Genetics and Genomics Commons^™

Unravelling The Layers Of Cell Wall Synthesis And Function In Rice, Ritu Mihani

Graduate Theses and Dissertations

The plant cell wall is of critical importance to plant growth and survival, functioning in maintaining structural integrity, supporting cell expansion, and acting as the first line of defense in response to biotic and abiotic stresses. The major components of the cell wall are cellulose, hemicelluloses, lignin, and pectin. Recent focus on the transcriptional machinery regulating cell wall biosynthesis in plants has revealed many key transcription factors responsible for orchestrating cell wall deposition. However, many of these TFs act redundantly and work coherently with a suite of TFs to activate the cell wall biosynthetic machinery. Heterologous expression of TFs is …

Involvement Of The Ino80 Complex In Chromosome Segregation, Jesus Moreno

Graduate Theses and Dissertations

Chromatin remodeling complexes are multi-protein complexes that regulate the dynamics of the nucleosomes in the genome. The INO80 chromatin remodeling complex participates in varied biological processes such as: transcription, DNA repair, DNA replication and chromosome integrity. It catalyzes the eviction of the H2A.Z variant histone as well as whole nucleosome eviction. This complex is comprised of 15 subunits and the contribution of each to chromosome segregations remains unknown. To evaluate the contribution of each subunit to chromosome segregation, we tested deletion mutants of the non-essential subunits for DNA content and benomyl sensitivity. Also, we assessed members of the SWR1 and …

Vascular Injury In Col3a1+/- Mice Model Of Vascular Ehler-Danlos Syndrome, Ping Zhou Ms

Dissertations and Theses (Open Access)

Vascular type of Ehlers-Danlos Syndrome (vEDS) is an inherited cardiovascular disease affecting the middle to large sized arteries, with an incidence rate of 1/5000. vEDS patients also show a significant phenotype of easily bruised skin, indicating aberrant wound healing and injury repair ability. Over 70% of the patients carry a glycine mutation located in their COL3A1 gene, which encodes the propeptide of type III collagen. Mutations in glycine residues lead to a disruption in the assembly and maturation of type III collagen. The goal and significance of the current study was to investigate the potential role of COL3A1 haploinsufficiency …

Phylogeny And Evolutionary Genomics Of Non-Photosynthetic Diatoms, Anastasiia Onyshchenko

Graduate Theses and Dissertations

Diatoms are prolific photosynthesizers responsible for some 20% of global primary production. In real terms, the oxygen in one of every five breaths traces back to photosynthesis by marine diatoms. Among the tens of thousands of diatom species, a small handful of colorless diatom species in the genus Nitzschia have lost photosynthesis altogether and rely exclusively on extracellular organic carbon for growth. I used DNA sequence data to reconstruct the phylogeny of this group, and found that nonphotosynthetic diatoms are monophyletic, indicating that photosynthesis was lost just one time over the course of some 200 million years of diatom evolution. …

Evolution Via Gene Duplication And Alternative Splicing In The Eukaryotic Ski7 And Hbs1 Genes, Alexandra Marshall

Dissertations and Theses (Open Access)

Gene duplication and alternative splicing are both recognized as important drivers of proteomic diversity and innovation during evolution, but the evolutionary changes over long periods of time or the interrelations of the two processes has not been extensively studied. Here I study these phenomena for the SKI7 and HBS1 gene pair. These Saccharomyces cerevisiae genes were created as part of a whole genome duplication (WGD) event and have since functionally diverged. Although both genes function in mRNA surveillance pathways, the two genes act on different RNAs and have different effects on the target mRNAs. Ski7 brings the Ski complex and …

Functional Similarity Of Prd-Containing Virulence Regulators In Bacillus Anthracis, Malik Raynor

Dissertations and Theses (Open Access)

Bacillus anthracis produces three regulators, AtxA, AcpA, and AcpB, that control virulence gene expression and are members of an emerging class of regulators termed “PCVRs” (Phosphoenolpyruvate-dependent phosphotransferase regulation Domain-Containing Virulence Regulators). AtxA controls expression of the toxin genes; lef, cya, and pag, and is the master virulence regulator and archetype PCVR. AcpA and AcpB are less well studied. AcpA and AcpB independently positively control transcription of the capsule biosynthetic operon capBCADE, and culture conditions that enhance AtxA activity result in capBCADE transcription in strains lacking acpA and acpB. RNA-Seq was used to assess the regulons of the …

Investigating The Impact Of Intragenic Dna Methylation On Gene Expression, And The Clinical Implications On Tumor Cells And Associated Stroma, Michael Mcguire

