Genetics and Genomics Commons^™

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

Capstone Experience: Master of Public Health

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 …

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 …

High-Performance Computing Frameworks For Large-Scale Genome Assembly, Sayan Goswami

LSU Doctoral Dissertations

Genome sequencing technology has witnessed tremendous progress in terms of throughput and cost per base pair, resulting in an explosion in the size of data. Typical de Bruijn graph-based assembly tools demand a lot of processing power and memory and cannot assemble big datasets unless running on a scaled-up server with terabytes of RAMs or scaled-out cluster with several dozens of nodes. In the first part of this work, we present a distributed next-generation sequence (NGS) assembler called Lazer, that achieves both scalability and memory efficiency by using partitioned de Bruijn graphs. By enhancing the memory-to-disk swapping and reducing 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 …

Phylogenetic Inference Of Multiscale Selection Pressures Using A Continuous State Birth-Death Process, Marco Hamins-Puertolas, David Rasmussen

Biology and Medicine Through Mathematics Conference

No abstract provided.

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

Biology and Medicine Through Mathematics Conference

No abstract provided.

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, …

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 …

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 …

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 …

Gene Co-Expression Networks Analysis Reveal Novel Molecular Endotypes In Alpha-1 Antitrypsin Deficiency, Jen-Hwa Chu, Wenlan Zang

Yale Day of Data

Rationale:Alpha-1 antitrypsin deficiency (AATD) is a genetic condition that predisposes to early onset pulmonary emphysema and airways obstruction. The exact mechanism through which AATD leads to lung disease is incompletely understood.

Objectives: To investigate the effect of AAT genotype and augmentation therapy on bronchoalveolar lavage (BAL) and peripheral blood mononuclear cells (PBMC) transcriptome, while examining the link between gene expression profiles, and clinical features of AATD.

Methods: We performed RNA-Seq on RNA extracted from BAL and PBMC on samples obtained from 89 AATD patients enrolled in the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study. Differential …

Non-Invasive Analysis Of The Sputum Transcriptome Discriminates Clinical Phenotypes Of Asthma, Xiting Yan

Yale Day of Data

Whole transcriptome wide gene expression profiles in the sputum and circulation from 100 asthma patients were measured using the Affymetrix HuGene 1.0ST arrays. Unsupervised clustering analysis based on pathways from KEGG were used to identify TEA clusters of patients from the sputum gene expression profiles. The identified TEA clusters have significantly different pre-bronchodilator FEV1, bronchodilator responsiveness, exhaled nitric oxide levels, history of hospitalization for asthma and history of intubation. Evaluation of TEA clusters in children from Asthma BRIDGE cohort confirmed the identified differences in intubation and hospitalization. Furthermore, evaluation of the TH2 gene signatures suggested a much lower prevalence of …

A Novel Pathway-Based Distance Score Enhances Assessment Of Disease Heterogeneity In Gene Expression, Yunqing Liu, Xiting Yan

Yale Day of Data

Distance-based unsupervised clustering of gene expression data is commonly used to identify heterogeneity in biologic samples. However, high noise levels in gene expression data and the relatively high correlation between genes are often encountered, so traditional distances such as Euclidean distance may not be effective at discriminating the biological differences between samples. In this study, we developed a novel computational method to assess the biological differences based on pathways by assuming that ontologically defined biological pathways in biologically similar samples have similar behavior. Application of this distance score results in more accurate, robust, and biologically meaningful clustering results in both …

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 …