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  • Tuesday, June 8, 2021

SC4ES: National Center for Genome Analysis Support Genomics Research webinar series

Featuring Lydia Bright, State University of New York, College at New Paltz, this monthly scientific series highlights the research of scientists who use computational resources provided by NCGAS.

Event details

  • Date & time
    Tuesday, June 8, 2021
    2pm-3pm
  • Location
    Online - Zoom

Register here

About this event

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The National Center for Genome Analysis Support (Links to an external site.) (NCGAS) helps researchers nationwide with the demanding—and often confusing— computations that genomics research requires. In this monthly series, scientists present their genomics research in pursuit of answers to some of the most confounding biological questions.

"NCGAS serves hundreds of researchers who apply genomics to their research, and we wanted to find out what their individual research projects entail. We hope to learn how they are using genomics in their studies, as an inspiration to other researchers." - Tom Doak, Chief Scientist, National Center for Genome Analysis Support

Talks will take place the second Tuesday of each month, 2-3pm EST.


Title of presentation: 
Uncovering molecular determinants of Holospora infection in Paramecium cells.

Presenter:
Lydia Bright (Links to an external site.)Department of Biology, Indiana University Bloomington and the Biology Department, State University of New York, College at New Paltz.


Abstract:
The endonuclear parasite Holospora undulata, which infects Paramecium caudatum, has been studied for over 50 years, but the host response has never been studied in an unbiased manner. We tracked the early response to H. undulata using whole-genome RNA sequencing of the host transcriptome. We found that ~19% of the total transcriptome of the host is responsive in these early stages, but that a very small number of genes had a greater than 2-fold expression change at either early timepoint examined. These differentially expressed genes are more likely to be conserved than other genes in the genome, and many of the predicted gene functions of these genes are consistent with an initial host response to a parasitic partner, including signaling molecules, transcription factors, transporters, and trafficking-related proteins.

While the differentially expressed genes are more likely to be conserved, the very highly upregulated genes in our analysis have an overrepresentation of unannotated and non-conserved genes, indicating that lineage-specific and perhaps fast-evolving genes may be the biggest players in response to this parasite. With this study, we have identified a workable number of genes for further functional study in an unbiased manner, including many unannotated genes that could not have been found using gene candidate approaches.

Catherine Kagemann1, Jean-Francois Gout2, Thomas G Doak3, Michael Lynch4, Oliver Kaltz5, and Lydia Bright3,6

1Department of Molecular Biology and Genetics, Cornell University; 2Department of Biological Sciences, Mississippi State University; 3Department of Biology, Indiana University Bloomington; 4Biodesign Center for Mechanisms of Evolution, Arizona State University, 5Departement Biologie Ecologie, Universite de Montpellier; 6Biology Department, State University of New York, College at New Paltz


The series (and archive):

View all the talks in this series as well as links to archive video of each talk (Links to external site.).


The Supercomputing for Everyone Series (S4ES) of workshops and seminars are led by personnel from Research Technologies (Links to external site.), a division of University Information Technology Services (Links to external site.). This series is led by the National Center for Genome Analysis Support (Links to external site.). Both are centers in the Pervasive Technology Institute (Links to external site.) at Indiana University.

The Supercomputing for Everyone Series (Links to external site.) aims to bring more users into the realm of advanced computing, whether it be visualization, computation, analytics, storage, or any related discipline. Let the Research Technologies staff take you to the next level of computing.