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Using Imputation As A Method Of Improving Genetic Data Analysis, Kimberly Diaz Perez 2017 Georgia State University

Using Imputation As A Method Of Improving Genetic Data Analysis, Kimberly Diaz Perez

Georgia State Undergraduate Research Conference

No abstract provided.


Genomic Analysis Of Factors Associated With Low Prevalence Of Antibiotic Resistance In Extraintestinal Pathogenic Escherichia Coli Sequence Type 95 Strains, Craig M. Stephens, Sheila Adams-Sapper, Manraj Sekhon, James R. Johnson, Lee W. Riley 2017 Santa Clara University

Genomic Analysis Of Factors Associated With Low Prevalence Of Antibiotic Resistance In Extraintestinal Pathogenic Escherichia Coli Sequence Type 95 Strains, Craig M. Stephens, Sheila Adams-Sapper, Manraj Sekhon, James R. Johnson, Lee W. Riley

Biology

Extraintestinal pathogenic Escherichia coli (ExPEC) strains belonging to multilocus sequence type 95 (ST95) are globally distributed and a common cause of infections in humans and domestic fowl. ST95 isolates generally show a lower prevalence of acquired antimicrobial resistance than other pandemic ExPEC lineages. We took a genomic approach to identify factors that may underlie reduced resistance. We fully assembled genomes for four ST95 isolates representing the four major fimH-based lineages within ST95 and also analyzed draft-level genomes from another 82 ST95 isolates, largely from the western United States. The fully assembled genomes of antibiotic-resistant isolates carried resistance genes exclusively on ...


Crispr-Based Knockout Screening In Primary Neurons, Ben Callif 2017 Marquette University

Crispr-Based Knockout Screening In Primary Neurons, Ben Callif

Master's Theses (2009 -)

Axon growth is coordinated by multiple interacting proteins that remain incompletely characterized. High content screening (HCS), in which manipulation of candidate genes is combined with rapid image analysis of phenotypic effects, has emerged as a powerful technique to identify key regulators of axon outgrowth. Here we explore the utility of a genome editing approach referred to as CRISPR (Clustered Regularly Interspersed Palindromic Repeats) for knockout screening in primary neurons. In the CRISPR approach a DNA-cleaving Cas enzyme is guided to genomic target sequences by user-created guide RNA (sgRNA), where it initiates a double-stranded break that ultimately results in frameshift mutation ...


Identifying Regulators From Multiple Types Of Biological Data In Cancer, Brittany Baur 2017 Marquette University

Identifying Regulators From Multiple Types Of Biological Data In Cancer, Brittany Baur

Dissertations (2009 -)

Cancer genomes accumulate alterations that promote cancer cell proliferation and survival. Structural, genetic and epigenetic alterations that have a selective advantage for tumorigenesis affect key regulatory genes and microRNAs that in turn regulate the expression of many target genes. The goal of this dissertation is to leverage the alteration-rich landscape of cancer genomes to detect key regulatory genes and microRNAs. To this end, we designed a feature selection algorithm to identify DNA methylation signals around a gene that would highly predict its expression. We found that genes whose expression could be predicted by DNA methylation accurately were enriched in Gene ...


Phytohormone Signaling In Chlorella Sorokiniana: Perspectives On The Evolution Of Plant Cell-To-Cell Signaling, Maya Khasin 2017 University of Nebraska-Lincoln

Phytohormone Signaling In Chlorella Sorokiniana: Perspectives On The Evolution Of Plant Cell-To-Cell Signaling, Maya Khasin

Dissertations and Theses in Biological Sciences

Cell-to-cell communication is a key aspect of microbial physiology and population dynamics, and a cornerstone in understanding the evolution of multicellularity. Quorum sensing in bacteria is a canonical example of microbial cell-to-cell signaling, in which bacteria use small molecule signals in order to monitor their population size and modulate their physiology accordingly. We propose that the evolution of plant hormone signaling arose in unicellular green algae, analogously to quorum sensing in bacteria, and that the complexity of these pathways required the recruitment of increasingly specific enzymes to increasingly sophisticated gene networks throughout the course of phytohormone signaling evolution. Using Chlorella ...


