The magazine of the Society for Applied Microbiology ■ June 2006 ■ Vol 7 No 2 ISSN 1479-2699

REGULARS MEETINGS FEATURES Microbiologist Vol 7 No.2 04Editorial 24 Summer 20 June 2006 Lucy Harper reviews Conference Bioremediation this issues top stories ISSN 1479-2699 2006 Bugs - keeping it 05 Contact Living together: clean. Teresa Belcher explores this Full contact polymicrobial important area information for all communities Committee members WRITE FOR US! 06Media Watch Microbiological news The editor is always looking for enthusiastic writers who wish to contribute articles to 07 Mailbox Microbiologist on their chosen Readers write in microbiological subject. Publisher: Society for 08President’s For further information please Applied Microbiology. email the editor, Lucy Harper column at: [email protected] Editor: Lucy Harper [email protected] 10 Med-Vet-Net Contributions: These are Infectious disease 27 Winter always welcome and should meeting in Malta 28 Cover story be addressed to the Editor Meeting at: [email protected] 12 Membership 2007 a one day meeting Advertising: Matters Julie Wright on Food and Health: Telephone: 01234 326661 13 Micro Break the most Applied [email protected] Photo competition microbiology Art and Design & layout: Pollard Creativity 14 Careers Biomedical Scientist Microbiology Production and printing: Pollard Creativity. in the news! All technical questions should 18 Overseas be addressed to: Development [email protected] 06 Tel: 01933 665617 Reports Reports from Ghana © Society for Applied and Reading Alun Anderson Microbiology 2006 reviews the Material published in Microbiologist may not be 38 Students controversial career reproduced, stored in a of Scientist Craig retrieval system, or into Work Venter who transmitted in any form without the prior permission reports discusses his latest of the Society. Avian influenza plan to make 42 The If you spot a microbes produce Society for Applied Microbiology, The Blore President’s microbiological story clean energy Tower, The Harpur Centre, Fund articles in the media which you Bedford MK40 1TQ, UK think should feature in 34 Stat Note 5 Microbiologist, please Tel: +44 (0)1234 326661 51 Books Is one set of data send it to the Editor at: Fax: +44 (0)1234 326678 more variable than [email protected] email: [email protected] 54 Join SfAM another? www.sfam.org.uk Editorial

Microbiologist N THE PREVIOUS ISSUE OF Vol 7 No.2 Microbiologist (March 2006, I Vol 7; No 1) I asked a rather June 2006 provocative question: When is a scientist not a scientist?” Answer: Contact the Editor: “When he / she is a business person”. [email protected] I was delighted by the response I received. Many of you think that the two Microbiologist copy Dates: contributors please disciplines can never be separated, that note that the final copy they are far from mutually exclusive. It’s dates in 2006/2007 will be: true to say that a successful scientist and a successful business person will both Vol 7 No.3 Sept 2006 have some very similar characteristics Friday 7 July 2006 and transferable skills — time and project management, accuracy, numeracy, Vol 7 No.4 Dec 2006 attention to detail, patience, and flexibility Friday 15 Sept 2006 to name but a few. In this sense the two go hand in hand. What do you think? To role in the Human Genome Project, Vol 8 No.1 March 2007 through his involvement in the company Friday 15 December 2006 join the debate contact me, the Editor at [email protected] or at the postal ‘Celera Genomics.’ This article was Vol 8 No.2 June 2007 address opposite. A couple of examples of written just as he was about to embark Friday 9 March 2007 different perspectives on this thorny topic upon new and apparently environmentally are described in the ‘Mailbox’ section friendly research, so ‘perhaps he’s not How to submit material (page 7). such a bad boy after all.’ We catch up Please submit all articles, with Venter at the latest stage of his reports, meetings endeavours, with an interview by Alun notifications, letters etc., as Anderson, former Editor-in-Chief of New plain text (*.txt) or rich text Scientist magazine. Venter gives us not files (*.rtf). Please submit only his opinion on the relationship all images as original photographic prints or between science and business, but also transparencies rather than describes the principles of the science scanned images and these involved, and its potential impact upon will be processed by us and the environment. returned to you promptly. On the subject of the environment, our If your images are only in second feature article is an overview of digital format please make Bioremediation (see page 20) the sure they are supplied at a dictionary definition of which is: ‘The use resolution of 300dpi (dots of plants or microorganisms to clean up or pixels per inch at a size pollution or to solve other environmental of not less than 100mm (4 inches) square. problems.’ This phenomenon has been recognised and researched scientifically Advertisers: if you wish to since the 1940s but also has state of the advertise in Microbiologist art applications, contributing to an area you should contact the which is high (though some might say not Society Office in the first high enough) on the political agenda — instance. Advertising rates the environment. and Guidelines on how to Bioremediation is also the subject of a submit advertisements are A scientist who is also a business session at our summer conference — given on the website and Living Together: Polymicrobial are also obtainable by person is the subject of our feature article emailing the editor at: (page 28). Craig Venter, the man behind Communities. The closing date for [email protected] the commercial arm of human genome registrations is now looming so get your sequencing. Considered by some a registration to us before 9 June 2006 to Website: the society maverick scientist — a ‘bad boy’ of prevent paying the late booking fee! website is a timely source science — he has now established both Spaces are limited and the conference is of up-to-date information for-profit and non-profit companies all filling up fast, so don’t delay. See page 26 on all Society matters and with a common goal — the exploitation of for a booking form or you can register maintains a comprehensive microorganisms for the commercial online at www.sfam.org.uk/sumconf.php archive of articles and production of energy. You may remember where you can fill in an online reports on a variety of registration form, or download a pdf microbiological topics. that we ran an article back in March 2003 (www.sfam.org.uk/pdf/features/ application form to complete offline. www.sfam.org.uk playgod.pdf) in which we described the I look forward to seeing you all in work of this controversial figure and his Edinburgh!

04 June 2006 www.sfam.org.uk Contact point

COMMITTEE MEMBERS 2005 - 2008

HON PRESIDENT: Dr Margaret Patterson, Agriculture and Food Science Centre, Newforge Lane, Belfast BT9 5PX [email protected] HON GENERAL SECRETARY: Dr Anthony Hilton, School of Life and Health Sciences, Aston University, Birmingham B4 7ET [email protected] HON MEETINGS SECRETARY: Professor Martin Adams, School of Biomedical & Molecular Sciences, University of Surrey, Guildford,Surrey GU2 7XH [email protected] HON TREASURER: Dr Valerie Edwards-Jones, Research Development Unit, Manchester Metropolitan University, Lower Chatham St, Manchester M15 5HA [email protected] HON EDITOR: Journal of Applied Microbiology Professor Arthur Gilmour, Agriculture and Food Science Centre, DARD and Queen’s University, Newforge Lane, Belfast BT9 5PX [email protected] HON EDITOR: Letters in Applied Microbiology Dr Jean-Yves Maillard, Welsh School of Pharmacy, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff CF10 3XF [email protected] HON EDITOR: Microbiologist Dr Lucy Harper, Society for Applied Microbiology, The Blore Tower, The Harpur Centre, Bedford MK40 1TQ [email protected]

ORDINARY COMMITTEE MEMBERS until July 2006

Dr David McCleery, Chief Specialist Microbiologist, Safe Food, Food Safety Promotion Board, 7 Eastgate Avenue, Little Island, Cork, Ireland [email protected] Dr Shona Nelson, Faculty of Applied Sciences, University of West of England, Coldharbour Lane, Bristol BS16 1QY [email protected] Professor Diane Newell, Veterinary Laboratories Agency, New Haw, Addlestone, Surrey, KT15 3NB [email protected]

ORDINARY COMMITTEE MEMBERS until July 2007

Dr John Coote, Infection and Immunity Division, Glasgow University, Joseph Black Building. Glasgow G12 8QQ [email protected] Professor Geoff Hanlon, School of Pharmacy and Biomolecular Sciences, University of Brighton, Moulsecoomb, Brighton BN2 4GJ [email protected] Dr Karen Stanley, Biosciences, Faculty of Health and Wellbeing, Sheffield Hallam University, Sheffield S1 1WB [email protected] Dr Susannah Walsh, H3.09b Hawthorne Building, School of Pharmacy, Faculty of Heath and Life Sciences, De Montfort University, The Gateway, Leicester LE1 9BH [email protected]

ORDINARY COMMITTEE MEMBERS until July 2008

Dr Tony Worthington, Department of Pharmaceutical and Biological Sciences, Aston University, Birmingham B4 7ET [email protected] Dr Andrew Sails, Health Protection Agency, Institute of Pathology, Newcastle General Hospital, Westgate Road, Newcastle-upon-Tyne NE4 6BE [email protected]

SOCIETY OFFICE STAFF CHIEF EXECUTIVE OFFICER: Philip Wheat [email protected] MEMBERSHIP CO-ORDINATOR: Julie Wright [email protected] EVENTS ORGANISER: Rachel Dowdy [email protected]

www.sfam.org.uk June 2006 05 MEDIAwatch MICROBIOLOGY IN THE NEWS If you spot a story in the media which you think should feature in this column, then send it to the Editor at: [email protected]. To keep up to date, don’t forget to look at our ‘News’ section on the SfAM website: www.sfam.org.uk/news.php

Science Media Centre Press Briefing on avian influenza. In my role as Communications Officer for SfAM I was lucky enough to be invited to a Press Briefing run by the Science Media Centre (SMC) on Avian Journalists from the UK Media attending Influenza. This was about one month a press briefing before the dead swan found in Today programme), Fergus (Walsh – Cellardyke Scotland, tested positive for BBC 10 o’ clock News) and then Roger H5N1. The briefing aimed to prepare have any effect on the warmth of the (Highfield – Telegraph).” The scientists journalists with good information about welcome I received from the Staff at the answered the questions precisely and what would happen if a case of H5N1 SMC. I crept into the back of the with great clarity and all dealt well with were found in the UK. briefing room where Dr Bob sometimes quite leading questions. For The topics covered included: McCracken, ex-President of the British a group of people who are often ■ Would it be safe to eat chicken and Veterinary Association, Dr Judith considered to be sometimes ineffective eggs? Hilton, Head of Microbiological Safety, communicators, I thought the scientists ■ What options would be available to Food Standards Agency and Dr John put across their points to great effect. the poultry industry? For example McCauley, Institute of Animal Health Whether this was pure co-incidence, vaccination or bringing free range were all explaining their position on canny choices on whom to put in the birds inside. avian influenza. They each gave us a spotlight, or a reflection of the effect ■ How would this affect the UK five minute talk on their role and stance the SMC is having on scientists poultry industry? on the subject of food safety aspects of attitudes to talking to the press, I don’t ■ What measures should the person H5N1, and then opened the floor to know. But if more scientists knew what in the street take to avoid avian questions. The charismatic director of good they could do by talking to the flu? the SMC, Fiona Fox was chairing the press, science reporting can only get ■ Who is most at risk of catching briefing, and she kept a tally of who better. For more information about the avian flu? was next to ask a question, referring to work of the SMC, please call Claire ■ What would it mean for wild birds each journalist by name. At this point I Bithell, Senior Press Officer on 020 in the UK? found it hard not to feel a little 7670 2980 or visit After a delayed rail journey, I was a starstruck: for example, “Ok, we’ll have www.sciencemediacentre.com. few minutes late, but this didn’t seem to questions from Tom (Fielden — BBC The briefing was over quickly – to allow the journalists to return to their desks, with more informal discussion SfAM POLICY ON THE MEDIA afterwards between the scientists and We will: ■ always do our best to provide facts, information and explanation. those journalists who could spare the ■ if speculation is required, explain the rationale behind that speculation. ■ desist from time. For me this was definitely an hour hyping a story—whether it is the journalist or the scientist doing the hyping. well spent.

06 June 2006 www.sfam.org.uk Mailbox

Would you like to contribute to the debate? If these letters make you want to put pen to paper or fingers to keyboard, then please feel free to contact the Editor, Lucy Harper at: [email protected] or at the postal address at the front of the magazine.

We’ve had quite a response to the somewhat contentious issue of science and commerce discussed in the last issue of Microbiologist. Here are two examples:

Hand in hand with Business Additionally it is pointed out that there is Quid pro quo? little (but not no) opportunity for people FROM: Russ Grant to take sabbaticals from their tenure FROM: Clive Blatchford SUBJECT: Science and Commerce positions to pursue commercialisation SUBJECT: Science and Commerce activities — they have to choose between I read with great interest your editorial one or the other scientist or businessman I read your editorial with interest, and the article on commercialisation of (unlike the USA). because I believe we have a problem with research in Microbiologist. I work as a Referring to your editorial and from scientists in business. I do not personally post doctoral researcher but I am lucky real-life experiences of science believe the two are incompatible, though I enough to carry out a good deal of commercialisation from Universities, I can appreciate the basis of the question. If business and scientific consultancy. Your understand why some scientists may want you look at the page facing your editorial, question, ‘When is a scientist not a to do their research for the love of it, but you will find a list of no doubt excellent scientist?’, and answer ‘When he/she is a I cannot understand why, in this age of scientists, of whom not one would appear business person.’, brings up several limited and competitive funding, they turn to be in a conventional business role, this points that have been recently addressed down the opportunity to obtain more despite the fact that SfAM is very by the BBC regarding innovation (Peter funding to continue their work. definitely and usefully orientated towards Day — ‘Universities Challenged’ and Contrary to this however in recent application. There may be many reasons ‘Real World Innovation’ on the developments there is now the spectre of for this bias, but it is self-perpetuating; www.bbc.co.uk website). However, it does losing control if commercialisation occurs my own contribution to SfAM being for rely on the fact that University innovation — often seen in start ups where the many years limited to looking through may be a good thing, with the best founder ends up as a scientific officer Microbiologist. It is difficult to justify evidence actually showing the opposite. when more business experienced using my company’s time and money to As a person who works in both fields, personnel are brought in and where attend meetings which always look my personal opinion is that science and shares are lost to raise further equity. interesting, but where there is little business go hand in hand. Similarities far As for being essential, it may become immediate value from attending. It is here out weigh differences. In the lab I plan this way, but at the same time over that the difference lies; businesses invest the experiments and order what is commercialisation will be damaging with money, which implies getting something needed, taking care of the cost and time it unsustainable losses leading in turn to tangible in return for the investment. It will take – generally the same as any fewer funded exploitations. Furthermore, may be that we should just accept that project manager. Keeping track of the it has been found that Universities are not applied for us goes as far as academic grants involves very basic bookkeeping. I really the ‘hot- bed’ of innovation they laboratories which work with industry, or attend meetings and conferences to learn have been made out to be, even in the US food testing laboratories, but somehow and share my work — in affect, where such revenue generation is seen as when one thinks of the number of marketing. I think of the best way to huge. Without getting political it appears microbiologists in business industry, this achieve the aim of the work — strategy. the recent investments are more public seem a pity. As a scientist I find myself doing many of appeasing than anything else. the things I do in business. What is That University innovation different however comes in the research commercialisation should be so low is no Erratum exploitation, where potential surprise if the evidence is examined — commercialisation requires knowledge of In the last issue of Microbiologist (March the biggest innovation comes from 2006), an article was published entitled: The fields outside those generally encountered challenging University educated H. Pylori Saga ends with the Nobel Prize. This in lab science. researchers with real world problems, in article first appeared in the ESCMID News The CEO of Intercell AG also recently the real world. More on this appears in and was reproduced with permission from wrote a report on commercialisation Peter Day’s articles from where interested the Editor. An acknowledgement was where expanding the knowledge of parties can continue their own fact mistakenly absent from our reproduction and students is increasingly being seen as the gathering. the Editor of Microbiologist apologises for way forward in commercialisation, to this error. increase awareness of situations. www.sfam.org.uk June 2006 07 the President’s Column

Dr Margaret and falling numbers of students studying and PhDs can bring to business growth core scientific disciplines. This point is Patterson and development. Gordon Brown’s budget looks echoed by the Biosciences Federation in announced plans to expand R & D tax at enthusing the its November 2005 report ‘Enthusing the credit support to medium-sized young to take up Next Generation’2. The report states: companies. Hopefully they will take full “Although the biosciences have not advantage of this and employ more of our science as a experienced the same course closures as graduates and spend more on research. career the physical sciences, this masks The total spend on R & D in the UK, as % undesirable variations in the strength of of GDP, is 1.86 of which 47% is financed XAMINATION SEASON IS upon interest and engagement across different by business (2002 figures). This is some us, making this one of the most areas of the discipline. Subjects such as way away from the 2010 EU target of 3% E stressful times of the year for sports science, psychology and forensic of GDP spent on R &D, of which two- young and old alike. Many science are increasingly popular in thirds comes from the private sector. young people are hoping for good grades universities whilst core subjects such as SfAM has recognised in our mission at GCSE and A-level so that they can biochemistry, pharmacology and statement that in the UK there are skill pursue their chosen career or university microbiology are finding it harder to deficiencies in applied microbiology and course. I wonder how many are planning recruit students.” that we will be involved in identifying on becoming ‘a scientist’? Probably not these deficiencies and will work towards that many, and this is not surprising due implementing solutions. We have still a lot to the poor public perception of such a of work to do in this area but we have career. However, applied microbiology, in made a start. We ran a very successful particular among the core sciences, design-a-bug competition for Primary cannot be accused of being irrelevant as school children a few years ago and we it impacts daily on our health, our food are sponsoring the MISAC (Microbiology and our environment. So what has gone in Schools Association Competition) this wrong? year. Our ‘Students into Work’ scheme I was interested to read that the has been very successful (see page 38) — President of the Royal Society, Lord Rees Those of us in the university sector will in fact Committee increased the budget of Ludlow, used the neglected and know that the unit of resource for for this grant this year, to allow as many decaying bust of Sir Isaac Newton as teaching science subjects does not usually undergraduates and recent graduates as symbolic of the way the UK regards cover the costs of courses. As a result, possible, the chance to gain valuable science and its scientists. Lord Rees used many students now graduate with a BSc laboratory experience. We will continue his speech in National Science Week in in a biological science but with little to promote the importance of our subject March to highlight the falling popularity hands-on experience, as practical classes at every opportunity and through the of science in schools and universities and are too expensive to run. Even in schools, collective work of others, such as the the knock-on effect this will have on the science teachers are shying away from Biosciences Federation. UK’s standing as a major player in the practical experiments (which I remember In the meantime, I am now off to set world of science and innovation. as the most exciting part of the lesson) some exam questions for a final year It seems that Lord Rees is not the only because of lack of resources, time and ‘Food Microbiology and Biotechnology’ one who feels that a strong science base worries over health and safety. Perhaps it paper, which I think is almost as is important if the UK economy is to grow is not too surprising, therefore, that many challenging as being on the receiving end and we are to compete effectively at the young people are not overly enthusiastic as a student. international level. Gordon Brown about having a career in science, Good luck to all those who are sitting mentioned the words ‘science’ and especially if it is perceived as being exams in the next few weeks. I hope at ‘scientific’ at least 18 times in his March boring, difficult and irrelevant to least some of you will end up with a budget. He also announced plans for everyday life. scientific career. creating an extra 3,000 posts for In addition, there is the concern over specialist science teachers. Currently, the the jobs that will be available to science References science curriculum in schools is not graduates, especially those interested in R ■ 1Moor et al (2006) Mathematics and always taught by those with a degree in & D, what their salary will be and the science in secondary schools. The that particular subject. I was surprised to career progression they can expect. The deployment of teachers and support staff to read in a recent report1 that around 10% recent news that university lecturers are deliver the curriculum. Research Brief RB708, of A-level biology, chemistry and physics taking strike action over pay is a case in Report for the Department for Education and was taught by those who either held no point. New lecturers, most of whom will Skills. ISBN 1 844786560 qualifications in that subject above post- have spent three years as a postgraduate ■ 2Enthusing the next generation. A report 16 level, or whose highest qualification in studying for a PhD and possibly a few on the bioscience curriculum by a working the subject was itself at A-level. years more as a postdoctoral fellow group established by the Biosciences This announcement on extra specialist working on a fixed term contract, can Federation. November 2005. science teachers is to be welcomed but I expect to earn only around £25,000 per am not sure where they will suddenly be year. Dr Margaret Patterson found, given the closure of a significant The private sector also needs to better President of the Society number of university science departments recognise the value well trained graduates

