Gramstain

New Blog Site

noreply@blogger.com (Adam Ratner) — Tue, 18 Jan 2011 21:09:00 +0000

We've moved the blog to WordPress. Please check us out there. The www.gramstain.org address should still work.

I saw a kid with chickenpox...

noreply@blogger.com (Adam Ratner) — Sat, 13 Mar 2010 02:03:00 +0000

I saw a kid with chickenpox. This isn't that unusual, as I'm a pediatrician and an infectious diseases specialist. Pediatricians have been coming home and saying "I saw a kid with chickenpox," to their spouses for a long, long time. It's less common now, because we have a safe, effective vaccine that prevents infection with varicella, the virus that causes chickenpox. Children get two shots -- the first at 12 months and the second at least three months later. In exchange for this, they get lifelong immunity against a disease that used to affect essentially all kids.

There are a reasonable number of people, some pediatricians included, who think that the varicella vaccine is superfluous. Why give a shot to prevent something that we all had as kids? After all, it didn't kill us, right? Well, before the vaccine was licensed in the United States, there were about 11,000 hospitalizations and 100 deaths per year due to chickenpox. These are relatively small numbers when compared to the size of any year's birth cohort, though that calculus changes pretty drastically if your kid is one of the 100. The vaccine has drastically decreased these numbers, though there are still cases, including severe ones. These may occur among immune compromised people, children who are too young to have received the vaccine, or those whose parents or pediatrician decided to forgo this protection.

Which brings us to the kid I saw. She was a beautiful two year-old with the classic dots of chicken pox studding her pale skin. They had passed the "dew drop on a rose petal" phase and were crusted over already, indicating that her immune system had the virus pretty well under control. What was less under control was the Streptococcus bacteria that had taken advantage of her damaged skin barrier to invade first the soft tissues of her neck and later her bloodstream. That's why we met in the intensive care unit, where a ventilator did her breathing, where Sharpie lines on her skin demarcated the spread of her infection since her arrival, and where her father told me that she was up to date on her vaccines. It was just that her pediatrician didn't give her the chickenpox shot at the 1 year-old visit.

When you sign up to be a pediatrician, you agree to sometimes argue with parents, to push and cajole and manipulate so that parents trust that, yes, even though the grandmother says to put the newborn baby on her stomach to sleep that it really truly is safer on the back. We ask questions about car seats and smoke alarms and guns in the house, all in the name of preventing tragedy. There are so many things that we can't vaccinate our patients against. If I had a child abuse vaccine, a car crash vaccine, a heartbreak vaccine -- I would use them all. It turns out that we only have a handful. So why, then, was I picking up the pieces of this family whose daughter was fighting bravely against one of the few things that we actually know how to prevent?

PLoS ONE Prokaryotic Genome Collection

noreply@blogger.com (Adam Ratner) — Tue, 09 Jun 2009 22:08:00 +0000

PLoS ONE unveiled their new Prokaryotic Genome Collection today, along with an editorial by Section Editor Niyaz Ahmed. Well done, Niyaz! Everyone else: send us your best genome papers!

Tara Smith on Swine Flu

noreply@blogger.com (Adam Ratner) — Sun, 26 Apr 2009 00:15:00 +0000

Tara Smith (Aetiology) has a great post on the unfolding swine flu outbreak in Mexico, California, New York... [Link].

Our new PLoS ONE paper is out!

noreply@blogger.com (Adam Ratner) — Thu, 16 Apr 2009 12:52:00 +0000

Our new paper about detection and inhibition of vaginolysin, the human-specific toxin from Gardnerella vaginalis, came out on line today! [Link] Please check it out and rate/comment if you can!

Kristof on pneumonia

noreply@blogger.com (Adam Ratner) — Fri, 03 Apr 2009 13:16:00 +0000

Nicholas Kristof has an excellent blog post about the overwhelming importance of pneumonia as a cause of childhood mortality worldwide. Preventable, treatable, often overlooked.

