Genetics and Genomics Commons^™

Effects Of Thymus Size And Involution On The Contribution Of Recent Thymic Emigrants To The Peripheral T Cell Pool, Michelle L. Bolner

Dissertations and Theses (Open Access)

The contribution of recent thymic emigrants (RTEs) to the peripheral naïve T cell population is necessary to maintain diversity of the T cell receptor (TCR) repertoire and produce immune responses against newly encountered antigens.

The thymus involutes with age, after irradiation or chemotherapy, and due to severe viral infections. Thymus involution results in decreased thymopoiesis and RTE output leading to a reduced diversity of peripheral T cells. This increases susceptibility to disease and impairs immune responsiveness to vaccines. Therefore, studies aimed at maintaining or regenerating thymic function are integral for maintaining and restoring peripheral TCR diversity.

Mice that express a …

Predictors Of Contralateral Breast Cancer In Brca Negative Women, Ann E. Simmons

Dissertations and Theses (Open Access)

Breast cancer is the most common cancer diagnosis and second leading cause of death in women. Risk factors associated with breast cancer include: increased age, alcohol consumption, cigarette smoking, white race, physical inactivity, benign breast conditions, reproductive and hormonal factors, dietary factors, and family history. Hereditary breast and ovarian cancer syndrome (HBOC) is caused by mutations in the BRCA1 and BRCA2 genes. Women carrying a mutation in these genes are at an increased risk to develop a second breast cancer. Contralateral breast cancer is the most common second primary cancer in patients treated for a first breast cancer. Other risk …

Mapping Quantitative Trait Loci Associated With Resistance To Bacterial Spot (Xanthomonas Arboricola Pv. Pruni) In Peach, Nannan Yang

All Dissertations

Bacterial spot, caused by Xanthomonas arboricola pv. pruni (Xap), is a serious disease that can affect peach fruit quality and production worldwide. This disease causes severe defoliation and blemishing of fruit, particularly in areas with high rainfall, strong winds, high humidity and sandy soil. The molecular basis of its tolerance and susceptibility in peach is yet to be understood. To study the genetics of the peach response to Xap, an F2 segregating population between two peach cultivars, `Clayton', a resistant phenotype, and `O'Henry', which is very susceptible to Xap, was created. Phenotypic data for leaf and fruit response to Xap …

Genetic Engineering Of Turfgrass For Enhanced Performance Under Environmental Stress, Man Zhou

All Dissertations

Turfgrass species are agriculturally and economically important perennial crops that are susceptible to biotic stress (e.g. fungal pathogens) and abiotic stress (e.g. salinity and drought). Every year, environmental stress significantly influences turfgrass quality and production causing economic loss globally. My research explores the feasibility of using two novel transgenes - Penaeidin4-1 (Pen4-1) from the shrimp, Litopenaeus setiferus, and microRNA319a (miR319a) from the rice, Oryza sativa, to genetically engineer turfgrass for enhanced tolerance to environmental stress.
The antimicrobial peptide - Pen4-1 has been reported to possess in vitro antifungal and antibacterial activities against various economically important pathogens. In this study, two …

Heterotopic Ossification: Cellular Basis, Symptoms, And Treatment, Brian Wolfe

Senior Honors Theses

Heterotopic ossification (HO) is the process by which calcified bone develops in soft tissues. Because of the abnormal calcification, complications such as bone deformation, loss of range of motion, and joint immobility adversely affect patients. There are many genetic types of heterotopic ossification, namely fibrodysplasia ossificans progressiva, progressive osseous heteroplasia, and Albright hereditary osteodystrophy. However, this condition can also arise from surgery, burns, or traumatic injuries, so it is seen as an important area for research in the future. There are various treatments available such as non-steroidal anti-inflammatory drugs and radiation therapy, as well as combinations of the two. The …

Revised Selection Criteria For Candidate Restriction Enzymes In Genome Walking, Ali Taheri, Stephen J. Robinson, Isobel Parkin, Margaret Y. Gruber

Agricultural and Environmental Sciences Faculty Research

A new method to improve the efficiency of flanking sequence identification by genome walking was developed based on an expanded, sequential list of criteria for selecting candidate enzymes, plus several other optimization steps. These criteria include: step (1) initially choosing the most appropriate restriction enzyme according to the average fragment size produced by each enzyme determined using in silico digestion of genomic DNA, step (2) evaluating the in silico frequency of fragment size distribution between individual chromosomes, step (3) selecting those enzymes that generate fragments with the majority between 100 bp and 3,000 bp, step (4) weighing the advantages and …

