Biology subjects

Russell, T. M.

Publications and source records attributed to Russell, T. M..

3 recordsLinked to original sources

bioRxiv2025

Locus-specific transcriptional regulation of transposable elements by p53

The tumor suppressor p53 protects genomic integrity in part by regulating transposable elements (TEs). Most studies of p53-TE interactions rely on synthetic DNA and reporter assays, which estimate expression only at the family or subfamily level and lack locus-specific resolution. To address this limitation, we developed a computational pipeline for ChIP-seq and RNA-seq analysis that employs advanced algorithms to accurately assign short reads mapping to multiple genomic locations. This approach enables precise quantification of TE transcripts at the locus level. By integrating p53 ChIP peaks with differentially expressed TE transcripts, we identified retroelements directly regulated by p53. Applying this framework to lung fibroblast IMR90 and colon cancer HCT116 cells treated with p53 activators, we observed a striking pattern: TEs were predominantly activated in normal IMR90 cells but repressed in HCT116 cancer cells. Analysis of 24 transcriptomes and 10 cistromes further confirmed this trend, distinguishing normal from cancer cell regulation. At the family level, normal cells showed broad TE upregulation, whereas cancer cells exhibited selective repression of Alu and LINE elements, with weaker effects on endogenous retroviruses. These findings provide the first comprehensive, locus-specific view of p53-mediated TE regulation, highlighting distinct chromatin-dependent dynamics in normal and cancer cells.

bioinformatics↗

bioRxiv2024

Increase of tropical seabirds (Sula) in the California Current Ecosystem with warmer ocean conditions

Climate change is impacting marine ecosystems in the California Current Ecosystem (CCE) through physical changes (e.g., an increase in the frequency and intensity of marine heatwaves) that manifest biologically at all trophic levels. We investigated range expansion into the CCE and correlations with environment for a group of tropical/sub-tropical seabirds. We assessed changes in the abundance (2002-2022) of five species from the genus, Sula (Cocos, Blue-footed, Red-footed, Masked, and Nazca Boobies), using a novel compilation of four data sources (at-sea surveys, n=82 observations, records from Southeast Farallon Island, n=600, the California Rare Birds Committee, n=593, and eBird -a citizen science mobile application, n= 20,529), and looked for relationships with the environment, including broad temporal and spatial scale dynamics (El Nino Southern Oscillation), local conditions where the bird was reported, and potential source conditions from Baja California Sur and the Gulf of California. All five species increased in abundance, and all, with the exception of Blue-footed, exhibited a northward range expansion by as much as 6.8 degrees latitude and increased range area of between 235-1013% within the CCE. There was increased abundance during warmer conditions (El Nino and warm SST) for Cocos, Red-footed, Masked, and Nazca Boobies, and all species increased by 692-3015% after the extreme marine heatwaves that began in late 2013. Our results document a tropical shift in seabirds of the CCE, which may present future challenges to resident species. As marine heatwaves are projected to increase in frequency and intensity, in addition to long-term warming, we hypothesize that these species will continue to expand their range northward in the CCE.

ecology↗

bioRxiv2024

Avian predator-prey dynamics in a changing climate along the Western Antarctic Peninsula; a scoping review

A unique characteristic of the food web along the Western Antarctic Peninsula (WAP), one of the fastest warming regions in the world, is that the avian tertiary predators seasonally rely on avian secondary predators for their subsistence. We conducted a scoping review to 1.) provide a summary of research on Antarctic avian predator-prey relationships, 2.) investigate potential avian predator-prey relationships and trends with the environment, and 3.) highlight research gaps and provide recommendations for future research. We searched Web of Science and Google Scholar for publications in English during any years. For our first aim, we searched using the terms "predator-prey dynamics" AND "Antarctica." We excluded results that did not include both avian predators and prey, which resulted in eight publications from around the Southern Ocean, and one along the WAP. For our second aim, we searched using the terms of each species common and scientific names (gentoo penguin, Pygoscelis papua, Adelie penguin, P. adeliae, chinstrap penguin, P. antarcticus, southern giant petrel, Macronectes giganteus, south polar skua, Stercorarius maccormicki, brown skua, S. antarcticus) AND "population" AND "Antarctic Peninsula." We refined our results (N=59) to publications with data on at least one prey and one predator avian species of all papers found in Web of Science, and the first 100 records of Google Scholar. We selected five locations that had data spanning over 10 years and that spread across the northern WAP. We compared predator-prey species trends across time along with sea surface and air temperature. We found that predator-prey dynamics between avian secondary and tertiary predators have had limited investigations in Antarctica. Along the WAP, the relationship between different penguin species and avian tertiary predators are highly variable and many population trends are decoupled from local temperature change. We include recommendations for future data collection and research on these interactions.

ecology↗