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I’m now in my second year of the BBSRC LIDo PhD programme. The first year was composed of two 4-month rotation projects, the first of which was based at both Birkbeck and UCL and is now my full-time PhD project. Like many others, March 17th was my final pre-lockdown day working in the lab and I was one month in on my second rotation project based at Barts Cancer Institute. The rest of the summer was a blur with days spent teaching myself to use command-line interfaces to run bioinformatic tools in an attempt to produce any data whatsoever for my project that had then become wholly computational. I managed to complete a coding course covering MATLAB, R and Python which was a mandatory part of my first year and a useful skill to learn as a biologist. All that remained was to return back to my old lab and officially start my PhD.
My first day back in the lab was July 27th – 4 and a half months post-lockdown. I had fastidiously read all the ‘returning to work’ documentation and was prepared for Birkbeck to look quite different to how I remembered it. Sure enough, the corridors were filled with COVID-19 safety measures and a 2-metre rule had been implemented. Luckily, I was already trained in the microbiology techniques I would need for the first month of my PhD thanks to my rotation project last year. My PhD researches the pathogenesis of the Kaposi Sarcoma-associated Herpes Virus with a particular focus on a viral oncogene it produces called vFLIP. I am interested in cancer biology having done a master’s degree in it, and my interdisciplinary PhD combines structural biology and virology. Overall, the majority of my PhD is wet lab based.
Being supervised while adhering to social distancing rules vaguely resembles a Quickstep dance. The 2-metre rule was recently relaxed to 1-metre with masks on at all times, which made it significantly easier for my supervisor to teach me how to use structural biology equipment. Later this month I will be demonstrating these techniques to undergraduate summer camp students and supervising an undergraduate placement student – both firsts in my career. Apart from eating our lunches at desks spaced 2-metres apart, the daily work routine is becoming relatively normal. I do look forward to the day we can attend seminars and lectures in-person rather than online. However, I will say that the switch to online talks gave me the courage to try a new profession – teaching! Overall, I’m thankful that my transition from working at home to experimenting in the lab has been smooth. I hope my story encourages others who may have some anxiety about returning to work to not be afraid and to believe in themselves!
The article below is written from the point of view of PhD students in the United States. It describes the experiences of Black, Indigenous and people of colour within a particular field of research but it is an informative framework to consider issues of importance for postgraduate researchers in other disciplines and for the wider postgraduate research community.
Hi my name
is Ogechi, I am currently a first year PhD psychology student at Birkbeck and
an NHS Mental Health worker. My previous
studies are Master of Public Health (MPH) and BSc (Hons) Biomedical Science.
My PhD journey has been great so far, acquiring new skills and knowledge in psychology. I have been very lucky to be a part of the Department of Psychological Sciences, and am grateful to my supervisor and mentor. My research is on medical help-seeking behaviours amongst the BME community which crosses over to my line of work in the NHS on a daily basis.
As well as registering my systematic review on Prospero, lecturing about what I do in work gave me a sense of joy to share the knowledge and attitude around how health psychology interventions are practised in NHS and NHS Mental Health settings. In these uncertain times, it can be quite challenging, but it is very important that everyone looks after their mental health during this time.
Balancing work and studies can be quite challenging as a mature student, but I’m determined that this will bring more benefit to the world of research and the field I am heading towards. COVID-19 has brought the world to a standstill and has shown us the possibilities of adjusting to this potential new normal. It has also highlighted the health inequalities and disparities seen in the BME community which is in line with my research, medical help-seeking and the barriers experiences by this group making it very relevant to today’s climate.
I hope the
next time I write another blog post, it will be me sharing my published
systematic review for all of you to share and read.
The Public Engagement Team provides advice, opportunities, and funding for engagement with research. The team was established to support Birkbeck’s commitment to making research results available to society. By working together with researchers, external partners, and organisations, we aim to create opportunities for knowledge exchange.
We would like to let researchers know that applications for our annual Public Engagement Awards are now open. This award recognises the inspiring public engagement work undertaken by Birkbeck researchers at various levels of their career, including doctoral researchers.
The team will be attending a research networking event hosted by the Birkbeck Institute for Social Research on Thursday 6th February, 12-2pm (G04, 43 Gordon Square) if you’d like to speak to them in person. You can contact firstname.lastname@example.org for more details or to reserve a seat.
Birkbeck doctoral researcher Jessica Massonnié(Department of Psychological Sciences) speaks about the development of her research exploring children’s perception of classroom noise which has led to collaboration between teachers and researchers. Jessica was recently the winner of of the PhD/ Early Career prize for at Birkbeck’s 2019 Public Engagement Awards for her entry ‘Noise Annoyance in Schools: is it a Fatality?’.
About my research
Public engagement always reminds me of who I am working for. I feel lucky to have quite an applied research topic: noise in schools. I am trying to understand how noise impacts pupils’ performance and well-being, and why children vary in their reactions to noise.
During the first year of my PhD, I designed “lab studies”: I prepared school exercises that children would do, as well as specific types of noise to display through headphones – hearing someone telling a story, or a more general babble noise. I assigned children to these different noise conditions and compared their performance in silence and in noise. This process had the advantage of fitting with the standard rules of scientific experiments, because it was highly controlled. But I often felt like a sales person when I was presenting the project to schools in order to try and convince them to participate. Although teachers and children were interested in the studies, and were enthusiastic about their participation, they were not directly involved in the creation of the research. All I could offer were some goodies to thank them for their participation, and feedback about the results several months later.
