Bioinformatics Commons^™

Association Of Gut Microbiota Composition With Alzheimer’S-Like Disease In A Rat Model, Hana Heiba

Theses and Dissertations

With many countries turning ‘grey’ and facing an issue with aging populations, the risk of developing one form of neurodegenerative disease is increasing. Dementia, being the most common syndrome resulting from neurodegeneration, severely affects memory and cognitive functions. Alzheimer’s disease (AD) is the most common neurodegenerative disorder, with an estimated 615,000 new cases will be added to the existing 5.7 million by 2030 (Alkasir et al., 2017).

In the current study, we establish a sporadic AD-like rat model by injecting STZ intracerebrally. Stool samples were collected at two time points; after three weeks for the acute stage, and 3 months …

Illuminating The Drivers Of Genomic Diversification In Lamprologine Cichlids Of The Lower Congo River, Naoko P. Kurata

Dissertations, Theses, and Capstone Projects

Freshwater fishes are extraordinarily diverse, considering their available habitats represent a tiny proportion of the earth’s surface. Rivers connect heterogeneous habitats in a linear form and provide excellent simplified models to understand how aquatic biodiversity evolves. In particular, the lower Congo River (LCR) in west Central Africa consists of a dynamic hydroscape exhibiting extraordinary aquatic biodiversity, endemicity, and morphological and ecological specialization. This system is thus an excellent natural laboratory for understanding complex speciation and population diversification processes. In my research, I explore various drivers of diversification, and adaptive evolution in rheophilic lamprologine cichlids endemic to the LCR, including Lamprologus …

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

Honors Theses, University of Nebraska-Lincoln

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 …

Deephtlv: A Deep Learning Framework For Detecting Human T-Lymphotrophic Virus 1 Integration Sites, Johnathan Jia, Johnathan Jia

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

In the 1980s, researchers found the first human oncogenic retrovirus called human T-lymphotrophic virus type 1 (HTLV-1). Since then, HTLV-1 has been identified as the causative agent behind several diseases such as adult T-cell leukemia/lymphoma (ATL) and a HTLV-1 associated myelopathy or tropical spastic paraparesis (HAM/TSP). As part of its normal replication cycle, the genome is converted into DNA and integrated into the genome. With several hundreds to thousands of unique viral integration sites (VISs) distributed with indeterminate preference throughout the genome, detection of HTLV-1 VISs is a challenging task. Experimental studies typically use molecular biology …

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.

The Genomics Of Autism-Related Genes Il1rapl1 And Il1rapl2: Insights Into Their Cortical Distribution, Cell-Type Specificity, And Developmental Trajectories, Jacob Weaver

MUSC Theses and Dissertations

Neuropsychiatric disorders have a significant impact on modern society. These disorders affect a large percentage of the population: schizophrenia has a world-wide prevalence of 1% and autism spectrum disorders (ASD) affects 1 in 59 school-aged children in the US. There is substantial evidence that most neuropsychiatric disorders have a genetic component. Thus, with the advent of high throughput sequencing much effort has gone into identifying genetic variants associated with these disorders. The emerging picture from these studies is a complex one where hundreds of genes with small effects interact with a varied landscape of common variants to result in disease. …

Molecular Biodiversity Of Foraminifera, Rabindra Thakur

Masters Theses

Foraminifera are a diverse clade of mostly shell-building single-celled organisms. Estimation of foraminiferal diversity is critical for understanding past and present climatic conditions, as they are highly sensitive to environmental perturbations. Biodiversity estimates of foraminifera began with the counting of test (i.e., shell) microfossils composed of calcium carbonate, as they are well preserved in sediment samples. However, this view has changed with molecular biodiversity estimates, which suggest that early-diverging single-chamber (i.e., "monothalamid") species that lack preservation ability are more diverse than anticipated. Although biodiversity estimates of foraminifera at the molecular level have changed our perceptions, they possess various challenges, especially …

The Genomic Dynamics Of Fermented Food Microbes

Doctoral Dissertations

Along with the agriculture and domestication revolution, humans have utilized bacteria, yeasts, and molds for millennia in the production of traditionally fermented foods and beverages. Fermentation is a very ancient practice of high relevance nowadays since it contributes with a great variety of foods worldwide. Microbial fermentation allows metabolic transformation of the raw food materials leading to biochemical changes that played a key role in food preservation, health benefits, nutrition, flavors, and texture, among others. Food fermentation practices could diverge from traditional artisanal spontaneous fermentation to industrialize methods with specialized microbial starters and although fermented environments tend to be very …

Be-03 Effects Of Dietary Iron On Taxonomic Composition And Function Of The Zebrafish Gut Microbiome, Megan D. Whisonant, Jeremiah L. Jackson, Sam L. Evans, Stuart Gordon Ph.D.

