The generation and maintenance of genetic novelty in helminth populations
Lead Research Organisation:
Wellcome Sanger Institute
Department Name: Pathogen Variation
Abstract
Helminths, commonly called parasitic worms, are a group of organisms that exploit an incredibly diverse range of hosts and life history strategies for their persistence across generations. Helminth infections of humans and animals of veterinary importance, such as companion and food-producing animals, are responsible for a significant disease burden in their hosts that causes pain, disability, developmental delay, and in some cases, death around the world. Worldwide, over 1.5 billion people and countless animals are infected with one or more helminth species at any given time. As such, human helminth infections are the target of large-scale mass drug administration campaigns, and in veterinary settings, hundreds of millions of animals are treated with anthelmintic drugs to prevent and/or cure infections. The importance of anthelmintics to treat helminth infections cannot be understated; the discovery and development of ivermectin as an anthelmintic was recognised by a Nobel Prize in Physiology or Medicine in 2015.
The ability of helminths to survive and adapt within or outside their hosts lies in their capacity to generate and maintain significant genetic novelty upon which selection can act, which in turn determines their adaptive potential. Two examples clearly illustrate this adaptive potential: (i) the ability of helminths to parasitise single or multiple host species has arisen from free-living ancestors independently many times throughout their evolutionary history, with different species of helminth exploiting distinct mechanisms to invade and establish in their host, and (ii) widespread and frequent use of anthelmintic drugs to control parasites has rapidly selected for drug-resistant parasites. Only three classes of broad-spectrum anthelmintics are available; in veterinary animals (and particularly in livestock), resistance to all of classes including to multiple classes simultaneously has been documented in many helminths species throughout the world, in as little as a few years after introduction of the drug. In humans, there are increasing concerns that reduced efficacy of these same drugs is evidence of emerging resistance, which threatens to reverse gains from up to 30 years of successful treatment and parasite control. The genetic basis for this adaptation is, however, poorly understood. This major gap in our knowledge, largely due to the high genetic diversity and experimental intractability of most helminth species, limits our ability to understand these processes, which need to be overcome to successfully treat disease and predict outcomes of long-term control programmes.
My work will identify the genetic mechanisms underpinning parasite adaptation. To do so, I will focus initially on the impact drug selection using ivermectin, a vitally important drug in human and animal health, has on the genetic diversity of Haemonchus contortus, a major economically important gastrointestinal parasite of livestock worldwide and a genetically tractable model used for drug discovery, vaccine development, and anthelmintic resistance research. Using a genetic cross between susceptible and ivermectin resistant H. contortus strains to control genetic diversity, together with high-throughput population and single-cell genomic approaches to sample genetic diversity over a multi-year evolution experiment, this research will dissect the interaction between genetic and phenotypic variation, and the impact that selection has on shaping this variation. Further, these data will show their potential for future adaptation, and identify evolutionary constraints that may be exploited for novel control interventions. More broadly, these data will inform practices to improve the health and welfare of animals exposed to parasites like H. contortus, and provide a novel experimental and theoretical framework toward understanding the adaptive potential of genetically intractable helminth species of human and veterinary medical importance
The ability of helminths to survive and adapt within or outside their hosts lies in their capacity to generate and maintain significant genetic novelty upon which selection can act, which in turn determines their adaptive potential. Two examples clearly illustrate this adaptive potential: (i) the ability of helminths to parasitise single or multiple host species has arisen from free-living ancestors independently many times throughout their evolutionary history, with different species of helminth exploiting distinct mechanisms to invade and establish in their host, and (ii) widespread and frequent use of anthelmintic drugs to control parasites has rapidly selected for drug-resistant parasites. Only three classes of broad-spectrum anthelmintics are available; in veterinary animals (and particularly in livestock), resistance to all of classes including to multiple classes simultaneously has been documented in many helminths species throughout the world, in as little as a few years after introduction of the drug. In humans, there are increasing concerns that reduced efficacy of these same drugs is evidence of emerging resistance, which threatens to reverse gains from up to 30 years of successful treatment and parasite control. The genetic basis for this adaptation is, however, poorly understood. This major gap in our knowledge, largely due to the high genetic diversity and experimental intractability of most helminth species, limits our ability to understand these processes, which need to be overcome to successfully treat disease and predict outcomes of long-term control programmes.
