The magazine of the Society for Applied Microbiology ■ December 2013 ■ Vol 14 No 4

■ Harnessing the collective intelligence in response to Chalara dieback

of ash ■ HPV vaccines and the media

■ Movie microbes under the microscope

■ Historical perspectives: MMR and the mediaINSI

DE

Microbiology in the media

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contentsthe magazine of the Society for Applied Microbiology

December 2013 ■ Vol 14 No 4 ■ ISSN 1479-2699

12

features

08 Harnessing the collective intelligence in response to Chalara dieback of ash

12 HPV vaccines and the media

14 Historical perspectives: MMR and the media

17 Movie microbes under the microscope

public engagement

20 Bad Bugs Bookclub: 5 years on

news

21 Biofocus: Mark Downs gazes into his crystal ball...

publications

22 Journal news: open access, a primer for UK authors

23 Journal watch

26 StatNote 35: are the data log normal?

28 Book review: Microbial Biofilms

meetings

29 Winter Meeting 2014 full programme

30 Activated sludge

32 The SfAM Activated Sludge Meeting full programme

33 Spring Meeting 2014 full programme

34 Summer Conference 2013 report

members

04 Editorial: microbiology in the media

06 President’s & CEO’s column: vision, mission and developments

43 New Members: we welcome our new Members

45 In the loop: public engagement

46 Careers: pupils to policy via public health

48 Students into Work Grant and President’s Fund: report

commercial

52 Advertisements and news from our Corporate Members

Microbiologist is published quarterly by the Society forApplied Microbiology. ISSN 1479-2699. Registered in theUK as a charity and Company limited by guarantee.Registered in England and Wales: 6462427. RegisteredCharity: 1123044.

© Society for Applied Microbiology 2007-2013. Materialpublished in Microbiologist may not be reproduced,stored in a retrieval system, or transmitted in any formwithout the prior permission of the Society.

Editor: Nancy Mendoza. nancy@sfam.org.uk

Contributions: These are always welcome and should beaddressed to the Editor at: nancy@sfam.org.uk

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Cover illustration: — Pollard Creativity.

Society for Applied Microbiology, Bedford Heights,Brickhill Drive, Bedford MK41 7PH, UK.Tel: +44 (0)1234 326661. Fax: +44 (0)1234 326678.

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information

14Historical perspectives:MMR and the media

17

Movie microbes underthe microscope

04

NancyMendoza

members

Microbiologist ispublished quarterly bythe Society for AppliedMicrobiology, aregistered charity. ISSN 1479-2699.

Copy Dates:

Vol. 15 No.1 March 2014Friday 20 Dec 2013

Vol. 15 No.2 June 2014Friday 21 March 2014

Vol. 15 No.3 Sept 2014Friday 27 June 2014

Vol. 15 No.4 Dec 2014Friday 26 Sept 2014

Disclaimer: The Societyassumes no responsibilityfor the opinionsexpressed bycontributors. The viewsexpressed by Societyofficers and staff do notnecessarily represent theofficial position of theSociety. Readers shouldnote that scientificmaterial is not refereedand represents only theviews of the authors.The claims of advertiserscannot be guaranteed.

Subscriptions:A subscription toMicrobiologist isincluded in the annualSfAM membership fee.For further informationabout the many benefitsof membership pleasesee page 42.

Advertising:Information aboutadvertising inMicrobiologist and howto submit advertise mentscan be found on theSociety website.

Website: our website(www.sfam.org.uk) isa timely source of up-to-date information on allSociety matters andmaintains acomprehensive archiveof articles and reports ona variety ofmicrobiological topics.

On Friday 6 January2006, at the end ofthe working day, I

joined my colleagues at thepub to celebrate my firstweek at the Science MediaCentre. No sooner had thetop been prised off a bottleof Mexican lager, than ourmobiles rang. The boss hadreceived a call from ajournalist; there was apatient in Weston-super-Mare, who had returnedfrom Southeast Asia withsuspected H5N1 avianinfluenza. We abandoned ourdrinks and hotfooted it backto the office.

On arrival, we discoveredit was a false alarm — the patient was very poorly but it wasn’t the deadlyH5N1. Had it been the UK’s first case, we would all, at 6pm on a Friday,

have been dialling the mobile phone numbers ofevery flu expert, virologist, epidemiologist,public health expert and X-ray crystallographer(essential if you want to explain how antiviraldrugs work) we knew.

Why? Because the chances of Editors pushingfor a sensationalized story, catastrophizing thatthis could be as bad as the 1918 flu pandemic,was almost certain; and there would be a rush tocover the news, given the timing was late on aFriday night. In this issue of Microbiologist,

John Illman, a health journalist who has reported for several of the UKdaily newspapers, discusses the importance of scientists stepping up, inthe moment, to have their voices heard when a controversial, orpotentially, scary story breaks.

The MMR vaccine scandal of the late 1990s and early 2000s is a case-in-point and one of the reasons that the House of Lords Science andTechnology Committee gave for the establishment of a Science MediaCentre. Criticism of the media over its reporting of MMR, which is thoughtto have contributed to low vaccination rates and the subsequent measlesoutbreak in South Wales during 2013, is, Illman says, justified. However,he is at pains to stress that both scientists and healthcare professionalsmust accept opportunities to represent their views, or the science behindthe story will go unheard and the dominant rhetoric is given over to thedissenters.

Of course planning helps, and if there is a chance to anticipate a story,there is absolutely no excuse for scientists and healthcare professionals toshy away from involvement. Margaret Stanley describes how in the run-upto the introduction of the HPV vaccination for girls, the media reportinghelped, rather than hindered, uptake of the vaccine. Stanley outlines acoordinated effort with clear messages; a flexible approach to meet theneeds of both the media and the audience; and clearly articulated scientificand medical information. It wasn’t all plain sailing, she says, and Stanleyand Illman agree on one point in particular: balance is the enemy of qualityscience reporting.

As well as looking at news coverage, we’ll also explore microbiology inthe movies and how scientists are using social media to crowdsource forresearch into Chalara ash dieback.

I hope you enjoy this issue and look forward to meeting many of you atour events in 2014.

editorialNancy Mendoza reviews the content ofthis issue of Microbiologist

We are always lookingfor enthusiastic writerswho wish to contributearticles to the magazineon their chosenmicrobiological subject.

For further informationplease email the editor,Nancy Mendoza at:nancy@sfam.org.uk

contribute

05

COMMITTEE MEMBERS

PRESIDENT: Professor Martin Adams, School of Biomedical & Molecular Sciences,University of Surrey, Guildford, Surrey GU2 7XHemail: m.adams@surrey.ac.uk

VICE PRESIDENT: Professor Christine Dodd, Division of Food Sciences, School ofBiosciences, University of Nottingham, Sutton Bonington Campus, Loughborough,Leicestershire LE12 5RD email: christine.dodd@nottingham.ac.uk

GENERAL SECRETARY: Professor Mark Fielder, School of Life Sciences, KingstonUniversity, Penrhyn Road, Kingston upon Thames, Surrey KT1 2EEemail: m.fielder@kingston.ac.uk

MEETINGS SECRETARY: Dr Andrew Sails, PHE Microbiology Services NewcastleLaboratory, The Medical School, Royal Victoria Infirmary, Newcastle NE1 4LPemail: andrew.sails@phe.gov.uk

TREASURER: Mr Steve Davies, Microbiology Department, Northern GeneralHospital, Herries Road, Sheffield S7 5AUemail: steve.davies@sth.nhs.uk

ORDINARY COMMITTEE MEMBER UNTIL JULY 2014

Dr Clare Taylor, School of Life, Sport & Social Sciences, Edinburgh Napier University,Sighthill Campus, Sighthill Court, Edinburgh, EH11 4BNemail: cl.taylor@napier.ac.uk

ORDINARY COMMITTEE MEMBERS UNTIL JULY 2015

Mr Mark Reed, Pro-Lab Diagnostics, 7 Westwood Court, NestonCheshire CH64 3UJemail: mreed@pro-lab.com

Dr Sally J Cutler, School of Health and Biosciences, University of East London,Stratford Campus, Romford Road, London E15 4LZemail: s.cutler@uel.ac.uk

Dr Nick Jakubovics, Oral Biology, School of Dental Sciences, Newcastle University,Newcastle upon Tyne NE2 4BWemail: nick.jakubovics@newcastle.ac.uk

Dr Samantha Law, NCIMB, Ferguson Building, Crabstone Estate, Bucksburn,Aberdeen AB21 9YAemail: s.law@ncimb.com

ORDINARY COMMITTEE MEMBERS UNTIL JULY 2016

Professor Valerie Edwards-Jones, School of Healthcare Science, The ManchesterMetropolitan University, John Dalton Building, Chester Street, Manchester, M1 5GDemail: v.e.jones@mmu.ac.uk

Dr Brendan Gilmore, School of Pharmacy, 97 Lisburn Road, Queen’s UniversityBelfast, Belfast, BT9 7BLemail: b.gilmore@qub.ac.uk

Dr Brian Jones, Pharmacy and Biomolecular Sciences, Moulsecoomb, Brighton, BN2 4GJ email: B.V.Jones@brighton.ac.uk

Professor John Threlfall, PHE Colindale, 61 Colindale Avenue, London, NW9 5EQ

CHIEF EXECUTIVE OFFICER: Philip Wheatemail: pfwheat@sfam.org.uktel: +44 (0)1234 326661

COMMUNICATIONS MANAGER: Nancy Mendozaemail: nancy@sfam.org.uktel: +44 (0)1234 350302

COMMUNICATIONS OFFICER: Clare Doggettemail: clare@sfam.org.uktel: +44 (0)1234 327679

MEMBERSHIP & FINANCE CO-ORDINATOR:Julie Wrightemail: julie@sfam.org.uktel: +44 (0)1234 326846

EVENTS ORGANIZER: Sally Hawkesemail: sally@sfam.org.uktel: +44 (0)1933 382191

ADMINISTRATOR: Julie Buchananemail: julieb@sfam.org.uktel: +44(0)1234 326661

executive committee

society office staff

contact pointSociety for Applied MicrobiologyBedford Heights, Brickhill Drive, Bedford MK41 7PH, UK.tel: +44 (0)1234 326661 ■ fax: +44 (0)1234 326678email: communications@sfam.org.uk ■ www.sfam.org.uk

FEATURES EDITORS:

Louise Fielding email: lfielding@uwic.ac.uk

Nick Jakubovics email: nick.jakubovics@newcastle.ac.uk

Ayuen Lual email: ayuen.lual@phe.gov.uk

Clare Taylor email: cl.taylor@napier.ac.uk

REGULAR CONTENT EDITOR:Louise Hill-King email: louise@hill-king.com

Microbiologist editorial group

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members

As many long-standing Members will know,the Society for Applied Microbiology(SfAM) was founded in 1931 and is the

oldest microbiology society in the UnitedKingdom. As well as facilitating an environmentfor furthering the science of microbiology by itsMembers, the Society has also always beenknown as friendly, promoting inclusivity andcordiality. Our current vision and missionstatements, and the values underpinning them tryto reflect these long-established aspirations. Inour vision statement:

“SfAM envisages a future where appliedmicrobiology research and development isstrong in the UK and beyond, andapplications of microbiology contributesignificantly to all global challenges facinghumanity, including infectious diseases; thechanging environment; sustainability of

energy, food, water andland resources; andeconomic growth.”

To this end, ourmission statementdeclares:

“This vision of SfAMwill be achieved bybeing the voice ofmicrobiology andadvancing, for thebenefit of the public, thescience of microbiologyin its application to theenvironment, humanand animal health,agriculture andindustry. SfAM willwork with sisterorganizations andmicrobiological bodies

to ensure that microbiology andmicrobiologists contribute to evidence-basedpolicymaking in the UK, Europe andworldwide. SfAM will build on a stronghistory of microbiology in the UK and willmove forward in step with the nextgeneration of microbiologists.”

The values underpinning these vision andmission statements are:

“SfAM is “The Friendly Society” and willalways offer value for money. We are modern,innovative and progressive; we valueintegrity, honesty and respect; and we seek topromote excellence and professionalism andto inspire the next generation ofmicrobiologists.”

The end of the year is an opportune momentfor us to reflect on developments over the last 12months, to review how well we are meeting ourobjectives and to look forward into next year.

Once again, we feel that SfAM has progressedduring 2013. If a learned society is to grow and

ceo’s andpresident’scolumnSfAM CEO Philip Wheat and President,Professor Martin Adams talk aboutthe vision and mission of the Society andreflect on past and future developments

develop it must always remain relevant to theMembers (and potential Members) it is there toserve, and meet their needs and expectations.One marker of whether this has been achieved isby looking at membership numbers. The totalnumber of Members at the end of 2012 was2,202. A conservative estimate of numbers forthe end of 2013 will be at least 2,400,representing an increase of 9% on the year. Thisincrease in membership numbers can be put intoa wider context by looking at the increase over alonger time period. So, for instance, if you lookat the membership number (1,220) at the end of2005 and compare this with the estimate for2013, it shows a very impressive increase ofnearly 97%.

It is also pleasing to report the success of twonew grants that were launched in 2013: theStudent Professional Placement Grant andthe PhD Studentship Grant. Both proved to bevery popular and the budgets for each have beenreached. Competition for the PhD Studentshipwas particularly intense and we are pleased toreport that Dr Dennis Linton (University ofManchester) and his nominated student DanielleWeaver were the successful applicants. The newStudent Professional Placement Grant alsoattracted some strong applications. It is designedfor students who have been awarded aprofessional work placement for over fourmonths. Two institutions were awarded grants in2013 — Public Health England and NottinghamTrent University — and a total of 17 students willbenefit as a result.

More generally, we estimate that in 2013 theSociety will have awarded at least £250000 ingrants to our Members. Competition for all theSociety’s grants has been very considerable thisyear and, though success rates remain high, wehave had to disappoint more people than usual.

Below: SfAM members in 1931

07

Martin AdamsPresident of the Society

Philip WheatChief Executive Officer

To give yourself the best chance of success, westrongly recommend that if you are going toapply for any SfAM grants in future you first readthe terms and conditions carefully and adhere todeadlines; applications must fully comply,otherwise they will not be considered.

Further good news for Members is that theExecutive Committee (EC) have once againdecided to retain the current membership fees;there has now been no membership fee increasefor over 10 years. Indeed, the EC have alsoagreed to continue the offer to existing FullMembers to take advantage of our ‘pay for twoyears and get the third year free’ scheme, ineffect lowering the membership fee to just over£33 per annum. If you include the additionalbenefits the Society has introduced over the lastfew years, this price, and indeed the standardmembership, offer terrific value for money.

As mentioned earlier, the Society alwaysendeavours to be inclusive for all its Membersand this includes encouraging under-representedgroups to become more involved. The Societyrecently introduced, within the ScientificMeeting Attendance Grant, the facility ofenabling new parents to claim childcare, shouldthe member (male or female) wish to attend ascientific meeting and need assistance withchildcare costs.

We are also pleased to report to Members thatat our (3 July) Annual General Meeting in Cardiff,Professor Christine Dodd (Food Sciences,University of Nottingham) was nominated (andaccepted by Members) as the next VicePresident of the Society. Christine will serve oneyear as the Vice President and will then beproposed as the next President at our annualmeeting in 2014. If the proposal is accepted,Christine will then become the second woman tohold the post out of the last four Presidents.

The year ahead sees a few changes to ournormal meetings schedule. The first meeting ofthe year is the Winter Meeting on 15 January2014. The topics covered will be “Foodcontamination: the food handler’s role” anda concurrent session covering “Biodefence”. Asin 2013, the meeting will be held at the RoyalSociety, London.

The first change to our normal schedule is inApril, when an extra meeting has been organized.This will be held in Manchester to celebrate thecentenary of the activated sludge sewagetreatment process, which was first developed byArdern and Lockett at the Davyhulme SewageWorks in Manchester. The meeting will be heldon the 1 April (pm) and 2 April at the nearby(up-wind) Lancashire County Cricket Ground.

Another change will be the Spring Meeting tobe held on the 30 April on the “Control ofinfection: current status and futureprospects”. Instead of the venue being atStratford-upon-Avon, this year it will be theHilton Hotel, Sheffield.

Finally, our Summer Conference has beenorganized in collaboration with the Med-Vet-NetAssociation. The meeting will take place from 30June to 3 July on the topic of “Zoonoses”. Thevenue is the prestigious Grand Hotel, Brighton. Afull delegate fee is only £250 (which includesthree nights hotel accommodation in the GrandHotel, most meals and full registration for themeeting). Demand is expected to be very high,so early booking at www.sfam.org.uk/summer ishighly recommended.

If you would like to attend any of ourmeetings, but do not have the funds to do so,why not apply for a relevant grant? If FullMembers submit an abstract (and it is accepted)for the Summer Conference they can apply for aPresident’s Fund award to enable attendance.In addition, if any Student Member wishes toattend, they should apply for a ConferenceStudentship where all their costs (with an upperlimit on travel costs) will be reimbursed. Fulldetails of all meetings, grants and studentshipscan be found by visiting www.sfam.org.uk.

Finally, it just remains for us to thank you allfor supporting the Society and to wish you all ahappy holiday period and a prosperous New Year.

08

features

interdisciplinary collaboration.Beyond scientific boundaries,

increasing the visibility of researchprovides a transparency that isnecessary to unlock the ivory tower ofscientific research within the publicarena. By cultivating the broad interestof the general public in science,researchers are now empowered toconsider ways to utilize their huge massand collective intelligence to acceleratescientific discoveries. This method is aform of “crowdsourcing”.

How do scientists design effectivecrowdsourcing projects?

Despite major advances incomputational systems and algorithms,researchers often remain reliant onmanual curation for fine-tuning analysisof complex datasets; with currentalgorithms producing a degree of falseor incomplete outputs. Manualintervention is essential to repair thesefalse outputs but this is extremely time-consuming. Crowdsourcing provides the

The 21st century scientist

The evolution of the Internet andthe explosion in social mediaportals has led to a dramatic shift

in the way scientific communities relayinformation and ideas, from traditionalunidirectional reporting tomultidirectional exchanges (Darling etal., 2013).

These online tools allow researchersto boost their professional visibilitywhilst sharing thoughts, opinions,articles and commentaries on varioustopics of interest. With at least 1 in 40scientists active on the micro-bloggingplatform Twitter, the benefits of anonline profile are far-reaching (Priem etal., 2012). For instance, many scientistshave found the use of social mediaoutlets effective in broadening interestin their research articles, as reflected inspikes in download rates (Terras, 2012).

With no geographical constraints onthese virtual communities and networks,scientists also often find these outletsconducive to the development of

Harnessing thecollectiveintelligencein response toChalara diebackof ash

means to utilize people power toaccelerate progress in these areas.However, to design effectivecrowdsourcing projects several keyquestions require careful consideration,such as: how can researchers motivatetheir target audience to participate in acrowdsourcing initiative? How do youreach the crowd? If targeting a non-specialist audience, how can researchersmould the required analysis into aninterface that can be broadlyunderstood? How will participants berecognized in future publications?

One way of capturing the interest ofthe general public is by integratinganalysis into an interactive game format.Games provide the opportunity to seeksolutions to scientific riddles inenjoyable, familiar frameworks. To date,several games have been developed bythe scientific community to addressspecific biological questions (Table 1).

Biogame is a diagnostic game whereplayers try to find malaria-infected cellsfrom multiple cell pictures (Mavandadi

09

et al., 2012). In MalariaSpot, playersmark malaria pathogens in a microscopyimage including white blood cells, withina limited time (Luengo-Oroz et al.,2012). Successful identifications givescores to players. The citizen sortproject developed an online game“Happy match” to classify photographsof organisms (Crowston & Prestopnik,2013). Playing EyeWire complementscomputational analysis for connectingneurons of the retina based onmicrographs. Foldit (Cooper et al.,2010) and EteRNA provideenvironments where players foldproteins to the correct shape or designRNAs through puzzles. In Phylo(Kawrykow et al., 2012) and Fraxinus(MacLean, 2013) players highlightdifferences in nucleotide sequencealignments to either flag potentialgenetic diversity or create moreaccurate alignments.

Particularly where projects are ofhigh interest to the general public, it isimperative that we harness their passion

and convert this into real contributionsto scientific progress.

The Facebook game FraxinusOne disease that has been met with

widespread anguish from the generalpublic is Chalara dieback of ash,commonly known as ash diebackdisease. The disease is caused by thefungus Chalara fraxinea whichemerged in Poland in the early 1990sand has since spread rapidly acrossEurope from east to west. In September2012, the first case of the disease innative woodland in the UK was reportedjust south of Norwich.

The vast media interest that ensuedreflects the very real threat that is posedto our 80 million ash trees here in theUK. For instance, in Denmark, the lossof up to 90% of the ash tree populationhas been attributed solely to ash diebackdisease.

With the ability to understand ouradversary paramount, and the cost andspeed of genome sequencing rapidly

decreasing, generating and publiclyreleasing sequence data is key toaccelerating research on emerging andre-emerging pathogens (Kamoun, 2012).In response, the OpenAshDieBackconsortium was set up, led by Norwichresearchers at The SainsburyLaboratory, The John Innes Centre andThe Genome Analysis Centre, andsupported by BBSRC.

The central goal of this project is togenerate and publicly release gene andgenome sequence data for the pathogenand host that can be analysed by theworldwide scientific community(http://oadb.tsl.ac.uk/; accessed23/09/2013). In addition, and in directresponse to the widespread concern ofthe general public, the Fraxinus gamewas conceived as part of thecrowdsourcing initiative.

By hosting Fraxinus on the Facebookplatform, participants automaticallysend invitations across their individualsocial networks when playing the game,to encourage competition between

Game

Fraxinus

Dizeez

EyeWire

BioGames

Phylo

MalariaSpot

GenESP

The Cure

Happy Match

EteRNA

Foldit

Year released

2013

2013

2012

2012

2012

2012

2012

2012

2012

2011

2008

URL

https://apps.facebook.com/fraxinusgame/

http://sulab.scripps.edu/dizeez/

https://eyewire.org

http://biogames.ee.ucla.edu

http://phylo.cs.mcgill.ca

http://www.malariaspot.com

http://sulab.scripps.edu/GenESP/fluid.htm

http://www.genegames.org/cure/

http://www.citizensort.org/web.php/happymatch

http://eterna.cmu.edu/web/

http://fold.it/portal/

Description

Puzzles. Sequencing alignments of ash-dieback pathogen genome

Quiz. Links of genes and disease

Mapping of connections between retinal neurons

Classification of malaria-infected cells

Puzzles. Sequencing alignments of human genome

Identification of malaria parasites

Quiz

Card game. Breast cancer

Classification of species

Puzzles. RNA design and structure prediction

Puzzles. Protein folding

Table 1. Games released as interfaces to scientific research for the general public

10

features

friends and family. With more than abillion active Facebook users(http://newsroom.fb.com/Timeline;accessed 23/09/2013), this provides asubstantial forum for the non-specialistaudience to contribute biologicallyrelevant analysis to the Fight BackAgainst Ash Dieback Disease.

Through the underlyingOpenAshDieBack research project, anabundance of genomic andtranscriptomic data was generated withthe aim to assess differences betweenvarious UK pathogen isolates and hostvarieties at the genomic level. Thisgenetic variation, in turn, can provideclues about how this pathogen may becausing disease and what makes aspecific tree variety potentially resistant.However, computational pipelines thatare commonly used to identify thesetypes of variation are notoriouslylimited. In contrast, the human eye ismuch better at recognizing these typesof patterns in large data sets.

