Summer Internships 2014

     
     

Join one of our research teams

By becoming an intern, you will be a member of one of our research teams, and your work will be an important contribution to the group’s discoveries. Summer Internships are an invaluable opportunity to gain hands-on experience in a research group and to get career advice from fellow students and mentors. They are also a great way to meet new people; we are a small, friendly department, located in the heart of London.

Eligibility

Our Summer Internships are largely funded by the Wellcome Trust or other learned societies. In order to be eligible for a research bursary from these organisations you must be:

  • Taking an undergraduate science degree
  • Considering research as a career
  • Expecting to achieve a First Class or good Upper Second Class degree result (references will be required)
  • In the middle years of your degree e.g. the internship will take place in the Summer vacation before the start of the final year of study
  • Registered at a UK university for the majority of your degree (for most funding bodies)

Working hours and stipend

  • Working hours will be 35 hours per week for between 6-8 weeks.
  • You can expect to receive a stipend of between £180 and 200 per week during your internship if the application for funding is successful. There are also opportunities for unpaid internships.

How to apply

Potential interns should contact chosen project supervisors by the end of January 2014 at the latest or by the date specified for specific projects below. When contacting supervisors please forward a copy of your current CV and a brief statement outlining your interest in the project and your suitability.

Internship projects available for Summer 2014

Molecular mechanisms of anti-tubercular specific action of NSAIDs

Drug resistance in the tuberculosis (TB) causing pathogen, Mycobacterium tuberculosis, was observed in 1940s when streptomycin was first introduced as a mono-therapy to treat the infectious disease. As of now, there is at least one reported case of an extensively drug-resistant (XDR) strain of the bacterium in 92 countries (1). A concerted effort to fight TB and develop novel therapeutic regimens to control and reverse the emergence of XDR-TB cases worldwide is on-going. As reported earlier by Ben Gold et al. and from our own studies, certain common non-steroidal anti-inflammatory drugs (NSAIDs) have proven to be selectively bactericidal against replicating, non-replicating and drug-resistant clinical isolates of M. tuberculosis (2, 3). Our primary focus is to repurpose these existing drugs and investigate their novel mechanisms of action in M. tuberculosis to help design more potent inhibitors in the future. We have identified the possible therapeutic targets of NSAIDs in M. tuberculosis to be unique from other bacteria and aim to characterise them further to characterise NSAIDs molecular mechanism of endogenous action. This project will involve molecular biology, biochemistry and related techniques to clone, express, purify the potential targets of NSAIDs as well as their interacting partners to develop assays for further characterisation of the recombinant enzymes from mycobacteria.

Key References:
1. World Health Organisation. Global Tuberculosis Annual Report 2013. London 2013.
2. Gold B, Pingle M, et al. Nonsteroidal anti-inflammatory drug sensitizes Mycobacterium tuberculosis to endogenous and exogenous antimicrobials. Proceedings of the National Academy of Sciences of the United States of America 2012; 109: 16004-11.
3. Guzman JD, Bhakta S. et al. (2013). Anti-tubercular specific activity of ibuprofen and other 2-arylpropanoic acids using the HT-SPOTi whole-cell phenotypic assay. BMJ Open 2013;3:6 e002672 doi:10.1136/bmjopen-2013-002672.

Please follow http://www.bbk.ac.uk/biology/our-staff/academic/sanjib-bhakta/publications or https://www.researchgate.net/profile/Dr_Sanjib_Bhakta/.
Further references for background literature studies, on individual research projects, are available on acceptance.

Project supervisor/ host lab:
Dr Sanjib Bhakta / ISMB-Mycobacteria Research Laboratory

Unravelling the genetic regulation of the kynurenine pathway and tryptophan metabolism using C. elegans

Tryptophan metabolism and the kynurenine pathway are emerging as key, evolutionary conserved regulators of many fundamental processes, such as neurodegeneration, cancer, ageing and death (see figure). Indeed, tryptophan catabolism is required for the generation of several important compounds, including the ubiquitous enzyme co-factor nicotine adenine dinucleotide (NAD), the neurotransmitter serotonin, and the vitamin niacin. However, how cells regulate this metabolic pathway to modulate these phenotypes is largely unknown. The nematode C. elegans is an exceptional model organism for the study of metabolism, disease and ageing, as well as an excellent tool for screening purposes. Furthermore, the kynurenine pathway is highly conserved between worms and humans. It has been shown that the long-lived and neurodegeneration-resistant insulin/IGF-like signalling worm mutants (daf-2) downregulate the kynurenine pathway via the transcription factor FOXO (daf-16), however the exact feedback mechanism remains to be elucidated. Here, we will develop a high-throughput biochemical technique using C. elegans for the fast, accurate and unbiased screening of all nematode transcription factors that could potentially regulate the kynurenine pathway. Subsequent validation of targets will be performed using quantitative RT-PCR.