My work will identify the genetic mechanisms underpinning parasite adaptation. To do so, I will focus initially on the impact drug selection using ivermectin, a vitally important drug in human and animal health, has on the genetic diversity of Haemonchus contortus, a major economically important gastrointestinal parasite of livestock worldwide and a genetically tractable model used for drug discovery, vaccine development, and anthelmintic resistance research. Using a genetic cross between susceptible and ivermectin resistant H. contortus strains to control genetic diversity, together with high-throughput population and single-cell genomic approaches to sample genetic diversity over a multi-year evolution experiment, this research will dissect the interaction between genetic and phenotypic variation, and the impact that selection has on shaping this variation. Further, these data will show their potential for future adaptation, and identify evolutionary constraints that may be exploited for novel control interventions. More broadly, these data will inform practices to improve the health and welfare of animals exposed to parasites like H. contortus, and provide a novel experimental and theoretical framework toward understanding the adaptive potential of genetically intractable helminth species of human and veterinary medical importance
Planned Impact
The overall aim of the proposed research is to understand how helminths generate and maintain genetic novelty, and how this novelty is used and changes in response to selection. These poorly understood aspects of helminth evolution will underpin the success or failure of any parasite control strategies in the future. The data and resources generated will inform the mechanisms by which helminths have become successful parasites, demonstrate their potential for future adaptation, and identify evolutionary constraints that may be exploited for novel control interventions.
The primary beneficiaries of this work are academic researchers working on H. contortus and/or related helminth species. In the short-term, these data will allow researchers to identify the context of "where" genes of interest are expressed, "when" during development this takes place, and "how" certain gene variants are used differently throughout the life cycle and in different cells of the parasite. Further, this rich transcriptional data will be incorporated into the H. contortus genome annotation and made available without restriction on the helminth community portal WormBase Parasite; this fine-grained information will not only benefit the H. contortus community, it will also provide very strong experimental evidence for gene annotations in other helminth species, many of which are only computationally predicted, have been poorly annotated, and/or contain no known functions.
In the longer term, the results generated here will impact broader questions related to the sustainable control of helminths that infect humans and animals globally. Over 1.5 billion people worldwide are infected with one or more helminth species at any given time, and countless animals are exposed or infected, such that human helminth infections are the target of large scale mass drug administration campaigns, and in veterinary settings, millions of animals worldwide are prophylactically treated with drugs to prevent and/or cure infection. Resistance to the few drugs available is already widespread in helminths of veterinary animals, while evidence of resistance is emerging in human-infective helminths treated with these same few compounds. New approaches to control these infections and manage resistance to maintain the efficacy of these drugs are desperately needed. The data generated here will inform this goal in a number of ways:
- A comprehensive understanding of the genome diversity at single-cell resolution will likely identify novel targets for alternative means to control the parasite;
- Understanding the relationship between phenotypic and genetic responses to resistance will allow for more precise diagnostic testing of resistance in the field, the detection of which may allow early intervention before there is an impact on human and/or animal health;
- Understanding fitness costs associated with resistant alleles will feed back into refugia-based management strategies that aim to limit the accumulation of resistant alleles;
- Surveillance of helminths using genomic tools will become increasingly common in health programs that aim to characterise, for example, treatment efficacy, transmission dynamics, and population decline toward infection elimination; the theoretical and empirical frameworks developed here will inform the development of such tools to monitor and/or predict change in helminth populations over time using genetic variation.
