Another Cell-ebration

Posted on 3 September, 2015 by Kevin

Last year we brought you details of the inaugural CBCB Symposium. In July the second CBCB symposium was held, and today we hear from the organisers, Kevin Waldron and Heath Murray, about this latest successful event.

The idea for an annual Centre for Bacterial Cell Biology (CBCB) symposium was originally conceived in 2013, and aimed to showcase both the high quality and the immense breadth of research activity that goes on in this unique Centre. It would also be an excellent opportunity to bring together the CBCB research community based in both the Medical School and in the Baddiley-Clark building to discuss their work and build future collaborations.

It wasn’t long after our 2014 Symposium was over when the organising team (Bernie Shaw, Heath Murray, Kevin Waldron and Jeff Errington) began planning for this year’s second event. Obviously we were delighted with the success of that first meeting, but of course it also applied a little pressure on us as organisers; this year’s event had to achieve a similar level of success. Fortunately, the feedback we had received from the 2014 event included a number of constructive suggestions from the CBCB community about how we might be able to improve the Symposium, and we tried to incorporate as many of these ideas as possible.

One of our postdoctoral researcher speakers, Yoshi Kawai, addresses the Symposium audience on the subject of L-forms

One suggestion was to include a number of more junior speakers in the Symposium Programme as well as PIs, and we are grateful to those postdocs who volunteered to present their work to the CBCB audience. Alexander Egan told us about his research in the Vollmer lab on the proteins that coordinate biosynthesis of the cell envelope during growth and division. Yoshi Kawai of the Errington lab explained how L-forms, bacteria that lack their cell wall, can be produced in the lab and how they propagate in a manner independent from the known bacterial cell division machinery, as well as speculating on their implications for early life forms on Earth. Marcin Dembek of the Salgado lab contrasted the mechanisms that govern sporulation in Clostridium difficile, a pathogen that primarily causes infections via spores, and the model organism Bacillus subtilis. Finally Didier Ndeh described his research in the Gilbert lab on how gut bacteria degrade the most structurally complex dietary polysaccharide known, rhamnogalacturonan II. PI speakers covered further topics relating to antibiotic discovery and their mechanisms of action and synthetic biology.

In addition to our CBCB researchers, we also again invited two high-profile external speakers. The day started with Mark Leake (University of York) who told us about his research using state-of-the-art microscopy for in vivo imaging of single molecules within the bacterial cell. And the Symposium was concluded by John Helmann (Cornell University) on the subject of transcriptional stress responses in one of CBCB researchers’ favourite model organisms, Bacillus subtilis.

Poster prize winner Lauren Drage

Another of the suggestions that we incorporated into the Symposium schedule this year was a poster session, which was accompanied by light refreshments (of course!) immediately after the day’s talks. We had a great turnout, with more than 20 posters on display, and the session generated a lot of lively scientific discussion. Again the Symposium organisers are very grateful to all those members of CBCB who participated in the poster session. We awarded three poster prizes, with congratulations to winner Lauren Drage for her excellent poster describing her research in the Aldridge lab looking for biomarkers for diagnosis of urinary tract infections, and to our two runners-up, Martin Sim (Wipat lab) and Clare Wilson (Errington lab); and of course thanks to our poster judges, Lucy Eland and Yulia Yuzenkova.

Finally, we all got to enjoy an informal barbecue dinner and drinks, where the science discussions could continue into the evening.

Jeff Errington and John Helmann in post-symposium discussions

Planning has already begun for next year’s Symposium, which will be held on the 8^th July 2016, and will feature two more external keynote speakers, Christine Jacobs-Wagner (Microbial Sciences Institute, Yale University) and Prof. Tracy Palmer (Molecular Microbiology, University of Dundee). We welcome your feedback too, so if you attended this year’s Symposium and you have any suggestions about how we might improve next year, please let us know.

Discovery at the Discovery Museum

Aside

Great Hall

Ready to replicate the success of last year’s Away Day, it was en masse outing time for ICaMB again! Time to find out who all the new faces are, and to find out exactly what that person you have a ‘hello and a nod in the corridor’ relationship with actually does at the bench all day. This year we headed to the Great Hall of the Discovery Museum. Despite the leaking roof caused by the downpour outside and the sometimes dodgy acoustics the day was still a success.

