www .labtimes.org

1/2015
SECTION II: ANTIBODY APPLICATIONS
CHAPTER 12: IMMUNOHISTOCHEMISTRY (IHC)
IHC Paraffin Protocol (using SignalStain® Boost Detection Reagent)
10. Wash sections three times with wash buffer for 5 min each.
*IMPORTANT: Please refer to the Applications section on the front page of product datasheet or product webpage to determine
whether a product is validated and approved for use on paraffin-embedded (IHC-P) tissue sections. Please see product datasheet
or product webpage for appropriate antibody dilution and unmasking solution.
11. Add 1 drop (30 µl) SignalStain® DAB Chromogen Concentrate to 1 ml SignalStain® DAB Diluent and mix well before use.
12. Apply 100–400 µl SignalStain® DAB to each section and monitor closely. 1–10 min generally provides an acceptable
staining intensity.
13. Immerse slides in dH2O.
A. Solutions and Reagents
14. If desired, counterstain sections with hematoxylin per manufacturer’s instructions.
NOTE: Prepare solutions with reverse osmosis deionized or equivalent grade water (dH2O).
15. Wash sections in dH2O two times for 5 min each.
1. Xylene
16. Dehydrate sections:
a. Incubate sections in 95% ethanol two times for 10 sec each.
2. Ethanol, anhydrous denatured, histological grade (100% and 95%)
3. Deionized water (dH2O)
b. Repeat in 100% ethanol, incubating sections two times for 10 sec each.
b. TBST/5% normal goat serum: To 5 ml 1X TBST, add 250 µl Normal Goat Serum (#5425).
c. PBST/5% normal goat serum: To 5 ml 1X PBST, add 250 µl Normal Goat Serum (#5425).
1X Phosphate Buffered Saline (PBS): To prepare 1 L 1X PBS: add 50 ml 20X PBS (#9808) to 950 ml dH2O, mix.
1X PBS/0.1% Tween® 20 (PBST): To prepare 1 L 1X PBST: add 1 ml Tween® 20 to 1 L 1X PBS and mix.
7. Antigen Unmasking Options:*
a. Citrate: 10 mM Sodium Citrate Buffer: To prepare 1 L, add 2.94 g sodium citrate trisodium salt dihydrate
(C6H5Na3O7•2H2O) to 1 L dH2O. Adjust pH to 6.0.
b. EDTA: 1 mM EDTA: To prepare 1 L add 0.372 g EDTA (C10H14N2O8Na2•2H2O) to 1 L dH2O. Adjust pH to 8.0.
c. TE: 10 mM Tris/1 mM EDTA, pH 9.0: To prepare 1 L, add 1.21 g Tris base (C4H11NO3) and 0.372 g EDTA
(C10H14N2O8Na2•2H2O) to 950 ml dH2O. Adjust pH to 9.0, then adjust final volume to 1 L with dH2O.
c. Repeat in xylene, incubating sections two times for 10 sec each.
17. Mount sections with coverslips.
For optimal results, always use the recommended primary
antibody diluent, as indicated on the product datasheet.
SignalStain® Antibody Diluent
#8112: IHC analysis of paraffinembedded human breast carcinoma
(top) and HCC827 xenograft (bottom)
using Phospho-Akt (Ser473) (D9E)
XP® Rabbit mAb #4060 or PhosphoEGF Receptor (Tyr1173) (53A5) Rabbit
mAb #4407 after dilution in either
#8112 (left) or TBST/5% NGS (right).
SignalStain® #8112
TBST-5% NGS
#4060
4. Hematoxylin (optional)
5. Wash Buffer: 1X Tris Buffered Saline with Tween® 20 (TBST): To prepare 1 L 1X TBST: add 100 ml 10X TBST (#9997) to
900 ml dH2O, mix.
6. Antibody Diluent Options:*
a. SignalStain® Antibody Diluent: (#8112)
A superior signal is achieved
when #4060 is diluted in #8112 as
compared with TBST/5% NGS.
d. Pepsin: 1 mg/ml in Tris-HCl, pH 2.0.
8. 3% Hydrogen Peroxide: To prepare 100 ml, add 10 ml 30% H2O2 to 90 ml dH2O.
No one diluent enables the optimal
performance of all antibodies.
9. Blocking Solution: TBST/5% Normal Goat Serum: to 5 ml 1X TBST, add 250 µl Normal Goat Serum (#5425).
10. Detection System: SignalStain® Boost IHC Detection Reagents (HRP, Mouse #8125; HRP, Rabbit #8114 )
#4407
11. Substrate: SignalStain® DAB Substrate Kit (#8059).
B. Deparaffinization/Rehydration
NOTE: Do not allow slides to dry at any time during this procedure.
1. Deparaffinize/hydrate sections:
a. Incubate sections in 3 washes of xylene for 5 min each.
b. Incubate sections in 2 washes of 100% ethanol for 10 min each.
c. Incubate sections in 2 washes of 95% ethanol for 10 min each.
2. Wash sections 2 times in dH2O for 5 min each.
IHC Frozen Protocol (using SignalStain® Boost Detection Reagent)
C. Antigen Unmasking*
NOTE: Consult product datasheet for specific recommendation for the unmasking solution/protocol.
1. For Citrate: Bring slides to a boil in 10 mM sodium citrate buffer, pH 6.0; maintain at a sub-boiling temperature for 10 min.
Cool slides on bench top for 30 min.
IMPORTANT: Please refer to the Applications section on the front page of product datasheet or product webpage to determine
whether a product is validated and approved for use on frozen (IHC-F) tissue sections. Please see product datasheet or product
webpage for appropriate antibody dilution.
2. For EDTA: Bring slides to a boil in 1 mM EDTA, pH 8.0: follow with 15 min at a sub-boiling temperature. No cooling
is necessary.
NOTE: Please see product datasheet and website for product-specific protocol recommendations.
3. For TE: Bring slides to a boil in 10 mM Tris/1 mM EDTA, pH 9.0: then maintain at a sub-boiling temperature for 18 min.
Cool at room temperature for 30 min.
A. Solutions and Reagents
4. For Pepsin: Digest for 10 min at 37°C.
2. Ethanol (anhydrous denatured, histological grade 100% and 95%)
3. Hematoxylin (optional)
NOTE: Consult product datasheet for recommended antibody diluent.
4. 1X Phosphate Buffered Saline (PBS): To prepare 1 L 1X PBS: add 50 ml 20X PBS (#9808) to 950 ml dH2O, mix.
1. Wash sections in dH2O 3 times for 5 min each.
5. Fixative Options: For optimal fixative, please refer to the product datasheet.
a. 10% neutral buffered formalin
2. Incubate sections in 3% hydrogen peroxide for 10 min.
3. Wash sections in dH2O 2 times for 5 min each.
b. Acetone
4. Wash sections in wash buffer for 5 min.
6. Remove blocking solution and add 100–400 µl primary antibody diluted in recommended antibody diluent to each section*.
Incubate overnight at 4°C.
7. Equilibrate SignalStain® Boost Detection Reagent to room temperature.
For more in-depth help with IHC,
please see our IHC Protocols and
Troubleshooting videos at
www.cellsignal.com/ihcvideos
212
c. Methanol
5. Block each section with 100–400 µl blocking solution for 1 hr at room temperature.
IHC Tips &
Techniques
T
V
Videos
8. Remove antibody solution and wash sections with wash buffer three times for 5 min each.
9. Cover section with 1–3 drops SignalStain® Boost Detection Reagent as needed. Incubate in a humidified chamber for
30 min at room temperature.
For Research Use Only. Not For Use in Diagnostic Procedures.
19
NOTE: Prepare solutions with reverse osmosis deionized or equivalent grade water (dH2O).
1. Xylene
D. Staining
d. 3% Formaldehyde: To prepare 100 ml, add 18.75 ml 16% formaldehyde to 81.25 ml 1X PBS.
6. Wash Buffer: 1X Tris Buffered Saline with Tween® 20 (TBS): To prepare 1 L 1X TBS: add 100 ml 10X TBS (#12498) to 900
ml dH2O, mix.
7. Methanol/Peroxidase: To prepare, add 10 ml 30% H2O2 to 90 ml methanol. Store at -20°C.
8. Blocking Solution: 1X TBS/0.3% Triton™ X-100/5% Normal Goat Serum (#5425). To prepare, add 500 µl goat serum and
30 µl Triton™ X-100 to 9.5 ml 1X TBS.
9. Detection System: SignalStain® Boost IHC Detection Reagents (HRP, Mouse #8125; HRP, Rabbit #8114 )
www.cellsignal.com/cstprotocols
/cstprotocols 213
See pg XXX for Application, Reactivity and Pathway Diagram keys.
SECTION III: WORKFLOW TOOLS
CHAPTER 19: DISCOVERY
Discovery
Complementary methods: immunoaffinity
immunoaffinity
and IMAC enrichment for phospho-peptides.
USING PEPTIDE IMMUNOAFFINITY ENRICHMENT AND LC-MS/MS
TO STUDY POST-TRANSLATIONAL
TRANSLATIONAL
TRANSLA
TIONAL MODIFICATIONS
MODIFICATIONS (PTMs)
How can I use PTM-specific
PTM-specific proteomics to enable discovery
of novel disease drivers and identification
cation of biomarkers?
A total of 27,372 unique phosphopeptides were isolated from MKN-45
cells using both IMAC and motif
antibody enrichment strategies. In
modified
this study, distinct sets of modified
ed by the two
peptides were identifi
identified
nity enrichment methods, with
affinity
affi
only 5.6% overlap between the MS/
identified peptides.
MS identified
Post-translational modifications
modifications such as phosphorylation, acetylation, methylation, ubiquitination, and
others are critical regulators of protein activity and function. Understanding the role of PTMs in disease
states and developing novel biomarkers and therapeutics are areas of intense research. However,
researchers who study PTMs are challenged by their inherent
ent low levels, which make them difficult
difficult to
identify and quantify from whole cell or native samples.
This challenge can be overcome
specific peptides
come by using immunoaffinity
immunoaffinity enrichment to isolate specific
containing PTMs of interest from a protease-digested cell or tissue extract. LC-MS/MS analysis is
proprietary to
then employed to identify and quantify the isolated peptides. PTMScan® TTechnology, proprietary
CST,
specificity of PTM-specifi
TT, utilizes
utilizes the specificity
PTM-specificc and motif antibodies to enrich target peptides from the
background of non-modified endogenous peptides, enabling the identifi
cation of modified
modified proteins that
identification
otherwise may not be detected. Hundreds to thousands of post-translationally modified peptides can
be identifi
ed and quantifi
ed in a single experiment. This approach can be used to study modifications
modifications
identified
quantified
such as phosphorylation, acetylation, methylation, ubiquitination, succinylation, or cleaved caspase.
The highly conserved nature of PTMs and substrate motifs across
oss many different
erent species also makes
this approach applicable to many different model systems.
PTM Site Discovery and Profiling
Profiling
• Discover candidate biomarkers linked to activation or repression of a specific class of PTMs.
• Perform a comprehensive proteomic survey of thousands of PTM sites associated with a wide
variety of organisms or a disease model system, integrating the results into known signaling
pathways or helping to defi
ne novel signaling networks.
define
• Detect substrates of novel signaling proteins (kinases, phosphatases, ubiquitin ligases,
deubiquitinases, acetyl transferases, methyl transferases, or succinyl transferases).
IMAC
(13,892)
All Antibody
(13,480)
How can I profi
le changes in specific
specific PTM sites on key target
profile
proteins to explore changes in critical signaling events?
Discovery workflow
workflow
for phospho-tyrosine
modificcations
ations
altered in NSCLC
5.6%
Cell or Tissue Samples
Identificcation
ation of Biomarkers
PTMScan TTechnology
echnology has been used to identify novel biomarkers in a number of different
erent model systems (2–6). One example
xample of the application of PTMScan TTechnology was conducted in a large-scale
large-scale
survey of tyrosine kinase activity in lung cancer, performed at CST.
ST. For
ST
For this study, we used a phosphotyrosine motif antibody to analyze changes in phosphorylation across the proteome in non-small cell
lung carcinoma (NSCLC) cell lines and tissues.
We surveyed the phospho-tyrosine status of receptor tyrosine
non-receptor
osine kinases (R
(RTK) and non-r
eceptor tyrosine
kinases in 41 NSCLC cell lines and over 150 NSCLC tumors. Over 50 tyrosine kinases and more than
ed. Two
2,500 downstream substrates that play roles in NSCLC growth and progression were identifi
identified.
T
findings from this study were the identification
identification of novel ALK and ROS1 C-terminal fusion
very exciting findings
proteins (EML4-ALK, CD74-ROS, SLC34A2-ROS) in some NSCLC cell lines and tumors (7). Further
investigation of ALK and ROS1 in other cancers led to the identifi
cation of a novel FN1-ALK fusion
identification
protein in ovarian cancer and a FIG-ROS1 fusion in cholangiocarcinoma (8,9).
Kinase Family Targeting
T
As one consequence of this study, a companion diagnostic immunohistochemistry (IHC) assay for
NSCLC
NSCL was developed. In 2011, the diagnostic IHC assay was approved
approved in the U.S. for patients with tumor samples that stain positive for ALK fusion protein expression for crizotinib treatment
eatment of NSCLC
NSCL (10).
Carcinoma-associated fusion proteins
discovered using PTMScan Technology
Immunoprecipitation
Using Motif Antibody
• Profile
Profile and quantify global effects of a candidate therapeutic
therapeutic on a specifi
specificc type of PTM,
identifying nodes of interest for further study.
• Understand how cross-talk among various PTMs (phosphorylation, ubiquitination, acetylation,
methylation) is related to a particular biological response or involved in cell development or
differentiation.
• Analyze downstream
eam effects of tar
targeted
geted gene silencing on signaling and potential activation
of alternative pathways.
• Identify protein-protein interaction binding partners along with their corresponding PTMs.
Discover Low Abundance PTM Sites
Immunoaffinity
Immunoaffi
nity enrichment allows you to identify low abundance modifi
modifications
cations by selectively capturing
the PTM in the context of the motif of interest from a population of endogenous peptides. For example,
the specificity of immunoaffinity
immunoaffinity enrichment complements that of IMAC, a charge-based
ge-based metal affinity
affinity
method commonly used for phospho-peptides. IMAC is driven by general coordination chemistry dictated
by the immobilized metal ion (1). IMAC can therefore lead to enrichment of peptides from more abundant
proteins for subsequent LC-MS/MS analysis, but not so readily for less abundant phospho-peptides.
254
ALK fusion protein
detection in human
lung carcinoma
ALK (D5F3) XP® Rabbit mAb #3633:
n-embedded
IHC analysis of paraffi
affin-embedded
affi
human lung carcinoma with high (left)
and low levels (right) of ALK fusion
protein expression using #3633.
LC-MS/MS and
Bioinformatic Analysis
www.cellsignal.com/discovery 255
See pg XXX for Application, Reactivity and Pathway Diagram keys.
For Research Use Only. Not For Use in Diagnostic Procedures.
SECTION I: RESEARCH AREAS
CHAPTER 03: CELL GROWTH AND DEATH
Death Receptor Signaling
Mitochondrial Control of Apoptosis
TNF-
TNF-
APO-3L/
TWEAK
FasL
TNF-R1
TNF-R2
FADD
Daxx
ASK1
Casp-8, -10
RIP
BID
IKK / /
TRAF2 TRAF1
cIAP1/2
ub
FLIP
I B
tBID
MKK1
JNR
IIb
Bcl-2
FADD
Microtubules
Casp-8,-10
Erk1/2
NF- B
p100
RelB
Akt
Bim
JNK
14-3-3
ROCK1
DFF45
Acinus
Cell Shrinkage
Membrane Blebbing
DNA
Chromatin
Fragmentation Condensation
Apoptosis
Arts
Casp-3
Transcription
Survival
Pro-Survival
ub
Apoptosis
PIDD
SirT2
Endo G
AIF
[NAD]
Bcl-2
HECTH9
Smac/
Diablo
Bcl-2 Family
Pro-Apoptotic
Puma
HtrA2
XIAP
RAIDD
Noxa
Cyto c
Casp-9
HSP60
CaMKII
Casp-2
Bcl-2
Bcl-xL
Apaf-1
p52 RelB
PARP
DFF40
Pro-Survival
Bad
Acetyl-CoA
Bax
Bak
Bax
Bak
14-3-3
Cytosolic
Sequestration
ARD1
NatA
Bcl-2
Mcl-1
Casp-7
Bax
Hrk
Calcineurin
Bad
JNK
Hrk
Bcl-2
Bmf
p70 S6K
Bad
Processing
Pro-Apoptotic
p53
ATM/
ATR
ING2
DNA Damage
Genotoxic Stress
Apoptosis can be induced through the activation of death receptors including Fas, TNFαR, DR3, DR4, and DR5 by their respective ligands. Death receptor ligands characteristically initiate signaling via receptor oligomerization, which in turn results in the recruitment of specialized adaptor proteins and activation of caspase cascades. Binding of FasL
induces Fas trimerization, which recruits initiator caspase-8 via the adaptor protein FADD. Caspase-8 then oligomerizes and is activated via autocatalysis. Activated caspase-8
stimulates apoptosis via two parallel cascades: it can directly cleave and activate caspase-3, or alternatively, it can cleave Bid, a pro-apoptotic Bcl-2 family protein. Truncated
Bid (tBid) translocates to mitochondria, inducing cytochrome c release, which sequentially activates caspase-9 and -3. TNF-α and DR-3L can deliver pro- or anti-apoptotic
signals. TNFαR and DR3 promote apoptosis via the adaptor proteins TRADD/FADD and the activation of caspase-8. Interaction of TNF-α with TNFαR may activate the NF-κB
pathway via NIK/IKK. The activation of NF-κB induces the expression of pro-survival genes including Bcl-2 and FLIP, the latter can directly inhibit the activation of caspase-8.
FasL and TNF-α may also activate JNK via ASK1/MKK7. Activation of JNK may lead to the inhibition of Bcl-2 by phosphorylation. In the absence of caspase activation, stimulation of death receptors can lead to the activation of an alternative programmed cell death pathway termed necroptosis by forming complex IIb.
The Bcl-2 family of proteins regulate apoptosis by controlling mitochondrial permeability. The anti-apoptotic proteins Bcl-2 and Bcl-xL reside in the outer mitochondrial wall
and inhibit cytochrome c release. The pro-apoptotic Bcl-2 proteins Bad, Bid, Bax, and Bim may reside in the cytosol but translocate to mitochondria following death signaling,
where they promote the release of cytochrome c. Bad translocates to mitochondria and forms a pro-apoptotic complex with Bcl-xL. This translocation is inhibited by survival
factors that induce the phosphorylation of Bad, leading to its cytosolic sequestration. Cytosolic Bid is cleaved by caspase-8 following signaling through Fas; its active fragment
(tBid) translocates to mitochondria. Bax and Bim translocate to mitochondria in response to death stimuli, including survival factor withdrawal. Activated following DNA damage, p53 induces the transcription of Bax, Noxa, and Puma. Upon release from mitochondria, cytochrome c binds to Apaf-1 and forms an activation complex with caspase-9.
Although the mechanism(s) regulating mitochondrial permeability and the release of cytochrome c during apoptosis are not fully understood, Bcl-xL, Bcl-2, and Bax may influence the voltage-dependent anion channel (VDAC), which may play a role in regulating cytochrome c release. Mule/ARF-BP1 is a DNA damage-activated E3 ubiquitin ligase
for p53, and Mcl-1, an anti-apoptotic member of Bcl-2.
Select Reviews:
Declercq, W., Vanden Berghe, T., and Vandenabeele, P. (2009) Cell 138, 229–232. • Fuchs, Y. and Steller H. (2011) Cell 147, 742–758. • Kantari, C. and Walczak, H.
(2011) Biochim. Biophys. Acta. 1813, 558–563. • Kaufmann, T., Strasser, A., and Jost, P.J. (2012) Cell Death Differ. 19, 42–50. • Lavrik, I.N. and Krammer, P.H. (2012)
Cell Death Differ. 19, 36–41. • Van Herreweghe, F., Festjens, N., Declercq, W., and Vandenabeele, P. (2010) Cell. Mol. Life Sci. 67, 1567–1579. • Wajant, H. and Scheurich, P. (2011) FEBS J. 278, 862–876.
Select Reviews:
Brenner, D. and Mak, T.W. (2009) Curr. Opin. Cell Biol. 21, 871–877. • Chalah, A., Khosravi-Far, R. (2008) Adv. Exp. Med. Biol. 615, 25–45. • Lindsay, J., Esposti, M.D.,
and Gilmore, A.P. (2011) Biochim. Biophys. Acta. 1813, 532–539. • Ola, M.S., Nawaz, M., and Ahsan, H. (2011) Mol. Cell. Biochem. 351, 41–58. • Pradelli, L.A., Bénéteau, M., and Ricci, J.E. (2010) Cell. Mol. Life Sci. 67, 1589–1597. • Rong, Y. and Distelhorst, C.W. (2008) Annu. Rev. Physiol. 70, 73–91. • Speidel, D. (2010) Trends
Cell Biol. 20, 14–24. • Suen, D.F., Norris, K.L., and Youle, R.J. (2008) Genes Dev. 22, 1577–1590.
©2002–2014 Cell Signaling Technology, Inc. • We would like to thank Prof. Junying Yuan, Harvard Medical School, Boston, MA, for reviewing this diagram.
©2003–2014 Cell Signaling Technology, Inc. • We would like to thank Prof. Junying Yuan, Harvard Medical School, Boston, MA, for reviewing this diagram.
For Research Use Only. Not For Use in Diagnostic Procedures.
See pg XXX for Application, Reactivity and Pathway Diagram keys.
www.cellsignal.com/customurlgoeshere 89
www.labtimes.org
LT_115_OC_OC.indd 2
DLC2
Bmf
Bcl-xL
p90RSK
Active
Caspase-8
p65/ NF- B
RelA p50
88
Mcl-1
BID
tBID
PKA
I B
XIAP
GAS2
HECTH9
PI3K
PKC
NIK
IKK
Casp-3
Actin
LC8
tBID
Casp-6
Lamin A
Bim
Casp-8,-10
cIAP1/2
RIP1
Smac
XIAP
Fas/
CD95
FADD
RIP
TRADD TRADD
FADD
TRAF3
MLKL
Apaf1
Casp-9
NF- B
IIa
FADD
Death Stimuli:
Survival Factor Withdrawal
FasL
Survival Factors:
Growth Factors, Cytokines, etc.
DR4/5
Casp-8
Casp-8
RIP1
FADD RIP3
Bcl-2
APO-2L/
TRAIL
DR3
APO-3
TRAF1
TRADD
RIP1
TRAF2
CYLD
cIAP1/2
TRAF2
Fas/
CD95
29.01.15 12:59
LT_115_IC_IC.indd 2
29.01.15 12:45
Editorial
1-2015
Lab Times
page 3
In a Modern Meritocracy…
Image: Fotolia/ Jeanette Dietl
…all that counts is how many loaves a baker can bake in a
PI. This is the objective that you will need to achieve in order for
given time frame or how many cars roll off the assembly line per
your performance to be considered at an acceptable standard.”
hour. Can you measure scientific performance the same way? Of
Up until this point, Grimm, working on apoptosis and tumoricourse, you can’t! Science isn’t done on a piece-work basis. But
genesis, had garnered more than 50 publications. His most recent
this doesn’t deter some university administrators from, now and
article on apoptosis inhibition at the outer mitochondrial memagain, evaluating their research personnel’s job performance. If
brane had just been published (EMBO Journal (33(23):2814-28).
a researcher does not publish a predetermined number of papers
In his posthumously published email, Grimm later writes,
in high-profile journals or does not secure enough funding, he or
“The reality is that these career scientists up in the hierarchy of
she is made redundant. (Monkey??) business as usual.
this organization only look at figures to judge their colleagues be
In 2012, exactly this kind of strategic,
it impact factors or grant income. (…) The
economic thinking stripped some biological
aim is only to keep up the finances of their
Assembly line production
and medical staff at the Queen Mary UniverDepartments for their own career advancedoesn’t work for science.
sity London of their jobs. Jeremy Garwood
ment.” He continues, “Did I regret coming
wrote about the “inexorable rise in business
to this place? I enormously enjoyed interactculture at UK universities” in his article “Acaing with my science colleagues here, but like
demic Values no Longer add up” (LT 4-2012,
many of them, I fell into the trap of confuspp. 20-24). Back then, the outcry was louding the reputation of science here with the
er than a pride of angry lions but not much
present reality. This is not a university anyseems to have changed, with perhaps tragic
more but a business with very few up in the
consequences. In September, Stefan Grimm,
hierarchy, like our formidable duo, profprofessor of toxicology at Imperial College
iteering and the rest of us are milked for
London, took his life; just months after he
money.”
was told his job would be at risk.
The complete letter and much more on
In their obituary, the German-based Max
the case is available on David Colquhoun’s
Planck Institute of Biochemistry, for which
blog www.dcscience.net.
Grimm worked as a group leader from 1998
For Colquhoun, all this does not come as
to 2004, described him as a “highly dedia surprise. For many years, the pharmacolcated scientist, insightful group leader and
ogist at the University College London has
friendly and obliging colleague”. Are those
been following the continued bullying at Imcharacter traits – dedication, empathy and
perial College and elsewhere. “The problem
diligence – no longer sufficient to survive
is by no means limited to Imperial. Neither
the science enterprise?
is it universal at Imperial: some departments
Of course, it’s not entirely clear whether the harsh working
are quite happy about how they are run. Kings College London,
climate at ICL was the sole reason behind his suicide. But email
Warwick University and Queen Mary College London have been
conversations suggest that it might have been. What exactly
just as brutal as Imperial. But in these places nobody has died.
brought an esteemed researcher to the verge of despair?
Not yet,” he sarcastically remarks.
An email, which emerged a month after Grimm’s death and
Whether the situation at Imperial College really led Grimm
which is signed by him, paints the picture of a deeply disappointto commit suicide or not is hard to tell. His death has, however,
ed and frustrated scientist. Subject: How Professors are treated
brought increased awareness, not only to many in the scientific
at Imperial College. The email begins, “On May 30th ’13 my boss,
world but also to the general public, of the working conditions at
Prof Martin Wilkins, came into my office together with his PA and
European research institutes, fuelling debates and giving food for
ask me what grants I had. After I enumerated them I was told
thought. “It’s impossible to manage research,” David Colquhoun
that this was not enough and that I had to leave the College withwrites. “If you want real innovation you have to tolerate lots and
in one year – ‘max’ as he said”.
lots of failure. ‘Performance management’ is an oxymoron. Get
Resurfacing emails sent by Wilkins to Grimm are riddled
used to it.”
with cold-hearted business talk. Care for an example? On March
10th, 2014, Wilkins writes, “I am of the opinion that you are
struggling to fulfil the metrics of a Professorial post at Imperial
College which include maintaining established funding in a programme of research with an attributable share of research spend
of £200k p.a. and must now start to give serious consideration as
to whether you are performing at the expected level of a Professor at Imperial College. Over the course of the next 12 months I
expect you to apply and be awarded a programme grant as lead
LT_115_03_03.indd 3
29/01/2015 13:27
page 4
Lab Times
Contents
1-2015
News
BioMed Central Design team ,CC-BY 4.0
Picture of the issue / University mega-merger in France / Standard file format for neuroscience
data / Recently Awarded / Costs of Open Access in the UK / EMBO Installation Grant winners
announced / Peer review scam at BioMed Central / German researchers discover that a plant
deceives its pollinator with the smell of fresh kill___________________________________ 6-10
Opinion
Observations of The Owl (52): Dear Customers______________________________________ 11
Research letter from... Belgium: The Armpit Doc will Smell you Now_______________________ 12
Over the Line? (19): A bit of a “Charlie”___________________________________________ 13
Photo: Klar et al., J Clin Invest, 124, 4773-80
Up until now, the role of individual authors
on a scientific publication has been unclear.
“Digital badges” are set to change that. Will
they work? (p. 18)
Analysis
Cover Story
Science is serious. But some research projects exhibit sparks of humour___________________ 14
Author Contributions
Can ‘digital badges’ clarify who has done what for a scientific publication?_________________ 18
Journal Club
Uppsala/Sweden A Pakistani family cannot sweat. What might be the underlying cause?_____ 24
Vienna/Austria A Brazilian plant does meiosis the other way around_____________________ 26
Budapest/Hungary Signal frequency determines nuclear import efficiency________________ 28
Publication Statistics
Photo: Bildergala/Fotolia
Sweat test at 32°C. The iodine-starch test
shows that the son of a Pakistani family is
unable to sweat. Niklas Dahl and Joakim Klar
found the responsible mutation (p. 24).
Toxicology research in Europe__________________________________________________ 30
What’s behind paper retractions? (26): A Second Chance for Fraudsters? __________________ 33
Biobusiness
News
Belgian UCB bags Parkinson’s disease collaboration deal / Successful financing for 3D
simulation tool / World’s richest doctor blamed for “fraudulent activities”__________________ 34
Airbrushed results at Asia’s leading contract research organisation?______________________ 35
Company Portrait
In search of polarity modulating compounds: Thelial Technologies (Lisbon, Portugal)__________ 36
Conflicts of Interest in Science (II): Undermined Authorities
Do public institutions always act in citizens’ best interests? And what happens when
companies persuade scientists to bias regulatory agencies in favour of their interests?_________ 39
Service
Photo: Tobias Frygar
Conflicts of interest, in particular of commercial nature, have undermined public regulatory authorities, Lab Times author Jeremy Garwood claims (p. 39).
Methods
Bench philosophy: Light-sheet microscopy_________________________________________ 44
Tips and tricks of the trade: Unexpected DNA binding activity of RNase A __________________ 46
Product survey: 1D gel electrophoresis systems ___________________________________ 47
New products _____________________________________________________________ 53
Book reviews
The Fall of the House of Rascher. The bizarre life and death of an SS doctor. By Siegfried Bär____ 54
Human Identity and Identification. By Rebecca Gowland and Tim Thompson________________ 55
Careers
Career strategies for young European scientists (LII)
Science and Society in Horizon 2020 and Beyond ___________________________________ 56
Jobs____________________________________________________________________ 61
Calendar________________________________________________________________ 62
Selective plane illumination microscopy
(SPIM) was outshined in the last years by
super­resolution microscopy. Now the door to
superresolution SPIM has opened (p. 44).
LT_115_04_05.indd 4
Humour
Paul the Postdoc___________________________________________________________ 06
Contact__________________________________________________________________ 64
Laboratory Tales ___________________________________________________________ 67
28.01.15 23:33
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LT_115_04_05.indd 5
28.01.15 23:33
Lab Times
News
1-2015
Photo: IRD/Jean-Marc Porte/Lengguru 2014
page 6
Picture of the issue
Kermit and his Friends
T
hese old water-splashers are most unlikely to turn into handsome young
princes anytime soon. But they do dwell in mysterious lands that hardly anyone has seen with his or her own eyes. That is until October last
year, when teams of French and Indonesian researchers set foot on the Lengguru
range in West Papua, Indonesia, to map the region’s unique fauna and flora.
“Karst [lime stone formations] form natural labyrinths scattered with huge networks of canyons, caves, underground galleries and fragmented rivers, sheltering a panel of very diversified ecosystems. (…) the karst masses are populated
by unique communities of birds, mammals, reptiles, fish and flora, most of them
unknown,” write the scientists. Diving to 100 metres below sea level and climbing to the tops of 1,400 metre high mountainous wedges, the expedition participants collected hundreds of specimens, including more than 50 bird species, 47
reptiles, 35 amphibians, 20 bats and some 300 orchid species. Now, the finds
will be analysed genetically (molecular barcoding, with additional nuclear and
mitochondrial markers) and morphologically to “confirm the discovery of at
least 50 new animal and plant species”.
-KG-
Paul the Postdoc
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page 8
Lab Times
News
1-2015
University mega-merger in France
Recently Awarded
New year, fresh prizes. In mid-January,
FEBS and EMBO announced that plant
biologist, Caroline Dean from the John
Innes Centre, UK, will be this year’s winner of the FEBS | EMBO Women in
Science Award. Honouring both the
lucky winner’s “outstanding achievements” in molecular biology and her role
in promoting and inspiring young female
scientists, Dean particularly impressed
the prize jury with her work on vernalisation, the acceleration of flowering by
prolonged cold. Also in outside research,
Dean has been active in pushing plant
biology. She is a founding member of
the steering committee for the Arabidopsis thaliana Genome Research Project, co-founder of the European Plant
Science Organization and a valuable
adviser for politicians. The award comes
with a prize money of €10,000.
After just winning the Breakthrough
Prize in Life Sciences (approx. €2.6
million) and the Ernst Jung Prize for
Medicine (€300,000), Emmanuelle
Charpentier from the Helmholtz Centre
for Infection Research in Braunschweig,
Germany, also pocketed the 2015
Louis-Jeantet Prize for Medicine
(approx. €610,000). All awards, of
course, honour her for her discoveries
revolving around the bacterial CRISPR/
Cas system, which, as a precise genome
editor, has since become one of the
most important tools in molecular biology. Charpentier will use the majority of
the prize money to continue her research
on the pathogenicity of Streptococcus
pyogenes, the bacterium that set off the
medical revolution. The second half of
the Louis-Jeantet Prize for Medicine went
to a slightly less prominent but not less
influential scientist, Rudolf Zechner
from the University of Graz, Austria. By
elucidating the pathways that control
lipolysis and lipid synthesis, the biochemist hopes to, one day, understand
what causes metabolic diseases like
obesity, insulin resistance and type 2
diabetes. Among his major discoveries
is adipose triglyceride lipase, an enzyme
essential for functional lipolysis.
-KG-
LT_115_06_11.indd 8
Straight to the Top
Bigger is better, as they say. Or plus grand
c’est, mieux c’est, as the French would perhaps phrase it. Earlier this year, a new super-university was created in the south of
Paris. If the French government’s plan pans
out, uniting two universities, ten “grandes
écoles” and seven research organisations
(among them CNRS, INRA and AgroParisTech) under one roof, or onto one campus
named Paris-Saclay, should secure them a
place in academic heaven and at the top
end of global university rankings. “To address ever-increasing global competition
in teaching, research and innovation, the
Founding Members of Université Paris-Saclay have decided to combine their resources by 2014 and create a joint teaching and
research project of the highest international
level,” the university’s press kit states.
Within the next decade, Paris-Saclay
wants to become serious competition for
Harvard, MIT, Oxford and Cambridge. “My
goal is to be a top 10 institution” in the
world, Dominique Vernay, current president of the Paris-Saclay campus, revealed
to BBC News. Within Europe, he aims for a
sunny spot among the top three. To make
it work, the French government supported
the project with an initial funding of 7.5 billion euros, for amongst others the construction of buildings and transportation. For instance, the Paris metro network is being extended to link the campus with the city and
the Orly airport.
On the 5.3 km2 large campus, 60,000
students (of which 12% are not from
France), and more than 10,000 researchers and teaching researchers are already
doing their daily work. More than 70 project leaders have been successful in winning grants from the European Research
Council. The campus was also built with
something else in mind: “Several fields of
scientific research teams are moving closer together on campus, in particular those
addressing the areas of food/agriculture,
pharmacy, nanosciences, cell biology, neurology, physics of lasers, high-performance
digital calculation, information science and
technology. Several thousands of researchers […] benefit from an environment specifically designed for enhanced interactions,” states the press kit. And there’s one
more treat for prospective students, who
want to come to France. They don’t need
to brush up their French language skills,
as some Masters courses are fully taught in
English. Dominique Vernay told BBC News,
“It’s not only allowed, it’s now encouraged
to teach in English.”
That being said, 49 Master degree programmes are on offer at the moment, including Biodiversity, Ecology & Evolution,
Bioinformatics and Public Health. The first
Master students, who take a ride on the
“next great historic wave of French higher
education”, will begin their studies in September.
Standard format for neuroscience data
One Format to...
Striving for uniformity mustn’t be a bad
thing. A uniform file format, for instance,
would make data sharing so much easier. That’s why, in late November, the first
hackathon of the recently formed Neurodata without Borders initiative took place
at the Janelia Farm Research Campus, USA.
Its goal: collecting ideas for the standardisation of neuroscience data on an international scale. The project’s first “problem child”
is cell-based neurophysiological data.
Amongst others, Ken Harris (University
College London), Christian Kellner (Ludwig
Maximilian University, Munich) and Vaclav
Papez (University of West Bohemia, Plzen)
travelled from Europe to the US to present
their suggestions. Pressing data from methods as diverse as extracellular array recordings, two-photon calcium imaging, intracellular recordings, video behaviour tracking
and “who knows what else in the future”,
as Harris put it, into one standard format
makes high demands on the candidate file
formats. It must be “sufficiently flexible and
extensible to incorporate present and future
electrophysiological and optical physiological data (i.e., cellular imaging) and […] to
include metadata (experimental variables),
Mistaken Identity
The photo that is supposedly depicting Vincent Noireaux in the
Journal Club from Israel article, in our last issue (see p. 34), shows
in fact Armando Hernandez-Garcia from Wageningen University, who
helped develop artificial viruses (see p. 22-25). The picture on the
left shows the real Vincent Noireaux. We apologise for the mistake.
29/01/2015 11:37
News
processed data (e.g. spike times, behavioral
events), intermediate level data (e.g. local
field potential, spike waveforms, position
data), and wide-band raw data for enabling
reproducibility and cross-validation”.
One format that meets all those requirements seems to be the HDF5 format, the
project’s current favourite. Developed in
the late 1980s, the Hierarchical Data Format has, over the years, found many fans.
NASA adopted it as the standard data and
information system for their Earth Observing System; R&D Magazine selected it as
“one of the 100 most technologically significant new products of the year 2002” and
special effect artists used it for the Lord of
the Rings movies. Now, HDF5 is perhaps going to revolutionise neuroscience.
According to its developers, HDF5 “supports an unlimited variety of datatypes,
and is designed for flexible and efficient
I/O and for high volume and complex data.
HDF5 is portable and is extensible, allowing
applications to evolve in their use of HDF5”.
Hence, it appears to be well-suited for the
neurophysiological data hotchpotch. And
the best thing about it, it’s open source and
distributed free of charge.
Should the HDF5 format make the cut,
the Neurodata Without Borders initiative
will test it on available datasets and then
share it with the broader neuroscience community (https://crcns.org/NWB).
1-2015
vited a number of UK higher education institutions and public sector research establishments to share their experiences in realising Open Access. Among the respondents
were: Imperial College London, King’s College London, the University of Edinburgh
and the University of Oxford. The resulting
report, Counting the Costs of Open Access,
and all data is available, free for everyone
to see and read, on the Research Consulting website.
The main findings: “Achieving compliance with Research Council UK’s open access Policy cost at least £9.2m in 2013/14
– with a further £11m or more spent on article processing charges (APCs)” and “The
time spent on increasing open access to research within UK research organisations in
2013/14 is equivalent to more than 110 fulltime equivalent staff members.”
Unsurprisingly, investment of money
and time differs considerably between the
two possible routes of OA – the gold route
(the author pays the journal an article processing charge) and the green route (an article is deposited in a publicly available repository). The report breaks down all the
costs involved and finds that “making an
article open access through the ‘gold’ route
Costs of Open Access in the UK
Worth the Money
The once unthinkable dream of freely available research articles is becoming a more
cherished reality for researchers and the
science-savvy public. This is especially true
in the UK, where the government pushes vigorously for Open Access to publicly
funded research for quite some time. Consequently, two of the largest funding providers in the country, Research Council UK
and Higher Education Funding Councils, introduced new Open Access policies, advising UK researchers to make their research
openly available, if they have the slightest
interest in receiving money from them.
While this move is a step in the right direction, Open Access publishing comes with
investments in the form of working time
spent on management, advocacy (telling
and advising researchers about their OA options) and infrastructure development. To
get an estimate of the true costs of OA in the
UK, UK-based consultancy, Research Consulting, devised a web-based survey and in-
LT_115_06_11.indd 9
takes two hours or more, at a cost of £81”.
