Alterations Of The Gut Mycobiome In Patients With Ms - A Bioinformatic Approach, 2022 University of Connecticut
Alterations Of The Gut Mycobiome In Patients With Ms - A Bioinformatic Approach, Saumya Shah
Honors Scholar Theses
The mycobiome is the fungal component of the gut microbiome and is implicated in several autoimmune diseases. However, its role in multiple sclerosis (MS) has not been studied. We performed descriptive and formal statistical tests using the R language to characterize the gut mycobiome in people with MS (pwMS) and healthy controls. We found that the microbiome composition of multiple sclerosis patients is different from healthy people. The mycobiome had significantly higher alpha diversity and inter-subject variation in pwMS than controls. Additionally, Saccharomyces and Aspergillus were over-represented in pwMS. Different mycobiome profiles, defined as mycotypes, were associated with different bacterial …
Scalable Software Infrastructure For The Lab And A Specific Investigation Of The Yeast Transcription Factor Eds1, 2022 Washington University in St. Louis
Scalable Software Infrastructure For The Lab And A Specific Investigation Of The Yeast Transcription Factor Eds1, Chase Mateusiak
McKelvey School of Engineering Theses & Dissertations
Individual biology labs handle increasingly large data sets. Ensuring accurate data entry, consistent sample metadata, and ease of access to the data once it is stored, are critical for both the integrity of analysis as well as productivity of the lab. Chapter 1 one of this thesis describes three implementations of software meant to facilitate handling data and metadata in the lab as the size of the data and complexity of analysis scale. The first piece of software is a database and entry interface for storing a large and varied amount of data on biological samples. The second is a …
Genomic Tools And Models For Investigating The Role Of Germline Diversity In Mouse Antibody Repertoire Development., 2022 University of Louisville
Genomic Tools And Models For Investigating The Role Of Germline Diversity In Mouse Antibody Repertoire Development., Justin T. Kos
Electronic Theses and Dissertations
Given the diversity and complexity within immunoglobulin (IG) loci, effective mouse models first require characterization of intra-strain differences and construction of high-quality reference assemblies for IG loci in several representative strains. To understand light chain germline diversity across biomedically significant mouse strains, we profiled the expressed IGK and IGL repertoires of 18 commonly used laboratory mouse strains using AIRR-seq. Across strains, we observed germline IGKV sequences shared by three different IGK haplotypes and a more conserved IGLV germline repertoire among common laboratory strains. Pacific Biosciences (PacBio) Single-Molecule Real-Time (SMRT) sequencing was used to sequence and assemble bacterial artificial chromosomes (BAC) …
Genomic Analysis Of Metabolic Differences Found In Clostridium Perfringens That Cause Necrotic Enteritis In Poultry, 2022 University of Nebraska-Lincoln
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 …
Using Machine Learning To Recognize Chronic Rhinosinusitis, 2022 Illinois Mathematics and Science Academy
Using Machine Learning To Recognize Chronic Rhinosinusitis, Irene Liu '23
Student Publications & Research
Chronic Rhinosinusitis (CRS) is a nasal disease characterized by the inflammation of the mucosa and paranasal sinuses with a duration of at least 12 consecutive weeks. So, to diagnose CRS, one needs to keep a record of their symptoms for ~12 weeks before they are recommended to get a tomography which will allow physicians to classify them as a patient with CRS or without. This is a timely and costly process; thus, machine learning should be used to speed the process up. Since patients with CRS have more obstructed noses, the sound produced should be different than an individual without …
Identification Of Dna Methylation Episignatures For Classification And Phenotype/Genotype Correlation In Mendelian Neurodevelopmental Disorders, 2022 The University of Western Ontario
Identification Of Dna Methylation Episignatures For Classification And Phenotype/Genotype Correlation In Mendelian Neurodevelopmental Disorders, John Reilly
Electronic Thesis and Dissertation Repository
ABSTRACT: Diagnosis for neurodevelopmental disorders poses numerous challenges, related to the lack of specific findings and limited understanding of clinical impact of the majority of genetic variation. Epigenomics mechanisms involve chemical modifications in DNA that involve a range of cellular mechanisms. DNA methylation is an epigenetic mechanism involving addition and removal of methyl groups to cytosine residues. These methylation signals form episignatures; patterns of methylation that can be used as biomarkers capable of differentiating neurodevelopmental disorders. EpiSigns have enabled molecular diagnosis of a number of genetic conditions, classification of variants of unknown significance, and provided insights into the pathophysiology of …
Annual Faculty Research Symposium 2022, 2022 Oakwood University
Annual Faculty Research Symposium 2022, Oakwood University
Proceedings
No abstract provided.
