Understanding the molecular mechanisms of resilience in marine invertebrates

Proposal by Zach Bengtsson

But first, a quick intro about me…

• BA in Biology from Boston University (2015)
• Advisor: John Finnerty
• 6 years professional work experience
• Genetics, gene expression, eDNA, remote sensing, GIS
• Interested in a career as a government or non-profit scientist

Resilience conveyed by epigenetics

To better understand how resilient organisms may be to climate change conditions, we need to examine the potential of molecular mechanisms to cope with environmental stress

Image Credit: University of Puget Sound, University of Hawaii, Virginia Institute of Marine Science

Heat stress response in Mytilus trossulus

• Response of 3 genes to chronic and variable heat conditions
• small heat shock protein 24.1 (small HSP24.1)
• heat shock cognate 70 (HSC70)
• heat shock protein 90 (HSP90)
• Code for chaperones that maintain protein folding and prevent aggregation under stress conditions
• More transcription of these genes is expected under stress conditions

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Research questions

• Does chronic heat exposure elicit a different response than variable heat stress?

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• What is the functional role of these genes?

Mytilus trossulus heat stress experiment

Stress related primers:

• small HSP24.1
• HSC70
• HSP90

Additional data:

• Paired respirometry measurements

Progress and current status

• Amplification observed for heat stress-related primers
• Primer for a normalizing gene must be run for reliable quantification
• β-actin
• Complete final HSC70 run
• QC assay

Chapter 1 Timeline

• Complete remaining lab work (Jan 2023)
• May lead in to early Feb depending on normalizing gene primer arrival
• Data analysis and finish rough draft of manuscript (Jan - Feb 2023)
• Manuscript revision and final edits (March 2023)
• Present results at National Shellfisheries Association Meeting (March 2023)

Long non-coding RNAs (lncRNAs) in Crassostrea virginica

• RNAs longer than 200 nucleotides that are not translated into functional proteins

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• lncRNAs have roles in various mechanisms of gene regulation

lncRNA functions

Figure Credit: Zhao, Sun, & Wang 2016

Research questions

• Are lncRNAs in Crassostrea virginica environmentally sensitive?

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• Could lncRNAs be used as a metric to assess organismal response to environmental stress?

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• What specific functions do lncRNAs serve?

Progress and current status

• lncRNA data files should be ready to go directly to differential expression analysis
• Predictions cover interactions between lncRNA and
• DNA
• RNA
• proteins

Chapter 2 timeline

• Prepare data and finalize study design (Feb 2023)
• Differential expression analysis (Mar 2023)
• OA exposure vs control
• Interaction predictions: lncRNA-DNA, -RNA, and -proteins (April 2023)
• Data analysis and rough draft manuscript (May 2023)
• Manuscript revision and final edits (June 2023)

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Questions?

Planning ahead for “by-pass”

• Submit by-pass application by the end of Spring Quarter (June 2023)
• Funding:
• Teaching & Student Assistantships - SAFS, PoE, and Marine Bio
• RA - Roberts lab projects (E5, shellfish work)
• Fellowships/Grants - SAFS fellowships, Hall Conservation Genetics

Chapters 3 & 4

• Build on Chapter 2 analysis pipeline, focusing on corals

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• Adding other pieces of expression landscape which may contribute to resilience
• miRNA, siRNA, other non-coding RNAs
• Focus on interactions with methylation

Course of study timeline

Full Tentative Timeline

• Mussel heat stress project (Jan - March 2023)
• Oyster lncRNA project (Feb - June 2023)
• By-pass application (June 2023)
• Plan of study submission (June 2023)
• Coral lncRNA only project (June 2023 - Sept 2023)
• Final committee formation (Aug - Sep 2023)
• Coral ncRNA project (Sep 2023 - )
• Dissertation proposal submission (Oct - Nov 2023)
• Qualifying exam (Jan - March 2024)
• General exam (Oct - Dec 2024)