These numbers are composed of 31 minutes and £24 at the author stage, where
the scientist figures out the requirements
for a gold OA publication and directs his
request to the institutes’ relevant department. It takes another, on average, 43 minutes and £24 for the administration to receive, review and process the request; 30
minutes and £17 to request, pay the invoice
Lab Times
page 9
and liaise with the publisher; and a final
30 minutes and £16 to confirm payment,
check article’s OA availability and its correct license. The survey respondents reported that most time is wasted liaising with the
publishers. In contrast, publishing an article via the green route takes about 45 minutes and costs £33. Here, the most common
time delay was a “lack of author familiarity
with the green OA process”.
Improvements in sharing knowledge,
policies and procedures, better automation and facilitating the depositing process
could help to cut the costs for OA further;
and thus make it an irresistible option for
all researchers and institutions.
EMBO Installation Grant winners
Back to the Roots
Since 2006, EMBO, the European Molecular Biology Organisation, is determined to
“strengthen science” also in European countries that are less blessed with a well-oiled
research infrastructure. Their Installation
Grants help young scientists to relocate to
the Czech Republic, Poland, Portugal, and
Turkey and get started with establishing independent laboratories. Up until today, a
total of 71 group leaders have received an
annual support of €50,000 for three to five
years and also a few more practical benefits like networking opportunities, access
to EMBL core facilities or a free job advert
in Nature.
In December, EMBO announced the
winners of the latest round of funding. Of
the eight grantees, relocating from universities in Canada, Germany and the United
States, three will set up research shop in
Turkey, two in the Czech Republic, two in
Portugal and one in Poland.
Ana Domingos, for instance, moved
from Rockefeller University in New York
to the Gulbenkian Institute of Science in
Portugal to study obesity. Using the latest neuro­genetic techniques, she wants to
“identify neurons that play a fundamental
role in eating behavior and metabolism”.
According to her website, Domingos is, by
the way, currently looking for “motivated
graduate students at Masters or PhD level”.
Also among the grant winners is ­Pavel
Plevka. After a four-year postdoc stay at
Purdue University, USA, he returned to his
home country, the Czech Republic, in 2013
to establish his own research group at the
Masaryk University in Brno. Plevka studies viruses, such as the human enterovirus
71 and the dengue virus. X-ray crystallog-
29/01/2015 11:37
page 10
Lab Times
News
1-2015
raphy and cryo-electron microscopy help
him and his group to zero in on the viruses’ structure.
Scientists, who could need a little support from EMBO and are at the moment applying for a full-time position at an institute
or university in the Czech Republic, Portugal, Poland or Turkey or have, in the past
two years, set up a lab in any of these four
countries, can note April 15th in their calendar, the next deadline for an EMBO Installation Grant proposal.
Peer review scam at BioMed Central
Faking it
As we already reported online (November 28th, 2014), the Open Access publisher ­BioMed Central recently fell victim to a
peer review scam. In as many as 50 cases,
author-suggested reviewers of manuscripts
turned out to be fake. Luckily, spelling mistakes and odd non-institutional email addresses gave most of them away. Five manuscripts, however, made it into the scientif-
ic record. BioMed Central suspected a third
party behind the fraud and promised to investigate thoroughly.
Meanwhile, more and more cases of
rigged reviews are coming to light. ­Elsevier
retracted 16 papers by economist Khalid Zaman, who submitted false contact information for the reviewers he suggested. And
also Medicine, a Wolters Kluwer title ranked
among the top journals for General & Internal Medicine, recently retracted two papers
by Chinese authors for “violating the peerreview process and publishing ethics standards”. In this case, a fictitious email account
fooled the journal editor into thinking the
manuscript was reviewed by a well-known
expert in the field.
Elsevier’s director of publishing services, Catriona Fennell, told Retraction Watch,
“About a year or two ago it became clear
these cases are not isolated. […] Our message for editors is, be alert but not alarmed.
This is a small minority but we do need to
start watching out for it.”
The ongoing BioMed Central investigations substantiated earlier suspicions of the
involvement of third party agencies, which
“may be providing services to authors [including] fabricated contact details for peer
reviewers during the submission process
and then supplying reviews from these addresses”.
Also COPE, the Committee on Publication Ethics, takes the scam seriously. In a
statement, they comment, “We are unclear
how far authors of the submitted manuscripts are aware that the reviewer names
and email addresses provided by these
agencies are fraudulent. However, given
the seriousness and potential scale of the
investigation findings, we believe that the
scientific integrity of manuscripts submitted via these agencies is significantly undermined. […] COPE is working with publishers, publishing organizations and relevant national bodies to determine how best
to address this situation in the longer term.
[…] We encourage anyone with information on these issues to contact COPE directly.” The contact form is available at publicationethics.org/contact-us
-KG-
Of Cheats, Thieves and Death
G
enerally, flowering plants depend on animals to get pollinised. To make it worthwhile for the pollinator, most plants
give something back: delicious pollen or nectar. But a small
number (4 - 6 % of angiosperms) cheat
by faking a certain scent or look, with no
reward for the pollinator. Researchers at
the Technical University of Dresden, Germany, recently discovered a fascinating,
new mimicry system in Aristolochia and
prove the existence of a new pollination
system in flowering plants (New Phytologist, doi: 10.1111/nph.13210).
Reminiscent of a “Dutchman’s pipe”,
plants of the genus Aristolochia have
specialised flowers to trap pollinators,
in their case flies. The flies, allegedly dung flies, are lured to the
plant through an irresistible smell of rotten fish, carrion and dung.
This strategy is called sapromyiophily. For their latest study, Stefan
Wanke and first author Birgit Oelschlägel analysed the tempting
odours in more detail and identified a clever trick.
Their first astonishing finding: A. rotunda’s (or smearwort) main
pollinators are not dung flies but fruit flies of the family Chloropidae
(Trachysiphonella ruficeps). Next, Oelschlägel et al. analysed the
chemical composition of the scent released by A. rotunda’s flowers and noticed compounds, which had previously been identified
in true bugs of the family Miridae. The bugs release these volatiles
LT_115_06_11.indd 10
when predators like spiders or ants attack them. Chloropidae fruit
flies, attracted by the dying bugs’ volatiles, join in on the feeding
frenzy as food thieves.
Fascinated by this interrelation, the
Dresden biologists created an artificial
‘Aristolochia-Miridae’ mix, containing
seven compounds that had elicited an
electrophysiological antennal response
in T. ruficeps. And as expected, the
chloropid fly was highly attracted to the
synthetic mix. For the researchers, this is
a sufficient proof that A. rotunda deceives
its pollinators by mimicking the scent of
freshly killed bugs, which the pollinator
otherwise prefers as food.
As this is the first study describing such a strategy, the authors
coined a novel term: ‘kleptomyiophily’ for pollination by kleptoparasites (parasitism by theft). Another novelty is the fact that the plant
releases compounds, known only from freshly killed rather than
living insects. And it shouldn’t go unmentioned that the flies have
been found to be exceptionally selfish. Rather than thinking about
feeding their young (like, for instance, bees), they think only about
filling their own empty tummies.
Karin Lauschke
(More research results from European labs on pp. 24-29)
Image: www.publicdomainpictures.net/George Hodan
German researchers discovered that a plant deceives its pollinator with the smell of fresh kill.
29/01/2015 11:37
Opinion
1-2015
Lab Times
page 11
Observations of the Owl (52)
Dear Customers
R
enaldo was here again!
reputation on the line. Therefore, it is essential to tell the truth
Years ago, I introduced you
and clear my reputation – particularly, in the light that they made
to Renaldo, the very best of
the final mistake. But they just refused to do so. You cannot treat
my veeery few human friends (LT
an author this way! After all, I gave them the privilege of publish6/2010: 16). Do you remember?
ing an exceptional review... This is so disappointing, it’s a nightExactly! That particular mouse gemare...”
neticist who regularly comes by
“Well I guess this wouldn’t have happened in bird science,” I
with some of his muscle-developasserted. “You know, in our world the publishing world follows a
ment mutants in his bag.
completely different principle: instead of submitting your paper
Yesterday evening, Renaldo
to just one journal, you sort of auction it to the highest bidder.”
served me his absolute “masterRenaldo’s face promptly turned from anger to perplexity,
pieces” to date. His freshest mu“What d’you mean?”
tants had definitely the most tender muscle meat I have ever de“In a nutshell, it works like this: The authors send a short outvoured. I went completely gaga over the five specimens and, in
line of their results to a whole number of appropriate journals, in
my ecstatic delight, almost gorged myself on them. The only senorder to screen who might indeed be willing to publish the whole
tence my drivelling beak could utter after quite a while was:
story. After that, the editors have to express their interest and
“Mmm, I’m sure they’ll bring you a major publication.”
convince the authors why their journal would be the best choice
This thoughtless remark, however, immediately pressed one
for the final publication – meaning they really have to bid for the
of his buttons. “I’ll tell you about ruddy publications,” he downpaper. The authors then select their two or three favourites and
right spat out. “Okay, tell me,” I brainlessly replied, while my beak
send them the complete manuscript. And if the editors still say,
was already aiming at the left-back hamstring of the fifth mouse.
‘Yes, we would consider it our privilege to publish your paper’ –
“Right.” He took a deep breath. “Well, a couple of months ago
the authors finally decide, which journal they actually wish to
I received an invitation from a certain physiology journal to write
grant that privilege.”
a comprehensive review about mammalian muscle development
“Sounds fantastic. But what about peer review?”
for them. I wasn’t exactly excited about it but, nevertheless, I
“Only some of our journals subject the manuscripts to an adagreed. So I emerged myself in this project... and, to my own surditional round of pre-publication review – not with the aim of
prise, I finally came out with the best piece I have ever written,
judging over their acceptance but rather to suggest further imat least in my own opinion. So, I happily sent the
provements. The majority of our journals, on the
manuscript to the editors at Elsewhere.”
other hand, just publish the authors’ final versions
“The journals have to
“Mmm... Wot?… Who?” I mumbled.
convince the authors, not and offer the possibility for everybirdy to comment
“Elsewhere – the publishing company.”
on the papers after publication. This is basically
the other way round.”
“Ah, okay.” Meanwhile, my focus had turned to
what you now call post-publication peer review.”
the extremely soft and succulent neck muscles...
“And it works this way?” Renaldo was still not convinced.
Renaldo continued. “Altogether they demanded two rounds
“Dear friend,” I replied. “Just imagine you have a really suof revision – no problem, that’s just how it goes. But before havperb discovery to sell. In that case, all journals would be bending finished the second round, the Elsewhere editors, completely
ing over backwards to publish your paper. And whom would you
out of the blue, published the manuscript ‘online before print’ on
finally grant the favour? Exactly, the journal that provides you
the journal’s webpage. Without any prior information.”
with the very best service.
“Okay, and that was a problem?”
“I can tell you, this way the journals are certainly much more
“Problem? It was a disaster! The reviewers, fortunately, had
aware that actually they are the service providers and we sciennoted two bigger mistakes – and I still hadn’t corrected them aptists are their dear customers. They
propriately when the ‘preliminary’ version suddenly appeared onhave to chase the authors rathline. With the mistakes still included, of course.”
er than the other way round. And,
“So they finally had to replace the online paper with a corby devil, they have to treat them in
rected version, I assume,” I said while licking off my beak.
the nicest­possible way to convince
“Guess what! They refused to,” Renaldo almost screamed.
them of their service. Otherwise,
“They didn’t even add a correcting note. Nothing! And it got even
they sincerely risk being swept
worse: From that day, the editors simply ignored all my requests
from the market.”
and protests and, in the end, also published the faulty version in
Stunned silence followed for a
print. Again no correcting note – nothing!”
couple of minutes, until Renaldo
“Phew, hard stuff,” I responded, now finally focussed on his
said with a strained smile, “Somestory. “Can it be that those Elsewhere blockheads are a bit too peatimes, I really wish I were a bird.”
cockish to tell the truth and admit having made a mistake?”
“Yes, it certainly seems so and this is the real scandal,” Renaldo replied. “By signing the paper as responsible author I put my
Comments: [email protected]
LT_115_06_11.indd 11
29/01/2015 11:37
page 12
Lab Times
Opinion
1-2015
Research Letter from:… Belgium
The Armpit Doc will Smell you Now
By our corresponding author, Winderige Oksel
Solutions for “the malodor generation”
In his latest research article – the “Microbial odour profile of polyester and cotton clothes after a fitness session” – Callewaert claims to be on the verge of revolutionising textiles (Appl Environ Microbiol,
80(21):6611-9). Using his findings, “the
textile industry can design adjusted clothing fabrics which promote a non-odour
causing microbiome”.
Human armpits (axillae) can contain
107 bacteria per cm2 from up to nine different phyla. Or as Callewaert told the Washington Post (13/08/14), “A lot of bacteria reside in our armpits. In fact, there are
more bacteria in your armpits than there
are humans on this planet. So you should
never feel alone!”
Our body odour is determined by specific bacterial species.
Although freshly secreted sweat has little odour, bacteria subsequently break down long-chain fatty acids, hormones and
sulphur compounds to smaller odoriferous molecules.
Our clothing helps create a warm, moist environment on
the skin that provides further potential for bacterial growth
and the generation of unpleasant odours. To study how different textiles affect these odours, Callewaert asked volunteers to
get hot and sweaty and then smelled their T-shirts.
Role of clothes in odour generation
Twenty-six healthy subjects, wearing freshly-washed cotton, polyester and mixed fibre T-shirts, participated in an intensive one hour session of bicycle spinning. Their sweaty T-shirts
were subsequently collected, placed in plastic bags and incubated for 28 hours in the dark at room temperature. This “sim-
LT_115_12_13.indd 12
ulated the home conditions” and let the microbial community
grow on the specific clothing textiles.
The individual T-shirts in the plastic bags were presented to
a panel of seven “selected and screened human assessors” who
sniffed them for their odour characteristics. The trained odoursmelling panel found that sweaty polyester smelled worse than
sweaty cotton. Not only did the polyester T-shirts smell less
pleasant, their odour was also found to be more intense, musty,
pungent of ammonia, strong, sweaty and sour.
Looking at Callewaert’s methods section, however, some
anomalies emerge. For example, why were the odour-testers
only presented with a clean cotton T-shirt as their “blank odour
measurement” and not a control polyester T-shirt? And why,
in addition to testing ten cotton and ten polyester T-shirts, are
there six with mixed fibres: four with 95%
cotton/5% elastane, one with 82% polyester/18% elastane, and one of 35% polyester/34% cotton/28% lyocell/3% elastane?
The answer would appear to be that all
26 participants used their own T-shirts. This
would also explain why Callewaert said he
had to test complete T-shirts when “incubating” them for bacterial growth – he couldn’t
simply cut-up his participants’ T-shirts to isolate the “armpit” region, even though he
wanted to compare them specifically to armpit swabs.
Photo: Fotolia/dandaman
H
umans are smelly animals! We naturally produce a
range of odours that we try to wash off or disguise. Yet
some people truly suffer from their smell and need scientific help. At least, this is the avowed goal of Chris Callewaert
– self-proclaimed ‘Doctor Armpit’ – whose mission at Belgium’s
Ghent University is to understand and regulate armpit odours.
On his ‘Dr Armpit’ website – www.drarmpit.com – Callewaert brings hope to the odour-challenged, with reassuring
messages like “Remember: if you have a body odour, it is not
your mistake: it is the mistake of your bacteria.”
His research focuses on “malodor-generating bacteria” and
how to counteract them in armpits, clothes, washing machines,
etc. Recent studies include the formulation of ‘synthetic sweat’
(J Microbiol Meths, 103:6-8). Apparently, this concoction permits all armpit bacteria to grow as they
would on armpit skin: “Even the formed
odour and malodor molecules resemble
the original odours.”
Small smelly samples
Callewaert has previously been criticised
for overstating findings from limited data. In
another study of only nine people, he looked
at the effect of deodorants and antiperspirants on armpit microbiomes and claimed that
the cosmetics “may actually make you smell
worse” (Arch Dermatol Res, 306:701). He later
admitted that the sample size was rather small but that he did
see “consistent outcomes” (Washington Post, 13/08/2014).
In the case of his T-shirt study, surely it would have been
better, given the unique microbiome in each person’s armpit, if
he had directly compared their T-shirts and armpit swabs. Furthermore, he could provide standardised T-shirts for each participant – one in cotton, one in polyester. Like that he could directly assess the match between armpit and textile; he could
even specifically amplify the armpit growth by cutting-out the
armpit regions of these T-shirts before incubating them.
But then, Dr Armpit does describe himself as a “pioneer”
and seems to be in a great hurry to be the first to cover new
ground. He even told the Washington Post that his ultimate objective was to solve the problem of body odour “by transplanting microbes from non-malodourous relatives to those afflicted”. Family armpit swaps could give a whole new sense to the
expression ‘keeping it in the family’!
29/01/2015 10:22
Opinion
1-2015
Lab Times
page 13
A bit of a “Charlie”
N
ero,
Post New Year reflection bears a heavy weight on a man’s
soul and I have been drawn to the nostalgia of an early seventies
footballing hero. The man in question was slight in size but astute
of foot. Yes, Charles Cooke or “Charlie”, as he was affectionately
known, was the Prince of Stamford Bridge.
Charlie was resplendent and an important contributor in the
pre-oligarch days of Chelski FC. In addition to his sporting prowess, Charlie had an impressive handlebar moustache. In my childlike mind, this gives him cartoon-like quality when in reality he
has the retrospective look of a 70s porn star (www.youtube.com/
watch?v=nypVOGzASr4).
Yes, Charlie had the ability to delight and offend depending
on how you chose to look at him. Charlie’s wing play was a thing
to behold. Wingers are the players who have fallen out of fashion
but used to regularly dazzle us out at the extremities of the pitch,
particularly in the attacking half as the creators of goals.
Ignoring left and right
This position has lost its significance in modern soccer ball,
as constraining the opposition and restricting more imaginative
individual skills seems to offend the modern coaches. They still
have a place as illustrated by the marmite (that some love and
others hate) pairing of “Blank
Rib-eye-ry” and his partnering
diva “Eye on Robbing”. These assimilated Bavarian wingers open
up ways to win that, assuming
you are Bavarian or from anywhere in Germany, cannot be disputed. Indeed, the greatest wingers like “Charlie” remind us that
movements and trickery at the
edges of the field can make the
heart sing.
Charlie was particularly
Dispatches from the
blessed as he could produce deborderlands of science
structive beauty on either wing.
He paid no attention to the left
and right wing that beyond football also defines the spectrum
of political and religious divides (www.theguardian.com/notesandqueries/query/0,5753,-1121,00.html). No, Charlie was enlightened and skilled enough to taunt his opposition and create
mayhem in the opposition’s defence from either side of the pitch.
An important attribute of Charlie-like wing men is, despite being
diminutive figures, they had the ability to bemuse the opposition
and often leave them on their backsides.
Over the Line?
Ridiculing the bullies who played outside the rules
Charlie plied his trade in a different time. He had to be brave
as his wing play was produced in the face of often insurmountable bullying. Ingerlish football was the self-proclaimed best. Most
teams were heavy-thighed, singularly committed and not con-
LT_115_12_13.indd 13
strained by the now widely accepted rule of fair play. A tackle often involved physical interaction with a Neanderthal defender.
Tackles were deemed legal even though they consisted of a preceding physical assault that would have led to a charge of grievous bodily harm if enacted on civic street. No Charlie and his artisan wing colleagues reminded us that although most of Ingerland
could run around a lot and were excellent at physical and verbal
violence, they were probably not playing football. Charlie and his
wingmen were brave and in doing so shone a light through the
dark days.
The persistence of these players and their predecessors means
that 40 years later we are now beginning to play the beautiful
game in Ingerland. Even, as is likely proclaimed by UKIP’s Nigel
Fromage, it is by overpaid foreign imports.
Un peu d’Universal Truth
The kind of bravery that Charles Cooke showed is not usually
required in our community. The rules of science are much clearer. They are based on objectivity, iterative consensus and a spirit
of live and let live. This has to be so. We are a melting pot of cultures, beliefs and non-beliefs focussed on defining the universal
truths of the world.
The splendidness of sage
conversation between Atheist and Buddhist or like you
and I, right- and left-footed
Christians, when trying to better-define sciences’ universal
truths, is one of the pursuit’s
great joys; don’t you think?
The rules and responsibility are that it does not get personal and we remain open to
and aware of the other ways,
even if we occasionally forget to cite those views. Mutual
consideration and respect until somebody gets ridiculous.
When this happens the views are aired and if they are dumb they
will be ignored.
Only rarely do we need to get brave. Those are the times
when we need to be persistent, to deliver messages that the wider community do not initially see. These often dislodge vested interests that subserve but do not shine light towards the universal
truths. However, usually the scientific method from Charlie Darwin to the present day progresses us towards the scientific principles of the universal truths.
Nero, “Parfois, nous avons tous besoin d’avoir un peu de Charlie” – with or without the handlebar moustache. But I bet you
would look good!
FinataNO’Toolex
29/01/2015 10:22
Photo: www.publicdomainpictures.net/George Hodan
Science and humour
Chasing the Funny
Side of Science
Science is a serious business, most of the time. Occasionally, scientists take a break from their daily work
and turn to more creative research questions. Is there a
place for humour in science?
I
n the summer of 2006, on the remote
high Arctic island of Edgeøya in Svalbard, Eigil Reimers, professor emeritus at the University of Oslo, found himself
dressed in white – toilet paper included –
stalking a herd of Svalbard reindeer. This
was not some lost bet (or perhaps it was)
but an impromptu field experiment where
someone needed to be the polar bear.
At the time, Reimers and his colleagues
were studying how the insular Svalbard
reindeer (Rangifer tarandus platyrhynchus) respond to human presence. They
were wrapping up their last footage, monitoring vigilance and fright & flight behaviour of the reindeer, when they noticed that
they were not the only ones doing the observing – a polar bear was also on the prowl.
The big polar bear disguise
The results published in 2012 in Arctic, Antarctic and Alpine Research showed
that the alert, flight initiation and escape
distances to the ‘polar bear’ were longer
than those to humans dressed in dark hiking gear. In other words, the reindeer took
notice of the ‘polar bear’ when it was much
further away than a human and, thus, reacted earlier.
Despite what must have been a truly Oscar-worthy performance by a well-respected
senior scientist stalking a group of reindeer,
outside the field of animal behaviour and
population ecology, this study would have
most likely gone unnoticed. But it didn’t!
Someone’s fancy got tickled and, unbeknownst to Reimers, submitted the study
to be considered for one of the most coveted awards in the field of science – the one
which provokes laughter and then deep
thought – the prestigious Ig Nobel award.
The research group was not too surprised. Polar bear protection laws estabImaginative and bizarre
lished in the 1970s in combination with the
The Ig Nobel prize is organised by the
decreasing sea ice meant that there were
people behind the bi-monthly journal Anmore bears in the Svalbard area. “Internals of Improbable Research (AIR). The reaction between reindeer and land-locked
search published is a little bizarre with a
polar bears is increasing and we thought
lot of imagination; it includes researchthat this earlier peaceful interaction has
ing those burning
changed the relationquestions we have
ship between the two,
“I like nonsense; it wakes up
all asked ourselves –
into a predator-prey rethe brain cells” – Dr Seuss
can rats tell the diflationship,” explains Reference between Japimers. Therefore, instead
anese spoken backward or Dutch spoken
of packing up and heading home, they did
backward (Linguistics prize, 2007); can we
the only sensible thing scientists could do
levitate frogs with a magnet (Physics prize,
at that moment – formulate a hypothesis,
2000); can a chimpanzee recognise another
which they immediately went about testchimpanzee by its rear end (Anatomy prize,
ing. They proposed that the reindeer had a
2012); why do onions make us cry (Chemislonger response distance (distance from aptry prize, 2013); and, how to brew a proper
proacher to reindeer) to a human disguised
cup of tea (Literature, 1999)? Since 1991,
as a polar bear than to a humanly-dressed
IgNobel awards have been handed out anhuman; hence the need for a disguise (see
nually by actual Nobel Prize laureates to reimages on p. 15).
LT_115_14_17.indd 14
searchers whose work supports the ideals
and spirit of AIR.
“Quite simply, there is not enough humour in science. Everyone is so serious, and
everyone takes themselves so seriously.”
Such are the opinions expressed by the architect behind The Science Web (thescienceweb.wordpress.com), a news site where the
author uses cutting humour to report on
science news from around the globe. “Miracle Ebola drug to be withheld until companies figure out how to make money from it”,
“Genome to become 110% functional”, “EU
to save on admin costs by funding exactly
the same people it did last time” or “Venter to become God in 2016; Jesus to step
down” are just some of the breaking news
headlines on the Science Web. None of it is
real, of course, but thinly veiled to voice one
man’s frustration with what is considered
‘progress’ in science today.
Hailing from the field of genomics,
which the author, who operates under the
pseudonym ‘jovial scientist’, currently finds
intellectually bankrupt and the funding decisions questionable, the blog has become
an outlet to vent frustrations using humour
– self-catharsis at its best. “There are some
amazing scientists involved”, acknowledges the blogger, “but 90% of genomics is
‘sequence first, think later’. One only has
to look at the 1,000 genome projects, the
10,000 genome projects, the 100,000 genomes project to understand that these
numbers are being pulled out of a hat and
are headline makers rather than having
anything to do with actual science.”
A bunch of absurdity
The first blog a year ago reported on the
sequencing of Bigfoot’s genome. Foolish? Of
course, but, as the blogger responds, “No
more absurd than the concept of extend-
29/01/2015 10:36
ing the lives of old people by sequencing
their genome, or any number of funded/
published projects we see every day.” The
posts will continue as long as there are absurd stories, stupid ideas or idiotic largescale projects to fuel them. There is also a
special penchant for people with huge, out
of control egos – an almost limitless source
available.
So, is there room for humour in science? This in itself is a multifaceted question with no simple answer. To start with,
there are certain expectations and stereotypes that scientists are expected to fulfil,
which is not helped by their portrayal in
popular media – stuffiness, strange sense
of humour, social awkwardness, Star Trek
lover. Thank you Big Bang Theory! It is also
expected that any attempt to communicate
science, whether to non-scientists, students
or even among peers, should be crammed
with as much terminology and aloofness
as possible.
“How to write consistently boring scientific literature” is a masterpiece of satirical
writing by Danish biologist, Kaj Sand-Jensen. Published in Oikos in 2007, Sand-Jensen
listed ten recommendations that scientists
should follow to establish themselves as
true writers of science: “Avoid focus; avoid
originality and personality; write long contributions; remove implications and most
speculations; leave out illustrations, especially good ones; omit necessary steps of
reasoning; use many abbreviations and
technical terms; suppress humour and flowery language; degrade species and biology
to statistical elements; and quote numerous
papers for self-evident statements.” His use
of humour to discuss what he deems taboo
in science communication is what makes his
opinions unforgettable.
Sociologist, Hauke Riesch is a little
more cautious when recommending humour in scientific communication, especially when the target audience is the general public. His recent paper cunningly en-
1-2015
titled “Why did the proton cross the road?
Humour and science communication” in
Public Understanding of Science, warns that
using humour may not always succeed in
engaging the desired response. “Humour
can set up and often strengthen boundaries, by either fostering in-group cohesion
through insider jokes and the construction
of reverse-dialogue re-appropriations of
the geek stereotype, or by excluding imagined out-groups by negative stereotyping.”
In other words, using humour is a sure-fire
way to separate people into those who ‘get
it’ from those who don’t. This can result
in feelings of inclusion or exclusion often
linked to intellect. On the other hand, he
does agree that humour can be an invaluable tool when properly used.
Lab Times
page 15
fessor at the Rabin Medical Center in PetahTiqva, Israel.
Leibovici’s findings showed that “remote intercessory prayer said for a group
of patients is associated with a shorter hospital stay and shorter duration of fever in
patients with a bloodstream infection, even
when the intervention is performed 4-10
years after the infection.” This was a classic case of present actions changing past
circumstances.
Taken too seriously
Leibovici’s message in irony generated over 60 follow-up publications, many of
which took the study at face value. Because
of this article and others like it, R
­ onagh
and Souder called for changes to publication guidelines – proper labelling of articles
Ethical dilemma
and exclusion from bibliographic databasWhere do we draw the line between hues. They even appealed for a retraction of
mour used to entice and keep the reader’s
Leibovici’s paper. There are many who disinterest, and spoof or parody science that
missed that a retraction was necessary, sugif misinterpreted or overlooked can lead
gesting that the article be accepted for what
to wasted time and finances in follow-up
it was – a spoof and a play on over-interpretstudies? How does a reader differentiate
ed data and unrealistic research questions.
between what’s real and what’s spoof, conLeibovici, in a letter to BMJ in 2002 residering the popular use of irony in the latsponding to comments to his article, sugter? Should spoof articles even be allowed
gests that scientists be a little more discernin ‘real journals’ without some indication
ing when it comes to interpreting data. He
of the authors’ intent?
writes, “The purpose of
What are the ethics inthe article was to ask
“If you want to tell people
volved? Maryam Ronthe following question:
the truth, make them laugh,
agh and Lawrence Soudwould you believe in a
otherwise they’ll kill you” –
er from the Department
study that looks methOscar Wilde
of Culture and Commuodologically correct but
nication at Drexel Unitests something that is
versity explored these iscompletely out of peosues in a recent article, “The Ethics of Ironple’s frame (or model) of the physical world
ic Science in its Search for Spoof” (Sci Eng
– for example, retroactive intervention or
Ethics, 2014, Dec 16), which was based on a
badly distilled water for asthma?” He then
spoof article more than ten years old (BMJ,
provides hints to help in the discernment
323(7327): 1
­ 450–1) entitled, “Effects of
process – and of his article, which, at the
remote, retroactive intercessory prayer on
surface appeared to be rooted in prayer, had
outcomes in patients with bloodstream innothing to do with religion. It demanded
fection: randomised controlled trial” by
that the reader reject the literal meaning
Leonard Leibovici, back then, medical proand search for the truth.
Photos(3): University of Oslo, M. Kardel
Photo: www.publicdomainpictures.net/George Hodan
Analysis
Worthy of an IgNobel prize: Eigil Reimers posing as a polar bear.
LT_115_14_17.indd 15
29/01/2015 10:36
page 16
Lab Times
Analysis
1-2015
was the absolute cheapest brand we could
much alcohol.” He needed immediate interfind.” The alcohol was vodka, which they
vention. The response was “a bit crazy” was
used in a foot bath for three hours, durhow corresponding author, Patrick Davies
ing which time a volunteer nurse collected
explained the media frenzy but, for him, the
blood samples every 30 minutes to measstudy “combined an important health mesure alcohol levels. Hansen and the three
sage with an entertaining background”. We
doctors who participated decided on an accan’t all be 007.
ronym because “all good studies need an
In 2014, Davies returned with anothacronym”. In the spirit of Christmas, they
er article for the Christmas issue. Wherechose Peace on Earth (Peras the year before his idea
cutaneous Ethanol Absorpwas based on fiction, ne“Happiness is good
tion Could Evoke Ongoing health and bad memory”
cessity was the motivation
Nationwide Euphoria And
in 2014 as he investigat– Ingrid Bergman
Wacky but not made-up
Random Tender Hugs). The
ed the accuracy of Google
That December morning, readers would
result – feet are impenetraTranslate in medical comhave noticed the tone was a little lighter,
ble to alcohol. Besides dispelling a popular
munication. The idea came about during
topics odd – butterfly sightings and the
myth, both national and international mea case, where he was trying to communigame of cricket were discussed; a saint,
dia were intrigued, leading to a crazy and
cate with the parents of a sick child. The
long dead, was diagnosed with anorexia; a
fun experience, while fulfilling the spirit
parents spoke no English and the hospital
report of a hanged woman from 1650, who
of the Christmas edition – it made people
could not find a translator, leading them to
came back to life, revisited. This was the
smile.
Google Translate. Their experience led the
first and what was to be the only Christdoctors to test the accuracy of the popular
007 delivers health message
mas edition of the BMJ, an attempt to focus
search engine’s ability to translate ten of the
“James Bond is an impotent drunk” was
on another side of medicine that explored
most commonly used medical statements
the headline on BBC’s health page in Dethe bizarre and reassess historical cases. As
into 26 languages. The results were evalucember 2013, and they weren’t the only
Tony Delamothe, editor of the Christmas
ated by native speakers. There was limited
ones reporting the scandal (see LT 1-2014).
edition, in a 2010 phone interview with USsuccess, showing that ‘just Google it’ does
Doctors from Nottingham Children’s Hosbased National Public Radio said, “The arnot work in medicine.
pital found that alcohol-induced tremors
ticles are a bit sort of quirky and wacky and
For example, a common translation for
were the reason for Bond’s shaken-notdifferent.”
‘your wife is stable’ was ‘your wife cannot
stirred Martini choice. The diagnosis came
These articles are not made up; in fact
fall over’ – not quite the same. Davies had
after reading 14 of Ian Fleming’s novels on
some could be in the ‘normal’ edition, as
this to say about the results, “The complexthe world’s best-loved MI5 agent and conthey address potentially important issues.
ity of the ideas, and the importance of what
servatively estimating the amount of alcoMost, however, fulfil the spirit of the BMJ’s
we are saying, is such that human beings
hol he imbibed to determine consumption.
Christmas edition as it was initially intendare still miles ahead of computers (when
ed – a voice for the bizarre; the
human beings are available).
different; the creative that makes
Computers would not be able to
getting in, according to clinical epdeal with the emotions involved
idemiologist, Bruce Arroll, from
in breaking bad news to parthe University of Auckland “the
ents.” When asked of the attracpinnacle of a research career”.
tion to publish in BMJ ChristTo select articles from the last
mas edition, Davies respond32 years is almost impossible. A
ed, “The Christmas BMJ is the
sampling, however, illustrates the
most read of all the issues of the
creativity that lies behind these
BMJ and is a highly competitive
articles. 2010 was a vintage year.
field. To publish in the ChristSleep was associated with attracmas edition gives great respect
tiveness; red heads were cleared
from many doctors. Some docof the popular charge that they
tors feel that it is a waste of time
bled more profusely and toleratbut, in general, I would rather
ed less pain than non-redheads;
work with those who appreciate
Dr Watson, sidekick of Sherlock, “The man with the Golden Liver” diagnoses Patrick Davies, MD, and
the humour and off-beat nature
contributed a case; and a group colleagues after analysing James Bond’s weekly alcohol consumption. of these papers.”
of Danes popped the bubble on an
Sports has also initiated
They concluded that “James Bond’s level of
urban Danish folklore that alcohol is only
some inventive research questions. There
alcohol intake puts him at high risk of mulabsorbed orally.
was cricket in the first issue, trout fishing in
tiple, alcohol-related diseases and an early
“One of the methods includes submerg1999 where a group of physicians identified
death. The level of functioning as displayed
ing feet in alcohol,” explains first author
the best artificial floating fly to be used as
in the books is inconsistent with the physChristian Stevns Hansen (MD/PhD stubait (both Poisson distribution and Fisher’s
ical, mental and, indeed, sexual functiondent). “We financed the alcohol ourselves.
test were used); unicycling and the public
ing expected from someone drinking this
It was bought in a local supermarket and
response it generates by Peter Froggatt, (reImage: Johnson G. et al., BMJ 2013;347:f7255
As many might have guessed, this article appeared in the notorious Christmas
edition of the BMJ. When the first of these
very special issues came out, it must have
been a shock! Some probably saw the humour and laughed. Others perhaps tossed
it in the garbage where they were convinced
it now belonged. The year was 1982, a few
days before Christmas when one of the top
medical journals around, the BMJ (then the
British Medical Journal), defied the status
quo.
LT_115_14_17.indd 16
29/01/2015 10:36
Analysis
tired vice chancellor of Queen’s University
in Belfast) explaining his post retirement
activities; and of course, football.
Goals and babies
In 2011, doctors from Manchester reported a case of Manchester United-induced
Addison disease, which they diagnosed in a
fan whose episodes were directly associated with the performance of the team. While
losing leads to adverse health effects, winning appears to induce euphoria; the consequences of which are life changing.
In 2009, Champion’s League semi-final, FC Barcelona’s central midfielder Andres Iniesta shot a 93rd minute goal against
FC Chelsea, which sent Barça to the finals.
Nine months later, there were reports of a
baby-boom in and around Barcelona – the
so-called ‘Iniesta effect’. A group of scientists and physicians from universities in Barcelona investigated the validity of this effect
by following the birth registers. In BMJ’s
2013 Christmas issue, they showed a 16%
spike in the number of births the following
February and 11% in March – approximately nine months following the goal.
1-2015
Lab Times
page 17
The punchline
Jesus Montesinos is responsible for reA 2008 essay published in the Journal of
search and innovation with the Althaia
Cell Science by biologist Martin A. Schwartz
Foundation in Barcelona and the first auexplores “The importance of stupidity in
thor. When asked if he thinks their study
scientific research”. This is not a spoof or
could be reproduced, the medical oncolomeant to be funny, though it is entertaininggist pointed to all the factors that must fit.
ly written, but a reminder that ‘not know“I think that this psychological effect of oping’ and ‘asking why’ are the foundation of
timism and euphoria could be done but is
scientific research. Schwartz introduces the
not frequent. In 2009, Barcelona football
term ‘productive stupidity’ encouraging sciclub broke all records for victories, the ecoentists to be “ignorant by choice” and adapt
nomic crisis in our country was very imfrom “learning what others once discovered
portant and the population certainly needto making your own discoved positive news. Also, the
ery”.
need to express the Cata“Never trust an atom;
It is in this spirit that
lan identity in our geothey make up everything”
scientists who have won
graphic area could have
– unknown
an ­­IgNobel or published in
had a summative effect.
BMJ’s Christmas issue conTo repeat these or similar
tinue their own research – by asking the
conditions is from my point of view an exseemingly ‘stupid’ questions and not beception.”
ing afraid to follow the results. Schwartz
Interestingly, the group did plan their
concludes in his essay that “The more comstudy for BMJ as Montesinos explains, “In
fortable we become with being stupid, the
the medical field BMJ is one of the most imdeeper we will wade into the unknown and
portant journals in the world and among
the more likely we are to make big discovother peculiarities have the ‘Christmas-iseries.”
sues’, in which are published research studRosemarie Marchan
ies that tend to have more levity.”
Our Selection Speaks Volumes
•
•
•
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•
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•
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Scissors
Retractors
Magnifiers
Probes & Hooks
Bone Instruments
Animal Identification
Hemostats
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Photo: Fotolia/ra2 studio
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Lab Times
Analysis
1-2015
Digital badges: An easier way to see and understand who does what in science
True Credentials
Being recognised as an author on research publications is of crucial importance to scientists because it is a unique
identifier of their scientific production. But who really did what and how much credit should be allocated or assumed?
Jeremy Garwood reports on a new, internet-based scheme offering ‘digital credentials’ that may allow researchers to
better display their research skills and achievements.
O
nce upon a time, many research reports were written by
a single author. In such cases, there could be little doubt
about who had done the research and written the article (assuming the author had not chosen to withdraw credit from
someone else). However, as even a cursory glance through the
current literature shows, most research papers in the life sciences now have multiple authors. Among reasons advanced to explain the lengthening list of authors are changes in the nature of
collaborative science, the associated use of specialised technology and the need for researchers to show that they are publishing
when being assessed for their “scientific productivity”.
However, what we cannot tell easily by reading a paper is who
actually did what. It is usually assumed that the first author did
most of the work and that the last author was some kind of directing presence. Yet, in many cases, it is only those who are directly involved with the projects in question who can really un-
derstand and explain what each of the authors contributed to the
final paper.
Problems with author lists
And this situation appears even more unfair when we realise that authorship of scientific papers is the major measure of
a researcher’s scientific productivity and “worth” when assessing who gets future research jobs, grants, awards, administrative
power, etc.
