Amplification Analysis

MP Biomedicals
Environmental Microbiology
One Call
Discover the World of Metagenomics
A Complete Solution From Sample Preparation
to Molecular Analysis
One Source
A World of
Microbiology
Optimize Your Environmental Workflow
Soil
Sediment
Sludge
Compost
Manure
Waste Water
Feces
Sand
Rock
Sample
Preparation
DNA/RNA Extraction
& Purification
Water
Snow
Clay
Airborne dust
Litter
Rhizosphere
Volcanic Rock
Glacier
Permafrost
Waste Oil
Gypsum
2
pages 4-5
FastPrep®
Homogenizers
and adapters
page 6
FastPrep®
Purification Kits
page 5
Lysing Matrix Tubes
page 9
Automated MPure-12TM
Platform
With MP Biomedicals Complete Solution!
• Thorough lysis in seconds of any bacteria present in environmental samples.
• Ready-to-use DNA & RNA for quantitative and qualitative characterization of microbial soil communities.
• Total removal of humic acids and PCR inhibitors for a successful investigation of microbial diversity.
• Excellent reproducibility for an optimum assay-to-assay consistency.
Amplification
Analysis
page 11
page 10
Buffers, Reagents for
Electrophoresis
PCR
page 10
page 11
Labware
RT-PCR
Learn more at
www.mpbio.com/environment
3
Sample Preparation
FastPrep® instruments
Find your optimal solution for grinding any environmental sample.
Ask for a FREE Trial
www.mpbio.com/demo
- Versatile, Fast & Intuitive - The most advanced sample prep system available!
• Powerful: Thorough grinding of up to 48 samples of most difficult environmental
specimens in just a few seconds.
• Intuitive: Interactive user-friendly interface and touchscreen with more than 70
pre-programmed protocols.
• Flexible: Easily interchangeable adapters to process any sample size (2 ml, 4.5 ml,
15 ml or 50 ml tubes) at cryogenic or room temperature.
Cat.No: 116005500
FastPrep-96™ - High Throughput Sample Grinding
• High Throughput: Process up to 192 samples simultaneously in 2 x 96 deep well
plates.
• Exceptional Versatility: Easily interchangeable adapters available for 2 x 96 deep
well plates, 96 x 2 ml tubes, 48 x 4.5ml tubes, 20 x 15 ml tubes, 8 x 50 ml tubes
and 2 x 250 ml bottles.
• True Linear Motion: Eliminates the need to reorient plates mid-cycle.
Cat.No: 116010500
- Portable Field Testing
• Thorough grinding: Omnidirectional motion with a unique crankshaft-slider mechanism.
• Time Saving: Complete sample lysis of most difficult samples in 5 to 15 seconds.
• Portable: Handheld system for lab and field use, with built-in battery power supply.
Cat.No: 116011500
Typical settings for grinding 50 mg of
various environmental samples with
the FastPrep-24TM 5G instrument and
Lysing Matrix E tubes:
4
Sample type
FastPrep® speed (m/s)
FastPrep® Time
Soil/Rock
5.5
2 x 30 sec
Sandy Sample
4.0
4 x 30 sec
30 sec
Litter
5.5
Brunisol Dark Gray Luvisol
5.5
40 sec
Soil from Grassland
5.5
2 x 30 sec
Rhizosphere
6.0
40 sec
Marine Sediment
5.5
2 x 40 sec
Asphalt-permeated Soil
6.0
40 sec
www.mpbio.com/FastPrepFamily
Sample Preparation - Unique Adapters & Lysing Matrix
FastPrep® instrument adapters
Many interchangeable adapters for any sample size and extraction temperature.
Room Temperature Adapters
Metal Adapters
FastPrep-96TM
FastPrep-24TM 5G
Cryogenic Adapters
FastPrep-24TM 5G
FastPrep-24TM 5G
Description
Cat.No
Description
Cat.No
Description
QuickPrep 24 x 2 ml
116002512
HiPrep 48 x 2 ml
116002527
2 x 96 deep well
plates
119696168
All Metal
QuickPrep 24 x 2 ml
116002545
QuickFlex 96 x 2 ml
116010570
TallFlex 48 x 4.5 ml
116010580
All Metal
BigPrep 2 x 50 ml
116002547
TeenFlex 20 x 15 ml
116010560
BigFlex 8 x 50 ml
116010550
LargeFlex 2 x 250 ml
116010590
TallPrep 24 x 4.5 ml
116002540
TeenPrep 12 x 15 ml
116002526
BigPrep 2 x 50 ml
116002525
Cat.No
Description
Cat.No
CoolPrep 24 x 2 ml
116002528
CoolTeenPrep 6 x 15 ml
116002530
CoolBigPrep 2 x 50 ml
116002531
FastPrep® Lysing Matrix
Tailored to environmental samples.
