Submission information
Submission Number: 103
Submission ID: 177
Submission UUID: 5a593c8d-3c9e-48b0-bff9-fffb022c2293
Submission URI: /form/project
Created: Wed, 07/14/2021 - 11:25
Completed: Wed, 07/14/2021 - 11:25
Changed: Tue, 01/10/2023 - 13:43
Remote IP address: 139.127.179.209
Submitted by: Joel Wilmore
Language: English
Is draft: No
Webform: Project
| Project Title | Metagenomic analysis to identify gene clusters associated with IgA production |
|---|---|
| Program | CAREERS |
| Project Image |
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| Tags | bioinformatics (277), biology (515), genomics (537), python (69), r (32), research-facilitation (442) |
| Status | Finishing Up |
| Project Leader | Joel Wilmore |
| wilmorej@upstate.edu | |
| Mobile Phone | |
| Work Phone | 315-464-5729 |
| Mentor(s) | Joel Wilmore, Neil McGlohon |
| Student-facilitator(s) | Eren Ada |
| Mentee(s) | |
| Project Description | The development of systemic IgA responses is highly dependent on the composition of the intestinal microbiome. We performed shotgun metagenomics on fecal bacteria based on the binding of serum IgA (IgA+ vs IgA-). Our goal is to identify genes or functional clusters of genes that are highly associated with serum IgA binding. We will then be able to target specific pathways, rather than specific species or classes of microbes. Identification of these pathways will provide the basis for improved mucosal vaccine design or inflammatory bowel disease treatments. |
| Project Deliverables | Analysis of existing shotgun metagenomics data (potentially some 16S data) to identify genes or clusters associated with IgA. Additional analysis of the microbiome will depend on the results. Some standard microbiome analyses will be likely as well (diversity, relative abundance, etc). Deliverables will include: A MIDAS database other researchers can use to analyze mouse gut microbiome data, either by itself or with phylogenize. A tree that includes both mouse MAGs and reference genomes. Evidence that this does (or does not) increase coverage. Genes associated with IgA binding (via phylogenize). |
| Project Deliverables | |
| Student Research Computing Facilitator Profile | The ability to analyze genomic data and learn to use new programs based on publications in the field. |
| Mentee Research Computing Profile | |
| Student Facilitator Programming Skill Level | Need help identifying |
| Mentee Programming Skill Level | |
| Project Institution | SUNY Upstate Medical University |
| Project Address | Syracuse , New York |
| Anchor Institution | CR-Rensselaer Polytechnic Institute |
| Preferred Start Date | |
| Start as soon as possible. | Yes |
| Project Urgency | Already behind2Start date is flexible |
| Expected Project Duration (in months) | 6 |
| Launch Presentation | |
| Launch Presentation Date | 05/11/2022 |
| Wrap Presentation | |
| Wrap Presentation Date | |
| Project Milestones |
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| Github Contributions | |
| Planned Portal Contributions (if any) | Deliverables will include: A MIDAS database other researchers can use to analyze mouse gut microbiome data, either by itself or with phylogenize. A tree that includes both mouse MAGs and reference genomes. Evidence that this does (or does not) increase coverage. Genes associated with IgA binding (via phylogenize). |
| Planned Publications (if any) | |
| What will the student learn? | |
| What will the mentee learn? | |
| What will the Cyberteam program learn from this project? | |
| HPC resources needed to complete this project? | |
| Notes | |
| What is the impact on the development of the principal discipline(s) of the project? | |
| What is the impact on other disciplines? | |
| Is there an impact physical resources that form infrastructure? | |
| Is there an impact on the development of human resources for research computing? | |
| Is there an impact on institutional resources that form infrastructure? | |
| Is there an impact on information resources that form infrastructure? | |
| Is there an impact on technology transfer? | |
| Is there an impact on society beyond science and technology? | |
| Lessons Learned | |
| Overall results |