Digital Commons Network^™

An Investigation Of Information Structures In Dna, Joel Mohrmann

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

The information-containing nature of the DNA molecule has been long known and observed. One technique for quantifying the relationships existing within the information contained in DNA sequences is an entity from information theory known as the average mutual information (AMI) profile. This investigation sought to use principally the AMI profile along with a few other metrics to explore the structure of the information contained in DNA sequences.

Treating DNA sequences as an information source, several computational methods were employed to model their information structure. Maximum likelihood and maximum a posteriori estimators were used to predict missing bases in DNA sequences. …

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) …

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) …

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 …

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 …

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 …

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 …

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 …

Co-Twin Relationship Quality As A Moderator Of Genetic And Environmental Factors On Urinary Cortisol Levels Among Adult Twins, Joseph A. Schwartz, Scott Jessick, Jessica L. Calvi, Douglas A. Granger

Athletic Performance Research

Previous research has indicated that genetic and environmental factors shape physiological activity. Cortisol levels, in particular, have received significant attention, with studies indicating substantive heritability estimates across various sampling techniques. A related line of research has indicated that genetic and environmental factors that explain variability in cortisol levels may vary across context and experiences by way of gene-environment interactions (G×Es). Despite these findings, a limited number of studies have examined the extent to which interpersonal relationships may operate as a moderator. The current study focused on co-twin relationship quality as a source of moderation, as twins are more likely to …

Exploration Of Genes Controlling Grain Yield Heterosis In Hybrid Wheat (Triticum Aestivum L.) Utilizing 3ʹ Rna Sequencing, Nichole Miller

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The implementation and future success of hybrid wheat (Triticum aestivum L.) is impacted by breeders’ inability to create consistent high yielding, high heterosis hybrids. This research addresses this problem by conducting an exploration of transcriptomes from hybrids and parent lines to determine what genes are active in heterotic or non-heterotic hybrids and how their level of expression can explain the phenotype of grain yield heterosis. Using hybrids that showed positive mid-parent heterosis (MPH), classified as heterotic in our study, and negative or no difference MPH hybrids, classified as non-heterotic, differentially expressed genes (DEGs) potentially related to heterosis and hybrid …

Genomic Analysis Of Metabolic Differences Found In Clostridium Perfringens That Cause Necrotic Enteritis In Poultry, Connor Aylor

School of Veterinary and Biomedical Sciences: Dissertations, Theses, and Student Research

Clostridium perfringens is a common member of gut microbiota in healthy animals, but can also be an important pathogen in human and veterinary medicine. It produces several protein toxins that contribute to both histotoxic and enteric diseases in animals. Necrotic enteritis in poultry has been associated with the NetB toxin of C. perfringens; however, this toxin alone is insufficient to cause disease in infected chickens. While considerable research has focused on the presence of toxins and virulence factors, little has been done to assess the function of metabolic factors on the ability of the bacteria to cause disease. In …

Ubjective Information And Survival In A Simulated Biological System, Tyler S. Barker, Massimiliano Pierobon, Peter J. Thomas

School of Computing: Faculty Publications

Information transmission and storage have gained traction as unifying concepts to characterize biological systems and their chances of survival and evolution at multiple scales. Despite the potential for an information-based mathematical framework to offer new insights into life processes and ways to interact with and control them, the main legacy is that of Shannon’s, where a purely syntactic characterization of information scores systems on the basis of their maximum information efficiency. The latter metrics seem not entirely suitable for biological systems, where transmission and storage of different pieces of information (carrying different semantics) can result in different chances of survival. …

Genomic Analysis Of Acetoanaerobium Sp. Vlb-1, An Anaerobic Bacterium Isolated From Nebraska's Eastern Saline Wetlands, Claire Martin

Honors Theses

Through the analysis of genetic code, the genomic and physiological characteristics of an environmental anaerobic bacterial isolate, Acetoanaerobium sp. strain VLB-1, can be determined and significant pathways can be identified in its significance to the environment. This particular organism was isolated from the Eastern Saline Wetlands in Lincoln, NE. With this isolate, an investigation into elemental and amino acid cycling via the Stickland reaction and the Wood-Ljungdahl pathway was conducted to determine possible metabolic products. The Stickland reaction is a relatively newly discovered pathway, observed in the genus Clostridium. A. sticklandii is the main model for this method of …

