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Cuticular Lipid Mass And Desiccation Rates In Glossina Pallidipes: Interpopulation Variation, Russell A. Jurenka, John S. Terblanche, C. Jaco Klok, Steven L. Chown, Elliot S. Krafsur 2016 Iowa State University

Cuticular Lipid Mass And Desiccation Rates In Glossina Pallidipes: Interpopulation Variation, Russell A. Jurenka, John S. Terblanche, C. Jaco Klok, Steven L. Chown, Elliot S. Krafsur

Elliot Krafsur

Tsetse flies, Glossina pallidipes (Diptera: Glossinidae) are said to have strong dispersal tendencies. Gene flow among these populations is estimated to be the theoretical equivalent of no more than one or two reproducing flies per generation, thereby raising the hypothesis of local regimes of natural selection. Flies were sampled from four environmentally diverse locations in Kenya to determine whether populations are homogeneous in desiccation tolerance and cuticular lipids. Cuticular hydrocarbon fractions known to act as sex pheromones do not differ among populations, thereby eliminating sexual selection as an isolating mechanism. Cuticular lipid quantities vary among populations and are not correlated ...


Long-Term Correction Of Very Long-Chain Acyl-Coa Dehydrogenase Deficiency In Mice Using Aav9 Gene Therapy, Allison M. Keeler, Thomas J. Conlon, Glenn Walter, Huadong Zeng, Scott A. Shaffer, Fu Dungtao, Kirsten E. Erger, Travis L. Cossette, Qiushi Tang, Christian Mueller, Terence R. Flotte 2016 University of Massachusetts Medical School

Long-Term Correction Of Very Long-Chain Acyl-Coa Dehydrogenase Deficiency In Mice Using Aav9 Gene Therapy, Allison M. Keeler, Thomas J. Conlon, Glenn Walter, Huadong Zeng, Scott A. Shaffer, Fu Dungtao, Kirsten E. Erger, Travis L. Cossette, Qiushi Tang, Christian Mueller, Terence R. Flotte

Thomas L. Shaffer

Very long-chain acyl-coA dehydrogenase (VLCAD) is the rate-limiting step in mitochondrial fatty acid oxidation. VLCAD-deficient mice and patients clinical symptoms stem from not only an energy deficiency but also long-chain metabolite accumulations. VLCAD-deficient mice were treated systemically with 1 x 10(12) vector genomes of recombinant adeno-associated virus 9 (rAAV9)-VLCAD. Biochemical correction was observed in vector-treated mice beginning 2 weeks postinjection, as characterized by a significant drop in long-chain fatty acyl accumulates in whole blood after an overnight fast. Changes persisted through the termination point around 20 weeks postinjection. Magnetic resonance spectroscopy (MRS) and tandem mass spectrometry (MS/MS ...


Iron Acquisition Strategies Employed By Staphylococcus Lugdunensis, Jeremy R. Brozyna 2016 The University of Western Ontario

Iron Acquisition Strategies Employed By Staphylococcus Lugdunensis, Jeremy R. Brozyna

Electronic Thesis and Dissertation Repository

Iron is crucial for many cellular processes including DNA synthesis and respiration. The majority of iron in mammals is in heme within hemoproteins, inside cells, or transported through circulation by the glycoprotein transferrin, which constitutes the greatest iron source in serum. Limiting iron availability is an important facet of nutritional immunity to help prevent infection.

Staphylococcus lugdunensis is a human skin commensal and opportunistic pathogen capable of causing a variety of infections, including particularly aggressive endocarditis. It is an emerging pathogen with elevated virulence compared to other species of coagulase-negative staphylococci. The versatility of S. lugdunensis to infect multiple niches ...