08 June 2006 www.sfam.org.uk the CEO’s Column

Philip Wheat reports on the latest developments within the Society

In the March 2006 issue of the Microbiologist the President of the Society highlighted that we were planning to become incorporated whilst still retaining our charitable status. I can confirm that we are progressing this initiative. New governing documents to replace the existing Constitution are being produced. We have been reviewing and revising the draft Articles and Memorandum of Association, which the Society’s solicitor has written. The change to become incorporated with charitable status was suggested by the Charity Commission and it should be noted that other learned Societies have proceeded down this line of organisation. The proposed changes for the Society for Applied Microbiology will ultimately have to be approved by the membership. Another initiative which was mentioned in the last issue of the Microbiologist was the Society potentially taking new improved office facilities. The Society has been planned or to promote future events the wide appeal of the topics the meeting occupied the current office since 1996. or other initiatives. In addition, we are is sure to be popular. Further information Whilst the Blore Tower is a building with now issuing a monthly email bulletin can be obtained from the preview on page plenty of character it is less than ideal as detailing any activities in the coming 27 of this issue of Microbiologist as well office space. I am currently assessing month. I am sure Lucy Harper will as the Society office. A booking form will alternative modern office facilities which provide you all with more information on be available on the website shortly. are still based in Bedford. A draft of the this initiative. Officers and myself have attended and proposed new lease for these premises Whilst on the subject of Lucy, I am are proposing to attend a number of has been received and if everything goes delighted to announce that the Trustees of national and international conferences in to plan it is proposed we will be moving the Society have decided to appoint Lucy the coming months. These have included offices in August/September this year. on a full-time basis as the Biomedica (Dublin 26-27 April), Communications Officer for the Society. American Society for Microbiology Lucy’s role will cover all aspects of (Orlando 22-24 May) and the communication. These will include being International Food Technology (Orlando responsible for all issues relating to the 26-28 June). In addition, I hope to meet website. She will also co-ordinate all areas many of you at the forthcoming SfAM concerned with public relations and Summer Conference (Edinburgh 3 – 6 affairs. This will include dealing with the July). I am sure the meeting will be an media and if appropriate, drafting and outstanding success. The scientific sending out any press releases and programme is topical and up to date with arranging press briefings. the latest research findings. In addition, Planning is well underway for next the social programme is complete with year’s Winter meeting. The meeting will many activities planned. All this, in the once again be held at the Royal Society, surroundings of the wonderful city of London. It will be a one day meeting on Edinburgh. I look forward to welcoming You should all by now have received a 11 January 2007. The topic of the you all as delegates at the meeting. questionnaire so that we can produce an meeting will be ‘Hospital Acquired updated members handbook. The Infections’ with a concurrent theme in Philip Wheat the afternoon entitled ‘Microbiology for information will also be used to keep you Chief Executive Officer informed of events which have already Environmental Health Officers.’ With

www.sfam.org.uk June 2006 09 Teresa Belcher reports on the gathering of international infectious disease experts in Malta to share research advances

keynote speakers attending the Net, to develop network relations with MED-VET-NET IS A EUROPEAN conference. Professor Patricia Smith from other representatives from outside of the Network of Excellence that aims to the Laboratory of Bio-Anthropology and network, widen participation to other improve research on the prevention Ancient DNA, Faculty of Dental Medicine, member states, and to raise awareness of and control of zoonoses by integrating The Hebrew University of Jerusalem, the state-of-art science inside and outside veterinary, medical and food science Israel, presented a talk entitled ‘The of the network. The meeting also research. Comprising 16 European zoonotic revolution: the impact of promoted further understanding of the partners and over 300 scientists, Med- domestication.’ Professor Scott McEwan network’s scientific aims and objectives Vet-Net will enable these scientists to from the Department of Population and provided an opportunity for the share and enhance their knowledge Medicine, University of Guelph, Canada development of collaborative ideas and and skills, and develop collaborative discussed ‘Uses and abuses of projects. research projects. microbiological risk assessment.’ Dr On the final day of the conference, a Eric Fèvre from the Centre for Infectious session covering ‘Networking for Food Safety’ Second General Scientific Disease, University of Edinburgh, was held. Dr Marta Hugas from ‘Emerging zoonoses, Meeting Scotland spoke on the European Food Safety Authority animal movements and disease risks.’ (EFSA) gave an outline of the newly- The very successful second Med-Vet- Professor Jean-Pierre Kraehenbuhl from formed body that is the keystone of EU Net General Scientific Meeting, took ISREC and Institute of biochemistry, risk assessment regarding food and feed place in Malta between 3-6 May 2006. Lausanne, Switzerland gave a safety. Dr Jan Sargent from the Public After nearly two years of joint activities presentation on ‘Host-microbial Health Agency of Canada (PHAC), spoke we are now beginning to see the outputs interactions at mucosal surfaces.’ about the Food Safety Research and of our collaborative efforts, many of which were presented at this meeting. Over 180 delegates met for four days Further Information at the Dolmen Resort Hotel on this sunny ■ For more information about Met-Vet-Net, Mediterranean island. Scientists from all visit our website at http://www.medvetnet.org/ or contact Teresa Belcher at the SfAM offices Med-Vet-Net institutes were represented, in Bedford on: +44 (0)1234 271020 and for the first time, the meeting was open to external delegates in order to share new research information and develop greater external collaborations worldwide. The meeting was opened by the Honourable Dr Louis Deguara, Maltese Minister for Health, the Elderly and Community Care. High-calibre presentations The topics selected for the meeting focused on aspects of zoonoses related to Conference Centre, Dolmen Hotel, Malta epidemiology and risk, detection and control, host-microbe interactions, Professor Gadi Frankel from the Response Network (FSRRN). The FSRRN microbial ecology as well as new and Department of Biochemistry, Imperial is a multi-institutional, multidisciplinary emerging zoonoses. The emphasis of the College London, England spoke on team of more than 50 food-safety scientific presentations was to promote ‘Application of contemporary specialists from 18 universities, state and current and new findings from both a molecular and cell biology technologies federal agencies and agricultural clinical and veterinary perspective, and to study host-microbe interactions.’ commodity stake-holder groups and is 70 scientists gave oral presentations. In funded by the U.S. Department of Serious science addition to this, over 150 posters were Agriculture. Dr Susanna Lukinmaa from also presented. The main aims of the annual General the Statens Serum Institut (SSI), Denmark Med-Vet-Net was fortunate to have a Scientific Meeting were to review explained the workings of PulseNet number of high-calibre, international scientific research supported by Med-Vet- Europe, the molecular surveillance

10 June 2006 www.sfam.org.uk Med-Vet-Net news

network for food-borne infections in the British. All have influenced Maltese Europe. In conclusion, Dr Claire Cassar life and culture to varying degrees and from the Veterinary Laboratories Agency many delegates took the opportunity to (VLA), UK spoke about the new network appreciate this aspect of local history. EUUS-SAFEFOOD, which aims to develop Several social events were organised to a transatlantic strategic alliance, between showcase the beauty of Malta. These food-borne zoonoses research networks in activities included ocean-side finger buffet the European Union and the United and wine reception for the first evening, a States. night’s entertainment comprised of a The Closing session saw Project short tour around Mdina, Malta’s Manager, Professor Diane Newell talk medieval capital, followed by a about the future of Med-Vet-Net followed champagne reception on the bastions by Dr Alfredo Caprioli and Dr Franco overlooking the island culminating with a Ruggeri who outlined plans for the next dinner at Bacchus, a reception venue Annual meeting to be held near Pisa in located in chambers built by the Knights Eating by the sea Italy. A summary of the meeting was given of Malta in 1657 on the second evening. by Chairman of the Med-Vet-Net countries, Malta. Inhabited since A relaxed poolside barbeque overlooking Advisory Panel, Professor Bill Reilly, and prehistoric times, and with an excellent the islands of St Paul was organised back closing remarks by Med-Vet-Net Project natural harbour, Malta has always at the hotel for the final evening. Coordinator’s Representative, Dr André maintained a strategic location at the Med-Vet-Net gratefully acknowledges Jestin. crossroads of the Mediterranean. It has the support from FAO, Malta Tourism frequently been a key prerequisite to Authority, Pfizer and Air Malta for the …sun, sea, scenery domination of the Mediterranean by running of this meeting. This year, Med-Vet-Net also departed various powers, being first colonised by from their current member countries to the Phoenicians and then subsequently by Teresa Belcher find the sun and sea in one of the the Romans, Arabs, Normans, the Knights Med-Vet-Net Communications Director European Union’s southern-most Hospitallers of St. John of Jerusalem, and

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www.sfam.org.uk June 2006 11 Membership matters

New Members is meant to complement the efforts of Sad News many universities in publicising their “schools talks” programmes. Geoffrey Talbot Banks The site now has nearly 450 speakers We would like to warmly welcome the (23/9/33 – 29/3/06). registered. Over the last 12 months the following new members and hope that We regret to inform members of the BSF have received about 200 email you will participate fully in the activities of loss of SfAM member, Geoffrey Talbot requests for talks. You may however rest the Society. Banks. Geoff will be remembered as a assured that speakers’ actual email lecturer and fermentation technologist at Australia addresses and phone numbers are not the Department of Biochemistry at accessible from our website. Dr E Bartowsky Imperial College, London. After a spell at If you already visit schools to give Glaxo in Barnard Castle in the early talks, or if you would like to start, then Denmark 1960s, Geoff joined Ernst Chain’s team at we would like to hear from you. Simply Imperial College, where he worked inter Dr A Gravesen send an email to: alia on interferon production, publishing [email protected] Egypt several papers in Nature. He retired from with your name, email address and Imperial College in the early 1990s, Mr Mohame Darwish university postcode (for location settling with his wife, Mary, in the Vale of purposes) together with your major Greece the White Horse. society affiliations to enable an Dr M Braoudaki appropriate society logo to appear with your entry in the database. India Upon registration we will then email Dr S Reddy Mondem you a password to enable you to complete your personal details and enter the full Ireland details of your talk(s).Further details of how to join this scheme can be found at: Ms L A Deering; Mr D Hayes; Dr K Horgan; Ms A-K Liliensiek; Miss L Lillis; Dr R Murphy; http://www.biology4all.com/join.asp Mr O Ojo; Mr P Sawulski; Miss U M Scallan Mexico SfAM School Dr C Wacher-Rodarte Associate United Arab Emirates

Mrs Ambika Rajesh Ambika Membership

United Kingdom

Mr G Aboagye; Mr P J Airey; Mr M Boateng; Dr C D Campbell; Mrs T Cheetham; Speakers for Miss P A Conway; Dr V Davenport; Dr A L Doran; Miss S Easton; Schools Mr M J Garland; Mr T Gibbs; Dr B F Gilmore; Mr A D Glancey; Database Mr V Gohel; Mr M T Jamal; Dr V Javid Khojasteh; Mr C Kwang-Kuk; On 12 September 2002 the Mrs E Langley; Dr S P Law; Miss S Lee; Biosciences Federation (BSF) Speakers Dr D Lowrie; Mrs A Newaj-Fyzul; Database was launched at the BA Festival Miss C Pope; Mr S N Tetteyfio; of Science. Dr John Thomson; Mr David Williams; This database enables university Mr J R Wingate academics to enter details of any talks or USA workshops that they are willing to give to local schools. The unique feature of this Mr H Chen; Dr B Green; Mr K Kauers; database is that it holds information Dr M Kendall; Dr A J Miller; Dr T B Norris; about the location of each speaker and Dr S Perkins; Dr Om Singh; Dr P Sreenivasan the distance that (s)he is willing to travel. Why not recommend SfAM membership CORPORATE MEMBERS Teachers then enter the postcode of their to your local school? school and the system delivers only those Bio-Rad Laboratories Ltd speakers who would be willing to travel to Benefits ■ Quarterly copies of Microbiologist Lab M Ltd that location. The database can be found at the ■ Full access to the Society website TCS Biosciences Ltd biology4all.com website: ■ Preferential rates at Society Meetings http://www.biology4all.com/talks.asp ■ All for only £15.00 per annum! This service is entirely free to use and

12 June 2006 www.sfam.org.uk Micro Break

SfAM Anniversary Photography Competition

Have you taken a striking photograph of your beloved bugs? Do you know someone who has and you’d like to see their work published? Or perhaps you’ve taken a photograph while attending an SfAM conference which you think is worthy of reproduction? The SfAM anniversary photograph competition offers you the chance to see your work become part of the society’s anniversary commemorations. We are offering the 12 best photographs the opportunity to appear in this years Christmas gift — a stunning desk calendar. The best overall photograph will also win a bottle of bubbly to help you celebrate 75 years of SfAM! To enter this competition, please send your photographs to the Editor. The photographs can be entered into one of two categories: 1. Scientific: photographs taken in the laboratory of your beloved organisms. 2. SfAM: artistic photographs taken whilst attending a SfAM event. Photographs in this category don’t necessarily need to be scientific.

To enter, please provide high quality, JPEG images or original prints, label them with their entry category and post them to: SfAM Anniversary Photographic Competition, Society for Applied Microbiology, The Blore Tower, The Harpur Centre, Bedford MK40 1TQ, UK, before the closing date of 28 July 2006. Alternatively, email your entry to: [email protected] with the subject ‘SfAM Anniversary Photographic Competition.’

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www.sfam.org.uk June 2006 13 Biomedical Scientists form the foundation of modern healthcare. Ian Cocking HEN YOU ASK THE GENERAL public ‘who tests the samples explores the rewards and challenges of this important work W Doctors and Nurses take from you in a hospital?’ it usually draws a blank facial expression. The fact is, there is an ‘unknown army’ of healthcare professionals dedicated to the analysis of patient samples of tissue and body fluids to diagnose disease and monitor treatment. CAREERS Biomedical Scientists (BMSs) in the NHS and private healthcare form the foundation of modern healthcare. Patient Biomedical Scientist treatment is based upon the results of vital tests and investigations performed by Biomedical Scientists. It is estimated that up to 70% of diagnoses of all illnesses are made on the basis of laboratory results. There are very few hospital departments that could function without the input from Biomedical Scientists. From A&E to Intensive Care, BMSs test and analyse patient samples to ensure patients obtain the optimal health support and treatment they expect from the NHS. Biomedical Scientists are based in hospital pathology departments surrounded by a myriad of sophisticated and expensive analysers and hi-tech laboratory equipment including microscopes, automated analysers and computers. They work continuously to provide essential patient healthcare; some departments are run 24hrs a day, 365 days a year. The work of Biomedical Scientists is diverse, complex and specialised. Within Pathology there are a network of departments working together to provide the service. These include: ■ Clinical Biochemistry ■ Haematology ■ Medical Microbiology ■ Histopathology ■ Cytology ■ Immunology These departments may then be sub- divided into smaller more specialised departments that include: ■ Virology ■ Molecular Genetics ■ Blood Transfusion/Blood Bank ■ Coagulation Career Progression and Training I stumbled into a career as a Biomedical Scientist accidentally, but in the eight years I have spent in this area I have found the career rewarding, and both physically and mentally challenging. If you want a career that is diverse and

14 June 2006 www.sfam.org.uk Careers

technically challenging on a daily basis, I continued to work at the RHH for a BMSs and decide how to manage the then this is the career for you. further four years, during which I laboratory sections to ensure every My career started as a student completed an MSc in Pathological section is adequately covered by a placement within the Microbiology Sciences at Sheffield Hallam University, combination of qualified BMS and Department at Northern General Hospital, along with various CPD activities. After Medical Laboratory Assistant (MLA) staff. Sheffield. This formed one year of the gaining my MSc and accruing sufficient Sitting at the bench it’s time to start four year sandwich degree course in experience and CPD points as a qualified reading the ‘Blood Culture’ bench. ‘Blood Biomedical Sciences (BSc Hons) at BMS, I met the requirements to progress culture’ is one of the few automated areas Sunderland University. After graduating in up the BMS career ladder. In 2003, I of Bacteriology, where complex analysers Biomedical Science, I returned to moved to Doncaster Royal Infirmary for continuously monitor blood samples from Sheffield, but this time to the Royal promotion to a Senior BMS. Three years patients with a suspected bacterial Hallamshire Hospital (RHH), to complete on, I now form part of an experienced infection of the blood. my training towards becoming a State laboratory team dedicated to providing a My first task involves removal of Registered Biomedical Scientist in quality diagnostic microbiology service to positive cultures from the analyser and Microbiology. At the time, this involved at the Doncaster and Bassetlaw NHS preparing Gram films to determine the least two years at the bench learning the Foundation Trust. presence of bacteria or yeasts within the basics of laboratory diagnosis in culture. Depending on the Gram reaction Duties of a Senior BMS Microbiology and completion of a of the isolates, I determine which logbook of competence. A viva-voce by A Senior BMS is responsible for the antibiotics to test against the isolate and an external assessor at the end of two supervision and management of other subculture the blood culture onto years determined whether you were BMS staff within a sub section of a appropriate agar plates for overnight competent to practice unsupervised as a laboratory. This requires a professional culture to confirm my diagnosis. qualified BMS. This has since been attitude and a broad knowledge and Next, its time to examine the culture superseded by the Health Professions understanding of the pathology discipline plates from the previous day to confirm Council (HPC) Registration of of your speciality. As a Senior BMS you initial laboratory findings. I examine the Competence Portfolio (6-12 months to are a point of reference for staff and plates and identify the bacteria present complete) to become a registered ensure all procedures within the and read the corresponding antibiotic Biomedical Scientist and the Institute of laboratory are performed according to sensitivity susceptibility plates to Biomedical Sciences (IBMS) Specialist standard operating procedure. determine the antibiogram of the Portfolio (1-2 years to complete) to Laboratory testing involves bacterial isolate. If I make a mistake here, become a Registered Specialist in a interpretation of test requests using the patient may be given the wrong chosen discipline(s). guidelines and personal judgement. This antibiotic, resulting in treatment failure, often requires the review of a patient’s causing a prolonged illness for the patient clinical history, current drug treatment, or worse. past exposure to disease and vaccination I record the details onto the laboratory status. The daily duties of a BMS involve computer system and worksheets before constant decision making, interpretation passing the details on to our Consultant of test results and reflex testing from that Microbiologist for approval. result. It’s 10:30 am — time for a break, but Within any laboratory, safety is my break is interrupted by the arrival of paramount and as a Senior BMS you are an urgent CSF sample from a young child responsible for monitoring health and with suspected bacterial meningitis. In safety within the department, regularly microbiology this can be a life or death performing risk assessments on situation and subsequent treatment of the laboratory procedures in conjunction with patient is highly dependent on the the laboratory manager to ensure safe laboratory findings. I examine the CSF working practice at all times. sample to determine the presence of infection. The CSF has a significant high Life as a Senior BMS white blood cell count, but I cannot see A normal day within the laboratory any bacteria in the Gram film (have I To be a competent Biomedical Scientist starts at 9:00am, whereby I first check missed them?). I ring the result to the requires life long learning. Continued my diary and emails for possible requesting clinician who informs me the Professional Development (CPD) is departmental meetings, training meetings child has already been administered fundamental to maintaining knowledge or appointments with sales antibiotics on attendance by the General and proof of Continual Professional representatives from the various Practitioner. That may explain the Competency (CPC) will soon become companies from which the department absence of bacteria in the Gram film. mandatory to ensure safe practice and purchase laboratory supplies/equipment. After a quick coffee with the other staff entitlement to stay on the HPC Register. After a few minutes (giving time for the and putting the world to rights, I return The career is structured in such a way late arrivals to try and sneak into the to finish my work in the section. Next I that CPD and higher degree/specialist laboratory unnoticed) it’s time to put on move to other benches to check progress qualifications are essential to career the white laboratory coat and enter the with other staff. My signature is required progression. laboratory to liaise with the other senior to verify confirmed isolates of Neisseria www.sfam.org.uk June 2006 15 gonorrhoea, from two people attending laboratory section and writing a new SOP between 12 and 1pm the next day and the hospital GUM clinic. I check the for the implementation of a new send it to the laboratory marked for my colony morphology on the culture plates, laboratory test kit for the rapid attention. Gram films and API NH profile identification of (MRSA) from routine The rest of the afternoon is spent (commercially available biochemical test culture agar plates. processing specimens as they arrive in kit) and authorise the results accordingly. Back in the laboratory, its time to the laboratory. As 5:30pm approaches the Next it’s the Faeces bench, and three ensure other staff are completing their daily workload of specimens is finally potential cases of Salmonella, four cases tasks and help out if required. It’s not cleared and it’s time to do some basic of Campylobacter and a faecal smear long before my opinion is required. A laboratory housekeeping. All BMS and containing Cryptosporidium have been fellow BMS has found an auramine smear MLA staff clean and restock laboratory detected by the BMS. I verify the results of sputum containing acid fast bacilli. A benches and maintain laboratory and forward them to the Consultants. review of the clinical details and patient equipment in readiness for another day at Where appropriate, the significant history indicate that the smear is from a the laboratory. isolates are saved and forwarded to a male returning from Africa after visiting Career Opportunities reference laboratory for typing. The family. He’s attended the A&E department results will form part of the national complaining of a persistent cough for Biomedical Science is a demanding surveillance and epidemiology of several weeks and complains of feeling career, both physically and mentally. It Salmonella, which, in liaison with hot and sweaty during the night. A requires personal expertise and this is Communicable Diseases and discussion ensues with the Consultant something all BMSs expand during their Environmental Health help serve to Microbiologist and it’s decided to isolate career. Biomedical Science is a protect the public from gastro-intestinal the patient and begin treatment for continually changing, dynamic profession infections. suspected Mycobacterium tuberculosis with long term career prospects including There’s no rest as an Infection Control (TB). I pass the details onto our Infection management, research, education and Nurse enters the laboratory to inform me Control Nurses who begin to contact specialised laboratory work. there is a potential Methicillin Resistant S. close contacts of the index case to be Current opinion is to expand the role aureus (MRSA) outbreak on one of our screened for possible cross infection. of BMS to a higher specialised level, hospital wards and they are screening possibly covering some of the roles potential contacts. A quick check of our currently performed by Medical media supply in the fridge confirms we Consultants. This would allow BMSs to are low on agar plates used to detect help, in light of the shortage of Medical MRSA. A quick phone call to our Consultants in the pathology disciplines. suppliers and they assure me more stocks Although in this career patient contact will arrive by tomorrow lunchtime — is minimal, the impact a Biomedical crisis averted. Scientist has on patient care is still highly An important role of a Biomedical regarded. As a BMS you have the reward Scientist is to research and evaluate of knowing your laboratory findings are current and new diagnostic techniques to contributing to patient care either in improve patient care. Currently I am hospitals, or in the community, even when evaluating a new chromogenic agar media it seems a thankless task. for the rapid screening of MRSA from NHS pathology laboratories are not the suspected cases. The new media is run in only place BMSs are employed. BMSs are parallel with our existing method and employed within the veterinary service, compared on a like-for-like basis. I sit the Health & Safety Executive, down at my desk to review the data so far universities, forensic laboratories, and after a few statistical calculations and pharmaceutical companies and Her costs, the results appear favourable Later that afternoon I have a meeting Majesty’s Forces. towards the new agar media. My next task with a Sales Representative from a is to present the findings of the evaluation laboratory equipment supplier. He Ian Cocking at next months departmental audit wonders if we are interested in a new Senior BMS, Microbiology Department, meeting. automated method for urine microscopy. Doncaster Royal Infirmary I manage to escape the laboratory for We review the literature on the system a lunch break. Afterwards, it’s time to and agree on a field visit to a local attend this months ‘Senior Management hospital to see the analyser in action. The If you are considering a career in Meeting.’ The pending Continuous visit gives me chance to speak to the BMS Biomedical Science then the following Pathology Accreditation (CPA) inspection staff that use the analyser and gauge their web sites provide further detailed is discussed between the senior and chief opinion. information: BMSs, Laboratory Manager and Back in the laboratory, I answer the ■ www.ibms.org.uk Consultants to determine what action is telephone to find a new Senior House required and who is responsible for Officer is unsure how to investigate a ■ www.nhscareers.nhs.uk carrying out that action. I am assigned patient for Bilharzia. I inform him that he ■ the task of updating Standard Operating needs to obtain a terminal urine specimen www.hpc-uk.org Procedure (SOP) documents for my (final passing of urine during micturition)

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www.sfam.org.uk June 2006 17 Report on a visit to the Kwame Nkrumah University Am I eligible - of Science and Technology (KNUST) Kumasi, Ghana can I apply?

