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2020

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Articles 1 - 30 of 562

Full-Text Articles in Genetics and Genomics

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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An Examination Of The Influence Of Multi-Scale Processes And Connectivity On The Population And Assemblage Dynamics Of Headwater Fishes, Josh P. Hubbell Dec 2020

An Examination Of The Influence Of Multi-Scale Processes And Connectivity On The Population And Assemblage Dynamics Of Headwater Fishes, Josh P. Hubbell

Dissertations

Typified by their branching pattern, headwaters are numerically abundant as the density of these habitats increases with increasing distance from the base of a dendritic river system. Connectivity among headwaters is complex, resulting in the spatial isolation of populations. Headwater specialists have evolved a suite of traits that permit these species to permanently reside within these habitats. The spatial configuration and connectivity of headwaters has repercussions for metapopulations and meta-assemblages. I investigated how multi-scale processes and connectivity influenced the patch occupancy, coexistence, movement ecology, population structure, and gene flow of headwater specialists. In chapter two, I used occupancy modeling to …

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Draft Genome Of The Common Snapping Turtle, Chelydra Serpentina, A Model For Phenotypic Plasticity In Reptiles, Debojyoti Das, Sunil Kumar Singh, Jacob Bierstedt, Alyssa Erickson, Gina L. J. Galli, Dane A. Crossley Ii, Turk Rhen Dec 2020

Draft Genome Of The Common Snapping Turtle, Chelydra Serpentina, A Model For Phenotypic Plasticity In Reptiles, Debojyoti Das, Sunil Kumar Singh, Jacob Bierstedt, Alyssa Erickson, Gina L. J. Galli, Dane A. Crossley Ii, Turk Rhen

Biology Faculty Publications

Turtles are iconic reptiles that inhabit a range of ecosystems from oceans to deserts and climates from the tropics to northern temperate regions. Yet, we have little understanding of the genetic adaptations that allow turtles to survive and reproduce in such diverse environments. Common snapping turtles, Chelydra serpentina, are an ideal model species for studying adaptation to climate because they are widely distributed from tropical to northern temperate zones in North America. They are also easy to maintain and breed in captivity and produce large clutch sizes, which makes them amenable to quantitative genetic and molecular genetic studies of …

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Persort Facilitates Characterization And Elimination Of Persister Subpopulation In Mycobacteria., Vivek Srinivas, Mario L Arrieta-Ortiz, Amardeep Kaur, Eliza Jr Peterson, Nitin Baliga Dec 2020

Persort Facilitates Characterization And Elimination Of Persister Subpopulation In Mycobacteria., Vivek Srinivas, Mario L Arrieta-Ortiz, Amardeep Kaur, Eliza Jr Peterson, Nitin Baliga

Articles, Abstracts, and Reports

Mycobacterium tuberculosis (MTB) generates phenotypic diversity to persist and survive the harsh conditions encountered during infection. MTB avoids immune effectors and antibacterial killing by entering into distinct physiological states. The surviving cells, persisters, are a major barrier to the timely and relapse-free treatment of tuberculosis (TB). We present for the first time, PerSort, a method to isolate and characterize persisters in the absence of antibiotic or other pressure. We demonstrate the value of PerSort to isolate translationally dormant cells that preexisted in small numbers within Mycobacterium species cultures growing under optimal conditions but that dramatically increased in proportion under stress …

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Biofilms Of The Non-Tuberculous Mycobacterium Chelonae Form An Extracellular Matrix And Display Distinct Expression Patterns, Perla Vega-Dominguez, Eliza Jr Peterson, Min Pan, Alessandro Di Maio, Saumya Singh, Siva Umapathy, Deepak K Saini, Nitin Baliga, Apoorva Bhatt Dec 2020

Biofilms Of The Non-Tuberculous Mycobacterium Chelonae Form An Extracellular Matrix And Display Distinct Expression Patterns, Perla Vega-Dominguez, Eliza Jr Peterson, Min Pan, Alessandro Di Maio, Saumya Singh, Siva Umapathy, Deepak K Saini, Nitin Baliga, Apoorva Bhatt

Articles, Abstracts, and Reports

No abstract provided.

