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University Open Days
The University's next Open Days are on June 23, July 16, September 10 and October 22. Members of the department will be available to show you round, answer questions and give presentations on our courses. We would prefer you to register in advance so we can plan numbers but this is not strictly necessary. You will have a chance to hear about MBB and have a tour of our teaching facilities. There are many other things on display at the open days, including our sister biology departments, accommodation and campus tours, and information about student life.
The Department also has open days for students who have applied via UCAS and accompanying people. Because of space restrictions these are not open to other visitors. Please contact us for more information via the link on the left.
How to make double stranded DNA (Agent Scully was right!)
Several episodes of the X-Files have Agent Scully suspecting that aliens have inserted branched DNA into her blood. Actually, we have known for a long time that branched DNA is made every time double stranded DNA is copied. DNA can only be synthesised in one direction (5' to 3'), but double helical DNA has two strands going in opposite directions. The solution used by all life is that one strand (the leading strand) is synthesised continuously, but the other (the lagging strand) is synthesised in fragments, each with an extra overlapping flap (in pink). Subsequently, an enzyme called flap endonuclease follows along and cuts off the flap to allow the fragments to be joined together. Research just published by Dr Rafferty in MBB shows that flap endonuclease has an arch that opens and closes to trap the flap and snip it off - see our Paper of the Month feature for details.
£3.5m for research on antibiotic resistance
The government have handed out a total of £9.5m to combat the growing threat of antibiotic resistance, to the Universities of Sheffield, Leeds and Bristol, with Sheffield getting £3.5m (May 19 2016). The money has gone to the Florey Institute, which is based jointly in MBB and the Medical School, and signals the government's determination to do somewething about bacterial resistance to antibiotics, which is the target of the Florey Institute.
MBB academic on Radio 4
Prof Simon Foster appeared on BBC Radio 4's flagship news programme, the Today Programme, on May 13, being interviewed by Tom Fielden about the threat of antibiotic resistance.
PhD students win prizes
In a rare double, PhD students Jason Wilson and Hayley Owen won first and second prize for their poster presentations at this year's British Crystallography Association meeting. The picture shows Jason (right) receiving the prize: appropriately enough, a piece of Blue John stone from the Peak District, and being presented by Matt Conroy, an ex-MBB student (undergraduate and PhD), now working at PDBE in Hinxton, Cambridge.
Panspermia hits the media again
Milton Wainwright FRAS, our guru on panspermia (the theory that life came to earth from outer space), has been making waves again. He was recently interviewed by the New York-based science magazine Nautilus, and an article on his work on panspermia can now be found online by searching Google for Nautilus. On a different level Milton has been invited to appear on BBC Radio Four’s Museum of Curiosity, in which panelists suggest, for discussion, a virtual museum piece. What is his exhibit? You will have to listen to the program to find out!
Third year PhD student poster presentations
On March 23 2016, third year PhD students from the three Biology departments presented posters of their work in Firth Hall. Sponsorship from various companies meant that we were able to provide coffee, cookies and three poster prizes, one of which went to Paul Galvin, who is supervised by Ewald Hettema and Jeremy Craven in MBB and uses computerised tracking of fluorescence microscopy images to follow the birth and development of peroxisomes in yeast cells.
Textbook translation into Japanese
Prof Williamson's textbook How Proteins Work has been translated into Japanese (the Japanese title means Essential Protein Science) and is available from Nankodo Ltd, Tokyo.
Prize for MBB Lecturer
Dr Matt Johnson, a lecturer in MBB, has been awarded the Society for Experimental Biology's President's Medal. The award recognises his work on photosynthesis in plants, and specifically his achievement in locating cytochrome b6f in the photosynthetic membrane using affinity-mapping atomic force microscopy. He commented: “I am deeply honoured and delighted to be awarded the prestigious SEB President’s Medal for Plant Science. The award provides wonderful recognition of my work on photosynthesis in the last nine years since my PhD. It means a great deal to be ranked alongside the many great scientists who have previously held the award.” For further details, see here.
MBB student at the UN Conference on Climate Change (COP21)
James Thackery is doing a PhD with Karim Sorefan on plant development, funded by the Grantham Centre for Sustainable Futures. In December 2015, he attended the UN Conference on Climate Change in Paris (COP21). He writes:
I went with professors from the Grantham Centre and from P3. Our aim was to highlight the importance of food security when considering how to tackle climate change. Our successful talks and events proved even more important considering that if we had not gone, there would have been no representation of the food security issues we face in the future. I also went with the purpose of meeting with organisations that I could work with after completing my PhD. I would like to work in science policy, so there were several organisations present that were worth getting to know. I also was able to attend many compelling talks on all aspects of climate change and meet several interesting people.
Overall, the trip was a success both for myself and for the University of Sheffield. We came away pleased with our efforts and with the event as a whole. The negotiations were widely regarded as a success. Strong agreements were made and they provide a good starting point for future developments. It was fantastic to see the range and variety of organisations from all over the globe working to reduce climate change. However, it was clear that the COP21 organisers felt strongly about three topics: conservation, renewable energy, and carbon capture and storage. Although these are important areas, very little attention was given to other, equally important topics, such as food and water security. There was also no mention of the importance of research to invent more efficient ways of dealing with climate change. Nonetheless, the whole event was a success both in awareness and in policy-making, and I am proud and delighted to have gone. Next up, COP22 in Morocco!
Focus on research: How cells decide what size and shape to be
Fundamental questions in biology are how do cells know what shape to be, when to stop growing and divide, and how to organise themselves? A recent research paper, from Prof Simon Foster and Dr Roy Chaudhuri and colleagues in MBB, has provided an answer to this question. They studied the spherical bacterium Staphylococcus aureus, a major hospital superbug, and discovered a group of proteins (one of which is the protein PlsY, shown in the image), which distribute themselves in a regular pattern around the outside of the cell. The key result, obtained by combining experimental observations with mathematical modelling, is that the information on where to go arises spontaneously within the cell, as a result of competition between the curvature that these proteins naturally impose on the cell wall, and random thermal motions. Thus, local interactions build up naturally to determine the overall cell shape and provide structural anchors within the cell, even though the proteins involved are much smaller than the overall cell dimensions. The work was published in Proceedings of the National Academy of Sciences of the USA 2015 vol 112 issue 51, pages 15725-15730.
Sheffield-based research network secures major new industrial biotechnology funding
The chemicals industry is a vital component of the world economy that is faced by the need to provide innovative and sustainable solutions to provide the resources required for a growing global population. One approach to a more sustainable chemicals industry is the use of microbial cell factories to produce key chemicals from sustainable feedstocks. However, a major barrier to commercial cell-factory-based chemical production is poor product yield. Often this is caused by intoxication of the cells resulting in sub-optimal performance. To address this problem, a £3 million research project (DeTox) to improve the sustainable production of chemicals and biofuels by microbes has been awarded by the Industrial Biotechnology Catalyst fund to a consortium of scientists led by the Sheffield-based Crossing Biological Membranes Network in Industrial Biotechnology (CBMNet). Professors Jeff Green and David Kelly along with sociologist Dr Susan Molyneux-Hodgson at the University of Sheffield are working with colleagues at the Universities of York, Nottingham and Cambridge and five companies (Green Biologics, ReBio, Lucite, CPI and Ingenza), to overcome poor product yields by focussing on how the properties of the bacterial cell membrane can be modified to create more robust cell factories.
So far CBMNet has funded seven Proof-of-Concept grants along with seven Vacation Scholarships (worth over £175,000) and five Business Interaction Vouchers (worth over £50,000). Many of these awards have focused on supporting students and early career researchers to ensure that the biotechnology expertise continues to grow.
MBB student to visit Canada for research collaboration
Tareq Omairi, who is a PhD student with Milton Wainwright, has obtained funding to travel to the University of Alberta in Canada, to work with Prof Konhauser to analyse meteorological samples to identify microbial bio-signatures and distinguish them from natural geological activities. The funding comes from the Worldwide Universities Network (WUN), a worldwide network of 18 leading international universities focussing on key international challenges.
Focus on research: Photosynthesis in plants
The energy neeeded for almost all life on earth ultimately comes from photosynthesis. The key processes of photosynthesis take place in specialised membrane structures called thylakoids, which not only carry out the capture of light but convert it efficiently to chemical energy, tune the process to environmental conditions such as light intensity, and make sure that the photosynthetic energy does not get diverted into other routes, such as oxidative damage. MBB's Dr Matt Johnson has published a review in the journal Nature Plants, discussing recent results that demonstrate the dynamic nature of thylakoids. In a second paper, also published in Nature Plants together with MBB professors Neil Hunter and Peter Horton, he has shown that there is a carefully regulated interplay between the light harvesting apparatus that captures sunlight and the photosystems that convert it to chemical energy, to maximise efficeincy and minimise oxidative damage.
The Krebs Fest was a series of events running through October and November 2015, to celebrate the achievements of Sir Hans Krebs, first Professor of Biochemistry at Sheffield and awarded the Nobel Prize for Physiology or Medicine in 1953. It kicked off with the installation of two stunning artworks in the Winter Gardens in Sheffield city centre, shown above. On the left is a giant inflatable E. coli cell, 28 m long (a human on this scale would stretch from the UK to Japan!), and on the right is an interpretation of Green Fluorescent Protein constructed in origami, complete with fluorescent centre. These have now been moved to Firth Court, where the combination of the 1905 red-brick building with these works of art is truly dramatic.
The festival also included lectures by three Nobel Prizewinners, a schools evening, and a public evening on November 13, which featured rap and dance, a film show projected against the walls of the Firth Court, and lots of hands-on science, plus an exhibition in the Western Bank library. For more details and photos, go to this link.
2015 Nobel Prize for Chemistry shared by Sheffield Honorary Graduate
The Nobel Prize for Chemistry 2015 was shared between three scientists for their work on DNA repair. One of these is Prof Tomas Lindahl, who has been an adviser both to the Institute of Cancer Studies and to MBB at Sheffield,and was awarded an honorary degree by Sheffield University in 2011. Several researchers in Sheffield work in a similar area, particularly Prof Sherif El-Khamisy, whose work is highlighted below.
Retirements of MBB staff
The end of September 2015 marked the retirement of Pam Scholes and Paul Brown, who have between them been providing technical support to the department for a grand total of 76 years! Their retirement was marked by a celebration, attended by many current and retired staff, including Profs Pauline Harrison and Peter Horton, whose labs they worked in for many years. Since then they have taken on many support roles in the department and they will be much missed.
Grant successes in summer 2015
Several MBB staff have been successful in attracting grant funding recently, including Profs Kelly, Green and Foster. However it is particularly noteworthy that four of our new staff have grant funding. Dr Steve West has landed three awards recently (see news item below), valued at well over £1m. In addition, we are delighted to report a grant of £538k to Dr Casson, for regulation of water use by plants in response to light levels; a grant of £526k to Dr Fagan, to study how the superbug C. difficile secretes molecules through its outer layer; and a grant of £528k to Dr Mesnage, to study cell surface display of bacterial proteins.
MBB student awarded Young Microbiologist of the Year
Joe Kirk, who is working in the lab of Dr Robert Fagan, was awarded the Society for General Microbiology Sir Howard Dalton Young Microbiologist of the Year award at their annual meeting in September 2015, and gave a presentation entitled 'Scratching the surface: Targeting the crystal shell of Clostridium difficile'.
The photo shows Joe being presented with his award by Prof. Dame Anne Glover (Vice Principal for External Affairs, University of Aberdeen).
