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Articles 811 - 840 of 3154

Full-Text Articles in Genetics

Sars-Cov-2 Reveals That Chimeric Agents Are The Bioweapons Of The Future, Rachel Craig Apr 2022

Sars-Cov-2 Reveals That Chimeric Agents Are The Bioweapons Of The Future, Rachel Craig

Senior Honors Theses

Bioweapons programs have existed since their development during the Cold War. These biowarfare programs initially utilized naturally occurring pathogens capable of infecting crops, livestock populations, and human populations. Anthrax is a widely exploited bioagent responsible for attacks ranging from the Germans’ deployment in World War I to the mailing of anthrax through the postal service in attempts on U.S. senators’ lives. With the development of genetic manipulations, the Soviet Union began modifying anthrax to resist detection and treatment. With the continued advancement of science and technology, a new bioagent has entered the scene – the man-made chimeric virus. Chimeric viruses …


The Utilization Of Healthcare Chaplains By Genetic Counselors, Elizabeth G. Hollingsworth Apr 2022

The Utilization Of Healthcare Chaplains By Genetic Counselors, Elizabeth G. Hollingsworth

Theses and Dissertations

Healthcare chaplains prioritize the spiritual and religious care a patient and their family may need during their healthcare experience. This study investigated the current utilization of healthcare chaplains by genetic counselors, as well as the ability, in time and skill, of the healthcare chaplains to see genetic counseling patients. Lastly, the study investigated if genetic counseling patients would accept a referral to meet with a healthcare chaplain. We hypothesized that genetic counselors are not utilizing healthcare chaplains, healthcare chaplains have the ability to see genetic counseling patients, and genetic counseling patients would consider meeting with a healthcare chaplain.

This study …


Origin And Epigenetic Regulation Of Cutaneous T Cell Lymphoma, Carly M. Harro Mar 2022

Origin And Epigenetic Regulation Of Cutaneous T Cell Lymphoma, Carly M. Harro

USF Tampa Graduate Theses and Dissertations

The pathogenesis of Cutaneous T cell lymphoma (CTCL) remains unclear. Using conditional knockout mice, we found that ablation of the genomic organizer Special AT-rich sequence-binding protein-1 (Satb1) caused malignant transformation of mature, skin-homing, Notch-activated CD4+ and CD8+ T cells into progressively fatal lymphoma. Mechanistically, Satb1 restrained Stat5 phosphorylation and the expression of skin-homing chemokine receptors in mature T cells. H3K27 and H3K9 trimethylation occluded the SATB1 promoter in Sézary cells, while inhibition of SUV39H1/2 methyltransferases (unlike EZH2 inhibition), restored protective SATB1 expression and selectively abrogated the growth of primary Sézary cells more effectively than romidepsin. Additionally, using single-cell RNA/TCR sequencing …


Alzheimer's And Patient Caregiver Burnout: A Review Of The Literature, Madeline Hekeler Mar 2022

Alzheimer's And Patient Caregiver Burnout: A Review Of The Literature, Madeline Hekeler

James Madison Undergraduate Research Journal (JMURJ)

The term “silent epidemic” is fitting for Alzheimer’s disease (AD), as its negative impact is widely felt but rarely discussed. Burnout among AD caregivers has become an epidemic of its own as caregivers experience an increase in health risks, stress, and financial burden. This literature review focuses on caregiver burnout and how imperative it is that caregivers are better supported in their role. Researchers have developed instruments to assess and intervene in caregiver burnout that have shown effectiveness among caregivers and their families.Nevertheless, further longitudinal research is warranted regarding more effective interventions, including stress management and social support mechanisms.


Meta-Analysis Of Two Rnaseq Datasets To Determine Diagnostic Biomarkers And Drug Target Candidates For Periodontitis, Carlos Moreno Mar 2022

Meta-Analysis Of Two Rnaseq Datasets To Determine Diagnostic Biomarkers And Drug Target Candidates For Periodontitis, Carlos Moreno

Annual Research Symposium

No abstract provided.


