Genetics and Genomics Commons^™

Regeneration Dynamics Of White Spruce, Trembling Aspen, And Balsam Poplar In Response To Disturbance, Climatic, And Edaphic Factors In The Cold, Dry Boreal Forests Of The Southwest Yukon, Canada, Shyam K. Paudel, Craig R. Nitschke, Suzanne W. Simard, John L. Innes

Aspen Bibliography

The southwestern region of the Yukon Territory of Canada has experienced an unprecedented spruce bark beetle outbreak (Dendroctonus rufipennis) and an increase in the frequency of forest fires that extend beyond historical trends and that have caused significant impacts on forest structure and composition. A Strategic Forest Management Plan (SFMP) for the Champagne and Aishihik Traditional Territory located in the southwest Yukon was implemented in 2004 in response to the spruce bark beetle (D. rufipennis) infestation and increased fire risk. The plan has recommended salvage harvesting of beetle-killed stands as a strategy to facilitate the development …

Anti-Cancer Activity Of Withaferin A In B-Cell Lymphoma., M K Mckenna, B W Gachuki, S S Alhakeem, K N Oben, V M Rangnekar, R C Gupta, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Withaferin A (WA), a withanolide from the plant, Ashwagandha (Withania somnifera) used in Ayurvedic medicine, has been found to be valuable in the treatment of several medical ailments. WA has been found to have anticancer activity against various solid tumors, but its effects on hematological malignancies have not been studied in detail. WA strongly inhibited the survival of several human and murine B cell lymphoma cell lines. Additionally, in vivo studies with syngeneic-graft lymphoma cells suggest that WA inhibits the growth of tumor but does not affect other proliferative tissues. We demonstrate that WA inhibits the efficiency of NF-κB nuclear …

Effects Of Proline And Glycine On The Cnidocyte Discharge Of Hydra Magnipapillata, Janine R. Appleton

Honors Theses and Capstones

The sense of taste enables animals to utilize environmental cues to detect favorable foods. Through specialized sensory receptors, Cnidarians employ stinging cells called cnidocytes to perform a variety of activities such as locomotion, capturing prey, inducing of feeding responses, and defense. Their discharge is highly regulated by mechanical and chemical signals that are mediated by a complex system including the opsin and taste pathways. Taste 1 Receptors (T1R) have previously been isolated in vertebrates but only until recently, have been noted in invertebrates. Receptors specific to L- amino acids corresponding to the taste sensation of umami, were studied to determine …

Draft Genome Sequence Of Cercospora Arachidicola, Causal Agent Of Early Leaf Spot In Peanuts, Valerie A. Orner, Emily G. Cantowine, Xinye Monica Wang, Amr Abouelleil, James Bochicchio, Chad Nusbaum, Albert C. Culbreath, Zaid Abdo, Renee S. Arias

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Cercospora arachidicola, causal agent of early leaf spot, is an economically important peanut pathogen. Lack of genetic information about this fungus prevents understanding the role that potentially diverse genotypes may have in peanut breeding programs. Here, we report for the first time a draft genome sequence of C. arachidicola.

Using Large Snp Datasets To Understand The Genetic Mechanisms Of Complex Traits In Arabidopsis Thaliana, Elisabeth S. Harrison

Open Access Theses

Arabidopsis thaliana, as a model species, has been widely genotyped and sequenced. Many studies have been done to understand the kinship and population structure of the species. This data and information is beneficial for understanding the genetic mechanisms of complex traits. In this thesis, we first used genotyped data for 5,967 accessions to study the occurrence of tetraploidy in the species. We found that tetraploidy is a transient character state, and the species is a diploid species. Secondly, we used 211K and 1.6M SNPs for 440 accessions to run genome-wide analyses (GWA) for four traits: glufosinate tolerance, hybrid incompatibilities, seed …

Directed Evolution Of Genetic Regulatory Elements Using Crispr/Cas Genome Engineering, Candice J. Coppola

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

No abstract provided.