MBB research inspires Chicago artist
Dr Milton Wainwright conducts research on panspermia – the theory that life on earth came here from space. This work has inspired Chicago artist Jerome Walker to create an artwork. Jerome said “I read your article on the sphere you recovered and it inspired me to create a large painting (121.92 cm x 243.84 cm), a diptych, depicting, among other things, the arrival of many such spheres in other times and other places and the possible, unusual results. I hope you enjoy it as much as I enjoy your work on panspermia.”
The painting comes at a time when interactions between science and art are being encouraged. Dr Wainwright says “It is of course a great thrill and privilege that a famous artist has been inspired by our work on life in space.”
National Student Survey results for 2015
The National Student Survey (NSS) results for 2015 were announced in August. The results are grouped rather differently to the structure of our degrees which makes it difficult to compare directly, but we are delighted to report that Microbiology scored 100% for overall student satisfaction, making us the best placed Microbiology department in the UK. We also scored well for our other degree subjects: Genetics was 2nd in England. In addition, the Students' Union was voted the best in the UK for the fourth year in a row.
Fellowship successes for Steve West
Steve West was appointed to MBB as a Senior Lecturer earlier this year, coming from the University of Edinburgh. His research looks at the processing of RNA, and how this can lead to disease. Since his arrival, he has won three prestigious awards:
- Most recently, he has been granted an Investigator Award worth nearly £1 million by the Wellcome Trust. The Wellcome Trust provides its Investigator Awards to only “the brightest researchers with the best ideas” so the competition is at the highest level.
- He has also been awarded a Lister Fellowship, which seek to “help support and nurture future leaders of biomedical research”. Prof El-Khamisy in MBB is also a Lister Fellow, and Profs Jon Waltho and David Rice in the Department were previous Lister Fellows, so he joins a distinguished group.
- He has been named as a European Molecular Biology Organization (EMBO) Young Investigator, a highly competitive Europe-wide programme to support the best young group leaders in Europe. Steve is one of only a handful of scientists to receive both an EMBO Young Investigator and a Lister Fellowship.
Congratulations to our graduates of 2015, who achieved one of the best results ever. Graduation day was at the end of July and turned out a nice day again. In addition to the ceremony itself, we hosted a lunch for graduates and their families, and tours of the department, and a good time was had by all.
Careers data for 2014 graduates
Careers data for undergraduates finishing in 2014 have just been published (in July 2015 - data collected in December 2014). The picture is fairly similar to the last few years: more than half of our graduates move on to a PhD or masters course, though the numbers of home students going on to Masters courses has declined gradually while the numbers going on to a PhD has increased. A pleasing statistic is that when asked 'How well did your degree prepare you for further employment?', the proportion answering Well or Very Well increased from 72 to 83%.
New appointment: Ling Hwang
Dr Ling Hwang joined MBB in May 2015, from the National Institutes of Health (NIH) in the USA. She is part of the growing team that make up Imagine, the joint project involving collaboration between MBB, Physics and Chemistry to develop advanced microscopy techniques for studying bacteria. She writes:
My research interests are in chromosome dynamics and the cell division machinery in bacteria. It is only recently with the advancement in fluorescence microscopy that we now know that bacteria are not just bags of enzymes, but instead contain complex spatial organization. Genomic DNA has to be properly organized and segregated to the daughter cells for genetic material to be faithfully transmitted to the next generation. My research aims to understand how partitioning proteins are involved in moving and positioning chromosomes prior to cell division. This same family of proteins is also involved in the organization of many important bacterial cell functions such as cell division, motility, chemotaxis and biofilm formation. Our research approach is multidisciplinary, from reconstitutive synthetic biology, biochemistry, biophysics to single-molecule fluorescence microscopy. Joining MBB and Imagine in Sheffield will expand our toolkit to include EM, AFM and super-resolution microscopy. I am excited to be part of this team and look forward to collaborations. When not in the lab, I like to be out in the sun, hiking, rambling, climbing, biking, swimming or just sitting.
New appointment: Egbert Hoiczyk
Dr. Egbert Hoiczyk joined the Department in April as a Senior Lecturer as part of the Imagine initiative. Before coming to Sheffield he was an Assistant Professor at Johns Hopkins University.
He writes: My research interests involve bacterial ultrastructure and cytobiology, a field that has recently experienced dramatic changes. Once thought to be simple, we now appreciate that bacteria possess elaborate architectures rivalling that of eukaryotic cells. My research focuses on the identification, and structural and functional characterization of the molecular complexes that underlie this surprisingly complex architecture. Specifically, I currently work on a family of bacterial cytoskeletal proteins termed bactofilins. Bactofilins are widely expressed and, like their well-studied eukaryotic counterparts, help organize the cytoplasm, play a role in cell shape maintenance, antibiotic resistance, chromosome segregation, cell division, and many other important cellular functions. Another area of research in my lab is studying the structure and function of bacterial motors such as type IV pili, cell appendages that allow cells to crawl over surfaces. The ultimate goal of this research is to devise new antibacterial therapeutic approaches that target these conserved structures. What attracted me to Sheffield are the world-class light and electron microscopic capabilities that the Imagine initiative offers, which should enable us to study these structures at an unprecedented level. When not in the lab, you will find me hiking, collecting fossils, or playing volleyball.
The best Students' Union in the UK
Sheffield University's Students' Union has just been voted the best in the UK for the seventh year running in the Times Higher Education Student Experience Survey. See here for more details.
Faulty DNA repair can lead to cancer
MBB's Professor Sherif El-Khamisy recently published a review in the journal Nature Reviews of Cancer, in which he discusses recent research linking faulty repair of DNA by the enzyme DNA topoisomerase to cancer. More details can be found here.
MBB teaching team win Sheffield Professional award
At a ceremony on March 26 2015, the team that runs the undergraduate practical lab for MBB (from left to right: Anne Holland, Mel Stapleton, Sarah Noble and Tom Hill) won the One Team category at the Sheffield Professional Awards. This award is 'for a team which, by the way they work together, is exceptional ... based on mutual respect, trust and team spirit'. The team organises all aspects of practicals, sometimes months in advance, and makes sure everything runs smoothly with 180 students passing through the lab every day.
New appointment: Steve West
Dr Steve West joined the department at the start of 2015 from the University of Edinburgh. He writes:
I recently joined the department as a Senior Lecturer. My research interest lies in gene expression, which is the process by which information encoded in our DNA is decoded to produce proteins. This occurs through an RNA intermediate that is transcribed from the DNA by RNA polymerase. In its primary form, RNA is unsuitable for protein synthesis and must undergo a number of maturation steps during transcription. We are interested in these maturation mechanisms and the proteins that control them. This research is very important because RNA synthesis is essential to every biological process in life. Reflecting this importance, defects affecting this part of the gene expression pathway are frequently a cause of disease. In gaining a much better understanding of how this essential process occurs, we hope to identify the molecular basis of the associated diseases and how to reverse their adverse effects. When not engaged in research, you are likely to find me in the Peak District – either hiking or trying to catch trout!
Our 4-year courses receive Advanced Accreditation from the Society of Biology
In February 2015, the Society of Biology conferred Advanced Accreditation status on all of our 4-year MBiolSci degree programmes. Accreditation is a recognition of academic excellence, and requires evidence that graduates from the programme meet defined sets of learning outcomes. It allows graduates to apply for membership of the Society of Biology after only two years of practice, rather than the standard three. This announcement adds to the accreditation of the MBiolSci in Biochemistry which happened in 2012. More details can be found here.
Research Excellence Framework (REF) 2014
Every few years there is a major review of research excellence across all UK Universities. In 1986, 1989, 1992, 1996, 2001 and 2008 this was called RAE (Research Assessment Exercise) and focused on research output, ie journal papers and books. In the 2008 RAE, Biological Sciences at Sheffield was rated 3rd in the UK. In 2014 the RAE was renamed REF because the measures used had changed: in particular, they also included an assessment of 'Impact', ie how much research had affected society, plus an increased measure of 'Environment' - mainly research facilities, people, and funding. The results were announced in December 2014.
In the 2014 REF, staff in MBB were mainly returned either in Biological Sciences or in Subjects Allied to Medicine. The Biological Science group also included most staff from the Department of Animal and Plant Sciences, while Subjects Allied to Medicine also included most staff from Biomedical Science and parts of the Medical School. In Subjects Allied to Medicine, Sheffield came first overall, out of a total of 94 institutions across the UK. In Biological Sciences, Sheffield came equal fifth out of 44 institutions, the top 5 being Institute of Cancer Research; Dundee; Edinburgh; Imperial; Sheffield, Newcastle and Oxford. The complete REF 2014 results can be found here.
New appointment: Bin Hu
Dr Bin Hu has joined MBB as a University Research Fellow. He writes:
My research interests lie in the field of cell cycle regulation. The cell cycle is a precise program leading to cell duplication and division. Progression through the cell cycle is tightly controlled and any error during the cell cycle could cause catastrophic consequences, for example cell death and cancer. This process is strongly influenced by environmental factors. My research aims to understand how cells incorporate environmental signals to cell proliferation and how cells make a decision on growth or death upon environmental stress. Understanding these processes will help us design new drugs to fight cancer and aging.
Grant income in 2014
In 2014, staff in MBB attracted grants of well over £5m. Notable grants included one of over £2m to Prof Neil Hunter from the European Commission, for the development of artificial photosynthetic systems based on bacteria, and two grants totalling over £1m to Prof Sherif El-Khamisy for studying the repair of damaged DNA. We have been awarded another grant of over £4m, which starts in 2015.
Congratulations to PhD graduates of 2014
In 2014, 22 students were awarded PhDs. We congratulate them on their achievements:
- F Almourfi (Baker) Structural genomic studies of lipoproteins from Mycobacterium smegmatis for drug design
- A Elbrghathi (Baker) Structural studies on dehydrogenases
- V Kent (Foster) Cell wall architecture and the role of wall teichoic acid in Staphylococcus aureus
- A Kabli (Foster) Identification and characterisation of cell division proteins in Staphylococcus aureus
- J Almohsen (Gilmour) Isolation and characterisation of halotolerant bacteria and algae and their potential for biofuel production
- O Iyiola (Goldman) Important roles of Ex01, Mre1, Sae2, SGS1,SPo11, Srs2 and Tell in the VDE-DSB repair during meiosis
- D Medhi (Goldman) Repair of double strand breaks catalysed by VMA1
- M Al Kuwayti (Hettema) The role of peroxisomes in sterol biosynthesis by the cellular slime mould Dictyostelium discoideum
- Y Aldawood (Hornby) Purification of E. coli McrBC complex and mapping inactive mutations in MrcB using error-prone PCR
- T Grieves (Hornby) Investigation of small molecule inhibitors of enzyme function
- A Nwokeoji (Hornby) Analysis of ribonucleoprotein complexes using affinity purification in conjunction with mass spectrometry
- S Hollingshead (Hunter) Investigating protein-protein interactions in the chlorophyll biosynthesis pathway
- Y Liu (Kelly) Novel aspects of the function and assembly of the electron transport chains in Campylobacter jejuni
- M Feigenbutz (Mitchell) Role of the exosome co-factor Rrp47 in RNA processing and surveillance
- W Garland (Mitchell) Analysis of nuclear exosome associated co-factors in Saccharomyces cerevisiae
- M Alkuriji (Piper) The yeast Cdc37 molecular chaperone: its association with Cak1 and its susceptibility to loss with oxidant and molybdate treatment
- F Al Malki (Rafferty) Structural studies on flap endonuclease complexes
- A Abd Aziz (Rice) Structural genomics on essential genes in Burkholderia
- J Greig (Sudbery) Phospho-regulation of Fkh2 in Candida albicans
- S Al Yahya (Wainwright) Studies on the microbiology and biogeochemistry of desert soils notably in relation to microbial phosphate solubilisation
- W Alwaneen (Wainwright) Use of fruit beetles, waxworm larvae and tiger worms in waste conditioning for composting
- M Bukhari (Wainwright) In vitro studies relating to honey as an alternative approach to wound therapy
New appointment: Ian Sudbery
Dr Ian Sudbery has joined MBB as a lecturer within the Bioinformatics Hub. He writes:
My research mostly focuses on exploration of the regulation of eukaryotic gene expression: How do cells decide which genes to express and where? How do these processes go wrong in disease? I am particularly interested in the functions of regulatory non-coding RNAs, and the effects of three dimensional chromatin structure on the cell. I use a range of techniques from functional genomics and computational biology. Although these days you’ll mostly find me behind a computer analysing large datasets, it wasn’t always so. My PhD and first postdoc were doing wet-lab science. After that I accepted an exceptional opportunity to spend three years in a postdoc training scheme that aimed to train lab scientists in computational biology. So I understand both lab and computational aspects of biology and don’t only speak geek! My work is necessarily collaborative and my door always open so come down and say hi whenever.
