News

Professor Colin Murrell joins UEA as a Director of ELSA
January 2012
Professor Colin Murrell is a microbial ecologist/biochemist, and comes to the UEA from Warwick. His research focuses on bacteria that feed on methane and other one Carbon compounds, in a wide range of environments including soils, peat bogs, hot springs and the oceans. He was co-inventor of an important technique called stable isotope probing, which shows which micro-organisms out of the many thousands of species present in any environmental sample are feeding on a particular carbon compound, an approach that is finding a central role in understanding the roles of microbial communities in biogeochemical cycles.

Next generation sequencing surveys Salmonella
January 2012
Salmonella bacteria cause over a billion cases of illness worldwide each year, and over 500,000 deaths. To help efforts to reduce this, Dr Arthur Thompson and colleagues at IFR have produced the first extensive and accurate map that shows where in the Salmonella genome genes are switched on and read from.

"Mapping where the majority of Salmonella genes start to be transcribed from and discovering non-coding RNAs is a major landmark, as this will allow us much greater insight into how the genes that are required for virulence are controlled," said Dr Thompson.

Legumes give nitrogen-supplying bacteria special access pass
December 2011
A 120-year debate on how nitrogen-fixing bacteria are able to breach the cell walls of legumes has been settled. A paper published by John Innes Centre scientists, with Professor Allan Downie as the lead author, reports that plants themselves allow bacteria in.

Once inside the right cells, these bacteria take nitrogen from the air and supply it to legumes in a form they can use, ammonia. Whether the bacteria breach the cell walls by producing enzymes that degrade it, or the plant does the work for them, has been contested since an 1887 paper in which the importance of the breach was first recognised.

"Our results are so clear we can unequivocally say that the plant supplies enzymes to break down its own cell walls and allow bacteria access," said Professor Allan Downie.

Tuberculosis drug target's structure to point to new therapies
November 2011
Scientists at the John Innes Centre led by Dr Stephen Bornemann and Dr Dave Lawson have worked out the structure of a class of enzyme that has been genetically validated as a new drug target in Mycobacterium tuberculosis, a pathogenic bacterium which is responsible for 2 million tuberculosis deaths worldwide each year. The scientists have been awarded over £500,000 by the Biotechnology and Biological Sciences Research Council (BBSRC) to work out how this enzyme works and is regulated, which will help in the development of new therapies against tuberculosis.

How parasites modify plants to attract insects
November 2011
Scientists, including Dr Saskia Hogenhout, from the John Innes Centre on Norwich Research Park have identified for the first time a specific molecule from a parasite that manipulates plant development to the advantage of the insect host.

"Our findings show how this pathogen molecule can reach beyond its host to alter a third organism," said Dr Hogenhout.

JIC success at Biotechnology YES
November 2011
A team of students from the John Innes Centre are through to the final of a national business plan competition, having won through from their regional heat. The Biotechnology Young Entrepreneurs Scheme (YES) is an annual business plan competition for PhD students and early career postdocs.

The winning team from JIC, HortiSense, included Daniel Tromans (working with Dr David Lawson), Farzana Miah (working with Dr Stephen Bornemann), Philippa Borrill and Tilly Eldridge.

Microbiology to play crucial role in ensuring food security
November 2011
Professor Mike Peck of the Institute of Food Research has joined other experts from the Society for General Microbiology in launching a position statement on food security and safety. This sets out the key role that microbiology will play in ensuring that the 7 billion people in the world have access to safe and nutritious food.

"Food security and safety is concerned with the production of sufficient safe food for all. The world is already experiencing a food security and safety crisis. These problems are likely to be exacerbated by the increase in the global population expected in the next few decades," said Professor Peck.

New NRP science magazine "Scisence" launched
October 2011
A group of PhD students from the John Innes Centre, The Institute of Food Research and the University of East Anglia have got together to launch a new science magazine "Scisense". The magazine, which is currently published electronically, http://www.scisensenrp.co.uk, is designed for students and is intended to promote the ground-breaking science taking place across the Norwich Research Park and across the world. The first issue includes articles on antibiotic research in the labs of Mervyn Bibb, Matt Hutchings, and Tony Maxwell as well as an interview with Professor Jon Clardy from Harvard Medical School.

Night at the museum for IFR scientists
October 2011
Combase, the predictive microbiology database co-ordinated by IFR, was recently showcased to a public audience at the Natural History Museum in London, at an event designed to let people get hands-on with cutting edge science and meet the people behind it.

Marina Munoz-Cuevas and Olivia Csernus (pictured on left), who work in Dr Jozsef Baranyi's research group at IFR, demonstrated the Combase system to hundreds of museum visitors on the night. The Combase database contains collections of data relating to how various food-borne microorganisms survive and grow in different food materials. The database is therefore incredibly valuable to food processing and packaging companies, who can consult it to ensure that their production lines and practices are safe.

