International Genetically Engineered Machine (iGEM) Competition

Purpose
BBSRC Research Experience Placements (REPs) are designed to:
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give promising undergraduates a first-hand opportunity to gain greater experience of research in
the biosciences
raise the profile of research careers amongst undergraduate students
interest students in postgraduate research in strategically important areas for BBSRC
Eligibility
Selected students must be:
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In the middle years of their first degree studies
Registered for a basic science (including mathematics and engineering) or veterinary degree at a
UK university
Expected to obtain a first or upper second class UK honours degree
Preference will be given to students who wish to use the placement to find out more about their suitability
and aptitude for further research, particularly if the project is in an area of science different from their main
subject area.
Duration
Each REP is for up to 10 weeks during the summer vacation 2015.
Support costs
The value of a REP is £2,500 to cover a stipend of £200 per week to the student and a contribution
towards research expenses during the placement.
We have two BBSRC REPs available at the University of Exeter this summer, and you can select from 8
projects (primary supervisors are listed first):
Projects:
1. Spatial and social networks in wild insects
Supervisor: Professor Tom Tregenza (Penryn)
We have been using 140 video cameras to monitor all the crickets in a field in Spain (see
www.wildcrickets.org). Every individual is tagged so that we can record their behaviours and DNA
fingerprinted so that we can identify how many offspring they have in the following generation. The project
would be to investigate the potential for individual crickets to have a particular personality that remains
stable over time, so that for instance, bold individuals are not just bold on one particular occasion but
consistently display that type of behaviour. This is an important issue in biology with implications for
understanding major questions such as how genetic diversity is maintained. Answering this question
would involve analysing a library of video recordings of individual crickets in the field to determine their
response to both artificial stimuli (experimenters frightening them) and to natural sources of danger. It
may also be possible to look for evidence of ageing through changes in movement rates or other
behaviours.
The project would ideally be carried out at the Tremough campus although a very self-motivated student
could do the work in Exeter after visiting Tremough and with regular skype and email contact. I would
anticipate that the work will result in at least one published study which the student would be a co-author
on.
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2. Butterfly genomics
Supervisor: Professor Richard ffrench-Constant (Penryn)
The student will help assemble and annotate a draft genome of the mimetic butterfly called the Diadem.
The Diadem shows sex limited Batesian mimicry whereby females mimic distasteful monarch butterflies.
The student will become familiar with basic web based annotation tools and simple gene searches.
Familiarity with computers would be a plus.
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3. The occurrence of ergothioneine in cyanobacteria
Supervisors: Prof. Nick Smirnoff, Dr. Anja Nenninger and Dr. Hannah Florance.
Ergothioneine is an antioxidant synthesised from histidine by fungi. It is proposed to have beneficial
effects in the human diet but its function is poorly-understood. There is one report of it occurring in
cyanobacteria (and possibly red algae). The aim of this project will be to develop a mass spectrometrybased assay for ergothioneine and then search for it in cyanobacteria. The project is suitable for a
student with an interest in biochemistry who will design the experiments with advice from the supervisors.
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4. Examining the effects of pesticides on bee behaviour using radar tracking
Supervisors: Prof Juliet Osborne and Dr Peter Kennedy (Penryn / Rothamsted)
We would like to offer a student the opportunity of 10 weeks research experience (between 22nd June
and 30th August 2015) working on a field experiment to identify whether sub-lethal doses of neonicotinoid
insecticides alter honeybee and bumblebee flight patterns, which may in turn affect their survival. The
project aligned with a BBSRC funded research grant using a systems approach to understanding the
impacts of insecticides on bees. This is an opportunity to work with unique and world class insect tracking
equipment and an expert team.
These field experiments will take place at Rothamsted Research centre in Hertfordshire: the student must
be prepared to spend 8 out of 10 weeks based at this location. The student will work alongside an
experienced Exeter Research Fellow, Dr Peter Kennedy, and the student will have the opportunity to
contribute to the design and implementation of the experiments. Each person in the radar tracking team
has their own particular role; so the student will be asked to take responsibility for part of the work and
analyse particular sections of the data. The experiments are weather dependent, so the student must be
prepared to work on any day of the week when conditions are favourable, and for long periods. A clean
driving licence would be beneficial. Travel & subsistence will be covered.