Papers

noreply@blogger.com (Adam Ratner) — Fri, 20 Mar 2009 16:10:00 +0000

I know that this has been widely publicized by Olivia Judson already, but Papers from mekentosj.com has changed my life. It is the most intuitive program I've encountered for organizing pdfs, searching PubMed and autoimporting, and letting me purge paper copies from my office. I've been importing manual and interlibrary loan scans of older papers as well. Amazing. It's $42 after the free trial and worth every penny.

Top picks in infectious diseases at PLoS ONE

noreply@blogger.com (Adam Ratner) — Fri, 20 Feb 2009 00:32:00 +0000

As a followup to the interview with Bora, I got to pick some of my favorite infectious diseases articles from PLoS ONE. http://www.plos.org/cms/node/444

PLoS ONE interview

noreply@blogger.com (Adam Ratner) — Wed, 18 Feb 2009 18:44:00 +0000

An interview that I did with Bora at PLoS ONE is now available at the PLoS site. We talked about infectious diseases, open access, and social justice. I also got to use the term "tyranny of the Impact Factor," which was fun...

A primer on funding labs and the consequences for creativity...

noreply@blogger.com (Adam Ratner) — Wed, 11 Feb 2009 11:57:00 +0000

Stephen Quake gets it right as a guest blogger at NYT today.

Using your kids as experimental subjects...

noreply@blogger.com (Adam Ratner) — Sun, 18 Jan 2009 13:00:00 +0000

MIT scientist attaches camera to his newborn's head, and the NY Times is there. (Link). This seems less surprising than they make it out to be, though the picture is quite cute. The article is mainly about people doing speech and vision studies, but there is mention of Salk giving his child the experimental polio vaccine. It isn't mentioned in the article, but Maurice Hilleman made the mumps vaccine using virus isolated from his daughter's throat (the Jeryl Lynn strain).

Full disclosure: I have a couple of my daughter's group A streptococcus strains from episodes of strep throat sitting in the -80C freezer in the lab.

PNAS allows authors to keep copyright...

noreply@blogger.com (Adam Ratner) — Tue, 06 Jan 2009 20:59:00 +0000

Welcome news from PNAS and another step toward open access.

Tree of Life Post on Thanksgiving

noreply@blogger.com (Adam Ratner) — Thu, 27 Nov 2008 14:52:00 +0000

A nice post over at Tree of Life on what scientists should be thankful for:

http://phylogenomics.blogspot.com/2008/11/what-scientists-should-be-thankful-for.html

Have a great Thanksgiving.

NIH Open Access Mandate Under Attack

noreply@blogger.com (Adam Ratner) — Fri, 19 Sep 2008 00:48:00 +0000

Here is a message from PLoS that was posted today. Legislation has been introduced that would effectively end the mandatory deposition of manuscripts reporting NIH-funded research into the freely available PubMed Central archive. Please contact your representatives and urge them to oppose this legislation and to preserve access to taxpayer-funded research. Thank you.

______________

NIH Mandate under attack - we need your help by 9.24

Hello Facebook page fans,

A rare individual note from us today but it is in a good cause. We don't like to bug our fans too much but sometimes we need your assistance.

We need you to make a noise for OA by contacting your representatives and senators to protest a new bill introduced into congress that would effectively reverse the NIH Public Access Policy. There's an especially nice post from David Dooling at PolITigenomics on the topic here http://www.politigenomics.com/2008/09/open-access-under-attack.html

The last time we asked our Facebook fans to take action in support of the mandate, you guys did such a good job that we were asked by certain folks who shall remain nameless to "call off the dogs" because they "had the point already"! Now we need to ask you to act again.

So what's the story? On September 11, 2008, the Chairman of the House Judiciary Committee (Rep. John Conyers, D-MI) introduced a bill that would effectively reverse the NIH Public Access Policy, as well as make it impossible for other federal agencies to put similar policies into place.

