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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 ...


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 ...


Separate F-Type Plasmids Have Shaped The Evolution Of The H30 Subclone Of Escherichia Coli Sequence Type 131., Timothy J Johnson, Jessica L Danzeisen, Bonnie Youmans, Kyle Case, Katharine Llop, Jeannette Munoz-Aguayo, Cristian Flores-Figueroa, Maliha Aziz, Nicole Stoesser, Evgeni Sokurenko, Lance B. Price, James R Johnson 2016 George Washington University

Separate F-Type Plasmids Have Shaped The Evolution Of The H30 Subclone Of Escherichia Coli Sequence Type 131., Timothy J Johnson, Jessica L Danzeisen, Bonnie Youmans, Kyle Case, Katharine Llop, Jeannette Munoz-Aguayo, Cristian Flores-Figueroa, Maliha Aziz, Nicole Stoesser, Evgeni Sokurenko, Lance B. Price, James R Johnson

Environmental and Occupational Health Faculty Publications

The extraintestinal pathogenic Escherichia coli (ExPEC) H30 subclone of sequence type 131 (ST131-H30) has emerged abruptly as a dominant lineage of ExPEC responsible for human disease. The ST131-H30 lineage has been well described phylogenetically, yet its plasmid complement is not fully understood. Here, single-molecule, real-time sequencing was used to generate the complete plasmid sequences of ST131-H30 isolates and those belonging to other ST131 clades. Comparative analyses revealed separate F-type plasmids that have shaped the evolution of the main fluoroquinolone-resistant ST131-H30 clades. Specifically, an F1:A2:B20 plasmid is strongly associated with ...


Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James Van Etten, Kenneth Nickerson 2016 University of Nebraska-Lincoln

Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James Van Etten, Kenneth Nickerson

Kenneth Nickerson Papers

Most animal–microbe symbiotic interactions must be advantageous to the host and provide nutritional benefits to the endosymbiont. When the host provides nutrients, it can gain the capacity to control the interaction, promote self-growth, and increase its fitness. Chlorella-like green algae engage in symbiotic relationships with certain protozoans, a partnership that significantly impacts the physiology of both organisms. Consequently, it is often challenging to grow axenic Chlorella cultures after isolation from the host because they are nutrient fastidious and often susceptible to virus infection. We hypothesize that the establishment of a symbiotic relationship resulted in natural selection for nutritional and ...


Adgrl3 (Lphn3) Variants Are Associated With A Refined Phenotype Of Adhd In The Mta Study, Maria T. Acosta, James Swanson, Annamarie Stehli, Brooke Molina, The MTA Team 2016 George Washington University

Adgrl3 (Lphn3) Variants Are Associated With A Refined Phenotype Of Adhd In The Mta Study, Maria T. Acosta, James Swanson, Annamarie Stehli, Brooke Molina, The Mta Team

Neurology Faculty Publications

Background

ADHD is the most common neuropsychiatric condition affecting individuals of all ages. Long-term outcomes of affected individuals and association with severe comorbidities as SUD or conduct disorders are the main concern. Genetic associations have been extensively described. Multiple studies show that intronic variants harbored in the ADGRL3 (LPHN3) gene are associated with ADHD, especially associated with poor outcomes.

Methods

In this study, we evaluated this association in the Multimodal Treatment Study of children with ADHD (MTA), initiated as a 14-month randomized clinical trial of 579 children diagnosed with DSM-IV ADHD-Combined Type (ADHD-C), that transitioned to a 16-year prospective observational ...


Enrichment Of Echinacea Angustifolia With Bauer Alkylamide 11 And Bauer Ketone 23 Increased Anti-Inflammatory Potential Through Interference With Cox-2 Enzyme Activity, Carlie A. LaLone, Nan Huang, Ludmila Rizshsky, Man-Yu Yum, Navrozedeep Singh, Cathy Hauck, Basil J. Nikolau, Eve S. Wurtele, Marian L. Kohut, Patricia A. Murphy, Diane F. Birt 2016 Iowa State University

Enrichment Of Echinacea Angustifolia With Bauer Alkylamide 11 And Bauer Ketone 23 Increased Anti-Inflammatory Potential Through Interference With Cox-2 Enzyme Activity, Carlie A. Lalone, Nan Huang, Ludmila Rizshsky, Man-Yu Yum, Navrozedeep Singh, Cathy Hauck, Basil J. Nikolau, Eve S. Wurtele, Marian L. Kohut, Patricia A. Murphy, Diane F. Birt

