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Old Dominion University

DNA

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Full-Text Articles in Physical Sciences and Mathematics

The Effect Of Metalation On Antimicrobial Piscidins Imbedded In Normal And Oxidized Lipid Bilayers, Ana Dreab, Craig A. Bayse Jan 2023

The Effect Of Metalation On Antimicrobial Piscidins Imbedded In Normal And Oxidized Lipid Bilayers, Ana Dreab, Craig A. Bayse

Chemistry & Biochemistry Faculty Publications

Metalation of the N-terminal Amino Terminal Cu(II)- and Ni(II)-binding (ATCUN) motif may enhance the antimicrobial properties of piscidins. Molecular dynamics simulations of free and nickelated piscidins 1 and 3 (P1 and P3) were performed in 3 : 1 POPC/POPG and 2.6 : 1 : 0.4 POPC/POPG/aldo-PC bilayers (POPC, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine: POPG, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol; aldo-PC, 1-palmitoyl-2-(9′-oxo-nonanoyl)-sn-glycero-3-phosphocholine) bilayer models. Nickel(II) binding decreases the conformation dynamics of the ATCUN motif and lowers the charge of the N-terminus to allow it to embed deeper in the bilayer without significantly changing the overall depth due to interactions of the charged half-helix …

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Analysis Of Subtelomeric Rextal Assemblies Using Quast, Tunazzina Islam, Desh Ranjan, Mohammad Zubair, Eleanor Young, Ming Xiao, Harold Riethman Jan 2021

Analysis Of Subtelomeric Rextal Assemblies Using Quast, Tunazzina Islam, Desh Ranjan, Mohammad Zubair, Eleanor Young, Ming Xiao, Harold Riethman

Computer Science Faculty Publications

Genomic regions of high segmental duplication content and/or structural variation have led to gaps and misassemblies in the human reference sequence, and are refractory to assembly from whole-genome short-read datasets. Human subtelomere regions are highly enriched in both segmental duplication content and structural variations, and as a consequence are both impossible to assemble accurately and highly variable from individual to individual. Recently, we developed a pipeline for improved region-specific assembly called Regional Extension of Assemblies Using Linked-Reads (REXTAL). In this study, we evaluate REXTAL and genome-wide assembly (Supernova) approaches on 10X Genomics linked-reads data sets partitioned and barcoded using the …

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Concordance Between Phylogeographic And Biogeographic Boundaries In The Coral Triangle: Conservation Implications Based On Comparative Analyses Of Multiple Giant Clam Species, Timery S. Deboer, Maria Rio Abdon Naguit, Mark V. Erdmann, Maria Carmen A. Ablan-Lagman, Ambariyanto, Kent E. Carpenter, Abdul Hamid A. Toha, Paul H. Barber Jan 2014

Concordance Between Phylogeographic And Biogeographic Boundaries In The Coral Triangle: Conservation Implications Based On Comparative Analyses Of Multiple Giant Clam Species, Timery S. Deboer, Maria Rio Abdon Naguit, Mark V. Erdmann, Maria Carmen A. Ablan-Lagman, Ambariyanto, Kent E. Carpenter, Abdul Hamid A. Toha, Paul H. Barber

Biological Sciences Faculty Publications

Marine habitats are in decline worldwide, precipitating a strong interest in marine conservation. The use of biogeographic data to designate ecoregions has had significant impacts on terrestrial conservation efforts. However, classification of marine environments into ecoregions has only become available in the last several years, based on biogeographic data supplemented by geomorphology, ocean currents, and water temperatures. Here we use a comparative phylogeographic approach to test for concordant phylogeographic patterns in three closely related species of Tridacna giant clams across the Coral Triangle, the most biodiverse marine region in the world and one of the most threatened. Data from a …

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Molecular And Physiological Responses Of Diatoms To Variable Levels Of Irradiance And Nitrogen Availability: Growth Of Skeletonema Costatum In Simulated Upwelling Conditions, G. Jason Smith, Richard C. Zimmerman, Randall S. Alberte Jan 1992

Molecular And Physiological Responses Of Diatoms To Variable Levels Of Irradiance And Nitrogen Availability: Growth Of Skeletonema Costatum In Simulated Upwelling Conditions, G. Jason Smith, Richard C. Zimmerman, Randall S. Alberte

OES Faculty Publications

Molecular mechanisms that drive metabolic acclimation to environmental shifts have been poorly characterized in phytoplankton. In this laboratory study. the response of light- and N-limited Skeletonema costatum cells to an increase in light and NO3 availability was examined. C assimilation was depressed relative to N assimilation early in enrichment, and the photosynthetic quotient (O2: CO2) increased, consistent with the shunting of reducing equivalents from CO2 fixation to NO3- reduction. The concomitant increase in dark respiration was consistent with the increased energetic demand associated with macromolecular synthesis. The accelerations of N-specific rates of …

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The Role Of The Voltage Gradient In The Agarose Gel Electrophoresis Of Dna, David Wheeler Apr 1990

The Role Of The Voltage Gradient In The Agarose Gel Electrophoresis Of Dna, David Wheeler

Theses and Dissertations in Biomedical Sciences

In Part I of this dissertation, empirical equations for predicting DNA mobility during agarose gel electrophoresis (AGE) from voltage gradient are developed from the data of McDonnel (36) for electrophoresis in a 1.6% agarose gel. These equations represented the data well for DNA between 2 and 10 kilobase pairs (KBp) in length. A computer program, called GELSIM, which incorporates these equations is described in Part II. GELSIM was designed to allow researchers to analyze electrophoresis data by predicting the effect on DNA migration of altering the voltage of electrophoresis. In this way, electrophoretic banding patterns produced using different voltages could …

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Population Variation In The Mitochondrial-Dna Of Two Marine Organisms: The Hard Shell Clam Mercenaria Spp. And The Killifish, Fundulus Heteroclitus, Bonnie Lynn Brown Apr 1989

Population Variation In The Mitochondrial-Dna Of Two Marine Organisms: The Hard Shell Clam Mercenaria Spp. And The Killifish, Fundulus Heteroclitus, Bonnie Lynn Brown

OES Theses and Dissertations

The two major topics are covered in this dissertation: the integration of molecular genetic tools with applied aquacultural research and short-term evolutionary dynamics. The first study investigated the extent of geographic differentiation of native clam stocks along the U.S. east and Gulf coasts. Clam mitochondrial DNA (mtDNA) demonstrated size polymorphism (16.5-19.0 kb) and restriction site heteroplasmy. Size heteroplasmic individuals occurred at a frequencies of 0-89% in clam populations. Restriction site heteroplasmy occurred in 12% of the 317 individuals assayed. Results of the study indicated that although harbouring a wealth of genetic variation, clams from northern regions were similar and lacked …

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