Genetics and Genomics Commons^™

48784 (Gmr17g08), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 48784

• Id - GMR 17G08
• Location 2L:2450278,2451074
• Base pairs – 796 bp

45437 (Gmr18b08), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 45437

• Id - GMR18B08
• Location - 2L:2455899,2457734
• Base pairs – 1835 bp

Tumor Cell Death After Electrotransfer Of Plasmid Dna Is Associated With Cytosolic Dna Sensor Upregulation, Katarina Znidar, Masa Bosnjak, Nina Semenova, Olga N. Pakhomova, Loree Heller, Maja Cemazar

Bioelectrics Publications

Cytosolic DNA sensors are a subgroup of pattern recognition receptors (PRRs) and are activated by the abnormal presence of the DNA in the cytosol. Their activation leads to the upregulation of pro-inflammatory cytokines and chemokines and can also induce cell death. The presence of cytosolic DNA sensors and inflammatory cytokines in TS/A murine mammary adenocarcinoma and WEHI 164 fibrosarcoma cells was demonstrated using real time reverse transcription polymerase chain reaction (RT-PCR), western blotting and enzyme-linked immunosorbent assay (ELISA). After electrotransfer of plasmid DNA (pDNA) using two pulse protocols, the upregulation of DNA-depended activator of interferon regulatory factor or Z-DNA binding …

Upregulation Of Dna Sensors In B16.F10 Melanoma Spheroid Cells After Electrotransfer Of Pdna, Katarina Znidar, Masa Bosnjak, Tanja Jesenko, Loree C. Heller, Maja Cemazar

Bioelectrics Publications

Increased expression of cytosolic DNA sensors, a category of pattern recognition receptor, after control plasmid DNA electrotransfer was observed in our previous studies on B16.F10 murine melanoma cells. This expression was correlated with the upregulation of proinflammatory cytokines and chemokines and was associated with cell death. Here, we expanded our research to include the influence of features of cells in a 3-dimensional environment, which better represents the tumors’ organization in vivo. Our results show that lower number of cells were transfected in spheroids compared to 2-dimensional cultures, that growth was delayed after electroporation alone or after electrotransfer of plasmid …

Evidence For The Genetic Basis And Inheritance Of Ocean And River-Maturing Ecotypes Of Pacific Lamprey (Entosphenus Tridentatus) In The Klamath River, California, Keith A. Parker

Cal Poly Humboldt theses and projects

Surveys of genetic variation have improved our understanding of the relationship between fitness-related phenotypes and their underlying genetic basis. However, how this information can be used to inform conservation has been unclear in many cases. The objective of this study was to combine next-generation genetic sequencing with traditional ecological knowledge to evaluate imperiled anadromous Pacific lamprey (Entosphenus tridentatus) and apply the findings to conservation in the context of resolving Native American traditional food security issues. In the Klamath River of California, a previously identified Pacific lamprey ocean-maturing ecotype was distinguished by a relatively advanced maturity of female fish …

Genes For Membrane Transport Proteins: Not So Rare In Viruses, Timo Greiner, Anna Moroni, James L. Van Etten, Gerhard Thiel

James Van Etten Publications

Some viruses have genes encoding proteins with membrane transport functions. It is unknown if these types of proteins are rare or are common in viruses. In particular, the evolutionary origin of some of the viral genes is obscure, where other viral proteins have homologs in prokaryotic and eukaryotic organisms. We searched virus genomes in databases looking for transmembrane proteins with possible transport function. This effort led to the detection of 18 different types of putative membrane transport proteins indicating that they are not a rarity in viral genomes. The most abundant proteins are K+ channels. Their predicted structures vary between …

Size-Dependent Catalysis Of Chlorovirus Population Growth By A Messy Feeding Predator, John Delong, Zeina Al-Ameeli, Shelby Lyon, James L. Van Etten, David Dunigan

