43:2 May 2016 43:2 May Are alive? viruses Are Astrobiology a sandbox God in playing Synthia: life of tree the on views Changing life of meaning the and Archaea What is life? TODAY

Microbiology Today 43:2 May 2016 What is life? 29/01/2016 11:07:41 and NINTH EDITION NINTH is intended for medical students and students medical for is intended www.garlandscience.com 978-0-8153-4551-0 • £60.00 978-0-8153-4551-0 978-0-8153-4512-1 • £41.00 978-0-8153-4512-1 April 2016 • Paperback • 928pp • 624 illus • Paperback April 2016 is a textbook for students studying immunology at immunology at studying students for is a textbook Immunobiology Janeway’s text, As an introductory school levels. and medical graduate, the undergraduate, while illustrations, and informative clear writing the book’s will appreciate students scope its comprehensive will value immunologists and working students advanced and depth. with up-to-date content the bringing revised been thoroughly has Edition The Ninth and immunity, innate topic of on the especially field, in the developments significant continuity. for better chapters topics across of the presentation improving instructors, to adopting available Bank is a Question Edition the Ninth to Also new assign to instructors which allows and the Garland Science Learning System the review topics and on specific immunology with assessments online tutorials via the instructor students, as individual well class, as of the entire performance dashboard. March 2016 • Paperback • 358pp • 255 illus 2016 • Paperback March Seventh Edition Edition Seventh Case Studies in Immunology, undergraduate and graduate students in immunology. It presents major topics of major topics It presents in immunology. students and graduate undergraduate the basic extend and reinforce cases that a selection of clinical immunology through science. facts about the immunological scientific essential by is preceded history case Each how demonstrate themselves cases The specific disorder. mechanisms of that by is followed in the clinic and each one deconstructed are problems immunological as discussion can serve which finding and questions summary of the clinical a concise points. text, be used as either a stand-alone and can of 55 cases The book includes a total Edition Immunobiology, Ninth Janeway’s to aid, or as a companion review Edition. , Fourth The Immune System University of Alabama at Birmingham, USA Birmingham, of Alabama at University

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CHLORAMPHENICOL 1 2 3,4 Adverse events should be reported. Reporting forms can be found at www.mhra.gov.uk/ and information events should also be reported to yellowcard. Adverse Essential Generics on 01784 477167. distension, pallid cyanosis, vomiting, progressing to vasomotor collapse, distension, pallid cyanosis, vomiting, progressing to vasomotor of irregular respiration and death within a few hours of the onset symptoms. Overdose: Stop chloramphenicol immediately if signs of adverse events oral develop. Treatment is mainly supportive. If an allergy develops, Baby antihistamines may be used. In severe overdosage e.g. Gray Resin Syndrome, reduce plasma levels of chloramphenicol rapidly. increase haemoperfusion (XAD-4) has been reported to substantially chloramphenicol clearance. Pack size and Price: 60 capsules £377.00 Legal Category: POM. Market Authorisation Number: PL17736/0075. Market Authorisation Holder: Chemidex Pharma Limited, 7 Egham UK. Business Village, Crabtree Road, Egham, Surrey TW20 8RB, Date of preparation: January 2016. for See Chloramphenicol Capsules Summary of Product Characteristics full prescribing information. References: 1. Martindale: The Complete Drug Reference. Chloramphenicol. [Online]. Available from: http://www.medicinescomplete.com [Accessed 17th September 2015]. 2. Fluit, A.C., Wielders, C.L.C., Verhoef, J., and Schmitz, F.J. Epidemiology and susceptibility of 3,051 Staphylococcus aureus isolates from 25 university hospitals participating in the European SENTRY Study. Journal of Clinical Microbiology. 2001; 39(10): 3727-3732. 3. Kelly, C., LaMont. Patient information: Antibiotic- cile (Beyond the associated diarrhea caused by Clostridium diffi Basics).June 2015. 4. Bartlett J.G. Antimicrobial agents implicated cile toxin-associated diarrhea of colitis. Johns in Clostridium diffi Hopkins Med J. 1981; 149(1): 6-9. 5. Feder. H, Chloramphenicol: What we have learned in the last decade. Southern Medical Journal. 1986; (79)9: 1129-34. 6. Weigel LM et al. High-Level Vancomycin-Resistant lm. Staphylococcus aureus Isolates Associated with a Polymicrobial Biofi Antimicrob Agents Chemother. 2007 Jan; 51(1): 231–238. 7. Ensminger, P., Counter, F., Thomas, L., Lebbehuse, P. Susceptibility, resistance development, and synergy of antimicrobial combinations against cile. Current Microbiology. 1982; 7: 59-62. 8. Poilane, Clostridium diffi I., Bert, F., Cruaud, P., Nicolas-Chanoine, MH., Collignon, A. Interest cile isolates of the disk diffusion method for screening Clostridium diffi with decreased susceptibility to antibiotics. Pathologie Biologie (Paris). 2007; 55(8-9): 429-33. 9. Cattoir, V., Ould-Hocine, ZF., Legrand, P. cile clinical isolates Antimicrobial susceptibility of Clostridium diffi collected from 2001 to 2007 in a French university hospital. Pathologie Biologie (Paris). 2008; 56(7-8): 407-11. 10. Brazier, JS., Levett, PN., Stannard, AJ., Phillips, KD., Willis, AT. Antibiotic susceptibility of clinical isolates of clostridia. Journal of Antimicrobial Chemotherapy. 1985; 15(2): 181-5. 1,5 1,5 1,5 7-10 1,5 1,5 1 2 6

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Grappling with the question ‘What is life?’ is not for the fainthearted. Reaching a consensus, even within the scientific community, is both a challenge and an aspiration. However, as a community of scientists, it is apparent that microbiologists are extremely well placed to influence the debate.

s technological and scientific of what it means to be alive, and this life. The new model supports two advances push forward our question has been at the heart of an domains instead of three, with Aknowledge boundaries, the ongoing debate that has been around eukaryotes originating from a common answer to ‘What is life?’ is becoming for more than a century. Different sides prokaryotic ancestor shared with tantalisingly closer. As I have learnt of the argument are presented by David Archaea. To coincide with the Molecular during my tenure at the Norwich Medical Bhella and Nigel Brown. Biology of Archaea Focused Meeting to School, scientists are not the only voices John Ward writes our next article. be held in London later this year, Hannah grappling with this question. He describes how astromicrobiology Marriott and Thorsten Allers pick up the Ethicists, the legal community and is perfectly placed to ask (and answer) Archaea story. They describe how this different religious communities to name whether there is life on Mars. Looking brand new of life contains more a few continue to debate this issue at microbial life forms that can survive than an exotic group of extremophiles. as scientists continue to advance the and thrive in extreme environments on In fact this ‘newest’ domain of life is one meaning of life and living as technology Earth is providing scientists with clues of the most ancient and ubiquitous. Our and scientific advances continue to about the possibility and viability of life previous conceptions of archaeal life progress. Very recently, researchers on our neighbouring planet. continue to be challenged as scientists working with Craig Venter published a The role of scientists in the ‘What continue to find new lineages. report in Science describing a bacterium, is life?’ debate is evolving too. Sarah Finally, Adam Staines from the Syn 3.0, that has been engineered to Richardson and Nicola Patron have BBSRC has written the Comment article. have the smallest genome of any freely co-authored an article that describes It focuses on one of the most important living organism. Its genome has been how synthetic biology is opening up new issues to occupy scientists’ minds after pared down to the bare essentials; just opportunities to manipulate, transplant the meaning of life question: what are 473 genes are needed to survive and and create new organisms. They also the policies that underpin funding for reproduce. The evidence that is coming describe why scientific advances cannot research? through seems to suggest that it is take place in a vacuum but require As our knowledge about the becoming more and more unlikely that a complete package of intellectual microbial world continues to expand, my ‘The answer to the ultimate question of property assessment, ethical debate money is on microbiologists finding the life, the universe and everything is going and philosophical review. answer to the question ‘What is life?’ to be 42’. So far the evidence is pointing Next, Martin Embley and Tom and also where did it begin? to 473. Williams describe how new models The first article asks the question based on molecular sequencing Laura Bowater ‘Are viruses alive?’ Clearly, viruses have and metagenomics analysis using Editor shaped history. Viruses by their very environmental DNA samples challenge [email protected] nature challenge our understanding the traditional three-domain tree of

Microbiology Today May 16 | www.microbiologysociety.org 49 Contents

Microbiology TODAY Articles Are viruses alive? 58 Nigel Brown & David Bhella Two microbiologists give opposing views.

Astrobiology 62 John Ward Is there life on Mars?

Synthia: playing God in a sandbox 66 Sarah M. Richardson & Nicola J. Patron Recombining and reordering life.

Only two domains, not three: 70 changing views on the tree of life T. Martin Embley and Tom A. Williams The modern phylogenic tree.

Archaea and the meaning of life 74 Hannah Marriott & Thorsten Allers The third domain of life. 43:2 May 2016 Features Regulars 83 Early Career Microbiologists’ 49 Editorial Forum 52 Council 2016 A great opportunity to get involved and have your say. 53 From the President 54 From the Chief Executive 84 Schoolzone – 55 News Life finds a way 78 Conferences Practical activities on how life forms and evolves. 80 Focused Meetings 93 Reviews

86 Outreach – Editor Dr Laura Bowater Crowdsourcing new antibiotics Managing Editor Ruth Paget Jake Newitt tells us about his work on the Small World Initiative. Editorial Board Phil Aldridge, David Bhella, Helen Brown, Emma Denham, Lorena Fernández-Martínez, Paul Hoskisson, James Redfern, Alison Sinclair, Nicola Stonehouse Address Microbiology Society, Charles Darwin House, 12 Roger Street, 88 Membership Q&A London WC1N 2JU T +44 (0)20 7685 2683 E [email protected] Suresh Mahalingam’s education and career. Design Ian Atherton, Corbicula Design (www.corbiculadesign.co.uk) Printed by Charlesworth Press, Wakefield © 2016 Microbiology Society 90 Membership review ISSN 1464-0570 A review of our membership offering is underway. The views expressed by contributors do not necessarily reflect official policy of the Society; nor can the claims of advertisers be guaranteed.

92 Best of the blog FSC Logo Ancient icemen, spinning electrons and baby marmosets.

95 Comment – Coloured scanning electron BBSRC funding for microbiology micrograph of strands of Adam Staines Actinomyces viscosus. Science BBSRC and its microbiology portfolio. Photo Library Council 2016

Executive Officers President – Professor Neil Gow College of Life Sciences and Medicine, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen AB25 2ZD; [email protected] General Secretary – Dr Evelyn M. Doyle School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield Dublin 4, Ireland; [email protected] Treasurer – Professor Chris Thomas School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT; [email protected]

Elected Members Professor Andrew Davison MRC-University of Glasgow Centre for Research, Church Street, Glasgow G11 5JR; [email protected] Dr Stephen Diggle School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD; [email protected] Professor Stephen Oliver Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA Professor David Pearce Faculty of Health and Life Sciences, Northumbria University, Northumberland Road, Newcastle-upon-Tyne NE1 8ST; [email protected] Dr Mike Skinner Section of , Imperial College London, Faculty of Medicine, St Mary’s Campus, Norfolk Place, London W2 1PG; [email protected] Professor Nicola Stonehouse School of Molecular and Cellular Biology and Astbury Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT; [email protected]

Chairs of Committees Communications Committee – Dr Paul A. Hoskisson Strathclyde Institute of Pharmacy & Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE; [email protected] Finance Committee – Professor Chris Thomas See ‘Treasurer’ above Professional Development Committee – Dr David Whitworth Institute of Biological, Environmental and Rural Sciences Room S22, Cledwyn Building, Aberystwyth University, Ceredigion SY23 3FG; [email protected] Policy Committee – Dr Pat Goodwin C3 Collaborating for Health, c/o Microbiology Society, Charles Darwin House, 12 Roger Street, London WC1N 2JU Publishing Committee – Professor Charles Dorman Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, College Green, Dublin 2, Ireland; [email protected] Scientific Conferences Committee – Dr Karen Robinson Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham NG7 2RD

52 Microbiology Today May 16 | www.microbiologysociety.org From the President

We are looking for your involvement in a number of issues in the coming months. The Society is about to enter a thorough review of our membership and is setting up a Membership Research Project Working Group.

he aim of the project is to themselves forward for vacancies on may, as a microbiologist, have gather data from members, non- Council and on some of our Committees. questions about whether he was the Tmembers and lapsed members In addition, we are looking for younger only living thing left on the Red Planet through structured questionnaires, focus members to become part of our newly and have been primed to think more groups and one-to-one interviews, to established Early Career Microbiologists’ about where microbial life exists outside enable us to understand and meet the Forum. It is important to me and the the Blue Planet. Also have a look at the needs of a changing membership in a Society that we have the widest possible articles by Sarah M. Richardson and sustainable manner. Our objective is to representation on our Committees, so Nicola J. Patron on synthetic ensure that the benefits we offer meet please consider getting involved. and the debate between two of our the needs of today’s members but are At the time of writing I am looking microbiology heavyweights – David also ‘fit for purpose’ for future members. forward to our annual meeting in Bhella and Nigel Brown – on whether The ballot for elections to Council, Liverpool, but there is also an exciting viruses can be considered to be ‘alive’. Committees and Divisions will open Focused Meeting being planned, titled We are therefore covering life, the Monday 23 May and I urge all eligible Molecular Biology of Archaea 5, taking universe and everything in one magazine member categories to utilise their right place 1–3 August. For information and considering the nature of life itself, to vote. It is important to the governance about registration, visit the website as well as how we can make new of the Society that we remain open and (http://microb.io/archaea5). ‘designer’ life forms. Beat that! transparent, and that the membership We always aim to cover the This issue also includes important is truly represented on the bodies whom length and breadth of microbiology information about our education and we trust to drive forward our strategy. in Microbiology Today, and this issue outreach activities and more information The ballot will be received electronically, may claim to extend the boundaries about the Early Career Microbiologists’ or via post from the Electoral Reform of biology, science and science fiction Forum. You can follow us, and get Services, who are administering the more than any previous one. We have regular updates on our activities in a process, so check your email spam notable articles that span the entire tree wide variety of other ways. I am told filters if you have not received it by of life on Earth, as well as an article on for example that we now have more Tuesday 24 May. Why not also think astrobiological ‘life off Earth’ and that than 10,000 Twitter followers, so I know about whether you personally should found in extreme climates, written by we are connecting through multiple be standing for election for one of our John Ward. These are complemented traditional and social media formats. posts in the Society? If you want to widen by a review of the archaea (by Hannah your influence and contribute to the field Marriott and Thorsten Allers) that of microbiology then there are some represent the third branch of life on Neil Gow interesting and important opportunities Earth along with the bacteria and President coming your way. Next January eukaryotes. If you’ve seen the movie [email protected] (2017) we will need applicants to put The Martian with Matt Damon you

