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Articles 3301 - 3330 of 9782

Full-Text Articles in Genetics and Genomics

The Origin Of Novel Trait Inferred From Transcriptomic Analysis And A Targeted Gene Approach In The Beetle Horns., Naureen Fatima Jan 2021

The Origin Of Novel Trait Inferred From Transcriptomic Analysis And A Targeted Gene Approach In The Beetle Horns., Naureen Fatima

Graduate Theses, Dissertations, and Problem Reports (ETD)

The origin of the evolutionary new trait (evolutionary novelty) and its subsequent evolution is of great interest for biologists in various fields, and beetle horns have been used to address this fundamental biological question. Previous studies on one of the horned beetle species, Onthophagus taurus, that utilized comparative gene expression analyses, suggested legs to be a strong candidate of the origin of horns. At the same time, their horns are secondary sexual traits whose development is regulated by the same gene (doublesex) as genitalia, which also originates from paired appendages such as legs. However, little is known …

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Open Problems In Extracellular Rna Data Analysis: Insights From An Ercc Online Workshop, Roger P Alexander, Robert R Kitchen, Juan Pablo Tosar, Matthew Roth, Pieter Mestdagh, Klaas E A Max, Joel Rozowsky, Karolina Elżbieta Kaczor-Urbanowicz, Justin Chang, Leonora Balaj, Bojan Losic, Eric L Van Nostrand, Emily Laplante, Bogdan Mateescu, Brian S White, Rongshan Yu, Aleksander Milosavljevic, Gustavo Stolovitzky, Ryan M Spengler Jan 2021

Open Problems In Extracellular Rna Data Analysis: Insights From An Ercc Online Workshop, Roger P Alexander, Robert R Kitchen, Juan Pablo Tosar, Matthew Roth, Pieter Mestdagh, Klaas E A Max, Joel Rozowsky, Karolina Elżbieta Kaczor-Urbanowicz, Justin Chang, Leonora Balaj, Bojan Losic, Eric L Van Nostrand, Emily Laplante, Bogdan Mateescu, Brian S White, Rongshan Yu, Aleksander Milosavljevic, Gustavo Stolovitzky, Ryan M Spengler

Faculty, Staff and Students Publications

We now know RNA can survive the harsh environment of biofluids when encapsulated in vesicles or by associating with lipoproteins or RNA binding proteins. These extracellular RNA (exRNA) play a role in intercellular signaling, serve as biomarkers of disease, and form the basis of new strategies for disease treatment. The Extracellular RNA Communication Consortium (ERCC) hosted a two-day online workshop (April 19–20, 2021) on the unique challenges of exRNA data analysis. The goal was to foster an open dialog about best practices and discuss open problems in the field, focusing initially on small exRNA sequencing data. Video recordings of workshop …

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Novel Mutations In The Gtpbp3 Gene For Mitochondrial Disease And Characteristics Of Related Phenotypic Spectrum: The First Three Cases From China, Hui-Ming Yan, Zhi-Mei Liu, Bei Cao, Victor Wei Zhang, Yi-Duo He, Zheng-Jun Jia, Hui Xi, Jing Liu, Fang Fang, Hua Wang Jan 2021

Novel Mutations In The Gtpbp3 Gene For Mitochondrial Disease And Characteristics Of Related Phenotypic Spectrum: The First Three Cases From China, Hui-Ming Yan, Zhi-Mei Liu, Bei Cao, Victor Wei Zhang, Yi-Duo He, Zheng-Jun Jia, Hui Xi, Jing Liu, Fang Fang, Hua Wang

Faculty, Staff and Students Publications

Combined Oxidative Phosphorylation Deficiency 23 (COXPD23) caused by mutations in GTPBP3 gene is a rare mitochondrial disease, and this disorder identified from the Chinese population has not been described thus far. Here, we report a case series of three patients with COXPD23 caused by GTPBP3 mutations, from a severe to a mild phenotype. The main clinical features of these patients include lactic acidosis, myocardial damage, and neurologic symptoms. Whole genome sequencing and targeted panels of candidate human mitochondrial genome revealed that patient 1 was a compound heterozygote with novel mutations c.413C > T (p. A138V) and c.509_510del (p. E170Gfs∗42) in GTPBP3 …

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Population Genetics Of A Reintroduced Fisher (Pekania Pennanti) Population In West Virginia, Caroline E. Harms Jan 2021

