Evgenia Markova and Laura Pokorny are PhD students who joined the UCL-Birkbeck MRC funded Doctoral Training Programme in Autumn 2016. PhD students on this programme complete rotation projects in year 1 before choosing and developing their PhD project. Both Evgenia and Laura are looking forward to increasing opportunities to engage with new intakes of students.
I obtained a BSc in Genetics from the University of York and during the course of my degree I completed summer internships in the Bulgarian Academy of Sciences and in Genika, a genetic medico-diagnostic laboratory. It was at this point that I started considering a career in science, as I was surrounded by experts in their respective fields who warmly welcomed me into their research environment. I also completed a year-long placement in a biotechnology company, Heptares Therapeutics, where I discovered a passion for biochemistry and structural biology, which ultimately determined my choice of a PhD topic.
Rotation Projects (Year 1)
‘My choice of PhD project emerged through engagement with rotation projects which took my research in novel directions. This flexibility to develop and mould the final project has been a great opportunity.’
Rotation 1: My first rotation project ‘Structural elucidation of a component of the COPII secretion system’ was with Dr. Giulia Zanetti (ISMB, Birkbeck) where I encountered electron microscopy for the first time and obtained preliminary structural information on a component of the COPII secretion system.
Rotation 2: My second rotation ‘Age-dependent neuroinflammation in the brain of a Wnt signaling pathway mutant’ was with Dr. Patricia Salinas at the MRC LMCB and utilised immunofluorescence to study the time-dependent brain inflammation profile of a Wnt signalling pathway-defective mouse model.
Rotation 3: Finally, I spent my third rotation ‘Single-molecule fluorescence investigation of the COPII coat assembly’ in Dr. Alan Lowe’s lab in (ISMB, Birkbeck) where I studied the dynamics of an endoplasmic reticulum membrane model as remodelled by purified COPII proteins.
‘The ISMB has excellent facilities which provide access to structural biology and cryo-EM. It has been easy to move between facilities at Birkbeck and UCL as part of the jointly run ISMB.’
PhD Project: The Kinetics and Assembly of the COPII Secretion System (Year 2 onwards)
The intracellular trafficking of biomolecules is an essential property of eukaryotic systems. The COPII vesicular transport system is responsible for anterograde intracellular transport processes at the ER membrane, where COPII component-lined vesicles incorporate protein and lipid cargoes. My project aims to investigate the mechanisms of COPII budding and coat assembly, which are currently poorly characterised. I will study COPII assembly and dissociation using an established membrane model,
Giant Unilamellar Vesicles (GUVs), and the mammalian COPII proteins, as expressed and purified from insect cell culture. I will utilise cryo-electron microscopy and single-molecule fluorescence in the study of the COPII coat assembly through in vitro reconstitution. My PhD supervisor is Dr Giulia Zanetti, ISMB, Birkbeck.
I studied for an undergraduate degree in Biochemistry at the University of York. In the summer between my second and third year I carried out a 2 month research placement in Paul Pryor’s lab at the Centre for Immunology and Infection at the University of York, where I was identifying chlamydial effector proteins involved in disrupting the trafficking of the bacterium to the host lysosome. I really loved working in a research setting and this was when I realised I wanted to do a PhD and pursue a career in research.
Rotation projects (Year 1)
Rotation 1: My first rotation ‘Manipulation of Nuclear Function by Chlamydia trachomatis’ was in Dr Richard Hayward’s lab (ISMB, Birkbeck). Previous research in the Hayward lab had identified alterations in nuclear architecture during infection by C. trachomatis. Namely, the nuclear shape becomes distorted in infected cells, lamin A/C is decreased at the inclusion distal face of the nucleus, and there was a degradation of nucleoporins at the inclusion proximal face of the nucleus. I confirmed these findings by aiming to understand the mechanism underlying the lamin A/C decrease.
Caspase 6 is a candidate for the degredation of lamin A/C due to the fact that lamin A/C is degraded by caspase 6 during apoptosis. By treating infected cells with a drug which inhibits caspase 6, I was able to block the lamin A/C decrease in infected cells. This was shown by confocal microscopy and by western blot.