Researchers to identify the secrets of Salmonella's survival
October 2011
IFR researchers are to investigate how Salmonella survives during its lifecycle within our bodies, as a way of finding chinks in its armour that can be exploited to develop new therapies. The researchers have been awarded over £400,000 by BBSRC to work together with colleagues at the University of Sheffield to identify the different ways in which Salmonella obtains its energy for growth and survival within the two types of host cells.

Once inside our bodies, Salmonella invades the epithelial cells that line the gut and reproduces, and can become systemic by invading and growing in macrophage cells, which are part of the body’s immune defences. "We inferred that Salmonella uses different pathways to generate the energy required for growth and survival in macrophages and epithelial cells," said Dr Arthur Thompson. "What we want to do now is work out what these pathways are. Does Salmonella use anything from the host cells to contribute to its growth?"

Crowd-sourcing the E. coli O104:H4 outbreak
September 2011
Ten variants of the deadly Escherichia coli strain that hit Germany in May 2011 have been sequenced across the world. The unprecedented level of collaboration across the scientific community should give insight into how the outbreak arose, says a scientist at the Society for General Microbiology's Autumn Conference 2011.

Sequencing of the bacterium started in early June at BGI, China. Their sequence was provided in draft form to the scientific community as a crowd-sourcing project. This allowed scientists, including those at The Genome Analysis Centre (TGAC) in Norwich to identify key disease-causing genes. Dr Lisa Crossman, Microbial Genome Project Leader at TGAC, explained, "We have found that the strain responsible for the outbreak carries a very high number of genes known to be involved in disease. These include genes that influence the bacterium's ability to attach to surfaces and survival genes that increase tolerance to high acidity, low oxygen, UV light and antibiotics."

Novel method for increasing antibiotic yields
September 2011
A novel way of increasing the amounts of antibiotics produced by bacteria has been discovered that could markedly improve the yields of these important compounds in commercial production. It could also be valuable in helping to discover new compounds. With the ever-growing threat from antibiotic resistance, these tools will be very useful in ensuring that we have enough of these useful compounds in the future.

The majority of antibiotics we know of today are produced naturally by a group of soil bacteria called Streptomyces. In work carried out initially at the John Innes Centre, Professor Mervyn Bibb and collaborator Dr Koji Yanai from a Japanse laboratory discovered 36 repeating copies of one gene cluster in a strain of Streptomyces that had been repeatedly selected to over-produce the antibiotic kanamycin. Based on this observation Prof Bibb and colleagues have developed a system for the targeted amplification of gene clusters which they believe will work for many other Streptomyces strains and antibiotics, and may also uncover new, undiscovered antibiotics by amplifying cryptic gene clusters in other Streptomyces species.

Read the full publication.

Tuning natural antimicrobials to improve their effectiveness at battling superbugs
August 2011
Clostridium difficile is a common and dangerous source of hospital-acquired infections. At the moment, antibiotics are used to treat infections, but C. difficile is adept at acquiring resistance, meaning the number of effective antibiotics is ever decreasing. This has driven the search for new antimicrobials, and at IFR Melinda Mayer and Arjan Narbad have been focussing on bacteriophage endolysins. These are relatively short proteins produced by viruses that specifically target certain species of bacteria and then break open the cell walls. New research is showing that it is possible to 'tune' these endolysins to increase their effectiveness and aid their development as a new weapon in the battle against superbugs. Working with colleagues at the European Molecular Biology Laboratory (EMBL) in Hamburg, the structure of the catalytic domain of endolysin CD27L has been solved and used to design mutants to investigate what controls the specificity and activity of the endolysins.

JIC student brings home new expertise to answer question in antibiotic resistance
August 2011
John Innes Centre researchers, Tung Le working with Professor Mark Buttner (pictured, standing on right) and Dr David Lawson, have worked out the structure of a complex formed when a protein binds to DNA. This has proved to be key in understanding how an antibiotic-producing organism controls resistance to its own antibiotic, and may be an example of how other antibiotic producers regulate export to prevent self-toxicity.

"This provides a mechanism that couples the potentially lethal biosynthesis of the antibiotic to its export, which has wider implications for resistance to clinically important antibiotics," commented Prof. Buttner. "However, we needed to know more detail about the interaction between SimR and DNA."

The crystal structure of the TetR family transcriptional repressor SimR bound to DNA and the role of a flexible N-terminal extension in minor groove binding, Le, T.B.K., Schumacher, M.A., Lawson, D.M., Brennan, RG and Buttner, M.J. Nucleic Acids Research.

Read the full publication.

