Laboratory Happenings

Summer

It's that time of year when we take a deep breath and prepare for the onslaught of work that accompanies the start of the academic year in the fall and look back on the past academic year.

We have had a great few months. To note a few recent advances:

  • We continue to learn a lot about Zika virus. We recently showed there is a theoretical risk of oral Zika virus transmission, but that the real-world transmission risk is low to non-existent. In collaboration with Matt Aliota, we developed a system for infecting macaque monkeys using Zika virus-infected mosquitoes. Coupled with a molecularly bar-coded Zika virus we prepared in collaboration with Greg Ebel and colleagues, we are looking forward to understanding the dynamics of Zika virus transmission and replication in pregnant and non-pregnant individuals.
  • Zika virus damages the eyes of fetuses born to mothers infected during pregnancy — does this mean that the risk to human babies is higher than currently thought? Or is this an artifact of the animal model that we study?
  • Exciting new genomics technologies allow us to explore immune genes with unprecedented resolution. We now have Illumina, Pacific Biosciences, Oxford Nanopore, HiC, and 10X Genomics data in the lab. Still learning how to best analyze and integrate all of these new types of data. We have also sequenced entire macaque transcriptomes using Pacific Biosciences isoSeq technology. We hope this will lead to better interpretation of macaque whole exome and whole genome sequencing data. I'm also hoping to replicate our Zika data sharing initiative to provide access to these interesting genomics datasets.
  • The more we learn about simian arteriviruses the more we are convinced they share worrisome features with simian immunodeficiency viruses and should be studied as possible future zoonoses.
  • We are working with several groups to identify viruses and virus-specific antibody responses in human and nonhuman primate samples. Our unique niche in this area is the ability to take interesting observations from sequencing and follow-up with laboratory studies, as we did when we created the first monkey model for understanding pegivirus infections. We have also used exciting new high-density peptide arrays to identify antibodies reactive to both known and unknown viruses; for example, we used this technology to identify regions of strong immunogenicity in Zika virus.

All of these projects are only possible because of the lab's great staff. This time of year is bittersweet, as we have staff transitioning to med school residency, medical school, and veterinary school. I am very excited to see what terrific work they will do in the future but it is sad to see them leave the lab.

If you are reading this because you are considering applying for a position in the lab or are an incoming student, I strongly encourage you to read about our research and my employment philosophy. I think my lab provides a fast-paced, challenging environment for highly motivated scientists who are committed to understanding the interplay of viral pathogenesis, genomics, and immunology.

Zika

A lot has happened in the past few months. Starting last November, we began working on a nonhuman primate model for studying Zika virus. We were fortunate to receive funding from NIH and pilot funding from the Wisconsin National Primate Research Center to support these studies. In turn, we made our results available to the community in real-time at http://zika.labkey.com/. A preprint of our first manuscript describing our efforts is available through Biorxiv and will hopefully be published in a peer-reviewed journal soon. There has been a lot of interest in both the data, our opinions about Zika virus research, and our decision to share it publicly. This has lead to an unusual amount of media attention, including:


Our work was even mentioned indirectly during a White House press conference!

In addition to Zika virus work, we've also been very busy studying macaque genetics and genomics. We are aggressively moving towards Pacific Biosciences long-read transcript sequencing for major histocompatibility complex and killer immunoglobulin receptor genotyping and allele discovery, work that will be funded by a newly awarded contract renewal from the National Institutes of Allergy and Infectious Diseases. Meanwhile, Michael Graham has been prototyping a new "virtual reality" browser that uses an Oculus Rift to visualize variation in human and macaque genomes. Also, lots of congratulations to go around….



I have also been busy since the start of the year, talking about our research at the:


Now that the summer is here I hope we will have time to take a deep breath for the first time in several months!

Chill

It's mid-November. Madison is getting cold again and everyone is preparing for another long winter. The best part of seasons in Madison is that each one has a distinctive character. Most years, I feel like these long days of winter are among the most productive, while in the summer it is more relaxed as people spend time outside.

2015 has been very busy. Many senior staff have had the opportunity to make exciting career transitions. Matt Reynolds, a Scientist in the lab, received his own NIH R01 grant to explore alloimmunization as an HIV vaccine. Adam Bailey successfully defended his PhD thesis and returned to med school to complete his MD. Justin Greene accepted a scientist position at the Oregon Health and Sciences University working with longtime friend of the lab Jonah Sacha. Finally, after our lab visited Promega Corporation this summer to discuss possible collaborations Michael Lauck was sufficiently impressed with their work that he joined their team. While these transitions are difficult for our lab, I'm delighted to see members of the lab advance and succeed in their careers.

Though we've had personnel turnover, it has been a productive year. We recently published a review paper on simian arteriviruses. Earlier in the year, we described the first animal model for human pegivirus infection and recently received a new NIH R01 grant to further develop this model. Understanding cellular immunity to HIV/SIV remains a priority and we continue to study cellular adoptive transfers and define CD8+ and CD4+ T cell epitopes. We are also doing a lot of work with immunogenetics and genomics. With help from the Center for High Throughput Computing, we used thousands of CPUs to analyze whole genome and whole exome sequences from hundreds of macaques. Technologically, the biggest change in the year has been our adaptation of Pacific Biosciences deep sequencing to characterize full-length MHC, KIR, and FCGR transcripts. For the first time, we are able to catalog hundreds of novel allelic variants at these loci, which will hopefully improve out understanding about how variation in these genes influences infectious disease resistance.

If you are reading this in anticipation of applying to do PhD research at UW-Madison in 2016, I am most likely to take students with three or more years of independent funding because this allows students the greatest flexibility in developing a research project that matches their interests. I have had open PVLs for technicians and scientists throughout 2015, so if you are interested in joining our team with a BS or PhD, I encourage you to apply or contact me for additional information. I seek motivated, talented, creative, team-oriented individuals who are interested in conducting world-class infectious disease research.

Refresh

It's been a while since I've updated the main page, but it isn't from lack of activity in the lab. The last year has been really eventful. Some highlights include:

- Several lab staff moving on to new opportunities in graduate and medical school
- Developing the first animal model for studying GB virus C…and showing that GBV-C may protect from Ebola mortality
- Discovering simian arteriviruses in captive baboons and new populations of wild primates
- Publishing a new method for studying HIV drug resistance efficiently
- Using whole genome sequencing to look for new genes associated with spontaneous HIV/SIV control
- Working towards characterizing all the genetic variation in Mauritian macaques
- Characterizing full-length major histocompatibility complex transcript and gene sequences using a variety of deep sequencing platforms.

I'm writing this on the heels of a busy fall of travel, which included trips to Cape Town, Washington D.C., Rio de Janeiro, Portland, and Sao Paulo. It is great fun to have such wonderful collaborators and colleagues to visit around the world.

Finally, I know this is the time of year when many people who visit my website are applying to UW-Madison for graduate school. Here is a short FAQ for you:

Are you taking new graduate students in fall, 2015? I will consider taking students who have three years or more independent funding. Most incoming students do not realize that it costs a lab like mine about $50,000 a year to support a graduate student. During the first two years, when students are taking classes and have other programatic requirements, time in the lab is limited - making the effective cost of a PhD student even higher. Moreover, students who have their own funding can have more flexibility by developing projects that are not funded by existing grants.

I am interested in your lab. Can I be directly admitted? No. I believe rotations in multiple labs are essential. Consequently, I do not accept students from programs that require one-on-one matching between students and investigators as a criteria for acceptance to UW-Madison.

