A crazy busy start to 2019 with 2 project meetings for our industrial biotechnology projects, two conferences attended and three papers published!
Our first meeting took Joyce, Reyme, Vicki, Ben and Gavin down to Cambridge to join the rest of the DETOX team for our 33 month meeting, hosted by the wonderful Kathryn Lilley at Jesus College Cambridge (the oldest and the best). Shortly afterwards some work Gavin did with Kathryn on the E. coli RNA-protein-interactome was published as part of her group's amazing new OOPs method paper in Nature Biotechnology. The same week we had our Microbiology Minisymposium in York Biology, which had a Staph-feel with our invited guest Prof. Matt Holden from St. Andrews and coincided with the visit of Prof. Simon Foster from Sheffield. Great talks all day, including Lisa, Michelle, Rebecca, Steve, Sarah and the flash-talks by the students in the morning worked really well. Well done to Michelle Rudden, Michael Bottery and Laura Clarke for organising this. Then the same week Rebecca Hall's long awaited paper on Sodalis metabolism was published in mBio, which was fab! Well done to her and to the other Thomas-lab co-authors - despite this being funded by a BBSRC studentship to Rebecca, three of our Wellcome CIDCATs students, Lindsey Flanagan, Michael Bottery and Steve Thorpe all contributed over the last 5 years (gosh) on the different stages of the paper. Shortly afterwards Ben's paper building on a Stage 3 project student Lindsay Dalzell's work with some help from Liam was published in Microbiology, using their new Short Communication format. Finally, team MeMBrane headed over to Valencia for our 9 month meeting, which was very nice (19oC) before Joyce and Gavin continued to Glasgow for the 5th IBioIC conference. Here Fujifilm Diosynth Biotechnologies launched their Universities Strategic partnership with York, Edinburgh and Manchester.
Lots of great lab news this month! First off, both Bryony Ackroyd and Sophie Rugg passed their PhD vivas with minor corrections - thanks Martin Walsh & Peter Henderson for being being great externals. Now to write some papers. We had our annual BBSRC White Rose DTP meeting in Sheffield and Caroline and Rebecca did great talks, with Rebecca winning the prize for the best research talk of the day! Liam presented a nice poster on his work. Gavin has been in Ljubljana from a TOPCAPI project meeting where he presented Emm's data from his research visit to Wilfred van der Donck's lab in Illinois. Also, apparently, he ate bear :-o. Thanks to Petko and Gregor and colleagues for organising a lovely couple of days in Slovenia. He also did a seminar at the University of Strathclyde and met all their friendly microbiologists. He also had to learn about an old protein friend, AmtB, and catch up with 15 years of literature to viva the excellent Gaeten Dias, who passed his viva with minor corrections. Also, after a couple of years we almost completely update the publication board..
After the fun of Edinburgh, back to normality. Our undergraduate project students finish in the lab and submit their reports - best of luck to Grace, Ilya, Nur, Tom, Lindsey and Cintia. Meanwhile my MBio student Pejvak Moghimi will be joining us again after his exams are finished to do some work on antibiotic transporters over the summer. Rebecca starts her PIP at the Yorkshire Museum and Caroline also starts hers soon at NYBEP and both will be doing some science communication and event management for outreach activities. Emm is also on his travels to South Korea for ISBA18. Also great news for Bryony as she wins the K.M. Stott award for her second year PhD talk - Eating the poison. Gavin, Reyme and Michelle also do some outreach with Pint of Science in the Fulford Arms in York. We spoke about our body odour project with Unilever and more generally about smell perception. Our sniff sticks from Unilever were great. Big plans now to roll this out for the Festival of Ideas in 2018. Alice Pearcy joins us for her MSc Industrial Biotechnology project and will be the first in the lab to use CRISPR-Cas for making scarless SNPs in E. coli - hope it works! ...and we get an Espresso maker...
The month of the Microbiology Society meeting in April, much anticipated by all in the lab and a great few days in Edinburgh. Many members of the group took posters and had great interactions with other scientists, with lots of new ideas to follow up. Rebecca was busy with the ECM Forum and Gavin was roped into judging posters with his fellow editors from Microbiology. And some of us also made it up Arthur's Seat and we came second in the quiz...
A busy month as the Easter teaching term finishes and our project students come to an end of their time in the lab. Also, 6 PhD students associated with the lab presented their work at our 2nd year PhD students talks symposium - well done to all for excellent talks (see pic below). We host the 12 month meeting of Project DETOX, which remind us how much we have achieved in the first year of this 5 year project. Hopefully the fruits of our labours will start emerging soon. Also, Sophie, Ivan and I sign up as advisors for York iGEM team 2017, for more fun over the summer....
