Quadram Institute Bioscience UKRI Innovation Fellowships: BBSRC Flexible Talent Mobility Accounts

Lead Research Organisation: Quadram Institute
Department Name: Directorate

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Publications

10 25 50
 
Description Hosting visiting scientist from University of Technology Sydney
Geographic Reach Australia 
Policy Influence Type Influenced training of practitioners or researchers
Impact Hosted a visiting postdoctoral scientist from the University of Technology Sydney (Australia) for 10 weeks, providing training in bioinformatics and genomics of bacterial pathogens and metagenomes.
 
Description Association of Salmonella with Protists in the aquatic environment
Amount $603,545 (USD)
Funding ID INV-051974 
Organisation Bill and Melinda Gates Foundation 
Sector Charity/Non Profit
Country United States
Start 11/2022 
End 11/2024
 
Description BBSRC Impact Accelerator Account
Amount £12,000 (GBP)
Funding ID BB/S506679/1 
Organisation Quadram Institute Bioscience 
Sector Academic/University
Country United Kingdom
Start 09/2019 
End 03/2020
 
Description Establishment of COVID-19 genome sequencing in Zimbabwe
Amount £20,000 (GBP)
Funding ID 43030-000-B 
Organisation Quadram Institute Bioscience 
Sector Academic/University
Country United Kingdom
Start 07/2020 
End 04/2021
 
Description Norwich Research Park Biosciences Doctoral Training Partnership
Amount £12,757,080 (GBP)
Funding ID BB/T008717/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2020 
End 09/2028
 
Description Research contract
Amount £183,890 (GBP)
Organisation Glycom A/S 
Sector Private
Country Denmark
Start 01/2018 
End 07/2019
 
Description Research contract
Amount £33,330 (GBP)
Organisation NutriLeads 
Sector Private
Country Netherlands
Start 03/2020 
End 08/2020
 
Description S. Typhi and protozoa in contaminated water in Zimbabwe
Amount $100,000 (USD)
Funding ID OPP1217121 
Organisation Bill and Melinda Gates Foundation 
Sector Charity/Non Profit
Country United States
Start 11/2019 
End 04/2021
 
Description Sustained Energy Release Starchy Food Products
Amount € 659,474 (EUR)
Funding ID 20169 
Organisation European Institute of Innovation and Technology (EIT) 
Sector Public
Country Hungary
Start 01/2020 
End 12/2021
 
Title Equipment for gut-on-chip 
Description Gut-on-chip system is run by specialised equipment consisting of two parts: Zoe and Orb. Zoe controls the rate of flow and peristalsis-like stretch for up to 12 chips, providing the environment cells need to live. Orb provides the precise mixture of gas, power, and vacuum stretch required by the Zoë culture module. 
Type Of Material Improvements to research infrastructure 
Year Produced 2019 
Provided To Others? Yes  
Impact Following initial experiments with gut-on-chip and demonstrating exciting results using this dynamic microfluidics system (as opposed to the conventional static methods such as trans wells) we were able to attract funding by an industrial collaborator for a pilot study using this state of the art method. 
URL https://www.emulatebio.com/products
 
Title Gut-on-chip technology established 
Description Gut-On-Chip microfluidic culture device recapitulates the microarchitecture and functions of living intestine. Using the organoid approach where intestinal stem cells isolated from human biopsies are processed to form intestinal villi oriented towards the channel lumen, and the epithelium in close apposition to human intestinal microvascular endothelium. This Gut-on-Chip GOC technology using donor-derived human intestinal cells therefore offers advantages over the current organoids and creates new opportunities for personalized medicine including the transport of nutrients, digestion, different intestinal disorders, and intestinal interactions with commensal microbes as well as pathogens. 
Type Of Material Model of mechanisms or symptoms - in vitro 
Year Produced 2018 
Provided To Others? Yes  
Impact Following initial experiments with gut-on-chip and demonstrating exciting results using this dynamic microfluidics system (as opposed to the conventional static methods such as trans wells) we were able to attract funding by an industrial collaborator for a pilot study using this state of the art method. 
URL https://www.nature.com/articles/s41598-018-21201-7
 