Microbiology Today May 16 | www.microbiologysociety.org 53 From the Chief Executive

When the Divisions met to begin discussing next year’s Annual Conference, it was easy to see the importance of microbiology just by looking at the day’s newspapers – three front pages were about the fight against malaria, the Zika virus, and the microbiome. This brought home to me how crucial it is for our community’s expert microbiological knowledge to feed effectively into public and political discussions about how we react to a whole range of major challenges.

ne of the four pillars of the to governments’ and parliaments’ Dublin, Belfast, Edinburgh and Cardiff. Microbiology Society’s strategy agendas, such as the response we made These activities are only a fraction Ois ‘engagement and knowledge (jointly with the Society for Applied of what the Society does in the policy transfer’. That means we work hard to Microbiology) to a UK parliamentary world on your behalf, overseen by a support members and share your unique, inquiry into the lessons learned from last Policy Committee. They are augmented deep and broad specialist understanding year’s Ebola outbreak. This topic was by a whole variety of events and with a wide range of people. One of the subject of a debate at our Annual partnerships that offer members the those audiences is the policy world – Conference and a number of fascinating chance to influence policy and to learn MPs and Lords in the UK, TDs in Ireland, papers in the Journal of General more about the policy process. These civil servants, government ministers, Virology. Our response, which drew on include sitting on external committees, European officials and parliamentarians, the expertise of members including attending Parliamentary events, blogging, and politicians and administrators in Ed Wright and Ian Goodfellow, was and helping to draft briefings, position Holyrood, Cardiff and Stormont. quoted repeatedly in the Parliamentary statements, responses to consultations These groups have different Committee’s final report. and other documents. These are things working practices and timescales from It is important to respond to such that it is often hard for active research researchers, so communicating with opportunities, but it is also crucial that scientists to get involved with, and the them can be challenging, especially the scientific community sets the agenda, Microbiology Society’s structures make when you are busy with your daily lives. drawing attention to issues that have not it possible for more of you to participate. The Society fosters communities and yet reached the notice of key decision One recent example was the Voice of the channels of communication to empower makers and influencers. During 2015, the Future event, at which members Rebecca your voices to be heard in policy debates. Society published briefings and position McHugh, Benjamin Johns, Andrew Day Following workshops with members statements on energy from food waste, and Rachel Edgar were able to quiz around the country, Council agreed a emerging zoonotic diseases, microbiology MPs and ministers directly on important policy roadmap that starts from the and climate change, food security from issues. overarching grand challenge of climate the soil microbiome, research and Please get in touch if you want change and sustainability, and then open access. Again, they were based on to know more about what the Society focuses on two major challenges where the expertise of members including Robin does in this area, or how to use microbiology has a big role – food Sen, Penny Hirsh and Thorunn Helgason. your microbiological expertise to security and infectious disease. Using They prompted questions in the Irish and help strengthen local, national and this framework, and with a very small, UK Parliaments, quotations in debates in international policies. highly focused team of staff, we can the House of Lords, face-to-face meetings have a real impact by concentrating your with members of the policy community, Peter Cotgreave knowledge and the valuable time you are and a sheaf of letters and requests for Chief Executive able to devote to policy work. more information from members of the [email protected] One way we do this is by responding parliaments and assemblies in London,

54 Microbiology Today May 16 | www.microbiologysociety.org News

Focused Meetings 2016 New subject category for Microbiology Focused Meeting 2016, Irish Division: The Society’s journal Microbiology has recently introduced a new biotechnology Host–Pathogen Interactions subject category and article submissions are now invited in this area. The journal has 30 June–1 July appointed two new Editors to cover the topic: Dr Louise Horsfall and Professor Saul Trinity College, Dublin, Ireland Purton. To find out more about the journal and how to submit your paper, go to Focused Meeting 2016: Molecular http://mic.microbiologyresearch.org. Biology of Archaea 5 1–3 August 2016 Small World Initiative – London School of Hygiene and Tropical Medicine, UK Research Councils help to search for new antibiotics Focused Meeting 2016, Irish Division: Exploring the Microbe–Immune System Interface 1–2 September Rochestown Park Hotel, Cork, Ireland Focused Meeting 2016: The Dynamic 5–7 September Mercure Exeter Rougemont Hotel, Exeter, UK Focused Meeting 2016: Molecular In Autumn 2015, Professor Melanie Biology and Pathogenesis of Avian Welham, Executive Director of Science at Professor Melanie Welham and Dr Simon Kerley at Viruses the Biotechnology and Biological Sciences Polaris House. Nancy Mendoza 27–29 September Research Council (BBSRC), and Dr Simon Charles Darwin House, London, UK Kerley, Head of Terrestrial Sciences at the Natural Environment Research Council (NERC), joined in the Society’s search for new antibiotics as part of the Small Deaths World Initiative. They kindly collected a It is with regret the Society notes the soil sample from the grounds of Polaris deaths of the following members. House in Swindon, home to the seven UK Professor Craig Pringle, who joined the Research Councils including the BBSRC Society in 1961. and NERC, which was sent to the University of East Anglia for analysis. It joined Mr Peter J. James, who joined the samples from our Citizen Science pop-up Society in 1965. events from last summer, a sample from Please contact mtoday@ 10 Downing Street and a sample from the microbiologysociety.org if you wish Arena and Convention Centre Liverpool, to notify the Society of the death of a collected by the Lord Mayor of Liverpool member whose details can be included to celebrate the Society’s 2016 Annual in this section. Conference in March.

Microbiology Today May 16 | www.microbiologysociety.org 55 Athena SWAN Biosciences Best Practice event In December last year, the Society led the organisation of the first Athena SWAN Biosciences Best Practice workshop, in partnership with the , Biochemical Society, British Ecological Society and Society for Experimental Biology. The workshop, held at the headquarters for all the named societies, Charles Darwin House in London, brought together staff from university bioscience departments that have received, or are applying for, Athena SWAN Awards. The Awards recognise commitment to tackle gender inequality in higher education. Delegates listened to inspiring talks from Dr Rachel Simmonds (University of Surrey) and Professor Jane Hill (University of York), who shared advice from their own departments’ successful applications for awards. Sarah Fink from the Equality Challenge Unit, which runs the Athena SWAN scheme, ran workshop sessions on how to collect and present data to support applications. The workshop was chaired by Professor Hilary Lappin-Scott, former President of the Microbiology Society and current Equality and Diversity External Advisor. This event came about as part of the work the Microbiology Society has been carrying out to embed equality and diversity across all of its activities. Alongside monitoring and collecting of data, the Society now has an Equality and Diversity Ambassador on Council and on each of its committees, who come together to share best practice and review collected data. Useful best practice information from the Athena SWAN workshop, including speaker interviews, slides and other resources, and further information about our equality and diversity activities, can be accessed here: http://microb.io/1nVEoER. For more information, please contact First Athena SWAN Biosciences Best Practice workshop at Charles Darwin the Society’s Policy team ([email protected]). House.

Nominations for Prize Lectures has re-opened Human Fungal Following our diversity check, the Society has re-opened the nominations process Diseases policy briefing to encourage broader representation of the microbiology community. The Society is The Society’s latest policy briefing supportive of Equality and Diversity issues and encourages members to consider Human Fungal Diseases was published the widest talent pool available when submitting nominations. in March. The briefing, which was We are accepting nominations for the 2017 Peter Wildy Prize, informed by experts working in medical Prize, Colworth Prize and Fleming Prize, and for the 2018 Microbiology Society Prize mycology, highlights the overlooked Medal. burden of these diseases and issues relating to diagnostics, antifungal The deadline for nominations is now Friday 29 July. Full information can be found on drugs, research and public health the Society website: www.microbiologysociety.org/nominations. surveillance. The briefing has been sent to UK and Irish parliamentarians and Society quoted in parliamentary report on Ebola policy-makers, but is also useful as an education resource. The fungal diseases In January, the UK House of Commons Science and Technology Committee briefing, and our past briefings, published the findings from their inquiry Science in emergencies: UK lessons from can be downloaded here: www. Ebola. The report criticised systematic delays in the UK’s response to the epidemic microbiologysociety.org/briefings. and lack of ‘research readiness’, and made recommendations to improve UK Contact our Policy Officer, Paul Richards preparedness for future disease emergencies at home and abroad. The report quoted ([email protected]) for issues and recommendations made in written evidence that was submitted by the further information about the Society’s Microbiology Society and the Society for Applied Microbiology, which was drafted in briefings and how to help with our consultation with members involved in the Ebola response and infectious disease policy work. research.

56 Microbiology Today May 16 | www.microbiologysociety.org Voice of the Future 2016 Grant deadlines

Voice of the Future 2016 took place at Date Grant Notes the Houses of Parliament in March. Science and engineering students 1 June 2016 Travel Grants For conferences and courses and early career researchers took the from 1 July onwards* seats of a Parliamentary Committee and grilled prominent witnesses 6 June 2016 Society Conference Grants For support to attend the about science policy, including the Inclusion Grant Focused Meetings on Molecular Government Chief Scientific Advisor Sir Undergraduate Student Biology of Archaea 5, and Host– Mark Walport and MPs from the House Conference Grant Pathogen Interactions of Commons Science and Technology 4 July 2016 Society Conference Grants Select Committee. The Microbiology For support to attend the Society was represented by members Inclusion Grant Irish Division Meeting on the Andy Day, Rachel Edgar, Benjamin Undergraduate Student Human Microbiome Johns and Rebecca McHugh. Andy and Conference Grant Rebecca asked questions about science funding and government preparedness 1 August 2016 Society Conference Grants For support to attend the for disease emergencies to Jo Johnson Inclusion Grant Focused Meeting on Molecular MP, the Minister for Universities Undergraduate Student Biology and Pathogenesis of and Science, and Labour’s Shadow Conference Grant Avian Viruses Science Minister, Yvonne Fovargue MP, respectively. The event was organised Rolling application by the Royal Society of Biology and Local Microbiology Event Sponsorship hosted by the Science and Technology Committee. You can read about All members can apply for funds to support microbiology-related events, Rachel’s experience on the Society e.g. sponsored talks. blog, Microbe Post. *Please note, you do not need to have received confirmation of abstract acceptance to apply for these grants as conditional offers will be made. In this case, evidence of Voice of the Future 2016 meeting. acceptance is required to claim your grant. Royal Society of Biology Elections for Council, member email address from Electoral Reform Services, who will administer the Committees and Divisions process. The Society elections for Council, Committee and Division members Contributions and feedback will launch later this month. If you are The Society welcomes contributions and an Honorary, Full, Full Concessionary feedback from members. Please contact or Postgraduate Student Member [email protected] with then you have a right to vote on who your ideas. represents the membership on these bodies. Benjamin Thompson Candidate information and the electronic Head of Communications ballot will open on 23 May. You will [email protected] receive an email to your registered

Microbiology Today May 16 | www.microbiologysociety.org 57 Are viruses alive?

What does it mean to be ‘alive’? At a basic level, viruses are proteins and genetic material that survive and replicate within their environment, inside another life form. In the absence of their host, viruses are unable to replicate and many are unable to survive for long in the extracellular environment. Therefore, if they cannot survive independently, can they be defined as being ‘alive’?

Taking opposing views, two microbiologists discuss how viruses fit with the concept of being ‘alive’ and how they should be defined.

Coloured transmission electron micrograph of a group of foot-and-mouth disease viruses. Nigel Brown & David Bhella Power and Syred / Science Photo Library

58 Microbiology Today May 16 | www.microbiologysociety.org but they carry their own transcriptional and translational machinery and fall into the evolutionary kingdom of No, viruses are not alive Bacteria. Like many other ‘difficult’ Nigel Brown pathogenic bacteria, we may eventually be able to grow them in cell-free systems. n many ways whether viruses are However, a crucial point is that Caetano-Anollés and colleagues living or non-living entities is a moot viruses are not capable of independent examined the phylogenomic Iphilosophical point. There can be few replication. They have to replicate within relationships of viruses to living organisms other than that have a host cell and they use or usurp the organisms through analysis of viral caused such devastation of human, host cell machinery for this. They do proteomes and assigned protein fold animal and plant life. Smallpox, polio, not contain the full range of required superfamilies. The authors concluded rinderpest and foot-and-mouth viruses metabolic processes and are dependent that viruses originated in ‘proto- are all well-known for their disastrous on their host to provide many of the virocells’ that were cellular in nature

effect on humans and . Less requirements for their replication. To and they implied that viruses and well known is the huge number of plant my mind there is a crucial difference modern bacteria evolved from common viruses that can cause total failure of between viruses and other obligate ancestors. They further claim that this staple crops. intracellular parasites, such as bacteria; means that viruses are indeed living In teaching about simple viruses, I namely, viruses have to utilise the host organisms. use the flippant definition of a virus as metabolic and replication machinery. This is not an argument I am ‘gift-wrapped nucleic acid’, whether that Intracellular bacteria may merely use comfortable with. If a virus is alive,

is DNA or RNA and whether it is double- the host as the environment in which should we not also consider a DNA or single-stranded. The gift-wrapping is they can supplement their limited molecule to be alive? Plasmids can virtually always a virus-encoded protein metabolic capacity and they usually transfer as conjugative molecules, or be and may or may not also include have their own replication machinery. passively transferred, between cells, and a lipid coat from the host. The viral Organisms such as Chlamydia spp. have they may carry genes obtained from the nucleic acid is replicated and the viral not yet been grown outside cell culture host. They are simply DNA molecules, proteins synthesised using the host cell’s “ although“ they may be essential for the processes. In many cases the virus also host’s survival in certain environments. encodes some of the enzymes required The argument reductio What about prions? The argument for its replication, a well-known example reductio ad absurdum is that any being reverse transcriptase in RNA ad absurdum is that any biologically produced mineral that can viruses. act as a crystallisation seed for further Over the last 15 years or so, biologically produced mineralisation (hence meeting the giant viruses found in amoebae have criterion of reproducibility) might also complicated our picture of viruses mineral that can act as a be classified as living! as simple non-living structures. crystallisation seed for The explicit sexism apart contained Mimiviruses and megaviruses can in the wording, I can do no better than to contain more genes than a simple further mineralisation quote Dr Kenneth Smith in the Preface bacterium and may encode genes for to his classic book Viruses (Cambridge information storage and processing. (hence meeting the criterion University Press, 1962): “As to the Genes common to the domains Archaea, question asked most frequently of all, Bacteria and Eukarya can be found of reproducibility) might also ‘Are viruses living organisms?’, that in different giant viruses, and some must be left to the questioner himself researchers argue on this basis that they be classified as living! to answer”. This questioner currently constitute a fourth domain of life. “ considers viruses to be non-living.