In the Fraxinus game, players act tomanually identify or curate anycomputationally problematic sequencevariation in comparisons betweenpathogen isolates or host varieties. Thecorresponding reference genomeappears as a series of coloured leaves,each representing a single nucleotidewithin a defined region of the pathogenor host genomes. The task is to match aseries of short stretches of 21 colouredleaves from a second sample isolateagainst this reference genome sequence(Figure 2). Mismatches represent

sequence differences that are used todetermine the genetic relatednessbetween the given sample and thereference isolate. As users steal patternsfrom their “friends” to improve the scoreassociated with the alignment, thesequence variations are verified overand over again. This, in turn, providesrobust analysis of the variation that is

Figure 1. The integration of social media into scientific communicationAs social media has grown in popularity numerous tools have been developed that can be utilised by scientits to promotecommunication both within the community and with the general public. Clip art images used with permission of Microsoft

Figure 2. FraxinusThe aim is to match the 21 nucleotide stretches of sequence patterns from one sampleagainst the target pattern at the top of the screen, which represents a region of thepathogen or plant genome sequences. Each nucleotide is represented by a singlecoloured leaf and mismatches relate to important genetic diversity between thesample and either the pathogen or tree genomes. The arrow buttons allow eachpattern string to be moved left or right, while individual leaves can be moved,deleted or inserted with click-and-drag movements. As the match improves so doesthe “Pattern value” with players able to “Claim this Pattern” when they have thehighest score

identified, eventually outputting theanalysis to a database that feeds backinto the researchers’ analysis. With over36,000 visits from approximately 18,000unique visitors from 126 countrieswithin the first week of its release, thisgame has really captured the enthusiasmof the non-specialist audience. The gamecontains 10,001 datasets that have all

11

been played to some extent, with theanalysis currently being transformedinto real scientific results.

The power of the crowdThe Fight Back Against Ash Dieback

Disease is built on an effectivecrowdsourcing network, with world-renowned plant biologists andbioinformaticians at its core. To thisaim, various forms of media have beenused to promote engagement from awide demographic. For instance, Twitterand traditional media have been used tospread awareness of the GitHub datarepository amongst scientists toencourage their contribution to vitalannotation. As a result, the analysis ofgenomic and transcriptomic sequencesfrom the pathogen and ash tree hasrevealed many genomic features andrepertoires of transcripts that are highlyexpressed during the infection stage(http://oadb.tsl.ac.uk/?page_id=223;

■ Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D.,Popovic, Z., and Players, F. (2010). Predicting protein structures with a multiplayer onlinegame. Nature, 466, pp756−760.

■ Crowston, S., and Prestopnik, N. R. (2013). Motivation and data quality in a citizen science game: a designscience evaluation. 46th Hawaii International Conference on System Sciences (HICSS).

■ Darling, E. S., Shiffman, D., Cote, I. M., and Drew, J. A. (2013). The role of Twitter in thelife cycle of a scientific publication. Ideas in Ecology and Evolution, 6, pp32−43.

■ Kamoun, S. (2012). Genomics of emerging plant pathogens: too little, too late.Microbiology Today, p140.

■ Kawrykow, A., Roumanis, G., Kam, A., Kwak, D., Leung, C., Wu, C., Zarour, E., Players, P.,and Sarmenta, L. (2012). Phylo: a citizen science approach for improving multiple sequencealignment. PLoS One, 7, e31362.

■ Luengo-Oroz, M. A., Arranz, A., and Frean, J. (2012). Crowdsourcing malaria parasitequantification: an online game for analyzing images of infected thick blood smears. Journalof Medical Internet Research, 14, e167.

■ Maclean, D. (2013). Cutting edge: Changing the rules of the game. eLIFE, 2.

■ Mavandadi, S., Dimitrov, S., Feng, S., Yu, F., Sikora, U., Yaglidere, O., Padmanabhan, S.,Nielsen, K., and Ozcan, A. (2012). Distributed medical image analysis and diagnosis throughcrowd-sourced games: a malaria case study. PLoS One, 7, e37245.

■ Priem, J., Costello, K., and Dzuba, T. (2012). Prevalence and use of Twitter among scholars.

■ Terras, M. (2012). The impact of social media on the dissemination of research: results ofan experiment. Journal of Digital Humanities, 1, p3.(http://figshare.com/articles/Prevalence_and_use_of_Twitter_among_scholars/104629)

references

Diane G.O. Saunders (left) and Kentaro Yoshida (right)The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.

accessed 01/10/2013). Furthermore, inan effort to understand how thepathogen successfully infects ash trees,researchers have identified andclassified genes that encode potentialeffector proteins (http://oadb.tsl.ac.uk/?p=622; accessed 01/10/2013).Effector proteins are secreted by anarray of plant and animal pathogens tomanipulate host physiology and helpsuccessful colonization.

Engagement with the general publichas also been crucial to reporting casesof infected ash trees in the wild throughthe AshTag smartphone application,where users submit photographs ofpotentially diseased ash trees to helptrack its spread(https://www.ashtag.org/; accessed01/10/2013). Employing a combinationof social and traditional media is anextremely powerful approach thatguarantees to reach the broadest ofdemographics.

How will crowdsourcing beintegrated into scientific researchin the future?

Crowdsourcing will undoubtedlycontinue to increase transparencywithin the process of scientificdiscovery, whilst further promotinginterdisciplinary collaboration.Computational scientists have longrelied on discussion forums and datarepositories to communicate. With “bigdata” becoming commonplace in allareas of research, we can look to ourcomputational colleagues to continue todevelop forums that include benchbiologists and act as central transparentcross-disciplinary hubs.

The integration of social media hasenabled scientists to start to dissolvebarriers between research and thegeneral public. However, this isdependent on scientists embracing thefull power of the crowd, regardless ofthe perceived complexities such asissues of data “ownership”, complexityof authorship and the threat of beingscooped. These issues can often bemanaged if addressed in the designstage of a project.

With the non-specialist audienceforming a vital resource that can beutilized to accelerate scientificdiscovery, it is our responsibility toensure that these issues are dealt witheffectively to make the most of thepower of the collective.

The integration of gaming technologyto crowdsourcing initiatives enables thegeneral public to help scientificprogression whilst ultimately havingfun!

As we look forward, we envisage afuture where the largely untappedresource and collective intelligence ofthe general public is fully embraced inall aspects of research.

One continuing issue is how tomaintain long-term engagement fromthe crowd. This remains a challenge andwill require scientists to fully appreciateand be dedicated to crowdsourcingmethodology, with active feedback tothe crowd and releasing new andexciting updates to any gamingtechnology to maintain interest.

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order to achieve a high coverage.Clearly, for the UK programme, both ofthese are and were met, but there isanother crucial need. The vaccinerecipients, teenage girls and in thisinstance their parents who will need toconsent, need to be convinced of threethings. They must be convinced that thevaccine is needed to prevent seriousdisease, that it works and that it is safe.Mass media coverage played a key rolein the perception by the public of thedesirability and therefore, acceptance ofthe HPV vaccine. It is important toremember that the vaccine wasintroduced at a time when the MMRcontroversy still featured in both thevisual and printed media, and in blogson the Internet. However, lessons hadbeen learnt by public health authoritiesand the immunization providers ingeneral, in the importance ofcommunication and the importance ofcommunicating what the HPV vaccinewas, what it would prevent and why itwas worthwhile.

Communication of the HPV vaccinefaced some very significant hurdles, notleast of which was that it prevented asexually transmitted infection and wasgoing to be delivered to 12-year-oldgirls. The general public and indeed

many of the health providers, doctors,nurses, paramedics, knew very little ornothing at all about HPV and its role inthe aetiology of cervical cancer. If thevaccine was to be perceived asnecessary in the “fight against cancer”then public awareness of HPV, thedisease and the vaccine needed toincrease. The messages that had to becommunicated were:

1) HPVs were very common viruses. Most of us acquired infection at some point in our lives, but most of us developed immunity and cleared the infection.

2) There were many HPV strains but only a few caused cancer. All cervical cancers were caused by HPV, but two types, 16 and 18, were the most important causing more than 7 out of 10 of all cervical cancers.

3) The HPV vaccines prevented infection with 16 and 18, and prevented the pre-cancers caused by them, one of the vaccines also prevented genital warts caused by other HPVs 6 and 11.

4) Despite the efficacy of the vaccine,women still needed to have pap smears since 3 out of 10 cervix cancers were caused by HPVs not covered by the vaccine.

This was really complicatedinformation, particularly for TV newsand radio broadcasts, where aninterview lasting more than one or twominutes was a rarity. So, how werejournalists engaged in the story of HPVvaccines? How were they briefed? Andwas it successful?

Pharmaceutical companiesmanufacturing and marketing the twovaccines, Cervarix and Gardasil, clearlyhad a vested interest in raising theprofile of the virus, the disease and thevaccine. Their communication and PRdivisions provided press releases,convened media briefings, to whichjournalists both print and visual wereinvited, at which medical expertspresented information on cervicalcancer, its treatment, the opportunitiesfor prevention and HPV virology andimmunology. In addition, socialpsychologists emphasized theimportance of raising awareness and thelow levels of knowledge about the virusand the disease. Media briefings andpress releases were provided bycharities and non-commercialorganizations, particularly Jo’s Trust, a

In September 2008, the HPVimmunization programme wasintroduced into the UK national

immunization schedule. The vaccine wasbadged as an anticancer vaccine,targeting HPV 16 and 18, the cause ofmore than 70% of cervical cancers.Despite a very successful call/recallcervical cancer screening programme,which has reduced the incidents andmortality of the disease by more than50% since its introduction in 1987, thereare still in the UK about 2,800 cases and950 deaths each year from this disease.Cervical cancer screening detects thehigh grade pre-cancers (the obligateprecursors to frank invasive cancer)allowing effective treatment by excisionor ablation and it is estimated that about20,000 cases of high grade pre-cancersare treated each year, at least 50% ofwhich are HPV 16/18 related. The HPVvaccine was introduced to reduce thisheavy burden of disease.

Genital HPV infection is acquiredsoon after the onset of sexual activityand the programme therefore, targetsgirls who are 12−13 years’ old as theongoing cohort and had, for the firsttwo years, a catch-up cohort of girls14−18 years’ old. To achieve theobjective of reducing disease andinfection by the HPV types in thevaccine and to be cost-effective, itneeded to achieve a high uptake rate.This was particularly important for girlsfrom deprived groups who have thehighest rates of cervical cancer —cervical cancer is a poor woman’sdisease even in affluent countries.Health economic models estimated thatcoverage rates exceeding 80% would beneeded for cost effectiveness, quite a bigask for a vaccine delivered in threeshots at zero, one or two, and sixmonths to teenage girls who arenotoriously needle averse. In fact, theUK school-based HPV vaccinationprogramme has been a huge successwith 86.8% uptake nationally for allthree doses in the most recent statisticsfor the 12−13-year-old cohort in2011−12,https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/244479/HPV_AnnualVaccineUptake2011-2012.pdf.

Successful vaccine implementationrequires that the vaccines are publiclyfunded and that there is an effectivepublic health and immunizationinfrastructure for vaccine delivery in

HPVvaccinesand themedia

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UK charity set up to support women andtheir families affected by cervicalcancer. Pharmaceutical companies andthe information they transmit is oftendistrusted, so information for journalistsfrom non-commercial or academic andmedical organizations such as the RoyalColleges, were central to advocacy forthe HPV vaccine and therefore, centralto how the media constructed andframed messages about the vaccine andthe immunization programme.

A number of scholarly analyses ofhow the media reported on the HPVvaccine, both in the UK (Hilton et al.,2010) and elsewhere (Kelly et al.,2009), have been published. Hilton andcolleagues report that from January2005 to December 2008 in the UK, 344news articles in both tabloid andbroadsheet journals included coverageof the virus and the vaccine.Importantly, the factual content in thesearticles in both tabloid and broadsheetwas overall correct. Articles describedthe development of the vaccine, theintroduction into the UK immunizationprogramme, the epidemiology ofcervical cancer, the association of HPVwith cervical cancer, why teenage girlsshould be the group to be vaccinatedand also the nature of HPV transmissiongenitally, i.e., sexually. Importantly, anti-immunization messages and rhetoricappeared in less than 20% of articles.Nonetheless, it is interesting that anti-immunization sentiments about theprogramme were more likely to appearin serious newspapers such as TheGuardian and The Independent.

The HPV vaccine story was attractiveto sub-editors of newspapers and newsEditors for TV programmes sinceoverall, it had very good news messages.Many articles conveyed the message of ascientific breakthrough and, indeed, thedevelopment of HPV virus-like particleswas a breakthrough. The vaccines wereremarkably efficacious; 98% efficacyagainst disease is remarkable and foronce the hyperbole about scientificbreakthroughs was justifiable. One ofthe most important, although tragic,events that propelled cervical cancerand HPV into the public’s awarenesswas the “fight” with cervical cancer ofJade Goody, a 27-year-old reality TVstar. Goody’s progress through herdiagnosis, treatment and ultimately herdeath were played out in the full glare ofthe media. Through Jade Goody, theeffect of treatment and the physical

deterioration that accompanies terminalcancer was communicated in all itspainful and agonizing reality to thepublic. The effect on cervical cancerawareness, uptake of cervical cancerscreening and the HPV vaccine wassignificant. Importantly, Jade Goody’sstory and the use by the media of thestories of other young women withcervical cancer focused attention on theseriousness of the disease and the factthat it occurred in young women notjust the over 70s. The risk benefits ofvaccine versus disease were put inperspective in the public mind.

One recurring issue was the fact thatgenital HPV is a sexually transmittedinfection and it was regularly voicedfrom various groups that the HPVvaccine would encourage girls to bepromiscuous and become sexuallyactive. The sound bite that the HPVvaccine was “a sex jab” was tooattractive to be resisted by the media.These views were espoused mainly, butnot exclusively, by some religiousorganizations who no doubt weresincere in their anxieties. However, itidentified what is a problem inengagement with the media and that is,balanced reporting. In media terms,balanced reporting is providing aplatform for grossly different views andwidely differing expertise in the subjectin question, often with the aim ofengendering confrontation, a techniqueparticularly favoured for TV and radio.As a consequence, the outcome isusually unbalanced with a clearpolarization of views that are unhelpfulin the communication of importantissues about the vaccine or the disease.Concerns about the vaccine sexualizingyoung girls and encouraging promiscuityin adolescent girls were commonplace inthe media. This actually focusedattention on the behaviour of women,not men, and risked stigmatizing womenwith cervical cancer or any other HPVassociated cancer (Waller et al., 2007).It is a continuing issue with respect tothe HPV vaccine.

Another issue with respect to balancein the media, and this is not just forHPV vaccines, but for scientific andmedical news in general, is the relianceof media organizations on a limitednumber of scientists or doctors to whomthey go for comment on particularissues. Journalists simply look at theircontacts page on their smart phone andring up their favoured scientist for a

comment or background to a news story.Vaccine safety is a major factor in the

public mind and anti-vaccine blogsabound on the internet, but overall HPVvaccine safety was intelligently analysedand discussed in the mainstream media.Importantly, when a potentially serioussituation arose, public health authoritiesreacted rapidly and effectively,communicating information clearly andquickly to the media. In September2009, a young girl in Coventry collapsedand died soon after the first dose ofvaccine, the local public health doctorsand the Department of Health providedinformation immediately. Within 24hours the cause of death, a cancer in thechest totally unrelated to the vaccine,was identified and the involvement ofthe media and family by the publichealth authorities was an example ofhow to manage a potentially seriousadverse event.

Overall, the media coverage for theHPV vaccine was positive andundoubtedly contributed to itsacceptance by the general public, but weshould not be complacent, social mediaplays an ever-increasing role incommunication and effective use ofthose channels will be critical in theintroduction of new vaccines.

■ Hilton, S., Hunt, K., Langan, M.,Bedford, H., and Petticrew, M. (2010).Newsprint media representations of theintroduction of the HPV vaccinationprogramme for cervical cancer preventionin the UK (2005−2008). Soc. Sci. Med., Jan9.

■ Kelly, B. J., Leader, A. E., Mittermaier, D.J., Hornik, R. C., and Cappella, J. N.(2009). The HPV vaccine and the media:how has the topic been covered and whatare the effects on knowledge about thevirus and cervical cancer? Patient educationand counseling, 77(2), pp308−313.

■ Waller, J., Marlow, L. A., and Wardle, J.(2007). The association betweenknowledge of HPV and feelings of stigma,shame and anxiety. Sex Transm. Infect.,83(2), pp155−159.

references

Margaret StanleyDepartment of Pathology,University of Cambridge

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historicalPerspectives

MMR andthe media

The measles, mumps and rubella triple vaccine (MMR) wasintroduced in the UK in 1988. In 1998, a report in The Lancet(Wakefield et al., 1998) suggested that it might cause autism.

MMR has been in the headlines ever since, generatingcomplaints about inaccurate, sensational and naive media

reporting. Such controversy discourages scientists andclinicians from working with reporters. This article suggests,

among other things, that this may be counterproductive.

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The backgroundThe paper published in The Lancet concerned 12 children

with bowel and behavioural problems. At a press conferencecalled by the Royal Free Hospital, London, the lead author, DrAndrew Wakefield, surprised colleagues by advocating singlevaccines instead of MMR. The paper did not propose this, butthe conference was outside peer review. No one should havebeen surprised — the single vaccine message had alreadybeen distributed in a video news release.

The study was very small, but The Lancet was a leadinginternational journal, the Royal Free was a leading teachinghospital and such press conferences were not everydayoccurrences. Media interest was thus legitimate, but only TheGuardian, The Independent and the Daily Mail reportedthe study, with heavy emphasis on Government advice todisregard Wakefield.

Supported by various newspapers, including the DailyMail, Wakefield subsequently raised further questions aboutMMR. In 2001, Prime Minister Tony Blair precipitatedextensive media coverage by refusing to confirm if his babyson Leo had been vaccinated. He insisted that this was aprivate matter, only to generate speculation that he did nottrust his own Health Secretary’s advice. (It later emerged thatLeo had been vaccinated.) In 1998−9, 88% of children hadbeen immunized against measles, mumps and rubella. By2003−4, coverage had fallen to 80% and to 61% in someLondon areas. In 2004, a Medical Research Council supportedstudy concluded that there was no evidence linking MMR toautism (Smeeth et al., 2004).

In 2010, the General Medical Council struck Wakefield offthe Medical Register for serious professional misconduct overhis research methods. Ironically perhaps, it was the tenacityand persistence of a journalist, Brian Deer, who uncoveredWakefield’s extensive conflicts of interest and unethicalresearch practice. Deer’s work in The Sunday Times led tothe retraction of the 1998 Lancet report.

In 2013, the Department of Health launched a nationalcatch-up vaccination campaign in response to a rise inmeasles cases and an epidemic in Swansea. This was mostlyattributed to unprotected 10−16 year olds who were notvaccinated in the late 1990s and early 2000s.

The cultural contextThe media is alleged to create health scares in order to

provoke panic and banner headlines. There is sometimes sometruth in these accusations, but the head-on collision betweentwo of the biggest drivers in contemporary life — science andthe preoccupation with risk — has created what thesociologist Frank Furedi calls a culture of fear. Previousgenerations did not ask: should we eat beef? Do mobilephones cause brain cancer? Does living near high-voltagepower lines cause cancer? Should we take aspirin to avoidheart attacks? Should we vaccinate our children?

The media did not create this culture, but it does fuel it.However, the media is primarily reactive, not proactive. Astudy of medical journals in Scandinavia and the UK between1967 and 1991 found a highly significant increase in the useof the term ‘risk’ (Skolbekken, 1995). During the first fiveyears the number of ‘risk’ articles published was about 1,000– for the last five years there were over 80,000. The mediashould and did reflect this trend.

During the same period, the relationship between doctors

and patients changed, and people became increasinglyinterested in their health. Again, this was not because of themedia, but because of the impact of consumerism; self-helpgroups; the women’s liberation movement, which campaignedagainst the medicalization of everyday life; and the HIV/AIDSlobby, which provided a template for thousands of advocacygroups for patients with diseases ranging from depression tobreast cancer.

How has science, the biggest ever driver of change,changed? Ironically, researchers are still encouraged, as theywere half a century ago, to remain at the bench and let theirpublications talk for them. However, the MMR story is one ofmany examples exploding the myth that evidence speaks foritself. This may be especially true of vaccination, which hasbeen controversial ever since Edward Jenner’s pioneeringwork against smallpox in the early 1800s.

Research suggests that scientists and healthcareprofessionals assume that the public will make the righthealthcare choices if they are provided with information; thisseems logical, but imagine the following scenario. Jane is ayoung mother who, ironically, because of the success ofvaccination, has never seen a case of measles and knowsnothing about herd immunity. After reading a harrowingaccount about a seven-year-old who developed autism afterMMR, she cancels her child’s vaccination appointment.

Storytelling: statistics versus case historiesShould such emotionally charged stories be published? I

believe so because vaccination is not risk-free. There were 24Government awards to vaccine-damaged children totallingmore than £2 million in the 10 years to 2013/14 (Pressstatement, September 2013). However, context is everything.Critics complain that the media has highlighted the plight ofthe tiny minority of vaccine-damaged children withoutstressing the benefits of vaccination to millions of others; thedangers of measles, mumps and rubella; and the risks ofsingle vaccines which leave children unprotected for longerand involve several clinic visits. Yet, to quote one example, the£3 million campaign launched by the Government in 2001,the year of the Leo Blair controversy, to allay parents’ fearswas widely reported.

So what went wrong? Scientists, I believe, over-estimate thepower of statistics in mass communication. Research intowhat persuaded people to give to charity showed that thebetter statistically informed the potential donors were, the lessmoney they gave (Small et al., 2008). People who read a shortemotional appeal about an African child at risk from hungergave more than twice as much as those who just saw rawstatistics about threats to millions of Africans. Thus, thefacelessness of statistics, one of the great strengths in science,can be an abject failure in mass communication.

This presents a unique challenge in the MMR story. A mediacase history about a child who has been successfullyvaccinated would be profoundly dull — the child would be oneof millions. Conversely, a story about a “vaccine-damaged”child may be extremely powerful by virtue of being different.

If case histories carry more weight than statistics, why notadopt more of a storytelling approach, combining casehistories with statistics? Storytelling is an integral part ofevery culture. From a very young age we listen to and tellstories. Medical stories are encapsulated in case histories inboth medical education and medical journalism. Stories help

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■ Boyce, T. (2007). In Health, Risk and News: The MMR vaccine andthe media. Peter Lang Publishing, p77.

■ Illman, J. (2013). How dangerous is measles?http://www.ovg.ox.ac.uk/blogs/ojohn/how-dangerous-measles.Accessed: 2 October 2013.

■ Press statement to John Illman from the Department of Worksand Pensions. September 2013.

■ Skolbekken, J-A. (1995). The Risk Epidemic in medical journals.Social Science and Medicine, 40 pp291−305.

■ Small, D. et al. (2008). Can insight breed callousness? The impactof learning about the identifiable victim effect on sympathy.http://fraudresearchcenter.org/2011/02/can-insight-breed-callousness-the-impact-of-learning-about-the-identifiable-victim-effect-on-sympathy/.

■ Smeeth, L. et al. (2004). MMR vaccination and pervasivedevelopmental disorders: a case-control study The Lancet, 364(9438), pp963−969.

■ Wakefield, A. J. et al. (1998). Ileal-lymphoid-nodular hyperplasia,non-specific colitis and pervasive development disorder in children.The Lancet, 351 (9103), pp637−641.

