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3,113 full-text articles. Page 6 of 121.

Iam Hiq—A Novel Pair Of Accuracy Indices For Imputed Genotypes, Albert Rosenberger, Viola Tozzi, Heike Bickeböller, Susanne M. Arnold, The INTEGRAL-ILCCO Consortium 2022 Georg-August-University Göttingen, Germany

Iam Hiq—A Novel Pair Of Accuracy Indices For Imputed Genotypes, Albert Rosenberger, Viola Tozzi, Heike Bickeböller, Susanne M. Arnold, The Integral-Ilcco Consortium

Markey Cancer Center Faculty Publications

Background: Imputation of untyped markers is a standard tool in genome-wide association studies to close the gap between directly genotyped and other known DNA variants. However, high accuracy with which genotypes are imputed is fundamental. Several accuracy measures have been proposed and some are implemented in imputation software, unfortunately diversely across platforms. In the present paper, we introduce Iam hiQ, an independent pair of accuracy measures that can be applied to dosage files, the output of all imputation software. Iam (imputation accuracy measure) quantifies the average amount of individual-specific versus population-specific genotype information in a linear manner. …


Chromomap: An R Package For Interactive Visualization Of Multi-Omics Data And Annotation Of Chromosomes, Lakshay Anand, Carlos M. Rodriguez Lopez 2022 University of Kentucky

Chromomap: An R Package For Interactive Visualization Of Multi-Omics Data And Annotation Of Chromosomes, Lakshay Anand, Carlos M. Rodriguez Lopez

Horticulture Faculty Publications

BACKGROUND: The recent advancements in high-throughput sequencing have resulted in the availability of annotated genomes, as well as of multi-omics data for many living organisms. This has increased the need for graphic tools that allow the concurrent visualization of genomes and feature-associated multi-omics data on single publication-ready plots.

RESULTS: We present chromoMap, an R package, developed for the construction of interactive visualizations of chromosomes/chromosomal regions, mapping of any chromosomal feature with known coordinates (i.e., protein coding genes, transposable elements, non-coding RNAs, microsatellites, etc.), and chromosomal regional characteristics (i.e. genomic feature density, gene expression, DNA methylation, chromatin modifications, etc.) of organisms …


Upregulation Of Cd36, A Fatty Acid Translocase, Promotes Colorectal Cancer Metastasis By Increasing Mmp28 And Decreasing E-Cadherin Expression, James Drury, Piotr G. Rychahou, Courtney O. Kelson, Mariah E. Geisen, Yuanyuan Wu, Daheng He, Chi Wang, Eun Y. Lee, B. Mark Evers, Yekaterina Y. Zaytseva 2022 University of Kentucky

Upregulation Of Cd36, A Fatty Acid Translocase, Promotes Colorectal Cancer Metastasis By Increasing Mmp28 And Decreasing E-Cadherin Expression, James Drury, Piotr G. Rychahou, Courtney O. Kelson, Mariah E. Geisen, Yuanyuan Wu, Daheng He, Chi Wang, Eun Y. Lee, B. Mark Evers, Yekaterina Y. Zaytseva

Surgery Faculty Publications

Altered fatty acid metabolism continues to be an attractive target for therapeutic intervention in cancer. We previously found that colorectal cancer (CRC) cells with a higher metastatic potential express a higher level of fatty acid translocase (CD36). However, the role of CD36 in CRC metastasis has not been studied. Here, we demonstrate that high expression of CD36 promotes invasion of CRC cells. Consistently, CD36 promoted lung metastasis in the tail vein model and GI metastasis in the cecum injection model. RNA-Seq analysis of CRC cells with altered expression of CD36 revealed an association between high expression of CD36 and upregulation …


Exploring The Functionality Of Putative Bop3 Post-Translational Modifications, Liliya Tkachuk, Rebecca Adams PhD 2022 Belmont University

Exploring The Functionality Of Putative Bop3 Post-Translational Modifications, Liliya Tkachuk, Rebecca Adams Phd

Belmont University Research Symposium (BURS)