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Polygenic Risk For Anxiety Influences Anxiety Comorbidity And Suicidal Behavior In Bipolar Disorder, Fabiana L. Lopes, Kevin Zhu, Kirstin L. Purves, Christopher Song, Ney Alliey Rodriguez Dec 2020

Polygenic Risk For Anxiety Influences Anxiety Comorbidity And Suicidal Behavior In Bipolar Disorder, Fabiana L. Lopes, Kevin Zhu, Kirstin L. Purves, Christopher Song, Ney Alliey Rodriguez

School of Medicine Publications

Bipolar disorder is often comorbid with anxiety, which is itself associated with poorer clinical outcomes, including suicide. A better etiologic understanding of this comorbidity could inform diagnosis and treatment. The present study aims to test whether comorbid anxiety in bipolar disorder reflects shared genetic risk factors. We also sought to assess the contribution of genetic risk for anxiety to suicide attempts in bipolar disorder. Polygenic risk scores (PRS) were calculated from published genome-wide association studies of samples of controls and cases with anxiety (n = 83,566) or bipolar disorder (n = 51,710), then scored in independent target samples (total n …

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Genetic And Mirna Transcriptomic Analysis Of Autoregulation Of Nodulation Signaling In Medicago Truncatula, Diptee Chauligain Dec 2020

Genetic And Mirna Transcriptomic Analysis Of Autoregulation Of Nodulation Signaling In Medicago Truncatula, Diptee Chauligain

All Dissertations

Legumes can source nitrogen from the air through biological nitrogen fixation inside root nodules formed in a symbiosis with rhizobia. A complex root-to-shoot-to-root signaling pathway called Autoregulation of Nodulation (AON) controls the number of nodules formed depending on the plant’s nitrogen requirements. In Medicago truncatula, the MtSUNN receptor complex in the shoot binds to the root-generated AON signals, peptides called MtCLEs, resulting in downregulation of miR2111 expression in the shoot, with the effect of decreased transport of miR2111 to the roots. Decreased miR2111 levels in the roots then cause an increase in transcript levels of the miR2111 targets MtTML1 …

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Gene Set Testing By Distance Correlation, Sho-Hsien Su Dec 2020

Gene Set Testing By Distance Correlation, Sho-Hsien Su

Graduate Theses and Dissertations

Pathways are the functional building blocks of complex diseases such as cancers. Pathway-level studies may provide insights on some important biological processes. Gene set test is an important tool to study the differential expression of a gene set between two groups, e.g., cancer vs normal. The differential expression of a gene set could be due to the difference in mean, variability, or both. However, most existing gene set tests only target the mean difference but overlook other types of differential expression. In this thesis, we propose to use the recently developed distance correlation for gene set testing. To assess the …

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Investigation Of Sulfur Cycling In Marine Sponge Cinachyrella Spp. From A South Florida Reef, Shelby K. Cain Dec 2020

Investigation Of Sulfur Cycling In Marine Sponge Cinachyrella Spp. From A South Florida Reef, Shelby K. Cain

All HCAS Student Capstones, Theses, and Dissertations

Symbionts within marine sponges are actively participating in the biogeochemical cycles. Among them, the role of symbiont microbes in the sulfur cycle remains a mystery. This study measured the abundance of microbes within the genus Cinachyrella before and after exposure to hydrogen sulfide. A four-part study was conducted: a) five-hour drop experiments, b) vertical distribution experiments, c) five-hour uptake experiments, and d) long-term exposure experiments. The five-hour drop experiment utilized a microsensor to measure sulfide levels, which was lowered 1.0 mm every thirty minutes for a total of 5 hours. Three trials were performed, each with one sponge and a …

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Modeling Neurofibromatosis Type Ii In Zebrafish, Hannah Nuszen Dec 2020

Modeling Neurofibromatosis Type Ii In Zebrafish, Hannah Nuszen

University Honors Program Senior Projects

Neurofibromatosis Type 2 (NF2) is a rare genetic disorder, classified as a neurocutaneous syndrome inherited through an autosomal dominant genetic mutation or deletion of the NF2 gene in humans. The tumor suppressor gene NF2 encodes the cytoskeletal protein MERLIN to promote apoptosis and inhibit abnormal cellular proliferation. Mutations in NF2 lead to a deficiency of functional MERLIN in humans and can result in hearing loss, disability, and premature death. These symptoms are due to uncontrollable growth of schwann cells generating bilateral benign tumors (schwannomas) within the nerve sheath of cranial nerve VIII. Here we seek to understand the function of …

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Genomics Education Partnership F Element Annotation Report, Amanda Moy Dec 2020

Genomics Education Partnership F Element Annotation Report, Amanda Moy

Honors Projects

The Genomics Education Partnership (GEP), headquartered at the University of Alabama, is a collection of over 100 universities that provide training and resources in order to provide students experiential learning in bioinformatics and genomics. The GEP hosts numerous research projects, including the F element project. The F element project has the main focus of annotating the F element genes of the fruit fly species D. ananassae, D. bipectinata, D. kikkawai, and D. takahashii. The Muller F element is the smallest chromosome in Drosophila species. However, the four species listed above have a notably larger F element than other …

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