2nd year PhD students Ivan, James, Aritha, Caroline, Rebecca (and Bryony - not pictured) successfully present their PhD progress at our 2nd year PhD talks day.
Mainly marking and teaching and marking this month. Did I mention marking? Hosted Andy Roe from Glasgow for departmental seminar and fun learning about how a transporter for D-serine has important roles in virulence. Also, catching up on the progress of EnteroBASE in my role in the advisory board - nearly topping out 100k Salmonella genomes. Finished article on Fred Griffith for the Oxford Dictionary of National Biography, which should be published later in this year.
Our first collaborative paper with Gregor Hageleuken is published in Biophysical Journal and gets a nice commentary from Gunner Jeschke. First use of PELDOR to investigate the conformational dynamics of a TRAP substrate binding protein (SBP) from our sialic acid TRAP system and the data clearly demonstrates that the protein exists in only two states - open unliganded and closed liganded.
We visit CPI at Darlington for our 9 month Project DETOX meeting, which is a very impressive new facility and was great to get a tour.
The month starts with Ivan, Rebecca, Emmanuele and Gavin attending the 28th Annual UK RNA Polymerase Workshop in York, which is lots of fun. Our BBSRC IB Catalyst project DeTox formally starts for 5 years (scary) and new lab technician Reyme Herman starts. Reyme has worked on L1 before, having undertaken a MSc by Research with my colleague Marjan van der Woude and spending some doing protein work in Prof. Jennifer Pott's lab. We have our formal kick-off meeting in York in a lovely period room in the Jacobean Heslington Hall. The month ends well with our Head of Department, Prof Ian Graham, being awarded Fellowship of the Royal Society.
The lab headed over to Liverpool for the Microbiology Society annual meeting. Gavin had organised a symposium on Transporters in Industrial Biotechnology, which was very popular and enjoyable. Bit of a whirlwind of committee meetings and other things, including recording this video for CBMNet about our activities. Ivan Gyulev presented a poster on the 2015 York iGEM team project and Sophie and Con also presented posters on their work. The science was excellent and I very enjoyable 3 days was had by all. Thanks to the Society for funding a number of travel grants to allow attendance at the meeting for Thomas lab PhD students and also undergraduate Pejvak Moghami.
The York iGEM team has been working hard all this month, with the help of Thomas-lab PhD student Sophie Rugg, on building and testing their parts for their project to make E. coli a better organism for removal of phosphate from drinking water. Sophie has also been helping Belina Sithole from Chemistry in assessing her new antibiotic conjugates for biological activity. Gavin presented at a BBSRC workshop on synthetic biology for biotechnology at the University of Surrey & also Chaired a CBMNet meeting in Sheffield on "Cell membrane stress, integrity and engineering". Con has been arranging his PIP placement, which will be at the Biorenewables Development Centre where he will be learning lots of new things about upstream processing of feedstocks and commercialization. Finally, our work demonstrating the key role of a highly conserved arginine residue in the function of TRAP transporters has been published in JBC.
OK, so I'm not great at keeping this up to date and this is going to morph into an occasional blog type thing when I have time to write about important microbiology stuff...March was a busy time for the lab as we prepared for and then decamped to Birmingham for the annual conference of my favorite society, the Society for General Microbiology. Sophie, Con and Dan all came along with Dan presenting his work on the microbiology of BO production in the underarm (see below). Dan's work was picked up by the excellent Ben Thompson at SGM and we prepared a press release in advance, working closely with Unilever. This got lots of coverage and Dan & I spent the whole of Monday afternoon talking to CNN, NPR, the BBC and the Daily Mail. Dan also spoke to Scientific American and BBC Hereford & Worcester and I also spoke to Minster FM (local York radio). A really fun experience, although right in the middle of it I got an Email from BBSRC saying that our grant hadn't been funded - keep smiling Gavin!
The year starts off again with our successful Microbiology Minisymposium, organised by Marjan van der Woude, and now including our expanded group of microbiologists with Profs. Maggie Smith, Peter McGlynn and Michael Brockhurst. Dan Bawdon talks about this PhD work with Unilever on bacterial transporter for malodour precursors. Welcome to Michael Bottery, who joins the lab to work on the aphid symbiont Sodalis glossinidius for his CIDCATs rotation project. Also welcome to David Virant, a MRes Postgenomic Biology student, who will be working with Rosanna on evolving E. coli to have increased resistance to growth in the presence of biofuels.
