Research Topics
Genomes and GenesSpecies | Helen PiontkivskaSummaryAffiliation: Kent State University Country: USA Publications
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Publications
Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcriptsHelen Piontkivska
2Department of BiologicalSciences, Kent State University, Kent, Ohio 44242, USA
BMC Genomics 10:189. 2009....- Molecular characterization and mRNA expression of two key enzymes of hypoxia-sensing pathways in eastern oysters Crassostrea virginica (Gmelin): hypoxia-inducible factor α (HIF-α) and HIF-prolyl hydroxylase (PHD)Helen Piontkivska
Department of Biological Sciences, Kent State University, OH 44242 0001, USA
Comp Biochem Physiol Part D Genomics Proteomics 6:103-14. 2011.... - Novel protein genes in animal mtDNA: a new sex determination system in freshwater mussels (Bivalvia: Unionoida)?Sophie Breton
Department of Biological Sciences, Kent State University, Kent, OH, USA
Mol Biol Evol 28:1645-59. 2011..Our results open new avenues for the identification, characterization, and functional analyses of ORFs in the intergenic regions, previously defined as "noncoding," found in a large proportion of animal mt genomes... - Comparative mitochondrial genomics of freshwater mussels (Bivalvia: Unionoida) with doubly uniparental inheritance of mtDNA: gender-specific open reading frames and putative origins of replicationSophie Breton
Department of Biological Sciences, Kent State University, Kent, Ohio 44242, USA
Genetics 183:1575-89. 2009..We propose that unassigned regions are the most promising candidate sequences in which to find regulatory and/or gender-specific sequences that could determine whether a mitochondrial genome will be maternally or paternally transmitted... - Frequent associations between CTL and T-Helper epitopes in HIV-1 genomes and implications for multi-epitope vaccine designsSinu Paul
Department of Biological Sciences, Kent State University, Kent, Ohio 44242, USA
BMC Microbiol 10:212. 2010..However, not much is known about the relationship among different types of HIV epitopes, particularly those epitopes that can be considered potential candidates for inclusion in the multi-epitope vaccines... 
Patterns of sequence evolution at epitopes for host antibodies and cytotoxic T-lymphocytes in human immunodeficiency virus type 1Helen Piontkivska
Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia SC 29208, USA
Virus Res 116:98-105. 2006..The pattern seen at CTL epitopes may represent the result of conflicting pressures favoring conservation of the amino acid sequence for functional reasons and amino acid replacements for reasons of CTL escape...- Analysis of gene expression in prostate cancer epithelial and interstitial stromal cells using laser capture microdissectionJennifer L Gregg
School of Biomedical Sciences, Kent State University, Kent, OH, USA
BMC Cancer 10:165. 2010..This report presents the first study of prostate tumor tissue that examines patterns of differential expression between specific cell types using laser capture microdissection (LCM)... - DNA repeat arrays in chicken and human genomes and the adaptive evolution of avian genome sizeAustin L Hughes
Department of Biological Sciences, University of South Carolina, Columbia SC 29208, USA
BMC Evol Biol 5:12. 2005..Birds have smaller average genome sizes than other tetrapod classes, and it has been proposed that a relatively low frequency of repeating DNA is one factor in reduction of avian genome sizes... - Environmental kinetoplastid-like 18S rRNA sequences and phylogenetic relationships among Trypanosomatidae: paraphyly of the genus TrypanosomaHelen Piontkivska
Department of Biological Sciences, 242 Cunningham Hall, Kent State University, Kent OH 44242, USA
Mol Biochem Parasitol 144:94-9. 2005..brucei (cause of African sleeping sickness) are not as closely related to each other as they were previously thought to be. Likewise, the results did not support monophyly of the genera Leishmania, Leptomonas, Bodo and Cryptobia... 