The legislation is HR6845: “Fair Copyright in Research Works Act” http://judiciary.house.gov/hearings/pdf/HR6845.pdf. You can read more about the intentions of this legislation here http://www.taxpayeraccess.org/nih/HR6845calltoaction.html

Please contact your Representative and Senators no later than September 24, 2008 to express your support for public access to taxpayer-funded research and ask that he or she OPPOSE HR6845.

Especially important are members of the House Judiciary Committee http://judiciary.house.gov/about/members.html and Senate Judiciary Committee http://judiciary.senate.gov/about/members.cfm.

Draft text and contact details are included below.

--------------------------

Dear [Representative/Senator];

On behalf of [your organization], I strongly urge you to OPPOSE HR 6845, the Fair Copyright in Research Works Act, introduced to the House Judiciary Committee, Subcommittee on the Courts, Intellectual Property and the Internet, on September 11, 2008. This bill would reverse the National Institutes of Health (NIH) Public Access Policy, prohibit American taxpayers from accessing any and all research funded by taxpayer dollars, and stifle critical advancements in lifesaving research and scientific discovery.

Because of the NIH Public Access Policy, millions of Americans now have access to vital health care information from the NIH’s PubMed Central database. Under the current policy, nearly 4,000 new crucial biomedical articles were deposited in the last month alone. HR6845 would prohibit the deposit of these articles so that, as a result, researchers, physicians, health care professionals, families and individuals will be seriously impeded in their ability to access NIH-funded, critical health-related information.

[Why you support taxpayer access and the NIH policy]. The NIH policy must be allowed to continue to ensure public access to the results of research funded by the agency with taxpayer dollars. Please OPPOSE HR6845.

Sincerely,

-------

CONTACT INFORMATION

SENATE COMMITTEE ON THE JUDICIARY

name state fax

Senator Patrick Leahy VT 202-224-3479 (Chairman)
Senator Arlen Specter PA 202-228-1229 (Ranking Member)
Senator Jeff Sessions AL 202-224-3149
Senator Jon Kyl AZ 202-224-2207
Senator Dianne Feinstein CA 202-228-3954
Senator Joseph Biden DE 202-224-0139
Senator Charles Grassley IA 202-224-6020
Senator Richard Durbin IL 202-228-0400
Senator Sam Brownback KS 202-228-1265
Senator Edward M. Kennedy MA 202-224-2417
Senator Benjamin Cardin MD 202-224-1651
Senator Charles Schumer NY 202-228-3027
Senator Tom Coburn OK 202-224-6008
Senator Sheldon Whitehouse RI 202-228-6362
Senator Lindsey Graham SC 202-224-3808
Senator John Cornyn TX 202-228-2856
Senator Orrin Hatch UT 202-224-6331
Senator Herb Kohl WI 202-224-9787
Senator Russell Feingold WI 202-224-2725

HOUSE COMMITTEE ON THE JUDICIARY

name state fax
Rep. John Conyers, Jr. TX 202-225-0072 (Chairman)
Rep. Lamar Smith TX 202-225-8628 (Ranking Member)
Rep. Artur Davis AL 202-226-9567
Rep. Trent Franks AZ 202-225-6328
Rep. Howard Berman CA 202-225-3196
Rep. Zoe Lofgren CA 202-225-3336
Rep. Maxine Waters CA 202-225-7854
Rep. Linda T. Sanchez CA 202-226-1012
Rep. Brad Sherman CA 202-225-5879
Rep. Adam Schiff CA 202-225-5828
Rep. Elton Gallegly CA 202-225-1100
Rep. Dan Lungren CA 202-226-1298
Rep. Darrell Issa CA 202-225-3303
Rep. Robert Wexler FL 202-225-5974
Rep. Debbie Wasserman Schultz FL 202-226-2052
Rep. Ric Keller FL 202-225-0999
Rep. Tom Feeney FL 202-226-6299
Rep. Hank Johnson GA 202-226-0691
Rep. Steve King IA 202-225-3193
Rep. Luis Gutierrez IL 202-225-7810
Rep. Mike Pence IN 202-225-3382
Rep. William D. Delahunt MA 202-225-5658
Rep. Keith Ellison MN 202-225-4886
Rep. Melvin Watt NC 202-225-1512
Rep. Howard Coble NC 202-225-8611
Rep. Jerrold Nadler NY 202-225-6923
Rep. Anthony Weiner NY 202-226-7253
Rep. Betty Sutton OH 202-225-2266
Rep. Steve Chabot OH 202-225-3012
Rep. Jim Jordan OH 202-226-0577
Rep. Steve Cohen TN 202-225-5663
Rep. Sheila Jackson Lee TX 202-225-3317
Rep. Louie Gohmert TX 202-226-1230
Rep. Chris Cannon UT 202-225-5629
Rep. Rick Boucher VA 202-225-0442
Rep. Robert Scott VA 202-225-8354
Rep. Bob Goodlatte VA 202-225-9681
Rep. J. Randy Forbes VA 202-226-1170
Rep. Tammy Baldwin WI 202-225-6942
Rep. F. James Sensenbrenner, Jr. WI 202-225-3190