Dissertations and Theses (Open Access)

Investigations into the function of non-promoter DNA methylation have yielded new insights into epigenetic regulation of gene expression. Previous studies have highlighted the importance of distinguishing between DNA methylation in discrete functional regions; however, integrated non-promoter DNA methylation and gene expression analyses across a wide number of tumor types and corresponding normal tissues have not been performed. Through integrated analysis of gene expression and DNA methylation profiles, we uncovered an enrichment of DNA methylation sites within the gene body and 3’UTR in which DNA methylation is strongly positively correlated with gene expression. We examined 32 tumor types and identified 57 …

Trim24 In Normal & Malignant Hematopoiesis, Justin Shaw

Dissertations and Theses (Open Access)

Treatment for acute myeloid leukemia (AML) has changed little in the past four decades. For the majority of AML patients, current treatment options include chemotherapy and allogeneic stem cell transplants, which also involves high-dose chemotherapy or radiation treatment. These options have little success in the long-run, as only an estimated 26% of patients survive five years post-diagnosis. In efforts to address this low survival rate, interest has increased for targeting epigenetic pathways in AML. This focus stems from the discovery that AML is frequently driven by blockades on hematopoietic stem cell differentiation, which involves a series of coordinated epigenetic changes. …

Phosphorylation Impairs Dicer1 Function To Accelerate Aging And Tumorigenesis In Vivo, Neeraj Aryal

Dissertations and Theses (Open Access)

Altered DICER1 protein levels are associated with developmental disorders, infertility, macular degenerative blindness, aging, and cancer in humans. Recently, post-translational regulation of Dicer1 via phosphorylation has been described in C. elegans. Oscillation of Dicer1 phosphorylation to regulate its activity is essential for germ cell development and embryogenesis in worms. These observations led us to posit that Dicer1 protein levels and activity are under tight regulation for normal mammalian homeostasis. To test whether phosphorylation of Dicer1 regulates its activity in mammals, I generated phospho-mimetic knock-in mouse models by replacing Serines 1712 and 1836 with Aspartic acids individually or together (dual …

Identification And Utility Of Dna In Exosomes, Paul Kurywchak

Dissertations and Theses (Open Access)

Cancer-associated mortality has been declining for two decades but remains a significant public health problem, especially when patients initially present with advanced disease. Early detection methods have improved survival rates but remain unavailable for a majority of cancers due to a lack of sensitive biomarkers or numerous limitations associated with current diagnosis strategies. Approaches to develop “liquid biopsies” by detecting tumor cells or DNA in the blood have led to several breakthroughs and create the potential for non-invasive, routine assessment of diseases status. However, these biomarkers are rare and currently difficult to isolate, especially in the early stages of disease. …

The Regulation Of Dna Methylation In Mammalian Development And Cancer, Nicolas Veland

Dissertations and Theses (Open Access)

DNA methylation is an essential epigenetic modification in mammals, as it plays important regulatory roles in multiple biological processes, such as gene transcription, maintenance of chromosomal structure and genomic stability, genomic imprinting, retrotransposon silencing, and X-chromosome inactivation. Dysregulation of DNA methylation is associated with various human diseases. For example, cancer cells usually show global hypomethylation and regional hypermenthylation, which have been implicated in genomic instability and tumor suppressor silencing, respectively. Although great progress has been made in elucidating the biological functions of DNA methylation over the last several decades, how DNA methylation patterns and levels are regulated and dysregulated is …

Multivalency Regulates Activity In An Intrinsically Disordered Transcription Factor, Sarah Clark, Janette B. Myers, Ashleigh King, Radovan Fiala, Jiri Novacek, Grant Pearce, Steve L. Reichow, Elisar J. Barbar

Chemistry Faculty Publications and Presentations

The transcription factor ASCIZ (ATMIN, ZNF822) has an unusually high number of recognition motifs for the product of its main target gene, the hub protein LC8 (DYNLL1). Using a combination of biophysical methods, structural analysis by NMR and electron microscopy, and cellular transcription assays, we developed a model that proposes a concerted role of intrinsic disorder and multiple LC8 binding events in regulating LC8 transcription. We demonstrate that the long intrinsically disordered C-terminal domain of ASCIZ binds LC8 to form a dynamic ensemble of complexes with a gradient of transcriptional activity that is inversely proportional to LC8 occupancy. The preference …

Genotype-Specific Insertion Of Cytotoxic Genetic Elements Into Cancer Cells, Ryan Englander