Response To A Water Bolus In Long Term Oral Contraceptive Users, Whitley C. Atkins, Brendon P. Mcdermott, Abigail T. Colburn, Stavros A. Kavouras Mar 2022

Response To A Water Bolus In Long Term Oral Contraceptive Users, Whitley C. Atkins, Brendon P. Mcdermott, Abigail T. Colburn, Stavros A. Kavouras

Health, Human Performance and Recreation Faculty Publications and Presentations

The purpose of our study was to determine the responses to an acute water bolus in long-term oral contraception (OCP) users. Seventeen female volunteers (27 ± 5 y, 64.1 ± 13.7 kg, 39.6 ± 5.9 kg/LBM) provided consent and enrolled in our study. All were long-term OCP users and participated in two trials, one during the active pill (High Hormone, HH) dose of their prescribed OCP and one during the sham pill (Low Hormone, LH) dose. Participants reported to the laboratory euhydrated, were fed breakfast, remained seated for 60 min and were provided a bolus of room temperature water in …


Evaluating And Improving A Novel Toolkit For Implementation And Optimization Of Lynch Syndrome Universal Tumor Screening, Tara M. Wolfinger Mar 2022

Evaluating And Improving A Novel Toolkit For Implementation And Optimization Of Lynch Syndrome Universal Tumor Screening, Tara M. Wolfinger

USF Tampa Graduate Theses and Dissertations

Individuals with Lynch syndrome (LS) have a hereditary predisposition to colorectal cancer (CRC), endometrial cancer (EC), and several additional cancer types. Universal tumor screening (UTS) is a systematic approach that increases identification of LS so affected individuals can benefit from targeted therapies and risk-reduction strategies to decrease cancer- related morbidity and mortality. Despite the known benefits of UTS, the practice is widely underutilized, likely due to the complexity of implementation and optimization. We developed a novel evidence-based toolkit to help institutions implement and optimize UTS programs. As part of an iterative evaluation process, we obtained feedback on the toolkit through …


Assessing Reported Use Of Clinical Genetic Counseling Skills, Nicole M. Wright Mar 2022

Assessing Reported Use Of Clinical Genetic Counseling Skills, Nicole M. Wright

USF Tampa Graduate Theses and Dissertations

Genetic Counseling (GC) is striving to become a more evidence-based field, but the absence of a clearly defined taxonomy of clinical skills is impeding efforts to systematically study and compare GC processes. Several frameworks such as the Reciprocal Engagement Model (REM) and FOCUS-GC have outlined strategies and behaviors used to meet patient needs, but neither include comprehensive descriptions of existing skills or delineate which are actually being used most commonly in clinical practice. The purpose of this study was to compile a large list of demonstrable genetic counseling skills and determine how often clinical genetic counselors (GCs) report using them …


Inaccuracies In Patient Self-Report Of Genetic Testing Results For Hereditary Cancer Risks Could Impact Risk-Management Practices, Brittany Faye Sears Mar 2022

Inaccuracies In Patient Self-Report Of Genetic Testing Results For Hereditary Cancer Risks Could Impact Risk-Management Practices, Brittany Faye Sears

USF Tampa Graduate Theses and Dissertations

Pathogenic variants (PV) or likely pathogenic variants (LPV) in a cancer risk gene increase lifetime risks of developing cancer. National guidelines provide evidence-based recommendations on cancer risk management (CRM) strategies tailored to the cancer risks associated with PV/LPV in different genes. Emotional responses after learning of a PV/LPV have been studied as predictors of patient adherence to CRM, but less attention has been given to whether patients remember their actual genetic test results and the impact this may have on subsequent adherence to CRM. We surveyed a group of 114 participants registered with the Inherited Cancer Registry (ICARE), all of …


Genetic Variation Of The Mitochondrial Dna Control Region Across Plains Bison Herds In Usa And Canada, Gaimi Davies, Blake Mccann, Lee Jones, Stefano Liccioli, Maria Cecilia Penedo, Igor V. Ovtchinnikov Mar 2022

Genetic Variation Of The Mitochondrial Dna Control Region Across Plains Bison Herds In Usa And Canada, Gaimi Davies, Blake Mccann, Lee Jones, Stefano Liccioli, Maria Cecilia Penedo, Igor V. Ovtchinnikov

Biology Faculty Publications

Once numbering in the tens of millions, bison (Bison bison) have faced a broad range of challenges over the past century, including genetic impacts from the population bottleneck in the 1800s, and significant loss and fragmentation of habitat resulting in little opportunity for population growth on remaining small, geographically isolated reserves. To identify best practices for bison stewardship against this backdrop, managers must understand the genetic composition of existing conservation herds. This study characterized 14 plains bison (Bison bison bison) herds managed by the U.S. Department of Interior and Parks Canada Agency based on complete mtDNA …