Identifying Molecular Markers For Early Detection Of Toxic Cyanobacteria And Dinoflagellate, 2022 St. Mary's University
Identifying Molecular Markers For Early Detection Of Toxic Cyanobacteria And Dinoflagellate, Shafqat F. Ehsan
Honors Program Theses and Research Projects
Harmful algal Blooms (HABs) develop when algal colonies grow out of control, causing toxicity or injury to humans, fish, shellfish, marine mammals, and birds. Most HABs of public health concern in saltwater generally are caused by eukaryotic dinoflagellates and diatoms. Prokaryotic cyanobacteria are usually responsible for freshwater blooms although they can contribute to saltwater and brackish blooms too. A common monitoring target of both groups is the saxitoxin-encoding genes. Saxitoxin(STX) is responsible for Paralytic shellfish poisoning, a foodborne illness developed from consumption of STX contaminated shellfish. Each cyanobacterial SXT gene cluster contains a set of core genes, common to all …
Comparative Modeling And Evolutionary Comparison Of Serine Protease, A Timber Rattlesnake Venom Protein, 2022 Jacksonville State University
Comparative Modeling And Evolutionary Comparison Of Serine Protease, A Timber Rattlesnake Venom Protein, Qawer Ayaz
Theses
The aim of this study is to create a homology model of VG35 serine protease and evaluate the evolutionary comparison of secondary structure on basis of protein model using YASARA. This method was furthermore used to predict the potential epitopes which can help in the investigation of future studies.
The VG35 was used to run a BLAST search which gave most resembled serine protease of different species which was then translated and modeled in YASARA. The modeled protein data was then used to determine the secondary structure. This was then used for evolutionary comparison of all proteins to VG35. Then …
Meta-Analysis Of Two Rnaseq Datasets To Determine Diagnostic Biomarkers And Drug Target Candidates For Periodontitis, 2022 Roseman University of Health Sciences
Meta-Analysis Of Two Rnaseq Datasets To Determine Diagnostic Biomarkers And Drug Target Candidates For Periodontitis, Carlos Moreno
Annual Research Symposium
No abstract provided.
A Machine Learning Framework For Identifying Molecular Biomarkers From Transcriptomic Cancer Data, 2022 Florida International University
A Machine Learning Framework For Identifying Molecular Biomarkers From Transcriptomic Cancer Data, Md Abdullah Al Mamun
FIU Electronic Theses and Dissertations
Cancer is a complex molecular process due to abnormal changes in the genome, such as mutation and copy number variation, and epigenetic aberrations such as dysregulations of long non-coding RNA (lncRNA). These abnormal changes are reflected in transcriptome by turning oncogenes on and tumor suppressor genes off, which are considered cancer biomarkers.
However, transcriptomic data is high dimensional, and finding the best subset of genes (features) related to causing cancer is computationally challenging and expensive. Thus, developing a feature selection framework to discover molecular biomarkers for cancer is critical.