Gavin get to live it up at the Houses of Parliament for an SGM reception for the release of their policy paper on STDs. There are some perks to the job....
Also, the BBSRC announce funding of their Networks in Industrial Biotechnology & Bioenergy, and the Crossing Biological Membranes (CBMNet) network that Gavin is the co-director of is funded! This is a 5 year network starting in April 2014. Look out for lots of meetings to do with transporters!
Henrique leaves York to return to São Paulo to finish off his degree. Good luck to him. He leaves a great legacy of transporter deletion (TD) strains in the Thomas lab strain collection!
We also welcome our colleagues from Green Biologics for their first meeting in York as part of our BBSRC TSB funded FLEX project using synthetic biology methods to upgrade the metabolic potential of solventogenic Clostridia sp.
Con Drousiotis, Corinne Shaw, Prof. Dave Kelly,
Prof. Paul Knox & Calum Pattrick enjoying York's finest tea.
October 2013 New academic term starts so busy with teaching and admin as well as research. We welcome our 5 new Stage 3 undergraduate project students to the lab who are here part-time until Easter. Antony Gann & Michael Knight are working on characterising some novel transporters in the lab, Anna Deal is working with Prof. Gideon Davies and myself on some sialic acid-related proteins and Raymond Li and James Hanna are working with Anne Routledge, Anne Duhme-Klair and me on the synthesis and testing of some novel antimicrobials. We had the kickoff meeting of our White Rose PhD network on engineering E. coli to utilise xylan from the biofuel crop plant Miscanthus and this ended with Gavin taking all who were still around at the end of the day for traditional tea and cake at Betty's in York (see picture). Gavin also did some more work for the SGM Equality & Diversity working group and we are now implementing a series of specific changes to SGM activities under the leadership of ex-President Hillary Lappin-Scott.
Sir William Chamber's 10-storey pagoda at Kew was a must see.
Another busy month with trips to Kew gardens for the Society of Biology awards for the accreditation of our Biochemistry with a Year in Industry degreeand news of 100% satisfaction in the all important last question on the NSS for our Biochemists - much appreciated! Also down to Brighton for the last of the SGM Autumn meetings and communications committee and equality & diversity committee meeting work to do. New BBSRC-funded postdoc Rosanna Hennessy started this month as well as new White Rose network funded PhD student Constantinos Drousiotis. Big welcome to them both. Summer student Laura finishes on a flourish with some expressed protein so everybody happy.
The first of Adam Hopkin’s PhD work is published in FEMS Letters where he showed that E. coli is able to use two additional carbon sources, N-glycolylneuraminic acid and KDN (deamino sialic acid). Hopefully the first of a number from Adam’s work. Sandy Macdonald, Angela Douglas and I have an article published in the Biochemist which was a summary of our recently published work on the role of the symbiotic bacteria in recycling nitrogen for their animal hosts. Also, Gavin traveled down to Green Biologics Limited (GBL) in Milton Park near Didcot for the kick off meeting of our new BBSRC/TSB funded project to engineer improved sugar utilisation properties into biofuel bacteria. Finally, the builders have arrived for the new Biology teaching building which is going up outside the West side of the department and will eventually hamper my views of Walmgate Stray!
With the students away, Gavin has been doing more work for the BBSRC, sitting on their BBR committee down in Birmingham and also helping SGM by attending a pre-Council meeting to agree on some exciting changes from the membership working groups and equality & diversity working groups. Also, SGM funded summer student Laura West joins us to get some TRAP transporter research moving again in the lab. iGEM students get started. Check out their site and YouTube videos!
Busy month as the end of the academic term and as Chair of Biochemistry Board of Studies, Gavin has his hands busy making sure all the final exam board meetings run smoothly. Fatima Nadat submits her MSc thesis for examination this month – fingers crossed on this. Gavin is down at SGM headquarters for a membership working party, which has brought about a variety of important changes to membership types. Gavin also down in Birmingham serving on the BBSRC Crowdsourcing panel.
We have a visit from the Society of Biology to determine whether our 4 year degree courses can gain accredited status. Went well, thanks to leadership of James Moir, and we’ll find out in the Autumn whether we were successful. Also, spent time talking to a keen set of undergraduates about iGEM and it looks like we will be running a team this year for the first time!