Students enjoying the open seminar

HE VISIT TOOK PLACE Lancaster to do a PhD on the ‘Seasonal between 24 October and 3 variation of indicator and pathogenic This new award is intended to assist T November 2005, during which bacteria in coastal and inland bathing Society members in developing countries time I gave five lectures on waters.’ Lancaster City Council provided and Eastern Europe to visit laboratories Health-Related Environmental the funds for the microbiological and give lectures and training in Microbiology to MSc students in the monitoring. This proved very successful appropriate areas of applied Department of Theoretical and Applied and resulted in six papers in peer- microbiology, or support overseas Biology. KNUST: reviewed journals and eight posters at members to visit UK laboratories to 1. Survival and persistence of international conferences. The work has receive training in appropriate areas of pathogens in the environment influenced the way in which regulatory microbiology, or to support technology 2. Zoonoses: Re-emerging infections bodies such as the Environment Agency transfer in applied microbiology for which sources of funding do not exist. 3. Zoonoses: Emerging disease view bathing waters. In particular, we 4. Pets and wild birds as reservoirs for showed that the time of the day that Nominations for awards will normally be disease and vectors of pollution samples are taken influences compliance considered by the Society's Awards panel 5. Epidemiology and environmental with the EU Bathing Water Quality in March, July and November each year. microbiology of Vibrio cholerae. Directive; and that flocks of wild birds are The last lecture was particularly timely major sources of pollution. To apply, please read the guidelines as it coincided with an outbreak of Since his return to Ghana in 1999, we below and then submit your application cholera in Kumasi. have continued our collaboration, by email or post to the Society Office. I also gave an open research seminar publishing papers on drinking water, all to the College of Science on ‘Wild birds of which have had a local impact above GUIDELINES and the spread of disease: bird flu.’ and beyond the usual scientific interest.

1. Individual awards up to a maximum of £5000 will be This was gratifyingly well attended and Dr. Elias Aklaku Integrated biological considered. produced some interesting questions. treatment and biogas production in a The collaboration in environmental small scale slaughter house in rural 2. The laboratory supporter must be a full member of the society and have held membership for at least 3 years. microbiological research between the Ghana, which has now been accepted for departments of Biological Sciences at publication in Water Environment 3. Detailed information must be provided about the Research. Elias, an engineer with an eye relevance of the application and the available local Lancaster University and KNUST grew out support. of a British Council Link programme in to solving local problems, has built a the mid 1990s to develop an MSc in small scale integrated abattoir and waste 4. Each application must be accompanied by full supporting documents. Environmental Science at KNUST. During digester in Ejura, a small rural my visits to Kumasi I realised that there communities north of Kumasi. The 5. A condition of the funding is that an appropriate report was useful health-related environmental digester converts waste from the animals must be written for publication in SfAM Microbiologist magazine together with photographs where possible. microbiological research that could be into methane, which provides energy for done and obtained funding from the singeing carcasses and for use by the 6. Applications should be sent by email or by post to the wider community. It also provides clean Society Office. Society for General Microbiology and UNESCO for further research visits, effluent that can be used for irrigation. In microbiological equipment and addition, there have been reductions in www.sfam.org.uk/members/prizes.php consumables. At that time, Kwasi Obiri- nuisance smells, flies, dogs and vultures. Danso, a lecturer at KNUST, came to The use of methane as energy has also

18 June 2006 www.sfam.org.uk Overseas Development Award

lessened the burden of wood collection broth and model foods and to use gene and reduced smoke levels in houses, Food Safety probe methods to gauge the frequency of which WHO has identified as a major toxigenic strains in food raw materials cause of death of women and children in Implications of and the environment. the Developing World. Neurotoxin Producing Part of the project would involve I also spent some very productive time working with toxigenic strains of visiting research field sites and discussing Clostridium species Clostridium butyricum and C. barati the current applied microbiology research and, although I am an experienced projects being done by Kwasi and his microbiologist, I had to receive specific research students. Tyhra Carolyn Kumasi training on working in a containment is working on the ways in which the water level 3 laboratory before starting this quality of the Barekese Reservoir, the aspect of the work. It took several weeks major source of water for Kumasi, is to complete the training and receive being affected by anthropomorphic approval from the Safety Officer. changes in land-use in its catchment area. Meanwhile, I familiarised myself with the Linda Aurelia Andoh is tracing the anaerobic techniques using non-toxigenic transfer of parasites from irrigation water strains to start with. It took the first used on farms onto salad vegetables, both couple of weeks to learn the technique of on the farm and at point of sale. Other culturing strict anaerobes, and to students are doing similar work but investigate their ability to grow at concentrating on tracing indicator different temperatures and on different bacteria from irrigation water onto fresh types of media for optimal growth and produce. This work fits in well with ARRIVED IN READING FROM spore production. I then examined the research that we are doing in Lancaster Nigeria on 1 June 2005 to growth of C. butyricum in dairy based and in the Western Balkans, funded by I begin a four month visit to the desserts and growth of C. barati, C WaterWeb, an EU programme, on the School of Food Biosciences at tertium and C. bifermentans in pate at connection between the microbial quality the University of Reading, supported by different temperatures and did some work of irrigation water and the contamination an Overseas Development Award from defining pH limits in broth. The of fresh fruit and vegetables at point of SfAM. physicochemical parameters of the food sale. Since this visit, I have returned to I reported to the School the following material such as pH and water activity Ghana with Joanna Heaton, a Lancaster day and was greeted by Dr Bernard were measured. I had an opportunity to PhD student working on this project, and Mackey — an old friend whom I first met use API strips to check the identity of the we have extended the range of bacteria nine years ago. I was then shown round test strains and also to identify being looked at in Kumasi to include the new laboratory facilities and Clostridium isolates obtained from food. Listeria, Aeromonas and Salmonella. introduced to my project team and other I also learned methods for DNA extraction Socially, the visit was great fun. I was members of the group. I was going to and the use of PCR for identification and well looked after by Kwasi and his work on a project looking at the growth detection of the toxin gene. colleagues, both from the University and properties of some potentially pathogenic This research project presented an the wider community. The adventure clostridia. opportunity to learn new techniques in highlight was a seven-story-high The main species of clostridia isolating and culturing strict anaerobes. rainforest canopy walk in the Kakum associated with foodborne illness are The most fascinating was a very simple National Park, Elmira, Cape Coast. Clostridium botulinum and C. modification of the standard plate count However, the evenings spent in the perfringens and much effort has been method. This will be very useful to my University Senior Staff House drinking directed towards understanding the colleagues and students back home. I Star lager and putting the World to rights, factors controlling their growth, toxin wish to thank Dr Richard Sherburn and linger longest and most fondly in the production and the resistance of their Dr Bernard Mackey who readily took on memory. spores. Other clostridia may cause the role of supervisor. I have benefited a I gratefully acknowledge the Overseas spoilage problems in cheese, canned fruit great deal from his wealth of experience Develpoment Award from SfAM that made and pasteurised acid sauces, but are not in research. I must not fail to mention my the visit possible. considered to be dangerous. Clostridium project mate Hamid who was always butyricum and C. barati are normally ready to assist me on any issue in the lab Further Information regarded as harmless but rare strains that and other members of our laboratory who on the connection between health-related have acquired the botulinum neurotoxin rendered help whenever necessary. Words environmental microbiology at Lancaster University and KNUST can be found on the gene have caused infant botulism or are not enough to express my sincere Lancaster Alumni web site : foodborne illness. Clostridium tertium gratitude to SfAM for giving me this and C. bifermentans occasionally occur opportunity, a rare asset to those of us ■ http://www.alumni.lancs.ac.uk/Upload/ Content/files/203/ParaFiles/STEPS2005.pdf in food in high numbers, but the food involved in teaching and research from safety implications of this, if any, are not developing countries. fully understood. The project I was Dr. Keith Jones joining, funded by the Food Standards Dr O.O. Aboaba Department of Biological Sciences, Lancaster Agency, aimed to examine the factors Department of Botany and Microbiology, Environment Centre, Lancaster University University of Lagos, Nigeria controlling growth of these organisms in www.sfam.org.uk June 2006 19 Bioremediation: bugs keeping it clean

N RECENT YEARS, SOCIETY chemical structure from natural organic that we live in. Microbes are the major has become increasingly compounds and are much harder to players in the synthesis and degradation I concerned with maintaining degrade. Additionally, other compounds of all sorts of molecules in the and preserving our natural such as polycyclic aromatic hydrocarbons environment. In all habitats, environment, with the treatment and (PAHs), produced by incomplete microorganisms degrade dead organisms, disposal of waste one of the most combustion of natural organic materials, making nutrients available for the future important problems facing mankind. are also toxic and those with higher growth of other living things. This is a The large-scale manufacturing, molecular weights, also more resistant to natural process, and understanding which processing and handling of chemicals degradation. There is clearly a definite microbes are in each ecological niche and have led to serious surface and need for new and more environmentally what they are doing there, is critical for subsurface soil contamination by a wide sound methods of disposal. our understanding of the world. Scientists variety of hazardous and toxic have also strived to better understand The good and the bad hydrocarbons. More and more waste is this, in order to enhance the process and being generated and the cumulative It is hard to imagine that the vast ultimately use bacteria to do even more effects of pollution have led to increased majority of life on this planet is good in an environmental sense. public concern, and stricter legislation for microscopic and it is even harder to What is bioremediation? the disposal of waste. Some wastes can be comprehend that we know hardly re-used, but in most cases, the removal anything about these microorganisms Bioremediation is the use of living and purification of waste poses two because fewer than 2% of them can be organisms to clean up environments that problems: the energy input required for grown in a laboratory. Generally, people have become contaminated with organic the process, and the problem of dealing tend to associate bacteria as being ‘bad’ – or inorganic substances. Bacteria and with the remaining concentrate. In in particular those causing disease. fungi ‘feed’ on the hazardous pollutants addition, many new chemicals such as However, in reality, many microbes and are able to convert them into less polychlorinated biphenyls (PCBs) and enhance our well-being and greatly toxic compounds. This is an ideal trichloroethylene differ substantially in influence and benefit the environment treatment method as it transforms the

20 June 2006 www.sfam.org.uk Features

pollutants rather than simply moving considered. Sometimes, extreme contaminated soil is removed from the them to another location. contaminant concentrations can be toxic polluted site and is treated in a ‘farm’. Bioremediation is both one of the to the microbes and inhibit their Frequent tilling provides the crucial oldest but also one of the newest effectiveness. Scientists need to oxygen for the microbes to survive, environmental remediation technologies. understand the specific microbial essential nutrients are supplied by It has been used throughout recorded environment and its threshold level to the application of fertilizers, and the soil is history to turn organic waste into relevant contaminants. In some cases, irrigated to provide water. An even more fertilizer by the use of compost heaps. high concentrations of contaminants can stringent variation of this is a Bioreactor Our sewerage wastes are treated using be toxic to the microbe, damaging the cell Landfill. These operate to rapidly biodegradation in wastewater treatment membranes. transform and degrade organic waste, plants, and the petroleum industry has The soil type of the area must be through the very controlled addition of relied on bioremediation for many years known in order to determine whether or liquid and air to enhance the microbial to clean contaminated soil. not in situ treatment is possible. In order processes. These can be configured to be Research has been conducted on the to treat soils, microbes must have aerobic, anaerobic (which produces possible uses of bioremediation since continual access to nutrients to promote methane gas often used for energy the1940s. Originally, much growth. Soils with high clay content are projects) or hybrid, utilizing a bioremediation focused on the breakdown more likely to restrict the flow of combination of methods. of organic contaminants to benign end- nutrients to the microbes. Conversely, Another ex situ method includes soil products, and since the 1970s has been sandy soils are well aerated and well washing. Here, contaminants sorbed onto used for the in situ clean up of fuel structured, allowing nutrients and oxygen fine soil particles are separated on the contaminated soil and groundwater. to flow and are therefore more suitable to basis of particle size from bulk soil in a Bioremediation has since developed into a bioremediation. water-based system. The wash water may popular method of pollution remediation. Proximity of groundwater must be have a basic leaching agent, surfactant, or Many new active remediation taken into account when trying to treat chelating agent added, or pH adjusted, to technologies utilize bioremediation: contaminated soil alone. If the help remove organics and heavy metals. bioventing, landfarming, bioreactors, groundwater is shallow, this could be The wash water and various soil fractions composting, bioaugmentation and easily be contaminated and allow further are usually separated using gravity biostimulation. movement of the pollutant. settling. Solvents can also be used in a similar way to separate organic and metal Influencing factors Helping things along contaminants from the soil in a process Through studying natural processes, If practical, the environment may be known as solvent extraction. researchers have been able to determine adjusted to provide optimum conditions Common forms of in situ the conditions necessary for degradation. for breakdown of the contaminants. biorementation include air sparging and Even though very often the actual Treating a contaminated site can be bioventing. Air sparging involves the microbes responsible for degradation are compared with looking after a farm and injection of air or oxygen through a not known, it is still possible to research growing crops: you need to provide the contaminated aquifer. Injected air which pollutants they can degrade and bacteria with optimal conditions for traverses horizontally and vertically in under what conditions this best occurs. growth. The main limiting factors in channels through the soil column, Several factors influence the success of bioremediation are the carbon source, creating an underground stripper that bioremediation including the oxygen, nitrogen, phosphorus and water. removes volatile and semi-volatile organic environment, contaminant type and If the right conditions are provided, then contaminants by volatilisation. The concentration, soil type, and the condition the bacteria will ‘eat’ at the optimal rate, injected air helps to flush the and proximity of groundwater. For and decomposition is facilitated. contaminants into the unsaturated zone. successful bioremediation, these factors Over time, ageing and weathering of Oxygen added to the contaminated have to be considered on a site-by-site the soil can make the contaminants less groundwater and vadose-zone soils can basis. The challenge of effective available due to chemical oxidation also enhance biodegradation of bioremediation is to provide both the reactions and the incorporation of contaminants below and above the water physical and chemical conditions which contaminants into the organic matter. table. Bioventing uses extraction wells to are most favourable to the growth of This decrease in bioavailability can be circulate air through the ground, these microbes and thereby maximizing overcome by the use of chemical or bio- sometimes pumping air into the ground. degradation of the pollutant. surfactants during the biodegradation Another in situ method includes soil The environment in which the process. vapour extraction where a vacuum is contaminated site exists influences the applied to the soil to remove volatile Bioremediation technologies type of organism that can be used. For contaminants. example, in cold environments (0°-15°C) Generally, bioremediation technologies Success stories: Exxon Valdez psychrophilic organisms would be can be classified as either ‘in situ’ or ‘ex spill effective, whereas in hot environments situ’. In situ bioremediation involves (>45°C) thermophilic organisms would treating the contaminated material at the One of the most famous cases of be effective. Temperature, pH, heavy site while ex situ involves the removal of bioremediation was in the clean up of the metal concentration, microflora and the contaminated material to be treated Exxon Valdez oil spill in Puget Sound, microbial diversity are some of the elsewhere. A common ex situ method is Alaska in 1989 when nearly 11 million environmental factors that must be landfarming. This is when the gallons of crude was spilt. At this point, www.sfam.org.uk June 2006 21 bioremediation had been studied to some environmentally sound remediation are extremely diverse, PAH-degrading degree, but the effectiveness of its technique, and its use has expanded to microbes need to either have a range of application on such a large area of areas such as sludges, surface waters and enzymes capable of accepting the contamination was unknown. Scientists process waters contaminated with different PAH substrates, or have enzymes studied the local contaminated pesticides, metals, crude oil and industrial with broad substrate specificity. environment and found a large solvents. Consequently, some of the more complex community of microorganisms which Interest in bioremediation of polluted PAHs may only be partially catabolized or made it advantageous to try soil and water has increased even further not transformed at all. There is also bioremediation and made it unnecessary in the past two decades after it was evidence that microorganisms have the to introduce microbes. They studied the recognized that microbes were able to capacity to evolve catabolic systems for limiting factors to the natural degradation degrade toxic xenobiotic compounds that mineralization of xenobiotics or newly of the hydrocarbons in the oil and found were previously thought to be resistant. introduced synthetic compounds. that concentrations of available nitrogen The microbial processes occurring are Genetic engineering is being studied as and phosphorous in seawater were the extremely complex, and while scientists a way to increase the biodegradation limiting factors. Tests found that the know that microbes have the primary capabilities of microbes. In order to application of fertilisers containing the catalytic role in bioremediation, their design improved, contaminant-degrading limiting reagents to test areas on the knowledge of the alterations occurring microbes, scientists need to understand shoreline assisted in the breakdown of the within the microbial communities remains the current metabolic processes and even oil, and a visible reduction in oil was seen relatively unknown. Research is create new metabolic routes. This is on rocks and sand particles. Additionally, continuing to look at the interactive and indeed an exciting and growing area, which will require the combined effort of expertise from microbiologists, biochemists and geneticists as well as chemical and environmental engineers. Additionally, combining chemical, physical and biological treatments may also improve the extent of degradation. For example, wood-rotting fungi have evolved biocatalytic systems that can make compounds more suitable for microbes to transform. Other agents such as ozone, potassium permanaganate or ferrate can also promote initial redox reactions. In light of new regulations requiring cleanup of many polluted sites and considering the expense of other remediation methods, bioremediation is definitely considered the best option for many situations in the future. Limiting factors in biodegradation can be tests of the tidal waters and the absence interdependent roles played by individual overcome by optimizing growth of algae growth concluded that excess species in these communities, and to conditions, improving activities of the levels of nitrogen and phosphorus where characterize key enzymatic reactions that natural soil flora, isolating or engineering not reaching the ocean. participate in contaminant better strains and designing microbial Overall, the clean up was regarded as a transformation. This knowledge will assist consortia of suitable organisms. successful example of the possibilities of in the engineering of biocatalysts with improved substrate specificities and bioremediation. It was estimated that References under natural conditions it would be five reaction rates. to ten years before natural conditions There has also been significant ■ Belcher, T. (1992) Optimal conditions for were achieved, whereas, with research into degradation in anaerobic decomposition of oily sludge, Honours thesis bioremediation, and the provision of environments, focusing on the catalytic ■ Sing, A. & Ward O.P (2004) optimal conditions, this would be possible mechanisms that facilitate the anaerobic ‘Biodegradation and Bioremediation – an in two to five. catabolism of pollutants. Anaerobic overview’ Soil Biology Volume 2 Springer- degradation systems require terminal Verlag, Berlin Heidelberg Current research activities and electron acceptors such as iron III, ■ http://www.clu-in.org/techfocus/ - the Future manganese oxide or nitrate to replace the Hazardous waste cleanup information Bioremediation is a continually function of oxygen in aerobic systems. ■ http://www.bact.wisc.edu/ University of growing field, and research is progressing The partial transformation of Wisconsin to further the cost-effectiveness and contaminants, known as ‘cometabolism’ is expand application possibilities. It is also an area of research that is of much Teresa Belcher becoming recognized as a powerful, interest. For example, as PAH molecules

22 June 2006 www.sfam.org.uk

Summer Conference 2006

75th Anniversary Conference CPD 1931 - 2006 ACCREDITATION A total of 13 credits have been awarded for Living together: this meeting polymicrobial communities Apex International Hotel, Edinburgh, UK Monday 3 to Thursday 6 July 2006 BOOK NOW TO BE SURE OF YOUR PLACE! The closing date for registration is Friday 9 June 2006, after which a late booking fee of £30.00 is payable.

