Biology subjects

Dimond, J. L.

Publications and source records attributed to Dimond, J. L..

3 recordsLinked to original sources

bioRxiv2024

Identification of an Outbreak of Bivalve Transmissible Neoplasia in Soft-Shell Clams (Mya arenaria) in the Puget Sound Using Hemolymph and eDNA Surveys

Bivalve transmissible neoplasia (BTN) is one of three known types of naturally transmissible cancer-- cancers in which the whole cancer cells move from individual to individual, spreading through natural populations. BTN is a lethal leukemia-like cancer that has been observed throughout soft-shell clam (Mya arenaria) populations on the east coast of North America, with two distinct sublineages circulating at low enzootic levels in New England, USA, and Prince Edward Island, Canada. Major cancer outbreaks likely due to Mya arenaria BTN (MarBTN) were reported in 1980s and the 2000s and the disease has been observed since the 1970s, but it has not been observed in populations of this clam species on the US west coast. In 2022, we collected soft-shell clams from several sites in Puget Sound, Washington, USA, and unexpectedly found high prevalence of BTN in two sites (Triangle Cove on Camano Island and near Stanwood in South Skagit Bay). Prevalence of BTN increased in subsequent years, reaching >75% in both sites in 2024, while it was not observed in other sites, suggesting the early stages of a severe disease outbreak following recent introduction. We observed that these cancer cells contain several somatic transposing insertion sites found only in the USA-sublineage of MarBTN, showing that it likely was recently transplanted from New England to this location. We then developed a sensitive environmental DNA (eDNA) assay, using qPCR to target somatic mutations in the MarBTN mitogenome, and showed that MarBTN can be detected in seawater at Triangle Cove, as well as several kilometers outside of the cove. We then used this assay to survey 50 sites throughout Puget Sound, confirming that the disease can be detected at high levels at Triangle Cove and South Skagit Bay, and showing that it extends beyond these known sites. However, while normal soft-shell clam mtDNA was widely detected, MarBTN was undetectable throughout most of Puget Sound and currently remains limited to the South Skagit Bay area and north Port Susan. These results identify a previously unknown severe outbreak of a transmissible cancer due to long-distance transplantation of disease from another ocean, and they demonstrate the utility of eDNA methods to track the spread of BTN through the environment.

ecology↗

bioRxiv2023

Multiple lineages of transmissible neoplasia in the basket cockle (Clinocardium nuttallii) with repeated horizontal transfer of mitochondrial DNA

Transmissible cancers are clonal lineages of neoplastic cells able to infect multiple hosts, spreading through populations in the environment as an infectious disease. Transmissible cancers have been identified in Tasmanian devils, dogs, and bivalves. Several lineages of bivalve transmissible neoplasias (BTN) have been identified in multiple bivalve species. In 2019 in Puget Sound, Washington, USA, disseminated neoplasia was observed in basket cockles (Clinocardium nuttallii), a species that is important to the culture and diet of the Suquamish Tribe as well as other tribes with traditional access to the species. To test whether disseminated neoplasia in cockles is a previously unknown lineage of BTN, a nuclear locus was amplified from cockles from Agate Pass, Washington, and sequences revealed evidence of transmissible cancer in several individuals. We used a combination of cytology and quantitative PCR to screen collections of cockles from eleven locations in Puget Sound and along the Washington coastline to identify the extent of contagious cancer spread in this species. Two BTN lineages were identified in these cockles, with one of those lineages (CnuBTN1) being the most prevalent and geographically widespread. Within the CnuBTN1 lineage, multiple nuclear loci support the conclusion that all cancer samples form a single clonal lineage. However, the mitochondrial alleles in each cockle with CnuBTN1 are different from each other, suggesting mitochondrial genomes of this cancer have been replaced multiple times during its evolution, through horizontal transmission. The identification and analysis of these BTNs are critical for broodstock selection, management practices, and repopulation of declining cockle populations, which will enable continued cultural connection and dietary use of the cockles by Coast Salish Tribes.

cancer biology↗

bioRxiv2019

Convergence of DNA methylation profiles in a novel environment in the reef coral Porites astreoides

Phenotypic acclimatization is an organismal response to environmental change that may be rooted in epigenetic mechanisms. In reef building corals, organisms that are severely threatened by environmental change, some evidence suggests that DNA methylation is an environmentally responsive mediator of acclimatization. We investigated changes in DNA methylation of the reef coral Porites astreoides in response to simulated environmental change. Coral colonies were sampled from a variety of habitats on the Belize Barrier Reef and transplanted to a common garden for one year. We used restriction site associated DNA sequencing, including a methylation-sensitive variant, to subsample the genome and assess changes in DNA methylation levels after a year in the common garden. Methylation changes among the 629 CpG loci we recovered were subtle, yet coral methylomes were more similar to each other after a year in the common garden together, indicating convergence of methylation profiles in the common environment. Differentially methylated loci showed matches with both coding and non-coding RNA sequences with putative roles in intracellular signaling, apoptosis, gene regulation, and epigenetic crosstalk. There was a weak but positive and significant relationship between genetic and epigenetic variation, providing evidence of methylation heritability. Altogether, our results suggest that DNA methylation in P. astreoides is at least somewhat responsive to environmental change, reflective of the environment, and heritable, characteristics necessary for methylation to be implicated as part of potential transgenerational acclimatization responses.

molecular biology↗