Serious faces, this is science

ICaMB is a fast paced, constantly evolving institute. Everybody is busy with their own research, making a break and a get-together once in a while a vital part of reminding ourselves of the vast range of expertise and diverse set of interests beavering away in our labs and offices. The answer to that tricky problem or that elusive technique is quite possibly just a few yards away.

But also fun!

With that in mind, this year’s Away Day felt particularly important as we welcomed 8 new academic groups to ICaMB from CAV (Campus for Aging and Vitality) as well new IRES fellows and a list of other recent recruits. Drs Victor Korolchuk and Gabi Saretzki from the CAV both spoke at the away day about their interests in neurodegenerative diseases and the role of oxidative stress in the ageing process.

As ever the day was kicked off by the Institute director, Bob (Professor Robert Lightowlers), who gave us a taster of ICaMB’s growth and success stories over the past year. Without breaking into the tune of that well known Christmas song; 7 Vacation Studentships, 6 BBSRC awards, 5 MRC awards, 2 Wolfson awards, 2 Senior Investigator awards and 1 Henry Dale ………. Not to mention all the promotions, outstanding research papers and commercial contracts = 1 happy Bob.

A cell-tastic morning then ensued: the completely dispensable nature of bacterial cell walls (Professor Jeff Errington); the role of NF-kB in the pathogenesis of lymphoma (Dr Jill Hunter); and the cell death independent functions of inhibitors of apoptosis (new IRES recruit Dr Niall Kenneth). The session was wrapped up by Dr Paula Salgado summarising 3.5 years of structural C. difficile research in 15min. Some feat Paula!

Of course just as last year, an absolute highlight of the day were the six, animated, three minute thesis presentations by our brave PhD students …….. Soon to be followed by the look of horror on several Professorial faces when it was suggested by PAN!C that at next year’s Away Day we have a session of 3 minute PI pitches! We can’t ignore the demands of our PhD students now can we? And congratulations to Mandeep Atwal from the Cowell/Austin lab who against steep competition was awarded the prize for best three minute thesis.

The possibilities of alginate bread?

A spot of oxidative stress and the evolution of peroxidases by Dr Alison Day, and some lunch completed the morning’s discovery. Though half an hour later and Dr Peter Chater had us all wishing we’d had an alginate packed lunch (and a go with the model gut!). Perhaps the Pearson lab can cater next year’s event? If it’s good enough for the One Show it’s good enough for the ICaMB Away Day.

A major focus of the Away Day is not just to learn about the breadth of exciting research carried out in our institute, but also to learn all about the very latest techniques and expertise ripe for exploitation. This year the focal point of new techniques came from Dr Alex Laude and the Bio-Imaging facility, with some beautiful images and super resolution microscopy techniques, which again left a number of the audience wanting a turn!

An afternoon transcribing and translating with Dr Danny Castro-Roa; learning about how the crucial nature of cell polarity means we really don’t mix up our arse from our elbow (thank you new IRES recruit Dr Josana Rodriguez); and last but by no means least, how on earth all that DNA manages to faithfully copy and repackage itself time after time from yet another new recruit, Professor Jonathan Higgins.

This completes our diverse and entertaining line-up, just leaving enough time for complementary wine, and the amusement as speakers and audience alike embarrass themselves at the ICaMB quiz (and I hear also in the pub afterwards).

More ICaMB winners! Doctoral Thesis Prize Success.

Posted on 15 July, 2014 by Suzanne

‘The Faculty of Medical Sciences Doctoral Thesis Prize is a mark of recognition of an outstanding level of achievement by the end of a research doctorate. Prizes are awarded biannually on a very limited basis following nomination by thesis examiners.’ Dr Tim Cheek, Post Graduate Tutor

Doctoral Bling!

