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Congratulations to the Senior Sophister Class of 2017 Who Graduated on Thursday, November 2nd

The Department of Microbiology congratulates the Senior Sophister Class of 2017.   We wish them every future success in the wide diversity of careers to which they are now headed. 06/11/17

Congratulations to Laura O'Connell, winner of the Microbiology Society Award

Congratulations to Laura O'Connell, winner of the Microbiology Society award for the highest Junior Sophister mark in 2016-17. Below (L to R) is Dr Alastair Fleming, Head of Department, Laura O'Connell and Dr Joan Geoghegan, JS Co-Ordinator. Sept/2017

dr joan geoghegan, js co-ordinator,  with laura o'connell, ms prize winer and dr alastair fleming, head of department

Microbiology Senior Sophister Class of 2016-17

Congratulations to the Microbiology Senior Sophister class of 2016-17 who celebrated their moderatorship classifications last Friday. All the staff at The Moyne are delighted with the students' excellent results. Retired Professor Cyril Smith presented his "Cyrils" to great joy.

Trinity microbiologists discover how to prevent infections spreading on medical devices

Microbiologists at Trinity College Dublin have discovered a new way to prevent bacteria from growing on medical devices such as hip replacements or heart valves implanted in the human body. The discovery is a step towards developing new preventive strategies that could have a direct impact on the recovery of patients in the immediate aftermath of a surgical operation.

Medical devices are routinely used in modern medicine to prevent and treat illness and disease but their use is compromised when an accumulation of b acteria called “biofilms” attach to the device surface after it is implanted in the human body. Communities of bacteria called “s taphylococci” growing on catheters, heart valves and artificial joints avoid being killed by antibiotics and the human immune system, meaning that the removal and replacement of the medical device is usually necessary. Each incident of biofilm infection costs €50,000-€90,000 to the healthcare system .

The research team led by Dr Joan Geoghegan, Assistant Professor of Microbiology at Trinity's School of Genetics and Microbiology is studying new ways to prevent medical device-related infection. A recent breakthrough published in the prestigious journal Proceedings of the National Academy of Sciences of the USA shows that it is possible to prevent communities of staphylococci from forming by targeting the linkages that hold the bacteria together.

Dr Joan Geoghegan and Leanne Hays' work may pave the way to new options for surgeons that reduce the risk of bacterial infection for patients.

In collaboration with atomic force microscopy expert Professor Yves Dufrêne and his team at the Université Catholique de Louvain, Leanne Hays, Irish Research Council-funded PhD student in the Department of Microbiology, has found that it is possible to stop bacteria from attaching to surfaces and to each other using a small blocking peptide. The target of the peptide was a protein attached to the surface of the bacteria called SdrC. In laboratory experiments the blocking peptide prevented the SdrC protein from recognising other bacteria and stopped the staphylococci from growing as biofilm communities.

Dr Geoghegan said: “ These new findings show that it is possible to stop bacteria from building communities using molecules that specifically target proteins attached to the surface of the bacteria. This exciting breakthrough will inform the design of new, targeted approaches to prevent biofilm formation by staphylococci and reduce the incidence of medical device-related infection.

The article can be accessed at http://www.pnas.org/content/early/2017/03/16/1616805114

Brewing up a storm: quiescent yeast cells are not so quiet.


It has been estimated that many cells spend the majority of their lifetime in a non-dividing, or quiescent state. During quiescence (or G0), these cells are often considered as ‘resting', whereby metabolic activity and gene expression are reduced. Another key characteristic of quiescence is that this state is reversible, and cells can re-enter the cell cycle to resume growth when specific conditions occur.

Numerous cells in the human body persist in this non-dividing state, including neurons and muscle cells. Stem cells also form quiescent populations which, for example, can re-enter the cell cycle in response to tissue damage to aid repair. Furthermore it is now known that cancer cells can become quiescent, during which time they are more resistant to drug treatments. However, research into this so-called ‘inactive' cellular state has often been over-looked, and the mechanisms that regulate quiescence are poorly understood.

A collaboration between Dr Alastair Fleming (Department of Microbiology), Dr Karsten Hokamp (Department of Genetics) and Prof Mary Ann Osley at the University of New Mexico, USA, has used the humble brewer's yeast, Saccharomyces cerevisiae , as a model organism in which to study cellular quiescence. The study mapped and compared the gene transcription machinery, and distinct chromosomal modifications that are associated with gene activity, across the entire genomes of actively-growing and quiescent yeast cells. Surprisingly, the study revealed that the genomes of the ‘inactive' quiescent cells retained many of the chromosomal signatures that are normally associated with actively growing cells, despite their shut-down in cellular activity. Furthermore the transcription machinery, although inactive, remained associated with most genes across the quiescent cell genome. Together, the study revealed that quiescent yeast cells are not inert, but are highly poised to resume growth and proliferation when the environment becomes favourable.

Dr Conor Young , a lead author of the study said, ‘the most interesting aspect of the study was that yeast showed a burst of transcription activity just before their exiting the cell cycle, during which many of the chromosomal marks required for active growth were deposited along the cell genome. It is like the yeast cells make a ‘last-gasp' attempt to arm themselves with the chromosomal attributes required to best ensure their survival and re-entry into the cell cycle' .

Assistant Professor of Microbiology, and co-senior author of the study, Dr Alastair Fleming stated, ‘This was an important study which mapped the chromosomal landscape of quiescent cells, and showed how this landscape was established. Our future aim is to uncover how the chromosomal modifications we have described contribute to the process of quiescence. By understanding the correct pathway cells take into and out of quiescence, it will be possible to identify where cells have deviated from this pathway during disease, which may yield future therapeutic targets'.

The study, funded by Science Foundation Ireland and the NIH , was published in the open-access BMC Genomics journal, and can be accessed here ( 10.1186/s12864-017-3509-9 ).

Young, Conor P. et al . ‘Distinct histone methylation and transcription profiles are established during the development of cellular quiescence in yeast'. BMC Genomics . 2017;18:107. doi:10.1186/s12864-017-3509-9.

 

Inner City Helping Homeless Christmas appeal

Staff and students of the Department of Microbiology generously put together shoeboxes for the Inner City Helping Homeless Christmas appeal. These shoeboxes included essentials such as gloves, hats, socks, clothes as well as chocolates, books and other small gifts which will be donated to the homeless community and to those in emergency accommodation. 