Pcr-Activated Cell Sorting As A General, Cultivation-Free Method For High-Throughput Identification And Enrichment Of Virus Hosts, Shaun W. Lim, Shea T. Lance, Kenneth M. Stedman, Adam R. Abate 2017 University of California, San Francisco

Pcr-Activated Cell Sorting As A General, Cultivation-Free Method For High-Throughput Identification And Enrichment Of Virus Hosts, Shaun W. Lim, Shea T. Lance, Kenneth M. Stedman, Adam R. Abate

Biology Faculty Publications and Presentations

Characterizing virus-host relationships is critical for understanding the impact of a virus on an ecosystem, but is challenging with existing techniques, particularly for uncultivable species. We present a general, cultivation-free approach for identifying phage-associated bacterial cells. Using PCR-activated cell sorting, we interrogate millions of individual bacteria for the presence of specific phage nucleic acids. If the nucleic acids are present, the bacteria are recovered via sorting and their genomes analyzed. This allows targeted recovery of all possible host species in a diverse population associated with a specific phage, and can be easily targeted to identify the hosts of different phages ...


A Novel Multi-Network Approach Reveals Tissue-Specific Cellular Modulators Of Fibrosis In Systemic Sclerosis, Jaclyn N. Taroni, Casey S. Greene, Viktor Martyanov, Tammara A. Wood 2017 Dartmouth College

A Novel Multi-Network Approach Reveals Tissue-Specific Cellular Modulators Of Fibrosis In Systemic Sclerosis, Jaclyn N. Taroni, Casey S. Greene, Viktor Martyanov, Tammara A. Wood

Open Dartmouth: Faculty Open Access Articles

Systemic sclerosis (SSc) is a multi-organ autoimmune disease characterized by skin fibrosis. Internal organ involvement is heterogeneous. It is unknown whether disease mechanisms are common across all involved affected tissues or if each manifestation has a distinct underlying pathology.We used consensus clustering to compare gene expression profiles of biopsies from four SSc-affected tissues (skin, lung, esophagus, and peripheral blood) from patients with SSc, and the related conditions pulmonary fibrosis (PF) and pulmonary arterial hypertension, and derived a consensus disease-associate signature across all tissues. We used this signature to query tissue-specific functional genomic networks. We performed novel network analyses to ...


Transcriptomic Responses To Environmental Temperature By Turtles With Temperature-Dependent And Genotypic Sex Determination Assessed By Rnaseq Inform The Genetic Architecture Of Embryonic Gonadal Development, Srihari Radhakrishnan, Robert A. Literman, Jennifer L. Neuwald, Andrew Severin, Nicole Valenzuela 2017 Iowa State University

Transcriptomic Responses To Environmental Temperature By Turtles With Temperature-Dependent And Genotypic Sex Determination Assessed By Rnaseq Inform The Genetic Architecture Of Embryonic Gonadal Development, Srihari Radhakrishnan, Robert A. Literman, Jennifer L. Neuwald, Andrew Severin, Nicole Valenzuela

Ecology, Evolution and Organismal Biology Publications

Vertebrate sexual fate is decided primarily by the individual’s genotype (GSD), by the environmental temperature during development (TSD), or both. Turtles exhibit TSD and GSD, making them ideal to study the evolution of sex determination. Here we analyze temperature-specific gonadal transcriptomes (RNA-sequencing validated by qPCR) of painted turtles (Chrysemys picta TSD) before and during the thermosensitive period, and at equivalent stages in soft-shell turtles (Apalone spinifera—GSD), to test whether TSD’s and GSD’s transcriptional circuitry is identical but deployed differently between mechanisms. Our data show that most elements of the mammalian urogenital network are active during turtle ...


P08. Unravelling Organelle Genome Evolution Architecture Using Rna-Sequencing Data, Matheus Sanita Lima, David Roy Smith 2017 Western University

P08. Unravelling Organelle Genome Evolution Architecture Using Rna-Sequencing Data, Matheus Sanita Lima, David Roy Smith

Western Research Forum

Background: Mitochondria genomes vary from 11 Mb to 6 kb, while plastids can vary from 1 Mb to 30 kb. Non-coding DNA accounts for most of this size variation, but the mechanistic and evolutionary reasons for that are still unknown. Next generation sequencing has generated unprecedented amounts of genomic and transcriptomic data that can be used for organelle genome evolution studies. However, most of these data is used only for the study of cell nucleus. Therefore, I decided to use these untapped data source to investigate the transcription of organelle genomes in plastid-bearing protists.

