Bioinformatics Commons^™

Development Of An Enhanced Sampling Workflow To Accelerate Molecular Docking With Sparse Biophysical Information, Zachary Stichter

Masters Theses & Specialist Projects

Rapid docking of flexible biological macromolecules remains a significant open challenge in protein structure determination. While rigid docking is relatively simple with toolkits such as TagDock, a key obstacle to rapid flexible docking is the complexity and roughness of the free energy surface associated with protein conformational motion (often termed the many-minima problem), meaning conventional molecular dynamics methods do not effectively sample protein conformations near the interaction complex in accessible timescales. Methods such as metadynamics and replica exchange molecular dynamics exist to ameliorate this obstacle, yet these methods use nonphysical biases or random swaps to enhance sampling. In contrast, high …

A Reliable Diabetic Retinopathy Grading Via Transfer Learning And Ensemble Learning With Quadratic Weighted Kappa Metric, Sai Venkatesh Chilukoti, Liqun Shan, Vijay Srinivas Tida, Anthony S. Maida, Xiali Hei

Computer Science Faculty Publications

The most common eye infection in people with diabetes is diabetic retinopathy (DR). It might cause blurred vision or even total blindness. Therefore, it is essential to promote early detection to prevent or alleviate the impact of DR. However, due to the possibility that symptoms may not be noticeable in the early stages of DR, it is difficult for doctors to identify them. Therefore, numerous predictive models based on machine learning (ML) and deep learning (DL) have been developed to determine all stages of DR. However, existing DR classification models cannot classify every DR stage or use a computationally heavy …

Integrated Rules Classifier For Predicting Pathogenic Non-Synonymous Single Nucleotide Variants In Human, Ahmed Barakat Hosseny, Marwa Said Hassan, A A. Shalan, Shymaa Khamis, M I. Dessouky

Basic Science Engineering

The most prevalent kind of genetic variants in humans are non-synonymous single nucleotide variants (nsSNVs). Several prediction tools have been launched to forecast the effect of amino acid substitutes on human protein function. These tools sort variants as pathogenic or neutral. We developed an Integrated Rules Classifier (Integration Score through JRip “ISTJRip”), which integrates the four individual tools that are publicly available; iFish, Mutation Assessor, FATHMM, and SIFT-based on the JRip machine learning technique. Additionally, we compared the ISTJRip approach with the other three created integration classifiers; Integration Score through J48 “ISTJ48”, Integration Score through RF “ISTRF”, and Integration …

Whole Genome Sequencing For The Millipede Cherokia Georgiana, Elena Cruz, Will Wittstock, Daniel Hastings, Arnab Sengupta, Bruce A. Snyder

Graduate Research Showcase

Out of thousands of known millipede species, only five sequenced genomes of species (in four of sixteen orders) are publicly available. No whole genomes and limited genetic information are available for incredibly diverse families such as Xystodesmidae. Our research goal is to sequence the whole genome of the millipede Cherokia georgiana. A de novo sequence of the complete genome of a North American species will facilitate future research in understanding gene expression under a variety of conditions. Many interesting biological processes in millipedes are poorly described, such as the production of a defensive hydrogen cyanide secretion found in the …

Using Single Cell Genomics To Explore The Impact Of Marine Viruses On Microbial Respiration., Paxton Tomko

MCB Articles

Viral metabolic reprograming of marine prokaryotes, through the use of virally encoded auxiliary metabolic genes (AMGs), plays a critical role in marine ecosystem function by influencing biochemical cycles and genetic diversity in these environments. Despite the fundamental role viruses play in global environmental ecosystems, they remain an understudied aspect of microbial ecology and evolution, in part due to the methods available for studying virus host interactions in natural systems. Thus far, metagenomic analyses have been used to study the interactions of virus host pairs, but these types of analyses have their limitations in accurately linking viruses to hosts, or culture-based …

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

Dissertations and Doctoral Documents from University of Nebraska-Lincoln, 2023–

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) …

Motif-Cluster: A Spatial Clustering Package For Repetitive Motif Binding Patterns, Mengyuan Zhou

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

Previous efforts in using genome-wide analysis of transcription factor binding sites (TFBSs) have overlooked the importance of ranking potential significant regulatory regions, especially those with repetitive binding within a local region. Identifying these homogenous binding sites is critical because they have the potential to amplify the binding affinity and regulation activity of transcription factors, impacting gene expression and cellular functions. To address this issue, we developed an open-source tool Motif-Cluster that prioritizes and visualizes transcription factor regulatory regions by incorporating the idea of local motif clusters. Motif-Cluster can rank the significant transcription factor regulatory regions without the need for experimental …

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) …

Predicted Structure And Analysis Of The Glycoprotein From Sars-Cov-2 Variants Of Interest, Boris Shabaltiy

