Transcripity Split: Course-Based Rna-Seq Analysis Using The Ultrafast Kallisto-Sleuth Pipeline, Ray A. Enke
Ray Enke Ph.D.
No abstract provided.
Nuclear Spindles Pave The Way To Metastasis, 2017 University of Kentucky
Nuclear Spindles Pave The Way To Metastasis, Patrick J. Hensley, Natasha Kyprianou
Urology Faculty Publications
No abstract provided.
Unseen Science: Modern Discoveries Too Far Away Or Tiny For Human Eyes, 2017 Cuny Graduate School of Journalism
Unseen Science: Modern Discoveries Too Far Away Or Tiny For Human Eyes, Lucy Huang
As science has progressed, scientists have realized that evidence goes beyond the realms of physical sight. Whether it is too small or difficult to find, scientists have developed different ways to get around this problem. We see this in cancer genomics and in extrasolar planetary research. Scientists use what they know and what they measure to validate their work.
Dna Barcoding Of Quercus Falcata, Quercus Palustris, Quercus Rubra, And Their Hybrids Using Rbcl, Matk, And Ycf1, 2017 Southern Adventist Univeristy
Dna Barcoding Of Quercus Falcata, Quercus Palustris, Quercus Rubra, And Their Hybrids Using Rbcl, Matk, And Ycf1, Mckinzie Johnson, Tim Trott
Research in Biology
No abstract provided.
Analysis, Visualization, And Machine Learning Of Epigenomic Data, 2017 University of Massachusetts Medical School
Analysis, Visualization, And Machine Learning Of Epigenomic Data, Michael J. Purcaro
GSBS Dissertations and Theses
The goal of the Encyclopedia of DNA Elements (ENCODE) project has been to characterize all the functional elements of the human genome. These elements include expressed transcripts and genomic regions bound by transcription factors (TFs), occupied by nucleosomes, occupied by nucleosomes with modified histones, or hypersensitive to DNase I cleavage, etc. Chromatin Immunoprecipitation (ChIP-seq) is an experimental technique for detecting TF binding in living cells, and the genomic regions bound by TFs are called ChIP-seq peaks. ENCODE has performed and compiled results from tens of thousands of experiments, including ChIP-seq, DNase, RNA-seq and Hi-C.
These efforts have culminated in two ...
Validation Of A New Rapid Hybridization Buffer For Fluorescence In Situ Hybridization With A Review On The Kinetics Of Dna Hybridization, Christine O'Connor
Honors Scholar Theses
Abbott Molecular recently developed the rapid Vysis IntelliFISH Hybridization Buffer for use in fluorescence in situ hybridization (FISH) assays. The hybridization step in a standard FISH assay requires an overnight incubation, thus the turnaround time for a patient result is at least 24 hours. The IntelliFISH buffer was designed to reduce hybridization time of probes to target DNA to about two hours, allowing the entire assay to be performed in a single day. A review of methodologies and commercial products has highlighted the importance of hybridization kinetics to a successful FISH assay. The purpose of the research was to investigate ...
Integrative Cancer Immunogenomic Analysis Of Serial Melanoma Biopsies Reveals Correlates Of Response And Resistance To Sequential Ctla-4 And Pd-1 Blockade Treatment, 2017 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
Integrative Cancer Immunogenomic Analysis Of Serial Melanoma Biopsies Reveals Correlates Of Response And Resistance To Sequential Ctla-4 And Pd-1 Blockade Treatment, Whijae Roh
UT GSBS Dissertations and Theses (Open Access)
Melanoma is the most malignant form of skin cancer. The five-year survival rate for metastatic melanoma is 19.9%. Although targeted therapy of BRAF and MEK inhibitors were developed for melanoma, resistance to therapy is inevitable. Immune checkpoint blockade, which reverses the suppression of the immune system, on the other hand, has shown a durable response in 20-30% of patients with metastatic melanoma. However, more predictive and robust biomarkers of response to this therapy are still needed, and resistance mechanisms remain incompletely understood. To address this, we examined a cohort of metastatic melanoma patients treated with sequential checkpoint blockade against ...