Population Genetics Of A Reintroduced Fisher (Pekania Pennanti) Population In West Virginia, Caroline E. Harms

Graduate Theses, Dissertations, and Problem Reports (ETD)

Fishers (Pekania pennanti) were reintroduced in West Virginia in 1969 with no population wide genetic analysis ever having been conducted. Genetic analysis of reintroduced populations is vital to assess genetic diversity as an indicative of population viability. My objective was to collect fisher samples throughout West Virginia, nearby states where fisher may be migrating (PA and NY), and the New Hampshire source population to provide a full genetic interpretation of the reintroduced West Virginia population. Genetic analysis was used to measure genetic diversity, admixture or delineation of subpopulations, and effective population size. Sample location and genetic data were …

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Initial And Advanced Stages Of Microbiota Establishment Within The Tsetse Fly, Miguel Eduardo Medina Munoz Jan 2021

Initial And Advanced Stages Of Microbiota Establishment Within The Tsetse Fly, Miguel Eduardo Medina Munoz

Graduate Theses, Dissertations, and Problem Reports (ETD)

Symbiosis is a long-term physical association between two or more species, although little is known regarding its evolutionary origins, particularly at the genetic level. Tsetse flies are the vector of African trypanosomes, causative agents of Human and Animal African Trypanosomiases. Tsetse provide an ideal model for studying initial and advanced stages of symbiosis. Tsetse have a simple digestive tract microbiota primarily consisting of two bacteria; the ancient mutualist Wigglesworthia glossinidia and the recently acquired Sodalis glossinidius. This work presents a chronological study in evolutionary terms of the history of a microbial-insect association. First, I present concepts on symbiosis and …

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Estrogen Disruption Of Hypothalamic Neural Activity, Princess Dickson Jan 2021

Estrogen Disruption Of Hypothalamic Neural Activity, Princess Dickson

Cal Poly Humboldt theses and projects

The brain is highly dependent on the endocrine system for proper neurodevelopment, as it plays a key role in many biological processes. Bisphenol A is a chemical found in plastics that has the potential to mimic the effects of Estrogen in the body, at least weakly. People interact with plastic that contains BPA regularly, and people are at risk for exposure even before being born. The abundance of BPA, along with other exogenous estrogens, makes examining the relationship between early exposure and changes in brain activity imperative. The current study aims to establish a relationship between disrupted estrogen function and …

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The Receptor Basis Of Serotonergic Modulation In An Olfactory Network, Tyler Ryan Sizemore Jan 2021

The Receptor Basis Of Serotonergic Modulation In An Olfactory Network, Tyler Ryan Sizemore

Graduate Theses, Dissertations, and Problem Reports (ETD)

Neuromodulation is a nearly ubiquitous process that endows the nervous system with the capacity to alter neural function at every level (synaptic, circuit, network, etc.) without necessarily adding new neurons. Through the actions of neuromodulators, the existing neural circuitry can be adaptively tuned to achieve flexible network output and similarly dynamic behavioral output. However, despite their near ubiquity in all sensory modalities, the mechanisms underlying neuromodulation of sensory processing remain poorly understood. In this dissertation, I address three main questions regarding the mechanisms of one modulator (serotonin) within one sensory modality (olfaction). I begin by establishing a "functional atlas" of …

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Tree Species Influence On Microbial Functional Gene Abundance And N Cycling In Riparian Soil, Elizabeth Matejczyk Jan 2021

Tree Species Influence On Microbial Functional Gene Abundance And N Cycling In Riparian Soil, Elizabeth Matejczyk

Graduate Theses, Dissertations, and Problem Reports (ETD)

Little is known about how above-ground vegetation may differentially influence the below-ground microbial community structure, abundance, and function. Abundance of soil microbial N cycling genes responsible for nitrification (amoA), denitrification (nirK and nirS), and nitrous oxide reduction (nosZ) may vary with tree species and increasing N availability, and these variables may be used to predict production of NO3- and N2O from soil. Variability of nitrification and denitrification rates have also been linked to tree mycorrhizal associations, with soil beneath tree species associated with arbuscular mycorrhizal (AM) exhibiting greater denitrification rates …

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Effects Of 4-Methylcyclohexanemethanol On Stress Response Pathway Regulators, In Saccharomyces Cerevisiae, Suk Lan Ser Jan 2021

Effects Of 4-Methylcyclohexanemethanol On Stress Response Pathway Regulators, In Saccharomyces Cerevisiae, Suk Lan Ser