To book your place, use the form on page 26 or visit the website where you can book online or download a PDF booking form for offline completion.

Student Session Making good use of your supervisor. An informal workshop with refreshments to help you get the most out of your supervisor. The session is on Wednesday 5 July from 16.30 to 18.00.

Please note that the ■ Including: Lewis B. Perry Memorial Lecture conference programme was correct at the time of going There will be sessions on: to press but may be subject to change. ■ Physiology and functionality of polymicrobial communities ■ Influencing polymicrobial communities For the latest information, please visit us online at: ■ The gut microflora www.sfam.org.uk ■ Bioremediation

24 June 2006 www.sfam.org.uk Programme

Monday 3rd July 13.00-14.00 Lunch/Trade Exhibition 11.50-12.25 Microbial interactions with the gut immune Arrive and Register: Apex International Session 2. Influencing system. Hotel, Edinburgh. polymicrobial communities. Dr Elizabeth Furrie, University of Dundee, UK. 18.00-19.00 Lewis B Perry 14.00-14.35 Combating polymicrobial 12.25 -13.30 Lunch. Memorial Lecture: Out of communities: learning a dusty archive – from from Nature. Session 4. SAB to SfAM, the first 75 Dr Jeremy Webb, University of ● Offered papers ● Student presentations ● years. Southampton, UK WH Pierce Prize ● Annual General Meeting. Professor Max Sussman.Lecture 19.30-20.00 Drinks reception Theatre, The Royal Museum of 14.35-15.10 Probiotic modulation of Scotland the oral flora. The Hub, The Royal Mile. Prof. Jeffrey Hillman, University 19.00-20.00: Drinks Reception. 20.00 - late: Conference and 75th of Florida, USA. From 20.00: Evening at leisure / Quiz Anniversary Dinner night (optional) 15.10-15.45 Using synbiotics to Thursday 6th July address major gut Tuesday 4 July problems. Session 5. Bioremediation Prof. Stig Bengmark, University Session 1. Physiology and College London, UK. 09.00-09.35 Bacterial and fungal functionality of polymicrobial transformations of communities. 15.45-16.15 Tea/posters metals, minerals and metalloids. 16.15-16.50 Impact of antibacterial 09.00-09.35 Interspecies signalling Dr Geoff Gadd, University of usage on polymicrobial communication. Dundee, UK. communities. Dr Miguel Camara, University of Prof. Peter Gilbert, University of 09.35-10.10 Contaminant degradation Nottingham, UK. Manchester, UK. in terrestrial 09.35-10.10 Co-ordination and environments: multiple Competition in 16.50-17.25 Impact of antimicrobial roles of fungi and specialised microbial residues on gut protists. communities. communities: are the new Dr Hauke Harms UFZ, Germany. Dr Andrew Whiteley, University regulations effective? 10.10-10.45 Phenolic degrading of Oxford, UK. Prof. Peter Silley, MB Consult, UK. communities: functional 10.10-10.45 Adaptation and evolution phylogeny, assembly and 17.30-19.00 Trade Show in a two-species stability. structured community. Dr Andrew Whitely CEH, Oxford, UK. Prof. Soren Molin, Technical Wednesday 5th July University of Denmark. 10.45-11.15 Coffee/ posters. 10.45-11.15 Coffee/ posters. Session 3. The gut microflora 11.15-11.50 Polymicrobial community 11.15-11.50 The role of niche 09.00-09.35 Bacterial metabolism and strategies for mediating differentiation in the interactions in the gut. the bioremediation of community assembly and Prof. Harry Flint, Rowett complex organic coexistence of uncultured Research Institute, Aberdeen, mixtures. bacteria from the UK. Dr Mike Larkin, Queen’s genus Achromatium. University, Belfast, UK. Dr Neil Gray, University of 09.35-10.10 Probiotics and gut Newcastle, UK. biofilms. 11.50-12.25 Themes and variation: 11.50-12.25 Genomics, ecophysiology Dr Sandra MacFarlane, emerging patterns in and interactions of yet University of Dundee, UK. microbial remediation of uncultured nitrifying spilled oil. bacteria. 10.10-10.45 The gut flora in early life. Dr Ian Head, University of Dr Holger Daims, Vienna, Dr Christine Edwards, University Newcastle, UK. Austria. of Glasgow, UK. 12.25-13.00 Natural attenuation 12.25-13.00 Living together while 10.45-11.15 Coffee/ posters. (or lack of it) in two being eaten: Bdellovibrio highly contaminated UK predation in 11.15-11.50 Intestinal bacteria aquifers. polymicrobial and ageing. Dr Roger Pickup, CEH, communities. Dr Emma Woodmansey, Smith Lancaster, UK. Dr Cary Lambert, University of and Nephew Research Centre, Nottingham, UK. York, UK. 13.00-14.00 Lunch and Close

www.sfam.org.uk June 2006 25 BOOKING FORM and INVOICE

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a one day meeting on Including: The Denver Russell Memorial Food and Health: Lecture: ‘Naturally Occurring The most Applied Microbiology Microorganisms and their Resistance to Physical and The Royal Society, Carlton House Terrace, London Chemical Agents’ given by Thursday 11 January 2007 Martin Favero, Advanced Sterilisation Products, Johnson & Johnson, USA.

Call for Posters! There will be an opportunity during the meeting to present posters in any relevant subject area. Abstracts of less than 500 words, to include aims and objectives, brief methodology, results, conclusions and implications of the work, should be submitted only as a Microsoft™ Word document A one day meeting with sessions on: attachement to an email ■ Hospital Acquired Infections and addressed to [email protected] ■ Food Microbiology (in collaboration with the Chartered Institute for with the subject line ‘January 2007 meeting submission’. Environmental Health) Topics to be covered will include: Hospital Acquired Infections: ● the government perspective; Please note that the meeting ● infection control team’s perspective; overview was correct at the time of going to press but ● clinical microbiologist’s perspective; may be subject to change. ● C.difficile ● MRSA ● Acinetobacter Simmering Questions in Microbiological Food Safety The full programme for this ● Is there a scientific basis for safe eating practice? ● How and why do enteropathogens make you ill? meeting will be available ● Norovirus and Hepatitus A — an important cause of foodborne illness? soon on the website at: ● How do foodborne pathogens emerge? www.sfam.org.uk

www.sfam.org.uk June 2006 27 Scientist, Craig Venter now plans to make microbes produce clean energy MAKING HISTORY

Alun Anderson reveiws the controversial career of Craig Venter

RAIG VENTER, billionaire (on paper, at least), sequence the human genome, he has raised a lot of money The maverick who and had just finished sailing is apparently up to - and I’ve for a new company looking at C led the private- around the world on your own come to meet him in his novel sources of energy, and sector human 95-foot yacht, what would you London hotel to hear more. If has just recruited a top US genome sequencing, now has do next? How about creating the stories were about anyone department of energy official, plans for clean energy. He life from scratch, saving the other than Venter, I would Aristides Patrinos, to join him. says he never aimed to Earth from global warming assume they were just dreams. Patrinos is well connected to “privatise” the genome and and, as a by-product, ending But he has a record of going those who set US energy thinks science and commerce western dependence on where no one else would dare, policy and is said to have had can be best friends. If you had imported energy? That’s what which is why he is described a hand in President Bush’s led a team that sequenced the Craig Venter, the scientist as a maverick, pirate, recent state of the union human genome, then became whose private company raced opportunist, egoist and the commitments to finding new the world’s first biotechnology the rest of the world to ‘bad boy’ of science. And now energy sources.

28 June 2006 www.sfam.org.uk Features

Venter is pacing his hotel him and ‘do the mouse had the biggest genome centre methods and untried room, blue-eyed and barefoot, genome’ instead. What in the world, and he was the mathematical algorithms, and as though still on the deck of followed was the scientific only player with no need to the quality of its work has his yacht. He was up until drama of the century. fear the US government been repeatedly attacked and 3am trying to out-drink the Sequencing the human cutting his funds if a private defended. Sulston claims that editor-in-chief of Nature and genome was a great scientific alternative seemed viable. He Venter’s team was merely a coffee is in plentiful supply. goal that was expected to give stuck firmly to his total ‘distraction’ and that the Before hearing about his a huge boost to biology and opposition to the commercial public programme did energy plans, I want to get his medicine. Many of the programme. everything important. Yet the side of the story of the race scientists involved were Venter insisted both to his public programme rapidly for the human genome and his brilliant overachievers who colleagues and to Congress changed its strategy in views on private versus public had their eyes set on a that the privately funded response to Venter, ruthlessly funding for science. I know he possible Nobel prize. But genome sequence would be ditching smaller, less efficient feels he has been unfairly although everyone wanted to made publicly available. But labs in the consortium, and attacked by the British press, win, no one wanted to admit no one quite believed him. buying many of the new fast including New Scientist, the he had entered into anything When Venter phoned Sulston machines to get to the finish magazine at which I was as unseemly as a race. to suggest collaboration ‘to line years earlier than editor-in-chief when the A former head of get the sequence out for planned, which suggests that human genome project was Georgetown University, an everyone,’ Sulston was Venter provided a kick to the going at full speed. institution founded by Jesuits, tempted, as he records in his consortium’s backside. But first some background once told me, ‘scientists are book The Common Thread, Of course, en route Venter on how Venter got that bad the only people more but refused, telling himself had annoyed lots of scientists boy reputation. Back in 1998, hypocritical than us Jesuits.’ that, wherever Venter had as well as some of the the vast publicly funded Just as a candidate for Pope been, ‘the decisions came business people in Celera, consortium to sequence the would not go around saying down to profit.’ For Sulston, a appearing to lean too much human genome had been ‘vote for me,’ but would clergyman’s son, that was not towards business for the rumbling along for years, first quietly murmur about his sole acceptable. scientists and too much under the leadership of James wish being to serve God, the Collaboration never towards free publication for Watson, the co-discoverer of scientist publicly claims his happened, however beneficial the business people. Back the structure of DNA, and then ‘god’ to be the progress of it might have been. Further then, everyone was caught up under Francis Collins, who truth. This progress can be peace meetings ended in in the tech bubble madness of discovered the gene for cystic achieved only by the sharing recrimination and, as the race the times. In little over a year, fibrosis. The planned of results: everyone stands on sped up, barrages of press some six biotech companies completion date was 2005. everyone else’s shoulders. releases from both teams raised a total of $4bn in Then, in May 1998, all hell But, of course, personal confused the media about who various stock offerings. That broke loose. Venter announced advancement only comes from was really ahead. President was something I wanted to ask he was going to set up a beating everyone else. In the Clinton stepped in as Venter about. The promise was privately funded company— world of science, competition peacemaker and the two that ‘genomics’ would deliver later named Celera—to always has to wear the mask teams agreed to stop fighting a quick way to create new sequence the entire human of co-operation. in public. A few months later, drugs and even ‘personalised genome, using radical new Scientists on the public on 26th June 2000 and only medicine,’ with drugs tailored methods at a fraction of the consortium wanted to win, but two years after the race to individual genetic cost of the public programme under the banner of co- began, Clinton, flanked by characteristics. Most of these and in only a couple of years. operation and ‘the principle of Venter and Francis Collins, things have proved very hard The reaction from the public free access to genetic announced that both sides had to realise, and patenting consortium was a mixture of information,’ as John Sulston, reached the finishing line genetic information has rage that anyone would dare who ran the British part of the together. A simultaneous provided no guarantee of a to compete with biology’s programme, put it. Every bit announcement was made by workable drug or a profit. equivalent of the Apollo of the data should be freely Tony Blair, although The human genome programme and fear that available to all scientists and inexplicably he failed to sequence is a great advance Venter’s company might not none of it used to give anyone mention the Sanger Centre. for basic research, but it has only beat it to the sequence a commercial edge or, even The race had officially ended been much slower to deliver but also obtain commercial worse, patented so that others in a dead heat, although at for the common good. The rights over the use of the data. would have to pay a fee to use that stage the teams had long slog of development and There was also much anxiety it. finished only drafts and much clinical trials continues much that governments might think Sulston worked at the work was still needed. as before, and the boom times twice about continuing their Sanger Centre (now the But even with the race long for biotech stocks, including funding at all. Venter had not Wellcome Trust Sanger over, the dust has never Celera, are long over. I was helped matters by suggesting Institute) in Cambridge. entirely settled. To put the interested in Venter’s views on that the global consortium of Thanks to hundreds of genome together at such this. But first I wanted to distinguished scientists should millions of pounds of funding speed, Venter’s team had know how he began to mix leave the human genome to from the Wellcome Trust, he employed radically new science and commerce. www.sfam.org.uk June 2006 29 AA: The human genome CV: Initially I had the genome.’ Everyone wanted to AA: That’s what led to the project turned you into a notion that the best way to keep going without trying launch of your company, figure of controversy. But you sequence the human genome anything new. The reaction Celera, and Watson’s were arguing with Jim Watson was to build a single was something like: ‘Very nice notorious remark that you over gene patenting long industrial-style centre. But the Mr Ford, you developed the ‘wanted to own the human before that. project took a different turn automobile, but you know our genome the way Hitler wanted CV: Back in 1992, I was a and became a giant horses and buggies are just to own the world.’ In Britain, government researcher at the international co-operative. It fine, thank you.’ The idea to John Sulston thought the National Institutes of Health planned to take $5bn of public turn these techniques into a same, writing that, ‘Craig was (NIH). I developed a method money and distribute it around privately funded project did aiming to gain total control of for labelling genes quickly and the planet. Every scientist and not come from me but from the information contained in the NIH tried to file patents on government in the world was the equipment-maker Applied the genome for commercial hundreds of genes. I was involved and it became a Biosystems (ABI). It gain.’ attacked by Watson and others political project with people developed a new instrument CV: They got it all wrong. I even though the so-called fighting to control the money. that is particularly powerful said to ABI that if I do set up ‘Venter patents’ were filed by New ideas were shut out. At when combined with the this company to sequence the NIH, not me, and I would human genome, I will need a never have gotten any money guarantee that I can publish it. from them. The irony is that, The response was, OK we’ll thanks to Watson attacking give you the $300m, but if you me, everyone heard about my want to publish the results work and I started to get big you’ll have to come up with a offers from biotech business plan. So I did. I knew companies. One of them that the 3bn-letter human offered me a $5m signing fee, genome was worthless without and when I turned it down the computing infrastructure because I wanted to keep and the software tools to do doing science, people saw it something with it. So my as a negotiating ploy. But I business model was to give eventually did a deal with the sequence away for free private investors. I said, if you and sell the necessary allow me to start my own not- software tools and the for-profit institute in parallel computer infrastructure. How with a for-profit institute, and is that against the public they are kept independent of interest? each other except for funding, AA: At least the stock I will do it. So I got $70m over market liked the idea. ten years to fund my lab called CV: It was insane. At one the Institute for Genomic point the market capitalisation Research (TIGR) with the of Celera reached $24bn, intellectual property rights making it bigger than any going to the for-profit institute British company. The model (Human Genome Sciences). could not justify that value. The scientific founders of But I could not say that in biotech companies are mostly the institute I had set up, shotgun sequencing and public as it was against SEC just looking for new ways to meanwhile, we were trying to offered to put up $300m to rules and would have caused a get their science funded, and develop new technology to create a new company to market crash. The irony was when the company comes sequence faster. It had taken sequence the genome using it. that Francis Collins and others under pressure to make scientists 13 years to It was not an altruistic move. in the public programme were products, the founder gets the sequence the genome of the They saw that this would help hyping the human genome, chop. I was trying to avoid bacterium E. coli, but using to sell a lot of these new describing it as the most that fate by coming up with a the new ‘shotgun’ methods I instruments, which it did. I important thing since the model that would allow me to developed with Hamilton looked at the prototype and moon landing. I was trying to do basic science and reap Smith (a Nobel prize-winner worked out that we could downplay it because you can commercial benefits. who works closely with probably sequence the human go to jail for hyping the stock! AA: The human genome Venter), we did the genome of genome in two or three years. I still became the world’s first project had started small Haemophilus influenzae in I told Ham Smith that I was biotech billionaire, but only on under James Watson, but by four months. Instead of people going to leave and try to paper—as head of the the time you entered the fray saying, ‘Wow, here is a faster sequence the human genome. company, I could not sell my it had grown into a global way to go,’ I just heard, ‘Oh He replied, ‘I don’t think it stock. project spread among many that could not possibly work will work, but I’m going with AA: You clearly have hurt labs around the world. on the scale of the human you! feelings about the press you

