Summer Research Lab Experience 2017

     
     

Join one of our research teams

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 research lab experience is 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

Opportunities 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. your visit 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 stay if the application for funding is successful. There are also opportunities for unpaid research lab experience.

How to apply

  • Potential applicants should contact chosen project supervisors by the end of January 2017 at the latest or by the date specified for specific projects below.
  • When contacting supervisors please forward: a copy of your current CV; a brief statement of support outlining your interest in the project and your suitability; the name of an academic referee.

Projects available for Summer 2017

 

Molecular mechanisms of anti-tubercular specific action of non-steroidal anti-inflammatory drugs (NSAIDs)

Project supervisor/ host lab
Dr Sanjib Bhakta
s.bhakta@bbk.ac.uk

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, 4, 5).

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 their structure, function, regulation and inhibition 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.

References

  1. World Health Organisation. Global Tuberculosis Annual Report 2016.
  2. Maitra A, Bates S, Shaik M, Evangelopoulos D, Abubakar I, McHugh TD, Lipman M, Bhakta S. (2016) Repurposing drugs for treatment of tuberculosis: a role for non-steroidal anti-inflammatory drugs. Br Med Bull. 2016 Jun;118(1):138-48. doi: 10.1093/bmb/ldw019.
  3. Maitra A, Bates S, Kolvekar T, Devarajan PV, Guzman JD, Bhakta S. (2015) Repurposing -a ray of hope in tackling extensively drug resistance in tuberculosis. Int J Infect Dis. 2015 Mar;32:50-5. doi: 10.1016/j.ijid.2014.12.031.
  4. 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.
  5. 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. "
 

Recycling of cell-wall peptidoglycan molecular machinery in bacteria

Project supervisor/ host lab
Dr Sanjib Bhakta
s.bhakta@bbk.ac.uk

Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains one of the leading causes of mortality across the world. Rise of drug resistant forms of the bacteria and HIV co-infection has made the development of new treatment strategies imperative (WHO annual TB report 2016), this in turn requires identification of novel therapeutic targets. The cell-wall peptidoglycan (PG) layer of M. tuberculosis is a fundamental part of the unique cell wall core of mycobacteria and is essential for its survival.

The host of enzymes involved in its biosynthetic, degradative, remodelling and recycling machinery have recently resurfaced as attractive targets for anti-infective drug development. PG is a dynamic structure- it is synthesised, broken down, remodelled or recovered every generation (1). Cell growth, division and septation require the co-ordinated of PG hydrolysing and synthesising enzymes. Peptidoglycan hydrolases form a vast group of enzymes and include glycosidases, amidases (2), endopeptidases and carboxypeptidases, which combined together, are capable of fully degrading the PG macromolecule. These degraded molecules are then recycled back into the PG synthesis as demonstrated in Escherichia coli (3). Apart from conserving resources and energy, PG recycling is also found to play a significant role in cell-wall monitoring, cell signalling and antibiotic resistance by β-lactamase induction. Its role in pathogen virulence, as well as the suppression of the innate immune response by effectively recovering cell-wall muropeptides that would otherwise stimulate immunity via PG-recognising proteins has been widely reported. However, current knowledge of PG recycling in pathogenic bacteria (such as M. tuberculosis, M. leprae, Staphylococcus aureus) is seriously lacking and through this project we aim to clone, express, purify and characterise structure, function, inhibition and regulation of the key enzymes involved in cell-wall PG recycling molecular machinery.

References

  1. Park JT, Uehara T. How bacteria consume their own exoskeletons (turnover and recycling of cell wall peptidoglycan). Microbiol Mol Biol Rev. Jun 2008;72(2):211-227, table of contents.
  2. Prigozhin D.M., Mavrici D.,Huizar J.P. et al. Structural and biochemical analyses of Mycobacterium tuberculosis N-acetylmuramyl L-alanine amidase Rv3717 point to a role in peptidoglycan fragment recycling. J. Biol. Chem. Sep 2013;288:31549-31555.
  3. Mengin-Lecreulx D, van Heijenoort J, Park JT. Identification of the mpl gene encoding UDP-N-acetylmuramate: L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase in Escherichia coli and its role in recycling of cell wall peptidoglycan. J Bacteriol. Sep 1996;178(18):5347-5352.
 
 

Cloning, expression and characterisation of kinesin motors from the malaria parasite

Project supervisor/ host lab
Professor Carolyn Moores
c.moores@mail.cryst.bbk.ac.uk

Malaria is caused by the intracellular Plasmodium parasite and infects over 300 million people a year, killing more than 1 million. The complex life cycle of the parasite, the small number of drugs available and emerging drug resistance mean that novel drug targets are desperately needed. Kinesins are ATP-dependent microtubule-based molecular motors and are potential targets for anti-malarial drugs. The overall aim of this project is to study the motor domains of kinesins from malaria. Motor domains from malaria kinesins will be cloned for recombinant expression in E. coli.