Thank you so much for everything you do to support us. Let's stop the madness.

Best wishes

PLoS

Sarah Palin and Botryotinia fuckeliana

noreply@blogger.com (Adam Ratner) — Sat, 06 Sep 2008 21:43:00 +0000

Enormous hat-tip to Jonathan Eisen for uncovering the evolutionary connection between Sarah Palin (or, more correctly, the peptide SARAHPALIN) and a hypothetical protein from -- wait for it -- B. fuckeliana. You could almost say that it looks intelligently designed... Link to Jonathan's blog post at Tree of Life here.

For profit, closed-access publishing

noreply@blogger.com (Adam Ratner) — Fri, 15 Aug 2008 15:49:00 +0000

An excellent post on for-profit publishers over at The Questionable Authority.

Ithaca, NY

noreply@blogger.com (Adam Ratner) — Sat, 02 Aug 2008 23:05:00 +0000

The Sciencenter (link) in Ithaca is the best children's science museum I've ever seen. The exhibits are attention-grabbing and (more impressively) attention-holding, even for an 8 year old. I've been twice in the past two days. We also did the Carl Sagan Planet Walk through Ithaca, which was a really cool way to think about relative sizes and distances in the solar system.

Olivia Judson on reading "Origin of Species"

noreply@blogger.com (Adam Ratner) — Wed, 09 Jul 2008 15:37:00 +0000

The column (link) is an easy read; the book, less so.

George Carlin

noreply@blogger.com (Adam Ratner) — Mon, 23 Jun 2008 09:20:00 +0000

Today is a sad, sad day. George Carlin, one of my favorite comedians, has died. I used to listen to his albums as I fell asleep as a junior high school student, and only much later realized how spot on he was about the absurdity of life and the hypocrisy of government. He has left at a time when we need his insights and his laughs more than ever.

Sour cream fudge cake.

noreply@blogger.com (Adam Ratner) — Mon, 23 Jun 2008 00:05:00 +0000

Joy of Cooking. Page 931. The sour cream fudge cake is the best cake recipe I've ever made. We've put it to the test twice now. Outstanding.

PLoS ONE

noreply@blogger.com (Adam Ratner) — Wed, 18 Jun 2008 20:02:00 +0000

I recently became the Section Editor for Infectious Diseases at PLoS ONE. While I've been an academic editor there since pretty close to the beginning, I'm really excited to take on this new role. Infectious diseases is already one of the largest article categories at PLoS ONE, and as a medical and scientific field with truly global reach, it is one that can benefit most from the open access model of publishing. I'm still getting the feel of my new role, but soon I hope to start collecting advice from friends and colleagues to help me grow the profile of PLoS ONE as a place where people submit and publish the best infectious diseases research.

More on Design and the Elastic Mind

noreply@blogger.com (Adam Ratner) — Wed, 14 May 2008 02:43:00 +0000

The NY Times has a story today about a piece in the Design and the Elastic Mind exhibit at MoMA (which I have blogged about in the past). It seems that a "living coat" made of mouse stem cells had to be put down due to aberrant growth. Link to story.

