Category: Misc.

A good thing: More and more biology papers showing up in arXiv

Good to see some more papers in microbiology & genomics and related topics going to the preprint server arXiv.

If you are interested in population and evolutionary genetics a good place to keep up with papers on this topic in arXiv is Haldane’s Sieve.  The good folks there in essence make a separate post about each paper of interest and then people can comment there on the papers, since the commenting functions at arXiv are, well, challenged.

In areas related to this blog, here are some recent papers in arXiv:

Am hoping more and more biologists start depositing papers in arXiv.  My brother has started doing it for all papers in his lab so I guess that means I should too.  And so should everyone else …
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Lab meeting May 7th 2013

Hello,
We will have our weekly lab meeting this week from 1:30 to 3pm in room 4202 of the Genome Center.
Dongying Wu is presenting.

The need for a phylogeny driven genomic encyclopedia of eukaryotes

Monday I gave a talk for the SMBE Eukaryotic Omics satellite meeting that has been going on at UC Davis.  When Holly Bik, a post doc in my lab asked me to talk at the meeting, I said, basically “Well, OK, but I don’t really do much work on eukaryotes.”  And then I came up with an idea – I could make my talk about how it might be good to have a better phylogenetic sampling of eukaryotic genome sequences.  I have been a bit obsessed for many many years about phylogenetic sampling of genomes and, well, though I have avoided eukaryotes mostly in most of my genome sequencing work, I figured, I should still get on my soap box about how phylogenetic sampling is a good thing.  So, well, I did.  And I think we (i.e., the scientific community) really needs a better sampling of eukaryotic genomes.

I have posted my talk to Slideshare and I recorded audio of my talk in synch with the slides and posted that to Youtube.  These are below.

I hereby am calling for those people interested in participating in such a phylogeny driven genomic encyclopedia of eukaryotes to make yourselves known.  We NEED to do this.

Related posts

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

I love this … "Dr. Eleanor’s Book of Common Ants" based in part on citizen science data

This is really cool:  Dr. Eleanor’s Book of Common Ants.  Free to download.  With incredible pics from Alex Wild.  And based in part on data from the School of Ants citizen science project.  You can download the PDF or the iBook from iTunes.  From the folks at “Your Wild Life” including Holly Menninger and Rob Dunn and others.  Definitely worth checking out.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

We are getting close to sequencing!

A few of the PCRs last week didn’t work so I’m finishing up the last PCR B’s right now that we’ve had to redo and then all we have to do is Gel confirmations. If I counted correctly there are 24 confirmations to do. I would like to do one now, but I have to catch the bus in 30 minutes and I wouldn’t finish in time 😦   I plan to come in on Friday and possibly Thursday as well and hopefully as a group we can completely finished and get our samples in the sequencer by the end of the week!

 

Then comes the hard part! Data analysis. I learned a lot about this portion of the project while I was preparing my part of the lab meeting presentation a few weeks ago so hopefully that knowledge helps me understand what’s to come. Like most things, I’m sure it’s much easier said then done!

Aquarium project poster at the UCD Undergraduate Research Conference

Here’s the poster that Lakshmi prepared for the conference.   The presentation went well!  Thanks to everyone who helped out.

S0357083

Trying to sort out all the STEM and STEM related departments, graduate programs , at #UCDavis

Well, I was in a meeting yesterday for the UC Davis ADVANCE program.  This program is an NSF funded project to improve presence of women and underrepresented minorities on the faculty in Science, Technology, Engineering and Math (STEM).  So I decided to see – how many departments at UC Davis might participate in such an initiative.  And, well, wow.  I knew there were a lot of STEM or STEM-related departments at UC Davis but I did not know there were this many.

Here is a list I compiled of UC Davis STEM or STEM-related Departments.  I included medical departments here since many people in such departments do medical/science research.  But clearly this is a broad definition of STEM.  But nevertheless, this gives some picture of the scope of science and medicine and related departments at UC Davis.

Vet School departments in Yellow
Med School departments in Red
College of Biological Sciences Departments are In Green
College of Agricultural and Environmental Sciences in Orange
College of Letters and Science in Light Blue
College of Engineering in Grey

