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Articles 1 - 15 of 15
Full-Text Articles in Genetics and Genomics
Magnetosome Gene Duplication As An Important Driver In The Evolution Of Magnetotaxis In The Alphaproteobacteria, Haijian Du, Wenyan Zhang, Wensi Zhang, Weijia Zhang, Hongmiao Pan, Yongxin Pan, Dennis A. Bazylinski, Long-Fei Wu, Tian Xiao, Wei Lin
Magnetosome Gene Duplication As An Important Driver In The Evolution Of Magnetotaxis In The Alphaproteobacteria, Haijian Du, Wenyan Zhang, Wensi Zhang, Weijia Zhang, Hongmiao Pan, Yongxin Pan, Dennis A. Bazylinski, Long-Fei Wu, Tian Xiao, Wei Lin
Life Sciences Faculty Research
The evolution of microbial magnetoreception (or magnetotaxis) is of great interest in the fields of microbiology, evolutionary biology, biophysics, geomicrobiology, and geochemistry. Current genomic data from magnetotactic bacteria (MTB), the only prokaryotes known to be capable of sensing the Earth’s geomagnetic field, suggests an ancient origin of magnetotaxis in the domain Bacteria. Vertical inheritance, followed by multiple independent magnetosome gene cluster loss, is considered to be one of the major forces that drove the evolution of magnetotaxis at or above the class or phylum level, although the evolutionary trajectories at lower taxonomic ranks (e.g., within the class level) remain largely …
Correction To: Transcriptome Analyses Of Tumor-Adjacent Somatic Tissues Reveal Genes Co-Expressed With Transposable Elements, Micky Chung, G. M. Jonaid, Sophia Quinton, Austin Ross, Corinne E. Sexton, Adrian Alberto, Cody Clymer, Daphnie Churchill, Omar Navarro Leija, Mira V. Han
Correction To: Transcriptome Analyses Of Tumor-Adjacent Somatic Tissues Reveal Genes Co-Expressed With Transposable Elements, Micky Chung, G. M. Jonaid, Sophia Quinton, Austin Ross, Corinne E. Sexton, Adrian Alberto, Cody Clymer, Daphnie Churchill, Omar Navarro Leija, Mira V. Han
Life Sciences Faculty Research
Following publication of the original article [1], the authors reported errors in Table 2 wherein all “KZFP” in the gene names should be changed to “ZNF”.
Complete Genome Sequences Of Mycobacterium Smegmatis Phages Nihilnomen And Carlyle, Isolated In Las Vegas, Nevada, Alicia Salisbury, Ryan Doss, Astha Mehta, Khadija Bhatti, Ciera Dapra, Audrey Huntsinger, Stephanie Rodriguez, Scott Yacek, Rylee Sandberg, Alexis Gildore, Jacinda Knudtson, Frances Tibayan, Tiannah Ohta, Neha Zafar, Guadalupe Mercado, Alan Le, Natalie Mekhaeel, Justin Willer, Edith Rodrich-Zuniga, Merissa Mcfarland, Kurt Regner, Christy Strong, Phillippos K. Tsourkas
Complete Genome Sequences Of Mycobacterium Smegmatis Phages Nihilnomen And Carlyle, Isolated In Las Vegas, Nevada, Alicia Salisbury, Ryan Doss, Astha Mehta, Khadija Bhatti, Ciera Dapra, Audrey Huntsinger, Stephanie Rodriguez, Scott Yacek, Rylee Sandberg, Alexis Gildore, Jacinda Knudtson, Frances Tibayan, Tiannah Ohta, Neha Zafar, Guadalupe Mercado, Alan Le, Natalie Mekhaeel, Justin Willer, Edith Rodrich-Zuniga, Merissa Mcfarland, Kurt Regner, Christy Strong, Phillippos K. Tsourkas
Life Sciences Faculty Research
We present the complete genomes of the Mycobacterium smegmatis phages Carlyle and NihilNomen, isolated from soil in Las Vegas, Nevada. The phages were isolated and annotated by undergraduate students enrolled in the Phage Discovery course offered by the School of Life Sciences at the University of Nevada Las Vegas.