Graduate Theses, Dissertations, and Problem Reports (ETD)

Hydrotropes are small molecules capable of inducing liquid-liquid phase separation by altering the solubility and conformation states of organic compounds that are increasingly becoming important in organizing chemical reactions and regulating complexes. They prevent protein aggregation causing these proteins to form condensates. Mediator, a highly conserved multi-subunit complex, plays an important role in transcription. Med15, a subunit found within the tail domain of the Mediator complex, works with stress-induced transcription factors and is regulated by many kinases, including CDKs and the AMP kinase, Snf1. Living cells respond by changing molecular and cellular pathways when they are exposed to stressful conditions. …

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A Hybrid Gene Selection Strategy Based On Fisher And Ant Colony Optimization Algorithm For Breast Cancer Classification, Mohammed Hamim, Ismail El Moudden, Mohan D. Pant, Hicham Moutachaouik, Mustapha Hain Jan 2021

A Hybrid Gene Selection Strategy Based On Fisher And Ant Colony Optimization Algorithm For Breast Cancer Classification, Mohammed Hamim, Ismail El Moudden, Mohan D. Pant, Hicham Moutachaouik, Mustapha Hain

EVMS School of Health Professions Faculty Publications

Breast cancer poses the greatest threat to human life and especially to women's life. Despite the progress made in data mining technology in recent years, the ability to predict and diagnose such fatal diseases based on gene expression data still reveals a limited prediction performance, which may not be surprising since most of the genes in expression data are believed to be irrelevant or redundant. The dimensionality reduction process may be considered as a crucial step to analyze gene expression data, as it can reduce the high dimensionality of the breast cancer datasets, which may result into a better prediction …

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Fungal Planet Description Sheets: 1112–1181, P. W. Crous, D. A. Cowan, G. Maggs-Kölling, N. Yilmaz, E. Larsson, C. Angelini, T. E. Brandrud, J. D. W. Dearnaley, B. Dima, F. Dovana, Et Al. Dec 2020

Fungal Planet Description Sheets: 1112–1181, P. W. Crous, D. A. Cowan, G. Maggs-Kölling, N. Yilmaz, E. Larsson, C. Angelini, T. E. Brandrud, J. D. W. Dearnaley, B. Dima, F. Dovana, Et Al.

Aspen Bibliography

Novel species of fungi described in this study include those from various countries as follows: Australia, Austroboletus asper on soil, Cylindromonium alloxyli on leaves of Alloxylon pinnatum, Davidhawksworthia quintiniae on leaves of Quintinia sieberi, Exophiala prostantherae on leaves of Prostanthera sp., Lactifluus lactiglaucus on soil, Linteromyces quintiniae (incl. Linteromyces gen. nov.) on leaves of Quintinia sieberi, Lophotrichus medusoides from stem tissue of Citrus garrawayi, Mycena pulchra on soil, Neocalonectria tristaniopsidis (incl. Neocalonectria gen. nov.) and Xyladictyochaeta tristaniopsidis on leaves of Tristaniopsis collina, Parasarocladium tasmanniae on leaves of Tasmannia insipida, Phytophthora aquae-cooljarloo from pond water, Serendipita whamiae as …

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A Cophylogenetic Analysis Of Fungus Gardening Ants And Their Symbiotic Fungi, Katherine Beigel Dec 2020

A Cophylogenetic Analysis Of Fungus Gardening Ants And Their Symbiotic Fungi, Katherine Beigel

Biology Theses

Fungus-growing ants (Tribe Attini) and their fungal cultivars share a 50-million-year coevolutionary history. Large scale phylogenetic analyses depict a strong co-phyletic signal among ants and their farmed fungi yet fungus sharing among unrelated ant lineages is somewhat widespread. An overview of sharing has been hampered by a lack of genetic markers that exhibit intraspecific variation and surveys across geographic regions. For example, previous studies have shown similar sequences of the internal transcribed spacer (ITS) region of fungus in different species of Trachymyrmex, suggesting that these ant species are farming the same fungal clone. To examine whether this was a …

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A Molecular Toolset For The In Vivo Detection Of A Sulfolobus Islandicus Leucyl Trna Synthetase Paralog, Nicholas Michael Bretz Dec 2020

A Molecular Toolset For The In Vivo Detection Of A Sulfolobus Islandicus Leucyl Trna Synthetase Paralog, Nicholas Michael Bretz