Title Integrated Models of the Human Gut 
Description The FTMA project undertaken by Suligoj has led to increased use of organ on chip technology at Quadram Institute. This has now been incorporated into a BBSRC-funded 'Integrated Models of the Human Gut' facility at the Institute. 
Type Of Material Improvements to research infrastructure 
Year Produced 2022 
Provided To Others? Yes  
Impact None yet. 
 
Description Collaboration between Juge Group and Emulate Inc 
Organisation Emulate, Inc.
Country United States 
Sector Private 
PI Contribution exchange of expertise
Collaborator Contribution Training and exchange of expertise
Impact Publication Research contract
Start Year 2019
 
Description Collaboration between Juge Group and Public Health England 
Organisation Public Health England
Country United Kingdom 
Sector Public 
PI Contribution We will be providing expertise on Emulate platform
Collaborator Contribution QIB (Juge group) is subcontractor on grant application
Impact Grant
Start Year 2020
 
Description Collaboration between QIB and Public Health England 
Organisation Public Health England
Department Public Health England Porton Down
Country United Kingdom 
Sector Public 
PI Contribution Intellectual input, site visit, sample collection, processing and analysis, consumables.
Collaborator Contribution Expertise in and provision of NHP model system, training, intellectual input, samples.
Impact The collaboration has generated new related projects and expanded to include additional partners at UK universities (UCL, Birmingham,Southampton). The original defined project is ongoing and will continue to grow as more samples become available over the course of 2020. Ultimately we aim to publish our results in high-impact journals and establish the model as a resource for other users.
Start Year 2019
 
Description UniPD_UniVR 
Organisation University of Padova
Country Italy 
Sector Academic/University 
PI Contribution - Our team introduced the use of NextFlow workflows for reproducible pipelines and how to package software in BioConda to allow for easy installation/distribution; - I delivered a research seminar at the University of Padua and a science dissemination talk for high-school students; - Hosted at UniPD for 10 days to collaborate on metagenomics methods
Collaborator Contribution - Prof. Chiara Romualdi organized and delivered a training session on "statistical methods for RNA-Seq analysis" - Prof. Nicola Vitulo organized and delivered a training session on "Interpreting data from metabarcoding experiments"
Impact - one-to-one session with Prof. Chiara Romualdi, statistician, resulted in improved statistical methods implemented in our microbiome statistical analysis; - collaborating with Prof. Nicola Vitulo, bioinformatician, we developed a pipeline for virome analysis that will be presented at the RECOMB2020 conference in May 2020.
Start Year 2019
 
Description UniPD_UniVR 
Organisation University of Verona
Country Italy 
Sector Academic/University 
PI Contribution - Our team introduced the use of NextFlow workflows for reproducible pipelines and how to package software in BioConda to allow for easy installation/distribution; - I delivered a research seminar at the University of Padua and a science dissemination talk for high-school students; - Hosted at UniPD for 10 days to collaborate on metagenomics methods
Collaborator Contribution - Prof. Chiara Romualdi organized and delivered a training session on "statistical methods for RNA-Seq analysis" - Prof. Nicola Vitulo organized and delivered a training session on "Interpreting data from metabarcoding experiments"
Impact - one-to-one session with Prof. Chiara Romualdi, statistician, resulted in improved statistical methods implemented in our microbiome statistical analysis; - collaborating with Prof. Nicola Vitulo, bioinformatician, we developed a pipeline for virome analysis that will be presented at the RECOMB2020 conference in May 2020.
Start Year 2019
 
