CATALYST FUND PROJECTS

While most Catalyst Science Fund projects are focused on studying a single species, the purpose of each is to catalyze development of genetic rescue biotechnologies that can be applied across many genetic rescue applications and for multiple species. The newest projects will run until June 2022 and support the development of an Advanced Coral Toolkit as well as Marine Banking & Sequencing, both of which were first proposed in our Ocean Genomics Horizon Scan.

Metabolomics As a Platform for Coral Monitoring and Conservation

Partners: Dr. Debashish Bhattacharya, Rutgers University and Hawaii Institute of Marine Biology, Oahu

Status: Active (September 2020–August 2022)

Focus: Genomic insight

Goal:Develop the knowledge needed to design and construct a portable coral stress monitoring instrument.

Why Now: Coral stress indicators may lead to earlier predictions of coral bleaching events. Learn more about coral bleaching

Catalytic Science: This instrument will rely on a panel of well-characterized antibodies and redox-based sensors of stress-related enzymes and metabolites, respectively—to assess coral health prior to bleaching and to allow time to enact appropriate interventions.

Mary Hagedorn.

Creation and Cryopreservation of Coral Nanofragments

Partners: Dr. Mary Hagedorn, Smithsonian’s National Zoo and Conservation Biology Institute

Status: Active (April 2020–April 2022)

Focus: Restoring diversity

Goal: Develop methods to cryopreserve and recover single-polyp nanofragments of model species of Hawaiian coral.

Why Now: Cryopreserved nanofragments, successfully thawed, could be used immediately for coral restoration or banked for centuries and reintroduced when ocean conditions are more hospitable.

Catalytic Science: An important advantage of nanofragment cryopreservation is that success will not depend upon coral reproductive events, which occur but once a year. New methods will be used to create minute (pin-head size) asexual coral nanofragments that exhibit stem cell qualities and apply existing cryopreservation and ultra-rapid warming methods developed in our laboratory to freeze, store, and reanimate these fragments. New methods will be developed to return the thawed nanofragments to seawater and demonstrate how to best utilize these fragments to create rapidly growing coral for restoration.

Marine Banking & Sequencing

Healthy sunflower sea stars predate upon sea urchins, helping to maintain kelp forests.

Pycnopodia helianthoides: Its Genomic Risk for Sea Star Wasting Disease and Potential for Genetic Rescue

Partners: Michael Dawson and Lauren Scheibelhut, University of California, Merced

Status: Active (June 2020–May 2022)

Focus: Genomic Insight

Goal: To discover genomic variation that confers resilience to sea star wasting disease (and other stressors) in the sunflower sea star (Pycnopodia helianthoides), and develop genetic rescue tools to increase captive breeding and reintroduction success.

Why Now: In 2013, an outbreak of sea star wasting disease (SSWD) impacted over 20 species of sea stars. The sunflower sea star, a keystone predator of urchins,  was all but eradicated (i.e. 80–100% mortality) from everywhere but the northern-most reaches (Alaska) of its >3000 km range. The ecological consequences—urchin populations increased 311%, kelp forest densities declined 30%—are showing no sign of rebound.

Catalytic Science: This project aims to discover genomic variation in the sunflower sea star that confers resilience to SSWD and other stressors. This project will provide a far fuller understanding of the genomic factors that shaped the high risk of sunflower sea stars to SSWD in 2013/2014, and the consequences of that event on remnant patterns of genomic diversity. This genomic insight will shape a captive breeding program that advances genomic resilience in the new population.

Interspecific Cloning of the Black-Footed Ferret (BFF)

Led By: Viagen Pets

Status: Active (May 2019–September 2020)

Focus: Restoring genetic diversity

Goal: Demonstrate the potential for interspecific cloning of BFFs using domestic ferret surrogates.