The response was excellent, with nearly 20 individual shoeboxes being donated by the microbiology department alone. These were brought to ICHH headquarters by MicroSoc and are now well on their way to making someone's Christmas. 

We are delighted with the response and would like to extend our sincere gratitude to all those who took part in the appeal: You have all made a difference this Christmas!

College Open Day 2016, Saturday 10th December

The Department would like to thank all our volunteers at the Microbiology stand for the College Open Day.

Microbiology Society Prize

01 November 2016

Congratulations to Senior Sophister student Kevin Lyons who was awarded the Microbiology Society Prize for the highest Junior Sophister mark in Microbiology in 2016.
Kevin Lyons Microbiology Society Prize

2016 Normanby Lecture in Microbiology

27 October 2016

The Normanby Lecture in Microbiology was established in 1996 in recognition of the considerable financial support that has been provided by the Normanby family in constructing, extending and refurbishing the Moyne Institute of Preventive Medicine over more than six decades. Normanby lecturers are leaders in microbiological research and in 2016 our speaker was Professor Tony Maxwell of the John Innes Institute in Norwich, UK. Professor Maxwell's lecture was entitled "Supercoils and Superbugs: exploiting DNA topoisomerases as targets for antibacterial activity". In this fascinating talk, the audience learned about efforts to control bacterial infection through the development of antibiotics that poison the activities of type II topoisomerases in microbes. Professor Maxwell reviewed the global problem of antibiotic resistance before going on to describe the biochemical activities of topoisomerases, the structures and mechanisms of action of the drugs that inhibit them and the types of academic-industrial partnerships that are driving modern developments in drug discovery. Recent efforts to employ anti-topoisomerase agents in the fight against tuberculosis were also covered. The talk was well attended and was followed by a reception organised by the TCD Microbiology Society.

Visualising how Salmonella genes are regulated

29 August 2016

In a collaboration with scientists at the University of Liverpool, Dr Aoife Colgan and Assistant Professor Carsten Kröger (both at the Department of Microbiology, Trinity College Dublin) have determined the roles of the important regulatory systems that allow the human pathogen Salmonella Typhimurium to cause disease.

We know that bacterial pathogens kill millions of people each year, and that bacteria carry “virulence” genes that allow them to cause disease. During infection of humans with Salmonella , the switching on and off of these virulence genes is carefully regulated to ensure expression at the “right time and right place”, but how is this process controlled?

Scientists based at the University of Liverpool and Trinity College Dublin have determined the roles of the important regulatory systems that allow the human pathogen Salmonella Typhimurium to cause disease. The team led by Professor Jay Hinton used the latest RNA-seq technology to study mutant bacteria that are unable to regulate key virulence processes, and defined the regulatory proteins that control expression of Salmonella coding genes and small RNAs during infection.

The lead author of the study, Dr. Aoife Colgan said “by using mutants of a single Salmonella strain that lack 18 different regulatory systems, we have generated a unique set of data. I am excited that the results are now available to all researchers at SalComRegulon, that my work can now be used to gain new insight into the process of Salmonella infection, and perhaps inspire new therapies”.

Professor Hinton said that he hoped that the data would contribute to our understanding of Salmonella -induced gastroenteritis, and to the lab's current research on a lethal disease in Africa called invasive non-typhoidal Salmonellosis.

The study is published in the open-access PLoS Genetics journal, and can be accessed here. All the data are freely available online at http://tinyurl.com/SalComRegulon.

Salmonella facts:

• Worldwide, Salmonella kills more than 1 million people each year.

• Symptoms of salmonellosis (food poisoning caused by Salmonella) are fever, headache, abdominal pain, diarrhoea, nausea and vomiting, and are usually self-limiting after a week. In some cases, particularly in the young and very elderly, dehydration can become severe and life threatening.

Salmonella Typhimurium is found in a broad range of animals, birds and reptiles, as well as the environment. Take care during the barbecue season - the bacterium causes food poisoning in humans mainly through the consumption of raw or undercooked contaminated food of animal origin - including poultry, eggs, meat, and milk, and also salad vegetables.

Plant Kingdom Provides Two New Antibiotic Candidates

21 June 2016

Scientists have isolated peptides (strings of amino acids) with antibiotic effects on bacteria that spoil food and cause food poisoning, after turning to the plant kingdom for help in boosting our arsenal in the ongoing war against antibiotic resistance.

The scientists found two small peptides from widely cultivated crop species (one from broad beans and one from cowpea) that were especially effective. 

Further work then confirmed that when these peptides were used together, and with a human peptide that is also an antimicrobial, their protective effects were beefed-up in a one-two antimicrobial punch.

Associate Professor and Head of Microbiology at Trinity College Dublin, Ursula Bond, led the team that has just published its research in the journal Applied and Environmental Microbiology.

Professor Bond  said: “There are two major advantages to these small peptides in that no resistance mechanisms have emerged yet, and in that they can be inexpensively synthesised in the lab. Initially, our aim was to identify peptides that provide protection against food-spoiling bacteria, but these peptides may also be useful as antibiotics against bacteria that cause serious human diseases.”

The research team behind the discovery had previously isolated a human peptide that is a potent antimicrobial agent against many of the bacteria that spoil beer during industrial fermentation. Instead of screening for other human peptides with similar desired effects, the scientists scanned plant peptides databases and focused on the peptides whose structural blueprints were similar to the human one with the desired characteristics.

Many of the most effective antibiotics are derived from proteins produced by plants, but there is a growing need to discover new therapeutic candidates as resistance is increasing in bacterial species that have major health and economic implications for society.

Professor Bond added: “We reasoned that natural peptides found in many plants and plant seeds might be useful new antibiotics, because plants have evolved these systems to protect themselves against the billions of bacteria and fungi they interact with in the soil every day.”

This work was funded by a grant from the Department of Agriculture, Food and the Marine. The journal article can be viewed here .

 

Microbiology Publications in Trinity Student Scientific Review (TSSR)

22 March 2016

Congratulations to Microbiology Sophister students Kelly Murray and Kevin Lyons on the publication of articles in the peer-reviewed undergraduate science journal Trinity Student Scientific Review ( TSSR ).

Senior Sophister Kelly Murray published a review entitled "A thief's toolbox: bacterial strategies to acquire iron from the human host". This is Kelly's second TSSR publication; she published "Immunoglobulin binding proteins of Staphylococcus aureus " in 2015.


