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Genomeblast: A Web Tool For Small Genome Comparison, Guoqing Lu, Liying Jiang, Resa M. K. Helikar, Thaine W. Rowley, Luwen Zhang, Xianfeng Chen, Etsuko N. Moriyama
Genomeblast: A Web Tool For Small Genome Comparison, Guoqing Lu, Liying Jiang, Resa M. K. Helikar, Thaine W. Rowley, Luwen Zhang, Xianfeng Chen, Etsuko N. Moriyama
Biology Faculty Publications
Background: Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inference of phylogenetic relationships in a given set of genomes.
Results: GenomeBlast is a Web tool developed for comparative analysis of multiple small genomes. A new parameter called "coverage" was introduced and used along with sequence identity to evaluate global similarity between genes. With GenomeBlast, the following results can be obtained: (1) unique genes in each …
Phycodnaviruses: A Peek At Genetic Diversity, David Dunigan, Lisa A. Fitzgerald, James L. Van Etten
Phycodnaviruses: A Peek At Genetic Diversity, David Dunigan, Lisa A. Fitzgerald, James L. Van Etten
Department of Plant Pathology: Faculty Publications
The family Phycodnaviridae encompasses a diverse collection of large icosahedral, dsDNA viruses infecting algae. These viruses have genomes ranging from 160 to 560 kb. The family consists of six genera based initially on host range and supported by sequence comparisons. The family is monophyletic with branches for each genus, but the phycodnaviruses have evolutionary roots that connect with several other families of large DNA viruses, referred to as the nucleocytoplasmic large DNA viruses (NCLDV). The genomes of members in three genera in the Phycodnaviridae have recently been sequenced and the purpose of this manuscript is to summarize these data. The …
Adaptive Evolution Of Chloroplast Genome Structure Inferred Using A Parametric Bootstrap Approach, Liying Cui, Jim Leebens-Mack, Li-San Wang, Jijun Tang, Linda Rymarquis, David B. Stern, Claude W. Depamphilis
Adaptive Evolution Of Chloroplast Genome Structure Inferred Using A Parametric Bootstrap Approach, Liying Cui, Jim Leebens-Mack, Li-San Wang, Jijun Tang, Linda Rymarquis, David B. Stern, Claude W. Depamphilis
Faculty Publications
Background
Genome rearrangements influence gene order and configuration of gene clusters in all genomes. Most land plant chloroplast DNAs (cpDNAs) share a highly conserved gene content and with notable exceptions, a largely co-linear gene order. Conserved gene orders may reflect a slow intrinsic rate of neutral chromosomal rearrangements, or selective constraint. It is unknown to what extent observed changes in gene order are random or adaptive. We investigate the influence of natural selection on gene order in association with increased rate of chromosomal rearrangement. We use a novel parametric bootstrap approach to test if directional selection is responsible for the …
Rdna Gene Region (18s-Its1-5.8s-Its2-28s) Of Biomphalaria Glabrata, Coen Adema
Rdna Gene Region (18s-Its1-5.8s-Its2-28s) Of Biomphalaria Glabrata, Coen Adema
Biomphalaria Genome Initiative
No abstract provided.
Atm-Dependent Erk Signaling In Response To Dna Double Strand Breaks, Ashraf Khalil
Atm-Dependent Erk Signaling In Response To Dna Double Strand Breaks, Ashraf Khalil
Theses and Dissertations
Ionizing radiation (IR) triggers many signaling pathways stemming from DNA damage, and, independently, from extra-nuclear events. To generate radio-mimetic DNA double-strand breaks (DSBs) without and minimizing the effects on extra-nuclear radiation targets, human (p53+) glioma and carcinoma cells containing bromodeoxyuridine (BrdU)- substituted DNA were treated with Hoechst 33258 followed by long wave-length UV (UV-A) (BrdU photolysis). BrdU photolysis resulted in well-controlled, dose-dependent generation of DSBs equivalent to 0.2 - 20 Gy of IR, as detected by pulse-field gel electrophoresis, accompanied by dose-dependent H2AX phosphorylation at ser-139 and ATM phosphorylation at ser-1981, indicating ATM activation. Furthermore, BrdU photolysis increased phosphorylation of …
Degenerate Oligonucleotide Primed - Polymerase Chain Reaction Evaluation And Optimization To Improve Downstream Forensic Str Analysis Of Low Quality/Low Quantity Dna, Lindsay Paige Thompson
Degenerate Oligonucleotide Primed - Polymerase Chain Reaction Evaluation And Optimization To Improve Downstream Forensic Str Analysis Of Low Quality/Low Quantity Dna, Lindsay Paige Thompson
Theses and Dissertations
When forensic biological samples yield low quality/low quantity DNA, thecurrent STR analysis methods do not generate acceptable profiles. Whole genomeamplification can be used to pre-amplify the entire genome for downstream analyses. A commercially available kit for DOP-PCR, a form of WGA, is currently being used in the clinical for downstream single locus targets. Forensic analyses utilize a multiplex amplification. This study determined that the "home brew" created by our lab performs the same as the commercially available kit. Future optimization studies of DOP-PCR can utilize this "home brew". Additionally, this research determined that a 10 second increase in electrokinetic injection …