Microbiology Today May 16 | www.microbiologysociety.org 59 Viruses assemble their from surprisingly few distinct protein folds, such that convergent evolution seems Yes, viruses are alive highly implausible. David Bhella A recent study has investigated viral origins by analysis of the evolution and conservation of protein folds in he question of whether viruses from genome sequence data. A striking the structural classification of proteins can be considered to be alive, example is domain duplication of the (SCOP) database. This work identified Tof course, hinges on one’s beta jelly roll motif which gives rise to a subset of proteins that are unique definition of life. Where we draw the line the pseudo-sixfold symmetry of trimeric to viruses. The authors conclude that between chemistry and life can seem hexon capsomeres in adenovirus. This is viruses most likely originated from early a philosophical, or even theological also found in viruses that infect insects, RNA-containing cells. If viruses made an argument. Most creation stories involve Gram-positive and Gram-negative evolutionary leap away from the cellular a deity that imbues inanimate matter bacteria and extremophile archaea. form, casting off its weighty metabolic with the ‘spark of life’. From a scientific perspective, attempting to find a working definition for ‘life’ seems to me to have little practical value, but it is fun to think about. Arguments over the life/not life status of viruses are often rooted in evolutionary biology and theories of the origins of life. All cellular organisms can claim a direct lineage to a primordial cell or cells, a continuous chain of cell divisions along which the ‘spark’ has been passed. Are viruses able to claim a similar ancestry? The contention that viruses have no place in the tree of life is often supported by the assertion that viruses do not have a comparable history – viruses are polyphyletic. Viruses are at a terrible disadvantage in this comparison, however. We are aware of only a tiny fraction of the total genetic diversity of viruses. Moreover, their genomes evolve far more rapidly than cellular organisms. So, from the small islands of sequence data we have, it is Human adenovirus type 5 (left – EM databank 1579) and sulfolobus turreted icosahedral virus 2 (right – hard to argue that a coherent phylogeny EM databank 1679) assemble their capsids from trimeric capsomeres in which each protomer comprises a does or does not exist. Interestingly, domain duplication of the beta jelly roll fold. This allows each trimer to pack with pseudo-sixfold symmetry – conservation of folds in viral proteins the geometric cage indicates the positions of local six-fold symmetry in the icosahedral capsid structure. has begun to highlight possible common This highly conserved feature has led to the proposal of a common viral lineage for these viruses that infect ancestries that could never be inferred eukaryotes and archaea, respectively. David Bhella

60 Microbiology Today May 16 | www.microbiologysociety.org shackles to opt for a more streamlined “ existence, did they cease to be life? Have All cellular organisms can claim a direct lineage to a they reverted to mere chemistry? Viruses are genetically simple primordial cell or cells, a continuous chain of cell divisions organisms; the smallest viral genomes are only 2–3 kbp while the largest are along which the ‘spark’ has been passed. Are viruses ~1.2 Mbp – comparable in size to the genome of Rickettsia. They all have able to claim a similar ancestry? surprisingly complex replication (life) cycles, however; they are exquisitely adapted to deliver their genomes to the ribosomes is a key ingredient. site of replication and have precisely Perhaps the most satisfying definition, Nigel Brown regulated cascades of gene expression. that explicitly excludes viruses, The University of Edinburgh Viruses also engineer their environment, emerges from the ‘metabolism first’ [email protected] constructing organelles within which model and concerns the presence they may safely replicate, a feature they of membrane-associated metabolic David Bhella share with other intracellular parasites. activity – a tangible ‘spark’ of life. This Centre for Virus Research, Sir Michael While a virion is biologically inert “draws a neat distinction between Stoker Building, 464 Bearsden Road, and may be considered ‘dead’ in the viruses and obligate intracellular Glasgow, UK same way that a bacterial spore or a parasites such as Chlamydia and [email protected] seed is, once delivered to the appropriate Rickettsia. This definition also confers environment, I believe that viruses are the status of life on mitochondria and Further reading very much alive. plastids, however. The endosymbiosis Bamford, D. H. & others (2002). Evolution Fundamental to the argument that that led to mitochondria is thought of viral structure. Theor Popul Biol 61, viruses are not alive is the suggestion to have given rise to eukaryotic life. 461–470. that metabolism and self-sustaining Mitochondria have metabolic activity Boyer, M. & others (2010). Phylogenetic replication are key definitions of on which we depend, they have and phyletic studies of informational genes life. Viruses are not able to replicate machinery to manufacture proteins in genomes highlight existence of a 4th without the metabolic machinery of and they have genomes. Most would domain of life including giant viruses. the cell. No organism is entirely self- accept that mitochondria are part of PLoS ONE 5, e15530. doi:10.1371/journal. supporting, however – life is absolutely a life form, but they are not independent pone.0015530. interdependent. There are many life. Moreira, D. & López-García, P. (2009). Ten examples of obligate intracellular I would argue that the only reasons to exclude viruses from the tree organisms, and eukaryote satisfactory definition of life therefore of life. Nat Rev Microbiol 7, 306–311 and that are critically dependent on the lies in the most critical property of associated commentary. metabolic activities of their host genetic heredity: independent Nasir, A. & Caetano-Anollés, G. (2015). A cells. Humans likewise depend on the evolution. Life is the manifestation of phylogenomic data-driven exploration of viral metabolic activity of nitrogen-fixing a coherent collection of genes that are origins and evolution. Sci Adv, e1500527. bacteria and photosynthetic plants along competent to replicate within the niche doi:10.1126/sciadv.1500527. with that of our microbiota. There are in which they evolve(d). Viruses fulfil Rybicki, E. P. (2014). A top ten list for very few (if any) forms of life on Earth this definition. economically-important plant viruses. Arch that could survive in a world in which all It is estimated that there are Virol. doi:10.1007/s00705-014-2295-9. chemical requirements were present but 1031 virus particles in the oceans – they Scheid, P. (2015). Viruses in close associations no other life. vastly outnumber all other organisms with free-living amoebae. Parasitol Res 114, So, what does define life? Some on the planet. Alive or not, viruses are 3959–3967. doi:10.1007/s00436-015-4731-5. have argued that the possession of doing rather well!

Microbiology Today May 16 | www.microbiologysociety.org 61 Astrobiology

I had just finished my first degree and was about to start a PhD when, in 1976, we were all gripped by the excitement of finding evidence of life on another planet. The Viking mission to Mars by NASA had experiments on board the lander that were designed to show whether there were any living organisms in the surface soil of Mars. The labelled release experiment showed a huge release 14 of radiolabelled CO2 when C labelled nutrients were mixed with a sample of Martian soil.

The Gusev Crater, Mars. JPL-Caltech / Cornell / NMMNH / NASA / Science Photo Library John Ward

62 Microbiology Today May 16 | www.microbiologysociety.org e know now that this was investigates life in extreme environments possibility that microbial life, if it had probably due to the highly on Earth such as extremely cold, dry evolved on Mars during those 200 million Wreactive oxidised compounds habitats like the Antarctic dry valleys, years, could have been carried from the in the soil created by solar UV radiation hot, dry desert environments such as surface of Mars by asteroid impacts and on the Martian surface. Mars has such a the Namib or Atacama Deserts and been deposited on Earth, possibly helping thin atmosphere and no ozone layer so volcanic-associated vents on land and or kick-starting life on Earth. UV from the Sun would not be absorbed in the deep ocean. Microbes are the The mass of Mars is about 10 times before reaching the ground. The UV reacts organisms that astrobiologists are less than that of Earth and the gravity to form highly oxidised chemicals that primarily interested in and it was in these on Mars is 38% that of Earth. Mars also would break down the nutrients added in extreme environments that the Archaea lost its magnetic field about 4 G yr BP

the Viking experiments releasing CO2. were first found. It’s a salutary lesson and a consequence of the low gravity and to us as microbiologists that it was only lack of magnetic field is that Mars would Life on Mars? recently in 2002 that we discovered the have started to lose its atmosphere soon Years later I would return to thinking most abundant free-living organism on after it formed. The solar wind exerts a about life on Mars and other planets in Earth. This is the bacterium Pelagibacter constant stripping pressure on a planet’s our Solar System when starting to do ubique SAR11 and there are estimated to outer atmosphere and a strong magnetic research in Astrobiology. Astrobiology be 2.4 x 1028 SAR11 cells in the world’s field, such as the one on Earth, prevents is the study of life in the universe and oceans. Often we fail to see what is charged particles from the Sun stripping also its origins here on Earth. It also there in front of us because of our fixed the outer layers of the atmosphere understanding of what we should be away. A dense atmosphere protects a looking for. planet’s surface from harmful solar radiation such as hard UV. Mars, unlike John Ward Mars–Earth history Earth, does not have a magnetic field, so Mars is small, a little more than half as Mars cooled and allowed microbial the diameter of Earth. In the history of life to evolve, its protective atmosphere formation of the Solar System when was gradually being stripped away. The all the planetary bodies were being current conditions at the surface of Mars formed by accretion of material around are an atmospheric pressure of only 6 the proto-Sun, Mars being smaller than mbar (Earth’s atmosphere is 1 bar, 166 Earth would have cooled more quickly. times more dense than Mars) and a If the conditions for life are liquid water, daytime temperature at the equator of protection from damaging radiation, and –58°C. This is below the triple point of nutrients and energy, then Mars would water so liquid water cannot exist stably have had these conditions before Earth. at the surface. The Earth is thought to have cooled at about 3.9 billion years (G yr) before Cosmic radiation on Mars present (BP). Mars could have cooled to A second consequence of the lack of have liquid water and an atmosphere a dense atmosphere on Mars is that as dense as the current Earth by about highly energetic charged particles 4 G yr BP. The first evidence for life on from the Sun (protons) and galactic Earth is about 3.8 G year BP and there cosmic rays (mainly protons and helium is good geological evidence for large nuclei) have nothing to block them amounts of material blasted off the until they hit the Martian surface. When surface of Mars by asteroid impacts these energetic particles hit Earth’s raining down on Earth in those early atmosphere they produce showers of days of the Solar System. So there is the secondary particles which themselves

Microbiology Today May 16 | www.microbiologysociety.org 63

produce further energetic charged particles in a spreading cone of radiation, reaching its peak at what is called the Pfotzer (or Regener) maximum, and on Earth this Pfotzer maximum is 15 km, about 5 km above the normal cruising “ height of modern commercial jets. On Mars the Pfozter maximum is in the top few metres of the soil surface. Thus, not only is the Martian surface effectively sterilised by solar UV, the Martian soil to a depth of a few metres will be exposed to sufficient radiation to destroy biomolecules over a period of 0.4 to 6 million years at a depth of 5 metres. We looked at the radiation Fig. 1. Coloured scanning electron micrograph of four Deinococcus radiodurans bacteria forming a tetrad. resistance of terrestrial cells such as Michael J. Daly / Science Photo Library Deinococcus radiodurans (Fig. 1) and Antarctic isolates combined with the annual radiation doses on Mars, and Given that phages are very tough and many can withstand calculated the survival time of dormant populations of the cells. Bacteria can be conditions that their hosts cannot, I would advise looking radiation-resistant because, when active, for phages on Mars. they successfully repair the DNA breaks caused by ionising radiation. However, when cells are dormant, such as frozen in the subsurface of Mars, they are preserved but unable to repair radiation damage, which accumulates to the point where the cell becomes permanently inactivated. At a 2-metre depth a radioresistant organism would have had to be reanimated to repair its DNA within the last 450,000 years to still be viable. Given “ that the temperature is too low for living processes at the surface we should look for evidence of life, e.g. biomolecules and microbes, at a depth below 5 metres.

Mars analogues on Earth Astrobiologists like to hunt for bacteria and archaea on Earth in places that could be thought to be similar to at least some of the conditions on Mars. The Antarctic Fig. 2. Miers Valley, Antarctica. Samantha Whiting dry valleys at McMurdo Sound (Fig. 2)

64 Microbiology Today May 16 | www.microbiologysociety.org are amongst the driest and coldest underground, then we should be looking Further reading places on Earth, and microbiologists for bacteria or their biosignatures. Dartnell, L. (2007). Life in the Universe: have sampled these valleys to determine We now understand that on Earth, A Beginner’s Guide, Astrobiology. Oxford: whether micro-organisms can survive bacteriophages, or phages (Fig. 4) – Oneworld Publications. there. There are in fact quite extensive viruses that infect bacteria – outnumber Dartnell, L. R. & others (2007). Martian sub- microbial communities in the soils bacteria by about 10 to 1. Given that surface ionizing radiation: biosignatures and there and even lichens (an algae or phages are very tough and many can geology. Biogeosciences 4, 545–558. cyanobacteria mutualism with fungi) withstand conditions that their hosts Dartnell L. R. & others (2009). Desiccation in the surface of rocks. Plating studies cannot, I would advise looking for phages resistance of Antarctic Dry Valley bacteria of Dry Valley micro-organisms (Fig. 3) on Mars. Of course we can’t use plaque isolated from contrasting locations. Antarctic and more recently 16S ribosomal DNA formation in soft agar to see whether Sci 22, 171–172. metagenomics show a large range of phages are present because we would Dartnell L. R. & others (2010). Low- bacteria, with Firmicutes, Proteobacteria need a live host for each phage type – a temperature ionising radiation resistance of and Actinobacteria being the main phyla real chicken-and-egg conundrum. But Deinococcus radiodurans and Antarctic Dry in all depths of soil down to 20 cm, filtering a sample of Martian regolith Valley bacteria. Astrobiology 10, 717–732. and the Acidobacteria, Actinobacteria, from about 2 to 5 metres underneath Dartnell L. R. & others (2012). Destruction of Bacteroidetes and Gammaproteobacteria the surface and using an electron Raman biosignatures by ionising radiation more abundant in the interface with the microscope to search for phages might and the implications for life-detection on permafrost. not be a bad idea. Mars. Anal Bioanal Chem 403,131–144. Stomeo F. & others (2012). Abiotic factors What should we look for on Mars? John Ward influence microbial diversity in permanently If the conditions were compatible for Department of Biochemical Engineering, cold soil horizons of a maritime-associated life to evolve on Mars in those few University College London, Bernard Antarctic Dry Valley. FEMS Microbiol Ecol 82, hundred million years before conditions Katz Building, Gordon Street, London 326–340. became too tough and possibly drove it WC1H 0AH, UK

Fig. 3. Miers Valley bacteria after 12 weeks’ growth. Samantha Whiting Fig. 4. T4 phage. Linda Wallace

Microbiology Today May 16 | www.microbiologysociety.org 65 Synthia: playing God in a sandbox

Sarah M. Richardson & Nicola J. Patron Coloured scanning electron micrograph of ‘synthetic’ bacteria. Thomas Deerinck, NCMIR / Science Photo Library In 2010 researchers at the J. Craig Venter Institute (JCVI) added a recombinant Mycoplasma mycoides genome into Mycoplasma capricolum cells and grew them until they shed their original genomes. It took 15 years of hard and steady work to develop and refine the technologies required to ‘transplant’ their chemically synthesised genome.

