REF 2014: Hurrah, we did really well – but is it really a good exercise?

Posted on 18 December, 2014 by Neil

By Neil Perkins

And so the REF 2014 results are upon us. If you listen closely you can hear academics all around the country trying desperately to find the method of expressing the results that most favours their own Institution (or downplays bitter rivals). Of course, this is a technique commonly used in publishing research articles so there is a lot of expertise in this area.

Anyway, however you wrangle the figures in ICaMB we think we’ve done pretty well (whisper it quietly, possibly better that we expected when our return was submitted).

Most ICaMB scientists went into UoA5 Biological Sciences, although a number of us also were included in the UoA1 (Clinical Medicine) and UoA3 (Allied Health Professions, Dentistry, Nursing and Pharmacy) submissions. In fact UoA5 contained only ICaMB members and was written and submitted by ICaMB members. So this is the right place to say congratulations to ICaMBs Professor Brian Morgan who masterminded, with the help of Amanda Temby, our UoA5 submission. We hope Brian has recovered from the ordeal by now.

So how did we do? If we go by the Times Higher Education table then Newcastle (i.e. ICaMB) came joint 5th overall. However, in the clearly much more important ‘Output’ table we come 2nd in the country!! I suspect that’s the one that will end up on the front page of our website. Our ‘Impact’ submissions dragged us down a bit. I remember the meetings where we struggled with the tight definition used for ‘Impact’, something not easy for an Institute that really focuses on fundamental science. We work on important and relevant subjects but the impact of this on medicine or biotechnology is often a few steps removed.

The Time Higher Education raking for Uo5, Biological Sciences. The most important section (cough) is highlighted.

It would be remiss of me not to point out that our sister UoA submissions in Newcastle also did well

UoA1 Clinical Medicine) came 9th out of 31, UoA3 (Allied Health Professions, Dentistry, Nursing and Pharmacy) was 15th out of 94 while Uo4 (Psychology, Psychiatry and Neuroscience was 9th out of 82.

Lies, damned lies and…..

I like this viewer put together by City University London

http://www.staff.city.ac.uk/~jwo/refviewer/

And if I tweak the parameters in just the right way……

……. Hurrah! Second again!

A big BUT

OK, if we were to be slightly self-critical it could be noted that our Uo5 submission had, relative to many Institutions, a relatively low number of staff associated with it, although this is the substantial majority of the people in ICaMB. It was very much the ICaMB submission, with many others in the Faculty of which we are a part, going into UoA1, Clinical Medicine.

However, this is also an exercise in who decodes the rules most successfully (and there was head scratching at times over ambiguities and what it really meant). So what better time, after having done well, so it cannot be said to be sour grapes, to repeat that the REF really is a bad way to go about assessing the relative research strengths of UK universities. The arguments for why this is the case have been aired before in detail (also here) and I will not go over them all again here. I think that every academic I speak with agrees with this. People involved with this work phenomenally hard at all levels in the university but it has to be said that it is a colossal, time consuming juggernaut of dubious worth. Speaking to colleagues who were members of REF panels, I was horrified at just how many papers they were expected to read. You do not need to go that far outside my area of expertise before my judgement becomes quite superficial. Quite how anyone thinks this process leads to an unequivocal assessment of research quality is beyond me. However, as an entire industry seems to have grown up around the REF, incentives for change are few.

So what could replace it? Well as academics we are judged and assessed continually as part of or our normal jobs. Our grant applications are rigorously reviewed. Our papers are refereed in detail. There are citation indices and download statistics showing if these are actually being read. While individual applications or submissions are subject to some randomness, over an Institution, over time, these are the measures that really assess how well we are doing. The information for these is already out there and would be relatively quick to compile.

Of course there are caveats to this. Different disciplines receive different levels of funding or are cited lightly relative to others. But it should not be beyond the wit of the academic community to come up with different weightings for different subject areas. Wouldn’t it be refreshing if someone at the top came out and said, ‘never again, there has to be a better way of doing this’. However, I suspect this might be wishful thinking. I’ll just fearfully wait for the email saying “Neil, about REF 2020, Brian did a great job last time and we’d really like it if you could…..”

The opinions expressed in this article are those of the author and do not reflect those of Newcastle University

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).

ECRs at ICaMB – Green transcription: how studying Cyanobacteria could change the world

Posted on 23 October, 2014 by Paula

In the latest of our series on the Early Career Researchers of ICaMB we asked Dr Yulia Yuzenkova to tell us about her research and the route that took her from a PhD in Moscow to being awarded a Royal Society University Research Fellowship in Newcastle.