What skills should a prospective student bring to the lab? See my graduate student philosophy, which still holds up pretty well even though I initially wrote it nearly ten years ago. It is now also essential that prospective students have a strong quantitative background because of the large datasets we are generating and analyzing. This doesn't mean you need to be an expert computer programmer when you join the lab, but it means you must be comfortable learning how to work with large datasets, command line tools, and basic programming (e.g., Python)


Happy ThanksTWiVing

Hi to anyone who is visiting this site after listening to This Week in Virology. It was great to have an opportunity to discuss our research. I’ll use Google Analytics to see if get a TWiV bump! If anyone is interested in getting more frequent updates on our work, I encourage you to follow me (@dho) on Twitter.

Here are a few links to topics we discussed on TWiV:

- Michael’s original paper on simian hemorrhagic fever viruses in red colobus monkeys [congrats to Michael, who finished his PhD in August!]
- Haddock and Dunn’s outstanding book ‘Practical Computing for Biologists
- information about the Illumina miSeq deep sequencer
- articles with my Brazilian friends describing deep sequencing of dengue, HIV [note, while looking for this URL I stumbled across an article in GenomeWeb I didn’t know existed!], and hepatitis C viruses

...and finally, my pick of the week (which didn’t make the podcast, unfortunately)...the Sonos Wireless Speaker System, which we just used to listen to TWiV in every room of our house!

It’s been a few months since the last website update, so here’s a quick summary of what we have been doing...

A lot of our time has been spent analyzing whole genome sequencing data from 20 SIV+ Mauritian cynomolgus macaques. These datasets are huge! Thanks to the outstanding best practices tutorials from the Broad Institute, we’ve begun calling and analyzing variants from these datasets. Adam Ericsen, Salendra Singh, and two rotating graduate students, Shelby Malone and Nick Florek, have done a great job exploring a possible relationship between a genomic region containing the granzyme B gene and control of SIV replication. The simple genetics of Mauritian macaques are ideal for exploring how immune genetics influence infectious disease resistance.

Our genetics team has also been working hard to understand macaque MHC diversity. Dawn Dudley described a new technique for identifying full-length MHC transcripts by deep sequencing (sorry about the paywall), we hosted a workshop to train other labs on macaque MHC genotyping, Patrick Bohn and Julie Karl presented new macaque genotyping methods at conferences, and Roger Wiseman wrote a review article summarizing our understanding of macaque MHC genetics (again, sorry about the paywall).

The last few months of virus discovery have also been productive. We helped explain the mysterious death of Mahal, an orangutan at the Milwaukee County Zoo. As part of our Kibale collaboration, we helped identify new pegiviruses in people, a novel hepacivirus in black-and-white colobus, novel SIV variants in black-and-white colobus (with a commentary), and divergent hepatocystis lineages in a variety of Kibale nonhuman primates. Michael Lauck, Sam Sibley, and Adam Bailey now have DNA viruses from Kibale monkeys in their sights; expect more news on these viruses by this time next year.

One of the most provocative new developments in the last year has come from our (as yet unpublished...sigh) studies of GB virus C in Kibale monkeys. This dovetails very nicely with research our colleague Esper Kallas is doing with GBV-C in Brazil and we are currently in the process of planning a series of collaborative studies together. Is GBV-C a “Good Boy” virus? An innocent bystander that just happens to be in the blood supply? Something else entirely? It is shaping up like these questions will be a major theme in Adam Bailey’s PhD project.

Finally, the last few months have been great fun. In addition to teaching our undergraduate class on HIV this fall (and getting a nice write-up of it in On Wisconsin!), we hosted a steady stream of visitors in addition to Vincent Racaniello: Jeff Rogers from Baylor, Jack Stapleton from the University of Iowa, and Ron Desrosiers (newly of the University of Miami). Shelby and I had the good fortune of visiting Atlanta and Sao Paulo to meet with collaborators a few weeks ago and I’m really excited to see how these joint research projects develop. In addition, I was delighted to learn that both of my graduate students received training grants this fall. Adam Ericsen is now a Virology Training Grant predoctoral trainee, while Adam Bailey received a Cellular and Molecular Pathology Training Grant.

Not but not least, I’m finally back to full productivity after spending most of the year coping with debilitating migraine headaches triggered by, among other things, blue light emitted from LCD screens and fluorescent light fixtures. If I ever give up virology, it will be to pursue the inexplicable but most certainly real relationship between allergies and migraines. It turns out that my migraines began within a month of discontinuing Zyrtec last winter and persisted until this fall when I began taking Zyrtec again for seasonal allergies. For the better part of the year, I couldn’t use iPads and had to severely limit how much time I spent staring at screens [as an aside, f.lux, which reduces the amount of blue light from computer monitors, single-handedly allowed me to remain productive]. While I’m not one to generalize from anecdotes, I do wonder whether others will experience similar migraine issues triggered by screens in the future. If so, my former technician Alex Blasky has coined the term ‘iGraines’ to describe them.

...and here are a few pictures from the last few months:
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Transitions

It’s a summer of transitions in the lab. Five of our staff are leaving. Three are going to medical school, one is going to graduate school, and one is pursuing a new career opportunity. In addition, a research associate in my wife Shelby’s lab also left to train as a Pathology Assistant. She was one of our first undergraduates back in 2006 and has seven years of accumulated knowledge about how our labs work. We are of course sad to see so many staff move on, but are delighted to see them continue their education and careers.

Next month, AVRL will be welcoming our friend David Evans. David and I have known each other since we were both graduate students training under David Watkins. I’m ecstatic to have David moving to Madison. He is a great friend and will soon be a wonderful colleague and member of our lab neighborhood.

The lab continues to do well. Congratulations to Julie, whose paper on Chinese rhesus macaque MHC genetics was recently published. Senior graduate student Michael has two papers already published this year, with another three in preparation. We have also published papers with our collaborators Brandon Keele and Tony Goldberg. It’s been a busy few months!

More locally, we also helped our UW-Madison veterinary colleagues and the Milwaukee Zoo identify a novel tapeworm that caused the unexpected death of a young orangutan. An article about this collaboration is here.

Finally, this summer I’m teaching a building-wide mini-course on computing. The course uses the excellent “Practical Computing for Biologists” book as its main text. I highly encourage students and researchers interested in my lab’s type of work to invest time to read and understand this book’s topics.

Recruiting

It’s been a whirlwind few months. Last fall I welcomed two new PhD students, Adam Ericsen and Adam Bailey, to the lab. Both are energetic and eager to begin working on their thesis research. If you are reading this as a prospective graduate student, I still anticipate taking only students with three or more years of independent funding this fall.

Research has been going very well. We have sequenced the entire genomes of nearly 20 Mauritian macaques and are currently learning how to analyze these massive datasets. Our work discovering novel viruses in Kibale has led us to a new interest in GBV-C, an apparently harmless virus that seems to offer some protection from AIDS mortality. We were also implicated in studying a virus that could be more ‘deadly, untreatable than Ebola.’ So I can cross ‘do research that could threaten all of humanity’ off my bucket list (note that the article is wildly and irresponsibly exaggerated). We continue to generate lots of MHC and virus sequencing data on the lab’s Illumina miSeq…figuring out how to manage this deluge of data is a pressing challenge right now.

I’m excited to report that several members of the lab are going to be starting medical school in the fall, so I may be hiring at least one research technician this summer. If you are graduating in May and are interested in working for us, please contact me so I can notify you of openings. Note that I am not going to sponsor visas for international scientists for technician positions.