With the use of MP Biomedicals Lysing Matrix E & Y in combination with FastPrep®
Instrument expect the best results for your sample preparation step.
Lysing Matrix E and Y tubes are designed to lyse all microorganisms including difficult
sources such as eubacterial spores and endospores, gram positive bacteria and yeast,
present in environmental samples.
Description
Composition
Lysing Matrix E tubes
1.4 mm ceramic beads, 0.1 mm silica beads and
4 mm glass beads.
Lysing matrix Y 96-Well Plates
Pack Size
Cat.No
50 x 2 ml
116914050
100 x 2 ml
116914100
500 x 2 ml
116914500
25 x 4.5 ml
116974025
25 x 15 ml
116934025
10 x 50 ml
116954010
1 x 96 well plate
116960001
10 x 96 well plate
116960010
0.5 mm Yttria-stabilized Zirconium Oxide Spheres
Barcoded 96 well plates are available on request.
Ask for your FREE Lysing Matrix sample Now!
www.mpbio.com/sample
5
DNA/RNA Extraction
Make your Experiments Easy with FastPrep® Extraction Kits
Ready-to-use protocols for DNA and RNA isolation from any environmental sample!
•
•
•
•
•
Rapid and reproducible sample lysis and purification process.
No cross-contamination with closed lysing matrix tubes.
Increased yields of high-quality DNA and RNA.
Integrity and size of DNA and RNA are retained.
Nucleic acids are ready-to-use in downstream applications.
FastRNATM Pro Soil-Direct Kit
Isolate total RNA from soil that is immediately ready for RT-PCR
•
•
•
•
50 preps - Cat N° 116070050
Up to 500 mg of soil or other environmental sample.
Lysing Matrix E tubes included for thorough sample lysis with a FastPrep instrument.
2 levels of purification to remove efficiently humic acids and other inhibitors.
Cellular RNases are inactivated during homogenization to prevent RNA degradation.
Clean RNA for Uninhibited RT-PCR.
Soil types differ in the type and amount of organic materials, and the largest
and most chemically significant fraction of natural organic matter is the humic
substances.
The amount and type of humic substances in a soil sample are established by
a combination of environmental conditions, vegetation and topography. Humic
substances frequently give soil a yellow/brown color and have been shown to
inhibit Taq polymerase activity at concentration as low as 0.1 mg/ml.
FastRNATM Pro Soil Kits purify RNA in a process that removes humic substances
and other inhibitors, and efficiently inactivates cellular Rnases during homogenization to prevent RNA degradation.
Each kit offers two levels of RNA purification that permit tailoring the protocol to
the soil sample and downstream applications.
FastRNATM Pro Soil-Indirect Kit
Isolate total RNA from soil supernatant that is immediately ready for RT-PCR
•
•
•
•
6
50 preps - Cat N° 116075050
Up to 1 g of soil or other environmental sample.
Initial separation of microorganisms and other biological specimens from soil .
Lysing Matrix E tubes included for thorough sample lysis with a FastPrep® instrument.
Efficient removal of PCR inhibitors and inactivation of cellular RNases during the
homogenization step.
- FastPrep® Kits
FastDNA Spin Kit for Soil
TM
A Gold Standard of Isolation of Pure Genomic DNA
•
•
•
•
BEST
SELLER!
Cited in more than
500 publications
50 preps - Cat N° 116560200
Up to 500 mg soil or other environmental sample.
Lysing Matrix E tubes included for thorough sample lysis with a FastPrep® instrument.
DNA purification by a silica-based spin filter method.
Efficient removal of humic acids and other PCR inhibitors.
FastDNATM 50ml Spin Kit for Soil
A Gold Standard of Isolation of Pure Genomic DNA
10 preps - Cat N° 116560600
• Up to 10 g soil or other environmental sample.
• 50ml garnet Lysing Matrix tubes included for thorough sample lysis with a
FastPrep® instrument.
• DNA purification by a silica-based spin filter method (50 ml Spin filter tubes).
• Efficient removal of humic acids/ polyphenols.
FastDNATM-96 Soil Microbe DNA Kit
Rapid, high throughput isolation of PCR-Ready Genomic DNA
2 x 96 preps - Cat N°119696200
• Up to 130 mg soil or other environmental sample.
• 96 deep-well plates with Lysing Matrix Y for sample lysis with the
FastPrep-96TM instrument.
• Yield is typically 5 µg of total DNA eluted in 50-100 µl of elution solution.
• Eliminates completely polyphenols and humic acids.
FastDNATM Spin Kit for Feces
Efficiently isolate of PCR-ready genomic DNA from human and animal stool samples
50 preps - Cat N° 116570200
• Up to 500 mg of feces.
