Genetics and Genomics Commons^™

Meiotic Dna Re-Replication And The Recombination Checkpoint, Nicole Ann Najor

Wayne State University Dissertations

Progression through meiosis occurs through a strict sequence of events, so that one round of DNA replication precedes programmed recombination and two nuclear divisions. Cyclin dependent kinase 1 (Cdk1) is required for meiosis, and any disruption in its activity leads to meiotic defects. The Cdk1 inhibitor, Sic1, regulates the G1-S transition in the mitotic cell cycle and the analogous transition in meiosis. We have employed a form of Sic1, Sic1deltaP^HA, that is mutated at multiple phosphorylation sites and resistant to degradation. Meiosis specific expression of Sic1deltaP^HA disrupts Cdk1 activity and leads to significant accumulation of over replicated …

Feed Intake Of Sheep As Affected By Body Weight, Breed, Sex, And Feed Composition, R. M. Lewis, G. C. Emmans

Department of Animal Science: Faculty Publications

The hypotheses tested were that genetic size-scaling for mature BW (A, kg) would reduce variation in intake between kinds of sheep and that quadratic polynomials on u = BW/A with zero intercept would provide good descriptions of the relationship between scaled intake (SI, g/A0.73 d) and degree of maturity in BW (u) across feeds of differing quality. Both sexes of Suffolk sheep from 2 experimental lines (n = 225) and from 3 breed types (Suffolk, Scottish Blackface, and their cross; n = 149) were recorded weekly for ad libitum feed intake and BW; recording of intake was from weaning through, …

A Candidate Subspecies Discrimination System Involving A Vomeronasal Receptor Gene With Different Alleles Fixed In M. M. Domesticus And M. M. Musculus, Robert C. Karn, Janet M. Young, Christina M. Laukaitis

Scholarship and Professional Work - LAS

Assortative mating, a potentially efficient prezygotic reproductive barrier, may prevent loss of genetic potential by avoiding the production of unfit hybrids (i.e., because of hybrid infertility or hybrid breakdown) that occur at regions of secondary contact between incipient species. In the case of the mouse hybrid zone, where two subspecies of Mus musculus (M. m. domesticus and M. m. musculus) meet and exchange genes to a limited extent, assortative mating requires a means of subspecies recognition. We based the work reported here on the hypothesis that, if there is a pheromone sufficiently diverged between M. m. domesticus and …

Biochemical Profiling Of Histone Binding Selectivity Of The Yeast Bromodomain Family, Qiang Zhang, Suvobrata Chakravarty, Dario Ghersi, Lei Zeng, Alexander N. Plotnikov, Roberto Sanchez, Ming-Ming Zhou

Interdisciplinary Informatics Faculty Publications

Background: It has been shown that molecular interactions between site-specific chemical modifications such as acetylation and methylation on DNA-packing histones and conserved structural modules present in transcriptional proteins are closely associated with chromatin structural changes and gene activation. Unlike methyl-lysine that can interact with different protein modules including chromodomains, Tudor and MBT domains, as well as PHD fingers, acetyl-lysine (Kac) is known thus far to be recognized only by bromodomains. While histone lysine acetylation plays a crucial role in regulation of chromatin-mediated gene transcription, a high degree of sequence variation of the acetyl-lysine binding site in the bromodomains has …

Dissecting The Biosyntheses Of Gilvocarcins And Ravidomycins, Madan Kumar Kharel

University of Kentucky Doctoral Dissertations

Gilvocarcin V (GV) and ravidomycin (RMV) exhibit excellent antitumor activities in the presence of near-UV light at low concentration maintaining a low in vivo cytotoxicity. Although, the exact molecular mechanism for in vivo actions of these antibiotics has yet to be determined, a [2+2] cycloaddition reaction of the vinyl side chain with DNA thymidine residues in addition to the inhibition of topoisomerase II and DNAhistone H3 cross-linking are reported for the GV’s mechanism of action. Such activities have made these molecules interesting candidates for the biosynthetic investigation to generate analogues with improved activity/solubility. Previous biosynthetic studies have suggested that the …