James Van Etten Publications

Many chloroviruses replicate in endosymbiotic zoochlorellae that are protected from infection by their symbiotic host. To reach the high virus concentrations that often occur in natural systems, a mechanism is needed to release zoochlorellae from their hosts. We demonstrate that the ciliate predator Didinium nasutum foraging on zoochlorellae-bearing Paramecium bursaria can release live zoochlorellae from the ruptured prey cell that can then be infected by chloroviruses. The catalysis process is very effective, yielding roughly 95% of the theoretical infectious virus yield as determined by sonication of P. bursaria. Chlorovirus activation is more effective with smaller Didinia, as larger …

Ictv Virus Taxonomy Profile: Chrysoviridae, Said A. Ghabrial, José R. Castón, Robert H. A. Coutts, Bradley I. Hillman, Daohong Jiang, Dae-Hyun Kim, Hiromitsu Moriyama, Ictv Report Consortium

Plant Pathology Faculty Publications

The Chrysoviridae is a family of small, isometric, non-enveloped viruses (40 nm in diameter) with segmented dsRNA genomes (typically four segments). The genome segments are individually encapsidated and together comprise 11.5–12.8 kbp. The single genus Chrysovirus includes nine species. Chrysoviruses lack an extracellular phase to their life cycle; they are transmitted via intracellular routes within an individual during hyphal growth, in asexual or sexual spores, or between individuals via hyphal anastomosis. There are no known natural vectors for chrysoviruses. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Chrysoviridae, which …

Ictv Virus Taxonomy Profile: Partitiviridae, Eeva J. Vainio, Sotaro Chiba, Said A. Ghabrial, Edgar Maiss, Marilyn Roossinck, Sead Sabanadzovic, Nobuhiro Suzuki, Jiatao Xie, Max Nibert, Ictv Report Consortium

Plant Pathology Faculty Publications

The Partitiviridae is a family of small, isometric, non-enveloped viruses with bisegmented double-stranded (ds) RNA genomes of 3–4.8 kbp. The two genome segments are individually encapsidated. The family has five genera, with characteristic hosts for members of each genus: either plants or fungi for genera Alphapartitivirus and Betapartitivirus, fungi for genus Gammapartitivirus, plants for genus Deltapartitivirus and protozoa for genus Cryspovirus. Partitiviruses are transmitted intracellularly via seeds (plants), oocysts (protozoa) or hyphal anastomosis, cell division and sporogenesis (fungi); there are no known natural vectors. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) …

Investigating Phosphorylation Patterns And Their Effect On The Activity Of Transcription Factor Taabf1 In Imbibing Cereal Grains, Grace Uwase

Honors Theses

The wheat transcription factor TaABF1 plays an important role in hormone-mediated regulation of seed dormancy and germination of cereal grains. Evidence shows that TaABF1 activity is regulated by phosphorylation, and previous work in our lab showed that when serine residues in its conserved regions; S36, S37, S113, S115 were altered to phosphomimetic aspartate, the 4xD TaABF1 mutant had increased activity as a transcription factor. However, when only S113 was altered, TaABF1’s activity was greatly reduced. The work presented here explored whether the S36D/S37D/S115D mutant would have stronger activity than the 4xD mutant. Using the particle bombardment technique to introduce the …

The Role Of Prrx1 And Snai2 As Master Regulators Of Fibroblast Identity, Huda A. Alzahrani

Masters Theses

Mammalian development involves a complex system of regulatory signals and reactions, leading to the creation of distinct tissues with specific structures and functions controlled by various gene expression profiles. Tissue-specific gene expression is by controlled specific combinations of transcription factors and cofactors that dictate cell differentiation via activation and repression of genes in mammalian cells.

Whole genome microarray analyses of fibroblasts have revealed candidate genes that may serve as master regulators of fibroblast identity, such as Prrx1 and Snai2, that activate downstream genes such as Bmp3, Twist, Shox2, Cfos, Slug, Sema3A, Spp1, and Col1a1. A previous study showed that Prrx1 …

Effects Of Gli-Similar 3 Knockout Mutations On The Expression Of Insulin Transcription And Pancreatic Islet Development In Zebrafish, Dylan James Hammrich

