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← Unlocking DNA: The Center for Comparative Genomics

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Showing Revision 8 created 02/06/2018 by Molly Michelson.

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  2. Probably the most appealing part for me was answering
  3. these long-standing questions that I've had since I was a kid.
  4. Evolutionary biology helps us understand the nature around us.
  5. First and foremost I'm interested in evolutionary questions.
  6. I'm very interested in the biodiversity that we see on Earth.
  7. Everything from species identification to deep, evolutionary questions
  8. can be addressed with DNA,
  9. and the CCG provides all of the resources necessary.
  10. So if someone's out collecting birds or reptiles or whatever,
  11. they bring it to the lab and they extract the DNA.
  12. They purify the DNA and separate all the cell material from the DNA,
  13. and then you have pure DNA.
  14. Once you have pure DNA, you can do all kinds of things with it.
  15. You can sequence that gene for many different organisms
  16. and then compare them to each other and build an evolutionary history
  17. or a "family tree" for genes and species.
  18. The main platform for sequencing for the past 30 years
  19. is Sanger sequencing.
  20. With that method we look at one section of the genome at a time.
  21. With next-gen sequencing methods the data
  22. we can get is massively increased because
  23. we can do a lot of the sequencing in parallel.
  24. We have the MiSeq sequencing machine here
  25. and we can produce 25 million sequences in one read.
  26. More recently there is a third generation sequencing.
  27. Here we have an Oxford Nanopore MinION machine.
  28. So by reading those electrical signals we're able to read the DNA.
  29. It fits in my pocket. It's amazing.
  30. (laughs)
  31. Matt Van Dam is currently working on weevils using this new technology
  32. to try to understand evolutionary history of the weevils.
  33. Weevils are a particular family of beetles.
  34. One of the problems in the genome assembly
  35. is that you have all these little bits of information.
  36. And then, sometimes, sticking them together
  37. in the right way is extremely complicated.
  38. The Nanopore does quite well for these longer reads.
  39. A group of us here at the Academy are sequencing
  40. the complete genome of the Pygmy Angelfish,
  41. and that includes all of the chromosomes,
  42. all of the mitochondria, and everything.
  43. It's very exciting work.
  44. Lauren is trying to look at which genes are active or turned on
  45. and what kind of combinations can be produced
  46. by these different genes being turned on and off.
  47. One of the craziest things is we have only characterized
  48. like 1% of scorpion venoms.
  49. A single individual scorpion might have
  50. 150 unique types of venom in its venom gland.
  51. And so it has genes to create all of these different venoms,
  52. and those venoms are highly specific.
  53. There's active research on using scorpion venom to treat cancer,
  54. to treat arthritis, to treat multiple sclerosis.
  55. So she is using something called RNA-Seq or transcriptomics,
  56. and what you do is you sequence all of the proteins,
  57. This is a way to sort of skip the whole genome sequencing
  58. and you can focus just on the RNA which is what produces the proteins.
  59. The seahorse project is something
  60. I've been involved with for many years.
  61. We've been trying to understand this very complex group.
  62. They apparently evolved very rapidly and created many different forms,
  63. so we have seahorses, pipefish, sea dragons,
  64. all these wild looking fish, and nobody really knows the relationships
  65. because they evolved and radiated very rapidly
  66. and in a very short period of time.
  67. We're using a new technology called ultra-conserved elements,
  68. and these are parts of the genome that are unchanged
  69. across hundreds of millions of years to reconstruct those branches.
  70. Our exhibits have lots of amphibians, so when we bring them in,
  71. we have to make sure that we don't spread
  72. chytrid fungus to the rest of our amphibians.
  73. If we put it in with the rest of the exhibits,
  74. they would probably all die.
  75. We essentially create these probes, which are pieces of DNA
  76. that match those unique markers to the chytrid fungus.
  77. If the probe matches, we know it has this fungus.
  78. If there is no match, then we can be pretty sure
  79. that there are no fungus infections.
  80. I think that the role of the CCG is to help every scientist
  81. answer their questions and there are very few questions
  82. you can address without genetic data.
  83. We have all of this information that's accumulated for decades
  84. by scientists and naturalists and they're depositing it
  85. in our collection with very good ecological data
  86. that's associated with it.
  87. It's very important that we can also unlock that knowledge.
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