Rotation 2: My second rotation ‘A novel mechanism of targeting and transport of a P. falciparum protein down the secretory pathway’ was in Dr Andrew Osborne’s lab (ISMB, UCL). The mechanism leading to protein transport, and in particular trans-membrane protein transport, in P. falciparum is not completely understood. Proteins destined for export must cross many membranes of the parasite before entering the host cell. Models have proposed whereby TM proteins are extracted from membranes at various stages of the secretory pathways and trafficked via chaperones (Papakrivos, Newbold and Lingelbach., 2005; Kneupfer et al., 2005; Gruring et al., 2012). However, the concept of pulling proteins out of membranes during protein export is unsupported outside the Plasmodium field. Recent work in the Osborne lab and others has provided evidence that the PNEP protein Pf332, which has a single TM domain, behaves in line with this extraction model. I used yeast as a model organism and showed that, when Pf332 is expressed in yeast, there is a subset of soluble protein. This suggests that the machinery needed to pull the protein out the membranes is conserved in eukaryotes. In this rotation I used techniques including western blotting, parasite culturing, cloning, and florescence microscopy.
Rotation 3: In my third rotation ‘Single-molecule studies of the molecular mechanisms of the nuclear pore complex during C. trachomatis infection’ in Dr Alan Lowe’s lab (ISMB, UCL) I used super-resolution microscopy to gain images of the nucleoporin degradation seen in my first rotation, and to learn more about the kinetics of importin-beta transport in the nucleus during infection. I used the technique of photoactivated localization microscopy (PALM). In short, PALM imaging uses the principle of stochastically activating, imaging and photobleaching photoswitchable fluorescent proteins in order to temporally separate closely spaced molecules (Betzig et al., 2006). The resolution achieved in PALM imaging is over an order of magnitude higher than the diffraction limit of light. By transfecting infected cells with importin-B (nuclear transport receptor) tagged to a photoswitchable fluorescent protein and imaging by PALM, we could gain a much higher resolution picture of the organisation of the nuclear pores, and could follow the kinetics of transport via single-particle tracking.
‘Working within the ISMB environment has been a great way to find out more about the work of other PhD students and staff through weekly presentations during term time known as Friday Wraps’
PhD project: Studying Vaccinia virus fusion using a minimal model system (Year 2 onwards)
Vaccinia virus (VACV) is the prototypical Poxvirus. Poxviruses enter cells by acid mediated fusion, using the most complicated virus fusion machinery identified. Whilst genetics indicates that poxvirus fusion relies on 12 viral proteins, to date the organisation of this machinery, its mechanism of fusion, its fusion peptide, and the structural and molecular details of poxvirus fusion remain a mystery. Therefore to address this lack in our knowledge, I aim to develop a new minimal model system to study VACV entry and fusion. This system will be amenable to super-resolution imaging studies allowing us an unprecedented view into the biological requirements of viral entry. My PhD supervisor is Dr Jason Mercer LMCB.
LIDo is one of the largest Doctoral Training Programmes in the country; a collaboration between six of London’s world-class universities and specialist science institutions (Birkbeck, Kings, LSHTM, Queen Mary, RVC and UCL). Students on the programme have a wide range of scientific backgrounds (e.g. cell biology, chemistry, genetics, physics, engineering, psychology, neuroscience, biochemistry, mathematics, statistics) but a common interest in solving problems in the life sciences. The consortium provides these students with a unique opportunity to pursue innovative interdisciplinary and cross-institutional research projects in the heart of one of the world’s most vibrant cities.
Which departments at Birkbeck are taking part in this DTP?
What strengths does Birkbeck bring to this Doctoral Training Programme?
Both Birkbeck departments are among the top ten university departments in the country in their subject area in terms of the quality of their research (REF 2014), and have a substantial profile of world class activity, particularly in structural biology and in understanding the processes of cognitive development.
How is the programme structured?
