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A Parallel Algorithm For Compression Of Big Next-Generation Sequencing Datasets, Sandino N. Vargas Perez, Fahad Saeed 2015 Western Michigan University

A Parallel Algorithm For Compression Of Big Next-Generation Sequencing Datasets, Sandino N. Vargas Perez, Fahad Saeed

Parallel Computing and Data Science Lab Technical Reports

With the advent of high-throughput next-generation sequencing (NGS) techniques, the amount of data being generated represents challenges including storage, analysis and transport of huge datasets. One solution to storage and transmission of data is compression using specialized compression algorithms. However, these specialized algorithms suffer from poor scalability with increasing size of the datasets and best available solutions can take hours to compress gigabytes of data. In this paper we introduce paraDSRC, a parallel implementation of DSRC algorithm using a message passing model that presents reduction of the compression time complexity by a factor of O(1/p ). Our experimental results ...


Identification Of Whole Mitochondrial Genomes From Venezuela And Implications On Regional Phylogenies In South America, Esther J. Lee, D. Andrew Merriwether 2015 Texas Tech University

Identification Of Whole Mitochondrial Genomes From Venezuela And Implications On Regional Phylogenies In South America, Esther J. Lee, D. Andrew Merriwether

Human Biology Open Access Pre-Prints

Recent studies have expanded and refined the founding haplogroups of the Americas using whole mitochondrial (mtDNA) genome analysis. In addition to pan-American lineages, a number of studies have identified specific variants that show higher frequencies in restricted geographical areas. In order to further characterize Native American maternal lineages and specifically examine local patterns within South America, we analyzed twelve maternally unrelated Yekuana whole mtDNA genomes from one village (Sharamaña) that include the four major Native American haplogroups A2, B2, C1, and D1. Our study proposes a reconfiguration of one subhaplogroup A2 (A2aa) that is specific to South America and identifies ...


Engaging Maori In Biobanking And Genetic Research: Legal, Ethical, And Policy Challenges, Angela Beaton, Barry Smith, Valmaine Toki, Kim Southey, Maui Hudson 2015 Te Tari Hauora me Te Tari Tikanga-ā-Hapori, Centre for Health and Social Practice, Waikato Institute of Technology

Engaging Maori In Biobanking And Genetic Research: Legal, Ethical, And Policy Challenges, Angela Beaton, Barry Smith, Valmaine Toki, Kim Southey, Maui Hudson

The International Indigenous Policy Journal

Publically funded biobanking initiatives and genetic research should contribute towards reducing inequalities in health by reducing the prevalence and burden of disease. It is essential that Maori and other Indigenous populations share in health gains derived from these activities. The Health Research Council of New Zealand has funded a research project (2012-2015) to identify Maori perspectives on biobanking and genetic research, and to develop cultural guidelines for ethical biobanking and genetic research involving biospecimens. This review describes relevant values and ethics embedded in Maori indigenous knowledge, and how they may be applied to culturally safe interactions between biobanks, researchers, individual ...


Role Of Metabolic Shifts In Protection From Mutation Damage: Characterizing Mitochondrial Membrane Potential In C. Elegans Gas-1 Mutants, Lauren S. Muñoz-Tremblay 2015 Portland State University

Role Of Metabolic Shifts In Protection From Mutation Damage: Characterizing Mitochondrial Membrane Potential In C. Elegans Gas-1 Mutants, Lauren S. Muñoz-Tremblay

PSU McNair Scholars Online Journal

Many terminal human diseases are caused by mutations affecting mitochondrial functioning. Mitochondria are essential organelles responsible for producing cellular energy, adenosine triphosphate (ATP) via oxidative phosphorylation (OXPHOS) at mitochondrial electron transport chains (ETC). Proper ETC functioning relies on maintenance of the electrochemical gradient essential for energy production, known as mitochondrial membrane potential (ΔψM). The inner mitochondrial membrane is the site of the ETC and is most closely in contact with the enzymatic processes occurring within the mitochondrial matrix. Mutations affecting protein components of the ETC are especially troublesome for organelle health. ETC mutants commonly express altered ΔψM, as well as ...