Impacts Of Climate, Geography And White-Nose Syndrome Mortality On The Population Genetic Structure And Variation Of Myotis Lucifugus In The Eastern United States, Shannon Marie Dodge Morgan

Legacy Theses & Dissertations (2009 - 2024)

A myriad of biotic and abiotic factors contribute to the fluctuations in geographic range and size of animal populations. In the Nearctic, bat species have experienced drastic historic changes in available habitat due to Pleistocene glaciations, and are recently imperiled by the introduction of a novel fungal pathogen, Pseudogymnoascus destructans within the last decade. Myotis lucifugus in particular has lost 90-95% of the population in the eastern US due to the fungal disease White-Nose Syndrome (WNS). A population decline of this magnitude will likely result in a loss of allelic diversity as a result of a genetic bottleneck. My study …

A Genetic Epidemiologic Investigation Of Breast Cancer Susceptibility, Cristy Ellen Stagnar

Legacy Theses & Dissertations (2009 - 2024)

Introduction

Genome-Scale Analyses Of Transcription And Transcriptional Regulation In Bacteria, Devon Marie Fitzgerald

Legacy Theses & Dissertations (2009 - 2024)

The textbook model of bacterial transcription regulation posits that promoters occur immediately upstream of genes and that transcription factors (TFs) modulate transcription through promoter-proximal binding. However, the recent application of unbiased genome-wide approaches, such as ChIP-seq and RNA-seq, has revealed a much more complex picture, including TF binding and transcription initiation occurring in unexpected locations. This dissertation describes the use of deep sequencing-based approaches to evaluate the genome-wide binding of transcription-related proteins and identify locations of transcription initiation. I have assessed the genome-wide binding of three Escherichia coli TFs and an alternative σ factor. Additionally, I have analyzed genome-wide patterns …

Foraminiferal Beta 2-Tubulin And Microtubule To Helical Filament Transition In Reticulomyxa Filosa, Ingrid Ann Hahn

Legacy Theses & Dissertations (2009 - 2024)

Foraminifera have unusually fast dynamic movements resulting in the reorganization of the microtubule cytoskeleton (Travis and Bowser, 1988; Travis et al., 1983). We are interested in using Reticulomyxa filosa as a model to investigate the mechanisms and factors that regulate such fast microtubule assembly/disassembly rates (Chen and Schliwa 1990; Travis and Bowser, 1991; Welnhofer and Travis, 1996). Compared to conventional microtubule assembly and disassembly models, foraminifera tubulin can exist in another assembly state termed helical filaments. A novel form of tubulin, β2, in foraminifera is likely critical to these unusual microtubule properties. This thesis investigates Reticulomyxa filosa, a freshwater foraminifera …

Whole-Genome Sequencing Of Kaposi’S Sarcoma-Associated Herpesvirus From Zambian Kaposi’S Sarcoma Biopsy Specimens Reveals Unique Viral Diversity, Landon Olp, Adrien Jeanniard, Clemence Marimo, Charles Wood

Nebraska Center for Virology: Faculty Publications

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiological agent for Kaposi’s sarcoma (KS). Both KSHV and KS are endemic in sub-Saharan Africa where approximately 84% of global KS cases occur. Nevertheless, whole-genome sequencing of KSHV has only been completed using isolates from Western countries—where KS is not endemic. The lack of whole-genome KSHV sequence data from the most clinically important geographical region, sub-Saharan Africa, represents an important gap since it remains unclear whether genomic diversity has a role on KSHV pathogenesis. We hypothesized that distinct KSHV genotypes might be present in sub-Saharan Africa compared to Western countries. Using a KSHV-targeted enrichment …

Observed And Expected Incidence Of Cervical Cancer In Lusaka And The Southern And Western Provinces Of Zambia, 2007 - 2012, Mulele Kalima, Kennedy Lishimpi, Jane L. Meza, Shinobu Watanabe-Galloway, Susan C. Msadabwe, Catherine K. Mwaba, Aaron L. Shibemba, Lewis Banda, Charles Wood, Robert M. Chamberlain, Amr S. Soliman

Nebraska Center for Virology: Faculty Publications

Objectives—Cervical cancer is increasing but underestimated in developing countries. We calculated the observed and expected incidence of cervical cancer in Lusaka and Southern and Western provinces of Zambia.

Methods/Materials—Data for 2007-2012 was obtained for the 3 provinces. Data included age, residence, year of diagnosis, marital status, occupation, HIV, stage, radiotherapy and chemotherapy. Expected incidence in Southern and Western provinces was calculated based on observed incidence for Lusaka province, adjusting for HIV.