All eukaryotic cells require that transcribed mRNAs undergo export form the nucleus to the cytoplasm where they can be translated into proteins. This process requires a host of proteins which are conserved between the unicellular budding yeast, S. cerevisiae, and humans. During this process, Mex67 and other associated proteins facilitate the mRNA to travel across the nuclear pore complex (NPC), doorways embedded in the nuclear envelope. Upon the exit of mRNA, Mex67 is released and recycled back into the nucleus to provide the export of more mRNA. This release occurs through the action of Dbp5, whose activity is regulated …


Predicting Gene Function Of Unknown Yeast Orfs Through Phylogenetic Comparative Analysis, Lewis Barr 2022 Georgia College

Predicting Gene Function Of Unknown Yeast Orfs Through Phylogenetic Comparative Analysis, Lewis Barr

Graduate Research Posters

Yeast (Saccharomyces cerevisiae) has been an instrumental model system for an extraordinary diverse array of research applications for over a century now. The S. cerevisiae genome was fully sequenced in 1996, and, as a result, 6,753 potential proteins were identified. These putative proteins were established by investigating likely open reading frames within the genome. Over the past few decades, nearly 5,000 open reading frames (ORFs) and their expressed proteins have been described, and the remaining undefined open reading frames are labeled as open reading frames of unknown function (ORFans). To better understand the remaining gaps within the S. …


Proteome Database, Mariana Rius, Jackie L. Collier, Joshua Rest 2022 SUNY Stony Brook

Proteome Database, Mariana Rius, Jackie L. Collier, Joshua Rest

SoMAS Research Data

No abstract provided.


Phylogenetic And Geographic Relationships Of Cheilostome Bryozoans In The Eastern Pacific, Hannah E. Lee 2022 Humboldt State University

Phylogenetic And Geographic Relationships Of Cheilostome Bryozoans In The Eastern Pacific, Hannah E. Lee

Cal Poly Humboldt theses and projects

The phylum Bryozoa is an incredibly diverse group of marine invertebrates with a widespread global distribution that is well suited for evolutionary studies but whose phylogenetic relationships are still poorly understood. Although recent studies on bryozoan taxonomies and phylogenies have increased, there is still a lack of assessment of species found at shallow water (<1 m) to intertidal depths. In this study, I aimed to expand the taxonomic sampling and assessment of the phylogenetic diversity of cheilostome bryozoans along the California coastline by utilizing mitochondrial DNA as well as inferring potential correlations between species presence and dispersal range both within and between rocky outer coast and sheltered harbor habitats. Illumina high-throughput sequencing was used to produce mitogenomes for cheilostome bryozoan samples collected off rocks from two rocky intertidal sites and off settlement panels from two harbor sites. Phylogenetic analyses generated evolutionary hypotheses of species relationships alongside geographic mapping of their distribution. This study identified 15 distinct species that represent 10 different families to form the first comprehensive phylogeny for multiple bryozoan families in California across a total range of approximately 973 km of coastline. Three genetically distinct species were found at multiple sites that are separated by a combination of rocky shores and sandy beaches, which indicates that the dispersal range of these species are not limited by geographic barriers along the coast of California. These results provide a future opportunity for further integration of this data with the phylogenies generated in this study to examine more robust evolutionary hypotheses for the phylogenetic and geographic relationships of Californian bryozoan species.


The Isolation And Characterization Of Bacteriophage Hasitha, Gillian Brown 2022 Western Kentucky University

The Isolation And Characterization Of Bacteriophage Hasitha, Gillian Brown

Mahurin Honors College Capstone Experience/Thesis Projects

Microbacteriophage Hasitha is a virus that infects Microbacterium foliorum, a bacterium associated with grasses that was first discovered in Germany. Hasitha was isolated from an enriched compost sample and is of particular interest due to its unusual growth pattern. Most bacteriophages require actively growing host cells to produce new phage progeny. However, Hasitha can infect and kill stationary (non-replicating) bacterial cells. We discovered this unusual characteristic through a fortuitous observation of infected lawns that were allowed to incubate in the lab workspace for approximately one month. During this time, a noticeable “halo” grew around the initial site of infection …