Traditional approaches for biomarker discovery calculate the fold change for each …
The Low Abundance Of Cpg In The Sars-Cov-2 Genome Is Not An Evolutionarily Signature Of Zap, 2022 UNSW Sydney, Australia
The Low Abundance Of Cpg In The Sars-Cov-2 Genome Is Not An Evolutionarily Signature Of Zap, Ali Afrasiabi, Hamid Alinejad-Rokny, Azad Khosh, Mostafa Rahnama, Nigel Lovell, Zhenming Xu, Diako Ebrahimi
Plant Pathology Faculty Publications
The zinc finger antiviral protein (ZAP) is known to restrict viral replication by binding to the CpG rich regions of viral RNA, and subsequently inducing viral RNA degradation. This enzyme has recently been shown to be capable of restricting SARS-CoV-2. These data have led to the hypothesis that the low abundance of CpG in the SARS-CoV-2 genome is due to an evolutionary pressure exerted by the host ZAP. To investigate this hypothesis, we performed a detailed analysis of many coronavirus sequences and ZAP RNA binding preference data. Our analyses showed neither evidence for an evolutionary pressure acting specifically on CpG …
Genetic And Environmental Regulation Of Plant Growth, 2022 University of Massachusetts Amherst
Genetic And Environmental Regulation Of Plant Growth, Kirk J-M Mackinnon
Doctoral Dissertations
Field grown crops are continually exposed to a variety of external stimuli that influence plant responses. Light, temperature, and water availability interact to affect many economically important traits including growth rate, size, and lifespan. My research is focused on the intersection of genetic and environmental factors influencing plant growth. Specifically, I am interested in elucidating the regulation of rhythmic genes in response to photo- and thermocycles and identifying novel candidate genes associated with growth and drought traits. Understanding the gene regulatory networks that mediate time-of-day signaling is vital to identifying candidate genes across the pan-genome associated with traits of interest.
Mapping Selected Polyphenols Metabolism By Gut Bacteria And Their Genes, 2022 University of Massachusetts Amherst
Mapping Selected Polyphenols Metabolism By Gut Bacteria And Their Genes, Ermin Zhao
Doctoral Dissertations
The human gut microbiome is a huge enzyme repository for dietary polyphenols metabolism, especially considering most of the polyphenols cannot be digested in the host and their biological functions are limited. Poor bioaccessibility based on traditional pharmaceutical ADME (absorption, distribution, metabolism, and excretion) assessment is the main problem facing the widely medical application of most polyphenols. Gut bacteria have the potential to mediate a wide range of biotransformation reactions of polyphenols, which leads to the production of many bioactive metabolites. In the past decades, mounting evidence in traditional ADME study have demonstrated gut bacteria play an irreplaceable role in dietary …
Modeling Jadera Haematoloma’S Phenotypic Variation In The Context Of Its Developmental Plasticity, 2022 Colby College
Modeling Jadera Haematoloma’S Phenotypic Variation In The Context Of Its Developmental Plasticity, Michael C. Yorsz
Honors Theses
Phenotypic plasticity is the ability of an organism to integrate information from environmental cues to inform the development of its phenotype and remains understudied in biology. Models of plasticity are needed because evolution in the presence of plasticity is poorly understood. Jadera haematoloma, a hemimetabolous true bug, is an excellent animal model of plasticity, exhibiting a non-linear plastic response to juvenile nutrition that biases adult development into groups with differences in flight capability, wing shape, and fecundity. However, there is a lack of literature consensus regarding the range of developmental outcomes in the species. Some publications report the presence …
Cbp60-Db: An Alphafold-Predicted Plant Kingdom-Wide Database Of The Calmodulin-Binding Protein 60 (Cbp60) Protein Family With A Novel Structural Clustering Algorithm, 2022 Wilfrid Laurier University
Cbp60-Db: An Alphafold-Predicted Plant Kingdom-Wide Database Of The Calmodulin-Binding Protein 60 (Cbp60) Protein Family With A Novel Structural Clustering Algorithm, Keaun Amani, Vanessa Shivnauth, Christian Castroverde
Biology Faculty Publications