Why Now: All living BFF trace their genetics to just 7 ancestors. Due to this, the current BFF population possesses just 85% of its original genetic diversity. Genetic drift will cause this diversity loss to continue. However, cryopreserved BFF cell lines at the San Diego Global Zoo’s Frozen Zoo possess genotypes that could greatly improve BFF biodiversity—if these genotypes can be cloned and bred into the current population. Learn more about the Black-footed Ferret.

Catalytic Science: Because every surviving BFF is vital to the recovery program, it is necessary to rely on domestic ferrets to act as surrogates in cloning the BFF. This project will determine if the interspecific cloning approach is a possibility for introducing new genetic variation into the breeding BFF community.

Engineering inherited VIP for Sylvatic Plague. (Click to enlarge.)

Inherited Vectored Immunoprophylaxis (VIP) for Sylvatic Plague in a Mouse Model

Partners: Texas A&M Institute for Genomic Medicine and United States Geological Survey (USGS) National Wildlife Health Center

Status: Active (July 2019–December 2020)

Focus: Facilitated adaptation

Goal: Demonstrate the potential to create heritable immunity to plague in the Black-footed ferret (BFF)

Why Now: Sylvatic plague caused by Yersinia pestis bacterium kills the BFF at nearly a 100% mortality rate. It is the largest obstacle to the self-sustaining recovery of this endangered prairie native. Learn more about the Black-footed Ferret.

Catalytic Science: This project will provide proof-of-concept for an approach to engineer gene-mediated plague resistance in the BFF. To quickly evaluate the efficacy of this approach, a mouse model will be used over multiple generations.

SB2 cells carry the Canine Distemper Virus. (Click to enlarge.)

Canine Distemper Virus (CDV) Removal from BFF Cell Culture

Led By: ImQuest BioSciences

Status: Active (July 2019–December 2020)

Focus: Restoring genetic diversity

Goal: Remove CDV particles completely from an infected BFF cell line, making those cells suitable genetic donors in subsequent cloning experiments.

Why Now: The Frozen Zoo at San Diego Zoo Global currently holds two cryopreserved cell lines from two BFFs—one male (SB2) and one female (SB10). Cloning these genomes and integrating them into the captive breeding program would effectively introduce two new founders into the living BFF population and boost their genetic diversity. Learn more about the Black-footed Ferret.

Catalytic Science: During the process of obtaining genomic sequences of SB2 and SB10, researchers at the Frozen Zoo discovered that the SB2 cell line is contaminated with an active infection of canine distemper virus (CDV). Therefore, SB2 is not currently able to serve as a source of donor nuclei for cloning experiments.

For these cells to be used in a cloning experiment, it is necessary that all CDV particles be removed from the SB2 cell line. This methodology will also need to preserve cell viability and genetic integrity, and render the cells suitable for cloning.

Heath Hen Revive & Restore

A Greater Prairie Chicken, like this one, is the closest living relative to the Heath Hen.

Developing Primordial Germ Cell Techniques for Germline Transfer

Led By: Dr. Rosemary Walzem, Texas A&M University

Status: Active (July 2019–June 2021)

Focus: De-extinction (Avian Genetic Rescue)

Goal: Identify key points in Primordial Germ Cell (PGC) biology to govern the success of PGC culture and transfer between wild and domestic bird species. 

Why Now: A critical step in avian genetic rescue will be the ability to isolate, culture, and expand avian PGCs (the cells that give rise to spermatozoa and oocyte cells) in vitro—a step that has not yet been accomplished for wild bird species. Learn more about the genetic rescue of the heath hen and the passenger pigeon.

Catalytic Science: Fundamentally, reproductive technologies available for genetic rescue in mammals do not work for birds. Egg-based reproduction presents a unique set of technical challenges. The success of this project will help enable genetic rescue projects for many avian species. In October, a flock of young greater prairie chickens from our breeder, Dan Snyder, arrived in Texas. New experiments to culture PGCs will begin when these birds lay eggs in 2020. Findings will be applied to support our heath hen de-extinction efforts and genetic rescue of its living relatives, including the critically endangered Attwater’s prairie chicken.