Theses and Dissertations

An ancient and ubiquitous set of enzymes known as the aminoacyl-tRNA synthetases are required for the viability of all organisms. The aminoacyl-tRNA synthetases catalyze the attachment of amino acids onto tRNA molecules. The aminoacylated, or charged, tRNA is then transported and utilized at the ribosome for the synthesis of proteins. The genome of the hyperthermophilic microorganism Sulfolobus islandicus (S. islandicus) harbors a unique leucyl-tRNA synthetase paralog, LeuRS-I, of unknown function. While its duplicate, LeuRS-F, carries out all the classical functions of LeuRS-family enzymes, LeuRS-I fails to charge leucine onto tRNALeu, despite its ability to activate this amino acid and bind …

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Genomic Adaptations And Evolutionary History Of The Extinct Scimitar-Toothed Cat, Homotherium Latidens, Ross Barnett, Michael V. Westbury, Marcela Sandoval-Velasco, Filipe Garrett Vieira, Sungwon Jeon, Grant Zazula, Michael D. Martin, Simon Y.W. Ho, Niklas Mather, Shyam Gopalakrishnan, Jazmín Ramos-Madrigal, Marc De Manuel, M. Lisandra Zepeda-Mendoza, Agostinho Antunes, Aldo Carmona Baez, Binia De Cahsan, Greger Larson, Stephen J. O'Brien, Eduardo Eizirik, Warren E. Johnson, Klaus Peter Koepfli, Andreas Wilting, Jörns Fickel, Love Dalén, Eline D. Lorenzen, Tomas Marques-Bonet, Anders J. Hansen, Guojie Zhang, Jong Bhak Dec 2020

Genomic Adaptations And Evolutionary History Of The Extinct Scimitar-Toothed Cat, Homotherium Latidens, Ross Barnett, Michael V. Westbury, Marcela Sandoval-Velasco, Filipe Garrett Vieira, Sungwon Jeon, Grant Zazula, Michael D. Martin, Simon Y.W. Ho, Niklas Mather, Shyam Gopalakrishnan, Jazmín Ramos-Madrigal, Marc De Manuel, M. Lisandra Zepeda-Mendoza, Agostinho Antunes, Aldo Carmona Baez, Binia De Cahsan, Greger Larson, Stephen J. O'Brien, Eduardo Eizirik, Warren E. Johnson, Klaus Peter Koepfli, Andreas Wilting, Jörns Fickel, Love Dalén, Eline D. Lorenzen, Tomas Marques-Bonet, Anders J. Hansen, Guojie Zhang, Jong Bhak

Biology Faculty Articles

Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1–4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6–8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread …

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Ogre-Faced, Net-Casting Spiders Use Auditory Cues To Detect Airborne Prey, Jay A. Stafstrom, Gil Menda, Eya I. Nitzany, Eileen A. Hebets, Ronald R. Hoy Dec 2020

Ogre-Faced, Net-Casting Spiders Use Auditory Cues To Detect Airborne Prey, Jay A. Stafstrom, Gil Menda, Eya I. Nitzany, Eileen A. Hebets, Ronald R. Hoy

Eileen Hebets Publications

Prey-capture behavior among spiders varies greatly from passive entrapment in webs to running down prey items on foot. Somewhere in the middle are the ogre-faced, net-casting spiders (Deinopidae: Deinopis) that actively capture prey while being suspended within a frame web. Using a net held between their front four legs, these spiders lunge downward to ensnare prey from off the ground beneath them. This “forward strike” is sensorially mediated by a massive pair of hypersensitive, night-vision eyes. Deinopids can also intercept flying insects with a “backward strike,” a ballistically rapid, overhead back-twist, that seems not to rely on visual cues. Past …

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Loss-Of-Function Genomic Variants Highlight Potential Therapeutic Targets For Cardiovascular Disease, Jonas B. Nielsen, Oren Rom, Ida Surakka, Sarah E. Graham, Wei Zhou, Tanmoy Roychowdhury, Lars G. Fritsche, Sarah A. Gagliano Taliun, Carlo Sidore, Yuhao Liu, Maiken E. Gabrielsen, Anne Heidi Skogholt, Brooke Wolford, William Overton, Ying Zhao, Jin Chen, He Zhang, Whitney E. Hornsby, Akua Acheampong, Austen Grooms, Amanda Schaefer, Gregory J. M. Zajac, Luis Villacorta, Jifeng Zhang, Ben Brumpton, Mari Løset, Vivek Rai, Pia R. Lundegaard, Morten S. Olesen, Kent D. Taylor, Donna K. Arnett Dec 2020

