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Mrub_3019 Casa Gene Is An Ortholog To E. Coli B2760, Kelsey Heiland, Dr. Lori Scott 2019 Augustana College, Rock Island Illinois

Mrub_3019 Casa Gene Is An Ortholog To E. Coli B2760, Kelsey Heiland, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This research is part of the Meiothermus ruber genome annotation project which aims to predict gene function with various bioinformatics tools. We investigated the function of Mrub_3019, which encodes the CasA protein involved in the multi-subunit effector complex for the CRISPR-Cas immunity system and predicted it to be an ortholog of E. coli K12 MG1655 b2760 (casA). We predicted that Mrub_3019 encodes the protein CasA, which is involved in PAM recognition of CRISPR interference pathway. Foreign DNA will bind to CasA, which signals Cas3 for helicase-mediated DNA degradation. Our hypothesis is supported by low E-values for pairwise alignment in NCBI ...


Heterodera Glycines Utilizes Promiscuous Spliced Leaders And Demonstrates A Unique Preference For A Species-Specifc Spliced Leader Over C. Elegans Sl1, Stacey N. Barnes, Rick E. Masonbrink, Tom R. Maier, Arun S. Seetharam, Anoop S. Sindhu, Andrew J. Severin, Thomas J. Baum 2019 Iowa State University

Heterodera Glycines Utilizes Promiscuous Spliced Leaders And Demonstrates A Unique Preference For A Species-Specifc Spliced Leader Over C. Elegans Sl1, Stacey N. Barnes, Rick E. Masonbrink, Tom R. Maier, Arun S. Seetharam, Anoop S. Sindhu, Andrew J. Severin, Thomas J. Baum

Office of Biotechnology Publications

Spliced leader trans-splicing (SLTS) plays a part in the maturation of pre-mRNAs in select species across multiple phyla but is particularly prevalent in Nematoda. The role of spliced leaders (SL) within the cell is unclear and an accurate assessment of SL occurrence within an organism is possible only after extensive sequencing data are available, which is not currently the case for many nematode species. SL discovery is further complicated by an absence of SL sequences from high-throughput sequencing results due to incomplete sequencing of the 5'-ends of transcripts during RNA-seq library preparation, known as 5'-bias. Existing datasets and ...


Human Survival Motor Neuron Genes Generate A Vast Repertoire Of Circular Rnas, Eric W. Ottesen, Diou Luo, Joonbae Seo, Natalia N. Singh, Ravindra N. Singh 2019 Iowa State University

Human Survival Motor Neuron Genes Generate A Vast Repertoire Of Circular Rnas, Eric W. Ottesen, Diou Luo, Joonbae Seo, Natalia N. Singh, Ravindra N. Singh

Biomedical Sciences Publications

Circular RNAs (circRNAs) perform diverse functions, including the regulation of transcription, translation, peptide synthesis, macromolecular sequestration and trafficking. Inverted Alu repeats capable of forming RNA:RNA duplexes that bring splice sites together for backsplicing are known to facilitate circRNA generation. However, higher limits of circRNAs produced by a single Alu-rich gene are currently not predictable due to limitations of amplification and analyses. Here, using a tailored approach, we report a surprising diversity of exon-containing circRNAs generated by the Alu-rich Survival Motor Neuron (SMN) genes that code for SMN, an essential multifunctional protein in humans. We show that expression of the ...


Identifying Genetic Regulators Of Cancer Stem Cell Differentiation For Glioblastoma Therapy, Ann Chen, Yang Xiao, Rong Fan, Jiangbing Zhou 2019 Yale University

Identifying Genetic Regulators Of Cancer Stem Cell Differentiation For Glioblastoma Therapy, Ann Chen, Yang Xiao, Rong Fan, Jiangbing Zhou

Yale Day of Data

Glioblastoma multiforme (GBM) is the most common and aggressive type of primary brain cancer. Even with treatment, GBM patients have a median survival rate of less than 15 months and a five-year survival rate of 2%. Poor therapeutic outcomes may be attributed to the presence of a subpopulation of cells within tumors, known as cancer stem cells (CSCs), which are resistant to conventional radiotherapy and chemotherapy. CSCs are capable of tumor initiation, sustained self-renewal, and differentiation into terminal cell types. These terminally differentiated cells make up the bulk of the tumor and are sensitive to GBM therapies. Therefore, CSC-directed therapies ...


