April 2024
Next week (8 - 11 April), Thomas lab will be heading to beautiful Edinburgh to attend one of the largest microbiology events - the Microbiology Society Annual Conference. Reyme and Imran will showcase their research on Tuesday and Thursday, while Daniel, a member of the AVERT project, will present his poster on Wednesday and Thursday. Get a sneak peek of Daniel's presentation through a short video link provided below. See you in Edinburgh!
Next week (8 - 11 April), Thomas lab will be heading to beautiful Edinburgh to attend one of the largest microbiology events - the Microbiology Society Annual Conference. Reyme and Imran will showcase their research on Tuesday and Thursday, while Daniel, a member of the AVERT project, will present his poster on Wednesday and Thursday. Get a sneak peek of Daniel's presentation through a short video link provided below. See you in Edinburgh!
March 2024
This quarter the Thomas’ lab celebrated several papers being accepted and published.
Abby and Emily published research that discovers an enzyme that may be involved in the virulence of multidrug resistant bacteria. The enzyme is the founding member of a previously unreported glycosyltransferase family – now known as GT118. Meanwhile, Bryony and Javeria shared their findings on ABC transporter linked to cAMP resistance. Through crystal structures and ligand binding studies, they revealed YejA's binding affinity for a unique N-terminal peptide extension, absent in other cluster C peptide ABC SBPs. This experimental data suggest that it is not an artefact of the crystallization process and hint at a potenital YejA's role in sensing of periplasmic or membrane stress. Finally, Rory's paper provided a comprehensive review of the diverse regulatory mechanisms governing bacterial transporter activity, encompassing small molecules, peptides, and larger signal transduction proteins.
Additonally, in March, the AVERT consortium held its quarterly progress meeting, kindly hosted by Henrik Strahl at the University of Newcastle. Two days of exciting discussions took place, paving the way for future research directions.
Furthermore, the team was involved in organising and facilitating the Microbiology Symposium at the Department of Biology. We invited a varied selection of internal and external speakers to present and discuss their research. The day included the James Burgess Lecture on Microbiology; a special talk dedicated to highlighting extraordinary research in the field of bacterial AMR. This year's James Burgess Lecture was given by Prof. Jess Blair (University of Birmingham).
Last but not least, several members of the lab will be attending the upcoming Microbiology Society annual conference in Edinburgh and presenting research on skin microbiome, bacterial stress response mechanisms and transport system. We are looking forward to seeing many of our colleagues and collaborators next month.
This quarter the Thomas’ lab celebrated several papers being accepted and published.
Abby and Emily published research that discovers an enzyme that may be involved in the virulence of multidrug resistant bacteria. The enzyme is the founding member of a previously unreported glycosyltransferase family – now known as GT118. Meanwhile, Bryony and Javeria shared their findings on ABC transporter linked to cAMP resistance. Through crystal structures and ligand binding studies, they revealed YejA's binding affinity for a unique N-terminal peptide extension, absent in other cluster C peptide ABC SBPs. This experimental data suggest that it is not an artefact of the crystallization process and hint at a potenital YejA's role in sensing of periplasmic or membrane stress. Finally, Rory's paper provided a comprehensive review of the diverse regulatory mechanisms governing bacterial transporter activity, encompassing small molecules, peptides, and larger signal transduction proteins.
Additonally, in March, the AVERT consortium held its quarterly progress meeting, kindly hosted by Henrik Strahl at the University of Newcastle. Two days of exciting discussions took place, paving the way for future research directions.
Furthermore, the team was involved in organising and facilitating the Microbiology Symposium at the Department of Biology. We invited a varied selection of internal and external speakers to present and discuss their research. The day included the James Burgess Lecture on Microbiology; a special talk dedicated to highlighting extraordinary research in the field of bacterial AMR. This year's James Burgess Lecture was given by Prof. Jess Blair (University of Birmingham).
Last but not least, several members of the lab will be attending the upcoming Microbiology Society annual conference in Edinburgh and presenting research on skin microbiome, bacterial stress response mechanisms and transport system. We are looking forward to seeing many of our colleagues and collaborators next month.
December 2023
This month, we hosted the inaugural meeting with the Scientific Advisory Board for our sLOLA AVERT project, funded by BBSRC. Spanning two days, the consortium shared updates on the research focused on understanding how IM30 proteins can restore membrane function in bacteria and other photosynthetic microbes. The productive discussion unfolded with the SAB members: Professor Jeff Green (University of Sheffield), Professor Martin Buck (Imperial College London), Professor Ben Engel (University of Basel), and Dr. Chris MacDonald (University of York), chaired by Professor Tracy Palmer (University of Newcastle).