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us — in a way that statistics cannot — to define ourselves andto compare ourselves with others, giving us a sense ofperspective about our place in the scheme of things.

No one recognized this better than the late children’sauthor Roald Dahl who declared: “It really is almost a crimeto allow your child to go unimmunized” (as quoted inIllman, 2013). Dahl knew the power of this sound bite. Hismessage was reinforced by the death of his own daughterfrom measles at the age of seven before a vaccine becameavailable. Hers is one of many powerful case histories.

Media case histories have their critics. For example,Professor Raymond Tallis complains about “the curse of themedia anecdote” and the habit of giving appealing individuals,with their moving stories, at least as much credence coverageas unappealing data; and of preferring faces to graphs andvox-pops to statistics. The anecdote may be an imperfect tool,but communication via p-values and confidence intervalsresonate with only a small minority. The real problem is not somuch the anecdote, as its misuse. The challenge is inachieving balance — easier said than done.

BalanceJournalists are trained to present both sides of the story in

the interest of objectivity and impartiality. This “balance” canwork well in a political story in which a Government ministerand an opposition spokesperson have equal time or space. Itmay not work so well in science stories in which two oppositeviewpoints are presented as if they are equal.

In Health, Risk and News: The MMR Vaccine and theMedia, Tammy Boyce complains that what is missing frommuch of the coverage is any sense of the weight of scientificevidence, which is firmly stacked on the side of the safety ofthe MMR vaccine (Boyce, 2007). When examining balance,she adds, it is not just a matter of counting which sideappeared more often. Balance is also influenced by the wayjournalists use scientific evidence. Boyce argues that byselecting equal numbers of scientists for and against MMR,journalists suggest that scientists and healthcare professionalsoverall are split on the issue when, in reality, the vast majoritysupport MMR. Mark Henderson’s The Geek Manifesto: WhyScience Matters, a must-read for any mass communicationstudent, also highlights this legitimate concern.

How does a journalist achieve “balance”? The answer inMMR may seem to be clear, but I have been puzzling over thisquestion for more than 30 years. The most difficult thing todo as a journalist is to present the evidence appropriately,especially in science which is inherently controversial. It iseasy enough to report what you are told, but this is rarelyenough. Evidence needs to be interpreted and spoken for, andit shifts and changes according to who is doing theinterpreting.

Working with the media — or not?In his widely acclaimed Bad Science, Dr Ben Goldacre

criticizes the media for poor reporting, especially over MMR.Much of what he says is true, but such attacks discouragescientists and clinicians from working with the media.Avoiding media questions for fear that they may exacerbatepublic alarm may open up the ground to commercial interestswho exploit fear for profit; and to pressure groups whodisseminate misleading information. Saying “no” to a mediainterview request may mean your view will go unrepresented

■ Furedi, F. (1997). Culture of Fear.

■ Henderson, M. (2012). The Geek Manifesto: Why ScienceMatters.

further reading

John IllmanJohn Illman Communications specializes inmedia and presentation skills training. A formerEditor of GP, he has also worked as medicalcorrespondent on the Daily Mail and HealthEditor on The Guardian. His sixth book,Handling the media: communication skills for

healthcare professionals, is due out early in 2014.

or be misinterpreted as meaning you have something to hide.For example, in 2003, Channel Five broadcast a

hagiographic drama about Wakefield, followed by a studiodebate with the man himself. Many experts on public health,paediatrics, autism and vaccination refused to take part. Thisprincipled, but misguided, stand robbed viewers of theauthority of those who were best able to challenge Wakefieldbefore a huge audience.

ConclusionCriticism of the media over its reporting in MMR is

justified, but healthcare professionals and scientists need torecognize that if they do not accept opportunities to representtheir views, they may be misrepresented or go unheard.

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Movie microbes under themicroscopeIt may surprise Microbiologist readers to learn that

microbes have been movie stars since the earliest days ofcinema. Between 1900 and 1930, moviegoers could watch

bacteria and other microbes cavort on the silver screen indozens of films with titles such as On the Trail of the Germs(1912) and The New Microbe (1912).

Louis Pasteur, Robert Koch and other scientists hadprovided convincing evidence for the germ theory of diseasein the later parts of the 19th century. The Lumière brothersheld the first public screening of projected motion pictures in1895. Not long afterwards, scientists began using the newtechnology as a research tool by attaching movie cameras tomicroscopes. And soon after that, film houses beganexhibiting these scientific films as public entertainment andfilm-makers began creating their own popular moviesfeaturing magnified microbes.

Cinema was an ideal technology for transformingphenomena that were invisible to the naked eye intospectacular visions. Films of microorganisms were popularbecause they invoked simultaneous reactions of attraction andrepulsion in audiences.

Films of microscopic organisms, such as documentary filmpioneer Charles Urban’s The Red Snow Germs (1905) andTyphoid Fever Germs (1905), allowed audiences to see forthemselves the previously invisible wriggling, writhing aliensthat actually lived around them, on them and in them. Yet,these films were also frightening because of the role thesemicroscopic monsters played in disease.

Many fictional films featuring microbes both reflected andfuelled this anxiety with titles such as The Dread of Microbes(1911) and Thomas Edison’s anti-tuberculosis propagandafilm The White Terror (1915).

One upshot of the public acceptance of germ theory wasthe frightening realization that germs were everywhere, ananxiety reinforced by early microbial movies. A large numberof these films featured scientist characters “discovering”microbes on everyday objects. Food was a particularlycommon subject as in The Unclean World (1903), TheScientist’s Lunch (1905) and A Bad Case (1909). In fact,one of the first acts of film censorship involved a film showingmicroscopic organisms found on food. In The Cheese Mites(1903), the normally invisible mites from a piece of Stiltoncheese were made to look like alien invaders when magnifiedon the screen. The film’s peek into this hidden world wasactually too revealing for some; the British cheesemakers hadthe film censored because they were afraid it would negativelyimpact the public’s perceptions of their product.

Many early films attributed germs with almost magicalproperties to influence human behaviour includingproblematic human behaviour such as alcoholism or violence.According to The Germ’s (1923) promotional literature, thefilm “Deals with a new scientific theory, that germs in theblood denote personality, and that serums can be foundthat will eradicate, these germs, after which a man cancommit no crime.” One of the most popular powers ascribedto microbes was the ability to act as an aphrodisiac as seen in

numerous comedies such as The Love Microbes (1907), TheKissing Germ (1909), The Love Germ (1912) and The Germin the Kiss (1914).

By 1930, film-makers began prominently featuring thebacteriologists who studied these killer pathogens in motionpictures. Paul de Kruif’s best-selling 1926 book The MicrobeHunters catalogued the scientific exploits of Louis Pasteur, PaulEhrlich, Walter Reed and other pioneering microbiologists. Asthe book’s title suggests, these “microbe hunters” were notfeeble old men working in dusty, darkened laboratories. Theywere idealistic adventurers who travelled to far off locales toestablish the truth about microbial dangers. de Kruif had alsoprovided scientific advice for Sinclair Lewis’ 1925 Pulitzer Prizewinning novel Arrowsmith, which followed the exploits of afictional scientist who studies a plague outbreak in an exoticcountry and who also conducts bacteriological experiments inthe backwoods of the American West.

The popularity of de Kruif’s and Lewis’ books made a filmadaptation of Arrowsmith inevitable. However, the criticaland financial success of 1931’s Arrowsmith paved the wayfor a host of films featuring stories of courageousbacteriologists.

Arrowsmith was entirely fictional, but the film had therealistic feel of a “bio-pic” which was also a popular genre atthe time. Studios figured that if they were successful with afictional bacteriologist, then why not make movies about real-life microbe hunters? Like Arrowsmith, The Story of LouisPasteur (1936) was not only a commercial hit, it was also acritical triumph — winning three Academy Awards as well asbeing nominated for best picture. Warner Brothers Studio alsotackled the story of Paul Ehrlich with 1940’s Dr Ehrlich’sMagic Bullet. The film hit a topical sweet spot for producersHarry and Jack Warner. It was an anti-fascist medical picturefeaturing a Jewish scientist whose research addressed animportant social problem (in this case syphilis).

Whether based on real-life scientists or entirely fictional,almost every bacteriologically based movie that followedborrowed narrative elements from Arrowsmith, especiallythose related to the theme of self-sacrifice. This led to films inwhich scientists travelled to disease outbreaks in exoticlocations or retreated to remote wildernesses in order toconduct experiments in isolation. In The Painted Veil (1934),for example, a bacteriologist travels to a remote part of Chinato study a cholera epidemic. While Green Light (1937) caststhe dashing Errol Flynn as a scientist who leaves the comfortsof the big city to work on a cure for Rocky Mountain spottedfever in the wilds of western Montana.

Film-makers also preferred real life scientists whoseresearch took place in dangerous locations such as YellowJack (1938), which focused on Walter Reed’s work in Cuba.These films also often featured an ethical dilemma reminiscentof Arrowsmith’s moral quandary about inoculating everybodywith his potential cure or maintaining his controlled study. InThe Crime of Doctor Hallet (1938), for example, themicrobiologist commits a crime in order to develop a vaccinefor red fever while working in the jungles of Sumatra.

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Although his indiscretion is the relatively uninteresting crimeof forgery, the film highlighted the lengths a microbiologistwas willing to go in order to save humanity from the menaceof infectious diseases.

We might think that there was nothing objectionable aboutstories of heroic scientists, but these films were not exempt fromcensorship. Some US state censor boards, for example, exciseda line of dialogue from The Crime of Doctor Hallet which hadimplied that we should be taking our moral cues from bacteria:“There’s something to be said for bacteria. They don’t wastetime moralizing. They eat-breed-die and kill.”

Animal experimentation was a major concern for censorsboth in the US and in the UK. There was also significantconcern within Hollywood’s censorship body at the time, theProduction Code Administration (PCA), about boycotts of TheStory of Louis Pasteur because Pasteur was considered the“father of vivisection.” In the UK, the film received extensivecuts before it could be shown for the same reasons.

The film facing the biggest struggle with censorship was DrEhrlich’s Magic Bullet. The PCA’s restriction on mentioningvenereal disease made things difficult for Warner Brothersgiven that the film was about Ehrlich’s discovery of Salvarsan,the first effective medical treatment for syphilis. In the end,the studio convinced censors that the final film was not aboutSalvarsan the drug, but about Ehrlich the man. By putting thefocus on the scientist and not the science, the story becamemorally acceptable to the censors.

The fad for movies about heroic bacteriologists did notsurvive the 1940s. During the Cold War, microbiologists wereno longer perceived as brave scientists attempting to cure

diseases; instead the public viewed them as mercenariesbetraying their scientific principles by using their knowledgeto create horrific biological weapons.

This change in public attitudes was reflected in the moviesand by the 1960s microbiologists had turned into movievillains. The success of the James Bond film Dr No in 1962led to a flood of imitation “superspy” films in the 1960s. Asurprising number of these films featured secret agents whosemission was to prevent the release of weaponized infectiousagents whether they were produced in the Soviet Union[Agent for H. A. R. M. (1966); The Nasty Rabbit (1965);Project X (1968)], by Western scientists [The Satan Bug(1965)] or within the lairs of “supervillains” [Billion DollarBrain (1967)].

One interesting exception to this period’s negativeportrayal of microbiologists was 1971’s The AndromedaStrain, where microbiologists are heroes using science tosave the world from the threat of killer microbes from space.

Two movies produced in the early 1970s, The Omega Man(1971) and The Crazies (1973), deviated significantly fromprevious bio-weapons films. The effect of these fictionalinfectious agents was not to cause illness or death. Instead,the weaponized pathogens in these films had a radicaltransformative effect on the hosts’ minds and bodies. In otherwords, infected people turned into monsters. Monster-spawning plagues became common in horror films of the nextseveral decades, especially when germs were combined withthe theme of GMOs as in Warning Sign (1985).

By the 2000s, microbial plagues had become whatradiation was in the 1950s, the go-to method for creating

Public acceptance of germ theory;microbes filmed via microscope forthe first time; fear of microbes,particularly in food; and magicalproperties of microbes

1895–1930

Courageous, adventurousmicrobiologists; and censorshipissues

1931–1940

The Cold War promotes distrust inthe motives of scientists andmicrobiologists are no longerdepicted as heroes

1941–1960

The Cheese Mites (1903)

The Unclean World (1903)

The Red Snow Germs (1905)

The Scientist’s Lunch (1905)

Typhoid Fever Germs (1905)

The Love Microbes (1907)

A Bad Case (1909)

The Kissing Germ (1909)

The Dread of Microbes (1911)

On the Trail of the Germs (1912)

The Love Germ (1912)

The New Microbe (1912)

The Germ in the Kiss (1914)

The White Terror (1915)

The Germ (1923)

Arrowsmith (1931)

The Painted Veil (1934)

The Story of Louis Pasteur (1936)

Green Light (1937)

The Crime of Doctor Hallet (1938)

Yellow Jack (1938)

Dr Ehrlich’s Magic Bullet (1940

19

David A. KirbyCentre for the History of Science, Technology, andMedicine, University of Manchester, ManchesterM13 9PL, UK

cinematic monsters. There have been dozens of recent filmswhere viral or bacterial “plagues” have broken out creatinghordes of zombies [28 Days Later (2002); Dawn of theDead (2004); World War Z (2013)], vampires [Blade(1998); I am Legend (2007); Daybreakers (2009)], andwerewolves [Underworld (2003)]. But these films areultimately not about infectious diseases. In today’s cinema,microorganisms predominantly serve as metaphors for a widerange of social issues such as conformity, consumerism andclassism.

Sensationalized news stories about killer E. coli andantibiotic resistant “superbugs” alongside dire warnings aboutemerging viruses in popular books, like Laurie Garrett’s TheComing Plague (1994), caused an increased anxiety aboutmicrobes in the 1990s. In the last two decades, there havebeen two prominent films that have specifically addressed theserious threat posed by emerging infectious diseases. In manyways Outbreak (1995) and Contagion (2011) recall theheroic microbiologist films of the 1930s with their plotsfeaturing virologists saving the world from devastatingpandemics. Both of these films raised awareness of emerginginfectious diseases far more than any popular science bookever could.

Movies have historically proven to be an effective way toconvince the public that a scientific issue needs more political,financial and scientific attention. In Lab Coats in HollywoodI refer to the connection between depictions of scientificdisasters in movies and increased public attention as the “WarGames effect” after the 1983 film.

Scientists believe that the more realistically a movie

catastrophe is visualized, the more motivated the public willbe to fund research in order to prevent the event fromoccurring in the real world. That is why many scientistswillingly signed up to act as science consultants on both thesefilms. Outbreak’s film-makers employed a host of leadingmicrobiologists as advisors including pioneering HIVresearcher Donald Francis. Contagion’s producers alsoutilized prominent microbiologist Ian Lipkin from ColumbiaUniversity as their main science consultant along withsignificant assistance from the CDC.

On Contagion, almost every member of the productionsought advice from the film’s scientific advisors from theactors to the scriptwriter to the set designers. Because of this,almost every scientific element in the film — the scientists,the laboratories, the source of the virus, the disease’sepidemiology and the response of the CDC — all feltauthentic.

Ultimately, the same “attraction and repulsion” that drewearly cinema audiences to films of microorganisms are thesame aspects that still fascinate modern audiences. Thetechnology of cinema adds an unreality to microbes thatmakes them appear both beautiful and disturbing at the sametime. For this reason, it is a good bet that we will continue tosee microbes in our movies for years to come.

Viral or bacterial plagues aredepicted but the microbes are nowmetaphors for wider social issues;and the hero microbiologists of the1930s have returned

1991–PRESENT

Super-spies prevent the release ofweaponized infectious agents

1961–1970

Infected people take on extreme,monsterous characteristics; geneticmodification is to be feared

1971–1990

The Satan Bug (1965)

The Nasty Rabbit (1965)

Agent for H. A. R. M. (1966)

Billion Dollar Brain (1967)

Project X (1968)

The Omega Man (1971)

The Crazies (1973)

Warning Sign (1985)

Outbreak (1995)

Blade (1998)

28 Days Later (2002)

Underworld (2003)

Dawn of the Dead (2004)

I am Legend (2007)

Daybreakers (2009)

Contagion (2011)

World War Z (2013)

20

public engagement

Joanna VerranManchester MetropolitanUniversity

■ Verran, J. (2013). The Bad BugsBookclub: science, literacy and enjoyment.J. Microbiology and Biol. Education, 14,pp110–112.

references

Bad BugsBookclub:5 years on

April 2009: National Science andEngineering Week marked thelaunch of the Bad Bugs Bookclub.

SfAM sponsored the screening of the filmOutbreak in theMammal Hall at theManchester Museumand subsequently alsohosted theaccompanyingdiscussion of thenovel The Hot Zoneby Richard Preston, ina hospitable bar inManchester. So in 2014we will be celebratingfive glorious years!

The Bad BugsBookclub comprises agroup ofmicrobiologists andnon-microbiologists(scientists and non-scientists). We read anddiscuss novels where infectious diseaseforms part of the plot. Since 2009, wehave met around six times each year,talking about 27 different books from allgenres: science fiction, horror, crime,classic, romance, historical and factual.Notes from every meeting are posted,with accompanying reading guides, onour website:www.hsri.mmu.ac.uk/badbugsbookclub.

There have been breakaway meetingsof the Bookclub at conferences (e.g.,ASM Conference on UndergraduateEducation; SfAM Summer Conferenceand FEMS Congress), and we have alsohosted accompanying events whereappropriate, often with funding support(for example, from SfAM and the Societyof General Microbiology, as well as fromother sources such as the ManchesterBeacon for Public Engagement). Theseevents have included community quiltmaking on World AIDS Day (2009 and2011), a musical tea party for WorldMalaria Day (2010), guided walks (forexample, around Eyam the plaguevillage and the Manchester of MaryBarton) and a series of film screenings.

The novel tells the story of TyphoidMary and really fleshes out the briefcaptions present in virtually allmicrobiology textbooks. The novel alsodescribes the living conditions, socialstrata and prejudices prevalent in NewYork at the beginning of the 20thcentury. It is easy to source historicalinformation about Typhoid Mary, thedisease, its current epidemiology andresearch, thus ‘hard science’ is accessedthrough the softer approach of apopular novel.

On the ‘literature’ side, I have madelots of friends at MMU’s Writing School,and have even taken a couple ofmodules on Gothic literature andCreative Writing! Even more terrifying, Iam also speaking at The TimesLiterature Festival in October, at anSGM-sponsored event (about ‘dirt’).

I wish that I were better at usingsocial media to encourage moreengagement of a wider audience. Iwould love to have other readerstweeting about our current book, andother Bookclubs using our books andreading guides, and contributing to ourdiscussions. Perhaps that can be myresolution for the next five years!

Our audienceshave also diversified.Undergraduatestudents were alwaysan intendedaudience and somehave hostedBookclub meetingsas part of theirfinal year projectwork. We alsointroduced a seriesof Bookclubmeetings into thesecond yearmedical

microbiology module tutorialprogramme (2012−2013), and wecapitalized on the prevalent interest invampire and zombie novels to conveyprinciples of infectious disease tochildren, teachers and families via theManchester Children’s Book Festival(2010, 2012) and the ManchesterGothic Festival (2013).

Personally, I have learnt so muchmore about microbiology — andliterature — through the Bookclub, but Ialso now appreciate that the ‘generalpublic’ is less aware of some aspects ofmicrobiology that I thought were almostcommon knowledge. It has been sointeresting to consider and clarifymisunderstandings during ourdiscussions, and to relate aspects of theplots to scientific principles ofmicrobiology and current epidemiologyof the different diseases described in thenovels.

For each book, we also consider howthe subject matter might be of value toundergraduate students — fordiscussion or for extension work. Forexample, at our most recent meeting, weread Fever by Mary Beth Keane (2013).

21

news

bioFocusMark Downs gazes into his crystal ball to view the Societyof Biology in 20 years

www.societyofbiology.org

Dr Mark Downs, PhD, FSBChief Executive, Society of Biology

Crystal ball gazing is a black art according to many.Those who look into the future to predict what mightbe, regularly get it wrong. After all, there is rarely

much application of science in the process and, where thereis, through good modelling, controversy oftenremains. Climate change is the obviousexample. For most, the future is simpleguess work or at best “educated” guesswork. It’s thus with sometrepidation that I try to answer thequestion asked frequently byMembers: “where do you seethe Society in 20 years’time?” As with all thesequestions, identifying thevariables is difficult enough,let alone their interaction,but for broad businessplanning purposes and theirresistible need to offer aview I’ll try to pen somethoughts.

Firstly, it is worth stressingthat the future of any umbrellaorganization is intimatelyconnected to the fate of itsmembership. After a fairly stable period,the next 10, and certainly 20, years areuncertain territory for many professional bodiesthat rely on publishing income to support their broadercharitable activity. Open access policies, of course, arecritical to this. The debate is often focused on the UK, withResearch Councils, The Higher Education Funding Councilfor England (HEFCE) and the Wellcome Trust driving theagenda. But, with most papers originating outside of the UK,it is likely to be the policies in North America and Asia thatdetermine the real impact on learned society publishers. Inthe short term, as open access and subscription fees co-exist, incomes may well rise whilst 10 years out it is likelythat many societies will see some decline in revenue. But theunderlying issue here is that technological advances are

creating new ways of communicating and using scienceinformation, and we have to find new ways of working to getthe best from these.

In my view, however, a key factor for the Society ofBiology 20 years on, will be how willing the life sciencessector has been to pool core functionality, and move towardsa more integrated approach to delivering membershipservices and support. There is often talk of mergers withinthe sector but this is far from the only option, and a mixedeconomy of continued independence and growth, contractionfor some and shared services for others are all likely. But,there will have to be some restructuring, as there has beenfor both chemistry and physics. With mounting pressure onall organizations to improve efficiency and drive down costs,it can no longer be sustainable for the biology sector to havemultiple membership service teams or the generic educationor policy work many of us undertake duplicated acrosssocieties. We also need to better reflect the way modernscience works where cross-discipline and multi-disciplineteams are the norm. There are strong and divergent views onthe need to maintain specialisms and consensus has not beenreached. But the debate is ongoing and we can’t ignore it.

To a large extent, individual memberships will drive theagenda. From the individual’s perspective it surely makessense to have one system and one bill for membership of

societies, allowing those with multiple interests asingle port of call? That doesn’t imply that all

the specialist services and communitiesassociated with sub-disciplines need

to disappear or give up anyindependence. But it could

improve efficiency for everyoneallowing more funds to bedirected towards support forindividual areas.

There is also politicalpressure to bring the lifesciences closer together. Asingle and strong voice forbiology is something that isalready bringing benefits,

allowing a coherent messageto be given to ministers and

the media with biology,chemistry, physics and maths

sitting at the same table arguingcollectively for the value and

contribution of science.I was inspired to hear James Burke on

Radio 4 recently, whom I’m sure many willremember for his engaging science TV programmes in the

1970s and 1980s. He was once asked to look 20 years intothe future and was scarily accurate in his predictions on theuse of technology, especially the information highway. As anavid viewer, I’m hoping I’ll have similar luck.

22

publications

The academic publishingenvironment is markedly morecomplex than in the years gone

by: mandates for both funded andunfunded open access areproliferating, and authors are oftenconfused by their options andobligations. Since the publication ofthe Finch Report last summer, therehave been numerous enquiries,debates and discussions on thesubject of open access, both ‘gold’(i.e., pay-to-publish services offeredby journals such as MicrobialBiotechnology orMicrobiologyOpen, or by theOnlineOpen option available for JAMand LAM) and ‘green’ (i.e., depositof the accepted manuscript in anonline repository), and what openaccess means for libraries,researchers, societies, universitiesand the UK economy.

