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Dmk_Dissertation_11.19.18.Pdf, Dana King 2018 Washington University in St. Louis

Dmk_Dissertation_11.19.18.Pdf, Dana King

Dana King

No abstract provided.


Dmk_Dissertation_11.19.18.Pdf, Dana King 2018 Washington University in St. Louis

Dmk_Dissertation_11.19.18.Pdf, Dana King

Dana King

No abstract provided.


20 - Putative Targets Of The Pp2a Serine/Threonine Phosphatase Complex In Regulating Dendritic Morphology, Andre Golshir, Shatabdi Bhattacharjee, Daniel N. Cox 2018 Georgia State University

20 - Putative Targets Of The Pp2a Serine/Threonine Phosphatase Complex In Regulating Dendritic Morphology, Andre Golshir, Shatabdi Bhattacharjee, Daniel N. Cox

Georgia Undergraduate Research Conference (GURC)

Proper dendritic development is essential for functional neuronal networks. Elucidating the molecular mechanisms that regulate dendritic diversification is therefore essential to understanding the formation and modulation of functional neural circuitry. PP2A is a serine/threonine phosphatase that is evolutionarily conserved from yeast to mammals. In Drosophila, the PP2A complex is composed of a catalytic subunit encoded by microtubule star (mts), a scaffolding subunit encoded by PP2A-29B and one of four alternate regulatory subunits encoded by widerborst (wdb), twins, PP2A-B’ and CG4733. Previous studies in the lab showed that specific RNAi-mediated knockdown of various PP2A subunits in CIV neurons severely impaired ...


Alternative Genes For Exploring Ranavirus Phylogenetics: Four Core Genes Compared To The Major Capsid Protein And The Whole Genome., Abigale Garner 2018 Gordon College - Barnesville

Alternative Genes For Exploring Ranavirus Phylogenetics: Four Core Genes Compared To The Major Capsid Protein And The Whole Genome., Abigale Garner

Georgia Undergraduate Research Conference (GURC)

The Iridoviridae is a family of virus that infects invertebrates and poikilothermic vertebrates such as amphibians, reptiles, and fish. Ranavirus is one of the five genera within the Iridoviridae. Ranavirus infections have been seen on every continent. The ranaviruses have 26 core genes, but our study focuses on the utility of: an immediate early protein ICP-46 [open reading frame (ORF) 91R in Frog virus 3 (FV3)]; a transcription elongation factor TIIS (ORF 81R in FV3); Evrl/Air family protein (ORF 88R in FV3); and a hypothetical/putative protein of unknown function (ORF 94R in FV3) as alternative genes for phylogenetic ...


The Future Of Biodiversity Assessment: Using Environmental Dna And Next-Generation Sequencing To Characterize Biological Communities In The Central Highlands Of Arizona, Courtney Turner-Rathbone 2018 Embry-Riddle Aeronautical University

The Future Of Biodiversity Assessment: Using Environmental Dna And Next-Generation Sequencing To Characterize Biological Communities In The Central Highlands Of Arizona, Courtney Turner-Rathbone

Undergraduate Research Symposium - Prescott

Historically ecological surveys require significant man hours in the field, utilizing methods which can stress species being observed. In using environmental DNA (eDNA) gathered from air, soil, and water, traditional methods may be supplemented or reduced in order to more efficiently utilize funding and reduce or eliminate stress on surveyed species. Water was collected in replicates using aseptic technique from two different sites, 60 miles apart, along the Verde River. Samples were vacuum filtered within 24 hours through 0.45 μm cellulose nitrate (CN) filters to collect eDNA. DNA extraction from the filters was performed. The polymerase chain reaction (PCR ...


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. 2018 Georgia Gwinnett College

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 ...