Non-Invasive Analysis Of The Sputum Transcriptome Discriminates Clinical Phenotypes Of Asthma, Xiting Yan 2019 Yale University School of Medicine

Non-Invasive Analysis Of The Sputum Transcriptome Discriminates Clinical Phenotypes Of Asthma, Xiting Yan

Yale Day of Data

Whole transcriptome wide gene expression profiles in the sputum and circulation from 100 asthma patients were measured using the Affymetrix HuGene 1.0ST arrays. Unsupervised clustering analysis based on pathways from KEGG were used to identify TEA clusters of patients from the sputum gene expression profiles. The identified TEA clusters have significantly different pre-bronchodilator FEV1, bronchodilator responsiveness, exhaled nitric oxide levels, history of hospitalization for asthma and history of intubation. Evaluation of TEA clusters in children from Asthma BRIDGE cohort confirmed the identified differences in intubation and hospitalization. Furthermore, evaluation of the TH2 gene signatures suggested a much lower prevalence ...


Analysis Of The Genetic And Neurological Components Of Opioid Addiction, With Public Health Perspectives Of The Opioid Epidemic In The United States Of America, Janhavi A. Dubhashi 2019 Georgia State University

Analysis Of The Genetic And Neurological Components Of Opioid Addiction, With Public Health Perspectives Of The Opioid Epidemic In The United States Of America, Janhavi A. Dubhashi

DISCOVERY: Georgia State Honors College Undergraduate Research Journal

Opioid addiction has reached epidemic levels around the world, with over-prescription of opioid pain relievers being an often-cited reason for the epidemic in the USA. This project looks at opioid addiction from three perspectives: a review of literature dealing with the neural pathways involved in opioid use and addiction; the underlying genetic differences that can increase the risk of opioid use disorder; and an overview of the public health aspects of the epidemic. The paper will conclude with a review of current and new treatments based upon a growing neurobiological and molecular understanding of opioid use disorder.


Investigating Neurogenesis As A Veritable Epigenetic Endophenotype For Alzheimer's Disease, Layne Wells 2019 Claremont Colleges

Investigating Neurogenesis As A Veritable Epigenetic Endophenotype For Alzheimer's Disease, Layne Wells

Scripps Senior Theses

Alzheimer's disease (AD) is the most common neurodegenerative disease, characterized by progressive amyloid plaque aggregation, neurofibrillary tangles, and cortical tissue death. As the prevalence of AD is projected to climb in coming years, there is a vested interest in identifying endophenotypes by which to improve diagnostics and direct clinical interventions. The risk for complex disorders, such as AD, is influenced by multiple genetic, environmental, and lifestyle factors. Significant strides have been made in identifying genetic variants linked to AD through the genome-wide association study (GWAS). It has been estimated in more recent years, however, that GWAS-identified variants account for ...


Vitamin D Receptor Gene Polymorphisms Knowledge And Breast Cancer In Texas, Ejike Roland Egwuekwe 2019 Walden University

Vitamin D Receptor Gene Polymorphisms Knowledge And Breast Cancer In Texas, Ejike Roland Egwuekwe

Walden Dissertations and Doctoral Studies

Breast cancer is a world health problem and is a leading cause of cancer-related death among women in the United States. However, breast cancer risks were reported to be reduced through exposure to Vitamin D through its Receptors identified as the p53 target gene. The purpose of this study was to assess the associations between VDR gene polymorphisms knowledge/awareness and decisions to reduce breast cancer risks and likelihood of mammogram screening among women in Texas. Data from survey were used. Roy adaptation model was the theoretical framework that guided this quasi- experimental, quantitative research. The dependent variables were decisions ...