Research Councils UK (RCUK)funds approximately 50% of UKresearch. Their current open accesspolicy applies to ‘peer-reviewed researcharticles...which acknowledge Research Councilfunding, that are submitted for publication from1st April 2013’, http://www.rcuk.ac.uk/documents/documents/RCUKOpenAccessPolicy.pdf. The policy clearly states thatdedicated funding for article processing charges(APCs) is provided in the form of block grantsspecifically allocated for publication charges,rather than research, which in turn hasnecessitated universities formulating their ownopen access policies, policies for distributing andmanaging the RCUK block grants, andcommunication plans aimed at helping theirresearchers answer a seemingly simple question:‘what do I have to do?’

In order to comply with RCUK’s definition of‘gold’, a journal must provide ‘via its ownwebsite, immediate and unrestricted access to thefinal published version of the paper, which shouldbe made available using the Creative CommonsAttribution (CC BY) licence’. This specific‘unrestricted’ open access license is required byboth RCUK and the Wellcome Trust, and allowsothers to modify, build upon and/or distribute thelicensed work, including for commercialpurposes, as long as the original author iscredited. Unless mandated to adopt CC BY,

authors might be well advised to considerpublishing under an alternative license that makesmore provision to safeguard their rights andlimits the use of an article by other parties tonon-commercial uses (for example, CC BY-NC orCC BY-NC-ND).

Although the wording of the initial RCUKpolicy favoured ‘gold’ open access over the fall-back option of ‘green’, the revised policy andsupporting guidance does make clear that ‘Thechoice of route to open access remains with theresearchers and their research organizations and,where funding for APCs is unavailable during thetransition period, longer embargo periods [i.e.,12 months rather than RCUK’s preferred sixmonths] will be allowable.’ In other words, anauthor may still comply with the RCUK policywithout paying a fee. The ‘Decision Tree’prepared by the Publishers Association representsa useful summary of what this all means inpractice (Finch et al., 2012).

At the time of writing, the House of CommonsBusiness, Innovation and Skills Committee Report(published September 2013) has concluded that‘The Government’s committed and proactivestance to increasing access to published researchfindings is admirable, as is its desire to achievefull open access. Gold open access, at scale, is a

journalNewsOpen access, a primer for UK authors

Open Access flowchart

Research publicly funded?

Yes No

No

No

Yes

Yes

Gold OA option availablefrom your publisher?

Are APC fundsavailable from

research funder?

Green OA after 6months (AHRC / ESRC

after 12 months)

Immediate Gold OAGreen OA after 12–24 months

23

Vicky JohnsonAssociate Editorial Director, Wiley,Research Communications, LifeScience

■ From the Publishers Association’s paper, ‘Finch,Willetts, RCUK, Green OA, and embargoes’ (2012).

references

desirable ultimate goal’, however, ‘The majormechanism of transition must be green openaccess, specifically through strong immediateself-archiving mandates set by funders andinstitutions, either as a funding condition or tiedto research assessment as appropriate’,(http://www.publications.parliament.uk/pa/cm201314/cmselect/cmbis/99/9902.htm).

The Higher Education Funding Council ofEngland (HEFCE) has begun its formalconsultation process on open access andsubmissions to the Research ExcellenceFramework (REF) post-2014, though conclusionsare yet to be drawn from submissions to that.

Although seemingly stepping back fromglimmering ‘gold’, BIS’ conclusions are perhapsmore in line with policies elsewhere around theglobe, which tend towards the unfunded ‘green’option. The tricky combination of unfundedmandates and short embargo periods, such asRCUK’s preferred six months, makes many STEM(science, technology, engineering andmathematics) journals, and societies whoseactivities rely on revenues received from thosejournals, nervous: ‘green’ open access relies onthe structure and organization provided bysubscription journals, which are unlikely tosurvive if libraries cancel their subscriptions tothose journals because the content is availableelsewhere (http://www.publishingresearch.org.uk/documents/ALPSPPApotentialresultsofsixmonthembargofv.pdf ).

It awaits to be seen what revision, if any, willbe made to the RCUK open access policyfollowing the BIS report and what other mandatesmay emerge, but the one conclusion that can bedrawn with certainty is that there is much morediscussion to be had in both the funded andunfunded open access debates.

Highlighted Articlesfrom the SfAM journals

Journal ofAppliedMicrobiology

Antimicrobial activityof phenoliccompoundsidentified in wildmushrooms, SARanalysis and dockingstudies.M. J. Alves et al.

Although the antimicrobial activity of extracts fromseveral mushroom species has been reported,studies with the individual compounds present inthose extracts are scarce. In this report, theantimicrobial activity of different phenoliccompounds identified and quantified in mushroomspecies from all overthe world wasevaluated.Furthermore, astructure-activityrelationship (SAR)analysis andmolecular dockingstudies were performed, in order to provide insightinto the mechanism of action of potentialantimicrobial drugs for resistant microorganisms. Itwas identified that phenolic compounds could beused as antimicrobial agents, namely against somemicroorganisms resistant to commercial antibiotics.bit.ly/JAM-Alves

Zinc as an agent for the prevention of biofilmformation by pathogenic bacteria.C. Wu et al.

Biofilm formation is important for the persistenceof bacteria in hostile environments. Bacteria in abiofilm are usually more resistant to antibiotics anddisinfectants than planktonic bacteria. The team atUniversity of Montreal, Canada, previouslyreported that low concentrations of zinc inhibitbiofilm formation of Actinobacilluspleuropneumoniae. This study evaluates the effectof zinc on growth and biofilm formation of otherbacterial swine pathogens. It found the antibiofilmactivity of zinc could provide a tool to fightbiofilms, and the non-specific inhibitory effect maywell extend to other important human and animalbacterial pathogens.bit.ly/JAM-Wu

For more information about Journal ofApplied Microbiology, visitwww.sfam.org.uk/JAM

journalWatchNews about the Society’s journals

The latest micropod is now online. This edition on'Open access publishing' features; SfAM's Phil Wheat,Deborah Kahn from BioMedCentral, and JenniferMcLennan at eLife, discussing what open accessmeans for the scientific community. It is availableonline at: http://www.sfam.org.uk/en/news-features/micropod.cfm/open-access-publishing.

OA podcast

24

publications

Letters in Applied Microbiology

Antimicrobial efficacy of liposome-encapsulated silver ions and tea tree oilagainst Pseudomonas aeruginosa,Staphylococcus aureus and Candida albicans.W. L. Low et al.

The activity of alternative antimicrobial agentssuch as tea tree oil (TTO) and silver ions (Ag+) withmultiple target sites impedes the development ofantibacterial resistance and might be useful inimproving the current treatment strategies forvarious chronic wound infections. Results showthat encapsulating silver (as the ion Ag+) and teatree oil (singly and in combination) in a controlledrelease liposomal carrier system can improve theirantimicrobial efficacy as well as reduce theeffective concentration required. These findingsmay impact on the problems of agent toxicitycaused by the need for high effective doses, ormicrobial resistance where long-term application isrequired.bit.ly/LAM-Low

Microbial diversity and prevalence offoodborne pathogens in cheap and junkfoods consumed by primary schoolchildren.M. J. Kim et al.

Food safety is especially important for children, butonly limited information is available about themicrobiological quality of cheap and junk foodsthat are consumed frequently by primaryschoolchildren (e.g., dried cakes, candies andchocolates). The present study investigated themicrobial quality of cheap and junk foods, and ourresults indicate that these foods are a potentialhealth risk for children, therefore, deeper concernabout the safety of these foods and effectivecountermeasures should be established to improvetheir microbiological safety. The present study maycontribute to the development of an appropriatechild food safety management system.bit.ly/LAM-Kim

For more information about Letters inApplied Microbiology, visitwww.sfam.org.uk/LAM

Microbial Biotechnology

Prebiotics, faecal transplants and microbialnetwork units to stimulate biodiversity of thehuman gut microbiome.P. Van den Abbeele et al.

Current society practices contribute to a decreasedmicrobial diversity of the human gut microbiome,thus disturbing the intimate association betweenhumans and the gut microbes. In this context, theauthors review existing (prebiotic) and novel

(faecal transplants, key microbial network units)approaches to manage the human gutmicrobiome.bit.ly/MBT-Abbeele

The SuperChip for microbial communitystructure and function from all environments.T. C. Hazen.

We have the technological capability to produce aSuperChip that would provide detailed analysis ofany sample for bacteria, archaea, viruses, fungi,microalgae, protists, etc. It would require puttingtogether a multidisciplinary, multi-institutional,multinational team but its applications and utilitywould truly be universal for all types of samples.bit.ly/MBT-Hazen

For more information about MicrobialBiotechnology, visit www.sfam.org.uk/MBT

EnvironmentalMicrobiology

Methane, microbesand models:fundamentalunderstanding of thesoil methane cyclefor futurepredictions. L. Nazaries et al.

Methane is an important greenhouse gas andmicrobes in the environment play major roles inboth global methane emissions and terrestrialsinks. However, a full mechanistic understandingof the response of the methane cycle to globalchange is lacking. Here, the authors synthesizerecent knowledge on soil microbial andbiogeochemical process, and the impacts ofclimate change factors on the soil methane cycle.They also identify the research gaps in each of thetopics identified above, provide evidence whichcan be used to demonstrate microbial regulationof the methane cycle and suggest thatincorporation of microbial data from emerging -omic technologies could be harnessed to increasethe predictive power of simulation models.bit.ly/EMI-Nazaries

Antimicrobial use in aquaculture re-examined:its relevance to antimicrobial resistance andto animal and human health. F. C. Cabello et al.

Approximately 80% of antimicrobials used inaquaculture enter the environment with theiractivity intact where they select for bacteria whoseresistance arises from mutations or moreimportantly, from mobile genetic elementscontaining multiple resistance determinants

25

Melissa McCulloch Wiley-Blackwell

transmissible to other bacteria. Such selectionalters biodiversity in aquatic environments and thenormal flora of fish and shellfish. The commonalityof the mobilome between aquatic and terrestrialbacteria, together with the presence of residualantimicrobials, biofilms and high concentrations ofbacteriophages, where the aquatic environmentmay also be contaminated with pathogens ofhuman and animal origin, can stimulate exchangeof genetic information between aquatic andterrestrial bacteria. Excessive use of antimicrobialsin aquaculture can potentially negatively impactanimal and human health as well as the aquaticenvironment and should be better assessed andregulated.bit.ly/EMI-Cabello

For more information about EnvironmentalMicrobiology, visit www.sfam.org.uk/EMI

EnvironmentalMicrobiologyReports

Assembly-freemetagenomicanalysis reveals newmetabolic capabilitiesin surface oceanbacterioplankton. H.Luo and M. A. Moran.

This study uses a recently developedcomputational method to confidently assignmetagenomic reads to microbial clades withoutthe requirement of metagenome assembly, bycomparing the evolutionary pattern of nucleotidesequences at non-synonymous sites betweenmetagenomic and orthologous reference genes.The authors found evidence for new, ecologicallyrelevant metabolic pathways in several lineages ofsurface ocean bacterioplankton using the GlobalOcean Survey (GOS) metagenomic data, includingassimilatory sulfate reduction and alkalinephosphatase capabilities in thealphaproteobacterial SAR11 clade, andproteorhodopsin-like genes in the cyanobacterialgenus Prochlorococcus. These findings raise newhypotheses about microbial roles in energy fluxand organic matter transformation in the ocean.bit.ly/EMR-Luo

Bacterial communities associated withMicrocystis colonies differ from free-livingcommunities living in the same ecosystem. B. Parveen et al.

The search for a better understanding of whycyanobacteria often dominate phytoplanktoncommunities in eutrophic freshwater ecosystemshas led to a growing interest in the interactionsbetween cyanobacteria and bacteria. Against this

background, we studied the location of bacteriawithin Microcystis colonies, and compared thestructural and phylogenetic diversity of Microcystis-attached and free-living bacterial communitiesliving in the same French lake, the Villerestreservoir. Our findings suggest that Microcystiscolonies constitute a distinct habitat for bacterialiving in freshwater ecosystems, and that directand indirect interactions (cell lysis, nutrientrecycling, etc.) may occur between them insidethese colonies. bit.ly/EMR-Parveen

For more information about EnvironmentalMicrobiology Reports, visitwww.sfam.org.uk/EMIR

About SfAM journals

Journal of Applied Microbiology

Journal of Applied Microbiology publishesresearch and review papers on all aspects ofapplied microbiology; including environmental,food, agricultural, medical, pharmaceutical,veterinary, taxonomy, soil, systematics, waterand biodeterioration.

Letters in Applied Microbiology

Letters in Applied Microbiology provides for therapid publication of short, high quality papersin the broad field of applied microbiology.

Microbial Biotechnology

Microbial Biotechnology publishes papers oforiginal research reporting significant advancesin any aspect of microbial applications,including biotechnologies related to chemicals,pharmaceuticals, energy, mining, materials,agriculture, food and environmental protection.

Environmental Microbiology

Environmental Microbiology provides a highprofile vehicle for publication of the mostinnovative, original and rigorous research in thefield. The scope of the Journal encompassesthe diversity of current research on microbialprocesses in the environment, microbialcommunities and microbial interactions.

Environmental Microbiology Reports

Environmental Microbiology Reports (EMIR)shares the same scope as EnvironmentalMicrobiology (EMI). This journal is availableonline only and holds compact research papersas an alternative to the full research paperspublished by EMI.

26

publications

In the 35th of a series of articles about statistics for biologists, Anthony Hilton &Richard Armstrong discuss:

Are the data log normal?

StatNote 35at least in the early stages and result in a size frequencydistribution of thalli that may be fitted by a log-normal model(Armstrong, 2013). This StatNote describes fitting the log-normal distribution with reference to two scenarios: (1) thefrequency distribution of bacterial numbers isolated fromcloths in a domestic environment and (2), the sizes oflichenized ‘areolae’ growing on the hypothallus ofRhizocarpon geographicum (L.) DC.

Scenario 1: Bacteria isolated from clothsA study was carried out to determine the degree of

bacterial contamination on dishcloths collected from domestickitchens (Hilton & Armstrong, 2005a). A total of 51 ‘in-use’dishcloths were collected from the kitchens and the aerobiccolony count from each material determined in the laboratory.As bacteria grow exponentially on the cloths, symmetricalvariation between cloths could result in a log-normaldistribution. The distribution of the data is shown in Figure 1.In StatNote 1, this distribution was tested for normality and itwas concluded that data exhibited a marked deviation from anormal distribution.

Scenario 2: Size of areolae in the lichen R.geographicum

The crustose lichen R. geographicum comprises yellow-green lichenized areolae which develop and grow inassociation with a non-lichenized fungal hypothallus(Armstrong, 2013). The areolae contain cells of the unicellulargreen alga Trebouxia and although they frequently maintaintheir individuality, they largely cover the surface of the fungalhypothallus. The areolae are highly variable in shape andmorphological differences between them may be attributableto their location on the thallus (Runemark, 1956). Hence,areolae that develop on the marginal hypothallus as itadvances (‘primary’ or ‘pioneer’ areolae) are generallypunctate or verrucose (warty), while those in the centre of thethallus (‘mature’ or ‘secondary’ areolae) have a more complexmorphology and are often angular or lobed. Areolae appear togrow exponentially on the surface of the fungal hypothallusand to be highly variable in size (Armstrong, 2013), whichsuggests a log-normal distribution may fit their sizedistribution.

Twenty-three thalli of R. geographicum, 0.5–2.4cm indiameter, growing on a south-facing slate cliff at a maritimesite were studied. Each thallus was photographed in its

Introduction

In many of the StatNotes described in this series, thestatistical tests assume the data are a random sample from anormal distribution (StatNote 1, Hilton & Armstrong,

2005a). These StatNotes include most of the familiar statisticaltests such as the ‘t’ test (StatNote 3, Hilton & Armstrong,2005b), analysis of variance (ANOVA) (StatNote 30, Hilton &Armstrong, 2012) and Pearson’s correlation coefficient (‘r’)(StatNote 14, Hilton & Armstrong, 2008). Nevertheless, manyvariables exhibit a more or less ‘skewed’ distribution. A skeweddistribution is asymmetrical and the mean is displaced either tothe left (positive skew) or to the right (negative skew). If themean of the distribution is low, the degree of variation largeand when values can only be positive (Limpert et al., 2001), apositively skewed distribution is usually the result. Manydistributions have potentially a low mean and high varianceincluding that of the abundance of bacterial species on plants(Hirano et al., 1982), the latent period of an infectious diseaseand the sensitivity of certain fungi to fungicides (Romero &Sutton, 1997). These positively skewed distributions are oftenfitted successfully by a variant of the normal distribution calledthe log-normal distribution (Hattis & Burmaster, 1994; Limpertet al., 2001).

Both the normal and log-normal distributions result frommany factors acting independently but without any singlefactor having a dominant influence. If the effects of thedifferent factors are ‘additive’, i.e., one would have to addtogether their individual effects to achieve the final ‘result’,then the data would be fitted by a normal distribution. If,however, effects are ‘multiplicative’ and therefore, have to bemultiplied together to achieve the final result, then theresulting distribution will also be log normal. Exponentialgrowth of a quantity in which variation is symmetrical, willalso result in a log-normal distribution. For example, if themean number of bacteria present in a culture is 1 x 106 andvariation is symmetrical, 1 cell division more or less will yield2 x 106 or 5 x 105 bacterial cells. The resulting range ofvalues achieved by sampling will be asymmetrical, i.e.,multiplied or divided by 2 around the mean and thedistribution will be skewed (Limpert et al., 2001). In addition,the size and age structure of many plant populations (Limpertet al., 2001) and the growth of fungal colonies on artificialmedia (Righelato, 1975) frequently follow a log-normaldistribution since exponential growth is likely to be involved.Similarly, the growth of symbiotic lichens may be exponential

27

entirety using a Canon IXUS-70 digital camera incorporating a12x zoom lens. A scale measure was placed next to eachthallus. The size of areolae was estimated using a PC and‘Image-J’ software developed by the National Institute ofHealth (NIH), Bethesda, USA and available as a free download(Syed et al., 2000; Armstrong, 2013). A transect line wasdrawn across the maximum diameter of each thallus. Themaximum diameter of each areola that touched the transectline was then determined. The frequency distribution ofareolae sizes from all thalli measured is shown in Figure 2.

How is the analysis carried out?A log-normal distribution was fitted to the numbers of

bacteria and size distribution of lichen areolae usingSTATISTICA software (Statsoft Inc., 2300 East 14th St, Tulsa,Ok, 74104, USA) (Pollard, 1979). A log-normal distribution isdefined as that of a variable X such that ln(X - Ø) is normallydistributed. The distribution has three parameters: Ø (where X> Ø), the mean (µ), and the variance (σ2). In manyapplications, the value of Ø can be assumed to be zero and atwo-parameter model fitted to the data. Goodness-of-fit to alog-normal model was tested using the Kolmogorov–Smirnov(KS) 1-sample test (StatNote 34, Hilton & Armstrong, 2013).

Interpretation: bacterial numbersThe number of bacteria isolated from the cloths was in the

range 20–220,000,000 (median = 33,000,000). Thefrequency distribution of bacterial numbers is shown in Figure1 and exhibits a degree of positive skew, i.e., the median ofthe distribution is to the left and the tail to the right of thedistribution. Although the log-normal distribution clearlyprovides a better fit to the data than the normal distribution,there are also significant deviations from a log-normaldistribution (KS = 0.20, P < 0.05). Hence, there were fewercloths with lower numbers of bacteria (<20,000,000) andmore than expected with larger numbers of bacteria(>20,000,000), compared with the predictions of a log-normal model. Hence, exponential growth of the bacteriatogether with symmetrical variation between cloths does notcompletely describe bacterial growth on domestic cloths andother factors are likely to be involved. The sample size wasquite small (N = 51), however, and a much larger sample ofcloths may be required to determine whether the log-normaldistribution actually describes this variable.

Interpretation: lichen areolaeThe size-class distribution of the mature areolae of the

lichen R. geographicum is shown in Figure 2 and is alsopositively skewed. The modal class is at an upper size limit of0.6mm and the maximum diameter of areolae is 2.8mm. Bycontrast with the cloths, a log-normal distribution significantlyfitted this distribution (deviation from model: KS = 0.05, P >0.05). This result has several implications regarding thegrowth of areolae of R. geographicum: (1) that growth maybe influenced by many factors acting independently and withmultiplicative effects and (2) that growth is likely to beexponential with a symmetrical pattern of variation betweendifferent areolae.

ConclusionThe data may not follow a normal distribution but a closely

related distribution called the log-normal distribution. Both

the normal and log-normal distributions are similar in thatthey result from a variety of factors acting independently. Ifthe effects of the different factors are additive, the result is anormal distribution and if effects are multiplicative, a log-normal distribution will be the result. Hence, bacterial andfungal growth (Righelato, 1975) may follow a log-normaldistribution and microbiologists should be alert to thispossibility if: (1) the data do not appear to follow a normaldistribution but exhibit a degree of positive skew, (2) themean of the distribution is low, the degree of variation large,and when values can only be positive, or (3) if there is thepossibility of exponential growth together with symmetricalvariation.

Figure 1. Histogram illustrating the observed distribution ofvalues for the cloth data and the predicted log-normal(continuous line) and normal (dotted line) distributions. TheKolmogorov–Smirnov (KS) tests the difference between theobserved and expected frequencies (KS = 0.20, P < 0.05).Because of the large absolute counts, the limits of each classare in scientific units, e.g., E7 represents 1 x 107

Figure 2. Size-class frequency distribution of areolae withinthe central region of 23 thalli of the crustose lichenRhizocarpon geographicum (L.) DC. Deviation from log-normalmodel (KS = 0.05, P > 0.05)

28

publications

■ Armstrong, R. A. (2013). Development of areolae and growth of theperipheral prothallus in the crustose lichen Rhizocarpon geographicum: animage analysis study. Symbiosis, 60, pp7−15.

■ Hattis, D. B., and Burmaster, D. E. (1994). Assessment of variability anduncertainty distributions for practical risk assessments. Risk Analysis, 14,pp713−730.

■ Hilton A., and Armstrong, R. A. (2005a). StatNote 1: Are the data normal?Microbiologist, Vol. 6, No.2, pp34−35.

■ Hilton, A., and Armstrong, R. A. (2005b). StatNote 3: Testing the differencebetween two groups. Microbiologist, Vol. 6, No.4, pp30−32.

■ Hilton, A., and Armstrong, R. A. (2008). StatNote 14: The correlation of twovariables (Pearson’s ‘r’) Microbiologist, Vol. 9, No.3, pp34−36.

■ Hilton, A., and Armstrong, R. A. (2012). StatNote 30: The one-way analysisof variance (ANOVA): Fixed effects model. Microbiologist, Vol. 13, No.3,pp32−35.

■ Hilton, A., and Armstrong, R. A. (2013). StatNote 34: The Kolmogorov-Smirnov test. Microbiologist, Vol. 14, No.3, pp28−30.

■ Hirano, S. S., Nordheim, E. V., Arny, D. C., and Upper, C. D. (1982). Log-normal distribution of epiphytic bacterial populations on leaf surface. Appliedand Environmental Microbiology, 44, pp695−700.

■ Limpert, E., Stahel, W.A., and Abbt, M. (2001). Log-normal distributionsacross the sciences: keys and clues. BioScience, 51, pp341−352.