66 Microbiology Today May 16 | www.microbiologysociety.org E. coli. ‘Designer’ doesn’t seem right, either, because M. mycoides JCVI-syn1.0, (in showman’s terms, Mycoplasma laboratorium or even ‘Synthia’) was not so much designed as copied. The genome is almost entirely the same as the previously sequenced genome of M. mycoides subspecies capri GM12. The final, synthetic genome differed only by the intentional inclusion of four non-functional ‘watermarks’ and one selectable marker, as well as 29

unintentional variations: 27 DNA single base pair (bp) changes, one 85 bp duplication, and the aforementioned E. coli transposon. The laudable work was the assembly itself – but while Synthia has the biggest piece of DNA ever crafted by humans to run a cell, she

doesn’t say anything new with it. Synthia is synthetic biology showing off – flexing muscle without doing any lifting. A goat pathogen would not usually be considered a prime candidate for synthetic biology; JCVI picked Mycoplasma for their tiny genomes, and M. capricolum specifically “ for its relatively rapid growth rate.

New in vivo technologies, Coloured scanning electron micrograph of ‘synthetic’ bacteria. Thomas Deerinck, NCMIR / Science Photo Library such as those adapted his project relied heavily on yeast cells. These 11 huge pieces were large-scale purchasing of DNA carefully separated from the yeast and from the recently famed Tfrom commercial vendors, then reintroduced to assemble into followed by assembly and sequencing. a final 1,000 kb molecule. This was CRISPR/Cas system make The researchers bought 1,078 carefully harvested from the yeast and introduced designed and sequence-verified 1 kb to competent, immune-compromised rebuilding a whole genome DNA fragments that they assembled Mycoplasma capricolum. At this stage, in 109 separate reactions into 10 kb the genome had been passaged through look as appealing as buying fragments by passage through yeast so many living cells that ‘chemically cells and then Escherichia coli bacteria. synthesised’ hardly seems applicable, monochrome cathode ray The 10 kb fragments were sequence especially in light of a transposon (a tube monitors. verified and then joined into 100 kb DNA sequence that can change its own fragments by a second passage through position) hitchhiker picked up from “

Microbiology Today May 16 | www.microbiologysociety.org 67 Then and today, the same final biology community through the technology is often ahead of ethical, genome sequence could be achieved establishment of an international policy and regulatory frameworks. without assembly and far more rapidly consortium to do the work and address In response to the arrival using established technologies for biosafety and ethical concerns: Sc2.0 of Synthia, the US Presidential mutating DNA and inserting new members must pledge that their Commission for the Study of Bioethical sequences into bacterial genomes. science will be done only in service Issues published a report on synthetic New in vivo technologies, such as to ‘peaceful purposes’ and that any biology. The Commission found that those adapted from the recently famed potential harm will be minimised. synthetic biology offers extraordinary CRISPR/Cas system make rebuilding Further, no intellectual property promise to create new products for a whole genome look as appealing as rights or restrictions on data and clean energy, pollution control and buying monochrome cathode ray tube materials sharing are to be exercised medicine; to revolutionise chemical monitors. Although synthetic biologists on the clones used to generate production and manufacturing, and to are now betting that industrial novel strains, intermediary strains, create new economic opportunities. production will make the shift from or the final ‘synthetic’ strain. These Despite the noise around Synthia, it chemical synthesis to biosynthesis, self-imposed guidelines satisfy the found no reason to endorse additional nobody is betting on complete genome scientific community but, just as with regulations or a moratorium on work synthesis; biosynthesising organisms other emerging areas of science, the in this field at this time. They are generally too large, too recalcitrant and too complex. Nevertheless, there is another player in the synthetic genome game: an academic team peopled mainly by undergraduate students. In 2014, they reported the redesign and production of a fully functional chromosome from the baker’s yeast Saccharomyces cerevisiae. Their eventual goal is a completely ‘synthetic’ yeast genome, but they do not intend to create a mere copy. They began with the publically available sequence and altered, removed, and added many different features Their ‘Sc2.0’ genome will be 12 times as big as Synthia and will result in an organism that is arguably functionally very different from its forbear. The yeast project may have avoided some of the criticism garnered by Synthia because it was published second and will take another 5 to 10 years to fully assemble, but also because S. cerevisiae has classically been regarded as non-pathogenic. The project also exemplified the values of The synthetic biology sandbox: sifting the environment for tools and pieces that will be useful in the the nascent academic synthetic laboratory. Sangeeta Nath

68 Microbiology Today May 16 | www.microbiologysociety.org No one in synthetic biology is inventing new life; we “ are not yet that knowledgeable or skilled. We are not making synthetic life, we are not inventing new things that have never been seen before; we still lack the ability to be that creative.

acknowledged our duty to attend All of this activity has been carefully to potential risks, be supported by a precipitous fall in Sarah M. Richardson responsible stewards, and consider the price for chemically synthesised Lawrence Berkeley National Laboratory, thoughtfully the implications for DNA, new technologies that improve University of California, CA, USA “ [email protected] humans, other species, nature and the ease with which synthesised the environment. Such discussions fragments can be assembled and Nicola J. Patron may be the most productive thing the development of easy-to-program The Sainsbury Laboratory, Norwich to come from the announcement of molecular tools for editing the Research Park, Norfolk, UK Synthia. sequences of existing genomes. [email protected] In the last six years the synthetic But no one in synthetic biology is biology community has blossomed: inventing new life; we are not yet Further reading iGEM, an international student that knowledgeable or skilled. We Cumbers J. (2015). These synthetic biology competition in synthetic biology, has are not making synthetic life, we are companies have raised half a billion dollars in grown from 37 teams in 2006 to 280 not inventing new things that have 2015. http://microb.io/1ojsxR8. Last accessed teams in 2015; investment in new never been seen before; we still lack 2 March 2016. synthetic biology companies has the ability to be that creative. We Gibson D. G. & others (2010). Creation surpassed a half billion dollars and a are recombining, sifting through the of a bacterial cell controlled by a chemically number of companies are now focused environment for tools and pieces, synthesized genome. Science 329, on engineering specific microbes for and using chemical DNA synthesis to 52–56. specific purposes. Oxford (UK)-based move them from the environment to New Directions. The ethics of synthetic Green Biologics uses Clostridium to the laboratory. More than synthetic biology and emerging technologies. A report produce biofuels and other industrial genomes, we need an even better by the Presidential Commission for the chemicals from sustainable feedstocks; understanding of what else we haven’t Study of Bioethical Issues (2010). http:// Boston (USA)-based Ginkgo Bioworks observed yet. The accurate copying microb.io/1L6zVKv. Last accessed 2 March design microbes that produce cultured of a genome in the laboratory was 2016. ingredients such as fragrances, flavours an excellent demonstration that the Pennisi, E. (2013). The CRISPR craze. and sweeteners while companies like technologies needed to support Science 23, 833–836. Synthace and Zymergen are focused a DNA-dependent biosynthesis Synthetic Yeast 2.0. SAVI. http://synthetic on improving the technologies for economy have come of age – but yeast.org/sc2-0/. Last accessed 2 March automating the selection of new strains now the field is headed in a different 2016. with machine learning. direction.

Microbiology Today May 16 | www.microbiologysociety.org 69 Only two domains, not three: changing views on the tree of life The Human family Tree from Haeckel’s Anthropogenie (1874) (French copy from 1886). Paul D. Stewart/Science Photo Library T. Martin Embley and Tom A. Williams In 1857, Charles Darwin sent a letter to Thomas Huxley in which he wrote: “The time will come I believe, though I shall not live to see it, when we shall have very fairly true genealogical trees of each great kingdom of nature.”

70 Microbiology Today May 16 | www.microbiologysociety.org has dominated debate about how to to use a mathematical model of how A tree for all of life – organise life’s diversity at the highest we think sequences evolve to infer the the three-domains tree level for the past 20 years or so, there evolutionary relationships between Genealogical or evolutionary trees show is now increasing evidence that it is them, typically expressed in a tree the relationships between organisms not the best-supported hypothesis for diagram. Because of their central based upon common ancestry, like the the evolutionary relationship between importance in the process of making family trees that we use to investigate eukaryotes and Archaea. trees, it is important to appreciate that our own parentage. For many biologists, all of these mathematical models use Darwin’s dream was realised on the Data and evolutionary models – simplifying assumptions to make the grandest scale when, in 1990, Carl how are trees made? analyses computationally tractable, Woese and colleagues proposed that all Although morphology has long been and that they are not accurate cellular life could be placed into one of used to classify animals and plants, representations of how sequences three separate fundamental groups or Archaea and Bacteria – which between really evolve: in the words of statistician ‘domains’ – the Bacteria, the Archaea them comprise much of Earth’s genetic George Box, “all models are wrong, but and the Eukarya, based upon sequence and biochemical diversity – lack the some are useful.” In the early days of comparisons of small subunit (SSU) wealth of morphological characters computational molecular evolution, the ribosomal (r) RNA sequences. According needed to reconstruct their relationships models used were very simple because to the ‘three-domains tree’, the Eukarya to each other or to eukaryotes. In 1965, the computers of the time were so slow. and Archaea are more closely related to double Nobel prize winner Linus Pauling It was during this period that the three- each other than they are to the Bacteria and his collaborator Emile Zuckerkandl domains tree first came to prominence, (Fig. 1). Hence, in this tree our closest proposed that the sequences of the so it is interesting to ask how the tree cousins are the Archaea, a group of DNA, RNA and proteins found in all has fared as both computers and models micro-organisms once thought to be cells were “documents of evolutionary have improved. restricted to anaerobic and other hostile history” and hence were the best source Most of the models traditionally habitats like hot springs and thermal of data for making global evolutionary used to make the three-domains tree vents in the deep ocean. However, trees. The basic procedure is to collect have assumed that the same sequences although the three-domains tree of life sequences from different species and in all organisms evolve in much the

Eukaryotes Euryarchaeota Euryarchaeota Eukaryotes Lokiarchaeota Crenarchaeota Crenarchaeota Thaumarchaeota Thaumarchaeota Aigarchaeota TACK/ Aigarchaeota TACK/ Korarchaeota eocytes eocytes Lokiarchaeota Korarchaeota Bacteria Bacteria

Three-domains tree Two-domains tree

Fig. 1. The three-domains and two-domains trees – competing hypotheses for the origin of eukaryotes. The iconic three-domains tree appears in most textbooks and divides cellular life into three separate major groups or ‘domains’: the Bacteria, the Archaea and the Eukaryotes. In this tree the Eukaryotes are held to have originated from a common prokaryotic ancestor shared with the Archaea (enclosed in the shaded box). By contrast, the two-domains/eocyte tree recovers Eukaryotes nested inside the Archaea with the newly discovered Lokiarchaeota currently thought to be the closest archaeal relatives of the Eukaryotes. In the two-domains/eocyte tree the eukaryotic lineage had an ancestor that was already an Archaea. Studying uncultured archaeal diversity in nature thus holds the promise of finding ever-closer relatives of Eukaryotes. The genomic and cellular features of these lineages could potentially illuminate important stages in the evolution of eukaryotic cells like our own. The Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota are commonly called the TACK Archaea in the literature. Modified from Williams et al. (2013) Nature 504, 231–236.

Microbiology Today May 16 | www.microbiologysociety.org 71 same way, but this is not supported by Two domains is better supported than limitations, they fit real sequence data real sequence data. For example, the three when new methods are used much better than the simpler models nucleotide composition of SSU rRNA Over the past few years, a number used in the past. Interestingly, when the sequences, which are by far the most of new models have been developed new models were first used to analyse the widely used molecules for making by statisticians to try and better molecular sequence data commonly taken broad-scale evolutionary trees, varies accommodate aspects of real molecular to support the three-domains tree, an dramatically in different species. This sequence evolution. For example, models alternative hypothesis for the relationship provides strong evidence that the are now available that recognise that between Archaea and eukaryotes called ways in which SSU rRNA sequences the same sequences in different species the ‘eocyte tree’ was better supported. have evolved in different species have can evolve differently in terms of their In the long-neglected eocyte tree, which changed over time. In tree building, using amino acid or nucleotide compositions, was first proposed by James Lake and a model of sequence evolution that does and other models have been developed colleagues in 1984 based upon ribosome not fit the data being analysed can often that allow individual sites in molecular structure, the Bacteria and Archaea produce an incorrect tree with strong sequences to evolve in different ways can still be considered distinct primary support. Recent work now suggests that to each other. Although it is widely domains but the eukaryotes originate this can explain why past analyses have recognised that even the best currently from within the domain Archaea recovered the ‘three-domains’ tree. available models have important (Fig. 1). In other words, in the ‘two- domains/eocyte tree’, the eukaryotic lineage has an archaeal parent.

Adding new groups of Archaea increases confidence in the new tree Microbiologists have long suspected that the micro-organisms that have been studied in the laboratory are only a tiny fraction of natural microbial diversity. The original eocyte Archaea included species like Sulfolobus (later called the Crenarchaeota in 1990 by Woese and colleagues) that live in hot acidic springs, so they were seen as rather unusual and exotic micro-organisms. In the past few years, sampling of the natural microbial world has greatly increased, driven by the availability of new molecular methods to investigate uncultured microbial diversity Fig. 2. Molecular methods can be used to identify environmental micro-organisms without cultivation. The figure (Fig. 2). Recently discovered Archaea on the right shows a light micrograph of an anaerobic ciliate protozoan called Trimyema that is commonly found related to the eocytes include a variety of in freshwater ponds in the UK and elsewhere. Trimyema is the host for a particular type of Archaea called a new lineages that have been informally methanogen because it makes methane. Like many environmental Archaea the intracellular methanogens have grouped together as the ‘TACK’ Archaea. not yet been isolated into laboratory culture but they can nevertheless be identified as a single new species of Some of the TACK Archaea have major Methanocorpusculum based upon their SSU rRNA sequences, which can be isolated and read using modern DNA roles in the soil and marine nitrogen technology. On the left a fluorescent DNA probe (green) was used to confirm that all of the many methanogens cycle, suggesting that their discovery living inside Trimyema have the same SSU rRNA sequence. Similar probes can facilitate isolation experiments and further study is not just important because they can be used to identify samples enriched in the target species and also to confirm when a target because of their potential relationship to species has been successfully cultured. Bars, 10 µm. Kindly provided by Mr Will Lewis (University of Newcastle) eukaryotes, but also for understanding

72 Microbiology Today May 16 | www.microbiologysociety.org The perspective on “ eukaryotic evolution provided by the two-domains/eocyte tree of life has already had a profound influence on ideas about how eukaryotes first evolved from their prokaryotic ancestors.