: Dr Yulia Yuzenkova

My early training was in Moscow, firstly as an undergraduate at Moscow State University and then for a PhD from the Russian Academy of Sciences. However, during my PhD I moved to the USA to study at the Waksman Institute (Rutgers University) with Prof Konstantin Severinov, where I was also a postdoc. My work in the laboratory was dedicated to the molecular mechanisms of inhibition of bacterial transcription by antibacterial peptides and small proteins from viruses. Transcription is the first step and critical regulatory checkpoint of gene expression. In all living organisms transcription is performed by multi-subunit RNA polymerases (RNAP). The central role of transcription in cellular metabolism and the presence of domains specific for bacteria make RNAP an obvious target for antibiotics. Yet, for decades, only one inhibitor of RNAP, rifampicin, has been used in the clinic to treat tuberculosis, while only recently, in 2011, lipiarmycin (fidaxomicin) was approved to eradicate Clostridium difficile. Two is a very small number, but this indicates that there is a good probability of finding new drugs that also work by targetting RNAP. Apart from their clinical significance, antibiotics and inhibitors of transcription in general have been proven to be very efficient molecular tools (see “RNAP details” below for more info).

During my second PostDoc in the lab of Prof Nikolay Zenkin in Newcastle, I have focused on the mechanisms controlling the fidelity of transcription. The copying of genetic information by RNAP is far from being absolutely precise, and RNAP whimsically dislikes reading some DNA sequences, resulting in ‘pauses’. RNAP is able to correct its own mistakes using a proofreading mechanism and the help of small proteins called transcript cleavage factors (explained in detail below). It seems to be important to have at least one cleavage factors; otherwise, the RNAP molecules stop, resulting in “traffic jams” as trailing molecules keep moving and bump into it.

Batch culturing of cyanobacteria

It was therefore a big surprise for me to learn that one large group of bacteria, cyanobacteria (details below), do not encode anything even remotely resembling cleavage factors. I started to look for an explanation for this extraordinary fact. Are there any factors that might compensate for the absence of cleavage factors? Is cyanobacterial RNAP so accurate and at the same time processive that it does not need them? In searching for the answer, I realised that almost nothing is known about the molecular details of transcription in cyanobacteria, and so I decided to apply for a Royal Society University Research Fellowship to try to answer these questions.

Microscopy image of membrane-stained cell
of Synechocystis sp 6803

In performing preliminary experiments for my application, I became fascinated with cyanobacteria, as they are truly amazing organisms to work with. They are the only prokaryotes that exhibit the classic circadian clock, and are the bacteria with the most complex intracellular organisation. Moreover, they are one of the most ecologically important groups on Earth. They live everywhere where sunlight is available and produce 30% of atmospheric oxygen; some can even convert inert atmospheric nitrogen into a digestible form.

The 2D projection of the membrane structure of cyanobacterium reminds me of a labyrinth

With my Royal Society University Research Fellowship I am planning to investigate the molecular details of the transcription machinery and will look for novel transcription factors that regulate this process. I am also going to test the metal requirements of cyanobacterial transcription, because metal composition of cyanobacterial cells is very different from other bacteria to suit the need of photosynthesis. Another fascinating question is how fast in the cyanobacterial cell, which is tightly packed with photosynthetic organelles, can molecules find their way through the membrane labyrinth.

The nitty-gritty science:

RNAP in detail:

Inhibitors of RNAP as molecular tools for understanding its functions. A wide range of targets of known inhibitors is mapped on the structure of bacterial RNAP. We contributed to understanding the modes of action of inhibitors marked in bold.

Studying the antibiotics and inhibitors modes of action have helped us and other groups to discover previously unknown functions and structural domains of RNA polymerase. For example, work on rifampicin shed light on geometry of the RNA exit path, long before the crystal structure of RNAP was solved. Moreover, streptolydigin led to the discovery of the novel catalytic domain, while microcinJ25 confirmed the proposed entry channel for substrates and tagetitoxin provided insight into the mechanisms of RNAP translocation along the template.

Newly synthesised RNA participates in the proofreading in a ribozyme-like manner. This method of proofreading, probably a remnant from the distant past, is extremely slow. To accelerate proofreading (and to escape from pauses), all 3 domains of life encode non-homologous, but very similarly folded, small proteins called transcript cleavage factors. In E.coli, GreA is an example of a protein that fulfils this role. Some bacteria have several homologs of GreA (in E.coli there are at least 6). It seems to be important to have at least one, because if these cleavage factors are depleted in the cell, the RNAP molecules on the actively transcribed genes stop, obstructing transcription, but also the chromosomal replication machinery moving along the same DNA.

Cyanobacteria:

Cyanobacteria have been hailed as future photobioreactors. Indeed, when supplied with little more than tap water and light, engineered cyanobacteria can produce all sorts of compounds from sunscreen to biofuels. Cyanobacteria can also be used for environmental applications such as greenhouse gas fixing and cleaning water from industrial pollutants. These initiatives, however, are compromised by slow growth of cyanobacteria and limited knowledge of their basic biology. By putting more effort into research, the potential abilities of cyanobacteria can eventually be harnessed on the industrial level. With this we could make a giant leap towards a future “greener” economy. With a little bit of imagination, it is not hard to envisage cyanobacteria helping humanity to colonise new worlds, and to permit them to inhabit the first lunar and martial greenhouses in not so distant future.

