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Articles 1 - 7 of 7
Full-Text Articles in Genetics and Genomics
A Machine Learning Approach For Using The Postmortem Skin Microbiome To Estimate The Postmortem Interval, Hunter R. Johnson, Donovan D. Trinidad, Stephania Guzman, Zenab Khan, James V. Parziale, Jennifer M. Debruyn, Nathan H. Lents
A Machine Learning Approach For Using The Postmortem Skin Microbiome To Estimate The Postmortem Interval, Hunter R. Johnson, Donovan D. Trinidad, Stephania Guzman, Zenab Khan, James V. Parziale, Jennifer M. Debruyn, Nathan H. Lents
Publications and Research
Research on the human microbiome, the microbiota that live in, on, and around the human person, has revolutionized our understanding of the complex interactions between microbial life and human health and disease. The microbiome may also provide a valuable tool in forensic death investigations by helping to reveal the postmortem interval (PMI) of a decedent that is discovered after an unknown amount of time since death. Current methods of estimating PMI for cadavers discovered in uncontrolled, unstudied environments have substantial limitations, some of which may be overcome through the use of microbial indicators. In this project, we sampled the microbiomes …
Evolutionary Interpretations Of Mycobacteriophage Biodiversity And Host-Range Through The Analysis Of Codon Usage Bias, Laura A. Esposito, Swati Gupta, Fraida Streiter, Ashley Prasad, John J. Dennehy
Evolutionary Interpretations Of Mycobacteriophage Biodiversity And Host-Range Through The Analysis Of Codon Usage Bias, Laura A. Esposito, Swati Gupta, Fraida Streiter, Ashley Prasad, John J. Dennehy
Publications and Research
In an genomics course sponsored by the Howard Hughes Medical Institute (HHMI), undergraduate students have isolated and sequenced the genomes of more than 1,150 mycobacteriophages, creating the largest database of sequenced bacteriophages able to infect a single host, Mycobacterium smegmatis, a soil bacterium. Genomic analysis indicates that these mycobacteriophages can be grouped into 26 clusters based on genetic similarity. These clusters span a continuum of genetic diversity, with extensive genomic mosaicism among phages in different clusters. However, little is known regarding the primary hosts of these mycobacteriophages in their natural habitats, nor of their broader host ranges. As such, it …
Comparative Population Genomics And Speciation Of Snakes Across The North American Deserts, Edward A. Myers
Comparative Population Genomics And Speciation Of Snakes Across The North American Deserts, Edward A. Myers
Dissertations, Theses, and Capstone Projects
Understanding the process of speciation is of central interest to evolutionary biologists. Speciation can be studied using a phylogeographic approach, by identifying regions that promote lineage divergence, addressing whether speciation has occurred with gene flow, and when extended to multiple taxa, addressing if the same patterns of speciation are shared across codistributed groups with different ecologies. Here I examine the comparative phylogeographic histories and population genomics of thirteen snake taxa that are widely distributed and co-occur across the arid southwest of North America. I first quantify the degree to which these species groups have a shared history of population divergence …
Phylogeny, Systematics And Biogeography Of Short-Tailed Opossums (Didelphidae: Monodelphis), Silvia E. Pavan
Phylogeny, Systematics And Biogeography Of Short-Tailed Opossums (Didelphidae: Monodelphis), Silvia E. Pavan
Dissertations, Theses, and Capstone Projects
