Google Analyzing

The last few months have been exciting. Ben Burwitz successfully defended his PhD in November and Melisa Budde defended hers right before Christmas. The lab has been productive. We have several papers in different stages of review and others that are being written. The work has been presented at several meetings. Ben Burwitz gave talks in New Orleans and Amsterdam, Shelby O’Connor spoke at a meeting in North Carolina, and I just got back from giving a talk in Paris.

It is a very exciting time to be doing HIV research. The recent data showing that a pill a day can reduce acquisition of HIV in men who have sex with men opens up an entirely new tool for HIV prevention. Additional research is needed, to be sure, however it is a landmark result that could have profound implications. With some of the new tools that are available for studying the virus and the immune response, vaccine and pathogenesis research are also progressing very quickly.

Visitors from 45 countries and 41 states have come to this website since September. Thank you and happy holidays to all who have taken the time to learn what we do.


I just fixed a slight display bug that caused all fonts on the website to break for the last few months. It was a small detail, a missing tag on the side of the page. Yet this small, seemingly inconsequential change had profound consequences on the overall appearance of the system, in this case, my website. This isn’t a terrible metaphor for our last few months - we have been collecting massive amounts of sequence data on our Roche/454 GS Junior and are painstakingly going through the data trying to figure out what it means and what clues it harbors for improving our understanding of HIV immunology. Some of this will be presented at the Nonhuman Primate Models for AIDS meeting in New Orleans in two weeks. Ben Burwitz will talk about viral sequencing at the meeting, while Roger Wiseman will discuss advances in our major histocompatibility complex genotyping. Shelby O’Connor and Michael Lauck will present posters describing SIV pathogenesis and novel pathogen discovery, respectively. I’m also going to this meeting to strategize with collaborators and learn more about others’ recent projects. While I’m not keen on scientific meetings in general, this one is loaded with content relevant to our lab.

The start of October has been hectic. Shelby O’Connor presented a poster at the annual CHAVI meeting as part of her Early Stage Investigator grant. While she was gone, Dr. Rodrigo Brindeiro flew to Madison from Rio de Janerio to learn more about Roche/454 viral sequencing. In addition to training Rodrigo, Julie Karl and Simon Lank are preparing to attend the Midwest Association of Core Directors meeting in two weeks.


The summer passed in a blur. It was incredibly busy, but fun. I spent the summer writing. I led an effort to resubmit an NIH NIAID contract to better understand nonhuman primate immunogenetics and the 200 page application was due in early July. I then began working on two NIH grants that were submitted last week. Both of these involved a lot of hard work, but I’m relieved that they are now being reviewed! I ended up submitting the grants from Sao Paulo, where we were visiting our colleague Esper Kallas the week the grants were due. Since Esper was a co-Principal Investigator on one of the grants, it was helpful that we were in the same city at the time of submission. Now I’m hopefully done writing grants for a few months....

...which should allow us to turn attention towards our undergraduate class Pathology 210: Sex, Science, and Society. Nearly 100 students are enrolled this semester and our teaching team is smaller than in years past, due to two maternity leaves. The recent success of a microbicide trial gives us optimistic news to share with the students, though the recession is threatening hard won gains against HIV in many countries. Nonetheless, teaching is a major commitment that takes a lot of time during the fall semester.

In graduate student news, congratulations to Justin Greene who successfully defended his PhD thesis and became Dr. Justin Greene in August. Melisa Budde and Ben Burwitz plan to follow in Justin’s footsteps and graduate by the end of the year. Our ranks are hardly depleted, though, as we recently welcomed Boaz Iga into the lab. Boaz is a lab manager at the Rakai Health Sciences Program in Rakai, Uganda and will be pursuing a PhD in the lab during the next few years.

The last few months have also been very exciting for our research program. Dawn Dudley and Ben Bimber wrote a manuscript describing whole HIV/SIV genome sequencing that was accepted in the Journal of Virology. Melisa Budde wrote a manuscript that demonstrated Roche/454 pyrosequencing can be used to assemble full-length MHC class I allele sequences that has been accepted at Immunogenetics. Finally, Simon Lank published a paper in Human Immunology describing high-throughput MHC typing of humans using Roche/454 pyrosequencing. Several other papers are in preparation and 2010 is shaping up to be a very productive year.