Description UniTO 
Organisation University of Turin
Country Italy 
Sector Academic/University 
PI Contribution - I introduced technical aspects on software engineering to Dr. Giovanni Birolo and Dr. Serena Aneli: Docker containers, packaging and distribution of software using BioConda, unit tests and continuous integration using Circle-CI; - Joint development of a novel tool for analysis of next generation sequencing alignments - Joint development of a novel tool for denoising of OTU table in 16S sequencing experiments
Collaborator Contribution - Dr. Serena Aneli delivered a seminar - Dr. Giovanni Birolo worked on a bioinformatics project at the Quadram Institute for one week, coding software (CovToBed and OTUSfocus)- - Dr. Giovanni Birolo delivered training on "Python - Pandas"
Impact - A publication describing "covtobed" has been submitted - The software "covtobed" has been released open-source, distributed on BioConda (> 1000 downloads) and Docker Hub. - A manuscript describing the OTU table cleaning tool is under preparation
Start Year 2019
 
Title BamToCov, an efficient toolkit for sequence coverage calculations 
Description BamToCov is a toolkit for rapid and flexible coverage computation that relies on the most memory efficient algorithm and is designed for integration in pipelines, given its ability to read alignment files from streams. The tools in the suite can process sorted BAM or CRAM files, allowing the user to extract coverage information via different filtering approaches and to save the output in different formats (BED, Wig or counts). The BamToCov algorithm can also handle strand-specific and/or physical coverage analyses. 
Type Of Technology Software 
Year Produced 2020 
Open Source License? Yes  
Impact A fast and memory-efficient method for the coverage analysis of genomics sequences allows a fast detection of undercovered regions (e.g. Sars-Cov-2 amplicon sequencing, KO genes,...) and counts of reads in regions of interests. 
URL https://github.com/telatin/BamToCov
 
Title Galru: rapid pathogen typing using CRISPR spacer repertoire 
Description Galru is a Python 3 program that defines CRISPR spacer repertoire directly from uncorrected metagenomic long reads. Galru first identifies long reads that map to CRISPR-associated genes and searches along the read for the CRISPR spacer array. This array is compared to a database of known arrays to identify the sequence type (MLST). 
Type Of Technology Software 
Year Produced 2019 
Open Source License? Yes  
Impact None yet 
URL https://github.com/quadram-institute-bioscience/galru
 
Title Singularity image of "covtobed" - a tool to convert coverage tracks to BED files 
Description Covtobed 1.0RC Read one (or more) alignment files (sorted BAM) and prints a BED with the coverage. It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range. https://github.com/telatin/covtobed/ 
Type Of Technology Software 
Year Produced 2019 
Open Source License? Yes  
Impact The singularity image allows to execute the software in HPC environments avoiding installation of libraries and dependencies. This image has been installed in the Norwich Research Park High Performance Cluster. 
URL https://zenodo.org/record/3600261
 
Title covtobed - a new tool to extract coverage information 
Description covtobed is a tool to generate BED coverage tracks from BAM files, that reads one (or more) alignment files (sorted BAM) and prints a BED with the coverage. It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range. 
Type Of Technology Software 
Year Produced 2019 
Open Source License? Yes  
Impact The software has been downloaded 1000 times from BioConda 
URL https://bioconda.github.io/recipes/covtobed/README.html
 
Description Bioinformatics workshop CLIMB 2020 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Training on Linux for bioinformatics with MRC CLIMB BIG DATA.
Year(s) Of Engagement Activity 2020
URL https://github.com/telatin/learn_bash/wiki/CLIMB
 
Description Bioinformatics workshop at the Evergreen Phage Meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact 30 postgraduate students and early career researchers attended a workshop on the use of command-line tools in the analysis of virome data, as part of the Evergreen International Phage Biology meeting in Olympia, WA, USA
Year(s) Of Engagement Activity 2019
 
Description Cardiff School of Medicine Science Seminar series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Invited keynote seminar at the University of Cardiff School of Medicine presentation entitled 'Salmonella Variants of Interest and Concern: carving a Niche in the pork industry'. Dissemination of key findings from a number of project from within my research group to an audience of approximately 50 students, postdoctoral scientists and prinicpal investigators.
Year(s) Of Engagement Activity 2021
 