Infocom, HHGG, and a blast from the past.

noreply@blogger.com (Adam Ratner) — Sun, 20 Apr 2008 13:02:00 +0000

For anyone who grew up as a computer geek in the 1980s, this blog post from Andy Baio will be of very great interest. It seems that he has come across the network drive from Infocom, the premier interactive fiction company of that time, and that one of the things on the drive is a fragment of an unreleased sequel to the Hitchhiker's Guide to the Galaxy game. There's not much to the fragment itself, but the comments on the site and the emails that he quotes are priceless.

Enjoy. (Link)

Last Day: Liveblogging the Molecular Evolution/Infectious Diseases Keystone Conference

noreply@blogger.com (Adam Ratner) — Sat, 12 Apr 2008 18:30:00 +0000

Day 3
Eun-Chung Park (NIAID) made an announcement about NIH funding opportunities for non-US investigators. There is a new PA for international research in infectious diseases PAR-08-130.

Morning Session
David Alland (UMDNJ) gave a fantastic talk on the evolution of drug resistance in M. tuberculosis. He uses SNP-based phylogenetic analysis to link specific mutations to drug resistance phenotypes. In the setting of confusing data as to which mutations actually cause resistance and which are simply epidemiologically linked, he showed that phylogenetic analyses can provide answers, including answers that impact patient care, that other techniques cannot.

M. Cristina Gutierrez spoke about “rethinking tuberculosis in the light of evolution.” She focused on smooth-colony variants of Mycobacterium tuberculosis (MTb), which are an uncommon but confusing cause of human disease. Using MLST, she showed that MTb can be divided into distinct lineages, which she calls MTb and Mycobacterium prototuberculosis. She provided estimates of the age of the split between the two lineages and hypothesized about the relevance of this to TB in hominid ancestors.

Bruce Levin delivered an “opinionated rant” about recombination in bacteria with a focus on transformation. Using a combination of equations, experiments, and “yak-yak,” he put forward a new hypothesis about the evolution of transformation and genetic competence. He hypothesizes that although competent bacteria may have a growth deficit in comparison to non-competent competitors, in the setting of occasional, punctuated selective pressure, the competent strains will predominate.

A short talk describing MLST analysis was given by Sebastien Gagneux from MRC. He focuses on the biogeography of MTb and links phylogenetic analysis to hypotheses about human migrations.

Anne Buboltz from Penn State gave a short talk about a strain of Bordetella bronchiseptica that has become less virulent due to a recombination event. Her group mapped this recombination, and using careful genetic studies linked the genes involved to the loss of virulence.

In the afternoon session, Jim Musser gave a phenomenal talk about his group’s integrated systems biology approach to group A streptococcus virulence. Using longitudinally collected human disease isolates, full genome sequencing, and unique animal models, they have linked single mutations on the streptococcal chromosome (including a single nucleotide change in one case) to both overall virulence and (in at least one case) to anatomic site specificity. Amazing, amazing work. I plan to go back and read several of the papers that he described again.

Nancy Moran gave an exciting talk about the evolutionary genomics of bacterial symbionts of insects. This is an area that has exploded recently, especially with the publication of the paper taking a genomic look at the dual sharpshooter symbiosis. She gave an overview of the field, focusing on the common characteristics of genomes of obligate symbionts (small size, loss of metabolic functions), the importance of maternal passage of symbionts to their evolution, and how more recently established symbioses may differ from ancient ones.

Mark Achtman (University College Cork) spoke about the complex and intimate relationship between Helicobacter pylori and humans. In addition to learning a tremendous amount about the organism itself, his group has used the rapid evolution and recombination within H. pylori to trace human migrations at a level of resolution that human genomic studies cannot approach. This is an extremely useful and creative use of evolutionary and phylogenetic analysis and a field that is just beginning.