Young elephants are especially susceptible to EEHV1A.

Assembling the EEHV1A Genome to Save the Endangered Asian Elephant from Disease

Led By: Dr. George Church, Harvard Medical School 

Status: Active (July 2019–December 2020)

Focus: Facilitated adaptation

Goal: Create a cell culture system for Elephant Endotheliotropic Herpes Virus 1A (EEHV1A) using a synthesized viral genome.

Why Now: Captive breeding efforts of the endangered Asian elephant (Elephas maximus) are currently hindered by the elephant endotheliotropic herpesviruses (EEHV), a widespread and highly fatal hemorrhagic disease that results in a 25% mortality rate for captive-born Asian elephant calves. Developing new strategies to fight this disease is essential for Asian elephant conservation. Unfortunately, all previous attempts to propagate the virus in cell culture models have failed. Without the ability to culture the virus in the laboratory, it is difficult to identify its’ mechanism of action, understand  its host-virus interactions, develop vaccines, or screen new antiviral drugs.

Catalytic Science: The Church lab has proposed taking two parallel approaches to assembling the complete EEHV1A genome from synthetic DNA fragments and transfecting it into Asian elephant endothelial cells to create a cell culture platform. Once this has been achieved, they plan to use electron microscopy to test whether viral particles are being made. Learn more about work from the Church Lab.

Science | Mouse | Revive & Restore

The use of a mouse model is helping develop new gene-editing technologies. 

Novel method for in vivo gene editing of vertebrate embryos

Led By: Dr. Alison Van Eenennaam, University of California Davis

Status: Active (June 1, 2019–May 31, 2020)

Focus: Invasive species control

Goal: Proof-of-concept for a novel method of in vivo gene editing to deliver gene-editing machinery into developing oocytes.

Why Now: There are many issues with current gene editing methods that preclude their use for conservation purposes. These include the inaccessibility of oocytes or embryos for microinjection, the inefficiency of microinjection and embryo transfer, and the unique culturing conditions required for oocytes and embryos of a variety of species. The Van Eenennaam lab has designed a novel method of gene editing that eliminates all of these steps by modifying early embryos in vivo.

Catalytic Science: This is a proof-of-concept effort to test a novel gene editing method based on cellular therapeutic technologies.

COMPLETED PROJECTS

Acropora hyacinthus | Revive & Restore

A graduate student from the Palumbi lab collects Acropora hyacinthus.

Coral Stress Triggers as Targets for Genetic Intervention and Climate Change Resilience

Led By: Dr. Steve Palumbi, Stanford University

Status: Completed (January to October 2019)

Focus: Facilitated adaptation

Goal: Establish a new research paradigm using pharmacological agents to explore the cellular controls that trigger coral bleaching.

Why Now: Coral death is precipitated by bleaching events—so-called because the coral’s symbiotic dinoflagellates (algae) exit the coral—which leave it white. Learn more about coral threats in our Ocean Genomics Horizon Scan. Recent studies show a set of cellular switches may be involved in triggering coral bleaching, the most promising of which is the unfolded protein response (UPR). While UPR is correlated with bleaching, it isn’t known whether UPR triggers bleaching. This project tested the possibility that UPR is a fundamental part of the coral bleaching trigger.

Catalytic Science: The typical way to test such a hypothesis is through genetic manipulation of cultured cells—yet traditional genetics techniques are not feasible in corals. Without the ability to manipulate coral genomes directly, coral geneticists cannot directly test their hypotheses. To make immediate progress in coral genetics, a novel strategy was borrowed from studies in cancer and cell biology. The Palumbi laboratory used pharmacological agents, that have specific effects on highly conserved proteins, to study coral cell biochemistry.

Results & Next Steps: The pharmacological agents were successful in manipulating coral gene expression, showing their utility for corals research. To inform strategies for intervening in the coral reefs’ destruction, high-throughput approaches to scale-up, and speed-up this approach to coral genetics research should be explored.