Modelling bacterial individuality during stress
Lead Research Organisation:
University of East Anglia
Department Name: Graduate Office
Abstract
It has recently been shown that Salmonella Typhimurium, which causes gastroenteritis, escapes the immune system of humans by diversification of its phenotypes. We would like to determine to what extent the same happens during food processing. The purpose of the study is to model subpopulations of resistant food-borne pathogens emerging from homogeneous populations when subjected to stress. An understanding of these phenomena would lead not only to improvements in food safety but also a better understanding of systems akin to those which induce antibiotic resistance.
To this end, we will first identify regulatory and metabolic mechanisms underlying bi-stable systems, and determine gene systems susceptible to giving rise to subpopulations, using network analysis of data in the literature. Molecular biology experiments will be carried out to check hypotheses about identified systems. The thesis will result in a new approach for predictive modelling.
To this end, we will first identify regulatory and metabolic mechanisms underlying bi-stable systems, and determine gene systems susceptible to giving rise to subpopulations, using network analysis of data in the literature. Molecular biology experiments will be carried out to check hypotheses about identified systems. The thesis will result in a new approach for predictive modelling.
People |
ORCID iD |
| Tamas Korcsmaros (Primary Supervisor) | |
| Marton Olbei (Student) |
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M011216/1 | 01/10/2015 | 31/03/2024 | |||
| 1799901 | Studentship | BB/M011216/1 | 01/10/2016 | 31/03/2021 | Marton Olbei |
| Description | I developed a protocol that can be used to find differences arising from different evolutionary pressures acting on closely related species. I have also developed/updated a database (SalmoNet) containing interaction information of multiple Salmonella strains. |
| Exploitation Route | The analysis method can be applied to a number of datasets, and is not constrained to biological networks. The interaction database developed can help specialists identify key interactions to understand evolution and adaptaion of Salmonella, or look for potential intervention targets. |
| Sectors | Agriculture, Food and Drink,Environment,Pharmaceuticals and Medical Biotechnology |
| Title | CytokineLink: an interactive cytokine communication map to analyse immune responses in inflammatory and infectious diseases |
| Description | In this project, we built a communication map between tissues and blood cells to show how cytokine feedback loops can build (and thus, possibly break) under pathophysiological conditions. We collated the most prevalent cytokines from literature, and assigned the proteins and their receptors to source tissue and blood cell types based on consensus RNA-Seq data from the Human Protein Atlas. To assign more confidence to the interactions, we integrated cytokine-cell interaction data from two systems immunology databases, immuneXpresso and ImmunoGlobe. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | I gave a virtual poster presentation on the tool at the ISMB 2020 conference. |
| Title | SalmoNet |
| Description | SalmoNet is a multi-layered network database of Salmonella enterica strains, containing protein-protein interaction, regulatory and metabolic interactions. The first version of the database has been published in 2017, and I am currently working on the second version, which includes more strains and additional information about them. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | The data within this database serves as the base of my PhD project, and as such all results come directly from this database. |
| URL | http://salmonet.org/ |
| Title | SalmoNet2.0 |
| Description | An integrated network resource containing regulatory, metabolic and protein-protein interactions For multiple Salmonella strains classified as gastro-intestinal or extra-intestinal pathogens An interaction resource with manually curated, high-throughput and predicted interactions Provides a strain specific and consensus networks Can be downloaded in a user-specified content and format |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation Métris A., Sudhakar P., Fazekas D., Demeter A., Ari E., Branchu P, Kingsley R.A., Baranyi J., Korcsmáros T. npj Systems Biology and Applications 3, Article number: 31 (2017) doi:10.1038/s41540-017-0034-z |
| URL | http://salmonet.org/ |
| Description | COVID Disease Map Consortia |
| Organisation | University of Luxembourg |
| Department | Luxembourg Centre for Systems Biomedicine |
| Country | Luxembourg |
| Sector | Academic/University |
| PI Contribution | We provide resourcs (SignaLink, OmniPath and VIralLink) to the curators of the project. And we participate in a weekly TC among 150 scientists from all around the world. |
| Collaborator Contribution | They provided domain expertise to optimise our tool development, and feedback on our study design. |
| Impact | Ostaszewski et al, bioRXiv, 2021; doi: 10.1101/2020.10.26.356014 |
| Start Year | 2020 |
| Description | Best poster award in the Signaling Resources category of the 2nd Interdisciplinary Signaling Workshop (2017) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I won the best poster prize award in the signaling resources category at the 2nd Interdisciplinary Signaling Workshop. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Conference Poster at Gordon Research Conference |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented my poster about the upcoming update to the SalmoNet database at the 2019 Gordon Research Conference on Salmonella Pathogenesis. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Interview on institute website on our recent publication on COVID-19 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Following our publication on cytokine responses caused by SARS-CoV-2 and similar viruses, the institute communications team made an interview with us to describe our findings |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/newsroom/could-our-immune-system-be-why-covid-19-so-deadly |