Peter Lawrence wrote a series of articles examining how the
politics of publication in science has resulted in a situation of
“rank injustice”, in which the misallocation of credit is endemic
(Nature, 415:835-6, Nature, 422:259-61), a position he discussed
further in Lab Times (LT 2-2011 p. 24,‘The heart of research is
sick’). “A common way to build rank is to annex credit from junior colleagues. To stop this I would like to see granting agencies
Photo: Fotolia/Olga Kovalenko
Types of Authorship Abuse
LT_115_18_23.indd 18
Coercion authorship – Use of intimidation tactics to gain authorship. Arguably a serious form of scientific misconduct
Honorary, guest, or gift authorship – Authorship awarded out of respect or friendship, in an attempt to curry
favour and/or to give a paper a greater sense of legitimacy. To qualify as an honorary author, you only have to
meet the following criteria: The author did not conceive or design the work, analyse or interpret the data, or collect data or other material. Nor did they write any part of the manuscript or revise the manuscript to make important changes in content, or approve the final version of the manuscript. In fact, such an author might not “feel
comfortable explaining the major conclusions” of the article.
Mutual support authorship – Agreement by two or more investigators to place their names on each other’s papers to give the appearance of higher productivity
Duplication authorship – Publication of the same work in multiple journals
Ghost authorship – Papers written by individuals who are not included as authors or acknowledged. This is a
situation that has often been linked to commercial interests, e.g. in articles that promote pharmaceutical drugs,
or that deny the toxicity of products, such as tobacco. Industry employees write the article and academic scientists receive ‘honorary’ authorship.
Denial of authorship – Publication of work carried out by others without providing them credit for their work with
authorship or formal acknowledgment. A form of plagiarism and therefore scientific misconduct
Source: “Authorship: why not just toss a coin?” by Kevin Strange Am J Physiol Cell Physiol. Sep 2008; 295(3): C567–75.
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Analysis
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1-2015
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meet, agree on and publicise principles of how the contribution
and responsibility of those scientists they support should be indicated in the list of authors of papers.”
“It is time for full disclosure of author contributions,” wrote
Sebastian Frische, biomedical scientist at Aarhus University,
Denmark, when calling for the use of online databases to increase fairness and transparency by fully documenting the role
of each contributor to a paper (Nature, 489:75). Authorship is
“key to getting grants and winning promotions. Yet authorship is
a dubious indicator. Sophisticated readers know that decoding
an author list in terms of actual contribution to the scientific paper is close to impossible, unless you are involved yourself.”
A striking example of this research opacity was provided by Bruno Lemaitre, currently Professor of Genetics at EPFL,
Lausanne. In 1996, Lemaitre, then a young researcher in Strasburg, published the discovery that the receptor protein Toll
was an essential part of the innate immune system in Drosophila (Cell, 86:973-83). In 2011, the work described in this paper was specifically cited as the reason why its last author, Jules
Hoffmann, was awarded that year’s Nobel Prize in Physiology or
Medicine. At which point, Lemaitre, first author on the article,
made a public protest, explaining that Hoffmann’s contribution
to the Toll discovery had been “distant” and amounted to little
more than editing the final manuscript.
To clarify what really happened, Lemaitre has provided a
detailed background description of this research discovery on
the ‘Behind Discoveries’ website (www.behinddiscoveries.com/
toll), and there is additional analysis at LT online (‘A Nobel Prize
not Immune from Error?’) and in LT 1-2012 p. 26 (‘Borrowed
Plumes’).
Why not just toss a coin?
A good overview of the authorship problem was provided
by Kevin Strange in ‘Authorship: why not just toss a coin?’ (Am J
Physiol Cell Physiol, 295: C567–75). His title’s provocative question should provoke a response. Obviously it appears grossly unfair to simply toss a coin when deciding if someone is an author
on an article or whether they have a ‘prominent’ position in the
list of authors. Unfortunately, the reality is that there is much
abuse of authorship status. Strange provides a list of some common mispractices in which researchers can steal and barter credit (see Textbox on p. 18).
At the heart of this abuse lies the problem of clearly identifying who should be recognised as an author. The ICMJE (International Committee of Medical Journal Editors) provides a strong
definition of authorship based on four criteria; they also distinguish contributions that they do not consider sufficient to justify authorship, including the obtainment of funds and general supervision (see Textbox on p. 21).
Ironically, Strange discusses how the discovery of scientific
fraud in research publications has served to reveal the extensive
use and abuse of ‘honorary’ and ‘gift’ authorships.
Take, for example, the Korean stem cell scandal. In 2005,
South Korean scientist, Woo Suk Hwang, was first author on a
high-profile Science paper that claimed embryonic stem cells
could be generated by somatic cell nuclear transfer (Science, 308:
1777–83). This paper was subsequently shown to contain fabricated data and was retracted. The senior/last author on the
paper was Gerald Schatten, from the University of Pittsburgh.
When the work was revealed to be fraudulent, Schatten made
significant efforts to distance himself from it. Although his uni-
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versity found no evidence that Schatten had falsified any aspect
of the Science publication, he was still found guilty of “scientific
misbehaviour”.
In effect, Schatten had not participated in any aspect of the
investigation and had little, if any interaction with his co-authors.
Therefore, Schatten could not take responsibility for the integrity of the studies, nor ensure that the listing of the co-authors reflected correct distribution of credit (or discredit in this case), or
certify that all co-authors had approved the manuscript for submission, even though he stated in a signed cover letter that they
had done so.
Nevertheless, investigators concluded that Schatten could
justify being an author given the role he played in writing the
fraudulent manuscript but they criticised his assumption of cocorresponding and senior authorship. Their report stated that,
“Dr. Schatten’s listing as the last author not only conferred considerable credibility to the paper within the international scientific community, but directly benefitted Dr. Schatten in numerous ways including enhancement of his scientific reputation, improved opportunities for additional research funding, enhanced
positioning for pending patent applications, and considerable
personal financial benefit.”
Another paper co-authored by Hwang and Schatten describing the cloning of a dog was also examined (Nature, 436:641).
This paper was not fraudulent but the investigating committee
questioned Schatten’s assumption of co-authorship since his only
contribution was to suggest “that a professional photographer be
engaged so that Snuppy (the dog) would appear with greater visual appeal”!
Strange concluded that “authorship abuse is not an infrequent occurrence. Indeed, of the various forms of unethical scientific conduct, I suspect that authorship abuse is the most prevalent and most tolerated. Authorship is awarded promiscuously
as an expedient solution to real or perceived problems and due to
outright unethical and unprofessional behaviour.”
Misrepresentation of authorship and research credit has also
been equated to scientific fraud. The research described in an article may not in itself be fraudulent but by claiming “inappropriate” credit for the work, researchers are effectively deceiving the
reviewers and committees who need to make decisions about future research funding, career appointments, promotions and
awards (‘Honorary and ghost authorship in high impact biomedical journals: a cross sectional survey’, BMJ, 343:d6128).
Digital Hopes – better digital credentials in the digital world
Can the power of the internet provide better and more transparent information about what researchers have really achieved?
Funding agencies, academic institutions, editors and publishers
have expressed growing interest. Many publishers now require
contribution disclosures upon article submission and funders are
developing ways of tracking the outputs and impact of their research investments.
In 2012, the Wellcome Trust and Harvard University co-hosted a workshop to explore alternative contributorship and attribution models (Nature, 508:312-3). The resulting ‘digital badge’
collaboration includes publishers BioMed Central (BMC) and the
Public Library of Science (PLoS); the Wellcome Trust; Mozilla Science Lab (Mozilla is the open software community behind the
Firefox browser and other programmes); the software and technology firm Digital Science; and ORCID (Open Researcher and
Contributor ID), the registry of unique researcher identifiers.
LT_115_18_23.indd 21
1-2015
Lab Times
page 21
Photo: www.publicdomainpictures.net/JB Stran
Analysis
What counts as Authorship?
The ICMJE (International Committee of Medical Journal Editors) includes The Lancet, the New England Journal of Medicine,
the British Medical Journal (BMJ) and the Public Library of Science (PLoS). It recommends that authorship be based on the following four criteria:
Substantial contributions to the conception or design of the
work; or the acquisition, analysis, or interpretation of data for the
work; AND
Drafting the work or revising it critically for important intellectual content; AND
Final approval of the version to be published; AND
Agreement to be accountable for all aspects of the work in
ensuring that questions related to the accuracy or integrity of any
part of the work are appropriately investigated and resolved.
All those designated as authors should meet all four criteria
for authorship.
In addition to being accountable for the parts of the work he
or she has done, an author should be able to identify, which coauthors are specifically responsible for other parts of the work.
Authors should also have confidence in the integrity of the contributions of their co-authors.
Non-Author Contributors
Contributors who meet fewer than all four of the above criteria
for authorship should not be listed as authors, but they should be
acknowledged.
Examples of activities that alone (without other contributions)
do not qualify a contributor for authorship are:
acquisition of funding;
general supervision of a research group or general administrative support;
writing assistance, technical editing, language editing and
proofreading.
Source: www.icmje.org/recommendations
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Lab Times
1-2015
Analysis
Digital badges reflect dissatisfaction with existing efforts to
include simple published descriptions of author contributions.
Not all journals insist on such a section and when it is present, it
is not standardised, meaning it’s often vague, with not enough
detail on the skills, techniques, or methods each author brought
to the work.
The digital badge scheme was presented in October, 2014 at
the Mozilla Festival in London. Kaitlin Thaney, director of Mozilla Science Lab said, “The parties behind the digital badge effort
are looking to change the behaviour of scientists in the competi-
tive dog-eat-dog world of academia by acknowledging contributions” (‘Could digital badges clarify the roles of co-authors?’, Science Insider, 3/11/14).
The proposed digital badges are based on Open Badge, an existing accreditation scheme developed by Mozilla that can theoretically be applied to any work situation. This offers a standardised digital credential corresponding to recognised work
skills and attainments. It intends to provide an alternative to traditional diplomas and qualifications that often fail to reflect what people learn in
their work environment. An example
that has received US government backing concerns former soldiers – such veterans often don’t have formal qualifications to show what they have learned
to do in the armed forces and this poses
problems
when looking for civilian jobs.
There are currently 14 suggested categories and corresponding badges.
Open Badge is already being used by some US
companies and organisations for internal profes1. Study conception - Provision of ideas; formulation of the
sional development, including Disney, NASA, and
research question; statement of hypothesis.
the Bill and Melinda Gates Foundation.
But the question is “Could badges work for
2. Methodology - Development or design of methodology; the
science?” (‘Contributorship badges: a new procreation of models.
ject’, 21/11/14, mozillascience.org). Mozilla is
hoping to apply similar principles to the world of
3. Computation - Programming or software development.
academic research. “As the research environment
becomes more digital, we want to test how we
4. Formal analysis - Application of statistical, mathematical
can use this medium to help bring transparency
or other formal techniques to analyse study data.
and credit for individuals in the publication process.(…) Badges can serve as a standardized digital credential for the work done by each author.
5. Investigation - They performed the experiments.
Research is increasingly reliant on a wider range
of skills from software to drafting to data cura6. Investigation - They collected the data/evidence.
tion. We want to avoid vague and unstructured
text descriptions of work completed by offering a
7. Resources - Provision of study materials, reagents, materials, patients, laboraset of well defined and standard badges.”
tory samples, animals, instrumentation or other analysis tools.
Digital Badges for Scientists
- The ‘Taxonomy’
8. Data curation - Management activities to annotate (produce metadata) and
maintain research data for initial use and later re-use.
9. Writing/manuscript preparation - Writing the initial draft.
10. Writing/manuscript preparation - Critical review, commentary
or revision.
Badge Images: BioMed Central Design team ,CC-BY 4.0
11. Writing/manuscript preparation - Visualization/data presentation.
12. Supervision - Responsibility for supervising research; project
orchestration.
13. Project administration - Coordination or management of research activities
leading to this publication.
14. Funding acquisition - Acquisition of the financial support for the project leading to this publication.
Source: Credit where credit is due, Nature, 2014 508: 312-13.
LT_115_18_23.indd 22
How digital science badges might work
Under the existing Open Badge system, a person or organisation issues a badge to a person
in recognition of skills, working experience and
achievements. These badges are validated
and kept together in a person’s digital
‘backpack’ or “digital credentialing website”, along with metadata on the criteria, description, issuer, evidence, standards, tags and data issued around that person’s badge. The “proposed work flow”
would have four steps:
Once an article is accepted, the publisher notifies the badging system and authors. BMC and PLoS will be the first publishers to test issuing and displaying the new badges on articles. A ‘PaperBadger matrix’ will be set
up for all authors to agree on who did what using
a detailed contributorship taxonomy. The badge
types and descriptions are based on a 14-role author contribution ‘taxonomy‘ (see Textbox on p.
22). This has already been tested on corresponding authors of recently published articles. Of the
29.01.15 12:55
Analysis
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Lab Times
page 23
authors who completed the survey, 82% felt the taxonomy presented the authorship in the work at least “the same” (37%) or
“better” (45%) than it had originally been shown.
Authors will fill out their roles based on the contributor taxonomy. After authors agree on who did what, the article is published. Mozilla’s Open Badges infrastructure will then issue each
author with badges that credit them for the work they contributed.
These badges appear next to the author’s name in the online version of the article and would also be linked directly to
their ORCID page.
Double-clicking on the badge takes you to the ORCID site
for that given author, where the badge would ‘live’, integrating
with an author’s entire ORCID record. ORCID provides a unique
ID to identify a researcher and will display all the badges earned
by that particular author.
This “lightweight system” will be put in place during 2015 as
a way to gather immediate feedback on the proposed workflow
and display. Mozilla’s Abigail Cabunoc says they are hoping to
use this prototype to “open dialogue with the research community and evaluate the effectiveness of a digital badge system.”
However, one factor that may initially limit the usefulness of
digital credentials is the massive amount of already published research, for which badges would still need to be implemented retroactively. Just think how many papers have been published and
the problems of retrospectively agreeing on each author’s contribution. Nevertheless, BMC’s Amye Kenall says that it will be possible to cover these older publications in “later versions of the
badge infrastructure.”
1-2015
Lab Times
page 23
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Just more metrics?
Mozilla’s Thaney thinks the badges could offer a more detailed, transparent measure of researcher productivity than existing metrics, and that this is the appeal of digital badges to universities and funding agencies. However, does science really
need more metrics? Many critics fear that increasing use of metrics has already adversely affected science (see, for example, LT
4-2012 p .20: ‘Academic values no longer add up’; LT 5-2013 p.
18: ‘Time to change how research is assessed’; LT 4-2014 p. 10:
Martin Fenner from PLoS on the development of alternative metrics to explore and evaluate scientific research).
Peter Lawrence told Lab Times that he was sceptical about
digital badges. He said that there remained the fundamental
problem of trying to numerically measure something that has no
numerical value. Furthermore, “all these things cost money and
take more and more out of science, just as endless grant applications and resubmission and rejection cycles do. I am sure this
junket will open new doors for fiddling and optimising appearance and lead into yet another tangled thicket.”
Nevertheless, the Open Badge scheme does seems to represent an attempt to provide a general chance for people to validate their experience away from formal education and diplomas.
Perhaps this could prove useful for all those research students
and postdocs who, whether by choice or lack of job opportunities, leave the research environment. After several years in research, they may have little more to show than a PhD thesis and
their name as co-author on one or two scientific publications.
Yet, they still have to explain just what they were doing during
all those years in the laboratory and how this relates to jobs in
other areas of the workforce.
Jeremy Garwood
www.sartorius.com/microsart
LT_115_18_23.indd 23
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Lab Times
Journal Club
1-2015
Photo: Fotolia/eunikas
page 24
Human genetics in Uppsala, Sweden
Working Up
a Sweat
Forty degrees in the shade and you are soaking wet. Sweating cools our bodies but members of a Pakistani family cannot rely on this bodily function, they suffer from anhydrosis. What causes this disorder? Joakim Klar in the
group of Niklas Dahl found a tiny mutation with big consequences.
I
magine the sun is shining outside. Without you giving it much thought, your
body is able to activate its in-built cooling system – aka sweat glands – and bring
your body temperature to a more pleasant
level. Sweating is a bodily function, ignored
at best and often cursed if in excess, but
without it, you may be in serious trouble.
Medically, this is known as anhydrosis and
for a particular family in Pakistan, it has become a daily plight for five of its members.
The affected family members have had
to develop ingenious ways to avoid hot
temperatures, including staying in a cellar
during the day and putting wet sheets over
their body to avoid increased heart rate and
heatstroke.
“Sweating is the number one
physical property we have to cool
down our body. What we can see
in our patients is that they completely lack sweating and they
cannot cool down when the temperature goes up,” says Joakim
Klar from Uppsala University
in Sweden and lead author in a
study published recently, looking
in-depth at what may be causing
the condition for this family (J
Clin Invest, 124, 4773-80).
After a little digging, a whole-genome
search revealed a single-amino acid mutation (glycine to serine) in amino acid 7492
in a gene called ITPR2. This gene encodes
for a type of inositol 1,4,5-triphosphate receptor, well-known for its involvement in
regulating calcium release from the endoplasmic reticulum into the cell cytosol.
What may at first glance seem like a mutation with mild consequences, has in fact a
very strong impact on receptor function. It
turns out that the “G-to-S” mutation is located in the pore domain and completely
obstructs the receptor’s ability to dispense
calcium. The mutated version of the receptor is still able to form its transmenbrane
structure with a normal calcium storage
late many cellular mechanisms throughout
the body, the next question soon became,
why is this mutation only affecting sweat
glands. The answer involves this receptor
– commonly referred to as a type 2 receptor – and two others, forming a family with
identical functions ubiquitously distributed
in the body. This means most cells will have
at least one fully working copy to compensate for the lack of active type 2 receptors.
An evolutionarily lucky deletion
LT_115_24_29.indd 24
Photo: Dahl lab
Rather incredibly, this includes the calcium storage section of the sweat glands
themselves, where type 3 receptors are
abundant. However, evolution “deleted”
these receptors from the release channels
in these glands, and only type 2
receptors seem to be present. As
a consequence, all family members affected are normal and
healthy, with the only exception
of not being able to sweat. “You
have these receptors in other
cells, and they’re important for
many functions in the body”,
says Klar, “but fortunately for
this family, the only thing that is
affected is the sweat gland, otherwise they would have problems in many cells.”
When sweating is impossible By the sweat on their brows, Niklas Dahl (centre), Joakim Dahl (2nd from
Since their discovery in the
It’s known that use of certain left) and the rest of the Uppsala team pinpointed the mutation that
late 1980s, studying these redrugs or skin conditions can affect leads to anhydrosis in a Pakistani family.
ceptors has attracted much ator block sweat glands, with the retention and their activity has
sult that sweating is impossible. In this case,
been associated with many different celluarea but this mineral cannot be evacuated
however, all family members have morpholar and physiological processes, from fertivia the excretory duct to trigger sweat prologically normal sweat glands. Intrigued by
lisation to hair loss.
duction. Not surprisingly, when the team
this conundrum, the team, led by genetiThis includes long time researcher in
conducted in vitro studies using mutated
cist Niklas Dahl, decided to explore further.
this field, Katsuhiko Mikoshiba, who has
versions of this receptor, they could not acDahl’s group often studies rare genetic dissuccessfully developed knockout mice lacktivate the cell’s normal response involving
orders, with the aim of identifying the muing each individual inositol receptor. As an
intracellular calcium oscillations.
tated genes behind them and developing
example, his team has shown that lack of
As the release of calcium from the enpotential treatments.
type 3 receptors affects taste perception for
doplasmic reticulum is essential to regu-
29/01/2015 10:03
Journal Club
1-2015
sweet, bitter and umami flavours, but not
sour or salty (J Biol Chem, 282, 37225-31).
Show me your paws
Their story was not so clear, though,
with regards to knockout mice lacking type
2 receptors. These mice managed to elude
their creators as to what their potential defects might be, until Dahl contacted the Japanese researchers and asked if they could
look at the mice’s paws. Once the reasoning
behind the curious request was explained, it
was clear why the defect had remained obscure: mice only have sweat glands in their
paws but they’re not exclusively dependant
on these glands to control their body temperature, at least certainly not to the same
extent as humans.
Not surprisingly, this made it very difficult to spot any mild problems. However, a
closer inspection in the presence of acetylcholine, working as a trigger to initiate calcium release, revealed that these animals
do lack the ability to produce sweat. Despite their once again normal sweat glands,
tests to the hind paws uncovered far less ac-
Top tip quality
for reliable analyses!
tive glands and a limited calcium release response in knockout mice compared to normal animals.
Curiously, the discovery of this mutation also gave the team some room to speculate about a potential novel treatment to
alleviate the opposite problem: too much
sweating. “If we were able to reduce this
gene function/expression, that could be
used to treat hyperhydrosis,” suggests Klar.
“Compared to anhydrosis, that is actually
quite a common problem.”
In theory, explains the researcher, this
would be simple to achieve in a cell or even
a mouse system but doing it in humans is
still in the realms of the imagination. “But
the idea is still valid and I think it would
work. It’s basically a kind of gene therapy,”
he adds.
A therapy for too much sweating
Currently, the team is planning to pursue this avenue further and have made
some preliminary progress to reduce this
gene’s function in a cell system. “It’s a big
step to go into the clinical field but we’ll
Lab Times
page 25
keep targeting this gene to see, for example,
if we can reduce sweating in different ways
in a mouse model. That is one thing we’re
planning to do in the future,” says Klar.
Anhydrosis is an extremely rare condition and before this family was discovered,
only one other example was clearly described in the literature from over ten years
ago. In the meantime, researchers and physicians have been able to identify two more
anhydrosis families, all with a similar mutation that totally blocks gene function. In
both cases the only defect seems to be lack
of sweating but future plans involve exploring further these mutations and comparing
all families affected by this condition.
As for Klar’s plans, the researcher intends to stay working with Dahl’s team,
at least for the foreseeable future. “As it is
now, I have my funding for 2015 and during
that time I’ll continue working with sweat
glands. I have quite a lot of different projects I’m working with but the sweat glands
are one of the most interesting ones. I’ll continue doing that,” he concludes.
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Plant meiosis in Vienna, Austria
The Curious Case of
R. pubera
ers in his latest paper (Nat Comm 5:5070)
how the quirky grass procreates using a
more extravagant solution. The Schlögelhofer lab’s decade-long interest has been to
understand meiotic recombination between
homologues, pairs of maternal and paternal
chromosomes, in plants.
Soon after DNA replication and at the
onset of meiosis, duplicated chromosomes
or ‘sister’ chromatids – conjoined all along
their lengths by ring-like protein complexes
– line up next to their duplex homologue,
setting the stage for recombination. Genetic exchange between homologous non-sister chromatids initiates when the DNA gets
a cut in the chromosomal arms. The protrusive strand at the cut invades the homologue and uses the latter’s complementary
sequence as a template to bandage its severed end in a repair process. Peter explains,
“During DNA repair, maternal and paterPhoto: Schlögelhofer lab
T
here’s one ulterior reason for organisms to love sex. Besides zapping our
pleasure centres, sex allows a species
to sustain itself against the odds. By increasing genetic diversity, it ensures that at least
some individuals can cope with changing
environments and protract the prevalence
of a species.
A seminal event in sexual reproduction
is meiosis. Meiosis is distinct from cell divisions of somatic cells in the way the chromosomes are distributed to daughter cells.
First, it fosters shuffling of parental DNAs
(recombination) and thus increases genetic variability. Second, it halves the chromosomal content so that the offspring receives
two sets of chromosomes, one from each
parent. These steps make but round one of
meiosis (M-I), the so-called ‘reductional’ division. The process is complete only after
the daughter cells of M-I go through round
two (M-II), which resembles the canonical
‘equational’ division seen in somatic cells.
Most sexually reproducing organisms
ditto the classical meiotic sequence, as even
subtle deviations can have dire effects in the
offspring. In humans, for instance, chromosomal errors can cause cognitive disability
such as in Down’s patients or infertility as
in Turner’s, while in plants, they account for
sterility and stunted growth among others.
Cut-copy-paste in sex cells
The sedge, a grass-like plant native to
tropical lands, is however, an exception.
Hailing from the family Cyperaceae, sedges of the Rhynchospora genus sport atypical
chromosomes that are incapable of enduring conventional meiosis. This would normally throttle breeding success but, surprisingly, these plants flourish in hot, Brazilian
wetlands. Peter Schlögelhofer, a group head
in the Department of Chromosome Biology,
Max F. Perutz Laboratories, Austria, uncov-
LT_115_24_29.indd 26
Lined-up in the regular order: Peter Schlögelhofer (last row, right), Gabriela Cabral (insert) and the rest of the team.
Photo: G. Cabral
Nature is ridden with exceptions. To Peter Schlögelhofer, the case of an exotic
sedge is a classic fit to the adage. The plant’s unusual type of chromosomes
makes cell division in sex cells rather challenging. But the flourishing species
has found a just as unusual solution to the formidable problem.
nal chromatids become chemically linked
at the cross-over site, termed chiasma, and
mutually exchange chromosomal parts, giving rise to new, chimeric genetic combinations.” This repeats at several chiasmata, resulting in patches of maternal and paternal
DNAs on both homologues.
In their previous work, the Austrian
group unveiled some of the molecular players in the repair process in the model plant
Arabidopsis. Peter elaborates, “It’s not just
about repairing the break but about shifting
the repair to the homologous chromosome
and, in the end, connecting maternal and
paternal chromosomal strands. Some of our
work has been addressing this aspect.”
The sedge paradox
Once the homologues have swapped
their DNAs, it’s time for them to segregate
into different daughter cells. To enable this,
the glue along the chromosomal arms dissolves, freeing the homologues, while sisters are still joined at the centromere. Molecular ropes or microtubules (MTs), from
the two ends of the cell, latch on to the centromere via the kinetochore protein complex. The MTs now pull the attached sister
chromatids to one pole of the dividing cell,
while the homologous non-sister chromatids are simultaneously drawn to the opposite pole. “In classical meiosis, homologues
are separated at M-I, while sister chromatids are still joined at the centromere and
migrate together. At M-II, the cohesion between sister chromatids that remained in
the region of the centromeres is lost and
the sisters now separate,” elaborates Peter.
The successive loss of the glue, first
along the chromosome arms and then at
the centromeres, is what preserves this meiotic sequence and ensures that the chromosomes are segregated in correct numbers
and as correct sets.
29/01/2015 10:03
Journal Club
“Our latest paper was inspired by a
shared student, Gabriela. She brought two
species of Rhynchospora – R. pubera and R.
tenius from her hometown in Brazil. They
do not have the typical monocentric chromosomes but instead exhibit holocentricity.” Conventional meiosis works for monocentric chromosomes (MCs) with a single centromeric region and localised kinetochore. “Here, the arms are free of kinetic
activity and can engage in cross-over, loosen up from the homologues and trail behind
the centromere when sister chromatids rise
towards the poles,” Peter explains.
Holocentric chromosomes (HCs), on
the other hand, bind kinetochore proteins
all along their lengths. “Cross-overs are
problematic [in HCs]…The recombined
DNA should not be attached to kinetic activity but be able to move around freely. Besides, there’s difficulty with proper segregation if everything is connected all the time,”
he continues. For the right chromosomes to
be packed into the right cells, it is important
for homologues to first pair up and sort out
and then, in a second round, have the sister
chromatids separate.
Nature’s quirky solution
Rhynchospora are not the only organisms with HCs. HCs have shown up time
and again, in both plants and animals, during evolution. It is not known, which came
first – the HCs or the MCs. How HCs crossover and sort out during meiosis has puzzled scientists for quite some time. There is
some evidence for alternative routes to canonical meiosis in these species. “It’s likely that the holocentric chromosomes still
behave as monocentrics, as in the worm
C. elegans. But a more interesting possibility is that they engage in inverted meiosis,
though there is only vague support for this
from insect studies,” Peter draws attention
to a novel form of meiosis, in which the sequence of events is reversed.
When they probed into the distribution
of chromosomes in R. pubera at M-I, the
Austrian group instantly realised what they
were getting at. For an organism with five
pairs of chromosomes, R. pubera should exhibit five pairs of sister chromatids at each
pole. But instead, there were up to ten individual chromatids at either pole. This
meant that the sister chromatids are already
separated at M-I in a likely inverted meiosis.
These chromatids mostly stayed connected
to their homologues by visible DNA threads.
The connections were presumably pivotal to
the proper segregation of the homologous
non-sister chromatids at M-II.
1-2015
Lab Times
page 27
In an elegant experiment using a hetero­
morphic chromosome pair, the group bolstered their findings. “The main moment
came when we generated plants with a broken homologue for chromosome 2,” Peter
recollects. The two fragments of the fractured homologue were replicated normally
and could be readily followed by DNA staining. If sisters separated first, they expected to see equal numbers of stained structures in both M-I daughter cells; whereas,
if homologues separated first, the structures would be distributed unequally, with
one cell receiving the intact and the other,
the fragmented version of chromosome 2.
It was clearly the first case, so they safely
concluded that R. pubera indeed exhibits
an upside-down meiosis.
“Step away from models”
“We always thought inverted meiosis
was amiss. There’s been very little evidence
in favour of it. But our studies on R. pubera
and R. tenius have both confirmed that it
does exist in nature.” R. tenius is even more
peculiar. It displays an achiasmatic inverted
meiosis, with no signs of genetic exchange
between homologues. “Besides these examples, Andreas Houben from the Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany has demonstrated inverted meiosis in yet another
plant, Luzula elegans,” Peter summons another paper, published in the same issue as
theirs with similar findings (Nat Commun,
5:4979). “We now appreciate that inverted
meiosis is a specific adaptation of sexually reproducing organisms with holocentric
chromosomes to distribute their chromosomes correctly during meiosis.”
It’s fascinating that Nature comes up
with novel solutions to quaint problems,
but why does it create them in the first
place? Peter responds wittily, “It’s just Nature’s way to reconcile innovation and tradition.” But he agrees that we do not yet
completely understand the implications of
such bizarreness. “We lack the resources for
comparative analysis of the biology of exotic species, to see how different they are. A
part of the problem is the over-reliance on
model organisms for research. These models do not represent the entire biodiversity.
But all our tools are derived from and represent only these prototypes,” he shirks. However, he ends on an optimistic note, “Novel
technologies such as deep sequencing and
CRISPR/Cas9 may make it easier for us to
expand our studies into diverse organisms.”
Eliminate the
hassle and expense
of spin columns
100% sample recovery – no loss
of PCR products regardless of the
fragment size
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Take the Challenge
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startup pack at:
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Madhuvanthi Kannan
© 2014 Affymetrix Inc.
All rights reserved.
LT_115_24_29.indd 27
29/01/2015 10:03
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Lab Times
Journal Club
1-2015
Preventive DNA repair in Budapest, Hungary
Import-ant Information
Despite their important role in nucleotide metabolism, the dUTPase enzyme family is everything but well-researched.
The enzymes’ nuclear import, for instance, is still far from being fully elucidated. But Beata Vértessy and Gergely
Róna are on the case.
T
dUTPase activity is a key element to achieve
this,” explains Beata Vértessy, group leader at the Laboratory of Genome Metabolism
and Repair at the Institute of Enzymology
of the Hungarian Academy of Sciences in
­Budapest, Hungary.
First contact
Vértessy has been doing research on
structures of dUTPases and also on their
contribution to correct replication of genetic information since her postdoctoral
fellowship at the University of Saarland,
Germany, where she first got in touch with
these hydrolases. Prior to that, Vértessy
studied at the Technical University in Budapest (BME) as well as at the University of
Chicago, USA, where she graduated with a
Master’s Degree in Biochemistry. Although
Images(2): Vértessy lab
o our current knowledge, the enzyme
family of dUTPases is found ubiquitously in all organisms as well as in
many viruses. It is responsible for preventive DNA repair and hence, maintenance of
genetic stability. In eukaryotic cells, this is
achieved by eliminating dUTP-nucleotides
in close proximity to DNA and thus, avoiding the incorporation of the base uracil,
which should only be present in RNA, into
the DNA strand, instead of the required thymine. This may occur since most DNA polymerases are not able to distinguish between
dUTP and dTTP. In consequence, the ratio
of dUTP and dTTP concentrations determines the composition of the newly synthesised DNA strand.
The fact that dUTPases are evolutionarily highly conserved underlines their im-
she founded a state-of-the-art structural bio­logy laboratory (www.biostruct.org/
bio­struct) at her alma mater BME. Now, the
biochemist focusses on preventive DNA repair via the dUTPases enzyme family and on
uracil-DNA signalling, combining structural and cell biology, from bacteria to human.
One of her latest papers describes how
nuclear localisation signals (NLS), as part
of the enzyme, influence the import of different dUTPases into the nucleus. This is
shown with the aid of different enzymes
derived from two Drosophila species and
an engineered artificial construct (FEBS J,
281(24):5463-78).
Translation of dUTPase mRNA into protein takes place in the cytoplasm. It is, however, assumed that dUTPases need to be
present within the nucleus, where DNA is
replicated, to fulfil their task. Since these
large enzymes are not able to enter the cell
nucleus through a nuclear pore complex by
diffusion, they need to be transported actively across the membrane. This entry is
promoted by a NLS that binds to an importin molecule, which, in turn, initiates the
cross-membrane import.
Molecular differences of fruit flies
A passion for essential enzymes: Beata Vértessy (in red),
Gergely Róna (front row, 3rd from left) and Co.
portance for proper DNA replication and
stabilising the genetic information within
the cell. “It is crucial for DNA replication
during the S phase of the cell cycle that the
strands are composed of the proper dNTPs.
LT_115_24_29.indd 28
she, from time to time, carried out her research abroad – in Sweden, Germany and
the USA – the Institute of Enzymology of
the Biological Research Centre in Budapest
can be seen as her home base. In addition,
The structure of all known dUTPases
is very similar. “Most dUTPases are homotrimers, such as the nuclear (Nuc) and cytoplasmic (Cyto) dUTPase isoform in D. melanogaster. Three identical subunits are held
together by non-covalent forces such as hydrogen bonds, van der Waals interactions
and ionic interactions,” explains Gergely
Róna, molecular biologist and lead author
of the FEBS paper. Interestingly, Vértessy
and Róna recently discovered and characterised a divergent dUTPase in D. virilis, in
which all three subunits are linked covalently. This pseudo-heterotrimer only possesses a single NLS in contrast to the Nuc-
29/01/2015 10:03
Journal Club
dUTPase of D. melanogaster that is equipped
with three NLSs, one at each subunit.
The researchers now hypothesised that
the number of NLSs influences the transport of molecules into the nucleus. To test
their assumption, they designed dUTPase
constructs with three, one or no NLS at all
and investigated those thoroughly in cell
culture and by using isothermal titration
microcalorimetry (ITC). This latter method enables the scientists to draw conclusions about complex formation of NLS-containing proteins with importin molecules by
measuring the increase in enthalpy of the
system. “ITC is a wonderful technique for
label-free interaction studies in the solution
phase,” Vértessy points out.
With their experiments, the Hungarian researchers could show that the number of NLSs correlates with the amount of
dUTPases detected within the nucleus: the
more NLSs a molecule possesses, the more
efficiently it is transported into the nucleus.
However, the mechanism behind that phenomenon is not yet entirely clear and still
needs to be investigated more thoroughly.
Can all NLSs of a single enzyme bind to several importins simultaneously? Does this, in
turn, lead to an accelerated translocation
into the nucleus? Or are there steric effects
that avoid the binding of more than one
importin in a physiological situation? Up
to now, this is not clear. But Róna describes
the outcome of a recent cell culture study,
“All in vitro data proved, beyond reasonable doubt, that every NLS site is accessible
and thus can bind to importin-α molecules.”
Prize-winning research
The work of Vértessy and her research
team is recognised internationally and was
also rewarded with several prizes, e.g.
the Scientia Europaea Prize, the l’Oréal-­
UNESCO prize and two International Scholar awards for biomedical scientists of the
Howard Hughes Medicines Institute (US).
Although the biochemist has been studying ­dUTPases for more than 20 years, the
enzymes are still shrouded in many mysteries. For instance, in eukaryotes, as mentioned above, nuclear presence is thought
to be indispensable for proper dUTPase
function. So far, there has been no experimental proof of this hypothesis. “It is generally accepted that dUTPase is essential
for viability of the cell. However, no direct
evidence has yet been published for the
essentiality of the nuclear presence,” explains Vértessy. She and her research team
are currently working on this aspect. Another interesting, and still mysterious, topic is
LT_115_24_29.indd 29
1-2015
Lab Times
page 29
the Cyto isoform in D. melanogaster. Since
this homo­trimer lacks any NLS, it cannot
be translocated into the nucleus. So, does
this protein serve any purpose at all? “Unfortunately, we do not know yet!” regrets
­Vértessy. Maybe this protein developed due
to loss-of-function, maybe there is more to
it. The research team is also currently addressing this question with the help of different knock-out models and rescue scenarios.
Your
SAFETY
is relevant to us!
Relevant for our species
Gergely Róna enjoys doing research at
Vértessy’s Laboratory of Genome Metabolism and Repair, where he is working on
his doctoral thesis at the moment, “One of
the best things about this lab is that you can
work around a biological problem with regard to many different aspects of structural biology, biochemistry or cell biology,” he
says. During his doctoral time, he was mainly focussing on the regulation of intracellular trafficking of different dUTPases. “We
found that the nuclear availability of the
dUTPases is regulated on several levels by
limited proteolytic digestion, NLS adjacent
phosphorylation as well as by the number
of NLSs.”
The team’s fly results may also be of
interest for us humans, as we also possess
dUTPases. Similar to D. melanogaster, there
are two different isoforms present in human cells: a nuclear and a mitochondrial
one, which are both homotrimers. The nuclear form is further characterised by three
NLSs. Vértessy and her group is also working very hard to reveal potential additional
physiological roles of uracil occurrences in
DNA. “Curiosity is among the most important factors of human development. Also,
scientific research is a process filled with
joy every day as we try to understand the intriguing questions of life. Yes, there are dark
moments, when nothing seems to work, but
these are easy to forget at the next discovery,” summarises Vértessy her profession
and why she is still happy about choosing
to be a scientist.
Lighting up the darkness
It is assumed that a dysfunction of
­ UTPases may lead to cell death. Hence,
d
Vértessy hypothesises that manipulation of
these hydrolases or the underlying mechanism of DNA repair could be used to specifically induce apoptosis in tumour cells.
Nevertheless, this mechanism still remains
in the dark. Vértessy and Róna are sure to
shine light on it, soon.
Stefanie Haas
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29/01/2015 10:03
Lab Times
Ranking
1-2015
Photo: Fotolia/manfredxy
page 30
Publication Analysis 2005-2011
Toxicology
“G
uilty” said the man in the back, “He’s guilty and must
die,” yelled another. The executioner, knowing, nodded his head and crushed the hemlock leaves to prepare the convict’s final drink. As the toxic liquid flowed through
his body, his feet became numb, then his legs – but he was still
wide awake. When the poison reached his diaphragm, he stopped
breathing and died a peaceful but tragic death.
Poison hemlock (Conium maculatum) is one of the most toxic
plants in Europe (besides the wolf’s bane, Aconitum napellus). Its
most potent toxin, coniine, binds to nicotinic acetylcholine receptors of the peripheral nervous system, causing ascending muscular paralysis. In ancient Greece, it was served as a death cocktail
to damned delinquents – just like philosopher Socrates. Having
toxicological knowledge, however, was not only advantageous in
old-fashioned jurisdiction; more recently toxins have also helped
to unravel basic biological relations. The insecticide rotenone,
for instance, was used to elucidate the workings of the respiratory chain in mitochondria and 19th century French physiologist,
Claude Bernard, studied the neuromuscular junction with the arrow poison, curare. Speaking of bows and arrows, the world ‘toxicology’ is derived from the ancient Greek word τόξον (tókson),
meaning bow.
