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Articles 1 - 30 of 987

Full-Text Articles in Genomics

Identification And Characterization Of Nitrogen Fixing Bacteria Associated With Kudzu Root Nodules, Chasity Lawless, Michelle Zedonek, Debbie Curtis, Jonda Scharringhausen, Jared Bryant, Wendy A. Dustman, Alexandra M. Kurtz, Bekah Ward Dr. Sep 2018

Identification And Characterization Of Nitrogen Fixing Bacteria Associated With Kudzu Root Nodules, Chasity Lawless, Michelle Zedonek, Debbie Curtis, Jonda Scharringhausen, Jared Bryant, Wendy A. Dustman, Alexandra M. Kurtz, Bekah Ward Dr.

Georgia Journal of Science

Pueraria montana, better known as kudzu, is an invasive species rapidly spreading throughout the southeastern United States. This plant can form root nodules which house nitrogen-fixing bacteria, allowing atmospheric nitrogen to be converted into biologically available forms of nitrogen for use by the plant host. Given the centrality of these bacteria to the spread of kudzu, isolates from nodules were characterized after collection from seven different locations across the metropolitan Atlanta area. Twenty-five isolates were grown on two different variants of nitrogen free media. Four different carbon sources were evaluated as well. Finally, growth under both aerobic and anaerobic conditions ...


The Transcriptome Of The Bermuda Fireworm Odontosyllis Enopla (Annelida: Syllidae): A Unique Luciferase Gene Family And Putative Epitoky-Related Genes, Mercer R. Brugler, M. Teresa Aguado, Michael Tessler, Mark Siddall Aug 2018

The Transcriptome Of The Bermuda Fireworm Odontosyllis Enopla (Annelida: Syllidae): A Unique Luciferase Gene Family And Putative Epitoky-Related Genes, Mercer R. Brugler, M. Teresa Aguado, Michael Tessler, Mark Siddall

Publications and Research

The Bermuda fireworm Odontosyllis enopla exhibits an extremely tight circalunar circadian behavior that results in an impressive bioluminescent mating swarm, thought to be due to a conventional luciferase-mediated oxidation of a light-emitting luciferin. In addition, the four eyes become hypertrophied and heavily pigmented, and the nephridial system is modified to store and release gametes and associated secretions. In an effort to elucidate transcripts related to bioluminescence, circadian or circalunar periodicity, as well as epitoky-related changes of the eyes and nephridial system, we examined the transcriptomic profile of three female O. enopladuring a bioluminescent swarm in Ferry Reach, Bermuda. Using ...


Combinatorial Genomic Data Refute The Human Chromosome 2 Evolutionary Fusion And Build A Model Of Functional Design For Interstitial Telomeric Repeats, Jeffrey P. Tomkins Jul 2018

Combinatorial Genomic Data Refute The Human Chromosome 2 Evolutionary Fusion And Build A Model Of Functional Design For Interstitial Telomeric Repeats, Jeffrey P. Tomkins

The Proceedings of the International Conference on Creationism

Evolutionists allege that human chromosome 2 is the product of an ancient fusion event in an ancient hominid ancestor descended from apes. However, both the alleged site of fusion and the so-called cryptic centromere of human chromosome 2 are situated inside active genes negating the idea of fusion. Not only are the alleged genomic fossils of fusion representative of functional intragenic sequence, but they are also both highly degenerate versions of their supposed evolutionary beginnings, suggesting something other than an evolutionary origin. Given that these data strongly refute an evolutionary fusion scenario, it behooves creationists to propose an alternative model ...


Genomic Analysis Of 48 Paenibacillus Larvae Bacteriophages, Casey Stamereilers, Christopher P. Fajardo, Jamison K. Walker, Katterinne N. Mendez, Eduardo Castro-Nallar, Julianne H. Grose, Sandra Hope, Philippos K. Tsourkas Jul 2018

Genomic Analysis Of 48 Paenibacillus Larvae Bacteriophages, Casey Stamereilers, Christopher P. Fajardo, Jamison K. Walker, Katterinne N. Mendez, Eduardo Castro-Nallar, Julianne H. Grose, Sandra Hope, Philippos K. Tsourkas

Life Sciences Faculty Publications

The antibiotic-resistant bacterium Paenibacillus larvae is the causative agent of American foulbrood (AFB), currently the most destructive bacterial disease in honeybees. Phages that infect P. larvae were isolated as early as the 1950s, but it is only in recent years that P. larvae phage genomes have been sequenced and annotated. In this study we analyze the genomes of all 48 currently sequenced P. larvae phage genomes and classify them into four clusters and a singleton. The majority of P. larvaephage genomes are in the 38–45 kbp range and use the cohesive ends (cos) DNA-packaging strategy, while a minority have ...