Results—Crude and age-standardized incidence rates (ASR) in Lusaka were 2-4 times higher than incidence in the other 2 provinces. Lusaka had a rate of 54.1/10⁵ and ASR of …

Crf07_Bc Strain Dominates The Hiv-1 Epidemic In Injection Drug Users In Liangshan Prefecture Of Sichuan, China, Lin Li, Daying Wei, Wan-Ling Hsu, Tianyi Li, Tao Gui, Charles Wood, Yongjian Liu, Hanping Li, Zuoyi Bao, Siyang Liu, Xiaolin Wang, Jingyun Li

Nebraska Center for Virology: Faculty Publications

The Liangshan prefecture in Sichuan province is an area in China severely affected by the HIV epidemic, with intravenous drug use (IDU) as the main risk factor. No reports on HIV subtypes prevalent in IDUs in Liangshan prefecture could be found. In this study, we have characterized the genotypes of HIV-1 in the IDU population in Liangshan prefecture and further determined the phylogenetic relationship of the CRF07_BC strains to HIV-1 sequences from the other regions of China, including Xinjiang and Yunnan provinces, to explore the pattern and possible diffusion pathway of HIV-1 in these regions. HIV-1-seropositive drug-naive IDUs identified in …

Exploring Birthparent’S Experiences Of Creating An Adoption Plan For Their Children With Special Needs, Sanjukta Tawde

Theses and Dissertations

Very little information is available regarding the experience and needs of families who create an adoption plan for their child with disability. The purpose of this study was to learn more about the experiences of birthparents who created an adoption plan after the diagnosis of Down syndrome so as to understand their needs during the process. Birthparents were invited to participate in the study through National Down Syndrome Adoption Network (NDSAN) by membership emails. Information about the study was made available on the organization’s website and social media pages. Potential participants also learned about the study from one of the …

Helping To Resolve Taxonomic Conflicts Within The Genus Amblyomma (Acari:Ixodidae) From A Molecular Perspective, Paula Lado

College of Graduate Studies: Theses & Dissertations

This work sought to reassess the taxonomic status of Amblyomma parvum Aragao, 1908 and of the A. maculatum group of ticks Camicas, 1998. By using different molecular markers, 12SrDNA, 16SrDNA, DL, COI, COII (mitochondrial) and ITS2 (nuclear), I analyzed the systematic relationships between these taxa and their closest relatives. Phylogenetic analyses by maximum parsimony, maximum likelihood, and Bayesian analysis were performed in order to determine relationships among species and populations, and to determine the evolutionary history of these ixodids. The data obtained supported the hypothesis of cryptic speciation occurring within A. parvum, with the northern populations of Central America being …

The Role Of Artificial Structures In Facilitating Range Expansion Of The Introduced Barnacle Megabalanus Coccopoma In The Southeastern U.S.A., Alicia M. Reigel

College of Graduate Studies: Theses & Dissertations

The barnacle Megabalanus coccopoma is a recent invader of the southeastern U.S.A. from the tropical eastern Pacific. In Georgia, M. coccopoma populations along the immediate coastline often suffer extensive mortality during the winter, but population rebuilding is common after these events suggesting that there may be nearby larval sources. I investigated the hypothesis that artificial structures (i.e., buoys, towers), occurring far enough offshore of Georgia for water temperatures to be moderated by the Gulf Stream, provide refuges for breeding adults of M. coccopoma and can serve as the larval source. I investigated this hypothesis by first developing thirteen microsatellite primer …

Evolution Of New Duplicate Genes In Arabidopsis Thaliana, Nicholas Curtis Marowsky

Wayne State University Theses

Abstract

Gene duplication is one of the major mechanisms by which organisms expand their genomes. The material added to the genome can then be acted upon by mutation and natural selection to increase the fitness of the species. By studying these duplicate sequences we can understand the process by which species evolve new functional genes. In a previous paper we identified 100 new duplicate genes through a genome wide comparison between A. thaliana and related species. We selected three of these new duplicate genes and investigated more closely their sequence and expression divergence from their parental gene. The three new …

An Assessment Of The Role Of Roads In Population Demography And Genetic Structuring In Two Species Of Lizards In The Northern Chihuahuan Desert, Kevin Floyd

Open Access Theses & Dissertations

Roads can fragment habitat and increase mortality rates of wildlife, potentially reducing population sizes and gene flow, which in turn can reduce genetic diversity through genetic drift. Although negative road impacts have been found in a variety of taxa, not all species are impacted. For instance, species that move less and rarely encounter roads and those that avoid the roads are predicted to not be negatively affected. Yet tests of these predictions are uncommon, especially for reptiles and particularly lizards. Side-blotched lizards (Uta stansburiana) are small sit-and-wait predators, while the larger marbled whiptails (Aspidoscelis marmorata) are active foragers. Their responses …

