Project title
Project director
Background to the project:
Patients suffering from neutropenia have reduced neutrophil counts due to increased rates of apoptosis. One congenital form of this disease is caused by a point mutation in a gene called VPS45 (resulting in mutation of Thr238 to Asn in the corresponding protein).
Vps45 is required for sorting of proteins through the endosomal system by mechanisms conserved through evolution, from yeast to humans.
My lab has introduced the disease causing mutation described above into the yeast
VPS45 and demonstrated that it abrogates function of the protein (please see Stepensky
P et al. Blood 2013;121:5078-5087.
This project will extend these findings and use the ease with which yeast can be manipulated to understand how defects in Vps45 function lead to increased rates of apoptosis.
Opportunities for experimental design, hypothesis development, data analysis, etc .:
Techniques that are likely to be used:
There are different avenues this project can take depending on student interest, including:

Phenotypic analyses of cells carrying disease causing mutations
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Creation of yeast strains carrying newly identified disease causing mutations
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Investigation of pathways through which Vps45 regulates
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Identification of genetic suppressors of disease causing Vps45 mutation(s)
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Yeast cell culture and transformation
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DNA manipulations
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SDS-PAGE and immunoblot analyses
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Project title
Project director
Background to the project:
Resistance to current antibiotic compounds is an increasing global risk to the health of the human population. A major challenge in the identification of novel antimicrobial compounds is the isolated growth of microbes that in the environment usually require a mixed community of organisms to thrive. This project will use novel isolation techniques for the growth of microbes from the environment that will then be screened, using more traditional techniques, for antimicrobial activities.
Opportunities for experimental design, hypothesis development, data analysis, etc.:
Students will need to investigate the literature to identify suitable screening strategies, design approaches that allow putative antibiotics to be classified, and for the producing species to be grown and investigated. A range of molecular methods could be used to identify species as new or known so that potential novel producers can be further characterised. Students will need to consider approaches to normalising the efficacy of different compounds, and identify means to differentiate between different modes of action (i.e. the pathways targeted by particular compounds).
Techniques that are likely to be used:
Aseptic technique, DNA extraction and sequencing, gas chromatography, mass spectrometry.
Microscopy, flow cytometry.
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Project title
Project director:
Background to the project:
Decisions on whether and how a male should deploy limited resources to mating rather than survival are complex. In the fly Drosophila melanogaster the intensity of courtship and the length of mating are influence by the physical and social environment (e.g. temperature, food quality and number of potential rivals). Females store sperm for later use, but sperm stocks might become depleted. Females also have an opportunity to accept or reject mating and their willingness to remate will be affected by their age and their prior experiences. Sperm competition, where the sperm from two or more males compete for fertilization within the female, does occur in Drosophila and males produce a variety of proteins which they transfer to females during mating which a ffect the female’s behaviour and lifespan – mating reduces survival.
Opportunities for experimental design, hypothesis development, data analysis, etc.:
Drosophila are very easy to keep in the lab and can be manipulated with simple changes to their environment. This means it is possible to design an experiment that manipulates more than one factor in a factorial design (e.g. an eight treatment design with all combinations of high/low quality food, young/old males, previously mated or not) to explore the interactions between those factors on easy to measure output variables (e.g. eggs laid, mating duration, activity, survival). This can all be analysed using an ANOVA style approach, althought other statistical approaches are also available.
We have a Drosophila activity monitor (DAM) available that measures activity of the flies by them passing through a beam in a small tube, passing the data direct to a PC. This is a very effective tool that can be used to measure 32 flies at a time
Techniques that are likely to be used:
Drosophila husbandry (keeping stocks going, getting flies of the correct age ready when required, manipulation of food, sexing flies, moving flies between tubes, etc.)
Data manipulation, synthesis and analysis (observation of mating behaviour and the
Drosophila activity monitor will generate a lot of data)
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Project title:
Project director:
Background to the project:
The transfer of pathogens between medical staff and patients in hospitals is a well-known problem. Recent cases of medical staff being contaminated with Ebola whilst treating infected patients is a good example of this. Whilst a range of studies has highlighted some of the transmission routes for these infections (e.g. poor hand washing practice, transfer via pens etc.), little is known about the survival and subsequent transfer of pathogens from fabrics used in health care settings. Different fabrics are used in health care settings e.g. uniforms, curtains, bed linen etc. and the type or material or the environment may influence the survival of pathogens and their subsequent transfer.
This project will use a standard quantitative method to investigate the survival and transfer of pathogens on and between fabrics as well as transfer between fabrics and other surfaces e.g. gloves or work surfaces.