Modern toxicologists are, however, a little bit less interested
in naturally occurring toxic substances. Many of them focus more
on man-made compounds with as yet unknown effects on health
and ecosystems, as we shall see later.
First, let’s have a look at European countries’ performance in
toxicology-themed research. As we haven’t yet figured out a way
to filter out toxicological papers from multidisciplinary journals,
the numbers for total citations, articles and the citation-per-article ratio are based on specialist journals like Aquatic Toxicology, Nanotoxicology or Toxicological Sciences only. For the most-cited authors in toxicology, we decided not to discriminate between
specialist and non-specialist journals.
Good ratios for Slovakia, Scotland and Switzerland
No surprise at the top of the nations’ performance list: England and Germany are the top two countries, far ahead of France
and Italy in third and fourth place. Turkey scored a good 12th
place but another country pushed itself to the fore even more.
Despite just about missing the top 20, Slovakia is the undisputed number one when it comes to citations-per-article (30.3). Not
even Scotland (28.1) and Switzerland (26.0) were able to keep
LT_115_30_33.indd 30
Toxicological research has turned from the
study of naturally occurring toxins to manmade contaminants, effecting our health and
ecosystems. Highly cited toxicology labs are
found all over Europe, with hot spots in Edinburgh and Stockholm.
up. The global comparison revealed one more surprise. Whereas in other disciplines they are usually way behind their US colleagues, here, European toxicologists received more citations per
article than their US peers, or from any of the analysed countries,
for that matter.
Now, we have arrived at toxicology’s hottest papers, published
between 2005 and 2011. Interestingly, four of the top five papers
are about cytotoxicity. How does basic cell biology relate to toxicology? In 2006, Sten Orrenius and Boris Zhivatovsky from the
Karolinska Institute in Stockholm rhetorically asked: Does it matter how cells die? Their prompt answer: “Yes, for our understanding of chemical hazards and the mechanisms by which toxicants
can damage our cells and tissues, it certainly does! Cell death is
the ultimate result of toxicity, and elucidating the signalling pathways involved is highly relevant for our understanding of the cellular targets and mechanisms of action of chemical toxins.”
With their cellular toxicology approach, Orrenius (16th) and
Zhivatovsky (4th) also secured themselves a spot in the top 30 toxicologists in Europe. Once again, it wasn’t easy to separate the
‘toxic’ wheat from the ‘non-toxic’ chaff. A most important criterion for inclusion was the number of papers in toxicology specialist
journals. To epidemiologists, we paid special attention and decided on a case-by-case basis.
‘Toxic clusters’ in Sweden and Scotland
Considering the researchers’ home affiliations, all four corners of Europe are well-represented in our top 30. North (Sweden, Denmark), East (Czech Republic), South (Spain, Italy, Portugal) and West (England, Belgium, Germany, Scotland, Austria, the Netherlands) – toxicology is an important research discipline almost everywhere in Europe. But there are ‘toxic clusters’:
the University of Edinburgh (fielding three researchers) is one
and the Karolinska Institute in Stockholm (fielding four) another.
Among our top 30 are also three women.
The dangers from eating poisonous plants seem to be more
or less eliminated but that doesn’t mean we are safe from toxic
harm. On the contrary, we, or our bodies, now have to deal with
modern poisons in the air, our food, drinking water, clothes and
homes. The majority of our top 30 toxicologists, thus, monitors
or studies health effects of exposure to toxic substances, such as
nanoparticles and nanomaterials (Vicki Stone, 5th; Rodger Duffin,
10th; Steffen Loft, 12th; Richard Handy, 22nd), metals, like cadmium, mercury and lead (Josep Domingo, 6th; Marie Vahter, 14th),
29/01/2015 11:13
Ranking
flame retardants used in furniture, for instance, (Adrian Covaci,
2nd; Åke Bergman, 19th), pesticides (Jürgen Angerer, 8th) and endocrine disruptors (Colin Janssen, 28th).
Environmental pollutants do not only affect human health.
Wildlife, particularly aquatic wildlife, has to cope with a mélange
of unnatural and toxic compounds in their habitat. Ecotoxicologists like Ronny Blust (11th), Charles Tyler (15th) and Amadeu
Soares (29th) want to understand whether or how these chemicals interfere with the physiological and or developmental processes of fish, water fleas and sea snails.
Not to forget the clinical toxicologists, who study the safety of
drugs. B. Kevin Park (9th), for instance, looks into drug-induced
liver injury and drug-induced cutaneous toxicity. Hans Maurer
(25th) experiments with designer drugs and their toxicity.
And finally, we come to the usual ‘outliers’, including our
number one, Mark Cronin from the University of Liverpool. He
approaches toxicology in the in silico way, predicting the toxicity
of industrial chemicals, pharmaceuticals, cosmetics and food additives. Currently, he coordinates the EU COSMOS project – Integrated In Silico Models for the Prediction of Human Repeated
Dose Toxicity of COSMetics to Optimise Safety. The project’s main
aim is to “develop freely available tools and workflows to predict
the safety to humans following the use of cosmetic ingredients”.
At the moment, the COSMOS database comprises more than
12,000 toxicity studies for more than 1,600 compounds.
Rudolf Krska (20th) is set apart from the majority of the other top 30 researchers by studying naturally occurring toxins, viz.
mycotoxins. In his lab in Tulln an der Donau, he works on methods to detect mycotoxins in food and feed.
What toxicology can teach us
As we have learnt during our current publication analysis,
toxicology also grapples with a well-known problem – reproducibility of research data. In a recent editorial in Particle and Fibre
Toxicology, Rodger Duffin and colleagues from Edinburgh and
The Netherlands, write: “The issue of reproducibility of results
in toxicology has long been a concern and, perhaps, at the back
of many of our minds but not necessarily at the forefront of our
thinking. Are the results we have published literally our results or
are they reproducible and truly part of a credible theory?”
In particular, Duffin et al. point out the importance of accurate
method description as “even minor modifications of conventional
in vitro toxicity assays (e.g. due to sample handling/preparation
issues) can have an important impact on study reproducibility”.
Hence, Duffin and co. suggest five ‘practical points’ every particle toxicologist should take to heart:
Be specific. If it’s graphene, then is it actually graphene, i.e.
a monolayer, or is it few-layer graphene, or graphite platelets?
Characterise, characterise, characterise. Characterise in relation to your hypothesis or research question.
Use statistics to question your results rather than simply
confirming a theory.
Write your hypothesis in advance of running the experiment. If your theory is robust it should survive your best efforts to
challenge it.
Take a ‘belts and braces’ approach to confirming findings.
Use multiple approaches, doses, time points, replicates and controls. You don’t want to be caught with your trousers down.
This advice surely applies not only to toxicology but to all biological disciplines.
Kathleen Gransalke
LT_115_30_33.indd 31
1-2015
.
Lab Times
page 31
Europe...
Country
1. England
2. Germany
3. France
4. Italy
5. Netherlands
6. Spain
7. Sweden
8. Switzerland
9. Denmark
10. Belgium
11. Norway
12. Turkey
13. Scotland
14. Finland
15. Portugal
16. Poland
17. Czech Rep.
18. Greece
19. Ireland
20. Austria
Citations
Articles
Cit./Art.
73,096
71,043
49,162
45,708
34,247
32,569
29,152
25,085
21,583
18,740
15,815
14,543
13,772
12,105
11,750
11,371
9,777
6,977
6,556
5,971
3,038
3,401
2,541
2,542
1,627
1,862
1,370
964
882
890
824
1,233
491
603
711
877
632
369
290
296
24.1
20.9
19.4
18.0
21.1
17.5
21.3
26.0
24.5
21.1
19.2
11.8
28.1
20.1
16.5
13.0
15.5
18.9
22.6
20.2
Articles appearing between 2005 and 2011 in ‘Toxicology’ journals as listed by SCImago and Thomson Reuters’ Web of Science. The citation numbers are accurate as of November 2014. A
country’s figures are derived from articles, where at least one author working in the respective European nation is included in the
authors’ list. Israel is included because it is a member of many
European research organisations and programmes (EMBO, FP7 of
the EU...).
... and the World
Citations
Articles
Cit./Art.
Europe
401,111
22,090
18.2
USA
China
Canada
Japan
India
South Korea
416,080
60,623
58,635
57,815
37,012
28,913
27,436
4,883
3,689
5,425
3,120
3,003
15.2
12.4
15.9
10.7
11.9
9.6
29/01/2015 11:13
page 32
Lab Times
Ranking
1-2015
Publication Analysis 2005-2011 – Toxicology
Most Cited Authors...
Cit- Artations icles
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
Mark T. D. Cronin, Pharm & Biomol Sci, Univ Liverpool
Adrian Covaci, Toxicol Ctr, Univ Antwerp
Ken Donaldson, Ctr Inflammat Res, Univ Edinburgh
Boris Zhivotovsky, Inst Environm Med, Karolinska Inst, Stockholm
Vicki Stone, Sch Life Sci, Heriot-Watt Univ, Edinburgh
Josep L. Domingo, Toxicol & Environm Hlth, Univ Rovira & Virgili, Reus
Kamil Kuca, Chem, Univ Hradec Králové
Jürgen Angerer, Prevent & Occupat Med, Univ Bochum
B. Kevin Park, Inst Translat Med, Univ Liverpool
Rodger Duffin, Ctr Inflammat Res, Univ Edinburgh
Ronny Blust, Biol, Univ Antwerp
Steffen Loft, Publ Hlth, Univ Copenhagen
Jan G. Hengstler, IfADo, Dortmund
Marie Vahter, Inst Environm Med, Karolinska Inst, Stockholm
Charles R. Tyler, Biosci, Univ Exeter
Sten Orrenius, Inst Environm Med, Karolinska Inst, Stockholm
Dominique Lison, Ctr Toxicol & Appl Pharmacol, UCL Brussels
Bernd Kaina, Toxicol, Univ Mainz
Åke Bergman, Environm Chem, Univ Stockholm
Rudolf Krska, Agrobiotechnol, Univ Nat Resources & Life Sci, Tulln
Bengt Fadeel, Inst Environm Med, Karolinska Inst, Stockholm
Richard D. Handy, Sch Biol Sci, Univ Plymouth
Ian Kimber, Fac Life Sci, Univ Manchester
Peter Møller, Publ Hlth, Univ Copenhagen
Hans H. Maurer, Exp & Clin Toxicol, Univ Saarland, Homburg
Stefano Bonassi, Clin Mol Epidemiol, San Raffaele Pisana, Rome
Micheline Kirsch-Volders, Lab Cell Genet, Vrije Univ Brussels
Colin R. Janssen, Environm Toxicol & Aquat Ecol, Univ Ghent
Amadeu M. V. M. Soares, CESAM, Univ Aveiro
Martin van den Berg, Inst Risk Assessment Sci, Univ Utrecht
... and Papers
6,202
6,139
5,705
5,071
4,278
3,689
3,612
3,596
3,580
3,561
3,541
3,524
3,516
3,381
3,307
3,082
2,986
2,841
2,802
2,767
2,733
2,699
2,674
2,568
2,519
2,514
2,508
2,470
2,439
2,410
84
150
71
74
54
151
261
101
106
42
162
103
101
92
80
34
72
76
88
85
69
44
97
60
104
66
54
128
161
53
Boris Zhivotovsky (4.)
Josep Domingo (6.)
Steffen Loft (12.)
Marie Vahter (14.)
Richard Handy (22.)
Colin Janssen (28.)
Amadeu Soares (29.)
Citations of articles published between 2005 and 2011
were recorded up until Nov. 2014 using the Web of Science database from Thomson Reuters. The “most-cited papers” had correspondence addresses in Europe or Israel.
1. Valko, M; Leibfritz, D; Moncol, J; Cronin, MTD; Mazur, M; Telser, J
Free radicals and antioxidants in normal physiological functions and human disease.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY 39(1):44-84 2007
2. Valko, M; Rhodes, CJ Moncol, J; Izakovic, M; Mazur, M
Free radicals, metals and antioxidants in oxidative stress-induced cancer.
CHEMICO-BIOLOGICAL INTERACTIONS 160(1):1-40 MAR 10 2006
3. Valko, M; Morris, H Cronin, MTD
Metals, toxicity and oxidative stress.
CURRENT MEDICINAL CHEMISTRY 12(10):1161-1208 2005
4. Van den Berg, M; Birnbaum, LS; Denison, M [...] Tysklind, M; Walker, N; Peterson, RE
The 2005 WHO reevaluation of human and mammalian toxic equivalency factors for dioxins and dioxin-like compounds.
TOXICOLOGICAL SCIENCES 93(2):223-241 OCT 2006
5. Bakkali, F; Averbeck, S; Averbeck, D; Waomar, M
Biological effects of essential oils - A review.
FOOD AND CHEMICAL TOXICOLOGY 46(2):446-475 FEB 2008
LT_115_30_33.indd 32
Vicki Stone (5.)
Citations
3,256
1,864
1,342
1,151
1,095
29/01/2015 11:13
Opinion
1-2015
Lab Times
page 33
What’s behind paper retractions? (26)
A Second Chance for Fraudsters?
Not for those who are recidivists. Retraction Watch will expose them.
I
Hiding a bad name
Photo: Photocase/zettberlin
n late December, we wrote about an
economist in Pakistan, Khalid Zaman,
who’d faked peer review on at least 16
papers. We also reported that Zaman had
been seeking a job at a new institution, and
that his application, which we’d obtained,
made no mention of his retractions, nor of
why he had suddenly left his previous institution.
A number of commenters on Retraction Watch said – some quite vehemently –
it wasn’t fair game for us to cover Zaman’s
search for employment. Some objected specifically to the fact that we had published
passages from his application, while others
argued more globally that we should stick
to retractions and not concern ourselves
with the effects on someone’s
career. Let hiring managers
figure that out, they wrote.
We were bullying Zaman.
We always appreciate constructive criticism and will
take all of those comments
to heart. But we believe very
strongly in the need to follow
up on retractions, particularly
their effect on careers. Here’s
why:
Although we certainly believe that everyone deserves a
second chance, it’s also clear
that many fraudsters aren’t really looking
for a fresh start as much as a place where
no one knows their bad name. Take, for example, the case of Scott Weber, a nursing scholar who left the University of Pittsburgh under a cloud but was able
to land a new job at another school because
Pitt did not provide a comprehensive reference. Or Michael Miller, who was found guilty
of misconduct using Federal U.S. grants and
was hired by a grant-writing consulting
firm, where his bio boasted of winning the
very grants on which he committed fraud.
He lost that job when we contacted the CEO
of that firm.
Or Yoshitaka Fujii, the record holder
for retractions, whose career of misconduct
spanned at least four Japanese medical centres that we’re aware of.
LT_115_30_33.indd 33
Or Igor Dzhura, who faked more than
70 images while at Vanderbilt, then landed a job at Novartis – which he lost as soon
as they learned that he had lied on his application.
To be sure, a common thread of these
cases is poor reference checks. But in our
experience, fraudsters tend to be recidivists. They cheat until they get caught and
if they have an opportunity to cheat again,
they take it.
Let’s be clear: The mere fact of having a retraction on one’s CV should by no
means be a disqualification for a job. After all, retractions often are a sign that science is working as it should by being selfcorrecting.
Indeed, Retraction Watch
has a category called “Doing the Right Thing” to commend researchers who correct the record even at personal expense. These authors should be rewarded,
not punished and, in fact,
evidence suggests that they
do experience a sort of trust
dividend among their colleagues.
Exposing deceivers
So it’s all the more important that scientists, who
take the opposite approach
by hiding their misdeeds from public scrutiny, trying to whitewash their resumes and
generally being dishonest about their work,
be exposed.
As blogger Neuroskeptic put it: “If he
were to quit academia and apologize, then
perhaps we could say ‘he’s learned his lesson’ and let’s leave him alone – but no, that
hasn’t happened. Instead he’s trying to take
an academic job that ought to go to someone more honest.”
“If he takes this job, an honest (most
likely Pakistani) economist will be unemployed in his stead,” Neuroskeptic continued. “That’s unfair.”
CytoPainter
staining reagents
Fluorescent dyes
for staining cells
and organelles
Multiple colours
Multiple applications
Maximum photostability
abcam.com/cytopainter
Adam Marcus and Ivan Oransky
(The authors run the blog Retraction
Watch: http://retractionwatch.com)
29/01/2015 11:13
page 34
Lab Times
Biobusiness
1-2015
Belgium: €430 million Parkinson’s deal
No More Tremors?
Photo: Albert Londe
A man with Parkinson’s
disease displaying
a flexed walking
posture.
Is there hope for those seven (or ten) million
globally who suffer from Parkinson’s disease
(PD)? After UCB, the Brussels drugmaker,
bagged a collaboration deal with Neuropore
(headquartered in San Diego), at least one
thing is clear: Again, a lot of money has been
raised to tackle the roots of PD. While current therapies aim to manage the early motor symptoms of the disease (and fail as the
disease progresses), the partners’ strategy is
to stabilise conformations of α-synuclein, the
brain protein whose misfolding is related to
the disease, by using NPT200-11. This experimental drug that, “addresses a fundamental pathological mechanism” and thus medicates PD “at the roots”, is an orally bioavailable small molecule that blocks the pathological protein misfolding and aggregation that
contribute to synaptic dysfunction and cell
death in PD. However, NPT200-11 has only
proved beneficial in animal models so far. So
it must first prove itself in human patients.
For junior partner Neuropore, the contract is unquestionably a jackpot. UCB’s
€430 million has ensured their survival for
years ahead. Later this year, both will start
phase I trials with NPT200-11.
-wk-
Belgium, Sweden: Successful financings
Planning Implants
Relief in Flanders: Belgium’s FEops, a supplier of 3D simulation tools for cardiovascular interventions, has secured a €1.3 million financing round. The money will, “support the launch of FEops’ first product, TAVIguide, in Europe and the US”. TAVIguide is a
cloud -based pre-operative planning service
for transcatheter aortic valve implantation
(TAVI) that aims to reduce time (“days in-
Photo: Nanthealth
Wo r ld ’s r ic h e s t d o c to r : “ f ra u d u l e n t a c tiv ities” ?
Fierce Accusations
Patrick Soon-Shiong is referred to as “the richest doctor who ever
lived” by Forbes Magazine. That might be correct, given his reputed fortune of €11.6 billion. Born 62 years ago in South Africa to
Chinese immigrant parents, Soon-Shiong became a doctor at the
age of 23, performed revolutionary human islet transplantations
in diabetes patients at the age of 41, invented protein nanoparticle delivery technologies for cancer treatment, issued 50 patents,
published 100 scientific papers and founded two pharmaceutical
companies that formed the basis for his wealth. In 2009, it was
reported that Soon-Shiong had returned to his alma mater, the
University of California, Los Angeles (UCLA), to work as a professor of microbiology, immunology, molecular genetics, and bioengineering (although your Lab Times reporter is sceptical that “the
wealthiest person in Los Angeles”, according to the LA Business
Journal, really spends time worth mentioning at UCLA).
The same magazine that reports annually on his wealth,
Forbes, now tells us that doctor Soon-Shiong is accused of involvement in “fraudulent activities”. Two former executives of one
of Soon-Shiong’s companies, NantHealth, claim that the company, “has repeatedly violated federal regulations, endangered
patient privacy and misled the public about what its technology
can do” (according to Forbes). NantHealth is a healthcare IT firm
that offers a cloud-based clinical operating system, which pools
vital signs and patient data from numerous hospital devices, thus
providing a real-time supply of medical information. Combining
LT_115 Business.indd 34
stead of months”) as well as cost. In Europe,
the implantation of coronary stents used to
reopen narrowed blood vessels has risen to
800,000 every year. When designing such
tiny implants, cardiovascular surgeons still
have to proceed in a clumsy process of trial and error. FEops’ pre-operative planning
technique has the potential to replace more
oldfashioned procedures, by combining preoperative CT imaging with advanced computer simulations, according to company officials. If that works, both patients as well as
health insurance companies will benefit. The
company was founded in 2009 as a spin-off
by scientists from the University of Ghent.
Swedish-American biotech Cortendo,
was also successful in getting private funding. The Gothenburg-based company raised
€24 million, dedicated to pushing their rare
disease drug candidate, COR-003, further
through late-stage trials. Just a few months
ago, in October 2014, Cortendo had raised
an initial €10 million to launch their phase
III project. COR-003 is a “safer and better targeted” version of the generic ketoconazole, which medicates Cushing’s syndrome, a potentially lethal orphan endocrine disorder that is characterised by an
-wkoverproduction of cortisol.
cloud computing, genomic analysis
and targeted drug development will,
according to Soon-Shiong, result in
faster diagnoses and better outcomes for cancer patients.
Combining a patient’s hospital data with genetic information – a Brave New Big Data World if it works, isn’t it? But the two
ex-employees actually hired to prepare NantHealth’s IPO, “discovered that [the company’s executives] were engaged in a multitude
of fraudulent activities, which would, if known to investment bankers, customers and the public... substantially devalue the company’s stock and likely cause the end of the IPO.” They claim that
NantHealth’s technology is of bad quality, more expensive than
competitors’ products and, even worse, was violating FDA regulations, according to a lawsuit they filed against NantHealth (http://
de.scribd.com/doc/252711149/NantHealth-lawsuit). Both
allege that they were dismissed after disclosing these issues to
NantHealth’s management and are suing for damages, based on
a Florida law designed to protect whistleblowers from being fired.
NantHealth’s COO, Steve Curd, told Forbes that all allegations
were “false”. Both were sacked because of their “improper behavior” and had then threatened to “launch a smear campaign” if they
didn’t get hush money (they supposedly demanded $2 million).
While “Soon-Shiong’s Big Data venture” (FierceBiotech) has now attracted more than €100 million in investment, the case raises serious doubts that their planned IPO will proceed as scheduled. -wk-
Patrick
Soon-Shiong
28.01.15 23:23
Biobusiness
1-2015
Lab Times
page 35
Airbrushed results at Asia’s leading contract research organisation?
Fishy Trials
I
t seemed no more than a routine trip
when a French regulatory inspector
arrived at GVK Bio’s clinical facility in
Hyderabad, India, on 19th May 2014. Sent
by the French drug regulatory authority,
ANSM, the scientist audited the medical reports of nine clinical trials of generic drugs
that were conducted by GVK between 2008
and 2013. In these “bioequivalence studies”,
a commercially-available brand product and
a potential generic product, are compared to
ensure that their therapeutic activities are,
to all intents and purposes, the same.
“Nothing extraordinary”, he may have
thought. But as the data became more puzzling, the Frenchman’s five-day flying visit
became explosive. At the end, none of the
nine reports could be signed off. Quite the
reverse: Some of GVK Bio’s staff had apparently falsified their findings, at least partly,
in all of the studies reviewed.
Fraudulent electrocardiograms
What happened then was a heated behind-the-scenes investigation. The initial findings from May were checked and
re-checked by European authorities over
the summer. In September, the ANSM announced that they had found systematically fraudulent check-out electrocardiogram
(ECGs) recordings of trial participants.
Some of these data were purely fictional.
At least ten different GVK Bio employees
were involved, over a period of at least five
years (2008 to 2013). Their motives are unknown, as is whether they were acting on
their own initiative.
European regulatory authorities concluded that there was a lack of compliance
with good clinical practices at GVK Bio, and
that studies conducted at the Hyderabad facility don’t meet necessary standards. This
raises the question of whether any of GVK
Bio’s bioequivalence studies met the requirements.
No media coverage for months
It is astonishing how long it took before
the European public learned of the sloppi-
LT_115 Business.indd 35
ness in India. Although the initial ANSM
an company isn’t a small facility, which can
investigation took place more than nine
be easily replaced. GVK Bio, headquartered
months ago and their appalling results were
in the 7 million metropolis of Hyderabad, is
published by the European Medicines AgenAsia’s leading contract research organisacy (EMA) online in September 2014, initialtion (CRO) with over 50,000 square metres
ly nobody uninvolved
noticed the enormous
Everything running smoothly?
consequences. It was
Apparently not!
an article in the German newspaper, Süddeutsche Zeitung, in
conjunction with simultaneously occurring reports on German
TV, that informed the
general public for the
first time on 4th December 2014. The frightened public learned that there were, “raised
of laboratory space and a scientific staff of
concerns about study data used to support
over 2,400 employees. According to their
the marketing authorisation applications
own statements, they have over 300 customof generic medicines” (as stated in the iners worldwide, many of them huge Western
itial EMA press release on 26th Sept 2014).
pharmaceutical groups. This scandal could
break the company’s neck if they fail to inRaised concerns about study data
vestigate their shortcomings properly.
Then all hell broke loose. The GerLessons learned?
man Bundesinstitut für Arzneimittel und
However, it doesn’t seem that GVK Bio’s
Medizinprodukte (BfArM) put on hold
executives have learned their lessons. For
more than a hundred drug approvals that
weeks, they refused to comment personalmay be based on falsified registration trily and, on their website, seem to be shrugals. A few days later, the French, Belgian
ging their shoulders of blame. According to
and Luxembourg authorities banned dozGVK Bio, “those ECGs are not essential for
ens of additional drugs. As this edition of
the demonstration of bioequivalence”, “the
Lab Times went to press, the number of restudies conducted are in accordance with
called drugs throughout Europe had risen
the GCP guidelines [and] the standard opto 750, according to the EMA. On 22nd January 2015, the EMA published a list of preperation procedures were followed stringentarations that should not be sold (www.ema.
ly”. Furthermore, they claim that GVK Bio
europa.eu/docs/en_GB/document_library/
has neither faked nor manipulated drug triOther/2015/01/WC500180894.pdf).
als. The identified deficiencies “are adminThe generic bioequivalence of an addiistrative”, and, in the last 10 years of operational 300 drugs was tested by other CROs.
tions, “GVK Bio has been inspected over 25
These drugs may be sold as before.
times by various regulatory agencies […]
Meanwhile, brand-name drugs that
None of these inspections reported any critwere tested in Hyderabad are being checked
ical findings.”
out. If the relevant studies also raise anomIn other words, in Hyderabad everyalies, patient safety could even be at risk.
thing is just fine. The question is therefore
For GVK Bio, the Hyderabad findings are
why on earth these irregularities arose in
Winfried Koeppelle
the ultimate worst case scenario. The Indithe first place.
Photo: GVK Bio
GVK Bio became many pharmaceutical companies’ first choice of partner to carry out clinical trials of generic drugs.
But a routine check revealed that, between 2008 and 2014, the Indian CRO allegedly conducted insufficient or
even fraudulent studies. As a consequence, 80 generic drugs from 16 European companies have been banned.
28.01.15 23:23
page 36
Lab Times
Biobusiness
1-2015
In search of polarity-modulating compounds: Thelial Technologies (Lisbon, Portugal)
Flying on Polarity
During beers and dinner in Lisbon, whilst playfully throwing ideas into the air, two Portuguese scientists set off
on the road to an astounding new form of targeted drug discovery.
O
ne thing is clear about eyepatches: they allow for rapid, unambiguous identification. Your Lab Times
reporter learned this when he arrived five
minutes late for his meeting with Richard
Hampson at Lisbon’s Ler Devagar (“to read
slowly”) bookshop. The spacious shop is full
of nooks and crannies where customers can
hide, including behind the decommissioned
industrial heavy machinery that serves as
decoration. But although your Lab Times
reporter had never seen Hampson before,
it was more than easy to identify him. The
shop’s owner, when asked if she had seen a
gentleman with an eyepatch, immediately
pointed in the right direction.
Identifying Hampson was by far the easier part of this meeting. The more difficult
part was finding out what happened to the
company that he helped create seven years
ago, Thelial Technologies.
Hampson began his career working on
DNA repair at the Imperial Cancer Research
Fund, London, for his PhD and continued
in the same area as a postdoc at Harvard
with Leona Samson (Samson’s lab has since
moved to MIT). It was during the course of
his second postdoc, back in London but this
time at King’s College, that Hampson’s career veered off the academic track. Working
on zebrafish development, he began experimenting with a novel mutagenesis strategy,
designed to produce frameshift mutations.
A novel mutagenesis strategy
At that point, says Hampson, “it became
clear that I was more interested in applied
rather than basic science”. The method was
taken up by a Spanish company, Oryzon,
that also took in Hampson.
Then, “after three years as a group leader in Barcelona, in 2006 my arm of the com-
pany came to an end (the company itself
is still around)”, says Hampson, “I realised
that I’m very happy trying to answer practical problems”.
Not long after, Hampson found himself
in Lisbon, Portugal, talking with a friend,
Drosophila researcher Rui Martinho, who
had moved from New York University to
start a group at the Instituto Gulbenkian
de Ciência. According to Martinho, “we
were having beers and dinner in Lisbon,
just throwing ideas up in the air.”
Every scientist I know engages in this
kind of conversation. Its most salient property is a growing enthusiasm that later
proves completely inconsequential. Martinho still sounds a bit surprised when remembering how, “six months later he (Hampson) came back because he thought some of
the ideas should be pursued.” As Hampson
puts it matter-of-factly, “Rui had an idea to
Photos (2): Thiago Carvalho
Richard Hampson of Thelial,
at the company’s LxFactory business headquarters
LT_115 Business.indd 36
28.01.15 23:23
Biobusiness
use flies to test for promising drugs. I had a
look and it seemed very appealing.”
Conversely, Martinho says his partner, “transposed the bureaucratic hurdles
and got the work to the stage where anyone could care about the idea”, emphasising that basic scientists underestimate how
much work goes into getting, “an idea to
a stage where an investor will just listen.”
1-2015
Lab Times
page 37
Drug discovery
technician, Teresa
Gomes, at the
Thelial laboratory
at Universidade
Nova de Lisboa’s
Chronic Diseases
Research Center
(CEDOC).
Using flies to test for drugs
Seven years later, amidst heavy machinery, Richard is sitting at the site of the
company he and Rui created, Thelial Technologies. The meeting with your Lab Times
reporter is at Thelial’s business headquarters, located in the hip LxFactory complex
in Lisbon’s Alcantara district. With 23,000
square metres of deactivated factory space
converted from an industrial ruin to a veritable hive of creative activity, LxFactory
houses a high density of aspiring entrepreneurs. Designers, software developers, architects and at least one biotech startup
mingle in the large collective office spaces.
On the ground floor are restaurants, trendy
shops, and the occasional art fair in its central street. Richard and your Lab Times reporter head off to lunch in a large canteen,
a spin-off of a now-defunct experimental
restaurant nearby that had specialised in
molecular gastronomy.
Focussing on oncology
Thelial Technologies’ basic pitch was
simple, to use flies to screen large quantities of potential drugs for in vivo effects.
The company proposed, and has since developed, a high-throughput proprietary
screening system, theLiTE, with the intention of focussing on potential applications
for oncology. Fly epithelium is similar to
simple human epithelium (like that of the
lung, for example), and the decision was
made early to analyse this tissue – as is evident from the company’s chosen name. A
short time into its existence, Thelial was rebranded as “The Polarity People”.
Strictly speaking, cellular polarity refers
to a simple but crucial fact: cellular content
is distributed asymmetrically and in highly
regulated ways. For an epithelial cell, polarity is crucial. As they regulate exchanges at the interface of tissues, epithelial cells
must know which side is ‘up’, and which
side is ‘down’ so that they are able to control, which molecules (or cells) traffic to
and from different sites. Loss of normal polarity is a hallmark of many diseases – in
particular of aggressive tumours. Because
polarity is also crucial in cellular position-
LT_115 Business.indd 37
ing and mobility, alterations in normal
polarity are an attractive target in invasive, metastatic
disease. Crucially, the cell polarity system
of Droso­phila and humans is very similar
and well characterised.
“We’re not looking for fly tumours”, says
Hampson, “but for a readout of particular
epithelial proteins and pathways that are
well conserved”. Thus, Thelial’s specific remit was to use a living model organism to
test compounds for effects on epithelial cell
polarity.
“A network is of crucial importance”
Thelial gained a foothold in Portugal
when the Instituto Gulbenkian de Ciência
(IGC) ceded laboratory space for a set of
pilot experiments to test the technology’s
feasibility. Funded at this stage by his severance package from Oryzon, Richard relocated to Lisbon to join Rui Martinho on
site. The challenge was to find supporters
and investors in a country with little tradition of innovation-driven business. Martinho again credits his partner with putting together enough support to get the company
off the ground, “Richard made all the contacts. It’s of crucial importance to build a
network in a positive way. Scientists underestimate how much work goes into effective
networking – we can be very defensive when
the business side criticises the project. How
to present [a project] to investors is a different level of knowledge. The aims are different from academia. If you don’t understand
that you can get very frustrated.”
Soon, Thelial had garnered one backer, BioCant Ventures, an angel investor specialising in biotechnology startups (or, as
their mission statement puts it somewhat
dramatically, to support life sciences ventures as they pass through their “valley of
death”). “The money was enough to pay
for a technician and lab materials”, says
Hampson.
Temporarily installed at the IGC, Thelial could benefit from the local Drosophila
community, and the surrounding research
institutions in the Oeiras campus. Thelial
soon began a collaboration at the adjacent
Institute of Chemical and Biological Technology (ITQB), in particular with mycologist Cristina Pereira, with whom they still
have an active research programme, screening secondary fungal metabolites for novel
biological activity – a project funded by the
Portuguese Science and Technology Foundation.
Holding hands all the way
Both founders also credit COTEC, a notfor-profit association established by a cluster of leading Portuguese companies to assist new business owners, for their continuing support since 2007. COTEC and Pedro Vilarinho, Director of their Technology
Commercialization Accelerator, provided
expert assistance in Thelial’s early stages.
COTEC advised on aspects such as formalising financing and writing a business plan,
free of charge (as Martinho put it, “holding
your hand all the way”).
By 2009, Thelial had completed its
proof-of-principle experiments, and the
company’s team was certain that their assay
system could both provide useful information and be scaled up to meet the needs of
high-throughput screening. Infrastructure
needs were modest – essentially space in a
good fly facility. Besides that, says Hampson, “you give us a fluorescent microscope,
we’re happy”.
At this point, Thelial went through
some major changes. The company
28.01.15 23:23
Lab Times
leased laboratory space at Lisbon University’s Institute of Molecular Medicine (IMM).
Fly wound-healing specialist Antonio Jacinto had moved his group there from the IGC,
and IMM offered very favourable terms to
the fledgling company.
Going through major changes
The next practical issue was which compounds to test, and where to get them. They
chose a clinical compound library maintained by Johns Hopkins University’s Parasitology Department, which shipped over
a thousand compounds for about $5,000
(€4,300). An additional thousand compounds were cobbled together from various other sources, and by 2013 Thelial had
screened 2,000 molecules for their effect on
fly epithelial cell polarity. They got 20 hits.
At this point, the pace of change accelerated. Rui Martinho made a decision to remain in academic science, accepted a position at Algarve University, and left Lisbon.
He remains with Thelial as a scientific advisor.
Shifting priorities
“The rules of the game between Richard and me were clear: the standards for the
science in the company and in my lab are
Image: Madalena Parreira
Thelial Technologies
uses flies to test for
promising drugs
LT_115 Business.indd 38
Biobusiness
1-2015
the same”, Martinho says. “The difference
is, the business side has decision power regarding the goals – the business perspective
sets the priorities. My curiosity is not the
driving force, unlike in my university lab.”
Meanwhile, Antonio Jacinto’s group,
which provided the required Drosophila infrastructure left IMM for Universidade Nova
de Lisboa’s Chronic Diseases Research Center (CEDOC). Thelial followed Jacinto’s relocation, and moved its research operation
to CEDOC, once again in the IGC’s Oeiras
campus (Richard’s company will soon have
been present in every major Lisbon area research institution). The company has found
what he calls a welcoming ecosystem – as
evidenced by the wide range of collaborations it established in a relatively short period of time. Martinho points to a highly qualified scientific workforce, still reeling from
the effects of the financial crisis on publicly
funded research, as an underused resource.
Intellectually challenged every day
Teresa Gomes has been with Thelial at
CEDOC for the past two and a half years,
working as a drug discovery technician.
Gomes joined the company after completing
her master’s degree in Drosophila development. Teresa describes a routine that has not
greatly changed, “We
do the experiments,
obtain the results, and
interpret them. It’s the
same basic process.”
Referring to one of
the main worries expressed by scientists
about working in a forprofit enterprise, Teresa emphasises that she
is still able to present
new ideas, “I am intellectually challenged
every day, I have to
keep up with the literature, and provide
the interpretation for
data.” Gomes sees
some clear advantages to being in a business, one of which includes stepping off
the fellowship merrygo-round (at a difficult
time in the Portuguese
science funding cycle).
More surprising,
and symptomatic of
the state of modern
academic research,
is the second positive point Gomes cites:
that of being evaluated by clients and investors. Because they have an interest in limiting cost and obtaining positive results, the
process side-steps one of the banes of the
academic scientist’s existence: the endless
round of often non-sensical experiments required by journal referees.
“Referees often propose random, disruptive things”, says Gomes, “clients are
more careful with the experiments they
ask for. After all, they are paying for them.”
Generating revenue
But who, effectively, is the client? That
is the interesting twist in the story. Unlike
so many biotech firms that absorb investment for as long as possible and then disappear without a trace, Thelial is now generating revenue. With their 20 positive hits,
Richard Hampson sought out new partners.
He found one in American pharmaceutical
company IC-MedTech.
“Cold calling is very unsuccessful, cold
emailing is also very unsuccessful, but
somewhat less so” says Hampson. IC-MedTech had a pre-existing interest in one of
the compounds, and has contracted Thelial
to continue in vivo testing. For Richard, it
was a compromise: on the one hand, his
company got much-needed income and
the LiTe system is implicitly validated by a
more established drug maker; on the other hand, as part of the deal, Thelial ceded property of the compound itself to ICMedTech.
This is not Thelial’s long term business
model. The company hopes to keep a proprietary interest in the compounds that it
develops in the future (and indeed is filing
for patents on the other 19 positive hits)
and to bring them to market at a much
more advanced stage by moving into clinical trials.
The company has to move now
Thelial Technologies is crossing what
their investor, BioCant Ventures, refers to
as the “valley of death” from concept to
proof of applicability. The company must
now move from screening hits to marketable compounds.
“Each round of the project has been a
bit bigger, but each round has also been
more defined”, says Hampson about Thelial’s 8-year existence. “We are now confident in the technology, and we’re looking
beyond service provision to making an income. The goal in the long term is to license
and stretch to clinical development”.
Thiago Carvalho
28.01.15 23:23
Photo: Bildergala/Fotolia
page 38
Conflicts of interest in science (II)
Biobusiness
Undermined
Authorities
1-2015
Lab Times
page 39
Photo: Bildergala/Fotolia
Do public institutions always
act in citizens’ best interests?
And what happens when companies
persuade scientists to bias regulatory agencies
in favour of their interests? Jeremy Garwood analyses how the tobacco
industry once, “changed industry-science relationships and public culture.”
T
he 1st part of this series discussed the
conflicts of interest that have resulted from closer ties between public researchers and industry, especially in US biomedical science since 1980 (see Lab Times
6-2014, page 45). This 2nd part will consider
the ways in which conflicts of interest have
undermined public regulatory authorities.
Such public authorities, whether at the national, European, or international level, need
expert advice and analysis in order to assess
situations, to understand whether problems
exist and how best to address them, and to
constantly update their actions in the light of
new knowledge. But private interests want
to influence this process in their favour.
How to withstand private interests?
In particular, commercial interests target
regulatory agencies because they can have a
major impact on business, on issuing scientific opinions and on decisions about industry products relating, for example, to safety
and pollution. If industry can control the information that these regulators need in order to do their work, they can control public regulation. To escape from this trap, public regulators need to maintain and develop independent sources of expertise. Their
successful operation depends on avoiding
conflicts of interest that may exist, not only
among their staff and management, but also
among experts in scientific committees or
similar technical bodies, who are not direct-
LT_115 Business.indd 39
ly employed by the agencies, but whose scientific and technical advice may play a crucial role in the decisions adopted by them.