Kelly Murray

Junior Sophister Kevin Lyons published a review article entitled "Elongation, termination and anti-termination: the final stages of transcription in Escherichia coli ". Kevin won the 2016 Prize for Best Overall Essay. This is a remarkable achievement, won against stiff competition from across all disciplines in science. The Provost presented Kevin with his award.


Amy Worrall (TSSR Life Sciences Editor), Kevin Lyons (Best Overall Essay), Dr. Patrick Prendergast (Provost)

The School of Genetics and Microbiology is very proud of its published student essayists and wishes them every success in their forthcoming examinations.

See the Provost’s address at the launch of Trinity Student Scientific Review here.

Charles Dorman
Professor of Microbiology
Head, School of Genetics and Microbiology

Secondary School Poster Competition

2 March 2016

Nineteen pupils currently in the transition year in local secondary schools participated in a poster competition hosted by the Microbiology Department TCD and the Trinity Access Programme. The students first attended a workshop led by Dr Ronan Smith from TAP at which they were given guidance in performing research and presenting their findings in a poster. The students were then asked to research and present on a topic of their choice concerning antibiotics. The student's posters were displayed in the foyer of the Moyne Institute at an event that was also attended by parents and teachers. Four winners were chosen and will spend a week on work experience in the Staphylococcal Research Group's laboratory in the Moyne. The competition has contributed to the work package on outreach activities that is part of the Horizon 2020-funded project NoMorFilm. Professor Tim Foster and Professor Joan Geoghegan from the Microbiology Department TCD are members of the NoMorFilm consortium which will discover and develop new antibiotics from microalgae in the sea.

The winners are:

Sophie Lyons, Assumption Secondary School, Walkinstown.
“Teixobactin: an antibiotic of the future”

Conor Comiskey, St Joseph's Secondary School, Rush.
“A Study on Tigecycline”

Aoife Dunne, Colaiste Bride, Clondalkin.
“Neomycin”

Kristine Segovia, Loreto College, Crumlin.
“Cephalosporin”

Pictures from the event:

 

Department of Microbiology hosts DAPI Symposium 

15 January 2016

Department of Microbiology hosts DAPI Symposium 
The sixth annual symposium of the Dublin Academy of Pathogenomics and Infection Biology (DAPI) was hosted by the Department of Microbiology on Friday, 15th January at the Moyne Institute. DAPI was established in 2010 to encourage enhanced synergy in research and teaching between researchers based in University College Dublin and in Trinity College Dublin with an interest in infection biology. This year's event saw more than 75 researchers attended the meeting. The keynote speaker was Dr. Suzan Rooijakkers from the University Medical Center Utrecht, The Netherlands. Suzan delivered a fascinating seminar about the molecular basis of the interaction between bacteria and the human immune system. She described her research on how complement kills bacteria and the various strategies that bacteria have evolved to resistant complement. Suzan's talk was sponsored by the Microbiology Society. The remainder of the talks were delivered by PhD students and postdocs from both universities offering an important opportunity for early stage researchers to gain experience of communicating the results of their research. The research being carried out in UCD and TCD was further showcased by the 28 participants who presented posters of their findings. The prize for best postgraduate speaker was awarded to Leanne Hays, (TCD) and the prize for the best poster presentation was awarded to Siobhan Turner (UCD). The DAPI meeting was a success in facilitating discourse between Infection Biology researchers across both TCD and UCD and will hopefully act as an incubator for further collaborations between the two universities in the future.  

Forces holding bacteria together in staphylococcal biofilm

6 January 2016

A collaboration between Assistant Professor Joan Geoghegan, Professor Tim Foster (both at the Department of Microbiology) and Professor Yves Dufrêne at the Université Catholique de Louvain, Belgium has resulted in the publication of several papers including one most recently in the Proceedings of the National Academy of Sciences of the USA . This paper uses Atomic Force Microscopy to study molecular forces that hold staphylococcal cells together in multicellular arrays called biofilm.

The ability of staphylococci (including MRSA) to colonize implanted medical devices such as catheters, artificial joints and heart valves is a major factor contributing to infection. Surgery is often required to remove and replace colonized devices. The bacteria adhere to the biomaterial and grow in multicellular communities called biofilm which are impervious to antibiotics and are resistant to host immune defences. Until recently the glue that held the biofilm cells together was considered exclusively to be a sugary polymer. The Staphylococcal Pathogenesis Laboratory discovered that many strains, including some MRSA, are held together by interactions between proteins attached to their surfaces.

Professor Dufr ê ne is a leading expert in the use of Atomic Force Microscopy to measure the interactions between single cells and molecules. Such nano-scale microbiological investigations have revealed novel insights into the strength of cell attachment to conditioned biomaterial and of the cell-cell interactions that occur as the biofilm develops. The current paper unravels the molecular forces that hold together cells promoted by one particular protein called SasG. This interaction is dependent on the presence of zinc ions which are not only required for the SasG-SasG interaction but also to modify the topology of the bacterial cell surface and to increase the exposure of SasG and its ability to interact with its partner. This work highlights the key role that molecular forces play in guiding cellular functions in staphylococcal biofilms.

Clearer understanding of the nature of cell cohesion and the forces that hold cells together will offer opportunities for the development of novel compounds to prevent or disrupt biofilm.

Formosa-Dague C, Speziale P, Foster TJ, Geoghegan JA, Dufrêne YF. Zinc-dependent mechanical properties of Staphylococcus aureus biofilm-forming surface protein SasG. Proc Natl Acad Sci U S A. 2015 Dec 29. pii: 201519265.[Epub ahead of print] PubMed PMID: 26715750.

