Genetics and Genomics Commons^™

Salvinia Radseq, Carol A. Rowe, Donald Hauber, Paul G. Wolf

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Killi-Data News (Winter), Tyrone Genade

Killifish Research Review

Valued readers, it is with a heavy heart that I inform you that this is the last issue of Killi-Data News. The good news is that we will be back as Killifish Research Review. The dissolution of Killi-Data International created a prob- lem: how can the newsletter of a defunct organization live on without that organization? But other additional problems were building in the background. The first issue numbered 15 pages. The previous issue was 28 pages. The number of killifish related papers is increasing while time on our end (the editorial team) is running out. It takes a lot …

Killi-Data News (Fall), Tyrone Genade

Killifish Research Review

Many interesting papers have been published over the last three months. The large volume of papers coupled with the start of the new college semester (and the workload it brings) delayed this issue of Killi-Data News. But better late than never—or so I hope! In this issue Richard van der Laan provides an insightful review of the recent Aphanius papers as to their taxonomic implications and questions. The systematic issues he raises show the importance of the Molecular project: we need to get more samples of the various cyprinodontiforme families to resolve unsettled systematic and taxonomic issues. In the Next …

Killi-Data News (Summer), Tyrone Genade

Killifish Research Review

Over the last three months several interesting and exciting pa- pers have been published. By now most of you have heard the Nothobranchius fish poo news emanating from the Valenzano lab. That paper is reviewed and certainly has repercussions for the health of our captive fish. Polaçik et al have published interesting data with ramifications as to how we breed and incubate annual killifish. The big news in this issue is the paper from the Reznick lab which Jean Huber reviews. The contents of that paper goes to the heart of the question of just what a killifish is. The …

Killi-Data News (Spring), Tyrone Genade

Killifish Research Review

This is the start of Killi-Data News’ second year. In this first issue of the year we have the usual review of research pub- lications as well as input from Martin Reichard on his lab’s Nothobranchius research. Martin is responding to my reviews of his lab’s work in the previous edition. I am serious about making sure the content in this newsletter is reliable but I erred in the previous edition and Martin has written extensively to correct my mistake in the section “Erratum”. This reply is welcomed and owed to readers. I must confess that I don’t know everything …

Killi-Data News (Winter), Tyrone Genade

Killifish Research Review

This is the fourth edition, and concluding issue of the first volume, of Killi-Data News and I am happy that it has been well received by readers. At 25 pages this issue is a bit thin- ner than the last but this is because we agreed to make the cut-off for submissions the 1 st of December so we could get this edition out by the New Year. This is an exciting edition full of new species descrip- tions and analyses that will keep taxonomists busy for years to come. Costa has given us two molecular phylogenies on Melanorivulus as …

Killi-Data News (Spring), Tyrone Genade

Killifish Research Review

This is the start of Killi-Data News’ second year. In this first issue of the year we have the usual review of research pub- lications as well as input from Martin Reichard on his lab’s Nothobranchius research. Martin is responding to my reviews of his lab’s work in the previous edition. I am serious about making sure the content in this newsletter is reliable but I erred in the previous edition and Martin has written extensively to correct my mistake in the section “Erratum”. This reply is welcomed and owed to readers. I must confess that I don’t know everything …

Manipulation Of Ploidy In Caenorhabditis Elegans, Erlyana K. Clarke, Katherine A. Rivera Gomez, Zaki Mustachi, Mikaela C. Murph, Mara Schvarzstein

Advanced Science Research Center

Mechanisms that involve whole genome polyploidy play important roles in development and evolution; also, an abnormal generation of tetraploid cells has been associated with both the progression of cancer and the development of drug resistance. Until now, it has not been feasible to easily manipulate the ploidy of a multicellular animal without generating mostly sterile progeny. Presented here is a simple and rapid protocol for generating tetraploid Caenorhabditis elegans animals from any diploid strain. This method allows the user to create a bias in chromosome segregation during meiosis, ultimately increasing ploidy in C. elegans. This strategy relies on the transient …

Non-Invasive Detection Of Adeno-Associated Viral Gene Transfer Using A Genetically Encoded Cest-Mri Reporter Gene In The Murine Heart, Shelby Meier, Assaf A. Gilad, Jason Anthony Brandon, Chenghao Qian, Erhe Gao, Jose F. Abisambra, Moriel Vandsburger