• Lysing Matrix E tubes included for thorough sample lysis with a FastPrep®
instrument.
• Typically isolates 10 µg- 20 µg of DNA from 500 mg of stool.
• Removes organic contaminates for downstream applications.
FastDNA-96TM Fecal DNA Kit
Efficiently isolate PCR-ready genomic DNA from stool samples in approximately 50mins
2 x 96 preps - Cat N° 119696400
• Up to 80 mg wet or dry stool per well.
• 96 deep-well plates with Lysing Matrix Y for sample lysis with the FastPrep-96TM
instrument.
• Yield is typically 5 µg of total DNA eluted in 50-100 µl of elution solution.
• Purification process that eliminates completely PCR inhibitors.
7
DNA Extraction & Purification From Environmental samples
FastPrep® extraction Kits have been specifically designed for the efficient recovery of inhibitor-free DNA from wide
range of tough-to lyse environmental samples.
DNA Extraction from Andisol, a Volcanic Ash Soil
Takada Y, et al. (2005). Japan Agricultural Research Quartorly. 39 (4): 247-52
Isolation of genomic DNA from 100 mg of Andisol samples using the FastDNA Spin Kit for Soil.
Samples were processed (40 sec at 6 m/s) using a FastPrep-24TM instrument.
Extracted genomic DNA (left) and PCR products (Right) from equivalent amounts of andisol
samples (1-7) were analyzed in agarose/ ethidium bromide gel. M is a DNA size marker.
The combination of the FastPrep® instrument and the FastDNATM SPIN Kit for soil have
demonstrated successful extraction of PCR-suitable DNA from recalcitrant soil samples.
DNA extraction from fecal samples
Harada T, et al. (2012). Journal of Clinical Microbiology. 50 (9): 2964-68.
Parasites DNA extraction from human fecal samples using three commercials DNA extraction Kits:
QIAamp DNA stool minikit (Qiagen); FastDNATM Spin Kit for Soil (MP Biomedicals); UltraClean fecal
DNA kit (MOBIO Laboratories). Superscript letters A to C indicate the DNA extraction efficiency
in each experiment, from high (A) to low (C), as determined using the Turkey-Kramer test with a
significance level (P) of 0.05.
The FastDNATM Spin Kit for Soil showed to be the best DNA extraction method providing the
highest PCR amplification (see Table). The FastPrep® technology gives higher yields and
increases detection limit threshold (CT) of PCR.
More application notes available at
8
www.mpbio.com/FastPrepLibrary
DNA/RNA extraction - Automated MPure-12TM Platform
MPure-12TM
Process up to 12 samples in a true walk away system.
The MPure-12TM allows rapid purification of nucleic acids from a wide variety of environmental samples
(water, soil, air...) using magnetic bead separation technology.
Combined with a uniquely designed magnetic bead processing chamber, the fully integrated and easy-to-use
pre-packaged reagent kits offer superior yields of nucleic acids and high-quality results at an affordable price.
• Fully automated and integrated platform that offers cost
and time savings.
NEW
• Reproducibility, lot-to-lot consistency, scalability,
ease-of-use & convenience.
• Highest quality & yield of DNA & RNA for downstream
applications.
• Flexibility & simplicity: 1-12 samples from a wide range
of bio-specimens processed in a single cycle.
• No cross-contamination of samples thanks to the unique
design of the platform.
• Minimized nucleic acid loss & degradation.
• Increased safety & efficiency through a closed system.
Description
Pack Size
Cat.No
MPure-12TM system
1 unit
117002200
MPure-12TM Bacterial DNA extraction kit
MPure-12TM Viral/Pathogen Nucleic Acids extraction kit B
48 preps
48 preps
117022600
117022130
MPure-12TM Cell & Tissue total RNA extraction kit
48 preps
117022160
‘‘MPurify your Nucleic Acid’’
Request your FREE Demo Now!
www.mpbio.com/mpure12
9
Amplification
PCR
Routine PCR: Taq DNA Polymerase
Description
Pack Size
Cat.No
MP Biomedicals’ highly purified, recombinant, Taq DNA
polymerase is supplied with a 10x Incubation PCR Buffer with
TAQ DNA POL (5U/ul)
250 U
11EPTQA025
MgCl2 at 1, 5 mM as final concentration.
TAQ & GO Ready to use
100
11EPTAG100
Taq & GO and Taq-&LOAD Mastermixes are 5x concentrated,
PCR MIX for 50 µl reactions
reactions
ready-to-use solutions, containing: high quality recombinant
TAQ-& LOAD PCR MasterMIX 100 reactions 11EPTAL100
Taq DNA polymerase, high purity dNTPs, optimized incubation
buffers and MgCl2. Moreover, Taq-&LOAD™ contains a densifying agent and a red purple dye for direct loading amplifications.