30 June 2006 www.sfam.org.uk Features

got in Britain, which often finite amount of money. If one its results in the journal Foundation into which I put followed Sulston’s line: thing is funded, another is not. Science on the same day as most of my stock from Celera. ‘there’s one bunch of people In the ‘we must race against the public project published I didn’t make much personally who are doing this for the Celera’ fervour, no one in its results in Nature, with the but my foundation got a benefit of humankind, and Britain really stopped to ask if sequence freely available to windfall. I have over 500 another bunch who are trying this made sense. Why didn’t researchers in a database, and people working for me at the to do it for their personal we just combine these projects conditions only for those with two research institutes. Then gain.’ and make them better, faster commercial aims. recently I raised $30m to start CV: A study of the global and cheaper? No one would AA: Then, just 11 months a new company called press coverage of the human answer those questions in after that day of joint Synthetic Genomics. Its goal is genome by a German Britain because national pride publication, you suddenly to build on our basic research university found that the ordained that you had to decided to leave Celera, the and find new commercial coverage in Britain was support Sulston. You have to company you had founded. energy alternatives that do not uniquely biased, and there was look at the whole system, not Why? cause global warming and will always this mano-a-mano just individual morals. CV: I was fired. end the massive dependence battle between me and Scientists can be working for AA: You were fired? on imported energy. The Sulston. He was one of the problem with trying to find players who made good novel sources of energy is that contributions, but there is governments in the US, nothing unique about him Britain and the rest of Europe except that he was railing aren’t supporting that kind of about how evil research. Our governments commercialisation was. But should be spending 10 per look at it this way: the public cent of their budgets on trying effort consumed about $5bn to find new energy sources of public assets. Celera, by that don’t add carbon to the contrast, used its own money atmosphere. It is vital for to sequence the genome for national security—we are $100m and gave it to the fighting all these wars over public for free. When you look energy sources instead of at the amount of medicine or developing independent education that $5bn could sources. It is also a priority have purchased, I think you for the health of the planet. can come up with quite a left- Climate change is real and if wing argument for letting the we don’t find alternatives to private sector play its part. burning coal and oil we are There are important issues going to be in trouble. here for government and AA: You are thinking about political leaders. Nations take using bacteria to produce pride in their scientific fuels like hydrogen. But you accomplishments, but if we need to create a new life form want to make national heroes to do it? out of people then it can lead CV: People have been to disaster. Look at what looking for naturally occurring happened in Korea where the altruistic reasons, people CV: Yes. I hadn’t gotten organisms to produce government pressured one funding the science can be along with the head of the hydrogen or methane. But it stem cell researcher to beat doing so for altruistic reasons, parent company from the does not make sense that the world and he ended up or they can be doing so out of beginning. I had sequenced anything would evolve faking data. We should be financial greed, but the greed the human genome, I had a naturally to produce asking whether the best is only satisfied if the science great customer database of all commercial amounts of decisions are being made is good and leads to a drug the top universities and methane or hydrogen. about the use of public money, that actually treats disease and companies. I had experience Organisms would use the and how to evaluate science as makes a body better. The in raising huge sums of money energy themselves. But if we a whole. At the same time as system overall is oblivious to and credibility in both the can design synthetic cells then those hundreds of millions of individual motivation. scientific and business we can make them put all dollars from the Wellcome Investors in Celera wanted to communities. I decided to their energy into pathways Trust were going to the human make money. But when we raise the money for a new that will drive methane or genome project here, a lot of asked employees why they company. I now have TIGR, hydrogen production. DuPont scientists lost funding for their wanted to work there, they my original institute, and the is a world leader in using work. Many left Britain during wanted to be part of history. new Venter Institute, both not- modified bacteria on an that period. We live in a zero- People like to make a for-profit laboratories funded industrial scale to transform sum game where there is a difference. Celera published through the Venter Science renewable natural www.sfam.org.uk June 2006 31 resources into products that AA: And that ties up with becomes a major source of making history? He’s already would normally have to come the project that has taken you energy—all of a sudden Latin made quite a bit of it through from oil. They are building a right around the world in your America and Cuba look very his enviable scientific $100m plant in Tennessee that yacht. attractive. It changes the publication record. That’s will turn corn sugar into CV: Yes, I’m just back from security landscape and it quite separate from the propanediol, a key polymer for a 40,000-mile trip around the changes how much carbon we notoriety which he acquired at making plastics, but it has globe on Sorcerer II. I bought are putting into the Celera. But the impression you taken them over five years to the yacht in New Zealand and atmosphere. There is a unique get on meeting Venter is that modify a bacterium so that it converted it, adding opportunity here, so let’s try he always needs to move on to will turn the sugars into the microscopes and sampling it. This is my third company the next project. If his polymer efficiently. Most of gear. All across the oceans we and I think this will be the one audacity works, and he and the work involved shutting have been extracting unknown that really works. Basic Hamilton Smith succeed in down existing pathways in the micro-organisms from sea research and creating a synthetic bacterium so that the sugar water, sending them to my commercialisation sit well bacterium, then they will start would end up as the polymer laboratory in Maryland and together. They are not a vast new field. The capacity and not be used for something sequencing their DNA. The separate worlds: in fact, the to build genomes opens up so else. The result showed that new discoveries are stunning. more they get together, the many possibilities, both in huge gains in efficiency are We only have the data from better for society. People make understanding life and in possible. the first quarter of the a distinction between business using bacteria as chemical My approach starts from a expedition but we have skills and science skills, but if factories. There will be new different place. I think that if already found 1.2m new you can run a science worries too: the technologies we can build a cell from genes—more than in the programme and inspire people will make biological weapons scratch with only the very whole history of molecular you can lead a business. easier to make. Whether bugs minimum of processes it biology. Among them are AA: You have set yourself can provide the next energy needs to survive, we won’t almost 800 genes involved in big goals. Is part of that supply is controversial. There need to go through this long converting sunlight into conditioned by your are plenty of simple creatures process of modifying an energy. experience in the Vietnam that make hydrogen as a by- existing bacterium to shut AA: So the oceans could war? product of their usual down all the pathways you provide a huge stock of new CV: I left home when I was metabolic processes but can don’t want. Instead, you can genes that you could slot into 17 to surf and explore life. anyone make them do so add to this ‘minimal cell’ the your ‘minimal cell,’ like Instead, I got drafted into the efficiently enough to drive a pathway you need in order to reprogramming a computer to war so I turned 21 in Vietnam. switch to a non-polluting make a specific product. I do different things? Being faced with the death of hydrogen economy? Venter is have been trying to CV: That’s the idea. thousands of people your own certainly right about one understand the minimum a AA: To do all this you are age and younger, and trying thing. Governments aren’t cell needs to survive for the once again running both non- (as a medical orderly) to save spending enough to find past ten years, as part of a profit and for-profit as many as you could are alternatives, or even to basic research project; the organisations. That means you tough lessons for someone at implement the solutions they fact that it has commercial have to be scientist and the end of their teens. already have. and social applications is businessman, what Francis Everybody that was there had wonderful. We sequenced a Collins described as a their lives changed. Many bacterium called Mycoplasma ‘Faustian’ situation that people changed for the genitalium which has the doesn’t work. Isn’t there a risk negative and did not recover smallest genome of any known that you’ll hear those words from the war, but I was free-living organism and have ‘you’re fired’ again? changed in such a way that I modified it to make it simpler CV: This time I’m making wanted to go on and make a and find the minimum set of sure to keep control of it. We difference. I thought it was genes an organism needs. have picked people as wrong, politically, that we At the same time, we’ve investors who all share the were in Vietnam, but none the been finding ways to build long-term view that this is a less, 30 years later, we are genomes artificially. The first national and international back in an almost identical time a team built a simple priority. I want to change the situation. virus genome from scratch, it world. A bacterium that makes AA: Many people say you Alun Anderson took three years. Using new gasoline from sugar in an have a very big ego. After all, Alun Anderson is a freelance techniques we did it in two academic lab doesn’t change the DNA you sequenced was writer and former editor-in-chief weeks. The genome of the the world unless someone mostly your own. of New Scientist. This article simplest bacterium is around develops it commercially. If, all CV: You have to have a first appeared in the April 2006 60 times bigger so it is much of a sudden, oil and energy strong sense of self to get issue of Prospect magazine more difficult, but we are could be produced locally and things done. I believe in (www.prospect-magazine.co.uk) moving towards creating the we were no longer reliant myself and my team and our and is reproduced with the kind first very simple living upon oil, global politics would ideas and making history. permission of the author and the magazine organism. be transformed. Sugar cane Will Venter succeed in

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www.sfam.org.uk June 2006 33 Stat Note 5 In the fifth of a series of articles about statistics for biologists, Anthony Hilton and Richard Armstrong ask: is one set of data more variable than another?

HERE MAY BE important assumption for the of variation and the (Hilton & Armstrong, 2005). A occasions when it is use of the ‘t’ test (Hilton & assumption of homogeneity of hypothetical experiment was T necessary to test Armstrong, 2005) or analysis variance may need to be carried out to investigate the whether the of variance (ANOVA) explicitly tested. This Statnote efficacy of two novel media variability of two or more sets (Armstrong & Hilton, 2004) is describes four such tests, viz., supplements (S1 and S2) in of data differ. that the variability of the the variance-ratio (F) test, promoting the development of An investigator, for different groups being Bartlett’s test, Levene’s test, cell biomass. Three ten-litre example, may wish to test compared is similar, i.e., that and Brown and Forsythe’s fermentation vessels were whether a new treatment they exhibit homogeneity of test. sterilised and filled with reduces the variability of a variance. Replicate identical growth media with The scenario particular microbial response measurements within a control the exception that the media compared with an older and a treated group, however, We return to the scenario in two of the vessels was treatment. In addition, an often exhibit different degrees first described in Statnote 3 supplemented with ten ml of

34 June 2006 www.sfam.org.uk Features

either medium supplement S1 calculations are slightly more or S2. The vessels were Table 1. Dry weight of bacterial biomass under unsupplemented complex and are given in (US) and two supplemented (S) growth conditions (S1 and S2) in allowed to equilibrate and Snedecor and Cochran (1980). a sample of 25 fermentation vessels. were subject to identical Interpretation of the environmental / incubation US S1 S2 US S1 S2 US S1 S2 results conditions. The vessels were then inoculated with a culture 461 562 354 506 607 556 518 617 714 In the worked example in of Bacterium x at an equal 472 573 359 502 600 578 527 622 721 Table 2, the value of χ2 was culture density and the 473 574 369 501 603 604 524 626 722 highly significant (P < 0.001) fermentation allowed to suggesting real differences 481 581 403 505 605 623 529 628 735 proceed until all the available between the variances of the nutrients had been exhausted 482 582 425 508 607 644 537 631 754 three groups. The previous F- and bacterial growth had 482 586 476 500 609 668 535 637 759 test suggested, however, that ceased. The entire volume of 494 591 511 513 611 678 542 645 765 the variance of the culture media in each unsupplemented data was 493 592 513 512 611 698 fermentation vessel was then similar to that of the growth removed and filtered to 495 592 534 511 615 703 medium S1. Therefore, it is recover the bacterial biomass, the effect of the growth Variances: US = 463.36. S1 = 447.88. S2 = 18695.24 which was subsequently dried Variance-ratio test comparing US and S1: F = 463.36/447.88 = 1.03 medium S2 that has and the dry weight of cells (2-tail distribution of F, P > 0.05) substantially increased the measured. This experiment variance of bacterial biomass. was repeated 25 times and the probability column has to be described above, but a better Hence, if these data were to dry weight of biomass used to obtain the 5% approach is to test all the be analysed by ANOVA produced in each of the three probability. variances simultaneously using (Armstrong & Hilton, 2004), groups recorded in Table 1. Bartlett’s test (Snedecor & the assumption of Interpretation of the Cochran, 1980). homogeneity of variance The variance-ratio test results would not hold and it may be How is the test done? If there are only two groups When the unsupplemented necessary to transform the involved, then their variances and S1 data are compared If there are equal numbers data to logarithms before can be compared by a two-tail (Table 1), a value of F = 1.03 of observations in each group, analysis to stabilize the variance ratio test (F-test) was obtained. This value is calculation of the test statistic variance. Data transformation (Snedecor & Cochran, 1980). less than the F value in the is straight-forward and a is described in more detail in 2.5% column (P > 0.05) and worked example is shown in Statnote 4 (Hilton & How is the test done? consequently, there is no Table 2. If the three variances Armstrong, 2006). The larger variance is evidence that the addition of do not differ from each other, The use of the χ2 divided by the smaller and the the medium S1 increased or then the ratio M/C is a distribution to test the resulting F ratio compared decreased the variance in member of the chi-square (χ2) significance of M/C is with the value in a table of the replicate flasks. distribution with (a – 1) questionable if the DF within variance ratio to obtain a P- degrees of freedom (DF), the groups are less than five Bartlett’s test value, entering the table for where ‘a’ is the number of and in such a case, there are the number of degrees of If there are three or more groups being compared. If the special tables for calculating freedom (DF) of the groups, then the different groups have different numbers the significance of the statistic numerator and denominator. groups could be tested in of observations in each (Pearson & Hartley, 1954). This test uses the two-tail pairs using the F-test (unequal ‘n’), then the Bartlett’s test is used less probabilities of F because we today and may not normally are testing whether or not the be available as part of a two variances differ rather Table 2. Comparison of the variances of three groups with equal statistics software package. than whether variance A is observations (v = 25) in each by Bartlett’s test. This is because the test is greater than variance B. regarded as being too Hence, this calculation differs Group Variance In (variance) ‘sensitive’ resulting in too from that carried out during a Unsupplemented 436.36 6.1385 many significant results typical ANOVA, since in the S1 447.88 6.1045 especially with data from long- latter, it is whether the tailed distributions (Snedecor S2 18695.24 9.8360 treatment variance is larger & Cochran, 1980). Hence use than the error variance that is of the test may raise being tested (Armstrong & Total 19606.48 22.079 unjustified concerns about Hilton, 2004). Published whether the data conform to 2 Σ 2 2 statistical tables of the F ratio M = v[a (ln s* ) – ln si ] where s* is the mean of the variances, ‘a’ the the assumption of (Fisher & Yates, 1963; number of groups, v = DF of each group, and ln = logarithms to base e. homogeneity of variance. As a Hence, M = 102.62 Snedecor & Cochran, 1980) consequence, Levene (1960) C = 1 + (a +1)/(3av) = 1.018 are usually in the form of one- developed a more robust test χ2 = M/C = 102.62/1.018 = 100.8 (DF = a – 1, P < 0.001) tail tables. Hence, the 2.5% to compare three or more www.sfam.org.uk June 2006 35 variances (Snedecor & for an ANOVA, that of than means, e,g., in analysing References Cochran, 1980). normality (Armstrong and data from experiments to Hilton, 2004). This problem determine whether a ■ Armstrong RA & Hilton A Levene’s test. How is becomes particularly acute if particular treatment alters the (2004) The use of analysis of the test done? there are unequal numbers of degree of variability or testing variance (ANOVA) in applied microbiology. Microbiologist, vol Levene’s test makes use of observations in the various the assumption of 5: No.4 18. the absolute deviation of the groups being compared. As a homogeneity of variance prior ■ individual measurements from consequence, a modification to other statistical tests. Brown MB & Forsythe AB (1974) Robust tests for the their group means rather than of the Levene test has been All of the tests described in equality of variances. J Am Stats the variance to measure the proposed by Brown and this Statnote have their Assoc 69: 264-267. variability within a group. Forsythe (1974). limitations. Bartlett’s test may ■ Fisher RA & Yates F (1963) Avoiding the squaring of be too sensitive but Levene’s Brown-Forsythe test. Statistical tables. Longman, deviations as in the calculation and the Brown-Forsythe tests How is the test done? London. of variance results in a also have problems. We would ■ Hilton A & Armstrong RA measure of variability that is This differs from Levene’s recommend the use of the (2005) Statnote 3: Comparing less sensitive to the presence test in that an ANOVA is variance-ratio test to compare the difference between two of a long-tailed distribution. performed not on the absolute two variances and the careful groups. Microbiologist, vol 6: An ANOVA (Armstrong & deviations from the group application of Bartlett’s test if No.4 30. Hilton, 2004) is then means but on deviations from there are more than two ■ Hilton A & Armstrong RA performed on the absolute the group medians. This test groups. (2006) Statnote 4: What if the deviations and if significant, may be more accurate than Considering that these tests data are not normal? the hypothesis of Levene’s test even when the are not particularly robust, it Microbiologist, vol 7: No.1 34 homogeneous variances is data deviate from a normal should be remembered that ■ Levene H (1960) In: rejected. distribution. Nevertheless, the homogeneity of variance Contributions to Probability and both Levene’s and the Brown- assumption is usually the least Statistics. Stanford University Interpretation of the Forsythe tests suffer from the important of those considered Press, Stanford, California. data same defect in that to assess when carrying out an ANOVA. ■ Pearson ES & Hartley HO A Levene’s test on the data differences in variance (1954) Biometrika Tables for in Table 1 using STATISTICA requires an ANOVA, and an Statisticians, vol1. Cambridge software, for example, gave a ANOVA requires the If there is concern about University Press. value of F = 52.86 (DF 2,72; assumption of ‘homogeneity of this assumption and especially ■ Snedecor G W & Cochran P < 0.001) confirming the variance,’ which some authors if the other assumptions of the W G (1980) Statistical Methods, results of Bartlett’s test. consider to be a ‘fatal flaw’ of analysis are also not likely to 7th Ed. Iowa State University Press, Ames Iowa. More recently, Levene’s test these analyses. be met, e.g., lack of normality has also been called into or non additivity of treatment Conclusion question since the absolute effects (Armstrong & Hilton, Dr Anthony* Hilton and deviations from the group There may be 2004) then it may be better Dr Richard Armstrong** means are likely to be highly circumstances where it is either to transform the data or *Pharmaceutical Sciences and skewed and therefore, violate necessary for microbiologists to carry out a non-parametric **Vision Sciences, Aston University, Birmingham, UK another assumption required to compare variances rather test on the data. Instant access!

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www.sfam.org.uk June 2006 37 Summer Project at Food Microbiology, Queen’s Am I eligible - University of Belfast. Gemma McClatchey reports on her project can I apply?

URING THE SUMMER, I WAS abnormalities noted in the previous work fortunate enough to be given when using a genetic fingerprinting assay D the opportunity to work in the known as AFLP (Assorted Fragment Food Microbiology branch of Length Polymorphism). A mathematics the Food Science Department at the software package, BioNumerics 4, was Queens University of Belfast. used to determine the genetic relatedness Being a Microbiology student about to of the food-borne Arcobacters. The enter my final year, this experience was package operates through analysing AFLP invaluable to me as it was an ideal profiles by clustering isolates into distinct opportunity to develop my research and groups according to their genetic banding laboratory skills. Furthermore, it also pattern. Values of 90% homology and highlighted the applications and above were used as an indication of importance of microbiology research. It identical isolates. AFLP profiles generated enabled me to gain hands-on experience during the research had shown a of microbiology within a research significant proportion of isolates gave institute setting. patterns with an unusually high number of bands. Grants can be made available to ANY The aim of my project was to examine FULL member who is able to offer a the isolates to see if the unusual AFLP suitable undergraduate student a work patters were due to mixed cultures placement for a period of up to 10 weeks during summer. The grant is £160 (species or genotypes) being analysed. per week for the student for a maximum Stored isolates were to be resuscitated of 10 weeks and up to £50 per week for then streaked to purity and AFLP analysis lab costs for a maximum of 10 weeks. To conducted. The resulting profiles would apply, visit be compared to the AFLP profiles gained www.sfam.org.uk/members/ previously. prizes.php Ten isolates were randomly chosen to be studied in detail and five pure cultures GUIDELINES were obtained from each isolate by 1. Any full member of the Society who can offer an repeated streaking to single colonies. undergraduate student, or a recent graduate (within 6 AFLP profiles were prepared and months of graduation) a work placement is eligible to apply for this grant. The placement can last up to a analysed from all fifty cultures. For eight maximum of 10 weeks, normally during the summer out of the ten original isolates studied, vacation. subcultures produced acceptable AFLP 2. The Grant will normally provide support at the rate of profiles showing over 90% profile £160 per week for the student and up to £50 per week for lab costs. The monies will usually be paid to the homology with the original isolate, when Department in which the student/graduate works unless a analysed using BioNumerics. This specific request is made for an alternative method of indicates that they were identical and can payment. Gemma McClatchey be used as a measure of colony purity. 3. Applications should be made by the supervisor using the PDF form provided on the website or the paper form My assigned project was designed Only one isolate gave results suggesting obtainable from the Society Office. around previous research into the that the original analysis was based on a 4. Successful applicants and their students/graduate must diversity of Arcobacter species in mixed culture. Multiple band profiles that write a report on the placement within 4 weeks of foodstuffs in Northern Ireland. Arcobacter had appeared in the initial AFLP profiles completing their placement which will be published in Microbiologist. Photographs of the applicant and/or the belongs to the family from the previous research were still work done during the placement are desirable. These Campylobacteraceae and are found in a present in the AFLP profiles generated in should be supplied as (a) digital images at a size of not range of animal origin foodstuffs. As yet my research, suggesting that they are less than 4 inches square at a resolution of not less than 300 pixels per inch, or (b) original photographic prints arcobacters have not been regarded as probably characteristic of some wild-type which will be scanned and promptly returned. significant food-borne pathogens, rather Arcobacter AFLP profiles. Two isolates 5. Normally a member may not apply for a further grant they can be thought of as emerging food- did not produce acceptable profiles and until a period of two years has elapsed. borne pathogens. these may be untypable by this specific 6.There is no closing date for this Grant and applications Previously, 104 cultures of Arcobacter method. The research has generated ideas can be made any time during the year. Applicants must apply at least 6 weeks before the proposed start date. had been stored in cryovials after for further research with Arcobacters and isolation from a range of foodstuffs as this is exciting as they continue to emerge part of previous PhD research that had as food-borne pathogens. www.sfam.org.uk/members/prizes.php finished in 2002. The main aim of this I thoroughly enjoyed my placement investigation was to study the and I feel that I have acquired a range of