It is a 4-year programme, based around projects that are proposed by a team of two (or more) supervisors from different disciplines. Around 40 studentships are available each year for students to undertake lab rotations in the first year with different supervisors in different institutions. Then, toward the end of their first year, they select their PhD project. They will subsequently be registered at their primary supervisor’s institution for their PhD. In addition, around 15 CASE projects are available each year that have an industrial co-sponsor. CASE students begin their PhD project right from the start and do not undertake rotations.
All students also undertake classroom training in the first year in computational modelling, statistics, aspects of biology driven commerce and ‘hot topics’ in biological research.
What kinds of resources and facilities are available to students who are offered a place on the programme?
Given the variety of the six institutions involved, it is impossible to summarise adequately. Somewhere in the consortium are resources and facilities for any particular area of research to more or less match anything available at any university in the world. Birkbeck and its neighbour UCL jointly operate a number of world class experimental facilities e.g. x-ray crystallography, NMR, electron microscopy, infra-red and magnetic resonance brain imaging.
What are the advantages for students taking part in this DTP in particular?
The camaraderie of being ‘in it together’ with a large and diverse group of students. The potential to undertake research in several of the colleges of the University of London in different research areas before deciding where to register for their PhD. The huge number and variety of projects that are available.
Are there any features of supervision within LIDo that you would like to highlight?
All students have at least two scientific supervisors to provide guidance and advice. In most of the institutions students will also be assigned a thesis mentor to act as an independent source of advice. LIDo keeps an eye on all the students, supervisors and host departments throughout the PhD. The LIDo representatives at each institution and the LIDO administrative staff are always available to help resolve (usually non-scientific) problems.
Are there any features of training or professional development and employability within LIDo that you would like to highlight?
To broaden student’s experience, all BBSRC-funded students also undertake a paid 3-month internship in an external organisation during their PhD. For CASE students this will be with their industrial partner. For other students the internship can be in any organisation able to provide an appropriate training environment. Students have taken placements in the biotech industry, in the voluntary sector, in a wide-range of start-ups, in policy roles, in government and in science communication. The program also has several networking events per year with invited participants from industry.
How can students find out about potential projects and supervisors at Birkbeck?
For students interested in the CASE studentships, a list of projects is available from November each year (for a following October start) at the LIDo website. Occasionally a few other specific projects affiliated to the programme are also advertised by the individual institutions. Most students are, however, initially recruited to the programme not a specific project or supervisor. For those students who are successful in their applications, a project list is provided in the Summer before they start their first year from which they choose labs to rotate in. There are usually over 200 projects to choose from, of those usually around 20 involve Birkbeck supervisors.
How would you describe your roles within the LIDo?
Multi-faceted. We have an oversight and pastoral role for LIDo students carrying out their PhD projects at Birkbeck. We represent Birkbeck’s views to the consortium. We work with staff from the other institutions in the consortium to take strategic and financial decisions for the DTP, and to organise bids for the funding to continue the programme (current grant funding is £20 million). We develop and enact policies regarding the student training aspects the programme. And finally, and by no means the least of our tasks, we work with staff from the other institutions to select students to join the programme from the many hundreds of applicants that LIDo receives each year.
What background and experience would successful students be able to demonstrate?
High level of recent academic achievement, typically either a First Class BSc or a Distinction at Masters level should be achieved or confidently predicted. Previous experience of research is also important, for example, through an extended undergraduate project, a Master’s degree project or one or more summer research internships. Almost all successful applicants will have spent at least 2-3 months working on a research project and have a good reference from their research supervisor. Applicants with more extensive experience in academia or industry in a research or technical role are regarded favourably even if their academic record is slightly less than perfect.
Where can potential students and supervisors find out more about LIDo?
Follow the application guidance available from the LIDo website – a completed application form, CV, references and transcripts need to be provided.
Are there any key dates to be aware of?
The closing date for studentships beginning in Autumn 2018 is 19 January 2018. Applicants should check the LIDo website for further information. It is advisable to begin the process at least a few weeks ahead of the deadline so that you can arrange for all the paperwork to be submitted before the deadline.