High Fidelity: ISIS Polymerase
Isis DNA polymerase is a proofreading Polymerase isolated from Pyrococcus abyssi.
• 40x more accurate than Taq DNA Polymerase
Description
• Reads through difficult secondary structure like GC rich domains
• Amplifies fragments up to 18 kb
ISIS DNA Polymerase
Pack Size
Cat.No
100 U
11EPSIS100
Hot-Start System: SurePRIME Polymerase
• Chemically modified Taq DNA polymerase
• Low background
• Highly specific amplification
Description
Pack Size
Cat.No
SurePRIME DNA Polymerase
250 U
11EPHSP025
RT-PCR
RT-&GO™ Mastermix and Random octamers
Mastermix for first strand cDNA synthesis
Description
Pack Size
Cat.No
RT-&GO Mastermix is a 2.5x concentrated Mastermix for efficient
Random
Octamers
100
µl
11RTOCT100
first strand cDNA synthesis, containing all the components
required for Reverse Transcription: M-MuLV Reverse Transcriptase,
RT-&GO™ Mastermix
100 reactions 11RTRAG100
Reverse Transcription Buffer, RNase inhibitor and dNTPs.
Random octamers may be used as universal primers in first strand cDNA synthesis, cDNA library construction and RT-PCR.
Related Products
10
Description
Pack Size
Cat.No
RNase ERASE (to remove RNase contamination)
250 ml
04821682
DNA ERASE (to remove DNA contamination)
500 ml
04821805
Water, DNA & RNAse Free
500 ml
04821932
dNTPs Set (100 mM each)
4 x 25 µmol
11NTACG100
dNTPs Mix (5 mM each) ready to use solution
5 µmol
11NTPMX050
Analysis
Buffers & Reagents for Electrophoresis
MP Biomedicals offers a large choice of Electrophoresis
buffers. TBE buffer for example is used for the electrophoresis of nucleic acids and gives an excellent resolution
of the DNA bands under low voltage. This buffer filtered
through 0,2 µm PTFE is RNAse, DNAse and Protease free.
Description
Pack Size
Cat.No
Tris Molecular biology grade
1 kg
11TRIS01KG
Tris Ultra pure
5 kg
04819638
EDTA
100 g
0520189280
TBE 10X Buffer
1L
11TBE10X02
Ethidium Bromide (10mg/ml)
10 ml
04802511
Agarose gels
Agarose First has high gel strength even at low concentrations. It is ideal for routine and rapid separation of DNA
and RNA fragments.
Standard Agarose (low EEO) is recommended for sharp resolution of nucleic acid fragments greater than 1000 bp..
Low Melting Point Agarose has finer sieving characteristics than standard agaroses. The low melting temperature
permits nucleic acid recovery without denaturation or damage. The agarose will remain in a liquid state at 37°C
allowing gel manipulations without prior DNA purification such as :
• Enzyme digestion
• DNA labelling
• Random priming
• PCR
• Sequencing
• Ligation
• Nick Translation
Description
Pack Size
Cat.No
Agarose First Low Price
500 g
11AGAF0500
Agarose Standard Low EEO
100 g
11AGAH0100
Agarose Low Melting Point
50 g
11AGAL0050
Why use MP Biomedicals agaroses?
• Highest quality and purity
• Certified molecular biology grade
• High resolution gels
• Absence of inhibitors to restriction enzymes
• Efficient Southern and Northern transfers
Labware
MiniCuve Electrophoresis Unit
• Absolutely leak-proof
• Low buffer volume
• Weighted and stable to avoid spillage
• Several combs sizes available
• Casting gel tray Kits
Description
Pack Size
Cat.No
Mini Cuve 8.10
1 unit
11INSE1100
www.mpbio.com/environment
11
MP Biomedicals,
The leader in the environmental field!
Many prestigious research labs have already put their confidence in MP Biomedicals’ products:
• Eurofins (France)
• INRA (France)
• Danone Eaux France (France)
• Austrian Institute of Technology (Austria)
• VEOLIA Recherche et Innovation (France)
• Julius Kühn Institut (Germany)
• Oxford University (UK)
• Helmholtz Centre for Environmental Research (Germany)
• Cambridge University (UK)
• Environment Agency (UK)
• CNRS Ecolab (France)
One Source for All Your Laboratory Needs
Molecular Biology
Biochemicals
Cell Biology
Adsorbents
Rare & Fine Chemicals
FastPrep® Sample Prep
Immunology
Labware
Culture Growth Media
Apoptosis
Research diets
SafTestTM Food Quality
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