Genetics and Genomics Commons^™

Characterization Of Bacterial Communities In Biscayne Bay Through Genomic Analysis, Eric Fortman

HCNSO Student Theses and Dissertations

Biscayne Bay is a shallow oligotrophic estuary in Southeast Florida. Channelization of rivers, and dredging of canals has greatly altered the historical flow of fresh water into the bay. This, coupled with the rise of a sprawling urban & suburban development, has greatly increased the nutrient load in the bay. This study examined the bacterial community at 14 stations throughout Biscayne Bay —6 stations were located at the mouths of canals; 1 upstream-canal station; 6 stations in the center of the bay; and one ocean influenced station, located near the entrance to the bay. One liter, surface water samples were …

Two Fields, One Pellet: Combining Demographics And Population Genetics Through Non-Invasive Sampling Of Snowshoe Hare Fecal Pellets In Michigan., Genelle Nicole Uhrig

Theses and Dissertations

As climate continues to change at a rapid rate, species are increasingly vulnerable to the resulting environmental changes. This is especially true for species whose fitness is closely linked to climate-associated environmental conditions. One of these vulnerable species is snowshoe hare, Lepus americanus, who depends on the timing and duration of snowfall to provide camouflage when they go through seasonal pelage changes from brown in the summer to white in the winter. Whereas snowshoe hare are stable across the core of their range, populations along the southern range edge are experiencing declines due to climate driven environmental changes that cause …

Overlap Matrix Completion For Predicting Drug-Associated Indications, Menhyun Yang, Huimin Luo, Yaohang Li, Fang-Xiang Wu, Jianxin Wang

Computer Science Faculty Publications

Identification of potential drug-associated indications is critical for either approved or novel drugs in drug repositioning. Current computational methods based on drug similarity and disease similarity have been developed to predict drug-disease associations. When more reliable drug- or disease-related information becomes available and is integrated, the prediction precision can be continuously improved. However, it is a challenging problem to effectively incorporate multiple types of prior information, representing different characteristics of drugs and diseases, to identify promising drug-disease associations. In this study, we propose an overlap matrix completion (OMC) for bilayer networks (OMC2) and tri-layer networks (OMC3) to predict potential drug-associated …

Inferred Function And Dynamics Of Microbial Communities From The Northern Gulf Of Mexico, Deepesh Tourani

HCNSO Student Theses and Dissertations

Microbial communities, or microbiomes, are the major drivers of global biogeochemical cycles, acting as primary producers and decomposers across the water column in the oceans. Thus, they reflect changes in physicochemical properties and nutrient composition of the ocean. However, this correlation between ecological changes and the function of marine microbiomes is poorly understood. Large-scale oceanic events such as the bottom-water oxygen-depleted zone (i.e., “dead zone”) and the Deepwater Horizon oil spill in the Gulf of Mexico (GoM) render the ecosystem fragile. These events decrease survival rates of pelagic and coastal macrofauna and affect the biodiversity of the region. As part …

Sdrap: An Annotation Pipeline For Highly Scrambled Genomes, Jasper Braun

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Network Structure And Dynamics Of Biological Systems, Deena R. Schmidt

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Loop Homology Of Bi-Secondary Structures, Andrei Bura

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Quantifying Pollen Traits To Build A Mathematical Model Of Pollen Competition - A Biologist's Perspective, Rob Swanson, Alex Capaldi

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Topology And Dynamics Of Gene Regulatory Networks: A Meta-Analysis, Claus Kadelka

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Acute Systemic Inflammatory Response To Lipopolysaccharide Stimulation In Pigs Divergently Selected For Residual Feed Intake, Haibo Liu, Kristina M. Feye, Yet T. Nguyen, Anoosh Rakhshandeh, Crystal L. Loving, Jack C. M. Sekkers, Nicholas K. Gabler, Christopher K. Tuggle

Mathematics & Statistics Faculty Publications

Background: It is unclear whether improving feed efficiency by selection for low residual feed intake (RFI) compromises pigs’ immunocompetence. Here, we aimed at investigating whether pig lines divergently selected for RFI had different inflammatory responses to lipopolysaccharide (LPS) exposure, regarding to clinical presentations and transcriptomic changes in peripheral blood cells.

