Genetics and Genomics Commons^™

Engaging Students In A Genetics Course-Based Undergraduate Research Experience Utilizing Caenorhabditis Elegans In Hybrid Learning To Explore Human Disease Gene Variants, Natalie Forte, Virginia Veasey, Bethany Christie, Amira Carter, Marli Hanks, Alan Holderfield, Taylor Houston, Anil Challa, Ashley Turner

Research, Publications & Creative Work

Genetic analysis in model systems using bioinformatic approaches provides a rich context for a concrete and conceptual understanding of gene structure and function. With the intent to engage students in research and explore disease biology utilizing the nematode Caenorhabditis elegans model, we developed a semester-long course-based undergraduate research experience (CURE) in a hybrid (online/in-person) learning environment—the gene-editing and evolutionary nematode exploration CURE (GENE-CURE). Using a combination of bioinformatic and molecular genetic tools, students performed structure-function analysis of disease-associated variants of uncertain significance (VUS) in human orthologs. With the aid of a series of workshop-style research sessions, students worked in teams …

Convolutional Neural Network-Based Gene Prediction Using Buffalograss As A Model System, Michael Morikone

Complex Biosystems PhD Program: Dissertations

The task of gene prediction has been largely stagnant in algorithmic improvements compared to when algorithms were first developed for predicting genes thirty years ago. Rather than iteratively improving the underlying algorithms in gene prediction tools by utilizing better performing models, most current approaches update existing tools through incorporating increasing amounts of extrinsic data to improve gene prediction performance. The traditional method of predicting genes is done using Hidden Markov Models (HMMs). These HMMs are constrained by having strict assumptions made about the independence of genes that do not always hold true. To address this, a Convolutional Neural Network (CNN) …

Repurposing Normal Chromosomal Microarray Data To Harbor Genetic Insights Into Congenital Heart Disease, Nephi Walton, Hoang Nguyen, Sara Procknow, Darren Johnson, Alexander Anzelmi, Patrick Jay

Department of Medicine Faculty Papers

About 15% of congenital heart disease (CHD) patients have a known pathogenic copy number variant. The majority of their chromosomal microarray (CMA) tests are deemed normal. Diagnostic interpretation typically ignores microdeletions smaller than 100 kb. We hypothesized that unreported microdeletions are enriched for CHD genes. We analyzed "normal" CMAs of 1762 patients who were evaluated at a pediatric referral center, of which 319 (18%) had CHD. Using CMAs from monozygotic twins or replicates from the same individual, we established a size threshold based on probe count for the reproducible detection of small microdeletions. Genes in the microdeletions were sequentially filtered …

A Review Of How Bioinformatics And Genome Sequencing Are Affecting Precision Medicine, Taylor S. Hickey

Honors Theses

Advancement in genomic sequencing and bioinformatics methods have been affecting biomedical research through precision medicine, especially in the area of cancer. Vaccine therapies can be developed using neoantigens that target specific mutations in tumors. The goals of this research are to identify mutations that lead to cancer and then define subpopulations in which patients can easily be identified. The future goal is to have targeted vaccines that are specific to each subpopulation ready to be used in treatment of their cancer. Limitations to reaching these goals have been due to tumor heterogeneity, cancer location, and difficulty in creating neoantigens for …

In Silico Characterization Of Protein-Protein Interactions Mediated By Short Linear Motifs, Heidy Elkhaligy

FIU Electronic Theses and Dissertations

Short linear motifs (SLiMs), often found in intrinsically disordered regions (IDPs), can initiate protein-protein interactions in eukaryotes. Although pathogens tend to have less disorder than eukaryotes, their proteins alter host cellular function through molecular mimicry of SLiMs. The first objective was to study sequence-based structure properties of viral SLiMs in the ELM database and the conservation of selected viral motifs involved in the virus life cycle. The second objective was to compare the structural features for SliMs in pathogens and eukaryotes in the ELM database. Our analysis showed that many viral SliMs are not found in IDPs, particularly glycosylation motifs. …

