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Efficient Alignment Algorithms For Dna Sequencing Data, Nilesh Vinod Khiste 2018 The University of Western Ontario

Efficient Alignment Algorithms For Dna Sequencing Data, Nilesh Vinod Khiste

Electronic Thesis and Dissertation Repository

The DNA Next Generation Sequencing (NGS) technologies produce data at a low cost, enabling their application to many ambitious fields such as cancer research, disease control, personalized medicine etc. However, even after a decade of research, the modern aligners and assemblers are far from providing efficient and error free genome alignments and assemblies respectively. This is due to the inherent nature of the genome alignment and assembly problem, which involves many complexities. Many algorithms to address this problem have been proposed over the years, but there still is a huge scope for improvement in this research space.

Many new genome ...


The Genome Of The Hi5 Germ Cell Line From Trichoplusia Ni, An Agricultural Pest And Novel Model For Small Rna Biology, Yu Fu, Yujing Yang, Han Zhang, Gwen Farley, Junling Wang, Kaycee A. Quarles, Zhiping Weng, Phillip D. Zamore 2018 Boston University

The Genome Of The Hi5 Germ Cell Line From Trichoplusia Ni, An Agricultural Pest And Novel Model For Small Rna Biology, Yu Fu, Yujing Yang, Han Zhang, Gwen Farley, Junling Wang, Kaycee A. Quarles, Zhiping Weng, Phillip D. Zamore

Open Access Articles

We report a draft assembly of the genome of Hi5 cells from the lepidopteran insect pest, Trichoplusia ni, assigning 90.6% of bases to one of 28 chromosomes and predicting 14,037 protein-coding genes. Chemoreception and detoxification gene families reveal T. ni-specific gene expansions that may explain its widespread distribution and rapid adaptation to insecticides. Transcriptome and small RNA data from thorax, ovary, testis, and the germline-derived Hi5 cell line show distinct expression profiles for 295 microRNA- and > 393 piRNA-producing loci, as well as 39 genes encoding small RNA pathway proteins. Nearly all of the W chromosome is devoted to ...


Transcriptome Analysis In Spleen Reveals Differential Regulation Of Response To Newcastle Disease Virus In Two Chicken Lines, Jibin Zhang, Michael G. Kaiser, Melissa S. Deist, Rodrigo A. Gallardo, David A. Bunn, Terra R. Kelly, Jack C.M. Dekkers, Huaijun Zhou, Susan J. Lamont 2018 Iowa State University

Transcriptome Analysis In Spleen Reveals Differential Regulation Of Response To Newcastle Disease Virus In Two Chicken Lines, Jibin Zhang, Michael G. Kaiser, Melissa S. Deist, Rodrigo A. Gallardo, David A. Bunn, Terra R. Kelly, Jack C.M. Dekkers, Huaijun Zhou, Susan J. Lamont

Jibin Zhang

Enhancing genetic resistance of chickens to Newcastle Disease Virus (NDV) provides a promising way to improve poultry health, and to alleviate poverty and food insecurity in developing countries. In this study, two inbred chicken lines with different responses to NDV, Fayoumi and Leghorn, were challenged with LaSota NDV strain at 21 days of age. Through transcriptome analysis, gene expression in spleen at 2 and 6 days post-inoculation was compared between NDV-infected and control groups, as well as between chicken lines. At a false discovery rate <0.05, Fayoumi chickens, which are relatively more resistant to NDV, showed fewer differentially expressed ...


Leveraging Genomic Prediction To Scan Germplasm Collection For Crop Improvement, Leonardo de Azevedo Peixoto, Tara C. Moellers, Jiaoping Zhang, Aaron J. Lorenz, Leonardo L. Bhering, William D. Beavis, Asheesh K. Singh 2018 Federal University of Vicosa

Leveraging Genomic Prediction To Scan Germplasm Collection For Crop Improvement, Leonardo De Azevedo Peixoto, Tara C. Moellers, Jiaoping Zhang, Aaron J. Lorenz, Leonardo L. Bhering, William D. Beavis, Asheesh K. Singh

Asheesh Singh

The objective of this study was to explore the potential of genomic prediction (GP) for soybean resistance against Sclerotinia sclerotiorum (Lib.) de Bary, the causal agent of white mold (WM). A diverse panel of 465 soybean plant introduction accessions was phenotyped for WM resistance in replicated field and greenhouse tests. All plant accessions were previously genotyped using the SoySNP50K BeadChip. The predictive ability of six GP models were compared, and the impact of marker density and training population size on the predictive ability was investigated. Cross-prediction among environments was tested to determine the effectiveness of the prediction models. GP models ...