Genomic Inference Of The Metabolism And Evolution Of The Archaeal Phylum Aigarchaeota, Zheng-Shuang Hua, Yan-Ni Qu, Qiyun Zhu, En-Min Zhou, Yan-Ling Qi, Yi-Rui Yin, Yang-Zhi Rao, Ye Tian, Yu-Xian Li, Lan Liu, Cindy J. Castelle, Brian P. Hedlund, Wen-Sheng Shu, Rob Knight, Wen-Jun Li Jul 2018

Genomic Inference Of The Metabolism And Evolution Of The Archaeal Phylum Aigarchaeota, Zheng-Shuang Hua, Yan-Ni Qu, Qiyun Zhu, En-Min Zhou, Yan-Ling Qi, Yi-Rui Yin, Yang-Zhi Rao, Ye Tian, Yu-Xian Li, Lan Liu, Cindy J. Castelle, Brian P. Hedlund, Wen-Sheng Shu, Rob Knight, Wen-Jun Li

Life Sciences Faculty Publications

Microbes of the phylum Aigarchaeota are widely distributed in geothermal environments, but their physiological and ecological roles are poorly understood. Here we analyze six Aigarchaeota metagenomic bins from two circumneutral hot springs in Tengchong, China, to reveal that they are either strict or facultative anaerobes, and most are chemolithotrophs that can perform sulfide oxidation. Applying comparative genomics to the Thaumarchaeota and Aigarchaeota, we find that they both originated from thermal habitats, sharing 1154 genes with their common ancestor. Horizontal gene transfer played a crucial role in shaping genetic diversity of Aigarchaeota and led to functional partitioning and ecological divergence among ...


Comparative Genetic And Genomic Analysis Of The Novel Fusellovirus Sulfolobus Spindle-Shaped Virus 10, David Andrew Goodman Jul 2018

Comparative Genetic And Genomic Analysis Of The Novel Fusellovirus Sulfolobus Spindle-Shaped Virus 10, David Andrew Goodman

Dissertations and Theses

Viruses that infect thermophilic Archaea are unique in both their structure and genetic makeup. The lemon-shaped fuselloviruses - which infect members of the order Sulfolobales, growing optimally at 80º C and pH 3 - are some of the most ubiquitous and best studied viruses of the thermoacidophilic Archaea. They provide a malleable and useful genetic tool for probing into the functions of their host, as well as the host responses to infection. Nonetheless, much about these viruses remains to be learned to further understand their morphological, genetic, and life cycle characteristics.

In order to investigate these aspects of these Fuselloviridae, as well ...


Computational Analysis Of Papionini Evolution Using Alu Insertions, Vallmer Edward Jordan Ii Jun 2018

Computational Analysis Of Papionini Evolution Using Alu Insertions, Vallmer Edward Jordan Ii

LSU Doctoral Dissertations

Alu elements are primate specific retrotransposons that have remained active throughout the course of primate evolution. As a result of this sustained mobilization. Alu elements are present in greater copy number in primate genomes than any other transposable element. An average of over one million Alu elements has been identified in every sequenced haplorrhine genome to date. These characteristics qualify Alu elements as ideal characters for studying evolutionary relationship among primates.

The increasing availability of whole genome sequencing data presents novel challenges and opportunities for comparative genomic analyses. Genomic data is now publicly available for most primate species. Such an ...


Draft Genome Sequence Of Bifidobacterium Longum Uma026, Isolated From Holstein Dairy Cow Feces, Korin Albert, David Sela Jun 2018

Draft Genome Sequence Of Bifidobacterium Longum Uma026, Isolated From Holstein Dairy Cow Feces, Korin Albert, David Sela

Open Access Articles

The draft genome sequence of an isolate identified as Bifidobacterium longum is communicated herein. This strain was isolated from the feces of a 1-week-old Holstein dairy cow. The draft genome of this Bifidobacterium longum isolate is 2.39 Mb in length, with a G+C content of 60.1%.