When I’m not working you’ll probably find me “swinging-out” on Sheffield’s swing and blues dance floors , climbing a mountain or in the pub drinking interesting beers.
New appointment: Rebecca Corrigan
Dr Rebecca Corrigan joined MBB in January 2015 on a Sir Henry Dale Research Fellowship, which is funded jointly by the Wellcome Trust and the Royal Society. She writes:
My research is focused on the bacterium Staphylococcus aureus, which is a human pathogen responsible for significant disease and morbidity worldwide. When it invades a human host it encounters a number of different stresses, such as nutrient limitation. The bacteria respond to these stresses by switching on a response called the stringent response, which results in the synthesis of two small nucleotides, collectively referred to as (p)ppGpp. These nucleotides bind to target proteins, causing the bacterial cells to shut down active growth and enter a persistent state that promotes survival. Relatively little is known about how these nucleotides are synthesised or the receptor proteins they interact with. My work will use a novel genome-wide approach to identify all protein targets to which (p)ppGpp bind in S. aureus in order to establish the pathways these nucleotides control. By doing so we will better understand how S. aureus can survive in the human host and can begin to design therapies to disrupt this process.
For those unfamiliar with Sheffield, this photo was not taken in Sheffield...
Congratulations to Dr Sherif El-Khamisy on his promotion
We are delighted to report that Dr El-Khamisy has been promoted to be a Professor. This is mainly because of his recent successes in grants, fellowships and high profile publications, as reported below.
Postgraduate support programme wins Times Higher Award
In the 2014 Times Higher awards at the end of November, Sheffield won three awards: for Widening participation/outreach; Outstanding international student strategy; and Outstanding support for early career researchers. The last of these is for our Think Ahead programme, which is a support programme for early career researchers. In the Faculty of Science, it is run by Sandrine Soubes, who is based in MBB. See http://www.sheffield.ac.uk/faculty/science/researchers for more details.
Visit from Nobel prizewinner
In November 2014, MBB hosted a visit from Sir Tim Hunt FRS, who was awarded the Nobel Prize for Medicine or Physiology in 2001 for his work on the cell cycle - the system used by cells to regulate when cells divide. He talked on the work he has carried out since then, showing that nothing in science is simple or straightforward, and that progress relies on never taking anything for granted. His lecture was the occasion of the annual Krebs Lecture, and was introduced by Prof Simon Foster (right), chair of the Krebs Institute.
The Fatberglars steal gold in Boston finals
The International Genetically Engineered Machine competition (iGEM) is a global synthetic biology initiative in which student teams are given biological parts, and use them to build new systems and operate them within living cells. This year there were 250 teams from across the world with over 4000 registered participants, 2500 of which were higher education students. One of these was a team from the University of Sheffield (three MBB students and five engineers). Over the past 7 months, the team have been working hard to tackle the current problem of fat accumulations called ‘fatbergs’ within sewerage networks across the country. (Google the images – it’s pretty disgusting!)
The team had discussions with experts from the university and the water industry, and designed a simple system within E. coli which would highly express and secrete lipase and keratinase enzymes to be released into the network. The project was then showcased at the Giant Jamboree on the 30th October – 3rd November held in Boston, USA. The University of Sheffield iGEM 2014 team came back with a gold medal at the finals! They also got an honourable mention in the New Yorker magazine - see this link.
Dr El-Khamisy awarded Lister Research Prize Fellowship
At a ceremony at the end of October, Dr El-Khamisy of MBB (left) was formally awarded a Lister Research Prize Fellowship by Sir Alex Markham (right, formerly CEO of Cancer Research UK), and then spoke about his research on DNA break repair and degenerative disease.
JK Rowling anagram solved here
On Oct 6 2014, JK Rowling tweeted an anagram, "Cry, foe! Run amok! Fa awry! My wand won't tolerate this nonsense", creating a flurry of interest from Harry Potter fans. A day later the anagram was solved by Emily Strong, a PhD student in the Department - "Newt Scamander only meant to stay in New York for a few hours", this being a summary of the start of the screenplay of the forthcoming film based on JK Rowling's prequel to the Harry Potter series, Fantastic Beasts and Where to Find Them, supposedly written by Newt Scamander. Congratulations Emily!
Successful end to bike ride
As reported below, Prof Goldman (our head of department) took part in a sponsored bike ride from Land's End to John O'Groats (from the southwest corner of the UK mainland to the northeast corner) in September 2014. The team completed the ride on schedule and without too many aches and pains, and succeeded in raising lots of money for Hearing Research.
Overall the team raised over £36,000. Alastair raised nearly £2000 (though it's still not too late to contribute!).
MBB students achieve sporting success
Over the summer of 2014, two of our students (now both in their second year) achieved notable successes. Jen Wood (left) took part in the Youth Olympic Games in Nanjing, China in August. Climbing was a 'showcased sport' there, meaning that the International Olympic Committee were testing it out to see if it would be suitable for the Olympics, so this was an exhibition rather than a competition. Jen was the only Team GB climber in Nanjing. Back home, she made the Junior team in 2012 and is now a member of the Senior GB bouldering team.
Jai Meyrick (right) competed in the Kick-Boxing World Cup competition and got a bronze medal. Jai is the Sports Secretary for the MBB Soc.
MBB at UN meeting
Dr Milton Wainwright researches on the possibility that life originated elsewhere and came to earth via space. In September he gave a talk at a meeting organised by the UN, called Astronomy and the United Nations.
Welcome to new teaching staff member
We are delighted to welcome Nick Zoulias, who will be helping out in the practical lab, to allow Lizzie time to assist in postgraduate teaching. Nick studied for his PhD at the University of Manchester in Plant Developmental Biology. His focus was on the role of auxin in flower head development in the Asteraceae (sunflower) Family.
Research grant successes for MBB
During the summer of 2014, we had two notable grants. One is for nearly £700,000, to support Rebecca Corrigan who will be joining the department as a Sir Henry Dale fellow to work with our microbiologists; and the other is for £4.3 million. This is a highly prestigious grant to Profs Neil Hunter, Per Bullough, Dr Matt Johnson and four others, to carry out research on using bacteria to produce solar energy. This is the second such grant to Neil, and is an indication of the strength of his research.
Graduation ceremony 2014
July 23 was our graduation ceremony, and it turned out to be a beautiful sunny day. The ceremony itself was in the Octagon Centre, with a reception in Firth Court, celebrated by students and staff alike: the staff wearing robes appropriate to the universities they graduated from, making a colourful splash.
New member of staff
Dr Janet Cronshaw has recently arrived as a Daphne Jackson Research Fellow working in the laboratory of Prof. Stuart Wilson. Her research interests lie in the field of nucleocytoplasmic transport - the mechanism by which proteins and RNAs move into or out of the nucleus. She is investigating a novel pathway of mRNA export and its implications for human disease.
Careers data from 2013 graduates
The careers data have just been published for students graduating in 2013. The statistics are all collected 6 months after graduation, ie in December 2013, and show a consistent pattern over the last few years, with over 90% of our graduates in jobs or full-time study by that time. Only about one-third of our graduates go directly into full-time employment, while over half go into further study, reflecting the nature of the job market for biology graduates. Most of these go straight to a PhD: of the students who responded to the survey, 23 are doing a PhD, 4 a Masters, 4 teacher training, one a law training course, and one is doing a first degree in medicine.
How to target a bacterial cell wall
Research from the department just published in Nature Communications (2014, vol 5 page 269) by Dr Stéphane Mesnage, Profs Foster and Williamson, and colleagues in France and Japan, has brought us a step nearer to being able to target the cell walls of specific bacterial species. This is an important goal because it is a key target for the development of new antibiotics.
Bacteria have a cell wall that is made up of a polysaccharide related to cellulose and starch, and closely related to chitin, which forms the cell wall of fungi and exoskeleton of insects. It is crosslinked by peptides, which are specific for each bacterial species. Bacteria continuously remodel their cell walls in order to grow, and to do this they attach the relevant remodelling enzymes to binding domains, to bring enzyme and substrate close together. The most common binding domain is called LysM, and this study shows how LysM domains recognise their specific cell walls and discriminate against other bacteria and fungi. The figure shows the close interaction between a LysM domain and the polysaccharide (light blue) and its peptide crosslinks (salmon pink).
MBB leads on research to transport molecules across membranes
The Biotechnology and Biological Sciences Research Council (BBSRC) fund most basic biological reseach in the UK. They have set up several Networks in Industrial Biotechnology and Bioenergy, one of which is coordinated by Prof Jeff Green in MBB. Its aim is to develop better ways of moving molecules across membranes, by linking universities and industry. Further details can be found on their website, Twitter feed [https://twitter.com/CBMNet_NIBB] or newsletter.
More images from discovery night
Apologies to our readers: this is not exactly news as discovery night was back in March. However these are such great pictures we couldn't resist including them. Shown are two children in the virtual reality suite, getting to grips with 3D protein structures; and our resident science guru Nate Adams with his hands full of (real) fire.
Award for ex-MBB student
The Biochemical Society have given one of their four 2014 Early Career Research Awards to Glyn Hemsworth. Glyn studied Biochemistry at Sheffield and went straight into a PhD with Pete Artymiuk, where he worked on structures of an enzyme that digests single-stranded DNA, and a leptin-binding domain from the human obesity receptor. He is now at the University of York, doing structural work on enzymes involved in the breakdown of plant cell walls. He is pictured here wearing a headband traditionally worn by PhD students in the X-ray crystallography groups as they are about to go into their PhD vivas (which he passed with flying colours!). The translation is roughly "fighting spirit".
Research fellowship awarded
We have just learnt that Dr Sherif El-Khamisy has been awarded a Wellcome Trust New Investigator Award entitled "The repair of oxidative and topoisomerase-induced chromosomal breaks: mechanism and implications for human health". This award supports him and his research team over the next 5 years and has a value of £802,230, and represents recognition of his research at a very high level.
New prayer room in MBB
Next week, room H1 in MBB will re-open as a prayer room for muslim students (throughout the University, not just in MBB).
Head of Department to take part in sponsored bike ride
Our Head of Department, Prof Alastair Goldman, is taking part in a bike ride this September from Land's End to John O'Groats (ie from the bottom left to the top right of the UK) with a team from the University to raise money for research into hearing. If you would like to sponsor him, go to this link which tells you more about the riders (who include our very own Pro-Vice Chancellor, Tony Ryan) and has a link to Alastair's JustGiving page.