Results: LPS injection induced acute systemic inflammation in both the low-RFI and high-RFI line (n = 8 per line). At 4 h post injection (hpi), the low-RFI line had a significantly lower (p= 0.0075) mean rectal temperature compared to the high-RFI line. However, no significant differences in complete blood count …

9th Annual Postdoctoral Science Symposium, University Of Texas Md Anderson Cancer Center Postdoctoral Association

Annual Postdoctoral Science Symposium Abstracts

The mission of the Annual Postdoctoral Science Symposium (APSS) is to provide a platform for talented postdoctoral fellows throughout the Texas Medical Center to present their work to a wider audience. The MD Anderson Postdoctoral Association convened its inaugural Annual Postdoctoral Science Symposium (APSS) on August 4, 2011.

The APSS provides a professional venue for postdoctoral scientists to develop, clarify, and refine their research as a result of formal reviews and critiques of faculty and other postdoctoral scientists. Additionally, attendees discuss current research on a broad range of subjects while promoting academic interactions and enrichment and developing new collaborations.

Nitric Oxide Is Involved In Heavy Ion-Induced Non-Targeted Effects In Human Fibroblasts, Megumi Hada, Premkumar B. Saganti, Francis A. Cucinotta

Health Physics & Diagnostic Sciences Faculty Publications

Previously, we investigated the dose response for chromosomal aberration (CA) for exposures corresponding to less than one particle traversal per cell nucleus by high energy and charge (HZE) particles, and showed that the dose responses for simple exchanges for human fibroblast irradiated under confluent culture conditions were best fit by non-linear models motivated by a non-targeted effect (NTE). Our results suggested that the simple exchanges in normal human fibroblasts have an important NTE contribution at low particle fluence. Nitric oxide (NO) has been reported as a candidate for intercellular signaling for NTE in many studies. In order to estimate the …

Effective Statistical Energy Function Based Protein Un/Structure Prediction, Avdesh Mishra

University of New Orleans Theses and Dissertations

Proteins are an important component of living organisms, composed of one or more polypeptide chains, each containing hundreds or even thousands of amino acids of 20 standard types. The structure of a protein from the sequence determines crucial functions of proteins such as initiating metabolic reactions, DNA replication, cell signaling, and transporting molecules. In the past, proteins were considered to always have a well-defined stable shape (structured proteins), however, it has recently been shown that there exist intrinsically disordered proteins (IDPs), which lack a fixed or ordered 3D structure, have dynamic characteristics and therefore, exist in multiple states. Based on …

Association Of Copy Number Variations With Chronic Hepatitis B In Chinese Population, Fang Niu

Capstone Experience

With one third of the Hepatitis B virus (HBV) infection population of the world, chronic Hepatitis B (CHB) has become a top burden in China. CHB is a lifelong infection with HBV which can cause serious health problems, like cirrhosis, liver cancer or even death. HBV infection is known to result in various clinical conditions, including asymptomatic HBV carriers to chronic hepatitis and primary hepatocellular carcinoma. Several studies have shown that host genetic susceptibility could be an important factor that determines these various outcomes of HBV infection. Many Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs) have been associated …

Using Hidden Markov Modeling For Biogeographical Ancestry Analysis, Melvin R. Currie

Journal of Humanistic Mathematics

This paper describes a methodology for analyzing X-chromosome data to establish biogeographical contributions to the author’s X chromosome. We present an exposition of how Hidden Markov Modeling (HMM) can be used as a black box for ancestry analysis and focus on a set of conditions that are not universal but fairly common. The first condition is that the ancestral populations are drawn from regions that have had very little or no contact with each other since prehistoric times. The second condition is that the number of possible ancestral populations is small. In this analysis, we assume that the ancestral populations …

Hierarchical Modeling And Differential Expression Analysis For Rna-Seq Experiments With Inbred And Hybrid Genotypes, Andrew Lithio, Dan Nettleton

Dan Nettleton

The performance of inbred and hybrid genotypes is of interest in plant breeding and genetics. High-throughput sequencing of RNA (RNA-seq) has proven to be a useful tool in the study of the molecular genetic responses of inbreds and hybrids to environmental stresses. Commonly used experimental designs and sequencing methods lead to complex data structures that require careful attention in data analysis. We demonstrate an analysis of RNA-seq data from a split-plot design involving drought stress applied to two inbred genotypes and two hybrids formed by crosses between the inbreds. Our generalized linear modeling strategy incorporates random effects for whole-plot experimental …