Cell-Free Dna Methylation Signatures In Cancer Detection And Classification, Jinyong Huang Mar 2022

Cell-Free Dna Methylation Signatures In Cancer Detection And Classification, Jinyong Huang

USF Tampa Graduate Theses and Dissertations

Early detection of cancer is believed as one of the best solutions to improve the therapeutic outcomes and overall survival of cancer patients. Analysis of circulating nucleic acids in bodily fluids, referred to as “liquid biopsies”, is rapidly gaining prominence for this purpose. Cell-free DNA (cfDNA) methylation has emerged as a promising biomarker for early cancer detection, tumor type classification, and treatment response monitoring. Currently, most cfDNA methylation profiling technologies are based on bisulfite conversion, while enrichment-based methods such as cfMeDIP-seq are beginning to show potential. To expand the use of enrichment-based methods in cfDNA methylation profiling, here, we report …


Characterization Of SccMec Instability In Methicillin-Resistant Staphylococcus Aureus Affecting Adjacent Chromosomal Regions, Including The Gene For Staphylococcal Protein A (Spa), Isabella A. Tickler, Fred C. Tenover, C. R. Scharn, R. V. Goering Mar 2022

Characterization Of SccMec Instability In Methicillin-Resistant Staphylococcus Aureus Affecting Adjacent Chromosomal Regions, Including The Gene For Staphylococcal Protein A (Spa), Isabella A. Tickler, Fred C. Tenover, C. R. Scharn, R. V. Goering

Biology Faculty Publications

Staphylococcal cassette chromosome mec (SCCmec) represents a sequence of clear clinical and diagnostic importance in staphylococci. At a minimum the chromosomal cassette contains the mecA gene encoding PBP2a but frequently also includes additional antibiotic resistance genes (e.g., ermA and aadC; macrolide and aminoglycoside resistance, respectively). Certain regions within SCCmec elements are hot spots for sequence instability due to cassette-specific recombinases and a variety of internal mobile elements. SCCmec changes may affect not only cassette stability but the integrity of adjacent chromosomal sequences (e.g., the staphylococcal protein A gene; spa). We investigated SCCmec stability …


Conservation Status Assessment Of The Egg-Mimic Darter (Percidae: Etheostoma Pseudovulatum) Using A Multi-Faceted Approach, Zachary L. Wolf, John W. Johansen, Rebecca E. Blanton Mar 2022

Conservation Status Assessment Of The Egg-Mimic Darter (Percidae: Etheostoma Pseudovulatum) Using A Multi-Faceted Approach, Zachary L. Wolf, John W. Johansen, Rebecca E. Blanton

Southeastern Fishes Council Proceedings

The imperiled Egg-mimic Darter (Etheostoma pseudovulatum) is a headwater-adapted fish restricted to an area less than 1000 km2 in Tennessee. It is found in only six tributaries of the Duck River and the large, mainstem of this system may act as a barrier to dispersal, restricting population connectivity. The only status assessment of this species was over two decades ago; genetic diversity and the degree of population connectivity have never been evaluated. We conducted a conservation status assessment using a multi-faceted approach to better inform conservation management plans, including examining its current distribution, assessing habitat quality, estimating …


Determining Some Quality Properties Of Oat Genotypes Collected From The Middle And West Black Sea Region, Zeki Mut, Hasan Akay, Ozge Doganay Erbas Kose, Ismail Sezer Mar 2022

Determining Some Quality Properties Of Oat Genotypes Collected From The Middle And West Black Sea Region, Zeki Mut, Hasan Akay, Ozge Doganay Erbas Kose, Ismail Sezer

The Philippine Agricultural Scientist

Healthy foodstuffs, including functional foods, are the key component of a healthy and prosperous life. Oat grains are rich in protein, soluble dietary fiber, β-glucan, starch, oil, some vitamins and minerals, and thus accepted as a healthy foodstuff. This study was conducted to determine physical and chemical quality traits of many different oat landraces/cultivars. In this study, 251 local oat genotypes, collected from 10 provinces of Western and Middle Black Sea Regions of Turkey and four standard oat cultivars were grown over the experimental fields of the Agricultural Application and Research Center at Samsun Ondokuz Mayıs University for two years …