■ Pollard, J. H. (1979). Numerical and Statistical Techniques. Cambridge:Cambridge University Press, p97.

■ Righelato, R. C. (1975). Growth of mycelial fungi. In: Smith, J.E., and Berry,D. R. (Ed.) The filamentous fungi Vol 1. Industrial Mycology, Arnold, London.

■ Romero, R. A., and Sutton, T. B. (1997). Sensitivity of Mycosphaerellafijensis, causal agent of black sigatoka of banana, to propiconozole.Phytopathology, 87, pp96−100.

■ Runemark, H. (1956). Studies in Rhizocarpon. I. Taxonomy of the yellowspecies in Europe. Opera Botanica, 2, pp1−152.

■ Syed, A., Armstrong, R. A., and Smith, C. U. M. (2000). Quantification ofaxonal loss in Alzheimer’s disease: an image analysis study. Alzheimer’sReports, 3, pp19−24.

references

Anthony Hilton1 and Richard Armstrong2

1Biology & Biomedical Sciences and 2Vision Sciences, Aston University, Birmingham, UK

Microbial Biofilms: Current Researchand Applications

Editor: Gavin Lear and Gillian D. LewisPublisher: Caister Academic PressISBN: 978-1-904455-96-7Reviewed by Alison Graham, Newcastle University

In this book, Gavin Lear and Gillian Lewis have broughttogether contributions from leading researchers on a widerange of topics related to biofilm biology. Inside there are

11 chapters that covereverything from the impact ofbiofilms in the environmentto their roles in disease andenergy generation.

The book starts with aninteresting chapter on therole of quorum sensing andmoves on to discuss biofilmsin two aspects of disease –host tissue infection andimplant-related infection. Thisis followed by a series ofchapters that collectivelycover the impact of biofilmsin the environment. Firstly,the significance of plant-associated biofilms, then the

role of biofilms in the soil, followed by applications in

book reviewbioremediation and wastewater treatment systems, andcorrosion and fouling. Chapter eight covers the importance ofbiofilm communities to freshwater rivers and streams, andhow measures of the community structure can provideindications of water quality and ecological health. This isfollowed by a review of extracellular enzymes in aquaticbiofilms.

The search for energy sources other than fossil fuels isbecoming ever more important. One potential method is toexploit microbial metabolic activity for biological energygeneration. The penultimate chapter reviews the biologicalprocesses associated with microbial fuel cells and theelectron transfer mechanisms of several model bacteria. Thefinal chapter then provides a thorough review of the use ofbiofilms in biocatalysis, discussing the developments inbiofilm reactor technology and challenges in using biofilmsfor biological catalysis.

The text throughout is full of up-to-date references to theoriginal research, and to other work, but with sufficientbackground to set the discussion in context. Withoutexception, the text flows well and is easy to read. This makesit an ideal starting point for undergraduate or postgraduatestudents entering the biofilm field. The figures and tables inthe book are useful and full of information; however, all areblack and white. It would have been nice for more images andillustrations to have been included and for at least some ofthese to have been in colour.

This book is useful for anyone interested in biofilms andparticularly microbiologists working in the environmental andremediation fields. Given the cost, it is more suited toinstitution or research group purchase. Overall, this bookmakes a valuable contribution to the growing literature onbiofilms and should have a place in all university libraries.

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meetings

To register online for this meeting please visit www.sfam.org.uk/winteror contact Sally Hawkes ■ Email: sally@sfam.org.uk ■ Telephone +44 (0)1933 382191

Wednesday 15 January 2014

The Royal Society, London, UK

Winter Meeting● Food contamination:

the food handler’s role● Biodefence

Including the Denver Russell Memorial Lecture

10.00 – 10.30 Tea, coffee and registration

Chair: To be confirmed

10.30 – 11.15 The Denver Russell Memorial Lecture:Food safety — current and future challengesColin Dennis

11.15 – 11.50 Nasty germs: in the bed or reds under the bed?Tim Brooks, Public Health England, UK

11.50 – 12.25 General introduction to food contaminationChris Griffith, retired

12.25 – 13.30 Lunch

Session A Food contamination: the food handler’s role

Chair: To be confirmed

13.30 – 14.05 The food manufacturerPeter McClure, Unilever, UK

14.05 – 14.40 The catererTayo Irawo, independent consultant

14.40 – 15.00 Tea and coffee

15.00 – 15.35 The retailerPeter Mather, Sainsbury’s Supermarkets Ltd, UK

15.35 – 16.10 The consumerEllen Evans, Cardiff Metropolitan University, UK

Session B Biodefence

Chair: To be confirmed

13.30 – 14.05 Biodefence over the ages and predictions for the futurePetra Oyston, DSTL, UK

14.05 – 14.40 If the anthrax does not get you the worms will! All you need to know aboutBacillus anthracis from nasty things in the mail to tea, sharks and green fluorescent nemotodesLes Baillie, University of Cardiff, UK

14.40 – 15.00 Tea and coffee

15.00 – 15.35 Glanders and melioidosis — past lessons and future perspectivesAndrew Simpson, DSTL, UK

15.35 – 16.10 Synthetic biology and biosecurityBrett Edwards, University of Bath, UK

Programme**Please note that this is a provisional programme and likely to change. For the latest information please visit

www.sfam.org.uk/en/events/index.cfm/Winter_meeting

30

meetings

On 1−2 April 2014, SfAM will hold a meeting inManchester to celebrate the centenary of the activatedsludge process. This will be an opportunity for

microbiologists and sanitary engineers to update theirknowledge of the microbiology of this important process.Papers include the use of cutting-edge molecular biology andbioinformatics tools to investigate the microbial consortiainvolved, as well as investigations of how the process can beused to remove priority pollutants and organic matter,suspended solids and pathogens. The meeting will also look tothe future, with presentations on granular sludge systems andfull-flow anaerobic treatment options. The following articlediscusses the development of the process, which is still inuse today.

Have you ever wondered what it was like to live throughthe industrial revolution? All those dark satanic millsbelching black smoke? Well, never mind the air, what aboutthe water? If you lived in the UK between 1850 and 1900, youhad a 20−25% risk of dying from a waterborne disease, withthe risk being highest in the overcrowded cities.

It is a sobering thought that in 1842, 17 years was theaverage age of death in a Manchester labourer’s family. In

Activated SludgeControl of waterborne disease: a century of theactivated sludge sewage treatment process

most cities, the middle classes lived on higher ground, partlyto avoid problems caused by occasional flooding. However,the urban poor were not so lucky, with their lower-lyingstreets and basement dwellings becoming flooded with whatwas effectively dilute sewage. Furthermore, most peopleobtained their drinking water from local wells, whichinevitably had become infected through groundwatercontamination — if not from floods, then from ‘night soil’(faeces) deposited onto the bare earth. The likelihood ofcontracting typhoid or some other diarrhoeal disease is onlytoo imaginable for a microbiologist. Even royalty fell victim,with Prince Albert dying of typhoid in 1861.

The unsanitary conditions in the UK led to variousinvestigations of the situation, e.g., Edwin Chadwick publishedhis Sanitary Report in 1842, followed in 1845 by a RoyalCommission report on the Health of Towns and PopulousPlaces. These reports were published before Pasteur’s germtheory of disease had been widely accepted, so the ‘miasma’(bad air) theory of disease transmission was dominant. Thus,following the London ‘Great Stink’ of 1858, there werevarious attempts to prevent odours, e.g., by sewage collection.For example, Joseph Bazalgette oversaw the construction of

See the fullprogrammeoverpage

31

sewers across London to contain the stench, so that by 1866most of the city was connected. However, initially, the sewagewas not treated but transported down the River Thames to bedischarged on the outgoing tide. It is interesting to speculatewhether political pressure would have been applied with suchforce if the Houses of Parliament had not been built on thebanks of the Thames, which was so badly polluted in 1858that curtains soaked in lime had to be hung at the windows tokeep out the ‘Great Stink’!

In 1898, the Royal Commission on Sewage Disposal wasestablished to determine what could be done about sewagepollution. The final report of this Commission, published in1912, set standards for wastewater treatment, some of whichare still in use. For example, the ‘20:30 Royal CommissionStandard’, whereby a treated effluent must not contain morethan 20mg/l of easily degraded organic matter (measuredusing the BOD5 test) and not more than 30mg/l of suspendedsolids (in both cases, so long as the receiving water dilutes theeffluent by at least 8-fold). This standard was soon adopted bymany other countries and is still in current use.

By 1894, the Manchester City Council Rivers Departmenthad established one of the first wastewater treatment facilitiesin the modern world, on the banks of the newly constructedManchester Ship Canal at Davyhulme, on land made availableby cutting off loops of the River Irwell. The treatment processat this works was initially based on the ‘sewage farm’ principle,where raw sewage was trickled over the land, which acted as aphysical filter and source of microorganisms to degrade thewaste. However, rather than the traditional grassland,Davyhulme developed a more efficient system of clinker beds(bacteria beds) with a herring-bone pattern of distributionchannels. (Incidentally, experiments to measure the activity ofslime growing on the clinker surface and reported in a 1902publication possibly constitute the first investigation of whatwe now call ‘biofilm’.) The use of bacteria beds reduced thearea required but the works still occupied a considerable areaof valuable land. Fortunately, necessity being the mother ofinvention, just across the River Irwell in Salford, the tricklingfilter had been developed by 1893, resulting in a 10-foldreduction in the land area requirement.

Nevertheless, the growing population of Manchester andthe connection of additional and new houses to the sewersystem meant that the Davyhulme site, though large, wouldstill be too small to even rely on the new trickling filtertechnology. Therefore, the scientists of the Rivers Departmentundertook research at Davyhulme on alternative processes.The team consisted of Gilbert Fowler, a consulting chemistwho had been responsible for directing research since 1904,Edward Ardern, a resident chemist since 1899 and WilliamLockett, a junior chemist. Lockett was also undertaking anMSc at Manchester University, under the supervision ofChaim Weizmann (a chemist and, incidentally, the Zionistleader who became the first President of Israel) and Fowler,who also held a university position. Weizmann’s lab wasrenowned as a centre of excellence for the development ofindustrial microbiology (including the production of acetoneand butanol using Clostridium butylicum), so Manchesterwas a natural choice for development of the microorganism-based activated sludge process. There was also the significantinfluences of Manchester being a major industrial city with ahistory of overcrowding and poor sanitation, and wealthyfrom cotton.

During a visit to the USA in 1912, Fowler witnessed thedevelopment of a novel system for sewage treatment, wherealgae and other microorganisms were grown as a biofilm oninclined slate panels in a tank of aerated sewage. This systemwas able to clarify the sewage and partially nitrify it over a 24hour period. On his return from the USA, Fowler instructedArdern and Lockett to conduct batch-culture experiments byaerating sewage in large bottles. Initially, it took five weeks forfull treatment but, by stopping aeration so that the biomasssettled before decanting the treated wastewater, a sludge ofactive microorganisms was produced (Ardern & Lockett,1914). Each subsequent batch increased the sludge volume sothat the process became quicker as the biomass concentrationincreased; an early example of process intensification throughbiomass retention! On 3 April 1914, this work wascommunicated at the spring meeting of the Society ofChemical Industry, in the Grand Hotel (now luxury flats) onAytoun Street in Manchester.

This process is now known as the Activated Sludgeprocess, because it relies on collecting and reusing settledsludge that had seemingly become ‘activated’ via aeration.Although microbiology was a fairly new science at the time, itwas soon established that the activity of this sludge relied onmicroorganisms, mostly flocculent bacteria and associatedprotozoa. Although initially developed as a batch process, thepracticalities of operating such a system with constantlyflowing sewage meant that a continuous process waseventually required. They also conducted experiments atDavyhulme on the best method of aeration, comparing surfacepaddles with surface inverted cone impellers (the ‘Simplex’system) and the use of compressed air from submerged pipes.Owing to practical difficulties at the time when using surfacepaddles or submerged aeration, the Simplex system wasadopted at Manchester’s Davyhulme works. Nowadays,submerged aeration tends to be used as it offers more efficientoxygen transfer. Incredibly, even 100 years after itsintroduction, the activated sludge process is still in use atlarger sewage treatment works across the globe.

Sewage treatment, principally through the metabolicactivities of bacteria and protozoa to remove organicpollutants and pathogenic microorganisms, together with thesupply of pure drinking water, has saved countless lives. Infact, it has been estimated that by breaking the cycle ofwaterborne disease, more lives have been saved than by allmedical interventions put together. Not bad for organismsthat, until Pasteur’s work, were not thought to exist and a citywith a false reputation for excessive rain.

M. J. DempseyManchester Metropolitan University and AdvancedBioprocess Development Ltd

■ Ardern, E., and Lockett, W. T. (1914). Experiments on the oxidation ofsewage without the aid of filters. J. Soc. Chem. Ind., 33 (10), pp523–539.

■ Chadwick, E. (1843). Report on the sanitary condition of the labouringpopulation of Great Britain. HMSO, London.

references

32

meetings

To register online for this meeting please visit www.sfam.org.uk/sludgeor contact Sally Hawkes ■ Email: sally@sfam.org.uk ■ Telephone +44 (0)1933 382191

Tuesday 1 April 2014

13.00 – 14.00 Tea, coffee and registration

Chair: To be confirmed

Session 1: History and microbiology

Chair: To be confirmed

14.00 – 14.30 Introduction: Development, success and future of the activated sludge processMike Dempsey, Manchester, UK

14.30 – 15.00 Faecal indicators of sewage pollutionDave Kay, Aberystwyth, UK

15.00 – 15.30 Microbial diversity in activated sludge (16S rRNA & FISH)Tom Curtis, Newcastle, UK

15.30 – 16.00 Tea and coffee

16.00 – 16.30 Metaproteomics for a functional insight to activated sludgePaul Wilmes, University of Luxembourg

16.30 – 17.00 Filamentous microorganisms in activatedsludgeMark van Loosdrecht, TU Delft, The Netherlands

Wednesday 2 April 2014

08.30 – 09.00 Tea, coffee and registration

Session 2: Pharmaceuticals, PCPs, heavy metals (keeping potable water potable)

Chair: To be confirmed

09.00 – 09.40 Effects of pharmaceutical compounds on selection for antibiotic resistance in aquatic microbesWilliam Gaze, Exeter, UK

09.40 – 10.20 Cytotoxic drugs, endocrine disruptors, and illegal drugs: where do they go? (Sex and drugs and rock ’n roll: where will it end up?)Mark Scrimshaw, Brunel University, London, UK

10.20 – 10.50 Tea and coffee

10.50 – 11.30 Pharmaceuticals, chiral drugs, illicit drugsand sewage epidemiologyBarbara Kasprzyk-Hordern, University of Bath, UK

11.30 – 12.10 Removal of hazardous chemicals during activated sludge treatmentElise Cartmell, Cranfield University, UK

12.10 – 13.10 Lunch

Session 3: Nitrification

Chair: To be confirmed

13.10 – 13.50 Ammonia and nitrite oxidizing bacteria in activated sludge: guild ecology & chaotic instabilityTo be confirmed

13.50 – 14.30 Nitrous oxide as early warning of nitrification failure in activated sludgeTom Stevenson, Cranfield University, UK

14.30 – 15.00 Tea and coffee

Session 4: Phosphate recovery

Chair: To be confirmed

15.00 – 15.40 Omics approaches to enhanced biological phosphate removalTo be confirmed

Session 5: Gene transfer

Chair: To be confirmed

15.40 – 16.20 Horizontal gene transfer in activated sludge via phageMichael Larkin, Queen’s University, Belfast, UK

Session 6: Epilogue

Chair: To be confirmed

16.20 – 17.00 Back to the future: upstream anaerobic digestionAna Soares, Cranfield University, UK

17.00 Meeting ends

Programme**Please note that this is a provisional programme and likely to change. For the latest information please visit

www.sfam.org.uk/en/events/meetings-diary.cfm/activatedsludge

The SfAM Activated Sludge MeetingControl of waterborne disease: a century of theactivated sludge sewage treatment processTuesday 1 – Wednesday 2 April 2014 ■ Lancashire County Cricket Club, Manchester, UK

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To register online for this meeting please visit www.sfam.org.uk/springor contact Sally Hawkes ■ Email: sally@sfam.org.uk ■ Telephone +44 (0)1933 382191

Wednesday 30 April 2014

The Sheffield Hilton Hotel, Sheffield, UK

Spring Meeting

● Control of infection: current status and future prospects

IBMSCPDACCREDITATION

6 POINTS

09.25 – 10.25 Tea, coffee, trade exhibition and registration

10.25 – 10.30 Chairman’s welcome

Chair: To be confirmed

10.30 – 11.00 Antibiotic resistance and its implications for infection controlHelena Parsons, Sheffield Teaching Hospitals,Sheffield, UK

11.00 – 11.30 Viruses and their infection control implicationsMichael Ankcorn, Sheffield Teaching Hospitals,Sheffield, UK

11.30 – 12.00 Challenges for the antimicrobial application of bacteriophage technologiesMichael Mattey, Fixed Phage, Glasgow, UK

12.00 – 12.30 Patient experience of surgical site infectionJudith Tanner, De Montfort University, Leicester, UK

12.30 – 14.00 Lunch and trade exhibition

Chair: To be confirmed

14.00 – 14.30 How clean is my hospital?Stephanie Dancer, NHS Lanarkshire, UK

14.30 – 15.00 Natural chemical diversity to combat infectious diseasesMarcel Jaspars, University of Aberdeen, UK

15.00 – 15.30 Natural antimicrobials, the future of infection control?Valerie Edwards-Jones, Manchester MetropolitanUniversity, UK

15.30 – 16.00 Infection controlMartin Kiernan, Southport and Ormskirk HospitalNHS Trust, UK

16.00 Close, tea and coffee

8th broadening microbiology horizons inbiomedical science meeting

Programme**Please note that this is a provisional programme and likely to change. For the latest information please visit

www.sfam.org.uk/en/events/index.cfm/springmeeting

34

meetings

Summer Conference 2013 reportHilton Cardiff Hotel, Cardiff, UK, Monday 1 July – Thursday 4 July 2013

■ Lactic acid bacteria and bifidobacterium■ Actinobacteria■ Including the Journal of Applied Microbiology (JAM) Inaugural Annual Lecture

This year’s Summer Conference was held at the Hilton Hotel Cardiff, 1–4 July. The conferencebegan with a preconference workshop on Public Engagement followed by the InauguralJournal of Applied Microbiology Lecture which was held at the National Museum Cardiff andwas presented by Professor Peter Setlow. The conference continued over the next three daysand covered the topics; ‘Lactic acid bacteria and bifidobacteria’, and ‘Actinobacteria’.

The first speaker of the ‘Lactic acid bacteria andbifidobacteria’ session was Todd Klaenhammer whogave an insight into the genomics of bacteria in starter

cultures and who started off by telling the audience that “youmust have a sequence to do biology”! In showing whygenomic sequences are important, Todd described some of hiswork that has helped us to better understand the dynamics ofcompetition and evolution in starter cultures includingmechanisms to help Lactococcus lactis resist attack fromvirulent phage and the adaptive evolution of Streptococusthermophilus to the dairy environment. Todd also describedfindings that may help to increase probiotic functionality suchas the use of lipoteichoic acid-deficient strains which have beenshown to increase IL-10 production in dendritic cells, reducinginflammation in a colitis model. Todd finished by describing theuse of lactic acid bacteria as oral delivery vehicles for thetargeted expression of anthrax protective antigen.

Oscar Kuipers continued the session with his talk on‘Synthetic approaches in engineering antimicrobialpeptides in lactococci.’ Oscar’s group are currently trying tofill the 20 year discovery void in the antibiotic pipeline byusing genetic approaches to modify bioactive peptides toproduce stable, novel antibiotics. Oscar outlined the four mainapproaches: 1) genome mining using BAGEL3; 2) usingmodularity to shuffle sequences; 3) hypermodification and 4)introduction of extracircular and heterocyclic modifications.After a refreshment break, Sylvain Moineau continued with‘New insights in viral protection in lactic acid bacteria.’Sylvain described current understanding of the CRISPR systemwhich has been described as a form of immunological memoryin bacteria to prevent reinfection with bacteriophage. Infectedbacteria acquire a sequence of spacer DNA from the infectingphage, resulting in a BIM (bacteriophage insensitive mutant)phenotype. The spacer sequence provides a ‘memory’ of thephage infection and protects against subsequent reinfection.Sylvain also described that the same phenomenon has beenobserved with the acquisition of plasmid spacers to give a PIM(plasmid interfering phenotype). The final speaker of thesession was Willem de Vos who gave an overview of‘Pangenomics of paradigm probiotics’ which focused onLactococcus rhamnosus. L. rhamnosus GG (LGG) iscommonly found in the GI tract and is used extensively as aprobiotic. LGG is unusual in that it is a non-pathogen whichproduces mucus-binding pili to enable it to maintain close

association with host cells. Recent genomic and functionalcharacterization which examined functions related tocarbohydrate transport and metabolism, production of mucus-binding pili, bile salt resistance, prophages and CRISPRadaptive immunity has revealed diversity amongst strains of L.rhamnosus and has provided insights into the adaptation ofthis organism to different, and in some cases, multiple niches.

Clare Taylor

The ‘Lactic acid bacteria and bifidobacteria’ sessioncontinued after lunch with four speakers covering a broadrange of topics. Luc de Vuyst, Brussels University, kicked offthe afternoon session with a fascinating talk on ‘Growth andphysiology of bifidobacteria’. Luc discussed thesefascinating bacteria, which make up a minor fraction of thehuman microbiota and yet play a vital role in carbohydratedegradation. Using a typical pathway these bacteria break downmonosaccharides such as glucose and fructose to producelactic acid and acetic acid in a 3:2 ratio, although this ratio isdependent upon substrate consumption. Luc went on to explainthat some strains of these bacteria are also able to break downinulin type fructans. The acetic acid produced by these bacteriathen cross feeds other colon bacteria. Luc’s talk gave a realinsight into some of the properties of these bacteria.

Douwe van Sinderen, University College Cork, was the nextspeaker of the afternoon. Douwe’s talk ‘Functionalgenomics of bifidobacteria for health’ began by discussingsome bifidobacteria in terms of their health promoting andprobiotic properties. Douwe explained that whilst we knowthat various bifidobacterial strains and species demonstrateprobiotic activity, the mode of action for this activity is largelya matter of speculation. Douwe went on to discuss recentgenomic exploration of bifidobacteria and the impact this hashad on our understanding of these organisms. From thedevelopment of genetic tools allowing access and modificationof the bifidobacterial genome to giving us a betterunderstanding of the particular adaptations to theirenvironment, Douwe demonstrated how important this area is.

After a break for tea the ‘Lactic acid bacteria andbifidobacteria’session concluded with two talks firstly JanKnol, Wageningen University, discussed ‘Intestinalmicrobiology in early life’ then Glenn Gibson, University ofReading, finished the session with a talk on ‘Targeting

35

bifidobacteria with prebiotics’. Jan explained that new-borns are essentially sterile, but that within the first few daysearly microbial colonizers help to develop a baby’s gutmicrobiota. These early colonizers can play a vital role in thedevelopment of this symbiotic relationship between humansand their gut microbiota and may even impact on the longterm composition and activity of the microbiota. For thisreason, Jan said, it is important to understand more about thedynamics that lead to this early development of the gut flora.Jan went on to discuss the importance of using this knowledgeto help develop milk substitute products for optimal gutmicroflora development.