Bioinformatic And Experimental Approaches For Deeper Metaproteomic Characterization Of Complex Environmental Samples, 2017 University of Tennessee, Knoxville
Bioinformatic And Experimental Approaches For Deeper Metaproteomic Characterization Of Complex Environmental Samples, Ramsunder Mahadevan Iyer
The coupling of high performance multi-dimensional liquid chromatography and tandem mass spectrometry for characterization of microbial proteins from complex environmental samples has paved the way for a new era in scientific discovery. The field of metaproteomics, which is the study of protein suite of all the organisms in a biological system, has taken a tremendous leap with the introduction of high-throughput proteomics. However, with corresponding increase in sample complexity, novel challenges have been raised with respect to efficient peptide separation via chromatography and bioinformatic analysis of the resulting high throughput data. In this dissertation, various aspects of metaproteomic characterization, including ...
Transcriptome-Based Gene Networks For Systems-Level Analysis Of Plant Gene Functions, 2017 University of Arkansas, Fayetteville
Transcriptome-Based Gene Networks For Systems-Level Analysis Of Plant Gene Functions, Chirag Gupta
Theses and Dissertations
Present day genomic technologies are evolving at an unprecedented rate, allowing interrogation of
cellular activities with increasing breadth and depth. However, we know very little about how the
genome functions and what the identified genes do. The lack of functional annotations of genes
greatly limits the post-analytical interpretation of new high throughput genomic datasets. For plant
biologists, the problem is much severe. Less than 50% of all the identified genes in the model plant
Arabidopsis thaliana, and only about 20% of all genes in the crop model Oryza sativa have some
aspects of their functions assigned. Therefore, there is an ...
Molecular Architectures Of Benzoic Acid-Specific Type Iii Polyketide Synthases, 2017 Iowa State University
Molecular Architectures Of Benzoic Acid-Specific Type Iii Polyketide Synthases, Charles Stewart Jr., Kate Woods, Greg Macias, Andrew C. Allan, Roger P. Hellens, Joseph P. Noel
Office of Biotechnology Publications
Biphenyl synthase and benzophenone synthase constitute an evolutionarily distinct clade of type III polyketide synthases (PKSs) that use benzoic acid-derived substrates to produce defense metabolites in plants. The use of benzoyl-CoA as an endogenous substrate is unusual for type III PKSs. Moreover, sequence analyses indicate that the residues responsible for the functional diversification of type III PKSs are mutated in benzoic acid-specific type III PKSs. In order to gain a better understanding of structure–function relationships within the type III PKS family, the crystal structures of biphenyl synthase from Malus × domestica and benzophenone synthase from Hypericum androsaemum were compared with ...
Comparative Oncogenomics Identifies Novel Regulators And Clinical Relevance Of Neural Crest Identities In Melanoma, 2017 University of Massachusetts Medical School
Comparative Oncogenomics Identifies Novel Regulators And Clinical Relevance Of Neural Crest Identities In Melanoma, Arvind M. Venkatesan
GSBS Dissertations and Theses
Cancers often resurrect embryonic molecular programs to promote disease progression. In melanomas, which are tumors of the neural crest (NC) lineage, a molecular signature of the embryonic NC is often reactivated. These NC factors have been implicated in promoting pro-tumorigenic features like proliferation, migration and therapy resistance. However, the molecular mechanisms that establish and maintain NC identities in melanomas are largely unknown. Additionally, whether the presence of a NC identity has any clinical relevance for patient melanomas is also unclear. Here, using comparative genomic approaches, I have a) identified a novel role for GDF6-activated BMP signaling in reawakening a NC ...