Regulatory rewiring improves bacterial fitness

3 December 2015

Knowledge of the regulatory circuits that govern the high-level global control processes that influence bacterial gene expression has been exploited to produce an organism that outperforms its natural ancestor under specific environmental conditions. No new genes were added and none was removed. Instead, the open reading frames of the genes encoding the H-NS and StpA nucleoid-associated proteins were exchanged on the chromosome of the bacterium Salmonella enterica. The new strain has enhanced competitive fitness that is tuneable by temperature and osmolarity. Although fitter than its natural ancestor under laboratory growth conditions, the new organism does less well under conditions found outside the lab, especially at low temperatures. The chromosome of the rewired organism is free from compensatory mutations. The basis for the change in fitness involves a rescheduling of the appearance of the stress and stationary-phase sigma factor, RpoS. This important component of RNA polymerase now appears in the early exponential phase of growth, hours earlier than it doe sin the ancestor. This work, funded by Science Foundation Ireland, was published online on December 3 rd in Scientific Reports (Nature Publishing Group). The paper can be read at:

Fitzgerald S, SC Dillon, C Tzu-Chiao, HL Wiencko, K Hokamp, ADS Cameron, CJ Dorman. 2015. Re-engineering cellular physiology by rewiring high-level global regulatory genes. Scientific Reports 5, 17653; doi: 10.1038/srep17653

 

New publication involving the Kröger Lab

High-resolution intracellular transcriptome of Salmonella enterica unveiled by Liverpool and Dublin microbiologists.

A comprehensive picture of gene expression of Salmonella enterica surviving inside macrophages has just been published. The study involved Jay Hinton (Professor of Microbial Pathogenesis, Institute of Integrative Biology, University of Liverpool), Carsten Kröger (Assistant Professor in Microbiology, Moyne Institute of Preventive Medicine, Department of Microbiology, TCD) and Dr Shabarinath Srikumar (Centre for Food Safety, UCD).

The Salmonella coding genes and transcriptional start sites that are expressed within macrophages during infection were defined. The transcriptional landscape of 280 small RNA molecules was determined at the level of the individual nucleotide. These data contribute to our understanding of the intricate transcriptional network that controls the “right time/ right place” expression of Salmonella virulence genes during intra-macrophage replication.

The study was funded by Science Foundation Ireland (SFI; Grants 08/IN.1/B2104 and 07/IN.1/B918) and the University of Liverpool.

The data have been made publically available in the “SalComMac” database with the help of Dr Karsten Hokamp (SFI Bioinformatics Research Officer, Smurfit Institute of Genetics, TCD): http://tinyu rl.com/SalComMac

The full study, published in PLoS Pathogens, can be accessed here: http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1005262

 

Congratulations to the Senior Sophister Class of 2015 who Graduated on Thursday, October 29th.

29 October 2016

 

 

PREVIOUS ARTICLES TO VIEW FROM MICROBIOLOGY NEWS

New Online-Only Open Access Journal Microbial Genomics (mGen):

31 March 2015

The Society for General Microbiology announced the launch of its new online-only open access journal Microbial Genomics (mGen) on March 31st during the Society's annual conference in Birmingham, UK. mGen will publish high quality, original research on archaea, bacteria, microbial eukaryotes and viruses.

Commenting on the launch, the chair of SGM's Publishing committee, Professor Charles Dorman, said that the superb quality of its editorial board ( http://mgen.sgmjournals.org/editorialboard.html ) will ensure that only the very best microbial genomics science will appear in mGen.

The new journal is now receiving manuscripts through its website at http://mgen.sgmjournals.org

 

Microbiology Undergraduate Success, Trinity Student Scientific Review:

March 2015

The Vice-Provost hosted a ceremony on March 11th to mark the publication of the Trinity Student Scientific Review, a new peer-reviewed publication for undergraduates.

Congratulations to our Junior Sophister Student Kelly Murray on her article "Immunoglobulin binding proteins of Staphylococcus aureus" which was published in the inaugural volume for Microbiology.
Three students from the School of Genetics and Microbiology were among the twenty whose articles were published, see School website for fruther information.

What the Trinity Scientific Review is About: Undergraduate students at Trinity College Dublin have combined to form the Trinity Student Scientific Review (TSSR). The TSSR will take the form of an online and print journal, published once a year, which will feature the top 20 science review articles written by undergraduates. The TSSR, which was inspired by the similarly minded Student Economics Review journal, will allow students to gain first-hand experience of the publishing process before completing their degrees(information taken from the FEMS website). Read More

For more information, and to read submission guidelines, see the TSSR website.

Lager Yeast Ancestors Were Full of Eastern Promise

26 February 2015

There are few drinks as iconic as a ‘pint of the black stuff'. It might, therefore, surprise beer connoisseurs to learn that the DNA of the all-important brewing yeast – the building blocks of the perfect Stout – is the same as that which encodes the yeast required to brew a clean, crisp lager.

That is the key implication to emerge from a genetic study carried out by researchers at Trinity College Dublin and UCD, which attempted to build a family tree of brewing yeasts through the ages. The geneticists analysed the genomes of 76 different strains of yeast taken from wineries, distilleries, bioethanol plants, bakeries, laboratories and natural isolates as they sought to paint a more complete picture of yeast evolution.

Lager yeasts are classified as either Group I or Group II. The Group II lager yeasts share DNA with Stout yeasts and, interestingly, with strains that are used to brew a South Indian speciality called ‘Toddy'. Such a connection implies that toing and froing between continents in years gone by helped introduce particular strains to our brewing armoury.

Associate Professor in Microbiology in the School of Genetics and Microbiology at Trinity College Dublin, Ursula Bond, was one of the researchers behind the discovery.

She said: “We know that lager yeasts are “hybrids” that emerged from a fusion between two yeast species about 500 years ago. The search has been on ever since to discover the parents that contributed to the genome of these species.”

The detailed findings, which have just been published in the peer-reviewed publication FEMS Yeast Research – provide other insights into how the two groups of modern-day lager yeasts evolved. The geneticists believe that Group I and II yeasts arose by independent fusion events with a yeast species that was only formerly discovered in 2011.

This species was found in Patagonia and in China, but has never been found in the wild in Europe. The current hypothesis used to explain its presence in some of our favourite beers is that it came here on ships returning from the New World, or from trade links established with China along the Silk Road.

Professor Bond added: “The research has uncovered new links between stout, ale and lager yeasts. Stout brewing originated in the British Isles. It is intriguing to speculate that the DNA similarities between stout yeasts, Group II lager yeasts and “Toddy” yeasts may indicate that colonial connections contributed to the exchange of yeast strains between India and England.”

Only further genome analysis will fully unravel the family tree connections. The group, which also comprises researchers Chandre Monerawela and Tharappel James from Trinity, and Ken Wolfe from UCD, is now involved in a project to sequence the Stout and Toddy yeast strains as they seek answers to some of these questions.