Martin Antonio spoke about Streptococcus pneumoniae, an extremely important cause of childhood mortality worldwide. His group looked at invasive S. pneumoniae disease in Africa and, through a detailed MLST analysis, linked a specific serotype to severity of disease.

Day 2: Liveblogging the Molecular Evolution/Infectious Diseases Keystone Conference

noreply@blogger.com (Adam Ratner) — Thu, 10 Apr 2008 22:59:00 +0000

Day 2
Morning Session: DNA viruses
Elliot Lefkowitz gave the opening session today. He spoke about gene acquisition and loss as driving factors in speciation of poxviruses. He focused on the orthopoxviridae (the group containing vaccinia, variola, monkeypox, and other pathogens). They have developed computational tools to do gene prediction and annotation across all known poxvirus genomes. This has allowed them to get around problems with inconsistency in annotation among deposited sequences. Gene acquisition in the core region appears to play much less of a role in orthopoxvirus speciation. These techniques have also enabled them to look at the process of gene fragmentation and loss over the evolutionary history of these viruses. They have begun to test these predictions, especially with regard to promoters. Some of this work is in a recent PNAS paper:
Assarsson, E., Greenbaum, J.A., Sundstrom, M., Schaffer, L., Hammond, J.A., Pasquetto, V., Oseroff, C., Hendrickson, R.C., Lefkowitz, E.J., Tscharke, D.C., Sidney, J., Grey, H.M., Head, S.R., Peters, B., Sette, A. (2008). Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes. Proceedings of the National Academy of Sciences, 105(6), 2140-2145. DOI: 10.1073/pnas.0711573105

The parvovirus family was the subject of the next talk, by Colin Parrish from Cornell. His title was “How to change your host range in a few easy steps: canine and feline parvoviruses.” In the 1970s, there was a host range shift within a feline parvovirus (FPV) that allowed it to infect dogs rather than cats. Within a year or two, this (now) canine parvovirus (CPV-2) spread through a wide geographic area and shifted again to allow efficient spread to both cats and dogs. All of the canine parvoviruses today appear to be descendants of this virus, and most are in the CPV-2a group. Nearly whole genome analysis has allowed description of geographically distinct clades within the CPV-2a group. Certain residues on the threefold spike of the capsid protein appear to control host range. The host receptor is the transferrin receptor, and binding to it triggers chathrin-mediated uptake.

Thomas Schultz talked about diversity within the rhadinoviruses (RV, which are gamma-2-herpesviruses, including KSHV – the causative agent of Kaposi’s sarcoma). There are two major branches within the RV lineage, and these are distant relatives of Epstein-Barr virus (EBV). Within KSHV, there was an early split into a number of geographically distinct lineages. More recently, there has been significant recombination among these lineages as well as introduction of sequences at the ends of the genome. KSHV protein K1, which contains hypervariable regions and has oncogenic properties, is located at one end of the genome at a position analogous to LMP-1 in EBV. KSHV protein K15, which activates host cell proinflammatory signaling, is at the other end. Homologues of K15 appear in other related viruses and seem to have distinct signaling profiles.

Mary Odom from the Lefkowitz lab gave a short talk about gene acquisition by poxviruses via horizontal transfer. She has developed bioinformatic techniques to look for putative transfer events. By looking at multiple databases (viral vs. eukaryotic or viral vs. bacterial), they can generate 2D plots of best BLASTP scores to generate leads.

Edgar Sevilla-Reyes gave a short talk about the dynamic gene content of human cytomegalovirus (CMV). Gene disrupting mutations occur after only a few passages in vitro. After more passages, larger deletions predominate, especially at the ends of the UL sequence. They studied genetic integrity at the ends of UL for 22 CMV isolates and found striking clustering of the sites of mutations. These same sites were also found to be mutated in a subset of non-passaged clinical CMV isolates, raising the question of what the selective pressures on these sites might be.