Basil Nikolau

Bauer alkylamide 11 and Bauer ketone 23 were previously found to be partially responsible forEchinacea angustifolia anti-inflammatory properties. This study further tested their importance using the inhibition of prostaglandin E2 (PGE2) and nitric oxide (NO) production by RAW264.7 mouse macrophages in the absence and presence of lipopolysaccharide (LPS) and E. angustifolia extracts, phytochemical enriched fractions, or pure synthesized standards. Molecular targets were probed using microarray, qRT-PCR, Western blot, and enzyme assays. Fractions with these phytochemicals were more potent inhibitors of LPS-induced PGE2 production than E. angustifolia extracts. Microarray did not detect changes in transcripts with ...


Metabolomics As A Hypothesis-Generating Functional Genomics Tool For The Annotation Of Arabidopsis Thaliana Genes Of “Unknown Function”, Stephanie M. Quanbeck, Libuse Brachova, Alexis A. Campbell, Xin Guan, Ann Perera, Kun He, Seung Y. Rhee, Preeti Bais, Julie A. Dickerson, Philip M. Dixon, Gert Wohlgemuth, Oliver Fiehn, Lenore Barkan, Iris Lange, B. Markus Lange, Insuk Lee, Diego Cortes, Carolina Salazar, Joel Shuman, Vladimir Shulaev, David V. Huhman, Lloyd W. Sumner, Mary R. Roth, Ruth Welti, Hilal Ilarslan, Eve S. Wurtele, Basil J. Nikolau 2016 Iowa State University

Metabolomics As A Hypothesis-Generating Functional Genomics Tool For The Annotation Of Arabidopsis Thaliana Genes Of “Unknown Function”, Stephanie M. Quanbeck, Libuse Brachova, Alexis A. Campbell, Xin Guan, Ann Perera, Kun He, Seung Y. Rhee, Preeti Bais, Julie A. Dickerson, Philip M. Dixon, Gert Wohlgemuth, Oliver Fiehn, Lenore Barkan, Iris Lange, B. Markus Lange, Insuk Lee, Diego Cortes, Carolina Salazar, Joel Shuman, Vladimir Shulaev, David V. Huhman, Lloyd W. Sumner, Mary R. Roth, Ruth Welti, Hilal Ilarslan, Eve S. Wurtele, Basil J. Nikolau

Basil Nikolau

Metabolomics is the methodology that identifies and measures global pools of small molecules (of less than about 1,000 Da) of a biological sample, which are collectively called the metabolome. Metabolomics can therefore reveal the metabolic outcome of a genetic or environmental perturbation of a metabolic regulatory network, and thus provide insights into the structure and regulation of that network. Because of the chemical complexity of the metabolome and limitations associated with individual analytical platforms for determining the metabolome, it is currently difficult to capture the complete metabolome of an organism or tissue, which is in contrast to genomics and ...


Plantmetabolomics.Org: Mass Spectrometry-Based Arabidopsis Metabolomics—Database And Tools Update, Preeti Bais, Stephanie M. Moon-Quanbeck, Basil J. Nikolau, Julie A. Dickerson 2016 Iowa State University

Plantmetabolomics.Org: Mass Spectrometry-Based Arabidopsis Metabolomics—Database And Tools Update, Preeti Bais, Stephanie M. Moon-Quanbeck, Basil J. Nikolau, Julie A. Dickerson

Basil Nikolau

The PlantMetabolomics (PM) database (http://www.plantmetabolomics.org) contains comprehensive targeted and untargeted mass spectrum metabolomics data for Arabidopsis mutants across a variety of metabolomics platforms. The database allows users to generate hypotheses about the changes in metabolism for mutants with genes of unknown function. Version 2.0 of PlantMetabolomics.org currently contains data for 140 mutant lines along with the morphological data. A web-based data analysis wizard allows researchers to select preprocessing and data-mining procedures to discover differences between mutants. This community resource enables researchers to formulate models of the metabolic network of Arabidopsis and enhances the research community ...