Loss-Of-Function Genomic Variants Highlight Potential Therapeutic Targets For Cardiovascular Disease, Jonas B. Nielsen, Oren Rom, Ida Surakka, Sarah E. Graham, Wei Zhou, Tanmoy Roychowdhury, Lars G. Fritsche, Sarah A. Gagliano Taliun, Carlo Sidore, Yuhao Liu, Maiken E. Gabrielsen, Anne Heidi Skogholt, Brooke Wolford, William Overton, Ying Zhao, Jin Chen, He Zhang, Whitney E. Hornsby, Akua Acheampong, Austen Grooms, Amanda Schaefer, Gregory J. M. Zajac, Luis Villacorta, Jifeng Zhang, Ben Brumpton, Mari Løset, Vivek Rai, Pia R. Lundegaard, Morten S. Olesen, Kent D. Taylor, Donna K. Arnett

Epidemiology and Environmental Health Faculty Publications

Pharmaceutical drugs targeting dyslipidemia and cardiovascular disease (CVD) may increase the risk of fatty liver disease and other metabolic disorders. To identify potential novel CVD drug targets without these adverse effects, we perform genome-wide analyses of participants in the HUNT Study in Norway (n = 69,479) to search for protein-altering variants with beneficial impact on quantitative blood traits related to cardiovascular disease, but without detrimental impact on liver function. We identify 76 (11 previously unreported) presumed causal protein-altering variants associated with one or more CVD- or liver-related blood traits. Nine of the variants are predicted to result in loss-of-function of …

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Absolute Quantification Of Transcription Factors In Human Erythropoiesis Using Selected Reaction Monitoring Mass Spectrometry., Mark A Gillespie, Carmen G Palii, Daniel Sanchez-Taltavull, Theodore J Perkins, Marjorie Brand, Jeffrey A Ranish Dec 2020

Absolute Quantification Of Transcription Factors In Human Erythropoiesis Using Selected Reaction Monitoring Mass Spectrometry., Mark A Gillespie, Carmen G Palii, Daniel Sanchez-Taltavull, Theodore J Perkins, Marjorie Brand, Jeffrey A Ranish

Articles, Abstracts, and Reports

Quantitative changes in transcription factor (TF) abundance regulate dynamic cellular processes, including cell fate decisions. Protein copy number provides information about the relative stoichiometry of TFs that can be used to determine how quantitative changes in TF abundance influence gene regulatory networks. In this protocol, we describe a targeted selected reaction monitoring (SRM)-based mass-spectrometry method to systematically measure the absolute protein concentration of nuclear TFs as human hematopoietic stem and progenitor cells differentiate along the erythropoietic lineage. For complete details on the use and execution of this protocol, please refer to Gillespie et al. (2020).

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Dna Polymerase Ε: Replication Error Prevention And Consequences Of A Cancer-Associated Mutation, Chelsea R. Bulock Dec 2020

Dna Polymerase Ε: Replication Error Prevention And Consequences Of A Cancer-Associated Mutation, Chelsea R. Bulock

Theses & Dissertations

Genome integrity is necessary to prevent mutations and disease. During eukaryotic DNA replication, DNA polymerases ε (Polε) and δ (Polδ) synthesize the leading and lagging strand, respectively. Polε and Polδ also have exonuclease activity that acts in series with post-replicative mismatch repair (MMR) to remove replication errors. Defects in proofreading and MMR lead to an increase in mutations and cause cancer in humans. This dissertation focuses on several unresolved issues involving the relationship between Polε and Polδ in replication error avoidance. First, despite an abundance of data supporting the one-strand-one-polymerase replication fork model, defects in the fidelity of Polε have …

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Multistrain Hiv-1 Elimination: A Crispr-Cas9 And Theranostics-Based Approach, Jonathan Herskovitz Dec 2020

Multistrain Hiv-1 Elimination: A Crispr-Cas9 And Theranostics-Based Approach, Jonathan Herskovitz