| Description | Interview with Medscape about COVID-19 publication |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I gave an interview following our publication on cytokine responses caused by SARS-CoV-2 and similar viruses. The interviewer asked great questions, and has asked medical professionals for comments on our publication. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.medscape.com/viewarticle/946900?src=soc_tw_share |
| Description | Participated in promotional video for research park |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Schools |
| Results and Impact | I participated in the shooting of a promotional video for the NBI. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.youtube.com/watch?v=jH_fmWD692s&feature=emb_title |
| Description | Participated in the "I'm a Scientist, Get me out of here" competition |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | I participated in the "Fast Computing Zone" of the competition, where we would chat with students daily for roughly 60 minutes about any questions they had aboust science. In the evenings I replied to their further questions. I talked to a lot of (100+) students throughout the event, and hopefully got them interested in my field of work. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://imascientist.org.uk/ |
| Description | Poster presentation at Genome 10K and Genome Science Conference: SalmoNet: an integrated multi-layered network for Salmonella |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented my poster about SalmoNet, an integrated Salmonella network resource to a wide variety of visitors at the Genome 10K and Genome science conference. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/genome-10k-and-genome-science-conference |
| Description | Poster presentation at "Modularity of signaling proteins and networks" conference: Reduce, reuse, rewire: Using network rewiring to gain insight into evolution and adaptation |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I showcased a workflow depicting how network rewiring can be used to highlight and explain evolutionary differences arising between different species or strains. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://meetings.embo.org/event/18-modularity |
| Description | Poster presentation at 2nd Interdisciplinary Signaling Workshop: SalmoNet: an integrated multi-layered network for Salmonella |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented my poster on SalmoNet, an integrated Salmonella network resource, at the 2nd Interdisciplinary Signaling Workshop. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/2nd-interdisciplinary-signaling-workshop-isw |
| Description | Poster presentation at ECCO'22 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | The 17th Congress of ECCO took place virtually on February 16-19, 2022. Over 7000 academics attended the conference. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.ecco-ibd.eu/ |
| Description | Poster presentation at ELIXIR UK All Hands 2018 meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The annual ELIXIR-UK All Hands brings together people working at ELIXIR-UK consortium member institutions for this two-day meeting, which for 2018 is hosted by Birmingham University. I presented a poster on the network resources developed and maintained by the Korcsmaros group. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/elixir-all-hands-2018 |
| Description | Poster presentation at EMBO conference on Bacterial Networks 2017: SalmoNet: an integrated multi-layered network for Salmonella, Host adaptation of Salmonella enterica strains investigated by an integrated network approach |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I showed the information contained in the SalmoNet database and its applications at the BacNet 2017 conference. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://meetings.embo.org/event/17-bacnet |
| Description | Poster presentation at ICSB2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented my poster at a prestigious systems biology conference (ICSB) where I got a lot of important feedback about my work. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation at Microbes in Norwich 2019: Integrated networks in Salmonella research |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | I presented a poster at the Microbes in Norwich conference, highlighting how using networks can influence the different facets of Salmonella biology. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://microbesinnorwich.org/ |
| Description | Presented a virtual poster at the ISMB 2020 conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented a virtual poster on CytokineLink, a cytokine communication interaction resource I have developed, in a special COVID-19 focused poster session. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Presented poster at the Network Inference in Biology and Disease workshop in Pozzuoli |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented my poster at the conference, which led to some interesting discussions regarding the project. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Runner up poster prize in Microbial Genomics at Genome 10K & Genome Science conference 2017 (2017) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | I received the runner up poster prize in Microbial Genomics at Genome 10K & Genome Science conference 2017, which included a membership to the Microbiology Society. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/genome-10k-and-genome-science-conference |
| Description | Written interview with institute website |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | I gave a written interview about my PhD project to the institute website, where we talked about what I have found so far, and what my plans are for the future. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/articles/network-biology-approaches-to-understanding-life?utm_campaign=Okt... |