Nitric Oxide Is Involved In Heavy Ion-Induced Non-Targeted Effects In Human Fibroblasts, Megumi Hada, Premkumar B. Saganti, Francis A. Cucinotta
Nitric Oxide Is Involved In Heavy Ion-Induced Non-Targeted Effects In Human Fibroblasts, Megumi Hada, Premkumar B. Saganti, Francis A. Cucinotta
Health Physics & Diagnostic Sciences Faculty Publications
Previously, we investigated the dose response for chromosomal aberration (CA) for exposures corresponding to less than one particle traversal per cell nucleus by high energy and charge (HZE) particles, and showed that the dose responses for simple exchanges for human fibroblast irradiated under confluent culture conditions were best fit by non-linear models motivated by a non-targeted effect (NTE). Our results suggested that the simple exchanges in normal human fibroblasts have an important NTE contribution at low particle fluence. Nitric oxide (NO) has been reported as a candidate for intercellular signaling for NTE in many studies. In order to estimate the …
A Frameshift Variant In The Chst9 Gene Identified By Family-Based Whole Genome Sequencing Is Associated With Schizophrenia In Chinese Population, Jingchun Chen, Jain-Shing Wu, Travis Mize, Marvi Moreno, Mahtab Hamid, Francisco Servin, Bita Bashy, Zhongming Zhao, Peilin Jia, Ming T. Tsuang, Kenneth S. Kendler, Momiao Xiong, Xiangning Chen
A Frameshift Variant In The Chst9 Gene Identified By Family-Based Whole Genome Sequencing Is Associated With Schizophrenia In Chinese Population, Jingchun Chen, Jain-Shing Wu, Travis Mize, Marvi Moreno, Mahtab Hamid, Francisco Servin, Bita Bashy, Zhongming Zhao, Peilin Jia, Ming T. Tsuang, Kenneth S. Kendler, Momiao Xiong, Xiangning Chen
School of Medicine Faculty Publications
Recent studies imply that rare variants contribute to the risk of schizophrenia, however, the exact variants or genes responsible for this condition are largely unknown. In this study, we conducted whole genome sequencing (WGS) of 20 Chinese families. Each family consisted of at least two affected siblings diagnosed with schizophrenia and at least one unaffected sibling. We examined functional variants that were found in affected sibling(s) but not in unaffected sibling(s) within a family. Matching this criterion, a frameshift heterozygous deletion of CA (–/CA) at chromosome 18:24722722, also referred to as rs752084147, in the Carbohydrate Sulfotransferase 9 (CHST9) gene, was …
Transcriptome Analyses Of Tumor-Adjacent Somatic Tissues Reveal Genes Co-Expressed With Transposable Elements, Micky Chung, G. M. Jonaid, Sophia Quinton, Austin Ross, Corinne E. Sexton, Adrian Alberto, Cody Clymer, Daphnie Churchill, Omar Navarro Leija, Mira V. Han
Transcriptome Analyses Of Tumor-Adjacent Somatic Tissues Reveal Genes Co-Expressed With Transposable Elements, Micky Chung, G. M. Jonaid, Sophia Quinton, Austin Ross, Corinne E. Sexton, Adrian Alberto, Cody Clymer, Daphnie Churchill, Omar Navarro Leija, Mira V. Han
Life Sciences Faculty Research
Background: Despite the long-held assumption that transposons are normally only expressed in the germ-line, recent evidence shows that transcripts of transposable element (TE) sequences are frequently found in the somatic cells. However, the extent of variation in TE transcript levels across different tissues and different individuals are unknown, and the co-expression between TEs and host gene mRNAs have not been examined. Results: Here we report the variation in TE derived transcript levels across tissues and between individuals observed in the non-tumorous tissues collected for The Cancer Genome Atlas. We found core TE co-expression modules consisting mainly of transposons, showing correlated …
Decline In Telomere Length By Age And Effect Modification By Gender, Allostatic Load And Comorbidities In National Health And Nutrition Examination Survey (1999-2002), Saruna Ghimire, Carl V. Hill, Francisco S. Sy, Rachelle Rodriguez
Decline In Telomere Length By Age And Effect Modification By Gender, Allostatic Load And Comorbidities In National Health And Nutrition Examination Survey (1999-2002), Saruna Ghimire, Carl V. Hill, Francisco S. Sy, Rachelle Rodriguez
Public Health Faculty Publications
Background: This study aims to assess the decline in telomere length (TL) with age and evaluate effect modification by gender, chronic stress, and comorbidity in a representative sample of the US population. Methods: Cross-sectional data on 7826 adults with a TL measurement, were included from the National Health and Nutrition Examination Survey, years 1999–2002. The population rate of decline in TL across 10-year age categories was estimated using crude and adjusted regression. Results: In an adjusted model, the population rate of decline in TL with age was consistent and linear for only three age categories: 20–29 (β = -0.0172, 95% …