University Scholar Projects

The new gene editing system CRISPR/Cas9, composed of a complex composed of a guide RNA and the Cas9 endonuclease, promises to revolutionize biological research and potentially allow clinicians to directly modify patient DNA in vivo. While its applications in the treatment of genetic diseases and in modifying immune cells for immunotherapy are currently being explored, CRISPR/Cas9’s potential utility as a modular system for targeting tumor-specific mutated sequences has not as of yet been explored. While CRISPR/Cas9 is specific enough to target small insertions and deletions or gross chromosomal rearrangements, it is not specific enough to reliably restrict editing to …

Effect Of Mutation Of Cvn7 Conservon Genes Sco6796 And Sco6798 Of Streptomyces Coelicolor., Caroline Fulmer

Undergraduate Distinction Papers

Abstract

Streptomyces coelicolor is a gram-positive Actinobacterium. It is a filamentous soil organism that performs complex multicellular development. Its physiological and morphological differentiation produces active secondary metabolite antibiotics that have pharmaceutical applications. Studies of S. coelicolor show that cyclic di-GMP proteins regulate physiological and morphological development. S. coelicolor has 13 copies of an operon that are collectively named “conservon” because they are highly conserved. The operons are named cvn1-13 and genes in each operon are denoted cvnA-D. RNA-Seq data of a cyclic di-GMP phosphodiesterase double mutant showed differential expression between wild type and many of the operons in the …

Identifying Rmda Protein Interactions In Streptomyces Using A Bacterial Two-Hybrid System, Rachel Nguyen

Undergraduate Distinction Papers

Streptomyces is a genus of the phylum actinobacteria most commonly found as soil bacteria and used as a major source of antibiotics. RmdA and RmdB are phosphodiesterases that break down the ubiquitous second messenger cyclic-di-GMP which determines colony morphology and development of Streptomyces. The objective of this research is to identify whether RmdA will have interactions with itself using the Bacterial Adenylate Cyclase Two-Hybrid (BACTH) System. Each gene was fused into one of two BACTH vectors that encode a different domain of a single protein (T18 and T25) and then cotransformed into the BACTH indicator strain. The transformants were …

The Identification And Characterization Of A Putative Chromosome Segregation Gene In Streptomyces Coelicolor, Sean Kirk

Undergraduate Distinction Papers

Streptomyces coelicolor is a soil bacterium that is a model for bacterial development. It is a filamentous, sporulating bacterium known to produce many medically utilized antibiotics. The goal of this research was to examine several developmental mutants and characterize novel genes of interest. Previously generated random transposon insertion mutants were analyzed using visual and microscopic phenotyping. Mutants of interest were further pursued and each transposon disruption site was identified by Inverse PCR and DNA sequencing. One of the novel genes is suspected to be involved in DNA segregation and codes for a putative membrane protein. Staining with propidium iodide was …

Efficient Reduced Bias Genetic Algorithm For Generic Community Detection Objectives, Aditya Karnam Gururaj Rao

Theses

The problem of community structure identification has been an extensively investigated area for biology, physics, social sciences, and computer science in recent years for studying the properties of networks representing complex relationships. Most traditional methods, such as K-means and hierarchical clustering, are based on the assumption that communities have spherical configurations. Lately, Genetic Algorithms (GA) are being utilized for efficient community detection without imposing sphericity. GAs are machine learning methods which mimic natural selection and scale with the complexity of the network. However, traditional GA approaches employ a representation method that dramatically increases the solution space to be searched by …

Characterizing The Role Of Cp1 In Drosophila Melanogaster: Its Effects On Basement Membrane Degradation And Signaling, Dane Alan Flinchum

Masters Theses & Specialist Projects

CP1 is a well-conserved cathepsin L-like protease essential for proper growth and development in Drosophila melanogaster. Previous research has demonstrated that CP1 has the ability to break down the extracellular matrix. Using the UAS-GAL4 system, immunohistochemistry, and antibody-staining, this research attempts to characterize the role of CP1 and its effects on basement membrane degradation and signaling. These effects include actions at the cellular level and on a known signaling pathway. The genes involved in this pathway are known to be required for proper development of the wing disc into the adult wing. We have demonstrated the collagenase activity of CP1 …

Neutrophils From Both Susceptible And Resistant Mice Efficiently Kill Opsonized Listeria Monocytogenes, Michelle G. Pitts, Travis A. Combs, Sarah E. F. D'Orazio

