Computational Biology Commons^™

Circadian Rhythmicity And Melatonin Sensitivity In The Human Gut Commensal Bacterium Klebsiella Aerogenes, Kinga Graniczkowska

Theses and Dissertations--Biology

While the expression of circadian rhythms is nearly universal among multicellular eukaryotic organisms, demonstration of this phenomenon in prokaryotes has been largely restricted to photosynthetic cyanobacteria until very recently. Further, growing interest in gastrointestinal microbiomes has revealed a complex temporal relationship between the gastrointestinal clock and the bacterial microbiome within. At least one member of the gut microbiome, Klebsiella (née Enterobacter) aerogenes, responds to the indoleamine hormone melatonin, secreted by the gastrointestinal system itself. Further research revealed that K. aerogenes also expresses a circadian rhythm in motility and gene expression that is temperature compensated. Although rhythmicity is unaltered …

Identification And Optimization Of Mirna Biomarkers For Body Mass Index (Bmi) Estimation In Forensic Samples, Jennifer J. Shealy

Master of Science in Forensic Science Directed Research Projects

DNA profiles do not provide as much evidentiary value when either all known samples can be excluded or when there is no known suspect. DNA phenotyping is a technique used for investigative purposes to predict externally visible characteristics (EVCs) based on specific markers found in the genome. Most phenotyping panels are currently restricted to markers stable over a lifetime within an individual and are not able to predict environmental or metabolic impacts on EVCs. It is known that miRNA expression levels change due to environmental and metabolic factors, such as BMI, and research has proven associations between circulating plasma miRNAs …

Fmri Feature Extraction Model For Adhd Classification Using Convolutional Neural Network, Senuri De Silva, Sanuwani Udara Dayarathna, Gangani Ariyarathne, Dulani Meedeniya, Sampath Jayarathna

Computer Science Faculty Publications

Biomedical intelligence provides a predictive mechanism for the automatic diagnosis of diseases and disorders. With the advancements of computational biology, neuroimaging techniques have been used extensively in clinical data analysis. Attention deficit hyperactivity disorder (ADHD) is a psychiatric disorder, with the symptomology of inattention, impulsivity, and hyperactivity, in which early diagnosis is crucial to prevent unwelcome outcomes. This study addresses ADHD identification using functional magnetic resonance imaging (fMRI) data for the resting state brain by evaluating multiple feature extraction methods. The features of seed-based correlation (SBC), fractional amplitude of low-frequency fluctuation (fALFF), and regional homogeneity (ReHo) are comparatively applied to …

Composition And Homology In The Taxonomic Classification Of Escherichia Coli, Tanya Irani

Theses and Dissertations (Comprehensive)

As new techniques have been introduced, specifically the possibility of complete genome sequencing, better methods of defining bacterial species have also been proposed. One of the most recently proposed methods, using bioinformatic techniques, is to calculate the average nucleotide identity (ANI) between the homologous genome segments of different isolates. Another method for species discrimination that has been tested successfully is the similarity of DNA compositional signatures. However, in a recent update, DNA signatures split the available Escherichia coli complete genomes into three groups. To check if this result was consistent with such genomes belonging to different species, we tested methods …

Age, Growth, And Mortality Of Atlantic Tripletail In The North-Central Gulf Of Mexico, Amanda E. Jefferson, Matthew B. Jargowsky, Meagan N. Schrandt, Pearce T. Cooper, Sean P. Powers, John Dindo, J. Marcus Drymon

University Faculty and Staff Publications

In the southeastern USA and the Gulf of Mexico (GOM), Atlantic Tripletail Lobotes surinamensis are increasingly targeted by recreational anglers, indicating that stock status should be assessed. A critical need for such assessments is age-specific data; however, previous studies have drawn conflicting conclusions regarding the most appropriate structure for aging. Moreover, growth parameters and mortality rates for GOM Atlantic Tripletail are unknown. Therefore, the goals of this study were to (1) evaluate sagittal otoliths and first dorsal spines as aging structures; (2) model combined and sex-specific growth; and (3) estimate mortality rates for GOM Atlantic Tripletail. From 2012 to 2019, …

Microbiome Community And Parasitic Infections In Wild Bees, Mark G. Young

Honors Theses

The microbiome is increasingly recognized for its complex relationship with host fitness. Akin to primates and other social animals, bumblebees harbor a specific microbiome derived from social contact. The bumblebee microbiome is characteristically species poor, with just a few “core” phylotypes accounting for the majority of total abundance. Genomic analyses reveal phylogenetic congruence and adaptation of the core endosymbionts to the bumblebee gut, indicating a shared evolutionary history. Prior investigations reveal that the relative abundance of core microbes is negatively associated with infection by a trypanosome, Crithidia bombi, and that the microbiome has a mechanistic role in immunity. As …