Development Of Genomic Resources In Vitis Riparia For Discoveries On Pre- And Post-Transcriptional Molecular Regulators Of Early Induction Into Endodormancy, Michael Robben 2022 South Dakota State University

Development Of Genomic Resources In Vitis Riparia For Discoveries On Pre- And Post-Transcriptional Molecular Regulators Of Early Induction Into Endodormancy, Michael Robben

Electronic Theses and Dissertations

Grapevine is one of the most important fruit crops in the world, responsible for billions in global sales annually. The largest threat to grapevine and other crop production is global climate change resulting human activities. This brings unpredictable and drastic changes in ambient air temperatures to many climates in which grapes are grown. Lower temperatures and inclement weather are already responsible for millions in lost revenue due to tissue damage of established plants. Thus, protecting grapevine crops from weather-related damage is the biggest concern to growers aside from pathogen- and diseaserelated crop damage. The primary mechanism for winter survival in …


Evaluación De La Posible Existencia Biológica De Proteínas A Partir De Secuencias De Arns Generados Por Modelamiento Computacional Pseudoaleatorio, Joan Sebastián Gutiérrez Sánchez, Andrés Reinaldo Chacón Prada 2022 Universidad de La Salle, Bogotá

Evaluación De La Posible Existencia Biológica De Proteínas A Partir De Secuencias De Arns Generados Por Modelamiento Computacional Pseudoaleatorio, Joan Sebastián Gutiérrez Sánchez, Andrés Reinaldo Chacón Prada

Biología

Las proteínas son biomoléculas fundamentales para el funcionamiento de los sistemas biológicos, por lo que entender como surgen y evolucionan es de gran interés teórico. Algunos autores consideran que el origen de las proteínas se dio por el ordenamiento aleatorio de secuencias polipeptídicas; por este motivo el objetivo de este trabajo es inferir si el proceso de creación de secuencias de ARN mensajeros es de carácter estocástico, mediante el diseño y programación de un código computacional en Python que genera secuencias de ARN de manera pseudoaleatoria; posteriormente, se tradujeron las secuencias de ARN obtenidas a aminoácidos para poder realizar un …


Improving Molecular Diagnosis Of Suspected Mendelian Disorders With Rna Splicing Analysis, Joseph Krittameth Aicher 2022 University of Pennsylvania

Improving Molecular Diagnosis Of Suspected Mendelian Disorders With Rna Splicing Analysis, Joseph Krittameth Aicher

Publicly Accessible Penn Dissertations

Exome sequencing is the most advanced standard-of-care genetic test for people with suspected Mendelian disorders. Yet, the diagnostic rate of exome sequencing is only 31%. RNA sequencing (RNA-seq) is a promising molecular test for detecting potentially pathogenic changes in RNA splicing as part of obtaining a molecular diagnosis. In this dissertation, I develop new computational tools and perform analyses towards improving how we detect these potentially pathogenic changes in RNA splicing with the goal of improving the molecular diagnostic rate. First, in Chapter 1, I review background on how we diagnose patients and how RNA splicing and RNA-seq could be …


A Systematic Analysis Of The Concordance Between Chromatin Accessibility And Gene Expression Changes, Karun Kiani 2022 University of Pennsylvania

A Systematic Analysis Of The Concordance Between Chromatin Accessibility And Gene Expression Changes, Karun Kiani

Publicly Accessible Penn Dissertations

A major goal in the field of transcriptional regulation is the mapping of changes in the binding of transcription factors to the resultant changes in gene expression. Recently, methods for measuring chromatin accessibility have enabled us to measure changes in accessibility across the genome, which are thought to correspond to transcription factor binding events. In concert with RNA-sequencing, these data in principle enable such mappings; however, few studies have looked at their concordance over short duration treatments with specific perturbations. Here, we used tandem, bulk ATAC-seq and RNA-seq measurements from MCF-7 breast carcinoma cells to systematically evaluate the concordance between …