Prizes were first awarded in 2009 and included two ICaMB students, Holly Anderson and Monika Olahova. This was followed in 2011 by David Adams and in 2012 by Graham Scholefield. However, 2013, was an absolute triumph, with three out of only five potential Faculty Prizes being bestowed on theses submitted by ICaMB students. Dr Andrew Foster from Professor Nigel Robinson’s Lab (currently a post-doc in the Robinson lab in Durham), Dr Fiona Cuskin from Professor Harry Gilbert’s lab (currently a post-doc in the Gilbert lab) and Dr Kristoffer Winther from Professor Kenn Gerdes lab (currently a post-doc in Gerdes lab). With their new roles keeping them busy, our 3 winners only just managed to get together recently to be presented with their medals by the Dean of Post Graduate studies. Andrew and Fiona tell us about their past and present research.

Dr Andrew Foster

Abstract by Dr Andrew Foster. Achieving metal selectivity is often more difficult than one might first imagine as the inherent chemical properties of metals often mean that a metalloprotein will preferentially select an incorrect metal over a correct one.

My PhD studies involved understanding metal selectivity among a group of proteins called metal sensors. These metal sensing, transcriptional regulators control the expression of genes of metal homeostasis and therefore influence the metallation of other proteins within the cell. I characterised a novel nickel sensor InrS and showed for the first time how metal selectivity could correlate with relative metal affinity across a class of proteins. The nickel sensor InrS has a tighter nickel affinity than the other sensors within the cell, thus InrS responds to nickel activating

Nickel

a nickel efflux gene so that the buffered nickel concentration within the cell does not rise high enough to mis-populate the sensors of other metals.

During my PhD studies our lab moved from Newcastle to Durham University but I remained registered at Newcastle. This move was obviously very disruptive but at the same time made me more focussed and determined to make a success of the work in spite of the disruption.

Busy Andrew

I am currently working with Professor Nigel Robinson at Durham University. My current work seeks to understand how the affinity of a metal sensor relates to the available concentration of the sensed element within the cell. Our model system involves the nickel sensor I discovered, InrS, and nickel supply to hydrogenase, a nickel enzyme capable of hydrogen production. Metal supply to enzymes will be a key biotechnological challenge as we seek to utilise microbial factories for the production of fuel and other useful products.

Dr Fiona Cuskin.

Abstract by Dr Fiona Cuskin. The use of complex carbohydrates in the food industry is wide and varied; a few examples include the use of polysaccharides and oligosaccharides as gelling agents, emulsifiers and fat replacements. Small oligosaccharides are being increasingly used as prebiotics for the vast array of “friendly” bacteria in the gut of both humans and animals. The addition of small fructose oligosaccharides by the food industry into yoghurts, amongst other foods, has been shown to promote a healthy gut flora, which in turn has a positive effect on the host gut health and immune system.

Having been in the lab for just a month my supervisor abandoned me and moved to America. Not to worry I tracked him down and moved there too for a few months. The subject of my PhD was to investigate how bacteria use enzymes called glycoside hydrolases to breakdown complex carbohydrates for utilisation. Part of this was to characterise a glycoside hydrolase that degraded the fructose containing polysaccharide, levan.This glycoside hydrolase contained two

Happy gut?

modules, the catalytic module and non-catalytic carbohydrate-binding module (CBM). CBMs are usually attached to enzymes that catalyse the breakdown of recalcitrant insoluble substrates to help target the catalytic module to the right carbohydrate. However, the CBM characterised in my PhD bound soluble fructan polysaccharides and potentiated the activity of the catalytic module ~100 fold. This work adds valuable knowledge to how bacteria breakdown complex polysaccharides. This knowledge can be exploited to better inform the use of prebiotics and to also choose enzymes that are efficient for the production of small oligosaccharides from polysaccharides.

We are very proud of our current winners. Who will be in the next batch of Doctoral Thesis Prize winners, adding to a growing list of ICaMB winners?

IPA Update: What’s it like to work for Nature?

Posted on 20 June, 2013 by Neil

By the IPA committee

Thursday 23^r^dMay saw the IPA’s second Science Lives Seminar. Following on from our first talk about the realities of establishing an independent research group in academia, the IPA wanted to explore what else a post-doc can do. What are our alternative careers?

To start answering this question, we invited Dr Andrew Jermy, a senior editor at Nature, to give us a talk on his career in journal editing.