  1. Anatomy, Physiology & Cell Biology
  2. Anesthesiology
  3. Animal Science
  4. Anthropology
  5. Applied Science
  6. Biochemistry and Molecular Medicine
  7. Biological and Agricultural Engineering
  8. Biomedical Engineering
  9. Cardiovascular Medicine
  10. Cell Biology and Human Anatomy
  11. Chemical Engineering and Materials Science
  12. Chemistry
  13. Civil and Environmental Engineering
  14. Computer Science
  15. Dermatology
  16. Electrical and Computer Engineering
  17. Emergency Medicine
  18. Entomology
  19. Environmental Science and Policy
  20. Environmental Toxicology
  21. Evolution and Ecology
  22. Family and Community Medicine
  23. Food Science and Technology
  24. Geology
  25. Human and Community Development
  26. Infectious Diseases
  27. Internal Medicine
  28. Land, Air and Water Resources
  29. Linguistics
  30. Mathematics
  31. Mechanical and Aeronautical Engineering
  32. Medical Pathology
  33. Medical Microbiology & Immunology
  34. Medicine and Epidemiology
  35. Microbiology and Molecular Genetics 
  36. Molecular and Cellular Biology
  37. Molecular Biosciences
  38. Nematology
  39. Neurobiology, Physiology and Behavior
  40. Neurological Surgery
  41. Neurology
  42. Nursing
  43. Nutrition
  44. Obstetrics and Gynecology
  45. Ophthalmology
  46. Pathology
  47. Pathology, Microbiology & Immunology
  48. Pediatrics
  49. Pharmacology
  50. Physical Medicine and Rehabilitation
  51. Physics
  52. Physiology and Membrane Biology
  53. Plant Biology
  54. Plant Pathology
  55. Plant Sciences
  56. Population Health and Reproduction
  57. Psychiatry
  58. Psychology
  59. Public Health Sciences
  60. Statistics
  61. Surgery
  62. Surgical and Radiological Sciences 
  63. Urology
  64. Viticulture & Enology
  65. Wildlife, Fish and Conservation Biology
And then of course UC Davis has a TON of graduate groups and almost all of these are separate from departments.  They do not hire faculty but they are a key part of the atmosphere and academics at UC Davis.  And there are an enormous number of these in STEM or STEM-related fields.  See below
Graduate Groups

Agricultural and Environmental Sciences Graduate Programs

  1. Agricultural and Environmental Chemistry
  2. Agricultural and Resource Economics
  3. Animal Biology
  4. Atmospheric Science
  5. Biological Systems Engineering
  6. Ecology
  7. Ecology (Joint Doctorate with San Diego State University)
  8. Entomology
  9. Food Science
  10. Genetics
  11. Geography
  12. Horticulture and Agronomy
  13. Hydrologic Sciences
  14. Master of Public Health
  15. Microbiology
  16. Nutritional Biology
  17. Pharmacology and Toxicology
  18. Plant Biology
  19. Plant Pathology
  20. Population Biology
  21. Soils and Biogeochemistry
  22. Transportation Technology and Policy
  23. Viticulture and Enology

Biological and Life Sciences Graduate Programs

  1. Animal Behavior
  2. Animal Biology
  3. Anthropology
  4. Avian Sciences
  5. Biochemistry and Molecular Biology
  6. Biochemistry, Molecular, Cellular and Developmental Biology
  7. Biological Systems Engineering
  8. Biomedical Engineering
  9. Biophysics
  10. Biostatistics
  11. Cell and Developmental Biology
  12. Clinical Research
  13. Comparative Pathology
  14. Ecology
  15. Ecology (Joint Doctorate with San Diego State University)
  16. Entomology
  17. Epidemiology
  18. Exercise Science
  19. Food Science
  20. Forensic Science
  21. Genetics
  22. Health Informatics
  23. Immunology
  24. Master of Public Health
  25. Maternal and Child Nutrition
  26. Microbiology
  27. Molecular, Cellular and Integrative Physiology
  28. Neuroscience
  29. Nursing Science and Health-Care Leadership (Doctor of Philosophy)
  30. Nursing Science and Health-Care Leadership (Master of Science)
  31. Nutritional Biology
  32. Pharmacology and Toxicology
  33. Plant Biology
  34. Plant Pathology
  35. Population Biology
Engineering Graduate Programs

  1. Applied Science Engineering
  2. Biological Systems Engineering
  3. Biomedical Engineering
  4. Chemical Engineering
  5. Civil and Environmental Engineering
  6. Computer Science
  7. Electrical and Computer Engineering
  8. Materials Science and Engineering
  9. Mechanical and Aeronautical Engineering
  10. Transportation Technology and Policy 

Health Sciences Graduate Programs

  1. Clinical Research
  2. Health Informatics
  3. Physician Assistant Studies
  4. Preventive Veterinary Medicine

Physical Sciences and Mathematics Graduate Programs

  1. Applied Mathematics
  2. Applied Science Engineering
  3. Atmospheric Science
  4. Biomedical Engineering
  5. Biophysics
  6. Biostatistics
  7. Chemistry
  8. Forensic Science
  9. Geography
  10. Geology
  11. Hydrologic Sciences
  12. Mathematics
  13. Physics
  14. Soils and Biogeochemistry
  15. Statistics