Estimating Weighted Panel Sizes For Primary Care Providers: An Assessment Of Clustering And Novel Methods Of Panel Size Estimation On Electronic Medical Records, Martin A. Lavallee 2022 Virginia Commonwealth University

Estimating Weighted Panel Sizes For Primary Care Providers: An Assessment Of Clustering And Novel Methods Of Panel Size Estimation On Electronic Medical Records, Martin A. Lavallee

Theses and Dissertations

Primary Care is on the frontlines of healthcare, thus they see the most diverse set of patients. In order to achieve high functioning primary care, a practice must establish empanelment, the pairing of patients to providers. Enumeration of empanelment, or estimating panel sizes, helps ensure that the demands of the patients demand the supply of providers and optimize the balance of primary care resources to improve quality of care. Further we can adjust panel sizes by using patient-level data on healthcare utilization and complexity extracted from the electronic medial record to determine the amount of care or burden of work …


Genomic Analysis Of Acetoanaerobium Sp. Vlb-1, An Anaerobic Bacterium Isolated From Nebraska's Eastern Saline Wetlands, Claire Martin 2022 University of Nebraska - Lincoln

Genomic Analysis Of Acetoanaerobium Sp. Vlb-1, An Anaerobic Bacterium Isolated From Nebraska's Eastern Saline Wetlands, Claire Martin

Honors Theses, University of Nebraska-Lincoln

Through the analysis of genetic code, the genomic and physiological characteristics of an environmental anaerobic bacterial isolate, Acetoanaerobium sp. strain VLB-1, can be determined and significant pathways can be identified in its significance to the environment. This particular organism was isolated from the Eastern Saline Wetlands in Lincoln, NE. With this isolate, an investigation into elemental and amino acid cycling via the Stickland reaction and the Wood-Ljungdahl pathway was conducted to determine possible metabolic products. The Stickland reaction is a relatively newly discovered pathway, observed in the genus Clostridium. A. sticklandii is the main model for this method of …


Prevotella Phylogeny: Genomic And Molecular Insights Into The Role Of The Human Commensal Prevotella In Cystic Fibrosis, Prioty Ferheen Sarwar 2022 University of Pennsylvania

Prevotella Phylogeny: Genomic And Molecular Insights Into The Role Of The Human Commensal Prevotella In Cystic Fibrosis, Prioty Ferheen Sarwar

Publicly Accessible Penn Dissertations

The genus Prevotella comprises of a diverse set of gram-negative anaerobes that are implicated in both health and disease. Prevotella is a common human commensal of various anatomic sites but can also be associated with the dysbiotic microbiomes of various chronic inflammatory diseases. Due to it’s association with both commensalism and disease, the role of Prevotella in disease progression is unclear. However, Prevotella has shown immunomodulatory potential, the ability to change the metabolic microenvironment and other cytotoxic phenotypes in both in vitro and in vivo studies. Despite this, Prevotella remains understudied both at the genomic and phenotypic levels. In this …


Multi-Omics Integration Through Single-Cell Copy Number Analysis In Cancer, Chi-Yun Wu 2022 University of Pennsylvania

Multi-Omics Integration Through Single-Cell Copy Number Analysis In Cancer, Chi-Yun Wu

Publicly Accessible Penn Dissertations

Genetic and epigenetic alterations combine to drive cancer progression. Heterogeneous cell populations within tumors are associated with poor prognosis and outcomes. Copy number aberrations (CNAs), a genetic variant commonly occurring in tumors, are used as markers to detect subclones and reconstruct tumor phylogeny. Multi-omics integration between CNAs and other modalities on tumor subclones facilitates studying the interplay between genome and epigenome, and their effects on transcriptome. So far, there is still a lack of computational methods for the multi-omics integration of different types of single-cell and ST tumor sequencing data. Therefore, the aim of this thesis is to extract (allele-specific) …


