Bioinformatics Commons^™

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 …

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 …

De Novo Sequencing Of Multiple Tandem Mass Spectra Of Peptide Containing Silac Labeling, Fang Han

Electronic Thesis and Dissertation Repository

The systematic studies of proteins has gradually become fundamental in the research related to molecular biology. Shotgun proteomics use bottom-up proteomics techniques in identifying proteins contained in complex mixtures using a combination of high performance liquid chromatography coupled with mass spectrometry technology. Current mass spectrometers equipped with high sensitivity and accuracy can produce thousands of tandem mass spectrometry (MS/MS) spectra in a single run. The large amount of data collected in a single LC-MS/MS run requires effective computational approaches to automate the process of spectra interpretation. De novo peptide sequencing from tandem mass spectrometry (MS/MS) has emerged as an important …

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 …

Deep Learning Methods For Prediction Of And Escape From Protein Recognition, Bowen Dai

Dartmouth College Ph.D Dissertations

Protein interactions drive diverse processes essential to living organisms, and thus numerous biomedical applications center on understanding, predicting, and designing how proteins recognize their partners. While unfortunately the number of interactions of interest still vastly exceeds the capabilities of experimental determination methods, computational methods promise to fill the gap. My thesis pursues the development and application of computational methods for several protein interaction prediction and design tasks. First, to improve protein-glycan interaction specificity prediction, I developed GlyBERT, which learns biologically relevant glycan representations encapsulating the components most important for glycan recognition within their structures. GlyBERT encodes glycans with a branched …

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 …

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.

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 …

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 …

Inverse Probability Weighting In Survival Analysis And Network Analysis, Yukun Lu

Doctoral Dissertations

Inverse probability weighting is a popular technique to accommodate selection bias due to non-random sampling and missing data. In the first chapter, we develop an inverse probability weighted estimator and an augmented inverse probability weighted estimator of regression coefficients for a linear model with randomly censored covariates, when the censoring mechanism may be dependent on the outcome. We investigate the asymptotic properties of both estimators and evaluate their finite sample performance through extensive simulation studies. We apply the proposed methods to an Alzheimer’s disease study. In the second chapter, we present an application of network analysis in a study of …

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 …

The Impacts Of Immune Challenges On Fish Behavior And Physiology, Teisha King

LSU Doctoral Dissertations

For species living in dominance hierarchies, social rank dictates access to resources and often contributes to reproductive success. To ensure survival, individuals constantly evaluate trade- offs between crucial biological systems, like the reproductive and immune systems, depending on their social rank and physiological state. Little is known about how social species balance interactions between immune system function, fluctuations in social status and reproductive fitness, and the performance of behaviors necessary for maintaining social status when sick, particularly in fishes, the largest and most diverse group of vertebrates. My dissertation research uses a whole animal approach to examine how physiological profiles …

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 …

Incorporating Sex Chromosomes In Transcriptome Prediction Models And Improving Cross-Population Prediction Performance, Daniel S. Araujo

Master's Theses

Transcriptome prediction models built with data from European-descent individuals are less accurate when applied to different populations because of differences in linkage disequilibrium patterns and allele frequencies. We hypothesized multivariate adaptive shrinkage may improve cross-population transcriptome prediction, as it leverages effect size estimates across different conditions - in this case, different populations. To test this hypothesis, we made transcriptome prediction models for use in transcriptome-wide association studies (TWAS) using different methods (Elastic Net, Matrix eQTL and Multivariate Adaptive Shrinkage in R (MASHR)) and tested their out-of-sample transcriptome prediction accuracy in population-matched and cross-population scenarios. Additionally, to evaluate model applicability in …

A Population Level Examination Of The Incredible Fruit Diversity In Astragalus Lentiginosus, Quinn Thomas

Master's Theses

Astragalus lentiginosus is the most taxomically diverse species in the North American flora with over 40 recognized varieties. The incredible diversity within A. lentiginosus, particularly in respect to its fruit morphology, makes it an exceptional model to study adaptation and evolution. However, it remains unknown whether fruit morphology is an adaptation and, if so, the extent to which selection or neutral evolutionary processes shape the striking diversity in this trait. In order to understand the adaptive significance of fruit morphology we must first understand the genetic structure of A. lentiginosus. Varieties of A. lentiginosus vary considerably in their range size …

Comparison Of Taxonomy Assignment And Strain Detection In Urobiome Communities Using 16s Rrna Sequencing And Shotgun Metagenomic Sequencing, Delaney Sauer

Master's Theses

Advancements in sequencing technologies have enabled scientists to gain insight into the microbes that inhabit the human body, including the urinary tract. Cataloging the bacteria that inhabit the urinary tract has primarily relied on amplification and sequencing of specific variable regions of the 16S rRNA gene enabling genus-level taxonomic identification. Recently, shotgun metagenomic sequencing has been employed such that bacterial taxonomy as well as the functionality that they encode can be inferred. In this study, we compare taxonomies assigned by 16S sequencing and shotgun metagenomic sequencing of the urinary microbiota (urobiome) of females with and without a clinical diagnosis of …