Complete Genome Sequences Of Paenibacillus Larvae Phages Bn12, Dragolir, Kiel007, Leyra, Likha, Pagassa, Pbl1c, And Tadhana, Jamison K. Walker, Bryan D. Merrill, Jordan A. Berg, Aziza Dhalai, Douglas W. Dingman, Chris P. Fajardo, Kiel Graves, Hunter L. Hill, Jared A. Hilton, Cameron Imahara, Bradley K. Knabe, James Mangohig, Josh Monk, Heejin Mun, Ashley M. Payne, Alicia Salisbury, Casey Stamereilers, Kathie Velez, Andy T. Ward, Donald P. Breakwell, Julianne H. Grose, Sandra Hope, Philippos K. Tsourkas Jun 2018

Complete Genome Sequences Of Paenibacillus Larvae Phages Bn12, Dragolir, Kiel007, Leyra, Likha, Pagassa, Pbl1c, And Tadhana, Jamison K. Walker, Bryan D. Merrill, Jordan A. Berg, Aziza Dhalai, Douglas W. Dingman, Chris P. Fajardo, Kiel Graves, Hunter L. Hill, Jared A. Hilton, Cameron Imahara, Bradley K. Knabe, James Mangohig, Josh Monk, Heejin Mun, Ashley M. Payne, Alicia Salisbury, Casey Stamereilers, Kathie Velez, Andy T. Ward, Donald P. Breakwell, Julianne H. Grose, Sandra Hope, Philippos K. Tsourkas

Life Sciences Faculty Publications

We present here the complete genomes of eight phages that infect Paenibacillus larvae, the causative agent of American foulbrood in honeybees. Phage PBL1c was originally isolated in 1984 from a P. larvae lysogen, while the remaining phages were isolated in 2014 from bee debris, honeycomb, and lysogens from three states in the USA.


A Systems Biology Approach For Studying Heterotopic Ossification: Proteomic Analysis Of Clinical Serum And Tissue Samples, Erin Crowgey, Jennifer Wyffels, Patrick Osborn, Thomas Wood, Laura Edsberg Jun 2018

A Systems Biology Approach For Studying Heterotopic Ossification: Proteomic Analysis Of Clinical Serum And Tissue Samples, Erin Crowgey, Jennifer Wyffels, Patrick Osborn, Thomas Wood, Laura Edsberg

Faculty Articles

Heterotopic ossification (HO) refers to the abnormal formation of bone in soft tissue. Although some of the underlying processes of HO have been described, there are currently no clinical tests using validated biomarkers for predicting HO formation. As such, the diagnosis is made radiographically after HO has formed. To identify potential and novel biomarkers for HO, we used isobaric tags for relative and absolute quantitation (iTRAQ) and high-throughput antibody arrays to produce a semi-quantitative proteomics survey of serum and tissue from subjects with (HO+) and without (HO−) heterotopic ossification. The resulting data were then analyzed using a systems biology approach ...


Recta: Regulon Identification Based On Comparative Genomics And Transcriptomics Analysis, Xin Chen, Anjun Ma, Adam Mcdermaid, Hanyuan Zhang, Chao Liu, Huansheng Cao, Qin Ma May 2018

Recta: Regulon Identification Based On Comparative Genomics And Transcriptomics Analysis, Xin Chen, Anjun Ma, Adam Mcdermaid, Hanyuan Zhang, Chao Liu, Huansheng Cao, Qin Ma

CSE Journal Articles

Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, regulon identification based on comparative genomics and transcriptomics analysis (RECTA), for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA on Lactococcus lactis MG1363 data to elucidate acid-response regulons. A total of 51 regulons were identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to ...