The Role Of Cuticle, Fatty Acids, And Lipid Signaling In Plant Defense, Ye Xia

Theses and Dissertations--Plant Pathology

Systemic acquired resistance (SAR) is initiated upon recognition of specific microbial effectors by cognate plant resistance proteins and immunizes distal tissues of plants against secondary infections. SAR involves the generation of a mobile signal at the site of primary infection, which then translocates to and activates defense responses in the distal tissues via some unknown mechanism(s). This study shows that an ACYL CARRIER PROTEIN 4 (ACP4), GLABRA1 (GL1) and ACYL CARRIER BINDING PROTEINS (ACBP) are required for the processing of the mobile SAR signal in distal tissues of Arabidopsis. Although acp4, gl1 and acbp plants generate the mobile signal, …

Sex, Mixability, And Modularity, Adi Livnat, Christos Papadimitriou, Nicholas Pippenger, Marcus W. Feldman

All HMC Faculty Publications and Research

The assumption that different genetic elements can make separate contributions to the same quantitative trait was originally made in order to reconcile biometry and Mendelism and ever since has been used in population genetics, specifically for the trait of fitness. Here we show that sex is responsible for the existence of separate genetic effects on fitness and, more generally, for the existence of a hierarchy of genetic evolutionary modules. Using the tools developed in the process, we also demonstrate that in terms of their fitness effects, separation and fusion of genes are associated with the increase and decrease of the …

Detection, Validation, And Downstream Analysis Of Allelic Variation In Gene Expression, Daniel C. Ciobanu, Lu Engle, Khyobeni Mozhui, Xusheng Wang, Manjunatha Jagalur, John A. Morris, William L. Taylor, Klaus Dietz, Perikles Simon, Robert W. Williams

Department of Animal Science: Faculty Publications

Common sequence variants within a gene often generate important differences in expression of corresponding mRNAs. This high level of local (allelic) control—or cis modulation—rivals that produced by gene targeting, but expression is titrated finely over a range of levels. We are interested in exploiting this allelic variation to study gene function and downstream consequences of differences in expression dosage. We have used several bioinformatics and molecular approaches to estimate error rates in the discovery of cis modulation and to analyze some of the biological and technical confounds that contribute to the variation in gene expression profiling. Our analysis of SNPs …

Strain Differences In Stress Responsivity Are Associated With Divergent Amygdala Gene Expression And Glutamate-Mediated Neuronal Excitability, Khyobeni Mozhui, Rose-Marie Karlsson, Thomas L. Kash, Jessica Ihne, Maxine Norcross, Sachin Patel, Mollee R. Farrell, Elizabeth E. Hill, Carolyn Graybeal, Kathryn P. Martin, Marguerite Camp, Paul J. Fitzgerald, Daniel C. Ciobanu, Rolf Sprengel, Masayoshi Mishina, Cara L. Wellman, Danny G. Winder, Robert W. Williams, Andrew Holmes

Department of Animal Science: Faculty Publications

Stress is a major risk factor for numerous neuropsychiatric diseases. However, susceptibility to stress and the qualitative nature of stress effects on behavior differ markedly among individuals. This is partly because of the moderating influence of genetic factors. Inbred mouse strains provide a relatively stable and restricted range of genetic and environmental variability that is valuable for disentangling gene–stress interactions. Here, we screened a panel of inbred strains for anxiety- and depression-related phenotypes at baseline (trait) and after exposure to repeated restraint. Two strains, DBA/2J and C57BL/6J, differed in trait and restraint-induced anxiety-related

behavior (dark/light exploration, elevated plus maze). Gene …

Srebp Pathway Genes As Candidate Markers In Country Ham Production, Benedicte Renaville, Kimberly L. Glenn, Benny E. Mote, Bin Fan, Kenneth J. Stalder, Max F. Rothschild

