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Articles 1 - 9 of 9
Full-Text Articles in Genetics and Genomics
Nuclear Spindles Pave The Way To Metastasis, Patrick J. Hensley, Natasha Kyprianou
Nuclear Spindles Pave The Way To Metastasis, Patrick J. Hensley, Natasha Kyprianou
Urology Faculty Publications
No abstract provided.
A Comparative Genome Analysis Of Cercospora Sojina With Other Members Of The Pathogen Genus Mycosphaerella On Different Plant Hosts, Fanchang Zeng, Xin Lian, Guirong Zhang, Xiaoman Yu, Carl A. Bradley, Ray Ming
A Comparative Genome Analysis Of Cercospora Sojina With Other Members Of The Pathogen Genus Mycosphaerella On Different Plant Hosts, Fanchang Zeng, Xin Lian, Guirong Zhang, Xiaoman Yu, Carl A. Bradley, Ray Ming
Plant Pathology Faculty Publications
Fungi are the causal agents of many of the world's most serious plant diseases causing disastrous consequences for large-scale agricultural production. Pathogenicity genomic basis is complex in fungi as multicellular eukaryotic pathogens. Here, we report the genome sequence of C. sojina, and comparative genome analysis with plant pathogen members of the genus Mycosphaerella (Zymoseptoria. tritici (synonyms M. graminicola), M. pini, M. populorum and M. fijiensis - pathogens of wheat, pine, poplar and banana, respectively). Synteny or collinearity was limited between genomes of major Mycosphaerella pathogens. Comparative analysis with these related pathogen genomes indicated distinct genome-wide repeat …
Comprehensive Genomic Profiling In Routine Clinical Practice Leads To A Low Rate Of Benefit From Genotype-Directed Therapy, Talal Hilal, Mary Nakazawa, Jacob Hodskins, John L. Villano, Aju Mathew, Gaurav Goel, Lars M. Wagner, Susanne M. Arnold, Philip Desimone, Lowell B. Anthony, Peter J. Hosein
Comprehensive Genomic Profiling In Routine Clinical Practice Leads To A Low Rate Of Benefit From Genotype-Directed Therapy, Talal Hilal, Mary Nakazawa, Jacob Hodskins, John L. Villano, Aju Mathew, Gaurav Goel, Lars M. Wagner, Susanne M. Arnold, Philip Desimone, Lowell B. Anthony, Peter J. Hosein
Markey Cancer Center Faculty Publications
Background: Describe a single-center real-world experience with comprehensive genomic profiling (CGP) to identify genotype directed therapy (GDT) options for patients with malignancies refractory to standard treatment options.
Methods: Patients who had CGP by a CLIA-certified laboratory between November 2012 and December 2015 were included. The medical records were analyzed retrospectively after Institutional Review Board (IRB) approval. The treating oncologist made the decision to obtain the assay to provide potential therapeutic options. The objectives of this study were to determine the proportion of patients who benefited from GDT, and to identify barriers to receiving GDT.
Results: A total of 125 pediatric …
Quaternary Interactions And Supercoiling Modulate The Cooperative Dna Binding Of Agt, Manana Melikishvili, Michael G. Fried
Quaternary Interactions And Supercoiling Modulate The Cooperative Dna Binding Of Agt, Manana Melikishvili, Michael G. Fried
Center for Structural Biology Faculty Publications
Human O6-alkylguanine-DNA alkyltransferase (AGT) repairs mutagenic O6-alkylguanine and O4-alkylthymine adducts in single-stranded and duplex DNAs. The search for these lesions, through a vast excess of competing, unmodified genomic DNA, is a mechanistic challenge that may limit the repair rate in vivo. Here, we examine influences of DNA secondary structure and twist on protein–protein interactions in cooperative AGT complexes formed on lesion-free DNAs that model the unmodified parts of the genome. We used a new approach to resolve nearest neighbor (nn) and long-range (lr) components from the ensemble-average cooperativity, ωave. We found …
The Mirnaome Of Catharanthus Roseus: Identification, Expression Analysis, And Potential Roles Of Micrornas In Regulation Of Terpenoid Indole Alkaloid Biosynthesis, Ethan M. Shen, Sanjay Kumar Singh, Jayadri S. Ghosh, Barunava Patra, Priyanka Paul, Ling Yuan, Sitakanta Pattanaik
The Mirnaome Of Catharanthus Roseus: Identification, Expression Analysis, And Potential Roles Of Micrornas In Regulation Of Terpenoid Indole Alkaloid Biosynthesis, Ethan M. Shen, Sanjay Kumar Singh, Jayadri S. Ghosh, Barunava Patra, Priyanka Paul, Ling Yuan, Sitakanta Pattanaik
Plant and Soil Sciences Faculty Publications