Adrenocortical Attunement, Reactivity, And Potential Genetic Correlates Among Parent-Daughter Dyads From Low-Income Families, Jennifer Byrd-Craven, Michael M. Criss, Jessica L. Calvi, Lixian Cui, Amanda Baraldi, Amanda Sheffield Morris

Athletic Performance Research

Examining the multitude of influences on the development of adolescent stress responses, especially among low-income families, is a critical and understudied topic in the field. The current study examined cortisol attunement between adolescent girls and parents (mostly mothers) from predominantly low-income, single parent, ethnic minority families before and after an in-laboratory disagreement discussion task. The sample consisted of 118 adolescents (M_age = 13.79 years, 76.3% ethnic minorities, 23.7% European Americans) and primary caregivers (M_age = 40.62 years; Mdn yearly income = $24,000; 43.2% single parents; 50% living below poverty line). We investigated oxytocin receptor (OXTR rs53576) …

Nematode Biodiversity In Lincoln, Nebraska's Tallgrass Prairie Corridor, Abigail Borgmeier

Department of Plant Pathology: Dissertations, Theses, and Student Research

The tallgrass prairie was once one of the most diverse grasslands on the planet, however over 95% has been converted to agriculture in the past 150 years. The remaining prairie is still host to a wide variety of plants, insects, mammals, and soil-dwelling microorganisms, creating an incredibly complex ecosystem. The first aim of this study is to compare three approaches for the measurement of nematode diversity within a 10-mile-long protected prairie habitat corridor near Lincoln, Nebraska. The methods are 1) a traditional morphological analysis of 150 nematodes per study site, 2) a metabarcoding analysis using the 18S genetic marker of …

The Differences Of Prokaryotic Pan-Genome Analysis On Complete Genomes And Simulated Metagenome-Assembled Genomes, Tang Li

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

Metagenomic assembly is often used in microbiome research. In metagenomic assembly, contigs are binned based on the shared nucleotide composition. These contig bins are called metagenome-assembled genomes (MAGs), each representing a unique bacterial genome recovered from metagenome sequencing. Hundreds of thousands of high-quality MAGs of various ecological environments have been published since 2017, and increasingly more MAGs are being used in pan-genome analyses where unculturable species or species without reference genomes are studied in microbiome research. However, compared to the traditional pan-genome analysis that uses isolate genomes (from a pure strain isolated from a mixed bacterial population), it is not …

Dynamic Observers For Unknown Populations, Chris Guiver, Nathan Poppelreiter, Richard Rebarber, Brigitte Tenhumberg, Stuart Townley

Brigitte Tenhumberg Papers

Dynamic observers are considered in the context of structuredpopulation modeling and management. Roughly, observers combine a known measured variable of some process with a model of that process to asymptotically reconstruct the unknown state variable of the model. We investigate the potential use of observers for reconstructing population distributions described by density-independent (linear) models and a class of density-dependent (nonlinear) models. In both the density-dependent and -independent cases, we show, in several ecologically reasonable circumstances, that there is a natural, optimal construction of these observers. Further, we describe the robustness these observers exhibit with respect to disturbances and uncertainty in …

Introduction To The R-Package: Usdampr, Elliott James Dennis, Bowen Chen

Extension Farm and Ranch Management News

Why the Need for the Package? In the 1990’s, concern over growing packer concentration and a hog industry market shock resulted in discontent among producers and packers. As a result, the United States Congress passed the Livestock Mandatory Reporting Act of 1999 (1999 Act) [Pub. L. 106-78, Title IX] which is required to be reauthorized every five years. See here for a full history of the Livestock Mandatory Reporting Background.

