Molecular Biology Commons^™

Environmental Controls On The Diversity And Distribution Of Endosymbionts Associated With Phacoides Pectinatus (Bivalvia: Lucinidae) From Shallow Mangrove And Seagrass Sediments, St. Lucie County, Florida, Thomas Walters Doty

Masters Theses

Lucinid bivalves are capable of colonizing traditionally inhospitable shallow marine sediments due to metabolic functions of bacterial endosymbionts located within their gills. Because lucinids can often be the dominant sediment infauna, defining their roles in sediment and pore fluid geochemical cycling is necessary to address concerns related to changes in coastal biological diversity and to understanding the sensitivity of threatened coastal ecosystems over time. However, there has been limited research done to understand the diversity and distribution of many lucinid chemosymbiotic systems. Therefore, the goals of this thesis were to evaluate the distribution of Phacoides pectinatus and its endosymbiont communities …

An Exploration Of The Phylogenetic Placement Of Recently Discovered Ultrasmall Archaeal Lineages, Jeffrey M. O'Brien

Honors Scholar Theses

In recent years, several new clades within the domain Achaea have been discovered. This is due in part to microbiological sampling of novel environments, and the increasing ability to detect and sequence uncultivable organisms through metagenomic analysis. These organisms share certain features, such as small cell size and streamlined genomes. Reduction in genome size can present difficulties to phylogenetic reconstruction programs. Since there is less genetic data to work with, these organisms often have missing genes in concatenated multiple sequence alignments. Evolutionary Biologists have not reached a consensus on the placement of these lineages in the archaeal evolutionary tree. There …

Positive Selection Drives Preferred Segment Combinations During Influenza Virus Reassortment, Konstantin Zeldovich, Ping Liu, Nicholas Renzette, Matthieu Foll, Serena Pham, Sergey Venev, Glen Gallagher, Daniel Bolon, Evelyn Kurt-Jones, Jeffrey Jensen, Daniel Caffrey, Celia Schiffer, Timothy Kowalik, Jennifer Wang, Robert Finberg

Celia A. Schiffer

Influenza A virus (IAV) has a segmented genome that allows for the exchange of genome segments between different strains. This reassortment accelerates evolution by breaking linkage, helping IAV cross species barriers to potentially create highly virulent strains. Challenges associated with monitoring the process of reassortment in molecular detail have limited our understanding of its evolutionary implications. We applied a novel deep sequencing approach with quantitative analysis to assess the in vitro temporal evolution of genomic reassortment in IAV. The combination of H1N1 and H3N2 strains reproducibly generated a new H1N2 strain with the hemagglutinin and nucleoprotein segments originating from H1N1 …

Translesion Synthesis And Mutations: On The Mutagenic Properties Of The Two Dna Lesions, 8-Oxo-G And Pt-Gg, And The Functions Of Y-Family Dna Polymerases And Rev3l On The Bypass Of Each Of The Dna Lesions In Mammalian Cells, Lizhen Guo

Electronic Thesis and Dissertation Repository

I studied the capabilities of the two DNA lesions 8-oxo-guanine and cisplatin intrastrand crosslinked 1,2-d(GpG) or Pt-GG to cause mutations in mammalian cells. Using isogenic cell lines generated from mice with selective gene knockouts of distinct DNA polymerases as models, I deduced the biological functions of the translesion DNA polymerases Pol eta, Pol kappa, Pol iota, Rev1 and Rev3L on bypassing each of the lesions 8-oxo-G and Pt-GG. My study takes advantage of the Next Generation Sequencing (NGS) technology to determine mutagenic effects of the DNA lesions in vivo and effects of translesion DNA polymerases on bypassing the lesions. Through …

Investigating Notch Signaling And Sequential Segmentation In The Fairy Shrimp, Thamnocephalus Platyurus, Sara Izzat Khalil

Senior Theses and Projects

Segmentation is a key feature of arthropod diversity and evolution. In the standard model for arthropod development, Drosophila melanogaster, segments develop simultaneously by a progressive subdivision of the embryo. By contrast, most arthropods add segments sequentially from a posterior region called the growth zone and in a manner similar to vertebrates.

Recent work, mainly focused on insects, suggests that Notch signaling might play a role in arthropods that segment sequentially. These studies document a potential regulatory similarity between sequentially segmenting arthropods and vertebrates. In vertebrates, somite formation involves a molecular oscillator that functions as a pacemaker, driving periodic expression …

Oxygenation Properties And Isoform Diversity Of Snake Hemoglobins, Jay F. Storz, Chandrasekhar Natarajan, Hideaki Moriyama, Federico G. Hoffmann, Tobias Wang, Angela Fago, Hans Malte, Johannes Overgaard, Roy E. Weber

Jay F. Storz Publications

Available data suggest that snake hemoglobins (Hbs) are characterized by a combination of unusual structural and functional properties relative to the Hbs of other amniote vertebrates, including oxygenation-linked tetramer-dimer dissociation. However, standardized comparative data are lacking for snake Hbs, and the Hb isoform composition of snake red blood cells has not been systematically characterized. Here we present the results of an integrated analysis of snake Hbs and the underlying α- and β-type globin genes to characterize 1) Hb isoform composition of definitive erythrocytes, and 2) the oxygenation properties of isolated isoforms as well as composite hemolysates. We used species from …