Theses & Dissertations

A critical barrier to achieving a functional cure for infection by human immunodeficiency virus type one (HIV-1) rests in the presence of latent proviral DNA integrated in the nuclei of host CD4+ T cells and mononuclear phagocytes. Accordingly, HIV-1-infected patients must adhere to lifelong regimens of antiretroviral therapy (ART) to prevent viral rebound, CD4+ T cell decline, and progression to acquired immunodeficiency syndrome (AIDS). Gene editing using clustered regularly interspersed short palindromic repeat (CRISPR)-Cas9 technology stands as one means to inactivate integrated proviral DNA. We devised a mosaic gRNA CRISPR-Cas9 system- TatDE- that targets viral transcriptional regulator genes tat / …

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Diagnosis And Distribution Of Florida Sand Darter, Ammocrypta Bifascia (Teleostei; Percidae), In The Flint River, Georgia, Camm C. Swift, Gregory R. Moyer, Christine E. Fallon, Brett Albanese Dec 2020

Diagnosis And Distribution Of Florida Sand Darter, Ammocrypta Bifascia (Teleostei; Percidae), In The Flint River, Georgia, Camm C. Swift, Gregory R. Moyer, Christine E. Fallon, Brett Albanese

Southeastern Fishes Council Proceedings

Abstract: In 2013, we observed the presence of an undocumented Ammocrypta species in the lower Flint River, Georgia. The occurrence represents the first record of the genus in Georgia. Subsequent surveys at 24 sites, using seining or snorkeling, documented additional specimens from mainstem sites (n = 3) between Albany and Bainbridge and from Ichawaynochaway Creek (n = 5 sites), a large tributary to the Flint River. We used morphological and genetic data to identify specimens to species. Morphological examination included 23 morphometric and 8 meristic characters from fifteen specimens that were compared to specimens from Williams (1975). For genetic analyses, …

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Single-Fluorophore Sensors For Mechanical Force In Living Cells, Sarah Kricheff Dec 2020

Single-Fluorophore Sensors For Mechanical Force In Living Cells, Sarah Kricheff

Honors Scholar Theses

Mechanotransduction is the process by which a mechanical stimulus is converted to a cellular signal. This process is heavily influential of cell morphology, differentiation, and behavior. However, altered levels of mechanical stimuli are also found in many pathological contexts. For example, cancerous cells have stiffer surrounding tissue than healthy cells, and research suggests that this alters cell behavior and promotes metastasis. Despite these findings, the cellular processes behind these signaling alterations remain widely unknown. Understanding these cascades is critical, as involved proteins can give us a deeper understanding of the role of mechanotransduction, and certain proteins can potentially be targeted …

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The Deleterious F109s Mutation Disrupts Binding Of Sex-Determining Region Y With Dna, Mohammed Baqur S. Al-Shuhaib Mbsa Dec 2020

The Deleterious F109s Mutation Disrupts Binding Of Sex-Determining Region Y With Dna, Mohammed Baqur S. Al-Shuhaib Mbsa

Karbala International Journal of Modern Science

Sex-determining region Y (SRY) protein is the master switch in the initiation of male sex differentiation. Mutation in SRY gene results in ambiguous genitalia and abnormalities in reproductive organs. Its function is mainly controlled by its high mobility group (HMG) box. Damage to the HMG box may cause dysfunction of the SRY protein, which may, in turn, lead to sex reversal. This study was conducted to prioritize the deleterious effects of the non-synonymous single nucleotide polymorphisms (nsSNPs) on SRY protein. A series of computational tools were applied to predict nsSNPs with the most harmful effects on protein structure, function, and …

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Innate Pathogenic Traits In Oral Yeasts, Ayat Ibrahiem Esmaeel Al-Laaeiby, Adnan A. Al-Mousawi, Inaam M.N. Alrubayae, Abdullah Al-Saadoon, Maysoon Almayahi Dec 2020

Innate Pathogenic Traits In Oral Yeasts, Ayat Ibrahiem Esmaeel Al-Laaeiby, Adnan A. Al-Mousawi, Inaam M.N. Alrubayae, Abdullah Al-Saadoon, Maysoon Almayahi

Karbala International Journal of Modern Science

The normal flora community plays a significant role in both healthy and patient individual’s bodies. It has improved its ability to change from beneficial to opportunistic organisms causing crucial infections in immunocompromised patients. This study was conducted to identify the community of yeast species, and to investigate potential virulence factors. Saliva samples were collected from healthy individuals, yeast species were isolated and identified using both traditional and advance molecular genetics technique. The results revealed that Candida albicans was the dominant isolate, while Meyerozyma caribbica was the least. The phylogenetic tree was constructed for 13 species using the Neighbour-Joining method, which …