Fine Grained Compositional Analysis Of Port Everglades Inlet Microbiome Using High Throughput Dna Sequencing, Lauren M. O'Connell, Song Gao, Donald S. Mccorquodale Jr., Jay M. Fleisher, Jose Lopez May 2018

Fine Grained Compositional Analysis Of Port Everglades Inlet Microbiome Using High Throughput Dna Sequencing, Lauren M. O'Connell, Song Gao, Donald S. Mccorquodale Jr., Jay M. Fleisher, Jose Lopez

Marine & Environmental Sciences Faculty Articles

Background

Similar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities (“microbiomes”) in major port inlets is important due to potential impacts on surrounding environments. We hypothesize seasonal microbial fluctuations, which were profiled by high throughput 16S rRNA amplicon sequencing and analysis.

Methods & Results

Surface water samples were collected every week for one year. A total of four samples per ...


Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Mourin Azar, Dr. Lori Scott May 2018

Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Mourin Azar, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of Escherichia coli and Meiothermus ruber proC genes using the complementation assay. In this research project, mutants of varying severity to the functional state of the protein were developed. The results showed that two or more amino acid deletions reduced or eliminated ProC function. Amino acid substitutions, on the other hand, were not severe enough to impact ProC function. Double and triple mutants ...


Characterizing Cultivable Bacteria From Trachymyrmex Septentrionalis Fungus Gardens, Hannah Beatty May 2018

Characterizing Cultivable Bacteria From Trachymyrmex Septentrionalis Fungus Gardens, Hannah Beatty

Honors Scholar Theses

The relationship between the fungus-growing ant Trachymyrmex septentrionalis, its symbiotic cultivar fungus, and the transient and residential community of microorganisms is a diverse and complex symbiosis that has evolved over space and time. The fungus garden, comprised primarily of the cultivar fungus belonging to the family Leucocoprineae,provides an environment that hosts many bacteria, which may also play an important role in this symbiosis. Although it is known that Pseudonocardia bacteria defend the ant host against fungal pathogens, other species of bacteria that are present in these fungus gardens also likely contribute to this symbiosis. Previous studies of this system ...


Bayesian Network Modeling And Inference Of Gwas Catalog, Qiuping Pan May 2018

Bayesian Network Modeling And Inference Of Gwas Catalog, Qiuping Pan

Theses and Dissertations

Genome-wide association studies (GWASs) have received an increasing attention to understand genotype-phenotype relationships. The Bayesian network has been proposed as a powerful tool for modeling single-nucleotide polymorphism (SNP)-trait associations due to its advantage in addressing the high computational complex and high dimensional problems. Most current works learn the interactions among genotypes and phenotypes from the raw genotype data. However, due to the privacy issue, genotype information is sensitive and should be handled by complying with specific restrictions. In this work, we aim to build Bayesian networks from publicly released GWAS statistics to explicitly reveal the conditional dependency between SNPs ...


Involvement Of The Ino80 Complex In Chromosome Segregation, Jesus Moreno May 2018

Involvement Of The Ino80 Complex In Chromosome Segregation, Jesus Moreno

Theses and Dissertations

Chromatin remodeling complexes are multi-protein complexes that regulate the dynamics of the nucleosomes in the genome. The INO80 chromatin remodeling complex participates in varied biological processes such as: transcription, DNA repair, DNA replication and chromosome integrity. It catalyzes the eviction of the H2A.Z variant histone as well as whole nucleosome eviction. This complex is comprised of 15 subunits and the contribution of each to chromosome segregations remains unknown. To evaluate the contribution of each subunit to chromosome segregation, we tested deletion mutants of the non-essential subunits for DNA content and benomyl sensitivity. Also, we assessed members of the SWR1 ...


Effects Of Mitochondrial Nadp+-Dependent Isocitrate Dehydrogenase Deficiency On Fructose-Induced Obesity In Mice, Allison Michelle Montalbano, Kaleigh Elizabeth Beane May 2018

Effects Of Mitochondrial Nadp+-Dependent Isocitrate Dehydrogenase Deficiency On Fructose-Induced Obesity In Mice, Allison Michelle Montalbano, Kaleigh Elizabeth Beane

Human Nutrition and Hospitality Innovation Undergraduate Honors Theses

Obesity prevalence in the United States continues to increase and is associated with health consequences such as type 2 diabetes, hypertension, atherosclerosis, and hyperlipidemia. Among many contributing factors to obesity, fructose may be one of the major reasons as it disrupts the antioxidant system thereby resulting in an accumulation of reactive oxidative species and leading to obese conditions. The enzyme, isocitrate dehydrogenase 2 (IDH2), reduces nicotinamide adenine dinucleotide phosphate from the TCA Cycle, hence might be implicated with not only energy metabolism but also cellular redox homeostasis. Therefore, the hypothesis was that IDH2 deficiency in mice would exacerbate hepatic lipid ...


