The Conservation Genetics Of Two Emydid Turtles: Emydoidea Blandingii And Malaclemys Terrapin, 2014 The University of Southern Mississippi
The Conservation Genetics Of Two Emydid Turtles: Emydoidea Blandingii And Malaclemys Terrapin, Charlotte Lizana Petre
Conservation of turtles is complicated by their sensitivity to habitat degradation and overexploitation. I used microsatellites and standard population genetic analyses to explore genetic diversity, population structure, paternity and demographic history in two emydid turtles that are currently experiencing threats to their survival. The Blanding’s turtle, Emydoidea blandingii, has experienced habitat fragmentation throughout its range, and this study focuses on a population in Massachusetts where hatchlings from one population are being translocated to establish a new population. I found evidence of multiple paternity within clutches and found no significant reduction in genetic diversity when comparing the source population and ...
Genetic Parameter Estimates And Breed Effects For Calving Difficulty And Birth Weight In A Multi-Breed Population, 2014 University of Nebraska - Lincoln
Genetic Parameter Estimates And Breed Effects For Calving Difficulty And Birth Weight In A Multi-Breed Population, Cashley Ahlberg
Theses and Dissertations in Animal Science
There are multiple breeds of beef cattle available to utilize in breeding systems to maximize production and economics. Calving difficulty (dystocia) is a significant cost to beef production and is more prevalent in first-calf heifers. The objectives of this study were to estimate genetic parameters and breed differences for calving difficulty and birth weight as a first step towards the development of across-breed adjustment factors for calving difficulty.
Two models were employed to analyze birth weight (BWT) and calving difficulty (CD) recorded on 4,579 first parity females from the Germplasm Evaluation program at the U.S. Meat Animal Research ...
Angelman Syndrome, 2014 Sacred Heart University
Angelman Syndrome, Stephanie Sorbara
Biology Undergraduate Publications
Angelman Syndrome (AS) is a neurogenetic disorder that is classically characterized by excessive laughter and a happy demeanor. Aggression, sleep disorders and epilepsy are other phenotypes associated with this disorder as well. Both happy and aggressive demeanors have been expressed in five different consumers at The Kennedy Center, a site which offers programs and services to individuals with varying disabilities. Research proposes several different genetic mechanisms responsible for the development of AS, each of which impact the function of the UBE3A gene located in the 15q11-13 region on chromosome 15. Additionally, from an evolutionary perspective, Emotion Signaling Theory and Kinship ...
Suppression Of Neurodegenerative Symptoms Via Suppressor Of Levy Mutation In Drosophila Melanogaster, 2014 SUNY Buffalo State
Suppression Of Neurodegenerative Symptoms Via Suppressor Of Levy Mutation In Drosophila Melanogaster, William Kaputa
Forensic Science Theses
Mutation of the levy gene on chromosome 2 of Drosophila melanogaster has previously been shown to cause temperature-induced paralysis and neurodegeneration. The Suppressor of levy mutation, Su(levy), also on chromosome 2, modulates the effects of the levy mutation and partly rescues the wild-type phenotype. The goal of this research was to determine if Su(levy) mutation alleviates the effects of neurodegeneration caused by mutations associated with Alzheimer’s and Parkinson’s diseases in humans. The mutant genes used were hLRRK2, α-Synuclein, DJ1-α, Pink, Parkin, and Aβ-42. To determine this, flies carrying the above-mentioned mutant genes were crossed ...