If successful, protein purification and biochemical characterisation will be performed. In particular, kinesin ATPase activity and the way the motors interact with microtubules in vitro will be studied and can provide considerable insight into their functions in vivo. These studies will contribute understanding of kinesin function in malaria and help identify suitable targets for screening of small molecule inhibitors. Outcomes Methods for cloning genes for recombinant expression in bacteria; optimisation of protein expression in bacteria; strategies for purifying recombinant protein from bacteria; assays to measure kinesin activity. Two internships are available in our lab.

Figure 1

References

  1. Morrissette NS, Sibley LD (2002) Cytoskeleton of apicomplexan parasites. Microbiol Mol Biol Rev 66, 21-38.
  2. Cross RA, McAinsh A (2014) Primer movers: the mechanochemistry of mitotic kinesins. Nature Reviews Molecular Cell Biology 15, 257-71
  3. Liu L, Richard J, Kim S, Wojcik EJ (2014) Small molecule screen for candidate antimalarials targeting Plasmodium kinesin-5. J Biol Chem 289, 16601-14"

Requirements for applicants
Applicants should be in their penultimate year of a biochemistry degree and be eligible to apply for studentship funding.

Deadline for enquiries
January 13th 2017

 

Computational analysis of transcriptomic data

Project supervisor/ host lab
Dr Irilenia Nobeli
i.nobeli@bbk.ac.uk

The project will concentrate on one of three areas of interest to the group:

a) The development and application of methods for quantifying differential transcription of the untranslated parts (5' and 3' UTRs) of transcripts and the effects that shortening or lengthening the ends of a gene might have on the fate and function of that gene.

b) The analysis of transcriptomic (NGS) data relating to neurodevelopmental diseases (in particular autism).

c) The structural and phylogenetic analysis of predicted riboswitches in bacteria.

A project will be designed to fit the student's skills and interests.

Requirements for applicants
The ideal applicant will be competent in using computers (preferably have experience with Unix-based OS) and will have some basic training in R and statistics. Alternatively, experience in programming in any language would be an advantage.

Deadline for enquiries
Students looking for funding should identify a funding body and apply to the group at least 4 weeks ahead of the deadline imposed by the body.

 

Interactions of complement factor H with its ligands

Project supervisor/ host lab
Professor Stephen Perkins - Structural Immunology Group; Molecular Interactions Facility
s.perkins@ucl.ac.uk

The project will address the molecular role of defective proteins in causing disease. As an example of such a project, 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 are presently unravelling the many interactions of complement factor H with its ligands and how these may be a crucial factor in causing AMD. In order to clarify the involvement of intact complement factor H with its ligands, the summer project will involve the purification of the homozygous high-risk and low-risk forms of factor H from patient plasma, or their recombinant fragments, then interaction measurements of the two forms with ligands will be made using surface plasmon resonance and/or analytical ultracentrifugation. Alternatively, to follow our mutations web-site (http://www.fh-hus.org/; to be updated), disease-risk mutations in recombinant Factor H fragments will be created by mutagenesis and studied using the same methods to show whether these are causative of disease.

References

Rodriguez E, Nan R, Li K, Gor J. & Perkins SJ (2015) A revised mechanism for the activation of complement C3 to C3b: a molecular explanation of a disease-associated polymorphism. J. Biol. Chem. 290, 2334-2350. Pubmed 25488663

Requirements
If based at UCL, ideally taking BIOC2004 (Protein Structure and Function) and/or IMMU2001 (Immunology). Please provide a brief CV, a supporting statement, the name of an academic referee, and your UCL PORTICO printout (or transcript) when applying.

Deadline for enquiries
One paid summer internship is available for 8 weeks. Applications by Monday 16th January 2017.

 

Oxidation in the cavity of protocells

Project supervisor/ host lab
Dr Salvador Tomas

s.tomas@sbc.bbk.ac.uk

It is believed that one of the key events in the origin of life was the formation of cell-like structures by the spontaneous assembly of primordial lipids in ancient waterholes. In the early stages of proto-cell evolution, they lacked the molecular machinery of modern cells. In the absence of efficient enzymes, chemical transformations would have been largely dependent on the environmental conditions. The aim of this project is to investigate how the inclusion of molecules within the cavity of protocell-like lipid vesicles would affect the oxidation and reduction of the confined molecules, as compared with molecules free in the environment. Understandings these differences will offer clues of how spontaneous chemical processes may have modulated proto-cell evolution.

References
Modulation of Reactivity in the Cavity of Liposomes Promotes the Formation of Peptide Bonds. A. Grochmal, L. Prout, R. Makin-Taylor, R. Prohens, S. Tomas, J. Am. Chem. Soc. , 2015 , 137, 12269-12275

 

 

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