I met Philippe Frasseto by a happy coincidence, when I was doing a training session about research methods in Psychology in Paris, for an external organization. Over a coffee break we discovered that we were both interested in the issue of noise in schools. As a teacher, he was at the front line, experiencing high levels of noise in his school, which he found pretty stressful for himself and for his students. He had the initial idea of creating visual displays that would raise children’s awareness about noise, by using a visual code (green for low noise levels; orange for moderate; red for high). We wanted to embed this tool within a broader workshop, introducing children to the concept of sound, noise, and music, and to the harmful effects of loud noises. Philippe and I were also involved in yoga and mindfulness practice, and having reviewed the scientific evidence for such practice, we decided to include it as a second type of workshop the children could benefit from. Yoga and mindfulness have the potential to calm children down, lower their stress levels, and make them more aware of their environment.
The actual implementation of these coffee-break ideas was made possible by the combination of several factors: Philippe’s contacts with an artist, sound engineer, and yoga teacher; the enthusiasm of his “inspector” (within a French equivalent of Oftsed), who helped us to recruit schools; the research support from Birkbeck and my supervisors (Denis Mareschal and Natasha Kirkham); and funding support from the Economic and Social Research Council, the Centre for Brain and Cognitive Development of Birkbeck University, and the Rectorat de Corse.
A collaborative approach
We designed the study together, and there was a lot of back and forth between the lab, and the school as we defined the main outcomes that we wanted to measure: noise levels; school performance; attention and memory skills. I then proposed some tasks and activities based on the available scientific evidence, and these were revised based on feedback from Philippe and participating teachers. This got me out of my comfort zone, by openly presenting the project before having finished it, or having any results. We were mostly focused on the collaborative process, coming up with a project that would benefit all of us.
I would say that one of the greatest challenges was to find a protocol that would answer the teachers’ interests and be flexible enough to fit with their everyday constraints, while still allowing us to conduct stringent analyses and derive reliable conclusions.
As Philippe says: “ The greatest challenge was coordination, to engage teachers and children and create a research project with classrooms that would not disturb their usual way of functioning.”
We followed the children over a 6-months period, collecting our assessments before, and after the interventions. The study was conducted in Corsica, an island in the south of France. I had the chance to be totally immersed in the project, living there for 3 months, during the key stages of the project. I was regularly meeting up with the team, visiting schools, observing the interventions, carrying out debriefing sessions with the children.
Continuation of my research
In the longer term, this research has allowed me to perceive scientific and experimental studies from a new angle, and I have become more involved in emerging fields in mind, brain and education, as I foster collaboration between teachers and researchers.
I am currently working with Michael Hobbiss (UCL) and Tracey Tokuhama–Espinosa (Harvard University, Flasco) to create an online platform connecting teachers and researchers willing to design scientific studies together. Feel free to read Michael’s blog post, and to get in touch with us, if you would like to participate, or to have more information.
On Thursday 2 May, Birkbeck doctoral students took part in the 2019 Three Minute Thesis Competition. Gabriella McGrogan was the overall winner and received a £500 prize.
2019 3MT Competition
On Thursday 2 May around 70 people attended the Birkbeck Three Minute Thesis Competition. This competition honed and tested the presentation skills of the PhD students who took part, and provided an exciting tour of a diverse range of our current doctoral research. Despite only having 3 minutes for each presentation, contestants (representing all Schools at Birkbeck) were able to convey their research in an insightful and meaningful way, and the event provided both celebration and insight arising from their achievements.
This event, which was held in the Clore Lecture Theatre, was the third time the Three Minute Thesis competition has been run at Birkbeck.
Winner: Gabriella McGrogan
During the exciting series of talks from Birkbeck PhD students, Gabriella McGrogan (Department of Law) was chosen as the overall winner for her compelling presentation ‘Against our Community Standards’- “Outsider” Witnessing of Atrocity and Social Media Censorship’. Gabriella is in her first year as a doctoral researcher in Criminology.
Gabriella told us her reaction on winning the competition:
“It was actually quite a shock! I went last, and had spent the short break prior to the competition repeating what I wanted to say over and over. I was a little overwhelmed by the brilliant calibre of all of the other contestants.
Not only was competing an excellent opportunity to practice public speaking (which I find daunting) but winning, and the conversations invoked afterwards, has helped to give me confidence that my work is interesting to a wide audience and may prove important. It has definitely encouraged me to consider how I can present it for public engagement again in the future.
Whilst competing is a little terrifying, the training and support of everyone at BGRS makes the experience much more comfortable – definitely have a go! It has helped me to condense a plethora of ideas and research into a manageable and coherent explanation. It’s also so enjoyable to engage with students from other departments and made me very proud of the diversity and innovation happening at Birkbeck.”
The overall winner and runner up were chosen by a panel of 5 Birkbeck experts (one from each of Birkbeck’s Schools) but the audience also played a key role and were asked to use their votes to choose a People’s Choice winner. The People’s prize was awarded jointly to ‘Lexter Woodley’ (Department of Geography) for her talk ‘An exploration on how female breadwinner couples experience and manage their home lives’
and to Pernelle Lorette (Applied Linguistics and Communication) for her presentation ‘How do you think they feel? Cross-linguistic and cross-cultural perception of emotion’.
2019 3MT Talks
A list of all the competitors and their talks is provided below.
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.