Finally, the flexibility and extended support that the UKRI Future Leaders Fellowship provides will positively impact my career progression as I establish an independent research group, and research agenda toward understanding aspects of the population biology of helminths using cutting-edge genomics. Further, the research proposed will also provide exciting opportunities for the PDF to receive training and acquisition of new skills that will benefit their career development towards independence.
The primary beneficiaries of this work are academic researchers working on H. contortus and/or related helminth species. In the short-term, these data will allow researchers to identify the context of "where" genes of interest are expressed, "when" during development this takes place, and "how" certain gene variants are used differently throughout the life cycle and in different cells of the parasite. Further, this rich transcriptional data will be incorporated into the H. contortus genome annotation and made available without restriction on the helminth community portal WormBase Parasite; this fine-grained information will not only benefit the H. contortus community, it will also provide very strong experimental evidence for gene annotations in other helminth species, many of which are only computationally predicted, have been poorly annotated, and/or contain no known functions.
In the longer term, the results generated here will impact broader questions related to the sustainable control of helminths that infect humans and animals globally. Over 1.5 billion people worldwide are infected with one or more helminth species at any given time, and countless animals are exposed or infected, such that human helminth infections are the target of large scale mass drug administration campaigns, and in veterinary settings, millions of animals worldwide are prophylactically treated with drugs to prevent and/or cure infection. Resistance to the few drugs available is already widespread in helminths of veterinary animals, while evidence of resistance is emerging in human-infective helminths treated with these same few compounds. New approaches to control these infections and manage resistance to maintain the efficacy of these drugs are desperately needed. The data generated here will inform this goal in a number of ways:
- A comprehensive understanding of the genome diversity at single-cell resolution will likely identify novel targets for alternative means to control the parasite;
- Understanding the relationship between phenotypic and genetic responses to resistance will allow for more precise diagnostic testing of resistance in the field, the detection of which may allow early intervention before there is an impact on human and/or animal health;
- Understanding fitness costs associated with resistant alleles will feed back into refugia-based management strategies that aim to limit the accumulation of resistant alleles;
- Surveillance of helminths using genomic tools will become increasingly common in health programs that aim to characterise, for example, treatment efficacy, transmission dynamics, and population decline toward infection elimination; the theoretical and empirical frameworks developed here will inform the development of such tools to monitor and/or predict change in helminth populations over time using genetic variation.
Finally, the flexibility and extended support that the UKRI Future Leaders Fellowship provides will positively impact my career progression as I establish an independent research group, and research agenda toward understanding aspects of the population biology of helminths using cutting-edge genomics. Further, the research proposed will also provide exciting opportunities for the PDF to receive training and acquisition of new skills that will benefit their career development towards independence.
Organisations
- Wellcome Sanger Institute (Fellow, Lead Research Organisation)
- University of Glasgow (Collaboration)
- Natural History Museum (Collaboration)
- Moredun Research Institute (Collaboration)
- University of Manchester (Collaboration)
- HARVARD UNIVERSITY (Collaboration)
- Instituto de Salud Global de Barcelona (Collaboration)
- University of Georgia (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
Publications
Antonopoulos A
(2022)
Allele specific PCR for a major marker of levamisole resistance in Haemonchus contortus.
in International journal for parasitology. Drugs and drug resistance
Antonopoulos A
(2024)
Functional validation of novel levamisole resistance marker S168T in Haemonchus contortus
in International Journal for Parasitology: Drugs and Drug Resistance
Baltrušis P
(2022)
Genome-wide analysis of the response to ivermectin treatment by a Swedish field population of Haemonchus contortus.
in International journal for parasitology. Drugs and drug resistance
Brann T
(2024)
Subtelomeric plasticity contributes to gene family expansion in the human parasitic flatworm Schistosoma mansoni
in BMC Genomics
Buddenborg SK
(2023)
The stage- and sex-specific transcriptome of the human parasite Schistosoma mansoni.
in Scientific data
Cotton JA
(2022)
A genetic TRP down the channel to praziquantel resistance.