Selected publications
van der Goot AT, Nollen EA (2013) Tryptophan metabolism: entering the field of aging and age-related pathologies. Trends in Molecular Medicine 19: 336-344

Coburn, C., Allman, E., Mahanti, P., Benedetto, A., Cabreiro, F., Pincus, Z., Matthijssens, F., Araiz, C., Mandel, A., Vlachos, M., et al. (2013). Anthranilate fluorescence marks a calcium-propagated necrotic wave that promotes organismal death in C. elegans. PLoS Biology 11, e1001613

Student requirements
Microbiology and/or molecular biology

Project supervisor/ host lab
Supervisor: Dr Filipe Cabreiro

Structural Studies of Transcriptional Activation in Eukaryotes

The activation of gene expression is a multistep process that begins with the binding of a transcription factor (TF) to the genome. TFs subsequently recruit coactivator complexes which can modify the chromatin environment around the gene and/or recruit the basal transcriptional machinery, both of which lead to the expression of that gene. This project is focused on two eukaryotic transcriptional coactivators called SAGA and NuA4 from Saccharomyces cerevisiae. These important complexes are conserved in all eukaryotes and consist of at least 13 subunits. They can enzymatically modify chromatin and also interact with parts of the basal transcriptional machinery. But the molecular mechanisms of these activities and how they cooperate to activate transcription remain largely unknown. Therefore, the aim of the intern student will be to dissect these complexes into smaller fragments that can be expressed in E. coli for structural analysis. This project is ideal for those interested in structural biology and/or transcription and will involve cloning, protein expression and protein purification of SAGA and NuA4 subunits to generate samples for subsequent study by x-ray crystallography, crosslinking or electron microscopy.

Project supervisor/ host lab
Dr Alan Cheung

Please note: This project is no longer available.

Towards an understanding of the molecular mechanisms underlying autism

Autism is a complex disorder and no single genetic factor can explain more than 1-2% of all cases. A number of genes have been implicated in Autism Spectrum Disorder (ASD) pathologies but a clear picture of what causes the disorder and what is simply a downstream effect is lacking. This project aims to identify homologues of human genes implicated in ASD in the model organism C. elegans. A list of such genes will allow us, for example, to explore the wealth of next-generation sequencing data available in C. elegans in order to gain a deeper understanding of the molecular mechanisms of autism in humans. This is an entirely computational project so the student should have a keen interest in computer-based work, and preferably a familiarity with Unix/Linux. Although no programming experience is required, an aptitude for installing and running software and for using computational tools on the web is expected.

Project supervisor/ host lab
Dr Irilenia Nobeli

Developing of biomimetic nano-containers

Simplistically, the complexity of function of living cells can be attributed to the localisation of incredibly intricate molecular machinery within the bounds of a lipid membrane (i.e., the cell membrane). The cell membrane fulfils the role of keeping the pieces together and of selecting what molecules go in and out. Based on this general concept, we aim to develop a new class of nanoparticles that respond to changes on the chemical composition of the environment, acting therefore as a sensor of this change and potentially releasing previously associated molecules. Briefly, these nanoparticles will be formed of lipid vesicles, containing within its cavity small molecules capable of assembling as a response of chemicals en the environment that are capable of crossing the lipid membrane barrier. The assembly will result in dramatic changes in the colour and/or fluorescent properties that can be used to quantify the change. You will synthesise the self-assembling molecules (termed SAM), build up the SAM-filled nanoparticles and characterise changes in optical spectroscopy upon changes in pH, ionic strength and the presence of specific chemical moieties.

Project supervisor/ host lab
Supervisor: Dr Salvador Tomas

 

Development of Anticancer Drug-Antibody Conjugates

Azinomycin A is a bacterial natural product with DNA crosslinking activity that has potential as an anticancer agent. Its toxicity limits its clinical potential, so the aim of this project is to develop methods to link azinomycin A to tumour targeting agents such as antibodies. We already know that an azinomycin analogue with an azide group can be produced in vivo. by adding an unnatural biosynthetic substrate. This project will involve scale-up synthesis of the substrate analogue, followed by production and purification of the modified azinomycin A. This will then be tested to see if it can be selectively modified by the azide-alkyne cycloaddition reaction. New compounds may be tested for anticancer activity in collaboration with the UCL Cancer Institute.

Student requirements
Applicants should have some practical experience of organic chemistry and/or microbiology.