Market reports were publicly issued in the form of .txt files with varying frequency from April 2000 to April 2020. Current and historical data were also housed in a USDA-AMS …

Using Bioinformatics Tools To Evaluate Potential Risks Of Food Allergy And To Predict Microbiome Functionality, Mohamed Abdelmoteleb

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

Novel foods and Genetically Engineered (GE) organisms are being developed for nutritional, industrial, and environmental applications. Dietary interventions have been used recently to mitigate methane emissions in ruminants. In this project, bioinformatics tools have been used to answer two main questions. The first question is the potential allergy risks for consumption of novel foods and GE organisms. The second question is the effects of dietary interventions on microbiome functionality related to methane production in ruminants.

To answer the first question, regulatory authorities in the United States and Europe now expect an evaluation of new proteins in novel foods or genetically …

Assembly And Identification Of Novel Viruses In The Aquatic Invertebrate Daphnia Magna, Freddy L. Gonzalez, Reilly O. Cooper, Clayton E. Cressler

UCARE Research Products

Microbiome studies have been critical to understanding host health and life history. Many studies primarily focus on understanding the impacts of bacteria on the host, while fewer examine the impacts of viruses on host fitness or the interaction between viruses and bacteria within a host. Here, we utilized shotgun sequencing to identify whether viruses were present in the model organism Daphnia magna. VIBRANT, a bioinformatic tool that utilizes hybrid machine learning and protein similarity to identify lytic genomes and other novel viruses, was used on sequencing data from four samples of adult and juvenile Daphnia. We found a …

On The Inadequacy Of Species Distribution Models For Modelling The Spread Of Sars-Cov-2: Response To Araújo And Naimi, Joseph D. Chipperfield, Blas M. Benito, Robert B. O'Hara, Richard J. Telford, Colin J. Carlson

Public Health Resources

The ongoing pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing significant damage to public health and economic livelihoods, and is putting significant strains on healthcare services globally. This unfolding emergency has prompted the preparation and dissemination of the article “Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate” by Araújo and Naimi (2020). The authors present the results of an ensemble forecast made from a suite of species distribution models (SDMs), where they attempt to predict the suitability of the climate for the spread of SARS-CoV-2 over the coming months. They argue that climate is …

Prospects And Challenges Of Population Health With Online And Other Big Data In Africa; Understanding The Link To Improving Healthcare Service Delivery, Rowland Edet, Bolarinwa Afolabi

Department of Sociology: Faculty Publications

Big data analytics offers promises to many health care service challenges and can provide answers to many population health issues. Big data is having a positive impact in almost every sphere of life in more advanced world while developing countries are striving to meet up. Even though healthcare systems in the developed world are recording some breakthroughs due to the application of big data, it is important to research the impact of big data in developing regions of the world, such as Africa and identify its peculiar needs. The purpose of this review was to summarize the challenges faced by …

Efficient Coi Barcoding Using High Throughput Single-End 400 Bp Sequencing, Chentao Yang, Yuxuan Zheng, Shangjin Tan, Guanliang Meng, Wei Rao, Caiqing Yang, David G. Bourne, Paul A. O'Brien, Junqiang Xu, Sha Liao, Ao Chen, Xiaowei Chen, Xinrui Jia, Ai-Bing Zhang, Shanlin Liu

Harold W. Manter Laboratory: Library Materials

Background

Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current highthroughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (for example, a maximum read length of 300 bp for the Illumina’s MiSeq system), or are hindered by a relatively high cost or low sequencing output (e.g. a maximum number of eight million reads per cell for the PacBio’s SEQUEL II system).

Results

Pooled cytochrome c oxidase subunit I (COI) barcodes from individual specimens were sequenced on the …

Repositories For Taxonomic Data: Where We Are And What Is Missing, Aurélian Miralles, Teddy Bruy, Katherine Wolcott, Mark D. Scherz, Dominik Begerow, Bank Beszteri, Michael Bonkowski, Janine Felden, Birgit Gemeinholzer, Frank Glaw, Frank Oliver Glöckner, Oliver Hawlitschek, Ivaylo Kostadinov, Tim W. Nattkemper, Christian Printzen, Jasmin Renz, Nataliya Rybalka, Marc Stadler, Tanja Weibulat, Thomas Wilke, Susanne S. Renner, Miguel Vences