SC Upstate Research Symposium

A healthy gut microbiota is essential to promote host health and well-being, therefore, effects of dietary components on the gut microbiome are important to investigate as the gastrointestinal tract can be a major route of infection. Iron—an essential component of heme and iron-sulfur proteins—plays a central role in many biological activities, including oxygen transport and cellular respiration.

In particular, the iron homeostasis system is one of the best characterized due to iron's causative relationship with iron-deficiency anemia. Dietary iron supplementation is a commonly used treatment for iron deficiency anemia; however, the known direct impacts of iron on the gut microbiome …

Biomarker Metabolite Discovery For Pancreatic Cancer Using Machine Learning, Immanuelle Kezia, Linda Erlina, Aryo Tedjo, Fadilah Fadilah

Indonesian Journal of Medical Chemistry and Bioinformatics

Pancreatic cancer is one of the deadliest cancers in the world. This cancer is caused by multiple factors and mostly detected at late stadium. Biomarker is a marker that can identify some diseases very specific. For pancreatic cancer, biomarker has been recognized using blood sample known as liquid biopsy, breath, pancreatic secret, and tumor marker CA19-9. Those biomarkers are invasive, so we want to identify the disease using a very convenient method. Metabolite is product from cell metabolism. Metabolites can become a biomarker especially from difficult diseases. In this paper, we want to find biomarker from metabolite using machine learning …

Identifying Non-Traditional Slippery Sequences Associated With Translational Frameshifts, Aaron J. Gin, Kari Lynn Clase

Graduate Industrial Research Symposium

Genetic frameshifts are a mutation in which
a nucleotide skip leads to a shift in the
reading frame. In viruses, these frameshifts
can be programmed using a slippery
sequence to bypass the stop codon
associated with the initial protein. This
allows for variable control of protein
expression. In bacteriophages, translational
frameshifts have been identified but only a
few have been proven experimentally. Using
experimental data and comparative
genomics, non-traditional slippery
sequences can be identified as assisting in
controlling the protein coding throughout
viruses. Novel slippery sequences can aid in
the understanding of protein expression in
biological environments and further the …

Intellectual Disability Related To De Novo Germline Loss Of The Distal End Of The P-Arm Of Chromosome 17: A Case Report, Eden Pope, Matthew Huertas, Amar Paul, Braden Cunningham, Matthew Jennings, Ryan Perry, Stephanie Chavez, John A. Kriak, Kyle B. Bills, David W. Sant

Annual Research Symposium

Hypothesis/Purpose: In this report we present a case of a 20-year-old female with congenital intellectual disability, stunted growth, and hypothyroidism. Competitive genetic hybridization (CHG) revealed a loss of 17p13.3, and the deletion was not present in either parent. This deletion has not previously been characterized, but mutations on the p-arm of chromosome 17 are responsible for Miller-Dieker Syndrome and Isolated Lissencephaly Sequence, both of which share symptoms in common with the patient.

Methods: Peripheral mononuclear cells (PBMCs) were used for karyotyping and competitive genetic hybridization (CHG). Bioinformatic analysis was carried out using the Genome Data Viewer (ncbi.nlm.nih.gov/genome/gdv).

Results: Karyotype was …

Vitamin C Contributes To Epigenetic Regulation Of Genes Related To Diabetic Retinopathy In Retinal Endothelial Cells, Elizabeth L. Turner, Jonathon Reynolds, Walker Kay, Marianne Becnel, Matthew Conway, Alexander Kim, John A. Kriak, Kyle B. Bills, David W. Sant

Annual Research Symposium

No abstract provided.

2d Respiratory Sound Analysis To Detect Lung Abnormalities, Rafia Sharmin Alice, Kc Santosh

SDSU Data Science Symposium

Abstract. In this paper, we analyze deep visual features from 2D data representation(s) of the respiratory sound to detect evidence of lung abnormalities. The primary motivation behind this is that visual cues are more important in decision-making than raw data (lung sound). Early detection and prompt treatments are essential for any future possible respiratory disorders, and respiratory sound is proven to be one of the biomarkers. In contrast to state-of-the-art approaches, we aim at understanding/analyzing visual features using our Convolutional Neural Networks (CNN) tailored Deep Learning Models, where we consider all possible 2D data such as Spectrogram, Mel-frequency Cepstral Coefficients …

Therapeutic Options For Covid-19: Drug Repurposing Of Serine Protease Inhibitor Against Tmprss2, Mohammad Wildan Abiyyi, Surya Dwira, Arleni Bustami, Linda Erlina