It should also be noted that a conflict of
interest is not the same as corruption, although a conflict of interest could lead to
corruption. Transparency International defines corruption as, “the abuse of entrusted
power for private gain. It hurts everyone
who depends on the integrity of people in
a position of authority.” Corruption can include consciously dishonest or fraudulent
conduct and bribery. However, those who
want to influence public decisions in their
favour have developed ways of doing this
that are much more subtle than simply bribing officials with money or promises of lucrative future jobs.
Industry strategies for influencing regulatory agencies are often based on personal contacts and systematic partnerships,
for example, inviting regulatory experts to
working sessions with industry scientists
and signing consultancy contracts with the
leading experts in a given field. What matters is to raise their awareness of, and sympathy for, industry’s priorities (see text box
1, Conflicts of interest and regulatory agencies, page 41).
Captured agencies
Public agencies can be brought under
the influence and control of private companies to ensure that they act in the com-
panies’ interests rather than those of the
general public. This is often referred to as
‘regulatory capture’ and occurs when a regulatory agency, created to act in the public interest, instead advances the commercial or special concerns of interest groups
that dominate the industry or sector it is
charged with regulating; it becomes a ‘captured agency’. When regulatory agencies
form expert bodies to examine policy, they
often come into contact with current or
former industry employees, or, at the very
least, individuals with contacts in the industry. To avoid pro-industry bias, public
authorities need to identify conflicts of interest and manage them, often by excluding
experts from policy-making meetings that
deal with topics where the expert’s potential conflict can manifest itself.
In the European Union (EU), there are
over 30 decentralised agencies with regulatory responsibilities. These include the European Environment Agency (EEA), European
Medicines Agency (EMA), European Chemicals Agency (ECHA), and the European Food
Safety Authority (EFSA). To meet their objectives, these agencies need to have access
to the highest level of expertise available in
each of their respective fields, but they must
also identify the risks of actual or perceived
conflicts of interest if they are to be effective
in advancing the public interest rather than
that of private groups (see text box 2, On
EFSA and conflicts of interest, page 42).
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Lab Times
Biobusiness
1-2015
Photo: Touchstone/Spyglass
The ‘Guidelines on the prevention and
management of conflicts of interest in EU
decentralised agencies’ state that, “A conflict of interest generally refers to a situation where the impartiality and objectivity of a decision, opinion or recommendation of an agency is or might be perceived as
being compromised by a personal interest
held or entrusted to a given individual” (europa.eu, 10th Dec 2013). It insists that, “not
only actual independence, but also perception of independence is important, since it
can impact on agencies’ reputation by raising doubts about the conclusions reached.
the world each year with many of these
deaths occurring prematurely. An additional 600,000 people are also estimated to die
from the effects of second-hand smoke. Tobacco kills more than tuberculosis, HIV/
AIDS and malaria combined.” The WHO estimates that tobacco consumption caused
100 million deaths in the 20th century (Tobacco – WHO Fact sheet N°339). “There
are more than 4,000 chemicals in tobacco
smoke, of which at least 250 are known to
be harmful and more than 50 are known to
cause cancer. There is no safe level of exposure to second-hand tobacco smoke.”
How is it possible that a
toxic product such as tobacco has continued to be
legally sold for 60 years?
Why did the public regulatory system fail to protect citizens? The 1999
Michael Mann film, Insider, summarises the
dramatic events that led
to the Tobacco Master
Settlement Agreement,
which compensates the
medical costs of caring
for people with smokingrelated illnesses.
The appearance of conflict of interest can
constitute a reputational risk to the agency, even if it turns out to be unsubstantiated.” The appearance of a conflict of interest is, in itself, considered a problem because it is crucial that public agencies remain credible. They are acting in the public
interest and their very authority depends on
the honesty and impartiality of their output.
Yet, the scientific evidence that tobacco consumption was directly linked to cancer dates back to the 1950s. How is it possible that such a toxic product has continued to be legally sold for 60 years? Why did
the public regulatory system fail to protect
the health of citizens despite clear evidence
that millions of them were dying prematurely from smoking-related disease?
The tobacco conspiracy
How tobacco created conflicts
To illustrate how damaging it can be
when industry distorts scientific debate to
influence public regulation, let’s consider
a very clearcut and well-documented example: tobacco. The tobacco industry successfully developed many of these strategies. This is why it continues to profitably
sell, “the only legal drug that kills many of
its users when used exactly as intended by
manufacturers”!
The 2012 World Health Organisation
(WHO) global report on ‘Mortality attributable to tobacco’ further notes the scale
of this human health disaster, “Direct tobacco smoking is currently responsible for
the death of about 5 million people across
LT_115 Business.indd 40
The answer is quite simply that the tobacco industry decided to protect its sales
by manipulating scientists, the media,
politicians, and the public. And we know
they did it because they gave us the information. After many years of legal action accusing the tobacco industry of selling a product known to be lethal, one finally succeeded. In 1998, the Master Settlement Agreement agreed to end the
lawsuits brought by 46 of the U.S. States
against cigarette manufacturers (see picture above). The tobacco companies were
fined $250 billion, to be paid over two decades. They were also ordered to make industry secrets public.
This resulted in the surrender of millions
of confidential documents by the major cigarette manufacturers that covered over 50
years of their activity. The documents are
stored in the Legacy Tobacco Documents
Library at the University of California, San
Francisco. There are more than 14 million
documents (around 80 million pages) relating to the advertising, manufacturing, marketing, sales, and scientific research activities of the tobacco industry (consultable online at: http://legacy.library.ucsf.edu).
That’s quite a lot to get through, but
there have already been a succession of
damning assessments based on their contents. The WHO found, “that tobacco companies have operated for many years with
the deliberate purpose of subverting the efforts of the World Health Organisation to
control tobacco use. The attempted subversion has been elaborate, well financed, sophisticated, and usually invisible” (Tobacco company strategies to undermine tobacco control activities at the World Health Organisation. 260-page WHO Report, 2000).
“What is now clear is the scale and intensity of their often deceptive strategies
and tactics. The tobacco companies’ campaign against WHO was rarely directed at
the merits of the public health issues raised
by tobacco use. Instead, the documents
show that tobacco companies sought to divert attention from the public health issues,
to reduce budgets for the scientific and policy activities carried out by WHO, to pit other UN agencies against WHO, to convince
developing countries that WHO’s tobacco control programme was a ‘First World’
agenda carried out at the expense of the developing world, to distort the results of important scientific studies on tobacco, and to
discredit WHO as an institution.”
Spent years studying the documents
Science historian Allan Brandt has spent
years studying the tobacco industry documents. In his article “Inventing Conflicts
of Interest: A History of Tobacco Industry
Tactics”, he identifies key elements in the
industry’s strategy that were initiated at a
meeting in December, 1953 at the Plaza Hotel in New York City (American Journal of
Public Health 2012 102:63-71). Here, the
heads of the tobacco companies met John
W. Hill, president of the leading public relations firm, Hill & Knowlton. The tobacco industry was deeply worried about scientific
evidence showing that smoking caused cancer, a finding that newspapers were beginning to report. They hoped that public relations could provide a solution.
28.01.15 23:23
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1-2015
Lab Times
page 41
Box 1 : Co n fl i c ts o f In te re st a n d Re g u l a tor y A genc ies
Close Enough to Be Potentially Biased
u ...front organisations.
These are usually non-profit groups that are established and funded by industry and claim to conduct
independent scientific research, but follow an
agenda determined by industrial interests, e.g. ILSI
– the International Life Science Institute. This Washington-based industry lobby group/think-tank has
been described as an almost perfect embodiment
of a regulatory capture tool. ILSI was co-founded
in 1978 by Coca-Cola, Heinz, Kraft, General Foods
and Procter & Gamble. It is financed by food, chemical, pesticide, biotechnology and pharmaceutical corporations.
There are 16 branches worldwide. ILSI systematically organises
work streams replicating the work of EFSA and other regulatory
agencies. It claims to bring together scientists from academia,
government, industry and the public sector in a spirit of “partnership”. ILSI invites all key agency experts in order to help blur the
borders between public and private interests. From 1983 to 1998,
ILSI, “provided assistance to the tobacco industry in its attempts
to subvert many attempts at legislative control over the industry’s
activities.” In 2006, following numerous examples of industry bias
in risk assessments, the WHO excluded ILSI from activities setting
safety standards for food and water. For EU regulatory agencies,
close links to ILSI now constitute a conflict of interest.
Hill proposed a strategy that directly
targetted science:
u 1. ‘Engineering science’. Create new science that creates doubt and controversy
about the findings that threaten your profits.
Hill said it was crucial for industry to
assert its authority over the scientific domain, but not by simply denying scientific
facts. Instead, he proposed that they seize
and control science, rather than avoiding
it. If science posed the principal threat to
the industry, Hill advised that the companies should now present themselves as
great supporters of science, “they should
demand more science, not less.”
The tobacco industry moved into the
production of scientific knowledge in order, “to undo what was now known: that
cigarette smoking caused lethal disease. If
science had historically been dedicated to
LT_115 Business.indd 41
u ...academic societies, meetings and journals.
Some academic societies that receive funding from industry are
also not considered independent, including The International
Society of Regulatory Toxicology and Pharmacology (ISRTP) and
the Institute of Food Technologists (IFT), which
are both regarded as ‘captured’ societies. This
bias extends to journals that they own – Regulatory Toxicology and Pharmacology, The Journal
of Food Science and Food Technology. Scientific
meetings may also receive extensive industry
sponsorship and feature a prominent industry
presence among speakers and organisers. For
example, a Lab Times article on honey bees and
pesticides described the dominating presence
of pesticide industry representatives at a meeting of the International Committee of Plant-Bee
Relationship (ICPBR) that subsequently fed
policy recommendations to EFSA (see Lab Times
7-2012, page 44). Although membership of academic societies
with commercial funds is not necessarily a problem, experts who
have leadership positions or scientific responsibilities within such
-jgassociations may have a conflict of interest.
Image: Bigmen/Fotolia
Scientists and other technical experts come into contact with
industry in various contexts. While public regulators need independent and unbiased information, some of these contacts are
considered to be close enough to constitute a conflict of interest.
Putative independent experts that are potentially
biased in favour of an industry position can be…
Sources:
- WHO (2001) The Tobacco Industry and Scientific Groups ILSI: A
Case Study.
- “Unhappy meal” – EFSA’s independence problem. S. Horel and
CEO report. October 2013.
- Honey bees and pesticides: The killing fields? (Lab Times
7-2012 p.44-49)
the making of new facts, the industry campaign now sought to develop specific strategies to ‘unmake’ a scientific fact”!
In effect, they declared, “the positive
value of scientific skepticism of science itself.” Hill pointed out that knowledge was
hard won and uncertain, and that there
would always be skeptics. “What better
strategy than to identify, solicit, support,
and amplify the views of skeptics of the
causal relationship between smoking and
disease?” The goal was to construct and
broadcast a major scientific controversy.
“The public must get the message that the
issue of the health effects of smoking remains an open question.”
u 2. Create a research institute to attract
and fund ‘skeptical’ scientists, to promote
their findings, and to counter other scientific findings with doubt and uncertainty.
Hill proposed creating an industrysponsored research entity – The Tobacco Industry Research Committee (TIRC) – arguing that the best public relations approach
for the tobacco industry was to become a
major sponsor of medical research.
“This tactic offered several essential advantages. The call for new research implied
that existing studies were inadequate or
flawed. It made clear that there was more
to know, and it made the industry seem a
committed participant in the scientific enterprise rather than a self-interested critic.”
The research institute would be promoted as an independent entity but its research
programme would be controlled by the industry. The explicit goal of the TIRC was to
control the scientific discourse about smoking and health. The public announcement
of its formation was made in a full-page advertisement in more than 400 news-
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Lab Times
Biobusiness
1-2015
Box 2 : T h e Eu ro p e a n Fo o d S a f e ty Au th or ity (E FSA ) and C onflic ts of Interest
Not So Independent As One Might Think
EFSA is one of the EU’s most important regulatory agencies. It has
a Scientific Committee and scientific panels that, “provide scientific opinions and advice, each within their own sphere of competence, and are composed of independent scientific experts.”
The panels include those regulating animal health and welfare,
biological hazards, plant health, food ingredients and packaging,
pesticides and nutrition.
EFSA’s scientific opinions are written by external experts
(around 1,200), who make up the scientific panels and their
working groups, and the Scientific Committee, which supports the
work of the panels. The activity of EFSA is of great interest to industry and there have been numerous accusations of pro-industry
bias and conflicts of interest.
Recent conflict of interest (COI) scandals discovered at EFSA
include:
u September 2010: the chair of EFSA’s Management Board,
Diana Banati, failed to declare that she was on the Board of Directors of ILSI Europe.
u February 2011: four members of the Management Board
(Kovac, Horst, Ruprich, Vanthemsche) were found to have links
with industry.
u June 2011: 11 out of the 20 members of the ANS (food
additives) panel had COIs with industry. In addition, four had not
declared links with ILSI Europe.
u November 2011: 12 out of 21 members of the GMO (genetically modified food) panel had COIs with industry, notably the
panel’s chair (Kuiper).
papers across the USA on 4th January, 1954
– the infamous ‘Frank Statement to Cigarette Smokers’ (source: Wikipedia).
The ‘Frank Statement’ started by casting doubt on the existing science linking
cancer and smoking, “...we feel it is in the
public interest to call attention to the fact
that eminent doctors and research scientists have publicly questioned the claimed
significance of these experiments. Distinguished authorities point out: 1. That
medical research of recent years indicates
many possible causes of lung cancer. 2.
That there is no agreement among the authorities regarding what the cause is. 3.
That there is no proof that cigarette smoking is one of the causes. 4. That statistics
purporting to link cigarette smoking with
the disease could apply with equal force
to any one of many other aspects of modern life. Indeed the validity of the statistics themselves is questioned by numerous scientists.”
LT_115 Business.indd 42
u December 2011: 10 out of 13 members of EFSA’s working
group on TTC (threshold of toxicological concern) have COIs with
industry.
Matters became so bad that EFSA was reprimanded by the
European Parliament and the European Court of Auditors. In
May 2012, the European Parliament delayed EFSA’s budget. In
October 2012, an investigation by the European Court of Auditors found EFSA’s management of conflicts of interest situations
“inadequate” and called for reform.
EFSA introduced a new policy and the Corporate Europe
Observatory (CEO) was invited to assess it. The CEO report ‘Unhappy Meal’, published in October 2013, described the naivety of
EFSA’s mangement towards the problems of regulatory capture.
Of the 209 experts comprising the scientific panels, it found that
122 (58%) had at least one conflict of interest with the commercial sector. Experts with conflicts of interest dominated all but one
of EFSA’s scientific panels. All but two panel chairs had conflicts
of interest. Seven chairs and vice-chairs should not even have
-jgbeen appointed according to EFSA’s own rules.
Sources:
- Unhappy Meal – EFSA’s independence problem. S. Horel and
CEO report. October 2013.
- Independence at the European Food Safety Authority: what is the
problem? Presentation by M. Pigeon, CEO, at the 25th meeting of
the EFSA Stakeholder Consultative Platform 4th June, 2014 (http://
corporateeurope.org/efsa/2014/11/efsas-credibility-loopholes)
But the industry wanted the public to
know that the citizens’ well-being was uppermost in their minds, “We accept an interest in people’s health as a basic responsibility, paramount to every other consideration in our business. We believe the products we make are not injurious to health.
We always have and always will co-operate
closely with those whose task it is to safeguard the public health.”
Which is why they were, “pledging aid
and assistance to the research effort into all
phases of tobacco use and health.” Brandt
explains that this “blurring” of the boundaries between industrial public relations and
academic science was critical to the industry’s success.
The TIRC set up a Scientific Advisory
Board (SAB), made up mostly of academic
researchers, who had been, “hand-picked
by Hill & Knowlton, which was always on
the lookout for skeptics (and, even better,
skeptics who smoked)”. The TIRC settled
into a programme of funding research principally on the basic science of cancer (e.g.
genetics), with little or no relevance to the
critical questions associated with the medical risks of smoking (i.e. environmental factors).
By steering funds away from the environmental effects of tobacco towards basic
science, the TIRC avoided the implication
that it served industry interests. SAB members were frequently in a position to secure
funding from the industry to support the
work of colleagues and associates, as well
as other research at their home institutions.
Such arrangements gave them considerable
influence and clearly sustained their loyalty to the TIRC.
“Doubt was no longer a matter of culture or training but the carefully crafted
centerpiece of an industry effort to sow confusion and heighten debate through explicit attempts to disrupt the process of normative science.”
28.01.15 23:23
Biobusiness
Tobacco tactics spread
Brandt has no doubt that the tobacco
industry’s public relations campaign permanently changed industry-science relationships and public culture. “Their disinformation campaign, built on a foundation
of conflicts of interest, demonstrates a series of problems that continue to evolve regarding the relationship between medical
science and industrial influence. The significance of industrial interests in shaping
scientific discourse and outcomes remains
undeniable.”
By the 1960s, tobacco sales were booming. Furthermore, due to the tobacco industry’s ‘public relations’ efforts, they had effectively captured the regulatory process.
The US federal government took no serious regulatory action against tobacco for
50 years. It was not until 2009 that the Food
and Drug Administration (FDA) was finally
given authority to regulate tobacco. Meanwhile in Europe, smoking bans in public
places only began in 2004.
When we know that tobacco has killed
millions of people but is still sold in vast
quantities, we can only marvel at the unscrupulous public relations strategies that
were created to achieve this. Other industries have carefully studied how it was done.
LT_115 Business.indd 43
Lab Times
page 43
As a result, they have come to better understand the fundamentals of influence within the sciences and the value of uncertainty
and skepticism in deflecting regulation, defending against litigation, and maintaining
credibility despite the marketing of prod-
other firms, including Shell, Zeneca, Tesco,
SmithKline Beecham, Bayer and Unilever, that helped secure binding changes to
the EU Treaty in 1997’s Treaty of Amsterdam (Working the System – British American Tobacco’s Influence on the European Union Treaty and Its Implications for Policy: An Analysis
Food industry tactics
of Internal Tobacco Indusresemble the
try Documents. K.Smith et
tobacco industry’s
al. (2010) PLoS Med 7(1):
e1000202).
In the mid-1990s,
BAT approached the European Policy Centre, a
prominent Brussels thinktank, which then created a
front group for them, the
‘Risk Assessment Forum’.
This front group lobbied
for changes to the Treaty
that required EU policymakers to minimise legisucts that are known to be harmful to public
lative burdens on businesses through the
health. They have also come to understand
EU’s impact assessment system. Impact asthat the invention of scientific controversy
sessments are tools for evaluating potential
undermines notions of the common good
legislative changes, each emphasising difby emphasising individual assessment, referent aspects of the ramifications of a govsponsibility, and judgment.
ernment choosing one particular law over
another. Some place great weight on enviSimilarities with Fast Food...
ronmental or health impacts, others on the
An article on ‘The Perils of Ignoring Hispotential financial loss to industry.
tory: Big Tobacco Played Dirty and Millions
…and pretty much everyone else
Died. How Similar Is Big Food?’ describes,
Monetary values are assigned to both
“significant similarities” in how the food inthe costs and benefits of a particular poldustry has reacted to health concerns about
icy, but, as the study’s authors note, it is
their products and the obesity epidemeasier to quantify business costs to indusic (The Milbank Quarterly, 2009, 87:259try than it is to quantify other, more fun94). Food industry tactics certainly resemdamental impacts, such as costs to human
ble the tobacco industry’s emphasis on perhealth and the environment. BAT believed
sonal responsibility, paying scientists to dethat its favoured system of impact assessliver research that instils doubt, criticising
ment, which is now EU law, would delay
the “junk” science that finds harm associrestrictions on public smoking and tobacated with smoking, making self-regulatoco advertising. The subsequent changes to
ry pledges, lobbying with massive resourcthe EU Treaty, “were translated into the apes to stifle government action, introducing
plication of a business-orientated form of
“safer” products, and simultaneously maimpact assessment (cost-benefit analysis).
nipulating and denying both the addictive
Both the tobacco and chemical industries
nature of their products and their markethave since employed impact assessments
ing to children.
in apparent attempts to undermine key asPerhaps it is not a coincidence that the
pects of European policies designed to protobacco industries diversified their wealth
Jeremy Garwood
tect public health.”
into processed food companies. For example, in the 1980s, cigarette company RJ
Reynolds merged with food giant, Nabisco
Freelance Biobusiness
Brands, and Philip Morris bought General
Writers Wanted
Foods and Kraft (The Long, Strange History
th
(Applications
from the UK, France
of Kraft Foods. WSJ 4 Aug 2011).
&
Scandinavia
especially welcome)
British American Tobacco (BAT) covertly led a lobbying campaign with a group
Please contact:
of chemical, food, oil, pharmaceutical and
[email protected]
Photo: Samuel Goldwyn Films
Hill further proposed...
u 3. Industrial benefits of scientific uncertainty – manage the political and media side of regulation, create a lobbying organisation.
The tobacco companies needed their
claims of proof and doubt to resist public
regulation and legal litigation. Because the
TIRC had been explicitly developed to sustain claims of independence, commitment
to science, and pursuit of the ‘‘truth’’ about
tobacco, its, “credibility and influence rested on perceptions of restraint and a narrow
scientific mission.” Therefore, Hill advised
the tobacco industry to establish another
group, separate from the TIRC, that would
act as a trade association that could openly lobby for the industry’s growing political
and public relations needs.
The Tobacco Institute, founded in 1958,
quickly emerged as one of Washington’s
most powerful, well-heeled, and effective
political lobbies. It pioneered new and aggressive approaches to managing its regulatory and political environment. But Brandt
says that it is, “critical to note that the lobbying and public relations efforts of the Tobacco Institute rested fundamentally on the
claims of the scientific doubt and uncertainty generated by the TIRC.”
1-2015
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Lab Times
Methods
1-2015
Bench philosophy (54): Light-sheet microscopy
Sliced by Light
Illuminating your specimen with a light-sheet means you can get a big increase in image resolution, and get deeper
penetration, quicker scans and lower toxicity with it. All with open source hardware and software.
­­­T
eral extras come included as standard: you
can image large tissues (even whole living
animals) and you can image over a long period. What is more, you can even convert
your old fluorescent scope into a SPIM setup using materials found in your kitchen
(provided you keep the right sort of things
in your kitchen).
Fluorescence microscopy’s downsides
So how does SPIM work? Let’s start
from the beginning. The basic problem with
standard fluorescence microscopy is that
you illuminate the whole specimen, even
though you are only focussing on one tiny
part. Doing that introduces all sorts of problems. For one, you get a lot of background
from the out-of-focus regions above and below your plane of focus. Second, irradiating a tissue with high energy electromag-
Photo: EMBL Heidelberg
here is a theoretical limit to the resolution of light microscopy. Way back
in 1873, Ernst Abbe broke the sad
news that the best resolution you can possibly get from any microscope is determined
by the diffraction properties of the light you
use. To the first approximation, the minimum distance you can resolve is more or
less half the wavelength of the light. One of
Nature’s non-negotiables, it seems.
Of course that’s why we had to invent
electron microscopy. If wavelength is what’s
causing the problem, then let’s switch to
“light” with a really small wavelength. A
beam of electrons has a wavelength about
100,000th that of visible light and that adds
up to a big leap in resolution.
The only problem is that using an electron beam means you can only see things
that are, or have been made, electron
SPIM solves these problems by the simple expedient of shining an ultra-thin sheet
of light through the specimen. The sheet
lies at a 90° angle to the observing objective, so light dispersed by stained objects is
detected by the objective. The sheet of light
itself is created from a dispersed laser beam
that is focused through a cylindrical lens.
Alternatively, the equivalent of a sheet can
be achieved by scanning a circular beam. Effectively, the specimen is optically sliced.
So what does this simple approach buy
us? First, you get better contrast images.
Gone is the background that mars conventional epifluorescence images. And given
the clarity of each slice, moving the sheet
through the sample, along the z-axis results
in a better-quality, reconstructed 3D image.
Then there is the speed factor. The lack
of background means you can get a good
quality image from a very rapid scan, so you
can image things that traditionally move
too quickly. Last year Jan Huisken at the
Max Planck Institute of Molecular Cell Biology and Genetics in Dresden used SPIM
to capture the first high-resolution images
of a beating heart of the zebrafish (Mickoleit et al. Nature Methods doi:10.1038/
nmeth.3037). This was made possible not
only because of the technique’s speed but
also because of its ability to penetrate thicker (>1 cm) tissues.
Image stacks
Ernst Stelzer (l.) and Jan Huisken pioneered the SPIM technology for life science applications. LT_115_Bench Philosophy.indd 44
netic radiation does a good job of slowly
micro-waving the specimen, placing a severe limit on how long you can image before the tissue hits medium-rare. That is a
big problem when your signal is weak and
you need a long time to overcome a poor
signal-to-noise ratio.
Sure, you can get around a lot of these
problems with confocal imaging, where a
beam of light converges on a point in the
specimen. But this comes at the expense
of a poor axial (z-plane) resolution, not to
mention great expense.
dense. Useless for all those amazing applications with fluorescent tags. And as for imaging living cells, just try putting your tissue
into an electron microscope and see what
happens.
But it turns out you can get around Abbe’s limit with a little bit of light trickery
and some clever computing. Selective plane
illumination microscopy (SPIM) is one such
hack that allows you to ramp up the resolution of your images without running the
expense of a confocal or two-photon setup.
And because of the way SPIM works, sev-
There are other advantages, too. With
SPIM you can easily rotate the sample,
keeping the imaging hardware fixed. The
significance of this is that you can build zstacks from different angles, which in turn
(with a bit of computer trickery called “multi-view fusion”) gives much better-resolved
reconstructions.
But does SPIM really give you super-resolution? Well, no at least not on its own.
The lateral resolution of a SPIM setup is still
limited by the diffraction limit and the numerical aperture of the lens.
But some recent reports have changed
all that: it seems you can get genuine superresolution microscopy if you fiddle about
with the fine details of the beam. And these
29.01.15 13:19
Methods
developments are causing quite a stir in the
field. Why? Because along with the superresolution you get super speed thrown in for
free.
Ultra-thin light-sheet
In 2011 Eric Betzig’s group at the HHMI
Janelia Research Campus, USA showed that
by making your light-sheet using a specially constructed beam (a “Bessel” beam), you
can get notably higher resolution. Last year
Betzig received the Nobel Prize in Chemistry together with Stefan Hell and William Moerner for “the development of super-resolved fluorescence microscopy”,
which brings “optical microscopy into the
nanodimension”. And even while Betzig
was waiting to hear about his prize, his
group was busy publishing a paper in Science showing that tweaking the light-sheet
further − using a non-diffracting “lattice
beam” − could push speed and resolution
even further up and toxicity even further
down (Bi-Chang Chen et al., Science 346,
6208: 1257998).
With all these high-tech optics, it may
come as a surprise that the idea behind
SPIM is not at all new. In fact, the basic idea
was described as far back as 1903 by Henry Siedentopf and Richard Zsigmondy, and
was given new impetus by Voie and co-authors in 1993, who used the idea of a lightsheet to optically section an entire cochlea
for the first time (Voie et al., J. Microsc. 170,
229-36). A period of exploration followed,
as experimenters toyed with different configurations of lens and illumination, until
Ernst Stelzer and Jan Huisken, then at the
EMBL in Heidelberg, developed the first
SPIM microscope suitable for life science
applications in 2004.
Whole bunch of applications
So how is SPIM being applied? It is one
of those foundational techniques that gets
the imaginative juices flowing in all sorts
of directions. For one thing, not frying your
specimen every time you image means you
can image for longer − you can track developing embryos at the cellular or even
subcellular level (remember what we said
about tissue penetration?).
Then again, SPIM’s ability to penetrate
tissues is especially interesting for 3D culture. There is an increasing awareness of
the importance of structure for cultured
cells. Where once we were happy growing
cells on the flat surface of a Petri dish, consensus is emerging that cells don’t grow
right unless they grow in 3D. Fortunately,
many cells are happy to grow in agarose,
LT_115_Bench Philosophy.indd 45
1-2015
Lab Times
page 45
to access the specimen from
two angles (the light-sheet
and the objective at 90°) is
a bit of an imposition if you
are using very large tissues.
Thinking of giving SPIM
a spin but don’t have a major research grant to spend
on a new setup? No worries
− you can build one yourself. At least that is the belief of the people behind the
OpenSPIM project (openspim.org), who think that
“every lab should have one”.
The site offers the plans and
even the complete assembly instructions for buildEricBetzig(r.)andhisgrouptookSPIMtothenextlevel.
ing your own SPIM system
which is also optically clear. That, coupled
that will occupy only 300 x 450 x 150 mm
with the enhanced penetration offered by
of space. They also offer a free and open
SPIM, opens up a host of possibilities.
source programme to control the system
But it is not just about anatomy −physthrough an Arduino (an open-access hardiology is getting a boost from SPIM, too. In
ware controller).
2013, Georges Debrégas’ group at the UniDIY-SPIM project
versity of Paris used zebrafish, geneticalAs has been the case with open source
ly modified to express a calcium indicator
software, it seems that open source micros(GCaMP3), to allow the activity of up to
copy is spawning a trend for do-it-yourself
5,000 neurons to be recorded simultane“hacking” (in the good sense of the word).
ously at 20 Hz. The resolution offered by
For instance, we have mentioned how
the SPIM approach allowed single-cell (or
Betzig used a Bessel beam to get a thinner
at least near single-cell) activity to be monlight-sheet but Bessel (and its alternative
itored (Panier et al., Frontiers in Neural Cir“Airy”) beams need some pretty expensive
cuits7:65).
components to make. To get around that,
The excitement about the neuro-physiKishan Dholakia’s lab at the University of
ological potential of SPIM is so intense that
St. Andrews showed a slight adjustment
Phillip Keller and Hans-Ulrich Dodt, from
to the OpenSPIM setup − by deliberately
the HHMI Janelia Research Campus, USA
(but judiciously) misaligning the cylindrical
and the Vienna University of Technology,
lens! (Yang et al. 2014 Biomed Opt Express
respectively, boldly declared two years ago
5, 3434-42). And if you want to see how to
that “Even samples up to the size of entire
set up a SPIM system and use it to image the
mammalian brains can be efficiently renematode, Caenorhabditis elegans, take a
corded and quantitatively analyzed” (Kellook at www.jove.com/video/51342/ where
ler and Dodt, Curr Opinion Neurobiology
Claire Chardès from the Institut de Biologie
22, 138-43). Optimistic, perhaps, but last
du Développement de Marseille, has posted
summer Keller’s lab reported that they had
a series of, how-to, videos. ,
imaged all the neurons in the brain of zeWhether or not the open source hardbrafish swimming in a virtual reality setup,
ware and software approach will bring
using the SPIM light-sheet to prevent illumiSPIM to the masses, SPIM and other lightnation of the retina (Vladimirov et al., 2014,
sheet applications continue pushing the
Nature Methods 11, 883-84).
boundaries of live-cell imaging to a new
As with any technique, SPIM is not
level.
Steven Buckingham
perfect. Slicing with a light-sheet causes
problems when the beam hits an optically dense target, causing a stripey pattern
in the downstream illuminated areas, alFancycomposinganinstallthough there are techniques to overcome
mentof“BenchPhilosophy”?
this. Then again, things go wrong when a
structure has a significantly higher refracContactLabTimes
tive index, resulting in an unwanted focusE-mail:[email protected]
sing of the beam around them. And having
29.01.15 13:19
page 46
Lab Times
Methods
1-2015
Tips and tricks of the trade
Expect the Unexpected
Researchers thought they knew most everything about RNase A: the RNA degrading enzyme was purified in the
1940s already, the structure was solved in the 1960s and the catalytic reaction mechanism can be found in detail
in every biochemistry text book. But RNase A may still catch you by surprise.
L ab Hin t
S
ome laboratory reagents are so familiar that we take them for granted
and yet these molecular workhorses
can occasionally surprise us, yielding unexpected and potentially misleading results in
standard procedures.
We were not expecting RNase A, an exceptionally well characterised enzyme, to
do anything other than degrade the RNA
in our samples but we actually observed
RNase A removing substantial quantities
of DNA under common experimental conditions. This activity confounds the results
of basic RNase susceptibility assays and has
the potential to introduce sequence bias
during DNA purification that would introduce artefacts in genome-wide analyses.
While searching for transcripts from
mouse major satellite repeat sequences by
Northern blot, we observed strong signals
in RNA samples derived from cultured fibroblasts. To ensure that these signals
did not represent contaminating genomic DNA, we performed a routine digestion
with RNase A and the signals disappeared
as expected. Other results, however, were
puzzling as the major satellite signals were
completely removed by DNase I but not by
some other ribonucleases.
Puzzling results
This unexpected result led us to suspect that the signals stemmed from genomic DNA and that RNase A may possess an innate activity against DNA. Confirming this
suspicion, we found that RNase A readily removed the signal of a major satellite
PCR product spiked into the assay (see Figure). This ability was not unique to a particular batch of RNase A and multiple other brands, including certified DNase-free
RNase A, displayed the same activity.
Anecdotal reports do suggest that RNase
A can degrade DNA but such reports receive
little credence as the well-understood catalytic mechanism of RNase A absolutely precludes DNA cleavage. It was shown long
the duplex transiently open), which occurs
at a sequence-dependent rate. The quantities of DNA removed are also not small;
1µg RNase A completely removes at least
50ng DNA from a sample, so a few µl’s of
commercially available RNase A (usually
10-20mg/ml) added to a DNA sample could
remove micrograms of DNA.
What to do?
A major satellite PCR product
is efficiently removed from an
RNA sample by
RNase A treatment and phenol/chloroform
purification.
RNase A from
three different
manufacturers
was tested.
ago, however, that RNase A can bind DNA
and our experiments reveal that RNase A
holds onto bound DNA with such ferocious
tenacity that DNA-RNase A complexes are
not dissolved by phenol:chloroform. When
phenol:chloroform extraction is used to
purify DNA samples treated with RNase A,
these complexes partition efficiently to the
organic phase and the DNA is lost.
DNA binding while ‘breathing’
Loss of DNA is not a peculiarity of major satellite sequences as a DNA molecular weight marker was also efficiently removed by RNase A. However, we predict
that there will be a sequence bias as RNase
A binds to single stranded regions of DNA as
it ‘breathes’ (a process in which regions of
There is no easy solution to this problem
as proteinase K digestion was insufficient to
completely release the bound DNA. The effect can be partially suppressed by increasing the salt concentration but DNA removal still occurs. Column-based purification
methods should avoid DNA loss but may
suffer the opposite problem of co-purifying
the RNase A leading to DNA migration defects, which we also observed.
We recommend that RNase A treatment
is avoided entirely for critical DNA purification applications, particularly on low abundance samples. RNase T1 did not show the
same effect in our hands and should, therefore, be usable for RNA removal post-purification.
Of course, RNase A finds many applications outside DNA purification; we suggest
that care is taken when interpreting any assay involving RNase A, to ensure that the results cannot be explained by strong binding
of RNase A to DNA or chromatin.
Federico Donà and Jon Houseley
(The Babraham Institute, UK)
Do you have any useful tips?
Contact us at:
[email protected]
Get your own copy – it’s free!
Lab Times is free of charge for non-profit institutions all over Europe. The life science journal is distributed to scientists and lab staff for free* wherever they work:
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LT_115_Tips and Tricks.indd 46
29.01.15 13:20
1-2015
Lab Times
page 47
Product survey: 1D Gel Electrophoresis systems
Electrophoretic
Race-Tracks
Though discontinuous gel electrophoresis of proteins turned fifty last year,
­it is still one of the most vital protein separation methods.
W
hen classifying the most archetypal life science techniques,
gel electrophoresis would most
probably rank amongst the top five. Almost
every researcher working with DNA and/or
proteins sooner or later will have to “run a
gel” to analyse his samples. Hence, life science researchers that have never performed
a one-dimensional gel electrophoresis aka
a 1D gel electrophoresis are a pretty rare
species.
The Swedish chemist Arne Tiselius applied electrophoresis already in the 1930s
to separate serum proteins and earned the
Nobel Prize for his invention in 1948. However, the real success story of gel electrophoresis took off in 1964 when Leonard
Ornstein and Baruch J. Davis, then working
at the Mount Sinai Medical Center in New
York, published two seminal papers describing a new, improved electrophoresis technique, which they termed disc(ontinuous)
electrophoresis. Since Ornstein and Davis
used polyacrylamide gels and kept the proteins in the native state, it is also referred to
as the native disc polyacrylamide gel electrophoresis or simply native disc-PAGE.
Back then, life science research was
rather adventurous. The two PAGE-pioneers built their electrophoresis apparatus
using carbon rods from old flash light batteries as electrodes and rumours tell, that
they had to “run from the basement of the
hospital to the roof in order to get enough
sunlight ... to aid the catalysis of polymerization of the stacking gels” (Reisfeld and
Williams, This week’s citation classics, 1981,
6, 95).
Round-edged electrophoresis tanks
Though a little sport hurts no body during a long day in the lab, the times of doubtful homemade electrophoresis chambers
and rusty bulldog clips to fix the gel cassettes are (hopefully) in the past.
Modern 1D gel electrophoresis systems
have turned from ugly, square-angled, greycoloured plastic boxes with wobbling electrodes into benchtop beauties that may
even please the legendary designer and
enthusiast of rounded edges, Luigi Colani.
The basic concept of native disc-PAGE, how-
LT_115_Product survey.indd 47
ever, has not changed in the last 50 years.
It is still based on the idea that the electrophoretic resolution of charged proteins
is considerably enhanced in a biphasic gelbuffer system consisting of stacking and resolving gel, which differ in pore size, i.e.
acrylamide concentrations, as well as in pH,
ionic strength and anions used in the electrode solutions. The classical system utilises
a Tris-chloride-glycine buffer system composed of Tris-glycine (running buffer) and
Tris-chloride (stacking and resolving gel,
anode buffer); the pH is kept at 6.8 in the
stacking gel in contrast to 8.8 in the resolving gel and the electrode solutions.
Soon after a voltage is applied, the chloride ions, already present in the stacking
gel, will take the lead in the race towards
the positively charged anode, while the only
slightly charged glycine ions (pKA: 6), flowing in from the cathode buffer, will lag behind.
Protein stacks
The voltage gradient established between chloride (leading ion) and glycine
(trailing ion), squeezes the proteins running between leading and trailing ions, to
form a thin protein staple that continuously moves isotachophoretically through the
wide pores of the stacking gel to the interface of stacking and resolving gel.
When entering the close-meshed resolving gel, the tightly packed proteins are soon
passed by the smaller and thus faster moving glycine ions, which run together with
chloride in front of the proteins towards the
anode. On their way through the meandering pores of the resolving gel, the individual proteins of the staple are separated zoneelectrophoretically, according to their size
and electrophoretic mobility.
The invention of the native disc-PAGE
was a milestone in protein research, however, the method has some shortcomings.
Native proteins can form, for example, erratic moving complexes or may be positively charged and migrate in the wrong direction. In 1970, the young Swiss scientist Ulrich Karl Lämmli, then working on the bacteriophage T4 at the Laboratory of Molecular Biology in Cambridge, had the simple
Photo: Srimoye Banerjee/Temple University
Products
Gel-shit happens−even with stylish, roundeged gel electrophoresis systems.
but brilliant idea of adding sodium dodecyl
sulfate (SDS) to the buffer system.
SDS denatures the proteins and binds
to them in a constant ratio to form evenly
charged, ellipsoidic SDS-protein complexes, which are separated in the resolving gel
solely according to their molecular weight.
SDS-PAGE has since become the standard
protein electrophoresis method and is almost synonymous with 1D gel electrophoresis. SDS-PAGE has stood the test of time and
recent modifications, especially in pre-cast
gels, are limited to variations of the trailing and leading ions (for example, MES or
MOPS instead of glycine and acetate instead
of chloride) and a neutral operating pH.