Lastly, I looked at the website’s analytics yesterday. More than 5,000 people visited this site last year, from all over the world. I’m impressed and humbled that people from so many different countries care about what we do.

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Heat waves

It is our typical summer of transitions. Several valued members of the laboratory are leaving to start the next chapter of their careers, while others will be joining the lab. Melisa Budde (biotech startup), Simon Lank (medical school), Adam Ericson (graduate school), Hannah Creager (graduate school), and Brittney Golbach (medical school) are all departing this summer. They will be missed! We recently welcomed two new undergraduates to our team and our first MD/PhD student, Adam Bailey, will be joining this fall.

Scientifically, the last few months have been exciting. Dawn Dudley published a paper describing the use of Roche/454 deep sequencing to study HIV drug resistance. Our projects describing novel viruses in African primates and understanding immune genes of humans and primates have exciting new data. Much of this data has been collected on our Illumina miSeq, a benchtop DNA sequencer that generates 10,000,000 sequence reads per instrument run! Considering we were only studying 96 sequences per run a few short years ago, this has created a new informatics challenge for the lab. Last week I even gave a talk to Illumina about the challenges of working with this type of data in an academic lab. If you had told me a few years ago that I’d be sequencing genomes dengue, HIV, hepatitis C, influenza, and a bunch of crazy novel viruses in my own lab, I wouldn’t have believed you!

A brief note to prospective graduate students. If you are interested in my lab, I strongly encourage you to read my graduate student philosophy and review my CV. Training graduate students is one of the best parts of running an academic laboratory. Unfortunately, the current funding climate is difficult for everyone. We are fortunate to have research support from NIH, but there is a strong possibility that NIH will take steps to more evenly distribute funding in coming years. For more details from NIH’s perspective, read this. In all likelihood, this will cause large labs like mine to downsize. Even though this will negatively affect the productivity of my group, I support the concept of funding more investigators in these difficult times.

A consequence of this probable change in NIH policy is that it will be increasingly difficult to support PhD students on Research Assistantships, particularly in pre-dissertator years when laboratory research time is split with courses and other obligations. Therefore, beginning this fall I plan on limiting rotation opportunities to students who have three or more years of independent financial support.

On the road again

The first few months of 2012 have been incredibly busy for the O’Connor lab. Our collaboration with Tony Goldberg and Tom Friedrich to discover new viruses brought me (along with graduate student Michael Lauck) to Kibale, Uganda in late January.

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While we were off in Africa, lab members were busy in the lab. We were involved in three recent publications:

Johnson, Z. P., R. D. Eady, S. F. Ahmad, S. Agravat, T. Morris, J. Else, S. M. Lank, R. W. Wiseman, D. H. O’Connor, M. C. Penedo, C. P. Larsen, and L. S. Kean. 2012. Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets. Immunogenetics 64:329-336:

Lauck, M., M. V. Alvarado-Mora, E. A. Becker, D. Bhattacharya, R. Striker, A. L. Hughes, F. J. Carrilho, D. H. O’Connor, and J. R. Rebello Pinho. 2012. Analysis of Hepatitis C Virus Intra-Host Diversity Across The Coding Region by Ultra-Deep Pyrosequencing. J Virol

Mudd, P. A., A. J. Ericsen, B. J. Burwitz, N. A. Wilson, D. H. O’Connor, A. L. Hughes, and D. I. Watkins. 2012. Escape from CD8+ T Cell Responses in Mamu-B*00801+ Macaques Differentiates Progressors from Elite Controllers. J Immunol

…with several more in the pipeline.

We were also saddened by the departure of Dr. David Watkins, a longtime mentor, colleague, and friend, for the University of Miami at the start of 2012. The entire lab wishes David the best of luck with this new chapter of his career. Two of David’s staff members elected to stay in Madison, so Dr. Matt Reynolds joined our lab in February and Adam Ericson joined our lab briefly to finish his MS thesis.

Spring will bring more interactions with other HIV labs. Melisa Budde presented recent data at the Conference on Retroviruses and Opportunistic Infections, while I presented some of this data at the Palm Springs Symposium on HIV/AIDS. In about two weeks, Shelby O’Connor and I will visit our colleagues in Brazil and participate in a short course on HIV pathogenesis. Busy times all around!

More Changes

It has been a great year for HIV prevention research thus far. A trial studying early HIV treatment in Africa proved the long-held speculation that HIV treatment IS HIV prevention. Real-world circumcision data demonstrated that reductions in HIV incidence could be achieved outside of clinical trials. And two studies show that treating high-risk heterosexuals with anti-HIV drugs can substantially reduce HIV acquisition. Nonetheless, the need for an HIV vaccine remains strong. All of these interventions, save for circumcision, rely on consistent behavioral modification. Circumcision does not, but its protection is not absolute nor is it useful for women. So we remain steadfast in our work and our hope that it can help inform vaccine development.

The lab is celebrating many transitions. Paul Hines, who has worked with us since last summer, recently left the lab to start medical school at the University of Minnesota. Ben Burwitz is leaving to work in Jonah Sacha's laboratory at the Oregon Health Sciences University. Ben will be deeply missed, as he has been in the lab since 2007 and developed much of our immunology expertise. Finally, Shelby O'Connor has accepted an Assistant Professor position at the University of Wisconsin-Madison and will be starting her own lab in September. Fortunately, she will not be moving far - her lab will remain in the AIDS Vaccine Research Laboratory, where she will share space with us, David Watkins's, and Thomas Friedirch's groups!

We welcomed four new staff to replace Paul (I did say he was valuable) and add support to newly funded projects. Ngoc Pham, Brian Cain, Matt Scarlotta, and Gabe Starrett are all acclimating to the lab. I'm certain you will be hearing more from them in upcoming blog updates.

We've had a number of new papers to celebrate (citations at the bottom of the post). Some come from our collaborators and some were written by members of our lab. Another two papers are currently out for review, so we are well on track to have a very productive 2011.

Moreland, A. J., L. A. Guethlein, R. K. Reeves, K. W. Broman, R. P. Johnson, P. Parham, D. H. O’Connor, and B. N. Bimber. 2011. Characterization of killer immunoglobulin-like receptor genetics and comprehensive genotyping by pyrosequencing in rhesus macaques. BMC Genomics 12:295: PMC3125267.

Budde, M. L., J. J. Lhost, B. J. Burwitz, E. A. Becker, C. M. Burns, S. L. O’Connor, J. A. Karl, R. W. Wiseman, B. N. Bimber, G. L. Zhang, W. Hildebrand, V. Brusic, and D. H. O’Connor. 2011. Transcriptionally abundant major histocompatibility complex class I alleles are fundamental to nonhuman primate simian immunodeficiency virus-specific CD8+ T cell responses. J Virol 85:3250-3261: PMC3067831.

Burwitz, B. J., Z. Ende, B. Sudolcan, M. R. Reynolds, J. M. Greene, B. N. Bimber, J. R. Almeida, M. Kurniawan, V. Venturi, E. Gostick, R. W. Wiseman, D. C. Douek, D. A. Price, and D. H. O’Connor. 2011. Simian immunodeficiency virus SIVmac239Deltanef vaccination elicits different Tat28-35SL8-specific CD8+ T-cell clonotypes compared to a DNA prime/adenovirus type 5 boost regimen in rhesus macaques. J Virol 85:3683-3689: PMC3067854.