Comparative Genomics Reveals Insights Into Avian Genome Evolution And Adaptation, 2014 University of Nebraska - Lincoln
Comparative Genomics Reveals Insights Into Avian Genome Evolution And Adaptation, Guojie Zhang, Cai Li, Qiye Li, Bo Li, Dennis M. Larkin, Chul Lee, Jay F. Storz, Agostinho Antunes, Matthew J. Greenwold, Robert W. Meredith, Anders Ödeen, Jie Cui, Qi Zhou, Luohao Xu, Hailin Pan, Zongji Wang, Lijun Jin, Pei Zhang, Haofu Hu, Wei Yang, Jiang Hu, Jin Xiao, Zhikai Yang, Yang Liu, Qiaolin Xie, Hao Yu, Jinmin Lian, Ping Wen, Fang Zhang, Hui Li, Yongli Zeng, Zijun Xiong, Shiping Liu, Long Zhou, Zhiyong Huang, Na An, Jie Wang, Quimei Zheng, Yingqi Xiong, Guangbiao Wang, Bo Wang, Jingjing Wang, Yu Fan, Rute R. Da Fonseca, Alonzo Alfaro-Núñez, Mikkel Schubert, Ludovic Orlando, Tobias Mourier, Jason T. Howard, Ganeshkumar Ganapathy, Andreas Pfenning, Osceola Whitney, Miriam V. Rivas, Erina Hara, Julia Smith, Marta Farré, Jitendra Narayan, Gancho Slavov, Michael N. Romanov, Rui Borges, João Paulo Machado, Imran Khan, Mark S. Springer, John Gatesy, Federico G. Hoffmann, Juan C. Opazo, Olle Håstad, Roger H. Sawyer, Heebal Kim, Kyu-Won Kim, Hyeon Jeong Kim, Seoae Cho, Ning Li, Yinhua Huang, Michael W. Bruford, Xiangjiang Zhan, Andrew Dixon, Mads F. Bertelsen, Elizabeth Derryberry, Wesley Warren, Richard K. Wilson, Shengbin Li, David A. Ray, Richard E. Green, Stephen J. O'Brien, Darren Griffin, Warren E. Johnson, David Haussler, Oliver A. Ryder, Eske Willerslev, Gary R. Graves, Per Alström, Jon Fjeldså, David P. Mindell, Scott V. Edwards, Edward L. Braun, Carsten Rahbek, David W. Burt, Peter Houde, Yong Zhang, Huanming Yang, Jian Wang, Avian Genome Consortium, Erich D. Jarvis, M. Thomas P. Gilbert, Jun Wang
Jay F. Storz Publications
Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses ...
An Active Role For The Ribosome In Determining The Fate Of Oxidized Mrna, 2014 Washington University in St. Louis
An Active Role For The Ribosome In Determining The Fate Of Oxidized Mrna, Carrie L. Simms, Benjamin H. Hudson, John W. Mosior, Ali S. Rangwala, Hani S. Zaher
Biology Faculty Publications
Chemical damage to RNA affects its functional properties and thus may pose a significant hurdle to the translational apparatus; however, the effects of damaged mRNA on the speed and accuracy of the decoding process and their interplay with quality-control processes are not known. Here, we systematically explore the effects of oxidative damage on the decoding process using a well-defined bacterial in vitro translation system. We find that the oxidative lesion 8-oxoguanosine (8-oxoG) reduces the rate of peptide-bond formation by more than three orders of magnitude independent of its position within the codon. Interestingly, 8-oxoG had little effect on the fidelity ...
Testing Gene-Environment Interactions In The Presence Of Measurement Error, Chongzhi Di, Li Hsu, Charles Kooperberg, Alex Reiner, Ross Prentice
UW Biostatistics Working Paper Series
Complex diseases result from an interplay between genetic and environmental risk factors, and it is of great interest to study the gene-environment interaction (GxE) to understand the etiology of complex diseases. Recent developments in genetics field allows one to study GxE systematically. However, one difficulty with GxE arises from the fact that environmental exposures are often measured with error. In this paper, we focus on testing GxE when the environmental exposure E is subject to measurement error. Surprisingly, contrast to the well-established results that the naive test ignoring measurement error is valid in testing the main effects, we find that ...
Ploidy Number For Panicum Virgatum (Switchgrass) From The Long Island Sound Coastal Lowland Compared To Upland And Lowland Cultivars., Tanisha Williams, Carol Auer
Plant Science Articles
Panicum virgatum L. (switchgrass) is a native, perennial grass in North America with important ecological function in ecoregions including the Long Island Sound Coastal Lowland in the Northeastern United States. In recent decades, switchgrass has become a model lignocellulosic bioenergy crop with a large research portfolio describing its distribution, genetics, genomics, phenology, traits, gene flow, and cultivation. Switchgrass has been divided into two ecotypes, the Lowland ecotype which is tetraploid (2n= 4x= 36 chromosomes) and the Upland ecotype which is tetraploid or octaploid (2n= 8x= 72). While most switchgrass research has focused on genotypes from the Midwest or Southeastern regions ...