Ethnic Disparity In 21-Hydroxylase Gene Mutations Identified In Pakistani Congenital Adrenal Hyperplasia Patient, Aysha Habib Khan, Muniba Aban, Jamal Raza, Naeem ul Haq, Abdul Jabbar, Tariq Moatter 2016 Aga Khan University

Ethnic Disparity In 21-Hydroxylase Gene Mutations Identified In Pakistani Congenital Adrenal Hyperplasia Patient, Aysha Habib Khan, Muniba Aban, Jamal Raza, Naeem Ul Haq, Abdul Jabbar, Tariq Moatter

Aysha Habib

Background: Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive disorders caused by defects in the steroid 21 hydroxylase gene (CYP21A2). We studied the spectrum of mutations in CYP21A2 gene in a multi-ethnic population in Pakistan to explore the genetics of CAH. Methods: A cross sectional study was conducted for the identification of mutations CYP21A2 and their phenotypic associations in CAH using ARMS-PCR assay. Results: Overall, 29 patients were analyzed for nine different mutations. The group consisted of two major forms of CAH including 17 salt wasters and 12 simple virilizers. There were 14 phenotypic males and 15 females ...


Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager 2016 University of Wisconsin-La Crosse

Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager

Spora: A Journal of Biomathematics

The development of an embryo from a fertilised egg to a multicellular organism proceeds through numerous steps, with the formation of the three germ layers (endoderm, mesoderm, ectoderm) being one of the first. In this paper we study the mesendoderm (the tissue that collectively gives rise to both mesoderm and endoderm) gene regulatory network for two species, \textit{Xenopus laevis} and the axolotl (\textit{Ambystoma mexicanum}) using Boolean networks. We find that previously-established bistability found in these networks can be reproduced using this Boolean framework, provided that some assumptions used in previously-published differential equations models are relaxed. We conclude by ...


A Long-Term Neuroepigenomic Profile Of Prenatal Alcohol Exposure, Benjamin I. Laufer 2016 The University of Western Ontario

A Long-Term Neuroepigenomic Profile Of Prenatal Alcohol Exposure, Benjamin I. Laufer

Electronic Thesis and Dissertation Repository

Fetal Alcohol Spectrum Disorders (FASD) represent the largest preventable cause of cognitive deficits in the western world. The mechanism(s) of how prenatal alcohol exposure (PAE) results in FASD remain unknown. Towards this end, mouse models of PAE have successfully recreated endophenotypes that are characteristic of FASD. This doctoral thesis examines the long-term epigenomic alterations associated with PAE. I have examined both mice with PAE and human patients with FASD.

In the first set of experiments, mice with PAE and matched controls were raised to adulthood and then their whole brains were examined for alterations to gene expression, non-coding RNA ...


Dyslexia And Language Impairment Associated Genetic Markers Influence Cortical Thickness And White Matter In Typically Developing Children, John D. Eicher, Jean A. Frazier, David N. Kennedy, Jeffrey R. Gruen 2016 Yale University

Dyslexia And Language Impairment Associated Genetic Markers Influence Cortical Thickness And White Matter In Typically Developing Children, John D. Eicher, Jean A. Frazier, David N. Kennedy, Jeffrey R. Gruen

Jean A. Frazier

Dyslexia and language impairment (LI) are complex traits with substantial genetic components. We recently completed an association scan of the DYX2 locus, where we observed associations of markers in DCDC2, KIAA0319, ACOT13, and FAM65B with reading-, language-, and IQ-related traits. Additionally, the effects of reading-associated DYX3 markers were recently characterized using structural neuroimaging techniques. Here, we assessed the neuroimaging implications of associated DYX2 and DYX3 markers, using cortical volume, cortical thickness, and fractional anisotropy. To accomplish this, we examined eight DYX2 and three DYX3 markers in 332 subjects in the Pediatrics Imaging Neurocognition Genetics study. Imaging-genetic associations were examined by ...


Genomic Insights Into The Ixodes Scapularis Tick Vector Of Lyme Disease, Monika Gulia-Nuss,, Daniel R. Caffrey, Neal S. Silverman, Adam R. Wespiser, Catherine A. Hill 2016 Purdue University

Genomic Insights Into The Ixodes Scapularis Tick Vector Of Lyme Disease, Monika Gulia-Nuss,, Daniel R. Caffrey, Neal S. Silverman, Adam R. Wespiser, Catherine A. Hill

Neal Silverman

Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing approximately 57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing ...