Our previous work on the Industrial Biotechnology (IB) Catalyst Project DETOX and its spin-in, the Multi-Omics Research Factory (MORF), received recognition in the BBSRC Impact Showcase 2023. The user-friendly tool now provides bioinformatics support to both academic and industrial projects. For more information about the MORF, please visit: https://www.morf-db.org/
As we bid farewell to a highly productive year and paused for the Christmas break, the Thomas lab celebrated with a day of fun, including an Escape room challenge and a festive Christmas lunch.
This month, we hosted the inaugural meeting with the Scientific Advisory Board for our sLOLA AVERT project, funded by BBSRC. Spanning two days, the consortium shared updates on the research focused on understanding how IM30 proteins can restore membrane function in bacteria and other photosynthetic microbes. The productive discussion unfolded with the SAB members: Professor Jeff Green (University of Sheffield), Professor Martin Buck (Imperial College London), Professor Ben Engel (University of Basel), and Dr. Chris MacDonald (University of York), chaired by Professor Tracy Palmer (University of Newcastle).
Our previous work on the Industrial Biotechnology (IB) Catalyst Project DETOX and its spin-in, the Multi-Omics Research Factory (MORF), received recognition in the BBSRC Impact Showcase 2023. The user-friendly tool now provides bioinformatics support to both academic and industrial projects. For more information about the MORF, please visit: https://www.morf-db.org/
As we bid farewell to a highly productive year and paused for the Christmas break, the Thomas lab celebrated with a day of fun, including an Escape room challenge and a festive Christmas lunch.
October 2023
We start the new academic year in Thomas lab by welcoming, over a cup of coffee, our new PhD students Beth, Connor and Daniel.
In the past month, several members of our lab had the opportunity to participate in various meetings and conferences. Javeria attended the 43rd British Mass Spectrometry Society Annual Meeting in Manchester. Meanwhile, Ben presented a poster at the 6th meeting on Microbial Responses to Stress at TU Wien, Vienna, organized by the Microbial Biotechnology Division of the European Federation of Biotechnology.
Gavin joined the Royal Society meeting on Glycans in Infection: challenges and opportunities. This interdisciplinary meeting brought leading experts together to share knowledge and explore the future challenges of exploiting sugars to combat infectious diseases. The meeting covered numerous topics relevant to the research in our lab, including work by Sloan Siegrist from the University of Massachusetts on cell wall recycling and outer membrane permeability, research from Nina van Sorge at Amsterdam UMC on the development of new therapeutic interventions against Staphylococcus aureus involving wall teichoic acids, and insights from Steve Townsend at Vanderbilt University on the outcomes of human milk oligosaccharides-mediated in vivo and ex vivo study on Streptococcus agalactiae infection. The meeting presented a good opportunity to discuss our work with previous and current lab collaborators: Syma Khalid from the University of Oxford, and Lucy Crouch-Myers from the University of Birmingham.
We start the new academic year in Thomas lab by welcoming, over a cup of coffee, our new PhD students Beth, Connor and Daniel.
In the past month, several members of our lab had the opportunity to participate in various meetings and conferences. Javeria attended the 43rd British Mass Spectrometry Society Annual Meeting in Manchester. Meanwhile, Ben presented a poster at the 6th meeting on Microbial Responses to Stress at TU Wien, Vienna, organized by the Microbial Biotechnology Division of the European Federation of Biotechnology.
Gavin joined the Royal Society meeting on Glycans in Infection: challenges and opportunities. This interdisciplinary meeting brought leading experts together to share knowledge and explore the future challenges of exploiting sugars to combat infectious diseases. The meeting covered numerous topics relevant to the research in our lab, including work by Sloan Siegrist from the University of Massachusetts on cell wall recycling and outer membrane permeability, research from Nina van Sorge at Amsterdam UMC on the development of new therapeutic interventions against Staphylococcus aureus involving wall teichoic acids, and insights from Steve Townsend at Vanderbilt University on the outcomes of human milk oligosaccharides-mediated in vivo and ex vivo study on Streptococcus agalactiae infection. The meeting presented a good opportunity to discuss our work with previous and current lab collaborators: Syma Khalid from the University of Oxford, and Lucy Crouch-Myers from the University of Birmingham.
