The Tree of Life: HIV

Wednesday, January 09, 2013

Notes from talk by Stephen J. O'Brien at #UCDavis

Stephen O' Brien talked at UC Davis a few days ago. I met with him in the afternoon before his talk. It was one of the more interesting discussions I have had in a long time. He has done some very interesting and important work (e.g., comparative genomics, HIV, feline evolution) though most of what we talked about was not work per se (e.g., we talked a lot about baseball and big cats since my kids are obsessed with big cats).

Anyway, below is a "Storification" of tweets from his talk. Best part - he signed a copy of his Tears of the Cheetah: The Genetic Secrets of Our Animal Ancestors book with a dedication to my kids.

View the story "Steven J. O' Brien talk at #UCDavis on CCR5/HIV/AIDS" on Storify Steven J. O' Brien talk at #UCDavis on CCR5/HIV/AIDS Storified by Jonathan Eisen· Mon, Jan 07 2013 20:12:09 Today at #UCDavis Stephen O Brien on "Three Decades of Genomics and AIDS" http://pic.twitter.com/dQG4tBsoJonathan Eisen Can't wait for talk at 4 PM today at #UCDavis Genome Ctr by Stephen O'Brien on "Three Decades of Genomics and AIDS" http://pic.twitter.com/dQG4tBsoJonathan Eisen @phylogenomics Wow! Interesting topic. Wish I was attending.Setor Amuzu As an evolutionary biologist am jealous of name of Obrien's "Theodosius Dobzhansky Center for Genome Bioinformatics" http://shar.es/4vIBYJonathan Eisen @phylogenomics any podcasts available?Cuquis R SJ Obrien - head of new Dobzhansky Inst - intro by Harris Lewin, discussing how Dobzhansky finished his career here at #UCDavis:Jonathan Eisen Lewin point out that Steven O Brien has been called the Indiana Jones of Genomes (e.g.., http://www.genomenewsnetwork.org/articles/2004/03/19/tears.php ) #ucdavisJonathan Eisen Lewin: Steven O' Brien is also one of the coordinators of the genome 10K project http://genome10k.soe.ucsc.edu/participants #UCDavisJonathan Eisen Steven O Brien launching into his talk at #ucdavis http://pic.twitter.com/RTadoUJmJonathan Eisen O'Brien at #UCDavis: Giving props to T. Dobzhansky and his pioneering work on population geneticsJonathan Eisen O'Brien at #UCDavis: discussing how population genetics help lead to many whole fields/areas incl. conservation genetics, DNA forensics, etcJonathan Eisen Stephen J. O'Brien: is on Plagues and people Contagion Genomics & Beyond. 3 areas: Gene Discovery, Conservation Genetics, DNA forensicsDawei Lin O'Brien at #UCDavis: began work on AIDS epidemic partly as model for way to connect human genetics and infectious diseaseJonathan Eisen O'Brien at #UCDavis: close to 30 million people have died of AIDS and close to 30 million more are infected w/ HIV & disease still spreadingJonathan Eisen @Curosik don't think soJonathan Eisen O'Brien at #UCDavis: heterogeneity in progression in HIV led him to try to use advances in human genetics to look for AIDS restrictive genesJonathan Eisen SJO: Oct. 1996 AIDS quilt is a symbol of the pandemic disease with 40K Tabard Emblems on that day at the Capitol Hill.Dawei Lin O'Brien at #UCDavis: early in AIDS epidemic got access to samples from different groups of people to test role of human genes in progressionJonathan Eisen O'Brien at #UCDavis: looked for genetic variation in AIDS resistance, progression rate, outcomes, response to HAART therapyJonathan Eisen O'Brien at #UCDavis: in 1996 5 groups discovered that CCR5 (a G coupled seven transmembrane receptor) was target of HIV for cell entryJonathan Eisen O'Brien at #UCDavis: looked for CCR5 mutations in cohorts of patients w/ HIV & found that homozygous mutations were protectiveJonathan Eisen SJO: CCR5 is the binding target for HIV. People with CCR5 delta with a 32 peptide deletions do not have HIV infections.Dawei Lin O'Brien at #UCDavis: those people heterozygous for CCR5 deletions showed slower progression of HIV infectionJonathan Eisen @phylogenomics would love to see the stats methods on thatLewis Lab @Lewis_Lab seems to be relatively old data ...Jonathan Eisen Obrien at #UCDavis: many scientists occasionally like to do more than publish in a good journal, some would like to translate to bedsideJonathan Eisen SJO: People study genes about infectious diseases should not stop at publishing on a good journal, should bring it to the bedside.Dawei Lin Obrien at #UCDavis: re: delta32 mutation in CCR5 and modifies Dobzhansky "nothing in medicine makes sense except in light of evolution"Jonathan Eisen Obrien at #UCDavis: discussing how frequency of CCR5 delta32 mutation has increased rapidly over time; suggest this is due to ++ selectionJonathan Eisen @phylogenomics I'm not seeing any open access/open data reports.Lewis Lab Obrien at #UCDavis: 20 mutations in CCR5 have been found outside of delta32 mutation; 18/20 are amino acid changing; suggests ++ selectionJonathan Eisen SJO: 1/5 people now is CCR5 delta 32 carriers. There are 22 variants. 