Two Students' Union awards for MBB
On May 22, the Students' Union held their annual ceremony to award staff for their support of students. We are delighted to report that our students nominated us for two awards, both of which we won! These were for the best departmental Staff-Student Committee (some of whom are pictured on the left), and for the late and sadly missed Prof Pete Artymiuk for the best student feedback. Thank you to all our students for your support.
MBB wins two Green Impact awards
In the 2014 Green Impact awards, MBB won a silver award (for the second time) plus a silver award specifically for labs. The awards are given for activities to reduce impact on the environment, such as reducing waste, energy efficiency, and turning things off when not in use, as well as spreading the word to be more environmentally aware.
Celebrating the MBBSoc
The MBBSoc is our undergraduate student society. It is affiliated to the Students' Union and organises a wide range of activities, both social and academic. This year's committee has been very active and is pictured left: (Top Row, Left to Right) Nicole Ackroyd (Social Secretary) Jordan Reed (Social Secretary) Arron Dougan (President) Guy Mayneord (Treasurer) Harriet Knafler (Charity and Outreach Officer)
(Bottom Row, Left to Right) Yasmin Proctor-Kent (Secretary) Leanne Miller (Publicity Officer) Lucy Spencer (Vice-President) Lara Grew (Publicity Officer) Olwen Seward (Female Sports Officer).
(On Committee but not present in the photograph) Charlotte Perry (Inclusions Officer), Rachel Plumb (Academic and Careers Officer), Alex Carter (Social Secretary) Jonny Korta ( Male Sports Officer).
The MBB Society has been nominated for “Outstanding Charitable Fundraising” at the Students’ Union Activities Awards. This year in particular was tough competition with the Union receiving over 350 nominations. MBBSoc has been nominated for its organisation of numerous charitable events throughout the year as well as strong links with Science Brainwaves and Sheffield RAG. Overall they have raised over £1300 for their adopted charity Teenage Cancer Trust, marking an incredible first year of fundraising, an initiative which was new to the society this year.
MBBsoc has also excelled in other areas this year. Achievements include: completing a successful rebranding of the society with a new logo, website and social media stream; gaining a record number of new members at the start of the year; and an amazing 38 applications for committee positions at their recent AGM.
MBB graduate sails into the history books
Three women have made history by becoming the first female submariners to serve in the 110-year history of the Royal Navy's Submarine Service. MBB graduate Lieutenant Penny Thackray (on the right) has completed months of specialised training, partly on the nuclear-powered Vanguard-class submarine HMS Vigilant, to earn her 'Dolphin'.
Penny obtained a 1st class degree in Biotechnology and Microbiology in 1995 and went on to do a PhD with Prof Anne Moir and a postdoc with Prof Jeff Green before joining the Navy. In her spare time (!) Penny represented Great Britain several times as a cross country runner, won the North of England cross country title in 1998, and got a bronze medal in the AAA 5000m.
Athena Swan Bronze award for MBB
We are delighted to announce that MBB have achieved a Bronze award from Athena Swan. Athena Swan awards recognise a department's commitment to advancing women's careers in science, technology, engineering, maths and medicine.
As part of our efforts, we have an MBB Women in Science section on the web page, which you can go to directly here. The site contains a range of links to further resources as well as a link to the documentation that we submitted in support of the award.
Prof Pete Artymiuk: in memoriam
We are saddened to announce the death of Prof Peter Artymiuk, at the age of only 61, after a brief battle with cancer.
Pete joined the Department in 1985 and has played a major role in the department since. He was a key player in the development of methods for refinement of crystallographic structures, including crystallographic B factors, and has determined structures of a wide range of proteins as well as developing software for recognising structural motifs, and being a founder member of the spinout company Asterion. His honesty, wit and passion for science will be sadly missed.
For a fuller account of Pete's life and achievements see here.
Congratulations to Varsity participants
Spring 2014 saw the annual Varsity sports competition between Sheffield University and Sheffield Hallam University. This year the competition included 42 sports, and Sheffield Uni won by a margin of 42 to 30.5. MBB saw a good number of participants, including (in the picture, L to R) Sam Wileman [#2 in tennis team, L1 Biochemistry], Sarah Gee [basketball, L1 Molecular Biology], Abdulla Altamimi [10-pin bowling, won 30-11, postgraduate student], John Rafferty [10K run, academic staff], and Jai Meyrick [boxing (men's English kickboxing champion 2013!), L1 Biochemistry]. Other MBB participants include Tom Champion and Jenny Ventress (10K run), Jennifer Wood (winning team in climbing), Chelsea Hodgson, Jonny Korta, Sam Swift and Giles Haynes (hockey), and many others including football, cheerleading, water polo, rugby league and rugby union.
Friday March 21 was Discovery Night at the University, when we opened our doors to showcase exciting research going on. MBB was represented by Nate Adams (below left) who set fire to soap bubbles in his hands, changed the colour of flowers, and lots more dramatic stuff; by our Atom Labs stand in Firth Hall (below right); and by George Mobbs showing off 3D proteins in the Virtual Reality suite.
Research highlights from MBB
Two members of the department have recently had their work published in high impact journals. Only the highest quality work gets into such journals, so this represents a strong vote of confidence in the importance of the research. Dr Robert Fagan has published a review in Nature Reviews in Microbiology about a layer on the outside of many bacteria (including the hospital pathogen C. difficile) called the S-layer, which is important for their growth and survival: and Prof Julie Gray has published research in Molecular Cell showing how plants signal using nitric oxide (also an important signal in humans, used to control blood pressure and the target of the drug ViagraTM). The Figure (right) shows that nitric oxide is required for the germination of plant seeds.
New appointment: Roy Chaudhuri
Roy joined the Department in January 2014, after postdocs at Birmingham and Cambridge, and a spell as Bioinformatics Team Leader at the Centre for Genomic research at Liverpool. He writes:
I am a computational biologist, and one of the founder members of the Sheffield Bioinformatics Hub. This is a cross-departmental initiative to establish a world-class bioinformatics capability in Sheffield, to facilitate collaborative research and the exploitation of next generation sequencing and other high-throughput technologies.
My research interests are primarily in the area of functional and comparative genomics of bacteria, particularly E. coli and Salmonella. I am interested in understanding the process of genome evolution and the differences in genome structure and function associated with commensal and pathogenic lifestyles, and with different host preferences.
Over the last few years I have been involved in the development of methods for the analysis and visualisation of data derived from Transposon directed insertion site sequencing (TraDIS). This is a sequencing-based transposon mutant screen which can be used to identify bacterial genes essential for survival, which represent potential targets for the development of novel antimicrobials. It can also be used to identify genes required for survival in an infection model or other selective screen, which can be used to select candidates for the development of new vaccines.
Away from work, I am a Manchester United season ticket holder, CAMRA member and regular at the Glastonbury festival.
An inspirational lecturer
Dr Milton Wainwright is giving a talk on March 27 2014 to Inspiration & Co, following nominations and votes organised by the Students' Union to find the most inspirational lecturers in Sheffield University. His talk is entitled Causing Trouble - In the Nicest Possible Way and covers his work on searching for extraterrestrial life in the stratosphere plus several other controversial topics.
Dr Wainwright has recently been elected as a Fellow of the Royal Astronomical Society, in recognition of his work on panspermia.
New teaching staff in the practical lab
We are delighted to welcome Drs Lizzie Alvey and Patrick Murphy, who are mainly to be found working in the practical labs, and will soon be very familiar faces to our undergraduate students.
Lizzie did a PhD at the John Innes Institute in Norwich on hormone signalling in plants, followed by a postdoc at Cambridge studying meiosis in early land plants. Patrick did a PhD at Manchester in yeast genetics, with particular relevance to protein synthesis.
An enterprising group of researchers from MBB have been awarded Wider Participation Funding from the university to buy a MakerBot Replicator 2 3D printer for use in outreach work. The printer works a lot like a hot glue gun, melting plastic made from corn-starch at 230oC to extrude a long strand that is laid down in layers to produce the final shape. It works well for any 3-dimensional model, for example a ball and stick structure of DNA or a model of the outer coat of the bacterial exosporium determined by Electron Microscopy (shown above). If you want to see it in action, come along to Discovery Night on the 21st March in Firth Hall, where it will be found on the Atom Labs stand.
Goodbye and welcome back
The Department bids farewell to Prof Peter Piper, who retires at the end of January. He is however returning as an Emeritus Professor, which means he will continue contributing to the Department. We are now starting to look for a new lecturer to take his place.
Research grant success in 2013
Research grants to members of the department in 2013 totalled £6m. This is an excellent achievement and includes large grants of £2m to Prof Hunter and £1.2m to Prof Foster. In total, 11 members of staff were awarded grants in 2013, thus spreading the new money around the department. We are happy to note that three of our new appointments (Drs El-Khamisy, Fagan and Mesnage) were successful in getting funding; and the funding also includes two fellowships to support early career researchers.
Prof Williamson's textbook How Proteins Work has been translated into Italian, with the title Come funzionano le proteine, published by Zanichelli; and Prof Sudbery's textbook Human Molecular Genetics has been translated into Italian [Genetica moleculare umana] and Spanish [Genética Molecular Humana].
Congratulations to new PhD graduates 2013
In 2013, 34 students were awarded their PhDs. We congratulate them on their achievements:
- Jayne Louise Wilson (Poole) The anti-microbial effects of carbon monoxide and carbon monoxide releasing molecule 3 (CORM-3)
- Richard Salmon (Artymiuk) Structural studies on proteins from pathogenic bacteria
- Laura Smith (Green) Characterisation of the essential transcription factor, WhiB1, from Mycobacterium tuberculosis
- Othman Baothman (Green) Characterisation of Salmonella aconitase proteins
- Peter Drake (Hettema) The first genome-wide screen for animal peroxins in Drosophila melanogaster
- Leenah Alaalm (Sudbery) Phospho-regulation of the Candida albicans hyphal repressor Nrg1 by the action of multiple kinases
- Magdah Ganash (Artymiuk) X-Ray crystallographic and electron microscopy studies on members of the ClyA/Nth family of the pore-forming toxins avian pathogenic E. coli Cytolysin A and B. cereus non-hemolytic enterotoxin
- Matthew Day (Rice) Structural studies on protein targets from the pathogenic bacterium Burkholderia pseudomallei
- Nuttawan Pramanpol (Baker) Structural studies on immunogenic proteins of Burkholderia pseudomallei
- Rober Howlett (Kelly) Analysis of Campylobacter jejuni amino acid metabolism and solute transport systems
- Christopher Marklew (Hunter) Structural and functional characterisation of magnesium protoporphyrin IX chelatase from Thermosynechococcis elongatus
- Khalid Alquthami (Wainwright) Medical implications of the effect of germanium etc
- Timothy Doheny-Adams (Gray) Manipulating stomatal density affects plant growth, yield and drought tolerance
- Salah Jaber (Wainwright) Canine faeces: The microbiology of an environmental health problem
- Qiang Wan (Bullough) Structure and assembly of bacillus spore proteins
- Sultan Alsharari (Wainwright) Studies on the microbiology and biogeochemistry of some industrial wastes and a preliminary evaluation of the use of biochar in spoil remediation
- I-Fang Teng (Wilson) Mapping mRNA export complex formation in living cells
- Peter Davis (Staniforth) Structural studies of cystatin B amyloid fibre, oligomer and novel therapeutic discovery
- Erika Pellegrini (Waltho) Dissection of enzymatic phosphoryl transfer from substrate recognition to the transition state
- Nathan Chan (Bullough) Electron microscopy of membrane proteins
- Mohammad Fakieh (Hettema) Trafficking of the peroxisomal membrane protein Pex3 in Saccharomyces cerevisiae
- Mariana Tinajero Trejo (Poole) The globins of Campylobacter jejuni: A functional study in a heterologous host
- Abdolkader Abosamaha Mohammed (Gilmour) Molecular identification and physiological characterization of moderately halophilic and alkaliphilic bacteria belonging to the genus Halomonas
- Mahsa Movahedi (Gray) Identifying stomatal signalling genes to improve plant water use efficiency
- Naji Al Ibrahim (Green) Characterisation of the Escherichia coli YdhY-T operon
- Ibrahim AlShubaith (Gilmour) Molecular identification and characterisation of extremophilic and pathogenic microorganisms from water samples collected in the UK and Saudi Arabia
- Shadi Zakai (Kelly) Biogenesis of the outer membrane of Campylobacter jejuni
- John Kendall (Kelly) The response of Campylobacter jejuni to hyperoxic conditions and the role of iron-sulphur cluster enzymes in microaerophily
- Nur Adeela Yasid (Williamson) Metabolite analysis of Escherichia coli in response to changes in oxygen levels
- Yueh-Ting Lu (Hornby) The mechanism of error-prone repair in Escherichia coli
- Helen Jesse (Poole) Carbon Monoxide and Carbon Monoxide - Releasing molecules as novel antibacterial agents: Mechanisms of toxicity and resistance
- David Mothersole (Hunter) Assembly, structure and organisation of photosynthetic membranes
- Marzieh Fanaei (Partridge) Investigating the role of tetraspanin proteins in multinucleated giant cell formation using recombinant proteins
- Yahya Aldawood (Hornby) Purification of E. coli McrBC complex and mapping inactive mutations in MrcB using Error-Prone PCR
A bumper month for research grants
In November 2013 members of the department won over £1.6m in research grants, from the BBSRC, Wellcome Trust and other sources, including grants to two of our new appointments (Robert Fagan and Sherif El-Khamisy).