38 June 2006 www.sfam.org.uk Students into Work report

important transferable skills. The The first part of my nine week project contained potassium nitrate which could development of independent working is a was to investigate the aerobic and low be utilised by P. aeruginosa as an large part of doing a project such as this oxygen (O2) growth of Pseudomonas alternative electron acceptor if oxygen and is certainly a skill that is essential in aeruginosa using a previously refined was unavailable. Biofilms were continually the area of scientific research. I found biofilm model. The second part was to perfused with CDM over the course of this to be a challenging experience but utilise environmental scanning electron several days. Viable counts were taken also highly stimulating and rewarding. It microscopy (ESEM) to attempt to throughout to determine the numbers of has been of great benefit to me and I visualise the biofilms produced in both bacteria being released from the biofilms would highly recommend it to any student the aerobic and low O2 systems. and also the final biofilm population. who has the opportunity to take part in The biofilm mode of growth of bacteria A section of the first part of my project such a scheme. I would like to extend my represents the major form of growth of was to modify the aerobic system to run gratitude to both my supervisors Dr bacteria. The process begins with under low oxygen conditions. Biofilms Madden and Mrs Moran for their bacterial attachment to inert surfaces and initially established under aerobic professional advice and also to Carmel formation of interactions with other conditions were subsequently perfused Kelly and Sarah Hamill who also assisted bacteria and the surface. A highly with an anaerobic gas mixture which me. I would particularly like to thank the organised 3D structure is formed, often created a low oxygen environment within Society for Applied Microbiology for composed of multiple species of bacteria the Sorbarod and biofilm. As with the enabling me to have taken part in such a and extracellular polymeric substance aerobic system, viable counting was valuable and rewarding experience. (EPS). Both the structure of the biofilm performed throughout every experiment, and the bacteria themselves contribute to and a final viable count of the Sorbarod Gemma L McClatchey the well documented phenomenon of biofilm population taken. After reaching a resistance. The EPS matrix creates steady state biofilm, both the aerobic and concentration gradients of O2, nutrients low oxygen biofilms were challenged with and even antibiotics. This can affect the ciprofloxacin to assess the efficacy of the The aerobic and low efficacy of some antibiotics, such as antibiotic under aerobic and low oxygen gentamicin, which rely on oxygen for conditions. During the antibiotic oxygen (O2) growth of active uptake into the bacterial cell. As perfusion into the system, viable counts Pseudomonas well as this, EPS can function as a were taken hourly to monitor the log drop molecular sieve trapping antibiotics. and recovery of the biofilm. aeruginosa. Bacterial physiology is also a factor in The second aim of the project was Chris Wright reports on his project biofilm resistance. As considered above, attempt to visualise the biofilms produced nutrient gradients exist within the EPS using ESEM. This was achieved using a creating regions of slow growing or control biofilm which was dissected and stationary phase cells which in turn will hydrated with sterile water. Under low affect the efficacy of antibiotics. This oxygen conditions, possible changes in growth as a biofilm can have serious and EPS production by P. aeruginosa could costly consequences for our use of produce visual differences in ESEM medical devices, such as central venous images. Furthermore, a change in EPS catheters and other indwelling prosthetic production could have an effect on the devices, should they become colonised antimicrobial susceptibility of the biofilm with microorganisms. As well as forming population. biofilms on inert substrata, such as Working in the microbiology lab at medical devices, P. aeruginosa is an UWE Bristol has been a great experience important opportunistic pathogen in and it has also made me realise that I cystic fibrosis (CF). In CF patients, a definitely want to do a PhD in the near decrease in pulmonary function caused by future. The project itself required good a loss of membrane ion channels and a time management skills and forward resultant incapacity to clear bacterial planning with the large scale media cells, leads to colonisation by preparation and organisation of the opportunistic pathogens. Once it has biofilm system. I would like to thank my colonised, P. aeruginosa is responsible supervisor, Dr Shona Nelson, and the ultimately for approximately 90% of microbiology researchers and technical FTER COMPLETING MY deaths in CF patients. staff at UWE for all their help and Applied Microbiology Honours The first part of my project was to support. Finally I would like to thank A degree at the University of the establish aerobic biofilms of P. SfAM for providing sponsorship for the West of England I wanted to aeruginosa using an established summer project which I have thoroughly gain more experience in a relevant protocol. This protocol involved the enjoyed. subject area and give myself a potential Sorbarod in vitro continuous flow system advantage in looking for a job. The SfAM of biofilm growth. Biofilms were cultured ‘Students into Work’ grant gave me the using a chemically defined medium opportunity to work in a microbiology (CDM) in which iron was the growth Chris Wright research laboratory. limiting factor. The medium also www.sfam.org.uk June 2006 39 Starch slurries extracted from maize mmol/L in both the decanted liquid and The use of starter (Fig 1) were inoculated with; the slurries by day three. In the control Lactobacillus plantarum (LP), samples coliform bacteria were detected cultures in the Pedicoccus acidilactic (PA), L. reuteri on day three in the slurries incubated at production of ‘Akamu’— (LR) with an uninoculated sample as a 30oC and on day one in slurries incubated control. The slurries were fermented at at 35oC. In the slurries inoculated with a Nigerian Fermented 30oC and 35oC for five days. The pH, starter cultures the coliforms were Maize Porridge used as short chain fatty acid and ethanol levels, detected on day five at 30oC and day coliforms, yeasts and LAB counts and the three at 35oC. Lactic acid bacteria a weaning food. sensory properties of the fermented numbers were ca 108 cfu/g in all slurries Patience Chisa Obinna-Echem reports on slurries were analysed. There were no including the controls. All of the slurries, statistically significant differences in inoculated and controls, had high yeast her project lactic acid, acetic acid or ethanol counts ca 106 cfu/g. In the sensory production between the treatments over analysis slurries inoculated with LP were the first three days of fermentation. the least liked in terms of sensory WISH TO EXPRESS MY attributes and general acceptance. profound gratitude to the Fig 1. Flow diagram for the production In this study the inoculation of maize Society for Applied I of Akamu with starter cultures of LAB did not Microbiology for giving me the appear to have any great benefit opportunity to gain experience of working Maize compared with the control slurries. In all in a microbiology research environment. ▼ cases initial lactic acid concentrations of I joined the research group of > 75 mmol/L were achieved. However, in Professor Peter Brooks and Dr Jane Beal 1. Cleaning the traditional Akamu making process the at the University of Plymouth who are benefits of high lactic acid concentrations working on lactic acid fermentation of ▼ are lost as most of the acid generated by cereal based diets for pigs and poultry. 2. Steeping @ 30OC for 24 hours LAB is discarded with the decanted liquid Spontaneous lactic acid fermentations are after the first 24 h fermentation. My study widely used to produce cereal based ▼ has raised a number of questions weaning food throughout Africa and regarding the safety of the traditional way 3. Decant water and wash parallels can be drawn between the two of making Akamu as well as questions processes. Therefore we decided that I ▼ regarding the dynamics of lactic acid would do some work on the use of starter production and interactions between µ Discard cultures in the production of a maize 4. Wet sieve (400 m) pomace lactic acid bacteria and yeasts in such based weaning food using the traditional systems. process. ▼ This research has broadened my The research was aimed at the knowledge on the safety quality of food 5. Sedimentation. determination of the effect of Lactic acid Add starter processing method as well as culture 18 hrs @ 30OC or 35oC bacteria (LAB) on the safety and fermentation and the activities of LAB. bacteriological quality of ‘Akamu’ a ▼ The practical research experiences gained fermented maize weaning food. Akamu is will in no doubt be of great benefit in any a traditional lactic acid fermented cereal- 6. Decant liquid food production and research sector. It based starchy meal, made from maize, has also heightened my interest in this sorghums or millet and it is a most ▼ area and I hope to be able to secure some popular weaning food for children in funding so that I can return and continue 7. Press in cheesebag Nigeria and other West African countries. this research as a PhD student. In Nigeria, diarrhoea is ranked as the ▼ second major cause of morbidity and mortality in children and up to 70% of all References 8. Cover cheesebag with water diarrhoeal episodes are caused either by ■ Beal, J. D., Niven, S. J., Campbell, A. and and ferment for 5 days contamination of food or drinking water Brooks, P. H. (2002) The effect of @ 30OC or 35oC. (Motarjemi et al., 1993). Weaning foods temperature on the growth and persistence Decant and replace fluid daily have been shown to be frequently of Salmonella in fermented liquid pig feed. contaminated with enteropathogens from International Journal of Food Microbiology 79, 99-104. various sources especially when stored at However, in all samples the liquid ambient temperature under poor hygienic decanted on the first day of fermentation ■ Motarjemi, Y., Kaferstein, F., Moy, G. and conditions and public sanitation, hence (Fig 1 - step 8) contained 70% of the Quevdo, F. (1993) Contaminated weaning exposing the infants to the risk of lactic acid produced, ca 60 mmol/L food: a major risk factor for diarrhoea and associated malnutrition. Bull WHO 71, (1) diarrhoea. However, if the food contains compared with ca 25 mmol/L remaining 79-92 sufficiently high levels of lactic acid (> in the slurry. Although the numbers of 75 mmol/L) contamination with LAB remained high in the remaining enteropathogens can be prevented (Beal slurries, lactic acid levels did not recover Patience Chisa Obinna-Echem et al., 2002). and were significantly reduced to <15

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www.sfam.org.uk June 2006 41 Am I eligible - can I apply? Bacterial Degradation of Technical Compounds and Formulated Mixtures

HE WORLD MARKET FOR However this is not to say that bioremediation — the use of information is not available on the T biological processes to treat degradation of xenobiotics in technical or contaminated areas, employing formulated forms. microbiology, biotechnology and To very briefly illustrate the ‘disparity’ engineering techniques — is increasing between technical compound (presuming greatly. It gained approximately U.S. $580 no impurities for clarity) and formulation million between 1994 and 2000 to a total biodegradation, a modern insecticide and of approximately $1050 million. a well known timber treatment product, Furthermore the cost of using appropriate both of which can give and have given bioremediation systems is around eight environmental problems, are described. times less than incineration and two and a Synthetic pyrethroids (SPs) are half times less than soil washing per ton insecticides now found in many The President's Fund provides limited of contaminated soil. Thus bioremediation applications, both household and grants to ALL members to assist can be seen to be not just a more agricultural. The largest agricultural them to attend scientific meetings or environmentally friendly technology for usage is in the treatment of flies and ticks workshops related to their area of contamination removal but commercially on sheep and cows; in the UK sheep dips work. Awards are made at the sole and economically attractive too. are one formulation. The SP cypermethrin discretion of the Honorary President. Microbial degradation is one of the is used as the active ingredient in many Please note that this Fund is open to processes of biodegradation. sheep dips and its degradation pathway members of all ages! Why not apply ‘Biodegradation’ itself is often used to (as a technical compound) is known. The to the Fund? The maximum grant encompass several further terms for fate in the environment is more of a available is normally £1,000. different processes such as problem because of the SP’s chemical biotransformation, biodetoxification and nature and its traceability. Incidents of SP To apply, visit biomineralisation; the connection usually based sheep dip pollution have occurred www.sfam.org.uk/members/ being the end result of observed loss of where aquatic life has been wiped out in prizes.php original xenobiotic to other product(s) rivers and lakes. The formulations are usually with a reduction in toxicity. Here (generally) designed to increase wool TERMS & CONDITIONS biodegradation may be through the uptake and maintain the stability and 1. The applicant must have been a member for at least indigenous population, selective isolates, potency of the SP after treatment. a full subscription year before the event to be attended or a supplemented population. Biodegradation has now been studied and must be a fully paid-up member at the time of application. A search of publications regarding the with the technical cypermethrin and 2. A successful applicant cannot re-apply to the Fund biodegradation of compounds will yield cypermethrin sheep dips, in both for three years from the date of the award. colossal numbers, but upon further laboratory and field applications. Without 3. Preference will be given to applicants who are inspection almost all of these relate to referring to individual and specific contributing to the meeting they wish to attend and/or either a technical or active ingredient, or results, degraders isolated from technical are unable to obtain funds elsewhere. a specific formulation as would be found cypermethrin cultures do appear to 4. Completed applications must include an abstract of any intended contribution to be made at the meeting or used in the (appropriate) environment. degrade SPs in a sheep dip formulation, and must be received by the Society Office not less than In many cases the active ingredient is but not as well as degraders isolated six weeks before the date of the event. described as the compound of study, using sheep dip cultures (with both 5. Student member applications must be supported by whereas it is actually a formulation isolations from non-SP containing media their supervisor and include the contact telephone number(s) and email address(es) of the supervisor or containing the compound that is used. from the same sources). However the head of department who is supporting their application. Additionally the matter measured (directly degraders isolated from sheep dip break 6. The maximum grant available is normally £1,000. or indirectly) may not be the technical down the technical SP to approximately 7. Under exceptional circumstances this maximum may compound but just as a constituent the same extent as the SP in a be exceeded. ingredient of the formulation. This may formulation. This may not seem 9. The award of this grant is at the sole discretion of not mean complete remediation of a unexpected but is interesting because the the Hon President of the Society. contaminated site from a technical SP active ingredient only constitutes 5- 10. The applicant must write a short article of between compound since formulation components 10% of a sheep dip formulation. Testing 400 - 600 words within 4 weeks of the meeting, the (which may or may not pose a risk) may different sheep dip formulations produces content of which will be agreed with the Editor of sfam Microbiologist and will be published in the magazine. remain. A good example of this is with similar results. For bioremediation of Photographs of the applicant and/or the subject of the polycyclic aromatic hydrocarbons (PAHs) used waste sheep dip the addition of article are desirable. These should be supplied as (a) digital files in TIFF or JPEG format at a size of not less in creosote, as presented below. previously isolated SP degraders than 4 inches square at a resolution of not less than Formulations themselves can have an significantly increases the rate of SP loss 300 pixels per inch, or (b) original photographic prints affect on the biodegradation of only by a little. This may in part be due to which will be scanned and promptly returned to the applicant. compounds, increasing stability, potency another potential problem – that of the of effect, adsorption and bioavailability. exact environment where the

42 June 2006 www.sfam.org.uk The President’s Fund

contamination is. other. Using a technical ingredient may be act as a reservoir for infection where PAHs are the main constituent of the only way to isolate a degrader, and previously decontaminated surfaces can creosote (the rest being mostly various using a formulation may be the only way be re-colonised when cells slough off the phenolics), which is used in the treatment to isolate a degrader that can be used in biofilm structure and disperse to these of timber to provide greater longevity; other formulations; similar formulation areas again. now banned or restricted in use in most uses are likely to have similar chemistries Microarray studies have confirmed of Europe. The carcinogenic and polluting after all. Equally, measuring a technical beyond any doubt that Salmonella nature of creosote and many PAHs are compound may be the only way to biofilm cells are distinct from their well documented as are many cases of monitor the loss of a formulation, but it is planktonic counterparts at the biodegradation and the bioremediation of the formulation that is almost always transcriptional level, and it has been contaminated sites. However in referred to as the pollutant. found that nearly 10% of the genome can biodegradation studies it is often PAH It should be remembered that in the be differentially expressed between the loss that is measured, and this is often environment it is highly unlikely that one two populations (Hamilton, 2005). extrapolated to creosote (not completely will find a technical compound that is not Various studies have shown that many unreasonable given the chemistry). Whilst in a formulation. The technical ingredient genes are required for biofilm formation, not wholly inaccurate, problems can arise may be the major pollutant but simply and the genetic mechanisms underlying with this approach, most obviously if only removing it alone is not removing the different aspects of the biofilm phenotype PAH degradation is taken as a sign of whole contamination. have been extensively studied over recent total creosote degradation in land years. However, while it is apparent that destined for another use (which does not References genes are differentially regulated in happen in reality); but the approach is ■ Bioremediation – Applied Microbial biofilm cells relative to their planktonic widely used in microcosm studies. A Solutions for Real-World Environmental cousins, much less is known about the problem does arise though when trying to Cleanup. 2005. Atlas, R.M. and Philp, J. eds. spatial and temporal expression of these isolate creosote degraders. The toxic ASM Press Washington. genes at a cellular level within the biofilm mixture requires heavy dilution relieving ■ Grant, R.J., Daniell, T.J. and Betts, W.B. structure. One of the most intriguing a good deal of selective pressure, but (2002) Isolation and identification of features of biofilms is their heterogeneity. using PAHs at concentrations nearer and synthetic pyrethroid degrading bacteria. Whether differential gene expression at those of use results in isolates with Journal of Applied Microbiology, 92, 534- plays a role in the development of this greater potential for use. In contaminated 540. heterogeneity or whether heterogeneity is sites it is not unusual to find low bacterial ■ Grant R.J., Muckian L.M., Clipson N. J.W. caused by environmental factors is concentrations whilst PAHs remain, but and Doyle E. M. (2003) Bioremediation of a currently unclear. It has been suggested be able to find PAH degrading isolates creosote contaminated site. In Situ and On- that the development of some features of and stimulate degradation through the Site Bioremediation, Magar V.S. and Kelley the biofilm structure are simply due to use of PAHs as carbon sources in the M.E. eds. Battelle Press, USA. ISBN 1-57477- stochastic environmental factors such as laboratory (energy models standardised). 139-6, 2004. the distribution of nutrients on the One additional affect of formulations ■ CL:AIRE. Contaminated Land: Application surface, rather than a programmed and technical compounds is upon the In Real Environments. 2 Queen Anne’s Gate genetic response to the environment. In microbial community. Increasingly Building, Dartmouth Street, London SW1H both scenarios differential gene researched upon with new tools and 9BD. www.claire.co.uk. Information on expression between biofilm cells is likely capabilities introduced by advances in bioremediation. to occur, either as part of a genetic molecular and biochemical biology, the program of development, or as a result of microbial ecology of contaminated sites Dr Russ Grant differing environments within the biofilm and the changes that occur during University College Dublin structure. So how do we find out what is bioremediation are attracting great going on in these structures? attention. However, at this next ‘level of There is an increasing body of resolution’ in bioremediation studies Shining a light on literature citing the use of Green disparity between the affects of a Fluorescent Protein (GFP) to determine technical compound and a formulation Biofilm Heterogeneity the spatial aspects of gene expression. are likely to be even greater making One of the first papers describing the use general studies more difficult or their OST SPECIES OF BACTERIA of GFP to investigate the spatial aspects results less encompassing. In possible will readily colonise surfaces of differential gene expression in the contradiction to this though is a result M and grow as a community of biofilm structure was by Kievit et al., presented here where the SP active cells embedded in an extra- 2000. They found that genes involved in ingredient appeared to be the greatest cellular polysaccharide matrix, commonly quorum sensing (a cell-to-cell signalling selecting factor for bacterial isolates referred to as a biofilm. mechanism dependant on bacterial cell- despite only constituting 5-10% of a Biofilm cells are physiologically density) were expressed at a higher level formulation. distinct from their planktonic in the cells located near the substratum To summarise, the biodegradation of counterparts and this mode of growth is than at the top of the biofilm. Several technical compounds and formulations associated with increased resistance to studies have followed on from this. A that contain the technical compound, may many antimicrobial regimes. This has recent example is the discovery that two be unique but this does not mean that one implications in the industrial, food and genes involved in quorum sensing are is not useful nor mutually exclusive to the medical settings, as biofilm formation can preferentially expressed at a higher level www.sfam.org.uk June 2006 43 in the ‘stalks’ of the mushroom type enables a very visual approach to UANTIFICATION OF GENE structure characteristic of Pseudomonas exploring this area further, and for me, expression by real time aeruginosa biofilms, as opposed to the this fascinating world can become truly Q quantitative reverse ‘caps’ (Lequette and Greenberg, 2005). It captivating when you can actually see transcription polymerase chain is this type of information that could something happening before your eyes. reaction (qRT-PCR) is becoming a widely prove vital in the development of new used technique replacing more time- prevention strategies. It is common References consuming and less sensitive ones such as practice to impregnate surfaces with Northern Blotting, RNase protection assay ■ Hamilton, M.S. (2005) Global approaches antimicrobials to prevent biofilm to identify genes involved in biofilm growth or conventional RT-PCR. contamination, such as is seen with many of Salmonella enterica serovar Typhimurium. However, several limitations need to be medically relevant surfaces. PhD Thesis. considered when real time qRT-PCR is However, if these substances target used, particularly normalisation, template ■ Hauterfort, I., Proenca, M.J. and Hinton, processes occurring in the upper parts of quality, operator variability and the C.D. (2003) Single-copy green fluorescent the structure, they may only stimulate the protein gene fusions allow accurate reverse transcription step itself. These uppermost regions of the structure to measurement of Salmonella gene expression and other features related to qRT-PCR for slough off, leaving the base layer in vitro and during infection of mammalian quantification of gene expression were untouched. Compounds that disrupt cells. Appl Environ Microbiol 69, 7480-7491. addressed in an intensive six days regulation near the base of the biofilm practical course organized at EMBL, ■ Kievit, T.R.D., Gillis, R., Marx, S., Brown, C. would be much more effective at actually and Iglewski, B.H. (2001) Quorum-sensing Heidelberg during summer 2005. removing the biofilm from the surface genes in Pseudomonas aeruginosa biofilms: Together with a group of 21 students, I and preventing reattachment. Knowing their role and expression patterns. Appl had the chance to learn the latest that certain genes involved in quorum Environ Microbiol 67, 1865-1873. developments in this technique from a sensing, for example, are expressed near group of knowledgeable experts in the ■ Lequette, Y., and Greenberg, E.P. (2005) the base of the biofilm may facilitate the Timing and localization of rhamnolipid field. From the beginning of the course, it development of compounds that target synthesis gene expression in Pseudomonas was clear to me that the 18 hour trip was this process. Recent advances in aeruginosa biofilms. J Bacteriol 187, 37-44. worth it, not only scientifically, but also molecular techniques coupled with because a particularly friendly ■ Scholz, O., Thiel, A., Hillen, W. and technological improvements have made environment prevailed among the Niederweis, M. (2000) Quantitative analysis investigations into this aspect of biofilms of gene expression with an improved green student’s group. This and the fact that the even more exciting. These include the fluorescent protein. Eur J Biochem 267, instructor’s team was a group of old development of reporter constructs using 1565-1570. friends, created an atmosphere where a bright variant of GFP that give a more having fun and learning were mixed. accurate representation of gene Besides the well structured practical Michael Pogson expression, (Scholz et al., 2000; and theoretical lectures, short sessions Hautefort et al., 2003), and highly were organised, so that each student had sensitive microscopy capable of detecting the chance to explain his/her research much lower levels of fluorescence than To treat or not to treat project and their experiences regarding was previously possible. Together these your RNA samples with qRT-PCR. Nearly all the projects were have shown promise as a suitable method related to issues concerning eukaryotic to elucidate the genetic regulation at the heavy duty DNase for gene expression. My work on the other single cell level within the biofilm quantitative RT-PCR hand is focused on gene expression in structure. This could lead to a level of bacteria with high GC content in their understanding about the development and assays: a necessary step genome. Therefore, the major problem I maintenance of the biofilm lifestyle that for high GC content was having with my qRT-PCR was previously unthinkable. experiments, i.e genomic DNA As our knowledge of the genetic bacterial strains? contamination of my RNA samples, regulation involved in the formation of seemed at glance a trivial difficulty to biofilms increases, so too will our ability most of the students. Despite this, to develop better control strategies to everyone engaged in an interesting minimise the economic and health costs troubleshooting session that allowed me incurred by their formation on industrially to come back to the lab with a couple of and medically important surfaces. While ideas on how to solve this problem. First there are many techniques that can be of all I realized that most of the in-column used to dissect the underlying techniques commercially available for mechanisms involved in this process, the RNA isolation are standardized for use of a reporter such as GFP has one eukaryotic cells and for some classical feature that sets it apart from the others. prokaryotes mainly E. coli. However, We know that it is ideal for providing when it comes to other prokaryotes, valuable spatial and temporal information particularly those with a resistant cell of gene expression in situ and in a non- wall, these isolation methods need further destructive manner. But perhaps the best standardisation. Since bacteria have a part about using GFP in this way is that it Course members at EMBL, Heildelberg smaller genome than eukaryotic cells, the