Department of Animal Science: Faculty Publications

Country hams are dry-cured products from the Southeastern region of the USA. This high value product requires quality fresh meat to avoid later processing problems. The marker SREBF1 is a transcription factor involved in the regulation of fatty acid synthesis and antioxidative enzyme transcription. The SREBF1 gene and its regulators, SCAP and MBTPS1, were investigated for associations with several meat quality traits in country hams. After single nucleotide polymorphism (SNP) identification, PCR-RFLP tests were designed for one polymorphism in each of the three investigated genes. Meat quality and physical traits were collected on 299 fresh hams. Significant associations were …

Plasmid Injection And Application Of Electric Pulses Alter Endogenous Mrna And Protein Expression In B16.F10 Mouse Melanomas, L. C. Heller, Y. L. Cruz, B. Ferraro, H. Yang, R. Heller

Bioelectrics Publications

The application of electric pulses to tissues causes cell membrane destabilization, allowing exogenous molecules to enter the cells. This delivery technique can be used for plasmid gene therapy. Reporter gene expression after plasmid delivery with eight representative published protocols was compared in B16.F10 mouse melanoma tumors. This expression varied significantly based on the pulse parameters utilized for delivery. To observe the possible influence of plasmid injection and/or pulse application on endogenous gene expression, levels of stress-related mRNAs 4 and 24 h after delivery were determined by PCR array. Increases in mRNA levels for several inflammatory chemokines and cytokines were observed …

Electroporation-Mediated Delivery Of A Naked Dna Plasmid Expressing Vegf To The Porcine Heart Enhances Protein Expression, W. G. Marshall Jr., B. A. Boone, J. D. Burgos, S. I. Gografe, M. K. Baldwin, M. L. Danielson, M. J. Larson, D. R. Caretto, Y. Cruz, B. Ferraro, L. C. Heller, K. E. Ugen, M. J. Jaroszeski, R. Heller

Bioelectrics Publications

Gene therapy is an attractive method for the treatment of cardiovascular disease. However, using current strategies, induction of gene expression at therapeutic levels is often inefficient. In this study, we show a novel electroporation (EP) method to enhance the delivery of a plasmid expressing an angiogenic growth factor (vascular endothelial growth factor, VEGF), which is a molecule previously documented to stimulate revascularization in coronary artery disease. DNA expression plasmids were delivered in vivo to the porcine heart with or without coadministered EP to determine the potential effect of electrically mediated delivery. The results showed that plasmid delivery through EP significantly …

Microarray Analysis Of Paramecium Bursaria Chlorella Virus 1 Transcription, Giane M. Yanai-Balser, Garry A. Duncan, James D. Eudy, Dong Wang, Xiao Li, Irina V. Agarkova, David D. Dunigan, James L. Van Etten

James Van Etten Publications

Paramecium bursaria chlorella virus 1 (PBCV-1), a member of the family Phycodnaviridae, is a large doublestranded DNA, plaque-forming virus that infects the unicellular green alga Chlorella sp. strain NC64A. The 330-kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To monitor global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDSs) was constructed. Competitive hybridization experiments were conducted by using cDNAs from poly(A)- containing RNAs obtained from cells at seven time points after virus infection. The results led to the following conclusions: (i) the PBCV-1 replication cycle is temporally …

The Differential Roles Of D-Pax2 Variants In Regulating Drosophila Eye And Bristle Development, Colin J. O’Shea

Honors Theses

The ability to appropriately interact with the environment is crucial to an organism’s survival. The establishment of functional sensory systems, such as the bristles and eyes in Drosophila, is a critical event during the development of the organism. The transcription factor D Pax2 is involved in the differentiation of the shaft and glial cells in the developing bristle (Kavaler et al., Dev, 126:2261-2272, 1999) and of the cone and primary pigment cells in the developing eye (Fu and Noll, Genes Dev, 11:389-405, 1997). How D-Pax2 contributes to distinct differentiative pathways in different cell types is not known. Recent work by …