Murray State Theses and Dissertations

Blood glucose homeostasis is a critical component in the physiological health of vertebrates. Regulation of blood glucose levels is the responsibility of the endocrine pancreas, which excretes hormones to the bloodstream in response to changes in glucose concentrations. The hormones excreted from the pancreas include insulin, which is secreted form the β cells of the pancreas and signals uptake of excess glucose by the peripheral tissues, and glucagon, which is secreted from the α cells and signals release of glucose to the bloodstream through gluconeogenesis in the liver. The Krüppel-like zinc finger protein Gli-Similar 3 (Glis3) is a transcription factor …

Trophic Interactions And Niche Partitioning Within A Post-White-Nose Syndrome Temperate Bat Community, Macy Kailing

Murray State Theses and Dissertations

The decline of cave-dwelling bats since the introduction of white-nose syndrome (WNS) to North America changed the way communities interact. Disease-mediated competition at the community level can influence the ability of imperiled species to recover because of competitive exclusion. In western Kentucky, tri-colored bats, Perimyotis subflavus, which are susceptible to WNS severely declined following WNS occurrence. During that same period, evening bats, Nycticeius humeralis, which are not susceptible to WNS increased markedly. To investigate the influence of WNS on community structure, the diets of sympatric tri-colored and evening bats were assessed. Guano was collected from evening (n=37) and …

Large Effect Quantitative Trait Loci For Salicinoid Phenolic Glycosides In Populus: Implications For Gene Discovery, Scott A. Woolbright, Brian J. Rehill, Richard L. Lindroth

Aspen Bibliography

Genomic studies have been used to identify genes underlying many important plant secondary metabolic pathways. However, genes for salicinoid phenolic glycosides (SPGs)—ecologically important compounds with significant commercial, cultural, and medicinal applications—remain largely undescribed. We used a linkage map derived from a full‐sib population of hybrid cottonwoods (Populus spp.) to search for quantitative trait loci (QTL) for the SPGs salicortin and HCH‐salicortin. SSR markers and primer sequences were used to anchor the map to the V3.0 P. trichocarpa genome. We discovered 21 QTL for the two traits, including a major QTL for HCH‐salicortin (R2 = .52) that colocated …

The Impact Of Reconstructed Soils Following Oil Sands Exploitation On Aspen And Its Associated Belowground Microbiome, Franck Stefani, Nathalie Isabel, Marie-Josee Morency

Aspen Bibliography

Oil sands surface mining in the Athabasca region of northern Alberta (Canada) is a significant anthropogenic disturbance that resets boreal forest development and succession to early stages. During surface mining, the vegetation is cleared, the topsoil is salvaged, and the overburden (the layer of sand and clay in between the topsoil and the oil sands) is piled (see Fig. 2 in Audet et al.1 for an explanation of the land-reclamation procedure). After mining is finished, the landforms (composed of overburden and tailings sand) are capped with organic matter-rich soil covers made of either upland-derived forest floor-mineral mix (FFMM) or a …

Hart Prairie Preserve Site Visit To Assess Aspen Health Nature Conservancy, Flagstaff, Az, Amanda Grady

Aspen Bibliography

On June 11, 2018, Amanda Grady, Entomologist, Arizona Zone, Forest Health Protection, performed a site visit to evaluate aspen health on the Nature Conservancy lands at Heart Prairie Preserve (HPP) near Flagstaff. Specifically, the evaluation was to determine whether or not the aspen within exclosures on Fern Mountain have symptoms or signs of Oystershell scale (OSS), an emergent forest pest contributing to aspen decline in northern Arizona.

Effects Of Climate Change On Forest Vegetation In The Northern Rockies Region, Robert E. Keane, Mary Frances Mahalovich

Aspen Bibliography

No abstract provided.

Climate-Induced Gradients Of Populus Sp. Forest Biomass On The Territory Of Eurasia, Usoltev Vladimir Andreevich, Omid Shobairi, Chasovskikh Viktor Petrovich

Aspen Bibliography

On the basis of the compiled database in a number of 413 sample plots with determinations of forest biomass of the genus Populus sp. on the territory of Eurasia from France to southern China and Japan statistically significant transcontinental decreasing of stem, above ground and total biomass as in the direction from northern temperate to subequatorial zonal belt and in the direction from the Atlantic and Pacific coasts to the continentality pole in Siberia is established. Unlike wood story, understory biomass in these directions has not decreased, and increasing. The root: shoot ratio increases in the range between northern temperate …