Genomic Insights Into The Mitochondria Of 11 Eastern North American Species Of Cladonia, Laurel M. Brigham, Luis M. Allende, Benjamin R. Shipley, Kayla C. Boyd, Tanya J. Higgins, Nicholas Kelly, Carly R. Anderson-Stewart, Kyle Keepers, Cloe S. Pogoda, James C. Lendemer, Erin A. Tripp, Nolan C. Kane Apr 2018

Genomic Insights Into The Mitochondria Of 11 Eastern North American Species Of Cladonia, Laurel M. Brigham, Luis M. Allende, Benjamin R. Shipley, Kayla C. Boyd, Tanya J. Higgins, Nicholas Kelly, Carly R. Anderson-Stewart, Kyle Keepers, Cloe S. Pogoda, James C. Lendemer, Erin A. Tripp, Nolan C. Kane

University Libraries Open Access Fund Supported Publications

Cladonia is among the most species-rich genera of lichens globally. Species in this lineage, commonly referred to as reindeer lichens, are ecologically important in numerous regions worldwide. In some locations, species of Cladonia can comprise the dominant groundcover, and are a major food source for caribou and other mammals. Additionally, many species are known to produce substances with antimicrobial properties or other characteristics with potentially important medical applications. This exceptional morphological and ecological variation contrasts sharply with the limited molecular divergence often observed among species. As a new resource to facilitate ongoing and future studies of these important species, we ...


A Unified Encyclopedia Of Human Functional Dna Elements Through Fully Automated Annotation Of 164 Human Cell Types, Maxwell Wing Libbrecht, Oscar Rodriguez, Zhiping Weng, Michael Hoffman, Jeffrey A. Bilmes, William Stafford Noble Apr 2018

A Unified Encyclopedia Of Human Functional Dna Elements Through Fully Automated Annotation Of 164 Human Cell Types, Maxwell Wing Libbrecht, Oscar Rodriguez, Zhiping Weng, Michael Hoffman, Jeffrey A. Bilmes, William Stafford Noble

University of Massachusetts Medical School Faculty Publications

Semi-automated genome annotation methods such as Segway enable understanding of chromatin activity. Here we present chromatin state annotations of 164 human cell types using 1,615 genomics data sets. To produce these annotations, we developed a fully-automated annotation strategy in which we train separate unsupervised annotation models on each cell type and use a machine learning classifier to automate the state interpretation step. Using these annotations, we developed a measure of the functional importance of each genomic position called the "functionality score," which allows us to aggregate information across cell types into a multi-cell type view. This score provides a ...


Transcriptomics To Develop Biochemical Network Models In Cyanobacteria, Bridget E. Hegarty, Jordan Peccia, Ratanachat Racharaks Apr 2018

Transcriptomics To Develop Biochemical Network Models In Cyanobacteria, Bridget E. Hegarty, Jordan Peccia, Ratanachat Racharaks

Yale Day of Data

Through targeted genetic manipulations guided by network modeling, we will create a flexible, cyanobacteria-based platform for the production of biofuel-precursors and valuable chemical products. To build gene-metabolite predictive models, we have characterized Synecococcus elongatus sp. UTEX 2973’s (henceforth, UTEX 2973) gene expression and metabolite production under a number of environmental conditions.


Viper: Visualization Pipeline For Rna-Seq, A Snakemake Workflow For Efficient And Complete Rna-Seq Analysis, Macintosh Cornwell, Mahesh Vangala, Len Taing, Zachary Herbert, Johannes Koster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, X Shirley Liu, Henry W. Long Apr 2018

Viper: Visualization Pipeline For Rna-Seq, A Snakemake Workflow For Efficient And Complete Rna-Seq Analysis, Macintosh Cornwell, Mahesh Vangala, Len Taing, Zachary Herbert, Johannes Koster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, X Shirley Liu, Henry W. Long

Open Access Articles

BACKGROUND: RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts.

RESULTS: Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis ...