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Molecular Identification, Antioxidant Efficacy Of Phenolic Compounds, And Antimicrobial Activity Of Beta-Carotene Isolated From Fruiting Bodies Of Suillus Sp, Shimal Yonuis Abdulhadi, Raghad Nawaf Gergees, Ghazwan Qasim Hasan Dec 2020

Molecular Identification, Antioxidant Efficacy Of Phenolic Compounds, And Antimicrobial Activity Of Beta-Carotene Isolated From Fruiting Bodies Of Suillus Sp, Shimal Yonuis Abdulhadi, Raghad Nawaf Gergees, Ghazwan Qasim Hasan

Karbala International Journal of Modern Science

Suillus species, in general, are edible mushrooms, and environmentally important that are associated mostly with pine trees in the tropics regions. These fungi considered a remarkable source of phenolic compounds that play a crucial role as antioxidants which may reduce the risk of most human chronic diseases such as cancer, diabetes, asthma, atherosclerosis, Alzheimer, and others. On the other hand, carotenoids (β carotene) are the most popular natural pigments which play an important role to protect the plants from photo-oxidative reactions. In human, these compounds prevent oxidative stress and expects to have antimicrobial activity. Here, the phenolic compounds were …

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The Role Of Anti-Inflammatory Cytokine Interleukin-10 (Il-10) In Tauopathies, Lea L. Weston Dec 2020

The Role Of Anti-Inflammatory Cytokine Interleukin-10 (Il-10) In Tauopathies, Lea L. Weston

Biomedical Sciences ETDs

Tauopathies are neurodegenerative diseases, including Alzheimer’s disease, that are associated with pathological accumulation of the microtubule associated protein tau (MAPT, or tau) (Lee et al., 2001). Abnormal hyperphosphorylated tau (pTau) strongly correlate with cognitive impairment (Nelson et al., 2012). Neuroinflammation is also associated with tauopathies (Gerhard et al., 2006b; Edison et al., 2008) and is implicated in driving tau pathology (Yoshiyama et al., 2007, Maphis et al., 2015b). Therefore, it is compelling to understand the role of anti-inflammatory cytokines in limiting neuroinflammation and tau pathology. Interleukin-10 (IL-10) is a well-established anti-inflammatory cytokine with roles in limiting inflammation in the central …

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Ultracontinuous Single Haplotype Genome Assemblies For The Domestic Cat (Felis Catus) And Asian Leopard Cat (Prionailurus Bengalensis), Kevin R. Bredemeyer, Andrew J. Harris, Gang Li, Le Zhao, Nicole M. Foley, Melody E. Roelke-Parker, Stephen James O'Brien, Leslie A. Lyons, Wesley C. Warren, William J. Murphy Dec 2020

Ultracontinuous Single Haplotype Genome Assemblies For The Domestic Cat (Felis Catus) And Asian Leopard Cat (Prionailurus Bengalensis), Kevin R. Bredemeyer, Andrew J. Harris, Gang Li, Le Zhao, Nicole M. Foley, Melody E. Roelke-Parker, Stephen James O'Brien, Leslie A. Lyons, Wesley C. Warren, William J. Murphy

Biology Faculty Articles

In addition to including one of the most popular companion animals, species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease, as well as for the study of phenotypic evolution and speciation. Previous diploid-based genome assemblies for the domestic cat have served as the primary reference for genomic studies within the cat family. However, these versions suffered from poor resolution of complex and highly repetitive regions, with substantial amounts of unplaced sequence that is polymorphic or copy number variable. We sequenced the genome of a female F1 Bengal hybrid cat, the …

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Pathway‐Extended Gene Expression Signatures Integrate Novel Biomarkers That Improve Predictions Of Patient Responses To Kinase Inhibitors, Ashis Bagchee‐Clark, Eliseos J. Mucaki, Tyson Whitehead, Peter Rogan Dec 2020

Pathway‐Extended Gene Expression Signatures Integrate Novel Biomarkers That Improve Predictions Of Patient Responses To Kinase Inhibitors, Ashis Bagchee‐Clark, Eliseos J. Mucaki, Tyson Whitehead, Peter Rogan