Autoantibodies To The Ny-Eso-1 Tumor Antigen In Metastatic Melanoma: Sialylation Of The Fc Region Of Immunoglobulin G Induces Differential Expression Signatures Of Inflammatory Molecules During Dendritic Cell Differentiation And Maturation, 2014 Aurora Health Care
Autoantibodies To The Ny-Eso-1 Tumor Antigen In Metastatic Melanoma: Sialylation Of The Fc Region Of Immunoglobulin G Induces Differential Expression Signatures Of Inflammatory Molecules During Dendritic Cell Differentiation And Maturation, Martin Oaks, Nathaniel Rein, John O. Richards, James Shaffer
Journal of Patient-Centered Research and Reviews
Purpose: We tested the hypothesis that different glycoforms of antibodies from patients with metastatic melanoma have different functional effects on human dendritic cell differentiation and maturation.
Methods: Antibodies to the cancer antigen NY-ESO-1 were affinity-purified from patients with melanoma and further fractionated into different glycoforms by lectin chromatography. Sialic acid-rich and sialic acid-poor fractions of these immunoglobulin G antibodies (IgG) were added to dendritic cell cultures during both differentiation and maturation, and the resulting cellular messenger RNA (mRNA) and culture supernatants were tested by microarray and enzyme-linked immunoassay for molecules related to inflammatory pathways.
Results: We identified unique mRNA and ...
Characterization Of The Transcriptome, Nucleotide Sequence Polymorphism, And Natural Selection In The Desert Adapted Mouse Peromyscus Eremicus, Matthew D. Macmanes, Michael B. Eisen
Molecular, Cellular and Biomedical Sciences Scholarship
As a direct result of intense heat and aridity, deserts are thought to be among the most harsh of environments, particularly for their mammalian inhabitants. Given that osmoregulation can be challenging for these animals, with failure resulting in death, strong selection should be observed on genes related to the maintenance of water and solute balance. One such animal, Peromyscus eremicus, is native to the desert regions of the southwest United States and may live its entire life without oral fluid intake. As a first step toward understanding the genetics that underlie this phenotype, we present a characterization of the P ...
Hla Class Ii Alleles In The Otomi Population Of The Mezquital Valley. A Genetic Approach To The History Of Interethnic Migrations In The Mexican Central Plateau, Ana Itzel Juárez-Martín, Blanca Zoila González-Sobrino, Ángel Eduardo Camarena Olvera, Ramcés Falfán-Valencia
Human Biology Open Access Pre-Prints
From a historic and genetic point of view, the Otomi of the Mezquital Valley are a frontier people that have played an important role in the making of the population dynamics of the Mexican Central Plateau. Due to their antiquity in the area, the Otomi may be bearers of ancient genetic variability, shared mainly today with other groups belonging to the Otomanguean linguistic family and with the Nahua.
This study analyzes the HLA class II allele frequencies reported in Mexican indigenous populations, in order to provide an intra-regional level historical perspective of the genetic relationships between the Otomi of the ...
Analysis Of Differential Mrna And Mirna Expression In An Alzheimer’S Disease Mouse Model, 2014 Liberty University
Analysis Of Differential Mrna And Mirna Expression In An Alzheimer’S Disease Mouse Model, Amanda Hazy, Matthew Dalton
Other Undergraduate Scholarship
Research has shown that changes in gene expression play a critical role in the development of Alzheimer’s Disease (AD). Our project will evaluate genome-wide RNA expression patterns from brain and blood in an AD mouse model. This analysis will provide insight regarding the mechanisms of AD pathology as well as determine a possible diagnostic tool utilizing RNA expression patterns found in the blood as biomarkers for AD.