Dr Yulia Yuzenkova’s ICaMB website: http://www.ncl.ac.uk/camb/staff/profile/yulia.yuzenkova

Royal Society University Research Fellowship: https://royalsociety.org/grants/schemes/university-research/

Recruiting the next generation of ICaMB scientists

Posted on 30 September, 2014 by Neil

In 2013, we created the IRES fellowship scheme to recruit potential new Principal Investigators to ICaMB. Now Faculty wide and renamed the Newcastle University Research Fellowships (NURFs) a new round of recruitment has just opened. Here, Neil Perkins reflects on the thinking behind the IRES scheme and why recruitment of early career researchers is so crucial.

It’s a moment for sober reflection when you realise that you can no longer be classified as a ‘young scientist’ and have now become part of a problematic group of rapidly ageing professors. Although when Bob Lightowlers, the ICaMB Director, told us a few years ago that we only had one Principal Investigator (PI) under the age of 40 I think we were all a bit shocked. Only one? Speaking as one of that cohort of over 40’s, I would of course defend our ability to still perform cutting edge science and stay on top of the latest developments in technology and social media. Well some of us anyway. However, as with many things, balance is important. Early career (to use the formal term) PIs bring vibrancy and energy to a department, generate new ideas and very importantly also challenge ingrained departmental behaviour. At least that’s how I like to fondly remember my time as a new PI in Dundee. I was probably just a pain in the neck.

To get back to the point, we had a problem and needed to find a way to fix it. In an act of skilful diplomacy, Bob Lightowlers managed to persuade the faculty leadership that we could begin the process of new recruitment immediately and that this would be funded by proleptic appointments. Yes, I had to go and look that up when I first heard it (after nodding my head as if I knew what he was talking about). In practical terms this meant that because we could anticipate retirements in future years, this future funding stream would be used to create new positions now. I assume the numbers add up.

We wanted to do something different with these new positions. In recent years, fellowships have become an increasingly popular mechanism to kick start someone’s career as a PI. They offer a transition period, where the new PI is protected from too onerous a teaching load (although all our new appointments will do some teaching), enabling them to focus on establishing an independent research programme. From the perspective of management, they provide the opportunity to assess whether a new appointee is really suited to this career before being offered a permanent position. So at the beginning of 2013 we created the Independent Researcher Establishment Scheme (or IRES). In the first instance this involved the creation of three 5-year fellowships. Importantly, after a rigorous assessment period, these should all lead to full academic positions with open contracts. It should be emphasised that there is no element of competition between our new IRES fellows (apart from some hopefully friendly rivalry). We want them all to succeed and get permanent positions.

When it came to recruiting the IRES fellows we were very conscious of the fact that we were recruiting future colleagues so we wanted to do more than the fashion parade that often passes for the interview process for new lecturer appointments at some UK universities (see rant to the right). We had 80 applications for the 3 IRES positions, many of which were of a very high standard. From this, after some heated debate by the ICaMB Research Committee, we whittled this down to a list of ten, all of whom were invited to Newcastle for an informal visit, where they gave a seminar, met colleagues and participated in a ’round table’ discussion about their future research and funding plans. We took them out to dinner and put them up in a hotel. Not quite the full Philip Cohen Dundee bird watching experience but a step in the right direction I think. From this list of 10 we created a final short list of 6, who all returned for a formal interview and from these we appointed 3 IRES fellows. All our IRES fellows are now in place and you can read about who we appointed here, in a previous ICAMBlog post. Will it work? Only time will tell but the early signs are very promising. We are very proud that our first arrival, Owen Davies, was recently awarded a prestigious Royal Society/Wellcome Trust Henry Dale Fellowship (more on this in the future). Our IRES appointments also join our growing cohort of successful early career PIs that includes Paula Salgado (recently awarded an MRC New Investigator Research Grant), Kevin Waldron (also recipient of a Royal Society Henry Dale Fellowship), Yulia Yezenkova (Royal Society University Research Fellowship), Suzanne Madgwick (Wellcome Trust Career Re-entry Fellow), Heath Murray (Royal Society University Research Fellow), Joao Passos (BBSRC David Phillips Fellowship) and Claudia Schneider (Royal Society University Research Fellow). I was very happy to hear that they had recently arranged a trip to the pub to begin the process of plotting and scheming.

: The author (3rd from left), in his youth, plotting and scheming with other new Dundee PIs in our traditional meeting place.

Imitation is the sincerest form of flattery, although not to be encouraged in undergraduate essays or academic publications, and now the ICaMB IRES scheme has been transformed into the Newcastle University Research Fellowships. Essentially, with some tweaking, our IRES fellowships have now been adopted by the entire Faculty of Medicine in Newcastle. Despite this, recruitment will still be handled by the Institutes themselves, so if you are reading this and are interested in becoming an ICaMB PI, then please get in touch. Here is our advert (ICaMBatNewcastle NURF advert final – pdf) and informal enquiries may be made to:

Bob Lightowlers, Institute Director (robert.lightowlers@ncl.ac.uk)

Janet Quinn, Search Committee (janet.quinn@ncl.ac.uk)

Kevin Waldron, Institute Fellowship Advisor (kevin.waldron@ncl.ac.uk)

Importantly, ICaMB is committed to the Athena SWAN Charter for women in science as detailed on our web site.

The opinions in this article are those of the author and not necessarily those of ICaMB or the Faculty of Medical Sciences at Newcastle University. Although the author thinks they really should be.