“However, the prize to be gained is Fig. 3. Part of the Soria Moria hydrothermal vent field along the Arctic Mid-Ocean Ridge. The picture was taken potentially enormous because success close to the Loki’s Castle sampling site from which the DNA samples used to recover the genome of Lokiarchaeota will bring the study of eukaryotic origins were isolated. The detailed methods used to reconstruct the Lokiarchaeota genome are described by Spang et al. much more firmly into the of (2015) Nature 521, 173–179. Kindly provided by Dr Rolf Birger Pedersen, Centre for Geobiology, University of Bergen, experimental science. Norway Martin Embley globally important nutrient cycles. that their genomes will be more similar Institute for Cell and Molecular Improved sampling of lineages often has to eukaryotes in their protein repertoires. Biosciences, University of Newcastle, a positive impact on the accuracy of tree This prediction appears to have been Newcastle-upon-Tyne, Tyne and Wear reconstruction, particularly if the new vindicated by the discovery of a new NE1 7RU, UK sequences populate parts of the tree archaeal lineage called the Lokiarchaeota [email protected] that were previously poorly sampled. (Fig. 3). The Lokiarchaeota are the closest Importantly, all of the recent analyses archaeal relatives of eukaryotes in Tom Williams that have included a broad sample of the evolutionary trees and, consistent with School of Earth Sciences, University new TACK Archaea have supported the that closer relationship (Fig. 1), their of Bristol, Senate House, Tyndall Avenue, two-domains/eocyte tree (Fig. 1). reconstructed genomes contain more Bristol BS8 1TH, UK genes for proteins that were previously [email protected] Can the new tree help us to better thought to be eukaryote-specific. These understand eukaryotic origins? include proteins that, in eukaryotes, are Further reading The perspective on eukaryotic evolution used for the cytoskeleton, in membrane Embley, T. M. & Williams, T. A. (2015). provided by the two-domains/eocyte remodelling and in phagocytosis, all Evolution: steps on the road to eukaryotes. tree of life has already had a profound features long-held to be unique to Nature 521, 169–170. influence on ideas about how eukaryotes eukaryotic cells. At present, the evidence Pester, M., Schleper, C. & Wagner, M. (2011). first evolved from their prokaryotic for the existence of Lokiarchaeota comes The Thaumarchaeota: an emerging view of ancestors. Eukaryotic cells have an from metagenomes constructed from their phylogeny and ecophysiology. Curr Opin internal structural complexity that is not environmental DNA samples so it is Microbiol 14, 300–306. found in and the origins of now critically important to isolate viable Spang, A. & others (2015). Complex archaea this complexity have long been a major cultures into the laboratory, to determine that bridge the gap between prokaryotes and evolutionary puzzle. A key prediction the cellular roles of their eukaryote-like eukaryotes. Nature 521, 173–179. of the two-domains/eocyte tree is that proteins. Achieving that goal may be Williams, T. A., Foster, P. G., Cox, C. J. & Archaea can be discovered that are more difficult and will require all of the classic Embley, T. M. (2013). An archaeal origin closely related to eukaryotes than the tools of microbiology, including selective of eukaryotes supports only two primary species that we already know about, and, isolation, microbial physiology and cell domains of life. Nature 504, 231–236. because of this closer common ancestry, biology, and cutting edge microscopy.

Microbiology Today May 16 | www.microbiologysociety.org 73 Archaea and the meaning of life

Above Carl Woese. Don Hamerman, Institute for Genomic Biology, University of Hannah Marriott & Thorsten Allers Illinois at Urbana-Champaign

Humans are inordinately fond of dividing things into two – our approach to taxonomic classification is no exception. The earliest system published by Linnaeus divided living organisms into animals and plants, and by the 1960s this was superseded by a more fundamental split between prokaryotes and eukaryotes. So it should come as no surprise that the idea of a third domain of life – Archaea – met with fierce resistance when it was proposed in the 1970s.

74 Microbiology Today May 16 | www.microbiologysociety.org Above Carl Woese. Don Hamerman, Institute for Genomic Biology, University of Illinois at Urbana-Champaign

Geothermal areas and hot springs from Waiotapu geothermal area (Roturua, New Zealand) and Yellowstone National Park (USA). Far left A mud pool, Waiotapu. Second from left Champagne Pool, Waiotapu. Centre A hot spring in Yellowstone National Park. Above Sulfur deposits, Waiotapu. Right Lady Knox Geyser, Waiotapu. All Ian Haidl, except centre Sonja-Verena Albers

A brief history of Archaea: Methanogens (archaea that However, he was surprised to find 1977 to present produce methane) and other groups of that they are fundamentally distinct to Archaea are widespread on Earth yet micro-organisms, including halobacteria bacteria. relatively little is known about them, (now called halophilic archaea) as Woese was using small-subunit outside of the select groups of people well as thermophiles, had already rRNA (ribosomal RNA) to build a new that study these fascinating organisms. been discovered, but they had been phylogenic tree. Small-subunit rRNA They are a mystery that is being slowly misclassified under the domain Bacteria. is an essential component of all self- unravelled since their ‘discovery’ in 1977 Woese found that these organisms replicating organisms and shows by Carl Woese and his group, including did not just share a love for extreme remarkable sequence conservation. This George Fox, while working at the environments, but also that they are made it a perfect choice for a molecular University of Illinois. phylogenetically related to each other. chronometer. At the time this molecular

Microbiology Today May 16 | www.microbiologysociety.org 75 Archaeal and Eukaryotic-like Discovery of an First archaeal Sulfolobus Discovery of the eukaryotic RNA promoters Presence of extreme acidophile DNA replication solfataricus found domain Archaea polymerases shown discovered in found that can grow below origin identified in to have multiple by Carl Woese to be similar archaea in archaea pH0 Pyrococcus abysii replication origins

1977 1980 1983 1986 1988 1990 1995 1996 2000 2004 2006 2009 2010 2013 2015

Archaea proposed First archaeal Proposal Archaea split into two First thermophile Archaea found Shotgun environmental by Woese as the genome sequenced: of ‘TACK’ groups: Crenarchaeota isolated with in the Antarctic sequencing shows third domain of life Methanococcus superphylum and Euryarchaeota optimum growth archaea are ubiquitous temp. of 100 °C jannaschii

Timeline of Archaea from their discovery to present day. Ian Haidl, Sonja Albers, Thorsten Allers approach to phylogeny was novel – environments such as soil and the tree changing as each new discovery is previous methods relied instead on ocean, and in environments where they made. visible characteristics such as cell shape cohabit with bacteria. For example, in or growth conditions. Woese found that the human gut archaea are responsible The origins of life? the prokaryotes are not one coherent for producing methane! However, unlike Archaea may look like bacteria at a domain, but are made up of two distinct bacteria, no pathogenic archaea have first glance and there are certainly many groups: Bacteria and Archaea. At the ever been found. superficial similarities, but dig deeper time they were named ‘Eubacteria’ and Almost 40 years have passed since and archaea have more in common ‘Archaebacteria’, respectively, but these their reclassification into a new domain with eukaryotes. In fact, it is now widely two groups of prokaryotes were found but still many more species of archaea accepted that archaea are the ancestors to be no more similar to each other are being discovered. DNA sequencing of all eukaryotes. than they were to eukaryotes. Woese has improved dramatically, meaning that Archaea, like bacteria, are single- proposed that the tree of life has three archaea no longer have to be cultured celled organisms with a circular equal branches – Archaea, Bacteria and to be characterised. This has led to double-stranded DNA genome, and Eukarya – and that the term ‘prokaryote’ the discovery of entirely new lineages. they have neither a nuclear membrane should be abandoned because it has no Based on phylogenetic data (16S rRNA nor organelles. This means that they taxonomic meaning. Unsurprisingly, his and other genes) the domain Archaea are similar to bacteria in terms of cell ideas were not universally popular. was originally split into two groups; the structure, although there are differences. As with any new discovery there Euryarchaeota and the Crenarchaeota. Archaea do not have a bacterial-style are sceptics, but biochemical data from However, since 2006 three more lineages cell wall and their plasma membrane is Wolfram Zillig supported the 16S rRNA have been discovered: Thaumarchaeota, different to that found in both bacteria data collected by Woese. Over time, the Aigarchaeota and Korarchaeota. These and eukaryotes. But on the inside of new domain of Archaea was accepted three new groups are often combined the cell, archaea show a striking family by the scientific community. Interest in with the Crenarchaeota to form the resemblance to eukaryotes. This is archaea increased further after whole ‘TACK’ superphylum (more on this especially so for the enzymic machinery genome sequencing took off in the later). Even more recently there have that processes genetic information 1990s, and researchers increasingly been reports of new lineages of ‘nano’ – DNA packaging and replication, switched from bacteria or eukaryotes archaea, which are characterised by transcription into RNA, and translation to working on these exotic micro- a small cell size with very few genes. into protein. All of these processes are organisms. But contrary to popular The constant unearthing of new species essentially the same in archaea and belief, not all archaea are extremophiles. and groups make the Archaea a very eukaryotes, and are quite distinct from They have also been found in ‘normal’ fluid domain, with the phylogenetic bacteria.

76 Microbiology Today May 16 | www.microbiologysociety.org Discovery of Haloferax volcanii superphylum of Archaea. One of the and Archaea. And more than anything ubiquitin-like found to grow protein modification faster without most exciting new discoveries of the last else, we should give credit to Carl Woese, in Haloferax volcanii replication origins year was the identification of a ‘missing whose taxonomic revolution has allowed link’ between Eukarya and Archaea. us to trace our ancestors all the way Called Lokiarchaeota, they were found back to their humble beginnings as 1977 1980 1983 1986 1988 1990 1995 1996 2000 2004 2006 2009 2010 2013 2015 near a hydrothermal vent at a site known archaeal cells. as Loki’s Castle in the Arctic Ocean. Can we use our knowledge of 1000th archaeal Proposal of only two Discovery of Hannah Marriott & Thorsten Allers genome is primary domains of new archaeal archaea to trace the origins of complex sequenced life: Bacteria and group: School of Life Sciences, University of life? Eukaryotic microfossils can be Archaea Lokiarchaeota Nottingham, Queen’s Medical Centre, dated back to 1.8 billion years ago but Nottingham NG7 2UH, UK biological methane has been found in rocks that are 3.4 billion years old. The Timeline of Archaea from their discovery to present day. Ian Haidl, Sonja Albers, Thorsten Allers only source of biological methane is Further reading This prompts the question: if methanogenic Euryarchaeota, so we Eme, L. & Doolittle, W. F. (2015). Archaea. archaea are more closely related to know that archaea have been around Curr Biol 25, R845–R875. eukaryotes than bacteria, then how do since the very beginnings of life on Earth. Spang, A. & others (2015). Complex archaea they fit in the tree of life? As for life on other planets, it is tempting that bridge the gap between prokaryotes and The phylogenetic tree proposed to speculate that archaea may have also eukaryotes. Nature 521, 173–179. by Woese was split into three equal colonised Mars – evidence is mounting Williams, T. A. & others (2013). An domains, with Archaea and Eukarya that methane in the Martian atmosphere archaeal origin of eukaryotes supports only sharing a common ancestor that has a biological origin. two primary domains of life. Nature 504, had already diverged from Bacteria. 231–236. However, biologists working on the Woese’s revolution Woese C. R., Kandler O. & Wheelis M. origins of life have recently concluded What do the recent discoveries mean L. (1990). Towards a natural system of that Eukarya and Archaea are not sister for us humans? Given our desire for organisms: proposal for the domains groups. Instead, eukaryotes are the dichotomy, we should be relieved that Archaea, Bacteria, and Eucarya. Proc Natl direct descendants of archaea, and our the tree of life has been pruned back to Acad Sci USA 87, 4576–4579. long-lost ancestor belongs to the ‘TACK’ just two primary branches – Bacteria

Eukarya

Archaea TACK Bacteria Euryarchaeota Crenarchaeota Eukarya Bacteria Eury- Thaum- Aigar- Cren- Korarchaeota

Archaea

Carl Woese’s New three-domain tree two-domain tree

Universal phylogenetic trees in rooted form, showing the three domains. Ian Haidl, Sonja Albers, Thorsten Allers

Microbiology Today May 16 | www.microbiologysociety.org 77 Annual Conference

Annual Conference 2016 | 21–24 March, ACC Liverpool

Thank you to all of our delegates, invited speakers and over 300 talks and 400 posters, all covering a range of exhibitors who helped make our Annual Conference one of microbiology, and this year we included additional lunchtime the Society’s best yet. During March, we welcomed over 1,400 and evening events as part of the conference experience. of you to the ACC in Liverpool to enjoy four days of science Particular highlights included our Prize Lectures, our Hot and socialising, which included our super talented band The Topic Lecture on Zika virus, and our social programme. Radicals, who brought the party atmosphere and encouraged As in previous years, research from our Conference received some movers and shakers to hit the dance floor! huge attention from the press, with researchers appearing Delegates attended the Conference from all over the globe to in newspapers, on radio stations and on television channels hear breakthrough research, take part in panels and debates, across the globe. and to network and build connections. Once again our 2016 Thank you to all those who gave us feedback; as always, we Conference featured a packed programme of 29 sessions, value your comments. Ian Atherton Society-sponsored events in 2016 Every year we provide financial support for microbiology events held by other organisations. Below are some of the events we have sponsored so far this year. The next deadline for 2016 event applications will be 17 June 2016.

11th Recently Independent Virology Researcher’s Meeting, 2016 (RIVR 2016) 4–5 January Derby 21st Glasgow Virology Workshop (GVW) 30 January Glasgow Legionella pneumophila (1976 to 2016) – From Whole Guinea Pigs to Whole Genome 31 March London Sequencing: Do We Understand it Any Better After 40 Years? The 7th European Spores Conference 18–20 April London 14th UK Meeting on the Biology and Pathology of Hepatitis C virus 20–22 May Cumbria Protistology-UK Spring Meeting 2016 6–8 June Bournemouth Young Microbiologists Symposium on Microbe Signalling, Organisation and 29–30 June Dundee Pathogenesis British Yeast Group 29 June–1 July Swansea Within Host RNA Virus Persistence: Mechanisms and Consequences 24–26 August St Andrews 8th Meeting of the European Society for Chlamydia Research 6–9 September Oxford Structural Aspects of Infectious Disease September Belfast

78 Microbiology Today May 16 | www.microbiologysociety.org Follow the Society on Twitter to keep up-to-date: Edinburgh. Convention Edinburgh @MicrobioSoc

Annual Conference 2017 3–6 April 2017, EICC Edinburgh #Microbio17 The countdown has begun to Conference 2017 and in preparation our Divisions have already started to create our next programme. Session titles

have now been confirmed and speakers are being identified to ensure that Peshkova/iStock/Thinkstock once again our Annual Conference provides delegates access to hot topics, Applications and new developments and leading research. proposals welcome Main symposia: • Regulation of RNA expression Our programme of events is developed during virus infection • Anaerobes in infection and driven from proposals submitted by • Synthetic and systems biology • Aquatic microbiology our members. In addition to the Focused applications in microbiology • Cell biology of pathogen entry Meeting proposals, we also welcome into host cells proposals for Conference sessions Virus workshops: to take place at our annual meeting • Circadian and cell rhythms • Antivirals and vaccines and applications for grants to support • Endemic mycoses • Clinical virology speaker expenses at external events. • Epigenetic and non-coding • Evolution and virus populations Further information can be found online, in eukaryotes • Gene expression and replication including terms and conditions and • Geomicrobiology • Innate immunity forms, at www.microbiologysociety. • Heterogeneity and polymicrobial • Pathogenesis org/proposals interactions in biofilms • Plant virology The next key deadlines are below: • Just passing through – virus infections of the gastrointestinal Prokaryotic forums: • Proposals for Focused Meetings 2017 tract • Environmental and Applied 17 June 2016 • Macromolecular machines Microbiology Forum • Society-Supported Conference Grants • Microbial cell surfaces • Microbial Physiology, Metabolism 2016/17 • Microbial genomics: whole and Molecular Mechanisms Forum 17 June 2016 population to single cell • Prokaryotic Genetics and Genomics • Proposals for Annual Conference 2017 • Microbial mechanisms of plant Forum 16 December 2016 pathology • Prokaryotic Microbial Infection • Protistology UK Annual Meeting Forum Further information can be found in our events section Add the date to your diary to not miss out next year. Sign up to our newsletter at www.microbiologysociety.org/newsletter to ensure you are online: receiving regular updates about the Conference and other Society news, and visit www.microbiologysociety.org/ www.microbiologysociety.org/events for further information. events

Microbiology Today May 16 | www.microbiologysociety.org 79 Focused Meetings Could you run a Focused Meeting with the Microbiology Society?