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Inbred mouse strains differ in their susceptibility to infection with the facultative intracellular bacterium Listeria monocytogenes, largely due to delayed or deficient innate immune responses. Previous antibody depletion studies suggested that neutrophils (polymorphonuclear leukocytes [PMN]) were particularly important for clearance in the liver, but the ability of PMN from susceptible and resistant mice to directly kill L. monocytogenes has not been examined. In this study, we showed that PMN infiltrated the livers of BALB/c/By/J (BALB/c) and C57BL/6 (B6) mice in similar numbers and that both cell types readily migrated toward leukotriene B4 in an in vitro chemotaxis assay. However, …

Characterization Of A Morphogenetic Furrow Specific Gal4 Driver In The Developing Drosophila Eye, Ankita Sarkar, Neha Gogia, Kevin Farley, Lydia C. Payton, Amit Singh

Biology Faculty Publications

The ability to express a gene of interest in a spatio-temporal manner using Gal4-UAS system has allowed the use of Drosophila model to study various biological phenomenon. During Drosophila eye development, a synchronous wave of differentiation called Morphogenetic furrow (MF) initiates at the posterior margin resulting in differentiation of retinal neurons. This synchronous differentiation is also observed in the differentiating retina of vertebrates. Since MF is highly dynamic, it can serve as an excellent model to study patterning and differentiation. However, there are not any Gal4 drivers available to observe the gain- of- function or loss- of- function of a …

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 …

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 …

Advancing Behavioural Genomics By Considering Timescale, Clare C. Rittschof, Kimberly A. Hughes

Entomology Faculty Publications

Animal behavioural traits often covary with gene expression, pointing towards a genomic constraint on organismal responses to environmental cues. This pattern highlights a gap in our understanding of the time course of environmentally responsive gene expression, and moreover, how these dynamics are regulated. Advances in behavioural genomics explore how gene expression dynamics are correlated with behavioural traits that range from stable to highly labile. We consider the idea that certain genomic regulatory mechanisms may predict the timescale of an environmental effect on behaviour. This temporally minded approach could inform both organismal and evolutionary questions ranging from the remediation of early …

New Classification Of The Dictyostelids, Sanea Sheikh, Mats Thulin, James C. Cavender, Ricardo Escalante, Shin-Ichi Kawakami, Carlos Lado, John C. Landolt, Vidyanand Nanjundiah, David C. Queller, Joan E. Strassmann, Frederick W. Spiegel, Steven L. Stephenson, Eduardo M. Vadell, Sandra L. Baldauf

Biology Faculty Research

Traditional morphology-based taxonomy of dictyostelids is rejected by molecular phylogeny. A new classification is presented based on monophyletic entities with consistent and strong molecular phylogenetic support and that are, as far as possible, morphologically recognizable. All newly named clades are diagnosed with small subunit ribosomal RNA (18S rRNA) sequence signatures plus morphological synapomorphies where possible. The two major molecular clades are given the rank of order, as Acytosteliales ord. nov. and Dictyosteliales. The two major clades within each of these orders are recognized and given the rank of family as, respectively, Acytosteliaceae and Cavenderiaceae fam. nov. in Acytosteliales, and Dictyosteliaceae …

A Model Species For Agricultural Pest Genomics: The Genome Of The Colorado Potato Beetle, Leptinotarsa Decemlineata (Coleoptera: Chrysomelidae), Sean D. Schoville, Yolanda H. Chen, Martin N. Andersson, Joshua B. Benoit, Anita Bhandari, Julia H. Bowsher, Kristian Brevik, Kaat Cappelle, Mei-Ju M. Chen, Anna K. Childers, Christopher Childers, Olivier Christiaens, Justin Clements, Elise M. Didion, Elena N. Elpidina, Patamarerk Engsontia, Markus Friedrich, Inmaculada García-Robles, Richard A. Gibbs, Chandan Goswami, Alessandro Grapputo, Kristina Gruden, Marcin Grynberg, Bernard Henrissat, Emily C. Jennings, Jeffery W. Jones, Megha Kalsi, Sher A. Khan, Abhishek Kumar, Fei Li, Vincent Lombard, Subba Reddy Palli, June-Sun Yoon

Entomology Faculty Publications

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and …

A New Toolset For Protein Expression And Subcellular Localization Studies In Citrus And Its Application To Citrus Tristeza Virus Proteins, Amit Levy, Choaa El-Mochtar, Chunxia Wang, Michael M. Goodin, Vladimir Orbovic

Plant Pathology Faculty Publications

Background

Transient gene expression is a powerful tool to study gene function in plants. In citrus, Agrobacterium transformation is the method of choice for transient expression studies, but this method does not work efficiently with many gene constructs, and there is a need for a more robust transient expression system in citrus leaves. Biolistic particle delivery is an alternative to Agrobacterium transformation, and in some plants, such as Arabidopsis, gives higher transformation rates in leaf tissues than Agrobacterium.