The Trim-Nhl Protein Nhl-2 Is A Co-Factor In The Nuclear And Somatic Rnai Pathways In C. Elegans, Gregory M. Davis, Shikui Tu, Jacqueline A. Wilce, Julie M. Claycomb, Zhiping Weng, Peter R. Boag 2018 Federation University

The Trim-Nhl Protein Nhl-2 Is A Co-Factor In The Nuclear And Somatic Rnai Pathways In C. Elegans, Gregory M. Davis, Shikui Tu, Jacqueline A. Wilce, Julie M. Claycomb, Zhiping Weng, Peter R. Boag

Program in Bioinformatics and Integrative Biology Publications and Presentations

Proper regulation of germline gene expression is essential for fertility and maintaining species integrity. In the C. elegans germline, a diverse repertoire of regulatory pathways promote the expression of endogenous germline genes and limit the expression of deleterious transcripts to maintain genome homeostasis. Here we show that the conserved TRIM-NHL protein, NHL-2, plays an essential role in the C. elegans germline, modulating germline chromatin and meiotic chromosome organization. We uncover a role for NHL-2 as a co-factor in both positively (CSR-1) and negatively (HRDE-1) acting germline 22G-small RNA pathways and the somatic nuclear RNAi pathway. Furthermore, we demonstrate that NHL-2 ...


The Role Of Fibrillin-1 In Eye Development And Disease, Wendell Brooks Jones 2018 Washington University in St. Louis

The Role Of Fibrillin-1 In Eye Development And Disease, Wendell Brooks Jones

Arts & Sciences Electronic Theses and Dissertations

The ciliary zonule of the human eye consists of a circumferential array of fibers that connect the ocular lens to the nonpigmented ciliary epithelium (NPCE) located at the inner wall of the eye. Zonular fibers consist of bundles of beaded filaments called microfibrils. Microfibrils are major structural elements of the extracellular matrix and are present in pure form in the ciliary zonule. Microfibrils are composed principally of fibrillin-1 (FBN-1); a large extracellular matrix glycoprotein. In humans, mutations in FBN1 underlie Marfan syndrome; a pleiotropic connective tissue disorder that profoundly affects the eye. Ocular manifestations include ectopia lentis (dislocated lenses), cataracts ...


Genetic Basis Of Thermal Divergence In Saccharomyces Species, Xueying C. Li 2018 Washington University in St. Louis

Genetic Basis Of Thermal Divergence In Saccharomyces Species, Xueying C. Li

Arts & Sciences Electronic Theses and Dissertations

The genetic architecture of phenotypic divergence is a central question in evolutionary biology. Genetic architecture is impacted by whether evolution occurs through accumulation of many small-effect or a few large-effect changes, the relative contribution of coding and cis-regulatory changes, and the prevalence of epistatic effects. Our empirical understanding of the genetic basis of evolutionary change remains incomplete, largely because reproductive barriers limit genetic analysis to those phenotypes that distinguish closely related species. In this dissertation, I use hybrid genetic analysis to examine the basis of thermal divergence between two post-zygotically isolated species, Saccharomyces cerevisiae and S. uvarum. S. cerevisiae is ...


Orbit: A New Paradigm For Genetic Engineering Of Mycobacterial Chromosomes, Kenan C. Murphy, Samantha J. Nelson, Subhalaxmi Nambi, Kadamba Papavinasasundaram, Christina E. Baer, Christopher M. Sassetti 2018 University of Massachusetts Medical School

Orbit: A New Paradigm For Genetic Engineering Of Mycobacterial Chromosomes, Kenan C. Murphy, Samantha J. Nelson, Subhalaxmi Nambi, Kadamba Papavinasasundaram, Christina E. Baer, Christopher M. Sassetti

Open Access Articles

Two efficient recombination systems were combined to produce a versatile method for chromosomal engineering that obviates the need to prepare double-stranded DNA (dsDNA) recombination substrates. A synthetic "targeting oligonucleotide" is incorporated into the chromosome via homologous recombination mediated by the phage Che9c RecT annealase. This oligonucleotide contains a site-specific recombination site for the directional Bxb1 integrase (Int), which allows the simultaneous integration of a "payload plasmid" that contains a cognate recombination site and a selectable marker. The targeting oligonucleotide and payload plasmid are cotransformed into a RecT- and Int-expressing strain, and drug-resistant homologous recombinants are selected in a single step ...