Activity Of The Porcine Gonadotropin-Releasing Hormone Receptor Gene Promoter Is Partially Conferred By A Distal Gonadotrope Specific Element (Gse) Within An Upstream Enhancing Region, Two Proximal Gses And A Retinoid X Receptor Binding Site, Rebecca Cederberg, Jacqueline Smith, Emily A. McDonald, Chanho Lee, Amy R. Perkins 2015 University of Nebraska - Lincoln

Activity Of The Porcine Gonadotropin-Releasing Hormone Receptor Gene Promoter Is Partially Conferred By A Distal Gonadotrope Specific Element (Gse) Within An Upstream Enhancing Region, Two Proximal Gses And A Retinoid X Receptor Binding Site, Rebecca Cederberg, Jacqueline Smith, Emily A. Mcdonald, Chanho Lee, Amy R. Perkins

Faculty Papers and Publications in Animal Science

Background: Regulation of gonadotropin-releasing hormone (GnRH) receptor (GnRHR) numbers on gonadotropes within the anterior pituitary gland represents a critical point for control of reproductive function. Binding of GnRH to its receptor regulates follicle stimulating hormone (FSH) and luteinizing hormone (LH) release and levels of this G-protein coupled receptor on the surface of gonadotropes determines their sensitivity to GnRH pulses. While transcriptional regulation of this gene has been studied in mice, rats, humans and sheep, little is known about its regulation in the pig, an important agricultural species and human research model.

Methods: We isolated 5118 bp of 5′ flanking sequence ...


Mitochondrial Dna Suggests A Western Eurasian Origin For Ancient (Proto-) Bulgarians, D V. Nesheva, S Karachanak-Yankova, M Lari, Y Yordanov, A Galabov, David Caramelli, Draga Toncheva 2015 Department of Medical Genetics, Medical University of Sofia

Mitochondrial Dna Suggests A Western Eurasian Origin For Ancient (Proto-) Bulgarians, D V. Nesheva, S Karachanak-Yankova, M Lari, Y Yordanov, A Galabov, David Caramelli, Draga Toncheva

Human Biology Open Access Pre-Prints

Ancient (proto-) Bulgarians have long been thought to as a Turkic population. However, evidence found in the past three decades show that this is not the case. Until now, this evidence does not include ancient mitochondrial DNA (mtDNA) analysis. In order to fill this void, we have collected human remains from the VIII-X century AD located in three necropolises in Bulgaria: Nojarevo (Silistra region) and Monastery of Mostich (Shumen region), both in Northeast Bulgaria and Tuhovishte (Satovcha region) in Southwest Bulgaria. The phylogenetic analysis of 13 ancient DNA samples (extracted from teeth) identified 12 independent haplotypes, which we further classified ...


Epigenetic Silencing Of Id4 In Prostate Cancer: Mechanistic Insight, Swathi Chinaranagari 2015 Clark Atlanta University

Epigenetic Silencing Of Id4 In Prostate Cancer: Mechanistic Insight, Swathi Chinaranagari

Electronic Theses & Dissertations Collection for Atlanta University & Clark Atlanta University

Inhibitor of DNA binding/differentiation protein 4 (ID4) is a dominant negative regulator of basic helix loop helix (bHLH) family of transcription factors. ID4 shares the homology of HLH domain with other ID proteins (ID1, ID2, and ID3) and lack the basic DNA binding region. Evidence suggested that unlike ID1, ID2 and ID3, ID4 acts as a tumor suppressor in prostate cancer by attenuating cell proliferation and promoting apoptosis. Consistent with these observations ID4 is epigenetically silenced in DU145 prostate cancer cell line. In this study we investigated whether ID4 is also epigenetically silenced in prostate cancer. We also examined ...