Alterations Of The Gut Mycobiome In Patients With Ms - A Bioinformatic Approach, Saumya Shah

Honors Scholar Theses

The mycobiome is the fungal component of the gut microbiome and is implicated in several autoimmune diseases. However, its role in multiple sclerosis (MS) has not been studied. We performed descriptive and formal statistical tests using the R language to characterize the gut mycobiome in people with MS (pwMS) and healthy controls. We found that the microbiome composition of multiple sclerosis patients is different from healthy people. The mycobiome had significantly higher alpha diversity and inter-subject variation in pwMS than controls. Additionally, Saccharomyces and Aspergillus were over-represented in pwMS. Different mycobiome profiles, defined as mycotypes, were associated with different bacterial …

Comparative Analyses Of De Novo Transcriptome Assembly Pipelines For Diploid Wheat, Natasha Pavlovikj

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Gene expression and transcriptome analysis are currently one of the main focuses of research for a great number of scientists. However, the assembly of raw sequence data to obtain a draft transcriptome of an organism is a complex multi-stage process usually composed of pre-processing, assembling, and post-processing. Each of these stages includes multiple steps such as data cleaning, error correction and assembly validation. Different combinations of steps, as well as different computational methods for the same step, generate transcriptome assemblies with different accuracy. Thus, using a combination that generates more accurate assemblies is crucial for any novel biological discoveries. Implementing …

Exploring The Functionality Of Putative Bop3 Post-Translational Modifications, Liliya Tkachuk

Honors Scholars Collaborative Projects

All eukaryotic cells require that transcribed mRNAs undergo export form the nucleus to the cytoplasm where they can be translated into proteins. This process requires a host of proteins which are conserved between the unicellular budding yeast, S. cerevisiae, and humans. During this process, Mex67 and other associated proteins facilitate the mRNA to travel across the nuclear pore complex (NPC), doorways embedded in the nuclear envelope. Upon the exit of mRNA, Mex67 is released and recycled back into the nucleus to facilitate the export of more mRNA. This occurs through the action of Dbp5, whose activity is regulated through …

Exploring The Functionality Of Putative Bop3 Post-Translational Modifications, Liliya Tkachuk, Rebecca Adams Phd

Belmont University Research Symposium (BURS)

All eukaryotic cells require that transcribed mRNAs undergo export form the nucleus to the cytoplasm where they can be translated into proteins. This process requires a host of proteins which are conserved between the unicellular budding yeast, S. cerevisiae, and humans. During this process, Mex67 and other associated proteins facilitate the mRNA to travel across the nuclear pore complex (NPC), doorways embedded in the nuclear envelope. Upon the exit of mRNA, Mex67 is released and recycled back into the nucleus to provide the export of more mRNA. This release occurs through the action of Dbp5, whose activity is regulated …

You Are What You Eat — Exploring The Microbiome Through Inquiry-Based Labs. Microbiome Lesson Plans, Karla S. Fuller

Open Educational Resources

If these commonly used spices have the ability to inhibit pathogenic bacterial growth, could they also potentially inhibit the growth of normal, harmless bacteria that live in your body? In this lab, we will test common bacteria for resistance to food additives.

Forward Genomics Of A Complex Trait: Mammalian Basal Metabolic Rate, Caleigh Charlebois

Honors College

The significance and nature of basal metabolic rate, a metabolic parameter recorded under specific laboratory conditions, are contested among biologists. Although it was most likely important in the evolution of endothermy in mammals and is associated with many other traits inter-and intra-specifically, the specifics of its heritability and its genetic determinants are largely unknown. Two bioinformatics pipelines are available which can associate traits with their genetic correlates given only whole genomes and phenotypes for each animal. However, extant pipelines were created with binary traits in mind. This leaves a void in our ability to associate continuous traits such as basal …

Analysis Of Subtelomeric Rextal Assemblies Using Quast, Tunazzina Islam, Desh Ranjan, Mohammad Zubair, Eleanor Young, Ming Xiao, Harold Riethman