Postdocs waiting to hear either (a) how to publish their papers in Nature or (b) how to work for Nature

Dr Jermy’s talk started by illustrating his personal experience. Like all of us, he completed a PhD in the biological sciences field and then did two short post-docs before he decided to leave academia to start a career in editing, first at Nature Cell Biology, followed by Nature Reviews Microbiology and now more recently at Nature. To achieve this, he used his networking skills as he had met someone currently working for Nature at conference. Hint, keep building up your contacts! It was very interesting for us all to understand the motivations that brought him to try a new and alternative career. “Getting bored of waiting for westerns to come out of the developer”, he repeated several times. Maybe he is not the only one?

Dr Jermy also described the several different job entry levels possible at Nature, something that applies generally to many of the larger scientific journals. We now have a much better idea of what working for a scientific journal actually entails and where we could slot in. He pointed out that in this kind of career you need a keen interest in all science, as well as being constantly on top of the cutting edge research in your specific editing field. The ability assimilate information quickly and handle up to 40-50 papers per month, while travelling to conferences and universities is also a must. On the other hand, Dr Jermy underlined that his job is not a simple 9-5 job. However, he can work from home and with the advantage of a permanent position as well as opportunities for career progression, this can make his career more family-friendly than what we post-docs are used to. Ultimately, this career seems ideal for those post-docs who no longer enjoy working at the bench, but still enjoy the other aspects of scientific life, such as reading, writing and networking at conferences.

Andrew demonstrates the Nature ‘secret handshake’

There was however much more to Dr Jermy’s talk than the career side… he gave practical tips to post-docs who want (or maybe its better to say wish) to submit a paper to Nature; from the title to the covering letter, from the abstract to the “style” of writing. Dr Jermy made a clear point that the philosophy of the journal is not to bin 90% of the papers they receive, but to focus on helping the top 10% of the articles emerge and get published. Finally, did you know you can send a pre-submission enquiry to Nature, asking if your scientific results are of interest before going through the long and painful online submission? Helpful for everyone!

After the seminar there was an informal chat-session, useful for post-docs to ask questions in a relaxed environment, helped of course by a beer in our hands!

The IPA wishes everyone a nice Summer and we will see you all for our next social event: a barbecue in September, a perfect occasion to give a warm welcome to new post-docs joining ICAMB as well as for all the current post-docs and final year PhD students to get together for the beginning of a new academic year.

Updates will follow on the website.

IPA Committee

IPA is run by Postdocs, for Postdocs. Get involved!

Links

IPA Facebook page: https://www.facebook.com/groups/462376430446559
Institute for Cellular and Molecular Biosciences: http://www.ncl.ac.uk/camb/
Newcastle University: http://www.ncl.ac.uk/
Nature Journal: http://www.nature.com/nature/index.html
Andrew Jermy’s twitter page: https://twitter.com/jermynation

IPA Update: Pub Quiz and Nature Editor visit

Posted on 9 May, 2013 by Neil

April 27^th saw the ICaMB postdoc association (IPA)’s second social event with a Friday Night at the North Terrace pub. Here the IPA committee describes the evening and upcoming VERY IMPORTANT EVENT

By the IPA

All those involved with the IPA social evening and pub quiz thought it was a terrific success, with a good turn out of Postdocs and final year PhD students letting off some steam after their hard week at work.

The pub quiz. Postdocs hard at work.

It was a great night and we all enjoyed the drinks and delicious North Terrace food, including generous portions of tasty potato skins and pizzas, which were very much approved of (even by Alessio). While some got serious over a game of darts, others chatted over pints – however the best part of the night was by far the PUB QUIZ.

Who is this man? One of the tough questions at the IPA pub quiz. Fortunately everyone got this one right.

The IPA committee prepared the questions with an international angle that went down well with our multi-national postdoc community. It was amusing to see the quality team-work used to answer questions on intercontinental cuisine and different languages. Particularly with the question “how does a Geordie spell the word home?”* Although the Italian Quiz Master occasionally struggled to read the questions in a ‘proper’ English accent, this just kept the postdocs on the ball! We had 4 competing teams, with every team randomly formed with different lab members, so everyone got to know and chat with new people.