Project supervisor/ host lab
Dr Philip Lowden

Cloning and expression of dyslexia susceptibility gene Dcdc2

Doublecortin domain-containing protein 2 (DCDC2) deficiency is associated with developmental dyslexia, one of the most common of the complex neurobehavioral disorders (Meng 2005, Schumacher 2006), characterized by reading impairment in 5-17% individuals with normal intelligence (Shaywitz 2003). DCDC2 is a microtubule associated protein (MAP) essential for brain development. The tandem repeat of globular doublecortin (DC) domains confers microtubule (MT) binding ability to the protein that can regulate MT cytoskeleton during neuronal migration. The aim of this project is to study the DCDC2 interaction with MTs in vitro to gain biochemical insights into MT regulation by DCDC2. This will involve: 1) cloning of Dcdc2 gene for expression in E. coli; 2) optimising protein expression conditions; and 3) chromatographic purification of the recombinant protein. This will enable functional testing of MT nucleation and stabilisation activity of DCDC2. Its binding affinity to MTs pre-stabilised with a drug paclitaxel will be assessed by cosedimentation assay (Moores 2006). These experiments will reveal important characteristics of the DCDC2 molecular mechanism of action and will help to understand its role in the regulation of the MT cytoskeleton.

Outcomes
Gene cloning techniques; optimisation of protein expression in E. coli; protein purification methods such as affinity chromatography and gel filtration; biochemical assays to measure MAP activity

References
Meng et al (2005). DCDC2 is associated with reading disability and modulates neuronal development in the brain. PNAS 102, 17053-8.

Schumacher et al (2006). Strong genetic evidence of DCDC2 as a susceptibility gene for dyslexia. Am J Hum Genet 78, 52-62.

Moores et al (2006). Distinct roles of doublecortin modulating the microtubule cytoskeleton. EMBO J 25, 4448-57. Shaywitz and Shaywitz (2003). Dyslexia (specific reading disability). Pediatr Rev 24, 147-53

Student requirements
Applicants should be in their penultimate year of a biochemistry/biomedicine degree and eligible to apply for studentship funding.

Deadline for enquiries
January 7th 2014

Project supervisor/ host lab
Dr Carolyn Moores

Interactions of complement factor H with its ligands

Age-related macular degeneration (AMD) is the main cause of blindness in the Western World in people over 55 years. Deposition of proteins, ions and lipids as "drusen" between the blood circulation and the retina is a major risk factor in AMD. Drusen usually grow in size and spread with age, disrupting the normal function of the retina, but may disappear. We recently discovered that the interaction between C-reactive protein and complement factor H may be a crucial factor in AMD (“Paper of the Week” in J.Biol.Chem. in January 2010). In order to prove further the involvement of intact complement factor H with this (or other ligands), the summer project will involve the purification of the homozygous high-risk and low-risk forms of factor H from patient plasma, then measurements will be made using surface plasmon resonance to define the conditions under which Factor H will interact with C-reactive protein (or other ligands) on sensor surfaces to which Factor H or C-reactive protein has been immobilised.

Student requirements
Examples of relevant training include UCL modules BIOC2004 and/or IMMU2001

Project supervisor/ host lab
Prof Steve Perkins, Structural Immunology Group. Molecular Interactions Facility

Please note: This project is no longer available.

Evaluation and development of chemical cross-linking mass spectrometry approaches for the mapping of macromolecular protein complexes.

A large number of cellular processes are seldom due to the action of individual proteins; rather, proteins come together and form macromolecular complexes in order to carry out their function. Knowing which proteins comprise these complexes and the structure of such complexes, provides insights into their mechanism of action. Obtaining structural information for macromolecular complexes using high resolution techniques, however, is not always possible.

Chemical cross-linking in combination with mass spectrometry (XL-MS) is a low resolution technique that provides information regarding the distance between lysine residues within a macromolecular complex [1]. XL-MS has advantages over other techniques in that it has low sample requirements, and can be applied to the study of heterogeneous samples [2]

While XL-MS has been successfully used to elucidate the structure of macromolecular complexes [3] and entire protein networks [4], a rate limiting step still lies in efficient sample cross linking and processing of the MS data which, almost always, requires significant manual validation. Subsequent mapping of the MS data, in order to obtain protein complex topology, also involves significant manual intervention.

This project will evaluate a number of existing approaches for performing chemical cross linking and for processing of the XL-MS data generated. Improvements to existing methods will be developed where necessary.

References
[1] A. Leitner, T. Walzthoeni, A. Kahraman, F. Herzog, O. Rinner, M. Beck, et al., Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics, Mol. Cell Proteomics. 9 (2010) 1634–1649.

[2] Thalassinos, K., Pandurangan, A.P., Xu, M., Alber, F., Topf, M. (2013) Conformational States of Macromolecular Assemblies Explored by Integrative Structure Calculation. Structure 21:1500-1508.

[3] J.W. Back, L. de Jong, A.O. Muijsers, C.G. de Koster, Chemical cross-linking and mass spectrometry for protein structural modeling, Journal of Molecular Biology. 331 (2003) 303–313.

[4] F. Herzog, A. Kahraman, D. Boehringer, R. Mak, A. Bracher, T. Walzthoeni, et al., Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry, Science. 337 (2012) 1348–1352.
Applicants should have some practical experience of organic chemistry and/or microbiology.

Project supervisor/ host lab
Dr Kostas Thalassinos

 

 

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Chemistry




   
   
   
     
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