Biochemistry Publications

Cancer chemotherapy responses have been related to multiple pharmacogenetic biomarkers, often for the same drug. This study utilizes machine learning to derive multi‐gene expression signatures that predict individual patient responses to specific tyrosine kinase inhibitors, including erlotinib, gefitinib, sorafenib, sunitinib, lapatinib and imatinib. Support vector machine (SVM) learning was used to train mathematical models that distinguished sensitivity from resistance to these drugs using a novel systems biology‐based approach. This began with expression of genes previously implicated in specific drug responses, then expanded to evaluate genes whose products were related through biochemical pathways and interactions. Optimal pathway‐extended SVMs predicted responses in …

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Karyotype Evolution In 10 Pinniped Species: Variability Of Heterochromatin Versus High Conservatism Of Euchromatin As Revealed By Comparative Molecular Cytogenetics, Violetta R. Beklemisheva, Polina L. Perelman, Natalya A. Lemskaya, Anastasiya A. Proskuryakova, Natalya A. Serdyukova, Vladimir N. Burkanov, Maksim B. Gorshunov, Oliver A. Ryder, Mary Thompson, Gina Lento, Stephen James O'Brien, Alexander S. Graphodatsky Dec 2020

Karyotype Evolution In 10 Pinniped Species: Variability Of Heterochromatin Versus High Conservatism Of Euchromatin As Revealed By Comparative Molecular Cytogenetics, Violetta R. Beklemisheva, Polina L. Perelman, Natalya A. Lemskaya, Anastasiya A. Proskuryakova, Natalya A. Serdyukova, Vladimir N. Burkanov, Maksim B. Gorshunov, Oliver A. Ryder, Mary Thompson, Gina Lento, Stephen James O'Brien, Alexander S. Graphodatsky

Biology Faculty Articles

Pinnipedia karyotype evolution was studied here using human, domestic dog, and stone marten whole-chromosome painting probes to obtain comparative chromosome maps among species of Odobenidae (Odobenus rosmarus), Phocidae (Phoca vitulina, Phoca largha, Phoca hispida, Pusa sibirica, Erignathus barbatus), and Otariidae (Eumetopias jubatus, Callorhinus ursinus, Phocarctos hookeri, and Arctocephalus forsteri). Structural and functional chromosomal features were assessed with telomere repeat and ribosomal-DNA probes and by CBG (C-bands revealed by barium hydroxide treatment followed by Giemsa staining) and CDAG (Chromomycin A3-DAPI after G-banding) methods. We demonstrated diversity of heterochromatin among pinniped karyotypes in terms of localization, …

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Systematic Comparison Of Sea Urchin And Sea Star Developmental Gene Regulatory Networks Explains How Novelty Is Incorporated In Early Development., Gregory A Cary, Brenna S Mccauley, Olga Zueva, Joseph Pattinato, William J R Longabaugh, Veronica F Hinman Dec 2020

Systematic Comparison Of Sea Urchin And Sea Star Developmental Gene Regulatory Networks Explains How Novelty Is Incorporated In Early Development., Gregory A Cary, Brenna S Mccauley, Olga Zueva, Joseph Pattinato, William J R Longabaugh, Veronica F Hinman

Articles, Abstracts, and Reports

The extensive array of morphological diversity among animal taxa represents the product of millions of years of evolution. Morphology is the output of development, therefore phenotypic evolution arises from changes to the topology of the gene regulatory networks (GRNs) that control the highly coordinated process of embryogenesis. A particular challenge in understanding the origins of animal diversity lies in determining how GRNs incorporate novelty while preserving the overall stability of the network, and hence, embryonic viability. Here we assemble a comprehensive GRN for endomesoderm specification in the sea star from zygote through gastrulation that corresponds to the GRN for sea …

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Aspen Soils Retain More Dissolved Organic Carbon Than Conifer Soils In A Sorption Experiment, Antra Boča, Astrid R. Jacobson, Helga Van Miegroet Dec 2020

Aspen Soils Retain More Dissolved Organic Carbon Than Conifer Soils In A Sorption Experiment, Antra Boča, Astrid R. Jacobson, Helga Van Miegroet

Aspen Bibliography

The effect tree species have on soil organic carbon (SOC) has been hotly debated but, so far, few clear patterns have emerged. One example of a differing tree species effect on SOC are aspen forests in North America, which have been found to have more stable SOC than adjacent conifer forest stands. An important source for the formation of stable organo-mineral complexes in soil is dissolved organic carbon (DOC). DOC concentrations in mineral soil are often higher under the thick O-horizons of conifer forests than under aspen forests, but this does not correspond to more stable mineral SOC. This suggests …

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