Social Sciences Graduate Programs

  1. Agricultural and Resource Economics
  2. Anthropology
  3. Child Development
  4. Ecology
  5. Geography
  6. Human Development
  7. Master of Public Health
  8. Maternal and Child Nutrition
  9. Nursing Science and Health-Care Leadership (Doctor of Philosophy)
  10. Nursing Science and Health-Care Leadership (Master of Science)
  11. Psychology

And then there are the Undergraduate Majors of which many are in STEM or STEM-related fields

    1. Aerospace Science & Engineering
    2. Agricultural & Environmental Education
    3. Animal Biology
    4. Animal Science
    5. Animal Science & Management
    6. Anthropology
    7. Applied Mathematics
    8. Applied Physics
    9. Atmospheric Science
    10. Biochemical Engineering
    11. Biochemistry & Molecular Biology
    12. Biological Sciences
    13. Biological Systems Engineering
    14. Biomedical Engineering
    15. Biotechnology
    16. Cell Biology
    17. Chemical Engineering
    18. Chemical Engineering/Materials Science & Engineering
    19. Chemical Physics
    20. Chemistry
    21. Civil Engineering
    22. Clinical Nutrition
    23. Computer Engineering
    24. Computer Science
    25. Computer Science and Engineering
    26. Ecological Management & Restoration
    27. Electrical Engineering
    28. Entomology
    29. Environmental Horticulture & Urban Forestry
    30. Environmental Policy Analysis & Planning
    31. Environmental Science & Management
    32. Environmental Toxicology
    33. Evolution, Ecology and Biodiversity
    34. Exercise Biology (suspended for 2013-14)
    35. Fiber & Polymer Science
    36. Food Science
    37. Genetics
    38. Geology
    39. Human Development
    40. Hydrology
    41. Linguistics
    42. Materials Science and Engineering
    43. Mathematical & Scientific Computation
    44. Mathematics
    45. Mechanical Engineering
    46. Mechanical Engineering/Materials Science & Engineering
    47. Microbiology
    48. Natural Sciences
    49. Neurobiology, Physiology & Behavior
    50. Nutrition Science
    51. Pharmaceutical Chemistry
    52. Physics
    53. Plant Biology
    54. Plant Sciences
    55. Psychology
    56. Science and Technology Studies
    57. Statistics
    58. Undeclared – Life Sciences
    59. Undeclared – Physical Sciences
    60. Undeclared – Social Sciences
    61. Viticulture & Enology
    62. Wildlife, Fish & Conservation Biology

    So – lots and lots of STEM stuff at Davis and lots of chances / opportunities to improve the presence / treatment / life of women and underrepresented minorities.




    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    Bad Ome-like word of the week: symbiome

    Well I got pointed to this paper: Transgenerational Transmission of the Glossina pallidipes Hytrosavirus Depends on the Presence of a Functional Symbiome

    And as many might guess – the word “symbiome” did not sit well with me.  Alas, they don’t define it in the paper.  So I can’t really quibble with their definition.  But I did find some other stuff out there that, well, at least helps see how other people are using the word:

    I can’t really tell from most of these if “symbiome” can be a useful term or not sometimes.  Certainly the iPhylo example above has potential.  But in general, the word seems awkward at best.  Now – as far as I can tell, nobody is using it in the context of “genomics” so this does not fit in with my “badomics” obsession.  But it still does not make me feel warm and fuzzy so I am going to give it a pseudo-award – the Bad Ome-like word award.

    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    UC Davis’ 2nd Annual BioBlitz will be sampling MICROBES!

    The first-ever MicroBioBlitz will be held tomorrow, April 27th, from 9am-2pm! Join the Eisen Lab and the UC Davis chapter of SEEDS (the Ecological Society of America’s Undergraduate Ecology Club) at the Putah Creek Riparian Reserve for their second annual BioBlitz. The event is open to the public, and SEEDS just finished putting out some traps, so there could be lots of fun critters to see tomorrow!

    I just chatted with the BioBlitz organizers, and they are super-excited to have us there to recruit the BioBlitz participants. As they catch frogs and butterflies, and identify flowers and trees, they will all be armed with a microbial sampling kit! Microbial samples will be sent to Jack Gilbert for sequencing as part of the Earth Microbiome Project!

    Bring friends, family, co workers, or anyone else you might know!

    Here is the link to iNaturalist, which is the site they will be using to upload all of their species accounts. Come out and help the UCD SEEDS chapter win the BIOBLITZ contest this year!!

    Hmmm… wonder if our microbial species will count for the contest???

    Here’s the official BIOBLITZ FLYER 

    and a BioBlitz Map

    Outreach & Communication for K-12 Students Workshop for Grad Students & Postdocs