Results

Here we describe an improved method for gene expression in epidermal cells of citrus leaves, using the Bio-Rad Helios gene-gun. …

Examination Of Orthologous Genes (Mrub_2518 And B3728, Mrub_2519 And B3727, Mrub_2520 And B3726, Mrub_2521 And B3725) Responsible For Abc Phosphate Transporters In Two Species M. Ruber And E. Coli, Margaret Meyer, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes b3725, b3726, b3727, b3728 and Mrub_2518, Mrub_2519, Mrub_2520 and Mrub_2521 (KEGG map number 02010). We predict that these genes encode the components of a Phosphate ABC transporter: Orthologous genes Mrub_2518 (DNA coordinates 2565359..2566438) and b3728 encodes the periplasmic phosphate binding component; Orthologous genes Mrub_2519 (DNA coordinates 2566499..2567485) and b3727, and Mrub_2520 (DNA coordinates 2567496..2568326) and b3726 encode for the two transmembrane proteins; Orthologous genes Mrub_2521 (DNA coordinates 2568338..2569159) and b3725 encode for the ATP binding protein within the cytoplasm. Within the two species, M. ruber and E. coli, …

Mrub_1325, Mrub_1326, Mrub_1327, And Mrub_1328 Are Orthologs Of B_3454, B_3455, B_3457, B_3458, Respectively Found In Escherichia Coli Coding For A Branched Chain Amino Acid Atp Binding Cassette (Abc) Transporter System, Bennett Tomlin, Adam Buric, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_1325, Mrub_1326, Mrub_1327, and Mrub_1328 (KEGG map number 02010). We predict these genes encode components of a Branched Chain Amino Acid ATP Binding Cassette (ABC) transporter: 1) Mrub_1325 (DNA coordinates 1357399-1358130 on the reverse strand) encodes the ATP binding domain; 2) Mrub_1326 (DNA coordinates 1358127-1359899 on the reverse strand) encodes the ATP-binding domain and permease domain; 3) Mrub_1327 (DNA coordinates 1359899-1360930 on the reverse strand) encodes a permease domain; and 4)Mrub_1328 (DNA coordinates 1711022-1712185 on the reverse strand) encodes the substrate binding domain. This system is not predicted to …

Predicted Ortholog Pairs Between E. Coli And M. Ruber Are B3456 And Mrub_2379, B3457 And Mrub_2378, B3456 And Mrub_2374, B3455 And Mrub_2376, And B3454 And Mrub2377, Which Each Code For Components Of A Prokaryotic-Type Abc Transporter For Branched-Chain Amino Acids, Elizabeth Paris, Tony Steinle, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_2379, Mrub_2378, Mrub_2374, Mrub_2376, and Mrub_2377 (KEGG map number 02010). We predict these genes encode components of a branched-chain amino acid ATP Binding Cassette (ABC) transporter: 1) Mrub_2374 (DNA coordinates 2424832-2425902 on the reverse strand) encodes one permease component (aka transmembrane domain); 2) Mrub_2378 (DNA coordinates 2429525-2430439 on the reverse strand) encodes the second permease component (aka transmembrane domain); 3) Mrub_2376 (DNA coordinates 2427858-2428613 on the reverse strand) encodes one of the ATP-binding domain (aka nucleotide binding domain); 4) Mrub_2377 (DNA coordinates 2428704-2429489 on the reverse strand) …

Mrub_1199 & Mrub_2272 Of Meiothermus Ruber Are Orthologous Genes To The B0262 Gene In Escherichia Coli While Mrub_1200, Mrub_1201, Mrub_2015 & Mrub_2271 Are Not Orthologous To The B0262 Gene Coding For The Iron (Fe3+) Abc Transport System, Kumail Hussain, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_1199, Mrub_1200, Mrub_1201, Mrub_2015, Mrub_2271 and Mrub_2272 (KEGG map number 02010). We predict these genes encode components of an Iron (Fe3+) ATP Binding Cassette (ABC) transporter: 1) Mrub_1199 (DNA coordinates [1211595-1212572] on the reverse strand) encodes the permease component (aka transmembrane domain); and 2) Mrub_1200 (DNA coordinates [1212612-1214093] on the reverse strand) encodes the ATP-binding domain (aka nucleotide binding domain); and 3) Mrub_1201 (DNA coordinates [1214347-1215309] on the reverse strand) encodes the substrate binding protein (aka the periplasmic component); and Mrub_2015 ( DNA coordinates [2053963-2054949] on the reverse strand) …