44 June 2006 www.sfam.org.uk The President’s Fund

number of bacterial cells to be used for assessed by visual inspection of samples RNA preparations needs to be much run on agarose gel electrophoresis. Campylobacter jejuni larger than the amount of cultured human Certainly, this does not guarantee or animal cells. Therefore the content of negligible Ct values during real time RT- and nitric oxide genomic DNA is larger, too. After PCR. performing some RNA preparations and In conclusion, the answer to the HE MOST COMMON RT-PCR assays, I found that good quality question raised in the title of this report is laboratory-confirmed bacterial RNA is more important than to have a yes, not only DNase treat your bacterial T cause of gastrointestinal large amount containing some DNA RNA samples but also perform a careful infection in England and Wales contamination. For this, the lysis validation of the assay before any continues to be Campylobacter. procedure is the critical step. An interpretation. Ideally, the data originated In 2004 alone, 42,146 cases were inefficient lysis step would release some from qRT-PCR should be analyzed reported to the Health Protection Agency. RNA but certainly would release more together with data gained by examining In reality this figure is known to be much DNA molecules resulting in a DNA other events or molecules relevant to the higher as many cases are not presented to contaminated RNA sample. It is not wise investigation. By these means, the the GP. Severity of the disease in humans to pursue qRT-PCR assays until an biological relevance of the qRT-PCR data varies from a few days to several weeks acceptable lysis procedure has been is reinforced. and causes a significant economic impact establish. I am grateful to Dr. Peter Green for through loss of working time. Symptoms The next critical step to consider is the encouraging me to apply for a President’s include headache, fever, diarrhoea and DNAse treatment of your sample. In spite Fund award and thank the SfAM for abdominal pain. This acute phase is of the hesitancy some researchers may awarding me this grant to attend the qRT- normally self-limiting, however have, this step is absolutely necessary if PCR course in Heidelberg. complications may include reactive real time qRT-PCR is being performed, arthritis and paralysis caused by Guillain- especially when prokaryotic RNA is used. References Barré syndrome. Most cases of infection Furthermore, in solution DNase treatment are sporadic and epidemiological studies ■ Aguena, M. & Spira, B. (2003). RT-PCR of suggest the route of transmission is of the RNA sample is strongly long prokaryotic operon transcripts without recommended even after in column DNase treatment. J Microbiol Methods 55, usually through the consumption of DNase digestion, since no commercial kit 419-423. contaminated poultry meat. Raw milk and can guarantee a DNA free preparation milk from bottles pecked by birds, ■ Ashkenas, J., Dennis, J. W. & Ho, C. Y. (Bustin, 2002; Peters et al., 2004). sewage, untreated water and contact with (2005). Simple enzymatic means to neutralize pets with diarrhoea have also been DNAse I is the commercially available DNA contamination in nucleic acid enzyme for this purpose and this poses a amplification. Biotechniques 39, 69-73. reported to cause infection. Cross challenge for those working with high GC contamination of foods in kitchens is also ■ content organisms such as Brucella. Bustin, S. A. (2002). Quantification of likely to be a significant risk if hygiene mRNA using real-time reverse transcription Genomic DNA contamination is persistent standards are poor. PCR (RT-PCR): trends and problems. J Mol Nitric oxide (NO) has become one of in Brucella RNA isolates regardless of the Endocrinol 29, 23-39. DNAse I concentration used, incubation the most intensively studied molecules. time or number of treatments. Recently, a ■ Dougherty, R. M., Phillips, P. E., Gibson, S. Before 1987 its role in human health was modified DNAse I, 600 times more & Young, L. (1993). Restriction endonuclease primarily as an irritant in air pollution. In digestion eliminates product contamination efficient than the previous existing one, 1998 the Nobel Prize in Physiology or in reverse transcribed polymerase chain Medicine was awarded to the scientists was made available and seems a good reaction. J Virol Methods 41, 235-238. choice to solve this problem. In cases as who discovered production of NO in the those described before, it is more realistic ■ Peters, I. R., Helps, C. R., Hall, E. J. & Day, body and identified its key role in intra- to think in terms of minimization of M. J. (2004). Real-time RT-PCR: and intercellular cell signalling. However, considerations for efficient and sensitive genomic contamination than of getting over- and under-production of NO assay design. contributes to numerous human diseases only background signal in the minus RT J Immunol Methods 286, 203-217. controls. It is the prerogative of the such as rheumatoid arthritis and researcher to decide, according to the Alzheimer’s disease. NO is a simple context, an acceptable minimisation level. Caterina Guzmán-Verri molecule with an unpaired electron However, it is important to keep in mind Universidad Nacional, Costa Rica making it a highly unstable and reactive - that any significant DNA contamination free radical. It can yield nitrite (NO2 ) and - would produce misleading and non nitrate (NO3 ) in aqueous systems and reproducible results. Other alternative reacts rapidly with the superoxide radical methods such as use of restriction NEED HELP? forming peroxynitrite anion (ONOO-). It endonuclease cocktails (Ashkenas et al., Could you benefit from a has numerous beneficial roles such as a 2005; Dougherty et al., 1993) or vasodilator and is the key bactericidal introduction of a non-homologous President’s Fund Grant? See component of macrophages. sequence at the 5´end of the cDNA page 42 for details of this Consequently pathogenic bacteria have during reverse transcription have been award or visit the website: evolved a number of activities that used to overcome this problem (Aguena & www.sfam.org.uk/prizes.php detoxify NO and its redox products and Spira, 2003). Nevertheless, the efficiency are able to modulate gene expression in of DNA removal of these techniques was response to it. www.sfam.org.uk June 2006 45 mycobacteria. C. jejuni contains both a superfamily. Mutant strains defective in Fig 1. single-domain globin and a truncated perR and fur showed unaltered inducible globin. The single-domain globin Cgb cgb expression and have been eliminated (Campylobacter globin) has significant as major regulators for cgb (Fig. 1). homology to the heme domain from E. However, when the gene encoding Cj0466 coli Hmp and other flavohaemoglobins, was mutated, inducible expression of Cgb however it does not possess the binding was almost totally abolished in the sites for FAD and NAD(P)H seen in these corresponding mutant (Fig. 1) suggesting two-domain globins. The role of Cgb was a prominent role for this regulator in NO- investigated by comparing oxidative and responsive cgb expression (Elvers et al., nitrosative stress resistance in the wild- 2005). Complementation of the NssR- type and cgb mutant. The cgb mutant was mutant by insertion of an intact copy of found to be hypersensitive to a the gene into an isolated pseudogene in nitrosating agent (S-nitrosoglutathione; the chromosome fully restored GSNO- GSNO) and sodium nitroprusside (SNP) inducible Cgb expression (Fig. 1). As a and NO releasing agent spermine result, Cj0466 was designated as NssR NONOate, yet sensitivities to peroxide, (Nitrosative stress sensing Regulator). organic peroxides and superoxide were Microarray experiments were conducted Cj0466 (NssR) mediates the inducible expression of Cgb in response to reactive nitrogen species. GSNO was added to Fig 2. growing cultures of wild type C. jejuni, cgb mutant, AV17 (Fur-), AV63 (PerR-), Cj0466- and complemented Cj0466. The expression of Cgb was detected at the times specified using anti-Cgb antibody. Bands corresponding to a protein of 16 kDa were detectable in all strains except cgb- and Cj0466-.

Campylobacters are likely to encounter elevated levels of NO during infection and must therefore respond to this bactericidal activity. Invasion of the epithelial mucosa plays an important role during Campylobacter infection and NO production from macrophages and enterocytes forms a key component of the Fig. 2a. The sequence of the cgb PCR product from 5’ RACE indicating the transcription start site. inducible defence. Possibly as a consequence of these mechanisms NO Fig. 2b. Transcription start sites (bases in red) of promoters upstream of cgb, Cj0645c (truncated haemoglobin), Cj0830, Cj0761 and nssR (Cj0466) as determined by 5’RACE. Proposed –10 synthesis is markedly increased in sequences are underlined. Putative NssR binding sites are boxed and nucleotides identical to the patients with infective gastroenteritis consensus TTAAC-N4-GTTAA shown in negative print while TG residues characteristic of extended (Forte et al., 1999). Campylobacters may –10 promoters are in grey boxes also be exposed to NO in the stomach since the chemical generation of NO can occur here as a consequence microbial equivalent to the wild-type. Construction in order to define the extent of the nitrite production in the mouth. of a reporter gene based on arylsulfatase regulon influenced by NssR. Eight genes Current research at the University of and Western analysis using a polyclonal were found to be over two-fold Surrey has investigated the mechanisms antibody prepared from purified Cgb upregulated in response to nitrosative underlying survival of Campylobacter showed that Cgb expression was strongly stress and these included cgb, the jejuni during oxidative and nitrosative and specifically induced after exposure to truncated globin, and six other genes of stress. Following publication of the C. nitrosative stress and absent in the cgb unknown function. Of these cgb, the jejuni NCTC 11168 complete genome mutant (Fig. 1). This suggested that there truncated globin and two others were sequence (Parkhill et al., 2000) two novel was a novel capacity for NO-related stress dependent on NssR. Consistent with NssR haemoglobins were identified (Elvers et sensing in this foodborne pathogen. being a Crp-Fnr superfamily member, a al., 2004). Bacterial haemoglobins can be Further analysis of the genome Fnr-like binding sequence (TTAAC-N4- classified into three broad groups, the sequence revealed a number of potential GTTAA) was found upstream of Cgb, the flavohaemoglobins for which the most regulators, which by analogy with other truncated globin and two of the other fully understood is Hmp of E. coli, the bacteria, might sense NO and mediate the genes (Fig. 2). Site-directed mutagenesis single domain globins first identified in NO-responsive expression of Cgb in C. confirmed that this cis acting motif Vitreoscilla and the truncated globins jejuni. These included Fur, PerR and mediates the nitrosative stress inducible two of which have been identified in Cj0466, a member of the Crp-Fnr expression of cgb.

46 June 2006 www.sfam.org.uk The President’s Fund

I would like to express my thanks and and is able to grow at very low shows for many food-borne pathogenic appreciation to the Society for Applied temperatures (2-4°C) (Farber et al., bacteria, exposure to sub-lethal Microbiology for their generous award 1991). It poses a particular threat to the environmental stress hardens these from The Presidents Fund, together with food processing industries owing to its bacteria, and as a consequence, stress- a University Research Support Fund, ability to form biofilms, which serve to adaptive strains have increased resistance which has allowed this work to be protect individual cells from operations to normally lethal levels of the same presented both orally and as a poster at designed to remove or inactivate (homologous) or different (heterologous) the 13th International Conference on microbial contaminants from food inimical stresses (Gahan, 1996). Campylobacter, Helicobacter and Related processing environments. The ability to Extensive research has been carried out Organisms, Australia, September 2005. adjust to such adverse conditions is on some of these stresses, including acid, probably important for survival and oxidative, low and high temperature References growth of the pathogen in contaminated stress in L. monocytogenes. food products, and within host organisms. Bacteria are commonly exposed to ■ Elvers, K.T., Wu, G., Gilberthorpe, N.J., alkaline stress in the food processing Poole, R.K. and Park, S.F. (2004) Role of an Filamentation of Listeria monocytogenes environment, particularly because of the inducible single-domain haemoglobin in at pH 9.2 alkaline nature of the detergents and mediating resistance to nitric oxide and disinfectants used to clean processing nitrosative stress in Campylobacter jejuni and Campylobacter coli. J Bacteriol 186, 5332- machinery and surfaces. They are also 5341. exposed to mild alkaline pH values in certain foods, in the phagolysosome ■ Elvers, K.T., Turner, S.M., Wainwright, during their pathogenic cycle and in parts L.M., Marsden, G., Hinds, J., Cole, J.A., of the intestine due to the alkaline nature Poole, R.K., Penn, C.W. and Park, S.F. (2005) NssR, a member of the Crp-Fnr superfamily of the pancreatic secretion. However, the from Campylobacter jejuni, regulates a focus of research on alkaline stress has nitrosative stress-responsive regulon that largely been directed toward gram- includes both a single-domain and a negative microorganisms such as truncated haemoglobin. Mol Microbiol 57, Escherichia coli and Salmonella. Less is 735-750. known about gram-positive foodborne ■ Forte, P., Dykhuizen, R.S., Milne, E., pathogens such as L. monocytogenes, McKenzie, A. Smith, C.C., and Benjamin, N. although the alkaline responses of Gram- (1999) Nitric oxide synthesis in patients with positive cells are likely to differ from infective gastroenteritis. Gut 45, 355-361. those of Gram-negative cells, because of ■ Parkhill, J.,Wren, B.W. Mungall, K., Ketley, differences in their cell wall structure. J.M., Churcher, C., Basham, D., et al., (2000) Knowledge concerning the The genome sequence of the foodborne mechanisms used by gram-positive pathogen Campylobacter jejuni reveals bacteria for adaptation and growth at hypervariable sequences. Nature 403, 665- alkaline pHs comes mainly from studies 668. of alkaliphilic strains of Bacillus species, although some information on Listeria is Karen T Elvers available. Taormina et al., (2001) School of Biomedical and Molecular Sciences, confirmed that L monocytogenes has the University of Surrey, Guildford, GU2 7XH. ability to survive in alkaline media under refrigeration and ambient temperatures, and reported enhanced thermotolerance due to alkaline stress. The extent of cross Morphological protection of Listeria against heat (56°C) alterations of Listeria increased in proportion to the length of The resistance of Listeria exposure time, but not the severity of monocytogenes monocytogenes to stresses is important alkaline challenge. It is likely that, as is in the food industry, where mild or the case with other bacteria, e.g. E. coli, ISTERIA MONOCYTOGENES inadequate treatments could allow the the alkaline stress response of L. is a causative agent of both survival and subsequent growth of small monocytogenes is transient. Thus L sporadic and epidemic food- numbers of contaminating cells, leading transfer of stressed cells into a non borne illness and has emerged to the subsequent development of alkaline environment, leads to reversion as an important human and animal sufficient cell numbers to constitute to the original levels of tolerance to a pathogen in the 1980’s. infectious doses in susceptible secondary chemical or physical assault Human listeriosis is quite rare but with individuals. (Taormina et al., 2001). a high mortality rate (30%). L. As addressed by Leistner (1995), food A number of rod-shaped bacterial monocytogenes is ubiquitous in nature borne pathogens are frequently stressed species, including some pathogens, form and is resistant to diverse environmental during food processing, distribution and elongated filamentous cells when exposed conditions such as low pH, high sodium storage. Compelling evidence that has to marginal growth conditions, suggesting chloride concentrations, low oxygen level, been gathered over the last years which that such bacteriostatic conditions inhibit www.sfam.org.uk June 2006 47 septation, leading to extensive cell References galacturonic acid (smooth regions) elongation and filamentation. Filamentous residues linked by α 1-4 glycosidic bonds ■ cells of Listeria have been reported in a Farber, J.M., and P.I. Peterkin. 1991 Listeria with alternating rhamnogalacturonan range of marginal growth conditions such monocytogenes, a food-borne pathogen branches (hairy regions). Microbiology Review 55: 476-511 as at 42.5°C (Rowan et al., 1998) and at The architecture of the plant cell wall aW 0.94 (Jorgensen et al., 1995). ■ Leistner L. 1995. Principles and is well adapted to resist attack from plant My study using Scanning Electron applications of hurdle technology. In: Gould pathogens, it is a highly insoluble Microscopy (SEM) has shown that GW, editor. New methods of food complex composed of cellulose, sublethal alkaline stress induced cell preservation. London: Blackie Academic & hemicellulose and pectins. The main role Professional. p 1-21. elongation, filamentation and formation of these cell wall polymers is related to of atypical chains in Listeria ■ Gahan C.G.M., O’Driscoll B, Hill C. 1996 cell expansion and mechanical strength. monocytogenes 10403S and its sigB Acid adaptation of Listeria monocytogenes The cellulose myofibrils are coated with deficient mutant. Morphology of some can enhance survival in acidic foods and hemicellulose and immersed in a pectin members of the population was during milk fermentation. Applied and matrix. Environmental Microbiology 62:3128-3132. significantly altered above pH 9.0. In Pectate lyase activity was first buffered media there was a relationship ■ Taormina, P.J. and L.R. Beuchat. 2001. identified in 1962 in cultures of Erwinia between the duration of alkaline Survival and heat resistance of Listeria caratovora and Bacillus sp; these treatment and the extent of monocytogenes after exposure to alkali and enzymes are secreted by both pathogenic morphological change. In non-buffered chlorine. Applied and Environmental and saprophytic microorganisms leading Microbiology 67:2555-2563. media, changes in cell morphology were to the maceration of plant tissue. (Star, less pronounced. Filamentation occurred ■ Rowan N. J. and Anderson J. G., 1998 M.P. and Moran, F., 1962). The best in parent and sigB deficient mutant Effects of Above-Optimum Growth studied microbial pectate lyases are those strains, suggesting that the process of Temperature and Cell Morphology on produced by Erwinia chrysanthemi, a filamentation is sigB independent. Thermotolerance of Listeria monocytogenes plant pathogen which causes severe Cells Suspended in Bovine Milk. Applied and Sublethally stressed cells regained normal maceration of parenchymatous tissue in Environmental Microbiology 64, 6: 2065- morphology and size within three hrs of 2071 various dicot plants. The bacterium enters transfer into neutral (pH 7.4) conditions. the plant through wounds produced by ■ Such changes in morphology may be Jørgensen, F., Stephens P. J., and Knochel either insects or harvesting, then an adaptation mechanism of the S. 1995 The effect of osmotic shock and multiplies in the intracellular spaces subsequent adaptation on the bacterium and might be important in the secreting large amounts of pectinolytic thermotolerance and cell morphology of ability of this pathogen to survive alkaline Listeria monocytogenes. Journal of Applied enzymes. challenge occuring during phagocytotic Bacteriology 79:274-281. Pectate lyases belong to the ingestion, and the application of alkaline polysaccharide lyase group of carbohydrate active enzymes and are detergents during cleaning of food Efstathios Giotis production environments. The University of Ulster, UK grouped into families based upon filamentation of major pathogen sequence similarity. (Coutinho, P.M. and especially those with a low infectious Henrissat, B., 1999). It is likely that all dose such as Listeria monocytogenes is Biochemical and pectate lyases secreted by pathogenic and of particular concern, since, in such saphrophytic bacteria share a common cases, the filamentous growth of even a Structural enzymatic mechanism. Major advances in single contaminating ‘unit’ in food, could Characterisation of a the understanding of these enzymes result in bacterial numbers that exceed catalytic mechanism has been made the infectious dose, on subsequent Pectate Lyase from through the recent structure septation and division. In addition, plate Clostridium determination of Pel1C and Pel9A from count techniques to enumerate bacteria the plant pathogen Erwinia during filamentation, fail to reflect the acetobutylicum ATCC chrysanthemi and Pel10A from increase in cell biomass (and future 824 Cellvibrio japonicus. (Kita, N. et al., infective potential) that is occurring. The 1996; Charnock, S. et al., 2002; Jenkins, development and presence of filamentous J. et al., 2004). forms, reduces the implicit relationship ECTATE LYASES ARE Clostridium acetobutylicum is a between colony forming units and polysaccharide lyases that gram positive, spore forming, anaerobic biomass, leading to underestimation of P catalyse the cleavage of the bacterium which resides in soil and lives the number/concentrations of potential glycosidic bond of pectic opportunistically on decomposing plant infectious units in foodstuffs, and polysaccharides via a α-elimination matter. This bacterium secretes an array incorrect prediction of the levels of risk reaction, resulting in the formation of a of carbohydrate active enzymes: it has posed to consumers. double bond at the newly formed non- been predicted that six genes encode Finally, I would like to thank the SfAM reducing end. Pectin is a major structural putative polysaccharide lyases, sixty four for giving me the opportunity to present component of the primary plant cell wall genes encode putative glycosyl and discuss this work at the 15th and is highly concentrated in the middle transferases, seventy one genes encode European Conference of Clinical lamella between the plant cells, it has a putative glycosidases and Microbiology and Infectious diseases complex structure consisting of a transglycosidases and twenty two encode (ECCMID) in Copenhagen, Denmark. backbone of partially methyl-esterified putative carbohydrate esterases. Open