Opportunities for experimental design, hypothesis development, data analysis, etc.:
Whilst the basic method involved in this project needs to be standardised in order to bring together the results of the different students doing this project, there is considerable scope to change the pathogen, the type of fabric or the method of transfer being investigated by individual students. Choice of pathogen will be limited to organisms that can be safely handled in an ACDP category 2 laboratory and can be grown on standard culture media under aerobic conditions. This limits the studies primarily to bacteria and some fungi, but bacteriophage could be used as a model for virus transmission / survival.
Techniques that are likely to be used:
The project will be based on the microbiology techniques previously encountered in Y1 practicals.
The technique for measuring survival and subsequent transfer of pathogens from fabric samples will be based on the following published paper
Sattar, S.A. et al (2001) Transfer of bacteria from fabrics to hands and other fabrics: development and application of a quantitative method using Staphylococcus aureus as a model. Journal of Applied Microbiology 90, 962-970
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Project title:
Project director:
Background to the project:
Measurement of plant species diversity and productivity is a central component of basic ecology. Understanding species diversity and species’ response to environment is essential if we are to predict how ecosystems will respond to climate change. The identity of plant species within a community can be determined, and by undertaking manipulation experiments, the response to change in that community can be determined. All plants, however, also occupy the soil niche. Soil is one of the most poorly understood ecological assemblages. Species in soil are difficult to observe, are often hard to identify, and their function in the soil may be obscure. However, by identifying appropriate variables, the response of soil communities to change can also be measured.
Opportunities for experimental design, hypothesis development, data analysis, etc.:
As a group, and in consultation with the Astrocampus team, you will agree on an appropriate manipulation experiment on the Astrocampus site. You will have the opportunity to think about randomisation, blocking,treatements and confounding variables, and then as a group, to design and implement a fully factorial blocked experiment, an key experimental design. Each of you will individually then identify a hypothesis that you can test within that experiment. You can split up into smaller groups to collect samples, and by the second half of the project you will be analysing your own set of samples for the write up.
Techniques that are likely to be used:
This platform can offer a wide variety of experiments. You can sample plants, their associated microbes, soil microbes, soil invertebrates or abiotic variables, such as available nutrients in soil water or plant tissues. You may choose to use techniquest from three broad areas:
1) Natural history identification of plants or invertebrates, and community analyses of the data.
2) Chemical analysis of plant or soil samples, to measure e.g. Phosphorous, C/N ratios,
Silicon, Nitrogen and so on.
3) DNA based techniques. DNA extraction from plants, invertebrates or microbes is possible. Within my group we have protocols for general amplification of plants, animals, fungi, bacteria and archaea, and also for some key functional genes in the nitrogen cycling pathway. Other targets can be developed. Either community samples or cloning and sequencing of particular individuals may be undertaken.
The experimental design will permit a range of statistical analysis, and you can develop this using R and also genetic analysis packages where appropriate.
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Project title:
Project director:
Background to the project:
Getting a better understanding of the molecular mechanisms that lead to tumour formation is important for the development of cancer therapies. In Drosophila , a wellestablished model organism for studying cancer, several tumour suppressor genes have been identified. Loss-of-function of the tumour suppressor gene discs large leads to neoplastic overgrowth of the brain and imaginal discs in Drosophila larvae. In addition, discs large homologues have been shown to be downregulated in human cancers, and the proteins encoded by them are targeted by oncoviruses.
Discs large has been shown to be implicated in a range of cellular processes that are altered in cancerous tissues, including cell proliferation, cell differentiation, cell signalling and cell polarity. This project aims to identify genetic modifiers of the discs large loss-offunction overgrowth phenotype, and to shed light on the importance of the various cellular functions of discs large in tumour formation. Two approaches will be used; an unbiased interactor screen using large chromosomal deletions, and a candidate screen testing for interaction with selected genes.
Opportunities for experimental design, hypothesis development, data analysis, etc.:
The project will give the students the opportunity to establish a protocol for the genetic screen, including the use of appropriate controls and the analysis of the results. The students will not only be involved in the planning of the experimental procedures, but will also shape the project by contributing to the selection of candidate genes tested in the screen. Quantitative data will be obtained, allowing for statistical analysis.
Techniques that are likely to be used:
- Drosophila husbandry and genetics
- dissection of Drosophila larvae
- light microscopy/fluorescence microscopy
- image analysis
- database interrogation
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Project title:
Project director:
Background to the project:
The nematode worm C. elegans is a model organism for studying development and signalling. The worms are typically fed on live bacteria, and thus it is possible to use C. elegans as a model for bacterial colonisation and virulence. Furthermore, the bacterial metabolism can impact on worm development and lifespan, as such the worm can be a model for testing the free radical theory of ageing [se e.g. Gomez et al. (2012) BMC
Microbiology 12, 300].