Carbapenemase-Producing Pseudomonas Aeruginosa – An Emerging Challenge, Fred C. Tenover, David P. Nicolau, Christian M. Gill Feb 2022

Carbapenemase-Producing Pseudomonas Aeruginosa – An Emerging Challenge, Fred C. Tenover, David P. Nicolau, Christian M. Gill

Biology Faculty Publications

Carbapenem-resistant Pseudomonas aeruginosa (CR-PA) is a major healthcare-associated pathogen worldwide. In the United States, 10–30% of P. aeruginosa isolates are carbapenem-resistant, while globally the percentage varies considerably. A subset of carbapenem-resistant P. aeruginosa isolates harbour carbapenemases, although due in part to limited screening for these enzymes in clinical laboratories, the actual percentage is unknown. Carbapenemase-mediated carbapenem resistance in P. aeruginosa is a significant concern as it greatly limits the choice of anti-infective strategies, although detecting carbapenemase-producing P. aeruginosa in the clinical laboratory can be challenging. Such organisms also have been associated with nosocomial spread requiring infection prevention interventions. The carbapenemases …


Allosteric Determinants Of The Sars-Cov-2 Spike Protein Binding With Nanobodies: Examining Mechanisms Of Mutational Escape And Sensitivity Of The Omicron Variant, Gennady M. Verkhivker Feb 2022

Allosteric Determinants Of The Sars-Cov-2 Spike Protein Binding With Nanobodies: Examining Mechanisms Of Mutational Escape And Sensitivity Of The Omicron Variant, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Structural and biochemical studies have recently revealed a range of rationally engineered nanobodies with efficient neutralizing capacity against the SARS-CoV-2 virus and resilience against mutational escape. In this study, we performed a comprehensive computational analysis of the SARS-CoV-2 spike trimer complexes with single nanobodies Nb6, VHH E, and complex with VHH E/VHH V nanobody combination. We combined coarse-grained and all-atom molecular simulations and collective dynamics analysis with binding free energy scanning, perturbation-response scanning, and network centrality analysis to examine mechanisms of nanobody-induced allosteric modulation and cooperativity in the SARS-CoV-2 spike trimer complexes with these nanobodies. By quantifying energetic and allosteric …


Escherichia Coli Alanyl-Trna Synthetase Maintains Proofreading Activity And Translational Accuracy Under Oxidative Stress, Arundhati Kavoor, Paul Kelly, Michael Ibba Feb 2022

Escherichia Coli Alanyl-Trna Synthetase Maintains Proofreading Activity And Translational Accuracy Under Oxidative Stress, Arundhati Kavoor, Paul Kelly, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Aminoacyl-tRNA synthetases (aaRSs) are enzymes that synthesize aminoacyl-tRNAs to facilitate translation of the genetic code. Quality control by aaRS proofreading and other mechanisms maintains translational accuracy, which promotes cellular viability. Systematic disruption of proofreading, as recently demonstrated for alanyl-tRNA synthetase (AlaRS), leads to dysregulation of the proteome and reduced viability. Recent studies showed that environmental challenges such as exposure to reactive oxygen species can also alter aaRS synthetic and proofreading functions, prompting us to investigate if oxidation might positively or negatively affect AlaRS activity. We found that while oxidation leads to modification of several residues in Escherichia coli AlaRS, unlike …


The Low Abundance Of Cpg In The Sars-Cov-2 Genome Is Not An Evolutionarily Signature Of Zap, Ali Afrasiabi, Hamid Alinejad-Rokny, Azad Khosh, Mostafa Rahnama, Nigel Lovell, Zhenming Xu, Diako Ebrahimi Feb 2022

The Low Abundance Of Cpg In The Sars-Cov-2 Genome Is Not An Evolutionarily Signature Of Zap, Ali Afrasiabi, Hamid Alinejad-Rokny, Azad Khosh, Mostafa Rahnama, Nigel Lovell, Zhenming Xu, Diako Ebrahimi

Plant Pathology Faculty Publications

The zinc finger antiviral protein (ZAP) is known to restrict viral replication by binding to the CpG rich regions of viral RNA, and subsequently inducing viral RNA degradation. This enzyme has recently been shown to be capable of restricting SARS-CoV-2. These data have led to the hypothesis that the low abundance of CpG in the SARS-CoV-2 genome is due to an evolutionary pressure exerted by the host ZAP. To investigate this hypothesis, we performed a detailed analysis of many coronavirus sequences and ZAP RNA binding preference data. Our analyses showed neither evidence for an evolutionary pressure acting specifically on CpG …