in Trends in parasitology
Crawford KE
(2024)
Genome-based tools for onchocerciasis elimination: utility of the mitochondrial genome for delineating Onchocerca volvulus transmission zones.
in International journal for parasitology
Description | The broad scope of our research is to understand how parasitic worms that infect animals and humans evolve over time. To do this, we have been developing genetic resources and tools to study and monitor how parasites differ from different places in the world. One example of developing resources is in the curated genome assembly of the sheep parasite, Haemonchus contortus, which forms a dataset upon which much of our future research, and that of many researchers working on helminth parasites around the world, is based. One example of understanding the diversity of parasites is our work focused on human whipworm Trichuris trichiura, where we sequenced parasites from around the world and up to 1000 years old (the oldest multicellular parasites ever sequenced), which demonstrated their relationships between each other and to non-human primates, which represent a zoonotic reservoir that may hinder control campaigns targeted this important human pathogen. Finally, we are establishing research to understand the fundamental building blocks of a parasite by sequencing every cell within the organism, which we believe will tell use more about how and why parasites are so successful and identify new ways to control them. |
Exploitation Route | We are generating significant amounts of data, curated genomic resources, and code/software that is all being made publicly available. We are actively encouraging others to use and build upon these data. We are also developing research frameworks for understanding genetic diversity in parasitic worms. We believe this will significantly impact the way this work is performed in the future. We are in the process of developing tools that can be used to inform the control of parasitic worms that affect over 1 billion people worldwide. |
Sectors | Agriculture Food and Drink Healthcare Pharmaceuticals and Medical Biotechnology Other |
URL | https://stephenrdoyle.github.io/ |
Description | European and Developing Countries Clinical Trial Partnership |
Amount | € 3,553,502 (EUR) |
Funding ID | 101103089 |
Organisation | European Commission |
Department | Directorate General for Research and Innovation |
Sector | Public |
Country | European Union (EU) |
Start | 06/2023 |
End | 06/2026 |
Description | Sanger Excellence Fellowship |
Amount | £218,221 (GBP) |
Organisation | The Wellcome Trust Sanger Institute |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 12/2023 |
End | 12/2026 |
Description | Whole-transcriptome and single-cell resolution spatial mapping of a model parasitic worm |
Amount | £10,241 (GBP) |
Organisation | The Wellcome Trust Sanger Institute |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 06/2024 |
End | 12/2024 |
Title | Code for publication "Population genomics of ancient and modern Trichuris trichiura". |
Description | Code for publication "Population genomics of ancient and modern Trichuris trichiura". |
Type Of Material | Computer model/algorithm |
Year Produced | 2022 |
Provided To Others? | Yes |
Impact | Code is being reused and adapted by members of the lab. Also had contact from students remotely who are reusing the code |
URL | https://github.com/stephenrdoyle/ancient_trichuris |
Title | Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm |
Description | Updated genome annotation for Haemocnhus contortus |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | Since publication in 2020, we have gone on to further curate genome annnotations for the parasite Haemonchus controtus, and released then for public use via WormBase Parasite. These data are used by a wide range of researchers, and are recognised by citations to the original paper. |
URL | https://parasite.wormbase.org/Haemonchus_contortus_prjeb506/Info/Index |
Title | Haemonchus contortus genome and annotation |
Description | Reference genome assembly and genome annotation that has been submitted to WormBase Parasite, the major repository for helminth genome data. The annotation in particular has been improved as part of the current funding. These data support researchers around the world in their wet lab and computational experiments. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | Many published research papers use these resources. |
URL | https://parasite.wormbase.org/Haemonchus_contortus_prjeb506/Info/Index/ |
Title | Schistosoma mansoni genome and annotation |