Root Type-Specific Reprogramming Of Maize Pericycle Transcriptomes By Local High Nitrate Results In Disparate Lateral Root Branching Patterns, Peng Yu, Jutta A. Baldauf, Andrew Lithio, Caroline Marcon, Dan Nettleton, Chunjian Li, Frank Hochholdinger

Dan Nettleton

The adaptability of root system architecture to unevenly distributed mineral nutrients in soil is a key determinant of plant performance. The molecular mechanisms underlying nitrate dependent plasticity of lateral root branching across the different root types of maize are only poorly understood. In this study, detailed morphological and anatomical analyses together with cell type-specific transcriptome profiling experiments combining laser capture microdissection with RNA-seq were performed to unravel the molecular signatures of lateral root formation in primary, seminal, crown, and brace roots of maize (Zea mays) upon local high nitrate stimulation. The four maize root types displayed divergent branching …

Genomic Neighborhoods For Arabidopsisretrotransposons: A Role For Targeted Integration In The Distribution Of The Metaviridae, Brooke D. Peterson-Burch, Dan Nettleton, Daniel F. Voytas

Dan Nettleton

Background: Retrotransposons are an abundant component of eukaryotic genomes. The high quality of the Arabidopsis thaliana genome sequence makes it possible to comprehensively characterize retroelement populations and explore factors that contribute to their genomic distribution.

Results: We identified the full complement of A. thaliana long terminal repeat (LTR) retroelements using RetroMap, a software tool that iteratively searches genome sequences for reverse transcriptases and then defines retroelement insertions. Relative ages of full-length elements were estimated by assessing sequence divergence between LTRs: the Pseudoviridae were significantly younger than the Metaviridae. All retroelement insertions were mapped onto the genome sequence and their distribution …

Gene Expression Profiling In Salmonella Choleraesuis-Infected Porcine Lung Using A Long Oligonucleotide Microarray, Shu-Hong Zhao, Daniel Kuhar, Joan K. Lunney, Harry Dawson, Catherine Guidry, Jolita J. Uthe, Shawn M. D. Bearson, Justin Recknor, Dan Nettleton, Christopher K. Tuggle

Dan Nettleton

Understanding the transcriptional response to pathogenic bacterial infection within food animals is of fundamental and applied interest. To determine the transcriptional response to Salmonella enterica serovar Choleraesuis (SC) infection, a 13,297-oligonucleotide swine array was used to analyze RNA from control, 24-h postinoculation (hpi), and 48-hpi porcine lung tissue from pigs infected with SC. In total, 57 genes showed differential expression (p < 0.001; false discovery rate = 12%). Quantitative real-time PCR (qRT-PCR) of 61 genes was used to confirm the microarray results and to identify pathways responding to infection. Of the 33 genes identified by microarray analysis as differentially expressed, 23 were confirmed by qRT-PCR results. A novel finding was that two transglutaminase family genes (TGM1 and TGM3) showed dramatic increases in expression postinoculation; combined with several other apoptotic genes, they indicated the induction of apoptotic pathways during SC infection. A predominant T helper 1-type immune response occurred during infection, with interferon …

Laser Microdissection Of Narrow Sheath Mutant Maize Uncovers Novel Gene Expression In The Shoot Apical Meristem, Xiaolan Zhang, Shahinez Madi, Lisa Borsuk, Dan Nettleton, Robert J. Elshire, Brent Buckner, Diane Janick-Buckner, Jon Beck, Marja Timmermans, Patrick S. Schnable, Michael J. Scanlon

Dan Nettleton

Microarrays enable comparative analyses of gene expression on a genomic scale, however these experiments frequently identify an abundance of differentially expressed genes such that it may be difficult to identify discrete functional networks that are hidden within large microarray datasets. Microarray analyses in which mutant organisms are compared to nonmutant siblings can be especially problematic when the gene of interest is expressed in relatively few cells. Here, we describe the use of laser microdissection microarray to perform transcriptional profiling of the maize shoot apical meristem (SAM), a ~100-μm pillar of organogenic cells that is required for leaf initiation. Microarray analyses …

Scanning Microarrays At Multiple Intensities Enhances Discovery Of Differentially Expressed Genes, David S. Skibbe, Xiujuan Wang, Xuefeng Zhao, Lisa A. Borsuk, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Motivation: Scanning parameters are often overlooked when optimizing microarray experiments. A scanning approach that extends the dynamic data range by acquiring multiple scans of different intensities has been developed.