Honors Theses

SARS-CoV-2 has had a devastating effect on the world, and while the public concern and severity of the diseased caused by it have decreased, it is still crucial to monitor the virus for mutations so we can rapidly identify new variants of concern, and then rapidly prepare new vaccines and treatments. The SARS-CoV-2 spike (S) protein from the first isolates of the virus (root variant) was structurally characterized in early 2021. The spike protein structure, designated 7CZW, was uploaded to RCSB Protein Data Bank (RCSB PDB). All subsequent mutations the S protein has accumulated are based on the amino acid …

Generative Ai-Assisted Pathway Analysis And Interpretation Of Rna-Seq Experiment Data, Junguk Hur

AI Assignment Library

No abstract provided.

Examining The Different Soil Horizons Of White Oak Mountain, Tn And Their Effect On The Soil Microbial Community, Ji Won Moon, Timothy D. Trott

Research in Biology

Soil microorganisms participate in the diverse interaction within virtually all ecosystems, consequently affecting the associated human and animal population. Identifying how edaphic variables alter the functional and taxonomic diversity of the soil microbial community requires an examination of total microbial soil diversity and abundance. This research study examined the effect of soil depth and horizon on the soil microbial community composition of White Oak Mountain. The soil microbial community was characterized by 16S/18S/ITS rDNA amplicon sequencing of the DNA extract of six samples from the three major soil types identified: HcE, MoE, and uMvC. OTU clustering analysis and both alpha …

The Impact Of Soil Disturbance On Soil Bacterial Community Composition, Marie A. Rodriguez, Mark Peach, Timothy D. Trott

Research in Biology

Soil bacterial communities are an important part of terrestrial ecosystems due to their roles in biogeochemical cycling processes. Consequently, understanding how soil disturbance affects the soil bacterial diversity is vital to understanding the entire ecosystem. In this study we examined the effects of soil disturbance (by mining) on the soil bacterial community composition from three sites on Bauxite Ridge in Southeast Tennessee compared to three undisturbed sites in a nearby location. The soil bacterial community was analyzed by 16S rDNA amplicon sequencing of total DNA extracted from the soil samples collected from each of the six sites. Characterization of the …

Exploring The Interactions Between Sars-Cov-2 And Host Proteins., Sojan Shrestha

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

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current pandemic, Coronavirus Disease 2019 (COVID-19). SARS-CoV-2 is considered to be of zoonotic origin; it originated in non-human animals and was transmitted to humans. Since the early stage of the pandemic, however, the evidence of transmissions from humans to animals (reverse zoonoses) has been found in multiple animal species including mink, white-tailed deer, and pet and zoo animals. Furthermore, secondary zoonotic events of SARS-CoV-2, transmissions from animals to humans, have been also reported. It is suggested that non-human hosts can act as SARS-CoV-2 reservoirs where accumulated …

Ranchsatdb: A Genome-Wide Simple Sequence Repeat (Ssr) Markers Database Of Livestock Species For Mutant Germplasm Characterization And Improving Farm Animal Health, Naveen Duhan, Simardeep Kaur, Rakesh Kaundal

Plants, Soils and Climate Student Research

Microsatellites, also known as simple sequence repeats (SSRs), are polymorphic loci that play an important role in genome research, animal breeding, and disease control. Ranch animals are important components of agricultural landscape. The ranch animal SSR database, ranchSATdb, is a web resource which contains 15,520,263 putative SSR markers. This database provides a comprehensive tool for performing end-to-end marker selection, from SSRs prediction to generating marker primers and their cross-species feasibility, visualization of the resulting markers, and finding similarities between the genomic repeat sequences all in one place without the need to switch between other resources. The user-friendly online interface …

Cellulosome-Forming Modules In Gut Microbiome And Virome, Jerry Akresi

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Cellulosomes are large multi-enzyme complexes encoded in the genomes of some microorganisms. Cellulosomes can degrade plant cell wall celluloses, commonly found in compost soils, forest floors and dietary fibers of farm animals. The hallmarks of cellulosome complexes are cohesins that form a large scaffoldin protein and dockerins that interact with cohesin to dock enzymes onto the scaffoldin. The dockerin-containing proteins often contain Carbohydrate Active Enzymes (CAZyme) domains, predominantly the cellulases (e.g., GH48 and GH9 enzymes), which enable them to break down celluloses. A fascinating question is, has Nature also evolved other similar protein complexes that target other types of complex …

Exploring The Genotypic And Phenotypic Differences Distinguishing Lactobacillus Jensenii And Lactobacillus Mulieris, Adriana Ene, Swarnali Banerjee, Alan J. Wolfe, Catherine Putonti