Temperature And Polyunsaturated Fatty Acid’S Effect On Daphnia Magna Reproduction, Mark Albright 2018 East Tennessee State University

Temperature And Polyunsaturated Fatty Acid’S Effect On Daphnia Magna Reproduction, Mark Albright

Electronic Theses and Dissertations

Organisms adapt to their environments by adjusting their biochemistry and physiology; such adaptation is limited by resource availability and physiological constraints. The freshwater crustacean Daphnia magna inhabits a wide range of environments and must survive and reproduce within a range of temperatures. One limit to low-temperature adaptation is thought to be the availability of unsaturated fatty acids necessary to maintain proper fluidity of cellular membranes. D. magna maintained at 10 ºC on a diet poor in unsaturated fatty acids have been observed to produce clutches that fail to develop. However, this has not been observed on a diet rich in ...


Investigating Autophagy Dysfunction Induced By A Parkinson's Disease-Causing Mutation In Vps35, Abir Ashfakur Rahman 2018 Boise State University

Investigating Autophagy Dysfunction Induced By A Parkinson's Disease-Causing Mutation In Vps35, Abir Ashfakur Rahman

Boise State University Theses and Dissertations

Parkinson’s Disease (PD) is an idiopathic disorder with no known cure. With number of cases steadily rising around the world, it is imperative to turn to the underlying cellular and molecular mechanisms of the disease manifestation and neurodegeneration to craft novel modes of therapy. VPS35 is one of the few genes that have identified and definitively linked to familial PD. The particular mutation that has been associated is known to cause dysfunction of a key cellular process known as autophagy. This process is primarily responsible for clearance of unwanted, damaged or misfolded proteins, among other things. Our study reveals ...


Genetic And Epigenetic Investigations On Pulmonary Hypertension Syndrome In Meat Type- Chickens, Khaloud Alzahrani 2018 University of Arkansas, Fayetteville

Genetic And Epigenetic Investigations On Pulmonary Hypertension Syndrome In Meat Type- Chickens, Khaloud Alzahrani

Theses and Dissertations

This dissertation presents a collection of studies that investigate the genetic and epigenetic associations to ascites phenotype in broiler chickens. Ascites is a significant metabolic disease associated with fast-growing meat-type chickens (broilers) and is a terminal result of pulmonary hypertension syndrome PHS. It is a multi-factorial syndrome caused by interactions between genetic, physiological, environmental, and managemental factors. It was estimated that ascites accounts for losses of about US$1 billion annually worldwide and for over 25% of broilers mortality. Although traditional and molecular genetic methods in the selection and in performance improvements, has greatly reduced ascites frequency, yet it has ...


Generation And Evaluation Of Modified Opaque-2 (O2) Popcorn Suggests A Route To Quality Protein Popcorn (Qpp), Ying Ren 2018 University of Nebraska-Lincoln

Generation And Evaluation Of Modified Opaque-2 (O2) Popcorn Suggests A Route To Quality Protein Popcorn (Qpp), Ying Ren

Theses, Dissertations, and Student Research in Agronomy and Horticulture

I have been working on a Quality Protein Popcorn breeding project where QPM conversion is carried out simultaneously for several elite popcorn germplasms. During my study in the graduate program, I led the following aspects of the Quality Protein Popcorn Breeding Project:

1. Identified suitable QPMs as opaque-2 allele donors.

2.Examined the feasibility of quick introgression of the opaque-2 allele into popcorn lines via marker-assisted selection.