Multi-Polygenic Risk Score Prediction Model For Bipolar Disorder, Travis Mize
Multi-Polygenic Risk Score Prediction Model For Bipolar Disorder, Travis Mize
UNLV Theses, Dissertations, Professional Papers, and Capstones
Bipolar disorder (BP), a severe mental disorder characterized by recurring manic and depressive episodes, has been shown to have a strong genetic underpinning. Current theory suggests that it is the summation of risk alleles, spread across the entirety of the genome, which contributes to the development of BP, as well as other polygenic traits. The comorbid nature of these polygenic traits are often problematic for diagnosticians as the symptomology of the disorders may vary substantially between individuals and can create diagnostic confusion. To alleviate issues such as these, a more objective measure, to be used alongside current diagnostic procedures, is …
Prioritization Of Variants For Investigation Of Genotype-Directed Nutrition In Human Superpopulations, Pascal D. Nilsson, Jacklyn M. Newsome, Henry M. Santos, Martin R. Schiller
Prioritization Of Variants For Investigation Of Genotype-Directed Nutrition In Human Superpopulations, Pascal D. Nilsson, Jacklyn M. Newsome, Henry M. Santos, Martin R. Schiller
Life Sciences Faculty Research
Dietary guidelines recommended by key health agencies are generally designed for a global population. However, ethnicity affects human disease and environment-gene interactions, including nutrient intake. Historically, isolated human populations with different genetic backgrounds have adapted to distinct environments with varying food sources. Ethnicity is relevant to the interaction of food intake with genes and disease susceptibility; yet major health agencies generally do not recommend food and nutrients codified by population genotypes and their frequencies. In this paper, we have consolidated published nutrigenetic variants and examine their frequencies in human superpopulations to prioritize these variants for future investigation of population-specific genotype-directed …
Paired-End Mappability Of Transposable Elements In The Human Genome, Corinne E. Sexton, Mira V. Han
Paired-End Mappability Of Transposable Elements In The Human Genome, Corinne E. Sexton, Mira V. Han
Life Sciences Faculty Research
Though transposable elements make up around half of the human genome, the repetitive nature of their sequences makes it difficult to accurately align conventional sequencing reads. However, in light of new advances in sequencing technology, such as increased read length and paired-end libraries, these repetitive regions are now becoming easier to align to. This study investigates the mappability of transposable elements with 50 bp, 76 bp and 100 bp paired-end read libraries. With respect to those read lengths and allowing for 3 mismatches during alignment, over 68, 85, and 88% of all transposable elements in the RepeatMasker database are uniquely …
A Method For Improving The Accuracy And Efficiency Of Bacteriophage Genome Annotation, Alicia Salisbury, Philippos K. Tsourkas
A Method For Improving The Accuracy And Efficiency Of Bacteriophage Genome Annotation, Alicia Salisbury, Philippos K. Tsourkas
Life Sciences Faculty Research
Bacteriophages are the most numerous entities on Earth. The number of sequenced phage genomes is approximately 8000 and increasing rapidly. Sequencing of a genome is followed by annotation, where genes, start codons, and functions are putatively identified. The mainstays of phage genome annotation are auto-annotation programs such as Glimmer and GeneMark. Due to the relatively small size of phage genomes, many groups choose to manually curate auto-annotation results to increase accuracy. An additional benefit of manual curation of auto-annotated phage genomes is that the process is amenable to be performed by students, and has been shown to improve student recruitment …
Position-Specific Metabolic Probing And Metagenomics Of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities At High Temperatures, Scott C. Thomas, Kevin O. Tamadonfar, Cale O. Seymour, Dengxun Lai, Jeremy A. Dodsworth, Senthil K. Murugapiran, Emiley A. Eloe-Fadrosh, Paul Dijkstra, Brian P. Hedlund
Position-Specific Metabolic Probing And Metagenomics Of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities At High Temperatures, Scott C. Thomas, Kevin O. Tamadonfar, Cale O. Seymour, Dengxun Lai, Jeremy A. Dodsworth, Senthil K. Murugapiran, Emiley A. Eloe-Fadrosh, Paul Dijkstra, Brian P. Hedlund