Physiology Faculty Publications

Research into gene therapy for heart failure has gained renewed interest as a result of improved safety and availability of adeno-associated viral vectors (AAV). While magnetic resonance imaging (MRI) is standard for functional assessment of gene therapy outcomes, quantitation of gene transfer/expression relies upon tissue biopsy, fluorescence or nuclear imaging. Imaging of gene expression through the use of genetically encoded chemical exchange saturation transfer (CEST)-MRI reporter genes could be combined with clinical cardiac MRI methods to comprehensively probe therapeutic gene expression and subsequent outcomes. The CEST-MRI reporter gene Lysine Rich Protein (LRP) was cloned into an AAV9 vector and either …

Sustained Maternal Inflammation During The Early Third Trimester Yields Fetal Adaptations That Impair Subsequent Skeletal Muscle Growth And Glucose Metabolism In Sheep, Cailtin N. Cadaret, Elena M. Merrick, Taylor L. Barnes, Kristin A. Beede, Robert J. Posont, Jessica Lynn Petersen, Dustin T. Yates

Department of Animal Science: Faculty Publications

Intrauterine growth restriction (IUGR) is linked to metabolic dysfunction in offspring, but the mediating mechanisms are still under investigation (Barker et al., 1993). IUGR fetuses adapt to their poor intrauterine environment by repartitioning nutrients to organs critical for survival (i.e., brain, heart) at the expense of tissues such as muscle (Yates et al., 2012c). These developmental adaptations help the fetus to survive in utero but have lifelong consequences in offspring; persistent reduction of highly metabolic muscle mass is detrimental to glucose homeostasis (DeFronzo et al., 1981). Glucose metabolism is regulated primarily by insulin, and nutrient depravation is associated with impaired …

The Determinants Of Nucleosome Patterns And The Impact Of Phosphate Starvation On Nucleosome Patterns And Gene Expression In Rice, Qi Zhang

LSU Doctoral Dissertations

In eukaryotic cells, DNA is a large molecule that must be greatly condensed to fit within the nucleus. DNA is wrapped around histone proteins to form nucleosomes, which facilitate DNA condensation, but on the other hand, may limit DNA processes. Organisms must respond to environmental stress in order to survive, and one strategy is by remodeling nucleosomes to promote changes in DNA accessibility to alter gene expression. Studies have demonstrated a clear correlation between nucleosome dynamics and transcriptional change in some eukaryotes, however factors that affect nucleosome positioning in plants are largely unknown, and the correlation between nucleosome dynamics and …

Data And Statistical Methods To Analyze The Human Microbiome, Levi Waldron

Publications and Research

The Waldron lab for computational biostatistics bridges the areas of cancer genomics and microbiome studies for public health, developing methods to exploit publicly available data resources and to integrate-omics studies.

Early Limb Patterning In The Direct‐Developing Salamander Plethodon Cinereus Revealed By Sox9 And Col2a1, Ryan R. Kerney, James Hanken, David C. Blackburn

Biology Faculty Publications

Direct‐developing amphibians form limbs during early embryonic stages, as opposed to the later, often postembryonic limb formation of metamorphosing species. Limb patterning is dramatically altered in direct‐developing frogs, but little attention has been given to direct‐developing salamanders. We use expression patterns of two genes, sox9and col2a1, to assess skeletal patterning during embryonic limb development in the direct‐developing salamander Plethodon cinereus. Limb patterning in P. cinereus partially resembles that described in other urodele species, with early formation of digit II and a generally anterior‐to‐posterior formation of preaxial digits. Unlike other salamanders described to date, differentiation of preaxial zeugopodial …

Breeding For Resistance In California Strawberry To Verticillium Dahliae, Zachary Christman

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

This article focuses on breeding resistant strawberries to the fungus Verticillium dahliae, common name Verticillium wilt. This is a serious fungal disease that can result in a loss of 50% or more of a strawberry harvest when grown in infested soil. The main goal is to provide an example of how a cultivar can be made more resistant to a plant pathogen with the use of plant breeding methods.

