Recommended Readings: Pardis Sabeti M.D., Ph.D. Friday, Nov 8

Friday, November 8, 2013
3:45 p.m., Caspary Auditorium

Pardis Sabeti M.D., Ph.D.
Senior Associate Member, Broad Institute of MIT and Harvard;
Associate Professor, Center for Systems Biology, Harvard University Department of Organismic and Evolutionary Biology, and Department of Immunology and Infectious Disease at Harvard School of Public Health

Evolutionary Forces in Humans and Pathogens

Recommended Readings:

Empirical Articles

The 100 Genomes Project Consortium. (2010). A map of human genome variation from population-scale sequencing. Nature, 467(7319), 1061–1073. doi:10.1038/nature09534

The International MapMap Consortium. (2005). A haplotype map of the human genome. Nature, 437(7063), 1299–1320. doi:10.1038/nature04226

Grossman, S. R., Andersen, K. G., Shlyakhter, I., Tabrizi, S., Winnicki, S., Yen, A., … Sabeti, P. C. (2013). Identifying recent adaptations in large-scale genomic data. Cell, 152(4), 703–713. doi:10.1016/j.cell.2013.01.035

Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z., Richter, D. J., Schaffner, S. F., … & Lander, E. S. (2002). Detecting recent positive selection in the human genome from haplotype structureNature419(6909), 832-837. doi:10.1038/nature01140

Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., … Gaudet, R. (2007). Genome-wide detection and characterization of positive selection in human populations. Nature, 449(7164), 913–8. doi:10.1038/nature06250

Review Papers

Biswas, S., Akey, J. M. (2006) Genomic insights into positive selection. Trends in Genetics, 22(8), 437-445. doi:10.1016/j.tig.2006.06.005

Kreitman, M. (2000). Methods to detect selection in populations with applications to the human. Annual Review of Genomics and Human Genetics, 1, 539-559. doi: 10.1146/annurev.genom.1.1.539

Nielsen, R., Hellmann, I., Hubisz, M., Bustamante, C., & Clark, A. G. (2007). Recent and ongoing selection in the human genome. Nature Reviews Genetics,8(11), 857-868. doi:10.1038/nrg2187

Sabeti, P. C., Schaffner, S. F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., … & Lander, E. S. (2006). Positive natural selection in the human lineage .Science, 312(5780), 1614-1620. doi:10.1126/science.1124309

Vitti, J. J., Cho, M. K., Tichkoff, S. A., Sabeti, P. C. (2012). Human evolutionary genomics: ethical and interpretive issues. Trends in Genetics, 28(3), 137-145. doi:10.1016/j.tig.2011.12.001

Recommended Readings: Maria M. Mota PhD March 13, 2013

Special Seminar Series

Malaria Infection, Superinfection and Co-infections: From Simple Models to Complex Interactions

Maria M. Mota,   PH.D.

Unit Leader, Malaria Unit

Instituto de Medicina Molecular

Monday      March 18,  2013

Recommended Readings:

Pinkevych, Mykola; Petravic, Janka; Chelimo, Kiprotich; et al.  2012.  The Dynamics of Naturally Acquired Immunity to Plasmodium falciparum Infection.   PLOS COMPUTATIONAL BIOLOGY.   8(10): e1002729   DOI: 10.1371/journal.pcbi.1002729  

 Klein, Eili Y.; Smith, David L.; Laxminarayan, Ramanan; et al.  2012. Superinfection and the evolution of resistance to antimalarial drugs. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES.   279( 1743):3834-3842   DOI: 10.1098/rspb.2012.1064  

 Portugal, Silvia; Drakesmith, Hal; Mota, Maria M. 2011. Superinfection in malaria: Plasmodium shows its iron will.  EMBO REPORTS.  12(12):1233-1242    DOI: 10.1038/embor.2011.213  

van Santen, Susanne; de Mast, Quirijn; Swinkels, Dorine W.; et al. 2011.  Hepcidin in malaria superinfection: can findings be translated to humans? NATURE MEDICINE.  17(11):1341-1341   DOI: 10.1038/nm.2488  

 Portugal, Silvia; Carret, Celine; Recker, Mario; et al. 2011.  Host-mediated regulation of superinfection in malaria.   NATURE MEDICINE.  17(6):732-U126    DOI: 10.1038/nm.2368  

 Templeton, TJ; Keister, DB; Muratova, O; et al.  1998. Adherence of erythrocytes during exflagellation of Plasmodium falciparum microgametes is dependent on erythrocyte surface sialic acid and glycophorins.   JOURNAL OF EXPERIMENTAL MEDICINE.  187(10 ):1599-1609   DOI: 10.1084/jem.187.10.1599

Recommended Readings: Beatrice H. Hahn, M.D.

Friday Lecture Series

Maclyn McCarty Memorial Lecture

Great Ape Reservoirs of Human AIDS and Malaria

Beatrice H. Hahn, M.D., professor, departments of medicine and microbiology,

University of Pennsylvania

 January 25, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Keele, B. F., J. H. Jones, K. A. Terio, J. D. Estes, R. S. Rudicell, M. L. Wilson, Y. Li, et al. 2009. “Increased Mortality and AIDS-Like Immunopathology in Wild Chimpanzees Infected with SIVcpz.” Nature 460 (7254): 515-519

Lee, H. Y., E. E. Giorgi, B. F. Keele, B. Gaschen, G. S. Athreya, J. F. Salazar-Gonzalez, K. T. Pham, et al. 2009. “Modeling Sequence Evolution in Acute HIV-1 Infection.” Journal of Theoretical Biology 261 (2): 341-360

Liu, J., B. F. Keele, H. Li, S. Keating, P. J. Norris, A. Carville, K. G. Mansfield, et al. 2010. “Low-Dose Mucosal Simian Immunodeficiency Virus Infection Restricts Early Replication Kinetics and Transmitted Virus Variants in Rhesus Monkeys.” Journal of Virology 84 (19): 10406-10412

Liu, W., Y. Li, G. H. Learn, R. S. Rudicell, J. D. Robertson, B. F. Keele, J. -B N. Ndjango, et al. 2010. “Origin of the Human Malaria Parasite Plasmodium Falciparum in Gorillas.” Nature 467 (7314): 420-425

Rayner, J. C., W. Liu, M. Peeters, P. M. Sharp, and B. H. Hahn. 2011. “A Plethora of Plasmodium Species in Wild Apes: A Source of Human Infection?” Trends in Parasitology 27 (5): 222-229

Sharp, P. M. and B. H. Hahn. 2010. “The Evolution of HIV-1 and the Origin of AIDS.” Philosophical Transactions of the Royal Society B: Biological Sciences 365 (1552): 2487-2494


Biologists Produce Malaria Vaccine From Algae

Biologists at the University of California, San Diego have succeeded in engineering algae to produce potential candidates for a vaccine that would prevent transmission of the parasite that causes malaria, an achievement that could pave the way for the development of an inexpensive way to protect billions of people from one of the world’s most prevalent and debilitating diseases. Initial proof-of-principle experiments suggest that such a vaccine could prevent malaria transmission.   Read the report of their research in PLoS ONE.