Glenn Gibson finished the session off with a veryentertaining talk on prebiotics. Glenn discussed some of thefascinating research he was involved in, looking at theeffects of prebiotics on different groups of people includingathletes and the elderly. Glenn went on to talk about somerecent research looking at using prebiotic supplements topromote health in the overweight and in those withmetabolic syndrome.

Clare Doggett

Following on from an attended poster session student,delegates had the opportunity to attend this year’s studentsession entitled “Career options — what’s next?” Manystudents, whether fresh out of an undergraduate degree or aPhD, with experience or not, are unsure of their next steps.This session offered a live student audience the opportunity toquestion an experienced and varied panel about careers inmicrobiology. As well as providing advice about commoncareer paths for young microbiologists – research andteaching, the panel also highlighted that a career inmicrobiology can be in other diverse areas, such as publicengagement and sales. Ali Ryan of the SfAM PECS Committeechaired the session, and introduced the panellists: Colin Hinds-Payne, Careers Advisor at Cardiff Metropolitan University;

Clare Doggett, Communications Officer for SfAM; LouiseFielding, Director of Research at the Cardiff School of HealthSciences, Cardiff Metropolitan University; Phil Wheat, CEO ofSfAM and Claire Hill, Project Manager at Medical Wire.

The first question asked was “What type of CV should Ihave?” The panellists gave plenty of advice! A CV needs to bebalanced, whilst being tailored specifically to each jobapplication. It is a document to sell yourself, so write to thereader. What are they looking for? How are you different?Why should they pick you? Look at the job specification,determine the skills required and adapt your CV appropriately.An important point raised was that a CV should be truthful —make sure you can do what it says you can. In order toenhance your CV, a number of suggestions were made. Takeall of the opportunities you can and more importantly makeopportunities as this shows initiative. Get involved withsocieties, go to conferences and engage with groups like thePECS Committee.

The second audience question came from a biomedicalscience undergraduate, “Can I complete my professionalportfolio through voluntary work?” Again the panellistsanswers were diverse. There isn’t a problem with the workbeing voluntary, but for any placement like this you will needto have financial support from elsewhere. An audiencemember contributed with their experience “voluntary isfinancially stressful, but sometimes necessary to make youstand out and to get your qualification”. To get work, trycontacting your local lab(s) and send them a speculative CV.Voluntary work shows motivation, enthusiasm and reliability. Itcan lead to paid employment in the future, so treat it as a paidjob. Relating back to question one, capitalize on newopportunities such as public engagement with SfAM — thiscan open doors to possible job opportunities. Colin Hinds-Payne posed a question to the audience: “What isemployability?” Colin explained it is about knowing yourskills, recognizing when to use them and then applying themto the situation.

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meetings

Question three: “I am ending my degree soon, and Idon’t see myself in academia, so I am considering othercareers like public health surveillance or policymaking.Have you got any advice?” Here it is important to becomeand stay informed, so watch the news, and attend events likeVoice of the Future and workshops run by organizations likeSense About Science. Learn as much as you can aboutparliament and policies. It would be advantageous to checkthe Society of Biology’s job section, as they are the umbrellasociety of about 80 life sciences societies, and will advertisejobs for all of them. Finally, try looking at the civil servantswebsite for jobs.

The fourth question asked was “My PhD funding ran outlast September, and I have been unable to find work since,I’ve tried everything I can think of. Interviewers say I amtoo skilled, and they can’t afford a PhD. I have triedmaking opportunities, but funding is scarce. I have alsovolunteered and been involved in public engagement.What else can I try to get a job?” You should start by visitingthe careers service of your university; they actually have athree year duty of care after you leave. Keep asking yoursupervisors, as they may be able to help you get funding.Make sure your interview techniques aren’t at fault, targetwhat skills they require and sell yourself. You may alreadyhave the skills, but not realize it, so really think about it.Another audience member commented on their experience “Itried a lot of avenues to get work. Some companies don’teven put through CVs for consideration. Having a PhD canalso make you too expensive to potential employers”. Somepostdoctoral job seekers don’t mention their qualification, toapply for lower grade jobs. If you are going for a job thatdoesn’t require a PhD, maybe you should be honest with theinterviewers, and state that you applying for the job for areason. Definitely don’t be afraid to talk about wages, howeversometimes you cannot negotiate down.

The final question of the session was “Employers wantyou to have experience when you apply, but I don’t have

enough, how can I get it?” Sometimes even if you don’t havethe experience, but you know you have the skills, make anapplication and sell yourself. If you don’t have the skills or theexperience, volunteering can be a great way to boost both.Whilst doing a PhD, take all opportunities given, especially ifyou are asked to teach. Some universities also offer stafftraining which you could benefit from. It is important to berealistic about the level of job you are applying for, sometimesyou need to start at the bottom and work your way up. Havingaspirations is crucial, but you need to be realistic to reachyour desired career. Make sure you work in yourundergraduate summers, and any gap years, take allopportunities. Mention what you have done on your CV, as thiscan make interviewers curious and want to ask you.

This was a brilliant session, which as an undergraduate, Ipersonally found very interesting and useful. Despiteemployment problems in our field (like many others), thepanel highlighted many ways in which you can improve yourprospects of following your chosen career path.

Stewart Barker

Wednesday morning was the start of the ‘Actinobacteria’session. The morning began with William Whitman, Universityof Georgia, providing an introduction with his talk on‘Bergey’s taxonomic outline of the Actinobacteria’.William talked about the recent changes to the taxonomicoutline of the Actinobacteria in the 2012 Bergey’s Manual ofSystematic Bacteriology. These changes have created moreconsistency between the Actinobacteria and otherprokaryotes, which William explained, facilitates comparisonsbetween phyla. William went on to talk about some of thechallenges with the classification of Actinobacteria and theneed for a continuously updated ‘living phylogenetic’ tree.

Following on from William, Gilles van Wezel, LeidenUniversity, discussed the ‘Evolution of sporulatingactinomycetes’. Gilles talked about the importance of

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accurate molecular taxonomy in the era of large genome datasets, and presented his work on a novel method of classifyingactinomycetes based on the conservation of SsgA and SsgBproteins. These proteins are developmental regulators and instreptomycetes are required for septum-site localizationduring sporulation-specific cell division. Gilles expanded onthis to explain how they were using these proteins to validateprevious taxonomic research into the actinomycetes as well assuggesting the possible reclassification of certain species.

The next speaker of the morning, William Fenical,University of California, took us on a journey to marineenvironments in his talk on ‘Accessing marineactinomycetes for drug discovery’. William discussed theuse of specific media and methods to isolate obligate marineactinomycetes as opposed to common isolation methods thatoften resulted in strains of actinomycetes which were closelyrelated to those isolated from terrestrial sources. William gavea couple of examples of recently isolated obligate marinestrains, which had been recently isolated. He explained thatthese strains could be characterized by the synthesis of uniquesecondary metabolites which could provide a new directionfor drug development.

After a coffee break we settled back in to hear two morespeakers for the morning session. Firstly Michael Goodfellow,Newcastle University, presented work on ‘Actinobacteriafrom extreme habitats: new opportunities for drugdiscovery’ before Francisco Barona-Gomez, NationalLaboratory for Genomics for Biodiversity, Iraputo, discussed‘Evo-mining: an evolution-inspired strategy for thediscovery of natural products in Actinobacteria’. Michaelbegan by reminding us that bacteria are, and always havebeen, the dominant form of life on this planet and are found innearly every environment. Michael discussed pioneeringresearch on actinobacteria which have been isolated from theActama Desert, the oldest and driest desert in the world.Innumerable novel actinobacterial species have been isolatedincluding those from ‘rare’ genera. Michael went on to say

that some of these species produce novel bioactivecompounds which may well pave the way for newpharmaceutical compounds.

Francisco concluded the morning’s session talking about‘Evo-mining’. Francisco used his presentation to demonstratehow evolutionary principles could guide the discovery of novelnatural products. Francisco explained that using an approachthey named ‘Evo-mining’ his team had been able to uncovernovel synthetic pathways including those in well-studiedlaboratory strains. Following a fantastic morning of talks webroke for lunch and further discussions on the mornings topics.

Clare Doggett

The ‘Actinobacteria’ session continued after lunch andposter viewing, chaired by Mike Goodfellow with two speakersaddressing different sources of actinobacteria in theenvironment. First, Martha Trujillo from the University ofSalamanca in Spain, outlined an accidental discovery ofMicromonospora while trying to isolate Rhizobia fromlegumes. As these organisms are slow growing, their presenceis not detected until the plates have been incubated for atleast 2 weeks, as opposed to the 3 days needed to growRhizobia. The Micromonospora, the most abundant of whichthey have found to be M. saelicesensis are normal inhabitantsof nitrogen-fixing nodules but their current function in rootnodules is unclear. Genomic analysis of M. lupini Lupac08revealed that there are approximately 680 genes that code fortransport and metabolism of carbohydrates and 200 hydrolyticenzymes, yet the organism is not pathogenic to plants. The‘Micromonospora Puzzle’ remains unclear but it ishypothesized that there is a plant/soil associated lifestyle andplant growth promotion traits may be a feature. The secondpresentation was by Matthew Hutchings of the University ofEast Anglia, who took us on a tour of ants and actinomycetes.The species of ants used in his lab, Aquamonas octopinosus,is unable to digest leaves or flowers and has developed a

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members

tripartite symbiotic relationship with a fungus andactinomycete bacteria (Pseudonocardia) to create massivehoneycomb-like garden structures. The ants have specializedglands that secrete food for the bacteria to absorb. ThePseudonocardia are vertically transmitted and while there isonly one species present per nest, as workers get older andleave the nest, an increase in microbial biodiversity is seen.Pseudonocardia, along with Streptomyces, has been foundto produce antimycins that have the potential to be developedas potent anticancer drugs via the Bcl anti-apoptotic route.The ants and their microbiomes can be seen at the universitywebcam: http://bit.ly/LCAntCam.

Louise Fielding

The student presentations session was chaired by thePostgraduate and Early Career Scientists (PECS) CommitteeChair, Emmanuel Adukwu. This session provided theopportunity for four PhD students to present their work ondifferent aspects of applied microbiology. The first speakerwas Xiaolei Ze from the University of Aberdeen, whodiscussed the role of keystone species on the degradation ofresistant starch in the human colon. The study investigatedthe inter-individual variation on the composition of the gutmicrobial community and its relationship with the ability toferment resistant starch (RS) in the human large intestine. Inthe study, anaerobic pure cultures and defined co-incubationswere performed to compare the abilities to degrade RS byfour of the most abundant amylolytic species present in thehuman colon. Each bacterial isolate was incubated in vitrowith the mixed bacterial communities from four volunteerswho showed remarkable differences in the digestibility of RSin vivo. From the study, it was concluded that Ruminococcusbromii exhibited a superior ability to degrade RS whencompared with other highly abundant species of amylolyticbacteria. This study provided an excellent example of akeystone species from within the human colonic microbial

community with respect to RS fermentation.Following on from Xiaolei; Benjamin McCutcheon from

Brighton University gave a presentation on the genomic,(meta)genomic and functional characterization of a novelRelBE type toxin-antitoxin addiction module associated withthe human gut microbiome. Benjamin and his researchcolleagues recently identified a RelBE type toxin-antitoxinmodule (p22-TAM) potentially enriched in the human gutmicrobiome. Here they examined i) carriage of this modulebetween different genetic units (plasmids, bacteriophage,chromosomes), ii) the prevalence of homologous sequences ina range of environments, iii) functions associated with geneneighbourhoods surrounding these modules, and iv) impact ofp22-TAM carriage on bacterial stress response. From this, theyfound that p22-TAM-like modules have a significantly higherabundance within the mammalian gut, are prevalent in theplasmid fraction and have a negative correlation with functionsnormally associated with the gut microbiome. The p22-TAM isimplicated in facilitating survival upon exposure to antibiotics,and may also play a role in other stress responses. Their studyconcluded that a higher prevalence of the novel p22-TAM withgut-associated plasmids, and the increased cell survival onexposure to antibiotics suggest carriage may be advantageousto gut microbes. This provides new insight into the structureand functions of the gut microbiome.

The penultimate presentation was given by Suzy Moodyfrom Swansea University entitled ‘The secret life of anantibiotic: albaflavenone and its novel role in vivo.’Albaflavenone is a sesquiterpene antibiotic produced byStreptomyces coelicolor. A disruption mutant incapable ofproducing albaflavenone was found to have a significantphenotype when grown under osmotic stress, being unable toproduce the pigmented antibiotics S. ceolicolor is renownedfor. Experiments were carried out to elucidate howalbaflavenone was mediating this change in phenotype.Phenotype, assays and qRT-PCR data provided evidence foralbaflavenone being a novel bacteria hormone and results

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point to a new signalling role for this antibiotic.To finish, Wan Zawiah from The University of Reading gave

a presentation on the survival of Salmonella under conditionsnot permitting growth. The aim of the study was to determinethe variations in survival among representative serovars ofSalmonella enterica under conditions not permitting growth.Wan presented results demonstrating that the survival ofSalmonella is affected by environmental conditions such astemperature, pH and water activity, but strain variation is alsoa significant source of variability. This is significant asmathematical models predict survival as a function ofenvironmental conditions.

The session was brought to an end by Professor MarkFielder who thanked and praised the students for theirexcellent presentations.

Christiana Adesanwo

The first of the SfAM award lectures was presented byCatherine Adamson of the University of St Andrews, whoreceived the New Lecturer Grant following her appointment toa lectureship in 2010. Her presentation, entitled ‘HIV-1maturation inhibitors: a novel class of antiretroviraldrug’, provided a fascinating overview of the development ofa class of drugs that target a previously neglected step in thelife cycle of HIV-1: the maturation of the viral particle.Catherine introduced the compound Bevirimat, which targetsthe Gag protein that is essential for assembly of viral particles.She presented data showing that Bevirimat inhibits theproteolytic activation of Gag. Furthermore, with somebeautiful cryo-electron tomography images, Catherinedemonstrated that blocking Gag proteolysis results in viralparticles that contain the hexagonal Gag lattice structure butlack the inner nucleocapsid-related layer. These immature viralparticles are non-infectious. Unfortunately, Phase II clinicaltrials of Bevirimat were suspended in 2010 when it was foundthat around 50% of HIV-1 infections are resistant to the drug

due to naturally occurring variants in the region of the gaggene that encodes the proteolytic cleavage recognition site.The aim is now to characterize this domain to enable therational design of new derivatives of Bevirimat with broadspecificity for HIV-1 variants.

The W H Pierce Prize was awarded to Lori Snyder,Reader in Bioinformatics at Kingston University. Lori gave anexcellent and informative presentation on ‘Finding sunkentreasure in the genome sequencing data flood’. Lori hasbeen on the front line of microbial genome sequencing formany years, and she described how the field has developedover the last decade or so. In particular, the introduction ofnext-generation sequencing technologies in 2006 led to adeluge of sequence data. Lori showed, somewhat reassuringly,that computers cannot process all this information accuratelyand that there is still a place for manual analysis of genomesequences. For example, careful analysis of genomesequences enabled the identification of large (32 kbp)tandem repeats in the Neisseria meningitidis genome andunusual inversions in the genome of Bacteroides fragilis.Lori described her work on Correia Repeat EnclosedElements (CREE) in the genome of Neisseria gonorrhoeae.These elements are similar to Insertion Sequences, but do notcode genes within them. Resequencing of a N. gonorrhoeaestrain following serial passage in the laboratory provided thefirst evidence that CREE sequences can invert in thisorganism. These elements contain outward-facing promoters,and it is possible that inversion may modulate the expressionof proximal genes. Lori also described the identification offlagellar genes within bacterial genome sequences, includingseveral species that have never been reported to be motile.Clearly, there is plenty of scope for fishing out importantbiological information from the vast oceans of microbialgenome data.

Nick Jakubovics

Daniel Amund winning first prize for his poster

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members

After an entertaining evening at the conference dinner, heldat Cardiff Castle, the Actinobacteria session continued onThursday morning with a talk on ‘Genome mining tounderstand and manipulate antibiotic production inactinomycetes’ by Mervyn Bibb. Mervyn discussed novelmechanisms of immunity and enzymology uncovered in thesearch for new antibiotics. This work has focused on theActinomycetes as they are an immensely important group forantibiotic production, producing two thirds of the knownantibiotics, with half being clinically used ones. Genes forantibiotic synthesis are generally clustered on thechromosome; using molecular methods this suggests arelatively simple strategy could be used for their isolation bysequencing and cloning the genes of interest into anexpression host easier to grow than the Actinomycete itself.However, cells making antibiotics need to express immunity tothe antibiotics themselves. In the native species this immunityis usually regulated to be expressed with antibiotic productionand cells may be sensitive at other times. Examples of studieswere given where immunity mechanisms were knocked outand the antibiotic was no longer made, showing a regulatorylink between immunity expression and antibiotic production.In other examples early induction of resistance allowedincreased production of antibiotics. Novel enzymology wasanother feature which has been seen. For example, cypemycinexhibits some of the features of a lantibiotic, but itsbiosynthetic gene cluster does not show typical features. Post-translational modifications such as dehydration of threonineswas shown to be due to an unusual enzyme, the gene forwhich was unique in the database. Bioinformatic analysisrevealed the widespread occurrence of cypemycin-like geneclusters within the bacterial kingdom and in the archaea.Thus, genome mining has identified both new synthesispathways and new mechanisms of control.

In ‘Application of phage integrases in streptomycetesand beyond’, Maggie Smith discussed the mode of action ofphage integrases and the advantages these present for genome

engineering. Phage integrases catalyse a highly directionalintegration of phage DNA into a host chromosome. Somecommonly used integrases need host factors to work, e.g.,phage λ integrase, but the examples presented do not needthese and so this makes them useful. These phage integrasesare interesting as they need only a very short homologoussequence and allow conservative site-specific recombination.Serine integrases are one example and their mechanism ofaction was discussed in detail. These mediate site-specificrecombination between short (40–45bp) attachment sites, attPin the phage and attB in the host. Mediated by the integrase,during recombination all four strands of DNA are cut at onceat precise points allowing only a 2bp overlap; strand exchangethen occurs by a 18° rotation and then the strands arereligated. This converts the attP and attB sites to the sites attLand attR. Reversal of this process (excision) at these two sitesis not possible without a recombination directionality factor(RDF) which reconfigures the integrase to excise not integrate.Work on streptomycete phage has shown that the integrasesfrom different phage have slightly different dinucleotidespecificity. Maggie then went on to describe examples of workwhich utilize these very precise site-specific recombinationabilities for synthetic biology engineering, for example, cloninga biosynthetic gene cluster and ensuring all the elements arerealigned in the right order.

In the talk ‘Biology of plant pathogenicstreptomycetes’, Dawn Bignell presented studies on thecharacteristics of Streptomyces species such as S. scabiesand S. acidiscabies which cause a variety of scab diseases ofplants (e.g., potato, beet, turnip); potato scab in particular isof great economic importance. A secondary metabolitethaxtomin A, a phytotoxin, is the cause of necrosis of potatotuber tissue and stunting of seedlings by inhibiting cellulosesynthesis. The six genes and regulator are conserved in a genecluster in the main pathogenic species S. scabies and S.acidiscabies. Another gene necI, needed for tissuecolonization, is also conserved in the plant pathogenic species

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and may suppress the plant’s defence responses to infection.Functional genomics studies have also identified otherpotential pathogenicity factors such as concanamycins; thosefrom S. scabies are phytotoxic. Expansin-like proteins havealso been described which loosen cell walls and may enableplant/microbe interactions. Another gene cluster found in S.scabies is highly similar to that for coronafacic acid (CFA),present in another plant pathogen Pseudomonas syringae. InPseudomonas, CFA is a component of the non-host specificphytotoxin, coronatine (COR), a known plant immunesuppressor. However, genes for the other biosyntheticcomponents of COR were not present in the S. scabies gene

cluster but unique genes were and so the exact pathogenicityfunction of the CFA-like molecule is currently unknown. Arecent study in Newfoundland isolated new pathogenic strainsfrom scaby potatoes which phylogenetic studies have shownare distinct from known Streptomyces pathogens; none madethaxtomin A or carried the gene; therefore strategies to makepotatoes thaxtomin resistant is not going to be a very usefulcontrol mechanism in the long run.

Paul Hoskisson’s talk on ‘Human PathogenicStreptomyces’ discussed a group of poorly understoodspecies which cause actinomycetoma — infections whichresult in tissue masses which are slow growing in deep tissueand bones, causing bone damage; antibiotic treatment islargely ineffective and so surgical intervention is typical whichmay result in limb amputation. Remaining infection can slowlyspread. This is now included by WHO on the list of neglectedtropical diseases. A range of types are found in areas such asrural Africa, the Middle East and the Neotropics, affecting thelower limbs and feet, mainly in those of low socio-economicstatus. This is typically seen in young farmers at an age whenthey are most active in fields, particularly foot infections afterrains and trauma (thorns). Little is known of the factorsneeded for virulence, for example, is morphology importantlike in fungi which cause the similar disease, eumycetoma?Genome sequencing presents a strategy to look for commonvirulence factors seen in other bacteria such as adhesionfactors, toxins, cell invasion, replication and host evasionmechanisms. Also, common genomic structures likepathogenicity islands could help identify important virulencefactors. Findings from sequencing of two type strains, S.somaliensis and S. sudanensis, and a clinical strain of S.somaliensis were discussed. The two species were found tobe almost identical with a high number of shared genes; thegenomes were typical of Streptomyces genomes but withfewer environmental regulators which may be an adaptation togrowth in the more stable environment of human tissue. Arange of potential virulence and multi drug resistance geneswere described. Surprisingly from this finding, when S.sudanensis and S. somaliensis were tested in the wax mothlarvae model system (Galleria mellonela) by injection intothe prohind leg, then S. sudanensis had no effect whereasboth S. somaliensis strains caused melanise (insect infectionresponse). Another surprising finding was that despite theknown epidemiology of the disease these species or theirgenes could not be isolated from soil, although otherStreptomyces species were present. This makes the diseaseepidemiology hard to establish despite the evidence fromother factors which suggest this is the main route of infection.

Christine Dodd

● Zoonoses

■ In conjunction with the Med-Vet-Net Association.

■ Including the Journal of Applied Microbiology (JAM) Lecture.

The Grand Hotel, Brighton, UK. 30 June – 3 July 2014.

Don’t miss next year’s...

...Summer Conference

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members

membership benefits

■ Full Ordinary Membership gives access to ourmany grants and awards, online access to the Journalof Applied Microbiology, Letters in AppliedMicrobiology, Environmental Microbiology,Environmental Microbiology Reports and MicrobialBiotechnology, copies of Microbiologist, preferentialregistration rates at Society meetings and access to themembers’ areas of the website.

■ Full Student Membership confers the samebenefits as Full Membership at a specially reduced ratefor full time students not in receipt of a taxable salary.

■ Associate Membership is only open to those withan interest in applied microbiology without it being aprime aspect of their job. For example, school teachersand those taking a career break; on maternity leave, orworking temporarily in other areas. It does not provideaccess to any journals or Society grants and awards.

■ Honorary Membership of the Society is by electiononly and this honour is conferred on persons ofdistinction in the field of applied microbiology.Honorary Members have access to our online journals.

■ Retired Membership is available to Full Membersonce they have retired from their employment. RetiredMembers are entitled to all the benefits of FullMembership except grants and access to the Society’sjournals.

■ eAffiliate Membership: This category ofmembership is open to microbiologists residing in BandI developing countries and is free of charge. It is anonline only membership and provides access to theeAffiliate bursary only.