Since 1930 the University of California, Davis, has been developing strawberry cultivars that are adapted to the agricultural industry and regional farms. Developing cultivars that require fewer inputs are of …

Morphogenetic Defects Underlie Superior Coloboma, A Newly Identified Closure Disorder Of The Dorsal Eye, Jennifer C. Hocking, Jakub K. Famulski, Kevin H. Yoon, Sonya A. Widen, Cassidy S. Bernstein, Sophie Koch, Omri Weiss, Forge Canada Consortium, Canada, Seema Agarwala, Adi Inbal, Ordan J. Lehmann, Andrew J. Waskiewicz

Biology Faculty Publications

The eye primordium arises as a lateral outgrowth of the forebrain, with a transient fissure on the inferior side of the optic cup providing an entry point for developing blood vessels. Incomplete closure of the inferior ocular fissure results in coloboma, a disease characterized by gaps in the inferior eye and recognized as a significant cause of pediatric blindness. Here, we identify eight patients with defects in tissues of the superior eye, a congenital disorder that we term superior coloboma. The embryonic origin of superior coloboma could not be explained by conventional models of eye development, leading us to …

Copy Number Variation In The Porcine Genome Detected From Whole-Genome Sequence, Rebecca Anderson

Honors Program: Senior Projects (Public)

Copy number variations (CNVs) are large insertions, deletions, and duplications in the genome that vary between individuals in a species. These variations are known to impact a broad range of phenotypes from molecular-level traits to higher-order clinical phenotypes. CNVs have been linked to complex traits in humans such as autism, attention deficit hyperactivity disorder, nervous system disorders, and early-onset extreme obesity. In this study, whole-genome sequence was obtained from 72 founders of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC) in Clay Center, Nebraska. This included 24 boars (12 Duroc and 12 Landrace) and …

Genetic And Molecular Mechanisms Underlying Symbiotic Specificity In Legume-Rhizobium Interactions, Qi Wang, Jinge Liu, Hongyan Zhu

Plant and Soil Sciences Faculty Publications

Legumes are able to form a symbiotic relationship with nitrogen-fixing soil bacteria called rhizobia. The result of this symbiosis is to form nodules on the plant root, within which the bacteria can convert atmospheric nitrogen into ammonia that can be used by the plant. Establishment of a successful symbiosis requires the two symbiotic partners to be compatible with each other throughout the process of symbiotic development. However, incompatibility frequently occurs, such that a bacterial strain is unable to nodulate a particular host plant or forms nodules that are incapable of fixing nitrogen. Genetic and molecular mechanisms that regulate symbiotic specificity …

Transcriptional Profiling Of Liver In Riboflavin-Deficient Chicken Embryos Explains Impaired Lipid Utilization, Energy Depletion, Massive Hemorrhaging, And Delayed Feathering, Larry A. Cogburn, Danielle N. Smarsh, Xiaofei Wang, Nares Trakooljul, Wilfrid Carré, Harold B. White Iii

Biology Faculty Research

Background

A strain of Leghorn chickens (rd/rd), unable to produce a functional riboflavin-binding protein, lays riboflavin-deficient eggs, in which all embryos suddenly die at mid-incubation (days 13-15). This malady, caused by riboflavin deficiency, leads to excessive lipid accumulation in liver, impaired β-oxidation of lipid, and severe hypoglycemia prior to death. We have used high-density chicken microarrays for time-course transcriptional scans of liver in chicken embryos between days 9-15 during this riboflavin-deficiency-induced metabolic catastrophe. For comparison, half of rd/rd embryos (n = 16) were rescued from this calamity by injection of riboflavin just prior to incubation of fertile …

Genetic Differentiation Between Two Species Of Buckwheat (Eriogonum), Paul G. Wolf, Jenessa B. Lemon

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Discovering the extent of genetic differentiation between closely related taxa facilitates decisions regarding species protection under the Endangered Species Act. Here, we analyze genotype data to explore the relatedness of two buckwheat species: Eriogonum soredium Reveal- a narrow endemic under consideration for protection, and a widespread close relative, Eriogonum shockleyi S. Watson. Eriogonum soredium grows only on Ordovician limestone outcroppings in west central Utah, whereas the range of E. shockleyi is broad, spanning the western United States from Colorado to California, and Idaho to Arizona. Eriogonum shockleyi is suspected of hybridizing with other buckwheats throughout this range. We detected higher …

Investigating The Genetic Structure Of Northern Long-Eared Bats In Nebraska, Jonathan Korbitz

UNO Student Research and Creative Activity Fair

Abstract:

The northern long-eared bat (Myotis septentrionalis) is one of many species of hibernating bats in North America affected by a recently discovered fungal disease called white-nose syndrome (WNS). Northern long-eared bats seem to be extremely susceptible to the disease with mass fatalities occurring among populations in eastern North America. Researchers in the eastern distribution of this species have performed mtDNA analysis to identify the population structure of the species; however, genetic analysis has yet to be done in western parts of its distribution. The goal of this study is to create a better understanding of the genetic …

Microbiome And Bacterioplankton Rrna Gene Sequence Data Collected From Gulf Of Mexico Seawater Samples, Cruises Dp03 And Dp04 From April - August 2016, Cole Easson, Lindsey Freed

DEEPEND Datasets

Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during planned DEEPEND cruise expeditions to the GOM in 2016. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable regions were generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Raw paired-end sequences were joined and quality filtered in the bioinformatics program, QIIME. Vertical baseline characterizations will track alpha and beta diversity at different depths ranging from 0 – 1500 m, assess seasonal …

Evolution Of Echovirus 11 In A Chronically Infected Immunodeficient Patient., Majid Laassri, Tatiana Zagorodnyaya, Sharon Hassin-Baer, Rachel Handsher, Danit Sofer, Merav Weil, Konstantinos Karagiannis, Vahan Simonyan, Konstantin Chumakov, Lester Shulman

Biochemistry and Molecular Medicine Faculty Publications

Deep sequencing was used to determine complete nucleotide sequences of echovirus 11 (EV11) strains isolated from a chronically infected patient with CVID as well as from cases of acute enterovirus infection. Phylogenetic analysis showed that EV11 strains that circulated in Israel in 1980-90s could be divided into four clades. EV11 strains isolated from a chronically infected individual belonged to one of the four clades and over a period of 4 years accumulated mutations at a relatively constant rate. Extrapolation of mutations accumulation curve into the past suggested that the individual was infected with circulating EV11 in the first half of …

Improving Eukaryotic Genome Annotation Using Single Molecule Mrna Sequencing., Vincent Magrini, Xin Gao, Bruce A Rosa, Sean Mcgrath, Xu Zhang, Kymberlie Hallsworth-Pepin, John Martin, John Hawdon, Richard K Wilson, Makedonka Mitreva

Microbiology, Immunology, and Tropical Medicine Faculty Publications

BACKGROUND: The advantages of Pacific Biosciences (PacBio) single-molecule real-time (SMRT) technology include long reads, low systematic bias, and high consensus read accuracy. Here we use these attributes to improve on the genome annotation of the parasitic hookworm Ancylostoma ceylanicum using PacBio RNA-Seq.

RESULTS: We sequenced 192,888 circular consensus sequences (CCS) derived from cDNAs generated using the CloneTech SMARTer system. These SMARTer-SMRT libraries were normalized and size-selected providing a robust population of expressed structural genes for subsequent genome annotation. We demonstrate PacBio mRNA sequences based genome annotation improvement, compared to genome annotation using conventional sequencing-by-synthesis alone, by identifying 1609 (9.2%) new …

A Comparison Of Oral And Intravenous Mouse Models Of Listeriosis, Michelle G. Pitts, Sarah E. F. D'Orazio

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Listeria monocytogenes is one of several enteric microbes that is acquired orally, invades the gastric mucosa, and then disseminates to peripheral tissues to cause systemic disease in humans. Intravenous (i.v.) inoculation of mice with L. monocytogenes has been the most widely-used small animal model of listeriosis over the past few decades. The infection is highly reproducible and has been invaluable in deciphering mechanisms of adaptive immunity in vivo, particularly CD8+ T cell responses to intracellular pathogens. However, the i.v. model completely bypasses the gut phase of the infection. Recent advances in generating both humanized mice and murinized bacteria, as well …

Genetic Diversity And Distinctness Of Wild Nebraska Hops And Hop Cultivars (Humulus Lupulus L.), Megan Franklin

Honors Program: Senior Projects (Public)

Background Commercial hop (Humulus lupulus) cultivars that are being grown in the Midwest are not performing as successfully as when they are grown in the Pacific Northwest, the region to which they are adapted. To increase adaptation to the Midwest environment, one strategy is to draw from the genetic pool of wild native Midwest hops, which have developed genes that allow them to grow successfully in this environment. Wild hop plants that are genetically distinct from commercial cultivars are likely to have more adaptations, such as pest/disease resistance and drought tolerance, which can be bred into commercial lines. The …