Workshop
short talk session

Nels Elde described an evolutionary arms race between poxviruses and their hosts. Protein kinase R (PKR) is a host factor with antiviral effects. In its dimeric (active) form, PKR phosphorylates eIF2alpha, which leads to a global transcriptional arrest. This blocks viral protein synthesis and can aid in host defense. As evidence of the importance of this strategy, several pathogenic viruses encode substrate mimics to block PKR. These mimics (K3L is the poxvirus example used here) are structurally similar to eIF2aplha and can block the PKR/eIF2alpha interaction. Analysis of the dN/dS ratio suggested that PKR was under positive selection but eIF2alpha was subject to purifying selection (i.e. PKR is undergoing adaptive evolution, while changes in eIF2alpha are generally selected against). By mapping specific sites in all three of the involved proteins (PKR, eIF2alpha, and K3L), the picture of a rapidly evolving selective race appears.

Willem van Ballegooijen talked about surveillance of hepatitis B virus (HBV) sequences following targeted vaccination of risk groups (not global vaccination!) in the Netherlands, starting in 1998. He used coalescent-based analysis of HBV DNA sequence and Bayesian analysis to provide statistical support for a decreasing incidence of infection, starting in about 2000.

Intrahost diversity and evolutionary dynamics of influenza were the topics of
Elodie Ghedin’s talk. Because of evidence of reassortment among cocirculating clades of influenza during a single season (see yesterday’s talks), she hypothesized that coinfection of individuals must occur. Using samples from human isolates, she examined diversity among influenza sequences. She found convincing evidence for double and even triple infections with influenza subtypes (which is something that we see clinically as well) and hypothesizes that this may be a source for flu reassortment and diversity during the active season.

Ma Luo from the University of Mannitoba discussed evolutionary interactions between HLA alleles and HIV-1 infection within an East African sex worker population. She studied women from the Pumwani sexworker cohort (high prevalence) and a mother-child cohort (low prevalence). They examined linkage of HLA class I alleles to the risk of seroconversion during the study and grouped these into “protective” and “susceptible” alleles. Over time (1985-1992 vs. 1993-2001) there was a decrease in the susceptible allele prevalence and an increase in the protective allele prevalence in the high-risk cohort.

Molly OhAinle talked about the evolution of the APOBEC3 locus of anti-retroviral elements in hominids. She presented evidence that the anti-retroelement of APOBEC3H, which is a broadly active member of the family, has undergone very recent changes. Macaque APOBEC3H efficiently inhibits HIV infectivity, which human APOBEC3H does not. The loss of this activity of APOBEC3H appears to have occurred independently at least twice in recent human evolution. Human APOBEC3H is considerably less stable than that of other primates, which accounts for its lack of activity. Ancestral sequence reconstitution suggests that recent human ancestors had stable (effective) APOBEC3H. Is there selection for non-functional APOBEC3H alleles in the human population?

Bouke de Jong (NYU) examined the phylogeography of the Mycobacterium tuberculosis complex, specifically the appearance of M. africanum in West Africa. By looking at genotypes of organisms from smear-positive tuberculosis (TB) cases and their contacts. A significant portion of TB in the Gambia appears to be caused by M. africanum. There are differences in risk of progression but not transmission or severity when comparing M. africanum with M. tuberculosis.

Joel Wertheim used Bayesian dating strategies to calibrate a molecular clock for SIV evolution. They used envelope and polymerase sequences to develop their model, which allowed specific estimation of dates for divergence of SIV clades as well as HIV-2.

Tsan Yuk Lam discussed transmission dynamics of natural reassortant H5N1 influenza in Indonesia. His analysis is consistent with a single clade arising from a single H5N1 introduction from China. There has been intralineage reassortment within Indonesia over a short time.

Evening Session: Retroviruses

Beatrice Hahn (UAB): Origins of HIV-1 and adaptation to its human host
John Moran (U. Michigan): Studies of a human transposable element (LINE elements)
Nathan Wolfe (UCLA): Cross-species transmission and establishment of novel human retroviruses.
Christine Clouser (U. Minnesota): Short talk: Exploiting the mutation rate of HIV