Welcome to new CIDCATs rotating PhD student Lindsey Flanagan, who is working on some interesting metabolic models of insect symbionts. Also welcome to Henrique Neves, a visiting Science without Borders undergraduate student from Brazil who will be with us until September. Gavin is awarded a TSB SPARK grant with Green Biologics Limited to start taking our studies on bacterial transporter into their applications in making biofuels. Also, our work with our friendly chemists Anne Duhme Klair and Anne Routledgeproduces another publication, this time on making staphyloferrin conjugates as novel antibiotics, but sadly they don’t work any better than the existing antibiotic.
Dan waiting for more beer by his poster at SGM Manchester.
March culminated in the excellent Society for General Microbiology meeting in Manchester, with Dan and Fatima presenting posters on their work and also Angela Douglas talking about Sandy's work on the Buchnera aphid symbiosis. A really strong meeting and got to meet Tyrrell Conway for the first time (after many years of communication by Email) which was great! This was preceded with SGM Communication Committee meeting where we planned some forthcoming issues of Microbiology Today. I had also been on SGM business earlier in the month in London serving on a Working group for Equality and Diversity, which was my first trip to Charles Darwin House where the SGM will be moving at the end of 2013. Met up with old supervisee Natasha Neil who now works for the Society of Biology in the same building.
Just before Easter Abbas and Amna Maqbool visited the lab from Norwich with baby Yusuf and great to see them all looking so well and getting on well in Norfolk.
Also good luck to Neeraj Patel who finished his successful third year project in the lab and now has to write it all up over Easter.
A busy month with trips to the Institute of Medical Sciences in Aberdeen and the Centre for Cardiovascular and Metabolic Research in Hull, both talking about our work using constraint-based modelling of metabolic networks to understand bacterial/insect symbioses. Thanks to my excellent hosts Ian Stansfield and Roger Sturmey for two highly enjoyable trips. Also, first trip over to Unilever at Port Sunlight for a progress meeting for Industrial CASE student Dan Bawdon and other collaborators. Interviewed candidates for our White Rose PhD network on hemicellulose utilisation by bacteria (the HUB project) and have appointed Constantinos Drousiotis, a current MBiolSc Molecular Biology student from the University of Sheffield, who will be joining us in September.
A new year and now my 11th in York (wow scary). Before I vanish in a pile of marking, big welcome to new PhD student Kazuki Iizuka who is working with Dr Jamie Wood and myself on using dynamic flux balance methods to model bacterial metabolism for applications in biotechnology and bioenergy. Also welcome to Lindsey Flanagan who will also be using flux balance analysis to understand the metabolic network of a bacterial symbiont of insects. Attended my first meeting of the SGM Communications committee after my last stint with SGM as Editor of Microbiology Today back in 2003-2006. Really great to be involved again and makes you realise how much great outreach and career development learned societies who are dependent on journal income can offer. Finch take note! Awarded a small SPARK grant from the Technology Strategy Board to do some synthetic biology with Green Biologics - hopefully the start of something big!
Dan spoke about his research on bacterial transporter involved in malodour production to our L1 research meeting, which went down very well and stimulated a lot of good questions. Great news for this month is that a White Rose PhD network application I led on has been funded (see HUB project on Our research pages) and we will be recruiting for able PhD candidates in the January. End of year tinged with sadness at the death of our colleage emeritus Prof. Guy Dodson FRS, who passed away on Christmas Eve.
Busy month of teaching and admin but a couple of small grants in preparation. Visited Green Biologics in Abingdon to talk about potential collaborations building on some of our studies on sugar transporters. Excited and enthused about what we might be able to do together and will be writing some grants soon. Dan Bawdon and I travelled to FERA for the launch of the White Rose DTP PhD training programme, which was a good chance to catch up with colleagues from Sheffield and Leeds.
New academic year so things pretty busy for most of the month. We welcome our new Stage 3 project students, Neeraj Patel, Joshua Sanderson, Emma Philips (with Paul Clarke, Chemistry) to the lab. Chris Carrick (joint PhD with chemists Anne Routledge and Anne-Duhme Klair) is in the lab this month also doing some biological screening. More good news for Abbas as some work he completed in his 'limbo' period on a Streptococcus pneumoniae methionine binding protein in collaboration with Prof. Jeremy Brown at UCL has just been accepted for publication in PLoS One.
Abbas's last day at the bench...
Abbas finally got his visa through and so was able to finally leave York with Amna and take up his position with Mark Banfield at the John Innes Centre. Best wishes to them both. Good month for Abbas also as our paper on the murein tripeptide carboxypeptidase MpaA was published in the Biochemical journal.