Sparse Forward-Backward Alignment For Sensitive Database Search With Small Memory And Time Requirements, David H. Rich

Graduate Student Theses, Dissertations, & Professional Papers

Sequence annotation is typically performed by aligning an unlabeled sequence to a collection of known sequences, with the aim of identifying non-random similarities. Given the broad diversity of new sequences and the considerable scale of modern sequence databases, there is significant tension between the competing needs for sensitivity and speed, with multiple tools displacing the venerable BLAST software suite on one axis or another. In recent years, alignment based on profile hidden Markov models (pHMMs) and associated probabilistic inference methods have demonstrated increased sensitivity due in part to consideration of the ensemble of all possible alignments between a query and …

Ensemble Protein Inference Evaluation, Kyle Lee Lucke

Graduate Student Theses, Dissertations, & Professional Papers

The Protein inference problem is becoming an increasingly important tool that aids in the characterization of complex proteomes and analysis of complex protein samples. In bottom-up shotgun proteomics experiments the metrics for evaluation (like AUC and calibration error) are based on an often imperfect target-decoy database. These metrics make the inherent assumption that all of the proteins in the target set are present in the sample being analyzed. In general, this is not the case, they are typically a mix of present and absent proteins. To objectively evaluate inference methods, protein standard datasets are used. These datasets are special in …

Novel Computational Methods For Cancer Genomics Data Analysis, Jinpeng Liu

Theses and Dissertations--Computer Science

Cancer is a genetic disease responsible for one in eight deaths worldwide. The advancement of next-generation sequencing (NGS) technology has revolutionized the cancer research, allowing comprehensively profiling the cancer genome at great resolution. Large-scale cancer genomics research has sparked the needs for efficient and accurate Bioinformatics methods to analyze the data. The research presented in this dissertation focuses on three areas in cancer genomics: cancer somatic mutation detection; cancer driver genes identification and transcriptome profiling on single-cell level.

NGS data analysis involves a series of complicated data transformation that convert raw sequencing data to the information that is interpretable by …

Applications Of Machine Learning In Microbial Forensics, Ryan B. Ghannam

Dissertations, Master's Theses and Master's Reports

Microbial ecosystems are complex, with hundreds of members interacting with each other and the environment. The intricate and hidden behaviors underlying these interactions make research questions challenging – but can be better understood through machine learning. However, most machine learning that is used in microbiome work is a black box form of investigation, where accurate predictions can be made, but the inner logic behind what is driving prediction is hidden behind nontransparent layers of complexity.

Accordingly, the goal of this dissertation is to provide an interpretable and in-depth machine learning approach to investigate microbial biogeography and to use micro-organisms as …

Statistical Methods In Genetic Studies, Cheng Gao

Dissertations, Master's Theses and Master's Reports

This dissertation includes three Chapters. A brief description of each chapter is organized as follows.

In Chapter 1, we proposed a new method, called MF-TOWmuT, for genome-wide association studies with multiple genetic variants and multiple phenotypes using family samples. MF-TOWmuT uses kinship matrix to account for sample relatedness. It is worth mentioning that in simulations, we considered hidden polygenic effects and varied the proportion of variance contributed by it to generate phenotypes. Simulation studies show that MF-TOWmuT can preserve the type I error rates and is more powerful than several existing methods in different simulation scenarios, MFTOWmuT is also quite …

Single-Fluorophore Sensors For Mechanical Force In Living Cells, Sarah Kricheff

Honors Scholar Theses

Mechanotransduction is the process by which a mechanical stimulus is converted to a cellular signal. This process is heavily influential of cell morphology, differentiation, and behavior. However, altered levels of mechanical stimuli are also found in many pathological contexts. For example, cancerous cells have stiffer surrounding tissue than healthy cells, and research suggests that this alters cell behavior and promotes metastasis. Despite these findings, the cellular processes behind these signaling alterations remain widely unknown. Understanding these cascades is critical, as involved proteins can give us a deeper understanding of the role of mechanotransduction, and certain proteins can potentially be targeted …

A Comparative Genomics Exploration Of Inter-Partner Metabolic Signaling In The Coral-Algal Symbiosis, Katherine E. Dougan