Results: Data from each of three scan intensities (low, medium, high) were analyzed separately using multiple scan and linear regression approaches to identify and compare the sets of genes that exhibit statistically significant differential expression. In the multiple scan approach only one-third of the differentially expressed genes were shared among the three intensities, and each scan intensity identified unique sets of differentially expressed genes. The set of differentially expressed genes from …

Microarray Gene Expression Profiles Of Fasting Induced Changes In Liver And Adipose Tissues Of Pigs Expressing The Melanocortin-4 Receptor D298n Variant, Sender Lkhagvadorj, Long Qu, Weiguo Cai, Oliver P. Coutoure, C. Richard Barb, Gary J. Hausman, Dan Nettleton, Lloyd L. Anderson, Jack C. M. Dekkers, Christopher K. Tuggle

Dan Nettleton

Transcriptional profiling coupled with blood metabolite analyses were used to identify porcine genes and pathways that respond to a fasting treatment or to a D298N missense mutation in the melanocortin-4 receptor (MC4R) gene. Gilts (12 homozygous for D298 and 12 homozygous for N298) were either fed ad libitum or fasted for 3 days. Fasting decreased body weight, backfat, and serum urea concentration and increased serum nonesterified fatty acid. In response to fasting, 7,029 genes in fat and 1,831 genes in liver were differentially expressed (DE). MC4R genotype did not significantly affect gene expression, body weight, backfat depth, or any measured …

Analysis Of Porcine Transcriptional Response To Salmonella Enterica Serovar Choleraesuis Suggests Novel Targets Of Nfkappab Are Activated In The Mesenteric Lymph Node, Yanfang Wang, Olivre P. Couture, Long Qu, Jolita J. Uthe, Shawn M. D. Bearson, Daniel Kuhar, Joan K. Lunney, Dan Nettleton, Jack C. M. Dekkers, Christopher K. Tuggle

Dan Nettleton

Background: Specific knowledge of the molecular pathways controlling host-pathogen interactions can increase our understanding of immune response biology as well as provide targets for drug development and genetic improvement of disease resistance. Toward this end, we have characterized the porcine transcriptional response to Salmonella enterica serovar Choleraesuis (S. Choleraesuis), a Salmonella serovar that predominately colonizes swine, yet can cause serious infections in human patients. Affymetrix technology was used to screen for differentially expressed genes in pig mesenteric lymph nodes (MLN) responding to infection with S. Choleraesuis at acute (8 hours (h), 24 h and 48 h post-inoculation (pi)) and chronic …

Distinct Peripheral Blood Rna Responses To Salmonella In Pigs Differing In Salmonella Shedding Levels: Intersection Of Ifng, Tlr And Mirna Pathways, Ting-Hua Huang, Jolita J. Uthe, Shawn M. D. Bearson, Cumhur Yusuf Demirkale, Dan Nettleton, Susan Knetter, Curtis Christian, Amanda E. Ramer-Tait, Michael J. Wannemeuhler, Christopher K. Tuggle

Dan Nettleton

Transcriptomic analysis of the response to bacterial pathogens has been reported for several species, yet few studies have investigated the transcriptional differences in whole blood in subjects that differ in their disease response phenotypes. Salmonella species infect many vertebrate species, and pigs colonized with Salmonella enterica serovar Typhimurium (ST) are usually asymptomatic, making detection of these Salmonella-carrier pigs difficult. The variable fecal shedding of Salmonella is an important cause of foodborne illness and zoonotic disease. To investigate gene pathways and biomarkers associated with the variance in Salmonellashedding following experimental inoculation, we initiated the first analysis of the whole …

Unique Genome-Wide Transcriptome Profiles Of Chicken Macrophages Exposed To Salmonella-Derived Endotoxin, Ceren Ciraci, Christopher K. Tuggle, Michael J. Wannemeuhler, Dan Nettleton, Susan J. Lamont

Dan Nettleton

Background: Macrophages play essential roles in both innate and adaptive immune responses. Bacteria require endotoxin, a complex lipopolysaccharide, for outer membrane permeability and the host interprets endotoxin as a signal to initiate an innate immune response. The focus of this study is kinetic and global transcriptional analysis of the chicken macrophage response to in vitro stimulation with endotoxin from Salmonella typhimurium-798.