Latest NSS scores show MBB in a strong position
The National Student Survey (NSS) is an official survey reporting views of undergraduates on their courses, maintained by unistats, and is therefore an important measure of the quality of teaching. In some years, NSS does not report results for all MBB courses, because there are not enough students for the results to be statistically significant. The 2013 results include all our courses, and show that MBB is in the top 5 for overall satisfaction nationally for all courses, as we have been consistently since the survey started (except for a blip last year). In Biochemistry and Molecular Biology we achieved an overall satisfaction rating of 98!
|Biochemistry and Mol. Biol.||Genetics||Microbiology|
Congratulations to Jeremy Craven on his promotion
We are delighted to report that Dr Jeremy Craven has been promoted to Senior Lecturer.
Making an impact – young researcher Carla Turner
Carla Turner is a PhD student in MBB, working on signalling pathways in plants. But she is a student with a difference – she is passionate about communicating science. She is head of communications for the Plant Environmental Physiology Group, a subgroup of the British Ecological Society and the Society for Experimental Biology. While on an internship at Syngenta, she was shortlisted for the Society of Biology’s young science research communicator of the year award, as part of which she went to Westminster to meet Andrew Miller MP, chair of the Science and Technology Committee. And she is an active member of Science Brainwaves, described elsewhere on this news page. For example, she regularly organises schools visits, and she co-presents a weekly slot on Forge Radio, Sheffield University’s very own radio station (check it out on http://forgetoday.com/radio/show/science-brainwaves/, or even better listen in at 11 am on Sunday mornings). The photo shows the excitement on the faces of budding young scientists as they watch an egg get sucked into a conical flask by atmospheric pressure alone.
MBB hosts visit by Nobel prizewinner
In October 2013, the Department hosted a research lecture by Professor Sir John Walker FRS, winner of the Nobel Prize in Chemistry in 1997, who talked about his recent research on the Fuel of Life, the molecular machine that generates ATP from a proton gradient across the mitochondrial membrane. Fittingly, this was the Krebs Memorial Lecture, since Hans Krebs' work centred on the fundamental energy-generating reactions in the cell. The visit was organised by Prof Neil Hunter FRS, whose own research is on the other main energy-generating system, photosynthesis.
Developments in bioinformatics
Bioinformatics is the use of computers to dig information from large biological datasets, for example genome sequences or lists of protein interactions. As the amount of data multiplies, bioinformatics is becoming even more important. The University of Sheffield has made a number of recent new appointments in bioinformatics, within Biology and Medicine, including two new academic staff in MBB: Roy Chaudhuri to start in December 2013 and Ian Sudbery in 2014. All these staff will be housed together in a new Bioinformatics Hub in MBB.
Evidence for life from space?
A research team led by Milton Wainwright, of the Dept of Molecular Biology and Biotechnology, has obtained particles from an altitude of between 22 and 27 km, during the recent Perseid meteor shower. Several of these look like they have a biological origin, in particular the diatom shown here, which resembles several terrestrial species. The team has done calculations to show that the probability of particles this high in the atmosphere coming up from the ground is very low. Analyses of isotope distribution will provide more detailed evidence on whether these particles really do come from meteors.
Welcome to two new members of staff
A warm welcome to two new members of staff: Rebecca Barnes (left) and Emma Jones (right). Rebecca studied the molecular biology of trypanosomes in Glasgow and Yale, while Emma worked on mitochondrial DNA replication, HIV vaccines and iron absorption in thalassaemia in Oxford. They will both be heavily involved in teaching within the Department. Rebecca is a year tutor for level 1 students and will develop level 1 practicals and tutorials, while Emma will work in a similar way with level 2 students. They are also giving some lectures and working with project students. They can be found in room D5b.
European Biology students gather in Sheffield
From July 28 to August 2 2013, the University of Sheffield is host to the annual SymBioSE meeting, at which biology students from all over Europe gather for a week of research presentations, worksops and social events. For more details, see http://www.sheffield.ac.uk/faculty/science/news/events/symbiose-2013
MBB researcher takes part in aikido World Championships
MBB postdoc Dr Caspar Chater, who works on the development of plants with Prof Julie Gray, was part of the UK team in the Aikido World Championships, which took place in July 2013 in Osaka, Japan. Caspar has been training in competitive aikido since 2006 in Sheffield, and got to the 3rd place playoffs. The UK team got as far as the quarterfinals, which is its best performance ever. Caspar said 'The next World Championship is in two years time in Brisbane, and we hope to do even better'. The picture shows Caspar in action; in the team photo he is the one taking a bite out his team-mate.
We had glorious weather for the graduation day. The picture below shows the level 4 and PhD students celebrating. A big selection of other photos can be found on our Facebook page, https://www.facebook.com/pages/MBB-University-of-Sheffield/105509697033
Welcome to two new members of staff..
We are delighted to welcome two new members of staff who will be arriving in September. Dr Rebecca Barnes comes to us from Yale Medical School, and Dr Emma Jones is from the University of Oxford. Their main roles will be to inject new life into our undergraduate teaching.
.. and farewell to retiring staff
This summer we have said goodbye to several members of staff who have been with us a long time. These are:
- Dr Charlie McDonald, who has been teaching Biochemistry here since 1984, and also introduced mammalian molecular biology to the Department.
- Prof Mike Fowler, who has been here since 1971. He became Professor of Biotechnology, and has founded and run several companies. More recently, he has nurtured our links with the University of Sharjah, creating what is now the largest department in that University.
- Dr Graham Warren, who started his PhD in Sheffield in 1974 and was appointed as a lecturer in Mike Fowler's Wolfson Institute of Biotechnology in 1985. Graham and Charlie have for many years been the backbone of our undergraduate teaching, and have regularly been awarded the MBB Teaching Prize (an award chosen by students).
- Ann Pease and Eileen Platts, who will be remembered by generations of undergraduates as the technical staff who cheerfully kept the practical labs running smoothly.
More detailed appreciations of Charlie, Mike and Graham can be found here.
Research from MBB: How bacterial cells grow
Bacterial cells are surrounded by a cell wall made out of a mesh of carbohydrates and peptides, which provides their structural strength. Many antibiotics (eg penicillin and vancomycin) work by disrupting synthesis of the cell wall, so it is important to understand how it is assembled. New research from MBB, published in the journal Nature Communications (2013, volume 4, page 1496) shows how the bacterium E. coli does it.
E. coli is rod shaped, and it has been known for a long time that it grows by inserting extra material into the cell wall to make the rod longer, until the cell is long enough to divide into two. The general assumption has been that the new material is added in strips into the middle of the rod. Prof Simon Foster in MBB has been collaborating with colleagues in the Department of Physics in Sheffield to develop new high-resolution microscopy techniques. They have shown that that the new material is added in patches (see picture on right), specifically to regions of the cell wall that are thinnest, and therefore that E. coli has a mechanism for detecting these weaker patches. This finding opens up routes for developing new antibiotics.
Congratulations to new appointment on a prestigious research fellowship
Congratulations to new research academic Dr Sherif El-Khamisy, who has been awarded a Lister Research Prize Fellowship by the Lister Institute of Preventative Medicine. Many Lister fellows have gone on to distinguished research careers, including two current professors in MBB, Jon Waltho and David Rice.
Dr El-Khamisy starts (as a Reader) in MBB in August 2013, and writes:
Our research is focused on understanding mechanisms of repairing oxidative and topoisomerase-mediated DNA damage and their association with human disease, such as cancer and neurodegeneration. Particularly, we are interested in studying how enzymes that repair trapped topoisomerases, such as tyrosyl DNA phosphodiesterase 1 (TDP1) and the newly discovered enzyme TDP2, participate in protecting our genetic material from genotoxic stress. The goal of our work is to expand our knowledge of DNA repair and translate this data into tangible ideas and next-generation treatment paradigms with improved patient quality-of-life. I enjoy playing squash and losing to my daughter at chess but my main recreation is sleeping.
New appointmen: Karim Sorefan
Karim joined the Department in May 2013, after postdoctoral appointments in the John Innes Centre and University of East Anglia. He writes:
I am interested in the molecular mechanisms that regulate plant development. My lab has a particular focus on understanding the function of small RNAs. Small RNAs may be tiny in stature, being only 20-30 nucleotides long, but they have a huge role in controlling biological processes. It is estimated that 40% of the human genes are targeted by small RNAs. In plants, small RNAs have many biological functions including the regulation of stress responses, epigenetic states and plant stem cell development.
All above ground plant tissues are derived from a small mound of undifferentiated stem cells called the meristem. My lab is interested in meristem differentiation, and how it is regulated by a network of transcription factors that control small RNA pathways. We are using next generation sequencing approaches to investigate the global expression patterns of genes and small RNAs.
New appointment: Stuart Casson
Stuart will arrive in August 2013 from the University of Bristol. He writes:
My research is focused on understanding the environmental and genetic control of plant development. I began my research career with Prof Keith Lindsey at Durham University studying the molecular genetics of plant embryogenesis and root development. I followed this with a move to the laboratory of Prof Alistair Hetherington at the University of Bristol where I began to use the stomatal system and developed my research on the environmental regulation of plant development and plant water use.
Stomata are found on the surface of plant leaves and consist of a pair of specialised guard cells surrounding a microscopic pore. They regulate gas exchange, primarily carbon dioxide and water, between the plant and the environment and are are considered to be one of the key innovations that allowed plants to colonise the land. In the short term, plants are able to regulate the aperture of the stomatal pore via changes in guard cell turgor. My research however, is interested in a longer term developmental response, whereby plants can modulate the number of stomata on their leaves in response to environmental change. In particular, I have focused on how light signals influence these changes in stomatal development and have demonstrated that the red light photoreceptor, phytochrome B, is a key component of light mediated changes in stomatal development. Sheffield has vast expertise in plant biology ranging from the molecular to global level, particularly in stomatal biology, and I’m looking forward to continuing my research in such a vibrant environment.