Roles Of The Drosophila Sk Channel (Dsk) In Courtship Memory, Ahmad N. Abou Tayoun, Claudio Pikielny, Patrick J. Dolph

Dartmouth Scholarship

A role for SK channels in synaptic plasticity has been very well-characterized. However, in the absence of simple genetic animal models, their role in behavioral memory remains elusive. Here, we take advantage of Drosophila melanogaster with its single SK gene (dSK) and well-established courtship memory assay to investigate the contribution of this channel to memory. Using two independent dSK alleles, a null mutation and a dominant negative subunit, we show that while dSK negatively regulates the acquisition of short-term memory 30 min after a short training session, it is required for normal long-term memory 24 h after extended …

A Streamlined Dna Tool For Global Identification Of Heavily Exploited Coastal Shark Species (Genus Rhizoprionodon), D. Pinhal, Mahmood S. Shivji, Pedro G. Nachtigall, Demian D. Chapman, Cesar Martins

Marine & Environmental Sciences Faculty Articles

Obtaining accurate species-specific landings data is an essential step toward achieving sustainable shark fisheries. Globally distributed sharpnose sharks (genus Rhizoprionodon) exhibit life-history characteristics (rapid growth, early maturity, annual reproduction) that suggests that they could be fished in a sustainable manner assuming an investment in monitoring, assessment and careful management. However, obtaining species-specific landings data for sharpnose sharks is problematic because they are morphologically very similar to one another. Moreover, sharpnose sharks may also be confused with other small sharks (either small species or juveniles of large species) once they are processed (i.e., the head and fins are removed). Here …

Widespread Diversity In African Toads (Anura: Amietophrynus), Nancy P. Conkey ^, Eli Greenbaum *

COURI Symposium Abstracts, Spring 2012

No abstract provided.

How Roads Affect The Population Genetic Structure Of The Lizard Uta Stansburiana In The Northern Chihuahuan Desert, Priscilla D. Duran ^, Kevin W. Floyd, Elizabeth J. Walsh *

COURI Symposium Abstracts, Spring 2012

Urbanization can have significant ecological effects on natural populations, including habitat fragmentation through increased road density. Roads may isolate populations, causing disruption of gene flow, inbreeding, and decreased genetic diversity. In this study we investigate how two roads, interstate highway I-10 and rural country road NM-9, affect population genetic structure of ideblotched lizards (Uta stansburiana) in the northern Chihuahuan Desert of New Mexico. Lizards were trapped on both sides of each road, plus one control site/road. Nine microsatellite loci were amplified to determine signatures of disrupted gene flow. Genotypes were obtained for 144 individuals from three sites, I-10 …

Resource Availability, Mortality And Fertility: A Path Analytic Approach To Global Life History Variation, Mark A. Caudell, Robert J. Quinlan

Human Biology Open Access Pre-Prints

Humans exhibit considerable diversity in timing and rate of reproduction. Life history theory suggests that ecological cues of resource richness and survival probabilities shape human phenotypes across populations. Populations experiencing high extrinsic mortality due to uncertainty in resources should exhibit faster life histories. Here we use a path analytic approach informed by life history theory to model the multiple pathways between resources, mortality rates, and reproductive behavior in 191 countries. Resources that account for the most variance in population mortality rates are predicted to explain the most variance in total fertility rates. Results indicate that resources (e.g., calories, sanitation, education, …

The Family Name As Socio-Cultural Feature And Genetic Metaphor: From Concepts To Methods, Pierre Darlu, Gerrit Bloothooft, Alessio Boattini, Leendert Brouwer, Matthijs Brouwer, Guy Brunet, Pascal Chareille, James Cheshire, Richard Coates, Paul Longley, Kathrin DräGer, Bertrand Desjardins, Patrick Hanks, Kees Mandemakers, Pablo Mateos, Davide Pettener, Antonella Useli, Franz Manni

Human Biology Open Access Pre-Prints

A recent workshop on "Family name between socio-cultural feature and genetic metaphor - From concepts to methods" was held in Paris on the 9th and 10th December 2010, partly sponsored by the Social Science and Humanity Institute (CNRS), and by Human Biology. This workshop was intended to facilitate exchanges on recent questions related to the names of persons and to confront different multidisciplinary approaches in a field of investigation where geneticists and historians, geographers, sociologists and ethnologists have all an active part. Here are the abstracts of some contributions.