Computer Science Faculty Publications

Genomic regions of high segmental duplication content and/or structural variation have led to gaps and misassemblies in the human reference sequence, and are refractory to assembly from whole-genome short-read datasets. Human subtelomere regions are highly enriched in both segmental duplication content and structural variations, and as a consequence are both impossible to assemble accurately and highly variable from individual to individual. Recently, we developed a pipeline for improved region-specific assembly called Regional Extension of Assemblies Using Linked-Reads (REXTAL). In this study, we evaluate REXTAL and genome-wide assembly (Supernova) approaches on 10X Genomics linked-reads data sets partitioned and barcoded using the …

Genomics Education Partnership F Element Annotation Report, Amanda Moy

Honors Projects

The Genomics Education Partnership (GEP), headquartered at the University of Alabama, is a collection of over 100 universities that provide training and resources in order to provide students experiential learning in bioinformatics and genomics. The GEP hosts numerous research projects, including the F element project. The F element project has the main focus of annotating the F element genes of the fruit fly species D. ananassae, D. bipectinata, D. kikkawai, and D. takahashii. The Muller F element is the smallest chromosome in Drosophila species. However, the four species listed above have a notably larger F element than other …

Polerovirus Genomic Variation And Mechanisms Of Silencing Suppression By P0 Protein, Natalie Holste

School of Biological Sciences: Dissertations, Theses, and Student Research

The family Luteoviridae consists of three genera: Luteovirus, Enamovirus, and Polerovirus. The genus Polerovirus contains 32 virus species. All are transmitted by aphids and can infect a wide variety of crops from cereals and wheat to cucurbits and peppers. However, little is known about how this wide range of hosts and vectors developed. In poleroviruses, aphid transmission and virion formation is mediated by the coat protein read-through domain (CPRT) while silencing suppression and phloem limitation is mediated by Protein 0 (P0)—a protein unique to poleroviruses. P0 gives poleroviruses a great advantage amongst plant viruses and diversifies polerovirus species, but the …

Integrate Structural Analysis, Isoform Diversity, And Interferon-Inductive Propensity Of Ace2 To Predict Sars-Cov2 Susceptibility In Vertebrates, Eric R. Sang, Yun Tian, Yuanying Gong, Laura C. Miller, Yongming Sang

Agricultural and Environmental Sciences Faculty Research

The current new coronavirus disease (COVID-19) has caused globally over 0.4/6 million confirmed deaths/infected cases across more than 200 countries. As the etiological coronavirus (a.k.a. SARS-CoV2) may putatively have a bat origin, our understanding about its intermediate reservoir between bats and humans, especially its tropism in wild and domestic animals are mostly unknown. This constitutes major concerns in public health for the current pandemics and potential zoonosis. Previous reports using structural analysis of the viral spike protein (S) binding its cell receptor of angiotensin-converting enzyme 2 (ACE2), indicate a broad potential of SARS-CoV2 susceptibility in wild and particularly domestic animals. …

10th Annual Postdoctoral Science Symposium, University Of Texas Md Anderson Cancer Center Postdoctoral Association

Annual Postdoctoral Science Symposium Abstracts

The Annual Postdoctoral Science Symposium (APSS) was initiated on August 4, 2011, by the MD Anderson Postdoctoral Association to provide a platform for talented postdoctoral fellows throughout the Texas Medical Center to present their work to a wider audience.

APSS is a scientific symposium organized by postdoctoral fellows from The University of Texas MD Anderson Cancer Center that welcomes submissions and presentations from postdoctoral fellows from all Texas Medical Center affiliated institutions and other Houston area institutions. The APSS provides a professional venue for postdoctoral scientists to develop, clarify and refine their research as result of formal reviews and critiques …

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.