48 June 2006 www.sfam.org.uk The President’s Fund

reading frame CAC1968 belongs to References a result the items are simply cleaned and polysaccharide lyase family 9, this gene low-level disinfectants used to reduce ■ has been cloned and the protein has been Charnock, S. Brown, I. Turkenburg, J .P. levels of bacteria. expressed and purified to homogeneity Black, G .W and Davies, G .J. (2002) The sterilisation of critical items is Convergent evolution sheds light on the anti- via immobilised metal affinity important requiring the removal of all B-elimination mechanism common to family chromatography and gel filtration. 1 and 10 polysaccharide lyases. Biochemistry. forms of microbial life, including spores, Preliminary biochemical assays show 99,19,12067-12072 to avoid patient to patient transfer of CAC1968 is active against infection. This is especially pertinent as ■ polygalacturonic acid, has a pH optimum Coutinho, P.M. and Henrissat, B. (1999) there is an expanding practice of re-using Carbohydrate Active Enzymes server at URL: of 7.0, a calcium chloride optimum of critical items such as pace-makers and http://afmb.cnrs.mrs.fr/~CAZY/index.html 0.2mM. narrow-lumened heart catheters. In the For structure determination a ■ Jenkins, J. Shevchik, V.E. and Hugouvieux- United States laparoscopes and selenomethionyl protein preparation of Cotte-Pattat, N. (2004) The Crystal Structure arthroscopes (critical items) that enter CAC1968 was required to facilitate of Pectate Lyase Pel9A from Erwinia sterile tissues are often not sterilised chrysanthemi. Journal of Biological multiple amorphous diffraction data between different patients and only Chemistry. 279, 10, 9139-9145 collection. However CAC1968 lacks any undergo high-level disinfection (Rutala et internal methonines, therefore a ■ Kita, N, Boyd, C.M, Garrett, M.R, Jurnak, F al., 1991). This seems inadequate as methionine mutant; I44M, was created. and Keen. N.T (1996) Differential effect of many of the high-level disinfectants An appropriate location for this mutation site-directed mutations on pel1C on Pectate available for clinical use are not effective lyase activity, plant tissue maceration and was identified via alignment of CAC1968 sporicidal agents. The medical devices elicitor activity. Journal of Biological with another family 9 pectate lyase, Pel9A Chemistry. 271, 26529-26533 themselves also offer an obstacle, due to from Erwinia chrysamthemi. (Jenkins, their design which often includes long ■ J. et al., 2004). Starr, M. P. and Moran, F. (1962) and narrow lumens and sharp angles. The Native CAC1968 and the I44M mutant Eliminative split of Pectic substances by presence of organic matter on medical phytopathogenic soft-rot bacteria. Science. were crystallised in the P3121 space group devices represents a further problem as 135, 920-921 with unit cell dimensions of a=56.2827Å, this limits the effectiveness of sterilisation b=56.2827Å, c=120.0700Å, each especially when the narrow lumens containing one molecule in the Mandy M Lyall contain a high organic load (Alfa et al., asymmetric unit. Data was obtained to a Chemical Biology Research Group, School of 1996). The prior cleaning of medical resolution of 1.8 Å. Applied Sciences, Northumbria University, devices is therefore paramount to the Newcastle-upon-Tyne, UK In addition two inactive mutants: effectiveness of sterilisation techniques. K209A and K209R were created and co- High-level disinfectants such as those crystallized with trigalacturonic acid to used in the USA for certain critical items, identify key enzyme substrate interactions Sterilisation of medical are not successful sporicidal agents as a to unravel the catalytic mechanism. These result of a number of factors. Bacterial crystals have been subjected to x-ray devices in hospitals endsospores are the most resistant living crystallography and diffraction data has structures known, as they have no been obtained and is awaiting analysis. IGH-LEVEL DISINFECTION of metabolism and as a result can withstand A greater understanding of these hospital items is a key measure a wide range of environmental assaults enzymes will inform the design of new H in the prevention of including heat, UV and solvents. Many of anti-microbials directed against nosocomial infections. the high-level disinfectants can not tackle phytopathogenic microbes, facilitate the Hospital items fall into three different this resistance, especially in the presence further exploitation of these enzymes in categories; critical, semi-critical and non- of organic matter, and are therefore often the fruit and vegetable industry and aid in critical items. Critical items are those not sporicidal. It is also known that for a the conversion of waste lignocellulose devices that carry a high risk of infection high-level disinfectant to be sporicidal biomass. if the item is contaminated with higher concentrations and often elevated microorganims or bacterial spores. temperatures are needed than for Therefore any item that enters sterile bactericidal activity, which would tissue or the vascular system must be inevitably increase the cost of the sterile. Items in this category include treatments. The need for complete catheters, needles, surgical instruments sterilisation of critical items is paramount NEED HELP? and surgical implants. Semi-critical to avoid the transmission of disease Could you benefit from a instruments such as endoscopes require between patients. high-level disinfection to destroy all Steam sterilisation is thought to be the President’s Fund Grant? See microorganims, but not high-levels of most effective sterilisation method as it is page 42 for details of this spores. Semi-critical items do not need to non-expensive, non toxic and sporicidal. award or visit the website: be free of spores as they only come into Autoclaving occurs at high temperatures, www.sfam.org.uk/prizes.php contact with intact mucous membranes most commonly 121ºC. Heat sensitive which are generally resistant to infection devices however require alternative by common bacterial spores. Non-critical methods of sterilisation as they can not items are those that do not come into survive the high temperatures and contact with skin such as bedpans and as pressures of the autoclave. The use of www.sfam.org.uk June 2006 49 The President’s Fund

Ethylene oxide for sterilisation of critical items has been used extensively, however SfAM School a ban on chlorofluorocarbons in 1995, which were used as a stabilising agent in Associate Membership combination with ethylene oxide (Rutala et al., 2001) reduced its use. At low temperatures ethylene oxide has very limited sporicidal activity, however this can be augmented as the temperature is increased. The use of alternative stabilising agents such as carbon dioxide and hydrofloourocarbons has allowed this chemical to continue to be used to sterilise critical items. Since the observation by Koch over 100 years ago that Bacillus anthracis Why not recommend SfAM membership could survive boiling there has been a to your local school? tremendous amount of research on the mechanisms of spores and their Benefits resistance. Through continued research, ■ Quarterly copies of Microbiologist the strict following of guidelines for the ■ Full access to the Society website sterilisation of critical and other medical ■ Preferential rates at Society Meetings devices, and effective staff training ■ All for only £15.00 per annum! programmes this may help to reduce the incidence of disease including those FREE attributed to the presence of spores. BOOKS! References

■ Alfa, M.J., DeGagne, P., Olson, R.T., and We receive loads of new books Puchalski, B.A. Comparison of ion plasma, from scientific publishers every vaporized hydrogen peroxide and 100% week and are always looking for ethylene oxide sterilizers to the 12/88 enthusiastic reviewers. ethylene oxide gas steriliser. Infection control and hospital epidemiology 1996; 17: 92-100. If we publish your review in ■ Rutala, W.A., and Weber, D.J. New Microbiologist — you get to disinfection and sterilisation methods. keep the book! Emerging infectious diseases 2001; 7: 348- The list of titles below is just a TINY 353 selection of the many titles available ■ Rutala, W.A., Clontz, E.P., Weber, D.J and for review on our website: Hoffman, K.K. Disinfection practices for endoscopes and other semi-critical items. An introduction to Practical Infection control and hospital epidemiology Microbiology (CD) 1991; 12: 282-288. Manchester Metropolitan University Antifungal Agents Jennifer Shackelford Humana Press, Ernst & Rogers Applied Bioremediation and Phytoremediation Advertise! Springer, Singh A & Ward O P With a highly targeted circulation of 2000 copies, Microbiologist is a cost- Biodegradation and effective way for members and non- NEED HELP? Bioremediation Springer, Singh A members to reach qualified & Ward O P microbiologists in industry, academia Could you benefit from a and public services, both in the UK, President’s Fund Grant? See Color Atlas of Medical Bacteriology and worldwide. page 42 for details of this ASM Press, de la Maza L, Pezzio M For more information about the award or visit the website: T, Shigei J T, Peterson E M benefits and costs of advertising your www.sfam.org.uk/prizes.php products or services in Microbiologist please contact the Society Office or visit TO SEE WHAT’S AVAILABLE, VISIT the website. www.sfam.org.uk/pubs/books.php

50 June 2006 www.sfam.org.uk Books

Principles of Virology

S. J. Flint, L. W. Enquist, V. R. Racaniello, and A. M. Skalka Publisher: ASM Press FREE ISBN No.: 1-55581-259-7. $109.95 Reviewed by: Wes P. Kuhne BOOKS! My first introduction, in detail at least, to the field of virology was with the 2nd Would you like to review a book for Microbiologist edition of The Biology of Animal Viruses and get to keep it? The by Frank Fenner, et al., while doing my Society receives several graduate studies. Principles of Virology new books every week takes a more student-reader friendly from publishers around approach. Many texts in this and other disciplines of microbiology have a mixed the world and are always and erratic style. It is apparent from the looking for enthusiastic text that the authors went to additional reviewers who extraordinary lengths to ensure a have an interest in the uniformity of style and presentation. subjects covered. While of some substance in its detailed approach to the field of virology, the text There is an up-to-date will be well suited for upper class ranking list of titles available for in undergraduate courses and graduate review on the Society’s work. The major determinant of this is website at: the heavy emphasis on the molecular biology of viruses and the host. www.sfam.org.uk/pubs/books.php. Two sections of the text demonstrate the authors’ application of current information. First, the section on To make an offer to review any book simply click its Molecular Biology of viruses takes the title. This will send an email request to the Editor of approach of studying the virus at this Microbiologist. In return for your efforts you get to level – the integration of biochemistry, keep the book! molecular genetics, and cell biology. The information presented is based on the You can also read online versions of book reviews latest research in the fields at the time of published in Microbiologist on the same web page. publication. Following a thorough tour of viral genomes and structure, the reader is immersed into the core of viral-host interaction with chapters on RNA virus genome replication, reverse transcription, DNA templates, DNA virus replication, and viral pre-mRNA. Additionally, the citation of various websites gives the reader some initial guidance in furthering their studies. Secondly, the final 2 chapters on the control and evolution of

Erratum The previous issue of Microbiologist contained an error in the contact details of T2 scientific, publishers of the ‘Microbiology of Drinking Water’ CD which was kindly reviewed by Alan Godfree. The correct email address is: [email protected] and the correct website address is: www.t2scientific.co.uk www.sfam.org.uk/pubs/books.php You can also make contact with T2 Scientific using the Contact Form on the website

www.sfam.org.uk June 2006 51 viruses and viral diseases bring in a unifying approach to the entire text. While the concept of evolution of infectious diseases is not new, its application in such a text takes the reader from a reductionist approach of studying virology to a much larger macrobiologic approach. These final 2 chapters help the reader put the wealth of information found in this text into a usable viewpoint that should be readily adaptable to taking laboratory theory and applying the information in the real world. As mentioned above, the authors did an excellent job unifying the writing styles of the various contributors. A conglomeration of different styles is often the downfall of many texts as they pose a constant shift in how to approach the information. Such is not the case here. Additionally, the authors make good use of color diagrams and artistic renderings of experimentally determined events. These are often tied to good clear electron micrographs and computer translation of experimentally derived electronic information. This approach is not limited to the main body of the text (molecular biology), but carries over into the section on pathogenesis. Many general texts present viral pathology as a subject relegated to the realm of the medical text book and only cover the topic with a courteous passing. This not the case here as the authors have allocated a good timely book on an issue that is very much portion of the book’s topics to in the news with numerous recent dissemination and virulence, host defense Revenge of the headlines concerning ‘superbugs’ and and immune response, patterns of Microbes: How bacterial hygiene in hospitals. infection, the ever present chapter on Despite the serious subject matter, the HIV, and oncogenesis. resistance is text is often light-hearted and humorous While the authors do not present any undermining the and gives the reader not only the new information to the field of virology, scientific facts but also deals with them in that is not the purpose of any textbook antibiotic miracle the modern social, economic and political really. The authors have done an context. The book is written mainly from outstanding job doing what they set out to Abigail A Salyers and Dixie D Whitt an American perspective but does retain a do. That is, prepare a text that presents a broadly international outlook. As they say 2005. ISBN 1-55581-298-8. £20.00 wealth of information in a uniform, ‘The need for new antibiotics is not a US readable, and utterly useful format. Reviewed by Bengü Said problem. It is an international problem.’ The text is well worth the investment The book is primarily about antibiotics by undergraduate, graduate, researchers, This book is not, as one could be and bacterial resistance but the authors and anyone needing a great, readable forgiven for assuming from the title, a also devote chapters to antiseptics and reference in the field of virology on their work of science fiction. Instead it is a disinfectants and to compounds that act book shelf. factual text and an ‘attempt to write a against viruses, fungi and protozoa. The book for the general public about authors explain terms, such as antibiotic, Want a FREE book? antibiotics and resistance to them.’ In antiseptic, and disinfectant, in clear writing for the general public the authors simple language in their introductory Would you like to review a book for have also written a book, which will be of chapter and return to these in more detail Microbiologist and get to keep it? interest to a wide-range of people, in later chapters. The narrative Then visit the website where you’ll find including students or professionals who progresses through a brief history of an up-to-date list of titles available for may require an introductory or basic antibiotics, how bacteria adapt and review. knowledge of antimicrobials. This is a develop strategies for circumventing the

52 June 2006 www.sfam.org.uk Books

action of antibiotics, the declining Morphogenesis). In the first chapter, there efficacy of antibiotics and where this is a succinct, but useful overview of the trend may lead. They identify a potential Essential Fungal origin, phylogeny and evolution of fungi crisis in antibiotic availability, with the Genetics that is then very well explained in chapter appearance of microbes resistant to the 9. In the second, the reader will find the antibiotic vancomycin, our last defence David Moore and LilyAnn Novak Frazer necessary information related to fungal against strains of Staphylococcus and sexuality, which is actually very complex Springer-Verlag, New York. 2002 Streptococcus species. but treated in a fairly understandable The core chapters of the book describe 357p + xi, 59 figs. € form. The last chapter is perhaps the the resistance strategies of bacteria: these ISBN 0-387-95367-1. 79.95 most outstanding as it covers very new usually involve a single resistance protein, Reviewed by: and important topics in fungal genetics. an enzyme that inactivates the antibiotic, Marcel Gutierrez-Correa Also, this chapter is developed as a or an altered antibiotic target that is no typical textbook issue that not only longer affected by the antibiotic. More Essential Fungal Genetics is a informs but motivates the reader to technical information on the actual concise but complete description of the search for further information, pushing structures of antimicrobial agents genetics of fungi in a textbook that covers one into the fascinating world of mentioned in the text and a description of traditional genetics, such as mutation, functional genomics and into systems how resistance is measured in clinical segregation and recombination, while biology. The book presentation omits laboratories are placed in the appendices. including the latest molecular biology reference citations so that readers can go At the end of each chapter in this book tools. Ten authoritative chapters treat undisturbed through the text. However, there is an ‘issues to ponder’ section and important aspects including genome lists of important publications and these are often thought provoking and interactions, wild types and mutants, websites ‘worth a visit’ and historical intended to stimulate further discussion. segregation genetics, recombination publications ‘worth knowing about’ are In addition the book also has a useful analysis, mechanisms of recombination, given at the end of each chapter. index so it can be dipped into or chapters the physical genotype, mapping the But humans are far from perfect and can be read as stand alones to get brief fungal genome, fungal phylogeny and so is their work! Core chapters 3 to 8 are but comprehensive information. In such a evolution, and fungal differentiation and written in quite a dense style, often concise text the authors can perhaps be morphogenesis. Although the authors’ demanding careful re-reading and there forgiven for the occasional over- goal is to integrate ‘fungal genetics into are fewer diagrams than are necessary for simplification and those who wish to learn current teaching by complementing major the understanding of tough topics. This is more can always turn to more traditional textbooks used in courses in general important for a textbook, particularly as scientific texts, such as those in the genetics, general organismal biology, and young people are being raised on highly suggested reading section. general mycology’, I found it valuable as a diagrammatic texts plenty of colored In their final chapters the authors textbook by itself for biology, pictures and schemes. As classical and suggest responses to the resistance microbiology and biotechnology advanced molecular fungal genetics are difficult problem. They give options including, undergraduate majors and, perhaps, for subjects even for mature scientists, less more prudent use of antibiotics to reduce graduate students in the fields of plant dense style and more colorful illustrations the selection pressures that encourage pathology (phytopathology), microbiology would help to attract the attention of resistant bacteria to emerge, or directly and industrial biotechnology. While young scientists. Basidiomycetes are targeting and inactivating bacterial reading the book, I though that a specific vindicated by the book but zygomycetes mechanisms for resisting antibiotics. It is course of fungal genetics is lacking in are again forgotten since really very few indeed hard to contemplate a world many schools, particularly in this century examples from this industrially important without antibiotics and the public health when fungal biotechnology is highly group are considered. Also, the adhesion impact this would have — ‘The bugs have relevant. process in filamentous fungi related to won! Here eat this root’ scenario. As stated before, this book has differentiation and gene expression is Fortunately, the authors remain included both classical and molecular missing in the discussion. Finally, I think optimistic that we can still act to preserve techniques together that makes for a that the revision notes at the beginning of the antibiotics we already have. ‘The keys satisfying read. From chapters 3 to 8 the each chapter are too numerous and would to future success in saving antibiotics are reader has an account of the above with be better if short summary sections were knowledge and the willingness of the the advantage that there are numerous considered. I am afraid that the price of public to take an informed interest not interesting examples ranging well beyond the book will discourage students from only in preserving the efficacy of the the normal model species used in purchasing it. antibiotics we have now but also in standard texts. In this sense, this book Despite these minor reservations, I will ensuring that future development of new differs from others on fungal genetics in certainly use this book to reinforce my antibiotics continues.’ that the examples chosen to illustrate advanced undergraduate Molecular So they conclude that ‘there is plenty various features tend to favour Microbial Genetics course which was in of hope’ that the current ‘detente’ we basidiomycetes and the less-often need of this source. For professionals have with the microbes will continue. referenced fungi. I particularly enjoyed searching for a summarised and up-to- After all they were here before us and chapter 1 (Why Study the Genomes of date basic information on fungal genetics they are not consciously malevolent, in Fungi?), chapter 2 (Genome this book is a highly valuable choice. fact many of them are vital to our Interactions), and chapter 10 (The existence. Genetics of Fungal Differentiation and www.sfam.org.uk June 2006 53 For more information about the Society, Society meetings, the benefits of membership, Microbiologist, or to join us please visit the Society website at www sfam.org.uk

i Benefits of sfam membership membership options Publications The Society for ■ Full membership gives online access to The Society publishes two monthly journals: Applied the Journal of Applied Microbiology, Letters Journal of Applied Microbiology and Letters Microbiology was in Applied Microbiology and Environmental in Applied Microbiology. We also produce our founded in 1931 and is Microbiology, copies of Microbiologist, own quarterly in-house colour magazine: dedicated to advancing preferential registration rates at Society meetings Microbiologist, which contains features, reports the study of microbiology. and access to the members areas of the website. topical news stories and full details of our Society members play a meetings. The Society is also a partner with leading role in shaping the ■ Full student membership confers the Blackwell Publishing in the monthly journal future of applied same benefits as Full Membership at a specially Environmental Microbiology. microbiology, and enjoy reduced rate for full time students not in receipt many benefits, including: of a taxable salary. Online journals ■ Reduced rates at ■ Associate membership this class of Society meetings Synergy is an online service provided by Blackwell membership is open to all current and new Publishing that gives Full and Student Members ■ Access to the Society members including existing Associate FREE access to the online versions of the members areas of Student Members and Retired members and Society’s three journals: Journal of Applied the Society website gives quarterly copies of Microbiologist and Microbiology, Letters in Applied preferential registration rates at all Society Microbiology and Environmental ■ Generous grants and meetings. Microbiology. Members can register for this awards service at http://www.blackwell-science.com. ■ Honorary membership of the Society is Members can also submit papers directly to our ■ FREE access to three by election only and this honour is conferred on journals via an online submission service. acclaimed journals persons of distinction in the field of applied For more information about Synergy or online Detailed information microbiology. manuscript submission, please visit the website. about all these benefits ■ and more can be found Corporate membership is open to all on the Society website. companies with an interest in microbiology. Grants & awards Corporate members benefits include: WEBSITE: Many awards and prizes are available to members ● Half page advertisement in each quarterly issue www.sfam.org.uk including the W H Pierce Memorial Prize and of Microbiologist (which can be upgraded to a Prizes for Student Oral Presentations and Posters The website is the best larger size at very attractive discounted rates). at the Summer Conference. In addition to these source of detailed substantial awards, the Society has funds to assist information on the Society ● Full page advertisement in the Members' members in their careers as microbiologists. These and it’s many activities. It Handbook. has a lively discussion include The President’s Fund, Conference forum and fully interactive ● FREE banner advert on the Society Website Studentships, Sponsored Lectures and the popular membership areas where with a direct link to your company site. Students into Work Scheme. you can book your place at Society meetings find ● Up to three members of company staff Full details of all the Society’s grants and awards and advertise jobs, display attending Society meetings at members' rate. can be found on the website together with easy- your CV and much more. (This means a 50% discount on non member to-use online application forms. registration rate). CONTACT: Society for Applied ■ Retirement membership Meetings Microbiology, The Blore Full Members can apply to go on the 'Retired Tower, The Harpur Centre, Members List' once they have retired from their We hold two annual meetings. The January Bedford MK40 1TQ, UK employment and have completed at least 20 Meeting comprises discussion sessions with the Tel: 01234 326661 years membership of the Society. Retired opportunity to display posters on related work. Fax: 01234 326678 members are entitled to all the benefits of Full The Summer Conference is held every July and email: [email protected] Membership except access to Journal of comprises a main symposium, a poster session, www.sfam.org.uk Applied Microbiology, Letters in Applied the AGM and a lively social programme. We also Microbiology and Environmental hold occasional joint ventures with other Microbiology. organisations on topics of mutual interest.

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