Association Among Obesity-Related Anthropometric Phenotypes: Analyzing Genetic And Environmental Contribution, Aline Jelenkovic, Esther Rebato

Human Biology Open Access Pre-Prints

Obesity has become a public health and policy problem in many parts of the world. Epidemiological and population studies in this field are usually based on different anthropometric measures, however, common genetic and environmental factors between these phenotypes have been scarcely studied. The objective of this work is to assess the strength of these factors on the covariation among a large set of obesity-related traits. The subject group consisted of 533 nuclear families living in the Greater Bilbao (Spain), and included 1702 individuals aged 2-61 years. Detailed anthropometric measurements (stature, breadths, circumferences and skinfolds) were carried out in each subject. …

Choline Supplementation And Dna Methylation In The Hippocampus And Prefrontal Cortex Of Rats Exposed To Alcohol During Development, Nicha K H Otero, Jennifer D. Thomas, Christopher Saski, Xiaoxia Xia, Sandra Kelly

Publications

BACKGROUND:

Some of the most frequent deficits seen in children with fetal alcohol spectrum disorders (FASD) and in animal models of FASD are spatial memory impairments and impaired executive functioning, which are likely related to alcohol-induced alterations of the hippocampus and prefrontal cortex (PFC), respectively. Choline, a nutrient supplement, has been shown in a rat model to ameliorate some of alcohol's teratogenic effects, and this effect may be mediated through choline's effects on DNA methylation.

METHODS:

Alcohol was given by intragastric intubation to rat pups during the neonatal period (postnatal days 2 to 10) (ET group), which is equivalent to …

Microgeographic Differentiation In Historical Yemen Inferred By Morphometric Distances, Maria Enrica Danubio, Emanuele Sanna, Fabrizio Rufo, Domenico Martorella, Elvira Vecchi, Alfredo Coppa

Human Biology Open Access Pre-Prints

This study analysed the variations in space of 8 body dimensions and 11 measures of the head of 1,244 adult Yemenite males, collected in 1933/34 by Coon in Yemen and in Hadhramawt. The aim was to evaluate the presence of geographic microdifferentiation of the populations settled in the different regions of Yemen at the time. Coon sub-divided the sample into 6 geographical areas according to birthplace and ethnicity of the individuals: Tihamah, the Western Mountains, the Central Plateau, the South Coast, the Eastern Mountains and Hadhramawt. The results of ANCOVA (age as covariate) show that the observed differences of all …

Replication Protein A (Rpa70c) Negatively Regulates Ribonucleotide Reductase (Rnr) In The Model Plant Arabidopsis Thaliana, Stacy Wong

Honors Theses and Capstones

Replication protein A (RPA) is a heterotrimeric single-stranded DNA-binding protein that plays an important role in cellular responses to DNA damage. For example, RPA can activate the cell-cycle checkpoint protein ATR in the presence of persisting DNA damage. The model plant Arabidopsis thaliana has 5 functional homologous RPA70 genes which may play specific roles in response to DNA damaging agents. One chemical that causes DNA damage in Arabidopsis is Hydroxyurea (HU), which blocks DNA replication by inhibiting activity in Ribonucleotide Reductase (RNR), an enzyme responsible for the production of free deoxyribonucleotides (dNTPs). In studies of Arabidopsis mutants, atr plants, but …

Transformation Of Tobacco With The Ba5 Cement Protein Gene From Balanus Amphitrite, Matt Marquis

Honors Theses and Capstones

Expressing barnacle cement proteins genes such as the BA5 gene in plants may enable individual study and analysis. This technique is effective since barnacle cement is difficult to work with as a whole in the lab setting. The BA5 gene extracted from Balanus amphitrite is transferred to tobacco leaf tissue using Agrobacterium tumefaciens.

The Dietary Isoprenoid Perillyl Alcohol Inhibits Telomerase Activity In Prostate Cancer Cells, Tabetha Sundin

Theses and Dissertations in Biomedical Sciences

This is the first evidence that a plant-derived compound–perillyl alcohol regulates telomerase activity via the mammalian target of rapamycin (mTOR) pathway in prostate cancer cells. Telomerase–the enzyme responsible for immortalizing cells through telomeric repeats addition–is de-repressed early in an aspiring cancer cell. We hypothesized that perillyl alcohol regulates hTERT (human telomerase reverse transcriptase) at the translational and post-translational levels via its effects on the mTOR pathway. A rapid suppression of telomerase activity was detected in prostate cancer cell lines (PC-3 and DU145) in response to biologically-relevant concentrations and short incubations of perillyl alcohol or the mTOR inhibitor—rapamycin.