Short-tailed opossums (genus Monodelphis) comprise the most species-rich genus of New World marsupials, with 25 currently recognized species. Monodelphis comprise small, terrestrial species collectively widespread in South America, which makes the group potentially informative about biogeographic processes that have shaped the continental fauna. The genus exhibits striking variation in several phenotypic characters, notably pelage coloration, behavior, and reproductive strategies. This diversity is unique among Neotropical marsupials, and makes the group particularly interesting to investigate the evolution and the adaptive significance of phenotypic trait variation. Despite this potential, missing knowledge on phylogeny and basic taxonomy precludes broader studies on evolution …
Comparative Genomics Explains The Evolutionary Success Of Reef-Forming Corals, Debashish Bhattacharya, Shobhit Agrawal, Manuel Aranda, Sebastian Baumgarten, Mahdi Belcaid, Jeana L. Drake, Douglas Erwin, Sylvian Foret, Ruth D. Gates, David F. Gruber, Bishoy Kamel, Michael P. Lesser, Oren Levy, Yi Jin Liew, Matthew Macmanes, Tali Mass, Monica Medina, Shaadi Mehr, Eli Meyer, Dana C. Price, Hollie M. Putnam, Huan Qiu, Chuya Shinzato, Eiichi Shoguchi, Alexander J. Stokes, Sylvie Tambutté, Dan Tchernov, Christian R. Voolstra, Nicole Wagner, Charles W. Walker, Andreas Pm Weber, Virginia Weis, Ehud Zelzion, Didier Zoccola, Paul G. Falkowski
Comparative Genomics Explains The Evolutionary Success Of Reef-Forming Corals, Debashish Bhattacharya, Shobhit Agrawal, Manuel Aranda, Sebastian Baumgarten, Mahdi Belcaid, Jeana L. Drake, Douglas Erwin, Sylvian Foret, Ruth D. Gates, David F. Gruber, Bishoy Kamel, Michael P. Lesser, Oren Levy, Yi Jin Liew, Matthew Macmanes, Tali Mass, Monica Medina, Shaadi Mehr, Eli Meyer, Dana C. Price, Hollie M. Putnam, Huan Qiu, Chuya Shinzato, Eiichi Shoguchi, Alexander J. Stokes, Sylvie Tambutté, Dan Tchernov, Christian R. Voolstra, Nicole Wagner, Charles W. Walker, Andreas Pm Weber, Virginia Weis, Ehud Zelzion, Didier Zoccola, Paul G. Falkowski
Publications and Research
Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals …
Diversity-Dependent Cladogenesis Throughout Western Mexico: Evolutionary Biogeography Of Rattlesnakes (Viperidae: Crotalinae: Crotalus And Sistrurus), Christopher Blair, Santiago Sánchez-Ramírez
Diversity-Dependent Cladogenesis Throughout Western Mexico: Evolutionary Biogeography Of Rattlesnakes (Viperidae: Crotalinae: Crotalus And Sistrurus), Christopher Blair, Santiago Sánchez-Ramírez
Publications and Research
Rattlesnakes (Crotalus and Sistrurus) represent a radiation of approximately 42 species distributed throughout the New World from southern Canada to Argentina. Interest in this enigmatic group of snakes continues to accrue due, in part, to their ecomorphological diversity, contributions to global envenomations, and potential medicinal importance. Although the group has garnered substantial attention from systematists and evolutionary biologists for decades, little is still known regarding patterns of lineage diversification. In addition, few studies have statistically quantified broad-scale biogeographic patterns in rattlesnakes to ascertain how dispersal occurred throughout the New World, particularly among the different major biomes of the …
The Evolution Of The Viral Rna Sensor Oas1 In Old World Monkeys And Cetartiodactyls, Ian Fish
The Evolution Of The Viral Rna Sensor Oas1 In Old World Monkeys And Cetartiodactyls, Ian Fish
Dissertations, Theses, and Capstone Projects
Animals produce an array of sensors patrolling the intracellular environment poised to detect and respond to viral infection. The oligoadenylate synthetase family of enzymes comprises a crucial part of this innate immune response, directly signaling endonuclease activity responsible for inhibiting viral replication. Oligoadenylate synthetase 1 plays a vital role in animal susceptibility to pathogens including flaviviruses such as dengue, West Nile, and hepatitis c virus. This thesis includes a population level analysis of OAS1 diversity within macaque and baboon species followed by a broader survey of the gene in nineteen Old World monkeys. My research found that at the species …