FIU Electronic Theses and Dissertations

At the foundation of coral reef ecosystems is the symbiosis between the coral host and its microbial community, particularly its photoautotrophic algae from the family Symbiodiniaceae. As a symbiosis centered around nutritional exchange, determining the mechanisms involved in the maintenance of this cooperative exchange is central to understanding how it breaks down. As the nutritional transfer primarily consists of sugars, this work first focuses on the cnidarian insulin signaling pathway, an evolutionarily important metazoan pathway involved in diverse functions, most notably metabolism. This dissertation unveiled 360 putative cnidarian insulin-like peptides (cnILPs) from existing transcriptomic datasets, where they were previously missed …

An Examination Of The Influence Of Multi-Scale Processes And Connectivity On The Population And Assemblage Dynamics Of Headwater Fishes, Josh P. Hubbell

Dissertations

Typified by their branching pattern, headwaters are numerically abundant as the density of these habitats increases with increasing distance from the base of a dendritic river system. Connectivity among headwaters is complex, resulting in the spatial isolation of populations. Headwater specialists have evolved a suite of traits that permit these species to permanently reside within these habitats. The spatial configuration and connectivity of headwaters has repercussions for metapopulations and meta-assemblages. I investigated how multi-scale processes and connectivity influenced the patch occupancy, coexistence, movement ecology, population structure, and gene flow of headwater specialists. In chapter two, I used occupancy modeling to …

Gene Set Testing By Distance Correlation, Sho-Hsien Su

Graduate Theses and Dissertations

Pathways are the functional building blocks of complex diseases such as cancers. Pathway-level studies may provide insights on some important biological processes. Gene set test is an important tool to study the differential expression of a gene set between two groups, e.g., cancer vs normal. The differential expression of a gene set could be due to the difference in mean, variability, or both. However, most existing gene set tests only target the mean difference but overlook other types of differential expression. In this thesis, we propose to use the recently developed distance correlation for gene set testing. To assess the …

Investigation Of Sulfur Cycling In Marine Sponge Cinachyrella Spp. From A South Florida Reef, Shelby K. Cain

All HCAS Student Capstones, Theses, and Dissertations

Symbionts within marine sponges are actively participating in the biogeochemical cycles. Among them, the role of symbiont microbes in the sulfur cycle remains a mystery. This study measured the abundance of microbes within the genus Cinachyrella before and after exposure to hydrogen sulfide. A four-part study was conducted: a) five-hour drop experiments, b) vertical distribution experiments, c) five-hour uptake experiments, and d) long-term exposure experiments. The five-hour drop experiment utilized a microsensor to measure sulfide levels, which was lowered 1.0 mm every thirty minutes for a total of 5 hours. Three trials were performed, each with one sponge and a …

Decoding The Evolutionary Response To Prostate Cancer Therapy Using Plasma Genome Sequencing, Naveen Ramesh

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

Investigating genome evolution in response to therapy is difficult in human tissue samples due to the difficulty in accessing metastatic tumor sites and logistical challenges of collecting longitudinal samples. To overcome these issues, we developed an unbiased whole-genome plasma DNA sequencing approach called PEGASUS that concurrently measures genomic copy number and exome mutations from archival cryostored plasma samples. This approach was applied to study longitudinal blood plasma samples from prostate cancer patients. A molecular characterization of archival plasma DNA from 233 patients and genomic profiling of 101 patients identified clinical correlations of aneuploid plasma DNA profiles with poor survival, increased …

Investigation Of Proliferation Suppressors In Genetic Fitness Screens, Walter Frank Lenoir Iv

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

Innovation of CRISPR gene-editing technology has provided scientists genome manipulation tools that allowed rapid advancement of scientific capabilities and thus improved our ability to systematically study mammalian genetic functional profiles. Genome-wide CRISPR knockout screens conducted in collections of human cell lines can knock out genes at multiple loci, and have provided new insights into functional roles for independent genes. This method has launched massive efforts in looking across genetic backgrounds for context specific genetic vulnerabilities within cancer. Much of the research effort thus far has been spent on optimizing phenotype distinctions between essential, genes required for cell fitness, and non-essential, …

Statistical Approaches Of Gene Set Analysis With Quantitative Trait Loci For High-Throughput Genomic Studies., Samarendra Das

Electronic Theses and Dissertations

Recently, gene set analysis has become the first choice for gaining insights into the underlying complex biology of diseases through high-throughput genomic studies, such as Microarrays, bulk RNA-Sequencing, single cell RNA-Sequencing, etc. It also reduces the complexity of statistical analysis and enhances the explanatory power of the obtained results. Further, the statistical structure and steps common to these approaches have not yet been comprehensively discussed, which limits their utility. Hence, a comprehensive overview of the available gene set analysis approaches used for different high-throughput genomic studies is provided. The analysis of gene sets is usually carried out based on …

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

Dissertations and Theses in Biological Sciences

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 …