Genetics and Genomics Commons^™

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 …

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 …

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 …

Direct Impacts Of Heat Stress On Illinois Soybeans, Jessica O'Connor, Charles Burroughs, Lisa Ainsworth

PRECS student projects

Rising global temperatures are challenging agricultural productivity and can affect soybean yield through many physiological and metabolic processes. Recent regression analyses indicate that soybean yield is depressed in warmer years. This research aims to help determine which processes are affected by heat stress, such as photosynthesis, plant development, leaf area index and yield. The experiment consists of two different varieties of commercial Illinois soybeans, which will be continually heated throughout the growing season in order to compare the physiological characteristics of the soybeans in the heated arrays to those growing in ambient conditions. Data collected on photosynthesis, plant development, leaf …

Effects Of Mycorrhizae On Struvite Dissolution Can Plant-Fungus Mutualism Increase The Viability Of A Sustainable Phosphorus Fertilizer?, Isako Battista Di Tomassi, Erinn Dady, Neha Chatterjee, Andrew Margenot

PRECS student projects

Phosphorus (P) is essential for all organisms. In agriculture, P, nitrogen (N) and potassium (K) are applied in large amounts as fertilizer. Monoammonium phosphate (MAP), a conventional fertilizer, is highly water soluble, causing high P and N concentrations in agricultural runoff, harming aquatic life. Struvite (NH4MgPO4 ·6H2O), a waste-water derived product with potential for use as a P fertilizer; has low water solubility, and phosphorus in struvite is not as accessible to plants as it is in MAP. Arbuscular mycorrhizal fungi (AMF) form mutualisms in which they receive carbon from plants in exchange for other nutrients, and assist in P …

Plasticity Or Local Adaptation?: Survival Of L. Parva Larvae In Varying Salinity, Kaitlyn Cortez, Lauren Mcdaniel, Becky Fuller

PRECS student projects

As environmental stressors continue to amplify, Lucania parva, or Rainwater Killifish, are expected to outlast other species in unpredictably fast changing environments, as they are unique in their ability to tolerate multiple salinities. The objective of this research is to understand what affects L. parva’s ability to tolerate salinity and discover the limitations the species might have to tolerating it. Understanding this fish’s biology will help with the conservation of aquatic ecosystems in Florida. Preliminary data and early trends suggest that during early larval stages, L. parva are plastic but the extent of their plasticity is limited as they cannot …

Construction Of A Tn5 Mutant Library In Xanthomonas Cucurbitae, Keirsten Kline, Rikky Rai, Sarah R. Hind

PRECS student projects

The health and yield of important crop plants around the world is a significant concern when faced with food scarcity in the generations to come. The Xanthomonas bacterial genus can infect more than 400 different plant species including economically important crops such as rice and soy. In Illinois, Xanthomonas cucurbitae can infect pumpkin and winter squash and cause bacterial spot disease (Figure 1) resulting in up to 100% yield loss of pumpkin crops. The disease caused by this pathogen has become one of the most significant threats to production of pumpkins in Illinois, the U.S. and the world.

There are …

Ranking And Clustering Of Drosophila Olfactory Receptors Using Mathematical Morphology, Jayanta Kumar Das, Pabitra Pal Choudhury, Neelambuj Chaturvedi, Mohd Tayyab, Sk Sarif Hassan

Journal Articles

This article introduces an alignment-free clustering method in order to cluster all the 66 DORs sequentially diverse protein sequences. Two different methods are discussed: one is utilizing twenty standard amino acids (without grouping) and another one is using chemical grouping of amino acids (with grouping). Two grayscale images (representing two protein sequences by order pair frequency matrices) are compared to find the similarity index using morphology technique. We could achieve the correlation coefficients of 0.9734 and 0.9403 for without and with grouping methods respectively with the ClustalW result in the ND5 dataset, which are much better than some of the …

Protocol Measuring Horizontal Gene Transfer From Algae To Non-Photosynthetic Organisms, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

Horizontal gene transfer (HGT) is a natural process for an organism to transfer genetic material to another organism that is a completely different species, for example, from a blue-green alga to a non-photosynthetic bacterium. The phenomenon of HGT is not only of an interest to the science of molecular genetics and biology, but also to the biosafety issue of genetic engineering. The novel protocol reported here for the first time teaches how to measure HGT from a genetically engineered (GE) blue-green alga (gene donor) to wild-type E. coli (recipient). This novel protocol can be used to measure HGT frequency for …

Simplicity Diffexpress: A Bespoke Cloud-Based Interface For Rna-Seq Differential Expression Modeling And Analysis, Cintia C. Palu, Marcelo Ribeiro-Alves, Yanxin Wu, Brendan Lawlor, Pavel V. Baranov, Brian Kelly, Paul Walsh