Web-Based, Participant-Driven Studies Yield Novel Genetic Associations For Common Traits, Nicholas Eriksson, J. Michael Macpherson, Joyce Y. Tung, Lawrence S. Hon, Brian Naughton, Serge Saxonov, Linda Avey, Anne Wojcicki, Itsik Pe'er, Joanna Mountain

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Despite the recent rapid growth in genome-wide data, much of human variation remains entirely unexplained. A significant challenge in the pursuit of the genetic basis for variation in common human traits is the efficient, coordinated collection of genotype and phenotype data. We have developed a novel research framework that facilitates the parallel study of a wide assortment of traits within a single cohort. The approach takes advantage of the interactivity of the Web both to gather data and to present genetic information to research participants, while taking care to correct for the population structure inherent to this study design. Here …

Development Of Protocols For Tissue Culture And Mutagenesis In Two Variegated Sansevieria Sp., Irmawati Akma Abdul Hapiz

Student Works (2010-2019)

Studies were conducted to develop the tissue culture protocol and mutagenesis through Gamma ray irradiation for two variegated Sansevieria species known as Sansevieria trifasciata var. Laurentii (goldband Sansevieria) and Sansevieria trifasciata var. Hahnii (birdnest Sansevieria). Seven combinations of BAP and NAA were chosen which are represented by letter A= 1.00 mg/I BAP, B = 1.00 mg/I BAP + 0.25 mg/I NAA, C = 2.00 mg/I BAP + 0.50 mg/I NAA, D = 2.00 mg/I BAP + 1.00 mg/I NAA, E = 3.00 mg/I BAP + 1.00 mg/I NAA, F = 4.00 mg/I BAP + 1.00 mg/I NAA and G = …

Molecular Identification Of Arowana Species Based On Cytochrome B And Cytochrome C Oxidase I (Coi) / Maryam Zahedi Fard, Maryam Zahedi Fard

Student Works (2010-2019)

Mitochondrial DNA (mtDNA) markers has been widely used to better resolve the taxonomic identification as well as display the genetic relatedness of different species and closely related fish. The highly cost ornamental fish, Asian arowana (Scleropages formosus) of family Osteoglossidae has different colored strains that are geographically distributed in different regions around Southeast Asia. The taxonomic classification of these different strains still remains unclear and disputable. The partial sequences of the cytochrome b and the DNA barcoding gene, cytochrome C oxidase were analyzed and assessed for molecular identification; to differentiate the colored varieties of this species. The results of this …

Group Ii Intron Dynamics In Heterologous Hosts, Venkata Raghavendra Aditya Chalamcharla

Legacy Theses & Dissertations (2009 - 2024)

Group II introns are ribozymes with an innate ability to self-splice. They are found predominantly in bacterial and bacterial-derived organellar genomes, but not in the nuclear genomes of eukaryotes. In bacteria, group II introns often behave as mobile retroelements, invading host DNA and exploiting its machinery to complete the retromobility process. The object of my studies is the group II intron found in the Lactococcus lactis relaxase gene. To determine the nature of the group II intron-host relationship, we performed a genetic screen and identified several host factors that affect group II intron retromobility in Escherichia coli, which provides a …

Stratifin Is Redundant In Cell Cycle Regulation But Essential For The Translational Control During Skin Development, Fang Liu

Legacy Theses & Dissertations (2009 - 2024)

Three phenotypically similar mouse mutations that cause severe defects in skin terminal differentiation have been identified in stratifin (Sfn, also known as 14-3-3σ), I-Kappa Kinase alpha (IKKα) and Interleukin regulatory factor 6 (Irf6). IKKα and Irf6 have been proposed to regulate skin differentiation at the level of transcription. Sfn has been studied intensively as a negative cell cycle regulator during DNA damage response; however, its role in skin development has not been fully characterized.