Therapeutic Raavrh10 Mediated Sod1 Silencing In Adult Sod1(G93a) Mice And Nonhuman Primates, Florie Borel, Gwladys Gernoux, Brynn Cardozo, Jake P. Metterville, Gabriela Toro Cabrera, Lina Song, Qin Su, Guang Ping Gao, Mai K. Elmallah, Robert H. Brown Jr., Christian Mueller 2016 University of Massachusetts Medical School

Therapeutic Raavrh10 Mediated Sod1 Silencing In Adult Sod1(G93a) Mice And Nonhuman Primates, Florie Borel, Gwladys Gernoux, Brynn Cardozo, Jake P. Metterville, Gabriela Toro Cabrera, Lina Song, Qin Su, Guang Ping Gao, Mai K. Elmallah, Robert H. Brown Jr., Christian Mueller

Christian Mueller

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease; survival in ALS is typically 3-5 years. No treatment extends patient survival by more than three months. Approximately 20% of familial ALS and 1-3% of sporadic ALS patients carry a mutation in the gene encoding superoxide dismutase 1 (SOD1). In a transgenic ALS mouse model expressing the mutant SOD1(G93A) protein, silencing the SOD1 gene prolongs survival. One study reports a therapeutic effect of silencing the SOD1 gene in systemically treated adult ALS mice; this was achieved with a short hairpin RNA, a silencing molecule that has raised multiple safety concerns ...


Relationship Between Morphogenesis And Secretion In The Filamentous Fungus Aspergillus Nidulans, Lakshmi Preethi Yerra 2016 University of Nebraska-Lincoln

Relationship Between Morphogenesis And Secretion In The Filamentous Fungus Aspergillus Nidulans, Lakshmi Preethi Yerra

Dissertations and Theses in Biological Sciences

Filamentous fungi have a long history in biotechnology for the production of food ingredients, pharmaceuticals and enzymes. The advancements made in recent years have earned filamentous fungi such as Aspergillus species a dominant place among microbial cell factories. Although the model fungus A. nidulans has been extensively studied, the genetic and regulatory networks that underlie morphogenesis and development have yet to be fully characterized. The Rho GTPases (Cdc42 and RacA) are one of the most important regulators of the morphogenetic processes among diverse eukaryotic organisms. Although the functions of these GTPases are relatively well-characterized, little is known about their downstream ...


Development Of Genomic Resources For The Evaluation Of Red Snapper, An Emerging Species Candidate For Marine Aquaculture And Stock Enhancement, Adrienne Elise Norrell 2016 University of Southern Mississippi

Development Of Genomic Resources For The Evaluation Of Red Snapper, An Emerging Species Candidate For Marine Aquaculture And Stock Enhancement, Adrienne Elise Norrell

Master's Theses

The northern red snapper (Lutjanus campechanus) is a highly targeted reef fish candidate for marine aquaculture and stock enhancement in the southern United States. This work aimed to develop genomic resources for the genetic management of aquaculture programs and to investigate population structure using high-throughput sequencing technologies. Eighty-four new microsatellite markers were developed through screening of Illumina paired-end sequencing reads. Microsatellite loci and Single Nucleotide Polymorphisms (SNPs) generated through Restriction Site Associated DNA (RAD) sequencing were assayed in 5 outbred full-sib families to construct a high-density linkage map of the red snapper genome. The map consists of 7,964 markers ...


Evolutionary Genetics: From Molecules To Morphology, Fredric J. Janzen 2016 Iowa State University

Evolutionary Genetics: From Molecules To Morphology, Fredric J. Janzen

Fredric Janzen

The past 35 years have witnessed a revolution in evolutionary genetics that, like the proverbial The Little Engine that Could going over the mountain pass, shows no signs of slowing, much less stopping. To a considerable extent, we owe much to one per­ son, Richard Lewontin, for getting this little train over the hump and conducting it while the masses have shoveled coal into the boiler. Indeed, few have had such a substantive and pervasive impact on evolutionary biology in general, and so this edited volume is a welcome and well-deserved tribute to the powerful and varied influence of Lewontin ...