Western blot analysis …

Modeling The Dispersion Of Eastern Oyster Larvae (Crassostrea Virginica) And Its Effects On The Movement Of Disease Resistant Genes In The Delaware Bay Estuary, Diego A. Narvaez

OES Theses and Dissertations

This study combines several models to address two primary research questions. How does the interaction of larval biology and environmental variability determine the spatial distribution of oyster larvae in Delaware Bay? What is the role of larval dispersion in the transference of disease-resistant genes? The particle-tracking module in the Regional Ocean Modeling System (ROMS) was converted into an Individual-Based model representing Eastern oyster larvae that has growth and vertical migration. Exchange of larvae between natural oyster reefs was estimated and used in an Individual-Based genetic model that simulates the genetic structure of eastern oysters. Particles were released from a number …

Studies On Enzyme Functional Evolution In The Sabath Multigene Family Using Phylogenetic And Biochemical Approaches, Ruiqi Huang

Masters Theses

Gene duplication is believed to be the major source for providing genetic materials for the innovation and diversification of protein functions; natural selection and/or neutral drift then works on these genetic materials to guide their evolutionary directions. Here, I used the salicylic acid/benzoic acid/theobromine (SABATH) multigene family to study how natural selection acted on duplicated genes to prompt functional diversification. Members in this family methylate plant secondary metabolites by transferring the methyl group from S-adenosyl-L-methionine (SAM) to the carboxyl group or ring nitrogen of the substrates. In the Apocynaceae and Solanaceae lineage of this family, I documented three putative gene …

Neurodegeneration - A Means To An End, Amit Singh

Biology Faculty Publications

Cell death, a global phenomenon found throughout the animal kingdom, is a mechanism to maintain tissue homeostasis and for adaptation to changes in the environment [1,2]. Millions of cells die in our body daily- they succumb to stress and commit suicide by a mechanism referred to as cell death or apoptosis [2-4]. Under normal conditions cells are continuously replaced by new cells from the stemor progenitor- cells. For example, an optimum balance in shedding of dead cells from the skin and their replenishment by new ones maintain our health and hygiene. In this context, apoptosis is a mechanism to eliminate …

Characterization Of Species C Human Adenovirus Serotype 6 (Ad6), Eric A. Weaver, Reeti Khare, Mathew L. Hillestad, Donna Palmer, Philip Ng, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

Adenovirus serotype (Ad5) is the most studied Ad. Ad1, 2, and 6 are also members of species C Ad and are presumed to have biologies similar to Ad5. In this work, we have compared the ability of Ad1, 2, 5, and 6 to infect liver and muscle after intravenous and intramuscular injection. We found that Ad6 was surprisingly the most potent at liver gene delivery and that Ad1 and Ad2 were markedly weaker than Ad5 and 6. To understand these differences, we sequenced the Ad6 genome. This revealed that the Ad6 fiber protein is surprisingly three shaft repeats shorter than …

Heme Oxygenase-1 Regulates The Immune Response To Influenza Virus Infection And Vaccination In Aged Mice, Nathan W. Cummins, Eric A. Weaver, Shannon M. May, Anthony J. Croatt, Oded Foreman, Richard B. Kennedy, Gregory A. Poland, Michael A. Barry, Karl A. Nath, Andrew D. Badley

Nebraska Center for Virology: Faculty Publications

Underlying mechanisms of individual variation in severity of influenza infection and response to vaccination are poorly understood. We investigated the effect of reduced heme oxygenase-1 (HO-1) expression on vaccine response and outcome of influenza infection. HO-1-deficient and wild-type (WT) mice (kingdom, Animalia; phylum, Chordata; genus/species, Mus musculus) were infected with influenza virus A/PR/8/34 with or without prior vaccination with an adenoviral-based influenza vaccine. A genome-wide association study evaluated the expression of single-nucleotide polymorphisms (SNPs) in the HO-1 gene and the response to influenza vaccination in healthy humans. HO-1-deficient mice had decreased survival after influenza infection compared to WT mice (median …

Pf19 Encodes The P60 Catalytic Subunit Of Katanin And Is Required For Assembly Of The Flagellar Central Apparatus In Chlamydomonas, Erin E. Dymek, Elizabeth F. Smith

Dartmouth Scholarship

For all eukaryotic cilia the basal bodies provide a template for the assembly of the doublet microtubules, and intraflagellar transport provides a mechanism for transport of axonemal components into the growing cilium. What is not known is how the central pair of microtubules is nucleated or how their associated polypeptides are assembled. Here we report that the Chlamydomonas pf19 mutation results in a single amino acid change within the p60 catalytic subunit of katanin, and that this mutation prevents microtubule severing activity. The pf19 mutant has paralyzed flagella that lack the central apparatus. Using a combination of mutant analysis, RNAi-mediated …

Dialogues, Dilemmas, And Disclosures: Genomic Research And Incidental Findings, Lynn W. Bush, Karen H. Rothenberg

Faculty Scholarship

No abstract provided.