Results: The 38535-probeset Affymetrix GeneChip Chicken Genome array was used to profile transcriptional response to endotoxin 1, 2, 4, and 8 hours post stimulation (hps). Using a maximum FDR (False Discovery Rate) of 0.05 to declare genes as differentially …

Complementation Contributes To Transcriptome Complexity In Maize (Zea Mays L.) Hybrids Relative To Their Inbred Parents, Anja Paschold, Yi Jia, Caroline Marcon, Steve Lund, Nick B. Larson, Cheng-Ting Yeh, Stephan Ossowski, Christa Lanz, Dan Nettleton, Patrick S. Schnable, Frank Hochholdinger

Dan Nettleton

Typically, F₁-hybrids are more vigorous than their homozygous, genetically distinct parents, a phenomenon known as heterosis. In the present study, the transcriptomes of the reciprocal maize (Zea mays L.) hybrids B73×Mo17 and Mo17×B73 and their parental inbred lines B73 and Mo17 were surveyed in primary roots, early in the developmental manifestation of heterotic root traits. The application of statistical methods and a suitable experimental design established that 34,233 (i.e., 86%) of all high-confidence maize genes were expressed in at least one genotype. Nearly 70% of all expressed genes were differentially expressed between the two parents and 42%–55% …

Comparative Efficacy Of Novel Endolysins In Queso Fresco, Daniella Smith, Maxwell J. Holle, Dr. Michael Miller

PRECS student projects

Listeria monocytogenes is problematic for the manufacturing, storage, and consumption of ready-to-eat foods. This bacterium may cause listeriosis upon consumption often with deadly complications. Queso Fresco (QF), a pasteurized Hispanic-style fresh cheese (HSFC), has been shown to support the growth of L. monocytogenes. QF is the most widely produced and implicated HSFC in the U.S., representing a significant health hazard to at risk populations such as infants, pregnant women, elderly, and the immunocompromised. The objective of this research project is to evaluate the efficacy of ten novel antimicrobial endolysins in combatting L. monocytogenes contamination in a miniaturized lab-scale queso fresco …

Stress Induced Remodeling In The Nematode C. Elegans, Becky Rose, Rebecca Androwski, Nathan E. Schroeder

PRECS student projects

Caenorhabditis elegans is a model organism for studying genetics and neuroscience C. elegans is frequently studied to understand how genes and the environment interact to produce new phenotypes. We take advantage of an organism-wide stress response and genetic tools that provide an excellent model for studying how phenotypes are impacted by stress.

Verification Of Successful Kainic Acid Injections In A Temporal Lobe Epilepsy Mouse Model, Adrian J. Garcia, Robbie J. Ingram, Catherine A. Christian

PRECS student projects

Temporal lobe epilepsy (TLE) is the most prominent form of partial epilepsy in adults. Reproductive endocrine comorbidities appear in patients with TLE at significantly higher rates than in the general population. These comorbidities include polycystic ovary syndrome, hypothalamic amenorrhea, hyperandrogenism, irregular menstrual cycle, lower testosterone levels, hypogonadism, erectile dysfunction, and decreased semen motility. It is believed that gonadotropin-releasing hormone (GnRH) neurons in the hypothalamus play an important role in the development of these comorbidities. The kainic acid (KA) mouse model is used to study epilepsy-associated changes in GnRH neurophysiology. Our lab recently observed that the activity of GnRH neurons is …

Fungal Endophytes Interact With Endophytic Yeast Isolated From Soybean Leaves, Baldemar Basurto, Natalie Christian, Katy Heath

PRECS student projects

Endophytes (endo = inside and phyte=plant) are microscopic fungi that live inside of the leaves of all species of plants and can have beneficial effects on their hosts. Previous work in our lab has shown a significant decrease of Sporobolomyces sp., an endophytic yeast, within soybean hosts exposed to elevated levels of CO₂. Sporobolomyces sp. has certain properties to enable them to act as natural biocontrol agents. This pink yeast may have untapped potential to protect crops from pathogenic organisms. If Sporobolomyces sp. interacts with fungal pathogens, it may have strong effects on other fungal endophytes in the community. The …