MicroRNAs (miRNAs) regulate numerous crucial biological processes in plants. However, information is limited on their involvement in the biosynthesis of specialized metabolites in plants, including Catharanthus roseus that produces a number of pharmaceutically valuable, bioactive terpenoid indole alkaloids (TIAs). Using small RNA-sequencing, we identified 181 conserved and 173 novel miRNAs (cro-miRNAs) in C. roseus seedlings. Genome-wide expression analysis revealed that a set of cro-miRNAs are differentially regulated in response to methyl jasmonate (MeJA). In silico target prediction identified 519 potential cro-miRNA targets that include several auxin response factors (ARFs). The presence of cleaved transcripts of miRNA-targeted ARFs in C. roseus …
A Comparative Genomic Analysis Of Putative Pathogenicity Genes In The Host-Specific Sibling Species Colletotrichum Graminicola And Colletotrichum Sublineola, Ester A. S. Buiate, Katia Viana Xavier, Neil Moore, Maria F. Torres, Mark L. Farman, Christopher L. Schardl, Lisa J. Vaillancourt
A Comparative Genomic Analysis Of Putative Pathogenicity Genes In The Host-Specific Sibling Species Colletotrichum Graminicola And Colletotrichum Sublineola, Ester A. S. Buiate, Katia Viana Xavier, Neil Moore, Maria F. Torres, Mark L. Farman, Christopher L. Schardl, Lisa J. Vaillancourt
Plant Pathology Faculty Publications
Background: Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized secondary metabolites (SSM), and small-secreted protein (SSP) effectors. Genes relevant to these categories were manually annotated in two co-occurring, contemporaneous strains of C. graminicola and C. sublineola. A comparative genomic and phylogenetic analysis was performed to address the evolutionary relationships among these and other divergent gene families in the two strains.
Results: Inoculation of maize with C. sublineola …
Genomic Perspectives On Amphibian Evolution Across Multiple Phylogenetic Scales, Paul Michael Hime
Genomic Perspectives On Amphibian Evolution Across Multiple Phylogenetic Scales, Paul Michael Hime
Theses and Dissertations--Biology
Genomes provide windows into the evolutionary histories of species. The recent accessibility of genome-scale data in non-model organisms and the proliferation of powerful statistical models are now providing unprecedented opportunities to uncover evolutionary relationships and to test hypotheses about the processes that generate and maintain biodiversity. This dissertation work reveals shallow-scale species boundaries and population genetic structure in two imperiled groups of salamanders and demonstrates that the number and information content of genomic regions used in species delimitation exert strong effects on the resulting inferences. Genome scans are employed to test hypotheses about the mechanisms of genetic sex determination in …
Differential Activity And Content Of High-Affinity Glutamate Transporters, Content Of Their Regulatory Proteins, And Capacity For Glutamine And Glutathione Synthesis In Tissues Of Finished Versus Growing Steers, Jing Huang
Theses and Dissertations--Animal and Food Sciences
Improvement of feeding regimens for production animals has been hindered by a lack of fundamental knowledge about how the capacity to regulate nutrient absorption across cell membranes affects the function of nutrient metabolizing enzymes. The objective is to determine if the activities and protein content of system X-AG glutamate transporter, its regulatory protein (GTRAP3-18 and ARL6IP1), glutamine synthetase (GS) and glutathione (GSH) content, changes in liver (Experiment 1), longissimus dorsi (LM) and subcutaneous adipose tissue (SF) (Experiment 2) as beef steers transitioned from predominantly-lean (growing) to -lipid (finished) tissue accretion phases. In liver (Experiment 1), system X- …
Characterization Of A Large Vertebrate Genome And Homomorphic Sex Chromosomes In The Axolotl, Ambystoma Mexicanum, Melissa Keinath
Characterization Of A Large Vertebrate Genome And Homomorphic Sex Chromosomes In The Axolotl, Ambystoma Mexicanum, Melissa Keinath
Theses and Dissertations--Biology
Changes in the structure, content and morphology of chromosomes accumulate over evolutionary time and contribute to cell, developmental and organismal biology. The axolotl (Ambystoma mexicanum) is an important model for studying these changes because: 1) it provides important phylogenetic perspective for reconstructing the evolution of vertebrate genomes and amphibian karyotypes, 2) its genome has evolved to a large size (~10X larger than human) but has maintained gene orders, and 3) it possesses potentially young sex chromosomes that have not undergone extensive differentiation in the structure that is typical of many other vertebrate sex chromosomes (e.g. mammalian XY chromosomes …