Application Of Genetics And Genomics To Wildlife Epidemiology, Julie A. Blanchong, Stacie J. Robinson, Michael D. Samuel, Jeffrey T. Foster 2018 Iowa State University

Application Of Genetics And Genomics To Wildlife Epidemiology, Julie A. Blanchong, Stacie J. Robinson, Michael D. Samuel, Jeffrey T. Foster

Julie A. Blanchong

Wildlife diseases can have significant impacts on wildlife conservation and management. Many of the pathogens that affect wildlife also have important implications for domestic animal and human health. However, management interventions to prevent or control wildlife disease are hampered by uncertainties about the complex interactions between pathogens and free-ranging wildlife. We often lack crucial knowledge about host ecology, pathogen characteristics, and host–pathogen dynamics. The purpose of this review is to familiarize wildlife biologists and managers with the application of genetic and genomic methodologies for investigating pathogen and host biology to better understand and manage wildlife diseases. The genesis of ...


Analysis For Science Librarians Of The 2017 Nobel Prize In Physiology Or Medicine: The Life And Work Of Jeffrey C. Hall, Michael Rosbash, And Michael W. Young, Neyda V. Gilman 2018 Binghamton University

Analysis For Science Librarians Of The 2017 Nobel Prize In Physiology Or Medicine: The Life And Work Of Jeffrey C. Hall, Michael Rosbash, And Michael W. Young, Neyda V. Gilman

Library Scholarship

Jeffrey C. Hall, Michael Rosbash, and Michael W. Young are the 2017 Nobel Prize in Physiology or Medicine Laureates, having earned the award for their “discoveries of molecular mechanisms controlling the circadian rhythm.” They identified the genes involved in the circadian rhythm mechanism and explained how all of the different pieces of the mechanism work together. These discoveries explain how the biological cycles of Earth’s organisms correspond to the rotation of the planet, acting as an inner clock. Their research also provides further opportunities to continue learning about the role of circadian rhythm and its relationship to human health ...


Practical Implications Of Erythromycin Resistance Gene Diversity On Surveillance And Monitoring Of Resistance, Elizabeth L. Rieke, Jinlyung Choi, Thomas B. Moorman, Michelle L. Soupir, Heather K. Allen, Schuyler D. Smith, Adina Howe 2018 Iowa State University

Practical Implications Of Erythromycin Resistance Gene Diversity On Surveillance And Monitoring Of Resistance, Elizabeth L. Rieke, Jinlyung Choi, Thomas B. Moorman, Michelle L. Soupir, Heather K. Allen, Schuyler D. Smith, Adina Howe

Agricultural and Biosystems Engineering Publications

Use of antibiotics in human and animal medicine has applied selective pressure for the global dissemination of antibiotic-resistant bacteria. Therefore, it is of interest to develop strategies to mitigate the continued amplification and transmission of resistance genes in environmental reservoirs such as farms, hospitals, and watersheds. However, the efficacy of mitigation strategies is difficult to evaluate because it is unclear which resistance genes are important to monitor, and which primers to use to detect those genes. Here we evaluated the diversity of one type of macrolide antibiotic resistance gene (erm) in one type of environment (manure) to determine which primers ...


A Mutator Phenotype Promoting The Emergence Of Spontaneous Oxidative Stress-Resistant Mutants In Campylobacter Jejuni, Lei Dai, Orhan Sahin, Yizhi Tang, Qijing Zhang 2018 Iowa State University

A Mutator Phenotype Promoting The Emergence Of Spontaneous Oxidative Stress-Resistant Mutants In Campylobacter Jejuni, Lei Dai, Orhan Sahin, Yizhi Tang, Qijing Zhang

Qijing Zhang

Campylobacter jejuni is a leading cause of foodborne illnesses worldwide. As a microaerophilic organism, C. jejuni must be able to defend against oxidative stress encountered both in the host and in the environment. How Campylobacter utilizes a mutation-based mechanism for adaptation to oxidative stress is still unknown. Here we present a previously undescribed phenotypic and genetic mechanism that promotes the emergence of oxidative stress resistant mutants. Specifically, we showed that a naturally occurring mutator phenotype, resulting from a loss of function mutation in the DNA repair enzyme MutY, increased oxidative stress resistance (OXR) in C. jejuni. We further demonstrated ...


