Genetic Signatures For Helicobacter Pylori Strains Of West African Origin,
2017
Vanderbilt University
Genetic Signatures For Helicobacter Pylori Strains Of West African Origin, Kennady K. Bullock, Carrie L. Shaffer, Andrew W. Brooks, Ousman Secka, Mark H. Forsyth, Mark S. Mcclain, Timothy L. Cover
Veterinary Science Faculty Publications
Helicobacter pylori is a genetically diverse bacterial species that colonizes the stomach in about half of the human population. Most persons colonized by H. pylori remain asymptomatic, but the presence of this organism is a risk factor for gastric cancer. Multiple populations and subpopulations of H. pylori with distinct geographic distributions are recognized. Genetic differences among these populations might be a factor underlying geographic variation in gastric cancer incidence. Relatively little is known about the genomic features of African H. pylori strains compared to other populations of strains. In this study, we first analyzed the genomes of …
Characterizing Mekk1: Candidate Behavioural Isolation Gene,
2017
The University of Western Ontario
Characterizing Mekk1: Candidate Behavioural Isolation Gene, Caryn Dooner
Electronic Thesis and Dissertation Repository
Behavioural isolation can occur due to divergence in aspects of courtship and mating, and can contribute to reproductive isolation. The purpose of this study is to determine how a gene, Mekk1, contributes to female rejection behaviour between D. melanogaster and D. simulans. Unique polymorphisms were identified within D. simulans Mekk1 that could contribute to behaviour, most of which are non-coding. Both transcripts of Mekk1 appear to be expressed at similar levels in D. simulans and D. melanogaster. These data also indicate that Mekk1 may be expressed in a specific region of the brain called the mushroom body, …
Genomic Data Reveal A Loss Of Diversity In Two Species Of Tuco-Tucos (Genus Ctenomys) Following A Volcanic Eruption,
2017
Chapman University
Genomic Data Reveal A Loss Of Diversity In Two Species Of Tuco-Tucos (Genus Ctenomys) Following A Volcanic Eruption, Jeremy L. Hsu, Jeremy Chase Crawford, Mauro N. Tammone, Uma Ramakrishnan, Eileen A. Lacey, Elizabeth A. Hadly
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Marked reductions in population size can trigger corresponding declines in genetic variation. Understanding the precise genetic consequences of such reductions, however, is often challenging due to the absence of robust pre- and post-reduction datasets. Here, we use heterochronous genomic data from samples obtained before and immediately after the 2011 eruption of the Puyehue-Cordón Caulle volcanic complex in Patagonia to explore the genetic impacts of this event on two parapatric species of rodents, the colonial tuco-tuco (Ctenomys sociabilis) and the Patagonian tuco-tuco (C. haigi). Previous analyses using microsatellites revealed no post-eruption changes in genetic variation in C. …
Exploiting Fission Yeast Genetic Interaction Data To Identify Disease-Specific Drug Targets For Tuberous Sclerosis Complex,
2017
The University of Western Ontario
Exploiting Fission Yeast Genetic Interaction Data To Identify Disease-Specific Drug Targets For Tuberous Sclerosis Complex, Ashyad Rayhan
Electronic Thesis and Dissertation Repository
Tuberous sclerosis complex (TSC) is an inherited genetic disorder caused by loss-of-function mutations in either TSC1 or TSC2. Their respective gene products regulate the mechanistic target of rapamycin (mTOR) signaling pathway, which serves as an activator of cellular proliferation, metabolism, and cell survival. Orthologs of the TSC1 and TSC2 genes exist in a wide range of organisms, including the commonly used and genetically tractable model eukaryote, Schizosaccharomyces pombe. To better understand the functional roles of S. pombe tsc1 and tsc2, I exploited recent advances in genetic interaction biology to identify and characterize genes that modulate the phenotypic …
Glutamylation Regulates Transport, Specializes Function, And Sculpts The Structure Of Cilia,
2017
Montclair State University