Description | Reference genome assembly and genome annotation that has been submitted to WormBase Parasite, the major repository for helminth genome data. The annotation in particular has been improved as part of the current funding. These data support researchers around the world in their wet lab and computational experiments. |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | Many publications describe the use of this dataset in academic research. |
URL | https://parasite.wormbase.org/Schistosoma_mansoni_prjea36577/Info/Index/ |
Title | Teladorsagia circumcincta genome and annotation |
Description | Reference genome assembly and genome annotation that has been submitted to WormBase Parasite, the major repository for helminth genome data. The annotation in particular has been improved as part of the current funding. These data support researchers around the world in their wet lab and computational experiments. |
Type Of Material | Database/Collection of data |
Year Produced | 2024 |
Provided To Others? | Yes |
Impact | `Key focus of our current research, however, we have shared it with collaborators to support their research. |
Title | The genome sequence of the Australian filarial nematode, Cercopithifilaria johnstoni |
Description | Wellcome Open Research is an Open Research platform. This publication is: version 2; peer review: 3 approved.We present a genome assembly and annotation of an individual female Cercopithifilaria johnstoni, a parasitic filarial nematode that is transmitted by hard ticks (Ixodidae) to infect a broad range of native Australian murid and marsupial hosts. The genome sequence is 76.9 Mbp in length, and although in draft form (N50 = 99 kbp, N50[n] = 232), is largely complete based on universally conserved orthologs (BUSCOs; genome = 94.9%, protein = 96.5%) and relative to other related filarial species. These data represent the first genomic resources for the genus Cercopithifilaria, a group of parasites with a broad host range, and form the basis for comparative analysis with the human-infective parasite, Onchocerca volvulus, both of which are responsible for similar eye and skin pathologies in their respective hosts. |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | We generated a genome sequence and annotation for the parasite Cercopithifilaria johnstoni, and submitted it for public use to WormBase Parasite, the major repository for helminth genomes. |
URL | https://opal.latrobe.edu.au/articles/journal_contribution/The_genome_sequence_of_the_Australian_fila... |
Title | stephenrdoyle/hcontortus_genome v1.0 |
Description | Release of code associated with analyses of genome of Haemonchus contortus, presented in the manuscript "Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm" by Doyle et al. 2020. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | These code have been used by my group and others interested in generating genome resources for helminth parasites |
URL | https://zenodo.org/record/4069269 |
Description | Analysing the genetic diversity of soil-transmitted helminths - supervision of PhD student Marina Papaiakovou |
Organisation | Natural History Museum |
Country | United Kingdom |
Sector | Public |
PI Contribution | I have recently started a collaboration with Cinzia Cantacessi at the University of Cambridge, UK and Tim Littlewood at the Natural History Museum, UK, as a second supervisor to the PhD student Marina Papaiakovou. I provide day to day support and mentorship to Marina, and have helped write the first publication of Marina's PhD. I will be helping to facilitate some of the genome sequencing required during Marina's PhD project. |
Collaborator Contribution | Cinzia and Tim both contribute to Marina's supervision and mentorship. |
Impact | We have just had a manuscript accepted for publication in Parasites and Vectors. |
Start Year | 2021 |
Description | Analysing the genetic diversity of soil-transmitted helminths - supervision of PhD student Marina Papaiakovou |
Organisation | University of Cambridge |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | I have recently started a collaboration with Cinzia Cantacessi at the University of Cambridge, UK and Tim Littlewood at the Natural History Museum, UK, as a second supervisor to the PhD student Marina Papaiakovou. I provide day to day support and mentorship to Marina, and have helped write the first publication of Marina's PhD. I will be helping to facilitate some of the genome sequencing required during Marina's PhD project. |
Collaborator Contribution | Cinzia and Tim both contribute to Marina's supervision and mentorship. |
Impact | We have just had a manuscript accepted for publication in Parasites and Vectors. |
Start Year | 2021 |
Description | Development of essential research tools for sustaining global programs for the elimination of human hookworms |
Organisation | Harvard University |
Department | Harvard T.H. Chan School of Public Health |
Country | United States |
Sector | Academic/University |