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Media Coverage

Irish Times, Wednesday 25th February, 2015

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More About Lager Yeasts

Yeasts have been used to ferment sugars into alcohol for several millennia, but fortune and chance were responsible for the emergence of the lager yeasts in Medieval Europe. With a nod to the discoverer of the microbe responsible for fermentation, Louis Pasteur, the new species was named Saccharomyces pastorianus .

The first fortuitous event was the introduction of a law in Bavaria in 1553, which restricted the brewing of beer to the winter months (from St Michaels Day to St Georges Day). This led to the natural selection of yeasts that could grow and ferment at low temperatures. The second contributing factor was the growing appetite in Europe for discovery and exploration of the New World.

Research Grants Awarded to Staff in Microbiology

Three grants have recently been awarded to staff in the Microbiology Department.

Professor Charles Dorman has been awarded a Principle Investigator programme grant valued at €1,228,466 to study bacterial nucleoid associated protein expression and stress resistance in pathogens.
Emeritus Professor Tim Foster is part of an EC H2020 consortium NOMORFILM novel marine biomolecules against biofilm, application to medical devices. This grant is worth €368,261 to TCD.
Assistant Professor Joan Geoghegan was successful in an application for a British Skin Foundation Research Award valued at £81,000 to investigate inhibitors of Staphylococcus aureus colonization of the skin of children with eczema.

Yeast is yeast? Not so when it comes to beer flavours

Researchers at Carlsberg Labs and in Trinity College are examining the genetic make-up of lager yeast in an effort to improve beer quality and develop new flavours

Beer disease was the curse of brewers and the drinking classes in the 19th century. Large amounts of lager could be brewed, but quality was erratic. The problem was solved in 1893 when Emil Christian Hansen of the Carlsberg Laboratory in Copenhagen realised that contamination from wild yeast was to blame.

“He made a pure lager yeast by diluting the yeast so much that there was only one cell left,” explains Dr Marie Bojstrup, senior scientist at the Carlsberg Lab. There was a marked difference in the very first brew that used this method, she says proudly. Famously, Carlsberg then made its pure yeast, Saccharomyces carlsbergensis , freely available to competitors.

Today, European lagers are often made with just malted barley , water , hops and yeast derived from the Carlsberg strain. Scientists who want to improve beer quality and develop new flavours look to the genetics of yeast, the single-celled maestros that convert carbohydrates to carbon dioxide and alcohols.

Magic ingredient

Microbiologist Dr Ursula Bond at Trinity College Dublin says different strains of yeast contribute to the different kinds of beer. Craft beers can range from cloudy gold to clear amber, taste malty with raspberry tones or perfumed with a hint of nutmeg, yet only the yeast is different. And yeast can conjure up hundreds of flavour and aroma compounds.

Dr Bond's lab is probing the genetic make-up of lager yeast and trying to understand strains' origins. “We're trying to tease out what makes them unique and useful for lager beer,” she says. “Ale yeast is a different kind, and we recently discovered that the yeasts used for making stouts are different again.” The brewer yeast does not live in the wild, but hundreds of strains evolved in breweries. Yeasts belong to the fungi kingdom.

Fermentation by yeast turns a stodgy mix of grain and water called “wort” into an alcoholic drink with light fizz: lager. Unlike ales, lagers require slow, low-temperature fermentations. Lager brewing began in Bavaria in the 15th century and was not permitted in summer, so lager yeast evolved for cold conditions.

“We have discovered specific regions of the genome that allow us to distinguish different groups of yeast,” Dr Bond explains.

“Altering or improving the flavour of beer is something people would like to do, but it is not easy. There are many genes controlling the myriad of enzymes required to produce the end flavours in beer, and subtle changes in enzyme levels can have unexpected effects.”

It was recently discovered that the enigmatic brewer's yeast Saccharomyces carlsbergensis (or S pastornianus ) is actually a hybrid (see panel). Carlsberg confirmed this in a report this summer.

They also probed the genetics behind a traditional split in lager yeasts into a Bavarian and an eastern European type – group I (Czech and Carlsberg beer) and group II (Weihenstephan and Heineken). The founder of Carlsberg had travelled to Munich in 1845 to obtain his yeast.

In the name of science, an 1886 bottle of Carlsberg beer was uncorked to obtain the original strain of lager yeast used. The beer tasted like port wine, says yeast scientist Dr Andrea Walther at Carlsberg Labs. “Our tasting panel said it was sherry-like, chocolate, with strong fruity aromas.”

When they tried the old strain, the beer was not so good. But after using a handwritten 19th-century protocol, “it was one of the best beers I've ever had”, Dr Walther recalls. The old way was to ferment at 4 degrees, not 17 degrees like today.

Trinity Microbiologists Win Harry Smith Vacation Studentships

May 20, 2014

Four microbiologists from Trinity College Dublin have won Harry Smith Vacation Studentships to support undergraduate research projects in their labs in the Moyne Institute of Preventive Medicine this summer. The studentships, awarded by the Society for General Microbiology, will underpin projects that span three of the major themes of microbiology: bacteriology, virology and eukaryotic microbiology.

One bacteriology project will attempt to better understand what causes strains of bacteria associated with eczema to stick to a protein in the skin, while the other will try to shed light on how ‘cold shock' proteins, expressed in cold temperatures, help regulate antibiotic resistance in a common bacterial strain of Salmonella. Students Elaine Moloney and Matthew Dorman will be working in the labs of Assistant Professors in Microbiology, Dr Joan Geoghegan and Dr Shane Dillon, respectively.

A virology research project will explore how the drug Oseltamivir decreases the cell-to-cell spread of the flu virus, and will be pursued by Dylan Sheerin in Dr Kim Roberts' lab. The eukaryotic microbiology project will investigate genetic functioning in the yeast, Saccharomyces cerevisiae, which is a key component in baking and brewing. Marina Bogue will work in the lab of Dr Alastair Fleming. Both Dr Roberts and Dr Fleming are Assistant Professors in Microbiology at Trinity.

Commenting on the awards, Head of Department and Professor of Microbiology at Trinity , Charles Dorman, said: “It is a tribute to our staff that they were awarded so many studentships over such a wide range of microbiological research themes. These awards will allow four talented undergraduate students to conduct real research over the summer months, which will significantly deepen their educational experience at Trinity.”