18 of them changes peptides.Dawei Lin @Lewis_Lab http://dobzhanskycenter.bio.spbu.ru/pdf/sjop/MS379_Martin.pdf ???Jonathan Eisen Obrien at #UCDavis: Suggests something influenced CCR5 mutations prior to AIDS epidemic (admits much of his theories on this controversial)Jonathan Eisen OBrien at #UCDavis now reading from Tears of the Cheetah http://www.amazon.com/Tears-Cheetah-Genetic-Secrets-Ancestors/dp/0312339003 his book on genetics / genomicsJonathan Eisen @Lewis_Lab maybe from this ??? http://journals.lww.com/jaids/Fulltext/1998/12010/Distinctive_Effects_of_CCR5,_CCR2,_and_SDF1.9.aspxJonathan Eisen O'Brien at #UCDavis: suggests that bubonic plague may have influenced CCCR5 mutation frequencies over timeJonathan Eisen O'Brien at #UCDavis: discussing plague epidemic in 1665 and 1666 (reading from his book)Jonathan Eisen @phylogenomics that got me the statistical test I was looking for--thanks. I don't find the article very intuitive, thoughLewis Lab O'Brien at #UCDavis: discussing their estimates of the age of the CCR5 delta 32 mutations by looking at the size of the linkage groupJonathan Eisen O'Brien at #UCDavis: estimates of the date of the origin of the spread of the CCR5 delta 32 mutation is correlated w/ plague epidemicJonathan Eisen O'Brien at #UCDavis: many many waves of plague epidemics over time (though he notes many other possible epidemics also at same general time)Jonathan Eisen @phylogenomics thanks. This is a good case study for the stats class.Lewis Lab "@phylogenomics O'Brien suggests that bubonic plague may have influenced CCCR5 mutation frequencies" No doubt a 1-2 insC mutation.Donald Atkinson SJO: Conspiracy theories of black death cause CCR5 mutation hike, which mostly found in Caucasians.Dawei Lin O'Brien at #UCDavis: refs a 2004 Nature study of mice w/ CCR5 delta 32 homozygous mutation; -/- have 90+% reduction in Y.pestis uptakeJonathan Eisen O'Brien at #UCDavis: after 9/11 & anthrax attack collaborated w/ people to look at smallpox infection in CCR5 delta 32 mutant cellJonathan Eisen "The O'Brien at #UCDavis" stream of tweets by @phylogenomics is fascinating. Must-read for biology folks.Rob Quarles @phylogenomics What is his book? I show the PBS vid he was in few years ago to my molec epi class each year to discuss CCR5/plague/HIVTara C. Smith O'Brien at #UCDavis: many other viruses have been screened for whether they make use of CCR5Jonathan Eisen @phylogenomics thanks for tweets re O'Brien lecture. Say hi to Steve for me!Kathy Belov @aetiology Tears of a Cheetah http://www.amazon.com/Tears-Cheetah-Genetic-Secrets-Ancestors/dp/0312339003Jonathan Eisen Obrien at #UCDavis: delta 32 mutations in CCR5 may lead to higher risk to West Nile virus ...Jonathan Eisen SJO: people with homozygous CCR5 delta mutations are susceptible to West Nile virus, not HIV.Dawei Lin Obrien at #UCDavis: looking back to 1996 b/c this is when HAART therapy for HIV was startedJonathan Eisen Obrien at #UCDavis: showing slide from Tony Fauci of FDA Approved antiretroviral drugs; now many new drugs going after CCR5 interactionJonathan Eisen @phylogenomics cool! I will order it.. Thanks for the link!Cuquis R @phylogenomics thanks!Tara C. Smith Obrien at #UCDavis: discussing "The Berlin Patient" (see http://articles.latimes.com/2012/jul/27/news/la-heb-hiv-cure-aids-meeting-20120727); had AML; prognosis bad; bone marrow tplant from CCR5delta32Jonathan Eisen OBrien at #UCDavis: 2008 Gero Hitter - the doctor for "The Berlin Patient" shows up at AIDS conference; news finally comes out in WSJ 2008Jonathan Eisen Obrien at #UCDavis: here is the WSJ news story about The Berlin Patient http://online.wsj.com/article/SB122602394113507555.htmlJonathan Eisen Obrien at #UCDavis: says the story of the Berlin patient is an anecdote; emphasizes it is one patient; need more information / data / casesJonathan Eisen Obrien at #UCDavis: refs SciAm article http://www.scientificamerican.com/article.cfm?id=blocking-hivs-attack where gene therapy for HIV patients reported; he's skeptical about peer reviewJonathan Eisen Obrien at #UCDavis: some researchers have been looking at how CCR5 might influence Graft Versus Host Disease (see http://www.nejm.org/doi/full/10.1056/NEJMc1209665)Jonathan Eisen Obrien at #UCDavis refs new Nature paper showing CCR5 is a receptor for MRSA leukotoxin (see http://www.sciencedaily.com/releases/2012/12/121214191518.htm)Jonathan Eisen @KathyBelov will do ...Jonathan Eisen SJO: Patients with bone marrow transplants with CCR5 negative genotypes remain HIV free without drug treatments. A potential breakthrough.Dawei Lin Obrien at #UCDavis giving props to George W. Bush for PEPFAR program http://www.pepfar.gov http://www.avert.org/pepfar.htmJonathan Eisen Obrien at #UCDavis: OBrien ends his talk by thanking the patients who have provided samples cc: @rebeccasklootJonathan Eisen Question at Obrien talk at #UCDavis: is CCR5 delta 32 the only restriction mutation? Obrien says yes but not yet translated to bedsideJonathan Eisen Comment at talk by Obrien at #UCDavis: primate center at UCDavis played a major role in work on HIVJonathan Eisen Comment at Obrien talk at #UCDavis: says to students in crowd that you have heard a talk about thinking which most people don't do anymoreJonathan Eisen @phylogenomics Nice. He definitely saw importance of donor appreciation/respect differently than most in the early days.Rebecca Skloot @phylogenomics I wanna know what happened to his amazing frozen zoo at NCI! Hope he took it w/him; he worried re who would take care of itRebecca Skloot @RebeccaSkloot he did not discuss this ...Jonathan Eisen Love @phylogenomics tweets on O'Brien's talk at #UCDavis. Everything he said on CCR5/HIV/Berlin pt is right up my alley.Nathalia Holt My kids are very happy w/ autographed copy of "Tears of the Cheetah" Steven O Brien gave me after his talk at #ucdavis http://pic.twitter.com/SCEh5AXkJonathan Eisen As follow up to post about "Tears of a cheetah" - my kids are a bit obsessed w/ big cats ... http://pic.twitter.com/M82V4fiHJonathan Eisen @phylogenomics How do the cats get along with all the microbes?Cindy Manson @CynthiaManson1 extremely well http://pic.twitter.com/joOoehUWJonathan Eisen

