Monday, November 09, 2015

The Past, Present, and Future of DNA

Last month I went to a Harvard Symposium on The Past, Present, and Future of DNA. They’ve posted the video of the event so here are my raw notes from it (any mistakes are mine).

The one-day science symposium will focus on the explosion of knowledge about past and present DNA, and will include discussions about possible directions and applications for future research. The event will include experts in ancient DNA, de-extinction, human origins, population genetics, forensic science, ethics, business, future synthetic life, and the personal genome.

9:30am WELCOME

  • Lizabeth Cohen, Dean of the Radcliffe Institute and Howard Mumford Jones Professor of American Studies, Department of History, Harvard University
  • First isolated in 1869
  • Microbes Hunters and The Eighth Day of Creation books

INTRODUCTION

  • Janet Rich-Edwards, Codirector of the Science Program, Radcliffe Institute; Associate Professor of Medicine, Harvard Medical School; Associate Professor in the Department of Epidemiology, Harvard T.H. Chan School of Public Health
  • Adding nucleotides to code more codons
  • Mitochondria have their own DNA, inherit item just from mom. Have less repair mechanisms than nuclear DNA.
  • Mitochondrial Eve, 150,000 years ago in Ethiopia
  • Spider-goat - transgenic goat whose milk can be strung into fibers 10x stronger than steel.

10am MAMMOTHS, NEANDERTHALS, AND YOUR ANCESTORS

video

Moderator: George Church

  • Robert Winthrop Professor of Genetics, Harvard Medical School

John Hawks

  • Vilas-Borghesi Distinguished Achievement Professor of Anthropology, University of Wisconsin-Madison
  • Has a blog, runs a MOOC
  • Goram caves, sites of Neanderthals
  • In last 20 years we have finally agreed on role of Neanderthals in our evolution
  • Living people today have Neanderthal ancestors, regionally distributed in surprising ways
  • East Asians more, then European, then African
  • Neanderthals come from European as well as central Asian sites
  • Denisova caves show a new humanoid species, that coexisted with Neanderthals
  • Field guide to Pleistocene Hookups
  • Every archaic human group interbred with each other
  • Every population before 40,000 years ago has been through a period of very high inbreeding
  • Neanderthals did not survive unaltered for 100,000s years. Much more dynamic
  • Europe has more mixing in it than we thought. Lots of colonization from other places, post-farming
  • Today’s populations are a mixture of ancient progenitor populations that no longer exist
  • Interbreeding with ancient populations provided raw materials for human adaptations
  • Changing excavation practices to get DNA

Beth Shapiro

  • Associate Professor, Department of Ecology and Evolutionary Biology, University of California, Santa Cruz
  • How to Clone a Mammoth
  • Sequencing the Dead
  • Found DNA in old stuff, like dinosaur DNA in Amber, wasn’t real. DNA decays
  • Organisms have DNA repair processes but of course these require energy
  • Cold helps. Oldest known DNA from Dawson Yukon, 700,000 years old (ash layer from volcano eruptions). In bad condition but were able to sequence whole genome. A horse.
  • Field is Ancient DNA. She started in 1999. Works in Beringia (Alaska, Russia)
  • Collect bones from animals, with DNA can find population size over time
  • Modern sequencers can do amazing things with short fragments. Other fields don’t like this, but these guys only have short fragments
  • Found a new camel species
  • Looked at horse domestication history
  • Can we clone a mammoth? No.
  • Asian elephants are closest relative to mammoth. 6 millions years of difference , not very much, just 1%
  • Hemoglobin difference is in three places, expressed these, found mammoths were better at delivering oxygen when it’s cold
  • Pleistocene Park. Guy introduced big animals like were there and just their presence over a few summers has brought back grass.

Spencer Wells

  • Scientist, author, entrepreneur, and former explorer-in-residence and director of the Genographic Project at National Geographic
  • The Human Journey -migration patterns
  • Apes 23m yrs ago
  • ~16m years ago africa bumped into Asia and species spread
  • Humans are 99.9% same genetically
  • African Adam and Eve 140,000–200,000 years ago
  • Only left Africa 60,000 years ago
  • The Genographic Project
  • 700,000 participants

Questions

  • While we each might have 3% Neanderthal genome, we each have different parts of it. Combine people in this room and you probably get close to half of Neanderthal genome.
  • ~75,000 years ago humans had a near extinction event, down to just 10,000 of us and we came back, so that’s a reason there’s so little variation.

1pm FORENSIC DNA INVESTIGATION

video

Introducer: Ronald S. Sullivan, Jr.

  • Clinical Professor of Law; Director, Criminal Justice Institute, Harvard Law School

Greg Hampikian

  • Professor, Department of Biological Sciences, Joint appointment in Department of Criminal Justice, Director of the Idaho Innocence Project, Boise State University
  • Happy Wrongful Convictions Day
  • Average time on death row before exoneration is 9 years
  • We know the genes and base pairs that do eye color (blue and brown, hazel is a little more difficult)
  • Databases with DNA, crime scene DNA, can look for exact match, but if none, look for half match to find family members.
  • Y-STRs are tied to last name, mitochondrial DNA is tied to mother. Public genealogy database combine these.
  • Sperm cells are different from other cells and we can separate them from others in samples
  • Given a profile, is a sample included or excluded or inconclusive. A statistics problem and it’s not always clear
  • Given tests to different labs, get back wildly different results

1:45pm THE ETHICAL FRONTIER OF DNA

video

Introducer: Danielle Allen

  • Director, Edmond J. Safra Center for Ethics, and Professor, Department of Government and Graduate School of Education, Harvard University

Arthur Caplan

  • Drs. William F. and Virginia Connolly Mitty Professor of Bioethics; Director, Division of Medical Ethics, Department of Population Health, NYU Langone Medical Center, NYU School of Medicine
  • Genetic Testing For Neurological Disorders: Ethical Challenges
  • We can test for Down’s syndrome and have been able for a while
  • It’s faced the ethical challenges that other testing will face
  • Given a prenatal tests, parents could do a lot of different things, some good some bad
  • Lookup Down’s on web, get different answer per website, Down’s, CDC, WebMD
  • Some states with laws about informing parents about down fetus and some banning aborting of down fetuses
  • Future is a big abortion battle based on testing

2:45pm THE FUTURE UTILITY OF DNA SCIENCE

video

Moderator: Christine Seidman

  • Thomas W. Smith Professor of Medicine, Harvard Medical School

Jacob Corn

  • Scientific Director, Innovative Genomics Initiative; Assistant Adjunct Professor of Biochemistry, Biophysics, and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley
  • The Genome Editing Revolution
  • Passed around a model of some enzyme (Cas9)
  • Reading DNA is faster than writing. Reading is growing faster than Moores law.
  • 1990s Zinc Fingered clueless
  • 2009 TAL Effector Nuclease - protein based recognition engineered Nuclease
  • 2012 CRISPR/Cas9 - targeting RNA endogenous Nuclease $100 and < 1 week
  • Cas9 is a bacterial immune system
  • Cas9 does a double stranded cut, not the edit
  • Gene editing to cure blood diseases
  • Seems to work everywhere, bacteria, virus, yeast, mice, chickens, cows, humans, etc.
  • Good for science testing. On organisms that we don’t know much about can use this to edit genes and see effects.
  • A German man was cured of HIV by getting a transplant from someone with a particular mutation (by coincidence), now looking to do this via editing

Alison Murdoch

  • Professor of Reproductive Medicine and Head of Department, Institute of Genetic Medicine, International Fertility Centre for Life, Newcastle University (United Kingdom)
  • The Science and Politics of Mitochondrial Donation (In the UK)
  • Large variety of mtDNA caused diseases
  • Nuclear DNA encode 32,000 genes
  • mtDNA encodes 37 genes
  • Mitochondrial transfer in embryos idea is 5 years old
  • Done in monkeys in 2009
  • Still not legal in UK on humans, is it ethical?
  • Just became legal in Oct 2015, treatment in a few months

Floyd Romesberg

  • Professor, Department of Chemistry, The Scripps Research Institute
  • Expanding the Genetic Alphabet
  • Predominantly hydrophobic nucleotides
  • Details of finding bases that pair well and don’t interfere with existing ones

4:15pm CLOSING REMARKS

Janet Rich-Edwards

4:30pm RECEPTION AND POSTER SESSION

1 comment:

Anonymous said...

Interesting! As our team are currently working on the R&D of bispecific antibodies, I don't get a chance for that.