A CBCB Cell-ebration

Posted on 24 July, 2014 by Kevin

Earlier this month, the Centre for Bacterial Cell Biology held its inaugural Symposium. Here, the CBCB’s Heath Murray and Kevin Waldron tell us about what happened at the event.

One of the aspects of ICaMB that makes it a unique institute is the Centre for Bacterial Cell Biology (CBCB), a group of researchers who are focused on understanding fundamental biological questions using bacteria as model organisms. The CBCB was founded by Professor Jeff Errington FRS and is the world’s first major research centre with a focus on bacterial cell biology. Since its inception, CBCB has relocated to a purpose-built £30 million facility in the Baddiley-Clark Building, and has grown to include more than 20 different research groups. In a relatively short time, CBCB members have made outstanding contributions to our understanding of numerous aspects of fundamental cellular processes in a wide range of bacteria.

Prof Kenn Gerdes from the CBCB discusses how bacteria can form dormant variants that evade the immune defence response.

In order to recognise the success and the breadth of science being generated in the Centre, we recently held the inaugural CBCB Symposium on July 9-10. More than 120 members of the CBCB community participated in the two-day event, underscoring the critical mass of researchers at Newcastle University working within the field. This excellent turnout certainly contributed to the overall success of the event.

Research themes covered by talks from group leaders in the CBCB included sporulation, infection, persistence, biofilms, metabolism, motility, and morphogenesis. We also heard about the emerging subject of synthetic biology, where bacterial organisms will be programmed much like computers to perform discrete biological tasks.The CBCB Symposium was highlighted by inspirational talks from three distinguished external scientists, Jan Löwe (Laboratory of Molecular Biology, Cambridge), Mervyn Bibb (John Innes Centre, Norwich), and Simon Foster (Department of Molecular Biology and Biotechnology, Sheffield).

Prof Simon Foster explains how the superbug Staphylococcus aureus grows and divides.

Professor Löwe discussed his work using a range of biochemical and structural approaches to analyse the bacterial cell division and morphogenesis machinery. Professor Bibb explained how his lab utilises a combination of next generation DNA sequencing and bioinformatics with classical genetic analysis to discover novel antibiotics. Professor Foster showed how studies on the fundamental aspects of bacterial cell biology can be harnessed to better understand host-pathogen interactions that can eventually be translated into vaccine development, with his focus on the ‘super bug’ Staphylococcus aureus..

Participants hold discussions over dinner and drinks following the Symposium.

At the end of the Symposium participants gathered together for dinner and drinks in the informal setting of the Forum. This provided an interactive end to the event that allowed researchers throughout the CBCB to meet one another, discuss the amazing science, and develop connections.

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?

ECRs at ICaMB: RNA Quality Control

Posted on 30 May, 2014 by Kevin

In the latest of our series focussing on the ECRs in ICaMB, we feature Dr Claudia Schneider. Claudia obtained her PhD from the Philipps-University in Marburg, Germany. She then moved to the UK to work with Prof David Tollervey at the Wellcome Trust Centre for Cell Biology in Edinburgh. In 2011, she was awarded a Royal Society University Research Fellowship and started her own lab at ICaMB. Here, Claudia describes her research, and how being alarmed during her postgraduate studies triggered her long-term research interest.

By Dr Claudia Schneider

Hi, my name is Claudia Schneider, and my Royal Society University Research Fellowship has allowed me to set up my own group here at ICaMB to study enzymes involved in RNA processing and quality control.

I am originally from Germany, where I did my undergraduate studies and my PhD. Many people might think that Germany is the land of cars or lederhosen – but in truth it is really the land of bread (and beer!). It might therefore not come as a surprise that baker’s yeast has become my favourite model organism.

Click on the image to find out how to make these budding buns!

During my undergraduate studies I was first introduced to RNA and I was (and am still) amazed by its many known and still emerging functions in the cell. We now know that almost the entire eukaryotic genome is transcribed, but only a small fraction of the transcripts are protein-coding messenger RNAs (mRNAs). The others are stable and unstable non-coding RNAs (ncRNAs), which are involved in all aspects of gene expression. RNA molecules are often extensively processed before they’re functional, and each processing step is subject to quality control mechanisms. If you want to know more about the life and death of non-coding RNAs, have a look at this recent review.

Yeast has not always been my first choice to study RNA metabolism, since the object of my PhD project in Prof Reinhard Lührmann’s lab turned out to be completely missing in baker’s yeast. Back then I worked on nuclear pre-mRNA splicing, the removal of non-coding introns from precursor mRNAs catalysed by the spliceosome. It was an exciting time in the splicing field: A second low abundance “minor” spliceosome had just been discovered in most multicellular eukaryotes (with the strange and still not readily explainable exception of C. elegans), and this complex is not present in yeast. The minor spliceosome recognises a rare class of introns (<0.5%) with different consensus sequences at the splice sites and has since been linked to a number of human diseases. During my PhD, I purified and biochemically characterised the snRNP components of this unusual pre-mRNA splicing machinery in human and Drosophila cells.