Description Coffee Break Science 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact About 100 QIB Employees attended the Coffee science meeting to hear a talk on in vitro models of human gut including hte latest developments on gut-on-chop technology. There was lots of interest by my colleagues to learn about it, they were asking about applications, training, feasibility, etc.
Year(s) Of Engagement Activity 2019
URL https://web.microsoftstream.com/video/77f38d25-d223-4b59-8a61-73d85c6b77fe
 
Description Darwin Day - Oral presentation for Italian students on the Gut Microbiome 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact Oral presentation (remote) for the National Darwin Day organized by UAAR for High School Students.

Live streamed to Facebook (https://www.facebook.com/95169492091/videos/3664473390326646) and YouTube (https://www.youtube.com/watch?v=sdQ11CKu7kI) with >1000 attendants and ~3000 view in the first week.
Year(s) Of Engagement Activity 2021
URL https://www.facebook.com/95169492091/videos/3664473390326646
 
Description Emulate Visit 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact About 15 staff from QI have attended the Emulate visit which took place at QIB with the intention to develop further collaboration and implementation of gut-on-chip tehnology at our Institute on a larger scale.
Year(s) Of Engagement Activity 2019
URL https://intranet.nbi.ac.uk/infoserv/cgi-bin/ResearchOutcomes/view.asp?ID=63775
 
Description Expert consultation on non-typhoidal Salmonella (NTS) and broadly protective Salmonella vaccines (NTS, paratyphoid A, typhoid) 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Third sector organisations
Results and Impact WHO convened this 2-day expert consultation as a forum for stakeholders to review the evidence on the epidemiology and the serovar distribution of invasive and diarrheal NTS disease, and to discuss how the geographic diversity of Salmonella serovars and the potential demand of endemic countries should be considered in the development of broadly protective Salmonella vaccines.
Year(s) Of Engagement Activity 2021
 
Description Invited lecture 23rd Biennial Evergreen International Phage Biology Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Invited lecture on phage taxonomy. The audience reported increased understanding of the importance of phage taxonomy in data analysis and changing behaviours.
Year(s) Of Engagement Activity 2019
 
Description Lotus tutorial 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact A hands-on session for 20 PhD students and Master Students on how to analyse metabarcoding experiments using Lotus.
This allowed to showcase a tool currently developed at the Quadram Institute and to engage in discussions with future researchers interested in microbiome experiments.
Year(s) Of Engagement Activity 2019
URL https://github.com/telatin/lotus-tutorial
 
Description Mapping the spread of SARS-CoV-2 in Zimbabwe using genomic epidemiology 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Blog of Quadram Institute role in assisting the emergency response of the Zimbabwe Government to the SARS-CoV-2 epidemic. The genomic analysis of Zimbabwe's 100 samples showed there were at least 25 separate independent introductions of SARS-CoV-2 into the country that were associated with eight global lineages. Ninety-five per cent featured the D614G genotype, a variant linked to increased transmissibility.
Year(s) Of Engagement Activity 2020,2021
URL https://quadram.ac.uk/blogs/mapping-the-spread-of-sars-cov-2-in-zimbabwe-using-genomic-epidemiology/
 
Description On line Blog of work on Typhoid fever in Zimbabwe 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact A blog was published on the Quadram Institute website that is accessible free of charge internationally. The blog describes in non-technical language the prpblem that endemic typhoid fever causes in Zimbabwe and the objectives of an award from the Bill and Melinda Gates foundation to study Salmonella Typhi and its association with protozoa in the the water environment in Zimbabwe.
Year(s) Of Engagement Activity 2020
URL https://quadram.ac.uk/collaboration-tackling-typhoid-fever-in-zimbabwe/
 