Evolutionary diversification of the avian fatty acid-binding proteinsAustin L Hughes
Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
Gene 490:1-5. 2011....- Discovery of novel targets for multi-epitope vaccines: screening of HIV-1 genomes using association rule miningSinu Paul
Department of Biological Sciences, Kent State University, Kent, Ohio 44242, USA
Retrovirology 6:62. 2009..To identify CTL epitopes in different genes that co-occur in HIV genomes, association rule mining was used... - Evolutionary conservation of zinc finger transcription factor binding sites in promoters of genes co-expressed with WT1 in prostate cancerKurtis Eisermann
School of Biomedical Sciences, Kent State University, Kent, Ohio, USA
BMC Genomics 9:337. 2008..To rapidly identify coordinately expressed prostate cancer growth control genes that may be regulated by WT1, we used an in silico approach... - Extreme primary and secondary protein structure variability in the chimeric male-transmitted cytochrome c oxidase subunit II protein in freshwater mussels: evidence for an elevated amino acid substitution rate in the face of domain-specific purifying seleEric G Chapman
Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
BMC Evol Biol 8:165. 2008..Additionally, male unionoidean bivalves have a approximately 550 bp 3' coding extension to the cox2 gene (Mcox2e), that is apparently absent from all other metazoan taxa... - Aspartic proteinase phylogeny and the origin of pregnancy-associated glycoproteinsAustin L Hughes
Department of Biological Sciences, University of South Carolina, USA
Mol Biol Evol 20:1940-5. 2003..The conservation of this ancestral change suggests that it may be important to PAG function, particularly the fact that PAGs lack proteinase activity in spite of the conservation of active site residues in most PAGs... - Between-host evolution of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1: an approach based on phylogenetically independent comparisonsHelen Piontkivska
Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29208, USA
J Virol 78:11758-65. 2004..The results support the hypothesis that CTL-driven selection has been a major factor in the long-term evolution of HIV-1... - Functional diversification of the toll-like receptor gene familyAustin L Hughes
Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29208, USA
Immunogenetics 60:249-56. 2008..Thus, the vertebrate TLRs provide an example of a multi-gene family in which gene duplication has been followed by extensive changes in certain aspects of gene function, while others have been conserved throughout vertebrate history... - Within-host evolution of CD8+-TL epitopes encoded by overlapping and non-overlapping reading frames of simian immunodeficiency virusAustin L Hughes
Department of Biological Sciences, University of South Carolina Columbia, SC 29208, USA
Bioinformatics 21:iii39-44. 2005.... - Identification of novel light-induced genes in the suprachiasmatic nucleusVeronica M Porterfield
School of Biomedical Sciences, Kent State University, Kent, OH 44242 USA
BMC Neurosci 8:98. 2007..Using laser capture microscopy, microarray analysis, and quantitative real-time PCR, we performed a comprehensive screen for changes in gene expression immediately following a 30 minute light pulse in suprachiasmatic nucleus of mice... - Phylogeny of Trypanosomatidae and Bodonidae (Kinetoplastida) based on 18S rRNA: evidence for paraphyly of Trypanosoma and six other generaAustin L Hughes
Department of Biological Sciences, University of South Carolina, USA
Mol Biol Evol 20:644-52. 2003..The results suggested that parasitism of vertebrates has probably arisen independently a number of times within the Trypanosomatidae... - Evolutionary analysis of glycosyl hydrolase family 28 (GH28) suggests lineage-specific expansions in necrotrophic fungal pathogensDaniel D Sprockett
Department of Biological Sciences, Cunningham Hall, Kent State University, Kent, OH 44240, USA
Gene 479:29-36. 2011..GH28 evolution among necrotrophs has likely been driven by a co-evolutionary arms race with plants, whereas the need to avoid plant immune responses has resulted in purifying selection within biotrophic fungi... - Molecular evolution of the nontandemly repeated genes of the histone 3 multigene familyAlejandro P Rooney
Department of Biological Sciences, Mississippi State University, P O Box GY, Mississippi State, MS 39762, USA
Mol Biol Evol 19:68-75. 2002..Further analyses of the structure of H3 proteins revealed that the histones of higher eukaryotes might have evolved from a replication-independent-like H3 gene...