A journey in ‘omics research from the bottom of the ocean to the top of a mountain

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A journey in ‘omics research from the bottom of the ocean to the top of a mountain April 9, 2020 Sacramento State University (NMS90) Dr. Rayna M. Harris Postdoc, UC Davis raynamharris 1

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What degree are you pursuing? 2

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Why did you pick that degree? 3

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What are your career aspirations? 4

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Part 1: My career path Ph.D. student Unpaid intern Lab tech and manager Postdoctoral researcher By Caitlin Friesen By Rayna Harris By Rayna Harris Etsy Teaching assistant Needpix.com 5

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Part 2: My current research “Transcriptional symphony of parental care” 6

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B.S. Biochemistry, University of Texas at Austin 2006 Why? It fulﬁlled all the pre-med requirements. But I soon realized I didn’t want to be that kind of doctor. 7

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What do you need to become a professor? 8

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Organic Chemistry Teaching Specialist, 2007-2009 9

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Instituto Nacional de Biodiversidad, Costa Rica, 2008 Research-driven scuba diving Culturing aquatic fungi Translating research 10

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Lab technician and manager, 2009-2012 11 Molecular biology, neuroscience Data science, bioinformatics

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Some molecular biology and data science keywords DNA RNA Protein genomics, genetics transcriptomics proteomics Molecular Biology Data Science/ Bioinformatics transcription (aka gene expression) translation 12

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PhD in Cell and Molecular Biology 2012-2017 13 https://www.biorxiv.org/content/10.1101/2020.02.05.935759v1

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Volunteer Instructor, The Carpentries 2015-2020 14 Translating lessons into Spanish Teaching Git in Argentina Instructor training in Latin America https://carpentries.org/

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Postdoc: Studying parental care while making science more inclusive to working mothers, 2019-current Image of parenting pigeons by Victoria Farrar Calisi & a Working Group of Mothers in Science 2018 PNAS 15 Calisi 2018 Science

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As a data scientist, I can work in the tropics, in the city or in the mountains 16 Home ofﬁce Truckee, CA Coffee shop Austin, TX Community center Old San Juan, PR

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What questions do you have about my career path? 17

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Part 2: My current research “Transcriptional symphony of parental care” 18

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“Transcriptional symphony”: the orchestrated expression of genes that regulate a biological process 19 DNA RNA Protein genomics, genetics transcriptomics proteomics Molecular Biology Data Science/ Bioinformatics transcription (aka gene expression) translation Biological process of interest

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Sonification: Turning data into sound! 20 https://en.wikipedia.org/wiki/Sonification

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Parental care: behavior that promotes offspring survival 21 Image from Google. Quote from https://global.oup.com/academic/product/the-evolution-of-parental-care-9780199692583?cc=ca&lang=en&

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Monogamous Rocks Doves provide bi-parental care 22

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The Rock Dove Transcriptomics Team Dr. Rayna Harris Dr. Suzanne Austin Dr. Andrew Lang Dr. Matthew MacManes Dr. Rebecca Calisi Rechelle Viernes Dr. Jesse Krause April Booth Victoria Farrar University of California, Davis University of New Hampshire Funded by the National Science Foundation 23

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A day in the life of parenting pigeons 24

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Research question: What genes in the reproductive axis (hypothalamus, pituitary, and gonads) promote parental care behavior in females and males? 25

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Boxplots are useful for comparing gene expression between groups 26

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Which groups are most different? 27 1. A and B 2. A and C 3. A and D 4. B and C 5. B and D 6. C and D

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Prolactin (PRL) gene expression is the highest at and around the hatch time point https://raynamharris.shinyapps.io/musicalgenes/ 28

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Genes that are co-expressed with PRL are known to influence development and cancer 29 https://github.com/macmanes-lab/DoveParentsRNAseq

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Musical genes: An app I made to visualize and sonify gene expression during parental care https://raynamharris.shinyapps.io/musicalgenes/ 30

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Breakout groups 31 Visit https://raynamharris.shinyapps.io/musicalgenes/. Pick a gene, tissue, and sex. Sonify and visualize its expression. Repeat and compare. Share your favorite.

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Pituitary prolactin orchestrates a symphony of gene expression that regulates parental care 32

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Many thanks to colleagues in the... 33 College of Natural Science, UT Austin Instituto Nacional de Biodiversidad, Costa Rica Neural Systems & Behavior Course, MBL The Carpentries Data-Intensive Biology Lab, UC Davis Birds, Brains & Behavior Lab, UC Davis Science & Technology Studies, UC Davis

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What questions do you have? Thank you for listening. Dr. Rayna M. Harris Postdoc, UC Davis raynamharris March 19, 2020 Sacramento State University (NMS90) 34