PI Contribution | I have made intellectual and grant writing contributions toward a project, recently recommended for NIH R21 funding. This work will bring a collaborator from Harvard to the Wellcome Sanger Institute to use methods developed during my current funding towards building genome resources for a hookworm parasite. |
Collaborator Contribution | This project is led by researchers at Harvard in collaboration with UGA and my group at Sanger. They have led the grant writing and project management to date. |
Impact | No specific outputs, other than recent recommendation for NIH R21 funding. This collaboration is multidisciplinary, combining parasitology, genetics, and genomics. |
Start Year | 2021 |
Description | Development of essential research tools for sustaining global programs for the elimination of human hookworms |
Organisation | University of Georgia |
Country | United States |
Sector | Academic/University |
PI Contribution | I have made intellectual and grant writing contributions toward a project, recently recommended for NIH R21 funding. This work will bring a collaborator from Harvard to the Wellcome Sanger Institute to use methods developed during my current funding towards building genome resources for a hookworm parasite. |
Collaborator Contribution | This project is led by researchers at Harvard in collaboration with UGA and my group at Sanger. They have led the grant writing and project management to date. |
Impact | No specific outputs, other than recent recommendation for NIH R21 funding. This collaboration is multidisciplinary, combining parasitology, genetics, and genomics. |
Start Year | 2021 |
Description | Evolution of drug resistance in the sheep gastrointestinal nematode, Teladorsagia circumcincta - supervision of PhD student Benedict Karani |
Organisation | University of Glasgow |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Joint supervision of a PhD student. Collaboration on project design. Advice on planned analyses. |
Collaborator Contribution | Primary supervision of the student by James Cotton, University of Glasgow, together with Roz Laing, and Jennifer McIntyre (Glasgow) and Fiona Kenyon (Moredun Research Institute) |
Impact | None yet, only running less than 6 months. |
Start Year | 2023 |
Description | Moredun Research Institute |
Organisation | Moredun Research Institute |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | This is a core collaboration for the project, which enables the maintenance and manipulation of parasites in sheep. We have regular interactions of experimental design and progress. This is a long term collaboration that began before this award, but is still very active and relevant to the current award. |
Collaborator Contribution | The collaborators do all of the handlings of sheep and parasites, and ship samples from Moredun to Sanger. |
Impact | We have had a number of recent publications within the scope of the current work, including: Morrison AA, Chaudhry U, Andrews L, Melville L, DOYLE SR, Sargison ND, Bartley DJ (2022) Phenotypic and genotypic analysis of benzimidazole resistance in reciprocal genetic crosses of Haemonchus contortus. Int. J Parasitol-DDR DOYLE SR, Laing R, Bartley D, Morrison A, Holroyd N, Maitland K, Antonopoulos A, Chaudhry U, Flis I, Howell S, McIntyre J, Gilleard JS, Tait A, Mable BK, Kaplan R, Sargison N, Britton C, Berriman M, Devaney E, Cotton J (2021) Genomic landscape of drug response reveals novel mediators of anthelmintic resistance. bioRxiv. Laing R, DOYLE SR, McIntyre J, Maitland K, Morrison A, Bartley DJ, Kaplan R, Chaudhry U, Sargison N, Tait A, Cotton JA, Britton C, Devaney E (2021) Transcriptomic analyses implicate neuronal plasticity and chloride homeostasis in ivermectin resistance and recovery in a parasitic nematode. bioRxiv. |
Start Year | 2015 |
Description | Population genomics of praziquantel treatment response by Schistosoma mansoni from Uganda - mentorship of PhD student Shannan Summers |
Organisation | Natural History Museum |
Country | United Kingdom |
Sector | Public |
PI Contribution | Mentorship to Shannan Summers, a PhD student at the Natural History Museum London. Provide experimental design, lab, bioinformatics and analysis support. |
Collaborator Contribution | Performing data generation and analysis. |
Impact | Manuscript in preparation |
Start Year | 2023 |
Description | STOP Consortium |
Organisation | Instituto de Salud Global de Barcelona |
Country | Spain |
Sector | Charity/Non Profit |
PI Contribution | I have been invited to be a member of the STOP Consortium, which aims to stop the transmission of parasites that infect humans, namely the soil-transmitted helminths, by evaluating and implementing new approaches to treatment. Since joining, I have - advised on genetic strategies to monitor drug resistance - supported a masters student on a summer placement with my group - contributed to grant writing to fund future work, submitted to NIH/CDC for $2.4 million USD. - contributed to writing a manuscript, which is about to be submitted for publication. |