Mathematics and Statistics: Faculty Publications and Other Works

Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus iners, and Lactobacillus jensenii are dominant species of the urogenital microbiota. Prior studies suggest that these Lactobacillus species play a significant role in the urobiome of healthy females. In our prior genomic analysis of all publicly available L. jensenii and Lactobacillus mulieris genomes at the time (n = 43), we identified genes unique to these two closely related species. This motivated our further exploration here into their genotypic differences as well as into their phenotypic differences. First, we expanded genome sequence representatives of both species to 61 strains, including publicly available …

Mechanistic Examination Of Protist-Mediated Plant Growth Through The Comparative Development Of Medicago Truncatula, Shane Connolly

University Scholar Projects

Protists are known to increase plant growth through two main mechanisms: the microbial loop and the alteration of the root microbiome. The microbial loop is a nutrient recycling method in which protists provide inorganic nitrogen ions to the plant. Alteration of root microbiome leads to the removal of plant pathogens and shifting communities towards plant growth-promoting bacteria (PGPB). This study aimed to elicit which mechanism could produce the largest boost in shoot weight for Medicago truncatula. A series of microcosm experiments were explored in which M. truncatula was grown with variable microbiome structures to allow for mechanism differentiation. The …

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 …

Exploring The Role Of Microrna-1 (Mir-1) On Skeletal Muscle Hypertrophy, Shengyi Fei

College of Education and Human Sciences: Dissertations, Theses, and Student Research

Skeletal muscle hypertrophy is a complex process that involves a range of signaling pathways and transcriptional regulators. Many hormones and growth factors can activate key signaling pathways, such as the PI3K/AKT/mTOR, MAPK, and cAMP pathways, which play a crucial role in the regulation of muscle hypertrophy. In Chapter 1, we reviewed some of the hormones and growth factors known to be associated with skeletal muscle hypertrophy, as well as the function of these key signaling pathways, and revealed some unresolved issues. In Chapter 2, we explored the role of microRNA-1 (miR-1) in skeletal muscle hypertrophy and aimed to determine the …

Soil Microbial Community Composition Of White Oak Mountain, Tennessee, Matthew Gano, Timothy D. Trott

Research in Biology

Abstract - Soil microbial communities are responsible for nutrient cycling in terrestrial ecosystems and have symbiotic and parasitic relationships with the plant community. However, little is known about the factors that determine the soil microbial community composition. In this study we examined how spring wildflower diversity and geographical factors influence the soil microbial community composition of the second growth oak hickory forests of White Oak Mountain in Southeast Tennessee. The characterization of the soil microbial community was completed with 16S/18S/ITS rDNA amplicon sequencing of total DNA extracted from soil samples that were normalized for each sample plot. Here we characterize …

Examining The Different Soil Horizons Of White Oak Mountain, Tn And Their Effect On The Soil Microbial Community, Ji Won Moon, Timothy D. Trott

Research in Biology

Soil microorganisms participate in the diverse interaction within virtually all ecosystems, consequently affecting the associated human and animal population. Identifying how edaphic variables alter the functional and taxonomic diversity of the soil microbial community requires an examination of total microbial soil diversity and abundance. This research study examined the effect of soil depth and horizon on the soil microbial community composition of White Oak Mountain. The soil microbial community was characterized by 16S/18S/ITS rDNA amplicon sequencing of the DNA extract of six samples from the three major soil types identified: HcE, MoE, and uMvC. OTU clustering analysis and both alpha …

Darwin Core Archive File, Stover-Ebinger Herbarium, Eastern Illinois University

Darwin Core Archive Download

ZIP file contains occurrences.csv, identivications.csv, and images.csv. The meta.xml document describes the content. Fields within the occurrences.csv file are defined by the Darwin Core exchange standard.

This file is updated as new occurrence records are added.

Hydropower To The People: Implications Of A Comparative Macroinvertebrate Study On Either Side Of The Central Hidroeléctrica Topo In Tungurahua, Ecuador, Grace Mazur

Independent Study Project (ISP) Collection

This study uses macroinvertebrates as bioindicators to assess the water quality upstream and downstream of a hydroelectric project in Ecuador’s eastern cloud forest. Ecuador has increasingly turned to hydropower to supply its energy needs as pressure mounts to turn away from fossil fuels. This transition has been realized on the Río Topo, located in the province of Tungurahua. This study aims to determine how the Central Hidroeléctrica Topo (CHT), a diversion hydroelectric project (HEP) constructed on the Río Topo in the 2010s, has affected the water quality of the river. Samples were taken of benthic (bottom-dwelling) macroinvertebrates in the Río …

Evaluation Of An Adaptive Sampling Approach To Characterize Microbes Associated With Pneumonia In White-Tailed Deer, Claire Nowak