Chlorella Viruses Encode Most, If Not All, Of The Machinery To Glycosylate Their Glycoproteins Independent Of The Endoplasmic Reticulum And Golgi, James L. Van Etten, James Gurnon, Giane M. Yanai-Balser, David Dunigan, Michael V. Graves

Nebraska Center for Virology: Faculty Publications

In contrast to all other viruses that use the host machinery located in the endoplasmic reticulum and Golgi to glycosylate their glycoproteins, the large dsDNA-containing chlorella viruses encode most, if not all, of the components to glycosylate their major capsid proteins. Furthermore, all experimental results indicate that glycosylation occurs independent of the endoplasmic reticulum and Golgi. (Review article)

The Drosophila Homolog Of The Mammalian Imprint Regulator, Ctcf, Maintains The Maternal Genomic Imprint In Drosophila Melanogaster, William A. Macdonald, Debashish Menon, Nicholas J. Bartlett, G Elizabeth Sperry, Vanya Rasheva, Victoria Meller, Vett K. Lloyd

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

CTCF is a versatile zinc finger DNA-binding protein that functions as a highly conserved epigenetic transcriptional regulator. CTCF is known to act as a chromosomal insulator, bind promoter regions, and facilitate long-range chromatin interactions. In mammals, CTCF is active in the regulatory regions of some genes that exhibit genomic imprinting, acting as insulator on only one parental allele to facilitate parent-specific expression. In Drosophila, CTCF acts as a chromatin insulator and is thought to be actively involved in the global organization of the genome.

Results

To determine whether CTCF regulates imprinting in Drosophila, we generated CTCF mutant alleles …

Functional Analysis Of B And C Class Floral Organ Genes In Spinach Demonstrates Their Role In Sexual Dimorphism, D Noah Sather, Maja Jovanovic, Edward M. Golenberg

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Evolution of unisexual flowers entails one of the most extreme changes in plant development. Cultivated spinach, Spinacia oleracea L., is uniquely suited for the study of unisexual flower development as it is dioecious and it achieves unisexually by the absence of organ development, rather than by organ abortion or suppression. Male staminate flowers lack fourth whorl primordia and female pistillate flowers lack third whorl primordia. Based on theoretical considerations, early inflorescence or floral organ identity genes would likely be directly involved in sex-determination in those species in which organ initiation rather than organ maturation is regulated. In this …

The Role Of Mitochondria In The Radiation-Induced Bystander Effect In Human Lymphoblastoid Cells, Sountharia Rajendran

Wayne State University Theses

This work evaluated the radiation-induced bystander effect in mitochondrial mutant cells and in normal cells treated with mitochondrial inhibitors. Although much research has been performed on the bystander effect, the underlying molecular mechanisms remain largely unknown. Cells without intact mitochondrial DNA have been shown to lack the bystander effect, which is an energy-dependent process. Based on these findings, cells harboring mutations in the mitochondrial genes responsible for ATP synthesis, and normal cells treated with mitochondrial inhibitors, were hypothesized to show a decreased bystander effect when compared to normal cells that were not treated with the mitochondrial inhibitors.

Radiation-induced bystander effects …

Towards An Understanding Of The Etiology Of Abdominal Aortic Aneurysms: Identification Of Genes Implicated In Aaa Risk And Development, John Hunt Lillvis

Wayne State University Dissertations

Abdominal aortic aneurysm (AAA) is a common disease for which mechanisms of formation are still not well understood. Despite a strong genetic component to AAA risk, specific risk alleles are still largely unidentified. AAA is also a localized disease with a majority occurring in the infrarenal abdominal aorta and is six times more common than aneurysms of the thoracic aorta. To determine whether risk alleles are present in functional positional candidate genes. we: 1. performed a genetic association study using DNA from AAA cases and controls in ten candidate genes and 2. performed exon sequencing on three genes with evidence …

Ancient Dna Analyses Exclude Humans As The Driving Force Behind Late Pleistocene Musk Ox (Ovibos Moschatus) Population Dynamics, Paula F. Campos, Eske Willerslev, Andrei Sher, Ludovic Orlando, Erik Axelsson, Alexei Tikhonov, Kim Aaris-Sorensen, Alex D. Greenwood, Ralf-Dietrich Kahlke, Pavel Kosintsev

