Course Description

This one-week intensive graduate-level course explores the intriguing intersection of climate change, epigenetics, and marine invertebrate physiology, with a significant emphasis on the application of functional genomics. The course aims to highlight the substantial yet often overlooked role of marine invertebrates in coastal ecosystems, underlining their ecological significance and their responses to climate change at an epigenetic level.

The course starts by establishing a strong foundational understanding of epigenetics, climate change, and marine invertebrate physiology. Following this, students will delve into the intricate role of functional genomics in understanding these connections. Real-world examples will be extensively used to discuss how changes in climate directly and indirectly lead to alterations in the epigenetic mechanisms of various coastal marine invertebrates.

By the end of the course, students should have a comprehensive understanding of how climate change can influence the epigenetics and physiology of coastal marine invertebrates and the potential broader implications for marine ecosystems. The course is suitable for students with a basic understanding of genetics and climate science, although students from all disciplines are welcome as the course starts from foundational principles.

Through a mix of lectures, discussions, and interactive case studies, students will develop a nuanced understanding of the course topics. This course is highly recommended for students interested in marine biology, genetics, climate change, and conservation biology.

Objectives:

Objective 1: Understanding the Interplay between Climate Change, Epigenetics, and Marine Invertebrate Physiology

The first objective of the course is to help students gain a comprehensive understanding of how climate change impacts the physiological processes of marine invertebrates, especially through the lens of epigenetics. Students will learn about the fundamentals of marine invertebrate physiology and the various ways in which climate change-related stressors can influence these physiological systems, causing significant changes at an epigenetic level.

Objective 2: Gaining Proficiency in Functional Genomics

The second objective is to ensure that students gain proficiency in the methodologies and applications of functional genomics, particularly in studying the epigenetic changes in marine invertebrates in response to climate change. Students will learn about various genomic techniques, their applications, and how to interpret data from these studies to gain insights into the epigenetic responses of marine invertebrates to climate stressors.

Objective 3: Developing Skills for Analyzing and Evaluating Scientific Research

The third objective is to develop students’ ability to critically analyze and evaluate scientific literature in the field of marine invertebrate epigenetics and climate change. Through case studies and discussions on recent research, students will hone their skills in analyzing experimental designs, interpreting results, and understanding the broader implications of research findings for climate change adaptation and marine conservation efforts.

Contents:

Basics of Epigenetics and Climate Change: This module provides an overview of climate change science and the principles of epigenetics. We discuss how the two fields intersect and introduce the concept of environmental epigenetics.

Physiology of Marine Invertebrates: This module focuses on the essential aspects of marine invertebrate physiology, covering topics such as feeding, digestion, reproduction, and response to environmental stressors.

Impact of Climate Change on Marine Invertebrate Physiology: This section explores the specific impacts of various climate change-related factors, such as ocean acidification, temperature rise, and salinity changes on the physiology of marine invertebrates.

Functional Genomics and Epigenetics: This module delves into the methodologies and applications of functional genomics in studying epigenetic changes. Various genomic techniques such as DNA methylation analysis, chromatin immunoprecipitation, and RNA sequencing will be discussed.

Case Studies and Current Research: The final module will involve an in-depth examination of recent research studies in the field. Students will be encouraged to critically analyze the studies and discuss the implications of the findings on our understanding of climate change impacts and the role of epigenetics in marine invertebrate adaptation.

Methodology:

Through a mix of lectures, discussions, and interactive data analysis, students will develop a nuanced understanding of the course topics. This course is highly recommended for students interested in marine biology, genetics, climate change, and conservation biology. The general format will be lecture in the morning and interactive data analysis in the afternoon. The latter will primarily involve using R and bash.

Bibliography:

Crandall, Grace, Rhonda Elliott Thompson, Benoit Eudeline, Brent Vadopalas, Emma Timmins-Schiffman, and Steven Roberts. 2022. “Proteomic Response of Early Juvenile Pacific Oysters (Crassostrea Gigas) to Temperature.” PeerJ 10 (October): e14158. https://doi.org/10.7717/peerj.14158.

Crandall, Grace, Pamela C. Jensen, Samuel J. White, and Steven Roberts. 2022. “Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes Bairdi).” Marine Biotechnology 24 (1): 216–25. https://doi.org/10.1007/s10126–022–10100–8.

