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Jonathan Eisen talk for 2019 ADVANCE Scholar Award Symposium

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Slides for my talk at the 2019 ADVANCE Scholar Award Symposium. Talk covered a little bit about mt research and more about STEM Diversity. See https://diversity.ucdavis.edu/2019-advance-scholar-award-symposium

Published in: Science
  • Copas Url to Read PDF Format === http://hailwoodmc.co.uk/books/Sei-chiodi-storti.-Santiago,-1976,-la-Davis-italiana.html
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Jonathan Eisen talk for 2019 ADVANCE Scholar Award Symposium

  1. 1. ######## #STEMDiversity #YAMMM #Manels #ClosedAccess The power and peril of social media in improving the culture and practice of science October 24, 2019 UC Davis ADVANCE Symposium Jonathan A. Eisen @phylogenomics University of California, Davis
  2. 2. Microbiomes: Communities of Microbes Image by Darryl Leja, NHGRI
  3. 3. Microbiomes: Mostly Ignored but Not Anymore Image by Darryl Leja, NHGRI
  4. 4. Google Trends Hits to Microbiome The Rise of the Microbiome
  5. 5. The Rise of the Microbiome 0 500 1000 1500 2000 2500 3000 3500 4000 4500 1956 1958 1961 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 Pubmed Hits to Microbiome vs. Year
  6. 6. Why Now I: Appreciation of Microbial Diversity
  7. 7. Why Now II: Post Genome Blues The Microbiome Transcriptome VariomeEpigenome Overselling the Human Genome?
  8. 8. Why Now III: Technological Advances
  9. 9. Why Now III: Technological Advances
  10. 10. Why Now IV: Microbiome Functions Turnbaugh et al Nature. 2006 444(7122):1027-31.
  11. 11. Why Now IV: Microbiome Functions Turnbaugh et al Nature. 2006 444(7122):1027-31. #1: Microbiome impacts key trait #2: Microbiome is transferable / modifiable
  12. 12. Why Now V: Importance of Other Microbiomes
  13. 13. Challenge I: Small, Hard to Study in Field • Microscope picture • Microbes are small • But diversity and numbers are very high • Appearance not a good indicator of type or function • Field observations of limited value
  14. 14. Challenge II: Diversity of Form
  15. 15. Challenge III: Diversity of Functions The Bad The Good The Unusual The Consumable The Burnable The Planet
  16. 16. Challenge IV: Evolutionary Diversity Viruses Bacteria & Archaea Other Eukaryotes Fungi
  17. 17. Challenge V: Microscale Localization Jessica L. Mark Welch, Blair J. Rossetti, Christopher W. Rieken, Floyd E. Dewhirst, and Gary G. Borisy PNAS February 9, 2016. 113 (6) E791-E800; published ahead of print January 25, 2016. https://doi.org/10.1073/pnas.1522149113 Jessica L. Mark Welch, Blair J. Rossetti, Christopher W. Rieken, Floyd E. Dewhirst, and Gary G. Borisy PNAS February 9, 2016. 113 (6) E791-E800; published ahead of print January 25, 2016. https:// doi.org/10.1073/pnas.1522149113
  18. 18. Microbiomes: Communities of Microbes Image by Darryl Leja, NHGRI
  19. 19. Solution for Eisen Lab: DNA Sequencing
  20. 20. Eisen Lab
  21. 21. Eisen Lab Jonathan Eisen’s Lab May the Microbes Be Ever in Your Favor A B C Input Sequences rRNA workflow protein workflow profile HMMs used to align candidates to reference alignment Taxonomic Summaries pa rallel op tio n hmmalign multiple alignment LAST fast candidate search pplacer phylogenetic placement LAST fast candidate search LAST fast candidate search search input against references hmmalign multiple alignment hmmalign multiple alignment Infernal multiple alignment LAST fast candidate search <600 bp >600 bp Sample Analysis & Comparison Krona plots, Number of reads placed for each marker gene Edge PCA, Tree visualization, Bayes factor tests eachinputsequencescannedagainstbothworkflows
  22. 22. UC Davis Microbiome Special Research Program • 2 year Special Research Program funded by the Office of Research and multiple campus Colleges • Goal: catalyze development and innovation in microbiome research on campus • 1: Catalyze research through seed funding programs • 2: Virtual hub for UCD Microbiome Research • 3: Organize quarterly meetings
  23. 23. Microbiomania vs. Germophobia Germophobia Microbiomania
  24. 24. Microbiomania vs. Germophobia Germophobia Microbiomania All Microbes Are Bad Use Antimicrobials in Everything Avoid all Microbes All Microbes Are Good Use Probiotics in Everything Embraces all Microbes Eat Dirt
  25. 25. Solution I: Citizen Microbiology Kitty Microbiome Jack Gilbert Project MERCCURI Phone and Shoes tinyurl/kittybiome Holly Ganz
  26. 26. Solution II: Outreach http://gut-check.net
  27. 27. Engage: Example
  28. 28. Diversity in STEM #DoSomething
  29. 29. Lesson 1: Organizations Can Change • Linda Katehi • Maureen Stanton • Linda Bisson • Kimberlee Shauman • Denneal Jamison-McClung
  30. 30. Lesson 2: Public Representation Matters
  31. 31. Lesson 2: Public Representation Matters
  32. 32. Lesson 2: Public Representation Matters
  33. 33. Lesson 3: Sexual Harassment & Assault is Pervasive
  34. 34. Lesson 3: Sexual Harassment & Assault is Pervasive
  35. 35. Lesson 3: Sexual Harassment & Assault is Pervasive
  36. 36. Lesson 4: Listen and Amplify Voices of Others
  37. 37. Lesson 4: Listen and Amplify Voices of Others
  38. 38. Lesson 5: UC Davis Rules
  39. 39. Lesson 5: UC Davis Rules Deb Niemeier, Ph.D. Colleen E. Clancy Sarah McCullough Maureen Stanton
  40. 40. Other Lessons
  41. 41. Other Lessons • Lesson 6: Tech Industry Needs To Change • Lesson 7: Not Just One Angle On Diversity • Lesson 8: Use Your Privilege • Lesson 9: Never Kick Down • Lesson 10: Apologize When Wrong …
  42. 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019 Lokiarchaea named after Loki’s Castle Vent Site
  43. 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019 Thorarchaeota http://sites.utexas.edu/baker-lab/2016/01/29/introducing-thorarchaeota/
  44. 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019 Asgard Archaea
  45. 45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019 Asgard Archaea Something is Wrong Here
  46. 46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019 Complaining on Twitter …
  47. 47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019 Response ..
  48. 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019 Helarchaeota
  49. 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019 Freya not next ..
  50. 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019 Helarchaeota
  51. 51. Eisen Lab

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