Insights Into Teleost Sex Determination From The Seriola Dorsalis Genome Assembly, Catherine M. Purcell, Arun S. Seetharam, Owyn Snodgrass, Sofia Ortega-García, John R. Hyde, Andrew J. Severin 2018 National Marine Fisheries Service

Insights Into Teleost Sex Determination From The Seriola Dorsalis Genome Assembly, Catherine M. Purcell, Arun S. Seetharam, Owyn Snodgrass, Sofia Ortega-García, John R. Hyde, Andrew J. Severin

Office of Biotechnology Publications

Background: The assembly and annotation of a genome is a valuable resource for a species, with applications ranging from conservation genomics to gene discovery. Genomic resource development is especially important for species in culture, such as the California Yellowtail (Seriola dorsalis), the likely candidate for the establishment of commercial offshore aquaculture production in southern California. Genomic resource development for this species will improve the understanding of sex and other phenotypic traits, and allow for rapid increases in genetic improvement for and economic gain in culture production.

Results: We describe the assembly and annotation of the S. dorsalis genome, and present ...


Evaluating The Quick Fix: Weight Loss Drugs And Cellular Respiration, Pamela L. Freeman, Jennifer A. Maki, Kara R. Thoemke, Monica H. Lamm, Clark R. Coffman 2018 The College of St. Scholastica

Evaluating The Quick Fix: Weight Loss Drugs And Cellular Respiration, Pamela L. Freeman, Jennifer A. Maki, Kara R. Thoemke, Monica H. Lamm, Clark R. Coffman

Monica H. Lamm

One key to student success in introductory and cell biology courses is a foundational knowledge of cellular respiration. This is a content area in which students often harbor misconceptions that make cellular respiration particularly challenging to teach. Conventional approaches presenting cellular respiration as a complex series of isolated steps creates a situation where students tend to memorize the steps but fail to appreciate the bigger picture of how cells transform and utilize energy. Instructors frequently struggle to find ways to motivate students and encourage deeper learning. The learning goals of this cellular respiration lesson are to understand energy transfer in ...


Molecular And Functional Analysis Of Anchorage Independent, Treatment-Evasive Neuroblastoma Tumorspheres With Enhanced Malignant Properties: A Possible Explanation For Radio-Therapy Resistance, Tamara Abou-Antoun, Javad Nazarian, Anthony Ghanem, Stanislav Vukmanovic, Anthony D. Sandler 2018 George Washington University

Molecular And Functional Analysis Of Anchorage Independent, Treatment-Evasive Neuroblastoma Tumorspheres With Enhanced Malignant Properties: A Possible Explanation For Radio-Therapy Resistance, Tamara Abou-Antoun, Javad Nazarian, Anthony Ghanem, Stanislav Vukmanovic, Anthony D. Sandler

Genomics and Precision Medicine Faculty Publications

Despite significant advances in cancer treatment and management, more than 60% of patients with neuroblastoma present with very poor prognosis in the form of metastatic and aggressive disease. Solid tumors including neuroblastoma are thought to be heterogeneous with a sub-population of stem-like cells that are treatment-evasive with highly malignant characteristics. We previously identified a phenomenon of reversible adaptive plasticity (RAP) between anchorage dependent (AD) cells and anchorage independent (AI) tumorspheres in neuroblastoma cell cultures. To expand our molecular characterization of the AI tumorspheres, we sought to define the comprehensive proteomic profile of murine AD and AI neuroblastoma cells. The proteomic ...


Rest Upregulates Gremlin To Modulate Diffuse Intrinsic Pontine Glioma Vasculature, Shavali Shaik, Bridget Kennis, Shinji Maegawa, Keri Schadler, Yang Yanwen, Javad Nazarian, +several additional authors 2018 George Washington University

Rest Upregulates Gremlin To Modulate Diffuse Intrinsic Pontine Glioma Vasculature, Shavali Shaik, Bridget Kennis, Shinji Maegawa, Keri Schadler, Yang Yanwen, Javad Nazarian, +Several Additional Authors

Genomics and Precision Medicine Faculty Publications

Diffuse intrinsic pontine glioma (DIPG) is a highly aggressive glial tumor that occurs in children. The extremely poor median and 5-year survival in children afflicted with DIPG highlights the need for novel biology-driven therapeutics. Here, we have implicated the chromatin remodeler and regulator of brain development called RE1 Silencing Transcription Factor (REST), in DIPG pathology. We show that REST protein is aberrantly elevated in at least 21% of DIPG tumors compared to normal controls. Its knockdown in DIPG cell lines diminished cell growth and decreased their tumorigenicity in mouse intracranial models. DIPGs are vascularized tumors and interestingly, REST loss in ...