June 2023
Finally updated the lab photo, although couple of key people were away, so will try again later in the summer. Did manage to get Vicki and Joyce in from team MORF, which was nice. Daniel sneaked in even though he doesn't start until September (although did his Master's project in the lab this Spring/Summer). Big paper in The Plant Cell for Justin Lau this week, who works in Luke Mackinder's lab and is co-supervised by Gavin, for his super cool work using TurboID-based proximity labeling technique to discovery new components in the Chlamydomonas reinhardtii pyrenoid.
Imran and Danos went over to Galway this month for the StaphGBI conference, which they enjoyed very much and ex-lab member Michelle Rudden, now in Hull, also presented.
Gavin also closed out 15 years working with Microbiology, stepping down as Editor in Chief at the end of June. More time to write some papers for the lab. We also had a visit from former-lab members Richard Horler who was up from the JIC, where he is going to be in charge of their new data centre (very exciting).
Finally updated the lab photo, although couple of key people were away, so will try again later in the summer. Did manage to get Vicki and Joyce in from team MORF, which was nice. Daniel sneaked in even though he doesn't start until September (although did his Master's project in the lab this Spring/Summer). Big paper in The Plant Cell for Justin Lau this week, who works in Luke Mackinder's lab and is co-supervised by Gavin, for his super cool work using TurboID-based proximity labeling technique to discovery new components in the Chlamydomonas reinhardtii pyrenoid.
Imran and Danos went over to Galway this month for the StaphGBI conference, which they enjoyed very much and ex-lab member Michelle Rudden, now in Hull, also presented.
Gavin also closed out 15 years working with Microbiology, stepping down as Editor in Chief at the end of June. More time to write some papers for the lab. We also had a visit from former-lab members Richard Horler who was up from the JIC, where he is going to be in charge of their new data centre (very exciting).
June started with Matt Rose's PhD viva, which went very well and thanks to Mark Shepherd from the University of Kent, who was the external. Some drinks afterwards with some good L1 banter (Pooja was a welcome addition). Later in the month Gavin was down at EMBL serving as external to Vivien Monzon who did her PhD on bioinformatic analysis of fibrillar adhesins in Actinobacteria and beyond.
May 2023
This month, Gavin, Rory, and Dr. Dani Ungar paid a visit to Glycome, to report on progress of his iCASE PhD project on oligosaccharide transporter. This was the last visit we did abroad before lock-down and nice to be back eating herring again. Gavin met Rosanne Hennessey, ex-Thomas lab PDRA, who is now lecturer at the Unversity of Copenhagen and we celebrate her landing a major personal grant from Novo Nordisk. At the Biology Graduate Conference, Ingrid Herdzik, a final year PhD student, presented her research on enhancing the stability of strains that express recombinant proteins.
We welcomed Dr. Anna Alessi to our team, who has joined us as the project manager on our AVERT sLOLA-funded project. Anna has a PhD in molecular microbiology, and previously worked on various large-scale interdisciplinary collaborative projects as a postdoctoral researcher at the University of York. In 2019, she transitioned to the Biorenewables Development Centre, where she successfully managed the £1.8 million Newton Bhabha project in partnership with academic and industry partners from the UK and India. Additionally, at the BDC, she oversees the management of the £1.2 million ERDF-funded ADCEY project, which provides funded packages to small and medium-sized enterprises (SMEs) in Yorkshire. In her new role as the AVERT project manager. Anna will closely work with research teams in York, Newcastle, Nottingham, and Cambridge to ensure the project's objectives are achieved in a timely manner.
This month, Gavin, Rory, and Dr. Dani Ungar paid a visit to Glycome, to report on progress of his iCASE PhD project on oligosaccharide transporter. This was the last visit we did abroad before lock-down and nice to be back eating herring again. Gavin met Rosanne Hennessey, ex-Thomas lab PDRA, who is now lecturer at the Unversity of Copenhagen and we celebrate her landing a major personal grant from Novo Nordisk. At the Biology Graduate Conference, Ingrid Herdzik, a final year PhD student, presented her research on enhancing the stability of strains that express recombinant proteins.