Glutamylation Regulates Transport, Specializes Function, And Sculpts The Structure Of Cilia, Robert O'Hagan, Malan Silva, Ken Cq Nguyen, Winnie Zhang, Sebastian Bellotti, Yasmin Ramadan, David Hall, Maureen M. Barr
Department of Biology Faculty Scholarship and Creative Works
Ciliary microtubules (MTs) are extensively decorated with post-translational modifications (PTMs), such as glutamylation of tubulin tails. PTMs and tubulin isotype diversity act as a “Tubulin Code” that regulates cytoskeletal stability and the activity of MT-associated proteins such as kinesins. We previously showed that, in C. elegans cilia, the deglutamylase CCPP-1 affects ciliary ultrastructure, localization of the TRP channel PKD-2 and the kinesin-3 KLP-6, and velocity of kinesin-2 OSM-3/KIF17, while a cell-specific α-tubulin isotype regulates ciliary ultrastructure, intraflagellar transport, and ciliary functions of extracellular vesicle (EV)-releasing neurons. Here, we examine the role of PTMs and the Tubulin Code in the cililary …
Mperiod2Brdm1 And Other Single Period Mutant Mice Have Normal Food Anticipatory Activity,
2017
University of Kentucky
Mperiod2Brdm1 And Other Single Period Mutant Mice Have Normal Food Anticipatory Activity, Julie S. Pendergast, Robert H. Wendroth, Rio C. Stenner, Charles D. Keil, Shin Yamazaki
Biology Faculty Publications
Animals anticipate the timing of food availability via the food-entrainable oscillator (FEO). The anatomical location and timekeeping mechanism of the FEO are unknown. Several studies showed the circadian gene, Period 2, is critical for FEO timekeeping. However, other studies concluded that canonical circadian genes are not essential for FEO timekeeping. In this study, we re-examined the effects of the Per2Brdm1 mutation on food entrainment using methods that have revealed robust food anticipatory activity in other mutant lines. We examined food anticipatory activity, which is the output of the FEO, in single Period mutant mice. Single Per1, Per2 …
An Undergraduate Laboratory Manual For Analyzing A Crispr Mutant With A Predicted Role In Regeneration,
2017
Rollins College
An Undergraduate Laboratory Manual For Analyzing A Crispr Mutant With A Predicted Role In Regeneration, Susan Walsh, Ashley Becker, Paxton S. Sickler, Damian G. Clarke, Erin Jimenez
Faculty Publications
Exposing students to undergraduate research has reportedly improved students’ development of knowledge and skills in the laboratory, self-efficacy, satisfaction with their research, retention, and perseverance when faced with obstacles. Furthermore, utilizing authentic course-based undergraduate research experiences (CUREs) includes all students enrolled in the class, giving those who may not otherwise have access to an independent undergraduate research project an opportunity to engage in the scientific process in context of an original, unanswered question. In the fall of 2016, second semester introductory biology students conducted a semester-long research project on the transcription factor Lin28a to determine the effect of Lin28a on …
Gene Expression Changes In The Mushroom Body Of Drosophila Melanogaster During A Time Course Of Long-Term Memory Formation And Maintenance,
2017
The University of Western Ontario
Gene Expression Changes In The Mushroom Body Of Drosophila Melanogaster During A Time Course Of Long-Term Memory Formation And Maintenance, Spencer G. Jones
Electronic Thesis and Dissertation Repository
Long-term memory (LTM) requires gene transcription. However, there is still much to learn about which genes are transcriptionally regulated during LTM and the biological roles they play. Here, gene expression changes were characterized in Drosophila melanogaster over a time course of LTM formation and maintenance in neurons of the mushroom body (MB), a structure required for normal learning and memory. I identified 120 genes differentially expressed (q < 0.2, fold change > 1.3) 24h after LTM induction. Among these were 13 potential downstream targets for RNA localization by the known memory genes pumilo, staufen and oskar, several genes encoding chromatin regulators and seven genes with …
All Roads Lead To Weediness: Stories About Weedy Rice Origins, Weedy Genes And Weed Competitiveness,
2017
University of Massachusetts Amherst