Biological Sciences Faculty Publications

The causes of the late Pleistocene megafaunal extinctions are poorly understood. Different lines of evidence point to climate change, the arrival of humans, or a combination of these events as the trigger. Although many species went extinct, others, such as caribou and bison, survived to the present. The musk ox has an intermediate story: relatively abundant during the Pleistocene, it is now restricted to Greenland and the Arctic Archipelago. In this study, we use ancient DNA sequences, temporally unbiased summary statistics, and Bayesian analytical techniques to infer musk ox population dynamics throughout the late Pleistocene and Holocene. Our results reveal …

An Intelligent Data-Centric Approach Toward Identification Of Conserved Motifs In Protein Sequences, Kathryn Dempsey Cooper, Benjamin Currall, Richard Hallworth, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

The continued integration of the computational and biological sciences has revolutionized genomic and proteomic studies. However, efficient collaboration between these fields requires the creation of shared standards. A common problem arises when biological input does not properly fit the expectations of the algorithm, which can result in misinterpretation of the output. This potential confounding of input/output is a drawback especially when regarding motif finding software. Here we propose a method for improving output by selecting input based upon evolutionary distance, domain architecture, and known function. This method improved detection of both known and unknown motifs in two separate case studies. …

Density Based Pruning For Identification Of Differentially Expressed Genes From Microarray Data, Jianjun Hu, J. Xu

Faculty Publications

Motivation

Identification of differentially expressed genes from microarray datasets is one of the most important analyses for microarray data mining. Popular algorithms such as statistical t-test rank genes based on a single statistics. The false positive rate of these methods can be improved by considering other features of differentially expressed genes.

Results

We proposed a pattern recognition strategy for identifying differentially expressed genes. Genes are mapped to a two dimension feature space composed of average difference of gene expression and average expression levels. A density based pruning algorithm (DB Pruning) is developed to screen out potential differentially expressed genes usually …

Using Jackknife To Assess The Quality Of Gene Order Phylogenies, Jian Shi, Yiwei Zhang, Haiwei Luo, Jijun Tang

Faculty Publications

Background
In recent years, gene order data has attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. If gene orders are viewed as one character with a large number of states, traditional bootstrap procedures cannot be applied. Researchers began to use a jackknife resampling method to assess the quality of gene order phylogenies.

Results
In this paper, we design and conduct a set of experiments to validate the performance of this jackknife procedure and provide discussions on how to conduct it properly. Our results show that jackknife is very useful to …

Insights Into Genome Functional Organisation Through The Analysis Of Interaction Networks, Andre Masella

Theses and Dissertations (Comprehensive)

Using computational techniques to identify orthology and operon structure, it is possible to find functional interactions between genes, which, together, define the genetic interactome. These large networks contain information about the relationships between phenotypes in organisms as genes responsible for related abilities are often co-regulated and reasserting of these genes can be detected in the operon structure. However, these networks are too large to analyse by hand In order to practically analyse the networks, a computational tool, gisql, was developed and, using this tool, the connectivity patterns in the genetic interactome can be analysed to understand high-level organisation of …

Isolation And Characterization Of Microsatellite Loci From Wild Striped Snakehead (Channa Striata)., Yasmeen Sameer Mahmoud Salah

Student Works (2010-2019)

Channa striata (better known as Haruan in Malaysia), is a freshwater species that is well known as a protein source and also for its pharmaceutical value among wounded patients. Unfortunately stocks have declined over the past few years, thus an in-depth study is needed to rule out genetic irregularities that might be causing the slow extinction of the species. This study was conducted for the purpose of studying the population diversity and genetic structure of Channa striata (striped snakehead) in seven different locations around the peninsular of Malaysia. Microsatellite markers were isolated and identified using Random Amplified Microsatellite (RAM) primers. …