We welcomed Dr. Anna Alessi to our team, who has joined us as the project manager on our AVERT sLOLA-funded project. Anna has a PhD in molecular microbiology, and previously worked on various large-scale interdisciplinary collaborative projects as a postdoctoral researcher at the University of York. In 2019, she transitioned to the Biorenewables Development Centre, where she successfully managed the £1.8 million Newton Bhabha project in partnership with academic and industry partners from the UK and India. Additionally, at the BDC, she oversees the management of the £1.2 million ERDF-funded ADCEY project, which provides funded packages to small and medium-sized enterprises (SMEs) in Yorkshire. In her new role as the AVERT project manager. Anna will closely work with research teams in York, Newcastle, Nottingham, and Cambridge to ensure the project's objectives are achieved in a timely manner.
September 2022
We are thrilled to announce that we have successfully secured a funding of £4 million from the BBSRC's strategic longer and larger (sLoLa) grant scheme. Over the next five years, our dedicated team, in collaboration with Prof. Luke Mackinder at CNAP, Dr. Jamie Blaza from the Department of Chemistry, and our partners from the Universities of Newcastle (Dr. Henrik Strahl), Nottingham (Dr. Boyan Bonev), and Cambridge (Prof. Kathryn Lilley), will work together on this exciting project.
The primary focus of our project revolves around the remarkable IM30 proteins, which are present in the majority of bacteria and plants. Our objective is to unravel the mysteries behind how these proteins can detect and repair damaged membranes, thereby enabling cells to withstand various stresses. This work builds upon the invaluable insights gathered during our DETOX project that discovered the activation of this response mechanism in diverse bacteria utilized in biotechnological applications for biochemicals production.
We announce our project as one of the five distinguished initiatives selected for funding, collectively receiving over £19 million from BBSRC. This financial support demonstrates the significance of our innovative research in addressing fundamental questions in the field of bioscience.
We are thrilled to announce that we have successfully secured a funding of £4 million from the BBSRC's strategic longer and larger (sLoLa) grant scheme. Over the next five years, our dedicated team, in collaboration with Prof. Luke Mackinder at CNAP, Dr. Jamie Blaza from the Department of Chemistry, and our partners from the Universities of Newcastle (Dr. Henrik Strahl), Nottingham (Dr. Boyan Bonev), and Cambridge (Prof. Kathryn Lilley), will work together on this exciting project.
The primary focus of our project revolves around the remarkable IM30 proteins, which are present in the majority of bacteria and plants. Our objective is to unravel the mysteries behind how these proteins can detect and repair damaged membranes, thereby enabling cells to withstand various stresses. This work builds upon the invaluable insights gathered during our DETOX project that discovered the activation of this response mechanism in diverse bacteria utilized in biotechnological applications for biochemicals production.
We announce our project as one of the five distinguished initiatives selected for funding, collectively receiving over £19 million from BBSRC. This financial support demonstrates the significance of our innovative research in addressing fundamental questions in the field of bioscience.
April 2022
We ended the month with the departure of Dr. Michelle Rudden (sob) for pastures new at HYMS in Hull (with Prof. Matt Hardman and Dr. Holly Wilkinson), where she will become an expert in wound healing methods. Michelle joined in 2016 on our BBSRC LINK project with Unilever and was driving force in our BO lyase story which we published in 2020. She had then developed our interests in the skin microbiome more generally as a side project while she was working on the EU TOPCAPI project after Emmanuele Severi departed for Prof. Tracy Palmer's group in Newcastle. We wish Michelle the best of luck and will be keeping her dry bench as she continues as a Visiting Researcher in the Department while now being based in Hull. Our MORF banner now has pride of place in the Biology Atrium to advertise our wares & Gavin finally spots Long Boi (our famous long necked duck) on campus!
We ended the month with the departure of Dr. Michelle Rudden (sob) for pastures new at HYMS in Hull (with Prof. Matt Hardman and Dr. Holly Wilkinson), where she will become an expert in wound healing methods. Michelle joined in 2016 on our BBSRC LINK project with Unilever and was driving force in our BO lyase story which we published in 2020. She had then developed our interests in the skin microbiome more generally as a side project while she was working on the EU TOPCAPI project after Emmanuele Severi departed for Prof. Tracy Palmer's group in Newcastle. We wish Michelle the best of luck and will be keeping her dry bench as she continues as a Visiting Researcher in the Department while now being based in Hull. Our MORF banner now has pride of place in the Biology Atrium to advertise our wares & Gavin finally spots Long Boi (our famous long necked duck) on campus!