Chromatin Accessibility Dynamics In The Arabidopsis Root Epidermis And Endodermis During Cold Acclimation, 2017 The University of Western Ontario
Chromatin Accessibility Dynamics In The Arabidopsis Root Epidermis And Endodermis During Cold Acclimation, Shawn Hoogstra
Electronic Thesis and Dissertation Repository
Understanding cell-type specific transcriptional responses to environmental conditions is limited by a lack of knowledge of transcriptional control due to epigenetic dynamics. Additionally, cell-type analyses are limited by difficulties in applying current technologies to single cell-types. A novel DNase-seq protocol and analysis procedure, deemed DNase-DTS, was developed to identify DHSs in the Arabidopsis epidermis and endodermis under control and cold acclimation conditions. Results identified thousands of DHSs within each cell-type and experimental condition. DHSs showed strong association to gene expression, DNA methylation, and histone modifications. A priori mapping of existing DNA binding motifs within accessible genes and the cold C-repeat ...
The Hoxd Cluster Is A Dynamic And Resilient Tad Boundary Controlling The Segregation Of Antagonistic Regulatory Landscapes, Eddie Rodriguez-Carballo, Lucille Lopez-Delisle, Ye Zhan, Pierre J. Fabre, Leonardo Beccari, Imane El-Idrissi, Thi Hanh Nguyen Huynh, Hakan Ozadam, Job Dekker, Denis Duboule
Program in Systems Biology Publications and Presentations
The mammalian HoxD cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of Hoxd genes in forearm cells, whereas the centromeric TAD subsequently regulates more posterior Hoxd genes in digit cells. Therefore, the TAD boundary prevents the terminal Hoxd13 gene from responding to forearm enhancers, thereby allowing proper limb patterning. To assess the nature and function of this CTCF-rich DNA region in embryos, we compared chromatin interaction profiles between proximal and distal limb bud cells isolated from mutant stocks where various parts of this boundary region ...
Integrative Microrna And Mrna Deep-Sequencing Expression Profiling In Endemic Burkitt Lymphoma, 2017 Maseno University
Integrative Microrna And Mrna Deep-Sequencing Expression Profiling In Endemic Burkitt Lymphoma, Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong'echa, Ann M. Moormann, Jeffrey A. Bailey
UMass Center for Clinical and Translational Science Supported Publications
BACKGROUND: Burkitt lymphoma (BL) is characterized by overexpression of the c-myc oncogene, which in the vast majority of cases is a consequence of an IGH/MYC translocation. While myc is the seminal event, BL is a complex amalgam of genetic and epigenetic changes causing dysregulation of both coding and non-coding transcripts. Emerging evidence suggest that abnormal modulation of mRNA transcription via miRNAs might be a significant factor in lymphomagenesis. However, the alterations in these miRNAs and their correlations to their putative mRNA targets have not been extensively studied relative to normal germinal center (GC) B cells.
METHODS: Using more sensitive ...
Gene Expression Changes In The Mushroom Body Of Drosophila Melanogaster During A Time Course Of Long-Term Memory Formation And Maintenance, 2017 The University of Western Ontario
Gene Expression Changes In The Mushroom Body Of Drosophila Melanogaster During A Time Course Of Long-Term Memory Formation And Maintenance, Spencer G. Jones
Electronic Thesis and Dissertation Repository
Long-term memory (LTM) requires gene transcription. However, there is still much to learn about which genes are transcriptionally regulated during LTM and the biological roles they play. Here, gene expression changes were characterized in Drosophila melanogaster over a time course of LTM formation and maintenance in neurons of the mushroom body (MB), a structure required for normal learning and memory. I identified 120 genes differentially expressed (q < 0.2, fold change > 1.3) 24h after LTM induction. Among these were 13 potential downstream targets for RNA localization by the known memory genes pumilo, staufen and oskar, several genes encoding chromatin regulators and seven genes ...