Radiation Exposure Determination In A Secure, Cloudbased Online Environment, Ben C. Shirley, Eliseos J. Mucaki, Joan H.M. Knoll, Peter Rogan 2022 Cytognomix Inc

Radiation Exposure Determination In A Secure, Cloudbased Online Environment, Ben C. Shirley, Eliseos J. Mucaki, Joan H.M. Knoll, Peter Rogan

Biochemistry Publications

Rapid sample processing and interpretation of estimated exposures will be critical for triaging exposed individuals after a major radiation incident. The dicentric chromosome (DC) assay assesses absorbed radiation using metaphase cells from blood. The Automated Dicentric Chromosome Identifier and Dose Estimator System (ADCI) identifies DCs and determines radiation doses. This study aimed to broaden accessibility and speed of this system, while protecting data and software integrity. ADCI Online is a secure web-streaming platform accessible worldwide from local servers. Cloud-based systems containing data and software are separated until they are linked for radiation exposure estimation. Dose estimates are identical to ADCI …


Cbp60-Db: An Alphafold-Predicted Plant Kingdom-Wide Database Of The Calmodulin-Binding Protein 60 (Cbp60) Protein Family With A Novel Structural Clustering Algorithm, Keaun Amani, Vanessa Shivnauth, Christian Castroverde 2022 Wilfrid Laurier University

Cbp60-Db: An Alphafold-Predicted Plant Kingdom-Wide Database Of The Calmodulin-Binding Protein 60 (Cbp60) Protein Family With A Novel Structural Clustering Algorithm, Keaun Amani, Vanessa Shivnauth, Christian Castroverde

Biology Faculty Publications

Molecular genetic analyses in the model species Arabidopsis thaliana have demonstrated the major roles of different CAM-BINDING PROTEIN 60 (CBP60) proteins in growth, stress signaling, and immune responses. Prominently, CBP60g and SARD1 are paralogous CBP60 transcription factors that regulate numerous components of the immune system, such as cell surface and intracellular immune receptors, MAP kinases, WRKY transcription factors, and biosynthetic enzymes for immunity-activating metabolites salicylic acid (SA) and N-hydroxypipecolic acid (NHP). However, their function, regulation and diversification in most species remain unclear. Here we have created CBP60-DB, a structural and bioinformatic database that comprehensively characterized 1052 CBP60 gene homologs …


Unmasking The Language Of Science Through Textual Analyses On Biomedical Preprints And Published Papers, David Nicholson 2022 University of Pennsylvania

Unmasking The Language Of Science Through Textual Analyses On Biomedical Preprints And Published Papers, David Nicholson

Publicly Accessible Penn Dissertations

Scientific communication is essential for science as it enables the field to grow. This task is often accomplished through a written form such as preprints and published papers. We can obtain a high-level understanding of science and how scientific trends adapt over time by analyzing these resources. This thesis focuses on conducting multiple analyses using biomedical preprints and published papers. In Chapter 2, we explore the language contained within preprints and examine how this language changes due to the peer-review process. We find that token differences between published papers and preprints are stylistically based, suggesting that peer-review results in modest …


Bone Marrow Stroma-Induced Transcriptome Signatures Of Multiple Myeloma As Modulated By Junb, Jasleen Kaur Gandhi 2022 West Virginia University

Bone Marrow Stroma-Induced Transcriptome Signatures Of Multiple Myeloma As Modulated By Junb, Jasleen Kaur Gandhi

Graduate Theses, Dissertations, and Problem Reports

The bone marrow (BM) microenvironment acts as a breeding ground for drug resistance in multiple myeloma (MM). The interaction with bone marrow stromal cells (BMSCs) confer environment-mediated drug resistance (EMDR) to multiple myeloma. We investigated BM stroma-induced transcriptome signatures of MM cells through a sophisticated analysis of gene expression. In particular, we defined transcription program modulated by JunB, an emerging regulator of MM pathogenesis and a member of the transcription factor superfamily activator protein 1 (AP-1), in response to BM stimulation. The data and results lay down a foundation for future studies to illustrate the regulatory role of JunB in …


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