The student will gain experience of field experiments, working with bees and beekeeping
methods/manipulations, high-tech insect tracking, fine scale experimentation with pesticides and working
at Rothamsted Research.
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5. From whole algae to crude oil – an interdisciplinary approach to tackle mine waste.
Supervisors: Mark van der Giezen, Steve Aves and Katy Jones (Streatham)
The increasing world population puts demands on the presence of clean water and increases reliance on
Earth's resources. Mining has deleterious environmental consequences and contributes greatly to
destruction of landscapes and water pollution. This is mainly through the generation and uncontrolled
release of acid mine drainage (AMD), a highly polluted water runoff from operating or abandoned mine
sites. It is caused by biological weathering of sulfide minerals exposed during mining operations. AMD is
highly acidic (pH <3.0) and transports heavy metals such as iron and copper and metalloids such as
arsenic from the mine into the wider environment and watercourses. It is a significant environmental
problem often requiring expensive and on-going treatment long after a mine has closed. Up to 1,000 km of
rivers and waterways are thought to be affected by AMD in the UK alone.
Thus far, algae have been trialled to remediate AMD but these systems are not competitive with chemical
treatment (rate-wise) or compost wetlands (cost-wise). Additionally, challenges in algal fuel production
include low growth rates, high costs of drying and lipid extraction.
Our interdisciplinary GW4 project (www.avarice.org.uk) uses thermochemical conversion of whole
microalgae into biocrudes, which can be further upgraded into chemicals and fuels. Oil is formed from the
entire biomass, allowing use of non-lipid producing algae more suited to bioremediation. A secondary
concentrated waste stream containing heavy metals is also produced, suitable for reprocessing and
additional valorisation. The student will be immersed in a highly novel and interdisciplinary project and will
start with an analysis of the microbial community from a local AMD site.
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6. Unique adenosine nucleotides associated with plant disease
Supervisor: Prof. Murray Grant (Streatham)
To date the majority of molecular plant pathology research has focused on genetic approaches to the
detriment of understanding the impact of small molecules. As a result we have few molecular plant
pathologists with analytical skills – both BBSRC skills deficit areas.
We are increasingly interested in the nature and functional role of host-derived small molecules induced
during disease development – therefore gaining insight into how a plant pathogen overcomes plant
defence. Previous research using unbiased high temporal resolution metabolic profiling of Pseudomonas
syringae infected Arabidopsis leaves identified 3-O-β-D-ribofuranosyl adenosine and closely related, but
not necessarily functionally equivalent, derivatives which rapidly and specifically increase in leaves of P.
syringae infected Arabidopsis, tomato and tobacco. 3-O-β-D-ribofuranosyl adenosine is a unique molecule
that is induced incredibly rapidly (~5hpi) and to very high abundance, prior to increase in pathogen growth.
In fact, qualitative comparisons suggest this reaches similar levels to foliar adenosine levels, thus
production of this compound imposes a major metabolic burden on the plant. 3-O-β-D-ribofuranosyl
adenosine could be a metabolic compound used as an energy source for the apoplastically localised
bacteria, a novel inhibitor of enzymatic (ATP related processes) that bacteria use to suppress plant
defences, or even part of a (failed) host defence strategy.
We have synthesized this compound BUT it does not have any affect on the infection phenotype. We
subsequently identified a family of 3-O-β-D-ribofuranosyl adenosine associated compounds, with m/zs of
400, 480, 494, 542 and 574, consistent with singly or doubly phosphorylated, or cyclic phosphate linkage
forming compounds.
We now have methods to identify these compounds and the studentship will involve characterization of
the infection dynamics and structure of these compounds using our mass spectrometer analytical facility
with co-supervision from Hannah Florance.
The project will involve:
Developing new extraction methods that will enable more quantitative recovery of these phosphorylated
forms as our current extraction procedure most likely causes hydrolysis of these residues (2 weeks).
Quantitating the abundance of the compound in wild-type, resistance and susceptible Arabidopsis and
looking for its present in other infected plant tissues, e.g. wheat/rice infected tissue (7 weeks).