Rates And Patterns Of Evolution In A Duplicated Genome In The Family Catostomidae, Megann Schmidt Apr 2018

Rates And Patterns Of Evolution In A Duplicated Genome In The Family Catostomidae, Megann Schmidt

Research in the Capitol

Whole genome duplication (WGD) is a process in which the entire genome of an organism is duplicated, making redundant genes which are subject to unique evolutionary forces. Various modes of selection create different genetic fates such as retention of ancestral function, development of new function, or loss of function. Because of these differing fates, WGD is hypothesized to be a major driving force behind diversification. In this project, DNA sequences from fish species in the family Catostomidae were examined to observe patterns of evolution following a known WGD. Gene trees were generated for 179 loci to determine the amount of ...


Numerous Recursive Sites Contribute To Accuracy Of Splicing Of Long Introns In Flies, Athma A. Pai, Joseph Paggi, Karen Adelman, Christopher B. Burge Mar 2018

Numerous Recursive Sites Contribute To Accuracy Of Splicing Of Long Introns In Flies, Athma A. Pai, Joseph Paggi, Karen Adelman, Christopher B. Burge

University of Massachusetts Medical School Faculty Publications

Recursive splicing, a process by which a single intron is removed from pre-mRNA transcripts in multiple distinct segments, has been observed in a small subset of Drosophila melanogaster introns. However, detection of recursive splicing requires observation of splicing intermediates which are inherently unstable, making it difficult to study. Here we developed new computational approaches to identify recursively spliced introns and applied them, in combination with existing methods, to nascent RNA sequencing data from Drosophila S2 cells. These approaches identified hundreds of novel sites of recursive splicing, expanding the catalog of recursively spliced fly introns by 4-fold. Recursive sites occur in ...


A Genetic Screen To Identify Fission Yeast Genes With Roles In Protecting Against Perturbation Of The Actin Cytoskeleton, Dorota Michalski Mar 2018

A Genetic Screen To Identify Fission Yeast Genes With Roles In Protecting Against Perturbation Of The Actin Cytoskeleton, Dorota Michalski

Electronic Thesis and Dissertation Repository

In the fission yeast, Schizosaccharomyces pombe, stress upon the cell division machinery leads to the activation of a cytokinesis checkpoint. This checkpoint results in a delay in cell cycle progression and the prolonged maintenance of a cytokinesis competent cellular state. In this state the cell is able to continuously reform/repair the actomyosin ring until cell division is achieved. To uncover genes that play a role in enforcing this checkpoint, the actin depolymerizing drug Latrunculin A (LatA) was used to perturb the cytokinetic machinery in a set of 3400 viable haploid S. pombe gene deletion mutants. Thirty-eight gene deletion mutants ...


Profiling Of Pluripotency Factors In Individual Stem Cells And Early Embryos, Sarah J. Hainer, Ana Boskovic, Oliver J. Rando, Thomas G. Fazzio Mar 2018

Profiling Of Pluripotency Factors In Individual Stem Cells And Early Embryos, Sarah J. Hainer, Ana Boskovic, Oliver J. Rando, Thomas G. Fazzio

University of Massachusetts Medical School Faculty Publications

Major cell fate decisions are governed by sequence-specific transcription factors (TFs) that act in small cell populations within developing embryos. To understand how TFs regulate cell fate it is important to identify their genomic binding sites in these populations. However, current methods cannot profile TFs genome-wide at or near the single cell level. Here we adapt the CUT&RUN method to profile chromatin proteins in low cell numbers, mapping TF-DNA interactions in single cells and individual pre-implantation embryos for the first time. Using this method, we demonstrate that the pluripotency TF NANOG is significantly more dependent on the SWI/SNF ...


Copy Number Variation In The Porcine Genome Detected From Whole-Genome Sequence, Rebecca Anderson Mar 2018

Copy Number Variation In The Porcine Genome Detected From Whole-Genome Sequence, Rebecca Anderson

Honors Theses, University of Nebraska-Lincoln

Copy number variations (CNVs) are large insertions, deletions, and duplications in the genome that vary between individuals in a species. These variations are known to impact a broad range of phenotypes from molecular-level traits to higher-order clinical phenotypes. CNVs have been linked to complex traits in humans such as autism, attention deficit hyperactivity disorder, nervous system disorders, and early-onset extreme obesity. In this study, whole-genome sequence was obtained from 72 founders of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC) in Clay Center, Nebraska. This included 24 boars (12 Duroc and 12 Landrace ...