3. Monitored modification by SDS-PAGE zein profiling and light box phenotypic selection to make sure multiple modifier loci for opaque-2 were incorporated each time generation advancement was carried out.

4. Carried out high ...


Evaluation Of Genetic And Environmental Influences On Broiler Meat Quality, Sara Katherine Orlowski 2018 University of Arkansas, Fayetteville

Evaluation Of Genetic And Environmental Influences On Broiler Meat Quality, Sara Katherine Orlowski

Theses and Dissertations

The effect of both genetic and environmental influences on broiler meat quality were evaluated over three experiments. Selection response was assessed for broiler lines selected for high (HBY4) and low (LBY4) four day percentage breast yield which were formed from a random bred control (RAN). A modern random bred population (MRB) created in 2015 was evaluated for differences in 4 day percentage breast yield and the resulting differences in the incidence and severity of the woody breast and white striping myopathies. Additionally, the use of embryonic thermal manipulation to impact cell division and early caloric feed restriction to slow growth ...


The Evaluation Of Genetic And Phenotypic Differences Associated With Short Term Selection Of Four Different Feed Efficiency Strategies In Japanese Quail, Alex David Gilley 2018 University of Arkansas, Fayetteville

The Evaluation Of Genetic And Phenotypic Differences Associated With Short Term Selection Of Four Different Feed Efficiency Strategies In Japanese Quail, Alex David Gilley

Theses and Dissertations

The concept of feed efficiency (FE), one unit of feed required to improve one unit of desired output, is relatively simple. However multiple outputs are desired in a commercial poultry breeding program, resulting in the need for nutrients to be partitioned in a particular manner. At the broadest level, nutrients are partitioned between production and maintenance requirements. The requirements for production and maintenance varies between birds. It is the poultry breeder’s responsibility to select individuals most aligned with the breeding objective. Irrespective of the breeding objective, various related and non-related traits influence a bird’s FE. To effectively improve ...


Identification Of Deubiquitinating Enzymes That Control The Cell Cycle In Saccharomyces Cerevisiae, Claudine E. Mapa 2018 University of Massachusetts Medical School

Identification Of Deubiquitinating Enzymes That Control The Cell Cycle In Saccharomyces Cerevisiae, Claudine E. Mapa

GSBS Dissertations and Theses

A large fraction of the proteome displays cell cycle-dependent expression, which is important for cells to accurately grow and divide. Cyclical protein expression requires protein degradation via the ubiquitin proteasome system (UPS), and several ubiquitin ligases (E3) have established roles in this regulation. Less is understood about the roles of deubiquitinating enzymes (DUB), which antagonize E3 activity. A few DUBs have been shown to interact with and deubiquitinate cell cycle-regulatory E3s and their protein substrates, suggesting DUBs play key roles in cell cycle control. However, in vitro studies and characterization of individual DUB deletion strains in yeast suggest that these ...


Phylogeny And Population Genetic Analyses Reveals Cryptic Speciation In The Bombus Fervidus Species Complex (Hymenoptera: Apidae), Jonathan B. Koch, Juanita Rodriguez, James P. Pitts, James P. Strange 2018 Utah State University

Phylogeny And Population Genetic Analyses Reveals Cryptic Speciation In The Bombus Fervidus Species Complex (Hymenoptera: Apidae), Jonathan B. Koch, Juanita Rodriguez, James P. Pitts, James P. Strange

Ecology Center Publications

Bumble bees (Bombus Latrielle) are significant pollinators of flowering plants due to their large body size, abundant setae, and generalist foraging strategies. However, shared setal coloration patterns among closely and distantly related bumble bee species makes identification notoriously difficult. The advent of molecular genetic techniques has increased our understanding of bumble bee evolution and taxonomy, and enables effective conservation policy and management. Individuals belonging to the North American Bombus fervidus species-complex (SC) are homogenous in body structure but exhibit significant body color phenotype variation across their geographic distribution. Given the uncertainty of the genealogical boundaries within the SC, some authors ...


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