The Role Of Histone H2a.Z Abundance In Modulating Responses To Phosphorus Deficiency In Rice, 2017 Louisiana State University and Agricultural and Mechanical College
The Role Of Histone H2a.Z Abundance In Modulating Responses To Phosphorus Deficiency In Rice, Sara Zahraeifard
LSU Doctoral Dissertations
Histone variants contribute to chromatin complexity by creating specialized nucleosomes. Here, to investigate the pattern of H2A.Z histone variant distribution and its role in modulating gene expression in rice (Oryza sativa L.), we performed genome-wide proﬁling of ARP6-dependent H2A.Z deposition in rice seedlings. We demonstrated that under controlled conditions, the majority of H2A.Z deposition is within protein-coding genes (PCG), and the most highly expressed genes are enriched with H2A.Z at their 5’ ends near the transcription start site (TSS), whereas the medium- to low-expressed genes contain H2A.Z across the entire gene. Based on H2A.Z ...
High-Throughput Single-Molecule Telomere Characterization, 2017 Old Dominion University
High-Throughput Single-Molecule Telomere Characterization, Jennifer Mccaffrey, Eleanor Young, Katy Lassahn, Justin Sibert, Steven Pastor, Harold Riethman, Ming Xiao
Medical Diagnostics & Translational Sciences Faculty Publications
We have developed a novel method that enables global subtelomere and haplotype-resolved analysis of telomere lengths at the single-molecule level. An in vitro CRISPR/Cas9 RNA-directed nickase system directs the specific labeling of human (TTAGGG) n DNA tracts in genomes that have also been barcoded using a separate nickase enzyme that recognizes a 7bp motif genome-wide. High-throughput imaging and analysis of large DNA single molecules from genomes labeled in this fashion using a nanochannel array system permits mapping through subtelomere repeat element (SRE) regions to unique chromosomal DNA while simultaneously measuring the (TTAGGG) n tract length at the end of ...
Selfish Mitochondrial Dna Proliferates And Diversifies In Small, But Not Large, Experimental Populations Of Caenorhabditis Briggsae, Wendy S. Phillips, Anna Luella Coleman-Hulbert, Emily S. Weiss, Dana K. Howe, Sita Ping, Riana I. Wernick, Suzanne Estes, Dee R. Denver
Evolutionary interactions across levels of biological organization contribute to a variety of fundamental processes including genome evolution, reproductive mode transitions, species diversiﬁcation, and extinction. Evolutionary theory predicts that so-called “selﬁsh” genetic elements will proliferate when the host effective population size (Ne) is small, but direct tests of this prediction remain few. We analyzed the evolutionary dynamics of deletion-containing mitochondrial DNA (ΔmtDNA) molecules, previously characterized as selﬁsh elements, in six different natural strains of the nematode Caenorhabditis briggsae allowed to undergo experimental evolution in a range of population sizes (N = 1, 10, 100, and 1,000) for a maximum of 50 ...
Interaction Of Cocoa Powder With Intestinal Microbiota, 2017 Louisiana State University and Agricultural and Mechanical College
Interaction Of Cocoa Powder With Intestinal Microbiota, Martha M. Escoto Sabillon
LSU Master's Theses
Cocoa is the fully fermented and dried seed of the cacao tree (Theobroma cacao L.) which has prebiotic properties, due to their high concentration of polyphenols. Therefore, the ingestion of cocoa could cause changes in the proportions of the intestinal microbiota that can influence the intestinal immune response. The objective of this study was to determine the effect of alkalization process of the cocoa bean in the diversity of the gut microbiota. The samples were “lavado” unprocessed cocoa powder, “natural” unprocessed cocoa powder, “D-11-S” as alkalized cocoa powder, “D-11-B” heavily alkalized cocoa powder, and raw cocoa “shells” and a control ...
The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription In The Swine Gut Microbiome, 2017 United States Department of Agriculture
The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription In The Swine Gut Microbiome, Timothy A. Johnson, Torey Looft, Andrew J. Severin, Darrell O. Bayles, Daniel J. Nasko, K. Eric Wommack, Adina Howe, Heather K. Allen
Carbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases. When the beta diversities of microbial FIGfam annotations were compared, the control and ...