All Roads Lead To Weediness: Stories About Weedy Rice Origins, Weedy Genes And Weed Competitiveness, Zhongyun Huang
Doctoral Dissertations
Weedy rice (Oryza spp.), a weedy relative of cultivated rice (O.sativa), infests and persists in cultivated rice fields worldwide. Many weedy rice populations have evolved similar adaptive traits, considered part of the ‘agricultural weed syndrome’, making this an ideal model to study the genetic basis of parallel evolution. Using population genetics analyses of South Asian and US weedy rice, my research reveals multiple independent evolution events giving rise to weed groups in the two geographic areas. Weeds in South Asia have highly heterogenous genetic backgrounds, with contributions from both cultivated varieties (aus and indica) …
Abnormal Contractility In Human Heart Myofibrils From Patients With Dilated Cardiomyopathy Due To Mutations In Ttn And Contractile Protein Genes,
2017
Imperial College London, UK
Abnormal Contractility In Human Heart Myofibrils From Patients With Dilated Cardiomyopathy Due To Mutations In Ttn And Contractile Protein Genes, Petr G. Vikhorev, Natalia Smoktunowicz, Alex B. Munster, O'Neal Copeland, Sawa Kostin, Cecile Montgiraud, Andrew E. Messer, Mohammad R. Toliat, Amy Li, Cristobal G. Dos Remedios, Sean Lal, Cheavar A. Blair, Kenneth S. Campbell, Maya E. Guglin, Ralph Knoll, Steven B. Marston
Physiology Faculty Publications
Dilated cardiomyopathy (DCM) is an important cause of heart failure. Single gene mutations in at least 50 genes have been proposed to account for 25–50% of DCM cases and up to 25% of inherited DCM has been attributed to truncating mutations in the sarcomeric structural protein titin (TTNtv). Whilst the primary molecular mechanism of some DCM-associated mutations in the contractile apparatus has been studied in vitro and in transgenic mice, the contractile defect in human heart muscle has not been studied. In this study we isolated cardiac myofibrils from 3 TTNtv mutants, and 3 with contractile protein mutations (TNNI3 …
Association Of Vitamin D Deficiency And Vdbp Gene Polymorphism With The Risk Of Ami In A Pakistani Population,
2017
Aga Khan University
Association Of Vitamin D Deficiency And Vdbp Gene Polymorphism With The Risk Of Ami In A Pakistani Population, Mujtaba Mubashir, Shaheena Anwar, Asal Khan Tareen, Naseema Mehboobali, Khalida Iqbal, Mohammad Iqbal
Department of Biological & Biomedical Sciences
OBJECTIVE: To investigate the relationship of vitamin D deficiency and risk of AMI in a Pakistani population, and to find out any associationbetween vitamin D binding protein (VDBP) genotypes and risk of AMI in this population.
METHODS: In a comparative cross-sectional study, 246 patients (age: 20-70 years; 171 males and 75 females) with first AMI were enrolled with informed consent. Similarly, 345 healthy adults (230 males and 115 females) were enrolled as controls. Their fasting serum samples were analyzed for 25 (OH) vitamin D, lipids and other biomarkers using kit methods, while DNA was analyzed for VDBP genotypes using PCR-RFLP …
High-Throughput Single-Molecule Telomere Characterization,
2017
Old Dominion University
High-Throughput Single-Molecule Telomere Characterization, Jennifer Mccaffrey, Eleanor Young, Katy Lassahn, Justin Sibert, Steven Pastor, Harold Riethman, Ming Xiao
Medical Diagnostics & Translational Sciences Faculty Publications
We have developed a novel method that enables global subtelomere and haplotype-resolved analysis of telomere lengths at the single-molecule level. An in vitro CRISPR/Cas9 RNA-directed nickase system directs the specific labeling of human (TTAGGG) n DNA tracts in genomes that have also been barcoded using a separate nickase enzyme that recognizes a 7bp motif genome-wide. High-throughput imaging and analysis of large DNA single molecules from genomes labeled in this fashion using a nanochannel array system permits mapping through subtelomere repeat element (SRE) regions to unique chromosomal DNA while simultaneously measuring the (TTAGGG) n tract length at the end of each …
Enrichment Of Putatively Damaging Rare Variants In The Dyx2 Locus And The Reading-Related Genes Ccdc136 And Flnc,