New appointment: Robert Fagan
Robert joined the Department in January 2013 after Postdoctoral positions at Imperial College London and a PhD from Trinity College Dublin. He writes:
My work focuses on the hospital superbug Clostridium difficile. C. difficile is a common member of the bacterial community in a healthy human gut. Treatment with antibiotics causes widespread disruption to this community and allows C. difficile to flourish.
I am primarily interested in how the bacterium colonises the human gastrointestinal tract. To that end my lab studies how the bacterium first secretes and then assembles the myriad proteins which coat the bacterial cell surface. These proteins mediate the interactions between the bacterium and its host, as well as carrying out many other essential tasks in the life cycle of the organism. Each C. difficile cell is covered with a continuous protein layer made up of about 500,000 individual proteins assembled into a symmetrical paracrystalline array or S-layer. Assembly of this layer requires enormous energy expenditure by the bacteria and its correct assembly is essential for bacterial survival and colonisation of the host.
New appointment: Matt Johnson
Matt first came to Sheffield as an undergraduate in 2000, before going on to complete a PhD in Professor Peter Horton's laboratory in 2007. From 2007-2011 he worked as a Posdoctoral Researcher in the lab of Professor Alexander Ruban at Queen Mary University of London before returning to Sheffield in 2011 as a Leverhulme Trust Research Fellowship. He writes:
My research is focused on the role of thylakoid membrane organisation in photosynthesis, the process that uses solar energy to transform water and carbon dioxide into the energy we consume and the oxygen we breathe. The enzymatic fixation of carbon dioxide into carbohydrate in the chloroplast stroma requires energy in the form of ATP and reducing power in the form of NADPH, which are provided by photosynthetic electron transport in the thylakoid membrane. The thylakoid membrane houses several major pigment-protein complexes involved in electron transport including photosystem II (the water-splitting enzyme), cytochrome b6f, photosystem I and ATP synthase. The efficiency of photosynthesis depends upon the rate of excitation energy transfer, the diffusion of electron carriers and the effectiveness of regulatory and repair processes, which in turn depend upon the spatial organisation of the pigment-protein complexes in the membrane.
I use a multidisciplinary approach combining high resolution imaging techniques such as atomic force microscopy, affinity-mapping AFM and stochastic super-optical microscopy (STORM/ PALM) with membrane biochemistry to elucidate how these complexes are spatially organised within the membrane. These state-of-the-art single molecule techniques allow me to gently image the membranes in their natural liquid environment thus preserving the native organisation of the pigment-protein complexes within. Armed with the complete picture of how the protein complexes of photosynthesis fit together in the membrane we can identify new genetic targets for improving the efficiency of photosynthesis for increased food and biofuel production. Understanding natural photosynthetic membrane organisation will also allow us to better imitate nature and so improve the design of artificial solar cells and carbon capture devices to provide green energy and a low carbon future for the planet.
Outside work I spend my time playing cricket for the University Staff Sunday XI, as Vice-Captain of the team (see photo) and preparing for my new life as a father- due to commence October 2013...
MBB researcher reaches out into the local community
MBB postdoctoral researcher Nathan Adams is not your average scientist. In addition to his day job in the Department, he works as a demonstrator for BBC Science, on shows such as Bang Goes the Theory and the One Show, as well as for the Royal Society of Chemistry and Biological Society, and enjoys going out there and enthusing others about science – he regularly goes out on the road giving talks enlivened with hands on experiments. In March 2013, the University of Sheffield organised an evening of talks and demonstrations on science and engineering, and Nate gave his ‘Kitchen Science Carnage’ talk to schoolchildren, showing how organic polymers can be used to absorb shock (see picture in the news item below), and setting fire to hydrogen bubbles (see picture below and on the Steel Science site). The show was so impressive that it made it on to BBC’s Look North.
But his interests extend also into the relationship between art and science. In a derelict urban site close to the University, Nate is creating an Installation called Neurone. This is an imaginative look at how neurones interact to create a thinking brain. It is constructed from hundreds of LEDs plus lots of wiring, netting and code that enables it to respond to you. For more, look here.
Six new lecturers appointed to department
In the last few months, we have appointed six new lecturers to the department. Left to right:
- Stéphane Mesnage joined in August 2012 from the University of Paris. He works on the bacterial cell wall.
- Matt Johnson joined in August 2012 following research posts at Queen Mary University of London and Sheffield. He works on the photosynthetic membrane in plants.
- Robert Fagan joined in January 2013 from Imperial College London. He works on the human pathogen ('superbug') Clostridium difficile, and how it interacts with its human host.
- Sherif El-Khamisy joins in August 2013 from the University of Sussex. He works on the repair of single-strand breaks in DNA, particularly using yeast as a model organism.
- Stuart Casson joins in August 2013 from the University of Bristol. He works on plant development, in particular the development of leaf iridescence and stomata.
- Karim Sorefan joined in May 2013 from University of East Anglia and works on the function of short RNA sequences.
Discovery Night March 18 2013
The University put on a series of demonstrations and exhibitions as part of the Sheffield Festival of Science and Engineering on March 18 2013. Several members of MBB took part. Shown here (left to right) are Dr Nate Adams, who is demonstrating the remarkable properties of polymers by hitting one hard with a hammer with his fingers underneath; Dr John Olsen, explaining the finer points of Atomic Force Microscopy; Rebecca Lowry ( a former undergraduate in MBB, now doing a PhD in the Dental school) showing how to make a model of bacterial flagella; and Dr Craven Jr who is hoping to extract sweets from a piñata, this being vaguely related to cancer. Nate was interviewed on BBC Radio Sheffield, and appeared on BBC Look North setting fire to bubbles containing hydrogen.
MBB wins silver in Green Impact Awards 2012/3
MBB were one of only three academic departments to get silver awards in the University's Green Impact sceme this year, which overall is calculated to have saved well over 300 tons of CO2 and £70,000 in the last year.
Research grants to MBB staff
Research grants announced in 2012 include grants to Profs Kathryn Ayscough, Alastair Goldman, Simon Foster, David Kelly, Stuart Wilson and Mike Williamson and Dr Jim Gilmour. There is not much money around for research at the moment, so these represent excellent achievements and genuine recognition for the quality of the research being carried out.
Congratulations to new PhD graduates 2012
In 2012, 26 students successfully defended their PhDs, and we congratulate them on their excellent achievement. In alphabetical order:
- Mohammed Al Malki (Gilmour): Molecular identification and characterisation of extremely acid tolerant microorganisms isolated from Rivelin and Limb valleys
- Heba Alhamal (Hornby): Tandem affinity purification of McrBC complex and mapping inactive mutations in McrC using error-prone PCR
- Nagat Ali (Gray): The function of guard cell expressed genes in Arabidopsis thaliana
- Reda Hassan Amasha (Wainwright): Studies on the environmental microbiology and biogeochemistry of desert surface soils
- Carlos Avila Ramirez (Poole): Response of Campylobacter jejuni to oxygen limitation and the caecal environment
- Claudine Bisson (Rice): Substrate and inhibitor binding in IGPD2
- Lesley Bowman (Poole): The impact of peroxynitrite on Escherichia coli
- Ruth Brown (Ayscough): Identification of novel endocytic cargo molecules in Saccharomyces cerevisiae
- Chung-Te Chang (Wilson): SRAG functions as a new mRNA export co-adaptor
- Adam Croucher (Goldman): Investigation of the expression and function of meiotic genes in human tumours
- Hugh Dannatt (Waltho): The role of enzyme dynamics in catalysis by ß-phosphoglucomutase
- Adham El-Shawaidhe (Staniforth): Role of human cystatin C in Alzheimer's disease
- Claudia Flemming (Artymiuk): Structural studies on DNA binding proteins
- Chris Glover (Bullough): Two-dimensional crystallisation of membrane transport proteins
- Joanna Griffin (Waltho): Investigations of the metal fluoride transition state and ground state analogue complexes of HAD superfamily proteins by NMR spectroscopy
- Abdullah Ibrahim (Gilmour): An investigation of the microbial diversity of Hoole Bank acid tar lagoon
- Yi Jin (Waltho): Metal fluorides as probes for enzyme catalysed phosphoryl transfer
- Michaela Livingstone (Wilson): Post-transcriptional gene regulation by LUZP4 and CIP29
- Tacita Nye (Poole): Dissection of the roles of individual terminal oxidases in E. coli: the third oxidase, cytochrome bdII
- Nur Zazarina Ramly (Rice): Molecular analysis on the superfamily of surface antigens from the apicomplexan parasite Eimeria tenella
- Sari Sabban (Helm): Development of an in vitro model system for studying the interaction of Equus caballus lgE with its high-affinity Fc receptor
- Sarawut Sattayakawee (Gilmour): Glucosylglycerol: A compatible solute in Arthrospira (Spirulina) platensis
- Adam Smith (Ayscough): The interactions and functions of Las17, the yeast homologue of mammalian WASP
- Martin Turner (Mitchell): An investigation of the C1D family of proteins in Saccharomyces cerevisiae
- Agnieszka Urbanek (Ayscough): Regulation of actin dynamics by YSC84 and LAS17 in yeast endocytosis
- Richard Wheeler (Foster): Peptidoglycan architecture and dynamics in Gram-positive bacteria
New treatment for organophosphorus poisoning
Organophosphorus (OP) agents are used widely as pesticides, although their use has been banned in much of the developed world. It is estimated that about 200,000 people die every year from OP poisoning. There also remain large stockpiles of OP agents such as sarin and VX, deleloped as nerve gases. There is an urgent need to develop scavengers which can inactivate OP agents, either immediately after accidental dosing or prophylactically for soldiers in danger of attack by nerve gases. Prof Mike Blackburn of MBB has been part of a collaborative team that recently reported (Proceedings of the National Academy of Sciences of the USA, 2013, vol 110(4), page 1243 the development of such a scavenger, which effectively protected mice against the nerve agent VR. More details can be found from the University of Sheffield's news feed.
Congratulations to Roger Anderson!
We are delighted to announce that in December 2012, our Director of Studies, Deputy Head of Department and head of teaching, Roger Anderson, was promoted to Professor, in recognition of his significant role in teaching and administration within the Department and across the University over many years. He was also elected a Fellow of the Society of Biology in January 2013, awarded to those who have made 'a prominent contribution to the advancement of biological sciences'.
Exciting research from MBB in 2012
Staff from MBB have published four papers during 2012 in Proceedings of the National Academy of Sciences of the USA (PNAS). This journal only publishes exceptional science, and these papers make important contributions.
- Prof Waltho published work in May (page 6910), looking at how the enzyme β-phosphoglucomutase catalyses the transfer of a phosphate group. This enzyme is a representative of the general group of enzymes called kinases, which are major drug targets, and accelerate reaction rates up to a remarkable 1021 times. His work showed that the enzyme works not just by binding the substrate correctly, but it also provides an adaptable environment that directs the whole pathway of phosphate transfer, and at the same time makes unwanted side reactions less favourable.
- Prof Hunter published work on photosynthesis on page 8570. All organisms that carry out photosynthesis have to deal with a major problem: how to convert light energy to chemical energy without damaging the cell as a result of oxidation. Solving this problem will be vital to the development of more efficient solar cells. Previous work from Sheffield has looked at how plants overcome the problem: this work looked at photosynthetic bacteria, and showed that the bacteria are protected by the red carotenoid pigment called spheroidene, which mops up the reactive oxygen.