D e le g a The Microbiology Society is now into our third year of Focused te s

vi ew Meetings, a series of events dedicated to exploring specific in g po st ers topics within the field. Working with members, we have so at the IAM MI m far produced five successful meetings on subjects ranging eetin 2015. g in London, UK, 9–10 November, from ‘Industrial Applications of Metal–Microbe Interactions’ to ‘Arboviruses and their Vectors’. This article explains why you The IMAV 2015 meeting was my first experience of running

should consider submitting an application for a meeting and how a Focused Meeting. It turned

the Society can help you make it a success. out to be a great occasion “that really fulfilled the aims Focused Meetings provide a forum for peers means that you can be a part of of bringing the community people working or studying in the same, the future direction of your field. It’s also together and showcasing“ or related, areas to network, collaborate a valuable skill to have when working in great science. The experience and learn from each other. They combine microbiology and looks great on a CV. and support of the Society talks from leading scientists with If you have an idea for a Focused team was hugely important in opportunities for new researchers to Meeting we advise you to discuss it the smooth organisation and present their work. first with your Division. You then need running of the event. There are many benefits to to submit an application, which will be becoming a Focused Meeting organiser: considered by the Society’s Scientific Alain Kohl, University of you get to play a key role in deciding the Conferences Committee. If your proposal Glasgow, Organiser, Focused

structure of the event, see papers at an is accepted, Society staff will work with Meeting 2015: International

early stage of their development, and you to organise a successful event. Meeting on Arboviruses and help shape the scientific programme. The Conference and Events Team their Vectors Organising a Focused Meeting for your will take care of all venue searching, A friendly atmosphere“ allowed for good conversation and discussion. I was able to make a couple of strong links that I hope to get further research “opportunities from. Delegate, Focused Meeting 2014: Emerging Challenges and Opportunities in Soil Microbiology

Delegates attend a session at the IAMMI m eeting. 80 Microbiology Today May 16 | www.microbiologysociety.org Upcoming Focused Meetings – abstract submissions and registration now open

administration and logistics. The D e Molecular Biology of Archaea 5 le Society will support you and the other g a te s 1–3 August 2016, London School of Hygiene and Tropical Medicine, London, UK speakers to create a solid scientific vi ew in programme, and will market the event Topics include: g po st effectively so you get the right people • DNA, chromosomes and cell cycle ers at the there. • RNA, CRISPR and viruses IAM MI m eetin 2015. To find out more about running • Molecular assemblies and protein modification g in London, UK, 9–10 November, a Focused Meeting, go to www. • Genomes and evolution microbiologysociety.org/proposals Early bird registration rate closes on: Monday 27 June 2016 or contact the Society’s Conference Grant application deadline: Monday 6 June 2016 and Events Team at conferences@ microbiologysociety.org. The deadline to T. A submit applications for Focused Meetings The Dynamic Fungus llers in 2018 is 31 December 2016. 5–7 September 2016, Mercure Exeter Rougemont Hotel, Exeter, UK

A full listing of Society Focused Meeting Topics include: events can be found at www.microbiology • Dynamics of the fungal cell society.org/focusedmeetings • Mathematical modelling in fungal science • Dynamics of cellular differentiation • Dynamics in fungal pathogenicity

We found organising a • Dynamic evolution and adaption of fungi Focused Meeting with the Early bird registration rate closes on: Monday 25 July 2016

Microbiology Society a Grant application deadline: Monday 27 June 2016 Ge ro Stei very pleasurable, hassle- nberg free experience. We were “ “ Molecular Biology and Pathogenesis of Avian Viruses extremely well supported by the administrative team at 27–29 September 2016, Charles Darwin House, London, UK the Society, which allowed us Topics include: to concentrate on putting an • Molecular biology and genetics of avian virus replication excellent scientific programme • Tropism and host range restriction • Pathogenesis of avian viruses together. • Host antiviral responses and virus immunomodulation Carol Munro, University • New and improved approaches to the control of avian viruses of Aberdeen, Organiser, Early bird registration rate closes on: Monday 1 August 2016 Focused Meeting 2014: Grant application deadline: Monday 4 July 2016 Mo nti Infection Models to Investigate cel llo / iStoc Microbial Disease and k / Thinkstock Further information on the programme and registration can be found Antimicrobial Therapies online: www.microbiologysociety.org/focusedmeetings

Delegates attend a session at the IAMMI m eeting. Microbiology Today May 16 | www.microbiologysociety.org 81 Focused Meetings –

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Exploring the Microbe– Immune System Interface 1–2 September 2016 Rochestown Park Hotel, Rochestown, Cork, Ireland

Further information for each meeting including the full programme, confirmed speakers, registration deadlines and grants can be found online: www. microbiologysociety.org/focusedmeetings

For further information contact [email protected]

e ut tit ns e I m 82 Microbiology Today May 16 | www.microbiologysociety.org bio cro Mi APC Early Career Microbiologists’ Forum: the Executive Committee

The Early Career Microbiologists’ (ECM) Forum is a new initiative that will bring our early career members together to play a key role in shaping the Society. This is part

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P o our membership – enabling early way, the Forum will have representation with the Communications Committee, m i s T s a career members to influence the work throughout our governance, giving it which oversees Microbiology Today, M r o s of the Society across all of its activities, a real opportunity to bring the ECM education and outreach activities and s fe ro including conference content, policy viewpoint to all proceedings, feeding in the Society’s other communications P d n a work, our journals and our professional the thoughts of the wider Forum. channels. ) n li b u development activities. We hope that it The roles that will be available D ge • The International Representative – le will play a major role in helping shape are: ol C ity the future development and governance who will work with the International rs ve ni of the Society. Quite simply, we want to • The Chair – who will work with Working Group, which ensures (U ry ar Council and the Professional the Society is considering its d B hear from you and learn what you want ral Ge Development Committee and international endeavours. Dr to see us do. To enable the Forum to feed into be a member of both Council, Each Executive Committee the way the Society is run, it will be which governs the Society, and member will serve a term of two years, represented by an Executive Committee the Professional Development to enable as many ECMs to benefit – voting for these representatives Committee. from a term in office as possible. Of will take place later this month. Early • The Treasurer – who will look after course, we want to ensure the work career members of the Society have the financial responsibilities of the and structure of the Forum is set by to register their interest in joining Forum. the Forum itself, so the committee will the Forum, to be able to vote for the evolve from these positions over time. Executive Committee. Each member of • The Conferences Representative – We think this will be a great who will work with the Scientific opportunity for early career Conferences Committee, which microbiologists within our membership. considers the scientific content of Join today to be involved in the Forum’s Society meetings. activities and make the most of the opportunity to have a real impact on • The Programmes Representative – our current work and future direction. who will work with both the Policy Contact: [email protected] and Publishing Committees, which look after the Society’s Maria Fernandes impact in the policy arena and Professional Development Officer oversee our journal outputs, [email protected] respectively.

Microbiology Today May 16 | www.microbiologysociety.org 83 Schoolzone Life finds a way

Concepts around when life evolved, and how life is formed, can be complex for students to understand. These examples of practical activities can be done with students to demonstrate how long microbes have been in existence, and also show how cells assemble, giving both large-scale and small-scale demonstrations of where life comes from. How do cells assemble? Have you ever wondered how cells 4. While the mixture is separating, What is happening form? Do they just appear immediately crack the egg into the smaller Water molecules are attracted to one at random as the beautifully coloured bowl. The egg yolk contains fats, another (hydrophilic) due to the polar structures we see in textbooks? Of oily compounds and phospholipid forces between them. Oil molecules, course not! Cells self-assemble due compounds. on the other hand, are non-polar to polar forces and interactions with 5. By now, the oil and water should (hydrophobic) and are repelled from phospholipids. In this experiment, you have completely separated and the water. This is why you see two can demonstrate how the cell wall can the oil has formed a layer on top distinct layers when oil and water are assemble in a clear and visible way. of the water. Take the eye dropper, placed together. Due to oil being less squeeze it and stab it into the dense, it forms the top layer. What you need centre of the yolk. Get Hydrophilic head • flask with a stopper – a sample of yolk and Hydrophobic tail Water a jar with a lid will suffice add a drop to the jar Water cooking oil with the water and oil. • Micelle • one egg The drop of yolk should Air • small bowl fall through the oil but • eye dropper float on top of the Water • water water layer. 6. Place the lid back on What to do the jar and shake again Water 1. Add 100 ml of water to the jar. for 3–5 seconds, like 2. Add 25 ml of oil. before. 3. Place the lid on the jar and give it 7. Watch what happens a good shake for 3–5 seconds. The to the oil layer this liquids should appear mixed at first time – there will be Illustration of phospholipids forming biological membranes. and then start separating. some movement! Science Photo Library

84 Microbiology Today May 16 | www.microbiologysociety.org Escherichia coli cultured to produce a phylogenetic tree showing the relatedness of primates. Gregory Lab/microbialart.com/Science Photo Library How old are microbes? The Earth is around 5 billion years • 20 small cards corresponding length along the old and a lot has happened since its • marker pen line from the ‘present day mark’. formation. Microbes have been around • metre ruler You may need to draw arrows when for a large portion of this time. For most • tape/glue it gets closer to present day as a lot people it is too hard to quantify this of events happen in a short space timescale – so let’s visualise it using What to do of time! significant events that led up to life as 1. Start by laying out the card so there 4. Once all twenty cards are stuck we know it today. is one long continuous length of 5 down along the timeline you can metres. This represents 5 billion appreciate the history of the world What you need years and the geological timescale and the origin of life timeline. • large pieces of card, making up you are working with. (Note – 5 metres in length every 1 metre represents 1 billion Questions to consider years and every 10 centimetres • How do you think scientists know represents 100 million years.) It the ages of organisms such as might be an idea to make a mark at dinosaurs and microbes? every metre to show when 1 billion • What factors do you think have Molecules within the yolk are years has occurred. influenced major events in the classed as phospholipids, which have 2. At one end of the line, mark this lifetime of the Earth? a hydrophilic ‘head’ and a hydrophobic with ‘present day’ and at the other • Why do you think single-celled ‘tail’, as shown by the diagram. This end mark with ‘5 billion years ago’. organisms have survived so long? means they can attract both polar and 3. Write each of the statements in • What was the difference between non-polar molecules. Phospholipids the table below on one of the the first cells and the first single- make up the majority of the cell wall, 20 cards and place them at the celled organisms? by forming a bilayer around polar Where on Where on Event Event molecules such as water, DNA or RNA. the timeline the timeline Two things are happening when Earth forms 4.6 m First cells appear 3.8 m the yolk is added to the oil layer. Firstly, Single-celled organisms appear 3.5 m Viruses are present 3.0 m phospholipid and oil molecules will Cyanobacteria appear 2.2 m First Ice Age 2.3 m combine and float to the top of the oil Eukaryotes divide into three groups layer and form a micelle. Secondly, a Eukaryotes appear 2.0 m 1.5 m (plants, fungi and animals) bilayer will be formed, similar to that Multicellular animals appear 80 cm Second Ice Age 7.7 cm pictured and encapsulate a water molecule, this will move to the lower Marine invertebrates appear 60 cm Earliest fish appear 50 cm half of the oil layer. Trees appear 35 cm Reptiles appear 30 cm As the centre of the bilayer has a Dinosaurs appear 23.5 cm Mammals are present 22 cm non-polar core, it makes it very difficult Extinction of dinosaurs 6.5 cm Flowering plants appear 4 cm for polar molecules to freely pass Humans diverge from their closest 6 mm Humans appear 0.005 mm through it (due to repulsive forces) and relatives therefore the contents within these vesicles will not leak out. This is how a Hannah Forrest cell keeps all of its important contents Public Affairs Administrator inside! [email protected]

Microbiology Today May 16 | www.microbiologysociety.org 85 Outreach Crowdsourcing new antibiotics

Research Associate Jake Newitt has been working hard at the University of East Anglia over the last six months on the samples from our pop-up events last August, as part of the Small World Initiative. Here, he gives his views on working on the project so far. Jake Newitt in the lab at UEA.

he Small World Initiative is giving the general public, students and Teducators in the UK and Ireland the opportunity to be part of a global initiative to discover new antibiotics from soil bacteria. The samples collected by the public at the pilot pop-up events are now at the University of East Anglia and I have been looking at each to identify any potentially interesting micro-organisms that are producing antibiotics. I feel that I am a science communicator at heart, which is why I was so enthusiastic to start my Research Associate position for the Microbiology Society. The work that I do entails a classical screening programme for natural products, with an emphasis on outreach and engagement with the general public. The pilot events were organised at Thetford Forest, Suffolk/ Norfolk, and Alice Holt, Surrey, for the general public to get involved with the hunt for new antibiotics by collecting soil samples and following their analysis online (www.microbiologysociety.org/ smallworld). At the University of East Participants collecting soil samples. Anglia (where I am based) I plated out

86 Microbiology Today May 16 | www.microbiologysociety.org to spot – they are usually white and thing that has really struck me about my fluffy – and many of them also inhibit time during this position is just how time the growth of other bacteria around flies. There is always more to be done. them. These were prime candidates for I have found that, in truth, science is a further analysis. Having isolated over 30 real labour. A labour of love, but a labour different bacteria (and counting), it was nonetheless. What keeps me going is my mission to show that they produced the idea that I’m pushing the frontiers compounds that had antimicrobial of the field forward. I believe that the properties. Initial bioassays were future of natural product discovery lies conducted using soft nutrient agar and with molecular engineering, modifying an indicator strain (a microbe that we existing organisms in ways that unlocks are testing for activity against). This silent pathways, producing compounds mixture was poured around a small spot never before seen under laboratory of bacteria (that I had isolated from soil), conditions. Whether we can find a new the indicator was given time to grow, and antibiotic this way using the samples then I would look for an area of inhibition from this project will be known with Jake Newitt in the lab at UEA. around the isolate. time! each of these soil samples and took The future of my work will focus photographs, which were shared with on the elucidation of these compounds; Jake Newitt the general public, who were encouraged many will likely be rediscovered known University of East Anglia, Norwich to try to identify some of the bacteria. compounds, but there is always a chance Research Park, Norwich NR4 7TJ, UK Additionally, I have filmed a video that a new compound may be found. One series called Lab Diaries, documenting the stages of this classical screening for natural products. This is in a video blog style that aims to break down barriers between the public and scientific research, which can all be viewed on YouTube (http://microb.io/1mvO4FT). I found this challenged me more than I thought it would, despite the fact that I was a writer and editor for a popular science magazine as an undergraduate! When it came to explaining my field of expertise I was so used to using technical jargon that I found it difficult to describe it in simple, understandable terms. When I was isolating bacteria, I was predominantly looking for Actinomycetes, and, in particular, Streptomyces. The reason for my focus on this group of bacteria is that more than half of all known antibiotics come from The interactive stand, where participants could look at Streptomyces strains and mixed cultures from soil Streptomyces. They are quite often easy samples as well as submit their soil sample.