In order to gain a better understanding of the interaction of a microbial agent with its host, it is useful to investigate the role of specific genes on this interaction. We are fortunate to have access to the Keio collection of E. coli -a collection which consists of mutant strains deficient in each of the non-essential genes from this bacterium.
In this project you will be able to explore the role of specific E. coli genes as colonisation and virulence determinants in the C. elegans model. It will also be possible to investigate the role of these specific genes on C. elegans lifespan.
Opportunities for experimental design, hypothesis development, data analysis, etc.:
Students will be able to explore the available literature on virulence / colonisation determinants, and decide on a set of genes of interest to explore further experimentally.
Having established colonies of C. elegans and cultures of various strains of E. coli (or other bacterial species, if students decide to explore other possibilities), students will have to adapt existing experimental methods in order to measure bacterial colonisation and survival inside the C. elegans host, set up competition experiments between bacterial strains, and measure the impact of different strains on C. elegans longevity. There will be potential to generate E. coli strains labelled with Green Fluorescent Protein (or equivalent) in order to monitor bacterial colonisation using microscopy-based approaches. There may be potential to monitor expression of key genes of interest using
Reverse Transcriptase PCR-based approaches. Quantitative data will be gathered on microbial numbers and worm survival, and analysed using appropriate statistical methodology.
Techniques that are likely to be used:
Core techniques will involve using aseptic technique for culturing bacteria, and basic husbandry of the C. elegans worms. You will use bright field microscopy to monitor worm development. There will be the potential for using some recombinant DNA technology
(e.g. to generate gfp -labelled E. coli ) and techniques for RNA extraction and amplification via RT-PCR. There may be some opportunity to use fluorescence microscopy, as appropriate depending on the experimental design that is developed in the project.
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Project title:
Project director:
Background to the project:
Maf1 is an evolutionarily-conserved transcription factor that binds and regulates RNA polymerase III to control the synthesis of noncoding RNAs such as tRNA. In yeast, loss of Maf1 undermines the response to diverse stress conditions. In fruitflies, Maf1 depletion enhances larval growth and development. This project aims to determine if
Maf1 influences how Arabidopsis grow and develop under normal and stress conditions.
Maf1 expression will be examined and evidence will be sought for post-translational modifications that might potentially respond to stress.
Opportunities for experimental design, hypothesis development, data analysis, etc.:
Designing the best ways to monitor plant growth and development and how these respond to stresses.
Developing hypotheses concerning the function(s) of Maf1 in plants.
Collection and analysis of data describing the growth & development of plants under normal and stress conditions.
Techniques that are likely to be used:
Plant culture and detailed monitoring.
Protein extraction, SDS-PAGE and western blot analysis.
RNA extraction and analysis.
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Project title:
Project director:
Background to the project:
Extracellular peptides are an important source of nutrients for many bacteria
– in other instances they perform signalling functions. Peptides are generally taken up by one or more of several transport systems. E. coli for example has two ABC-type peptide transporters, an oligopeptide permease for the uptake of peptides 2-5 residues in length and a dipeptide permease which takes up dipetides. Each transporter has a set of membrane spanning and ATPase components as well as an extracellular receptor protein component which binds the substrate and defines the specificity of the system. Curiously,
Bacillus anthracis has coding sequences for 14 peptide binding proteins. This project aims to determine the ligand binding specificity of these transporter proteins.
Opportunities for experimental design, hypothesis development, data analysis, etc.:
Prior to embarking on experiments, this project will involve sequence retrieval and comparison of sets of sequences with one another and in the context of crystal structure information. Here there is opportunity for hypothesis development and discovery. What can sequence tell us about the likely function of the chosen proteins? At this point each student will have a pair of coding sequences to work on by themselves. They will be expected to contribute to a group evaluation of what the most promising candidates for experimental analysis are. There will later also be a reasonable degree of experimental interpretation.
Techniques that are likely to be used:
This will be followed by primer design for the amplification of coding sequences from chromosomal DNA. Following PCR and gel analysis of the resulting amplified DNAs, the fragments will be captured in an expression plasmid using a ligation independent cloning technique and the resulting plasmids will be introduced into E. coli . Plasmid minipreps will be carried out and the products analysed for the presence of the expected inserts. Small scale expression tests will be carried out and cell lysates will be examined by SDS-PAGE for the overproduction of the desired recombinant protein. The proteins will be partially purified by Ni-chelation chromatography. As peptide binding proteins often co-purify with their substrates, it may be possible to determine the nature of the bound ligands by mass spectrometry. Alternatively, binding of specific peptides may be monitored by spectroscopy.
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