Life Sciences Faculty Research
Temperature is a primary driver of microbial community composition and taxonomic diversity; however, it is unclear to what extent temperature affects characteristics of central carbon metabolic pathways (CCMPs) at the community level. In this study, 16S rRNA gene amplicon and metagenome sequencing were combined with 13C-labeled metabolite probing of the CCMPs to assess community carbon metabolism along a temperature gradient (60–95°C) in Great Boiling Spring, NV. 16S rRNA gene amplicon diversity was inversely proportional to temperature, and Archaea were dominant at higher temperatures. KO richness and diversity were also inversely proportional to temperature, yet CCMP genes were similarly represented across …
Novel Algorithms For Ldd Motif Search, Peng Xiao, Martin Schiller, Sanguthevar Rajasekaran
Novel Algorithms For Ldd Motif Search, Peng Xiao, Martin Schiller, Sanguthevar Rajasekaran
Life Sciences Faculty Research
Background: Motifs are crucial patterns that have numerous applications including the identification of transcription factors and their binding sites, composite regulatory patterns, similarity between families of proteins, etc. Several motif models have been proposed in the literature. The (l,d)-motif model is one of these that has been studied widely. However, this model will sometimes report too many spurious motifs than expected. We interpret a motif as a biologically significant entity that is evolutionarily preserved within some distance. It may be highly improbable that the motif undergoes the same number of changes in each of the species. To address this issue, …
The Anti-Sigma Factor Muca Of Pseudomonas Aeruginosa: Dramatic Differences Of A Muca22 Vs. A Δmuca Mutant In Anaerobic Acidified Nitrite Sensitivity Of Planktonic And Biofilm Bacteria In Vitro And During Chronic Murine Lung Infection, Warunya Panmanee, Shengchang Su, Michael J. Schurr, Gee W. Lau, Xiaoting Zhu, Zhaowei Ren, Cameron T. Mcdaniel, Long J. Lu, Dennis E. Ohman, Daniel A. Muruve, Ralph J. Panos, Hongwei D. Yu, Thomas B. Thompson, Boo Shan Tseng, Daniel J. Hassett
The Anti-Sigma Factor Muca Of Pseudomonas Aeruginosa: Dramatic Differences Of A Muca22 Vs. A Δmuca Mutant In Anaerobic Acidified Nitrite Sensitivity Of Planktonic And Biofilm Bacteria In Vitro And During Chronic Murine Lung Infection, Warunya Panmanee, Shengchang Su, Michael J. Schurr, Gee W. Lau, Xiaoting Zhu, Zhaowei Ren, Cameron T. Mcdaniel, Long J. Lu, Dennis E. Ohman, Daniel A. Muruve, Ralph J. Panos, Hongwei D. Yu, Thomas B. Thompson, Boo Shan Tseng, Daniel J. Hassett
Life Sciences Faculty Research
Mucoid mucA22 Pseudomonas aeruginosa (PA) is an opportunistic lung pathogen of cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) patients that is highly sensitive to acidified nitrite (A-NO2-). In this study, we first screened PA mutant strains for sensitivity or resistance to 20 mM A-NO2- under anaerobic conditions that represent the chronic stages of the aforementioned diseases. Mutants found to be sensitive to A-NO2- included PA0964 (pmpR, PQS biosynthesis), PA4455 (probable ABC transporter permease), katA (major catalase, KatA) and rhlR (quorum sensing regulator). In contrast, mutants lacking PA0450 (a putative phosphate transporter) and PA1505 (moaA2) were A-NO2- resistant. However, …
Investigating The Dna-Binding Site For Virb, A Key Transcriptional Regulator Of Shigella Virulence Genes, Using An In Vivo Binding Tool, Monika M.A. Karney, Joy A. Mckenna, Natasha Weatherspoon-Griffin, Alexander D. Karabachev, Makensie E. Millar, Eliese A. Potoceck, Helen J. Wing
Investigating The Dna-Binding Site For Virb, A Key Transcriptional Regulator Of Shigella Virulence Genes, Using An In Vivo Binding Tool, Monika M.A. Karney, Joy A. Mckenna, Natasha Weatherspoon-Griffin, Alexander D. Karabachev, Makensie E. Millar, Eliese A. Potoceck, Helen J. Wing
Life Sciences Faculty Research
The transcriptional anti-silencing and DNA-binding protein, VirB, is essential for the virulence of Shigella species and, yet, sequences required for VirB-DNA binding are poorly understood. While a 7-8 bp VirB-binding site has been proposed, it was derived from studies at a single VirB-dependent promoter, icsB. Our previous in vivo studies at a different VirB-dependent promoter, icsP, found that the proposed VirB-binding site was insufficient for regulation. Instead, the required site was found to be organized as a near-perfect inverted repeat separated by a single nucleotide spacer. Thus, the proposed 7-8 bp VirB-binding site needed to be re-evaluated. Here, we engineer …