Detection Of Methicillin-Resistant Staphylococcus Aureus Infections Using Molecular Methods, Fred C. Tenover, Isabella A. Tickler Feb 2022

Detection Of Methicillin-Resistant Staphylococcus Aureus Infections Using Molecular Methods, Fred C. Tenover, Isabella A. Tickler

Biology Faculty Publications

The application of molecular detection methods for bacterial pathogens has dramatically improved the outcomes of septic patients, including those with methicillin-resistant Staphylococcus aureus (MRSA) infections. Molecular methods can be applied to a variety of clinical specimens including nasal swabs, growth in blood culture bottles, and wounds. While data show that the overall accuracy of molecular tests for MRSA is high, results can be confounded by the presence of multiple staphylococcal species in a specimen, insertions and deletions of DNA in and around the Staphylococcal Cassette Chromosome mec (SCCmec) element, and point mutations in mecA. Herein, we explore the complexities of …


Novel Strategies For Glutamate Clearance In The Glia-Deprived Synaptic Hub Of C. Elegans, Joyce Chan Feb 2022

Novel Strategies For Glutamate Clearance In The Glia-Deprived Synaptic Hub Of C. Elegans, Joyce Chan

Dissertations, Theses, and Capstone Projects

As the major excitatory neurotransmitter in the mammalian brain, Glutamate (Glu) is critical for normal neuronal physiology. Disruption in Glu clearance results in hyper-stimulation of glutamatergic circuits, potentially leading to excitotoxic neurodegeneration. The canonical model of brain connectivity describes glutamatergic synapses as well insulated and enveloped by glia. These glia express Glu Transporters (GluTs) which work to clear Glu following synaptic activity. However, critical areas of the brain such as the mammalian hippocampus display poor synaptic isolation, which may result in Glu spillover between adjacent synapses and subsequent loss of circuit specificity. How accurate signal transmission is achieved in these …


Identifying Gene Network Patterns And Associated Cellular Immune Responses In Children With Or Without Nut Allergy, Khui Hung Lee, Anthony Bosco, Michael O'Sullivan, Yong Song, Jessica Metcalfe, Kan Yu, Benjamin J. Mullins, Richard Loh, Guicheng Zhang Feb 2022

Identifying Gene Network Patterns And Associated Cellular Immune Responses In Children With Or Without Nut Allergy, Khui Hung Lee, Anthony Bosco, Michael O'Sullivan, Yong Song, Jessica Metcalfe, Kan Yu, Benjamin J. Mullins, Richard Loh, Guicheng Zhang

Research outputs 2022 to 2026

Background: Although evidence suggests that the immune system plays a key role in the pathophysiology of nut allergy, the precise immunological mechanisms of nut allergy have not been systematically investigated. The aim of the present study was to identify gene network patterns and associated cellular immune responses in children with or without nut allergy. Methods: Transcriptome profiling of whole blood cells was compared between children with and without nut allergy. Three genes were selected to be validated on a larger cohort of samples (n = 86) by reverse transcription-polymerase chain reactions (RT-qPCR). The composition of immune cells was inferred from …


Extensive Identification Of Genes Involved In Congenital And Structural Heart Disorders And Cardiomyopathy, Nadine Spielmann, Gregor Miller, Tudor I Oprea, Chih-Wei Hsu, Gisela Fobo, Goar Frishman, Corinna Montrone, Hamed Haseli Mashhadi, Jeremy Mason, Violeta Munoz Fuentes, Stefanie Leuchtenberger, Andreas Ruepp, Matias Wagner, Dominik S Westphal, Cordula Wolf, Agnes Görlach, Adrián Sanz-Moreno, Yi-Li Cho, Raffaele Teperino, Stefan Brandmaier, Sapna Sharma, Isabella Rikarda Galter, Manuela A Östereicher, Lilly Zapf, Philipp Mayer-Kuckuk, Jan Rozman, Lydia Teboul, Rosie K A Bunton-Stasyshyn, Heather Cater, Michelle Stewart, Skevoulla Christou, Henrik Westerberg, Amelia M Willett, Janine M Wotton, Willson B Roper, Audrey E Christiansen, Christopher S Ward, Jason D Heaney, Corey L Reynolds, Jan Prochazka, Lynette Bower, David Clary, Mohammed Selloum, Ghina Bou About, Olivia Wendling, Hugues Jacobs, Sophie Leblanc, Hamid Meziane, Tania Sorg, Enrique Audain, Arthur Gilly, Nigel W Rayner, Impc Consortium, Genomics England Research Consortium;, Marc-Phillip Hitz, Eleftheria Zeggini, Eckhard Wolf, Radislav Sedlacek, Steven A Murray, Karen L Svenson, Robert E Braun, Jaqueline K White, Lois Kelsey, Xiang Gao, Toshihiko Shiroishi, Ying Xu, Je Kyung Seong, Fabio Mammano, Glauco P Tocchini-Valentini, Arthur L Beaudet, Terrence F Meehan, Helen Parkinson, Damian Smedley, Ann-Marie Mallon, Sara E Wells, Harald Grallert, Wolfgang Wurst, Susan Marschall, Helmut Fuchs, Steve D M Brown, Ann M Flenniken, Lauryl M J Nutter, Colin Mckerlie, Yann Herault, K C Kent Lloyd, Mary E Dickinson, Valerie Gailus-Durner, Martin Hrabe De Angelis Feb 2022