Methods: I mapped the transcriptomes over ...


The Mirnaome Of Catharanthus Roseus: Identification, Expression Analysis, And Potential Roles Of Micrornas In Regulation Of Terpenoid Indole Alkaloid Biosynthesis, Ethan M. Shen, Sanjay Kumar Singh, Jayadri S. Ghosh, Barunava Patra, Priyanka Paul, Ling Yuan, Sitakanta Pattanaik 2017 University of Kentucky

The Mirnaome Of Catharanthus Roseus: Identification, Expression Analysis, And Potential Roles Of Micrornas In Regulation Of Terpenoid Indole Alkaloid Biosynthesis, Ethan M. Shen, Sanjay Kumar Singh, Jayadri S. Ghosh, Barunava Patra, Priyanka Paul, Ling Yuan, Sitakanta Pattanaik

Plant and Soil Sciences Faculty Publications

MicroRNAs (miRNAs) regulate numerous crucial biological processes in plants. However, information is limited on their involvement in the biosynthesis of specialized metabolites in plants, including Catharanthus roseus that produces a number of pharmaceutically valuable, bioactive terpenoid indole alkaloids (TIAs). Using small RNA-sequencing, we identified 181 conserved and 173 novel miRNAs (cro-miRNAs) in C. roseus seedlings. Genome-wide expression analysis revealed that a set of cro-miRNAs are differentially regulated in response to methyl jasmonate (MeJA). In silico target prediction identified 519 potential cro-miRNA targets that include several auxin response factors (ARFs). The presence of cleaved transcripts of miRNA-targeted ARFs in C. roseus ...


Defining The 5 And 3 Landscape Of The Drosophila Transcriptome With Exo-Seq And Rnaseh-Seq, Shaked Afik, Osnat Bartok, Maxim N. Artyomov, Alexander A. Shishkin, Sabah Kadri, Mor Hanan, Xiaopeng Zhu, Manuel Garber, Sebastian Kadener 2017 The Hebrew University, Jerusalem

Defining The 5 And 3 Landscape Of The Drosophila Transcriptome With Exo-Seq And Rnaseh-Seq, Shaked Afik, Osnat Bartok, Maxim N. Artyomov, Alexander A. Shishkin, Sabah Kadri, Mor Hanan, Xiaopeng Zhu, Manuel Garber, Sebastian Kadener

UMass Center for Clinical and Translational Science Supported Publications

Cells regulate biological responses in part through changes in transcription start sites (TSS) or cleavage and polyadenylation sites (PAS). To fully understand gene regulatory networks, it is therefore critical to accurately annotate cell type-specific TSS and PAS. Here we present a simple and straightforward approach for genome-wide annotation of 5- and 3-RNA ends. Our approach reliably discerns bona fide PAS from false PAS that arise due to internal poly(A) tracts, a common problem with current PAS annotation methods. We applied our methodology to study the impact of temperature on the Drosophila melanogaster head transcriptome. We found hundreds of previously ...


Utility Of Comprehensive Genomic Sequencing For Detecting Her2-Positive Colorectal Cancer, Yoshifumi Shimada, Stephen Lyle, Toshifumi Wakai 2017 Niigata University Graduate School of Medical and Dental Sciences, Japan

Utility Of Comprehensive Genomic Sequencing For Detecting Her2-Positive Colorectal Cancer, Yoshifumi Shimada, Stephen Lyle, Toshifumi Wakai

Open Access Articles

HER2-targeted therapy is considered effective for KRAS codon 12/13 wild-type, HER2-positive metastatic colorectal cancer (CRC). In general, HER2 status is determined by the use of immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). Comprehensive genomic sequencing (CGS) enables the detection of gene mutations and copy number alterations including KRAS mutation and HER2 amplification; however, little is known about the utility of CGS for detecting HER2-positive CRC. To assess its utility, we retrospectively investigated 201 patients with stage I-IV CRC. The HER2 status of the primary site was assessed using IHC and FISH, and HER2 amplification of the primary site ...