Professor Harry Smith, CBE FRS (1921-2011), was a major figure in microbiology in the 20th Century. He was the first to discover a bacterial toxin (anthrax) in 1954 while he was working at the Microbiological Research Establishment at Porton Down. This landmark event developed the field of microbial pathogenesis, and Harry became the leading advocate worldwide for the study of disease-causing microbes in the environment of their hosts.

He held the Chair of Microbiology at Birmingham University (1965-1988) and was a key advisor to Trinity in filling its Chair of Microbiology in 1976 and 1993. Professor Smith served as President of the Society for General Microbiology (1975-1978) and was instrumental in establishing the Federation of European Microbiology Societies.

Following his death in 2011, the Society for General Microbiology named its summer vacation studentship scheme in his honour. Harry Smith Vacation Studentships provide a stipend for each undergraduate researcher as well as some support for their research costs. Further information about the scheme is available here .

Versatility in Genetic Expression Aids Rapid Microbial Evolution

Mar 31, 2014

Microbiologists from Trinity College Dublin have discovered that an identical protein is used differently by two species of bacteria to help them cope with distinct types of environmental stress. The discovery reveals an extraordinary level of versatility in the way different genes are ‘switched on' in bacteria, which in turn helps to explain how they evolve so quickly.

The microbiologists showed that the same protein, called ‘OmpR', which is responsible for binding to specific sections of DNA, governs the way a large cohort of genes function in both a human-friendly strain of Escherichia coli (E. coli) and in the potentially deadly Salmonella enterica serovar Typhimurium ( S. Typhimurium) .

In E. coli, OmpR is central to the ability of the bacterium to survive sudden stress caused by water moving in and out of its cells due to changing external conditions. In S. Typhimurium, however, OmpR is a key regulator of a series of actions that enable individual bacteria to respond to and survive acid stress. Such conditions are experienced, for example, in the hostile environment found in the bacteria-destroying vacuoles of macrophages, which are cells of the immune system that Salmonella can defeat using specialist pathogenic genes.

The microbiologists identified all the OmpR binding sites in the chromosomes of both species and investigated the features that attracted OmpR to them. The sites were rich in the DNA bases adenine (A) and thymine (T), which bind to one another to help form the classic double helix structure associated with DNA.

Importantly, the DNA of S. Typhimurium alters its shape after a bacterium is exposed to acid. This change in shape, called DNA relaxation, enhances the attractiveness of the OmpR binding sites for the OmpR protein. The same relaxation does not occur in E. coli.

Professor and Head of Microbiology at Trinity , Charles Dorman, said: “This work shows that DNA is not a passive partner when genes are switched on, but that it is an active and dynamic participant in the process. And, among the many OmpR targets possessed by S. Typhimurium that are not present in E. coli are the genes that make Salmonella pathogenic, and problematic for people.”

Scientists believe that the pathogenic genes were acquired through horizontal gene transfer. This process is mediated by direct contact between bacteria, by special viruses called bacteriophages, or by direct uptake of DNA from the environment. The transfer essentially represents the passing of DNA's all-important codes between individuals, and is often associated with the development and evolution of antibiotic resistance.

The scientists suspect that this DNA code sharing occurred after Salmonella and E. coli separated from their last common ancestor, earlier in the two species' unique evolutionary journeys, which is why the pathogenic genes are not present in E. coli . The DNA sequences of these genes confirm that they are very rich in A and T bases, which is a key characteristic they share with the OmpR binding sites.

Functionally, this means that these genes have the appropriate structural profile for rapid interaction with the OmpR DNA binding protein, which regulates when, and to what degree, they are ‘switched on'. This profile, coupled with the DNA relaxation that accompanies acid stress in Salmonella , may have allowed OmpR to 'tame' these imported genes and embed them in the acid stress response of Salmonella bacteria.

The work, which was funded by Science Foundation Ireland, has just been published in the high-impact online journal PLoS Genetics . Research Fellows in Microbiology at Trinity, Dr Heather Quinn and Dr Andrew Cameron (now at the University of Regina, Canada), worked with Professor Dorman to make the discovery.

A copy of the journal article is available here .

Trinity Represents Ireland in Women's Cricket World Cup

Mar 20, 2014

Third year Microbiology student, Jennifer Gray, Zoology PhD student, Rebecca Rolfe and Trinity graduate, Cecelia Joyce, are representing Ireland in the Irish Women's Cricket Squad currently competing at the ICC Cricket World Cup Twenty20 Finals in Bangladesh.

Jennifer represented the Irish Senior Squad in Qatar earlier this year. She represented Leinster and Ireland at Under 17 level as well as the Ireland A Ladies in 2011/12 and the Irish Senior Development Squad in early 2013.

Rebecca Rolfe is representing Ireland following a decision by the ICC to increase the official playing squad for the ICC World Twenty20 2014from 14 to 15. The 27 year old batter plays her club cricket for Leinster Cricket Club.

Cecelia, one of Ireland's most consistent performers, has been capped 44 times for the Irish Ladies Senior Squad. Cecelia made her Irish debut at the age of 17 in College Park and went on to represent DUWCC while studying here, receiving a Pink in 2006.

The Irish Team has one warm up match left against India on March 21 before starting their campaign against New Zealand on March 25. They lost the first warm up match to Ski Lanka. During the tournament the women's team will also face Australia, South Africa and Pakistan.

Further information is available at http://www.cricketireland.ie/news/article/ireland-women-announce-icc-world-twenty20-squad

Trinity Past and Present Selected for Irish Cricket Ladies Team

Jan 10, 2014

Third year micro-biology student, Jennifer Gray, has been selected for the Irish Senior Ladies Cricket squad travelling to Qatar this month. The trip to Qatar is a warm up tournament for the upcoming Cricket World Cup, taking place in Bangladesh in March.

Having represented Leinster and Ireland at Under 17 level as well as the Ireland A Ladies in 2011/12 and then the Irish Senior Development Squad in early 2013, it was a natural progression for Jennifer to be selected for the Senior Squad.

Jennifer is an accomplished bowler but proved herself as an all-rounder when she scored her maiden century in College Park in 2013 when the club played against North Kildare securing the win with 156 runs to 103. Jennifer batted 104 runs, more than the entire opposing team She is the first player to have scored a hundred runs in DUWCC history.