Sperm Dna Oxidative Damage And Dna Adducts, Hueiwang Anna Jeng, Chih-Hong Pan, Mu-Rong Chao, Wen-Yi Lin

Community & Environmental Health Faculty Publications

The objective of this study was to investigate DNA damage and adducts in sperm from coke oven workers who have been exposed to polycyclic aromatic hydrocarbons. A longitudinal study was conducted with repeated measurements during spermatogenesis. Coke-oven workers (n =112) from a coke-oven plant served the PAH-exposed group, while administrators and security personnel (n=67) served the control. Routine semen parameters (concentration, motility, vitality, and morphology) were analyzed simultaneously; the assessment of sperm DNA integrity endpoints included DNA fragmentation, bulky DNA adducts, and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dGuo). The degree of sperm DNA fragmentation was measured using the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling …

Developing Microbial Biomarkers To Non-Invasively Assess Health In Wild Elk (Cervus Canadensis) Populations, Samuel B. Pannoni

Undergraduate Theses, Professional Papers, and Capstone Artifacts

The composition of the intestinal bacterial community (intestinal microbiome) of mammals is associated with changes in diet, stress, disease and physical condition of the animal. The relationship between health and the microbiome has been extensively demonstrated in studies of humans and mice; this provides strong support for its potential utility in wildlife. When managing elk (Cervus canadensis), federal and state agencies currently must rely on invasive sampling and coarse demographic data on which to base their decisions. By developing microbiome-based biomarkers that vary as a function of elk body condition and disease (i.e. microbial biomarkers), we hope to …

On The Comparison Of State- And Transition-Based Analysis Of Biological Relevance In Gene Co-Expression Networks, Kathryn Dempsey Cooper, Prasuna Vemuri, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

Traditional correlation network analysis typically involves creating a network using gene expression data and then identifying biologically relevant clusters from that network by enrichment with Gene Ontology or pathway information. When one wants to examine these networks in a dynamic way - such as between controls versus treatment or over time - a "snapshot" approach is taken by comparing network structures at each time point. The biological relevance of these structures are then reported and compared. In this research, we examine the same "snapshot" networks but focus on the enrichment of changes in structure to determine if these results give …

Up Regulation Of Heat Shock Protein 70b (Hsp70b) And Ssa1 In Chlamydomonas Reinhardtii Via Hsp70a-Rbcs2 And Psad Promoter, B. Kirtley Amos

Theses and Dissertations--Biosystems and Agricultural Engineering

Fabrication of effective algae cultivation systems adjacent to coal-fired power plants to fixate waste CO₂ would represent a sizable step towards achieving a carbon neutral energy cycle. However, emission gas would elevate the algal cultivation system temperature and decreases its pH without expensive preprocessing. Increased temperature and acidity constitutes a profound stress on the algae. Although stressed algae produce heat shock proteins (HSPs) that promote protein folding and protect against stress, the ordinary biological response is insufficient to protect against coal flue gas. Experimental upregulation of HSPs could make algae respond to the stress caused by high temperatures and …

The Role Of Batf2 In Lps/Ifnγ Polarized Macrophages, Marie A. Gehman

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

Transcription factors regulate distinct macrophage functions by regulating gene expression in response to micro-environmental cues. This functional plasticity is critical for regulating innate and adaptive immune responses during infection and during chronic disease processes including inflammatory diseases and cancer. Microarray analysis of macrophages polarized to a pro-inflammatory (M1) phenotype with LPS and IFNγ revealed that basic leucine zipper transcription factor ATF-like 2 (Batf2), a member of the AP1 transcription factors, is selectively upregulated in M1 macrophages compared to anti-inflammatory IL-4-polarized (M2) macrophages. The initial hypothesis was that Batf2 is a master regulator of gene expression that orchestrates M1 polarization. To …

Target-Directed Biosynthetic Evolution: Redirecting Plant Evolution To Genomically Optimize A Plant’S Pharmacological Profile, Dustin Paul Brown