April 2021
April culminated in the Microbiology Society Annual Conference (AC2021), which is entirely on-line this year. We have Ben Willson presenting on his Clostridial multi-omics work in the Biotechnology session, with DETOX postdoc Joe Webb (Sheffield) also presenting in the same session on our work on understanding styrene toxicity in producing strains of Escherichia coli. Also, DETOX Co-I Prof. Alex Conradie heads off the session so lots of DETOX contribution to this symposium. Else where Sarah Tindall has a poster on her work on the bacterial AT3 proteins (Poster 489) and Gavin and Emm Severi's work with Andrew Bell (Quardram) is also presented on a poster (P474).
Dr. Lisa Miller leaves the lab as she takes on a new PDRA position in York with Steve Johnson and Thomas Krauss and we hope to continue to see her around whenever she needs some microbiology and proteins :-). Also, celebrations in the lab as our research associate Reyme Herman gets his permanent residency in the UK.
April culminated in the Microbiology Society Annual Conference (AC2021), which is entirely on-line this year. We have Ben Willson presenting on his Clostridial multi-omics work in the Biotechnology session, with DETOX postdoc Joe Webb (Sheffield) also presenting in the same session on our work on understanding styrene toxicity in producing strains of Escherichia coli. Also, DETOX Co-I Prof. Alex Conradie heads off the session so lots of DETOX contribution to this symposium. Else where Sarah Tindall has a poster on her work on the bacterial AT3 proteins (Poster 489) and Gavin and Emm Severi's work with Andrew Bell (Quardram) is also presented on a poster (P474).
Dr. Lisa Miller leaves the lab as she takes on a new PDRA position in York with Steve Johnson and Thomas Krauss and we hope to continue to see her around whenever she needs some microbiology and proteins :-). Also, celebrations in the lab as our research associate Reyme Herman gets his permanent residency in the UK.
March 2021
Important month for PhD student liam Chapman, who submitted his thesis on time following a 6-month COVID-related extension. Thanks for the White Rose DTP for this and for Liam's hard work, persistance and determination to get this submitted on time.
Important month for PhD student liam Chapman, who submitted his thesis on time following a 6-month COVID-related extension. Thanks for the White Rose DTP for this and for Liam's hard work, persistance and determination to get this submitted on time.
January 2019
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.
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.
December 2018
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..
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..
May 2017
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...
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...
April 2017
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...
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...
March 2017
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....
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....
February 2017
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.
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.
January 2017
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.
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.
April 2016
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 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.
March 2016
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 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.
September 2015
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.
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.
March 2015
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!
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!
January 2014
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.
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.
December 2013
Celebrating with the department the success of our first ever iGEM team who won a Gold medal at the European Jamboree. They followed an idea to create gold nanoparticles by bacteria being used in microbial fuel cells to increase their conductivity. Thanks for support from the University Alumni fund and other kind supporters.
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!
Celebrating with the department the success of our first ever iGEM team who won a Gold medal at the European Jamboree. They followed an idea to create gold nanoparticles by bacteria being used in microbial fuel cells to increase their conductivity. Thanks for support from the University Alumni fund and other kind supporters.
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!
November 2013
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.
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.
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.
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.
September 2013
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 degree and 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.
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 degree and 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.
August 2013
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!
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!
July 2013
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!
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!
June 2013
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.
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.
May 2013
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!
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!
April 2013
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 Routledge produces another publication, this time on making staphyloferrin conjugates as novel antibiotics, but sadly they don’t work any better than the existing antibiotic.
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 Routledge produces another publication, this time on making staphyloferrin conjugates as novel antibiotics, but sadly they don’t work any better than the existing antibiotic.
March 2013
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.
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.
February 2013
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.
January 2013
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!
December 2012
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.
November 2012
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.
October 2012
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.
September 2012
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).
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).
August 2012
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.
July 2012
James Chong, Marjan van der Woude & Gavin
Welcome to Callum Chaplain and Rhiannon Roberts how have joined the lab for this summer to do some serious genome mining. Thanks to the Society of General Microbiology for supporting Callum. Rokas Juodeikis goes back to Lithuania for a holiday but will be back in September for a short period to finish off some work before he starts a PhD at the University of Kent, Canterbury. The BBSRC has picked up our paper in Proc. Roy. Soc. B on the aphid/Buchnera symbiosis and have included it in their most recent BBSRC Business magazine. Also, Abbas graduated PhD!
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.
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.
June 2012
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.
May 2012
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...
April 2012
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.
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.
March 2012
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.
February 2012
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.
January 2012
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.
December 2011
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.
November 2011
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.
October 2011
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.