Since then, I have been fascinated by biochemical and enzymatic assays involving RNA such as in vitro splicing assays, where in vitro transcribed pre-mRNAs are mixed with purified spliceosomes. The goal of such an experiment is to observe precise and (hopefully) pretty intron removal in the test tube – but, to my great annoyance, success was every so often hampered by a powerful ribonuclease (RNase) contamination in the assay that completely trashed the precious RNA substrates. Generic and aggressive RNases like RNase A are found on our skin, are incredibly stable and can even survive boiling.

Common decoration on lab surfaces during my PhD

It is therefore fair to say that my scientific career was majorly influenced by constant warnings by my mentor, who told me that all RNases are evil and must be destroyed. However, for my postdoc, I decided to face my fears and look these evil RNases in the eye, in the humble model system yeast. During my time with Prof David Tollervey at the University of Edinburgh, I learned that there are many different types of RNases, and only very few of them are promiscuous and chop RNA to bits.

The majority of RNases are very sophisticated and versatile enzymes. Several RNases are capable of degrading only specific RNA molecules, or only function under certain circumstances, and protein co-factors often assist in substrate recognition. RNases are crucial elements in RNA quality control or surveillance systems, which distinguish aberrant from “normal” RNA molecules. One clinically important RNA surveillance pathway is called “nonsense-mediated decay” or NMD, and this system recognises and degrades a specific class of defective mRNAs to limit the synthesis of truncated and potentially toxic proteins. NMD defects are linked to ~30% of all inherited human diseases (e.g. Duchenne muscular dystrophy and forms of b-thalassemia) as well as certain types of cancer. In addition to quality control/surveillance, where RNAs are mostly completely degraded, a growing number of RNases have been shown to be responsible for precise processing or “trimming” of precursor RNA molecules to produce their functional forms.

Exonucleases were long believed to be the main players involved in RNA recognition and processing/turnover. However, this model was recently challenged by the identification of endonucleases containing PIN (PilT N-terminus) domains, which appear to play key roles in RNA metabolism. Eight PIN domain proteins and therefore putative endonucleases are encoded in the genome of budding yeast, and this includes three largely uncharacterised “orphan” nucleases.

Overall it is still puzzling to me how individual RNases “make the decision” to either completely degrade or carefully process a specific RNA. Given the ever-growing number of non-coding transcripts in the cell, I am also keen to know which RNases are responsible for which substrates and what the so-far uncharacterised putative PIN domain endonucleases in yeast are doing!

To this end, our lab is using an RNA-protein cross-linking method called “CRAC” (UV cross-linking and analysis of cDNA) to identify the targets of PIN domain endonucleases on a transcriptome-wide scale. The CRAC method and the machinery to cross-link yeast cultures were developed by Sander Granneman at the University of Edinburgh, when we were both PostDocs in Prof David Tollervey’s lab. Sander now has his own lab too, and he runs a CRAC-blog. Interestingly, the cross-linking device we are using was originally designed to sterilise sewage water, but it is now also commercially available for research. With this setup, yeast cells are cross-linked while they are growing in culture, which is crucial to identify the often very transient interactions between nucleases and their target RNAs. This system provides a huge advantage over more traditional cross-linkers like the “Stratalinker”, which requires pelleting and cooling the cells on ice before cross-linking. It is, however, also much bigger and takes up a whole bench in the lab – but I guess there is a drawback to everything! In any case: if you want to find RNA targets for your favourite yeast protein – get in touch!!

Cultures of Saccharomyces cerevisiae can be “zapped”, while they are growing: It only takes 100 seconds!

Transcriptome-wide RNA-protein interaction analyses generate huge datasets and we use RNA binding and nuclease assays, as well as co-precipitation studies, to validate the in vivo cross-linking results for individual PIN domain endonucleases.

With the help of an ERASMUS exchange student, Franziska Weichmann, who spent 6 months in my lab last year, we have made good progress with two putative PIN domain endonucleases that are linked to ribosome biogenesis. We were able to identify their binding sites on the pre-ribosomal RNAs, as well as co-factors that are important to recruit them into the pre-ribosome. We have also set up an in vitro system with recombinant proteins, and we are currently trying to convince one of them to specifically cleave its proposed rRNA substrate in the test tube – and we are slowly getting there…..

Like the other ICaMB ECRs, who posted on this Blog before, I would like to finish by saying that having my own lab has been an exciting and (on most days) enjoyable adventure so far – and I am looking forward to the next set of challenges…

Antisense Science: A Science Blog by Students

Posted on 9 May, 2014 by Paula

Blogs are now a widespread science communication tool, with many researchers taking to the blogosphere to discuss the latest scientific discoveries, explain the basic concepts in their research field to a wide audience or just talk about science and scientists. Our 3rd year bioscience students have done just that, and this week we have a guest post prepared by them.

by Antisense Science

Antisense Science is a science blog founded by a group of 3rd year bio-scientists from Newcastle University. As a team, we recognise that science is not as accessible to the general public as it should be. We therefore make it our primary aim to translate complex scientific principles and research articles that interest us personally, into topical, thought provoking blogs accessible to everyone.