The Dublin University Women's Cricket Club (DUWCC) will be well represented on the Qatar tour not only by Jennifer but also by alumna, Cecelia Joyce. One of Ireland's most consistent performers, Cecelia has been capped 44 times for the Irish Ladies Senior Squad. Cecelia made her Irish debut at the age of 17 in College Park and went on to represent DUWCC while studying here, receiving a Pink in 2006

 

TCD was awarded the prestigious ‘Green Flag'  as part of An Taisce's Green-Campus programme , recognising the quality of its environment.
The Green Flag is an international award and comes following years of work by those at the university. Green-Campus  is operated by the Environmental Education unit of An Taisce on behalf of the internationally-based Foundation for Environmental Education. Trinity College is now only the second university to hold this status. The flag is flown beside the Moyne Institute, Trinity's Department of Microbiology which assisted in development of the EcoSchools project in the EU, the international Blue Flag scheme, WHO standards for recreational waters and many other aspects of water research.

TCD Researchers Discover How the Bacterium Staphylococcus Aureus that plays a vital role in spread of MRSA Colonises the Human Nose

Jan 29, 2013

Staphylococcus aureus: why it gets up your nose!

A collaboration between researchers at the School of Biochemistry and Immunology and the Department of Microbiology at Trinity College Dublin has identified a mechanism by which the bacterium Staphylococcus aureus (S. aureus) colonises our nasal passages. The study, recently published in the prestigious journal PLOS Pathogens, shows for the first time that a protein located on the bacterial surface called clumping factor B (ClfB) recognises a protein called loricrin that is a major component of the envelope of cells in the nose and skin.

S. aureus is an important human pathogen, with the potential to cause severe invasive diseases. It is a major concern in hospitals and healthcare facilities, where many infections are caused by strains such as MRSA that are resistant to commonly used antibiotics. Interestingly, S. aureus persistently colonises about 20% of the human population by binding to skin-like cells within the nasal cavity. Being colonised predisposes an individual towards becoming infected so it is vital that we understand the mechanisms involved.

ClfB was previously shown to promote S. aureus colonisation in a human nasal volunteer study. This paper now identifies the mechanism by which ClfB facilitates S. aureus nasal colonisation. ClfB binding to loricrin was shown to be crucial for successful colonisation of the nose in a mouse model. A mouse lacking loricrin allowed fewer bacterial cells to colonise its nasal passages than a normal mouse. When S. aureus strains that lacked ClfB were used nasal colonisation was dramatically reduced. Finally it was shown that soluble loricrin could reduce binding of S. aureus to human nasal skin cells and that nasal administration of loricrin reduced S. aureus colonisation of mice.

Trinity's Assistant Professor at the School of Biochemistry and Immunology Rachel McLoughlin and Professor of Molecular Microbiology Tim Foster, the study's corresponding authors concluded: “Loricrin is a major determinant of S. aureus nasal colonisation. This discovery opens new avenues for developing therapeutic strategies to reduce the burden of nasal carriage and consequently infections with this bacterium. This is particularly important given the difficulties associated with treating MRSA infections”.

This project was supported by a Science Foundation Ireland Programme Investigator award and the Wellcome Trust.

The paper describes research performed by Michelle Mulcahy, postgraduate student in Microbiology, with the assistance of Joan Geoghegan (Assistant Professor of Microbiology and Ian Monk (postdoctoral associate, Microbiology) and Kate O'Keefe (PhD student, Biochemistry and Immunology).

CITATION: Mulcahy ME, Geoghegan JA, Monk IR, O'Keeffe KM, Walsh EJ, et al. (2012) Nasal Colonisation by Staphylococcus aureus Depends upon Clumping Factor

B Binding to the Squamous Epithelial Cell Envelope Protein Loricrin. PLoS Pathog 8(12): e1003092. doi:10.1371/journal.ppat.1003092

The paper was published December 27th 2012 in the Open Access journal PLOS Pathogens, http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1003092

PLOS Pathogens ( www.plospathogens.org ) publishes outstanding original articles that significantly advance the understanding of pathogens and how they interact with their host organisms. All works published in PLOS Pathogens are open access

 

Serial Academic Inventor

September, 2012

Prof. Tim Foster, B.A., Ph.D.(BRIST.), S.F.T.C.D-

is Professor of Molecular Microbiology and Director of Postgraduate Teaching and Learning in Microbiology. He is worldrenowned for his pioneering research on Staphylococcus aureus, a bacterium that can cause serious infections in humans and farm animals, and is notorious for being resistant to many antibiotics (MRSA). By studying proteins from the bacterial cell surface he tries to understand the mechanisms that allow the bacterium to colonize human skin as well as occasionally to cause invasive disease. His excellence in research has afforded him inventorship on multiple patent portfolios, many of which are currently licenced to multi-national companies for both animal and human vaccine development. Much of Tim’s early work on S. aureus binding proteins is patent protected, with many patents granted internationally. This patent portfolio has been licenced to Inhibitex/Pfizer for development. In recent years, a novel protein, patent protected in numerous countries, has been licensed for development by a major international pharmaceutical company as a vaccine to combat S.aureus infections. This licence deal has brought in revenue of over €350,000 to Trinity College and the inventors to date. Intervet/Schering-Plough Animal Health, the European market leader in equine vaccines, has developed EQUILIS® StrepE, the only strangles vaccine for horses in Europe. The key component of the vaccine was developed by the Foster lab and is licensed to Intervet.

Article taken from: Trinity Technology Transfer News, September addtion http://www.tcd.ie/research_innovation/assets/PDF%20Open%20Access/TTO%20ezine%20-%20Sept%202012.pdf

Flu is Transmitted before Symptoms Appear, Study Suggests

August 30, 2012

Research examining influenza transmission in ferrets suggests that the virus can be passed on before the appearance of symptoms. If the finding applies to humans, it means that people pass on flu to others before they know they're infected, making it very difficult to contain epidemics.