Molecular genetic analyses in the model species Arabidopsis thaliana have demonstrated the major roles of different CAM-BINDING PROTEIN 60 (CBP60) proteins in growth, stress signaling, and immune responses. Prominently, CBP60g and SARD1 are paralogous CBP60 transcription factors that regulate numerous components of the immune system, such as cell surface and intracellular immune receptors, MAP kinases, WRKY transcription factors, and biosynthetic enzymes for immunity-activating metabolites salicylic acid (SA) and N-hydroxypipecolic acid (NHP). However, their function, regulation and diversification in most species remain unclear. Here we have created CBP60-DB, a structural and bioinformatic database that comprehensively characterized 1052 CBP60 gene homologs …
Evaluación De La Posible Existencia Biológica De Proteínas A Partir De Secuencias De Arns Generados Por Modelamiento Computacional Pseudoaleatorio, 2022 Universidad de La Salle, Bogotá
Evaluación De La Posible Existencia Biológica De Proteínas A Partir De Secuencias De Arns Generados Por Modelamiento Computacional Pseudoaleatorio, Joan Sebastián Gutiérrez Sánchez, Andrés Reinaldo Chacón Prada
Biología
Las proteínas son biomoléculas fundamentales para el funcionamiento de los sistemas biológicos, por lo que entender como surgen y evolucionan es de gran interés teórico. Algunos autores consideran que el origen de las proteínas se dio por el ordenamiento aleatorio de secuencias polipeptídicas; por este motivo el objetivo de este trabajo es inferir si el proceso de creación de secuencias de ARN mensajeros es de carácter estocástico, mediante el diseño y programación de un código computacional en Python que genera secuencias de ARN de manera pseudoaleatoria; posteriormente, se tradujeron las secuencias de ARN obtenidas a aminoácidos para poder realizar un …
Degradation And Nitrogen Cycling In The Context Of Biodiversity-Ecosystem Function Relationships In The Inquiline Bacterial Community Of Darlingtonia Californica, 2022 Humboldt State University
Degradation And Nitrogen Cycling In The Context Of Biodiversity-Ecosystem Function Relationships In The Inquiline Bacterial Community Of Darlingtonia Californica, Megan Teigen
Cal Poly Humboldt theses and projects
Biodiversity-ecosystem function (BEF) research aims to explain how species and their environments interact with each other. Microbial communities engage in vital biogeochemical pathways in a variety of natural ecosystems, and yet there are large knowledge gaps about the specific metabolic pathways in which they are involved. Degradation specifically contributes to nitrogen cycling globally through the breakdown of large organic nitrogen compounds into small inorganic nitrogen that is necessary for the survival of many other organisms. In this study, I focused on the degradative function of the inquiline microbial communities found within the carnivorous pitcher plant, Darlingtonia californica. Darlingtonia grows in …
Identifying Epidermal Enriched Genes Required For Planarian Regeneration- Sp. Schmidtea Mediterranea, 2022 University of Kentucky
Identifying Epidermal Enriched Genes Required For Planarian Regeneration- Sp. Schmidtea Mediterranea, Pallob Barai
Theses and Dissertations--Biology
The outer epithelial layer covering an organism, commonly known as the epidermis, is crucial for maintaining homeostasis and for the wound healing processes after injury. The planarian epidermis allows flatworms to heal their wounds and virtually restore any missing tissues. Immediately after amputation, planarians contract their muscle and stretch their epidermis to heal the wound area. However, how the planarian epidermis coordinates with other tissues and mechanisms after the initial wound healing processes begins is not understood in detail. I hypothesized that epidermal cell stretching upon wound healing induces transcriptional changes that are required for effective regeneration. To test this …
An Integrative Investigation Of The Synechococcus A/B Clade During Adaptive Radiation At The Upper Thermal Limit Of Phototrophy, 2022 University of Montana, Missoula
An Integrative Investigation Of The Synechococcus A/B Clade During Adaptive Radiation At The Upper Thermal Limit Of Phototrophy, Christopher L. Pierpont
Graduate Student Theses, Dissertations, & Professional Papers
Thermophilic microorganisms have been scientifically observed since the early nineteenth century and have spurred many questions about the limits of life and the capacity of organisms to survive extreme conditions. Decades of research on thermophile proteins and genomes have yielded several proposed correlates of temperature that may contribute to adaptation of bacteria and archaea to high temperature. However, many of the generalizations reported are drawn from analyses of deeply divergent taxa or from individual case studies in isolation from mesophilic relatives. Members of the Synechococcus A/B (SynAB) group are the only cyanobacteria with members able to grow above 65 °C …