Extensive Identification Of Genes Involved In Congenital And Structural Heart Disorders And Cardiomyopathy, Nadine Spielmann, Gregor Miller, Tudor I Oprea, Chih-Wei Hsu, Gisela Fobo, Goar Frishman, Corinna Montrone, Hamed Haseli Mashhadi, Jeremy Mason, Violeta Munoz Fuentes, Stefanie Leuchtenberger, Andreas Ruepp, Matias Wagner, Dominik S Westphal, Cordula Wolf, Agnes Görlach, Adrián Sanz-Moreno, Yi-Li Cho, Raffaele Teperino, Stefan Brandmaier, Sapna Sharma, Isabella Rikarda Galter, Manuela A Östereicher, Lilly Zapf, Philipp Mayer-Kuckuk, Jan Rozman, Lydia Teboul, Rosie K A Bunton-Stasyshyn, Heather Cater, Michelle Stewart, Skevoulla Christou, Henrik Westerberg, Amelia M Willett, Janine M Wotton, Willson B Roper, Audrey E Christiansen, Christopher S Ward, Jason D Heaney, Corey L Reynolds, Jan Prochazka, Lynette Bower, David Clary, Mohammed Selloum, Ghina Bou About, Olivia Wendling, Hugues Jacobs, Sophie Leblanc, Hamid Meziane, Tania Sorg, Enrique Audain, Arthur Gilly, Nigel W Rayner, Impc Consortium, Genomics England Research Consortium;, Marc-Phillip Hitz, Eleftheria Zeggini, Eckhard Wolf, Radislav Sedlacek, Steven A Murray, Karen L Svenson, Robert E Braun, Jaqueline K White, Lois Kelsey, Xiang Gao, Toshihiko Shiroishi, Ying Xu, Je Kyung Seong, Fabio Mammano, Glauco P Tocchini-Valentini, Arthur L Beaudet, Terrence F Meehan, Helen Parkinson, Damian Smedley, Ann-Marie Mallon, Sara E Wells, Harald Grallert, Wolfgang Wurst, Susan Marschall, Helmut Fuchs, Steve D M Brown, Ann M Flenniken, Lauryl M J Nutter, Colin Mckerlie, Yann Herault, K C Kent Lloyd, Mary E Dickinson, Valerie Gailus-Durner, Martin Hrabe De Angelis

Faculty, Staff and Students Publications

Clinical presentation of congenital heart disease is heterogeneous, making identification of the disease-causing genes and their genetic pathways and mechanisms of action challenging. By using in vivo electrocardiography, transthoracic echocardiography and microcomputed tomography imaging to screen 3,894 single-gene-null mouse lines for structural and functional cardiac abnormalities, here we identify 705 lines with cardiac arrhythmia, myocardial hypertrophy and/or ventricular dilation. Among these 705 genes, 486 have not been previously associated with cardiac dysfunction in humans, and some of them represent variants of unknown relevance (VUR). Mice with mutations in Casz1, Dnajc18, Pde4dip, Rnf38 or Tmem161b genes show developmental cardiac structural abnormalities, …


Conservation, Comparative Genomics And Species Delimitation Of The Reindeer Lichens (Cladonia), Jordan R. Hoffman Feb 2022