A Microrna Family Exerts Maternal Control On Sex Determination In C. Elegans, Katherine McJunkin, Victor R. Ambros 2017 University of Massachusetts Medical School

A Microrna Family Exerts Maternal Control On Sex Determination In C. Elegans, Katherine Mcjunkin, Victor R. Ambros

Program in Molecular Medicine Publications and Presentations

Gene expression in early animal embryogenesis is in large part controlled post-transcriptionally. Maternally contributed microRNAs may therefore play important roles in early development. We elucidated a major biological role of the nematode mir-35 family of maternally contributed essential microRNAs. We show that this microRNA family regulates the sex determination pathway at multiple levels, acting both upstream of and downstream from her-1 to prevent aberrantly activated male developmental programs in hermaphrodite embryos. Both of the predicted target genes that act downstream from the mir-35 family in this process, suppressor-26 (sup-26) and NHL (NCL-1, HT2A, and LIN-41 repeat) domain-containing-2 (nhl-2), encode RNA-binding ...


Messenger Rna And Microrna Transcriptomic Signatures Of Cardiometabolic Risk Factors, David D. McManus, Jian Rong, Tianxiao Huan, Sean Lacey, Kahraman Tanriverdi, Peter J. Munson, Martin G. Larson, Roby Joehanes, Venkatesh Murthy, Ravi Shah, Jane E. Freedman, Daniel Levy 2017 University of Massachusetts Medical School

Messenger Rna And Microrna Transcriptomic Signatures Of Cardiometabolic Risk Factors, David D. Mcmanus, Jian Rong, Tianxiao Huan, Sean Lacey, Kahraman Tanriverdi, Peter J. Munson, Martin G. Larson, Roby Joehanes, Venkatesh Murthy, Ravi Shah, Jane E. Freedman, Daniel Levy

UMass Center for Clinical and Translational Science Supported Publications

BACKGROUND: Cardiometabolic (CM) risk factors are heritable and cluster in individuals. We hypothesized that CM risk factors are associated with multiple shared and unique mRNA and microRNA (miRNA) signatures. We examined associations of mRNA and miRNA levels with 6 CM traits: body mass index, HDL-cholesterol and triglycerides, fasting glucose, and systolic and diastolic blood pressures through cross-sectional analysis of 2812 Framingham Heart Study who had whole blood collection for RNA isolation for mRNA and miRNA expression studies and who consented to genetic research. We excluded participants taking medication for hypertension, dyslipidemia, or diabetes. We measured mRNA (n = 17,318; using ...


Ethical Consequences Of Full Human Genome Testing, Michael Lupton 2017 Bond University

Ethical Consequences Of Full Human Genome Testing, Michael Lupton

Law Faculty Publications

A Genome is the entire set of hereditary instructions for building, running, maintaining an organism and passing on life to the next generation. A Genome is divided into chromosomes, the chromosomes contain genes and the genes are made of DNA. Genomes are found in cells; which are the microscopic structures that make up all organisms. With few exceptions, each of your body’s trillions of cells contains a copy of your genome. The human genome may be commonplace but it is quite powerful, because the information in the genome affects every aspect of a person’s behaviour and physiology. The ...


Estimating The Probability Of Clonal Relatedness Of Pairs Of Tumors In Cancer Patients, Audrey Mauguen, Venkatraman E. Seshan, Irina Ostrovnaya, Colin B. Begg 2017 Memorial Sloan-Kettering Cancer Center

Estimating The Probability Of Clonal Relatedness Of Pairs Of Tumors In Cancer Patients, Audrey Mauguen, Venkatraman E. Seshan, Irina Ostrovnaya, Colin B. Begg

Memorial Sloan-Kettering Cancer Center, Dept. of Epidemiology & Biostatistics Working Paper Series

Next generation sequencing panels are being used increasingly in cancer research to study tumor evolution. A specific statistical challenge is to compare the mutational profiles in different tumors from a patient to determine the strength of evidence that the tumors are clonally related, i.e. derived from a single, founder clonal cell. The presence of identical mutations in each tumor provides evidence of clonal relatedness, although the strength of evidence from a match is related to how commonly the mutation is seen in the tumor type under investigation. This evidence must be weighed against the evidence in favor of independent ...