Data analysis and write –up (1 weeks).
The student benefits: The project will provide mass spectrometric training, method development and data
interpretation and presentation skills.
The added value to Biosciences: The project will provide the requisite data to finish a detailed publication
on the dynamics of 3-O-β-D-ribofuranosyl adenosine accumulation AND its derivatives in plant defence
(Salmond et al. in prep). This publication is required to underpin an application to BBSRC.
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7. Bridging Microfluidics and Oceanography: development of microfluidic devices to
capture marine microbes
Supervisors: Dr Stefano Pagliara and Dr Adam Monier (Streatham)
Oceans are experiencing fast ecological changes. Rising temperatures and atmospheric CO2 are altering
water chemistry and the way water moves around the oceanic basins. Such change is thought to cause
intense stress on marine species, including the very foundations of oceanic food webs —microbes. Ocean
systems and their biological communities are composed of an incredibly diverse collection of microorganisms, from microbes that predate on other microbes, to tiny phytoplankton (single-celled plant-like
organisms). It is difficult to accurately sample single-cells of the microbes that live in marine environments
using standard tools. Microfluidics allow the manipulation of small fluids and particles. As part of this
project, we will design, test and use microfluidic devices to capture microbial cells of specific size sampled
from Devonian coastal waters. Using DNA amplification/sequencing, we will then compare and contrast
the genetic diversity of marine microbes recovered from distinct cell size chambers, within the microfluidic
device. A part of this research project will be dedicated to bioinformatics analyses of this microbial
molecular diversity, to determine if the microbial assemblages are correctly size-fractionated. Bridging
microfluidics and genetic identification of natural single-cells will enable a new understanding of how
microbial assemblages are altered by environmental change.
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8. Would you like sea salt with that? Using physiology to improve the sustainability of
marine aquaculture
Supervisors: Dr. Rod Wilson, Dr. Eduarda Santos and Dr. Mauricio Urbina (Streatham)
Aquaculture will soon overtake wild-capture fisheries as our dominant source of seafood (1) and is vital to
future food security. Aquaculture of salmon and trout involves transfer of freshwater juveniles to sea
cages, but mortalities from osmoregulatory stress create fish welfare, sustainability and production
problems. Diets with elevated NaCl content can help to prepare freshwater juveniles for seawater transfer
(2). However, this only addresses the requirements for gill function, as this organ exclusively processes
+
excess monovalent ions (Na and Cl ) that must be excreted by fish in seawater. The kidney and gut are
2+
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also vital for successful seawater acclimation as these organs excrete excess divalent ions (Ca , Mg
2and SO4 ) that are limiting factors for survival in seawater (3). The student will join a dynamic and wellfounded team to investigate whether physiological knowledge can help design better diets to prepare all
vital osmoregulatory organs (gills, intestine and kidney) of juvenile fish for a more successful seawater
transfer. The student will aid in designing feeding experiments and will learn standard physiological
measurements to assess seawater adaptability. The student will also have scope for analysing and
interpreting gene/protein expression changes in the tissues that play key roles in successful preparation
for seawater survival (4). Dietary stimulation of marine adaptability also has the potential advantage to
make fish ready for marine aquaculture at a much younger age than previously possible. This could have
major economic and welfare benefits to the global aquaculture of salmonids, and potentially other
important aquaculture species.
References Cited:
1) FAO, 2014. The State of World Fisheries and Aquaculture 2014. UN Food and Agriculture Organization, Rome.
2) Perry, S.F. et al. (2006). Fooling a freshwater fish: how dietary salt transforms the rainbow trout gill into a seawater
gill phenotype. J. Experimental Biology 209(23): 4591-4596.
3) Wilson, R.W. et al. (2009). Contribution of Fish to the Marine Inorganic Carbon Cycle. Science 323(5912): 359-362.
4) Urbina, M. A., et al. (2013). Differential expression of Na+, K+-ATPase α-1 isoforms during seawater acclimation in
the amphidromous galaxiid fish Galaxias maculatus. J. Comparative Physiology B - 183(3): 345-357.
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