Reducing False-Positive Prediction Of Minimotifs With A Genetic Interaction Filter, Jerlin Camilus Merlin, Sanguthevar Rajasekaran, Tian Mi, Martin Schiller

Life Sciences Faculty Research

Background

Minimotifs are short contiguous peptide sequences in proteins that have known functions. At its simplest level, the minimotif sequence is present in a source protein and has an activity relationship with a target, most of which are proteins. While many scientists routinely investigate new minimotif functions in proteins, the major web-based discovery tools have a high rate of false-positive prediction. Any new approach that reduces false-positives will be of great help to biologists.

Methods and Findings

We have built three filters that use genetic interactions to reduce false-positive minimotif predictions. The basic filter identifies those minimotifs where the source/target …

Occurrence Of Hormonal Residues In Feedlot Cattle Waste, Terry L. Mader, Leslie J. Johnson, Shannon L. Bartelt-Hunt, Daniel D. Snow, William Kranz, Charles Shapiro, Simon Van Donk, David P. Shelton, David Tarkalson, T. C. Zhang, Steve Ensley

Department of Animal Science: Faculty Publications

Two identically designed studies were conducted in separate years at the UNL Haskell Agricultural Laboratory using 192 crossbred heifers (96/study). Within a study heifers (initial weight = 386kg) were randomly assigned to 2 groups (3 42.4 m × 14.6 m pens/group/year): 1) treatment (TRT) animals were administered synthetic hormones via subcutaneous implants [d 1, 36 mg zearalonal; d 35, 140 mg trenbolone acetate (TBA) and 14 mg of 17β-estradiol benzoate (Revalor-H)] and fed Melengesterol Acetate (MGA), and 2) control (CON) animals with no synthetic hormone provided. Throughout each study, feedlot pen surface samples were obtained from 4 equally-sized zones (5 …

Proteins: Form And Function, Roy D. Sleator

Department of Biological Sciences Publications

An overwhelming array of structural variants has evolved from a comparatively small number of protein structural domains; which has in turn facilitated an expanse of functional derivatives. Herein, I review the primary mechanisms which have contributed to the vastness of our existing, and expanding, protein repertoires. Protein function prediction strategies, both sequence and structure based, are also discussed and their associated strengths and weaknesses assessed.

Use Of A Complete-Feed Diet (Ramp) To Rapidly Transition Cattle To A Finishing Diet, C. J. Schneider, Brandon L. Nuttelman, Dirk Burken, Terry J. Klopfenstein, Galen E. Erickson

Department of Animal Science: Faculty Publications

A study evaluated transitioning cattle from RAMP to a finishing diet with fewer intermediate step diets and days fed during transition. Yearling crossbred steers (n = 390; BW = 341 ± 14 kg) were blocked and stratified by BW, and assigned randomly within strata to 40 feedlot pens, with 9 or 10 steers per pen. Treatments were different grain adaptation programs (27 or 28 d) involving blends of RAMP and finishing diet. A control adaptation program involved decreasing RAMP and increasing a 62.5% corn finishing diet (62.5% high moisture corn (HMC), 25% sweet bran, 7.5% alfalfa hay (AH), and 5% …

Anaerobic Digestion Of Finishing Cattle Manure With And Without Distillers Grains In The Diet., Andrea K. Watson, Terry J. Klopfenstein, Galen E. Erickson, Samodha C. Fernando, Jana L. Harding, Adam L. Shreck

Department of Animal Science: Faculty Publications

Two treatments (cattle diet) were used in anaerobic digestion of finishing cattle manure. Diet 1 contained 82.5% dry rolled corn (DRC) (CONT) and diet 2 contained 40% wet distillers grains plus solubles (DM basis) replacing DRC (WDGS). Cattle were housed in stanchions for 3 d with complete manure collection in a cement pit. Manure (feces and urine) was sampled and analyzed for minerals, DM and OM. Manure collected was weighed into individual allotments based on DM and frozen. Continuously stirred anaerobic digesters (n = 7, 1 L capacity) were inoculated and maintained for 5 mo before the trial to ensure …