Genotype-Phenotype Correlation In Nf1: Evidence For A More Severe Phenotype Associated With Missense Mutations Affecting Nf1 Codons 844-848, M Koczkowska, Y Chen, T Callens, A Gomes, A Sharp, Rhonda Schonberg, +several additional authors 2018 George Washington University

Genotype-Phenotype Correlation In Nf1: Evidence For A More Severe Phenotype Associated With Missense Mutations Affecting Nf1 Codons 844-848, M Koczkowska, Y Chen, T Callens, A Gomes, A Sharp, Rhonda Schonberg, +Several Additional Authors

Pediatrics Faculty Publications

Neurofibromatosis type 1 (NF1), a common genetic disorder with a birth incidence of 1:2,000–3,000, is characterized by a highly variable clinical presentation. To date, only two clinically relevant intragenic genotype-phenotype correlations have been reported for NF1 missense mutations affecting p.Arg1809 and a single amino acid deletion p.Met922del. Both variants predispose to a distinct mild NF1 phenotype with neither externally visible cutaneous/plexiform neurofibromas nor other tumors. Here, we report 162 individuals (129 unrelated probands and 33 affected relatives) heterozygous for a constitutional missense mutation affecting one of five neighboring NF1 codons—Leu844, Cys845, Ala846 ...


Taming The Beast—A Community Teaching Material Resource For Beast 2, Joelle Barido-Sottani, Veronika Boskova, Louis du Plessis, Denise Kuhnert, Carsten Magnus, Venelin Mitov, Nicola F. Muller, Julia Pecerska, David A. Rasmussen, Chi Zhang, Alexei J. Drummond, Tracy A. Heath, Oliver G. Pybus, Timothy G. Vaughan, Tanja Stadler 2018 ETH Zurich

Taming The Beast—A Community Teaching Material Resource For Beast 2, Joelle Barido-Sottani, Veronika Boskova, Louis Du Plessis, Denise Kuhnert, Carsten Magnus, Venelin Mitov, Nicola F. Muller, Julia Pecerska, David A. Rasmussen, Chi Zhang, Alexei J. Drummond, Tracy A. Heath, Oliver G. Pybus, Timothy G. Vaughan, Tanja Stadler

Ecology, Evolution and Organismal Biology Publications

Phylogenetics and phylodynamics are central topics in modern evolutionary biology. Phylogenetic methods reconstruct the evolutionary relationships among organisms, whereas phylodynamic approaches reveal the underlying diversification processes that lead to the observed relationships. These two fields have many practical applications in disciplines as diverse as epidemiology, developmental biology, palaeontology, ecology, and linguistics. The combination of increasingly large genetic data sets and increases in computing power is facilitating the development of more sophisticated phylogenetic and phylodynamic methods. Big data sets allow us to answer complex questions. However, since the required analyses are highly specific to the particular data set and question, a ...


Analyzing Metabolomics Data For Association With Genotypes Using Two-Component Gaussian Mixture Distributions, Jason Westra, Nicholas Hartman, Bethany Lake, Gregory Shearer, Nathan L. Tintle 2018 Iowa State University

Analyzing Metabolomics Data For Association With Genotypes Using Two-Component Gaussian Mixture Distributions, Jason Westra, Nicholas Hartman, Bethany Lake, Gregory Shearer, Nathan L. Tintle

Faculty Work Comprehensive List

Standard approaches to evaluate the impact of single nucleotide polymorphisms (SNP) on quantitative phenotypes use linear models. However, these normal-based approaches may not optimally model phenotypes which are better represented by Gaussian mixture distributions (e.g., some metabolomics data). We develop a likelihood ratio test on the mixing proportions of two-component Gaussian mixture distributions and consider more restrictive models to increase power in light of a priori biological knowledge. Data were simulated to validate the improved power of the likelihood ratio test and the restricted likelihood ratio test over a linear model and a log transformed linear model. Then, using ...


Qatar: Diabetes, DiAngelo Gonzalez 2018 Augustana College, Rock Island Illinois

Qatar: Diabetes, Diangelo Gonzalez

Global Public Health

The State of Qatar is a developed nation that is located in the Middle East and borders the Persian Gulf and Saudi Arabia. The nation is a constitutional monarchy and is currently led by Amir Tamim bin Hamad Al Thani. The 2,300,000+ people of Qatar face many major challenges. Although it is one of the wealthiest nations in the Middle East, Qatar faces issues of human trafficking, migrants willing to work in poor conditions, and Middle Eastern Respiratory Syndrome (MERS). The most critical issue that plagues this county is diabetes, both I and II. Diabetes is a disease ...