The Pharmacogene Variation (Pharmvar) Consortium: Incorporation Of The Human Cytochrome P450 (Cyp) Allele Nomenclature Database, Andrea Gaedigk, Magnus Ingelman-Sundberg, Neil A. Miller, J Steven Leeder, Michelle Whirl-Carrillo, Teri E. Klein

Manuscripts, Articles, Book Chapters and Other Papers

The Human Cytochrome P450 (CYP) Allele Nomenclature Database, a critical resource to the pharmacogenetics and genomics communities, will be transitioning to the Pharmacogene Variation (PharmVar) Consortium. In this report we provide a summary of the current database, provide an overview of the PharmVar consortium and highlight the PharmVar database which will serve as the new home for pharmacogene nomenclature.

Whole-Genome Analysis Of Mycobacterium Tuberculosis From Patients With Tuberculous Spondylitis, Russia, Ekaterina Chernyaeva, Mikhail Rotkevich, Ksenia Krasheninnikova, Andrey Yurchenko, Anna Vyazovaya, Igor Mokrousov, Natalia Solovieva, Viacheslav Zhuravlev, Piotr Yablonsky, Stephen J. O’Brien

Biology Faculty Articles

Whole-genome analysis of Mycobacterium tuberculosis isolates collected in Russia (N = 71) from patients with tuberculous spondylitis supports a detailed characterization of pathogen strain distributions and drug resistance phenotype, plus distinguished occurrence and association of known resistance mutations. We identify known and novel genome determinants related to bacterial virulence, patho-genicity, and drug resistance.

Draft Genome Sequence Of A Dictyoglomus Sp. From An Enrichment Culture Of A New Zealand Geothermal Spring, Anna-Louise Reysenbach, John A. Donaho, John F. Kelley, Emily St. John, Christina Turner, Mircea Podar, Matthew B. Stott

Biology Faculty Publications and Presentations

A draft genome of a novel Dictyoglomus sp., NZ13-RE01, was obtained from a New Zealand hot spring enrichment culture. The 1,927,012-bp genome is similar in both size and G+C content to other Dictyoglomus spp. Like its relatives, Dictyoglomus sp. NZ13-RE01 encodes many genes involved in complex carbohydrate metabolism.

Characterization Of The Roles Of Muscle-Synthesized Brain-Derived Neurotrophic Factor And Presynaptic Tyrosine Receptor Kinase B In Motor Neuron Axonal Transport, Luke A. Vanosdol

All NMU Master's Theses

Brain-derived neurotrophic factor (BDNF) is a small, diffusible protein essential for the development and function of neurons. It is synthesized by many types of tissue, including muscle. BDNF actions are mediated via binding to its receptor, tyrosine receptor kinase B (TrkB). The BDNF-TrkB complex is endocytosed into a specialized vesicle, which induces downstream signaling cascades locally in the dendrites, or, more often, is delivered to the cell soma via retrograde axonal transport, where it modulates gene expression. BDNF activation of TrkB is critical for the initiation of axonal transport, and this cellular process relies on the interaction of numerous adaptor …

Bmilf And I-Motif Structure Are Involved In Transcriptional Regulation Of Bmpoum2 In Bombyx Mori, Kangkang Niu, Xiaojuan Zhang, Huimin Deng, Feng Wu, Yandong Ren, Hui Xiang, Sichun Zheng, Lin Liu, Lihua Huang, Baojuan Zeng, Sheng Li, Qingyou Xia, Qisheng Song, Subba R. Palli, Qili Feng

Entomology Faculty Publications

Guanine-rich and cytosine-rich DNA can form four-stranded DNA secondary structures called G-quadruplex (G4) and i-motif, respectively. These structures widely exist in genomes and play important roles in transcription, replication, translation and protection of telomeres. In this study, G4 and i-motif structures were identified in the promoter of the transcription factor gene BmPOUM2, which regulates the expression of the wing disc cuticle protein gene (BmWCP4) during metamorphosis. Disruption of the i-motif structure by base mutation, anti-sense oligonucleotides (ASOs) or inhibitory ligands resulted in significant decrease in the activity of the BmPOUM2 promoter. A novel i-motif binding protein (BmILF) …