Victory went to the ‘baby PINK team’ after winning the tie break question with their closest answer to “What is the length of the River Nile?”** Not easy! Their 1^st place prize was North Terrace Deli sandwich vouchers. Yummy!

The result. A close run thing.

The IPA committee is looking forward to our next social; a barbecue in September! We are in the process of seeking a good venue!

Before this we have our next Science Lives Seminar with the invited Nature Microbiology senior editor Dr Andrew Jermy giving an exclusive talk to our Postdocs and final year PhDs. Get Thursday 23^rd May 4pm blocked now in your busy diaries – you can’t miss hearing about how this former postdoc established a career in editing for one of the most renowned journals in our field. We, as postdocs, need to keep our career options open, and this does not seem like a bad one! The PIs are perhaps even more excited than us about his visit, not that they are invited to the seminar (haha unlucky), but we can expect some serious sweet-talking in Andrew Jermy’s tight schedule of meetings with ICaMB academics the following day! We all know that PIs don’t have much time, but all of them have managed to rearrange their outlook calendars for this guest!

* Answer is ‘yem’
** Answer is 6,650 km (4,130 miles)

If you have any suggestions for themes for future events please get in touch with the IPA committee.

Links

The IPA: Run By Postdocs, For Postdocs!

Posted on 14 March, 2013 by Neil

The ICaMB Postdoc Association (IPA) was created in 2012. It’s motto is ‘Run by postdocs, for postdocs’. Here we have asked the IPA committee to describe what they do and some of the events they have been organising.

by the IPA

Post-docs are the engine room of any lab. Let’s face it, we are the ones at the bench doing the experiments that get into those high impact publications (hopefully!). However, in many institutes we are also the forgotten proportion of the scientific workforce. This is something we, the post-docs of ICaMB, are trying to change. Six of us (Alessio, Claire, Jackie, Jill, Luisa and Matt) formed the ICaMB Post-doc Association (IPA) in mid-2012 with a view to bringing the post-docs of our institute together and giving us a voice. Yes, we want to talk to each other about our science and share our ideas and expertise but the IPA is also about establishing new friendships and having a laugh too.

One of the main aims of the IPA, is to address some of the challenges faced by post-docs today – realistically we know that not all of us will make it to Principal Investigator (PI), or even necessarily want to. So, we have started a seminar series looking at ‘Science Lives’ in which we invite speakers from diverse jobs to talk to the post-docs about their career choices after post-docing. Our first speaker was ICaMB’s very own, Heath Murray, a Royal Society Fellow based in the CBCB. He gave a very honest account of making that transition from post-doc to PI. Heath discussed his personal highs and his love for science, but also the difficulties he faced when applying for Fellowships, together with the challenges he now faces when carving out his own independent lab.

The next speaker in the series is Andrew Jermy on May 23^rd at 4pm. Andrew is the senior microbiology editor at Nature and will come to talk to us about a career in editing and publishing at pretty much the biggest journal in our field. Many of the post-docs in ICaMB have told members of the committee that editing is something they would like to learn about as they consider other career options in science. On the other hand, many of the academic staff are also very excited by the prospect of Andrew coming to ICaMB so they can all show off the great science being done here!

An IPA Social

The IPA is also about the post-docs getting to know one another away from the lab…we all like to let our hair down by having a party and some of us even enjoy a glass of wine (or two!). Our first event was a social held at the Forum Café in the CBCB where the ICaMB post-docs based in the Medical School and those in the CBCB could get to know each other. We don’t often get lots of time to interact, being in separate buildings, and everyone seemed to really enjoy themselves!

Our next social event will be at the North Terrace Pub on April 26^th starting at 5pm – expect lots of food, drinks, a pub quiz and lots of other fun and games!

The IPA Committee, from left to right, Alessio, Claire, Luisa, Jackie, Jill and Matt

If you have any suggestions for themes for future events please get in touch with IPA committee (ipda@newcastle.ac.uk).

Find the IPA on facebook and look out for the new look ICaMB website coming soon where the Post-docs will have their own section!