Coral Genomics: An assessment of metabolic pathways and genes influencing coral bleaching. Implications for the development of hydra as a model organism.

Project Title: Coral Genomics:  An assessment of metabolic pathways and genes influencing coral bleaching. Implications for the development of hydra as a model organism.
Program:
CAREERS (323)

Project Image: https://support.access-ci.org/system/files/webform/project/242/CoralPolyp_SI.jpg
Tags:
genomics (537)

Status: Complete
Project Leader
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Project Leader:
Milton Muldrow

Email: milton.x.muldrow@wilmu.edu
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Project Personnel
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Mentor(s):
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Student-facilitator(s):
Natalie Vazquez Beales (1722)

Mentee(s):
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Project Information
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Project Description:
This project is predicted to be a multi-semester project to broadly assess genes metabolic function found in both humans, coral (Acropora palmata, A. cervicornis, A. millepora) and the hydra Aiptasia pallida.   

The first goal is to train students on basic coral biology, and issues influencing coral decline.  Students will also be trained to perform blast analyses. 

Second, as a lab, we aim to characterize our own strain of Aiptasia, including:
1. Develop inoculated and bleached strains, along with conducting imaging of the strains. 
2. Conduct genetic sequencing of the hydra.  This initial goal is to provide gene sequencing training, for both the instructor and student, and gather preliminary sequencing data.  This would be a new competency to the lab.   
3. Test novel substances on hydra hypothesized to influence both growth rate and bleaching resilience. 
This will include development of experimental design.
Aiptasia pallida is a model organism for coral reef studies, and these cnidarians are an interesting potential model organism for humans in comparison to the fruit fly.  Implications here include:
* potential insight into coral bleaching mechanisms 
* insight into human evolution and assessment of potential model organisms 
* development of hydra as a model organisms for both corals and humans.  Hydra are already well developed as coral models, although this needs significant development.

Lastly, students will examine the DARWIN cluster and how it might aid project development.

Project Information Subsection
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Project Deliverables:
A project summary and assessment of evolutionary relationships among hydra and humans in regard to metabolic genes.

Project Deliverables:
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Student Research Computing Facilitator Profile:
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Project Institution: Wilmington University
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Anchor Institution: CR-University of Delaware
Preferred Start Date: 02/07/2022
Start as soon as possible.: No
Project Urgency: Already behind3Start date is flexible
Expected Project Duration (in months): 3
Launch Presentation: https://support.access-ci.org/system/files/webform/project/242/LaunchPresentationCAREERS_Natalie_Vasquez_Beales%20.pptx
Launch Presentation Date: 03/09/2022
Wrap Presentation: https://support.access-ci.org/system/files/webform/project/242/WrapPresentationCAREERS_Natalie_Vasquez_Beales.pptx
Wrap Presentation Date: 05/11/2022
Project Milestones:
- Milestone Title: Beginning
  Milestone Description: Examine hydra and coral metabolic function as well as learn how to both access and interpret bioinformatic data (ex: BLAST). Give a Launch presentation.
  Completion Date Goal: 2022-03-09
  Actual Completion Date: 2022-03-09
- Milestone Title: Middle
  Milestone Description: Apply understanding of both hydra and coral metabolic function and bioinformatics data formatting and databases to conduct an analysis on genetic implications of coral metabolic function.
  Completion Date Goal: 2022-04-13
  Actual Completion Date: 2022-04-13
- Milestone Title: End
  Milestone Description: In end, the student will interpret data and analysis to derive conclusions, and develop new hypotheses based on the analysis. Student should develop a poster. Give a Wrap-up presentation.
  Completion Date Goal: 2022-05-11
  Actual Completion Date: 2022-05-11

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What will the student learn?:
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What will the Cyberteam program learn from this project?:
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HPC resources needed to complete this project?:
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Final Report
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What is the impact on the development of the principal discipline(s) of the project?:
Here, the student was able to perform some analyses we were long looking to conduct.  Their work answered key questions regarding our research.

Natalie has received two previous NASA Space Grant awards (NASA Grant NNX15AII9H), and will continue her work this summer examining the basic biology and genomics of corals, along with exploring ways to make them more robust to climate change via genetic engineering.

What is the impact on other disciplines?:
Examination of sirtuin genes may have broad implications of these highly conserved genes throughout the animal kingdom.

Is there an impact physical resources that form infrastructure?:
We did not utilize any new physical resources, although CAREERS did introduce us to the DARWIN resource, which we may incorporate in our research over time.

Is there an impact on the development of human resources for research computing?:
N/A

Is there an impact on institutional resources that form infrastructure?:
N/A

Is there an impact on information resources that form infrastructure?:
N/A

Is there an impact on technology transfer?:
N/A

Is there an impact on society beyond science and technology?:
Our goal is to assist corals in becoming more resilient to climate change.  If we are successful, this would have broad societal benefits, including economic, cultural and intrinsic benefits.

Lessons Learned:
From Natalie’s wrap presentation:

We were able to access and interpret the bioinformatic data collected, when comparing the sequences.
We were able to analyze Sirtuins proteins and transcripts.
We still have to analyze the genetic implication of what actually triggers the stress. Meaning to have a comparison of a coral before and after the stress.

Overall results:
From Natalie’s wrap presentation:

We can determine that there’s a lot of similarities in the Query Cover between Aipatasia and human sirtuins, in that they may overlap in their metabolic functions. These functions of gene maintenance and metabolism may influence bleaching.