Fernandez, C. S., J. C. Reece, U. Saepuloh, R. De Rose, D. Ishkandriati, D. H. O’Connor, R. W. Wiseman, and S. J. Kent. 2011. Screening and confirmatory testing of MHC class I alleles in pig-tailed macaques. Immunogenetics 63:511-521:

Greene, J. M., R. W. Wiseman, S. M. Lank, B. N. Bimber, J. A. Karl, B. J. Burwitz, J. J. Lhost, O. E. Hawkins, K. J. Kunstman, K. W. Broman, S. M. Wolinsky, W. H. Hildebrand, and D. H. O’Connor. 2011. Differential MHC class I expression in distinct leukocyte subsets. BMC Immunol 12:39:

Reed, J. S., J. Sidney, S. M. Piaskowski, C. E. Glidden, E. J. Leon, B. J. Burwitz, H. L. Kolar, C. M. Eernisse, J. R. Furlott, N. J. Maness, A. D. Walsh, R. A. Rudersdorf, W. Bardet, C. P. McMurtrey, D. H. O’Connor, W. H. Hildebrand, A. Sette, D. I. Watkins, and N. A. Wilson. 2011. The role of MHC class I allele Mamu-A*07 during SIV(mac)239 infection. Immunogenetics

Colantonio, A. D., B. N. Bimber, W. J. Neidermyer, R. K. Reeves, G. Alter, M. Altfeld, R. P. Johnson, M. Carrington, D. H. O’Connor, and D. T. Evans. 2011. KIR Polymorphisms Modulate Peptide-Dependent Binding to an MHC Class I Ligand with a Bw6 Motif. PLoS Pathog 7:e1001316: PMC3053351.

Creager, H. M., E. A. Becker, K. K. Sandman, J. A. Karl, S. M. Lank, B. N. Bimber, R. W. Wiseman, A. L. Hughes, S. L. O’Connor, and D. H. O’Connor. 2011. Characterization of full-length MHC class II sequences in Indonesian and Vietnamese cynomolgus macaques. Immunogenetics

Changes

Summer is here and the lab is once again in an enjoyable transition. Technician Paul Hines is leaving to start medical school in the fall. He will be replaced by Ngoc Pham, who will be joining us from the East coast. Two other grants were recently funded in the lab, paving the way for us to hire two other technicians who will be starting later this month. Finally, a grant we wrote to compare a human genetic typing method we developed (using Roche/454 sequencing to study HLA genes, for those of you with a scientific bent) was just funded. Simon Lank, who has been developing this method in our lab, will be the lead technician on this new project.

In addition, we are celebrating several new research manuscripts that have been published in the last few months. Michael Lauck published his first paper as a PhD student, describing a novel simian hemorrhagic fever virus in colobus monkeys living in Uganda. This paper is particularly exciting for us because it is the first (of hopefully several) papers produced in collaboration with Drs. Thomas Friedrich and Tony Goldberg. Together, we hope to identify new viruses in primates living in forest fragments in Uganda.

We continued our good run of undergraduate first author manuscripts earlier this month, when Hannah Craeger’s paper describing MHC class II genes in cynomolgus macaques from different locations appeared in Immunogenetics. Congratulations to Hannah and the rest of her research team!

Members of the lab also appeared as authors on papers from Stephen Kent’s group at the University of Melbourne and Dave Evans’s group at the New England Primate Research Center. As always, details on our most recent papers are available from the ‘Lab Publications’ link.

Despite a very productive 2011 to date, we are also remembering that it was 30 years ago this June when HIV was first officially documented. While the virus undoubtedly circulated for decades before its ‘discovery’, the 30 year anniversary provides a convenient opportunity to look back at the successes and failures of our field, while looking ahead to promising opportunities that may avert millions of infections that would otherwise occur in the next three decades. Male circumcision, female microbicides, ‘treatment as prevention’, improved access to antiretroviral treatment, pre-exposure prophylaxis...the list of potential interventions goes on and on. And, of course, one cannot forget the essential and immutable goal of developing a preventative vaccine that would confer long-lasting immunity against HIV in people who are uninfected.

Good stories on the 30th anniversary of the discovery of HIV here, here, and here.

Recruiting

Just in time for graduate student recruiting, I updated the lab publication list and our research interests. The lab is entering a very exciting time. We just published two manuscripts in the Journal of Virology that used next-generation DNA sequencing to understand macaque MHC genetics and acute phase SIV pathogenesis. We expect to publish additional studies using similar methodologies later this year.

We are also anxiously awaiting the completion of two macaque genome sequences from MHC-identical macaques that had dramatically different control of SIV infection. I don’t yet know how we will analyze the 3,000,000,000 DNA bases from each animal, but hopefully we will start to learn!

I also recently started the UW-Madison Global Infectious Disease working group to bring together campus researchers studying pathogens, primarily viruses, that cause significant disease worldwide. We had our first meeting in early February and had nearly 30 people attend. I’m hoping that this continues to grow in 2011.

Also, the lab has been busy presenting data at conferences and meetings. Emily is giving a poster presentation at the upcoming Conference on Retroviruses and Opportunistic Infections in Boston. I will be going to Boston a week later to present at a Center for AIDS Research symposium. Next month Shelby and I will be traveling to Sao Paulo to teach in an HIV pathogenesis course. Exciting, but tiring!

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.

Haystacking

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.

Whirlwind

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.

Springtime!

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.

Uganda

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.

Snow Day

Today is a rarity; a snow day at UW-Madison. It comes in the middle of a busy week. We hosted a visitor from Israel on Monday and will be hosting another from Rochester on Friday. One of our collaborators from Sao Paulo, Brazil is also visiting until next Wednesday. The next few days will be very hectic.

I’m happy to announce that Michael Lauck has joined the laboratory as a PhD student. The total number of PhD students is unchanged, however, since Ben Bimber defended his PhD thesis successfully on Monday. Congratulations Ben!

Roger and Julie are missing the blizzard as they visit a collaborator in Connecticut. They are the lucky ones!

In other news, we will be presenting our research to the UW-Madison provost next week. Shelby and I gave presentations on our research in Sao Paulo, Brazil two weeks ago and there will likely be several more presentations within the next month. I’m also beginning to make serious arrangements for my upcoming trip to Uganda with Jim Sosman and Tom Friedrich. We are very excited to visit our collaborators in Rakai and Mbarara.

It Starts Anew

So...here we are again. The end of summer is nearly upon us; I inadvertently drove into undergrad move-in preparations yesterday and realized that fall and winter are on the way. Undergrad move-in is a good time to shake the cobwebs off the website and give some updates on our lab. Gosh, where to begin...

First, if you are a graduate student interested in a rotation, please read by graduate student training philosophy and review my research program.

Last month we said goodbye to Claire O’Leary who left our lab to start grad school at the University of Pennsylvania. Ann Detmer left to become an Assistant Track coach at Cal (I imagine it is easy to be a track coach when your runners are motivated by a hungry Golden Bear). Kevin Campbell, a four year undergraduate in the lab, also left to start medical school at the University of Wisconsin School of Medicine and Public Health.

The new faces from earlier this summer are already well integrated in the lab. All four undergraduates supported by ARRA money presented lab meetings on their projects and I have high hopes that most of this work will eventually be published. Claire’s work has already been submitted for publication.

Speaking of publications....we are still anxiously awaiting publication of a high profile manuscript in a journal-that-shall-remain-nameless-because-of-a-manuscript-embargo. In papers that I can talk about, Julie Karl published an MHC techniques paper in the creatively named journal ‘Methods’. Ben Bimber’s paper in collaboration with Ha Youn Lee from the University of Rochester was published in ‘Retrovirology’. In addition to the aforementioned papers in press and under submission, I expect Shelby and Justin to each submit a paper within the next few weeks, with more papers following soon thereafter from Ben Burwitz and Melisa Budde.

We’ve had a fairly relaxing summer in terms of presentations. Dawn Dudley presented her work in South Africa at the 5th IAS Conference on HIV Pathogenesis, Treatment, and Prevention and then traveled to Uganda to meet with potential collaborators in Uganda. But I stayed home this summer - I think this is my first summer without business travel in more than five years! Perhaps this reclusive behavior isn’t by choice? After all, I did give a Neil Diamond themed presentation at Harvard University in April. The acknowledgements video (with help from our friends in the AIDS Vaccine Research Lab) pretty much says it all.

Let’s see...what else...we are very happy to report that an NIH R01 grant that I co-authored with Dr. Tom Friedrich scored very well and may be funded. If the grant is funded, we will explore the importance of broadly directed cellular immune responses in an animal model of HIV/AIDS. In addition, we received a favorable score for a renewal of an NIH R24 application to improve our understanding of macaque genetics. I also contributed to several ARRA applications that received promising evaluations. I think that now I am genuinely done writing grants for a while*.

*(at least 2 weeks)

Lastly, thanks to the miracle of Google Analytics, I still track who comes to visit my lab’s web page. A big thanks to Jen Lhost’s secret admirer, whose google search represents a whopping 12.28% of all traffic to the site in the last month. Also, like Styx, we’re (relatively) huge in Asia.




Craziness

The last few months have been incredibly busy. In addition to the challenges inherent in tracking my 9 month old son, the lab has experienced a surge of productivity that has kept everyone on their toes.

Two manuscripts describing our forays into next-gen DNA sequencing have been accepted for publication in really good journals. Justin Greene is preparing another manuscript for submission, hopefully in the next few weeks. And Julie Karl just published a review article in the journal Methods.

It has also been a busy time for grants. We submitted a renewal of our R24 grant that characterizes MHC genetics in different populations of macaques. We also submitted two grants to the Gates Foundation, one in collaboration with our friend Rodney Phillips, to study HIV evolution by deep sequencing. NIH has awarded us a supplement to support the salaries of five summer undergraduate students and we are awaiting word on several other supplements. Until a week ago, I felt like the grant madness would never cease!

Our nascent international HIV research program is starting to gain traction. We are working with our friends in Sao Paulo to sequence HIV from their patients. We are also working with Dr. Frank Graziano here at the University of Wisconsin to investigate HIV sequence diversity in Ugandan and Wisconsin HIV+ patients. Dawn Dudley will be representing the lab at the 5th IAS Conference on HIV Pathogenesis, Treatment, and Prevention in Cape Town, South Africa in July. She will also be visiting prospective collaborators in Uganda during her time in Africa.

Lastly, it is the time of year when familiar faces leave us and new ones join the team. We will be saying goodbye to Kevin Campbell (med school), Ann Detmer (grad school), and Claire O’Leary in the coming weeks...but we will be saying ‘hi!’ to Ericka Becker (who will be replacing Ann). Hannah Creager and Benji Sudolcan are joining our undergraduate ranks.

Springtime!

In the two months since the last update of this webpage, we’ve been very busy. I spent a week in Washington DC in February, talking about our latest research at NCI and NIAID. I got back to Madison late on Friday night and then turned right around and flew down to Brazil on Monday. Shelby and I taught in a class for Brazilian scientists and clinicians before taking a week of vacation on the Sao Paulo coast. Dawn Dudley accompanied us to Brazil and spent time in research labs expanding the scope of our collaborations with our Brazilian counterparts. We are now eagerly awaiting a return visit from one of their senior scientists in May.

Other individuals in the lab have also been very busy. Ben Burwitz had a manuscript accepted for publication in the Journal of Virology. Congratulations, Ben!!

Also, I refreshed the pictures in the Lab Pictures page.

Phew!

The last two months have been incredibly hectic in the O’Connor Lab. As Shelby and I adjust to having four-month old Eli in our lives, the lab continues to forge ahead.

In December, we wrapped up our teaching for the fall semester. We were very happy with Pathology 210, our 100 student undergraduate course on HIV/AIDS, whose curriculum we completely revamped this year. The day after the final exam, Shelby and I left for the nonhuman primate models for AIDS conference in San Juan, Puerto Rico. The week passed in a blur. I gave a presentation at an NIH NIAID-sponsored satellite meeting on Systems Biology in NHP Research, co-chaired the conference session on Genetics, and watched as two years of planning culminated in a meeting that was well received by nearly all the 250 participants. We’re happy that the meeting we planned went so well, though we’re even more happy that we won’t have to plan another one for several more years!

After we returned from the meeting, we hosted two special visitors in the lab. Susan Gold, a pediatric nurse who does educational outreach in Kenya, met with the lab and toured our facilities. She visited with a colleague, Nicholas Makau, who manages the Nyumbani Villiage, a village for HIV/AIDS orphans. During our discussion, we learned that they have their own laboratory facilities. To see if our work can help their important work in any way, we are sending Simon and Jen from the lab to visit for several weeks in February. This month we were visited by Bob Bowers who told us about living with HIV since 1983. We are definitely lucky to have so many wonderful speakers interested in sharing their experiences with us.

We also had the good fortune of presenting our research to others. Ben Bimber and Julie Karl gave platform talks at the NHP AIDS meeting, while Shelby, Roger, Justin, Dawn, and Ben Burwitz presented posters on their research. Justin, Shelby, and I presented our work to the new UW-Madison Chancellor in late December. Shelby is giving a talk at the UW-Madison Global Health Symposium on our collaborative projects with researchers in Sao Paulo, Brazil. Next month I am going to Frederick, MD and Bethesda, MD to share our most recent research with scientists from NCI and NIAID. Lastly, in early March Shelby and I will be going to Sao Paulo, Brazil to teach in an HIV/AIDS course and spend time with our collaborator Esper Kallas.

In addition, we have been busy with papers and grants. Tom Friedrich and I submitted a grant to study cellular immune responses against HIV. Shelby and Dawn are preparing grants for the Early Career Investigator Scholar Award. Ben Burwitz is preparing a manuscript on his research that will hopefully be submitted next week, while a manuscript describing our MHC typing of macaques using next-generation DNA sequencing will hopefully be submitted tomorrow.

So it has been a busy time around here, but it certainly isn’t dull!

Thanksgiving

Welcome to students who are considering applying to graduate school at the University of Wisconsin-Madison. Hopefully we will meet with some of you later this spring.

The last weeks have been exciting. Shelby and I attended an NIH-sponsored workshop on nonhuman primates and AIDS vaccine design in Washington D.C. The next day, we flew to Miami and attended another workshop on the use of nonhuman primates and organ transplants. We were joined in Miami by Roger Wiseman, Julie Karl, and Ben Bimber from the lab. An exciting outcome from the meeting is that we will hopefully be working closely with dbMHC to create a publicly available resource for understanding nonhuman primate major histocompatibility complex genetics.

Since returning from Miami, we’ve been finalizing preparations for the 26th Annual Nonhuman Primate Models for AIDS meeting that we are co-hosting with the Caribbean Primate Research Center. Going into the last work week before the conference starts, I am happy to report that our planning is complete! Our lab will be well represented at the meeting. Julie Karl and Ben Bimber will be giving platform talks, I will be chairing a session, and Roger Wiseman, Ben Burwitz, Justin Greene, Dawn Dudley, and Shelby O’Connor will present posters.

Crutching

The past two weeks have been interesting. Last Tuesday I sprained my ankle badly playing basketball. Today, nearly two weeks later, is the first day that I can hobble around without an aircast. For the first week after the injury, I was on crutches. Unfortunately, the injury came two days before a trip to New York (to visit IAVI) and Washington D.C. (to visit NIAID). Navigating the Northeast on cructhes isn’t very much fun.

But while I was gone, there was lots of activity in the lab. Ben Bimber’s manuscript on killer immunoglobulin receptors in macaques received a very favorable review. Chad Pendley departed the lab to start medical school at the Medical College of Wisconsin, while Alex Blasky left to start a PhD program at the University of Colorado-Denver. Very soon, their replacements Ann Detmer and Jen Tuscher will arrive. Now we await the start of the academic year that will coincide with Shelby’s due date. Managing the responsibilities of lab with the responsibilities of parenthood promises to be interesting.

Busy as a Bee

In the last few years, I’ve discovered that fewer and fewer hours at work are mine - most of the time I’m either coming from a meeting or going to a meeting. And when I’m not in meetings, I’m being asked about my availability for yet more meetings. It sometimes feels strange anything gets accomplished at all. And while I need to attend meetings, I’m trying to be a bit more saavy in scheduling. To wit, notice the newest addition to my toolbar, ‘Dave’s Schedule.’ This handy link takes my calendars and puts them into an HTML viewable form (without disclosing what I’m actually doing). Hopefully this will simplify meeting planning, if only a little.

In other news, at night we now face the age old struggle - work on our soon-to-be-due grants or watch DVDs of ‘How I Met Your Mother’. The last two nights, Doogie has won.

Eritrea!

A few people have asked about the countries where our visitors have come from. Here is a map showing where their geographic distribution:



We’ve even had a visitor from Eritrea! Soon the sun will never set on the O’Connor lab web empire.

In the last two weeks we submitted a manuscript for consideration by the Journal of Immunology. Hopefully the reviewers will like it. Even if they don’t, the lead author, Ben Bimber, probably won’t care too much since he is getting married this weekend! Congratulations Ben!

Shelby is still very pregnant, though both of us are scurrying to submit grants for the September 7 NIH deadline.

We are also starting to prepare for this fall’s offering of the UW-Madison undergrad class Pathology 210: HIV: Sex, Science, and Society that I am coordinating along with Dr. Tom Friedrich.

Lastly, we are preparing for this year’s nonhuman primate models for AIDS meeting in December. I am co-chairing the meeting with help from staff at both UW-Madison and the Carribbean Primate Research Center. Early response is incredibly positive. We are a month away from the abstract deadline and already we are running short of hotel rooms for the nights immediately before and after the meeting.

We're Huge in Asia!

We now have more than a month of tracking data from Google Analytics. It is amazing to me how far-flung some of our visitors are. Our little lab web site has been visited by people from places that I couldn’t point to on a map (Carlisle, UK? Kuantan, Malaysia? Really?).

I’m writing this at the tail end of the long Independence Day weekend. Though I frittered my Sunday away watching the Wimbledon finals, the lab has been positively hopping the last few weeks. With Alex Blasky and Chad Pendley weeks from starting grad school and med school, and their replacements already busy at work, we have never seemed like such a large lab before. Hopefully we haven’t reached our carrying capacity yet!

Let’s see...other news:

• Alex Blasky had his paper on reference-strand mediated conformational analysis accepted for publication at Immunogenetics
• Ben Burwitz passed his graduate school Prelim A with aplomb
• Ben Bimber is preparing a paper for submission to the Journal of Immunology while preparing for his upcoming nuptuals
• Shelby O’Connor is now 30 weeks pregnant and looking the part
• We are busily writing grants for the upcoming NIH AIDS grant deadline and bracing ourselves for this fall’s Pathology 210 class

That’s all for now. Big thanks to those of you taking the time to read about our lab from afar.







My Complex

I’ve spent the last week researching an NIH R21/R33 grant I hope to submit in early September. Concentrated researching means shutting off email, closing the door to my office, and trying to stay focused on identifying and reading papers. Terrific software like Bookends makes the process much easier than it used to be, yet it is still tough sledding. Occasionally I look for a diversion. Yesterday I found one - setting up Google Analytics to analyze traffic to this web site after learning of two people who discovered that Shelby and I are expecting from reading this lab web page.

That just can’t be right, so I decided to investigate it (you see, I’m a scientist. That’s what I do. I investigate things). I thought that stats would show that no one visits the site except for wayward students and people from the lab. It turns out that I might have been wrong - while we certainly aren’t ESPN.com, we’ve logged more traffic than I expected. Which puts me under pressure to make sure that I keep this page updated. And worry that I’m going to say something wrong. Or accidentally divulge that Chicken McNuggets based HIV vaccine I’ve been working on.

In more germane news, congratulations to Alex Blasky, whose research paper describing a new type of genetic testing recived very positive reviews and will hopefully be published later this year. Alex, Julie Karl, and Justin Greene described their recent research at the UW-Madison Immunology Symposium last week. We also just migrated our lab’s entire information management system from a series of Mac Minis held together by a load-bearing series of firewire cables to a fancy new XServe. I’m excited because I can leverage the new technology to harass the staff twice as much in half the time. Progress!

It's Memorial Day!

It's been an exciting month in the O'Connor lab. In addition my mounting excitement over being a new dad (and Shelby's, of course, of being a new mom!), we have begun planning for a fall semester where we will be on maternity/paternity. Except for the Path 210 class we teach. And except for the NHP AIDS 2008 meeting that we are co-chairing. And except for all the other exceptions that we haven't identified yet! But really, we will be MIA for most of the fall (we hope) as we welcome our newest family member to the world.

Other exciting news:

-Justin Greene's paper on adoptive transfers in nonhuman primates was accepted at PLsS ONE.
-Chad Pendley and Ericka Becker's paper on MHC genetics of Indonesian cynomolgus macaques was accepted at Immunogenetics.
-Ben Bimber and Justin Greene have passed their Prelim B, while Ben Burwitz is gearing up to take his Prelim A at the end of May
-Dawn Dudley submitted a grant application for UW-Madison ICTR Pilot Project Funding
-Joe Mankowski from Johns Hopkins visited us for two days in early May, right before the weather got nice
-Simon Lank and Ann Detmer will be joining the lab as Associate Research Specialists in our Genetics Unit after graduation in May

And the Pirate Monkeys, a soccer team comprised mainly of players from our lab and David Watkins's lab, have started the spring season on a 4-0 tear.

Where in the World is the O'Connor Lab?

As Madison creeps closer to 100 inches of total snowfall this winter, members of the laboratory have been abandoning the city in the name of science! Shelby and I just returned from Sao Paulo, Brazil where we spent a week with our collaborator Esper Kallas. During our time in Brazil, we met with research staff and taught Brazilian scientists and clinicians about HIV pathogenesis and genetics. Now that we are back, Julie Karl and Ben Bimber have left to spend a week working with computer programmers at Connexio in Perth, Australia. Alex Blasky is also out of the lab right now as he vies for graduate school admission.

Even with all the traveling, we have had a very good start to the year. We received NIH R01 funding for a project to study adoptive transfer of vaccine elicited immunity. The Wisconsin National Primate Research Center conducted an exciting site visit of its activities. And I recently received a UW-Madison Vilas Associate Award to support a study of HIV superinfection in collaboration with Dr. Kallas in Brazil. Now we can start to gear up for spring (if winter ever ends!).

Happy New Year!

Happy New Year from your friends in the O'Connor laboratory! Around this time of year we often receive inquiries from prospective students considering graduate study at the University of Wisconsin-Madison. Our laboratory is affiliated with the Cellular and Molecular Pathology program, the Cellular and Molecular Biology program, and, most recently, the Microbiology program. Additionally, we train students in the Molecular Biosciences Training Grant, regardless of their graduate program.

The last few months have been really exciting. Julie Karl's manuscript on Chinese rhesus macaque MHC genetics was published in the journal Immunogenetics. Two of our undergraduate researchers (Chad Pendley and Ericka Becker) are working with Shelby O'Connor to submit a manuscript describing Indonesian cynomolgus macaque MHC genetics. Justin Greene is submitting a third manuscript exploring adoptive transfer in macaques. 2008 is already shaping up as a busy year for publications.

It has also been a busy time for travel. Dave visited Washington D.C. twice and New York in November. Dave and Shelby took a much-needed vacation to Hawaii in December and will be traveling together to Sao Paulo, Brazil in February to lecture on HIV to Brazilian scientists.

Lastly we would like to welcome our newest undergraduate researcher, Kelly Sandman. In other personnel news, Chad Pendley has accepted a full-time position in our laboratory following his graduation in December. Additionally, undergraduate Kevin Campbell recently won a Mary Shine Peterson scholarship to support his continuing research in our laboratory. We are exceedingly proud of our undergraduate's high quality work, but will likely not be hiring any additional students (unless they are exceptionally well-qualified scholastically, GPA > 3.75) during the spring semester.

Free Fallin'

A chill is in the air and the days are getting shorter in Madison. But there is no shortage of work in the lab. Alex Blasky and Justin Greene are preparing manuscripts for submission while Shelby and I just finished hosting Dr. Denis Nansera, a pediatrician from Uganda, and Dr. Esper Kallas, a clinician/researcher from Sao Paulo, Brazil. A crazy and hectic week!

Earlier this month I gave a seminar to transplantation researchers in Washington D.C., a city I will be visiting twice more by the end of November. October was also a busy month for teaching. Shelby and I lectured extensively in Pathology 210, HIV: Sex, Science, and Society and Pathology 803.

The lab is happy to welcome our newest member, Dr. Dawn Dudley, who joins us after getting her PhD in Dr. Eric Arts's laboratory at Case Western Reserve University.

dave

Off the Road Again

In the last month we've had lots of travel. Roger visited our collaborator Dan Geraghty in Seattle and attended the AIDS Vaccine 2007 conference. Meanwhile, Shelby and I visited Kim Hasenkrug in Hamilton, Montana. We got to spend a few days talking about adoptive transfer of cellular immunity, learn about the NIH's Rocky Mountain Labs, and enjoy the natural beauty of western Montana.

Shelby and I submitted 2 NIH R01 applications in the week after we returned from Montana. Now we keep our fingers crossed and hope for the best!

Last week Shelby, Alex Blasky, and I attended the 25th Annual Nonhuman Primate Models for AIDS meeting in Monterey, CA. Outside the meeting (where Dave had a talk and debuted a video previewing next year's conference), we spent time hiking with our friends Stephen Kent from the University of Melbourne and Dave Evans from the New England Primate Research Center. Later the same day we got to snorkel in Monterey Bay with other scientists from the New England Primate Center. Who knew there were so many sea lions in California (not us!)?

Congratulations to Justin Greene who submitted a manuscript in August and also completed his Pathology Department Preliminary Written exam. Julie Karl also submitted a manuscript last month. Hopefully the next website update will reflect the positive peer review of these papers!

Chaotic

I am writing this from the LaGuardia airline terminal in New York. When many flights are delayed - as they are now - the already small gate areas can begin feeling entirely claustrophobic. Combine with two parts screaming babies and a good time is has by all.

I am in New York to meet with our friends at the International AIDS Vaccine Initiative. They provided support for our pilot research into nonhuman primate adoptive transfer experiments and I visited today to give a status update on this project. If all goes well, we will continue our relationship with IAVI into the future.

Last week I also visited with HIV treaters at the Medical College of Wisconsin. If our subsequent interactions are as positive as the ones we had last week, Milwaukee and Madison HIV treaters and researchers may be working together very soon.

In other late breaking lab news, I'm pleased to announce that Dr. Dawn Moore-Dudley, formerly of Dr. Eric Arts' laboratory at Case Western Reserve, will be joining our team in October. Welcome Dawn!

Chaotic

I am writing this from the LaGuardia airline terminal in New York. When many flights are delayed - as they are now - the already small gate areas can begin feeling entirely claustrophobic. Combine with two parts screaming babies and a good time is has by all.

I am in New York to meet with our friends at the International AIDS Vaccine Initiative. They provided support for our pilot research into nonhuman primate adoptive transfer experiments and I visited today to give a status update on this project. If all goes well, we will continue our relationship with IAVI into the future.

Last week I also visited with HIV treaters at the Medical College of Wisconsin. If our subsequent interactions are as positive as the ones we had last week, Milwaukee and Madison HIV treaters and researchers may be working together very soon.

In other late breaking lab news, I'm pleased to announce that Dr. Dawn Moore-Dudley, formerly of Dr. Eric Arts' laboratory at Case Western Reserve, will be joining our team in October. Welcome Dawn!

Returned

We're back in Madison after a week of whirlwind traveling to Florida and Brazil. With classes done, the lab is busier than ever with graduate students and undergrads spending entire days in lab. Hopefully it will be a productive summer!

Congratulations to O'Connor lab alumnus (Sr. Vice President in Charge of Awesomeness) Kendall Krebs -- he tied the knot last weekend and is moving to Cleveland with Christi to work with Dr. Eric Arts.

In a highly anticipated matchup, the original lab soccer team, Incompetent United (with the Drs. O'Connor, Ben Burwitz, and Chad Pendley), solidly thrashed the motley upstart lab team the Long-Term Non-Progressors (which includes Alex Blasky, Justin Greene, and Ericka Becker) 3-1. Rumor has it that the LTNP were so distraught that they disbanded their team for the summer.

A few other developments to pass along:

- Undergraduate Chad Pendley won a prestigious Hilldale Undergraduate Research Fellowship for his studies on Indonesian cynomolgus macaque MHC genetics
- 1st year PhD student Ben Bimber was selected to give an oral presentation at the University of Wisconsin Immunology Symposium
- Assistant Scientist Roger Wiseman participated in an NIH think tank on nonhuman primate genetics in late May
- The website for the Knowledge Vaccine Project can now be accessed
- I was just named the Wisconsin Primate Research Center's interim Associate Director for Research Services in addition to my responsibilities as head of the Primate Center's Genetics Service.
- Shelby and I also started a new project with our friends and co-geeks Angie Mabb and Scott Svendsen to simplify supplies purchasing for academic labs. For more details, visit http://www.lab-hound.com.

Grants

New research proposals have been the story of the last few months. We submitted an expanded proposal to the International AIDS Vaccine Initiative, revised a proposal for the MERC New Investigator award program, and submitted our lab's first NIH R01 grant application. This summer will see us writing at least two more grants, an NIH R13 travel grant for the 26th Symposium for Nonhuman Primate Models for AIDS (I am the Scientific Chair!) and revision of a program grant. Needless to say, it has been busy!

In a way, the next few weeks will be more relaxing. I am preparing a talk for the American Association of Immunologists meeting in Miami and a visit to our collaborator Esper Kallas in Sao Paulo, Brazil.

Thawing

The temperature in Madison has finally climbed out of the teens, though we still may see more snow before the end of winter (note added 2/23 - we're supposed to get over a foot of snow this weekend!). The last few months in the lab have been very productive. Roger Wiseman submitted a review article and Shelby O'Connor recently resubmitted a manuscript on Mauritian cynomolgus macaque MHC class II genetics. The two Bens, Bimber and Burwitz, recently joined the lab as graduate students, willingly submitting themselves to several years of working around here. We also hired a new undergraduate researcher, Ann Detmer, bringing our total number of undergrads to four. I am also happy to report that Jason Wojcechowskyj, one of our former technicians, paused his tour of the world long enough to get accepted into graduate school at the University of Pennsylvania. Congratulations Jason!

Growing

Welcome to the O'Connor lab website. We enjoyed a very successful end to 2006. Two papers from our lab were published back-to-back in the Journal of Virology, Roger Wiseman is finalizing a review article for Transplantation Reviews, and Shelby O'Connor is preparing a paper for submission to Immunogenetics. Meanwhile, other members of the lab are pursuing projects including the adoptive transfer of immunity between SIV-infected monkeys, improving tools for studying macaque genetics, and conducting pilot experiments with Affymetrix GeneChips. Three rotating graduate students helped with these projects during the fall semester and at least one of these students will be joining our laboratory in the spring. We look forward to a productive and exciting 2007.

Publishing

Welcome to the O'Connor lab website. The last few weeks have been very good to our lab. The Journal of VIrology accepted two manuscripts detailing the relationship between monkey genetics and SIV infection. Roger Wiseman described some of these results at the Nonhuman Primate Models for AIDS meeting in Atlanta, GA. Shelby and Dave also attended. All three even had a chance to do some sightseeing at the Georgia Aquarium and CNN center. The lab also obtained its first HIV research sample from a volunteer in Madison. Dave is busy reviewing grants, teaching classes, and generally making a nuisance of himself.

Freedom

After several months, I am finally able to edit this webpage from my laptop! With my newfound freedom, I will...um...I guess I don't have much to say right now. We currently have two papers under consideration by the Journal of Virology and are keeping our fingers crossed. As for me, a return trip from New York last week took nearly 12 hours, giving me and my trusty ipod plenty of time to contemplate the larger issues confronting the world, such as 'when and where did kool recruit his gang?' and 'have I always been blind to the quality of early Phil Collins records?'.

Transitions

The summer is coming to an end, and with it comes the annual immigration and emigration of lab personnel. This month we say goodbye to Tobi Gopon and Jason Wojcechowskyj who will be spending the next year overseas. We hope to welcome two to three new lab personnel this fall, including at least one graduate student. If you are a CMB, CMP, or MBTG graduate student interested in my lab, please take a moment to read my graduate student philosophy and consider whether my lab might be a good fit for you.

This has been a terrific summer for research productivity. We prepared two manuscripts for consideration by the Journal of Virology and received approval to conduct HIV research in conjunction with UW-Hospitals and Clinics. Researchers in the lab successfully developed new assays for virus sequencing and genetic testing. We purchased animals for an exciting new vaccine research project and began working with outside labs to help characterize the genetics of their research animals. Hopefully we can continue this momentum into the fall and winter.

Redesign

Wow, it's been several months since the last web page update. The lab has grown dramatically in the last few months. We received a new NIH award to study SIV pathogenesis in genetically defined monkeys and are currently waiting to hear about another manuscript under submission. The lab now has six full-time members and two undergraduates, plus me. We plan on accepting rotating graduate students from the both the CMB and Pathology graduate programs this fall, so if you are reading this and considering labs, please look at my graduate student philosophy.

Anniversaries

It was one year ago this week that Kendall Krebs and I first set foot in my new lab. Our first experiment came about 10 days later, on 2/25/05. Since then, we have grown dramatically -- what started as just the two of us is now me, a lab manager, a PhD student, three technicians, and an undergraduate researcher (even though the website doesn't reflect this reality yet). Our ambitions and goals scaled with our size, we are now characterizing the genetics of different macaque populations, undertaking SIV pathogenesis trials in macaques, initiating HIV research in conjunction with UW-Madison clinicians, and toying with the idea of becoming more involved with HIV preexpoosure prophylaxis research. Phew. Quite a year. On another note, I'd like to welcome any prospective CMB or CMP graduate students who are browsing my website. Madison is a terrific city and the UW-Madison is an outstanding institution for advanced study.

Bustling

It has been two months since our last update. The lab has been exceptionally busy. Tobi Gopon joined our group in mid-October and we have hosted two rotating graduate students from the UW-Madison Department of Pathology. In terms of progress, our first grant, an NIH R24, was awarded late in September. Our lab's first paper was published in the Journal of Immunology. Yesterday, I submitted an invited review article to the new journal Future Virology. I taught several classes throughout October and culminated the month by serving on an NIH study section in Washington DC.

We have also been conducting our first SIV infection trial with Mauritian Cynomolgus macaques. As of now, we are six weeks into the infection and learning new things each and every day.

Repopulation

Since returning from Brazil, the lab has been a hotbed of chaotic activity. Kendall departed to take a job in Chicago, Ben started chiropractor school, Justin began graduate school, and Jason returned to his undergraduate studies. A new crop of talented and capable researchers have been hired to take their place. Nathan Vakharia and Roger Wiseman are already contributing to the productivity of the lab. An eager set of rotating graduate students are circulating through the lab this fall, and we may take one if the fit is right.

We've also received good news on several research fronts. Our Journal of Immunology manuscript on Mauritian Cynomolgus macaques is now in press, while our first studies using these animals are slated to begin in early October. I've been furiously writing grants to help subsidize these preliminary experiments!

Harried

Another month in the O'Connor lab is in the books. We expanded to 4.25 members this month, held our first lab meetings, submitted two grant proposals and one revised manuscript, purchased our first Mauritian Cynomolgus macaques, and participated in educational outreach programs with South Africa.

The pace should relax a little during July. I am participating in the 3rd IAS Conference on HIV Pathogenesis and Treatment in Brazil. After the meeting, my wife and I are spending 10 days on the island of Fernando de Noronha.

In other exciting lab news, Kendall Krebs will be leaving us in August when he moves to Chicago. He is going to continue HIV/AIDS research in the lab of our collaborator, Steven Wolinsky.

Work Opportunities

A section on work opportunities within the lab is now available. In addition to describing the types of employment within the lab, the page describes the lab philosophy and our expectations for its workers.

Submitted

Our lab submitted its first manuscript for peer-review today. While we have been involved in many publications, this is the first one led by Dr. O'Connor. Now we'll keep our fingers crossed and wait the 4-?? weeks until it is peer-reviewed (or returned to us without review right away!).

Welcome

Welcome to the inaugural website of David O'Connor's laboratory. We are members of the Department of Pathology and Laboratory Medicine at the University of Wisconsin-Madison.

Our laboratory plans on studying the pathogenetics of AIDS infection, though right now we are preoccupied with equipping the laboratory and making it functional.

We recently presented results at the 2005 Seattle International Conference on Primate Genomics. A pdf of our presentation is now available.