B-Type Natriuretic Peptide And C-Reactive Protein In The Prediction Of Atrial Fibrillation Risk: The Charge-Af Consortium Of Community-Based Cohort Studies, 2014 University of Massachusetts Medical School
B-Type Natriuretic Peptide And C-Reactive Protein In The Prediction Of Atrial Fibrillation Risk: The Charge-Af Consortium Of Community-Based Cohort Studies, Moritz F. Sinner, Emelia J. Benjamin, Alvaro Alonso, David D. Mcmanus
Meyers Primary Care Institute Publications and Presentations
AIMS: B-type natriuretic peptide (BNP) and C-reactive protein (CRP) predict atrial fibrillation (AF) risk. However, their risk stratification abilities in the broad community remain uncertain. We sought to improve risk stratification for AF using biomarker information.
METHODS AND RESULTS: We ascertained AF incidence in 18 556 Whites and African Americans from the Atherosclerosis Risk in Communities Study (ARIC, n=10 675), Cardiovascular Health Study (CHS, n = 5043), and Framingham Heart Study (FHS, n = 2838), followed for 5 years (prediction horizon). We added BNP (ARIC/CHS: N-terminal pro-B-type natriuretic peptide; FHS: BNP), CRP, or both to a previously reported AF risk ...
Investigating The Role Of Micrornas In The Response To Nitrogen Deprivation In The Green Alga Chlamydomonas Reinhardtii, 2014 University of Nebraska - Lincoln
Investigating The Role Of Micrornas In The Response To Nitrogen Deprivation In The Green Alga Chlamydomonas Reinhardtii, Adam Voshall
Dissertations and Theses in Biological Sciences
Microalgae are gaining attention as a potential feedstock for the production of biodiesel, mainly derived from triacylglycerols (TAG). In many algae, TAG synthesis increases dramatically upon certain stresses but this is often accompanied by growth retardation. Rational improvements to strain productivity are limited by the scant knowledge on algal lipid metabolism and gene regulatory mechanisms. In this context, systems-level approaches aimed at understanding and modeling metabolic and regulatory networks may enable hypothesis-driven genetic engineering strategies. The green microalga Chlamydomonas reinhardtii accumulates significant amounts of TAGs under nutrient starvation and provides a genetically tractable model for manipulating biosynthetic pathways. In order ...
De Novo Transcriptome Of The Hemimetabolous German Cockroach (Blattella Germanica), 2014 University of Nebraska - Lincoln
De Novo Transcriptome Of The Hemimetabolous German Cockroach (Blattella Germanica), Xiaojie Zhou, Kun Qian, Ying Tong, Junwei Jerry Zhu, Xinghui Qiu, Xiaopeng Zeng
Publications from USDA-ARS / UNL Faculty
Background: The German cockroach, Blattella germanica, is an important insect pest that transmits various pathogens mechanically and causes severe allergic diseases. This insect has long served as a model system for studies of insect biology, physiology and ecology. However, the lack of genome or transcriptome information heavily hinder our further understanding about the German cockroach in every aspect at a molecular level and on a genome-wide scale. To explore the transcriptome and identify unique sequences of interest, we subjected the B. germanica transcriptome to massively parallel pyrosequencing and generated the first reference transcriptome for B. germanica.
Methodology/Principal Findings: A ...
Modeling T Cell Receptor Recognition Of Cd1-Lipid And Mr1-Metabolite Complexes, 2014 University of Massachusetts Medical School
Modeling T Cell Receptor Recognition Of Cd1-Lipid And Mr1-Metabolite Complexes, Brian G. Pierce, Thom Vreven, Zhiping Weng
Open Access Articles
BACKGROUND: T cell receptors (TCRs) can recognize diverse lipid and metabolite antigens presented by MHC-like molecules CD1 and MR1, and the molecular basis of many of these interactions has not been determined. Here we applied our protein docking algorithm TCRFlexDock, previously developed to perform docking of TCRs to peptide-MHC (pMHC) molecules, to predict the binding of alphabeta and gammadelta TCRs to CD1 and MR1, starting with the structures of the unbound molecules.
RESULTS: Evaluating against TCR-CD1d complexes with crystal structures, we achieved near-native structures in the top 20 models for two out of four cases, and an acceptable-rated prediction for ...