Investigating The Role Of Wolbachia Endosymbionts In The Expansion Of The F Element In Drosophila Ananassae, Elizabeth J. Chen 2015 Washington University in St Louis

Investigating The Role Of Wolbachia Endosymbionts In The Expansion Of The F Element In Drosophila Ananassae, Elizabeth J. Chen

Undergraduate Theses—Unrestricted

At 4.2 Mb overall, the Drosophila melanogaster Muller F element (dot chromosome) is an unusual autosome; it is broadly heterochromatic, but the distal 1.3 Mb has a gene density and expression pattern similar to other autosomes. More intriguing is the large expansion of the D. ananassae F element (~20 Mb). Elucidating the factors that contribute to this expansion could improve our understanding of how heterochromatic domains are maintained and amplified.

Previous analyses show that the lateral gene transfer (LGT) of Wolbachia (the most widespread intracellular bacteria in the Rickettsiales order) into the D. ananassae genome is an important ...


Environmental Stimuli And Intragenerational Epigenetics, Nicholas J. Napier 2015 Wofford College

Environmental Stimuli And Intragenerational Epigenetics, Nicholas J. Napier

Student Scholarship

Epigenetics is the study of any change in gene expression that is not mediated by DNA sequence. The effects of environmental stimuli on epigenetic changes have been studied extensively in recent years. Multiple reviews have provided comprehensive summations of the effects of environmental stimuli on transgenerational epigenetic changes, but few reviews have focused upon environment-induced intragenerational epigenetic changes. This review will summarize current knowledge of the intragenerational epigenetic changes that are induced by two groups of well-studied environmental stimuli: nutritional deficiencies and carcinogens. This survey of intragenerational epigenetic changes will focus upon the mechanisms behind them, the disorders associated with ...


Deciphering The Functional Collaboration Of Mid And Bric-A-Brac 2 As Potential Regulators Of Cellular Proliferation Within Adult Drosophila Ovaries, Petra Visic 2015 University of Southern Mississippi

Deciphering The Functional Collaboration Of Mid And Bric-A-Brac 2 As Potential Regulators Of Cellular Proliferation Within Adult Drosophila Ovaries, Petra Visic

Master's Theses

Stem cell niches are highly organized and specialized microenvironments located within specific tissues of both vertebrate and invertebrate organisms [1]. In Drosophila melanogaster, three distinct stem cell niches have been identified within the ovary including the germline stem cell (GSC), follicle stem cell (FSC), and escort stem cell (ESC) niche. Recently, Fregoso-Lomas et al. [2] reported that Gurken/Epidermal Growth Factor Receptor (EGFR) signaling is modulated within posterior ovarian follicle cells by Midline (Mid). The mid gene encodes a T-box transcription factor protein that specifies cell fates in the developing heart [3][4], central nervous system [5][6], epidermis [7 ...


Short Germ Insects Utilize Both The Ancestral And Derived Mode Of Polycomb Group-Mediated Epigenetic Silencing Of Hox Genes, Yuji Matsuoka, Tetsuya Bando, Takahito Watanabe, Yoshiyasu Ishimaru, Sumihare Noji, Aleksander Popadic, Taro Mito 2015 University of Tokushima

Short Germ Insects Utilize Both The Ancestral And Derived Mode Of Polycomb Group-Mediated Epigenetic Silencing Of Hox Genes, Yuji Matsuoka, Tetsuya Bando, Takahito Watanabe, Yoshiyasu Ishimaru, Sumihare Noji, Aleksander Popadic, Taro Mito

Biological Sciences Faculty Research Publications

In insect species that undergo long germ segmentation, such as Drosophila, all segments are specified simultaneously at the early blastoderm stage. As embryogenesis progresses, the expression boundaries of Hox genes are established by repression of gap genes, which is subsequently replaced by Polycomb group (PcG) silencing. At present, however, it is not known whether patterning occurs this way in a more ancestral (short germ) mode of embryogenesis, where segments are added gradually during posterior elongation. In this study, two members of the PcG family, Enhancer of zeste (E(z)) and Suppressor of zeste 12 (Su(z)12), were analyzed in ...