End Sequence Analysis Toolkit (Esat) Expands The Extractable From Single Cell Rna-Seq Experiments, Alan G. Derr, Chaoxing Yang, Rapolas Zilionis, Alexey Sergushichev, David Blodgett, Sambra D. Redick, Rita Bortell, Jeremy Luban, David Harlan, Sebastian Kadener, Dale L. Greiner, Allon Klein, Maxim Artyomov, Manuel Garber 2016 University of Massachusetts Medical School

End Sequence Analysis Toolkit (Esat) Expands The Extractable From Single Cell Rna-Seq Experiments, Alan G. Derr, Chaoxing Yang, Rapolas Zilionis, Alexey Sergushichev, David Blodgett, Sambra D. Redick, Rita Bortell, Jeremy Luban, David Harlan, Sebastian Kadener, Dale L. Greiner, Allon Klein, Maxim Artyomov, Manuel Garber

Open Access Articles

RNA-seq protocols that focus on transcript termini are well-suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed for global RNA-seq produce computational artifacts. To remedy this we created the End Sequence Analysis Toolkit (ESAT). As a test, we first compared end-sequencing and bulk RNA-seq using RNA from dendritic cells stimulated with lipopolysaccharide (LPS). As predicted by the telescripting model for transcriptional bursts, ESAT detected an LPS-stimulated shift to shorter 3'-isoforms that was not evident by conventional computational methods. Then, droplet-based microfluidics was used to generate 1,000 ...


Comparative Evolutionary Analysis Of Organellar Genomic Diversity In Green Plants, Weishu Fan 2016 University of Nebraska - Lincoln

Comparative Evolutionary Analysis Of Organellar Genomic Diversity In Green Plants, Weishu Fan

Theses, Dissertations, and Student Research in Agronomy and Horticulture

The mitochondrial genome (mitogenome) and plastid genome (plastome) of plants vary immensely in genome size and gene content. They have also developed several eccentric features, such as the preference for horizontal gene transfer of mitochondrial genes, the reduction of the plastome in non-photosynthetic plants, and variable amounts of RNA editing affecting both genomes. Different organismal lifestyles can partially account for the highly diverse organellar genomes across the tree of green plants. For example, endosymbiotic and parasitic lifestyles can dramatically affect the genomic architectures of plant mitochondria and plastids. In this study, the organellar genomes of several green plants with atypical ...


Integrative Analysis Of The Caenorhabditis Elegans Genome By The Modencode Project, Sarah Petersen, et al. 2016 Kenyon College

Integrative Analysis Of The Caenorhabditis Elegans Genome By The Modencode Project, Sarah Petersen, Et Al.

Sarah Petersen

We systematically generated large-scale data sets to improve genome annotation for the nematodeCaenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor–binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor–binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with ...


A Transcriptional Program Promotes Remodeling Of Gabaergic Synapses In Caenorhabditis Elegans, Sarah Petersen, et al. 2016 Selected Works

A Transcriptional Program Promotes Remodeling Of Gabaergic Synapses In Caenorhabditis Elegans, Sarah Petersen, Et Al.

Sarah Petersen

Although transcription factors are known to regulate synaptic plasticity, downstream genes that contribute to neural circuit remodeling are largely undefined. In Caenorhabditis elegans, GABAergic Dorsal D (DD) motor neuron synapses are relocated to new sites during larval development. This remodeling program is blocked in Ventral D (VD) GABAergic motor neurons by the COUP-TF (chicken ovalbumin upstream promoter transcription factor) homolog, UNC-55. We exploited this UNC-55 function to identify downstream synaptic remodeling genes that encode a diverse array of protein types including ion channels, cytoskeletal components, and transcription factors. We show that one of these targets, the Iroquois-like homeodomain protein, IRX-1 ...


A Spatial And Temporal Map Of C. Elegans Gene Expression., Sarah Petersen, et al. 2016 Selected Works

A Spatial And Temporal Map Of C. Elegans Gene Expression., Sarah Petersen, Et Al.