Only slight variations
While SDS-PAGE is almost exclusively
performed in vertical gel chambers, molecular biologists prefer horizontal submarine
electrophoresis units equipped with agarose or poly acrylamide gels for the electrophoresis of nucleic acids. Submarine gel
boxes are basically rectangular plastic containers with a cavity on each side connected
by a bridge. The electrodes are mounted at
the bottom of the cavities and coupled to a
jack in the safety lid. The gel is placed onto
the bridge and drowned in electrophoresis
buffer, usually Tris-acetate-EDTA (TAE) or
Tris-borate-EDTA (TBE).
Connecting the electrodes to a power
supply and applying a DC current to the
gel will force the negatively charged DNA
to migrate towards the anode in a size-dependent manner. However, this only holds
true for DNA fragments smaller than approx. 50 kbp, since long DNA cannot be separated in a gel applying a constant electric
field. Separating long stretches of DNA requires a pulse field electrophoresis (PFGE)
system that creates an unsteady, periodically-changing electric field.
PFGE systems are pretty sophisticated
devices, with one type using, for example,
free rotating electrodes to establish a pulsed
electric field. But after all, they still exploit
the same basic electrophoretic principles
that were pioneered by the inventors of gel
electrophoresis some 50 years ago. Harald Zähringer
29.01.15 13:21
page 48
Lab Times
Products
1-2015
1D Gel Electrophoresis Systems
Company/Distributor Name of device
Purpose & application | Gel size Miscellaneous, Specialities, Generally
Price [EUR]
Analytik Jena
Compact Family: Compact XS/S, Compact
M, Compact, MultiWide Compact L/XL
Horizontal gel electrophoresis with
agarose gels |
Gel size (cm): 8.2 x 7.1/10.5; 12.4 x
14.5; 15.0 x 7.0/10.0/ 15.0/18.0;
23.9 x 20.0/25.0
Robust systems with thick chamber walls | Unique casting systems
for leak-proof gel casting | Multichannel-pipette-compatible combs
| UV-transparent gel trays
Starting at
347.–
Horizon Family:
Horizon 58, Horizon
11.14, Horizon 20.25
Horizontal gel electrophoresis with
agarose gels |
Gel size (cm): 5.7 x 8.3; 11.0 x 14.9;
20.0 x 25.0
Compact systems with turn-up lid | Chambers made of resistant ABS Starting at
plastic | Buffer recirculation ports | UV-transparent gel trays
465.–
Eco-Line:
Eco-Mini, Eco-Maxi
Vertical gel electrophoresis with polyacrylamide gels + tank blotting |
Gel size (cm): 9.4 x 8.0; 19.4 x 18.5
Robust tank systems with thick chamber walls | Gel casting system
for up to 4 gels | For 2 or 4 mini gels or for 2 maxi gels | Thick glass
plates with fixed glass spacers
Starting at
847.–
Double gel design | Leak-proof gel sandwiches with silicone seal
| Low buffer volume required | Thick glass plates with fixed glass
spacers | With ports for water cooling
Starting at
1,040.–
Starting at
1,850.–
Biometra Product Line
Jena, Germany
www.bio.analytik-jena.com
Contact:
lifescience@analytik-jena.
com
Phone +49 36 41 7770
Vertical gel electrophoresis with
Minigel Family:
Minigel Twin, Multigel/ polyacrylamide gels |
Gel size (cm): 8.6 x 7.7; 11.0 x
Long Maxigel
7.0/12; 17.0 x 18.0
Bio-Budget
Technologies
Sequencing System
S2
Vertical gel electrophoresis with
polyacrylamide gels |
Gel size (cm): 31.0 x 38.5
Adjustable levelling feet and built-in levelling indicator | Integral
aluminum plate for even heat distribution | Removable lower buffer
tray | Built-in integral clamps hold the gel in place | Gasket sealing
system ensures leak-free operation
Horizontal Minigel
Electrophoresis
Systems
Separation of nucleic acids on
agarose gels |
Gel size (cm): 7 x 8; 9 x 11;
12 x 14; 14 x 10
Ready-to-use-system | Microtiter-format combs available |
Starting at
Quick and leak-proof seal | High-quality, fixed platinum electrodes | 400.–
Robust construction
Separation of nucleic acids on
agarose gels |
Gel size (cm): 15 x 15; 23 x 14
Ready-to-use-system | Microtiter-format combs available |
Starting at
Quick and leak-proof seal | High-quality, fixed platinum electrodes | 745.–
Robust construction
Horizontal Maxigel
Electrophoresis
Systems
Separation of nucleic acids on
agarose gels |
Gel size (cm): 13 x 25; 15 x 25; 20 x
25; 23 x 25; 23 x 40
Ready-to-use-system | Microtiter-format combs available; integrated buffer recirculation available on selected units | Quick and
leak-proof seal | High-quality, fixed platinum electrodes | Robust
construction
Starting at
715.–
Vertical Electrophoresis Systems
Separation of proteins or nucleic acids
on acrylamide gels |
Gel size (cm): 10 x 10 (mini); 20 x 10
(wide);16 x 14 (midi); 20 x 20 (maxi)
Ready-to-use-system | Quick and leak-proof gel casting or compatible with a wide range of precast gels | High-quality, fixed platinum
electrodes | Ports for water-cooling for minimising “smiling effect” |
Robust construction
Starting at
955.–
Part of the V3 Western Workflow | Small format | Protein separation
in less than 15 min
Starting at
437.–
Krefeld, Germany
www.biobudget-shop.de
Contact:
Horizontal Midigel
info@ bio-budget.de
Electrophoresis
Phone +49 2151 6520830 Systems
Bio-Rad Laboratories
Munich, Germany
www.bio-rad@com
Contact: techsupport.
germany@bio-rad. com
Phone +49 89 31 8840
LT_115_48_52.indd 48
Mini-Protean Tetra Cell Vertical electrophoresis system |
Gel size (cm): Up to 4 gels; 8.6 x 6.8
(precast); 8.3 x 7.3 (handcast)
Mini-Protean 3
Dodeca Cell
Vertical electrophoresis system |
Gel size (cm): Up to 12 gels; 8.6 x 6.8
(precast); 8.3 x 7.3 (handcast)
Part of the V3 Western Workflow | High-throughput | Small format |
Protein separation in less than 20 min
Starting at
3,387.–
Criterion Cell
Vertical electrophoresis system |
Gel size (cm): Up to 2 gels; 13.3 x 8.7
(precast)
Part of the V3 Western Workflow | Midi format | Protein separation
in less than 25 min
544.–
Criterion Dodeca Cell
Vertical electrophoresis system |
Gel size (cm): Up to 12 gels; 13.3 x
8.7 (precast)
Part of the V3 Western Workflow | High-throughput | Midi format |
Protein separation in less than 25 min
3,506.–
Protean II xi Cell
Vertical electrophoresis system |
Gel size (cm): Up to 4 gels; 16 x 16
(handcast); 16 x 20 (handcast)
Large format
Starting at
1,658.–
Protean II xi Multi-Cell
Vertical electrophoresis system |
Gel size (cm): Up to 6 gels; 16 x 16
(handcast); 16 x 20 (handcast)
Medium-throughput | Large format
5,459.–
Protean i12 IEF
System
Isoelectric focussing of proteins using
IPG strips |
Gel size (cm): Up to 12 IPG strips;
lengths: 7, 11, 17, 18, 24
High-capacity running platform | Individual lane control
10,775.–
Experion Automated
Electrophoresis
System
System for automated protein and
nucleic acid separation using
microfluidic technology |
n.s.
Optional 21 CFR Part 11 compliance | Proteins: Up to 10 samples;
Starting at
RNA: Up to 12 samples; DNA: Up to 11 samples | Sample separa13,378.–
tion, staining, destaining, imaging, band detection, quantitation, and
data analysis in 30 min
Sub-Cell Horizontal
Electrophoresis
Systems
Submerged horizontal electrophoresis
cells |
Gel size (cm): 7 x 7; 7 x 10; 15 x 7;
15 x 10, 15 x 15; 15 x 20; 15 x 25;
25 x 10
Greatest choice of gel lengths, sample combs, and separation
modes | All cells include components for casting gels | The MiniSub cell systems can be used with ReadyAgarose precast gels |
UV-transparent gel trays with fluorescent ruler | For DNA gel
electrophoresis and Southern and Northern blotting protocols
Starting at
355.–
Pulsed Field Gel
Electrophoresis CHEF
Systems
CHEF systems incorporate different
technologies such as PACE, FIGE, and
AFIGE |
Gel size (cm): 14 x 13; 14 x 21
Different blocks of run conditions can be programmed | Depending
on the model, specify any electrophoresis angle (0 to 360°) |
Separation of chromosome-sized DNA can be achieved in almost
half the time previously possible
On request
29.01.15 15:27
Products
1-2015
Lab Times
page 49
1D Gel Electrophoresis Systems
Company/Distributor Name of device
Purpose & application/Gel size Miscellaneous, Specialities, Generally
Price [EUR]
Biostep
Mini, midi and maxi
vertical systems of
GV series & Desaphor
VA150/VA300
SDS-PAGE of mini, midi and maxi
gels |
Gel size (cm): 10 x 10; 20 x 10; 20 x
20; 25 x 15; 25 x 30
No transfer of glass plates at GV series | Gel casting module = gel
running module | Optionally with cooling coil | Stable glass plates
with fixed spacers
Starting at
635.–
Desaphor HF 210
Multi-tasking system for isoelectric
focussing and horizontal gel
electrophoresis |
Gel size (cm): 21 x 26
Integrated cooling plate | Insertion of a third or fourth electrode for
double focussing | Up to 108 samples with double focussing | For
all common carrier foils | High voltage up to 3,000 V possible
1,645.–
High flexibility | Colour-coded combs | UV-transparent gel casting
trays
Starting at
325.–
Burkhardtsdorf, Germany
www.biostep.de
Contact: Silvana Böhme
[email protected]
Phone +49 3721 3905 24
DNA and RNA separation |
Large range of
horizontal chambers of Gel size (cm): Gel width 7 / 10 / 15 /
20 / 26 (different lengths)
GH series
Biozym Scientific
Hessisch Oldendorf,
Germany
www.biozym.com
Contact: Anja Röben
[email protected]
Phone +49 5152 9020
CometPlus
Comet Assay for light-sensitive single
cell gel electrophoresis |
Gel size: For 10, 20 or 40 slides
Simultaneous separation of many DNA samples in agarose gels |
High efficiency cooling for enhanced resolution
Starting at
495.–
EasyPhor Mini
Systems
DNA- and RNA gel electrophoresis |
Gel size (cm): 7 x 7 and/or 7 x 10
Economic low gel and buffer volumes | Small lab bench footprint |
Different combs available
Starting at
290.–
EasyPhor Midi
Systems
DNA- and RNA gel electrophoresis |
Gel size (cm): 10 x 7 and/or 10 x 10)
Run up to 100 samples | Low buffer volumes | Ideal for rapid
electrophoresis | Different combs available
Starting at
318.–
EasyPhor Medi
Systems
DNA- and RNA gel electrophoresis |
Gel size (cm): 15 x 7, 15 x 10 and/
or 15 x 15
Run up to 210 samples | Low buffer volumes | Multichannelpipette-compatible combs for speed loading (marked with MC) |
Different combs available
Starting at
330.–
For higher resolution separation of more samples over a longer distance | Low buffer volumes | 4 multichannel-pipette-compatible,
28-sample combs for speed loading included | Different combs
available
Starting at
381.–
EasyPhor Medi Stretch DNA- and RNA gel electrophoresis |
Gel size (cm): 15 x 20 or 15 x 25
Systems
EasyPhor Maxi
Systems
DNA- and RNA gel electrophoresis |
Gel size (cm): 20 x 25, 20 x 20, 20 x
15 and/or 20 x 10
Run up to 550 samples | Low buffer volumes | Ideal for extended
separations | Different combs available
Starting at
521.–
EasyPhor PAGE Mini
System
PAGE electrophoresis (protein, nucleic
acids) |
Gel size (cm): 10 x 10
High throughput capability, run a maximum of 4 gels | PAGE insert,
used for both gel casting and running | Also for most common precast gels | Interchangeable modular inserts for slab gels, 2-D electrophoresis and electroblotting available | Different combs available
Starting at
474.–
EasyPhor PAGE Mini
Electrophoresis and
Blotting System
PAGE electrophoresis (protein, nucleic
acids), tank blotting |
Gel size (cm): 10 x 10
High throughput capability, run a maximum of 4 gels | PAGE insert,
used for both gel casting and running | Also for most common
precast gels | Different combs available | Including a tank blotting
module
Starting at
793.–
PAGE electrophoresis (protein, nucleic
EasyPhor PAGE Mini
Electrophoresis and HI acids), tank blotting |
Gel size (cm): 10 x 10
Blotting System
High throughput capability, run a maximum of 4 gels | PAGE insert,
Starting at
used for both gel casting and running | Also for most common pre845.–
cast gels | Different combs available | Including a HI (High Intensity)
tank blotting module
EasyPhor PAGE Mini
Wide System
PAGE electrophoresis (protein, nucleic
acids) |
Gel size (cm): 20 x 10
High throughput capability, run a maximum of 4 gels | PAGE insert,
Starting at
used for both gel casting and running | Interchangeable modular
661.–
inserts for slab gels, 2-D electrophoresis and electroblotting available
| Different combs available
EasyPhor PAGE Mini
Wide Electrophoresis
and Blotting System
PAGE electrophoresis (protein, nucleic
acids), tank blotting |
Gel size (cm): 20 x 10
High throughput capability, run a maximum of 4 gels |
Rapid casting | Different combs available | Including a tank blotting
module
Starting at
1,049.–
High throughput capability, run a maximum of 4 gels | Rapid
casting | Different combs available | Including a HI (High Intensity)
tank blotting module
Starting at
736.–
PAGE electrophoresis (protein, nucleic
EasyPhor PAGE Mini
acids), tank blotting |
Wide Electrophoresis
and HI Blotting System Gel size (cm): 20 x 10
Carl Roth
EasyPhor PAGE Maxi
WAVE Electrophoresis
System
PAGE electrophoresis (protein, nucleic
acids) |
Gel size (cm): 20 x 20
High Throughput Capability, run a maximum of 4 gels | Rapid casting | Starting at
Vertical screwclamp technology reduces the number of screws required 972.–
for set up | No top tank assembly | Different combs available
EasyPhor PAGE Maxi
WAVE Electrophoresis
and Blotting System
PAGE electrophoresis (protein, nucleic
acids), tank blotting |
Gel size (cm): 20 x 20
High Throughput Capability, run a maximum of 4 gels | Rapid
casting | Vertical screw clamp technology reduces the number of
screws required for set up | Different combs available | Including
a tank blotting module
Starting at
1,331.–
PAGE electrophoresis (protein, nucleic
EasyPhor PAGE Maxi
WAVE Electrophoresis acids), tank blotting |
and HI Blotting System Gel size (cm): 20 x 20
High Throughput Capability, run a maximum of 4 gels | Rapid
casting | Vertical screw clamp technology reduces the number of
screws required for set up | Different combs available
Starting at
1,567.–
Rotiphorese Unit
1D vertical separation of proteins,
nucleic acids, peptides /
Electro-transfer of proteins and nucleic
acids / Isoelectric focussing |
Gel size (cm): 10 x 10
Fast-clamping technique | Generally coolable, different versions
725.– to
with casting module for precast gels etc. | For running of up to 4 gels 855.–
in parallel | Compatible with all major brands of 10 x 10 to 8 x 10
cm precast gels | Wide range of additional accessories, compatible
tank-blotting module available
Rotiphorese Unit
PROclamp Maxi
1D vertical separation of proteins,
nucleic acids, peptides /
Electro-transfer of proteins and nucleic
acids / Isoelectric focussing |
Gel size (cm): 20 x 20
Wave-screw-clamp technology | Set with all necessary accessories
for self-casting, coolable | For running of up to 4 gels in parallel
| Wide range of additional accessories, compatible tank-blotting
module available
PROclamp Mini
Karlsruhe, Germany
www.carlroth.com
Contact: Elke Drotleff
[email protected]
Phone +49 721 5606 1037
LT_115_48_52.indd 49
1,600.–
29.01.15 15:27
page 50
Lab Times
Products
1-2015
1D Gel Electrophoresis Systems
Company/Distributor Name of device
Purpose & application/Gel size Miscellaneous, Specialities, Generally
Carl Roth (continued)
Mini Vertical Dual
Plate Electrophoresis
Unit
1D vertical separation of proteins,
Made of heavy acrylic glass | Different versions available |
676.– to
nucleic acids, peptides /
With glass plate stops – for reliable pouring of gels | Compatible with 1,073.–
Electro-transfer of proteins and nucleic most 10 x 10 cm precast gels | Wide range of additional accessories
acids / Isoelectric focussing |
Gel size (cm): 10 x 10
Maxi Vertical Dual
Plate Electrophoresis
Unit
See above |
Gel size (cm): 20 x 20
Flat Bed Electrophoresis Unit Multi
1D flat bed gel electrophoresis /
Rugged acrylic construction for high voltage electrophoresis up to
1,800.–
Isoelectric focussing applications using 5000 V | Adjustable glass electrode frame | Ceramic cooling plate |
IEF gels or IPG strips |
Buffer drainage system | Wide range of accessories
Gel size (cm): 25 x 25
MiniVE
1D/2D electrophoresis |
Gel size (cm): Gel cassettes up to
10 × 10.5
Cast, run and blot mini-gels in four streamlined components |
Run two mini-gels or four mini-blots at once | Choose precast gels
from a variety of manufacturers | Perform two second-dimension
separations using 7-cm IPG strips in 1.5 h
Amersham ECL Gel
Box
1D electrophoresis |
Gel size (cm): Dedicated precast gels
8 x 10
Horizontal electrophoresis system with virtually no assembly required 83.–
| Used together with dedicated precast gels | Everything required to
access and cut the gel is included in the Amersham ECL Gel cassette
SE 400 Vertical Unit
1D electrophoresis |
Gel size (cm): 16
Economical and secure vertical slab electrophoresis units | Rugged
injection-molded construction for easy assembly and durability |
Built-in casting stand seals sandwiches leak-free without tape
1,260.–
Maintain temperature between 1 and 45°C | Run two gels simultaneously-or run four gels | Cast single or multiple gels | Perform second-dimension separations using two 7 cm IPG strips side-by-side
--
Contact: see page 49
GE Healthcare Europe
Freiburg, Germany
www3.gehealthcare.de
Contact:
[email protected]
SE 600 Ruby Standard 1D/2D |
Gel size (cm): Up to 16
Dual Cooled Vertical
Unit
1,073.– to
1,499.–
1,485.–
SE 250 Mini-Vertical
Unit for Two Slab Gels,
complete
1D electrophoresis |
Gel size (cm): 8 x 10
Premium, multi-option, mini-vertical electrophoresis unit | Fast results 1,446.–
| Run two gels at once in a single unit | Assemble gel sandwiches and
electrophoresis units quickly and easily | Cast up to four gels at once
SE 260 Mini-Vertical
Unit for Two Slab Gels,
complete
1D electrophoresis |
Gel size (cm): 10.5 x 10
See above
Amersham WB System 1D electrophoresis and Western blotting |
-cPAGE Chamber
Gentaur (Distributor)
(100-240 V)
Aachen, Germany
Contact: Viktor Kadrinov
[email protected]
cPAGE Twin Chamber
Phone +49 241 5600 9968
Atto (Manufacturer)
Labnet International
Made of heavy acrylic glass | Different versions available |
With glass plate stops – for reliable pouring of gels | Wide range of
additional accessories
Price [EUR]
1,533.–
Dedicated consumables and reagents | Optimised prelabeling of
On request
samples with Cy5 NHS chemistry | Reliable normalisation by
multiplexing target and control fluorescent signals on the same blot |
Western blot workflow achieved in less than 4 h
Compact-slab size electrophoresis sys- Integrated power supply | For hand-cast and precast gels
tem with built-in Power Supply |
Gel size (cm): 6 x 6
575.–
Up to two gels | Pressure plate | Gel cast for two or four gels
included
394.–
mPAGE Chamber
Mini-slab size electrophoresis system | Leakage prevention | Temperature control | For precast gels
Gel size (cm): 9.0 x 8.0 x 0,1
394.–
mPAGE Chamber
See above
Leakage prevention | Temperature control | For hand-cast gels
Dual Mini Slab
Chamber
See above
Up to two gels | Pressure plate, | Leakage prevention | Temperature 589.–
control
Enduro Gel XL
-DNA gel box with integrated power
supply |
Gel size (cm): 12.5 x 12; 12.5 x 6 and 6x6
Edison (NJ), USA
europe.labnetinternational.
com
Contact:
Enduro Horizontal Gel
Phone: +1 732 417 0700 Boxes
Compact-slab size electrophoresis
system for two gels |
Gel size (cm): 6 x 6
394.–
610.–
DNA agarose gel analysis |
Gel size (cm): 7 x 7, 7 x 10, 10 x 10,
15 x 10, 15 x 15 and 20 x 20
--
320.– to
548.–
Enduro VE 10 Vertical
Gel System
Protein mini gels and blotting |
Gel size (cm): 10 x 10 and most miniprecast gels
--
608.–
Enduro VE20 Vertical
Gel System
Protein full size gels and blotting |
Gel size (cm): 16 x 17.5
--
1,343.–
Life Technologies
Gels in different concentrations, gradients and for different sample
Novex Bolt Gel Electro- Precast polyacrylamide protein gels
designed for optimal protein separavolumes available | Bolt Welcome Pack A available: Including gel
phoresis System
tion and ideal for use with Western blot tank and all necessary gels and buffers
transfer and analysis |
Gel size (cm): 8 x 8
About
332.–
(Welcome
pack)
MoBiTec
Dark Reader GelHead DNA/ RNA separation and detection |
(combined electropho- Gel size (cm): 12 x 8 x 0.5
resis/non-UV transilluminator unit)
1,112.–
Thermo Fisher Scientific
Carlsbad (CA), USA
www.lifetechnologies.com
Goettingen, Germany
www.mobitec.com
Contact: Arne Schulz
[email protected]
Phone +49 551 70722 0
LT_115_48_52.indd 50
Electrophoresis unit with integrated transilluminator | Allows DNA
bands to be watched in real time as they migrate through a gel | Gel
only needs to be run until the DNA bands of interest are separated |
Results in 30 min or less
29.01.15 15:27
Products
1-2015
Lab Times
page 51
1D Gel Electrophoresis Systems
Company/Distributor Name of device
Purpose & application/Gel size Miscellaneous, Specialities, Generally
Price [EUR]
Nippon Genetics
Europe (Distributor)
Horizontal gel electrophoresis for DNA
and RNA gels |
Gel size (cm): Mini and Maxi gels, up
to 104 samples
All-in-one system (power controller, casting stand, gel trays, combs
are included)
On request
Real-Time DNA detection during
electrophoresis |
Gel size (cm): Mini and Maxi gels, up
to 104 samples
DNA detection, safe LED technology, real-time | Compatible with
Mupid One
On request
Vertical electrophoresis chamber for
protein electrophoresis |
Gel size (cm): 8 x 10 precast gel
cassettes
Small size | 2 gels can be used simultaneously | Reduced buffer
volume
On request
Gel Systems
Horizontal gel electrophoresis |
Gel size (cm): 7 x 8 - 23 x 40
3 years warranty | 6 mm CNC-milled acrylic glass | Gold-plated
banana plugs | Corrosion-protected platinum electrodes |
Optional buffer revolution technology
400.– to
1,195.–
PerfectBlue Vertical
Gel Systems Twin
Vertical gel electrophoresis /PAGE |
Gel size (cm): 10 x 10 – 20 x 20
3 years warranty | 6 mm CNC-milled acrylic glass | Gold-plated
banana plugs | Corrosion-protected platinum electrodes |
Highest safety standards
825.– to
1,435.–
BlueVertical PRiME
Polyacrylamide gel electrophoresis
(PAGE) of vertical mini gels |
Gel size (cm): 10 x 10
Leak-free clamp system to keep the plastic cassettes of precast gels
in correct position | Up to 2 gels per run | Easy and safe to handle
| Smart design
695.–
Flatbed system for horizontal
electrophoresis |
Gel size (cm): max. 26 x 20.5
High capacity cooling plate suitable for high voltage applications |
For all kinds of film-backed flatbed gels, self-cast or precast |
Easy sample loading | Economical reagent usage | Smart design
3,795.–
Mupid One
Düren
www.nippongenetics.eu
Contact:
Mupid One LED Lid
[email protected]
Phone +49 2421 2084690
Advance (Manufacturer)
Peqlab Biotechnologie
FastGene Protein
Chamber
Erlangen, Germany
www.peqlab.com
Contact: [email protected]
Phone +49 9131 610 7020 PerfectBlue Horizontal
Serva Electrophoresis
(Distributor)
Heidelberg, Germany
www.serva.de
HPE BlueHorizon
Contact: Judith Koch
Phone +49 6221 13840 44
[email protected]
HPE BlueHorizon Multi
Decks
High capacity cooling plate suitable for high voltage applications
Stack of 2, 3 or 4 HPE BlueHorizon On request
systems for horizontal electrophoresis | | Modular, multilevel system | For all kinds of film-backed flatbed
gels, self-cast or precast | Economical reagent usage | Smart design
Gel size (cm): max. 26 x 20.5
HPE Tower
Multilevel flatbed system for horizontal Unmatched resolution and reproducibility | Up to 4 gels per run |
Up to 25 % more spots compared to traditional vertical 2D PAGE |
electrophoresis |
Smart design
Gel size (cm): max. 26 x 20.5
On request
HPE Tower System
Multilevel flatbed system for horizontal Unmatched resolution and reproducibility | Up to 4 gels per run |
Up to 25 % more spots compared to traditional vertical 2D PAGE |
electrophoresis |
Smart design
Gel size (cm): max. 26 x 20.5
On request
BlueMarine 100
Submarine agarose gel electrophoresis Max. 28 samples | Contains main unit and 1 removable UV-transparent gel tray, 2 gel casting gates, 1 comb | Colored loading strips
Gel size (cm): 7 x 10
for easy sample application | Optional accessories available
465.–
BlueMarine 200
Submarine agarose gel electrophoresis |
Gel size (cm): 15 x 15; 15 x 20
Max. 62 samples (15 x 15 tray) | Max. 124 samples (15 x 20 tray)
| Contains main unit and 2 removable UV-transparent gel trays,
2 gel casting gates, 2 combs | Coloured loading strips | Optional
accessories available
640.–
BlueMarine HTS
Submarine agarose gel electrophoresis |
Gel size (cm): 17.5 x 19.2
Max. 102 samples | By changing the left/right orientation of the
comb the sample wells can be positioned one upon the other or
shifted to each other | Coloured loading strips | Contains main unit
and 1 removable UV-transparent gel tray, 2 aluminum gel casting
gates, 6 combs
1,095.–
Elchrom (Manufacturer)
Origins by Elchrom
Scientific
Horizontal electrophoresis |
Gel size (cm): 10.8 x 27.8
Temperature control | Suitable for self-cast agarose gels and
5,950.–
Elchrom ready-to-use gels | Unit contains integrated cooling/heating
system, integrated temperature control, integrated pump for buffer
circulation | Working temperature ranges from 4 to 55 °C
Hoefer (Manufacturer)
Hoefer SE250 Mighty
Small II Mini Vertical
Electrophoresis Unit
Polyacrylamide gel electrophoresis
(PAGE) of vertical mini gels |
Gel size (cm): 10 x 8
Up to 2 gels per run | Complete unit contains the basic unit with gel
casting accessories | Optional accessories available
575.– to
845.–
Hoefer SE260 Mighty
Small II Mini Vertical
Electrophoresis Unit
Polyacrylamide gel electrophoresis
(PAGE) of vertical mini gels |
Gel size (cm): 10 x 8; 10 x 10.5
Up to 2 gels per run | Compatible with SERVAGel precast vertical
mini gels | Complete unit contains the basic unit with gel casting
accessories | Optional accessories available
595.– to
875.–
Hoefer SE300 miniVE
Integrated Vertical
Electrophoresis and
Blotting Unit
Blotting and polyacrylamide gel
electrophoresis (PAGE) of vertical mini
gels |
Gel size (cm): 10 x 8, 10 x 10.5
Up to 2 gels per run | Compatible with SERVAGel precast vertical
mini gels | Complete unit contains the basic unit with gel casting
accessories | Optional accessories available
725.– to
895.–
Hoefer SE400
Air-cooled Vertical
Electrophoresis Unit
Polyacrylamide gel electrophoresis
(PAGE) |
Gel size (cm): 18 x 16
Up to 2 gels per run | Rugged and economical unit ideal for
educational laboratories with multiple users | Complete unit
contains the basic unit with gel casting accessories | Optional
accessories available
995.– to
1,095.–
Hoefer SE410 Tall
Air-Cooled Vertical
Electrophoresis Unit
Polyacrylamide gel electrophoresis
(PAGE) |
Gel size (cm): 18 x 24
Up to 2 gels per run | Rugged and economical unit ideal for
educational laboratories with multiple users | Optional accessories
available
1,275.–
Hoefer SE640
Wide-Mini Vertical
Electrophoresis Unit
Polyacrylamide gel electrophoresis
(PAGE) |
Gel size (cm): 18 x 8
Up to 2 gels per run | Extra wide format ideal for quick, high through- 985.– to
put runs | Complete unit contains the basic unit with gel casting
1,175.–
accessories | Optional accessories available
LT_115_48_52.indd 51
29.01.15 15:27
page 52
Lab Times
Products
1-2015
1D Gel Electrophoresis Systems
Company/Distributor Name of device
Purpose & application/Gel size Miscellaneous, Specialities, Generally
Price [EUR]
Serva (continued)
Hoefer SE600
Standard Dual Cooled
Vertical Unit
Polyacrylamide gel electrophoresis
(PAGE) |
Gel size (cm): 18 x 8; 18 x 16
Up to 2 gels per run | Complete unit contains the basic unit with gel
casting accessories | Optional accessories available
1,335.– to
1,375.–
Hoefer SE600X
Chroma Deluxe Dual
Cooled Vertical Unit
Polyacrylamide gel electrophoresis
(PAGE) |
Gel size (cm): 18 x 8; 18 x 16
Up to 2 gels per run | Ergonomically designed unit for easier
handling and sample application | Complete unit contains the basic
unit with gel casting accessories | Optional accessories available
1,450.– to
1,575.–
Hoefer SE660 Tall
Standard Dual Cooled
Vertical Unit
Polyacrylamide gel electrophoresis
Up to 2 gels per run | Tall format unit for 24 cm long gels to increase 2,275.– to
(PAGE) |
resolution | Complete unit contains the basic unit with gel casting
2,385.–
Gel size (cm): 18 x 8; 18 x 16; 18 x 24 accessories | Optional accessories available
Hoefer HE33Mini
Horizontal Agarose
Electrophoresis Unit
Mini horizontal unit for agarose gel
electrophoresis |
Gel size (cm): 7 x 10
For rapid separation of DNA fragments | Max. 32 samples |
Complete unit includes basic unit, comb, comb back | Optional
accessories available
375.– to
410.–
Hoefer HE99X Max
Horizontal Agarose
Electrophoresis Unit
Horizontal agarose gel electrophoresis | To design the gel for optimal resolution of DNA fragments |
Gel size (cm): 15 x 10; 15 x 15; 15 x 20 Complete unit includes basic unit with casting and running tray,
comb, comb back | Optional accessories available
475.– to
665.–
Hoefer SUB6 Mini
Submarine Gel
Electrophoresis Unit
Horizontal agarose gel electrophoresis |
Gel size (cm): 6 x 7.5
Max. 32 samples | Allows gel casting directly in the tank |
360.–
Unit includes buffer chamber assembly with running tray with silicone
gasket, 1 mm thick, 8 well combs – 2 pcs, coloured loading strips |
Optional accessories available
Hoefer SUB10
Mini-Plus Submarine
Gel Electrophoresis
Unit
Horizontal agarose gel electrophoresis |
Gel size (cm): 10 x 11.5
Max. 80 samples | Allows gel casting directly in the tank |
410.–
Unit includes buffer chamber assembly with running tray with silicone
gasket, 1 mm thick, 16 well combs – 2 pcs, coloured loading strips |
Optional accessories available
Hoefer SUB13 Midi
Submarine Gel
Electrophoresis Unit
Horizontal agarose gel electrophoresis |
Gel size (cm): 12.8 x 15
Max. 112 samples | Allows gel casting directly in the tank |
435.–
Unit includes buffer chamber assembly with running tray with silicone
gasket, 1 mm thick, 16 well combs – 2 pcs, coloured loading strips |
Optional accessories available
Hoefer SUB15
Standard Submarine
Gel Electrophoresis
Unit
Horizontal agarose gel electrophoresis |
Gel size (cm): 15 x 15
Max. 120 samples | Highly versatile option for screening samples,
490.–
ranging from DNA mini-preps to PCR products | Buffer recirculation
ports | Unit includes buffer chamber assembly with running tray with
silicone gasket, 1 mm thick, 16 well combs – 2 pcs, coloured loading
strips | Optional accessories available
Hoefer SUB20
Maxi-Standard
Submarine Gel
Electrophoresis Unit
Horizontal agarose gel electrophoresis |
Gel size (cm): 20 x 20
Max. 160 samples | Buffer recirculation ports | Unit includes buffer
chamber assembly with running tray with silicone gasket, 1 mm
thick, 16 well combs – 2 pcs, coloured loading strips | Optional
accessories
Hoefer SUB20C
Maxi-Cooled
Submarine Gel
Electrophoresis Unit
Horizontal agarose gel electrophoresis |
Gel size (cm): 20 x 20
Max. 160 samples | Buffer recirculation ports | Unit includes buffer 905.–
chamber assembly with cooling ports, running tray with silicone
gasket, 1 mm thick, 16 well combs – 2 pcs, coloured loading strips |
Optional accessories
Hoefer SUB25
Maxi-Plus Standard
Submarine Gel
Electrophoresis Unit
Horizontal agarose gel electrophoresis |
Gel size (cm): 25 x 30
Max. 624 samples | Buffer recirculation ports | Unit includes buffer
chamber assembly with running tray with silicone gasket, 1 mm
thick, 26 well combs – 6 pcs, coloured loading strips | Optional
accessories
875.–
Hoefer SUB25C
Maxi-Plus Cooled
Submarine Gel
Electrophoresis Unit
Horizontal agarose gel electrophoresis |
Gel size (cm): 25 x 30
Max. 624 samples | Buffer recirculation ports | Unit includes buffer
chamber assembly with cooling ports, running tray with silicone
gasket, 1 mm thick, 26 well combs – 6 pcs, coloured loading strips,
buffer recirculation port | Optional accessories
1,085.–
Sysmex Partec
CyFox – All-In-One
Gel Electrophoresis
System
Horizontal gel electrophoresis system
for size separation of nucleic acids
(DNA/RNA) |
Gel size (cm): 7 x 11
All-in-one device | Live observation process | Time-controlled
recording | No darkroom needed, non-toxic staining |
Automatic analysis software
On request
Takara Bio Europe
MupidOne Gel
DNA & RNA electrophoresis |
Gel size (cm): 13 x 5.95 or 13 x 12.2
Complete and compact system | Includes gel tank and detachable
power supply | Supplied with heat-resistant gel casting set: gel trays
and combs | Multichannel-pipette-compatible
585.–
Wako Chemicals
SuperSep Phos-tag
Separation of phosphorylated and
non-phosphorylated proteins by SDSPAGE |
Plate (cm): 10,0 x 10,0 x 0,3
Gel size (cm): 9.0 x 8.5 x 0,1
13 and/or 17 wells
Efficient separation of phosphorylated and non-phosphorylated
On request
proteins with sharp bands | Long-term stability (stable for 6 months)
| Applicable with the following systems: Nihon Eido, Bio-Craft,
Cosmo-Bio, Tefco | Applicable with special handling: Atto AE-6500
Dual Mini Slab (careful installation), Invitrogen Xcell SureLock
Mini-Cell
Contact: see page 51
Goerlitz, Germany
www.sysmex-partec.com
Contact:
[email protected]
Phone +49 3581 8746 0
Electrophoresis
(Distributor)
St Germain-en-Laye, France System
www.clontech.com
Contact: Phone
+33 1 3904 6880 (Europe)
0808 234 8063 (UK)
0800 182 5178 (DE)
0800 563 629 (CH)
[email protected]
Advance (Manufacturer)
(50 µmol/l) Gels
Neuss, Germany
www.wako-chemicals.de
Contact: biochem@
wako-chemicals.de
Phone +49 2131 311 155
LT_115_48_52.indd 52
675.–
29.01.15 15:27
New Products
1-2015
Lab Times
page 53
New Products
Cell Culture
Product: Bioreactor
Name & Manufacturer: Biostat A from Sartorius Stedim Biotech
Technology: The system’s control tower features
a complete array of measurement and control
functions like easy-load peristaltic pumps, an
aeration module, conveniently accessible probe
ports and supply connections. The aeration system provides automatic flow control over the full
range of each gas used. The bioreactor is available with various single-walled borosilicate glass
culture vessels with maximum working volumes
of 1, 2 or 5 litres.
Advantages: Thanks to the intuitive user interface, operating the new bioreactor is ideal
for beginners because it prevents operating
errors and reduces training time to a minimum.
Optional operation with a tablet or smartphone
allows to monitor and control the system,
whether you’re on the go, in the lab, in the office
or even at home.
More Information: www.sartorius.com
Pipetting
Product: Electronic Pipette
Name & Manufacturer: Viaflo II from Integra
Biosciences
Technology: The new 50 µl multichannel electronic pipette range combines ultra lightweight
design and operational comfort. GripTips snap
into place with minimal tip loading effort.
Advantages: The new 50 µl models available
for single-, 8-, 12- and 16-channel VIAFLO II
pipettes, deliver optimised precision pipetting.
More Information: www.integra-biosciences.
com
LT_115_New Products.indd 53
Immunohistochemistry
Product: Protein Detection System
Name & Manufacturer: SNAP i.d. 2.0 from
Merck Millipore
Technology: Traditional immunohistochemistry
(IHC) methods may be subject to process variability. The protein detection system addresses
these challenges by systemising the handling
of multiple slides. It decreases slide handling
time and enables parallel processing of up to
24 slides at once, reducing slide-to-slide process variation without incurring the costs of automation. In addition, the system speeds wash
steps and allows antibodies to be recovered
and reused, saving researchers valuable time
and resources. The system produces robust
and consistent staining, without causing tissue
degradation or blotchy artifacts. It also offers
the flexibility for researchers to perform Western blotting and IHC experiments in parallel, facilitating use of the system by multiple users at
once, and also makes it possible to simultaneously assess relative abundance of an antigen
(by Western blotting) and spatial distribution
(by immunohistochemistry).
Advantages: The power of IHC lies in its capacity to localise antigens within tissue samples,
thereby identifying the cell types and subcellular compartments in which antigens are located.
This is particularly important for heterogeneous
tissues (i.e., tissues made up of many different
cell types, such as the brain and tumors), for
which other antigen detection methods do not
reveal spatial information.
More Information: www.merckmillipore.com/
snap.
Microscopy
Product: Confocal microscope
Name & Manufacturer: LSM 800 with­
Airyscan from Zeiss
Technology: The microscope system is continually monitoring and calibrating the scanner
position to guarantee a stable field of view and
equal pixel integration times over the whole
field of view. The linear scanning regime gives
a constant signal-to-noise level and uniform
exposure to the illuminating laser throughout
the scanned area, including manipulated regions of interest. Gallium arsenide phosphide
photomultiplier tubes (GaAsP PMTs) display
high light collection efficiencies over a broad
spectral range. The gain in signal-to-noise ratio
(SNR) will increase productivity by achieving
faster scan speeds while preserving high image
quality. The optional Airyscan module delivers
1.7 times higher resolution and higher sensitivity than conventional confocal microscopes.