Evaluating Nubian Population Structure From Cranial Nonmetric Traits: Gene Flow, Genetic Drift, And Population History Of The Nubian Nile Valle, Kanya Godde, Richard L. Jantz

Human Biology Open Access Pre-Prints

Paleolithic archaeological and skeletal remains from the Nile Valley have yielded a complex picture of life along the river. Sociocultural and sociopolitical events during this timeframe shaped population structure, while gene flow and genetic drift further developed it. In this paper, we take a population genetics approach to modeling Nubian biological relationships in an effort to describe how an accumulation of events formed Nubian population structure. A variety of Nubian samples were utilized, spanning the Mesolithic-Christian time periods, and geographically, from just above the first through the third cataracts. Population genetics statistics were employed to estimate and depict biological affinities …

Repetitive Elements And Genomic Rearrangements, Emily Hartsell

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Three Methodological Innovations In Race And Ethnicity Research, Jeffrey Napierala

Legacy Theses & Dissertations (2009 - 2024)

This dissertation examines topics related to racial and ethnic diversity through three essays. Each essay takes a new perspective on a current issue in the literature and utilizes a unique statistical methodology to address that issue. The first essay uses the Monte Carlo Simulation Method to develop a measure of segregation for the ACS and uses it to assess whether the ACS is useful for measuring segregation in places with different sizes. The second essay considers whether a relatively unexplored factor, genetics, is correlated with migration. This perspective broadens our understanding of why migration occurs and is perpetuated over time. …

Mechanistic Analysis Of The Type I-E Crispr-Cas System In Escherichia Coli, Lauren A. Cooper

Legacy Theses & Dissertations (2009 - 2024)

In CRISPR-Cas immunity systems, short CRISPR RNAs (crRNAs) are bound by CRISPR-associated (Cas) proteins, and these complexes target invading nucleic acid molecules for degradation in a process known as interference. In type I CRISPR-Cas systems, the Cas protein complex that binds DNA is known as Cascade. Association of Cascade with target DNA can also lead to acquisition of new immunity elements in a process known as primed adaptation. Here, we assess the specificity determinants for Cascade-DNA interaction, interference, and primed adaptation in vivo, for the type I-E system of Escherichia coli. Remarkably, as few as 5 bp of crRNA-DNA are …

Multivariate Analysis To Identify Potential Biomarkers For Prognosis And Treatment Resistance In Head And Neck Cancer Patients, Christina Ann Wicker

Theses and Dissertations--Toxicology and Cancer Biology

It is estimated that nearly 50,000 individuals in the United States will be diagnosed with head and neck cancer in 2017 (American Cancer Society www.cancer.org). Ninety percent of oral cancers are head and neck squamous cell carcinoma (HNSCC). Major obstacles in the treatment of HNSCC are recurrence and treatment resistance, which contributes to increased mortality. Therefore, there is increased need to determine genetic alterations in HNSCC that may be ideal novel drug targets, and biomarkers to improve diagnostic and prognostic testing.

Abnormal localization and overexpression of base excision repair protein and transcriptional regulator Apurinic/Apyrimidic endonuclease (APE1) has been associated with …

An Investigation Of Atomic Structures Derived From X-Ray Crystallography And Cryo-Electron Microscopy Using Distal Blocks Of Side-Chains, Lin Chen, Jing He, Salim Sazzed, Rayshawn Walker

Computer Science Faculty Publications

Cryo-electron microscopy (cryo-EM) is a structure determination method for large molecular complexes. As more and more atomic structures are determined using this technique, it is becoming possible to perform statistical characterization of side-chain conformations. Two data sets were involved to characterize block lengths for each of the 18 types of amino acids. One set contains 9131 structures resolved using X-ray crystallography from density maps with better than or equal to 1.5 Å resolutions, and the other contains 237 protein structures derived from cryo-EM density maps with 2-4 Å resolutions. The results show that the normalized probability density function of block …

Non-Naturally Occurring Porcine Reproductive And Respiratory Syndrome Virus (Prrsv) And Methods Of Using, Hiep Lai Xuan Vu, Fernando Osorio, William W. Laegreid, Asit K. Pattnaik, Fangrui Ma

Nebraska Center for Virology: Faculty Publications

A non-naturally occurring porcine reproductive and respiratory syndrome virus (PRRSV) is provided herein, and methods of making and using the non-naturally occurring PRRSV also are provided.