Sarah Petersen

The C. elegans genome has been completely sequenced, and the developmental anatomy of this model organism is described at single-cell resolution. Here we utilize strategies that exploit this precisely defined architecture to link gene expression to cell type. We obtained RNAs from specific cells and from each developmental stage using tissue-specific promoters to mark cells for isolation by FACS or for mRNA extraction by the mRNA-tagging method. We then generated gene expression profiles of more than 30 different cells and developmental stages using tiling arrays. Machine-learning-based analysis detected transcripts corresponding to established gene models and revealed novel transcriptionally active regions ...


Dietary Weight Loss Advice In Us Health Magazines And Its Relation To Ancestral Diet, Risa J. Stein, Marium A. Choudhry, Thomas J. Murray Jr. 2016 Rockhurst University

Dietary Weight Loss Advice In Us Health Magazines And Its Relation To Ancestral Diet, Risa J. Stein, Marium A. Choudhry, Thomas J. Murray Jr.

Journal of Evolution and Health

As rates of overweight and obesity have risen in the US, the public has sought effective strategies for weight loss through dietary modification. A proliferation of processed foods and changing governmental nutrition guidelines have both impacted dietary intake patterns. While physicians are considered respectable sources of weight-loss information, increasingly the public has turned to the media, particularly magazines, for weight loss advice. This study investigated the dietary recommendations found in the five leading US health-related magazines and compared those recommendations to ancestral diets. With a couple notable exceptions, leading health magazines present consistent recommendations for dietary modifications to promote weight ...


Sex Chromosome-Wide Transcriptional Suppression And Compensatory Cis-Regulatory Evolution Mediate Gene Expression In The Drosophila Male Germline, Emily L. Landeen, Christina A. Muirhead, Lori Wright, Colin D. Meiklejohn, Daven C. Presgraves 2016 University of Rochester

Sex Chromosome-Wide Transcriptional Suppression And Compensatory Cis-Regulatory Evolution Mediate Gene Expression In The Drosophila Male Germline, Emily L. Landeen, Christina A. Muirhead, Lori Wright, Colin D. Meiklejohn, Daven C. Presgraves

Faculty Publications in the Biological Sciences

The evolution of heteromorphic sex chromosomes has repeatedly resulted in the evolution of sex chromosome-specific forms of regulation, including sex chromosome dosage compensation in the soma and meiotic sex chromosome inactivation in the germline. In the male germline of Drosophila melanogaster, a novel but poorly understood form of sex chromosome-specific transcriptional regulation occurs that is distinct from canonical sex chromosome dosage compensation or meiotic inactivation. Previous work shows that expression of reporter genes driven by testis-specific promoters is considerably lower—approximately 3-fold or more—for transgenes inserted into X chromosome versus autosome locations. Here we characterize this transcriptional suppression of ...


Dynamics Of Marine Bacterial Community Diversity Of The Coastal Waters Of The Reefs, Inlets, And Wastewater Outfalls Of Southeast Florida, Alexandra Mandina Campbell, Jay Fleisher, Christopher D. Sinigalliano, James R. White, Jose V. Lopez 2016 Nova Southeastern University Oceanographic Center

Dynamics Of Marine Bacterial Community Diversity Of The Coastal Waters Of The Reefs, Inlets, And Wastewater Outfalls Of Southeast Florida, Alexandra Mandina Campbell, Jay Fleisher, Christopher D. Sinigalliano, James R. White, Jose V. Lopez

Jose Lopez

Coastal waters adjacent to populated southeast Florida possess different habitats (reefs, oceanic inlets, sewage outfalls) that may affect the composition of their inherent microbiomes. To determine variation according to site, season, and depth, over the course of 1 year, we characterized the bacterioplankton communities within 38 nearshore seawater samples derived from the Florida Area Coastal Environment (FACE) water quality survey. Six distinct coastal locales were profiled – the Port Everglades and Hillsboro Inlets, Hollywood and Broward wastewater outfalls, and associated reef sites using culture-independent, high-throughput pyrosequencing of the 16S rRNA V4 region. More than 227,000 sequences helped describe longitudinal taxonomic ...


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