Finally, we have some new projects that are very exciting. We learned in July that our grant to detect novel primate pathogens in collaboration with Drs. Tony Goldberg and Tom Friedrich was funded by the Wisconsin Center of Infectious Diseases, while a collaborative project to sequence to genomes of two cynomolgus macaques in collaboration with Dr. Jeff Rogers at the Baylor Genome Center was initiated earlier this month.

Memorial Day

The last few weeks have been pretty chaotic. I attended meetings in Washington D.C. and Seattle in April. Fortunately, I will be traveling less during the summer, with only one trip planned between now and August. We are busy writing and renewing grants and working with next-generation DNA sequencing. Ben Burwitz from our group presented some of our data at the launch webinar for the Roche/454 GS Junior. Both Ben and Justin Greene are also preparing manuscripts for publication and eagerly anticipating graduation later this year.

The summer is also a time of transition. Two of our staff will be leaving to start Medical School in the fall, while a third will be departing for graduate school. We’re in the midst of interviewing a very impressive set of job applicants. Additionally, we will be hosting an MD/PhD student rotator in July and are preparing for new PhD student Boaz Iga’s arrival from Uganda in late August. Busy times.

Lastly, I appeared on the local CBS news two weeks ago to describe our research and its implications for HIV/AIDS prevention. You can watch the interview here. Very few people visited my website for more information after the interview aired.


The last few months have been exciting. Tom Friedrich, Jim Sosman, and I spent nearly two weeks in Uganda. We visited colleagues at the Rakai Health Sciences Program and Mbarara Hospital. After a few weeks back in Madison, Shelby and I flew to Brazil to teach in a short course on HIV pathogenesis. Several of the other instructors, including Esper Kallas, Kim Hasenkrug, and Mary Carrington, are also collaborators and friends of the lab, so it was good to see them and discuss potential experiments. After a brief break in March, I’ll be going to Washington D.C. and Seattle in April. In Seattle, I’ll be giving an invited presentation at the International Conference on Primate Genomics. Other members of the lab have also been busy. Melisa Budde gave a poster discussion at the 17th Conference on Retroviruses and Opportunistic Diseases in San Francisco, while Dawn Dudley and Justin Greene are presenting posters at the Keystone Symposium on HIV Vaccines. Meanwhile, Roger Wiseman is currently in Munich, Germany presenting recent genetics data at the Analytica 2010 conference.

We have published several papers in the first few months of 2010. A collaborative project describing cell transfer in macaques was published by Claus Ohlen’s group from the National Cancer Institution. Our colleagues at Merck published a paper describing a vaccine trial in macaque monkeys that deepens our understanding of a vaccine candidate that failed to protect people in a large clinical trial. Closer to home, Justin Greene described a comparison of immune cells from the lung and blood of vaccinated macaques in the Journal of Virology. Our close collaborator Austin Hughes performed advanced analyses on a next-generation DNA sequencing dataset that we originally published last May. Finally, Science Translational Medicine published a manuscript suggesting that macaques who mount narrow immune responses fare poorly compared to macaques who mount broader immune responses. This paper was noticed by some journalists. Shelby was interviewed by the Voice of America and Milwaukee Public Radio.

The lab’s research is going very well. We are expanding our collaboration with HIV clinicians in Brazil and recently received more than 100 samples for genetic analysis. We hope to receive similar samples from Uganda later this year. Our studies with simian immunodeficiency virus and macaque genetics are also yielding new insights that we hope will help inform the development of an HIV vaccine.


Exciting times in lab. Justin’s paper was just accepted at the Journal of Virology. Go team! Other manuscripts are pending and out for peer review. Everyone is now back from the holidays and it is bustling in the lab. Just in time for...me to leave! I’m going to Uganda to meet future grad student Iga Boaz and visit long-time colleague and friend Denis Nansera. Tom Friedrich and Jim Sosman are joining me on this trip. It should be fascinating; none of us have been to Uganda before. In the spirit of trying new things, I’m going to setup a little Twitter feed on the right toolbar.