■ eStudent Membership: This category ofmembership is open to undergraduate students only. Itis an online only membership and is free of charge.This category of membership does not provide accessto the Society’s grants or journals.

■ Corporate Membership is open to all companieswith an interest in microbiology. Corporate Membersbenefits include:● Quarter page advertisement in each issue of Microbiologist (which can be upgraded to a larger size at discounted rates).● The opportunity to publish press releases, company news, etc., in each issue of Microbiologist.● FREE banner advert on the Society website with a direct link to your company site.● Up to three members of company staff attending Society meetings at members’ rate (this means a 50% discount on non member registration rate).

JOIN US!

You can apply for membership on, or offline. To applyoffline, please contact the Membership & Finance Co-ordinator, Julie Wright on +44 (0)1234 326846, oremail julie@sfam.org.uk.

options The Society for Applied Microbiology is the voice of appliedmicrobiology within the UK and was founded in 1931. Society membersplay a leading role in shaping the future of applied microbiology, and enjoymany benefits, including:

■ The opportunity to apply for one of our many grants or funds.■ Eligibility to win any of our awards or nominate a candidate for the

SfAM Communications Award.■ Access to our five peer–reviewed Journals: Journal of Applied

Microbiology, Letters in Applied Microbiology, Environmental Microbiology, Environmental Microbiology Reports and Microbial Biotechnology.

■ Free access to the entire collection of digitized back files for JAM and LAM dating back to 1938.

■ A topical quarterly magazine, Microbiologist.■ Substantially reduced rates for attendance at SfAM meetings and

conferences.■ Networking with worldwide professionals in over 80 countries.■ Access to private members’ area of the SfAM website.■ Monthly email bulletins with the latest news from SfAM.■ Invitation to the annual Environmental Microbiology lecture.■ Fostering cross disciplinary research.■ A 25% discount on the extensive Wiley–Blackwell collection of titles. Detailed information about all these benefits and more can be found on

the Society website at: www.sfam.org.uk.

GRANTS & AWARDS: Many grants, awards and prizes are available tomembers including the W H Pierce Memorial Prize and prizes for studentoral presentations and posters at the Summer Conference. In addition tothese substantial awards, the Society has funds to assist members in theircareers as microbiologists. These include the President’s Fund, ConferenceStudentships, Sponsored Lecture Grants and the popular Students intoWork Scheme.

Full details of all the Society’s grants and awards can be found on thewebsite together with application forms.

JOURNALS: The Society publishes two monthly journals: Journal ofApplied Microbiology and Letters in Applied Microbiology. We alsoproduce this quarterly colour magazine, Microbiologist, which containsfeatures, topical news stories and full details of our meetings. The Societyis also a partner with Wiley–Blackwell in the monthly journals:Environmental Microbiology, Environmental Microbiology Reportsand Microbial Biotechnology.

All Full and Student Members receive free access to the online versionsof the Society’s journals, and can also submit papers to our journals via anonline submission service.

MEETINGS: We hold three annual meetings; the Winter Meeting is aone-day meeting with parallel sessions on topical subjects. The SpringMeeting is a one–day meeting tailored for personnel in clinicalmicrobiology. The Summer Conference is held every June/July andcomprises a main symposium, a poster session, the AGM and a lively socialprogramme. All members are invited to our prestigious annual lecture heldto commemorate the success of our Environmental Microbiology journal.We also hold joint ventures with other organizations on topics of mutualinterest.

WEBSITE: The website is the best source of detailed information on theSociety and its many activities. It has fully interactive membership areaswhere you can find archive issues of Microbiologist, exclusive SfAMdocumentation and much more.

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NEW MEMBERSWe would like to warmly welcome the following new members andhope that you will participate fully in the activities of the Society.

Australia

K. A. Hammer; R. McLean; S. Muehlen

Belgium

B. A. Stenuit; C. Vinueza

Canada

J. A. Tetro

China

Z. Liu

Columbia

F. A. Ramos Rodriguez

France

C. Baliere

Germany

T. R. Vonnahme

Ghana

F. Adzitey

India

R. Dewanti; I. Ghosh; J. Jublee

Indonesia

L. Nuraida

Ireland

A. Crowley; E. Ferguson; C. Guinane

Korea

C-J. Cha

Malta

D. Spiteri

Mexico

L. Espinosa Tolentino

New Zealand

R. Fraser

Nigeria

F. Adeoshun; A. Afolayan; O. A. Aregbesola; C. C. Egbe; T. O. Egwuatu; K. E. Eimuhi; J. O. Eimuhi; V. A. Njoku; I. A. Odetokun; C. T. Olateru; P. Oleghe; A. O. Olugbile; O. O. Omobofe; S. O. Samuel

Pakistan

F. Syed

Portugal

C. Silva Pereira

South Korea

M. Rahman

Uganda

S. Bagaaya

UK

F. Alberti; T. Arif; W. Armour; M. Ben Khala; N. Blackwell; G. H. Boother; C. Bowen; V. Bratby; B. Chadwick; S. Challa; S. Charles; D. Childers; H. Y-L. Choo; L. Cieslak; C. Cooper; F. Coukan; H. Davey; P. Druggan; H. El Kadri; F. Ferrara; S. H. Fisher; D. Flynn; L. P. Fossier; A. Frangleton; C. Gachon; I. Garaiova; M. Gibson; Z. S. Goh; F. Goodwin; A. Green; A. Green; R. Griffin; C. Grob; J. Harris; K. Hataglou; R. Hatch;S. Hawkings; C. Hendy; N. Holdforth; E. J. Holmes; A. Howat;A. L. Irvine; R. Jenkins; R. Johns; C. Johns-Gardner; P. Kane; D. Keen; J. Kelly; T. Korin; R. Koy; S. Kuehne; J. Lock; L. Mackay; C. M. Madden; A. Majeed; S. McClarty; S. McGrath; C. Moore; C. Mur’Tala; Z. Mycroft; P. Nash; V. Nkwenti; L. O’Brien; J. O’Donnell; E. Oluwadare; A. Otter; F. Parkinson; L. Pickthall; D. A. Poole; C. Price; G. Pritchard; T. Puttick; B. M. Rabi’u; K. Randall; D. Reddiar; S. Rout; H. Sharma; S. H. Simms; D. Smith; S. Starkings; S. Stewart; V. Taylor; V. Tennyson; J. K. Thomas; C. B. Thomson; K. Thorley;S. L. Tingey; S. Tylisczuk; L. Vanchieri; Y. Wang; D. Weaver; J. Webb; E. Wilcox; G. Wilson; L. Wright; P. A. Zaman

USA

N. Blanco Herrera; A. Chakraborty; H. E. Fisher; L. J. Harris; W. Ju; R. Oni; B. Portoni; S. Ruengvisesh; A. Sayler; C. Sevilla; J. Wall; Y. Wang; A. Xu; P. Zoder

Losses

We were saddened to learn of the death of the followingMember of the Society:

George A. Prentice.

Membership changes

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members

New Committee MembersBrendan F Gilmore

Brendan graduated with a BSc (Hons) in Pharmacy(1999) and a PhD in Medicinal Chemistry (2004) fromQueen’s University Belfast. He was appointed to aLectureship in Pharmaceutics (PharmaceuticalMicrobiology) in July 2004 in the School of Pharmacy atQueen’s. In 2005 he was a visiting researcher in the

laboratory of ProfessorHoward Ceri, University ofCalgary, where he remainsa visiting scientist in theBiofilm Research Group.He was promoted toSenior Lecturer inPharmaceuticalMicrobiology in 2010. Hisresearch aims to elucidatethe mechanistic andbiochemical pathwayscentral to the process ofmicrobial biofilm

formation and to uncover novel targets for prevention ofmicrobial biofilms; spanning microbiology, chemicalbiology, and synthetic/medicinal chemistry directed towardantimicrobial and anti-biofilm applications. His maininterests include the role of proteolytic enzymes in biofilmformation and development of novel approaches for biofilmcontrol in chronic infections. He has an active researchinterest in antibiotic biodiscovery from marine bacteria andarchaea (extreme halophiles). Brendan is the 2013recipient of the Royal Pharmaceutical Society ScienceAward for his research contributions in the field of biofilmcontrol and pharmaceutical microbiology. He is an Editorof the textbook ‘Hugo & Russell’s PharmaceuticalMicrobiology’ (8th Ed) and is responsible for teaching allaspects of pharmaceutical microbiology and infectiousdiseases to undergraduate pharmacy students at QUB.

Brian Jones

Brian graduated from Cardiff University in 2000 with aBSc (Hons) in Genetics. He completed a PhD in 2004, alsoat Cardiff University, investigating the role of swarming in

the pathogenesis ofProteus mirabilis urinarytract infections. In 2004,he joined the AlimentaryPharmabiotic Centre andMicrobiology Departmentat University College Cork,Ireland, where he began towork on the human gutmicrobiome and associatedmobile metagenome. In2008, he took up aposition at the Universityof Brighton, where his

research group continues to study the pathogenesis ofdevice-associated infections, as well as the structure andfunction of the human gut microbiome.

Val Edwards-Jones

Val worked for 20 years in the NHS as a diagnosticmicrobiologist and then transferred to academia afterundertaking her PhD on toxic shock syndrome in burned

patients. Since then, Valhas continued to researchand has published inseveral areas of medicalmicrobiology includingrapid diagnostictechniques, woundinfection, biofilms andantimicrobial agents.

Val is very interested inthe role of biofilms inchronic wounds andcontinues to work withthe healthcare

professionals and industry to help improve these issues.Val also works as a microbiological advisor with MaverickTV who produce the series Embarrassing Bodies onChannel 4.

John Threlfall

Since being awarded a PhD in Microbial Genetics in1969, John has worked in the UK Health ProtectionAgency (HPA) (formerly the Public Health LaboratoryService, now Public Health England) in a variety of roles.Most recently he served as Director of the HPALaboratory of Enteric Pathogens from 2004 to 2008 andas Head of R&D in the Gastrointestinal, Emerging andZoonotic Infections Department from 2008 to 2010.

In 2007, he wasappointed Project Directorfor the EU-funded Med-Vet-Net Network ofExcellence and continuedin this role in the Med-Vet-Net Association until2011.

From 2010 to 2012John was employed asProgramme Manager forthe HPA for the EU-funded EURLOP (EUHuman ReferenceMicrobiology Options

Project) and ECDC-funded EU-LabCAT project, whichwere targeted at rationalizing various aspects of humanreference microbiology within the EU. Therecommendations from these projects are currently beingimplemented. He was appointed to the European FoodSafety (EFSA) Biohazards (BIOHAZ) Panel in 2009 andhas recently been elected for a second three-year term ofoffice.

His principal interests are antimicrobial drug resistancein bacterial zoonotic pathogens and the molecularepidemiology of foodborne zoonoses; he has publishedextensively in these areas.

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Agnieszka Piotrowska

News from the SfAM Postgraduate andEarly Career Scientist Committee

Firstly, the term public engagement, asdefined by the Higher Education FundingCouncil for England, is ‘the involvementof specialists listening to, developingtheir understanding of, and interactingwith, non-specialists’. In other words it isgetting people involved in science byexplaining it at a level that can beunderstood. But why exactly do scientificsocieties want to get actively involved?Very importantly, misrepresentedscientific research, and generallyunsubstantiated ‘science’ is sometimesgiven a platform in the media which canbe misleading to the lay person. This canoccur in many media forms available intoday’s society, so it is important for thepopulation to be aware of the possiblemisinterpretations and misconceptionsthat exist. It is essential, therefore, tomake sure the public is well informed onhow to critically interpret scientific news.A good example of this is theorganization Sense About Science. Theywork with scientists and members of thepublic to change public debates, and toequip people to make sense of scienceand evidence.

Furthermore, as scientists we shouldalways encourage greater understandingof science for many reasons, forexample, public health issues. SeveralSfAM public engagements events haveaimed to give children (and theoccasional adult!) a better understandingof pathogenic bacteria, and the processin which bacterial illnesses are identified.One of the take-home messages is theimportance of good hygiene, in additionto getting children interested in ‘behindthe scenes’ science. This is not onlybeneficial for public health, but couldalso set the path for the next generationof microbiologists!

It can be a daunting task to organizean outreach event and get a goodturnout. The easiest way is to arrange itin a family friendly environment. Anexample could be to join a local fair andask a school teacher if they would beinterested in taking part in a publicengagement event. There are alsovarious events already organized forScience, Technology, Engineering andMathematics (STEM) ambassadors — it isfree to join the STEMNET and you needonly commit to participating in one eventa year. STEM ambassadors contributethrough clubs, careers days, and regularlessons to give a fresh perspective toyoung people and engage their interestand imagination.

Alternatively, if you are creative andwould like to organize your ownoutreach event, there are opportunitiesto find support and funding from manyprofessional bodies that would be happyto support you, and may even offer helpand support with the organization. Thisyear the PECS Publications Officer, Jenni,participated in a Science Communicationtraining day; “…this workshop wasdesigned to enhance our skills anddemonstrate the impact and benefits ofour research to schools and the public.We were shown interactive ways todeliver activities and become confidentto use resources and engage with wideraudiences”. These days can be usefultraining and are also good networkingopportunities.

You need to have a clear end-goal inmind when organizing an event; it reallyneeds to be planned well. One of thefirst things to ask yourself whenplanning an event is ‘What do you reallywant the audience to remember whenthey have left you’? Your event can befunny and interesting, but you need toensure that people visiting leave withthis message. Organizing hands-onactivities can be a great way to keepkids engaged — it can be messy thoughso beware! A good example of a verywell-known activity is the ‘handwashingexperiment’. Using UV glow cream anda UV light you can show them how wellthey washed their hands, explaininghow important it is to do so and whatthe potential consequences are if theydon’t. If possible, try to have somefreebies for them to take home —preferably with some information aboutyour activity or a link to a websitewhere they can learn more.

If it is successful, hopefully they willpass on what they learnt to their familymembers and friends. You can also usethe time with your captive audience toadvertise other public engagementevents taking place.

Even if you don’t organize your ownevent, there are many societies that carryout public engagement, and I’m surethat you will find something that is rightfor you. Just do it – it is fun and veryrewarding (it is also very good for yourCV!).

Don’t forget — SfAM has a PublicEngagement Grant you could apply forand the Society also gives opportunitiesto Members to volunteer at publicengagement events they are taking partin. Get involved!

Publicengagement

In recent years public engagement hasbeen a hot topic. But what is it? Whyhas it become so important and why

are scientists so keen to get involved?

46

members

careersPupils topolicy viapublic health

Given the magazine and itsaudience, I think it’s only rightand proper to declare up front

that my degree was in pharmacology,therapeutics and toxicology, and I enjoybooks on particle physics. Specializingin a particular field was not for me,though, and my career since has mostlybeen jobs where I get to work with, orapply knowledge from, a number offields. I’m happy to be a jack-of-all-trades (less so a master of none)because for me, it’s the way of thinkingthat comes with working in sciencethat’s most interesting.

Graduating without any firmconvictions as to career paths, I tookadvantage of the freedom and applied toVoluntary Service Overseas (VSO). Atthat time, VSO ran a scheme to placescience or maths graduates as teachersin secondary education level abroad. Forme, this was an opportunity to live andwork abroad; experiencing anotherculture rather than floating by with arucksack on my back.

Passing the interviews and sittingthrough the teacher training courses, Iwas placed as a general science teacherin the village of Bongo in the UpperEast Region of Ghana. At the time,general science comprised everythingfrom optics to fish farming, something Iwas completely unprepared for. I mean,how many of you could design a fishfarm in sub-Saharan Africa based on

your university education? My first threemonths were spent combattinglanguage/accent issues (the locallanguage of Gurune and Welsh didn’tmix easily) and removing spiders fromthe neglected laboratories.

Dusty: a stock answer when anyoneasks me about my experiences abroad,but how can you condense two yearsinto a few sentences? I’m not going totry here.

I brought many things back with mefrom Ghana: a love of teaching science,the malaria parasite, long hair and achieftaincy title (Naba Asikoulga II forthe curious reader) to name a few. Thebiggest impact on my life, though, hasbeen perspective. To this day I lookback at the knowledge, experiences andemotions of my time in Bongo to put mycurrent situation, whether personal orprofessional, in its place.

Returning to the UK and still nonethe wiser about a career, I simply lookedfor opportunities to use and work withscience. I never once consideredteaching because of the differencesbetween the education systems in theUK and Ghana. In Ghana, every studentwanted to learn, regardless of theirability. That made a huge difference.There were also laxer health and safetycontrols, which as a science teacheropened up a world of possibilities. Mymother, a head teacher, subsequentlyconfirmed I would probably have been

sacked in the UK for some of mypractical lessons. My students, on theother hand, got better results than anyprevious year group at the school.

Combing job adverts, I spotted arecruitment drive for scientific officersat the Food Standards Agency (FSA).Just the sort of thing I was looking forand a move to London as well. Movingto the anonymity of London from thegoldfish bowl of Bongo would be awelcome change. I was successful,having given an interview presentationon the MMR media coverage, andrecruited into the somewhat oddly titled‘incidents branch’.

Food law is there to make sure thatall food is safe and fit for consumption.When it goes wrong somewhere alongthe food chain, the incidents branch arecalled. They are there to link betweenthe reports from local authorities,industry or the public and those whoassess the risk to consumers. Once therisk has been assessed, decisions mustthen be taken on how to manage therisk and how this should becommunicated. The work coveredeverything from outbreaks of foodbornedisease to chemical spills and labellingdiscrepancies.

As the scientific officer within theteam, I was there to explain the riskassessments in a languageunderstandable to non-scientists. Thescience teaching stood me in good stead.

Hefin Davies describes hisvaried career journey

47

My first brush with microbiology wasan investigation into levels of Listeriaspp. in cooked sliced meat. Notnecessarily a safety issue, but indicativeof hygiene failings at some point in thechain. I quickly learned how difficult itwas to pin down a source of bacterialcontamination (a spill is so mucheasier). Thanks to the knowledge of theFSA’s own microbiologists and thosewithin the Health Protection Agency(now Public Health England)Salmonella spp. and E. coli spp.followed soon after, picked up by one ofthe tens of thousands of food samplestaken annually.

Is it safe? A question that seems sosimple yet can be incredibly tricky. Wehave regulatory standards and nationalguidance on unsafe levels of pathogensin food to help us, certainly, but that’sonly part of the story. Can one resultfrom a shop-bought product besufficient to require action against tonsof product up and down the country inpeople’s homes? Sometimes. It’s rarelyblack and white and has to beconsidered 200−300 times a year [317microbiological incidents in 2012 (FSAannual report of incidents 2012)].

My first big outbreak was SalmonellaMontevideo in 2006 and what anoutbreak to start with. A well-knownconfectionary company’s chocolateproducts were identified as the probablecause resulting in a UK-wide recall of

products and a lot of scrutiny from allquarters. Being at the centre of theinvestigation as the situation developedwas fast-paced and exciting, especiallyas details emerged of the extent towhich the company were aware of thecontamination at one of its sites. Theresulting prosecution and fine of £1million were seen as thoroughlyjustified.

The key to any outbreak response isbringing together the microbiological,environmental and epidemiologicalevidence as quickly and thoroughly aspossible to try and establish the likelysource. We rarely have all the evidencewe would like but decisions are neededto prevent further cases. We only haveto look at the E. coli O104 outbreak inEurope during 2011 to see what canhappen when quick decisions have to bemade on incomplete evidence.

Having been away from Wales for fiveyears, I decided it was time to returnand took a job with the FSA’s office inCardiff. My incidents role was fairlysimilar but now, ‘microbiologist’ hadbeen added to my job title. I wasresponsible for microbiological riskassessment work, using my experiencefrom the previous few years.

I ended up working with a lot ofpeople in different organizations whohad been involved in the South Wales E.coli O157 outbreak in 2005, whichtragically resulted in the death of a

■ FSA annual report of incidents. (2012).http://www.food.gov.uk/multimedia/pdfs/incidents-report-2012.pdf.

references

young boy. The outbreak and resultingPennington enquiry set the landscapefor my role over the next few years. Igot to know staff from local authoritiesand Public Health Wales very well,which ultimately benefited the responseto incidents and outbreaks. For anyoutbreak control team, I would alreadyknow most of the other people aroundthe table, making the communicationslicker and easier.

Despite the job title, my roleincluded environmental contaminationand managing the post-Chernobyl sheepmovement restrictions in North Wales;therefore, I had to add radiologicalprotection to my ever-increasingscientific bow. As the role developed,genetic modification andnanotechnology joined the party.

With my Ghana experience showingthrough, I started sharing thisknowledge with others by preparingteaching sessions on pretty muchanything for anyone who was preparedto listen. Whether FSA staff, boardmembers, university students or foreignvisitors, I would happily don myEinstein wig and talk about carbonnanotubes.

Ultimately, I became a scientificadvisor and support to the entire officein Wales. It was more than just‘explaining all the long words’ andmeant that I got to experience and workon everything that the FSA isresponsible for. Breadth of experience iswhat I enjoy and what keeps meinterested.

I have now moved on and work ondeveloping food safety policy andnegotiating legislation in Europe. The‘scientific’ jobs may have gone but theskills I’ve developed, the knowledge I’vegained and the way of thinking thatcomes with scientific inquiry; well, theystay with me.

Hefin DaviesOfficial Feed and FoodControls Policy, FoodStandards Agency

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members

Bdellovibrio and Salmonella isolation from reptiles

Human salmonellosis remains amajor public health burden, with over99,000 reported cases in the EU in 2010(http://www.efsa.europa.eu/en/efsajournal/pub/2597.htm). However, the trueincidence of salmonellosis may be muchhigher than this (up to 2,000 timeshigher in some countries) according toone recent serological study(Falkenhorst et al., 2012). Salmonellosisis usually considered to be a foodbornedisease, but an increasing number ofcases have been linked to contact withpet reptiles (Bertrand et al., 2008).Exotic animals have becomeincreasingly popular pets in recentyears. More than 500,000 pet reptileswere imported into Frankfurt airportalone during 2007 (Bertrand et al.,2008). Salmonella colonizes manyreptiles asymptomatically, with theprevalence in some species reachingalmost 100% (Caine et al., 2009). Theuse of antimicrobials to reduceSalmonella numbers in reptiles is notadvised because of emerging problemswith resistance and the high prevalenceof this pathogen in reptiles. Biologicalcontrol using bacteriophages may be anoption, as phages have been used tocontrol Salmonella in poultry and pigsin experimental trials (Atterbury et al.,2007; Wall et al., 2010). However,bacteriophages tend to have a restrictedhost range and continual use of phagesusually results in the emergence ofresistant populations of bacteria.

An alternative biological controlexists in the form of the Gram-negativebacterium Bdellovibrio bacteriovorus.Bdellovibrio is a predatory bacteriumthat invades and kills other Gram-negative bacteria, including pathogenssuch as Salmonella. Unlike

am I eligible — can I apply?Yes — if you are FULL Member who can offer an undergraduatemicrobiology student the chance to obtain work experience. If youwould like to read about the experiences of students who havebenefited from this grant, you can do so below.

For further information visit: http://www.sfam.org.uk/siw

Students into Work Grant report

bacteriophages, resistance toBdellovibrio predation cannot arisefrom a single mutation event. In fact,only one resistance mechanism hasbeen found so far, the production of anintact S-layer (Sockett, 2009).Bdellovibrio and like organisms(BALO) have been isolated from thefaeces of some animals and humans(Schwudke et al., 2001); however, todate, no studies have attempted toisolate Bdellovibrio from reptiles. Inour study, we attempted to isolate BALOfrom reptiles as a first step towardsdeveloping a biological treatment toreduce Salmonella in pet reptiles.