Dang, Xin, Yong-Kian Lim, Yang Li, Steven B. Roberts, Li Li, and Vengatesen Thiyagarajan. 2023. “Epigenetic-Associated Phenotypic Plasticity of the Ocean Acidification-Acclimated Edible Oyster in the Mariculture Environment.” Molecular Ecology 32 (2): 412–27. https://doi.org/10.1111/mec.16751.

Dimond, James L., and Steven B. Roberts. 2016. “Germline DNA Methylation in Reef Corals: Patterns and Potential Roles in Response to Environmental Change.” Molecular Ecology 25 (8): 1895–1904. https://doi.org/10.1111/mec.13414.

Eirin-Lopez, Jose M., and Hollie M. Putnam. 2019. “Marine Environmental Epigenetics.” Annual Review of Marine Science 11 (January): 335–68. https://doi.org/10.1146/annurev-marine–010318–095114.

Gallardo-Escárate, C., V. Valenzuela-Muñoz, S. Boltaña, G. Nuñez-Acuña, D. Valenzuela-Miranda, A. T. Gonçalves, C. Détrée, et al. 2017. “The Caligus Rogercresseyi miRNome: Discovery and Transcriptome Profiling during the Sea Lice Ontogeny.” Agri Gene 4 (June): 8–22. https://doi.org/10.1016/j.aggene.2017.03.002.

Gallardo-Escárate, Cristian, Gabriel Arriagada, Crisleri Carrera, Ana Teresa Gonçalves, Gustavo Nuñez-Acuña, Diego Valenzuela-Miranda, and Valentina Valenzuela-Muñoz. 2019. “The Race between Host and Sea Lice in the Chilean Salmon Farming: A Genomic Approach.” Reviews in Aquaculture 11 (2): 325–39. https://doi.org/10.1111/raq.12334.

Gallardo-Escárate, Cristian, Valentina Valenzuela-Muñoz, Gustavo Nuñez-Acuña, Diego Valenzuela-Miranda, Fabian J. Tapia, Marco Yévenes, Gonzalo Gajardo, et al. 2023. “Chromosome-Level Genome Assembly of the Blue Mussel Mytilus Chilensis Reveals Molecular Signatures Facing the Marine Environment.” Genes 14 (4). https://doi.org/10.3390/genes14040876.

Gavery, Mackenzie R., and Steven B. Roberts. 2014. “A Context Dependent Role for DNA Methylation in Bivalves.” Briefings in Functional Genomics 13 (3): 217–22. https://doi.org/10.1093/bfgp/elt054.

Gurr, Samuel J., Shelly A. Trigg, Brent Vadopalas, Steven B. Roberts, and Hollie M. Putnam. 2022. “Acclimatory Gene Expression of Primed Clams Enhances Robustness to Elevated pCO2.” Molecular Ecology 31 (19): 5005–23. https://doi.org/10.1111/mec.16644.

Juárez, Oscar E., Fabiola Lafarga-De la Cruz, Ignacio Leyva-Valencia, Edgar López-Landavery, Zaúl García-Esquivel, Fernando Díaz, Denisse Re-Araujo, Brent Vadopalas, and Clara E. Galindo-Sánchez. 2018. “Transcriptomic and Metabolic Response to Chronic and Acute Thermal Exposure of Juvenile Geoduck Clams Panopea Globosa.” Marine Genomics 42 (December): 1–13. https://doi.org/10.1016/j.margen.2018.09.003.

Núñez-Acuña, Gustavo, Constanza Sáez-Vera, Diego Valenzuela-Miranda, Valentina Valenzuela-Muñoz, and Cristian Gallardo-Escárate. 2023. “Whole-Genome Resequencing in the Sea Louse Caligus Rogercresseyi Uncovers Gene Duplications and Copy Number Variants Associated with Pesticide Resistance.” Frontiers in Marine Science 10. https://doi.org/10.3389/fmars.2023.1112691.

Putnam, Hollie M., Shelly A. Trigg, Samuel J. White, Laura H. Spencer, Brent Vadopalas, Aparna Natarajan, Jonathan Hetzel, et al. 2022. “Dynamic DNA Methylation Contributes to Carryover Effects and Beneficial Acclimatization in Geoduck Clams.” bioRxiv. https://doi.org/10.1101/2022.06.24.497506.

Roberts, Steven B., and Mackenzie R. Gavery. 2012. “Is There a Relationship between DNA Methylation and Phenotypic Plasticity in Invertebrates?” Frontiers in Physiology 2 (January): 116. https://doi.org/10.3389/fphys.2011.00116.