Collaborator Contribution | The partners have contributed in many of the activities described above. They have also provided samples from their archives for developing protocols and methodologies that will complement both of our research programs moving forward. I have made note of this "in kind" contribution as £1 GBP, however, these samples are invaluable and impossible for me to collect in any other practical way. |
Impact | - manuscript about to be submitted for publication - grant submitted to NIH/CDC This collaboration is multidisciplinary, combining parasitology, epidemiology, genomics, statistical analyses. |
Start Year | 2021 |
Description | University of Cambridge - Maria Duque-Correa |
Organisation | University of Cambridge |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We are developing single-cell genomics protocols for parasitic worms, led by postdoctoral fellow Sarah Buddenborg in my lab. We are sharing materials and protocols. We are also collaborating on RNAseq experiments, and supporting bioinformatic analysis |
Collaborator Contribution | Maria's lab have provided parasite material for single cell sequencing. They are running wetlab experiments and generating samples for sequencing. |
Impact | Protocols have been optimised, and a manuscript is in preparation. |
Start Year | 2023 |
Description | University of Manchester - Richard Grencis |
Organisation | University of Manchester |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Supported experimental and analysis design. Performed bioinformatic analyses. |
Collaborator Contribution | Collaboration with Richard Grencis and Kelly Hayes. Performed wetlab experiments, sequencing, and data analysis. |
Impact | Manuscript in preparation: "Stable lentiviral-mediated transgenesis of the murine parasitic nematode Trichuris muris" |
Start Year | 2023 |
Description | Berlin Parasitology Seminar series |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited presentation to the Berlin Parasitology Seminar series, which is a forum held between a number of research institutions in Berlin, Germany |
Year(s) Of Engagement Activity | 2021 |
Description | British Association for Veterinary Parasitology (Invited Panel Member for ECR Careers session) |
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 | Was invited to speak in a panel discussion on career progression for the British Association for Veterinary Parasitology |
Year(s) Of Engagement Activity | 2022 |
Description | Genomics Lite |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | Speaker for the Wellcome Connecting Science's Genomics Lite series aimed at A-Level students. The topic was titled "Parasitic Nematodes". There was a one hour presentation that was recorded followed by a Q&A session from students and their teachers. A recording was posted to YouTube |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.youtube.com/watch?v=CwR2sglF_sI |
Description | Helminth Bioinformatics Wellcome Connecting Science course, Khon Kaen, Thailand |
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 | Lead a bioinformatics course targeted at building bioinformatics capacity in Asia Pacific region. 30 postgraduate students attended the week long course at Khon Kaen Univerity. We also ran a public engagement event at the local natural history museum, for school-aged children. Nearly 200 children, including some from the general public, attended. |
Year(s) Of Engagement Activity | 2023 |
Description | Interview with undergraduate students from University of Florida |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Undergraduate students |
Results and Impact | Invited interview with University of Florida undergraduate students to discuss my career and research |
Year(s) Of Engagement Activity | 2022 |
Description | Invited plenary speaker at 5th Parasitic Nematode Workshop: Bridging the Divide |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited plenary speaker at 5th Parasitic Nematode Workshop: Bridging the Divide |
Year(s) Of Engagement Activity | 2021 |
Description | Invited plenary speaker at Molecular Helminthology: An Integrated Approach |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited plenary speaker to discuss current research, which generated a lot of interesting followup discussion |
Year(s) Of Engagement Activity | 2021 |
Description | LSHTM Masters Course lightning talk |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | I gave a lightning talk for Masters students on parasite genomics in the Wellcome Connecting Science Open Lab at the Wellcome Genome Campus. We also had a networking event afterwards to discuss careers and research opportunities in genomics. |