Faecal samples were collected frompet reptile species (bearded dragon,milk snake, corn snake, tortoise) at theSchool of Veterinary Medicine,University of Nottingham, and speciesfrom the reptile section of TwycrossZoo. The faecal samples were dilutedapproximately 1:10 in Ca-HEPES buffer.Volumes, 1ml of each faecal suspensionwere cultured for Salmonella byselective enrichment in Rappaport-Vassiliadis (RV) broth, followed bystreaking onto a selective medium(Brilliant Green agar). PutativeSalmonella isolates were confirmed byagglutination with poly-O antiserum.The resistance of the Salmonellaisolates to a range of antimicrobials wasdetermined using the disc diffusionmethod.

Bdellovibrio isolation from thefaecal samples was performed byadding a cocktail of prey bacteria(Salmonella and E. coli) to the faecalsuspensions and incubating at 30°C forup to two weeks. Bdellovibrio isolationfrom some sources requires prolongedincubation, and therefore, 1ml volumes

of the faecal enrichment cultures weretaken every three days to examine forthe presence of Bdellovibrio by bothlight microscopy and direct cultureusing a double-layer agar overlaycontaining prey bacteria (Lambert &Sockett, 2008). The plates wereincubated for up to two weeks at 30°Cand regularly examined for the presenceof typical Bdellovibrio plaques.Putative Bdellovibrio plaques weretransferred to Ca-HEPES buffercontaining prey bacteria and incubatedfor 2−3 days at 30°C.

In this study, we found that 4/25(16%) faecal samples tested positive forSalmonella spp., all of these sampleswere taken from the pet reptile speciesat the university. This result is in linewith previous suggestions that apresence of Salmonella in reptiles is tobe connected to a specific area insteadof individual animals (Caine et al.,2009). All four Salmonella isolatesfrom the pet reptiles were resistant topenicillin, erythromycin and ampicillin,but limited or no resistance wasrecorded for tetracycline,chloramphenicol and streptomycin. Theresistance of these isolates to ampicillinis particularly worrying as this is one ofthe antimicrobials often relied upon totreat invasive Salmonella infections(Crump et al., 2011). A number offaecal samples (8/25, 32%) includingboth samples from the university(bearded dragons, milk and cornsnakes) and Twycross Zoo (monitorlizard, boa constrictor, glass lizard),contained small, highly motile bacteriawhich resembled Bdellovibrio. We planto confirm whether or not these bacteriaare Bdellovibrio or like organisms by16S rRNA gene sequence analysis, and

49

Kostijn van GinkeltUniversity of Nottingham

References■ Atterbury, R. J., Van Bergen, M. A.,Ortiz, F., Lovell, M. A., Harris, J. A., DeBoer, A., Wagenaar, J. A., Allen, V. M., andBarrow, P. A. (2007). Bacteriophagetherapy to reduce Salmonella colonizationof broiler chickens. Appl. Environ.Microbiol., 73, pp4543−4549.

■ Bertrand, S., Rimhanen-Finne, R., Weill,F. X., Rabsch, W., Thornton, L.,Perevoscikovs, J., Van Pelt, W., and Heck,M. (2008). Salmonella infections associatedwith reptiles: the current situation inEurope. Euro. Surveill., 13, pp1−6.

■ Caine, C., Tyre, D., and Ferraro, D.(2009). Incidence of Salmonella on reptilesin the pet trade. RURALS: Review ofUndergraduate Research in Agriculturaland Life Sciences, 4, p12.

■ Crump, J. A., Medalla, F. M., Joyce, K.W., Krueger, A. L., Hoekstra, R. M.,Whichard, J. M., and Barzilay, E. J. (2011).Antimicrobial resistance among invasivenontyphoidal Salmonella enterica isolatesin the United States: National AntimicrobialResistance Monitoring System, 1996 to2007. Antimicrob. Agents Chemother., 55,pp1148−1154.

■ Falkenhorst, G., Simonsen, J., Ceper, T.H., Van Pelt, W., De Valk, H., Sadkowskq-Todys, M., Zota, L., Kuusi, M., Jernberg, C.,Rota, M. C., Van Duynhoven, Y. T., Teunis,P. F., Krogfelt, K. A., and Molbak, K.(2012). Serological cross-sectional studieson Salmonella incidence in eight Europeancountries: no correlation with incidence ofreported cases. BMC Public Health, 12,p523.

■ Lambert, C., and Sockett, R. E. (2008).Laboratory maintenance of Bdellovibrio.Curr. Protoc. Microbiol., Chapter 7, Unit 7B2.

■ Schwudke, D., Strauch, E., Krueger, M.,and Appel, B. (2001). Taxonomic studies ofpredatory bdellovibrios based on 16S rRNAanalysis, ribotyping and the hit locus andcharacterization of isolates from the gut ofanimals. Syst. Appl. Microbiol., 24,pp385−394.

■ Sockett, R. E. (2009). Predatory lifestyleof Bdellovibrio bacteriovorus. Annu. Rev.Microbiol., 63, pp523−539.

■ Wall, S. K., Zhang, J., Rostagno, M. H.,and Ebner, P. D. (2010). Phage therapy toreduce preprocessing Salmonella infectionsin market-weight swine. Appl. Environ.Microbiol., 76, pp48−53.

by culturing with a range of potentialprey bacteria.

In conclusion, Salmonella spp. wasisolated from reptile species which arecommonly kept as pets in the UK; inaddition, bacteria resemblingBdellovibrio and like organisms wereisolated from a number of faecalsamples taken from the university andTwycross Zoo. If these isolates areconfirmed as Bdellovibrio or likeorganisms, this may be a first steptowards using this bacterium to reducethe prevalence of Salmonella in petreptile species. As a veterinary studentwith a strong interest in microbiologyand public health, this project has

provided me with invaluable practicallaboratory experience, beyond the scopeof the veterinary curriculum, in the fieldof zoonoses, which will undoubtedly aidmy career potential in this field. Thisproject would not have been possiblewithout the generous grant from theSociety for Applied Microbiology, forwhich I thank the Societywholeheartedly, the guidance of mysupervisor Dr Robert Atterbury, thehelpful practical advice and scientificinput from Professor Liz Sockett, andthe willingness of the University ofNottingham and Twycross Zoo to supplyme with the necessary samples forwhich I am grateful.

50

members

am I eligible — can I apply?It is not only our Student Members who require our help. Seniormicrobiologists often find difficulty in funding attendance atmeetings. If you are in this position you are eligible for this fund.

For further information visit: http://www.sfam.org.uk/presidents-fund

President’s Fund report

The role of fungi in biodegradation of compostable plastic polylactic acid

Conventional plastics such aspolyethylene terephthalate (PET),polyvinylchloride (PVC), polyethylene(PE), polypropylene (PP), polystyrene(PS) and polyamide (PA) have beenused for decades in a diverse range ofapplications as they are easilyprocessed, available in large quantities,inexpensive and they have favourablemechanical characteristics. However,

they are non-biodegradable and whenthey are used as short shelf-lifeproducts, as they are resistant tomicrobial attack, they accumulate in theenvironment and cause waste disposalproblems. Recycling has not developedsufficiently to keep up with increasingamounts of plastic consumption anddemand. In addition, the vast majorityof conventional plastics are derived

from petrochemicals and theirmanufacture is dependent on non-renewable fossil fuels.

Poly(lactic acid) (PLA) is a syntheticaliphatic polyester with a hydrolysablebackbone that is susceptible todegradation and uses starch as arenewable feedstock. Since its rawmaterial is lactic acid, it can beobtained from renewable resources such

Figure 1. Compostable disposable PLA containers

51

References■ Jarerat, A., and Tokiwa, Y. (2001).Degradation of poly(L-lactide) by a fungus.Macromolecular Bioscience, 1, pp136−140.

■ Sangwan, P., and Wu, D. Y. (2008). Newinsights into polylactide biodegradationfrom molecular ecological techniques.Macromolecular Bioscience, 8, pp304−315.

as starchy materials. PLA hasfavourable properties including ease offabrication, no toxicity, biocompatibility,high mechanical strength and it is alsocompostable. Lactic acid, the precursorof PLA, can be produced by bacterialfermentation and it is much cheaperthan producing PLA as a petrochemical-derived product. PLA has beenpreferred in the medical area andcurrently, food-packaging films havebeen produced from PLA for shortshelf-life products.

The most accepted mechanism ofPLA degradation involves a two-stepmechanism involving chemicalhydrolysis in the presence of water,followed by microbial degradation inwhich microorganisms mineralizepolymer breakdown productsgenerating carbon dioxide underaerobic conditions and methane underanaerobic conditions. This is a distinctfeature of PLA because typicallybiodegradable polymers are degradedby microbial attack in a single step.However, there is some evidence tosuggest that microbial enzymes existcapable of directly degrading highmolecular weight PLA.

High molecular weight PLAdegradation solely by microorganismsand enzymes is poorly understood andto date, most identified PLA degradersare actinomycetes. Sangwan and Wu(2008) suggested that there were likelyto be far more PLA degradingmicroorganisms still to be identified, asthe techniques employed to date werebased on classical cultivation methodsthat favoured the fastest growingmicroorganisms by employing brothenrichment rather than solid material,and because the majority ofenvironmental microorganisms cannotreadily be grown on laboratory media.As a result of this study it is suggestedthat phyla Actinobacteria (especiallythose belonging to the generaThermomonospora andThermopolyspora) and Ascomycota(genus Paecilomyces) might playsignificant roles in the biodegradationof PLA under composting conditions.

Since PLA short shelf-life productsare thrown away after their use (Figure1), understanding the PLA degradationmechanism and monitoring thedegradability of PLA, in differentenvironment conditions, are the mainconcerns of this study. In addition, withthe exception of Tritirachium album,

Mehlika Karamanlioglu

no PLA degrading fungi have beenidentified (Jarerat & Tokiwa, 2001).

Therefore, the aims of this studywere to investigate the degradation ofPLA in different environmentalconditions; to determine the relativeimportance of biological and chemicalfactors in PLA degradation bycomparing the rate of degradation inmicroorganism-rich compost and soilwith the rate of hydrolysis in sterilewater; identify the role of fungi asputative PLA degraders; and todetermine the diversity of fungalcommunities growing on the surface ofPLA buried in compost and soil by anon-culture based study.

The rate of PLA degradation incompost and soil was compared withsterile water at a temperature range todecide the role of hydrolysis andmicroorganisms in PLA degradation.Degradation was assessed by measuringtensile strength. The loss of tensilestrength in microorganism-richcompost and soil was faster thanhydrolysis in sterile water at 50ºC,indicating a role for microbialdegradation (Figure 2).

Putative fungal PLA degraders wereisolated from the surface of PLA buriedin compost and soil at 25 and 50ºC,and identified by ribosomal DNAsequencing. Abundant fungal growthwas observed on the surface of PLArecovered from compost at 50ºC byenvironmental scanning electronmicroscopy (ESEM) and were theprinciple microbes recovered from thesurface, suggesting thermophilic fungiplay an important role in thedegradation process. Terminalrestriction fragment lengthpolymorphism (TRFLP) was used as a

non-culture based method forcommunity analysis of PLA buried incompost and soil at 25 and 50ºC. PLAburied in compost and soil either at 25or 50ºC had less fungal diversity withless evenness than compost and soil,with no PLA suggesting enrichment forPLA degraders on the surface of PLA.

The project will determine the abilityof isolated and identified fungi todegrade PLA and also the impact ofPLA on the quality and microbialdiversity of compost by non-culturebased methods, including TRFLP andnext generation sequencing.

I would like to thank the Society forApplied Microbiology for thePresident’s Fund award, whichenabled me to attend the 14thInternational Symposium on MicrobialEcology in Copenhagen, Denmark, inAugust 2012. This gave me the chanceto communicate with colleagues in myfield and learn about the latestdevelopments and methods in microbialecology such as next generationsequencing. I also would like to thankmy supervisor Dr Geoff Robson for hishelp and support throughout myproject.

Figure 2. Tensile strength changes of PLA incubated in compost, soil and sterile waterat 50ºC for 60 days

52

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Microbiologics has extended their offering ofShiga-toxin producing Escherichia coli (STEC)products to include Epower™. Epower™ is aready-to-use QC microorganism product whichdelivers a specific number of colony forming units(CFU) and is used for quantitative microbiologicalquality control testing.

Under USDA regulation, E. coli serogroups O26,

Biological back-up servicesat NCIMB

While most laboratories and researchorganisations will have an automated system inplace for backing up information held oncomputers, systems for backing up microbialcultures and genetic material may be less rigorous.However, these collections can represent alifetime’s work and may be effectively irreplaceablein the event of accidental loss or damage.

The World Federation of Culture Collectionsproduces guidelines for culture collections whichinclude the use of two methods of preservationand having an off-site back-up storage facility. In

order to minimise the riskof losing key biologicalresources, researchorganisations andlaboratories can followsimilar guidelines butpreservation techniquessuch as freeze-drying aretime consuming and theskills and equipmentrequired may not beavailable in-house.

NCIMB offers a rangeof commercial off-site storage services for bacteria,yeasts, actinomycetes, bacteriophages, purifiedDNA, plasmids/cosmids and seeds that can helpyou to securely and confidentially preservebiological resources.

We can use a range of techniques to preservecultures prior to storage or accept them readyprepared, and can store material with a hazardrating and physical containment level no greaterthan ACDP category 2 or ACGM class 1.

further Information

Visit: www.ncimb.comTel: +44 (0)1224 711100Email: s.law@ncimb.com

Leatherhead Food Research:food safety & productintegrity

Leatherhead’s food safety portfolio provides acomprehensive range of products and services tohelp food and drink companies maintain thehighest possible standards of safety and stability intheir products. We provide a broad array ofmicrobiological food testing, analysis andconsultation covering microbiological food safety,training and advice, and bespoke testing, ifrequired.

Our main focus areas include:■ Shelf life and challenge testing (including Cl.

botulinum) ■ Microbial inactivation kinetics (to aid food

processing) ■ Molecular diagnostics including speciation of

bacteria, yeasts and moulds, and horsemeat■ Enteric virus research and detection ■ Antimicrobial screening and alternative

natural preservation technologies■ HACCP training and studies including

troubleshooting and audits ■ Biofilm study and control ■ Method development and validation of rapid

detection methods ■ Validating and advice on cleaning and

disinfection procedures Additionally, our Food Safety & Product

Integrity Department is supported by expertise

corporatenewsThe latest news, views and microbiologicaldevelopments from our Corporate Members

O103, O45, O111, O121 and O145, alsocommonly referred to as the ‘Big 6 E. coli’, areprohibited from raw ground beef, its components,and tenderized steaks. In addition to the Big 6 E.coli strains, Microbiologics also offers serogroupsO157 and O104. Beef testing laboratories useMicrobiologics QC microorganisms for validation,verification and routine quality control checks oftheir STEC testing processes, material, equipmentand personnel proficiency.

Epower™ QC microorganisms are packaged ina vial of 10 lyophilized pellets consisting of a singleenumerated microorganism strain. Also included isa peel-off Certificate of Assay detailing the identityand mean assay value of the pellets for quick andeasy documentation. Customers especially likeEpower™ because of the versatility the productoffers; Epower™ pellets can be easily manipulatedto deliver a wide range of CFU concentrations, ormultiple strains can be combined for a mixedmicroorganism population.

further information

Visit: www.microbiologics.comTel: 00+1 320 253 1640Email: info@microbiologics.com

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Same time and reduce errorswhen using MALDI–TOF

MALDI–Trace™ is a system created specificallyfor the traceability of organism identification testsperformed using seeded target plates and Matrix-Assisted Laser Desorption Ionization — Time ofFlight (MALDI–TOF) technology.

The system provides a platform thatidentifies which area on a MALDI targetplate needs to be inoculated. Thisinformation is transferred to theMALDI–TOF and onceidentification has taken placethis is registered directly ontothe LIMS — no need tocomplete manual worksheetsfor the transfer of data. MALDI–Trace™ allows laboratorypersonnel to keep track of culture isolates withoutthe risk of transcription errors.

■ MALDI–Trace™ is designed to be conveniently used inside a laminar flow cabinet.

■ Full traceability of information related to the seeded target plate (patient information, specimen description, presumptive culture isolate name and other patient identifiers).

■ Accurate management of isolates and their correct placement on target spots.

■ Automatic on-screen display of the number and location of target spots seeded.

■ Different operational modes and integration with different systems: HighFlexX, WASPLab™ Image Recording.

■ Open flexible system for future integrations with other laboratory Middleware or LIMS systems.

■ Ergonomic target plate holder that prevents accidental contamination of perimeter target spots during transport prior to insertion into the MALDI–TOF.

further information

Visit: www.dwscientific.co.ukTel: + 44 (0)1274 595728Email: sales@dwscientific.co.uk

New video shows Lab M’snew µPREP™ media formatin action

Lab M’s new video shows how quick and easy itis to prepare and use the company’s µPREP™ lineof bagged, ready-to-reconstitute microbiologicalculture media. µPREP™ Buffered Peptone WaterISO (BPW) is the first medium to be produced inthis new format, which is designed for maximumconvenience and ease of use. It saves laboratorytime and resources in media preparation for highthroughput testing while minimising storagerequirements. The 5-minute video provides a step-by-step guide on how to prepare, use and storethe pre-enrichment medium:http://bit.ly/LabMBPW

Formulated to ISO 6579, Lab M’s BufferedPeptone Water ISO (BPW) supports the recovery ofsublethally damaged salmonellae prior to selectiveenrichment. This nutrient medium is free frominhibitors and is well buffered to maintain pH 7.0for the incubation period. Sublethal injury tosalmonellae occurs in many food processes andsuch pre-enrichment steps greatly increaserecovery of these organisms.

µPREP™ media take up minimal storage space,offer quick, convenient, time-saving reconstitution

from across Leatherhead. For example, we cancheck the safety/shelf life of a reformulation,whilst ensuring that it meets the required sensoryand nutritional properties. We can also provideregulatory advice so that the product meets therequired legislation for the countries in which is itsold.

further information

Visit: www.leatherheadfood.comTel: +44 (0)1372 376761Email: help@leatherheadfood.com

with no need to autoclave, and can be preparedwith minimal training. The product is suppliedsterile in boxes of 10 highly robust bags, eachmaking 20 litres of complete media. To view theµPREP™ video visit: http://bit.ly/LabMBPW

further information

Visit: www.labm.comTel: +44 (0)161 820 3833Email: info@labm.com

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Are you a CorporateMember of the Society?If so, this section ofMicrobiologist is foryou. Here you canpublish short pressreleases, acquisitionnotices, news of newstaff appointments,technical developmentsand much more.

Each CorporateMember of the societymay publish up to 200words on a topicrelated to their field ofactivity in each issue ofMicrobiologist. Forfurther informationplease contact NancyMendoza by email at:nancy@sfam.org.uk

Both CorporateMembers and OrdinaryMembers of the Societywill find a wealth ofuseful information andresources in thissection.

information

commercial

NEW — rapid detection ofCarbapenemase resistancemechanism in less than twohours.

Rapid Carbapenemase Screen is a simple, twohour, test that will detect the presence ofcarbapenem resistant organisms in fresh culture,blood culture and urine specimens.

Based on the Carba-NP as described byNorddmann, Poirel & Dortet and mentioned in theboth the HPA (PHE) document on detectingcarbapenemases and the Eucast draft guidelinesfor detecting resistance mechanisms. Rosco’s RapidCarbapenemase Screen has the required reagentsin tablet form together with a negative control tohelp interpret borderline reactions (product code98021).

Carba NP is a microtitre based method which(at the time of writing — September 2013) is notcommercially available. However, promisingevaluations have been published, both on platecultures, and on pellets obtained by centrifugingblood cultures by laboratories with the facilities to

Comprehensive veterinaryvaccines productdevelopment service

VLA Scientific offers a range of services forlivestock pharmaceutical and vaccine research anddevelopment. Our services extend from datageneration during initial research through to batchtesting on finished products.

We have a wealth of experience of in-vitro andin-vivo techniques with expertise in infectiousdisease modelling, efficacy and safety testing.Benefits include access to comprehensive librariesof bacterial, viral and parasitic organisms and ourextensive facilities enable us to work withorganisms requiring containment ACDP level 3and SAPO category 4.

In addition to these services, our clients haveaccess to world leading livestock disease experts inpathology, epidemiology, microbiology,parasitology and virology who can advise onrecent research findings as well as modeldevelopment and study design.

Our vaccine development services include: ■ Primary research ■ Antigen development■ Antibody and antigen detection ■ Testing for attenuation■ Extraneous agents testing■ Efficacy, safety and bioequivalence testing Where necessary, our services are performed in

accordance with Good Laboratory Practice, GoodManufacturing Practice and Good Clinical Practice(veterinary) with a minimum site standard for allactivities of ISO 9001 and ISO17025 for most ofthe testing work.

further information

Visit: www.ahvlascientific.comTel:+44 (0)1932 357641Email: ahvlascientific@ahvla.gsi.gov.uk

reproduce the test method in-house. AlthoughRapid Carbapenemase Screen has yet to havepublished evaluations early results from a LondonTeaching hospital show the test is easy to performand read and gave 100% correlation with knowncarbapenemases and non-carbapenemases.

To find out more about this new product andhow they can help in your laboratory testingplease visit the BioConnections website,alternatively contact us by email or by telephone.

further information

Visit: www.bioconnections.co.ukTel: +44 (0)1782 516010Email: welcome@bioconnections.co.uk

Swabs for every application

Medical Wire is the specialist in swab-basedspecimen collection. In addition to manufacturingTranswab®, the leading range of liquid and semi-solid medium transport swabs, it offers anexceptional range of dry swabs for everyconceivable application. Whether swabbing frogsin the Amazon forests for chytrid fungus, chickensfor avian flu, or pipework for biofilm, whethertesting is conventional or molecular, Medical Wirehas the device.

Dry swabs come with advanced bud materialsincluding PurFlock® and HydraFlock® multifilamentflocked fibres, Sigma-Swabs® with cellularpolyurethane foam, or spun fibres rayon andpolyester. Shafts are available in plastic or wirewith varying flexibility or rigidity. Swabs with nylonbristles are used for cervical smears, while somevery long swabs with bud or brush ends are usedfor larger animals.

Dry swabs are supplied in three formats.Labelled tubes with the swab mounted in the capare self-contained and ideal for the transport ofcertain specimens. Individual swabs in sterile peelpouches are convenient when a test is performedimmediately. Multiple packs may be suitable whensamples are to be pooled.

further information

Visit: www.mwe.co.ukTel: +44 (0) 1225 810361Email: sales@mwe.co.uk

events in 2014

Wednesday 15 January 2014

The Royal Society, London, UK

Wednesday 30 April 2014

The Sheffield Hilton Hotel, Sheffield, UK

30 June – 3 July 2014

The Grand Hotel, Brighton, UK

For further information on these events please visit www.sfam.org.uk/eventsor contact Sally Hawkes ■ Email: sally@sfam.org.uk ■ Telephone +44 (0)1933 382191

Save the dates!Winter Meeting● Food contamination:

the food handler’s role

● BiodefenceIncluding the Denver Russell Memorial Lecture

Spring Meeting

● Control of infection: current status and future prospects

Summer Conference● Zoonoses■ In conjunction with the Med-Vet-Net Association

■ Including the Journal of Applied Microbiology(JAM) Lecture

8th broadening microbiology horizons in biomedicalscience meeting