Roberts, Steven B., and Mackenzie R Gavery. 2017. “Epigenetic Considerations in Aquaculture.” PeerJ 5 (December): e4147. https://doi.org/10.7717/peerj.4147.

Sadler, Kirsten C. 2023. “Epigenetics across the Evolutionary Tree: New Paradigms from Non-Model Animals.” BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology 45 (1): e2200036. https://doi.org/10.1002/bies.202200036.

Silliman, Katherine, Laura H. Spencer, Samuel J. White, and Steven B. Roberts. 2023. “Epigenetic and Genetic Population Structure Is Coupled in a Marine Invertebrate.” Genome Biology and Evolution 15 (2). https://doi.org/10.1093/gbe/evad013.

Spencer, Laura H., Erin Horkan, Ryan Crim, and Steven B. Roberts. 2021. “Latent Effects of Winter Warming on Olympia Oyster Reproduction and Larval Viability.” Journal of Experimental Marine Biology and Ecology 542–543 (September): 151604. https://doi.org/10.1016/j.jembe.2021.151604.

Spencer, Laura H., Yaamini R. Venkataraman, Ryan Crim, Stuart Ryan, Micah J. Horwith, and Steven B. Roberts. 2020. “Carryover Effects of Temperature and pCO2 across Multiple Olympia Oyster Populations.” Ecological Applications: A Publication of the Ecological Society of America 30 (3): e02060. https://doi.org/10.1002/eap.2060.

Timmins-Schiffman, Emma B., Grace A. Crandall, Brent Vadopalas, Michael E. Riffle, Brook L. Nunn, and Steven B. Roberts. 2017. “Integrating Discovery-Driven Proteomics and Selected Reaction Monitoring To Develop a Noninvasive Assay for Geoduck Reproductive Maturation.” Journal of Proteome Research 16 (9): 3298–3309. https://doi.org/10.1021/acs.jproteome.7b00288.

Timmins-Schiffman, Emma, Samuel J. White, Rhonda Elliott Thompson, Brent Vadopalas, Benoit Eudeline, Brook L. Nunn, and Steven B. Roberts. 2021. “Coupled Microbiome Analyses Highlights Relative Functional Roles of Bacteria in a Bivalve Hatchery.” Environmental Microbiome 16 (1): 7. https://doi.org/10.1186/s40793–021–00376-z.

Trigg, Shelly A., Yaamini R. Venkataraman, Mackenzie R. Gavery, Steven B. Roberts, Debashish Bhattacharya, Alan Downey-Wall, Jose M. Eirin-Lopez, et al. 2022. “Invertebrate Methylomes Provide Insight into Mechanisms of Environmental Tolerance and Reveal Methodological Biases.” Molecular Ecology Resources 22 (4): 1247–61. https://doi.org/10.1111/1755–0998.13542.

Valenzuela-Muñoz, Valentina, Juan Antonio Váldes, and Cristian Gallardo-Escárate. 2021. “Transcriptome Profiling of Long Non-Coding RNAs During the Atlantic Salmon Smoltification Process.” Marine Biotechnology 23 (2): 308–20. https://doi.org/10.1007/s10126–021–10024–9.

Venkataraman, Yaamini R., Alan M. Downey-Wall, Justin Ries, Isaac Westfield, Samuel J. White, Steven B. Roberts, and Kathleen E. Lotterhos. 2020. “General DNA Methylation Patterns and Environmentally-Induced Differential Methylation in the Eastern Oyster (Crassostrea Virginica).” Frontiers in Marine Science 7. https://doi.org/10.3389/fmars.2020.00225.

Venkataraman, Yaamini R., Samuel J. White, and Steven B. Roberts. 2022. “Differential DNA Methylation in Pacific Oyster Reproductive Tissue in Response to Ocean Acidification.” BMC Genomics 23 (1): 556. https://doi.org/10.1186/s12864–022–08781–5.

Wanamaker, Shelly A., Kaitlyn R. Mitchell, Rhonda Elliott Thompson, Benoit Eudeline, Brent Vadopalas, Emma B. Timmins-Schiffman, and Steven B. Roberts. 2020. “Temporal Proteomic Profiling Reveals Insight into Critical Developmental Processes and Temperature-Influenced Physiological Response Differences in a Bivalve Mollusc.” BMC Genomics 21 (1): 723. https://doi.org/10.1186/s12864–020–07127–3.