Microbiology Today May 16 | www.microbiologysociety.org 87 Membership Q&A This is a regular column to introduce our members. In this issue, we’re pleased to introduce Suresh Mahalingam. S. Mahalingam S.

Where are you currently based? cater very well to students in remote as the grant success rate is often very low I am currently a research professor at the villages, and so I was keen to finish school and a lot of good grants don’t get funded. Institute for Glycomics at Griffith University and head to Kuala Lumpur to follow We have been very lucky to secure funding on the sunny Gold Coast in Queensland, my passion for biology. My second-year for our research from the Australian Australia. research project informed me clearly National Health and Medical Research that my passion lay in biomedical Council. One other important thing is to be What is your area of specialism? research. I was fortunate to obtain a PhD able to get interest from pharmaceutical I am a virologist, with a particular interest scholarship at the John Curtin School companies. We are also trying to foster in the pathogenesis and treatment of viral of Medical Research at the Australian collaboration with biotechnology and big inflammatory diseases. National University, which had a very high pharmaceutical companies, and at times And more specifically? performing viral immunology programme, this can be challenging as they may have In the past 10 years we have focused on and I was inspired by the Nobel Prize- different priorities and goals. I have found understanding how viral infections cause winning work of Rolf M. Zinkernagel and it most beneficial to meet with directors disease in humans. We use animal models Peter C. Doherty that had been done there of biotechnology and pharmaceutical to dissect the mechanisms and we also in the 1970s. This was an exciting time companies to discuss their drugs or work closely with clinicians to obtain for me and confirmed that biomedical vaccines, and apply them to my research as human tissue samples so that we can research was my true vocation. part of a collaboration. We’re also working hard to increase our collaborations bridge the gap between basic and clinical Where did your interest in with clinicians, so that we can take our data. My work focuses on a number of viral microbiology come from? research from the bench to the bedside. infections in humans, particularly those As a child, I was always fascinated by The best science comes about from being that cause viral inflammatory disease, biology. During my undergraduate years surrounded by the right environment – and such as chikungunya virus, Ross River in Kuala Lumpur, I came down with it is particularly important to be in a strong virus and dengue virus. We also work dengue fever (caused by dengue virus and intellectual environment, with a critical with respiratory viruses that affect young transmitted by mosquitoes) and spent a mass of researchers with overlapping children, particularly respiratory syncytial very uncomfortable two weeks in hospital. areas of interest. virus and human metapneumovirus, for The fact that there were no vaccines which we have very reliable animal model or specific antivirals for this virus What is the best part about ‘doing systems. Once we know the mechanisms stimulated a desire to work in the area of science’? that are involved, we can look at current infectious disease, with a goal of helping I get enormous satisfaction from the drugs in the market that can be used people suffering from dengue and other scientific process. The thrill of conclusively against the virus. We are also developing infectious diseases. My goal remains to proving (or disproving) a hypothesis is vaccines. use my research skills to make a real hard to beat, followed by the challenge difference, particularly for emerging virus Tell us about your education to date of convincing the scientific community, diseases that affect poorer, developing I was raised in a small rural village in particularly the reviewers of high countries. Malaysia near the east coast, with little impact journals! I also get considerable surrounding it in any direction except What are the professional challenges satisfaction from doing basic science that the Malaysian jungle. It was a simple that present themselves and how do can influence change in clinical practice upbringing, without the distractions of you try to overcome them? or provide a new pathway to therapeutic big city life. The education system didn’t The main challenge in research is funding, development.

88 Microbiology Today May 16 | www.microbiologysociety.org I feel a deep sense of gratitude for What do you do to relax? Tell us one thing that your work the opportunities that have come my My wife Helen and I have two children, colleagues won’t know about you! way, and I am passionate about giving and these days it is family life that I am highly trained in Indian classical back to the scientific community. I take keeps me busy outside of the lab. One music, playing the mirthangam, a South special pleasure in nurturing the younger of my sons is autistic, which presents Indian drum. My father taught me and generation of scientists and the career its own challenges, but he is still the I used to give numerous concerts in development of scientists in my lab is sweetest and most lovable boy I know. Malaysia and Australia. a high priority. I am also on the national My wife often teases me that I am If you weren’t a scientist, what board of the Australian Institute of Policy married to my work, but the truth is would you be? & Science and serve this institute as a that family life is the most important to I can’t think of any job I would prefer, Tall Poppy Campaign Ambassador. This me, and I work very hard to maximise but perhaps a CEO of a large company, involves recognising Australian scientific my family time. I also enjoy watching particularly one that supports the excellence and encouraging younger tennis and listening to Indian classical community and gives something back to Australians to follow in the footsteps of music. our outstanding achievers. the community.

Who is your role model? What one record and luxury item If you would like to be featured in I greatly admire leading researchers in would you take to a desert island? this section or know someone who the field for their achievements. There I would bring my drum to play and listen may, contact Paul Easton, Head of are several that I look up to and aspire to to classical performances of great South Membership Services, at follow in their footsteps. Indian musicians. [email protected]

Microbiology Today May 16 | www.microbiologysociety.org 89 Membership review What will Society membership look like in 2017 and beyond? Look out for the opportunities to have your say

The Society will be undertaking a review of its membership offering during the course of 2016 to ensure it remains relevant and continues to deliver what members want from it. For those who couldn’t attend the Conference in March to give us their views, there will be other opportunities for members to give feedback through a range of consultation meetings, questionnaires and surveys. Do look out for them.

embership has been identified as a key Society pillar through Mwhich we aim to deliver our goals. Indeed, it is an essential component of our plan to deliver our mission and vision. Going forward, our goal is to “enhance the membership experience so it not only meets but exceeds expectations and members feel valued, heard and part of a community”. Our review will ask the questions necessary to help us deliver this goal, no matter

which community members feel part of. Olechowski/iStock/Thinkstock Rafal

90 Microbiology Today May 16 | www.microbiologysociety.org ourselves to continue to deliver a valued available to the widest range of people. service to members for the next 10, 15, We support individual members with 20 years? grants. We offer career-enhancing Some may argue that in the age of governance opportunities. We provide the internet, learned societies have no work experience opportunities. We offer place. After all, every one of us now has peer recognition through a range of the potential to build our own networks prizes and awards. We influence policy- and find sources of reliable information makers. None of this would be possible online. Why would we pay to join an without our membership. organisation when we can get these So, in looking forward to what benefits for free? It’s a valid question. space we seek to occupy in the future, So where can we add value? How perhaps a challenge for all of us is can the Society ensure its relevance to work harder to raise members’ going forward? consciousness above the level of the Part of the answer will lie in individual and the tangible, to the wider making much more of the experiences view that speaks more about the sense that cannot easily be replicated online. of ‘microbiological community’ and Our events for example, offer unique belonging that comes with membership, opportunities for people to meet each and the impact we can have on the other face-to-face, interact, and be part collective whole. Maybe we all need of a wider discussion and conversation. to work harder at demonstrating and Many of the benefits of attending communicating this.

Comstock/Stockbyte/Thinkstock conferences and meetings can’t be If you have thoughts and views to As preparation for taking part in the easily quantified. These occasions share about membership, we’d love to consultation process, we would ask you always bring the unexpected – the hear them. What are the questions we to start thinking now about some of the introduction you didn’t know would lead should be asking? What do you get out of bigger challenges facing organisations to the samples you needed; the offer membership? What do we do well? What like ours. of help made by someone you weren’t don’t we do that we should be doing? We operate in a very different aware of working on the same problem; If we were starting the Society from environment now compared with the a contact about a job; a discussion about scratch today, how different would it one just 10 years ago. How we received a possible funding lead. They are all look? How can we ensure what we offer and paid for our information then looks examples of face-to-face interactions is sustainable? Here’s your opportunity very different to how many of us receive that add value to being part of our wider to let us know your thoughts so please it now. Cheques, CDs and hard copy microbiological community. do! were still very much the currency of the And it is perhaps being part of this Look out for the opportunities day. Compare this with now. Anywhere, wider community where membership to contribute during the year, or if you anytime and very often for free are really comes into its own. Individually, of can’t wait, send your comments now today’s expectations. Keeping pace course, we pursue our own career and to [email protected]. with the rate of change in technology professional agendas, whether online These will feed into the review process presents challenges for all of us. or off. But only by acting collectively, on your behalf during 2016. But more importantly for through societies like ours, can we really membership organisations like ours, support each other and strengthen the Paul Easton is our need to keep pace with what our standing and impact of our profession. Head of Membership Services members and prospective members Through membership, we are able to [email protected] expect from us. How should we position provide opportunities and make them

Microbiology Today May 16 | www.microbiologysociety.org 91 Best of the blog

s the weather warms up for those of us here in the Northern AHemisphere, I thought it might be right to look at some of the temperature- related blog posts we’ve had over the past few months. Firstly in this roundup, we learnt about the ancient ‘Iceman’, also known as Ötzi, whose body was discovered in Ötzi, the ‘Iceman’. Thilo Parg / Wikimedia Commons 1991 after spending millennia buried under snow and ice in the Alps. This You know what’re warm? Hand past few months. Some of my remarkable find gave researchers the driers are warm (alright, this is getting a favourites include: Lactobacillus chance to gaze far back into our past. little tenuous now). Might the air coming wasatchensis from aged cheddar One of these researchers is Dr Frank out of the jet hand driers be responsible cheese (http://microb.io/1Uajtu9); the Maixner, who has been studying Ötzi’s for spreading viruses in public ultramicrobacteria Aurantimicrobium gut microbiota. Frank spoke to our washrooms? We spoke to Dr Patrick minutum (http://microb.io/1SwuG8x); Multimedia Producer Anand Jagatia Kimmitt at the University of Westminster, and three new species of Bifidobacterium about the work, which may help us better who has been researching this issue isolated from the faeces of baby understand human migration thousands (http://microb.io/1pvgyRy). marmosets (http://microb.io/1Uajtu9). of years ago (http://microb.io/1UPpY6l). We don’t tend to find many At the time of writing, we’re yet to When the weather’s warm, I like to microbiology-related papers in the have this year’s Annual Conference, but go surfing. Sadly, I am quite bad at it and journal Nature Physics, but this is exactly if the quality of the abstracts is anything spend more time in the sea than on my the source of some new research we to go by, I’m sure you’ll have an amazing board. Might this lead to me increasing covered in a podcast earlier this year. We time. There’ll be a host of Conference- my risk of coming into contact with learnt from the University of Cambridge’s related posts and podcasts on our site, so antibiotic-resistant bacteria? Anand went Professor Raymond Goldstein about how don’t forget to have a read of the Microbe to Cornwall to interview Anne Leonard, the mathematical principals can be Post to see what you might have missed. a PhD student at the University of Exeter used to explore both the swimming of Medical School, who is running the bacteria and the spin of electrons Benjamin Thompson Beach Bum Survey to assess the gut (http://microb.io/21Vn99m). Head of Communications bacteria of surfers in Southwest England We’ve learnt about a lot of [email protected] (http://microb.io/1QRL2t1). newly discovered microbes over the

92 Microbiology Today May 16 | www.microbiologysociety.org Reviews

Thermophilic Microorganisms by the leading experts in each field. It Edited by F. Li covers subjects such as the ecology of deep-sea thermophiles and their Caister Academic Press (2015) genetic systems, the diversity of £159.00 ISBN 978-1910190135 thermophiles and their roles in carbon cycling and biomass degradation, and Thermophilic micro-organisms the biochemical properties of a variety are quite a diverse group of micro- of heat-active enzymes and their current organisms and have brought and possible applications. Each chapter us fascinating scientific and is concise and readable, providing biotechnological interests, such as lucid explanations about the current the diversity and evolutional history understanding and prospective views of these thermophiles, their ecological of the fields. roles and adaptation mechanisms to This book would be an invaluable high temperature environments, and resource for any researcher interested their applications in bioprocessing and in these exotic microbes and their bioremediation scenes. applications, from senior undergraduates Takashi Itoh This book presents 10 selected and postgraduates to scientists and RIKEN BioResource Center topics of thermophilic micro-organisms engineers.

Microbiology Today May 16 | www.microbiologysociety.org 93 Microbiology: A Clinical Approach (2nd Edition) Written by A. Strelkauskas, A. Edwards, B. Fahnert, G. Pryor and J. Strelkauskas Garland Science (2015) £60.00 ISBN 978-0815345138

There is no shortage of textbooks that deal with general or clinical microbiology. I have nine in my own office and many other microbiology textbooks that deal with more specialist topics. It is important therefore that books introduced into this market approach the topic from a different angle. My initial thought on being sent this book was that there is little space for a new text in the market or even on my shelf, but having spent time reading this book I believe that it has succeeded in differentiating itself from other apparently similar offerings. The book is aimed mainly at nursing and allied health students and, based on my own experience, I believe that this would be a useful resource for the pharmacy students that I teach. The topics and depth of coverage reflect a ‘need-to-know’ approach for the intended readership, reflecting the way that allied health disciplines are often taught. Material is presented clearly and with emphasis at the start of each chapter on why a given topic is important. Each chapter has been colour-coded with ‘fast fact’ and ‘keep in mind’ sections that condense the main messages and provide relevant context. To facilitate learning, chapters have sections titled: ‘self-evaluation’ and ‘chapter-confidence’, with a series of multiple choice questions; ‘depth of understanding’, with more discursive questions; and ‘clinical corner’, which reinforces the clinical relevance of chapter material. The book is nicely illustrated throughout and well supported by a website, which incidentally is also excellent. The ‘bug parade’ section of the website even has embedded sound files to cover the pronunciation of bacterial names and links these to morphology, disease and to the associated chapters in the book. A large number of excellent videos are also available. In summary, this is an excellent learning resource that is targeted at pre-nursing and allied health students but would be a useful resource for medical and microbiology students and their lecturers.