- Prof Green published work on page 15734, looking at how the gut bacterium E. coli senses the presence of oxygen. This process is vital, because E. coli has to adapt very rapidly between growing without oxygen (in the gut) and growing with oxygen (outside the body): it is its ability to do this that allows it to act as a food-borne pathogen. He showed that it uses a sensing molecule that has iron atoms at its core, which cycles between oxidised and reduced states using an evolutionarily ancient mechanism.
- Prof Waltho published the fourth of these papers in November, on page 19563. The question was a fundamental one: how proteins fold up so quickly to their complicated three-dimensional shapes. The classic explanation is that proteins follow a smooth pathway, not unlike skiing down a bumpy hillside. Using a novel experimental approach, he showed that the ride is much bumpier than this: at every point and on every scale, there are big energy barriers. This slows down the folding, but also helps the protein avoid going down blind alleys.
MBB wins Green award
The University recently started a 'Labs Switch Off' campaign, encouraging us all to switch off unwanted equipment and thus save electricty. MBB are the first winners, having reduced our energy consumption by 14% compared to the same time last year.
Researchers' Night in the Festival of the Mind
The University of Sheffield opened its doors in September 2012 for the Festival of the Mind. As part of this, MBB researchers took part in Researchers' Night on September 28, with a varied set of contributions, covering (left to right) the use of Atomic Force Microscopy to investigate structures in bacteria, extracting DNA from strawberries, the history of the discovery of penicillin (in Sheffield), and whether life arrived on earth from outer space.
Graduation party 2012
As usual, we celebrated our new graduates with a party in July: a celebration lunch, speeches, prizes, tours of the Department, the graduation ceremony itself, and of course lots of photos. To see many more pictures, visit our Facebook page.
New Head of Department
We are happy to report that Prof Dave Hornby has done his bit for the Department and has been replaced by the new Head, Prof Alastair Goldman (the one in the tasteful green and pink gown in the photo). Dave is smiling broadly over his shoulder.
New insight into protein production
Prof Stuart Wilson in MBB, in collaboration with scientists at Harvard University, has published important research in the journal Nature Communications (2012, Vol 3 page 1006). In humans, DNA is copied to RNA in the nucleus, and the RNA then is exported from the nucleus into the cytoplasm to be made into protein. Errors in this process lead to a wide range of diseases including motor neuron disease, myotonic dystrophy and cancer. His work explains how RNA is tagged to allow it to leave the nucleus. He comments: "Until now, it has not been clear how the cell knows when the mRNA should be given a passport allowing passage to the cytoplasm. Now we have identified how the passport is issued." It turns out that it requires a protein called TREX.
Science Brainwaves receives the Sir Walter Bodmer award
Science Brainwaves is an enthusiastic group of science communicators, made up of undergraduate, Masters and PhD students from science departments at the University of Sheffield, as well as postdocs. They organise a wide variety of activities in and around Sheffield, with the aim of showing that science is fun and that scientists are not mad boffins in white coats. They are a branch of the British Science Association, in fact the most active group outside London, which is why they were awarded the 2012 Sir Walter Bodmer Award, recognising the achievement of volunteers within the BSA. The awarding committee gave special praise to Tacita Nye, a PhD student from MBB, who chaired it in 2011-12 until she stood down in order to write up her PhD thesis.
Science Brainwaves organises a wide range of outreach activities for schoolchildren, including the popular A question of taste, in collaboration with the University of Sheffield and the Association for Science and Discovery Centre, supported by the Wellcome Trust, in which students carry out analysis of their own DNA to investigate their sense of taste. They have organised sell-out events for the general public, including pub quizzes, film nights, a radio show at Sheffield Live, and hands-on talks such as Weird physics, Science of cocktails, Botany of gin and Better looking, better loving.
Science Brainwaves is part of the British Science Association, Registered Charity 212479 and SCO39236.
Developing links with the University of Sharjah
Staff from MBB, led by Emeritus Prof Mike Fowler (programme director for the course), have been helping the University of Sharjah develop a new degree programme in Biotechnology, as a collaborative venture with the University of Sheffield. The first 8 graduates from the 4-year course graduated in June 2012, and the course continues to grow in popularity, with well over 360 currently enrolled. We are delighted to welcome some students from the course to Sheffield over the summer of 2012, who are visiting as part of the Erasmus programme.
The course has been awarded an International Recognition Certificate by the Society of Biology, and is the first international course to receive such recognition. UK-based external examiners have visited Sharjah, reported on the first cohort to graduate, and approved the standards of the course.
Sharjah is the third largest emirate within the UAE and borders Dubai and Abu Dhabi. The University of Sharjah was founded in 1997; the Biotechnology course is the flagship course of the Department of Applied Biology and is now the largest course within the College of Sciences.
Senate Award for teaching for Dr Anderson
We are delighted to report that Dr Roger Anderson, our Head of Teaching, was recently awarded a 2012 Senate Award for his sustained contributions to teaching and learning in the University.
Latest careers data for MBB graduates
Data are now available for undergraduate students graduating in summer 2011. Students are surveyed in the December following their graduation. The results show a very consistent pattern over the last few years, with about 90% of graduates in work or further study (a very high figure by comparison to national averages), and 80% of these in graduate level jobs. Graduates continue to find jobs in major biology-based employers such as GE Healthcare and Sanofi-Aventis. There is a trend for an increasing number of our graduates to go on to further study. Of the 2011 graduates, 22 went on to PhDs, 10 to Masters courses and 4 to PGCEs. Further details can be found on our Careers page.
Green Impact award for MBB
MBB won a bronze award for Green Impact at a ceremony led by the Vice-Chancellor in April 2012. Green Impact is a flagship project run by the National Union of Students, designed to help staff change environmental practices, and the award recognises the effect already achieved by practical changes in working practices.
MBB student success
We congratulate final year student Sav Cardamone and his dance partner Charlie Lowe. At the Inter-Varsity Dance Competition in Blackpool on March 4 2012, they won the award for Varsity Most Promising Couple as well as winning in Ballroom and Latin categories.
Breakthrough in fight against meliodosis
Meliodosis is a disease that affects millions of people in South East Asia and North Australia and is one of the top three causes of death by infectious disease in some regions. It is caused by the bacterium Burkholderia pseudomallei, but the molecular basis of pathogenicity is poorly defined. An international team led by Prof David Rice of MBB and including scientists from Malaysia and Singapore, as well as other research labs in the UK, has stumbled across a previously unknown toxin while investigating proteins of unknown function in B. pseudomallei.
This work, published in the journal Science in the 11 November 2011 issue (Vol 334, page 821), identifies an enzyme called Burkholderia Lethal Factor 1 as the toxin, and shows that it has a similar structure to a toxin produced by the well-known bacterium Escherichia coli. Crucially, the structures of their active sites are very similar (Figure). This provided the crucial clue as to how it works: it turns out that although the reaction it catalyses is identical (deamidation of a glutamine), the biological consequence is quite different. In B. pseudomallei, it deamidates a protein required for translation of RNA into protein, and thereby halts protein synthesis in infected human cells. This work paves the way for the design of drugs against meliodosis. The team are also working on the possibility of using the toxin to target cancer cells and kill them.
This figure shows a comparison of the active sites of B. pseudomallei toxin (blue) and the related E. coli toxin (red). The crucial catalytic residues are Cys94 and His106, which are in very similar spatial positions.
100% success in national student satisfaction survey
The results for the 2011 Student Satisfaction Survey are now out. MBB scored a remarkable 100% score for overall student satisfaction over all its courses: see this link for more detail.
Research grants awarded in 2011
To do research, you need people, equipment and chemicals. These all cost money, and most research funding is obtained from research grants, which are provided by government and charities as a result of a competitive process, with the judges being other research scientists. This means that obtaining a research grant is recognition that your research is seen as internationally excellent. We are happy to announce grant funding in 2011 spanning a wide range of research areas in the department:
- A grant to Prof Williamson to study the structure and function of a protein involved in the formation of cysts in the kidney
- A grant to Prof Gray to study the development of stomata (the pores on plant leaves that allow water to evaporate)
- A grant to Prof Piper to study how the chaperone Hsp90 is involved in causing cancer
- A grant to Prof Artymiuk to develop agonists and antagonists of human growth hormone (see the news item below about spin-out companies)
- A grant to Prof Foster to develop a vaccine against Staphylococcus aureus (also described in the news item about spin-out companies)
- A grant to Prof Sudbery to investigate hyphae in the pathogenic fungus Candida albicans (see the news item Research Highlights ftrom MBB in 2010 for more details on this story)
- A grant to Prof Kelly to understand how the food pathogen Salmonella grows and survives
- A grant to Prof Wilson to study the export of RNA from the nucleus to the cytoplasm
Congratulations to new PhD graduates 2011
In 2011, 39 PhD students graduated (compared to 24 in 2010!), and we congratulate all of them on their hard work and achievement.
- Rebecca Jones (Dr Mitchell) A study into the nuclear exosome cofactor, Rrp47
- Fawaz Alshammari (Dr Wainwright) Application of molecular identification of ultrasmall bacteria
- Susana Gomez Escalante (Prof Piper) Studies on the human and yeast VNC-Y5 myosin folding molecular chaperone
- Yvonne Rauter (Prof Foster) The interaction of Staphylococcus aureus and human skin fatty acids
- Holly Smith (Prof Poole) The response of Campylobacter jejuni to oxygen and toxic haem ligands
- Nagah Abubaker (Dr Gilmour) Molecular identification and physiological characterisation of bacteria to grow at high salinity
- Andrew Hitchcock (Prof Kelly) The role of the twin-arginine translocase in the assembly and function of the electron transport chains in the pathogen Campylobacter jejuni
- Soheil Aghamohammedzadeh (Prof Ayscough) The assembly and disassembly of endocytic complexes in Saccharomyces cerevisiae
- Farhat Marston (Dr Craven) NMR structure analysis and identification of the DNA binding site of the C-terminal domain of the Bacillus subtilis protein DnaD
- Pawel Gardzielewski (Dr Hettema) Studies on the role of Pex25p in peroxisome maintenance
- Jonathan Smart (Prof Kelly) The role of molybdenum and tungsten in Campylobacter jejuni
- Chatchawal Phansopa (Prof Kelly) Structural and biochemical characterisation of major antigenic proteins of Campylobacter jejuni
- Cassandra Terry (Prof Bullough) Assembly of the Bacillus exosporium
- James Marston (Prof Waltho) Kinases: charge balance & structural tightening in the transition state
- Hannah Regan (Prof Sudbery) Molecular mechanisms of hyphal growth in Candida albicans
- Samir AlHarbi (Prof Hornby) Design and analysis of DNA polymerase for use in random mutagenesis
- Stephen Harper (Dr Rafferty) Structural investigation of tungstate and molybdate transport in Campylobacter jejuni
- Rebecca Hill (Prof Rice) Pilot studies on the purification and analysis of macromolecular protein complexes in Saccharomyces cerevisiae
- Mostafa Ismaeil Omar Ibrahim (Prof Waltho) Biophysical studies of the structure and backbone dynamics of gsPGK using NMR relaxation methods
- Thibaut Angevin (Dr Goldman) Role of cohesin complex subunit SCC3 in DNA-damage response pathways in yeast Saccharomyces cerevisiae
- Abimael Cruz (Prof Rice) Structural studies on BPSL1549 protein, a putative determinant of pathogenicity in Burkholderia pseudomallei
- Daniel Canniffe (Prof Hunter) Engineering the haem and chlorophyll biosynthetic pathways
- Khalid Al'Abri (Dr Wainwright) Use of molecular approaches to study the occurrence of extremophiles and extremodures in non-extreme environments
- Ismaeel Bozakouk (Prof Foster) Characterization of the effect of mammalian serum on Staphylococcus aureus
- Sulaiman Alnaimat (Dr Wainwright) A contribution to the study of biocontrol agents, apitherapy and other potential alternatives to antibiotics
- Robert Paramore (Dr Staniforth) Studies on the mechanism of amyloid formation by cystatin B
- Laila Alfageih (Prof Hornby) Biochemical and genetic studies of bacterial C5-DNA methyltransferases
- Muhammad Sameer Qureshi (Prof Hornby) Development and analysis of a generic high-throughput proteomic methodology for systematic isolation and characterisation of eukaryotic recombinant protein complexes as a key to deciphering and mapping the cellular interactome
- Bassam Al-Johny (Dr Wainwright) Studies on silicon microbiology
- Andrew Proudfoot (Prof Williamson) Structural studies of the enzyme NADPH: protochlorophyllide oxidoreductase
- Salah Hajomer (Dr Wainwright) Studies on the autecology of the fungus Aureobasidium pullulans
- Mohamed Bumadian (Dr Gilmour) Molecular identification and physiological characterisation of extremely halotolerant bacteria isolated from a freshwater environment
- Roderick Katete (Prof Hornby) Biophysical characterisation of the manganese transporter MntH from Enterococcus faecalis
- Chatrudee Suwannachart (Dr Rafferty) Investigation of actin regulatory proteins
- James Lightfoot (Dr Martinez-Perez) The roles of SCC-2 during C. elegans meiosis
- Kathrine Mcaulay (Prof Foster) Glycosylation of Staphylococcus aureus surface proteins
- Fabia Allen (Dr Baker) Structural studies of SFSA, a novel nuclease
- Amy Bottomley (Prof Foster) Identification & characterisation of the cell division machinery
- Peter Adams (Prof Hunter) Structure, organisation and assembly of light-harvesting complexes in bacterial photosystems
Major new undergraduate text from Department
Prof Mike Williamson published the major textbook called How Proteins Work in July 2011. This is the second important textbook to be written by staff in MBB, following on from Prof Pete Sudbery's Human Genetics (see below).