Crisprseek: A Bioconductor Package To Identify Target-Specific Guide Rnas For Crispr-Cas9 Genome-Editing Systems, 2014 University of Massachusetts Medical School
Crisprseek: A Bioconductor Package To Identify Target-Specific Guide Rnas For Crispr-Cas9 Genome-Editing Systems, Lihua Julie Zhu, Benjamin R. Holmes, Neil Aronin, Michael H. Brodsky
Program in Gene Function and Expression Publications and Presentations
CRISPR-Cas systems are a diverse family of RNA-protein complexes in bacteria that target foreign DNA sequences for cleavage. Derivatives of these complexes have been engineered to cleave specific target sequences depending on the sequence of a CRISPR-derived guide RNA (gRNA) and the source of the Cas9 protein. Important considerations for the design of gRNAs are to maximize aimed activity at the desired target site while minimizing off-target cleavage. Because of the rapid advances in the understanding of existing CRISPR-Cas9-derived RNA-guided nucleases and the development of novel RNA-guided nuclease systems, it is critical to have computational tools that can accommodate a ...
Single Point Mutation In Rabenosyn-5 In A Female With Intractable Seizures And Evidence Of Defective Endocytotic Trafficking, 2014 University of Massachusetts Medical School
Single Point Mutation In Rabenosyn-5 In A Female With Intractable Seizures And Evidence Of Defective Endocytotic Trafficking, Sylvia Stockler, Silvia Corvera, David G. Lambright, Kevin E. Fogarty, Ekaterina Nosova, Deborah Marie Leonard, Robert Steinfeld, Cameron Ackerley, Casper Shyr, Nicolas Au, Kathrin Selby, Margot Van Allen, Hilary Vallance, Ron Wevers, David Watkins, David Rosenblatt, Colin J. Ross, Elizabeth Conibear, Wyeth Wasserman, Clara Van Karnebeek
Open Access Articles
Background. We report a 6.5 year-old female with a homozygous missense mutation in ZFYVE20, encoding Rabenosyn-5 (Rbsn-5), a highly conserved multi-domain protein implicated in receptor-mediated endocytosis. The clinical presentation includes intractable seizures, developmental delay, microcephaly, dysostosis, osteopenia, craniofacial dysmorphism, macrocytosis and megaloblastoid erythropoiesis. Biochemical findings include transient cobalamin deficiency, severe hypertriglyceridemia upon ketogenic diet, microalbuminuria and partial cathepsin D deficiency.
Methods and results. Whole exome sequencing followed by Sanger sequencing confirmed a rare (frequency:0.003987) homozygous missense mutation, g.15,116,371 G inverted question mark > inverted question markA (c.1273G inverted question mark > inverted question markA), in ...
Mapping Regions Of Rnf168 Required For Its Degradation By Icp0, 2014 Chapman University
Mapping Regions Of Rnf168 Required For Its Degradation By Icp0, Andrea Cyr, Matthew Weitzman
e-Research: A Journal of Undergraduate Work
Viruses establish infection by overtaking host cell processes and developing mechanisms that promote viral replication. Herpes simplex virus undergoes lytic and latent cycles of infection throughout the lifespan of its host. The viral genome is transcriptionally silent during latency, but viral proteins are produced upon reactivation. Herpes simplex virus type 1 encodes the ICP0 protein, an E3 ubiquitin ligase required for reactivation from latency of the infectious virus. The immediate-early protein ICP0 regulates the herpes simplex virus by activating viral gene expression thereby initiating lytic infection. Cellular proteins are degraded by ICP0, promoting the virus to enter the lytic cycle ...
Haplotype Variety Analysis Of Human Populations: An Application To Hapmap Data, 2014 Chapman University
Haplotype Variety Analysis Of Human Populations: An Application To Hapmap Data, Michelle Creek, Cyril Rakovski
e-Research: A Journal of Undergraduate Work
We undertake a study to investigate the haplotype variety of distinct human populations. We use a natural measure of haplotype variety, the total number of haplotypes (TNH) present that reflects the number of haplotypes with nonzero frequencies estimated from the data at hand for each selection of multiple loci. For the analysis of real human populations, we use the haplotype data of the Denver Chinese, Tuscan Italians, Luhya Kenyans, and Gujarati Indians from release III of the HapMap database. Moreover, we show that the TNH statistic is biased in small sample data scenarios such as the HapMap and implement a ...