Theses and Dissertations--Neuroscience

The dissertation describes a novel method for plant drug discovery based on mutation and selection of plant cells. Despite the industry focus on chemical synthesis, plants remain a source of potent and complex bioactive metabolites. Many of these have evolved as defensive compounds targeted on key proteins in the CNS of herbivorous insects, for example the insect dopamine transporter (DAT). Because of homology with the human DAT protein some of these metabolites have high abuse potential, but others may be valuable in treating drug dependence. This dissertation redirects the evolution of a native Lobelia species toward metabolites with greater activity …

Novel Computational Methods For Transcript Reconstruction And Quantification Using Rna-Seq Data, Yan Huang

Theses and Dissertations--Computer Science

The advent of RNA-seq technologies provides an unprecedented opportunity to precisely profile the mRNA transcriptome of a specific cell population. It helps reveal the characteristics of the cell under the particular condition such as a disease. It is now possible to discover mRNA transcripts not cataloged in existing database, in addition to assessing the identities and quantities of the known transcripts in a given sample or cell. However, the sequence reads obtained from an RNA-seq experiment is only a short fragment of the original transcript. How to recapitulate the mRNA transcriptome from short RNA-seq reads remains a challenging problem. We …

Comparative Analysis Of Prostate Cancer Gene Regulatory Networks Via Hub Type Variation, Pegah Khosravi, Vahid H. Gazestani, Mohammad Akbarzadeh, Samira Mirkhalaf, Mehdi Sadeghi, Bahram Goliaei

Publications and Research

Background

Prostate cancer is one of the most widespread cancers in men and is fundamentally a genetic disease. Identifying regulators in cancer using novel systems biology approaches will potentially lead to new insight into this disease. It was sought to address this by inferring gene regulatory networks (GRNs). Moreover, dynamical analysis of GRNs can explain how regulators change among different conditions, such as cancer subtypes.

Methods

In our approach, independent gene regulatory networks from each prostate state were reconstructed using one of the current state-of-art reverse engineering approaches. Next, crucial genes involved in this cancer were highlighted by analyzing each …

The Genetic Ancestry Of African Americans, Latinos, And European Americans Across The United States, Katarzyna Bryc, Eric Y. Durand, J. Michael Macpherson, David Reich, Joanna Mountain

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans (brought largely by the trans-Atlantic slave trade), shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasive mixed ancestry and asymmetrical male and female ancestry contributions in all groups studied. We show that regional ancestry differences reflect historical …

The Mechanisms Of Α-Amanitin Resistance In The Fruit Fly Drosophila Melanogaster, Chelsea L. Mitchell

Dissertations, Master's Theses and Master's Reports

Insect pesticide resistance has become a costly problem in the US. To make things more problematic, resistance to one pesticide is often associated with cross-resistance to other toxins, including pesticides that have not yet even been developed. In this study, we investigated a possible type of cross-resistance in the model fruit fly Drosophila melanogaster, some stocks of which are resistant to the very potent mushroom toxin α-amanitin. Because α-amanitin is solely produced by mushrooms, and because D. melanogaster does not feed on mushrooms in nature, the fruit flies should not be resistant to this toxin. In order to understand …

A Therapeutic Approach For Senile Dementias: Neuroangiogenesis, Charles T. Ambrose

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Alzheimer's disease (AD) and related senile dementias (SDs) represent a growing medical and economic crisis in this country. Apart from cautioning persons about risk factors, no practical, effective therapy is currently available. Much of the recent research in AD has been based on the amyloid cascade theory. Another approach assumes a vascular basis for SDs. This paper presents evidence from a score of studies that cerebral capillary density (CCD) declines during old age in animals and people as well as in AD. Neuroangiogenic (NAG) factors initiate and maintain capillaries in the brain. Thus a waning level of these factors and …

Chromosomal Rearrangements Directly Cause Underdominant F1 Pollen Sterility In Mimulus Lewisii-M. Cardinalis Hybrids, Angela M. Stathos

Graduate Student Theses, Dissertations, & Professional Papers

Chromosomal rearrangements can contribute to the evolution of postzygotic reproductive isolation directly, by disrupting meiosis in F₁ hybrids, or indirectly, by suppressing recombination among genic incompatibilities. Because direct effects of rearrangements on fertility imply fitness costs during their spread, understanding the mechanism of F₁ hybrid sterility is integral to reconstructing the role(s) of rearrangements in speciation. In hybrids between monkeyflowers Mimulus cardinalis and M. lewisii, rearrangements contain all quantitative trait loci (QTLs) for both premating barriers and pollen sterility, suggesting that they may have facilitated speciation in this model system. I used artificial chromosome doubling and …