Differential Analysis Of Chromatin Accessibility And Histone Modifications For Predicting Mouse Developmental Enhancers, Shaliu Fu, Qin Wang, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Kaili Fan, Cuihua Gu, Cizhong Jiang, Ruixin Zhu, Anshul Kundaje, Aiping Lu, Zhiping Weng 2018 Tongji University,China

Differential Analysis Of Chromatin Accessibility And Histone Modifications For Predicting Mouse Developmental Enhancers, Shaliu Fu, Qin Wang, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Kaili Fan, Cuihua Gu, Cizhong Jiang, Ruixin Zhu, Anshul Kundaje, Aiping Lu, Zhiping Weng

Program in Bioinformatics and Integrative Biology Publications and Presentations

Enhancers are distal cis-regulatory elements that modulate gene expression. They are depleted of nucleosomes and enriched in specific histone modifications; thus, calling DNase-seq and histone mark ChIP-seq peaks can predict enhancers. We evaluated nine peak-calling algorithms for predicting enhancers validated by transgenic mouse assays. DNase and H3K27ac peaks were consistently more predictive than H3K4me1/2/3 and H3K9ac peaks. DFilter and Hotspot2 were the best DNase peak callers, while HOMER, MUSIC, MACS2, DFilter and F-seq were the best H3K27ac peak callers. We observed that the differential DNase or H3K27ac signals between two distant tissues increased the area under the precision-recall ...


Genetic Architecture Of Gene Expression Traits Across Diverse Populations, Lauren S. Mogil, Angela Andaleon, Alexa Badalamenti, Scott P. Dickinson, Xiuqing Guo, Jerome I. Rotter, W. C. Johnson, Hae Kyung Im, Yongmei Liu, Heather E. Wheeler 2018 Loyola University Chicago

Genetic Architecture Of Gene Expression Traits Across Diverse Populations, Lauren S. Mogil, Angela Andaleon, Alexa Badalamenti, Scott P. Dickinson, Xiuqing Guo, Jerome I. Rotter, W. C. Johnson, Hae Kyung Im, Yongmei Liu, Heather E. Wheeler

Bioinformatics Faculty Publications

For many complex traits, gene regulation is likely to play a crucial mechanistic role. How the genetic architectures of complex traits vary between populations and subsequent effects on genetic prediction are not well understood, in part due to the historical paucity of GWAS in populations of non-European ancestry. We used data from the MESA (Multi-Ethnic Study of Atherosclerosis) cohort to characterize the genetic architecture of gene expression within and between diverse populations. Genotype and monocyte gene expression were available in individuals with African American (AFA, n = 233), Hispanic (HIS, n = 352), and European (CAU, n = 578) ancestry. We performed expression ...


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 2018 NYC College of Technology (CUNY)

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 2018 Institute for Creation Research

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 2018 University of Nevada, Las Vegas

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 ...


Elimination Of Pcr Duplicates In Rna-Seq And Small Rna-Seq Using Unique Molecular Identifiers, Yu Fu, Pei-Hsuan Wu, Timothy J. Beane, Phillip D. Zamore, Zhiping Weng 2018 University of Massachusetts Medical School

Elimination Of Pcr Duplicates In Rna-Seq And Small Rna-Seq Using Unique Molecular Identifiers, Yu Fu, Pei-Hsuan Wu, Timothy J. Beane, Phillip D. Zamore, Zhiping Weng

Open Access Articles

BACKGROUND: RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting material, but not every molecule amplifies equally, causing some to be overrepresented. Unique molecular identifiers (UMIs) can be used to distinguish undesirable PCR duplicates derived from a single molecule and identical but biologically meaningful reads from different molecules.

RESULTS: We have incorporated UMIs into RNA-seq and small RNA-seq protocols and developed tools to analyze the resulting data. Our UMIs contain stretches of random nucleotides whose lengths sufficiently capture diverse molecule species ...


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

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 2018 Louisiana State University and Agricultural and Mechanical College

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 2018 University of Massachusetts Amherst

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 2018 Brigham Young University

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 2018 Daemen College

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 2018 Tianjin University,

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 2018 Nova Southeastern University

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 ...


Characterizing Cultivable Bacteria From Trachymyrmex Septentrionalis Fungus Gardens, Hannah Beatty 2018 University of Connecticut

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 ...


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