Conservation, Comparative Genomics And Species Delimitation Of The Reindeer Lichens (Cladonia), Jordan R. Hoffman

Dissertations, Theses, and Capstone Projects

The genus Cladonia represents one of the most speciose genera of lichenized fungi, with more than 500 known species encompassing a diverse array of morphologies and habits. These lichens form keystone species in many habitats, serving a variety of ecological roles. However, despite being among of the more well studied lichens, there is much still unknown or under-studied about them. As is the case with most lichen study systems, phylogenetic study has been limited to a small number of partial loci, while adoption of next-generation sequence methods has been slow. As a consequence, there are still knowledge gaps in Cladonia …


A Crispr Toolbox For Generating Intersectional Genetic Mouse Models For Functional, Molecular, And Anatomical Circuit Mapping, Savannah J Lusk, Andrew Mckinney, Patrick J Hunt, Paul G Fahey, Jay Patel, Andersen Chang, Jenny J Sun, Vena K Martinez, Ping Jun Zhu, Jeremy R Egbert, Genevera Allen, Xiaolong Jiang, Benjamin R Arenkiel, Andreas S Tolias, Mauro Costa-Mattioli, Russell S Ray Jan 2022

A Crispr Toolbox For Generating Intersectional Genetic Mouse Models For Functional, Molecular, And Anatomical Circuit Mapping, Savannah J Lusk, Andrew Mckinney, Patrick J Hunt, Paul G Fahey, Jay Patel, Andersen Chang, Jenny J Sun, Vena K Martinez, Ping Jun Zhu, Jeremy R Egbert, Genevera Allen, Xiaolong Jiang, Benjamin R Arenkiel, Andreas S Tolias, Mauro Costa-Mattioli, Russell S Ray

Faculty, Staff and Students Publications

BACKGROUND: The functional understanding of genetic interaction networks and cellular mechanisms governing health and disease requires the dissection, and multifaceted study, of discrete cell subtypes in developing and adult animal models. Recombinase-driven expression of transgenic effector alleles represents a significant and powerful approach to delineate cell populations for functional, molecular, and anatomical studies. In addition to single recombinase systems, the expression of two recombinases in distinct, but partially overlapping, populations allows for more defined target expression. Although the application of this method is becoming increasingly popular, its experimental implementation has been broadly restricted to manipulations of a limited set of …


Data-Driven Modeling Predicts Gene Regulatory Network Dynamics During The Differentiation Of Multipotential Hematopoietic Progenitors, Joanna Handzlik, Manu Jan 2022

Data-Driven Modeling Predicts Gene Regulatory Network Dynamics During The Differentiation Of Multipotential Hematopoietic Progenitors, Joanna Handzlik, Manu

Biology Faculty Publications

Cellular differentiation during hematopoiesis is guided by gene regulatory networks (GRNs) comprising transcription factors (TFs) and the effectors of cytokine signaling. Based largely on analyses conducted at steady state, these GRNs are thought to be organized as a hierarchy of bistable switches, with antagonism between Gata1 and PU.1 driving red- and white-blood cell differentiation. Here, we utilize transient gene expression patterns to infer the genetic architecture—the type and strength of regulatory interconnections—and dynamics of a twelve-gene GRN including key TFs and cytokine receptors. We trained gene circuits, dynamical models that learn genetic architecture, on high temporal-resolution gene-expression data from the …


Clinical Performance Of The Xpert® Ct/Ng Test For Detection Of Chlamydia Trachomatis And Neisseria Gonorrhoeae: A Multicenter Evaluation In Chinese Urban Hospitals, Fred C. Tenover, Yan Han, Mei-Qin Shi, Qing-Ping Jiang, Wen-Jing Le, Xiao-Lin Qin, Han-Zhen Xiong, He-Ping Zheng, Yi-Wei Tang, Yue-Ping Yin Jan 2022

Clinical Performance Of The Xpert® Ct/Ng Test For Detection Of Chlamydia Trachomatis And Neisseria Gonorrhoeae: A Multicenter Evaluation In Chinese Urban Hospitals, Fred C. Tenover, Yan Han, Mei-Qin Shi, Qing-Ping Jiang, Wen-Jing Le, Xiao-Lin Qin, Han-Zhen Xiong, He-Ping Zheng, Yi-Wei Tang, Yue-Ping Yin

Biology Faculty Publications

Background: We aimed to evaluate the clinical performance of the GeneXpert® (Xpert) CT/NG assay for the detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) using urine and cervical swabs collected from patients in China.