Honors College

Infectious diseases have a tremendous global impact, adversely affecting the health and well-being of humans, domestic livestock, and wildlife. Consequently, pathogen surveillance in wild animals is essential for managing the risk of disease transmission to humans and domesticated animals, as well as for understanding host-pathogen interactions. However, pathogen detection methods are often focused on one to a few pathogen species, which limits our understanding of the distributions and effects of multiple co-infecting pathogens on host individuals and populations. In this study, I employed a metagenomic sequencing approach to (1) characterize the microbial community in a white-tailed deer (Odocoileus virginianus …

Editorial: Special Issue “Protein Modeling And Simulation: Selected Articles From The Computational Structural Bioinformatics Workshop 2021”, Negin Forouzesh, Kamal Ai Nasr

Computer Science Faculty Research

No abstract provided.

Complet+: A Computationally Scalable Method To Improve Completeness Of Large-Scale Protein Sequence Clustering, Rachel Nguyen, Bahrad A. Sokhansanj, Robi Polikar, Gail L. Rosen

Henry M. Rowan College of Engineering Faculty Scholarship

A major challenge for clustering algorithms is to balance the trade-off between homogeneity, i.e., the degree to which an individual cluster includes only related sequences, and completeness, the degree to which related sequences are broken up into multiple clusters. Most algorithms are conservative in grouping sequences with other sequences. Remote homologs may fail to be clustered together and instead form unnecessarily distinct clusters. The resulting clusters have high homogeneity but completeness that is too low. We propose Complet+, a computationally scalable post-processing method to increase the completeness of clusters without an undue cost in homogeneity. Complet+ proves to effectively merge …

A Growth Model For Arctica Islandica: The Performance Of Tanaka And The Temptation Of Von Bertalanffy—Can The Two Coexist?, John M. Klinck, Eric N. Powell, Kathleen M. Hemeon, Jillian R. Sower, Daniel R. Hennen

CCPO Publications

Organisms increase in size over time (age) due to excess assimilation over metabolic (respiration) energy demands. Most organisms reach a maximum size with increasing age as gain and loss balance. The von Bertalanffy length-at-age relationship, which is commonly used in fishery assessment calculations, imposes such a maximum size. However, some fished species, such as ocean quahogs, Arctica islandica, are long lived and continue to grow at old age. The Tanaka age-at-length relationship has continued growth at old age, but is rarely used in stock assessment models. A modified form of the von Bertalanffy model is presented, which mimics the …

Teloportwrapper: A New Tool For Understanding The Dynamic World Of Fungal Telomere Ends, Trey Stansfield

Mahurin Honors College Capstone Experience/Thesis Projects

Telomeres are repetitive DNA sequence motifs found at eukaryote chromosome ends. Telomeres help protect chromosome ends from DNA damage and promote chromosome stability. Chromosomes play important roles in aging, mutation, and cancer. Eukaryotic pathogens also use telomeres to mutate and manage virulence genes. In response to chromosome end breakage newly formed telomeres, called de novo telomeres, are formed to recreate the lost telomere and sub-telomeric regions.

Magnaporthe oryzae is a fungal pathogen which causes wheat blast, a deadly plant disease in wheat. Magnaporthe oryzae is also known for its highly variable sub-regions which show high amounts of induced variability due …

Adjusting For Gene-Specific Covariates To Improve Rna-Seq Analysis, Hyeongseon Jeon, Kyu-Sang Lim, Yet Nguyen, Dan Nettleton

Mathematics & Statistics Faculty Publications

Summary

This paper suggests a novel positive false discovery rate (pFDR) controlling method for testing gene-specific hypotheses using a gene-specific covariate variable, such as gene length. We suppose the null probability depends on the covariate variable. In this context, we propose a rejection rule that accounts for heterogeneity among tests by employing two distinct types of null probabilities. We establish a pFDR estimator for a given rejection rule by following Storey's q-value framework. A condition on a type 1 error posterior probability is provided that equivalently characterizes our rejection rule. We also present a suitable procedure for selecting a tuning …

Radiation Exposure Determination In A Secure, Cloud-Based Online Environment, Ben C. Shirley, Eliseos J. Mucaki, Peter Rogan

Biochemistry Publications

Rapid sample processing and interpretation of estimated exposures will be critical for triaging exposed individuals after a major radiation incident. The dicentric chromosome (DC) assay assesses absorbed radiation using metaphase cells from blood. The Automated Dicentric Chromosome Identifier and Dose Estimator System (ADCI) identifies DCs and determines radiation doses. This study aimed to broaden accessibility and speed of this system, while protecting data and software integrity. ADCI Online is a secure web-streaming platform accessible worldwide from local servers. Cloud-based systems containing data and software are separated until they are linked for radiation exposure estimation. Dose estimates are identical to ADCI …