Our project is small but our ambition is big! Since our founding in October 2013 we have published 58 articles covering psychoactive baths salts, human evolution and the neurobiology of love, to name a few, and with a growing following (we’ve had over 6000 hits since inception) we were thrilled to be given the opportunity to guest post on ICaMBlog. As Newcastle University students, our interest in research was stirred by the professors at Newcastle University, including those who founded this blog. With planned guest posts focusing on research by Prof Rick Lewis among others, maybe YOU will feature on Antisense Science in the near future! We foresee (we hope!) that our blog can form a bridge between researchers here at Newcastle and the student body, raising awareness of what is actually being discovered right under our noses. By forming mutually beneficial collaborations, we hope to diversify and grow our following and expose our current readers to a continual stream of stimulating articles which never fail to pique the interest of the curious.

Meet the Antisense Science team

Currently, we have a total of 7 writers, all of whom enjoy sharing the intrigue of the latest developments in science, from biochemistry to microbiology (and even physics) and we have no plans of stopping. Although many of us will be moving on from our BScs to ever greater things, Antisense Science will remain and we are even in the process of recruiting further up and coming bio-scientists as writers (keep your eyes peeled for blogs from first year students Bethany Lumborg and Lucy Gee, as well as our fellow third year Emily Lawson and a multitude of guest posters from across the student body). The future looks bright and we’re very glad with the progress we have made thus far!

For an example of what we do, here is an article on depression written by our very own Joe Sheppard. We hope you enjoy it! If you ever want to be involved in any of our projects feel free to drop us a message. We also have Facebook (www.facebook.com/antisensescience) and Twitter (@AntisenseSci) so there are plenty of ways to keep in the loop.

The Confounding Contradictions of Depression

If you currently have or have had depression then you may already be able to tell your MAOIs from your SSRIs, but if you haven’t then what you read here might actually help. Knowledge is power and I believe learning a little something about depression could contribute a bit of control to an otherwise daunting and often underestimated medical condition.

Depression is perhaps the ultimate “common complex disorder”. Unlike pathogens or mutations that affect physical body tissue, depression is a condition that alters the very consciousness and emotional state of an individual making it a truly unique affliction. Throughout the course of our lives 1 in 5 of us will experience depression or anxiety of some kind, yet the majority of people conceive depression simply as a disease of “sadness” when the truth is much more complex. “Anhedonia“, an inability to feel joy in anything and “congruent memory bias”, the inability to remember or altered recall of specific memories, are extremely common cognitive behaviours in depression that we often inflict upon ourselves on a day to day basis.

It may surprise you to know that modern science can say with little certainty what neuro-physiological changes initiate depression, and linking those that we do think are involved to the broad psychiatric manifestations seen in cases of depression is even harder as human experience and consciousness is beyond the understanding of molecular neuroscience (and by extension, definitely me). But from the murky depths of our own minds patterns do emerge, and as such there are a few good theories out there.

Rather confusingly the best fitting theory of depression is actually based on the drugs WE ALREADY USE to treat it, not a common theme in medicine, I might add. “The monoamine theory of depression” states that depressed brains have reduced signalling between neurons via a group of specific chemical neurotransmitters called monoamines. Two in particular called 5-hydroxytryptophan (hereafter referred to as serotonin) and dopamine are released into a synapse to induce electrical signals between neurons in the midbrain. These two neurotransmitters and the resulting electrical signals are most notably perceived as feelings of joy, euphoria, reward and attention. And there is some evidence to back this up: depletion of tryptophan, an amino acid essential for serotonin synthesis in the brain, caused mood congruent memory bias, and altered reward-related behaviours. Biochemical evidence exists too, abnormalities of the protein that binds serotonin in the brain called the 1A receptor have been noted in multiple brain areas of major depressive disorder (MDD) patients. Why does serotonin decline in patients with depression? Well, search my pockets, you will find no answers.

Rather reassuringly this hasn’t stopped treatment of depression at all, and several drugs for which the theory is named are all targeted at increasing serotonin, and so good feelings, within the brain. The so named selective serotonin re-uptake inhibitors (those “SSRIs” I snuck in earlier, such as fluoxetine and sertraline) are the most prescribed group of antidepressants and work in a way best aided pictographically:

Schematic representation of neuron activity

Serotonin is synthesised in the presynaptic neuron from tryptophan, from here it is packaged into vesicles and upon nerve impulse firing (see previous article “ shedding light on neural networks”) is released in the synaptic cleft (the space between neurons). Serotonin then binds to receptors on the postsynaptic neuron, stimulating a similar nerve impulse. However, serotonin is also able to control its own release: By binding to the 1A receptor on the presynaptic neuron it prevents continued release of serotonin, allowing the proposed channel protein SCL6A4 to re-absorb serotonin in the presynaptic neuron to be destroyed.

This is where SSRIs come in. Believed to bind to SCL6A4 and prevent the re-absorption of serotonin, it allows serotonin to remain in the synaptic cleft for longer and therefore stimulate nerve impulses in the post synaptic neuron for longer, and so increase the degree of monoamine signalling.