Description Oral presentation at the Norwich Research Park Earth & Life Systems Alliance (ELSA) workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Virtual workshop showcasing research done at the Norwich Research Park to improve knowledge exchange across the park and engage postgraduate students.
Year(s) Of Engagement Activity 2020
 
Description PHAVES: Ask Me Anything 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Virtual Debate in the Ask Me Anything format organised by the international non-profit organisation Phage Directory in order to promote phage research and international collaboration across the globe.
Year(s) Of Engagement Activity 2020
 
Description Postgraduate Student Knowledge Exchange Trip to University of Parma, Italy 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The Knowledge Exchange Trip is a yearly exchange visit with a University or institute in Europe which has a similar research focus to Quadram Institute Bioscience (QIB). The purpose of the trip, is for students to present their PhD research projects to a group of students and group leaders from the host institute and then the host institutes students also present their research to the QIB students. The students also receive a tour of the facilities at the host institute. 11 students attended the trip and gained experience presenting their research to an audience that does not necessarily specialise in the same area of research as them. Students gained knowledge of other research areas and also learnt about new techniques that could benefit their own research. It was also an opportunity to promote QIB and the excellent research that goes on within the institute, which may lead to future collaborations between QIB and the University of Parma.
Year(s) Of Engagement Activity 2018
 
Description Talk for the the Organ-on-a-Chip Technologies Network 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I gave a talk on how sugars from human milk affect human gut barrier function. This presentation on advanced models of human gut triggered an interesting discussion on how the field of in vitro modelling is advancing and what is being done to also include anaerobic bacteria in to the gut-on-chip models.
Year(s) Of Engagement Activity 2020
URL https://www.organonachip.org.uk/events/4647/organ-on-a-chip-symposium
 
Description Video for BioRepository 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Study participants or study members
Results and Impact I took part in making a video for the BioRepository webpage to explain the importance of research and how collaboration with the biorepository improves the research we can deliver on the park to benefit the wider community. The use of state of the art in vitro gut models (including gut on chip) was metnioned. The videos were recorded back in November and are currently in the process of editing. Once they go live, the activity will reach a lot more people than listed above for this point in time.
Year(s) Of Engagement Activity 2020
 
Description Visit to National Microbiology Reference Lab, Zimbabwe 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Two members of the Kingsley group visited Dr Sekesai Zinyowera and her team at the National Microbiology Reference Lab in Harare, Zimbabwe. Project planning, further collaboration and capacity building at NMRL for investigation of food and water-borne bactewrial infections was discussed. We also met with The Douglas Mangwanya, Director of Laboratory Sevices in Zimbabwe and delegates from the City of Harare Authorities involved in water treatment to investigate areas of cooperation.
Year(s) Of Engagement Activity 2020
 
Description Wellcome/BMGF NTS CHIM Workshop invited speaker 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Third sector organisations
Results and Impact Nontyphoidal Salmonellae, particularly Salmonella enterica serovars Typhimurium and Enteritidis, are a major cause of enterocolitis globally. In sub-Saharan Africa NTS are also responsible for invasive disease known as invasive NTS disease or iNTS disease: bacteraemia and/or meningitis which particularly affect young children and HIV-infected individuals and have high associated case fatality rates (1,2). Effective treatment of iNTS disease is hampered by the lack of a pathognomonic clinical presentation, need for blood culturing to make a diagnosis and increasing levels of antimicrobial resistance. For these reasons, development of a vaccine against iNTS disease could have a major global public health impact.
New candidate vaccines against iNTS disease have recently entered or are about to enter first-in-human trials, alone or in combination with licensed typhoid conjugate vaccine, making this workshop particularly timely. A controlled human infection model (CHIM) could have a role in the pathway to vaccine registration for healthy and special populations,
Objectives of the Meeting
1. Understand possible roles for an NTS CHIM
2. Gauge utility of an NTS CHIM for vaccine development
3. Discuss different approaches to NTS CHIM development
4. Prime Wellcome's call for Expressions of Interest for NTS CHIM development
Year(s) Of Engagement Activity 2021