Friday, June 17, 2011

Twisted tree of life award: @Discovermag for article on Lynne Margulis

Well, if you can, for a minute, ignore that fact that in Discover Interview: Lynn Margulis Says She's Not Controversial, She's Right | Evolution | DISCOVER Magazine Discover Magazine in essence is promoting some of the refuted ideas Lynne Margulis has about HIV. Sure they hint in part that they think she is over the top but they also give her a soapbox to spout some of her latest absurdities on HIV and such. I would suggest you don't even read the main part of the Discover article. Just read Tara Smith's discussion of it: Margulis does it again : Aetiology. Margulis should not be given such prominence in a magazine like Discover. But that is not what I am hear to write about. I am hear to point out that Discover also sets up a red herring for Margulis. In the beginning of the article, it is written:

"A conversation with Lynn Margulis is an effective way to change the way you think about life. Not just your life. All life. Scientists today recognize five groups of life: bacteria, protoctists (amoebas, seaweed), fungi (yeast, mold, mushrooms), plants, and animals. Margulis, a self-described “evolutionist,” makes a convincing case that there are really just two groups, bacteria and everything else."

Seriously? Scientists today do not recognize five groups. Scientists today have moved past that to recognize and/or argue about bacteria, archaea and eukaryotes - the three domains of life. These three groups were first proposed in 1977 by Carl Woese and colleagues. Did Discover somehow miss the last 34 years of science? WTF? For setting up such an evolutionary red herring in this painful interview with Lynne Margulis, I am giving Discover Mag my coveted "Twisted tree of life award". Past winners are: