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!