Department of Computer Science Publications

One of the key challenges for transcriptomics-based research is not only the processing of large data but also modeling the complexity of features that are sources of variation across samples, which is required for an accurate statistical analysis. Therefore, our goal is to foster access for wet lab researchers to bioinformatics tools, in order to enhance their ability to explore biological aspects and validate hypotheses with robust analysis. In this context, user-friendly interfaces can enable researchers to apply computational biology methods without requiring bioinformatics expertise. Such bespoke platforms can improve the quality of the findings by allowing the researcher to …

Root Hair Single Cell Type Specific Profiles Of Gene Expression And Alternative Polyadenylation Under Cadmium Stress, Jingyi Cao, Congting Ye, Guijie Hao, Carole Dabney-Smith, Arthur G. Hunt, Qingshun Q. Li

Plant and Soil Sciences Faculty Publications

Transcriptional networks are tightly controlled in plant development and stress responses. Alternative polyadenylation (APA) has been found to regulate gene expression under abiotic stress by increasing the heterogeneity at mRNA 3′-ends. Heavy metals like cadmium pollute water and soil due to mining and industry applications. Understanding how plants cope with heavy metal stress remains an interesting question. The Arabidopsis root hair was chosen as a single cell model to investigate the functional role of APA in cadmium stress response. Primary root growth inhibition and defective root hair morphotypes were observed. Poly(A) tag (PAT) libraries from single cell types, i.e., root …

Do Metabolic Networks Follow A Power Law? A Psamm Analysis, Ryan Geib, Lubos Thoma, Ying Zhang

Senior Honors Projects

Inspired by the landmark paper “Emergence of Scaling in Random Networks” by Barabási and Albert, the field of network science has focused heavily on the power law distribution in recent years. This distribution has been used to model everything from the popularity of sites on the World Wide Web to the number of citations received on a scientific paper. The feature of this distribution is highlighted by the fact that many nodes (websites or papers) have few connections (internet links or citations) while few “hubs” are connected to many nodes. These properties lead to two very important observed effects: the …

What Can We Do? Puzzling Over The Interpretation Of Heredity And Variation From Galton To Genetic Engineering, Peter J. Taylor

Working Papers on Science in a Changing World

First six chapters of a book motivated as follows: When I had mentioned to colleagues that I was exploring some significant issues overlooked by both sides in nature-nurture debates, the typical response was “we know, of course, that nature and nurture are intertwined”; they never asked “which nature-nurture science are you referring to?” It occurred to me that, in the long history of nature-nurture debates, opposing sides had always assumed or implied that these different scientific approaches were speaking to the same issues. If that were the case, then the challenge—something I was already puzzling over—was how best to draw …

Incorporating Pathway Information Into Feature Selection Towards Better Performed Gene Signatures, Suyan Tian, Chi Wang, Bing Wang

Biostatistics Faculty Publications

To analyze gene expression data with sophisticated grouping structures and to extract hidden patterns from such data, feature selection is of critical importance. It is well known that genes do not function in isolation but rather work together within various metabolic, regulatory, and signaling pathways. If the biological knowledge contained within these pathways is taken into account, the resulting method is a pathway-based algorithm. Studies have demonstrated that a pathway-based method usually outperforms its gene-based counterpart in which no biological knowledge is considered. In this article, a pathway-based feature selection is firstly divided into three major categories, namely, pathway-level selection, …

Lab Practicum For Bias In Algorithms, Ameet Soni, Krista Karbowski Thomason

Digital Humanities Curricular Development

This is a course assignment to demonstrate potential biases encoded in algorithms (this can be linked more specifically to natural language processing, machine learning, or artificial intelligence) using the Word Embedding Association Test. In lab, students will work with programs that demonstrate the usefulness of word embedding algorithms in finding relationships between words. Then, students will use an implementation of the algorithm in "Semantics derived automatically from language corpora contain human-like biases" by Caliskan et al. to detect gender and racial bias encoded in word embeddings. The assignment has students design and run an experiment using the WEAT algorithm to …

Fys: Ethics And Technology (Phil 07/Cpsc 15) Syllabus, Ameet Soni, Krista Karbowski Thomason

Digital Humanities Curricular Development

There has been an accelerated shift in the influence of computing technology and the use of algorithms in our daily lives. With this technology comes serious ethical questions. Philosophers are often well-equipped to wrestle with ethical questions, but less well-equipped to wrestle with questions of technology itself. Computer scientists are well-equipped to deal with the problems and challenges of technology, but less well-equipped to deal with the ethical problems and challenges that technology can pose. In this co-taught course, we bring together the two fields to address ethical questions involving social media, data mining, self-driving cars, artificial intelligence, and other …