2017
Yale University
Enrichment Of Putatively Damaging Rare Variants In The Dyx2 Locus And The Reading-Related Genes Ccdc136 And Flnc, Andrew K. Adams, Shelley D. Smith, Dongnhu T. Truong, Erik G. Willcutt, Richard K. Olson, John C. Defries, Bruce F. Pennington, Jeffrey R. Gruen
Psychology: Faculty Scholarship
Eleven loci with prior evidence for association with reading and language phenotypes were sequenced in 96 unrelated subjects with significant impairment in reading performance drawn from the Colorado Learning Disability Research Center collection. Out of 148 total individual missense variants identified, the chromosome 7 genes CCDC136 and FLNC contained 19. In addition, a region corresponding to the well-known DYX2 locus for RD contained 74 missense variants. Both allele sets were filtered for a minor allele frequency ≤0.01 and high Polyphen-2 scores. To determine if observations of these alleles are occurring more frequently in our cases than expected by chance in …
Uncovering Tasselsheath3. A Genomic And Phenotypic Analysis Of A Maize Floral Mutant.,
2017
University of Massachusetts Amherst
Uncovering Tasselsheath3. A Genomic And Phenotypic Analysis Of A Maize Floral Mutant., Thompson Zhang
Masters Theses
In the modern era, maize has become the most successful crop grown in the United States. According to the USDA over 90 million acres of land are planted to corn and 96.2% of the U.S feed grain production is made up of the cereal. Part of the success of maize is due to its floral architecture, and its pollination technique in which the flower opens, exposing stamens containing pollen into the air. A unique organ called the lodicule functions as a release mechanism, forcing the flower to open. Lodicules from grasses and eudicot petals are homologous, yet there is little …
Pattern Discovery In Brain Imaging Genetics Via Scca Modeling With A Generic Non-Convex Penalty,
2017
Northwestern Polytechnical University, China
Pattern Discovery In Brain Imaging Genetics Via Scca Modeling With A Generic Non-Convex Penalty, Lei Du, Kefei Liu, Xiaohui Yao, Jingwen Yan, Shannon L. Risacher, Junwei Han, Lei Guo, Andrew J. Saykin, Li Shen, Michael W. Weiner, Paul Aisen, Ronald Petersen, Clifford R. Jack, William Jagust, John Q. Trojanowki, Arthur W. Toga, Laurel Beckett, Robert C. Green, John Morris, Leslie M. Shaw, Zaven Khachaturian, Greg Sorensen, Maria Carrillo, Lew Kuller, Marc Raichle, Steven Paul, Peter Davies, Howard Fillit, Franz Hefti, David Holtzman, Charles D. Smith, Gregory Jicha, Peter A. Hardy, Partha Sinha, Elizabeth Oates, Gary Conrad
Neurology Faculty Publications
Brain imaging genetics intends to uncover associations between genetic markers and neuroimaging quantitative traits. Sparse canonical correlation analysis (SCCA) can discover bi-multivariate associations and select relevant features, and is becoming popular in imaging genetic studies. The L1-norm function is not only convex, but also singular at the origin, which is a necessary condition for sparsity. Thus most SCCA methods impose ℓ1-norm onto the individual feature or the structure level of features to pursuit corresponding sparsity. However, the ℓ1-norm penalty over-penalizes large coefficients and may incurs estimation bias. A number of non-convex penalties are proposed to reduce …
Characterization Of Plant-Spider Mite Interactions And Establishment Of Tools For Spider Mite Functional Genetic Studies,
2017
The University of Western Ontario
Characterization Of Plant-Spider Mite Interactions And Establishment Of Tools For Spider Mite Functional Genetic Studies, Nicolas Bensoussan
Electronic Thesis and Dissertation Repository
The two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), is one of the most polyphagous herbivores feeding on cell contents of over 1100 plant species including more than 150 crops. However, despite its important pest status and a growing understanding of the molecular basis of its interactions with plant hosts, knowledge of the way mites interface with the plant while feeding and the plant damage directly inflicted by mites is lacking. Likewise, while the use of the reverse genetic tools in plants facilitated our understanding of the establishment of defense mechanisms against spider mite herbivory, such tools are lacking for …