Andrew McBain University of Manchester

94 Microbiology Today May 16 | www.microbiologysociety.org Comment

Biotechnology and BBSRC funding Biological Sciences Research Council (BBSRC) for microbiology invests in world-class bioscience research and training on behalf of Adam Staines the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond. BBSRC

unded by Government, and with In 2015, I led a review of the entire Firstly some data: BBSRC’s an annual budget of around £509m BBSRC microbiology portfolio, covering microbiology portfolio over the last Fin 2014–2015 (£459m on research the period 2008–2014. One of the six years accounted for over 30% of and capital grants, and £50.5m for interesting aspects that arose was the our research portfolio, with spend training and fellowships), we support cross-cutting nature of microbiology, and consistently averaging over £80m research and training in universities how pervasive it is across the BBSRC per year. This consisted of over 2,100 and strategically funded institutes. portfolio. It might be the scientist in me grants to almost 100 institutions. This BBSRC research and the people we but I must admit to a liking for in-depth spend has also been on the increase fund are helping society to meet major portfolio analysis – looking for patterns since 2012. challenges, including food security, green and trends in the data, and reading a So what were the pleasant energy and supporting people to have range of exciting grant proposals from surprises? Well, for one we seemed to healthier, longer lives. Our investments across our portfolio. fund a broad range of research across underpin important UK economic There was a combination of drivers kingdoms: predominantly bacteria (47%), sectors, such as farming, food, industrial for this analysis: it is a key research area viruses (20%) and fungi (17%), with biotechnology and pharmaceuticals. for BBSRC; the community had raised understandably smaller (but multi- Despite my past research life some concerns about the balance of our million) annual investment in protista which involved the manipulation and portfolio; and no cross-cutting analysis (3%), archaea (1%) and ‘other’ (1%), a characterisation of bacterial enzymes, of microbiology had been undertaken for classification which covers the range I could not profess to call myself a almost eight years. What the analyses of species that the then President of microbiologist. However, one of the revealed was a positive surprise both for the Microbiology Society described attractive aspects of working for a me and the expert group that reviewed as species where the ‘classification funding agency is the exposure we get to the analyses, which also allows us to is still under debate’. The breadth of an exciting range of novel research. dispel some myths. this portfolio continued across model

Microbiology Today May 16 | www.microbiologysociety.org 95 Replacing Feeding fossil fuels Staying a growing healthier population for longer

Committee A 15% Committee D 36% Committee B 33%

Committee C 16% examples of Research Councils working together such as the new AMR 12 programme. 10 Though the BBSRC microbiology 8 portfolio is very healthy there are some 6 areas where we need to do more work 4 2 in partnership with the community. 0 Plant virology and research on animal 2008/ 2009/ 2010/ 2011/ 2012/ 2013/

Spend in AMR-related microbiology (£m) microbiology Spend in AMR-related 09 10 11 12 13 14 fungal pathogens form relatively small BBSRC parts of the portfolio – there is a need species, and microbes that interact with much was funded through the other to encourage the next generation of animal, human or plant systems. committees and mechanisms. researchers into these fields – and levels So one of the myths I would like to Another myth I was pleased to of funding on foodborne pathogens has dispel is the type of research BBSRC dispel was around success rates. The been falling at a time when Defra and supports. I have heard comments that we data demonstrated that microbiology the Food Standards Agency funding only support basic microbiology in model does better than the average success has also reduced. BBSRC is currently systems or that we are only interested rates in three out of four committees, discussing these issues through our in applied microbiology. Well, in keeping and better than average overall. I think various advisory structures. I would note with our strategic priorities, which cover there is an inherent frustration from if anyone is interested in joining a BBSRC both areas, the good news is we invest in applicants when grant proposals are panel or committee, our annual call for the continuum of microbiology research, unsuccessful, and with 20–25% success new members opens in May. from fundamental discovery science, rates that is most applicants, most of the through to more translational and time. But I can reassure the microbiology Acknowledgements applied areas. This is also reflected in the community that they do well in our This analysis fed into an expert sources of funding, which include ~40% Responsive Mode system. working group chaired by Professor funding through the Responsive Mode There were also a number of Sarah Gurr, and I would like to thank mechanism, and the rest is split pretty pleasing trends in the portfolio; we have all the participants for their time and evenly between initiatives and institute been investing in an increasing level consideration on this. programmes. of human gut and skin microbiome One of the strengths of the research; the use of industrial schemes Adam Staines microbiology community is that has doubled in the last six years too (12% Head of Strategy (joint): Agriculture and their research spans all four BBSRC of the microbiology portfolio). We also Food Security, BBSRC Responsive Mode Committees, identified many new exciting impacts [email protected] depending on the nature of the research from the research we have invested in. question. The downside of this is that We often find ourselves discussing For more information about any individual committee member with the community how we handle BBSRC, our science and our impact only has visibility of a subset of the interdisciplinary proposals. An RCUK- see: www.bbsrc.ac.uk. microbiology grants we fund. I think wide agreement ensures all Responsive this has, in part, led to some of the Mode research proposals have a home, To note: ‘microbiology’ is defined by misconceptions about our portfolio; and where proposals have elements investments containing a substantial one committee member who reviewed in other councils’ remits, co-funding is component investigating the microbes the portfolio apologised to me for often provided. There was no evidence themselves, i.e. excluding microbes just being ‘grumpy’ about microbiology from the portfolio of an issue in this being used as a research tool. investments when he saw how regard; and there are lots of positive

96 Microbiology Today May 16 | www.microbiologysociety.org

Size: 297 x 210 mm 210 x 297 Size: Job no: 00536 no: Job PDF hi-res as Supply mm 5 Bleed:

Journal: Microobiology Today Microobiology Essential Generics: Chloramphenical Ad Chloramphenical Generics: Essential 02/02/2016 16:03 CHL25060 O65995 ALLIANCE: MOVIANTO: AAH: CHL600B PIP: 106-5796 CAPSULES

CHLORAMPHENICOL 1 2 3,4 Adverse events should be reported. Reporting forms can be found at www.mhra.gov.uk/ and information events should also be reported to yellowcard. Adverse Essential Generics on 01784 477167. distension, pallid cyanosis, vomiting, progressing to vasomotor collapse, distension, pallid cyanosis, vomiting, progressing to vasomotor of irregular respiration and death within a few hours of the onset symptoms. Overdose: Stop chloramphenicol immediately if signs of adverse events oral develop. Treatment is mainly supportive. If an allergy develops, Baby antihistamines may be used. In severe overdosage e.g. Gray Resin Syndrome, reduce plasma levels of chloramphenicol rapidly. increase haemoperfusion (XAD-4) has been reported to substantially chloramphenicol clearance. Pack size and Price: 60 capsules £377.00 Legal Category: POM. Market Authorisation Number: PL17736/0075. Market Authorisation Holder: Chemidex Pharma Limited, 7 Egham UK. Business Village, Crabtree Road, Egham, Surrey TW20 8RB, Date of preparation: January 2016. for See Chloramphenicol Capsules Summary of Product Characteristics full prescribing information. References: 1. Martindale: The Complete Drug Reference. Chloramphenicol. [Online]. Available from: http://www.medicinescomplete.com [Accessed 17th September 2015]. 2. Fluit, A.C., Wielders, C.L.C., Verhoef, J., and Schmitz, F.J. Epidemiology and susceptibility of 3,051 Staphylococcus aureus isolates from 25 university hospitals participating in the European SENTRY Study. Journal of Clinical Microbiology. 2001; 39(10): 3727-3732. 3. Kelly, C., LaMont. Patient information: Antibiotic- cile (Beyond the associated diarrhea caused by Clostridium diffi Basics).June 2015. 4. Bartlett J.G. Antimicrobial agents implicated cile toxin-associated diarrhea of colitis. Johns in Clostridium diffi Hopkins Med J. 1981; 149(1): 6-9. 5. Feder. H, Chloramphenicol: What we have learned in the last decade. Southern Medical Journal. 1986; (79)9: 1129-34. 6. Weigel LM et al. High-Level Vancomycin-Resistant lm. Staphylococcus aureus Isolates Associated with a Polymicrobial Biofi Antimicrob Agents Chemother. 2007 Jan; 51(1): 231–238. 7. Ensminger, P., Counter, F., Thomas, L., Lebbehuse, P. Susceptibility, resistance development, and synergy of antimicrobial combinations against cile. Current Microbiology. 1982; 7: 59-62. 8. Poilane, Clostridium diffi I., Bert, F., Cruaud, P., Nicolas-Chanoine, MH., Collignon, A. Interest cile isolates of the disk diffusion method for screening Clostridium diffi with decreased susceptibility to antibiotics. Pathologie Biologie (Paris). 2007; 55(8-9): 429-33. 9. Cattoir, V., Ould-Hocine, ZF., Legrand, P. cile clinical isolates Antimicrobial susceptibility of Clostridium diffi collected from 2001 to 2007 in a French university hospital. Pathologie Biologie (Paris). 2008; 56(7-8): 407-11. 10. Brazier, JS., Levett, PN., Stannard, AJ., Phillips, KD., Willis, AT. Antibiotic susceptibility of clinical isolates of clostridia. Journal of Antimicrobial Chemotherapy. 1985; 15(2): 181-5. 1,5 1,5 1,5 7-10 1,5 1,5 1 2 6

infections including: C.diffi cile with C.diffi implicated Rarely Widely distributed throughout the body, including CSF including the body, throughout distributed Widely levels to i.v. comparable Oral levels Typhoid Legionella Rickettsia MRSA VRSA Neisseria

E. coli

C.diffi cile C.diffi

H. infl uenzae H. infl against serious Effective Abbreviated Prescribing Information Chloramphenicol Capsules BP 250mg Presentation: Hard Gelatin Capsules. particularly Indications: Typhoid fever and life-threatening infections, uenzae, where other antibiotics will those caused by Haemophilus Infl ce. not suffi Posology: For oral administration. doses. For Adults and elderly: 50 mg/kg body weight daily in 4 divided be doubled severe infections (meningitis, septicaemia), this dose may Children: initially, but must be reduced as soon as clinically possible. Not recommended. Contra-indications: Known hypersensitivity or toxic reaction to used chloramphenicol or to any of the excipients. Should not be active for the prophylaxis or treatment of minor infections; during liable to immunisation; in porphyria patients; in patients taking drugs by breast- depress bone marrow function; during pregnancy, labour or feeding mothers. Special warnings and precautions for use: Use only if other treatments are ineffective. Use should be carefully monitored. Reduce dose and monitor plasma levels in hepatic or renal impairment; in the elderly; and in patients concurrently treated with interacting drugs. Interactions: Chloramphenicol prolongs the elimination, increasing the blood levels of drugs including warfarin, phenytoin, sulphonylureas, tolbutamide. Doses of anticonvulsants and anticoagulants may need to be adjusted if given concurrently. Complex effects (increased/decreased plasma levels) requiring monitoring of chloramphenicol plasma levels have been reported with co-administration of penicillins and rifampicin. Paracetamol prolongs chloramphenicol half-life and concurrent administration should be avoided. Chloramphenicol may increase the plasma levels of calcineurin inhibitors e.g. ciclosporin and tacrolimus. Barbiturates such as phenobarbitone increase the metabolism of chloramphenicol, resulting in reduced plasma chloramphenicol concentrations. In addition, there may be a decrease in the metabolism of phenobarbitone with concomitant chloramphenicol use. There is a small risk that chloramphenicol may reduce the contraceptive effect of oestrogens. Chloramphenicol reduces the response to hydroxocobalamin. Chloramphenicol is contra-indicated in patients taking drugs liable to suppress bone marrow function e.g. carbamazepine, sulphonamides, phenylbutazone, penicillamine, cytotoxic agents, some antipsychotics including clozapine and particularly depot antipsychotics, procainamide, nucleoside reverse transcriptase inhibitors, propylthiouracil. Pregnancy and Lactation: The use of chloramphenicol is contra- indicated as the drug crosses the placenta and is excreted in breast milk. cant effect Effects on ability to drive and use machines: No signifi on driving ability. Undesirable Effects: Reversible dose related bone marrow depression, irreversible aplastic anaemia, increased bleeding time, hypersensitivity reactions including allergic skin reactions, optic neuritis leading to blindness, ototoxicity, acidotic cardiovascular collapse, nausea, vomiting, glossitis, stomatitis, diarrhoea, enterocolitis, Gray Baby Syndrome particularly in the newborn, which consists of abdominal For further information, please contact: Essential Generics, 7 Egham Business Village, Crabtree Road, Egham, Surrey TW20 8RB, UK For further information, please contact: Essential Generics, 7 Egham Business Village, Crabtree Road, EG/CH/JAN/2016/01a 00536_Chloramphenicol Ad_Microbiology Today_AW.indd 1 43:2 May 2016 43:2 May Are viruses alive? viruses Are Astrobiology a sandbox God in playing Synthia: life of tree the on views Changing life of meaning the and Archaea What is life? Microbiology TODAY

Microbiology Today 43:2 May 2016 What is life? 29/01/2016 11:07:41 and NINTH EDITION NINTH is intended for medical students and students medical for is intended www.garlandscience.com 978-0-8153-4551-0 • £60.00 978-0-8153-4551-0 978-0-8153-4512-1 • £41.00 978-0-8153-4512-1 April 2016 • Paperback • 928pp • 624 illus • Paperback April 2016 is a textbook for students studying immunology at immunology at studying students for is a textbook Immunobiology Janeway’s text, As an introductory school levels. and medical graduate, the undergraduate, while illustrations, and informative clear writing the book’s will appreciate students scope its comprehensive will value immunologists and working students advanced and depth. with up-to-date content the bringing revised been thoroughly has Edition The Ninth and immunity, innate topic of on the especially field, in the developments significant continuity. for better chapters topics across of the presentation improving instructors, to adopting available Bank is a Question Edition the Ninth to Also new assign to instructors which allows and the Garland Science Learning System the review topics and on specific immunology with assessments online tutorials via the instructor students, as individual well class, as of the entire performance dashboard. March 2016 • Paperback • 358pp • 255 illus 2016 • Paperback March Seventh Edition Edition Seventh Case Studies in Immunology, undergraduate and graduate students in immunology. It presents major topics of major topics It presents in immunology. students and graduate undergraduate the basic extend and reinforce cases that a selection of clinical immunology through science. facts about the immunological scientific essential by is preceded history case Each how demonstrate themselves cases The specific disorder. mechanisms of that by is followed in the clinic and each one deconstructed are problems immunological as discussion can serve which finding and questions summary of the clinical a concise points. text, be used as either a stand-alone and can of 55 cases The book includes a total Edition Immunobiology, Ninth Janeway’s to aid, or as a companion review Edition. , Fourth The Immune System University of Alabama at Birmingham, USA Birmingham, of Alabama at University

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