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  • Tuesday, March 9, 2021

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

Featuring Petra Lenz, University of Hawai'i at Manoa, this monthly scientific series highlights the research of scientists who use computational resources provided by NCGAS.

Event details

  • Date & time
    Tuesday, March 9, 2021
  • Location
    Online - Zoom

Register here

About this event

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: 
Environmental transcriptomics of seasonal dormancy in a sub-arctic copepod, a key crustacean zooplankter at the base of the metazoan food web.

Petra Lenz (Links to an external site.) received her B.A. degree in Biology from the University of California San Diego in 1976 and her Ph.D. in Biological Sciences from the University of California Santa Barbara in l1983. She joined the research faculty of the Pacific Biosciences Research Center at the University of Hawaiʻi Mānoa in 1990, where she pursued a career investigating the physiological ecology of planktonic organisms. Her early work included the first measurements of sensitivity of copepod mechanoreceptors, the quantitative analysis of fast and powerful escape reactions, and the unexpected discovery of myelin in the nervous systems of some but not all copepods. More recently, she has explored the world of ‘omics for non-model species, generating molecular resources for marine copepods. Her recent research focuses on the application of environmental transcriptomics to elucidate organism-environment interactions in sub-arctic copepods with complex life histories, which has included identifying patterns of gene activation that underlie both the preparation for and the awakening from their annual winter dormancy. She is currently a rotator at the National Science Foundation serving as Program Director for Biological Oceanography in the Directorate of Geosciences.

Matthew C. Cieslak, Ann M. Castelfranco, Daniel K. Hartline (U. Hawai‘i at Mānoa)
Vittoria Roncalli (Stazione Zoologica Anton Dohrn, Naples, Italy)

Exceptionally productive, economically-valuable fisheries in high-latitude marine systems are supported by lipid-rich planktonic prey at the base of the food chain. Periods of poor recruitment and survival of commercially important fishes have been linked to low abundances of lipid-rich prey, which notably include the large copepods in the family Calanidae. These copepods have a complex life history, with their growth cycle synchronized to the annual spring phytoplankton bloom. This synchronization is achieved through a developmentally programmed seasonal dormancy termed "diapause," which lasts for months and is completed at depths below 300 meters. Population models project declines or even local extinctions of these lipid-rich copepods as a consequence of global climate change. Uncertainty in some of these models has arisen owing to insufficient data on the biology and physiological ecology of the copepods, which are difficult to study in situ, and are not amenable to laboratory culture.

Recently, however, transcriptomics applied to samples taken from the wild under known environmental conditions has opened new avenues to studying non-model species that are central players in ecosystems. The sub-arctic copepod, Neocalanus flemingeri, a key member of the northern Gulf of Alaska ecosystem, is a capital breeder that depends on a short phytoplankton bloom for growth and the accumulation of resources to fuel diapause and reproduction. We have used environmental transcriptomics to examine its physiological responses to orders of magnitude differences in local food availability and to interannual differences in bloom dynamics. Functional analysis of gene expression differences have been aimed at understanding the copepod’s strategies for survival in the face of this variability. These studies are highlighting the degree to which organisms regulate gene expression in the natural environment. Diapause transcriptional phenotypes were characterized in females field-collected from depth and then followed through post-diapause awakening in the lab. Experimental incubations included gene expression profiling over a 10-week time series from collection through spawning. The transcriptomic analysis focused on characterizing the progression of transcriptional profiles from the environmentally-determined state of diapause through the play-out of the subsequent reproductive program and allocation of resources to balance organismal function with the cost-of-reproduction. The transition from diapause to post-diapause follows a complex pattern of changes in gene expression as the females awaken and progress through oogenesis. 

The series (and archive):

View the video archive (Links to a YouTube video).

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.