An Agrobacterium-Delivered Crispr/Cas9 System For High-Frequency Targeted Mutagenesis In Maize, Si Nian Char, Anjanasree K. Neelakandan, Hartinio Nahampun, Bronwyn Frame, Marcy Main, Martin H. Spalding, Philip W. Becraft, Blake C. Meyers, Virginia Walbot, Kan Wang, Bing Yang 2017 Iowa State University

An Agrobacterium-Delivered Crispr/Cas9 System For High-Frequency Targeted Mutagenesis In Maize, Si Nian Char, Anjanasree K. Neelakandan, Hartinio Nahampun, Bronwyn Frame, Marcy Main, Martin H. Spalding, Philip W. Becraft, Blake C. Meyers, Virginia Walbot, Kan Wang, Bing Yang

Genetics, Development and Cell Biology Publications

CRISPR/Cas9 is a powerful genome editing tool in many organisms, including a number of monocots and dicots. Although the design and application of CRISPR/Cas9 is simpler compared to other nuclease-based genome editing tools, optimization requires the consideration of the DNA delivery and tissue regeneration methods for a particular species to achieve accuracy and efficiency. Here, we describe a public sector system, ISU Maize CRISPR, utilizing Agrobacterium-delivered CRISPR/Cas9 for high-frequency targeted mutagenesis in maize. This system consists of an Escherichia coli cloning vector and an Agrobacterium binary vector. It can be used to clone up to four ...


An Assessment Of Potential False Positive E.Coli Pyroprints In The Cplop Database, Skyler A. Gordon 2017 California Polytechnic State University, San Luis Obispo

An Assessment Of Potential False Positive E.Coli Pyroprints In The Cplop Database, Skyler A. Gordon

Master's Theses and Project Reports

The genetic information found in each species of organism is unique, and can be used as a tool to differentiate at the molecular level. This has caused rapid genotyping methods to become the cornerstone of a new area of research dependent on reading the genome as a form of identification. One of these specific identification methods, known as pyroprinting, relies on the small variation of DNA sequences within the same species to develop a unique, reproducible fingerprint. By simultaneously pyrosequencing multiple polymorphic loci within the ribosomal operons known as the intergenic transcribed spacers, a reproducible output is obtained, known as ...


Genome Sequence Of The First Coleopteran Iflavirus Isolated From Western Corn Rootworm, Diabrotica Virgifera Virgifera Leconte, Sijun Liu, Yuting Chen, Thomas W. Sappington, Bryony C. Bonning 2017 Iowa State University

Genome Sequence Of The First Coleopteran Iflavirus Isolated From Western Corn Rootworm, Diabrotica Virgifera Virgifera Leconte, Sijun Liu, Yuting Chen, Thomas W. Sappington, Bryony C. Bonning

Entomology Publications

The genome sequence of a novel iflavirus was identified from the transcriptome of the western corn rootworm, Diabrotica virgifera virgifera. The RNA sequence consists of 9,823 nucleotides (nt) with a 3′ polyadenylated tail, containing a single open reading frame that encodes a 3,028-amino-acid polyprotein.


Microbial Repopulation Following In Situ Star Remediation, Gavin Overbeeke 2017 The University of Western Ontario

Microbial Repopulation Following In Situ Star Remediation, Gavin Overbeeke

Electronic Thesis and Dissertation Repository

In situ STAR (Self-sustaining Treatment for Active Remediation) is an emerging remediation technology which uses smouldering combustion to destroy nonaqueous phase liquid (NAPL) contamination in the subsurface. Since STAR smouldering travels through contaminated soils slowly (~0.5 to 5 m/day) and subjects them to high temperatures (400–1000°C), it is expected that this technology will thoroughly dry and sterilize the zones which it treats. Further, soils surrounding the treatment zone which are not smouldered will be heated, although not smouldered, by virtue of their proximity to STAR, impacting microbial communities within them. Therefore, the objectives of this work ...


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