Year(s) Of Engagement Activity | 2023 |
Description | Life Sciences foundation course |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Undergraduate students |
Results and Impact | I was a speaker for the University of Lincoln's Life Sciences foundation course. I gave a 30 minute talk on parasitic worms and genomics followed by a Q&A with students and teachers. I also discussed career options and my career path with students. |
Year(s) Of Engagement Activity | 2023 |
Description | NTD Day, York Biomedical Institute, UK |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Invited talk on NTD research in the UK. |
Year(s) Of Engagement Activity | 2023 |
Description | Parasitic Helminths: New Perspectives in Biology and Infection, Hydra, Greece |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Oral presentation of research to world-leading scientists and colleagues |
Year(s) Of Engagement Activity | 2023 |
Description | Parasitology meeting - functional validation of parasitic nematode genes |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Invited to speak at a workshop on "functional validation of parasitic nematode genes", which aimed to bring together experts to discuss challenges and opportunities in our field. |
Year(s) Of Engagement Activity | 2023 |
Description | Podcast for "Two Brad for You" |
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 | Media (as a channel to the public) |
Results and Impact | From the podcast page: Stephen Doyle is a molecular and computational biologist who uses whole genome sequencing to study how parasites evolve resistance to drugs. He was also able to explain how genome sequencing works and just how powerful that technology and data can be, especially in the context of the ongoing coronavirus situation. You've heard of corona variants, well Stephen helps sort out what this means and how genomics is used to track these outbreaks. We also discussed the benefits of pre-print for the field of genomics and the importance of open science. |
Year(s) Of Engagement Activity | 2021 |
URL | https://podcasts.apple.com/gb/podcast/tbfy-in-conversation-21-sharing-genomes-and-more/id1268436621?... |
Description | Presentation to Barcelona Institute for Global Health |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited talk to the Barcelona Institute for Global Health and STOP Consortium working group, which generated a lot of discussion and interest in using genomics to survey parasites. |
Year(s) Of Engagement Activity | 2021 |
Description | Promotional material for postdoctoral researchers at the Wellcome Sanger Institute |
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 | Postgraduate students |
Results and Impact | Participated in the generation of promotional material for the Wellcome Sanger Institute in collaboration with New Scientist magazine. |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.youtube.com/watch?v=1-vxm2nBmFA |
Description | STEM Ambassador |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | Regular "meet the scientist" events where I present what a day in the life of scientists looks like. Variety of ages from secondary school-college. |
Year(s) Of Engagement Activity | 2022,2023 |
Description | Talk at Helminth Bioinformatics, Accra, Ghana |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Invited presentation during a workshop focused on building bioinformatics capacity in low and middle-income countries. |
Year(s) Of Engagement Activity | 2021 |
Description | Talk at World Association for the Advancement of Veterinary Parasitology (WAAVP) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Gave a talk at World Association for the Advancement of Veterinary Parasitology (WAAVP) |
Year(s) Of Engagement Activity | 2021 |
Description | Wellcome Connecting Science Open Lab |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | Conducting student tours at the Open Lab at the Wellcome Genome Campus. |
Year(s) Of Engagement Activity | 2023 |
Description | Working with Pathogen Genomes (Latin America) (Virtual) |
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 | Ran a virtual bioinformatics course for 30 participants in Latin America. |
Year(s) Of Engagement Activity | 2022 |
URL | https://coursesandconferences.wellcomeconnectingscience.org/event/working-with-pathogen-genomes-lati... |
Description | ZAPworms |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Talk on our research and the need to improve helminth genomes. Resulted in a lot of discussion and followup interactions. One followup was invite to co-organise a conference in Toronto in September 2024. |
Year(s) Of Engagement Activity | 2023 |