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 …

Mrub_3019 Casa Gene Is An Ortholog To E. Coli B2760, Kelsey Heiland, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This research is part of the Meiothermus ruber genome annotation project which aims to predict gene function with various bioinformatics tools. We investigated the function of Mrub_3019, which encodes the CasA protein involved in the multi-subunit effector complex for the CRISPR-Cas immunity system and predicted it to be an ortholog of E. coli K12 MG1655 b2760 (casA). We predicted that Mrub_3019 encodes the protein CasA, which is involved in PAM recognition of CRISPR interference pathway. Foreign DNA will bind to CasA, which signals Cas3 for helicase-mediated DNA degradation. Our hypothesis is supported by low E-values for pairwise alignment in NCBI …

Mrub_3015 Is Orthologous To The B2757 Gene Found In Escherichia Coli Coding For Casd, Ramona Collins, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of the gene Mrub_3015, which we hypothesize is a component of the CRISPR-Cas prokaryotic defense system. We predict that Mrub_3015 (DNA coordinates 3055550...3056245) encodes the the CRISPR-associated protein cas5, which is integral in maintaining the crRNA-DNA structure, keeping the complex from base pairing with the target phage DNA. Our hypothesis is supported by identical hits for Mrub_3015 and b2527 to the KEGG, Pfam, TIGRfam, CDD and PDB databases as well as a …

Mrub_3018 Is Orthologous To E. Coli B2759 (Casb), Kyle Parker, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We studied the biological activity of the Mrub_3018 gene, which we hypothesize is orthologous to E. coli gene B2759. We predicted that Mrub_3018(DNA coordinates 3057916… 3058524) encodes the protein CasB. CasB is a protein in the CRISPR CASCADE that will function as a structural protein. When the rest of the proteins form an “S” formation CasB will connect the front and back of the “S” creating a back bone for the structure. It will help bind DNA …

The N-Glycan Structures Of The Antigenic Variants Of Chlorovirus Pbcv-1 Major Capsid Protein Help To Identify The Virus-Encoded Glycosyltransferases, Immacolata Speciale, Garry A. Duncan, Luca Unione, Irina Agarkova, Domenico Garozzo, Jesus Jimenez-Barbero, Sicheng Lin, Todd L. Lowary, Antonio Molinaro, Eric Noel, Maria Elena Laugieri, Michela Tonetti, James L. Van Etten, Cristina De Castro

James Van Etten Publications

The chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1) is a large dsDNA virus that infects the microalga Chlorella variabilis NC64A. Unlike most other viruses, PBCV-1 encodes most, if not all, of the machinery required to glycosylate its major capsid protein (MCP). The structures of the four N-linked glycans from the PBCV-1 MCP consist of nonasaccharides, and similar glycans are not found elsewhere in the three domains of life. Here, we identified the roles of three virus-encoded glycosyltransferases (GTs) that have four distinct GT activities in glycan synthesis. Two of the three GTs were previously annotated as GTs but the third …

Integrated Analysis Of Competing Endogenous Rna Network Revealing Potential Prognostic Biomarkers Of Hepatocellular Carcinoma, Xiwen Liao, Xiangkun Wang, Ketuan Huang, Chuangye Han, Jianlong Deng, Tingdong Yu, Chengkun Yang, Rui Huang, Xiaoguang Liu, Long Yu, Guangzhi Zhu, Hao Su, Wei Qin, Xianmin Zeng, Bowen Han, Quanfa Han, Zhengqian Liu, Xin Zhou, Yizhen Gong, Zhengtao Liu, Jianlv Huang, Cheryl A. Winkler, Stephen J. O'Brien, Xinping Ye, Tao Peng

Biology Faculty Articles

Objective: The goal of our study is to identify a competing endogenous RNA (ceRNA) network using dysregulated RNAs between HCC tumors and the adjacent normal liver tissues from The Cancer Genome Atlas (TCGA) datasets, and to investigate underlying prognostic indicators in hepatocellular carcinoma (HCC) patients. Methods: All of the RNA- and miRNA-sequencing datasets of HCC were obtained from TCGA, and dysregulated RNAs between HCC tumors and the adjacent normal liver tissues were investigated by DESeq and edgeR algorithm. Survival analysis was used to confirm underlying prognostic indicators. Results: In the present study, we constructed a ceRNA network based on 16 …