MBB to provide science education in national project
Postgraduate students in MBB have obtained support for an innovative science education project. In association with the UK Association for Science and Discovery Centres and the Wellcome Trust, they will deliver a workshop to school pupils in Sheffield, exploring their ability to taste a bitter chemical called phenylthiocarbamide (PTC). This is determined by genetic makeup, and about 30% of people cannot taste it at all. The workshop will involve DNA isolation, PCR (polymerase chain reaction) and gel electrophoresis. The project is to be delivered by Science Brainwaves, whose Director is a PhD student in MBB. For more detail about Science Brainwaves, see the science outreach link below, and for more on this story see this link.
MBB teacher wins Students’ Union Personal Tutor of the Year Award
At their annual Academic Awards ceremony on May 12 2011, The Students’ Union presented an award for Personal Tutor of the Year to Dr Rosie Staniforth, a lecturer in MBB. One of her tutees commented ‘She is always available for personal one-to-one sessions and was incredibly supportive of any decisions I have made, both academic and personal.’ Dr Staniforth said "It is a great honour to receive this award. I am extremely touched but also highly encouraged to feel that I can make a difference simply by providing the care and attention they so very much deserve." The award follows one in 2009 given to Dr Charlie McDonald from MBB.
Dr Gilmour introduces microbiology to schoolchildren
Dr Jim Gilmour introduced a group of 90 13- and 14-year olds to the science of microbiology, as part of a program of encouraging local schoolchildren to consider a career in medicine. Pupils learnt about good and bad microbes. The session received a writeup in the Sheffield Star. See this link for more details.
Congratulations on MBB promotion
We congratulate Dr Ewald Hettema on being promoted to Reader, in recognition of his outstanding research on peroxisomes, which are organelles found in almost all eukaryotic cells that carry out a range of both degradative and synthetic reactions.
A busy year of science outreach activities
2010/11 has seen MBB staff and students involved in a wide range of outreach activities. We have delivered creative science workshops aimed at exciting primary school pupils about science. These have covered topics such as microbes and bacteria, DNA and proteins, cells and their structures, microscopy, the use of animals in research, evolution and natural selection, as well as genetic manipulations. The photo below shows a product from a “Design a Bug” workshop, creating bacteria adapted to particular environments. In the workshops we have worked with artists from Art in the Park to enhance pupils’ experience. Pupils have produced songs, poems, short dramas, artworks and models based on the science.
Dr Sandrine Soubes collaborated with the theatre company the Babbling Vagabonds to deliver science and theatre workshops exploring the topic of Synthetic Biology in two local primary schools. The project engaged over 150 Y6 pupils who were engaged for a whole week of science and art workshops. In each school, pupils delivered a performance to the rest of the schools and parents.
At the Sheffield Children’s Festival in June 2010 we delivered science workshops to families on a busy Saturday. These were run with the help of Science Brainwaves, a group of postgraduate and undergraduate students from Sheffield, mainly from MBB, whose aim is to educate and entertain – to communicate science.
A group of postgraduates, mainly from MBB, have got together to form the Café Forum, a regular venue for presentation and lively discussion of cross-disciplinary science.
For more details and pictures click here.
Research Highlights from MBB in 2010
Members of the Department published about 90 papers in research journals in 2010. We have selected three, which are explained in more detail in the link below. The first, from Prof Sudbery, decribes how the pathogen Candida albicans pushes its way into the bloodstream to cause lethal infeactions. The second, from Prof Foster, describes how the spherical bacterium Staphylococcus aureus ‘knows’ in which direction to split in half. And the third, from Prof Williamson, describes how the binding of one protein (UBA) to another (ubiquitin) is regulated by dimerisation, faults in which lead to Paget’s disease of bone.
MBB develops new spin-out company
Prof Simon Foster is the founder of Absynth Biologics, a company developing vaccines and antibodies against the MRSA superbug Staphylococcus aureus. In 2010, Absynth signed an agreement with the German company MorphoSys AG to develop therapeutic targets.
We took our first venture into spin-out companies back in 2001 with Asterion, a company developing proteins that bind to cytokine receptors as treatments for a wide range of disorders, involving Prof Pete Artymiuk as a co-founder.
BioServ UK was also launched in early 2009, a company that produces quality antibodies and recombinant proteins. The company is based in the Department, with Dr Lynda Partridge as Scientific Director and Dr Simon Smith (previously a Departmental PhD student) as Technical Director. Both companies are still going strong, not a bad record in the Biotech market.
Congratulations to Prof Peter Horton on being elected FRS
We congratulate Professor Horton as the second MBB academic to be awarded an FRS in the area of photosynthesis (see details of Prof Hunter’s award below). An FRS is the highest accolade for British scientists.
Prof Horton has wide interests in photosynthesis. A major interest has been in working out how plants respond to excess light. In this era of global climate change, excess light is a major problem, which can lead to severe damage to plant tissues. This interest has led to his being involved in Project Sunshine, a major initiative by the University of Sheffield to tackle the food and energy needs of the world in an integrated way.
Research grants awarded in 2010
MBB received research grants totalling over £4 million in 2010. These include:
- A grant of £499k to Dr Jim Gilmour by the Carbon Trust, for the development of new biofuels from algae. This is part of a major UK initiative to develop more ecologically friendly fuels, and has large commercial potential.
- A grant of just over £0.5m to Prof Simon Foster to study bacterial cell walls. These are major antibacterial drug targets, and the mechanisms by which bacteria remodel their cell walls and split them in two to divide are the key to developing new drugs.
- A grant of over £1m to Profs Robert Poole and Jeff Green for studying how bacteria respond to changes in oxygen levels. Bacteria that live in the gut such as E. coli grow in an environment without oxygen, but when they pass out of the gut they suddenly move into an oxygen-rich environment. They make major changes in their metabolism very quickly to cope with this, which is the key to their success, and also to their ability to act as food-borne pathogens. The grant is to develop a ‘systems biology’ approach, involving the integration of a wide range of data.
- A grant of £586k to Prof David Rice for the development of new herbicides based on X-ray crystal structures of drug targets bound to plant proteins.
- A grant of £464k to Prof Jon Waltho to study how enzymes transfer phosphate groups from one molecule to another. This enzyme activity (‘kinase’) contributes to many cancers, and the research uses basic science to address a problem of great medical importance.
Congratulations to new PhD graduates 2010
In 2010, we saw 24 PhD students graduate, and we congratulate all of them on their hard work and achievement.
- Melissa Lacey: Characterisation of Escherichia coli YfgF: a cyclic di-GMP phosphodiesterase
- Glyn Hemsworth: Structural studies on the flap endonuclease ExolX from Escherichia coli
- Jamie Jackson: Neural differentiation in human embryonic stem cells
- Tooba Alizadeh: Insight into folding and activity of phosphoryl transfer enzymes
- Christopher Penfold: Modelling meiotic chromosome behaviour in space and time
- Alastair Robertson: The role of Ysc84/SH3yl-1 in regulating actin dynamics during endocytosis
- Megan Lewis: The flavohaemoglobins of Botrytis cinera
- Mark Street: Assessing potential allergenicity of latex proteins with the aim of devising therapeutic intervention strategies
- Mustafa Alsull: Physiological and molecular characterisation of an alkalophilic Bacillus isolated from the river Lathkill in the Derbyshire Peak District
- Claire Davies: Structural studies of glutamate racemase
- Plykaeow Chaibenjawong: Desiccation tolerance in Staphylococcus aureus
- Laura Jones: Mechanisms of hyphal tip growth in the human fungal pathogen Candida albicans
- Alexis Bloom: Identification and structural insights into immobilised metal ion affinity purified nuclear protein complexes
- Esmaeil Sadroddiny: A proteomics approach to the study of the functional consequences of IgE-mediated activation of mast cells
- Samera Suleman: Molecular characterisation of peroxisome transport and biogenesis in Aspergillus nidulans
- Noha Hassuna: The role of tetraspannins in the uptake of intracellular pathogens
- Rachel Hulme: Defining the active sites of tetraspannins
- Carrie-Anne Sharma: Elucidating the topology of cystatin B amyloid fibrils
- Jill Shepherd: Roles for the adherent matrix and the cell cycle in the self-renewal and differentiation of human embryonic stem cells
- Adam Hodgson: Resection analysis of the VDE-DSB during meiosis
- Victoria Green: Structural studies of Holliday junction resolvase 67RuvC from Lactococcus lactis
- Arunya Jiraviriyakul: Strategies for generating antibodies for the study of tetraspannin proteins: Characterisation of tetraspannin Tspan11
- Hongtu Ye: Study of the structure/function relationship in canine and human IgE as the basis for the development of rational therapeutic strategies in allergic disease
- Muhammad Lokman: Development of post-meiotic germ cells from human embryonic stem cells in vitro
New edition of popular textbook on Human Genetics Feb 2010
MBB’s Professor Peter Sudbery has brought out the third edition of his popular textbook, Human Molecular Genetics, in collaboration with his son Ian.
Congratulations to Prof Neil Hunter on being elected FRS
We congratulate Professor Neil Hunter on his election to FRS. Prof Hunter works on photosynthesis, with particular interests in bacterial photosynthesis and the biosynthesis of chlorophyll. His work is therefore of great relevance to development of greener technologies and cleaner energy, as is being developed for example in the University of Sheffield’s Project Sunshine.