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Articles 1 - 6 of 6
Full-Text Articles in Genetics and Genomics
Able: Blockwise Site Frequency Spectrafor Inferring Complex Population Histories And Recombination, Champak R. Beeravolu, Michael J. Hickerson, Laurent A. F. Frantz, Konrad Lohse
Able: Blockwise Site Frequency Spectrafor Inferring Complex Population Histories And Recombination, Champak R. Beeravolu, Michael J. Hickerson, Laurent A. F. Frantz, Konrad Lohse
Publications and Research
We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide multi-locus data (for example, RADSeq) and can also accommodate arbitrarily large samples. We use simulations to demonstrate the accuracy of this method to infer complex histories of divergence and gene flow and reanalyze whole genome data from two species of orangutan. ABLE is available for download at https://github.com/champost/ABLE.
Integration Of Bmp And Insulin/Igf-1 Signaling Regulates Multiple Homeostatic Functions In Caenorhabditis Elegans, James F. Clark
Integration Of Bmp And Insulin/Igf-1 Signaling Regulates Multiple Homeostatic Functions In Caenorhabditis Elegans, James F. Clark
Dissertations, Theses, and Capstone Projects
The maintenance of homeostatic functions is key to the survival and well-being of an organism. Regulation of homeostasis relies on varied inputs, both intrinsic and extrinsic, to potentiate a web of interconnected signaling relays. Insulin/IGF-1 signaling (IIS) is a well-known regulator of glucose and lipid metabolism, as well as having far reaching effects in other homeostatic mechanisms. On the other hand, bone morphogenetic protein (BMP), a member of the transforming growth factor beta signaling superfamily, is known for its role in differentiation and development, with only recent studies highlighting potential roles in metabolic homeostasis. Here we elucidate new functions for …
The Transcriptome Of The Bermuda Fireworm Odontosyllis Enopla (Annelida: Syllidae): A Unique Luciferase Gene Family And Putative Epitoky-Related Genes, Mercer R. Brugler, M. Teresa Aguado, Michael Tessler, Mark Siddall
The Transcriptome Of The Bermuda Fireworm Odontosyllis Enopla (Annelida: Syllidae): A Unique Luciferase Gene Family And Putative Epitoky-Related Genes, Mercer R. Brugler, M. Teresa Aguado, Michael Tessler, Mark Siddall
Publications and Research
The Bermuda fireworm Odontosyllis enopla exhibits an extremely tight circalunar circadian behavior that results in an impressive bioluminescent mating swarm, thought to be due to a conventional luciferase-mediated oxidation of a light-emitting luciferin. In addition, the four eyes become hypertrophied and heavily pigmented, and the nephridial system is modified to store and release gametes and associated secretions. In an effort to elucidate transcripts related to bioluminescence, circadian or circalunar periodicity, as well as epitoky-related changes of the eyes and nephridial system, we examined the transcriptomic profile of three female O. enopladuring a bioluminescent swarm in Ferry Reach, Bermuda. …
Using Molecular Markers To Trace The Population History Of Volant Organisms At Differing Temporal Scales, Noah A. Burg
Using Molecular Markers To Trace The Population History Of Volant Organisms At Differing Temporal Scales, Noah A. Burg
Dissertations, Theses, and Capstone Projects
Using molecular markers to test phylogenetic and phylogeographic hypotheses is critical for tracking the population origin of invasive, introduced species (Chapter 2, Chapter 4) and to identify the systematic relationships of disparate lineages at both shallow and deep evolutionary time scales (Chapters 3, Chapter 4). In this thesis, Sanger Sequencing was used to generate datasets based on fresh and preserved tissue from specimens collected in the field, as well as museum tissue vouchers granted from various institutions in the US and Europe. In combining these source materials, data were generated for three focal studies: 1) In the first research section …
A Contribution Toward A Global Monograph Of Gyroporus: Taxonomy, Phylogeny, Biogeography, Naveed Davoodian
A Contribution Toward A Global Monograph Of Gyroporus: Taxonomy, Phylogeny, Biogeography, Naveed Davoodian
Dissertations, Theses, and Capstone Projects
Gyroporus (Sclerodermatineae, Boletales, Agaricomycetes, Basidiomycota, Fungi) is a genus of ectomycorrhizal mushroom-forming fungi distributed throughout the world in suitable habitats. Previous attempts to untangle the diversity of this genus proved difficult due to the presence of semi-cryptic species and equivocal results from phylogenetic analysis of ribosomal RNA markers. To overcome these obstacles, a combined taxonomic and phylogenetic (emphasizing protein-coding genes) approach is used here to delimit species and elucidate geographic and evolutionary patterns of Gyroporus. Careful study of relevant literature and herbarium specimens was augmented by field work in North America, Australia, and East Asia for observation and collection …
Regulation Of The Tubulin Homolog Ftsz In Escherichia Coli, Monika S. Buczek
Regulation Of The Tubulin Homolog Ftsz In Escherichia Coli, Monika S. Buczek
Dissertations, Theses, and Capstone Projects
Escherichia coli is a well-known pathogen, and importantly, a widely used model organism in all fields of biological sciences for cloning, protein purification, and as a model for Gram-negative bacterial species. And yet, researchers do not fully understand how this bacterium replicates and divides. Every year additional division proteins are discovered, which adds complexity to how we understand E. coli undergoes cell division. Due to their specific roles in cytokinesis, some of these proteins may be potential targets for development of antibacterials or bacteriostatics, which are much needed for fighting the current global antibacterial deficit. My thesis work focuses on …