Mrub_3014 Is Orthologous To B2756, Samir Abdelkarim, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of the gene Mrub_3014, which we hypothesize is a component of the CRISPR-Cas prokaryotic defense system. We predict that Mrub_3014 (DNA coordinates 3054943..3055575) encodes CRISPR-associated protein Cse3/case which function as an endonuclease. Our hypothesis is supported by identical hits for Mrub_3014 and b2756 to the KEGG, Pfam, TIGRfam, CDD and PDB databases, as well as a low E-value for a pairwise NCBI BLAST comparison. Both protein products are predicted to be localized …

M. Ruber Mrub_3013 Is Orthologous To E. Coli B2755, Laura Butcher, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of gene Mrub_3013, which we hypothesize is orthologous to b2755 in E. coli K12 MG1655 (a.k.a. Cas1). We investigated the biological function of a gene with the M. ruber locus tag of Mrub_3013, which we hypothesize is a component of the CRISPR-Cas prokaryotic defense system in M. ruber. We predict that Mrub_3013 (DNA coordinates 3,053,978-3,054,940) encodes the protein Cas1 which as part of the CRISPR-Cas system, selects and cuts the foreign …

Mrub_3020, A Paralog Of Mrub_1489, Is Orthologous To E. Coli Casc (Locus Tag B2761), Alfred Dei-Ampeh, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological functions of two genes: mrub_3020 and mrub_1489. We make two hypotheses in this investigation: a) mrub_3020 is orthologous to the gene b2761 in E. coli K12 MG1655 (a.k.a. casC); b) mrub_1489 is a paralog of mrub_3020. We also predict that the two genes encode unique proteins: mrub_3020 with DNA coordinates 3060491…3063190 encodes a CRISPR – associated helicase (Cas3) that supports the Cascade complex of the CRISPR – Cas adaptive immune system …

Effects Of Temperature On Crispr/Cas System, Eddie Beckom, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the effect of temperature on the complexity of CRISPR/Cas systems in bacterial organisms across temperature classifications. We predict that temperature extremes would result in CRISPR/Cas systems with multiple operons, repeating cas genes, and complex systems. CRISPR/Cas systems can be classified into three types with a number of subtypes based on the CRISPR-associated genes, cas genes, present in a given organism. Our hypothesis is supported by the presence of multiple operons in thermophilic organisms based on …

An Investigation Into The Relationship Between Mrub_3013, Mrub_1477, And Mrub_0224: Are They Paralogs?, Melette Devore, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of mrub_3013 and the nature of its relationship with mrub_1477 and mrub_0224. We hypothesized that mrub_3013 is orthologous to b2755 in E. coli K12 MG1655 (a.k.a. cas1). We predict that mrub_3013 encodes the enzyme Cas1, which is involved in spacer acquisition in the CRISPR-Cas prokaryotic defense system. Our hypothesis is supported by identical hits for b2755, mrub_3013, mrub_1477, and mrub_0224 from the CDD and Pfam databases and highly similar hits from …

Characterization Of Mrna Polyadenylation In The Apicomplexa, Ashley T. Stevens, Daniel K. Howe, Arthur G. Hunt

Plant and Soil Sciences Faculty Publications

Messenger RNA polyadenylation is a universal aspect of gene expression in eukaryotes. In well-established model organisms, this process is mediated by a conserved complex of 15–20 subunits. To better understand this process in apicomplexans, a group of unicellular parasites that causes serious disease in humans and livestock, a computational and high throughput sequencing study of the polyadenylation complex and poly(A) sites in several species was conducted. BLAST-based searches for orthologs of the human polyadenylation complex yielded clear matches to only two—poly(A) polymerase and CPSF73—of the 19 proteins used as queries in this analysis. As the human subunits that recognize the …

Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Maureen Azar, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of Escherichia coli and Meiothermus ruber proC genes using the complementation assay. In this research project, mutants of varying severity to the functional state of the protein were developed. The results showed that two or more amino acid deletions reduced or eliminated ProC function. Amino acid substitutions, on the other hand, were not severe enough to impact ProC function. Double and triple mutants …