Transgneic Endothelin 3 Regulates Murine Pigment Production And Coat Color,
2017
Florida International University
Transgneic Endothelin 3 Regulates Murine Pigment Production And Coat Color, Javier Pino
FIU Electronic Theses and Dissertations
Pigmentation plays a protective role against damage caused by ultraviolet (UV) irradiation. Humans with fair skin and light hair have a higher susceptibility to UV-induced DNA damage that can lead to the development of skin cancers. The melanocytes found in the skin and hair follicles depend on different signaling molecules for their proper development and pigment production. α-Melanocyte Stimulating Hormone (α-msh) binds to the Melanocortin 1 receptor (Mc1r) to regulate pigment production and the switch between eumelanin and pheomelanin. Lethal yellow mice (Ay) overexpress the agouti signaling protein, which inhibits the binding of α-msh, resulting in a yellow …
Characterization Of Acaricide Resistance, Plant-Mediated Rnai Against Two-Spotted Spider Mites (Tetranychus Urticae Koch), And Assessing Off- And Non-Target Effects,
2017
The University of Western Ontario
Characterization Of Acaricide Resistance, Plant-Mediated Rnai Against Two-Spotted Spider Mites (Tetranychus Urticae Koch), And Assessing Off- And Non-Target Effects, Hooman Hosseinzadeh Namin
Electronic Thesis and Dissertation Repository
The two-spotted spider mite (TSSM), Tetranychus urticae (Koch), is one of the most damaging agricultural pests in the world. It feeds on over 150 crops, causing considerable yield losses in greenhouses and agricultural fields. Currently, using synthetic acaricides is the main method to control TSSM. However, it can develop resistance to acaricides with repeated exposure, and typically resistance can occur within two to four years. To understand the underlying mechanisms of spider mite adaptation to acaricides is an essential part of resistance management strategy. The resistance ratio of the pyridaben-selected strain compared with the pre-selection strain was estimated at greater …
Hne-Modified Proteins In Down Syndrome: Involvement In Development Of Alzheimer Disease Neuropathology,
2017
Sapienza University of Rome, Italy
Hne-Modified Proteins In Down Syndrome: Involvement In Development Of Alzheimer Disease Neuropathology, Eugenio Barone, Elizabeth Head, D. Allan Butterfield, Marzia Perluigi
Sanders-Brown Center on Aging Faculty Publications
Down syndrome (DS), trisomy of chromosome 21, is the most common genetic form of intellectual disability. The neuropathology of DS involves multiple molecular mechanisms, similar to AD, including the deposition of beta-amyloid (Aβ) into senile plaques and tau hyperphosphorylating in neurofibrillary tangles. Interestingly, many genes encoded by chromosome 21, in addition to being primarily linked to amyloid-beta peptide (Aβ) pathology, are responsible for increased oxidative stress (OS) conditions that also result as a consequence of reduced antioxidant system efficiency. However, redox homeostasis is disturbed by overproduction of Aβ, which accumulates into plaques across the lifespan in DS as well as …
Landscape Genetics Of The California Tiger Salamander: Inferences From Multiple Methods,
2017
Western Kentucky University
Landscape Genetics Of The California Tiger Salamander: Inferences From Multiple Methods, Samantha Gabrielle Thomas
Masters Theses & Specialist Projects
Landscape genetics is a rapidly growing field of study that compares patterns of gene flow among populations with habitat heterogeneity across a landscape to infer the interaction between dispersal of individuals and their physical environment. Empirical data generated from a landscape genetics study can inform conservation and management strategies, making the field increasing popular. However, concerns have arisen in the literature that the field is expanding faster than the analytic framework that supports it. Multiple methods for generating estimates of the association among habitat types and dispersal (i.e., least-cost paths and resistance surfaces) have been proposed, and there is a …