Let’s not forget our friend dopamine:

Dopamine too is a monoamine consistently found reduced in the blood of patients with depression, as a result of decreased synthesis and degradation in the brains of these patients. Neurons that signal using dopamine (as opposed to serotonin) are found in a region of the brain called the substantia nigra that degenerates during Parkinson’s disease. Interestingly the motor impairment (shaking) in this disease is often preceeded by major depressive disorder in 50% of Parkinson’s cases!

This brings me quite nicely to my final point. Since so little is known about the basis of psychiatric disorders their treatment has been almost purely symptomatic for the last 60 years. Thomas Insel, director of the US National Institute for Mental Health was quoted in 2013 as saying “In the rest of medicine, this would be equivalent to creating diagnostic systems based on the nature of chest pain, or the quality of fever.” This was following the release of the 5th edition of the diagnostic and statistical manual of mental disorders (DSM-5), that diagnoses psychiatric conditions based on common symptoms presented by each condition. Despite the strong agreement with Insel by many psychiatrists that this method is outdated, the shift to a more objective and molecular diagnostic is years away given the outstanding complexity of these diseases. But keep the hope, recent booms in neuroscience research are a sure step towards a less archaic means of treating depression and other mental disorders.

A new approach spearheaded by the same Thomas Insel called “Research Domain Criteria” or RDoC is already doing just that by utilizing genomic sequencing technology, fMRI imaging techniques and cognitive science to develop an entirely new platform for diagnosis based on new data being attained all the time, rather than the laboured DSM-5 classification. While still in its infancy this new approach aims to start looking at broader groups for diagnosis rather than classification of different disorders by the symptoms they present. For instance, by looking at a group of patients with different disorders but all experiencing anhedonia will not only allow a greater insight into a unifying cause for these symptoms, but also speed up treatments in the future.

Of course, there are always two sides to each argument and depression does in some sense stand alone from other psychiatric disorders such as schizophrenia in that it imparts a greater emotional influence on the sufferer – if “precision medicine” were able to prescribe a pill for the treatment of emotional conditions, would you want it to? Of course this is a quandary we won’t face for some time, but worth a thought.

Some interesting but by no means comprehensive reviews on depression, its far too huge for 3 articles!

Hasler G (2010). Pathophysiology of depression: do we have any solid evidence of interest to clinicians? World psychiatry : official journal of the World Psychiatric Association (WPA), 9 (3), 155-61 PMID: 20975857

Martinowich K, Manji H, & Lu B (2007). New insights into BDNF function in depression and anxiety. Nature neuroscience, 10 (9), 1089-93 PMID: 17726474

Frances, A. (2013) One manual shouldn’t dictate US mental health research
(Accessed: 07/01/14).

Deep Impact

Posted on 24 April, 2014 by Suzanne

Alginate bread on a pedestal under show-biz lights.

Another excellent post by ICaMB’s Dr Matthew Wilcox as the fame of alginate spreads and seaweed bread goes on tour!

Well, I was kindly invited along to the BBSRC Fostering Impact awards ceremony in London a couple of weeks ago and although I wasn’t up for anything, Newcastle University were.

Fostering impact is a scheme run by the BBSRC to capture the economic and social impact of research funded by them. There are three competitions that fit the fostering impact scheme; ‘innovator of the year’, ‘activating impact’ and ‘excellence with impact’. The first is for an individual researcher, the second is for the knowledge exchange teams and the final award is for research organisations (runs from 2013 – 2015).

The knowledge exchange and commercialisation team at Newcastle University has changed substantially over the past couple of years. What was once a centralised Business Development Directorate has now become the Research Enterprise Service, comprised of three teams, each embedded in one of the Faculties. Each Institute or School now has their own dedicated business development manager (BDM), with ICAMB’s BDM being Laura Rush (who is very nice). They are now much easier to contact, whether it’s just a quick question or the drafting of patents.

Home baking practice.

Newcastle’s application for the Activating Impact award was submitted back in October 2013 and used the wonderful research done by the beautiful people of ICAMB as its basis. In January the RES team found out that they had successfully made it to the final five (from 18) and through to the grand final in London. Newcastle was up against the knowledge exchange and commercialisation teams from King’s college London, Queen Mary University of London, University College London and University of Aberdeen. One of the requirements of the competition was to bring along someone to the final who had worked with RES, a ‘user’ (according to the BBSRC). They also wanted an iconic object?! Alginate bread it was then. Back in the kitchen I went. How many loaves would I need to feed the people there? Two should do it, right?

Martin and Laura on the train gearing up for competition.

In London Martin Cox presented the case for Newcastle in front of a panel of scientists, business types and other technology transferers, assembled by the BBSRC. Demonstrating what Newcastle does well, how BDM’s have been embedded into each institute and also what they would do with the money if we won (£100k). He also described the additional internal funds that are available to help activate impact. FMS has two funds available; the first is to help with data collection for translational grant applications, the second is to support further claims in patent applications. The two internal grants can both potentially support a post doc salary for three months, plus consumables.

Dengue fever carrying mosquito.

The awards ceremony combined the ‘innovator of the year’ and ‘activating impact’. I got a glitzy stand for my bread and also had the chance to look around the other pretty amazing stuff that was on display, like Dr Luke Alphey’s work. Luke ended up being named both social innovator and overall innovator of the year for his work on the genetic control of pests, including the dengue fever carrying mosquito.