Callum has finished up his bioinformatics project which was very successful and thanks to the Society for General Microbiology for supporting him over the summer. Rokas meanwhile has returned for a few weeks to finish making some strains before he starts his PhD at the University of Kent in October.
Gavin delivered a public lecture at the York Castle Museum on the history of microbiology around 1914 as part of the build-up to their commemorations of the 1914-1918 war. He talked about bombs (Clostridium and acetone fermentation), bacteriophage (discovered by Frederick Twort in this period) and Bartonella (the causative agent of trench fever, which was described by Allied doctors on the Western Front).
Nadine's work on sialic acid in Corynebacterium glutamicum is publised in FEMS Letters. This was a great little paper from 3-months work and suggests that sialic acid might have a physiological role in the soil environment as this bug grows remarkably well on sialic acid and has a full repertoire of genes for its use. Also, first publication from the group on an Actinobacteria! Abbas has been appointed to a job at the John Innes Centre with Mark Banfield and is waiting for his new visa before he can start and so is busy finishing up loose ends in York. Sandy Macdonald is now finishing his MRes Computational Biology and is starting a Bioinformatics job in the department working on the C2D2 project.
The PI's and postdocs from Biology went to Hazelwood Castle for our annual Research Away Day. Lots of interesting talks and chances to talk to other faculty about our research and a historic tour of the house - the seat of the Vavasour family for many years. You can see a range of other photos from the day taken by Phil Roberts here.
Marking all done and gearing up towards the end of the academic year as Gavin is now Chair of the Biochemistry Board of Studies. Ex-postdoc Sandy Macdonald represents the lab and talks about our recent work on the aphid/Buchnera symbiosis at the EU COST Action FA0701 meeting "Arthropod Symbiosis: from fundamental studies to pest and disease management" in Ile d’Oléron, France. We are joined over the summer by Rokas Juodeikis who is helping construct some E. coli strains with various transporter defects and Amna Afzal who is working on a new TRAP transporter we are investigating.
With Fidelma Boyd's group in Delaware, USA, we demonstrate that the VC1777-9 genes (siaPQM) encode the sole sialic acid transporter in Vibrio cholerae and that another reported sialic acid TRAP transporter from this organism, VC1927-9, is actually a C4-dicarboxylate transporter. Gavin also travels to Tuscany to talk about sialic acids and bacteria at the 'Prokaryotes in Cortona' meeting sponsored by the Italian Society of General Microbiology & Biotechnology. Sunshine, good food, good company and great science - its doesn't get much better than this...
Sandy's paper with Angela Douglas's group at Cornell is published in Proc. Roy. Soc. B with an accompanying Press release which has been picked up by BBSRC. Also, a big welcome to Fatima Nadat, a MSc by Research student who is working on the sialic acid project for her thesis. Ahmad, Stuart and Sandy finish their PhD/MRes rotation projects and are heading out on external projects - good luck to them.
We have some new funding through the Wellcome Trust funded C2D2 programme which is priming some research with Prof. Jennifer Potts on the structural biology of some interesting bacterial surface proteins and using this money we have appointed Vashek Stemberk for 6 months as a postdoc.
Abbas Maqbool passes with PhD viva with minor corrections. Well done to Abbas! Also welcome to Ahmad Abd-el-Aziz, one of our CIDCATs students who is doing some DNA gyrase assays in my lab as part of his internal project.
There is a press release about Chris Mulligan's SiaPQM paper from Vibrio cholerae. This has also been picked up by our funders the BBSRC and the publishers of the journal. We welcome Stuart McEwen and Dr. Sandy Macdonald to the lab, both of whom of Master's students undertaking their internal research project in the Thomas lab.
Congratulations to Abbas Maqbool who has submitted his PhD! Chris Mulligan's paper on the sialic acid TRAP transporter from Vibrio cholerae is accepted for publication in the Journal of Biological Chemistry. Sadly we say goodbye to Nadine Grutser who returns to Cologne after her short placement in the lab. An extremely productive 3 months for all.
We publish a short note with Fidelma Boyd on the likely sialic acid transporter of Vibrio cholerae after the publication of another paper that argues that a different TRAP transporter is the sole sialic acid transporter in this organism.
Welcome to new undergraduate project students, Kimberley Barnes (with Dr Jamie Wood, YCCSA), Stephanos Hadjiprokopis, Rokas Juodeikis, Katie Norville and Miranda Smith who are undertaking various experimental and computational projects in the lab.