During the early phase of the 2009 influenza pandemic, attempts were made to contain the spread of the virus. Success of reactive control measures may be compromised if the proportion of transmission that occurs before overt clinical symptoms develop is high. In this study we investigated the timing of transmission of an early prototypic strain of pandemic H1N1 2009 influenza virus in the ferret model. Ferrets are the only animal model in which this can be assessed because they display typical influenza-like clinical signs including fever and sneezing after infection. We assessed transmission from infected animals to sentinels that were placed either in direct contact or in adjacent cages, the latter reflecting the respiratory droplet (RD) transmission route. We found that pre-symptomatic influenza transmission occurred via both contact and respiratory droplet exposure before the earliest clinical sign, fever, developed. Three of 3 animals exposed in direct contact between day 1 and 2 after infection of the donor animals became infected, and 2/3 of the animals exposed at this time period by the RD route acquired the infection, with the third animal becoming seropositive indicating either a low level infection or significant exposure. Moreover, this efficient transmission did not temporally correlate with respiratory symptoms, such as coughs and sneezes, but rather with the peak viral titre in the nose. Indeed respiratory droplet transmission did not occur late in infection, even though this was when sneezing and coughing were most apparent. None of the 3 animals exposed at this time by the RD route became infected and these animals remained seronegative at the end of the experiment. These data have important implications for pandemic planning strategies and suggest that successful containment is highly unlikely for a human-adapted influenza virus that transmits efficiently within a population. See Link to Paper: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0043303

Click on the news links for extra reading: http://www.independent.co.uk/life-style/health-and-families/health-news/flu-may-spread-before-symptoms-show-8095489.html , http://www.dailymail.co.uk/health/article-2195649/Flu-spread-symptoms-finds-study-ferrets.html?ito=feeds-newsxml

Discovery of Missing Links for Salmonella's Weapon System (Extract from Communications Office)

Apr 24, 2012

Scientists have discovered multiple gene switches in Salmonella that offer new ways to curb human infection. The discovery of the mechanisms of gene regulation could lead to the development of antibiotics to reduce the levels of disease caused by Salmonella. The breakthrough was made by Professor Jay Hinton, Stokes Professor of Microbial Pathogenesis, Trinity College Dublin and his research team and has just been published in the leading journal Proceedings of the National Academy of Sciences (PNAS).   Science Foundation Ireland funded the research.

Salmonella causes food poisoning and kills around 400,000 people worldwide every year. The bacteria are particularly effective at causing human infection because they can survive a series of harsh conditions that kill most bacteria including strong acids in the stomach and the anaerobic and salty environment of the intestine.

Professor Jay Hinton and Dr Carsten Kroger. 

“It's a decade since we discovered the Salmonella genes active during infection of mammalian cells,” said Professor Hinton. “Now we have found the switches that control these critical genes. My team has gained an unprecedented view of the way that Salmonella modulates the level of the weapon systems that cause human disease.”

Salmonella bacteria use a variety of proteins that act as weapons to hijack and attack human cells. Despite many decades of research throughout the world, little was understood about the way that Salmonella genes that control this weapon system are switched on. Now Professor Hinton's team has used a new approach to identify the switches of the Salmonella Typhimurium genes. The exciting new findings show that Salmonella bacteria have more than 1,800 switches, called ‘promoters' and reveals how they work.

Understanding how Salmonella switches on its genes should aid the discovery of new antibiotics that will knock out the weapon systems of Salmonella and stop the bacteria causing infection.

The researchers also identified 60 new RNA molecules, called ‘small RNAs'.  Some of these can actually override the switches of Salmonella genes.

“Just five years ago, we didn't realise that small RNAs played such an important role – or that the switches of so many Salmonella genes were controlled by small RNAs. Identifying these small RNAs could lead to completely new ways to prevent bacterial disease, but this will take at least a decade, ” said Professor Hinton.

Professor Hinton's team worked in collaboration with the Wellcome Trust Sanger Institute and the University of Würzburg, and used several cutting edge techniques during the project, called chip-chip and RNA-seq. “I think one reason that our findings are making such impact is that this combination of the new technologies has not been used before for a bacterial pathogen” says lead author Dr Carsten Kröger.

The research was led by scientists at Trinity College Dublin, and involved the following collaborating institutions: Institute of Food Research, UK; University College Dublin, Ireland;  University of Wurzburg, Germany; Wellcome Trust Sanger Institute, UK; Technical University of Denmark.

Full title of Proceedings of the National Academy of Sciences (PNAS) article: "The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium"

Normanby Visit to Department (October 27, 2011) - Extract from Communications Office

Research Laboratories Refurbished at Moyne Institute of Preventive Medicine - Communications office

The research laboratories in the east wing of the Moyne Institute of Preventive Medicine, which houses the Department of Microbiology , were recently reopened following an extensive refurbishment project funded in part by a donation of €250,000 from the Normanby Trust.  To mark the occasion the chairman of the trust, Constantine Phipps, the Marquess of Normanby, visited the Moyne Institute accompanied by his wife, Nicola and son, Tom.  Members of the Department of Microbiology and academic staff who occupy the research laboratories were on hand to demonstrate some of the research conducted in the laboratories.

The refurbished laboratories will house the research of Head of the Department, Dr Ursula Bond, who focuses on yeast, concentrating on industrial yeasts such as those used for making beer and lagers.  In one project she is using knowledge gained from genome analysis and transcriptional profiling to understand better how yeasts function during fermentation in the manufacture of beer.  Another project aims to modify yeast so that it can use cellulose waste products as a source of sugars for the production of biofuels.

Constantine Phipps, the Marquess of Normanby, with his wife, Nicola and son, Tom at the Moyne Institute of Preventive Medicine.

Lecturer in Microbiology, Dr Alastair Fleming is researching the coordination of cell rest, knows as quiescence, and controlled cell death, known as apoptosis, which represent two processes required for the correct development of organisms.  Dr Fleming is using the yeast Saccharomyces cerevisiae as a model organism to study the epigenetic changes that occur during cell growth and cell death, with a view to shedding light on diseases in which these processes are aberrant, including cancer.

Science Foundation Ireland Stokes Professor of Microbial Pathogenesis, Professor Jay Hinton is investigating an exciting new class of small RNA molecules that control the ability of pathogenic Salmonella to cause disease. These bacteria have the unusual ability to survive within macrophages, one of the main types of cell involved in defending humans against microbial attack.  Salmonella is responsible for severe gastroenteritis, and one particularly nasty serotype causes typhoid fever.

The Moyne Institute of Preventive Medicine was built in 1953 and was funded by a gift from Constantine's mother, Grania Guinness. Since then the Normanby Trust has funded three extensions to the building, the last being opened in 1995.  The memorial plaque in the foyer of the Moyne Institute records the opening of the building in May 1953 in memory of Grania Guinness's father, the first Lord Moyne.

Dublin Academy of Pathogenomics and Infection Biology

MS - Microbiology Society

 


Last updated 6 November 2017 by Microbiology (Email).