I even got to meet the new (ish) CEO of the BBSRC, Professor Jackie Hunter, who was definitely not snapped stuffing free stuff into her bag!

BBSRC's CEO Jackie Hunter enjoying the exhibition

On the right BBSRC’s CEO Professor Jackie Hunter enjoying the exhibition.

Unfortunately Newcastle did not win, but being down to the last five of the competition is brilliant and should give confidence to ICAMB scientists that when help is required in achieving impact (social or economic), we have a great team to help.

Queen Mary University of London, whose entry was also being supported by a previous BBSRC Enterprise Fellow and King’s College London, ended up being joint winners each scooping £100k.

Perhaps if a few more of the world leading researchers in ICaMB engaged with the Enterprise team, they might not have to only take some eejit and his bread to the competition next year and increase NU’s chance of winning!

ECRs at ICaMB: Copying the blueprint of life – Understanding DNA replication

Posted on 4 April, 2014 by Kevin

In the latest of our series focussing on the Early Career Researchers (ECRs) in ICaMB, we feature Dr Heath Murray. After completing undergraduate studies at the University of California, Los Angeles and then obtaining his Ph.D. from the University of Wisconsin-Madison, Heath came to the UK to join the lab of Prof Jeff Errington in Oxford. From there he re-located to ICaMB, and in 2009 was awarded a Royal Society University Research Fellowship. Here, Heath describes his research into the mechanisms of DNA replication, and explains why he became interested in this field.

By Dr Heath Murray

Hello, my name is Heath Murray and I’m a Royal Society University Research Fellow in ICaMB’s Centre for Bacterial Cell Biology (CBCB) studying DNA replication. DNA is one of the most important molecules required for life because it encodes the information, or the blueprint, used to build a cell (i.e. the most basic unit of an organism). In order for a cell to create new cells it must synthesize an exact copy of its DNA, an extraordinary process when you consider that the genomes of most cells contain millions of individual DNA subunits!

Bacillus subtilis is a useful model system as it proliferates rapidly and is amenable to genetic, cell biological, biochemical, and structural analyses

Bacteria are ideal model systems to study this fundamental process because they are much less complex than human cells (e.g. all of their DNA is encoded by a single chromosome, whereas humans have 23), and this allows us to understand how they work at the greatest possible level of detail.

I was introduced to bacteria when I was an undergraduate student and the effect was transformative. My mentors taught me how to add a specific gene (a DNA sequence) to a bacterial cell, and if it worked properly then the bacteria would turn blue!

Bacterial colonies turn blue if they contain a gene that degrades specific sugars.

That basic genetic experiment was one of the coolest things I had ever done, and from that point on I worked hard to learn the trade of “bacterial genetics”.

Today my research group focuses on understanding how DNA replication is controlled so that each new cell will end up containing an exact copy of the genetic material from its predecessor. We employ a wide range of complementary experimental techniques: genetic engineering of bacterial strains, biochemical analysis of purified proteins, and fluorescence microscopy.

In the hot room to check my plates…. I haven’t even stopped to take my jacket or backpack off yet!

Fluorescence microscopy is a particular strength of the CBCB because there are several bespoke systems specifically designed for bacterial cells (bacteria are 10-100 times smaller than most human cells). One of the core approaches we use is to genetically engineer a protein we want to study so that it will be fused to a special reporter protein called GFP (Green Fluorescent Protein, originally isolated from jellyfish!) within the cell. Using this approach we can then visualize where our test protein is because it fluoresces when exposed to a specific wavelength of light. Some of our microscopes are so sophisticated that we can observe the location of single proteins and track their movements within living cells.

At the bench.

One of the approaches we often use is to visualize specific regions of the genome within living cells. First, a specific DNA binding protein ( called “LacI”) is genetically fused to GFP. Second, the DNA sequence recognized by LacI (called “lacO”) can be genetically integrated into any location of the genome. Since I study DNA replication, I am particularly interested in the site of the bacterial chromosome where DNA synthesis is initiated (called the “replication origin”). Third, fluorescent dyes are added to cells that bind to the cell membrane and the DNA. Finally, we utilize our fluorescent microscopes to visualize the location of replication origins within individual cells. In the image shown, the live bacterial cells contain chromosomes that are in the process of being replicated, and therefore they have duplicated and separated their replication origins!! This image also emphasizes the fact that although bacteria lack the organelles found in eukaryotic cells, they are nonetheless highly organized (notice how the replication origins are characteristically located at the outer edge of each chromosome).

The GFP protein from jellyfish can be used to fluorescently tag proteins in vivo. Fluorescence microscopy can then be used to localise the tagged protein within the bacterial cell.

Well that’s it for my first ICaMB blog! I hope you enjoyed hearing about how I became interested in bacterial genetics and about my work on bacterial DNA replication. Please feel welcome to contact me if you have any questions or if you would like further information regarding my research.

Links

Royal Society URF http://royalsociety.org/grants/schemes/university-research/

Centre for Bacterial Cell Biology (CBCB) http://www.ncl.ac.uk/cbcb/