Divergent Activity Of The Gonadotropin Releasing Hormone Receptor Gene Promoter Among Genetic Lines Of Pigs Is Partially Conferred By Nuclear Factor (Nf)-Kb, Specificity Protein (Sp)1-Like And Gata-4 Binding Sites, Emily A. McDonald, Jacqueline E. Smith, Rebecca A. Cederberg, Brett R. White 2016 University of Nebraska - Lincoln

Divergent Activity Of The Gonadotropin Releasing Hormone Receptor Gene Promoter Among Genetic Lines Of Pigs Is Partially Conferred By Nuclear Factor (Nf)-Kb, Specificity Protein (Sp)1-Like And Gata-4 Binding Sites, Emily A. Mcdonald, Jacqueline E. Smith, Rebecca A. Cederberg, Brett R. White

Faculty Papers and Publications in Animal Science

BACKGROUND: Binding of gonadotropin-releasing hormone (GnRH) to its receptor (GnRHR) on gonadotropes within the anterior pituitary gland is essential to reproduction. In pigs, the GnRHR gene is also located near a genetic marker for ovulation rate, a primary determinant of prolificacy. We hypothesized that pituitary expression of the GnRHR gene is alternatively regulated in genetic strains with elevated ovulation rates (Chinese Meishan and Nebraska Index) vs. standard white crossbred swine (Control).

METHODS: Luciferase reporter vectors containing 5118 bp of GnRHR gene promoter from either the Control, Index or Meishan swine lines were generated. Transient transfection of line-specific, full length, deletion ...


Functional Characterization Of Recombinant Interleukin (Il)-17a/F1 In The Japanese Pufferfish (Takifugu Rubripes), Jun-ichi Hikima Dr., Koshin Mihara, Shun Maekawa, Han-Ching Wang, Takashi Aoki, Tomoya Kono, Masahiro Sakai 2016 University of Miyazaki, Faculty of Agriculture

Functional Characterization Of Recombinant Interleukin (Il)-17a/F1 In The Japanese Pufferfish (Takifugu Rubripes), Jun-Ichi Hikima Dr., Koshin Mihara, Shun Maekawa, Han-Ching Wang, Takashi Aoki, Tomoya Kono, Masahiro Sakai

2nd International Conference of Fish & Shellfish Immunology

No abstract provided.


Identification And Characterization Of Heat Shock Transcription Factor 1 Isoforms In Orange-Spotted Grouper (Epinephelus Coioides), Tingyu Wang 2016 National Cheng Kung University

Identification And Characterization Of Heat Shock Transcription Factor 1 Isoforms In Orange-Spotted Grouper (Epinephelus Coioides), Tingyu Wang

2nd International Conference of Fish & Shellfish Immunology

No abstract provided.


Rna-Seq Analysis In Gills Of Atlantic Salmon (Salmo Salar) Infected With Newly Identified Isav Strains In The Atlantic Canada Region, Francis LeBlanc 2016 Fisheries and Oceans Canada

Rna-Seq Analysis In Gills Of Atlantic Salmon (Salmo Salar) Infected With Newly Identified Isav Strains In The Atlantic Canada Region, Francis Leblanc

2nd International Conference of Fish & Shellfish Immunology

No abstract provided.


Heterologous Expression Of A Rice Mir395 Gene In Nicotiana Tabacum Impairs Sulfate Homeostasis, Ning Yuan, Shuangrong Yuan, Zhigang Li, Dayong Li, Qian Hu, Hong Luo 2016 Clemson University

Heterologous Expression Of A Rice Mir395 Gene In Nicotiana Tabacum Impairs Sulfate Homeostasis, Ning Yuan, Shuangrong Yuan, Zhigang Li, Dayong Li, Qian Hu, Hong Luo

Publications

Sulfur participates in many important mechanisms and pathways of plant development. The most common source of sulfur in soil –SO42−– is absorbed into root tissue and distributed into aerial part through vasculature system, where it is reduced into sulfite and finally sulfide within the subcellular organs such as chloroplasts and mitochondria and used for cysteine and methionine biosynthesis. MicroRNAs are involved in many regulation pathways by repressing the expression of their target genes. MiR395 family in Arabidopsis thaliana has been reported to be an important regulator involved in sulfate transport and assimilation, and a high-affinity sulphate transporter and ...


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