Characterization Of A Novel Clade Of Transporters In Phytophthora, Stephanie Padula, Paul F. Morris Dr, Howard Casey Cromwell Dr., Menaka Ariyaratne, Andrew Wagner 2015 Bowling Green State University - Main Campus

Characterization Of A Novel Clade Of Transporters In Phytophthora, Stephanie Padula, Paul F. Morris Dr, Howard Casey Cromwell Dr., Menaka Ariyaratne, Andrew Wagner

Honors Projects

The oomycete Phytophthora parasitica has a worldwide distribution and is an economically important pathogen of more than 100 species4. RNA-seq analysis showed that one gene, PPTG_16698 has the 5th highest level of expression of all transport proteins in the zoospore stage, and is highly conserved throughout Phytophthora species. This project attempts to characterize the important biological role that PPTG_16698 plays in P. parasitica and other oomycetes. Three strategies have been implemented to accomplish this goal: growth analysis by heterologous expression in yeast, metabolite analysis in yeast, and construction of a GFP fusion protein to enable localization of the ...


Examination Of Polymorphism In The Serine Proteinase Inhibitor Gene In The Eastern Oyster, Crassostrea Virginica., Aine Lehane 2015 University of Rhode Island

Examination Of Polymorphism In The Serine Proteinase Inhibitor Gene In The Eastern Oyster, Crassostrea Virginica., Aine Lehane

Senior Honors Projects

Oysters are a keystone species; they are filter-feeders and reef-builders. Additionally, oysters are extremely important within the shellfish aquaculture industry; they are the second most widely produced species in world aquaculture production. Eastern oysters, Crassostrea virginica, are produced in aquaculture and are unfortunately susceptible to Dermo disease. Dermo is caused by a protozoan parasite, Perkinsus marinus, and infection is often fatal in oysters due to widespread tissue damage and blockage of blood vessels. Research in oyster disease is particularly needed because disease is one of the largest impediments faced by the aquaculture industry as entire oyster populations can be decimated ...


The Cancer Genome Atlas (Tcga): Breast And Ovarian Cancers, Laura Ann Riccio 2015 University of Rhode Island

The Cancer Genome Atlas (Tcga): Breast And Ovarian Cancers, Laura Ann Riccio

Senior Honors Projects

The field of genomics originated in the 1970’s starting with the sequencing of small organisms’ genomes such as the bacterium, Haemophilus influenzae, and the yeast, Saccharomyces cerevisiae. A genome is the complete ordered sequence of DNA bases (A, C, G, and T) comprising all of the protein- and RNA-coding genes, as well as all of the regulatory sequences necessary for the construction of an organism. Over time, scientists sequenced the genomes of larger and more complex organisms, eventually leading to the sequencing of the human genome. The Human Genome Project (HGP) was initiated in 1990 and took over ten ...


Bioinformatic Game Theory And Its Application To Cluster Multi-Domain Proteins, Brittney Keel 2015 University of Nebraska-Lincoln

Bioinformatic Game Theory And Its Application To Cluster Multi-Domain Proteins, Brittney Keel

Dissertations, Theses, and Student Research Papers in Mathematics

The exact evolutionary history of any set of biological sequences is unknown, and all phylogenetic reconstructions are approximations. The problem becomes harder when one must consider a mix of vertical and lateral phylogenetic signals. In this dissertation we propose a game-theoretic approach to clustering biological sequences and analyzing their evolutionary histories. In this context we use the term evolution as a broad descriptor for the entire set of mechanisms driving the inherited characteristics of a population. The key assumption in our development is that evolution tries to accommodate the competing forces of selection, of which the conservation force seeks to ...


Dominance Of Old End Growth Is Inherited In Fission Yeast, Julie Tia Rich 2015 University of Tennessee, Knoxville

Dominance Of Old End Growth Is Inherited In Fission Yeast, Julie Tia Rich

University of Tennessee Honors Thesis Projects

No abstract provided.