Advantages: The LSM 800 is an affordable system with a good price-performance ratio: robust
and easy to use, with a small footprint. Minimal
setup requirements, minimal maintenance, and
self-calibration paired with low overall energy
consumption make it an economical choice.
More Information: www.zeiss.com
Protein Purification
Product: Medium-Pressure Chromatography
Systems
Name & Manufacturer: NGC Discover and
NGC Discover Pro from Bio-Rad Laboratories
Technology: The systems are available with a
10 ml/min pump module or with the NGC 100
ml/min pump module. They are able to load
multiple samples and run up to 15 columns sequentially. The Pro System can collect 12 largevolume fractions via its outlet valve.
Advantages: All NGC Systems feature the same
modular design with interchangeable plug-andplay modules that allow researchers to scale
the system according to their throughput needs.
All systems can be operated in compliance with
21CFR Part 11 regulations.
More Information: www.bio-rad.com/NGCpr
29.01.15 14:41
page 54
Lab Times
Book Review
1-2015
Book review: The bizarre life and death of the SS doctor Sigmund Rascher
An Ordinary Scientist
During the Third Reich, he was the prototype of a Nazi monster. If he were alive today, however,
he would probably be a popular physician in alternative medicine, claims the author of an
equally disturbing and entertaining biography on Nazi medical experimenter, Dr Sigmund Rascher.
D
r Sigmund Rascher has a poor reputation as one of the worst of the
Nazi medical experimenters, the
prototype of a Nazi monster. In his various
experiments during World War 2, over 200
people are thought to have died. But Siegfried Bär’s book, The Fall of the House of Rascher, is about more than just Rascher’s
deadly research. It is, in effect, a biography
of Rascher (1909-1945), his family, his education, his helpers, co-workers and superiors. Bär says he wrote it because there was
enough material to reconstruct Rascher’s
life in the “finest detail” – some hundred
personal letters from his close family and
friends, documents from the years 1936 to
1944, and testimony from the 1947 Doctors’
Trial at Nuremberg. He traces the influences that shaped Dr. Rascher, “an average person like you and me who happened to live
through a dark and strange adventure unparalleled by any other.”
“An average person like you and me”
Rascher’s family were early adherents
of Rudolf Steiner’s spiritual movement,
the Anthroposophical Society (founded in
1913). Sigmund attended the first Waldorf
school, a hotbed for children of educated
middle class Anthroposophists. Here, he
came under the direct influence of Ehrenfried Pfeiffer, an ‘apostle’ who played a
major role in developing Steiner’s ideas on
biodynamic farming (that are still popular today).
Rascher went on to study medicine, but
was drawn to research by Pfeiffer’s ideas
about the influences of cosmic rhythms on
life processes. In particular, Pfeiffer claimed
to show that spiritual forces could influence
the crystallization of copper chloride. Starting in 1934, Rascher hoped to get his doctoral degree by proving that hormones affect this crystallization process and that
it could be used as a pregnancy test. He
claimed that his test worked, but there were
doubts and funding problems.
His research career was saved when he
fell in love with an influential older woman, Karoline “Nini” Diehl, a former crooner.
LT_115 Books.indd 54
While Rascher was working on his crystal
studies, the Nazis were firmly establishing
their power in Germany. Nini just happened
to be a close friend of a top Nazi – Heinrich
Himmler, head of the SS and, as General
Plenipotentiary, one of the most powerful
men in Nazi Germany. Trained as an agronomist, Himmler himself had plenty of ideas about science. In 1935, he founded the
Ahnenerbe, the ‘Study Society for Primordial Intellectual history, German Ancestral
Heritage’. At its height, the Ahnenerbe comprised 46 departments and 300 employees.
Not much of a researcher
After Nini lobbied Himmler on behalf
of her beloved, Rascher duly completed his
thesis in 1939 and started a five point research contract under Himmler’s patronage. Unfortunately, Rascher was not much
of a researcher. In 1941, fearing he would
lose favour with Himmler, he began a research project investigating the effect of low
pressure on adult men. The Luftwaffe were
concerned that their pilots flying at high altitudes would suffer from low air pressure
should their planes be hit by enemy fire. Rascher took prisoners from the Dachau concentration camp (near Munich) as substitutes for Luftwaffe pilots, and began sticking them in a vacuum chamber to see what
happened. Not surprisingly, they suffered
agony and occasionally died.
A year later, Rascher moved on to a
new problem. Luftwaffe air crews who
parachuted into the North Sea were freezing to death. What is the cause of death by
freezing? How can frozen men be warmed
again? Prisoners were duly placed in ice
cold water baths. More deaths.
However, Rascher was now preoccupied
with getting enough research results for his
Habilitation (the German university teaching qualification). For this, he needed to
write an extensive thesis. He began to collect projects like others collect stamps (Rascher was, in fact, also a keen philatelist).
In Dachau, he had a team of prisoner technicians who proposed projects for which
he could claim all the credit. These includ-
ed patented mashed potatoes, an anti-rust
agent, a cancer cure, and a hemostatic, Polygal. The latter, when taken orally, is supposed to stop bleeding in wounded soldiers.
It is actually a pectin preparation normally
used to make jams and jellies.
Rascher’s downfall ...
Bär presents and analyses many of Rascher’s dubious research projects. Nothing really worked, but that didn’t matter as
long as Himmler was happy. Ironically, Rascher’s downfall came from his wife’s fertility – Nini was suspiciously old to be having babies. She gave birth, in mysterious
circumstances, to a first son in 1939. Then
she had a second and a third.
The scandal errupted at the end of a
fourth pregnancy in 1944 – Nini was accused of baby-snatching at Munich railway
station. The police investigation discovered
that she had been ‘hiring’ babies. Rascher,
however, had noticed nothing (at least, this
is what he claimed).
... caused by his wife’s fertility
Himmler was not happy. Nini and Rascher were duly imprisoned and, as Nazi
Germany descended into chaos, they were
finally executed in 1945.
Siegfried Bär has written a highly documented biography. He finds that Sigmund
Rascher was not a monster, “Apart from his
personal ambition, he had no outstanding
mental or emotional gifts, not even a disposition for cruelty.”
And yet he initiated and performed
these deadly experiments on living humans.
Bär suggests that if Rascher were alive today, “he would probably be a popular physician in alternative medicine.”
Jeremy Garwood
The Fall of the House of Rascher: The bizarre
life and death of the SS doctor Sigmund Rascher. By Siegfried Bär. Kindle edition, English, 1436 KB (the equivalent of about 500
pages), €7,66 Euro (sold by Amazon Media
EU S.à r.l.). ASIN: B00MBOFX5K.
28.01.15 22:39
Book Review
1-2015
Lab Times
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Book review: Human Identity and Identification
Our Identity:
from Skin to DNA
W
Photo: University of Durham
ho are you? What gives you your
identity? Is it the DNA that you
inherited from your parents? Or
your brain, which is in charge of recording
what happens in your life? As you probably
guessed, the answer is not that simple. Although DNA affects how you look and behave, and your brain charts your daily experiences, the many other parts of the body,
taken together, comprise the person you are
and influence how you live your life and
build an identity.
Rebecca Gowland, an archaeologist at
Durham University, and Tim Thompson,
an anthropologist at Teesside University,
wrote a book about this relationship between body, identity and society. Through
Human Identity and Identification they travel
inside and outside of our bodies and explain
their components’ influence in understanding individuals in biological, medical, social,
forensic and even anthropological contexts.
Gowland and Thompson explore the
body in its different layers. They start with
Authors Rebecca Gowland and Tim Thompson organise courses in forensic science,
studying and practising techniques of
body location, recovery and analysis.
LT_115 Books.indd 55
the skin, discussing its role in identification
(just think of fingerprints, palmprints, footprints and, yes, you heard right, earprints).
Later they look deeper into what lies be-
Photo: NIH
How does our body define us? How does it connect with our environment and influence others’ perceptions of us? What role does it play
in human identification in the context of forensics and archaeology?
Two English scientists explore these and similar questions.
One of the main aims of the authors is
to look at the human body not only from the
biological and physical perspective, but including the social boundaries, discontinuities and tensions associated with it. Each
body part is placed in its social and historical context.
Forbidden interaction with blood
Rebecca Gowland, lecturer in bioarchaeology
at the University of Durham, is doing research
on skeletal remains discovered in Rome. Her
new book examines the relationship between
social identity and biological tissues.
neath: the skeleton, blood, guts and body
fat. They tackle and discuss many forensic
techniques, including the most conventional, such as fingerprints, analyses of blood
stains, and the study of the isotopic composition of tissues, which is helpful when
guessing what an individual has ingested
(a procedure that has been used for forensic cases but which is particularly common
in archaeological research).
Finally, they review the biomolecular
machinery involved in our identity. DNA,
for instance, which has also played an important role in forensic identification in recent decades. Interestingly, in this same
chapter the authors review more recent advances, such as the study of bacterial and
other microbial communities that can help
in forensic cases associated with terrorism
or bite marks. These new developments in
microbiology, including the potential understanding that the study of microbiomes
can give, also open a door to using the microscopic communities in our bodies as determinants of identity.
The concept of blood is an example of a
body component that not only has an enormous role in forensic identification, but also
carries a highly emotional definition and
has been the subject, as the authors recognise, “of mythologies, hate (and) religious
fervour”. Religious identity influences how
a person takes decisions regarding his or
her blood in a medical context. In some religions, such as amongst Jehovah’s Witnesses for instance, interaction with blood is forbidden, which also affects whether an individual is allowed to receive blood transfusions and whether he or she pays a moral
cost in order to get them.
In summary, Human Identity and Identification discusses the role of the body in human identity, providing an update on current methods in forensic science. It is therefore recommended to readers involved or
interested in this field, with the caveat that
it offers a good introduction to the topic
rather than highly specialised content.
Additionally, both forensic scientists and
laypeople will be encouraged that the discussion is taken from both a biological and
a social viewpoint, aiming to better clarify how the body influences identity. This
book will provide answers to all those curious about how each of our body parts can
say something about us and how society has
perceived individual traits throughout human history.
Alejandra Manjarrez
Human Identity and Identification. By Rebecca Gowland and Tim Thompson. Cambridge
University Press, 2013. 233 pages, £30 (€35).
28.01.15 22:39
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56
Lab Times for young
1-2015 European scientists (LII)
Career
strategies
Careers
Science and Society
The idea of supporting the best science for the world and not that in the world
has become popular. Science-society issues have also gained momentum in the ongoing EU Framework Programme, Horizon 2020. Participating scientists and their institutions
are faced with new challenges, including modified rules for publication and data sharing.
E
uropean Framework Programmes for
Research and Technological Development were launched about 30 years
ago. Approximately €80 billion have been
earmarked in the current eighth consecutive programme (2014-2020) for all sorts
of research, development and innovation,
with the ultimate goal of increasing the
economic competitiveness of the European
Research Area. Horizon 2020’s three main
funding pillars are scientific excellence, industrial leadership and societal challenges.
In addition, there are smaller programmes,
such as Science with and for Society whose
mission it is to bridge the gap between the
scientific community and society.
But societal topics are not confined to
EU research agendas and academic discourse. In Horizon 2020, they have arrived
at the level of the individual research project and the scientist involved. For example,
requirements for compliance with ethical
standards, or for sharing publications and
are just a few recent concepts, which are becoming increasingly relevant not only in the
context of EU programmes, but may also influence the way science is funded at the national level in the future. Here, Lab Times
will provide some insights into recent developments, with a focus on open access in
Horizon 2020 and beyond.
Humble beginnings
The promotion of research and innovation in order to create new knowledge, technologies and products has always been at
the core of the EU Framework Programmes
(FP). As well as research, addressing the
scientific outcome and broader impact of
EU-supported projects and programmes has
gained importance over the years. More emphasis has also been gradually placed on research and additional activities, targeting
legal, ethical and societal issues associated
with science and technology. The funding
of small-scale pilot projects, including tech-
Maria Leptin, EMBO Director, Heidelberg, Germany: “Data
are indeed an essential component of publications. In our
view, an important element of the open sharing of research
is unrestricted access (which means Open Access with a license that does not impose undue restrictions) to the data
published in papers with sufficient context to allow use
and reuse of this data. With its SourceData project, EMBO
is currently developing editorial tools to make this vision
possible. Open access to data in research papers can be
achieved without necessarily converting the journal to OA.”
research data, must either be compulsorily addressed or on an optional basis for the
time being. In some funding programmes,
new criteria such as gender balance have
been included as ranking factors for applications, receiving the same score during
evaluation. Moreover, scientists must now
justify their research proposal by estimating its economic impact and societal benefit, in addition to its scientific value and European added value. Responsible research,
open access, Science 2.0 and citizen science
LT_115_56_60.indd 56
nology assessment and foresight studies,
but also larger programmes, were to some
extent motivated by novel emerging technologies and their applications (such as, for
example, genetic engineering in the past
and, more recently, nanotechnology and
geoengineering), or by disease outbreaks
and environmental catastrophes.
In the late 1980s, intensifying communication with the public and getting to
know the public’s opinion on and knowledge of science and technology were on
Photo: Fotolia/ptnphotof
in Horizon 2020 and Beyond
the EU agenda. In the 90s, the policy focus shifted slowly towards the integration
of social and ethical aspects of science and
engineering research, for example, by using
the Targeting Socio-Economic Research FP4
programme. To improve the understanding
of the benefits and limitations of scientific
and technological research by the general
public, programmes such as the FP5 Raising Awareness Programme were launched,
aimed at sensitising scientists to matters of
concern to the public.
Societal issues pick up speed & Euros
The Commission working paper Science, Society and the Citizen in Europe,
published in 2000, was a key document that
culminated in the first Science and Society Action plan of the European Commission. Subsequently, new concepts promoting dialogue and participation were put forward in FP6 (2002-2007), for example, by
the €80 million Science and Society programme and the €225 million Citizen and
Governance in Knowledge-based Society
programme.
The shift from Science and Society to Science in Society was made in FP7
(2007-2013) to stress that both areas are
not separate entities but highly interconnected. The €330 million programme enabled hundreds of research, coordination
and support actions as well as initiatives,
conferences, seminars and expert groups.
In a recent presentation by the DG RTD B7,
the Unit of the Directorate-General for Research and Innovation in charge of science
and society issues at the European Commission, three main outcomes of previously funded science-society projects were emphasised. First, good marketing alone is no
longer sufficient to gain public acceptance
of technology. Second, the key to innovation adequacy and acceptability is the early
and continuous engagement of the public.
Finally, to achieve greater creativity and to
promote better results in the whole research
process, diversity at all levels and in all as-
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Careers in academia
pects of the research process has become a
must. The interested reader may find further details in the policy briefing Science in
Society: caring for our futures in turbulent
times published by the European Science
Foundation in 2013 and in a very recent
review by the National Research Council
of Italy on the main priorities and achievements of science-society activities funded
in FP6 and FP7.
Science at the service of society?
Integrating society in science and innovation (ISSI), making science education and
careers attractive for young people (SEAC),
promoting gender equality in research and
innovation (GERI) and developing governance for the advancement of responsible
research and innovation (GARRI). All proposals have to take up and support the new
Responsible Research and Innovation (RRI)
approach in Horizon 2020, which will be
explained in detail below.
Whereas in the past the results of science-society programmes often went unnoticed by the greater scientific community
and public, more emphasis has been placed
in Horizon 2020 on dissemination beyond
a closing expert-level conference, a major
publication or website that will eventually
become outdated. In order to receive financial support, applications in the programme
have not only to give proof of their innovative character but also of their social, eco-
Societal challenges, with their assignment to push research and innovation for
the society’s benefit, has become one of
three major funding priorities in Horizon
2020. Roughly 40% of the whole FP budget is earmarked for seven topics, which have
been identified as key societal challenges in
the Europe 2020 strategy for smart, sustainable and inclusive growth. They include, for
example, health, food security, clean and
efficient energy, resource efficiency and raw materials, Jack Stilgoe, Department of Science and Technoland will be tackled by re- ogy Studies, University College of London: “Under
search and innovation activiHorizon 2020, there will certainly be growing support
ties, bringing together differfor open access. But open science does not only
ent disciplines, technologies
speed up research and innovation, it brings new
and actors.
Social sciences and hu- responsibilities, too. It questions the boundaries that
manities research were separate science from the rest of society. I think we
stressed as important ele- underestimate how difficult will be the vital task of
ments in these efforts, main- turning open science into responsible science.”
ly to counteract continuing
nomic and environmental sustainability becriticism of being largely underrepresentyond the funding period. The topic of Scied with respect to funding opportunities
ence within and for the Society has defiand research budgets. Research and innovanitely drawn considerable attention within
tion activities are accompanied by the €500
the scientific community and beyond. This
million Science with and for Society prois evident, for example, from the number
gramme (SWAFS), which was not holed up
of proposals in the first calls for Horizon
beneath major funding lines as previously,
2020 and from the crowd of 600 attendbut was implemented as an independent
ees in the booked-up international conferand clearly visible element. According to
ence on ‘Science, Innovation and Society:
the work programme, the aim of SWAFS is
Achieving Responsible Research and Innoto build an effective cooperation between
vation’ in Rome last November.
science and society, to recruit new talents
for science and to pair scientific excellence
Responsible research and innovation
with social awareness and responsibility.
The concept of responsibility in science
For the first time in the history of EU prois nothing new. Its meaning extends beyond
grammes, research and innovation to socipure research ethics and varies widely, for
ety’s benefit and activities bridging the gap
example between scientific disciplines such
between science and society have been poas biomedicine or physics and research topsitioned prominently. Whether this was just
ics under consideration, such as geneticala clever move to justify an increased budgly modified crops, nuclear energy and IT
et for Horizon 2020 in times of economic
security.
turbulence or indeed a strong commitment
Various definitions of RRI have been
that will not soon be abandoned for the sake
put forward recently, for instance by a
of economic impact remains to be seen.
group of scientists in the UK consisting
SWAFS funding announcements, with
of Jack ­Stilgoe, Richard Owen and Phil
deadlines in September 2015, will fall with­Macnaghten, by the Dutch agricultural sciin the following four broad thematic topics:
LT_115_56_60.indd 57
entist and philosopher René von Schom­
berg, working for the European Commission on research and innovation policies,
and by the European Commission itself. The
UK scientists described the four dimensions
of RRI: anticipation in governance, reflexivity by actors and institutions, inclusion of
new voices and responsiveness in the innovation systems. Von Schomberg defined
RRI in his article A vision of Responsible
Research and Innovation as a “transparent,
interactive process by which societal actors
and innovators become mutually responsive to each other with a view to the (ethical) acceptability, sustainability and societal desirability of the innovation process
and its marketable products in order to allow a proper embedding of scientific and
technological advances in our society.”
In the EU context, Responsible Research
and Innovation (RRI) surfaced during the
programming period of Horizon 2020, towards the end of FP7, as a compromise between economic and
societal aspects of research and
innovation. RRI has been implemented as a cross-cutting issue with relevance for all three
major funding areas of Horizon
2020, and should be taken into
consideration and promoted
throughout the whole FP.
The European Commission settled on six RRI key elements in 2012: 1) open access to the results
of publicly-funded research for all societal
actors to increase their impact and to make
research and innovation more transparent,
2) ethics as a way of ensuring high quality results and increased acceptability of research and innovation, 3) gender equality
in the context of research and innovation,
4) science education to bring more talent
into research and to create a science-literate society, 5) engagement of all societal actors and their participation in the research
and innovation process and, finally, 6) governance as a tool to implement the five previous keys and to prevent harmful and unethical developments in research and innovation.
One might argue that RRI is just an omnium gatherum of the European Commission to gain acceptance for a bundle of highly diverse topics, which are directly or indirectly linked to research and innovation but
do not have too much in common and have
been widely addressed before. The rest of
this article will be confined to the RRI key
element of open access and how it is put
into practice in Horizon 2020.
29/01/2015 10:15
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Careers
Careers in academia
The practice of providing online acagencies have responsibilities, too. These
tation of results, nor an obligation to pubcess to scientific information that is free of
include, for example, the definition of instilish. The scientist receiving financial supcharge to any end-user and is re-usable is
tutional policies and the provision of fundport for a project in Horizon 2020, also
a brief definition of open access. The Euing for the dissemination of scientific incalled the beneficiary in FP language, still
ropean Commission reasoned a couple of
formation, including E-infrastructure (e.g.
decides whether all or part of his research
years ago that “information already paid
hardware, software and skilled personnel
results are secured, exploited or dissemifor by the public purse should not be paid
to run the infrastructure) in order to secure
nated. However, open access becomes manfor again each time it is accessed or used,
long-term preservation and re-use.
datory as soon as he chooses to publish reand that it should bensults originating from
efit European compaa Horizon 2020-fundnies and citizens to the
ed project.
full”. Open access was
Open access inScience with and for Society in Horizon 2020 – http://ec.europa.eu/research/swafs
put forward as a way
cludes two steps: deto optimise the impact
positing a publication
European Commission RRI Twitter – @RRI_EC
of publicly-funded rein a repository for sciESF briefing – www.esf.org/uploads/media/spb50_ScienceInSociety.pdf
search. This should be
entific publications
Review on science-society projects in FP6 and FP7 – www.bit.ly/1y6MOsL
translated into action,
and providing open
Euroscientist special issue on RRI – www.euroscientist.com/rri/?format=pdf
for example, by inaccess not only to the
FP7 Project RRI Tools – www.rri-tools.eu
corporation of scienpublication itself but
tific information and
also to its bibliographOpen access in Horizon 2020 has a legal
knowledge gained in the past into new reic metadata. The metadata in the repositobasis in the Framework Programme itself
search projects, thereby promoting the rery identify the deposited publication and
and its Rules of Participation. Specific reuse of scientific information, avoiding dushould include a persistent identifier, such
quirements for the dissemination of results
plication of efforts, creating transparency
as a DOI (Digital Object Identifier), the puband open access are laid down in Article
and fostering scientific collaboration.
lication date, data referring to the original
29 of the Model Grant Agreement, which
funding announcement (name of action),
Setting the landmarks for open access
has to be signed after positive evaluation
the project acronym and the grant numAs an immediate outcome, the prospect
of the research proposal in order to receive
ber as well as the terms “EU” and “Horiof savings in R&D expenditure and an inEU funds.
zon 2020”. In addition, authors funded by
creased return on public R&D investments,
a Horizon 2020 project, should aim to deBasics of open access in Horizon 2020 posit research data needed to validate the
but also the acceleration of the research
According to the current Guidelines on
and discovery process with a shortened
results at the same time.
Open Access to Scientific Publications and
time from the innovation to the market, was
Pick your colour: OA in practice
Research Data in Horizon 2020, the most
highlighted. Alongside the EU flagship initiDepositing a publication and granting
relevant scientific information are peer-reatives Digital Agenda for Europe and Innoopen access to it may take place simultaneviewed scientific research articles in acavation Union, a couple of major policy docously or not, depending on the publishing
demic journals as well as research data givuments that paved the way for open access
model. There are two major routes: archiven as data underlying publications, curated
in Horizon 2020 were published in 2012. A
ing by the author himself or his representdata or raw data. In addition, making open
communication entitled “Towards better acative (green open access) or open access
access available to other publications such
cess to scientific information – boosting the
publishing by the publisher (gold open acas monographs, books and conference probenefits of public investments in research”
cess). Green open access means that the auceedings is encouraged.
set three major targets: to establish nationthor publishes his article as usual, for examResearch data can be defined as paral policies for open access in all EU Memple, in a subscription-based journal, and deticular facts or numbers, which are collectber States by 2014; to increase the share
posits either a machine-readable electroned to be examined and considered as a baof publicly-funded scientific articles under
ic form as, for example, a PDF file of the
sis for reasoning, discussion or calculation
open access at EU-level from 20% to 60%
published article or the final peer-reviewed
and are available in digital form, including
by 2016; and to make all scientific publicamanuscript as soon as possible, or, at the
experimental results, measurements, statistions resulting from Horizon 2020 available
latest, on publication in an online database
tics, observations resulting from fieldwork,
under open access.
or repository. Repository software might alsurvey results, interview recordings or imIn “On access to and preservation of
low the author to delay access to the article.
ages. However, no legally binding definition
scientific information”, EU Member States
This embargo period must be within a maxiof open access is given. Open access to sciwere informed about the cornerstones of
mum of six months in STEM disciplines (scientific publications is understood to include
the national implementation of open acence, technology, engineering, mathematthe right to read, download and print as
cess. In the meantime, so-called National
ics), in case of publications in the social sciwell as to copy, distribute, search, link and
Points of Reference for open access have
ences and humanities within a maximum
mine, whereas open access to data means
been established in almost every EU counof twelve months. The embargo may also
that they can be accessed, exploited, mined,
try with the task of coordinating efforts at
be imposed by the publisher, whose polireproduced and disseminated.
a national level. It was further stressed that
cies make provisions for an embargo period
Open access in Horizon 2020 is by no
open access is not the sole responsibility of
during which he is able make some money,
means at odds with securing intellectual
the scientist himself but that other actors,
for example, via pay-per-view or by grantproperty rights or the commercial exploiincluding research institutions and funding
Science-Society Links
LT_115_56_60.indd 58
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Careers in academia
ing institutions the right to use it for educational purposes.
Gold open access involves the publication of the article in an open access journal, upon which it becomes immediately accessible. In addition, there are also hybrid
journals that are subscription-based with a
paid open access option. In this case, your
institution will have to pay the subscription,
while the EC, your institution or you have to
take care of the fees for open access.
Nevertheless, in all three scenarios the
article has to be archived in a repository to
ensure long-term preservation. The costs of
publishing in open access journals, referred
to as article processing charges (APC) or a
publishing fee, are eligible for reimbursement during the duration of a Horizon 2020
project, and should be estimated and requested in your funding application as part
of the dissemination budget. A price cap
on fees for publication costs is currently not imposed by the EC. Björk and Solomon published a study last year on APC and
found that the average costs of publishing
are about €1,020 for established open access journals and €1,980 for hybrid journals. However, the actual costs for a given
journal may be much higher. Since many
publications appear after the funding period of a project, a mechanism for dealing
with golden access publication charges after grant expiration will be sought in the
frame of a pilot project as part of the European Research Infrastructures Work Programme, under the topic e-Infrastructure
for open access.
Data are next: open access pilot
data repository of their choice and take
measures that will allow the data to be accessed, exploited, mined, reproduced and
disseminated free of charge. Moreover, details on instruments and tools, which are
necessary for validating the results presented in publications and, where possible, the
tools themselves, have to be placed at the
disposal of the beneficiary. Seven areas,
accounting for about a fifth of the whole
budget for Horizon 2020 in this period, are
participating in the pilot and include projects in the Industrial Leadership (ICT only)
programme and Future and Emerging Technologies, three subprogrammes of the society challenges funding pillar and SWAFS actions. Additional areas are able to take part
on a voluntary basis.
Opting in – opting out
Projects in the seven areas of the pilot
may opt out in part or full at any stage of
the project. The justification for opting out
has to be included in the original or updated DMP. An initial indication of whether a
project plans to opt out or not has to be given in the proposal at the submission stage,
but has no impact on the evaluation of the
project. A project may opt out, for example, if there are conflicts with obligations
regarding commercial exploitation or personal data protection, as well as if confidentiality or security issues exist. Moreover, a
project may opt out if it does not collect or
generate any data or if its main aim is compromised by making specific data publicly available.
The DMP of a project is not part of the
funding proposal but has to be developed
during the first six months of a project and
updated if necessary. However, all project
Making research data available and
ready for re-use is currently being tested
and implemented by
a limited two-year
Krishnaraj Rajalingam, Heisenberg Professor, Molecular
Open Research Data
Signalling Unit, Research Center for Immunotherapy, UniverPilot in Horizon 2020.
sity of Mainz, Germany: “Science has to be open and transThe pilot focusses on
parent. For scientists in my field the main obstacle for not
the “underlying data”
publishing their best work in an open access journal is our
needed to validate
current evaluation system, which unfortunately still heavily
the results of publicarelies on numerical indexes like the journal impact factor.
tions and their associWithout any changes, scientists will be hesitant to publish
ated metadata as well
their scholarship in open access journals. Further, young inas additional data and
vestigators need additional support from the granting agentheir associated metacies to cover the costs incurred for open access publishing.”
data, which are specified by the scientist in
the data management plan (DMP) of the
proposals, both research and innovation acEU-funded project. A template for the DMP
tion and innovation action, have a section
is provided, for example, in Annex 1 of the
on data management, which is subjected
Guidelines on Data Management in Horito evaluation under the impact criterion. It
zon 2020. Beneficiaries have to deposit the
should provide details on the nature, scale
digital data of their project in a research
and origin of data to be collected or gen-
LT_115_56_60.indd 59
erated, on the data standards to be used
and the way metadata are produced, on the
type of data that will be either exploited or
made accessible and how this will be implemented, on how the data are processed and
preserved for long-term usage, storage and
back-up, and how associated costs will be
covered after the expiry of the project. The
exploitation and dissemination of results,
including efforts to ensure open access, will
be monitored once the project is funded by
periodic and final reports. As outlined in
article 43 of the Model Grant Agreement,
failure to comply with Horizon 2020 policies (involving measures for dissemination
and exploitation of results) may result in
the reduction of the grant.
For funded projects taking part in the
pilot, any costs relating to the implementation of the pilot will be reimbursed and additional technical and professional support
services will be provided. One would expect
the majority of projects to opt out but a preliminary analysis of roughly 3,000 project
proposals from Horizon 2020’s first calls revealed that opt-out rates are below 30% in
the seven areas of the pilot with a range for
individual areas from nine to 29%. In other
areas, about 27% of projects opted in on a
voluntary basis with an area-specific range
of nine to 50%.
Any assistance needed?
The scientist dealing with open access
for the first time in the context of EU programmes may get help via a number of different channels. Support is provided either by the European Commission itself, by
FP7- or Horizon 2020-funded projects addressing responsible research and innovation, including open access, or by National
Contact Points, which
have been established
in almost all EU countries and may give advice to do with applications, legal and financial matters and
science-society issues.
Various stakeholder
organisations, such as
UNESCO, the Global
Research Council, the
Research Data Alliance
and the League of European Research Universities (LERU) have
established expert and working groups on
open access topics and published reports
and guidelines, which might provide insights beyond the scope of Horizon 2020.
Finally, many of the major research funding
29/01/2015 10:15
page 60
Lab Times
Careers
1-2015
Careers in academia
and research performing organisations have
established their own open access policies
and may give advice and limited financial
support for their applicants and members.
You can find documents relevant to
open access in the Horizon 2020 Participant
Portal under the heading Reference Documents. To get some background on open
access, which might fuel into your research
proposal, the regulations establishing Horizon 2020 (article 18), the Rules for Participation (article 43), the Specific Programme
(preamble 1.3) and the Work Programme
2014-15 are helpful. For legal and practical aspects consult the Model Grant Agreement (especially article 29.2
and 29.3), the 656-page Annotated Model Grant Agreement
and the two Guidelines on
Open Access to Scientific Publications and Research Data as
well as on Data Management
in Horizon 2020. You may also
contact directly the European
IPR helpdesk, which has also
published a sheet of frequently asked questions on open access or the
European Commission’s Open Access Team
at [email protected]. Members of the European Commission Central
Library have created a portal, which presents, amongst other things, a selection of
links to search tools and repositories as well
as the latest news on open access (www.netvibes.com/open-access).
Even more help for scientists
Researchers participating in Horizon
2020 are free to publish anywhere, as long
as they make sure that the publication or
data are made publicly available. But many
researchers do not know, which open access and copyright options are available for
their favourite journals (see, for example,
the service portal SHERPA/RoMEO at www.
sherpa.ac.uk/romeo), or whether an open
access journal applies a quality control system to guarantee its content (white list Directory of Open Access Journals at www.
doaj.org), or whether it is of questionable
quality (so-called predatory journals, black
list at http://scholarlyoa.com/publishers).
Other questions arising include where
to deposit publications or data, which format should be used for depositing publications, data and associated metadata, or
which licensing model should be applied
for the re-use of data. In addition, there are
databases with links to free tools and online
services that support the researcher, e.g. in
writing a data management plan according
LT_115_56_60.indd 60
to EC regulations or providing letter templates that might be instrumental in dealing with publishers. The EU-funded project
FOSTER (Facilitate Open Science Training
for European Research, www.fosteropenscience.eu) is a two-year project that started
in 2014 and aims to produce a Europe-wide
training programme that will help researchers and others to incorporate open access
approaches into their research work. In addition, the project’s portal has already assembled a huge amount of existing material on open access from various sources that
may be re-used and may help the researcher
to become familiar with open access. Other
find additional repositories via registries,
such as OpenDOAR (www.opendoar.org),
ROAR (http://roar.eprints.org), the REgistry of REsearch Data REpositories (www.re3data.org) or OpenAire.
Outlook
Responsible research and innovation,
open access and science with and for society are topics that are heavily promoted
and strongly supported in the Horizon 2020
Framework Programme. Whereas some issues have been implemented throughout
the whole programme, such as open access
to publications, others are still in their infancy and are being checked out
in pilots, such as the open data
Eduardo Moreno, Institute of Cell Biology,
pilot or in research and dissemiUniversity of Bern, Switzerland: “I am a big
nation projects, aimed at genersupporter of open access journals because
ating and sharing best practice
research that is paid by taxpayers should be
solutions. The scope of the topaccessible to the public that paid for it, not only
ics covered in this article is very
to academics. It will also contribute to increase
broad. Not all aspects could be
the scientific education of Europeans and,
covered sufficiently and only a
therefore maintain the EU as a knowledge hub.” small selection of links to further
information has been included.
EU-projects worth mentioning as a source
Open access issues and the future of
of support and background on open access
scientific publishing have been widely adare OpenAire and OpenAire+, which have
dressed recently in primary scientific joursignificantly contributed to the implemennals. Latest news includes, for example, the
tation of open access in Europe and will be
Bill and Melinda Gates Foundation’s ancontinued by Open AIRE2020 in 2015.
nouncement of the world’s most abrasive
policy on open access, which might prevent
Repositories at your fingertips
researchers funded by the foundation from
There are institutional, disciplinary
publishing in certain top journals. Publishand multidisciplinary repositories for pubers have reacted to the new developments,
lications and/or research data. The EC entoo, and installed new journals or modified
courages the use of discipline-specific rebusiness models. For example, Science Adpositories, which often have the advantage
vances, an online-only open access journal
of being widely accepted and used by the
will join the family of Science publications
scientific community of the depositing sciin 2015 and will charge about €4,650 per
entist and to have more features, visibility
article and a surcharge of €1,270 if articles
and higher user-friendliness in comparison
exceed ten pages. The publisher AAAS has
to smaller institutional repositories. Discibeen criticised by the scientific community
plinary repositories include, for example,
not only for its price tag but also for its li­arXiv, which was launched in 1991 at Corcensing model, one that is not used by some
nell University and just announced that
research funders such as the Wellcome
more than one million articles have been
Trust. The Nature Publishing Group anuploaded by physicists, computer scientists
nounced that starting from October 2014,
and mathematicians as preprint before peer
all papers submitted to Nature Communireview. Another example in the Life Scienccations must be published in open access
es/Biomedicine sector is Europe PubMed
and that during a one-year pilot, subscribCentral, which provides full-text access to
ers and media will get access to read-only
more than 2.6 million articles. In case the
research papers in PDF format, including
scientist does not want to use or is not able
those in Nature and 48 additional journals.
to find a subject-specific repository, multiThese papers cannot be printed but may be
disciplinary repositories, such as the “catchannotated and shared via a link provided.
all” repository Zenodo may be used (www.
Ralf Schreck
zenodo.org). Zenodo is co-funded by the
European Commission and was launched
More information and interviews online
by CERN and OpenAIRE in 2013. You may
at www.labtimes.org.
29/01/2015 10:15
Job Appointments
1-2015
International Max Planck
Research School
Molecular Biomedicine
and
Cells in Motion
Graduate School
Joint PhD program of the University of Münster and the Max Planck Institute for Molecular Biomedicine
16 PhD Fellowships in
Life and Natural Sciences
The International Max Planck Research School – Molecular Biomedicine (IMPRS-MBM) and the Cells in Motion Excellence Cluster
(CiM) offer 16 PhD Fellowships in Life and Natural Sciences. More
PhD positions financed by work contracts may be offered depending
on availability.
CiM and IMPRS-MBM – jointly run by the University of Münster
and the Max Planck Institute for Molecular Biomedicine – offer
integrative approaches to biomedical research with a strong
emphasis on imaging. PhD projects range from the analysis of basic
cellular processes to clinical translation, from the generation of
mathematical models to the development of new imaging-related
techniques and compounds.
Research areas:
Cell and Molecular and Biology • Developmental and Stem
Cell Biology • Vascular Biology • Immunology •
Microbiology • Neurobiology • In vivo Imaging • High
Resolution Optical Imaging • Biophysics • Chemical Biology
• Label Chemistry • Mathematical Modelling • and more
Applications for the 3-year PhD program can be submitted from
10 February – 15 April 2015. Projects start in October 2015. Applications can only be submitted via our online system.
Lab Times
page 61
Hannover Biomedical
Research School (HBRS)
Graduate School of Excellence
PhD
Opportunities
in a First Class
Research
Environment
Hannover Biomedical Research School, as part of Hannover Medical School (MHH),
invites applications for the above PhD studentships, to commence in October
2015. The three-year study programs, taught in English, are aimed at postgraduates in Medicine, Veterinary Medicine as well as those from Life Science
fields. The PhD program “Regenerative Sciences” is also open to students from
the various disciplines of Natural and Materials Sciences. As well as working on a
research project, students also attend seminars, lab and soft-skill courses,
congresses and summer schools. Successful candidates will be awarded a PhD,
alternatively Dr. rer. nat. Scholarships are fully funded by the DFG (Excellence
Initiative), MHH and partner institutes.
We are looking for highly-motivated candidates who have an active interest in
one of the fields associated with one or more of the programs on offer. Excellent
written and spoken English skills are required. With nearly two thirds of our
students coming from outside Germany, international applicants are welcome.
Deadline for completed applications is April 1st, 2015. Online applications are
invited at www.mh-hannover.de/hbrs.html
PhD “Molecular Medicine”: The program aims to form a bridge between Science
and the Clinic, in research as well as in teaching.
PhD “Infection Biology”: Students focus on the main topics in Infection, Immunology, Microbiology, Virology and Cell Biology.
PhD “Regenerative Sciences”: Research and teaching concentrate on basic topics
in regenerative sciences, regeneration of the 4 organ systems covered in the
Cluster of Excellence REBIRTH, additional organ systems, enabling technologies,
regulations and processes involved in translation from bench to bedside, ethics.
For online application and further information go to
www.cim-imprs.de
The program offers excellent scientific and transferable skills training,
a competitive tax-free fellowship and support with administrative
matters, accomodation, visas etc. There are no tuition fees. The program language is English. We invite applications from highly qualified
and motivated students of any nationality from biological sciences,
chemistry, mathematics, computer sciences and physics. We are
looking forward to your application for a PhD fellowship in Münster,
“the world’s most liveable city” (LivCom Award 2004).
Contact: [email protected]
Get your own copy of
Lab Times – it’s free!
Lab Times is free of charge for non-profit institutions all over Europe. The life
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2nd Cologne Summer School in Neural circuit
analysis on the cellular and subcellular level
Understanding nervous system activity in its physiological and pathophysiological conditions is a fundamental goal of the neurosciences.
We examine nervous system function in health and disease across
the molecular, cellular and network level. For eighteen Master’s
students we announce a ten-day summer program with lectures
and hands on experiments in neural circuit analysis.
The summer school will take place
from July 13th - 22nd in the
biological department
and medical faculty
of the University
of Cologne.