Computational Analysis Of Large-Scale Trends And Dynamics In Eukaryotic Protein Family Evolution, Joseph Boehm Ahrens

FIU Electronic Theses and Dissertations

The myriad protein-coding genes found in present-day eukaryotes arose from a combination of speciation and gene duplication events, spanning more than one billion years of evolution. Notably, as these proteins evolved, the individual residues at each site in their amino acid sequences were replaced at markedly different rates. The relationship between protein structure, protein function, and site-specific rates of amino acid replacement is a topic of ongoing research. Additionally, there is much interest in the different evolutionary constraints imposed on sequences related by speciation (orthologs) versus sequences related by gene duplication (paralogs). A principal aim of this dissertation is to …

Feature Selection For Longitudinal Data By Using Sign Averages To Summarize Gene Expression Values Over Time, Suyan Tian, Chi Wang

Biostatistics Faculty Publications

With the rapid evolution of high-throughput technologies, time series/longitudinal high-throughput experiments have become possible and affordable. However, the development of statistical methods dealing with gene expression profiles across time points has not kept up with the explosion of such data. The feature selection process is of critical importance for longitudinal microarray data. In this study, we proposed aggregating a gene’s expression values across time into a single value using the sign average method, thereby degrading a longitudinal feature selection process into a classic one. Regularized logistic regression models with pseudogenes (i.e., the sign average of genes across time as predictors) …

Unified Methods For Feature Selection In Large-Scale Genomic Studies With Censored Survival Outcomes, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

One of the major goals in large-scale genomic studies is to identify genes with a prognostic impact on time-to-event outcomes which provide insight into the disease's process. With rapid developments in high-throughput genomic technologies in the past two decades, the scientific community is able to monitor the expression levels of tens of thousands of genes and proteins resulting in enormous data sets where the number of genomic features is far greater than the number of subjects. Methods based on univariate Cox regression are often used to select genomic features related to survival outcome; however, the Cox model assumes proportional hazards …

Substantial Red Wolf Genetic Ancestry Persists In Wild Canids Of Southwestern Louisiana, Jennifer R. Adams, John J. Cox, Lisette P. Waits

Forestry and Natural Resources Faculty Publications

Concerns over red wolf (Canis rufus) extinction caused by hybridization with coyotes (C. latrans) led to the capture and removal of remnant wild wolves from southwestern Louisiana and southeastern Texas, United States, during the 1970s. Here we show that despite decades of unmitigated hybridization, and declaration of endangered red wolves as functionally extinct in the wild, red wolf mitochondrial or nuclear DNA ancestry persists in ∼55% of contemporary wild canids sampled in southwestern Louisiana. Surprisingly, one individual had 78–100% red wolf ancestry, which is within the range for 75% red wolf, red wolf backcross, or putative …

Genome-Wide Association Studies For Yield-Related Traits In Soft Red Winter Wheat Grown In Virginia, Brian P. Ward, Gina Brown-Guedira, Frederic L. Kolb, David A. Van Sanford, Priyanka Tyagi, Clay H. Sneller, Carl A. Griffey

Plant and Soil Sciences Faculty Publications

Grain yield is a trait of paramount importance in the breeding of all cereals. In wheat (Triticum aestivum L.), yield has steadily increased since the Green Revolution, though the current rate of increase is not forecasted to keep pace with demand due to growing world population and increasing affluence. While several genome-wide association studies (GWAS) on yield and related component traits have been performed in wheat, the previous lack of a reference genome has made comparisons between studies difficult. In this study, a GWAS for yield and yield-related traits was carried out on a population of 322 soft red …

Conformational Flexibility In The Enterovirus Rna Replication Platform, Meghan S. Warden, Kai Cai, Gabriel Cornilescu, Jordan E. Burke, Komala Ponniah, Samuel E. Butcher, Steven M. Pascal

Chemistry & Biochemistry Faculty Publications

A presumed RNA cloverleaf (5′CL), located at the 5′-most end of the noncoding region of the enterovirus genome, is the primary established site for initiation of genomic replication. Stem–loop B (SLB) and stem–loop D (SLD), the two largest stem–loops within the 5′CL, serve as recognition sites for protein interactions that are essential for replication. Here we present the solution structure of rhinovirus serotype 14 5′CL using a combination of nuclear magnetic resonance spectroscopy and small-angle X-ray scattering. In the absence of magnesium, the structure adopts an open, somewhat extended conformation. In the presence of magnesium, the structure compacts, bringing SLB …