Harold W. Manter Laboratory: Library Materials

Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000–20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4,113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use …

Connectivity Differences Between Gulf War Illness (Gwi) Phenotypes During A Test Of Attention, Tomas Clarke, Jessie Jamieson, Patrick Malone, Rakib U. Rayhan, Stuart Washington, John W. Vanmeter, James N. Baraniuk

Department of Mathematics: Faculty Publications

One quarter of veterans returning from the 1990–1991 Persian Gulf War have developed Gulf War Illness (GWI) with chronic pain, fatigue, cognitive and gastrointestinal dysfunction. Exertion leads to characteristic, delayed onset exacerbations that are not relieved by sleep. We have modeled exertional exhaustion by comparing magnetic resonance images from before and after submaximal exercise. One third of the 27 GWI participants had brain stem atrophy and developed postural tachycardia after exercise (START: Stress Test Activated Reversible Tachycardia). The remainder activated basal ganglia and anterior insulae during a cognitive task (STOPP: Stress Test Originated Phantom Perception). Here, the role of attention …

Transcriptomic Analyses And Computational Modeling Reveal That Fatty Acid Transport Protein 2 (Fatp2) Impacts The Transcriptional Activity Of Pparα Thus Altering The Lipid Metabolic Landscape, Vincent M. Perez

Department of Biochemistry: Dissertations, Theses, and Student Research

Fatty acid transport protein 2 (FATP2) is highly expressed in liver, small intestine, and kidney where it functions in both the uptake of exogenous long chain fatty acids (LCFAs) and in the activation of very long chain fatty acids (VLCFAs). Here we address the phenotypic impacts of deleting FATP2 with the following three separate approaches: [1] Utilizing an unbiased next-generation sequencing analysis of FATP2-null (fatp2-/-) mice fed a standard chow diet; [2] Utilizing an unbiased next-generation sequencing analysis of fatp2-null (fatp2-/-) mice fed a high-fat ketogenic diet (KD) and fasted for 24-hours [3] Building dynamic computer models built with data …

Genome-Wide Association Studies In Maize And Sorghum, Preston Hurst

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Genome-wide association studies are used to identify genetic variants associated with a particular phenotype. GWAS has been used in a variety of taxa, from humans, to fish to plants . The present analysis is focused on two species important to the human species: maize and sorghum. A GWAS in maize was carried out on the modification of the Ga1-s allele. The Ga1 locus has long been studied as being involved in a unilateral crossing barrier . However, it has long been suspected that the locus is modified by background genetic factors . GWAS was used to observe candidates for this …

Changes On Movement Control Of Dart Throwing Under Distance And Target Weight Constraints, Carlos E. Campos, Guilherme M. Lage, Andre G.P. Andrade, Crislaine R. Couto, Suziane P. Santos, Vitor L.S. Profeta, Herbert Ugrinowitsch

Athletic Performance Research

The aim of the study was to verify the effects of dart weight and target distance on kinematic variables of the movement control of the underarm dart throwing task. Four women and one man performed the task of throwing a dart at two horizontal circular targets located at 2m (Nt) and 3m (Ft) away, with two different weights, 22g (Ld) and 44g (Hd). On the first phase of the experiment, the human volunteers performed 200 trials per day during four sessions. On the fifth day, it had 40 more trials in a pseudo random order that were recorded and analysed. …

Contemporary Sexual Selection Does Not Explain Variation In Male Display Traits Among Populations, J. Colton Watts, Allissa Flynn, Brigitte Tenhumberg, Eileen Hebets

Brigitte Tenhumberg Papers

Sexual selection is widely hypothesized to facilitate the evolution of reproductive isolation through divergence in sexual traits and sexual trait preferences among populations. However, direct evidence of divergent sexual selection causing intraspecific trait divergence remains limited. Using the wolf spider Schizocosa crassipes, we characterized patterns of female mate choice within and among geographic locations and related those patterns to geographic variation in male display traits to test whether divergent sexual selection caused by mate choice explains intraspecific trait variation. We found evidence of phenotypic selection on male behavior arising from female mate choice, but no evidence that selection varied …