Jak/Stat Signaling Regulates Gametogenesis And Age-Related Reproductive Maintenance, Michelle Suzanne Giedt 2018 University of Kentucky

Jak/Stat Signaling Regulates Gametogenesis And Age-Related Reproductive Maintenance, Michelle Suzanne Giedt

Theses and Dissertations--Biology

Cell signaling is central to integration of internal and external cues that regulate development and homeostasis. Most development is thought of as pre-adult, but limited developmental processes occur in adults. Gametogenesis incorporates elements of both these facets, with a distinct developmental plan for gamete synthesis which is regulated by integration of homeostatic inputs such as nutrient status, and environmental cues. Signaling pathways integrate and transduce information from these cues to evoke a response. A decline in homeostasis and subsequent cues occurs over time, in the case of reproductive tissues leading to a progressive loss of fertility. The Janus Kinase and ...


Draft Genome Sequence Of Streptomyces Sp. Strain Jv178, A Producer Of Clifednamide-Type Polycyclic Tetramate Macrolactams, Yunci Qi, John M. D’Alessandro, Joshua A.V Blodgett 2018 Washington University in St. Louis

Draft Genome Sequence Of Streptomyces Sp. Strain Jv178, A Producer Of Clifednamide-Type Polycyclic Tetramate Macrolactams, Yunci Qi, John M. D’Alessandro, Joshua A.V Blodgett

Biology Faculty Publications & Presentations

Here, we report the draft genome sequence of Streptomyces sp. JV178, a strain originating from Connecticut (USA) garden soil. This strain produces the polycyclic tetramate macrolactam compounds clifednamides A and B. The draft genome contains 10.65 Mb, 9,045 predicted protein coding sequences, and several natural product biosynthetic loci.


Mitochondrial Dna Analysis Of Mazahua And Otomi Indigenous Populations From Estado De Mexico Suggests A Distant Common Ancestry, Angelica González-Oliver, Ernesto Garfias-Morales, D G. Smith, Mirsha Quinto-Sánchez 2018 Facultad de Ciencias, Departamento de Biología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México

Mitochondrial Dna Analysis Of Mazahua And Otomi Indigenous Populations From Estado De Mexico Suggests A Distant Common Ancestry, Angelica GonzáLez-Oliver, Ernesto Garfias-Morales, D G. Smith, Mirsha Quinto-Sánchez

Human Biology Open Access Pre-Prints

The indigenous Mazahua and Otomi have inhabited the same localities in Estado de Mexico since pre-Columbian times. Their languages, Mazahua and Otomi, belong to the Otomanguean linguistic family, and, while they share cultural traditions and a regional history that suggest close genetic relationships and common ancestry, the historical records concerning their origin are confusing. To understand the biological relationships between Mazahua and Otomi we analyzed the mitochondrial DNA (mtDNA) genetic variation. We identified the mtDNA haplogroups by restriction fragment length polymorphism typing and sequenced the hypervariable region I of the mtDNA control region in 141 Mazahua and 100 Otomi. These ...


Examination Of Orthologous Genes (Mrub_2518 And B3728, Mrub_2519 And B3727, Mrub_2520 And B3726, Mrub_2521 And B3725) Responsible For Abc Phosphate Transporters In Two Species M. Ruber And E. Coli, Margaret Meyer, Dr. Lori Scott 2018 Augustana College, Rock Island Illinois

Examination Of Orthologous Genes (Mrub_2518 And B3728, Mrub_2519 And B3727, Mrub_2520 And B3726, Mrub_2521 And B3725) Responsible For Abc Phosphate Transporters In Two Species M. Ruber And E. Coli, Margaret Meyer, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes b3725, b3726, b3727, b3728 and Mrub_2518, Mrub_2519, Mrub_2520 and Mrub_2521 (KEGG map number 02010). We predict that these genes encode the components of a Phosphate ABC transporter: Orthologous genes Mrub_2518 (DNA coordinates 2565359..2566438) and b3728 encodes the periplasmic phosphate binding component; Orthologous genes Mrub_2519 (DNA coordinates 2566499..2567485) and b3727, and Mrub_2520 (DNA coordinates 2567496..2568326) and b3726 encode for the two transmembrane proteins; Orthologous genes Mrub_2521 (DNA coordinates 2568338..2569159) and b3725 encode for the ATP binding protein within the cytoplasm. Within the two species, M. ruber ...


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