Atacseqqc: A Bioconductor Package For Post-Alignment Quality Assessment Of Atac-Seq Data, Jianhong Ou, Haibo Liu, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson, Lihua Julie Zhu Mar 2018

Atacseqqc: A Bioconductor Package For Post-Alignment Quality Assessment Of Atac-Seq Data, Jianhong Ou, Haibo Liu, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson, Lihua Julie Zhu

University of Massachusetts Medical School Faculty Publications

BACKGROUND: ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. While several tools have been developed or adopted for assessing read quality, identifying nucleosome occupancy and accessible regions from ATAC-seq data, none of the ...


Evidence For A Unique Dna-Dependent Rna Polymerase In Cereal Crops, Joshua T. Trujillo, Arun S. Seetharam, Matthew B. Hufford, Mark A. Beilstein, Rebecca A. Mosher Feb 2018

Evidence For A Unique Dna-Dependent Rna Polymerase In Cereal Crops, Joshua T. Trujillo, Arun S. Seetharam, Matthew B. Hufford, Mark A. Beilstein, Rebecca A. Mosher

Genome Informatics Facility Publications

Gene duplication is an important driver for the evolution of new genes and protein functions. Duplication of DNA-dependent RNA polymerase (Pol) II subunits within plants led to the emergence of RNA Pol IV and V complexes, each of which possess unique functions necessary for RNA-directed DNA Methylation. Comprehensive identification of Pol V subunit orthologs across the monocot radiation revealed a duplication of the largest two subunits within the grasses (Poaceae), including critical cereal crops. These paralogous Pol subunits display sequence conservation within catalytic domains, but their carboxy terminal domains differ in length and character of the Ago-binding platform, suggesting unique ...


Identification Of Novel Genetic Variations For Amyotrophic Lateral Sclerosis (Als), Guang Xu Feb 2018

Identification Of Novel Genetic Variations For Amyotrophic Lateral Sclerosis (Als), Guang Xu

GSBS Dissertations and Theses

A list of genes have been identified to carry mutations causing familial ALS such as SOD1, TARDBP, C9orf72. But for sporadic ALS, which is 90% of all ALS cases, the underlying genetic variants are still largely unknown. There are multiple genome-wide association study (GWAS) for sporadic ALS, but usually a large number nominated SNP can hardly be replicated in larger cohort analysis. Also majority of GWAS SNP lie within noncoding region of genome, imposing a huge challenge to study their biological role in ALS pathology. With the rapid development of next-generation sequencing technology, we are able to sequence exome and ...


Novel Candidate Genes Important For Asthma And Hypertension Comorbidity Revealed From Associative Gene Networks, Olga V. Saik, Pavel S. Demenkov, Timofey V. Ivanisenko, Elena Yu. Bragina, Maxim B. Freidin, Irina A. Goncharova, Victor E. Dosenko, Olga I. Zolotareva, Ralf Hofestaedt, Inna N. Lavrik, Evgeny I. Rogaev, Vladimir A. Ivanisenko Feb 2018

Novel Candidate Genes Important For Asthma And Hypertension Comorbidity Revealed From Associative Gene Networks, Olga V. Saik, Pavel S. Demenkov, Timofey V. Ivanisenko, Elena Yu. Bragina, Maxim B. Freidin, Irina A. Goncharova, Victor E. Dosenko, Olga I. Zolotareva, Ralf Hofestaedt, Inna N. Lavrik, Evgeny I. Rogaev, Vladimir A. Ivanisenko

Open Access Articles

BACKGROUND: Hypertension and bronchial asthma are a major issue for people's health. As of 2014, approximately one billion adults, or ~ 22% of the world population, have had hypertension. As of 2011, 235-330 million people globally have been affected by asthma and approximately 250,000-345,000 people have died each year from the disease. The development of the effective treatment therapies against these diseases is complicated by their comorbidity features. This is often a major problem in diagnosis and their treatment. Hence, in this study the bioinformatical methodology for the analysis of the comorbidity of these two diseases have been ...