Methods: This study was conducted from September 2016 to September 2018 in three Chinese urban hospitals. The results from the Xpert CT/NG test were compared to those from the Roche cobas® 4800 CT/NG test. Discordant results were confirmed by DNA sequence analysis.

Results: In this study, 619 first void urine (FVU) specimens and 1,042 cervical swab specimens were included in the final dataset. There were …


Design Of A Synthetic Temperature-Activated Epigenetic Biocontainment System, Owen Rivers Page Jan 2022

Design Of A Synthetic Temperature-Activated Epigenetic Biocontainment System, Owen Rivers Page

Theses and Dissertations

The need for an internal control to govern engineered strain survival is becoming apparent when considering the biosafety and ethics within biotechnological research. Using understudied regulatory elements known as RNA thermometers (RNATs) that can modulate protein translation based on temperature changes and a Type II restriction modification system, we posit the creation of a synthetic temperature-activated epigenetic biocontainment system, termed the ‘sentinel switch’. We have mined a wide variety of bacteria from Yersinia pestis to Synechocystis sp. looking for novel RNATs. A complementary synthetic biology approach based on library generation and screening of chimeric RNATs (ChRNATs) was also conducted. RNATs …


Cross Species Use Of Human Microarray Genotyping Technology For Bornean Orangutan (Pongo Pygmaeus) Snp Discovery, Ruth Ella Linsky, R. Steven Wagner, Reniastoetie Djojoasmoro, Joseph G. Lorenz, Biruté M. F. Galdikas Jan 2022

Cross Species Use Of Human Microarray Genotyping Technology For Bornean Orangutan (Pongo Pygmaeus) Snp Discovery, Ruth Ella Linsky, R. Steven Wagner, Reniastoetie Djojoasmoro, Joseph G. Lorenz, Biruté M. F. Galdikas

Student Published Works

Previous genetic studies of orangutans (Pongo spp.) have relied mainly upon mitochondrial DNA or microsatellite short tandem repeats (STR) for genomic genotyping analysis. Scientists have yet to take advantage of the genetic closeness of the great apes to humans for genomic analysis by using advanced techniques available for human genotyping. To genotype orangutans at Tanjung Puting National Park, we developed a novel combination of a methyl-based magnetic enrichment capture of genomic fecal DNA with genotyping on a human targeted single nucleotide polymorphism (SNP) microarray, and compared this to additional microsatellite (STR) micro-capillary genotyping. We successfully isolated 125 known human genomic …


Characterization Of Cofilin And Its Potential Role In The Epha4 Pathway, Brian Donald Condron Jan 2022

Characterization Of Cofilin And Its Potential Role In The Epha4 Pathway, Brian Donald Condron

Master's Theses and Doctoral Dissertations

EphA4 is a receptor tyrosine kinase that is responsible for cellular adhesion and locomotion using repulsion signaling in early development of Xenopus laevis. EphA4 regulates cellular locomotion by controlling proteins within its signal transduction pathway, which may include the protein cofilin. Cofilin actively severs and removes actin monomers, thus altering the actin cytoskeleton, leading to the cessation of cellular crawl. During the gastrulation phase of embryonic development, individual cells are relocating to create the three primary germ layers of the organism. Failure of this process to occur results in attrition of the embryos, frequently by way of embryonic exogastrulation. …


Effects Of Sunrise/Sunset Lighting On Corticosterone Levels In Coturnix Quail (Coturnix Coturnix), Hannah M. Feuerborn, Sara K. Orlowski Jan 2022

Effects Of Sunrise/Sunset Lighting On Corticosterone Levels In Coturnix Quail (Coturnix Coturnix), Hannah M. Feuerborn, Sara K. Orlowski

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

Both genetics and environment play important roles in the growth, performance, and overall welfare of poultry species. Current commercial production practices typically do not mimic the natural environmental conditions of ancestral poultry species, specifically lighting. The current study aimed to evaluate the impact of genetics and the effect of sunrise/sunset lighting on the stress response of 4 genetic lines of Coturnix quail. The 4 lines utilized in this study included high stress (H), low stress (L), stress control (R), and Arkansas randombred (A) quail lines. Day old chicks from these lines were placed in one of two environmentally controlled rooms. …