Application
deadline:
April 30,
2015
For more detailed information please visit the website:
http://rtg-nca.uni-koeln.de/12642.html
Please submit your application via email to:
Dr. Isabell Witt,
Email: [email protected]
Zülpicher Str. 47a, D-50674 Cologne, Germany
Phone: +49(0)221 470 1683,
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LT_115_61_66.indd 61
29.01.15 13:07
page 62
Lab Times
Conferences
1-2015
Calendar
2015
18/2–20/2 Berlin (DE)
1st International CRC 973
Symposium: Bridging Ecology and
Molecular Biology – Organismic
Responses to Recurring Stress,
Info: www.sfb973.de/Meeting/
Symposium2015
19/2–20/2 Halle/Saale (DE)
5th Conference on Recombinant
Proteins, Info: www.biochemtech.
uni-halle.de/halle_conference
21/2–27/2 Lucca/Barga (IT)
Gordon Research Seminar
and Conference: Quantitative
Genetics & Genomics, Info: www.
grc.org/programs.aspx?id=12072
24/2–25/2 Munich (DE)
Cell Culture World Congress 2015:
Applied Solutions for Biomanufacturing, Info: www.terrapinn.
com/conference/cell-culture
25/2–27/2 Leipzig (DE)
The Human Mutation Rate
Meeting (THMR2015), Info:
www.eva.mpg.de/genetics/
conferences/thmr2015
26/2–28/2 Innsbruck (AT)
EASL (European Association for
the Study of the Liver) Monothematic Conference: Microbiota,
Metabolism and NAFLD (Nonalcoholic Fatty Liver Disease),
Info: www.easl.eu/_events
26/2–28/2 Kiel (DE)
Inflammation at Interfaces: 5th International Annual Cluster Symposium, Info: www.symposium-iai.org
10/3–12/3 Ghent (BE)
Plant Organ Growth Symposium,
Info: www.psb.ugent.be/
plantorgangrowthsymposium
18/3–20/3 Tuebingen (DE)
European Molecular Imaging
Meeting (EMIM 2015), Info:
www.e-smi.eu/index.php?id=1976
27/2 London (UK)
Abcam Conference on
Mitochondria, Energy Metabolism
and Cancer, Info: www.abcam.
com/mitochondriaFEB
10/3–12/3 London (UK)
The 2015 Forensic Forums, Info:
www.regonline.co.uk/forensic15
18/3–20/3 Cambridge (UK)
Wellcome Trust Conference on
Innate Immune Memory,
Info: www.hinxton.wellcome.ac.uk
28/2–6/3 Lucca/Barga (IT)
Gordon Research Conference: Glycobiology – Glycans as Mediators
of Interactions Between Molecules, Cells & Organisms, Info: www.
grc.org/programs.aspx?id=11358
2/3–4/3 Paris (FR)
13th International Congress on
Targeted Anticancer Therapies,
Info: www.tatcongress.org
5/3–8/3 Monaco (MC)
World Cord Blood Congress V
and Innovative Cell Therapies,
Info: www.esh.org/conference/
world-cord-blood-congress
6/3–8/3 Lisbon (PT)
3rd ESCMID Conference on Vaccines – for Mutual Protection, Info:
www.escmid.org/research_projects
7/3–13/3 Lucca/Barga (IT)
Gordon Research Conference: RNA
Editing – Diversifying the Transcriptome: Consequences for
Development & Disease, Info: www.
grc.org/programs.aspx?id=12665
8th International Meeting
Stem Cell Network NRW
April 21–22, 2015, Plenary Chamber WCC, Bonn, Germany
• listen to experts like Fred Gage, Juergen Knoblich and
Shoukhrat Mitalipov
• show your work in the poster sessions
• exchange your thoughts with biotech companies
• register for free
www.congress.stemcells.nrw . de
LT_115_61_66.indd 62
10/3–13/3 Bremerhaven (DE)
9th Central European Diatom Meeting, Info: www.awi.de/cediatom9
11/3–13/3 Cambridge (UK)
Wellcome Trust Conference:
The Challenge of Chronic Pain,
Info: www.hinxton.wellcome.ac.uk
12/3 Bristol (UK)
Immunotherapy 2015 – Understanding and Applying Immunotherapy in Allergy, Autoimmunity,
Cancer and Transplant Tolerance,
Info: https://bsi.immunology.org/
page.aspx?pid=1503
12/3–14/3 Sorrento (IT)
3rd International Congress on
Controversies in Rheumatology
and Autoimmunity (CORA 201),
Info: http://cora.kenes.com
15/3–18/3 Vimeiro (PT)
EFB Meeting on Bacterial
Electron Transfer Processes and
Their Regulation,
Info: www.efb-central.org/index.
php/bacterial_electron_transfer
15/3–20/3 Lucca/Barga (IT)
Gordon Research Conference:
Polar Marine Science – Polar
Shelves and Shelf Break
Exchange in Times of Rapid
Climate Warming, Info: www.
grc.org/programs.aspx?id=12641
16/3–18/3 The Hague (NL)
4th Beneficial Microbes
Conference, Info: www.bastiaansecommunication.com/bm2015
17/3–18/3 Berlin (DE)
Lab-on-a-Chip & Microfluidics,
Biodetection & Biosensors, Pointof-Care Diagnostics and Microarray Technology, Info: https://
selectbiosciences.com/BB2015
18/3–22/3 Naples (IT)
International Conference on
Stress Biology and Crop
Fertility, Info:
http://3rdconference.spot-itn.eu
18/3–22/3 Nice (FR)
12th International Conference
on Alzheimer’s and Parkinson’s
Diseases and Related
Neurological Disorders,
Info: www2.kenes.com/adpd
21/3–25/3 Dubrovnik (HR)
EMBO Conference: Mechanisms
and Regulation of Protein
Translocation, Info: http://events.
embo.org/15-translocase
21/3–27/3 Lucca/Barga (IT)
Gordon-Kenan Research Seminar
and Conference: Cardiac
Arrhythmia Mechanisms – The
Surprising Heart: A HeteroCellular, Multi-Physics, and InterDisciplinary Challenge, Info: www.
grc.org/programs.aspx?id=13281
23/3–24/3 Amsterdam (NL)
The Global Bioequivalence Harmonisation Initiative – International
Conference, Info: www.gbhi.eu
23/3–27/3 Freising (DE)
qPCR & NGS 2015 Event: Advanced Molecular Diagnostics for
Biomarker Discovery: 7th International qPCR Symposium & Exhibition, Info: www.qpcr-ngs-2015.net
24/3–26/3 London (UK)
The 2015 TB Summit, Info:
www.regonline.co.uk/TB2015
25/3 Birmingham (UK)
Metabolic Drivers of Immunity,
Info: www.biochemistry.org/
Conferences
29.01.15 13:07
Conferences
25/3–26/3 London (UK)
Superbugs & Superdrugs –
A Focus on Antibacterials,
Info: www.smi-online.co.uk/
pharmaceuticals/uk/
superbugs-superdrugs
25/3–27/3 Hannover (DE)
Big Data in a Transdisciplinary
Perspective – Herrenhausen
Conference, Info: www.
volkswagenstiftung.de/bigdata
1-2015
8/4–10/4 Graz (AT)
BioNanoMed 2015: Nanotechnology Enables Personalized Medicine – 6th International Congress,
Info: www.bionanomed.at
26/3–28/3 Mosbach (DE)
66th Mosbach Kolloquium: Metals
in Biology – Cellular Functions and
Diseases, Info: www.gbm-online.
de/gbm-tagungen.html
29/3–31/3 Heidelberg (DE)
EMBO-EMBL Symposium: Frontiers
in Stem Cells and Cancer, Info:
www.embo-embl-symposia.org/
symposia/2015/EES15-01
12/4–15/4 Warsaw (PL)
19th Annual International Conference on Research in Computational Molecular Biology (RECOMB
2015), Info: www.recomb2015.pl
30/3–31/3 Oxford (UK)
Location, Location, Location: The
Matrix and the Microenvironment,
Info: www.bsmb.ac.uk/location
12/4–17/4 Lucca/Barga (IT)
Gordon Research Conference:
Cancer Genetics & Epigenetics –
Deciphering the Cancer Genome
and Epigenome to Develop Novel
Therapies, Info: www.grc.org/
programs.aspx?id=12552
30/3–31/3 Toulouse (FR)
1st International Consensus Conference of the European EUCelLEX
Project (Cell-based Regenerative
Medicine: New Challenges for
EU Legislation and Governance,
Info: www.eucellex.eu
30/3–1/4 York (UK)
Repetitive, Non-Globular Proteins:
Nature to Nanotechnology, Info:
www.biochemistry.org/Conferences
31/3–2/4 Luxembourg (LU)
5th International Human
Microbiome Congress,
Info: www.ihmc2015.org
31/3–2/4 Paris (FR)
Forum Labo and Biotech 2015,
Info: www.forumlabo.com
6/4–10/4 Leipzig (DE)
10th International Congress on
Autoimmunity, Info:
http://autoimmunity.kenes.com
7/4–11/4 Soelden (AT)
17th International Neuroscience
Winter Conference, Info:
www.winterneuroscience.org/2015
LT_115_61_66.indd 63
13/4–16/4 Jena (DE)
MiCom 2015 – 5th International
Student Conference on Microbial
Communication,
Info: www.micom.uni-jena.de
13/4–16/4 Lisbon (PT)
3rd International Molecular Diagnostics Europe: Prenatal Molecular Diagnostics, Cancer Sequencing, Advanced Diagnostics for
Infectious Disease & Circulating
Cell-Free Nucleic Acids,
Info: www.moleculardxeurope.com
15/4–18/4 Chester (UK)
ATP Binding Cassette
Transporters from Mechanism to
Organism, Info:
www.biochemistry.org/Conferences
15/4–18/4 Heidelberg (DE)
EMBO-EMBL Symposium:
Cellular Heterogeneity – Role
of Variability and Noise in
Biological Decision-Making, Info:
www.embo-embl-symposia.org/
symposia/2015/EES15-02
page 63
“The right patient
for the right therapy.”
9/4–11/4 Hamburg (DE)
1st CSSB International Symposium
on Systems in Infection Biology –
From Molecules to Organisms,
Info: www.cssb-symposium2015.de
12/4–15/4 Edinburgh (UK)
Festival of Neuroscience
2015 (British Neuroscience
Association), Info:
www.physoc.org/bna2015festival-of-neuroscience
Lab Times
CANCER IMMUNOTHERAPY
13th CIMT
Personalized Immunotherapy
Tumor Vaccination
New Targets & New Leads
ANNUAL
MEETING
Tumor Biology & Interaction
with the Immune System
MAY 11-13, 2015
Immunomonitoring
RHEINGOLDHALLE CONGRESS CENTER
Cellular Therapy
MAINZ, GERMANY
Improving Immunity
meeting.cimt.eu
Abstract Submission Deadline: February 27, 2015
17/4 London (UK)
The Tumour Microenvironment
– Fundamental Biology and
Translational Research, Info:
http://cpd.rvc.ac.uk/courses/
the-tumour-microenvironment
18/4–24/4 Lucca/Barga (IT)
Gordon Research Conference:
Cell Biology of Megakaryocytes
& Platelets – Bridging the Divide
Between Megakaryocytes and
Platelets, Info: www.grc.org/
programs.aspx?id=13253
20/4–21/4 Edinburgh (UK)
Exploiting the New Pharmacology
and Application to Drug
Discovery,
Info: www.bps.ac.uk/meetings/
NewPharmaDrugDiscovery
20/4–21/4 London (UK)
Oxford Global Conferences: 8th
Annual Proteins and Antibodies
Congress, 2nd Annual Peptides
Congress & 3rd Annual Biosimilars
and Biobetters Congress,
Info: www.proteins-congress.com
21/4–24/4 Vienna (AT)
18th Annual Meeting of the European Biosafety Association/EBSA:
Orchestrating a (Bio)Safe World,
Info: www.ebsaweb.eu/ebsa_18
21/4–22/4 Bonn (DE)
8th International Meeting of the
Stem Cell Network North Rhine
Westphalia, Info: www.congress.
stemcells.nrw.de/en.html
22/4 Marburg (DE)
SYNMIKRO Symposium 2015:
Microbial Biosensors & Regulatory
Circuits, Info: www.synmikro.com
22/4–24/4 Budapest (HU)
Tribbles Pseudokinases on the
Crossroads of Metabolism,
Cancer, Immunity and
Development, Info: www.
biochemistry.org/Conferences
22/4–24/4 Cambridge (UK)
Wellcome Trust Conference on
the Biology of Regenerative
Medicines, Info:
www.hinxton.wellcome.ac.uk
22/4–24/4 Mallorca (ES)
8th Conference on Recombinant
Protein Production (RPP8),
Info: www.efb-central.org/
index.php/RPP8
22/4–26/4 Vienna (AT)
International Liver Congress 2015:
50th Meeting of the European
Association for the Study of the
Liver, Info: https://ilc-congress.eu
29.01.15 13:07
page 64
Lab Times
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Conferences
1-2015
23/4–26/4 Strbske Pleso (SK)
Hot Topics in Microbiology –
International Conference for
Young Scientists,
Info: http://htmicro.sk
25/4–1/5 Lucca/Barga (IT)
Gordon-Kenan Research
Conference: Multi-Drug Efflux
Systems – A Paradigm Shift from
Fundamental Mechanisms to
Practical Applications, Info: www.
grc.org/programs.aspx?id=13928
27/4–30/4 Leiden (NL)
13th International Symposium
on Mutation in the Genome:
Detection, Genome Sequencing
& Interpretation, Info: http://
wired.ivvy.com/event/MD2015
29/4–1/5 Cambridge (UK)
Wellcome Trust Conference on
Genomics of Rare Diseases:
Beyond the Exome, Info:
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2/5–8/5 Lucca/Barga (IT)
Gordon Research Seminar and
Conference: Antimicrobial
Peptides – Basic and Translational Aspects, Info: www.grc.org/
programs.aspx?id=12633
5/5–8/5 Berlin (DE)
European Pharma Summit: 9th
Drug Design & Medicinal Chemistry / 2nd Bioanalytical Sensors /
2nd Tissue Models & Phenotypic
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Protein Kinases in Drug Discovery
Conference / 2nd GPCR Targeted
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6/5–8/5 Cambridge (UK)
Wellcome Trust Conference
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6/5–10/5 Heidelberg (DE)
EMBO Conference: Chromatin and
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training/events/2015/CHR15-01
12/5–14/5 London (UK)
The 2015 Controlling Cancer
Summit, Info: www.
regonline.co.uk/cancer2015
7/5–8/5 London (UK)
2nd Microbiome Forum: Europe –
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Microbiota Research, Probiotics,
Health and Disease, Info: www.globalengage.co.uk/microbiota.html
13–17/5 Jaroszowice/Krakow (PL)
5th Conference on Biomolecules
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7/5–9/5 Bucharest (RO)
European Biotechnology
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International Conference on the
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International Meeting on
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Abcam Conference on Adult Neurogenesis: Evolution, Regulation and
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18/5–20/5 Cambridge (UK)
Wellcome Trust Conference on
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Conferences
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programs.aspx?id=13318
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30/5–3/6 Hamburg (DE)
35th Blankenese Conference:
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Gordon Research Conference:
CAG Triplet Repeat Disorders,
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aspx?id=12982
1-2015
4/6–7/6 Mainz (DE)
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1st European Chemokine and
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9/6–11/6 London (UK)
Stem Cells: From Basic Research
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Biophysics in Drug Discovery
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Gordon Research and Conference:
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2015
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Lab Times
THE 2015
IMB CONFERENCE
DNA Repair &
Genome Stability in a
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MAINZ, GERMANY | 4 – 7 JUNE 2015
KEYNOTE SPEAKERS: Susan
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Titia Sixma – Netherlands Cancer Institute, NL
SPEAKERS:
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Leiden University
Medical Center, NL
Dana Branzei
FIRC Institute of
Molecular Oncology, IT
Fabrizio d’Adda
di Fagagna
The FIRC Institute of
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Nico Dantuma
Jessica Downs
Karl-Peter Hopfner
Brendan D. Price
Steve Jackson
Björn Schumacher
Brandeis University,
USA
Joe Jiricny
Evi Soutoglou
Ian D. Hickson
Niels Mailand
University of Sussex, UK Ludwig-MaximiliansUniversity, DE
Daniel Durocher
Lunenfeld-Tanenbaum
Research Institute, CA
James E. Haber
University of
Copenhagen, DK
Karolinska Institutet, SE
Cambridge University,
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University of Zurich, CH
University of
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IMB Mainz, DE
IMB Mainz, DE
University of Cologne,
DE
Institute of Genetics
and Molecular and
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Memorial Sloan
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Yossi Shiloh
Helle Ulrich
University of
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Petra Beli
Dana-Farber Cancer
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Tel Aviv University, IL
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15/6–16/6 London (UK)
3rd Annual Next Generation
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Plant Wax 2015: From
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20/6–26/6 Lucca/Barga (IT)
Gordon Research Conference:
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20/6–23/6 Berlin (DE)
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page 66
Lab Times
Conferences
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Enabling Technologies for
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24/6–25/6 Vienna (AT)
Biopharmaceutical Raw Materials
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24/6–27/6 Stockholm (SE)
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Gordon Research Conference:
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Intestinal Microbiota in Chronic
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Congress of Translational
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22/6–26/6 Potsdam (DE)
Unravelling Glycan Complexity
– 4th Beilstein GlycoBioinformatics Symposium,
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symposien/glyco-bioinformatics
23/6–25/6 Budapest (HU)
International Scientific Conference on Probiotics and Prebiotics,
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LT_115_IC_IC.indd 2
29.01.15 12:45
1/2015
SECTION II: ANTIBODY APPLICATIONS
CHAPTER 12: IMMUNOHISTOCHEMISTRY (IHC)
IHC Paraffin Protocol (using SignalStain® Boost Detection Reagent)
10. Wash sections three times with wash buffer for 5 min each.
*IMPORTANT: Please refer to the Applications section on the front page of product datasheet or product webpage to determine
whether a product is validated and approved for use on paraffin-embedded (IHC-P) tissue sections. Please see product datasheet
or product webpage for appropriate antibody dilution and unmasking solution.
11. Add 1 drop (30 µl) SignalStain® DAB Chromogen Concentrate to 1 ml SignalStain® DAB Diluent and mix well before use.
12. Apply 100–400 µl SignalStain® DAB to each section and monitor closely. 1–10 min generally provides an acceptable
staining intensity.
13. Immerse slides in dH2O.
A. Solutions and Reagents
14. If desired, counterstain sections with hematoxylin per manufacturer’s instructions.
NOTE: Prepare solutions with reverse osmosis deionized or equivalent grade water (dH2O).
15. Wash sections in dH2O two times for 5 min each.
1. Xylene
16. Dehydrate sections:
a. Incubate sections in 95% ethanol two times for 10 sec each.
2. Ethanol, anhydrous denatured, histological grade (100% and 95%)
3. Deionized water (dH2O)
b. Repeat in 100% ethanol, incubating sections two times for 10 sec each.
b. TBST/5% normal goat serum: To 5 ml 1X TBST, add 250 µl Normal Goat Serum (#5425).
c. PBST/5% normal goat serum: To 5 ml 1X PBST, add 250 µl Normal Goat Serum (#5425).
1X Phosphate Buffered Saline (PBS): To prepare 1 L 1X PBS: add 50 ml 20X PBS (#9808) to 950 ml dH2O, mix.
1X PBS/0.1% Tween® 20 (PBST): To prepare 1 L 1X PBST: add 1 ml Tween® 20 to 1 L 1X PBS and mix.
7. Antigen Unmasking Options:*
a. Citrate: 10 mM Sodium Citrate Buffer: To prepare 1 L, add 2.94 g sodium citrate trisodium salt dihydrate
(C6H5Na3O7•2H2O) to 1 L dH2O. Adjust pH to 6.0.
b. EDTA: 1 mM EDTA: To prepare 1 L add 0.372 g EDTA (C10H14N2O8Na2•2H2O) to 1 L dH2O. Adjust pH to 8.0.
c. TE: 10 mM Tris/1 mM EDTA, pH 9.0: To prepare 1 L, add 1.21 g Tris base (C4H11NO3) and 0.372 g EDTA
(C10H14N2O8Na2•2H2O) to 950 ml dH2O. Adjust pH to 9.0, then adjust final volume to 1 L with dH2O.
c. Repeat in xylene, incubating sections two times for 10 sec each.
17. Mount sections with coverslips.
For optimal results, always use the recommended primary
antibody diluent, as indicated on the product datasheet.
SignalStain® Antibody Diluent
#8112: IHC analysis of paraffinembedded human breast carcinoma
(top) and HCC827 xenograft (bottom)
using Phospho-Akt (Ser473) (D9E)
XP® Rabbit mAb #4060 or PhosphoEGF Receptor (Tyr1173) (53A5) Rabbit
mAb #4407 after dilution in either
#8112 (left) or TBST/5% NGS (right).
SignalStain® #8112
TBST-5% NGS
#4060
4. Hematoxylin (optional)
5. Wash Buffer: 1X Tris Buffered Saline with Tween® 20 (TBST): To prepare 1 L 1X TBST: add 100 ml 10X TBST (#9997) to
900 ml dH2O, mix.
6. Antibody Diluent Options:*
a. SignalStain® Antibody Diluent: (#8112)
A superior signal is achieved
when #4060 is diluted in #8112 as
compared with TBST/5% NGS.
d. Pepsin: 1 mg/ml in Tris-HCl, pH 2.0.
8. 3% Hydrogen Peroxide: To prepare 100 ml, add 10 ml 30% H2O2 to 90 ml dH2O.
No one diluent enables the optimal
performance of all antibodies.
9. Blocking Solution: TBST/5% Normal Goat Serum: to 5 ml 1X TBST, add 250 µl Normal Goat Serum (#5425).
10. Detection System: SignalStain® Boost IHC Detection Reagents (HRP, Mouse #8125; HRP, Rabbit #8114 )
#4407
11. Substrate: SignalStain® DAB Substrate Kit (#8059).
B. Deparaffinization/Rehydration
NOTE: Do not allow slides to dry at any time during this procedure.
1. Deparaffinize/hydrate sections:
a. Incubate sections in 3 washes of xylene for 5 min each.
b. Incubate sections in 2 washes of 100% ethanol for 10 min each.
c. Incubate sections in 2 washes of 95% ethanol for 10 min each.
2. Wash sections 2 times in dH2O for 5 min each.
IHC Frozen Protocol (using SignalStain® Boost Detection Reagent)
C. Antigen Unmasking*
NOTE: Consult product datasheet for specific recommendation for the unmasking solution/protocol.
1. For Citrate: Bring slides to a boil in 10 mM sodium citrate buffer, pH 6.0; maintain at a sub-boiling temperature for 10 min.
Cool slides on bench top for 30 min.
IMPORTANT: Please refer to the Applications section on the front page of product datasheet or product webpage to determine
whether a product is validated and approved for use on frozen (IHC-F) tissue sections. Please see product datasheet or product
webpage for appropriate antibody dilution.
2. For EDTA: Bring slides to a boil in 1 mM EDTA, pH 8.0: follow with 15 min at a sub-boiling temperature. No cooling
is necessary.
NOTE: Please see product datasheet and website for product-specific protocol recommendations.
3. For TE: Bring slides to a boil in 10 mM Tris/1 mM EDTA, pH 9.0: then maintain at a sub-boiling temperature for 18 min.
Cool at room temperature for 30 min.
A. Solutions and Reagents
4. For Pepsin: Digest for 10 min at 37°C.
2. Ethanol (anhydrous denatured, histological grade 100% and 95%)
3. Hematoxylin (optional)
NOTE: Consult product datasheet for recommended antibody diluent.
4. 1X Phosphate Buffered Saline (PBS): To prepare 1 L 1X PBS: add 50 ml 20X PBS (#9808) to 950 ml dH2O, mix.
1. Wash sections in dH2O 3 times for 5 min each.
5. Fixative Options: For optimal fixative, please refer to the product datasheet.
a. 10% neutral buffered formalin
2. Incubate sections in 3% hydrogen peroxide for 10 min.
3. Wash sections in dH2O 2 times for 5 min each.
b. Acetone
4. Wash sections in wash buffer for 5 min.
6. Remove blocking solution and add 100–400 µl primary antibody diluted in recommended antibody diluent to each section*.
Incubate overnight at 4°C.
7. Equilibrate SignalStain® Boost Detection Reagent to room temperature.
For more in-depth help with IHC,
please see our IHC Protocols and
Troubleshooting videos at
www.cellsignal.com/ihcvideos
212
c. Methanol
5. Block each section with 100–400 µl blocking solution for 1 hr at room temperature.
IHC Tips &
Techniques
T
V
Videos
8. Remove antibody solution and wash sections with wash buffer three times for 5 min each.
9. Cover section with 1–3 drops SignalStain® Boost Detection Reagent as needed. Incubate in a humidified chamber for
30 min at room temperature.
For Research Use Only. Not For Use in Diagnostic Procedures.
19
NOTE: Prepare solutions with reverse osmosis deionized or equivalent grade water (dH2O).
1. Xylene
D. Staining
d. 3% Formaldehyde: To prepare 100 ml, add 18.75 ml 16% formaldehyde to 81.25 ml 1X PBS.
6. Wash Buffer: 1X Tris Buffered Saline with Tween® 20 (TBS): To prepare 1 L 1X TBS: add 100 ml 10X TBS (#12498) to 900
ml dH2O, mix.
7. Methanol/Peroxidase: To prepare, add 10 ml 30% H2O2 to 90 ml methanol. Store at -20°C.
8. Blocking Solution: 1X TBS/0.3% Triton™ X-100/5% Normal Goat Serum (#5425). To prepare, add 500 µl goat serum and
30 µl Triton™ X-100 to 9.5 ml 1X TBS.
9. Detection System: SignalStain® Boost IHC Detection Reagents (HRP, Mouse #8125; HRP, Rabbit #8114 )
www.cellsignal.com/cstprotocols
/cstprotocols 213
See pg XXX for Application, Reactivity and Pathway Diagram keys.
SECTION III: WORKFLOW TOOLS
CHAPTER 19: DISCOVERY
Discovery
Complementary methods: immunoaffinity
immunoaffinity
and IMAC enrichment for phospho-peptides.
USING PEPTIDE IMMUNOAFFINITY ENRICHMENT AND LC-MS/MS
TO STUDY POST-TRANSLATIONAL
TRANSLATIONAL
TRANSLA
TIONAL MODIFICATIONS
MODIFICATIONS (PTMs)
How can I use PTM-specific
PTM-specific proteomics to enable discovery
of novel disease drivers and identification
cation of biomarkers?
A total of 27,372 unique phosphopeptides were isolated from MKN-45
cells using both IMAC and motif
antibody enrichment strategies. In
modified
this study, distinct sets of modified
ed by the two
peptides were identifi
identified
nity enrichment methods, with
affinity
affi
only 5.6% overlap between the MS/
identified peptides.
MS identified
Post-translational modifications
modifications such as phosphorylation, acetylation, methylation, ubiquitination, and
others are critical regulators of protein activity and function. Understanding the role of PTMs in disease
states and developing novel biomarkers and therapeutics are areas of intense research. However,
researchers who study PTMs are challenged by their inherent
ent low levels, which make them difficult
difficult to
identify and quantify from whole cell or native samples.
This challenge can be overcome
specific peptides
come by using immunoaffinity
immunoaffinity enrichment to isolate specific
containing PTMs of interest from a protease-digested cell or tissue extract. LC-MS/MS analysis is
proprietary to
then employed to identify and quantify the isolated peptides. PTMScan® TTechnology, proprietary
CST,
specificity of PTM-specifi
TT, utilizes
utilizes the specificity
PTM-specificc and motif antibodies to enrich target peptides from the
background of non-modified endogenous peptides, enabling the identifi
cation of modified
modified proteins that
identification
otherwise may not be detected. Hundreds to thousands of post-translationally modified peptides can
be identifi
ed and quantifi
ed in a single experiment. This approach can be used to study modifications
modifications
identified
quantified
such as phosphorylation, acetylation, methylation, ubiquitination, succinylation, or cleaved caspase.
The highly conserved nature of PTMs and substrate motifs across
oss many different
erent species also makes
this approach applicable to many different model systems.
PTM Site Discovery and Profiling
Profiling
• Discover candidate biomarkers linked to activation or repression of a specific class of PTMs.
• Perform a comprehensive proteomic survey of thousands of PTM sites associated with a wide
variety of organisms or a disease model system, integrating the results into known signaling
pathways or helping to defi
ne novel signaling networks.
define
• Detect substrates of novel signaling proteins (kinases, phosphatases, ubiquitin ligases,
deubiquitinases, acetyl transferases, methyl transferases, or succinyl transferases).
IMAC
(13,892)
All Antibody
(13,480)
How can I profi
le changes in specific
specific PTM sites on key target
profile
proteins to explore changes in critical signaling events?
Discovery workflow
workflow
for phospho-tyrosine
modificcations
ations
altered in NSCLC
5.6%
Cell or Tissue Samples
Identificcation
ation of Biomarkers
PTMScan TTechnology
echnology has been used to identify novel biomarkers in a number of different
erent model systems (2–6). One example
xample of the application of PTMScan TTechnology was conducted in a large-scale
large-scale
survey of tyrosine kinase activity in lung cancer, performed at CST.
ST. For
ST
For this study, we used a phosphotyrosine motif antibody to analyze changes in phosphorylation across the proteome in non-small cell
lung carcinoma (NSCLC) cell lines and tissues.
We surveyed the phospho-tyrosine status of receptor tyrosine
non-receptor
osine kinases (R
(RTK) and non-r
eceptor tyrosine
kinases in 41 NSCLC cell lines and over 150 NSCLC tumors. Over 50 tyrosine kinases and more than
ed. Two
2,500 downstream substrates that play roles in NSCLC growth and progression were identifi
identified.
T
findings from this study were the identification
identification of novel ALK and ROS1 C-terminal fusion
very exciting findings
proteins (EML4-ALK, CD74-ROS, SLC34A2-ROS) in some NSCLC cell lines and tumors (7). Further
investigation of ALK and ROS1 in other cancers led to the identifi
cation of a novel FN1-ALK fusion
identification
protein in ovarian cancer and a FIG-ROS1 fusion in cholangiocarcinoma (8,9).
Kinase Family Targeting
T
As one consequence of this study, a companion diagnostic immunohistochemistry (IHC) assay for
NSCLC
NSCL was developed. In 2011, the diagnostic IHC assay was approved
approved in the U.S. for patients with tumor samples that stain positive for ALK fusion protein expression for crizotinib treatment
eatment of NSCLC
NSCL (10).
Carcinoma-associated fusion proteins
discovered using PTMScan Technology
Immunoprecipitation
Using Motif Antibody
• Profile
Profile and quantify global effects of a candidate therapeutic
therapeutic on a specifi
specificc type of PTM,
identifying nodes of interest for further study.
• Understand how cross-talk among various PTMs (phosphorylation, ubiquitination, acetylation,
methylation) is related to a particular biological response or involved in cell development or
differentiation.
• Analyze downstream
eam effects of tar
targeted
geted gene silencing on signaling and potential activation
of alternative pathways.
• Identify protein-protein interaction binding partners along with their corresponding PTMs.
Discover Low Abundance PTM Sites
Immunoaffinity
Immunoaffi
nity enrichment allows you to identify low abundance modifi
modifications
cations by selectively capturing
the PTM in the context of the motif of interest from a population of endogenous peptides. For example,
the specificity of immunoaffinity
immunoaffinity enrichment complements that of IMAC, a charge-based
ge-based metal affinity
affinity
method commonly used for phospho-peptides. IMAC is driven by general coordination chemistry dictated
by the immobilized metal ion (1). IMAC can therefore lead to enrichment of peptides from more abundant
proteins for subsequent LC-MS/MS analysis, but not so readily for less abundant phospho-peptides.
254
ALK fusion protein
detection in human
lung carcinoma
ALK (D5F3) XP® Rabbit mAb #3633:
n-embedded
IHC analysis of paraffi
affin-embedded
affi
human lung carcinoma with high (left)
and low levels (right) of ALK fusion
protein expression using #3633.
LC-MS/MS and
Bioinformatic Analysis
www.cellsignal.com/discovery 255
See pg XXX for Application, Reactivity and Pathway Diagram keys.
For Research Use Only. Not For Use in Diagnostic Procedures.
SECTION I: RESEARCH AREAS
CHAPTER 03: CELL GROWTH AND DEATH
Death Receptor Signaling
Mitochondrial Control of Apoptosis
TNF-
TNF-
APO-3L/
TWEAK
FasL
TNF-R1
TNF-R2
FADD
Daxx
ASK1
Casp-8, -10
RIP
BID
IKK / /
TRAF2 TRAF1
cIAP1/2
ub
FLIP
I B
tBID
MKK1
JNR
IIb
Bcl-2
FADD
Microtubules
Casp-8,-10
Erk1/2
NF- B
p100
RelB
Akt
Bim
JNK
14-3-3
ROCK1
DFF45
Acinus
Cell Shrinkage
Membrane Blebbing
DNA
Chromatin
Fragmentation Condensation
Apoptosis
Arts
Casp-3
Transcription
Survival
Pro-Survival
ub
Apoptosis
PIDD
SirT2
Endo G
AIF
[NAD]
Bcl-2
HECTH9
Smac/
Diablo
Bcl-2 Family
Pro-Apoptotic
Puma
HtrA2
XIAP
RAIDD
Noxa
Cyto c
Casp-9
HSP60
CaMKII
Casp-2
Bcl-2
Bcl-xL
Apaf-1
p52 RelB
PARP
DFF40
Pro-Survival
Bad
Acetyl-CoA
Bax
Bak
Bax
Bak
14-3-3
Cytosolic
Sequestration
ARD1
NatA
Bcl-2
Mcl-1
Casp-7
Bax
Hrk
Calcineurin
Bad
JNK
Hrk
Bcl-2
Bmf
p70 S6K
Bad
Processing
Pro-Apoptotic
p53
ATM/
ATR
ING2
DNA Damage
Genotoxic Stress
Apoptosis can be induced through the activation of death receptors including Fas, TNFαR, DR3, DR4, and DR5 by their respective ligands. Death receptor ligands characteristically initiate signaling via receptor oligomerization, which in turn results in the recruitment of specialized adaptor proteins and activation of caspase cascades. Binding of FasL
induces Fas trimerization, which recruits initiator caspase-8 via the adaptor protein FADD. Caspase-8 then oligomerizes and is activated via autocatalysis. Activated caspase-8
stimulates apoptosis via two parallel cascades: it can directly cleave and activate caspase-3, or alternatively, it can cleave Bid, a pro-apoptotic Bcl-2 family protein. Truncated
Bid (tBid) translocates to mitochondria, inducing cytochrome c release, which sequentially activates caspase-9 and -3. TNF-α and DR-3L can deliver pro- or anti-apoptotic
signals. TNFαR and DR3 promote apoptosis via the adaptor proteins TRADD/FADD and the activation of caspase-8. Interaction of TNF-α with TNFαR may activate the NF-κB
pathway via NIK/IKK. The activation of NF-κB induces the expression of pro-survival genes including Bcl-2 and FLIP, the latter can directly inhibit the activation of caspase-8.
FasL and TNF-α may also activate JNK via ASK1/MKK7. Activation of JNK may lead to the inhibition of Bcl-2 by phosphorylation. In the absence of caspase activation, stimulation of death receptors can lead to the activation of an alternative programmed cell death pathway termed necroptosis by forming complex IIb.
The Bcl-2 family of proteins regulate apoptosis by controlling mitochondrial permeability. The anti-apoptotic proteins Bcl-2 and Bcl-xL reside in the outer mitochondrial wall
and inhibit cytochrome c release. The pro-apoptotic Bcl-2 proteins Bad, Bid, Bax, and Bim may reside in the cytosol but translocate to mitochondria following death signaling,
where they promote the release of cytochrome c. Bad translocates to mitochondria and forms a pro-apoptotic complex with Bcl-xL. This translocation is inhibited by survival
factors that induce the phosphorylation of Bad, leading to its cytosolic sequestration. Cytosolic Bid is cleaved by caspase-8 following signaling through Fas; its active fragment
(tBid) translocates to mitochondria. Bax and Bim translocate to mitochondria in response to death stimuli, including survival factor withdrawal. Activated following DNA damage, p53 induces the transcription of Bax, Noxa, and Puma. Upon release from mitochondria, cytochrome c binds to Apaf-1 and forms an activation complex with caspase-9.
Although the mechanism(s) regulating mitochondrial permeability and the release of cytochrome c during apoptosis are not fully understood, Bcl-xL, Bcl-2, and Bax may influence the voltage-dependent anion channel (VDAC), which may play a role in regulating cytochrome c release. Mule/ARF-BP1 is a DNA damage-activated E3 ubiquitin ligase
for p53, and Mcl-1, an anti-apoptotic member of Bcl-2.
Select Reviews:
Declercq, W., Vanden Berghe, T., and Vandenabeele, P. (2009) Cell 138, 229–232. • Fuchs, Y. and Steller H. (2011) Cell 147, 742–758. • Kantari, C. and Walczak, H.
(2011) Biochim. Biophys. Acta. 1813, 558–563. • Kaufmann, T., Strasser, A., and Jost, P.J. (2012) Cell Death Differ. 19, 42–50. • Lavrik, I.N. and Krammer, P.H. (2012)
Cell Death Differ. 19, 36–41. • Van Herreweghe, F., Festjens, N., Declercq, W., and Vandenabeele, P. (2010) Cell. Mol. Life Sci. 67, 1567–1579. • Wajant, H. and Scheurich, P. (2011) FEBS J. 278, 862–876.
Select Reviews:
Brenner, D. and Mak, T.W. (2009) Curr. Opin. Cell Biol. 21, 871–877. • Chalah, A., Khosravi-Far, R. (2008) Adv. Exp. Med. Biol. 615, 25–45. • Lindsay, J., Esposti, M.D.,
and Gilmore, A.P. (2011) Biochim. Biophys. Acta. 1813, 532–539. • Ola, M.S., Nawaz, M., and Ahsan, H. (2011) Mol. Cell. Biochem. 351, 41–58. • Pradelli, L.A., Bénéteau, M., and Ricci, J.E. (2010) Cell. Mol. Life Sci. 67, 1589–1597. • Rong, Y. and Distelhorst, C.W. (2008) Annu. Rev. Physiol. 70, 73–91. • Speidel, D. (2010) Trends
Cell Biol. 20, 14–24. • Suen, D.F., Norris, K.L., and Youle, R.J. (2008) Genes Dev. 22, 1577–1590.
©2002–2014 Cell Signaling Technology, Inc. • We would like to thank Prof. Junying Yuan, Harvard Medical School, Boston, MA, for reviewing this diagram.
©2003–2014 Cell Signaling Technology, Inc. • We would like to thank Prof. Junying Yuan, Harvard Medical School, Boston, MA, for reviewing this diagram.
For Research Use Only. Not For Use in Diagnostic Procedures.
See pg XXX for Application, Reactivity and Pathway Diagram keys.
www.cellsignal.com/customurlgoeshere 89
www.labtimes.org
LT_115_OC_OC.indd 2
DLC2
Bmf
Bcl-xL
p90RSK
Active
Caspase-8
p65/ NF- B
RelA p50
88
Mcl-1
BID
tBID
PKA
I B
XIAP
GAS2
HECTH9
PI3K
PKC
NIK
IKK
Casp-3
Actin
LC8
tBID
Casp-6
Lamin A
Bim
Casp-8,-10
cIAP1/2
RIP1
Smac
XIAP
Fas/
CD95
FADD
RIP
TRADD TRADD
FADD
TRAF3
MLKL
Apaf1
Casp-9
NF- B
IIa
FADD
Death Stimuli:
Survival Factor Withdrawal
FasL
Survival Factors:
Growth Factors, Cytokines, etc.
DR4/5
Casp-8
Casp-8
RIP1
FADD RIP3
Bcl-2
APO-2L/
TRAIL
DR3
APO-3
TRAF1
TRADD
RIP1
TRAF2
CYLD
cIAP1/2
TRAF2
Fas/
CD95
29.01.15 12:59