A Two-Component Regulatory System Associated With Scytonemin Biosynthesis In Nostoc Punctiforme Atcc 29133, Jacob P. Janssen 2015 Indiana University - Purdue University Fort Wayne

A Two-Component Regulatory System Associated With Scytonemin Biosynthesis In Nostoc Punctiforme Atcc 29133, Jacob P. Janssen

Masters' Theses

As phototrophic bacteria, cyanobacteria are continually exposed to ultraviolet radiation as they harvest solar energy. In particular, long-wavelength ultraviolet radiation (UVA) damages living cells by releasing reactive oxygen species. To mitigate damage to the cell, some cyanobacteria produce a UVA-absorbing pigment in the extracellular sheath, known as scytonemin. Scytonemin is a heterocyclic, dimeric molecule that is only produced upon induction by UVA. In Nostoc punctiforme ATCC 29133, it is hypothesized that scytonemin is regulated by the two component regulatory system (TCRS) of NpF1277 (sensor kinase) and NpF1278 (response regulator). Gene expression of the TCRS was studied after exposure to UVA ...


Genetic Approaches To The Conservation Of Migratory Bats: A Study Of The Eastern Red Bat (Lasiurus Borealis), Maarten J. Vonhof, Amy L. Russell 2015 Western Michigan University

Genetic Approaches To The Conservation Of Migratory Bats: A Study Of The Eastern Red Bat (Lasiurus Borealis), Maarten J. Vonhof, Amy L. Russell

Amy L. Russell

Documented fatalities of bats at wind turbines have raised serious concerns about the future impacts of increased wind power development on populations of migratory bat species. However, for most bat species we have no knowledge of the size of populations and their demographic trends, the degree of structuring into discrete subpopulations, and whether different subpopulations use spatially segregated migratory routes. Here, we utilize genetic data from eastern red bats (Lasiurus borealis), one of the species most highly affected by wind power development in North America, to (1) evaluate patterns of population structure across the landscape, (2) estimate effective population size ...


Tracking Plastid Gene Migration In Karenia Brevis, Kelly E. Scott 2015 The University of Southern Mississippi

Tracking Plastid Gene Migration In Karenia Brevis, Kelly E. Scott

Honors Theses

Karenia brevis is a marine dinoflagellate responsible for the harmful algal blooms (also known as red tides) in the Gulf of Mexico. K. brevis expresses antisense (AS) RNAs, each of which has a complementary region to the messenger RNA (mRNA) of a variety of genes. In dinoflagellates, many plastid (and mitochondrial) genes have migrated to the nuclear genome. It is unknown whether chloroplast genes, such as photosystem – D2, have migrated in K. brevis. It is also unknown where the gene that expresses the AS RNA for photosystem D2 resides. The protein-coding gene and the AS RNA-expressing gene could both reside ...


Phosphotransacetylase And Xylulose 5-Phosphate/Fructose 6-Phosphate Phosphoketolase: Two Eukaryotic Partners Of Acetate Kinase, Tonya Taylor 2015 Clemson University

Phosphotransacetylase And Xylulose 5-Phosphate/Fructose 6-Phosphate Phosphoketolase: Two Eukaryotic Partners Of Acetate Kinase, Tonya Taylor

All Dissertations

Although acetate is a predominant metabolite produced by many eukaryotic microbes, far less attention has been given to acetate metabolism in eukaryotes than in bacteria and archaea. Acetate kinase (Ack), which catalyzes the reversible phosphorylation of acetate from ATP, is a key enzyme in bacterial acetate metabolism. Ack primarily partners with phosphotransacetylase (Pta), which catalyzes the generation of acetyl phosphate from acetyl-CoA, but can also partner with xylulose 5-phosphate/fructose 6-phosphate phosphoketolase (Xfp), which produces acetyl phosphate from either xylulose 5-phosphate or fructose 6-phosphate. The Ack-Pta pathway, found primarily in bacteria, is also present in lower eukaryotes such as the ...


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