Indonesian Journal of Medical Chemistry and Bioinformatics

The SARS-Coronavirus 2 (SARS-CoV-2) outbreak is a serious global public health threat. Researchers around the world are conducting mass research to control this epidemic, starting from the discovery of vaccines, to new drugs that have specific activities as antivirals. Drug repurposing is a potential method of using drugs with known activity for reuse as COVID-19 therapy. This method has the advantage that it can reduce costs and also the duration in the development of potential drugs. The initial step in drug repurposing can be done computationally to determine the effectiveness and specificity of the drug on the target protein. Molecular …

Virtual Screening On Indonesian Herbal Compounds As Sars-Cov-2 Spike (S2) Glycoprotein Inhibitors: Pharmacophore Modelling & Molecular Docking Approaches, Syailendra Karuna Sugito, Artha Uli Cristina, Putri Saskia Harimurti, Gabriella Regita Cendani, Fauzi Azhar Insani, Linda Erlina, Rafika Indah Paramita, Fadilah Fadilah

Indonesian Journal of Medical Chemistry and Bioinformatics

Background: There are still no specific treatments for coronavirus disease (COVID-19) until present days. Several studies have been conducted to determine whether herbal medicine can be an option to be used as a definitive medicine for COVID-19. S2 subunit of spike protein which is responsible for SARS-CoV-2 entry to the host cell, is a potential drug target to inhibit the viral infection. In this study, we aimed to find some compounds from the HerbalDB database that have potential as SARS-CoV-2 spike (S2) glycoprotein inhibitor.

Methods: The 6LXT protein was used as the target protein. The procedure in this study consisted …

Investigating The Potential Role Of Termites As Pathogen Vectors In The Decline Of Ironwood Trees (Casuarina Equisetifolia) In Guam, Garima Setia

LSU Master's Theses

Termites have been found associated with the decline of Casuarina equisetifolia (ironwood), an important agro-forestry species in Guam. While the ironwood tree decline (IWTD) was first reported in 2002, its association with termites as well as with bacteria Ralstonia solanacearum and Klebsiella species (K. oxytoca and K. variicola) was determined in 2010 and 2012 respectively. In 2019, the termite species attacking the ironwood trees were identified as Nasutitermes takasagoensis, Coptotermes gestroi, and Microcerotermes crassus. However, the role of termites in IWTD is not known. Since termites are repositories of bacteria and consume wood, termite foragers might …

Bioinformatics Lab: A Course-Based Undergraduate Research Experience Curriculum, Kristen M. Deangelis, Mallory Choudoir, Ashley Eng, Maureen A. Morrow

Microbiology Educational Materials

This is a computer lab course intended to give students technical and practical experience in analyzing sequencing data. We focus on bacterial genomes from recently isolated bacteria, so there is a possibility of discovery of new microbial diversity. Collaborative learning will be encouraged, but students will work individually to assemble, annotate, and analyze a bacterial genome.

Each week will begin with a review on the topic to be covered for that week. When applicable, there will be pre-recorded lectures to introduce lab topics, and students are expected to have watched these before coming to class. Our time in class will …

Analysis Of Ab Initio Protein Structure Prediction Methods, Maytha Alshammari, Jing He

College of Sciences Posters

Protein structure prediction produces atomic models of three-dimensional structure of a protein from its amino acid sequence. Understanding the function mechanism of proteins requires knowledge of three-dimensional structures. When developing new enzymes and drugs, it's essential to understand the structure of the target protein. In this study, we analyze models predicted using two ab initio protein structure prediction methods, trRosetta and Quark. A set of thirty protein chains was used to evaluate the effectiveness of the methods. The thirty chains were collected from Protein Data Bank (June – November, 2020). The length and the relative position of the predicted secondary …

Attack Of The Clones: Elucidating The Role Of Clonality In The Invasion Success Of Carpobrotus Edulis, Eduardo Luis Cruz

Electronic Theses, Projects, and Dissertations

Transcriptomics is a modern technique in genomics that utilizes RNA sequences to get a snapshot of genetic expression. This is a powerful tool in non-model species lacking a reference genome. Thus, the application of comparative transcriptomics has the potential to help us elucidate the evolutionary mechanisms that facilitate species invasion. Carpobrotus edulis is a prolific and widespread invasive succulent plant belonging to the Aizoaceae family. A native to South Africa, this species has become a dominant invader of many Mediterranean coastal areas. In this study, we leveraged the use of RNAseq to investigate evolutionary changes among invasive populations. RNA-seq data …