Antibiotic production controls unravelled to help in clinical development
July 2011
JIC scientists researching a new antibiotic have pieced together the way it is produced by a soil bacterium by working out the functions of its genes. Microbisporicin is produced by a soil bacterium from Indonesia called Microbispora corallina. A clearer understanding of how microbisporicin's synthesis is regulated by the bacterium will provide the basis for finding ways of optimising its production and so become a new weapon in the fight against multi-drug resistant pathogens.

Lantibiotics are a class of antibiotics produced by bacteria, and microbisporicin represents a potent example of the class, which has so far been under-exploited for clinical use. That could now change, as preclinical trials are showing that it is highly active against a large range of bacteria. To aid its pharmaceutical development, Professor Mervyn Bibb and Dr Lucy Foulston at the John Innes Centre, identified the genes that Microbispora corallina uses to regulate microbisporicin production.

Feed-Forward Regulation of Microbisporicin Biosynthesis in Microbispora corallina, Foulston, L. and Bibb, M. Journal of Bacteriology, p. 3064-71, Vol. 193. Read the full publication.

John Innes Foundation Prizes for Excellence in Scientific Research and Excellence in Science Communication
July 2011
Four postgraduate research students from the John Innes Centre and The Sainsbury Laboratory have received awards from the John Innes Foundation for the excellence of their research and how well they communicate it.

Dr Lucy Foulston (top left in picture), formally of Prof Mervyn Bibb's lab, and Dr Ben Schwessinger (top right of picture), formally of the Zipfel group, were both awarded the JIF Prize for Excellence in Scientific Research.

The John Innes Foundation also awarded prizes to current students Liliana Cano (bottom left in left in picture), in Prof Sophien Kamoun's group, and Alaa Aljabali (bottom right in picture), in David Evan's group, for Excellence in Science Communication.

Transatlantic award for microbiology student
July 2011
Daniel Tromans has received the Heatley-Payne Award from the Society of General Microbiology, which has allowed him to travel to the US to carry out a short research visit and present his work at the Annual Meeting of the American Society of Microbiology (ASM).

Daniel is a second year Norwich Research Park PhD student based at the School of Chemistry at the University of East Anglia and the John Innes Centre. His studentship is jointly supervised by UEA's Rebecca Goss, and David Lawson and Mervyn Bibb at JIC. He is investigating the biosynthesis of pacidamycin, a naturally produced antibiotic made by the soil bacterium Streptomyces.

Genome analysis will reveal how bacteria in our guts make themselves at home
June 2011
Dr. Lisa Crossman and other researchers from TGAC and IFR have published the genome sequence of a gut bacterium to help understand how these organisms evolved their symbiotic relationships with their hosts.

The IFR and TGAC researchers are now hoping to use this information to elucidate exactly what it is that restricts certain Lactobacillus reuteri strains to specific hosts.

L. reuteri confers certain health benefits, and has a role in modulating the immune system. A greater understanding of how L. reuteri host adaptation will help in efforts to exploit these health benefits, for example in the production of new probiotics.

Genome sequence of a vertebrate gut symbiont Lactobacillus reuteri ATCC 53608. J. Bacteriol. 2011 Read the full publication.

Microbelog - blogging the latest developments in microbiology
June 2011
Dr Matt Hutchings along with Dr Ben Thompson, who writes science blogs for the Wellcome Trust, have created a new blog which opens up the amazing and hidden world of microbes (bacteria, archaea, fungi and viruses) and brings awareness about the latest developments in microbiology. See their blog Microbelog for more information.

TGAC helps in crowd-sourcing analysis of E. coli strain
June 2011
Scientists from The Genome Analysis Centre (TGAC) have identified several genes which may be key factors in the recent E.coli outbreak of strain 0104:H4. The strain has now been implicated in a number of hospitalisations and deaths, particularly in Germany. The outbreak has also had a high economic impact on the fresh vegetable market, particularly in Spain and across the EU. The studies have been made possible by the public release of genome sequence data from BGI, China.

Dr. Lisa Crossman, TGAC Microbial Genomes Project Leader said "By studying the genetic factors involved in the survival of this bacterium on surfaces we hope to get an angle on how this organism has been able to get a foothold in the global food chain."

Bridging the gap – JIC hosts South African biotechnology students
June 2011
Three research students from the University of Pretoria are currently visiting and working at the John Innes Centre in prominent biotechnology laboratories, learning the skills needed to work in this field.

Discovery opens the door to electricity from microbes
May 2011
Using bacteria to generate energy is a signifiant step closer following a breakthrough discovery by scientists at the University of East Anglia. The project is led by Dr Clarke, Prof David Richardson and Prof Julea Butt, in collaboration with colleagues at the Pacific Northwest National Laboratory in the US.

The discovery means scientists can now start developing ways to 'tether' bacteria directly to electrodes - creating efficient microbial fuel cells or 'bio-batteries'. The advance could also hasten the development of microbe-based agents that can clean up oil or uranium pollution, and fuel cells powered by human or animal waste.