Recruiting
25 January 2013
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.
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.
Heat waves
17 July 2012
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.
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
10 March 2012
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!
.
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
26 July 2011
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
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
05 June 2011
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.
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.