Electrotransfer Of Different Control Plasmids Elicits Different Antitumor Effectiveness In B16.F10 Melanoma, Masa Bosnjak, Tanjo Jesenko, Urska Kamensek, Gregor Sersa, Jaka Lavrencak, Loree Heller, Maja Cemazar

Bioelectrics Publications

Several studies have shown that different control plasmids may cause antitumor action in different murine tumor models after gene electrotransfer (GET). Due to the differences in GET protocols, plasmid vectors, and experimental models, the observed antitumor effects were incomparable. Therefore, the current study was conducted comparing antitumor effectiveness of three different control plasmids using the same GET parameters. We followed cytotoxicity in vitro and the antitumor effect in vivo after GET of control plasmids pControl, pENTR/U6 scr and pVAX1 in B16.F10 murine melanoma cells and tumors. Types of cell death and upregulation of selected cytosolic DNA sensors and cytokines were …

Draft Genome Sequence Of Streptomyces Sp. Strain Jv178, A Producer Of Clifednamide-Type Polycyclic Tetramate Macrolactams, Yunci Qi, John M. D’Alessandro, Joshua A.V Blodgett

Biology Faculty Research

Here, we report the draft genome sequence of Streptomyces sp. JV178, a strain originating from Connecticut (USA) garden soil. This strain produces the polycyclic tetramate macrolactam compounds clifednamides A and B. The draft genome contains 10.65 Mb, 9,045 predicted protein coding sequences, and several natural product biosynthetic loci.

Why Doesn’T A Mother Reject A Genetically Different Fetus?, Devora Krumholtz

The Science Journal of the Lander College of Arts and Sciences

Many basic multicellular organisms possess some form of immune response to protect themselves against the invasion of foreign objects. It was not until British scientist, Peter Medawar proposed a fundamental question that changed the way researchers studied the maternofetal relationship. A fetus, being genetically different from its mother should be rejected by the maternal immune system, however, it is not. Researchers have since discovered and developed several mechanisms that aim to explain how the maternal immune system prevents fetal rejection. The formation of a mechanical barrier, general and local suppression of the maternal immune system, and a shift in cytokine …

Uvb Induced Mutation Of P53 In Non Melanoma Skin Cancer, Raizy Berger

The Science Journal of the Lander College of Arts and Sciences

There is a clear correlation between excessive sun exposure and the development of skin cancer. UVB radiation from the sun is potent, and as the ozone layer gets depleted, more UVB can reach Earth and cause cell damage. UV radiation causes DNA lesions, such as 6-4 photoproducts and cyclobutane pyrimidine dimers. Cyclobutane pyrimidine dimers are more abundant and take longer to be repaired and therefore are responsible for most of the mutation and DNA damage. These DNA lesions lead to mutation of the p53 gene. The signature mutation on p53 from UV radiation is a CC to TT mutation, which …

Genotype-Phenotype Study In Patients With Valosin-Containing Protein Mutations Associated With Multisystem Proteinopathy, Ebaa Al-Obeidi, Sejad Al-Tahan, Abhilasha Surampalli, Namita Goyal, Annabel K. Wang, Andreas Hermann, Molly Omizo, Charles D. Smith, Tahseen Mozaffar, Virginia Kimonis

Neurology Faculty Publications

Mutations in valosin‐containing protein (VCP), an ATPase involved in protein degradation and autophagy, cause VCP disease, a progressive autosomal dominant adult onset multisystem proteinopathy. The goal of this study is to examine if phenotypic differences in this disorder could be explained by the specific gene mutations. We therefore studied 231 individuals (118 males and 113 females) from 36 families carrying 15 different VCP mutations. We analyzed the correlation between the different mutations and prevalence, age of onset and severity of myopathy, Paget's disease of bone (PDB), and frontotemporal dementia (FTD), and other comorbidities. Myopathy, PDB and FTD was present in …