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Changes In The Proliferation And Gene Expression Of Huvecs In Response To Treatment With Plant Secondary Metabolites, Caleigh Howard 2018 Pepperdine University

Changes In The Proliferation And Gene Expression Of Huvecs In Response To Treatment With Plant Secondary Metabolites, Caleigh Howard

Seaver College Research And Scholarly Achievement Symposium

Medicinal plants have historically been a valuable source of new drugs, and Southern California possesses a rich collection of native plants which have been used as medicines by native people groups for thousands of years. Angiogenesis is the biological process of new blood-vessel growth from endothelial cells. It is an essential part of the wound-healing process, and increased angiogenesis has also been implicated in the growth of some types of cancerous tumors. In this study, extracts of the Southern Californian native plants Red shanks (Adenostoma sparsifolium) and the alkaloid extract of Jimson weed (Datura wrightii) were tested for their angiogenic ...


Investigating The Genetic Structure Of Northern Long-Eared Bats In Nebraska, Jonathan Korbitz 2018 University of Nebraska at Omaha

Investigating The Genetic Structure Of Northern Long-Eared Bats In Nebraska, Jonathan Korbitz

Student Research and Creative Activity Fair

Abstract:

The northern long-eared bat (Myotis septentrionalis) is one of many species of hibernating bats in North America affected by a recently discovered fungal disease called white-nose syndrome (WNS). Northern long-eared bats seem to be extremely susceptible to the disease with mass fatalities occurring among populations in eastern North America. Researchers in the eastern distribution of this species have performed mtDNA analysis to identify the population structure of the species; however, genetic analysis has yet to be done in western parts of its distribution. The goal of this study is to create a better understanding of the genetic makeup of ...


Improving Eukaryotic Genome Annotation Using Single Molecule Mrna Sequencing., Vincent Magrini, Xin Gao, Bruce A Rosa, Sean McGrath, Xu Zhang, Kymberlie Hallsworth-Pepin, John Martin, John Hawdon, Richard K Wilson, Makedonka Mitreva 2018 George Washington University

Improving Eukaryotic Genome Annotation Using Single Molecule Mrna Sequencing., Vincent Magrini, Xin Gao, Bruce A Rosa, Sean Mcgrath, Xu Zhang, Kymberlie Hallsworth-Pepin, John Martin, John Hawdon, Richard K Wilson, Makedonka Mitreva

Microbiology, Immunology, and Tropical Medicine Faculty Publications

BACKGROUND: The advantages of Pacific Biosciences (PacBio) single-molecule real-time (SMRT) technology include long reads, low systematic bias, and high consensus read accuracy. Here we use these attributes to improve on the genome annotation of the parasitic hookworm Ancylostoma ceylanicum using PacBio RNA-Seq.

RESULTS: We sequenced 192,888 circular consensus sequences (CCS) derived from cDNAs generated using the CloneTech SMARTer system. These SMARTer-SMRT libraries were normalized and size-selected providing a robust population of expressed structural genes for subsequent genome annotation. We demonstrate PacBio mRNA sequences based genome annotation improvement, compared to genome annotation using conventional sequencing-by-synthesis alone, by identifying 1609 (9 ...


Identification Of Novel Genetic Variations For Amyotrophic Lateral Sclerosis (Als), Guang Xu 2018 University of Massachusetts Medical School

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 ...


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 ...


Genetic Diversity, Breed Composition And Admixture Of Kenyan Domestic Pigs, Fidalis Denis Mujibi, Edward Okoth, Evans K. Cheruiyot, Cynthia Onzere, Richard P. Bishop, Eric M. Fèvre, Lian Thomas, Charles Masembe, Graham Plastow, Max Rothschild 2018 Nelson Mandela Africa Institution of Science and Technology

Genetic Diversity, Breed Composition And Admixture Of Kenyan Domestic Pigs, Fidalis Denis Mujibi, Edward Okoth, Evans K. Cheruiyot, Cynthia Onzere, Richard P. Bishop, Eric M. Fèvre, Lian Thomas, Charles Masembe, Graham Plastow, Max Rothschild

Animal Science Publications

The genetic diversity of African pigs, whether domestic or wild has not been widely studied and there is very limited published information available. Available data suggests that African domestic pigs originate from different domestication centers as opposed to international commercial breeds. We evaluated two domestic pig populations in Western Kenya, in order to characterize the genetic diversity, breed composition and admixture of the pigs in an area known to be endemic for African swine fever (ASF). One of the reasons for characterizing these specific populations is the fact that a proportion of indigenous pigs have tested ASF virus (ASFv) positive ...


Genome-Wide Association Study For The Relationship Between Temperature And Feed Intake In Beef Cattle, Robel Ghebrewold 2018 University of Nebraska - Lincoln

Genome-Wide Association Study For The Relationship Between Temperature And Feed Intake In Beef Cattle, Robel Ghebrewold

Theses and Dissertations in Animal Science

The interaction of livestock with the environment they live in is complex and plays a significant role in their production performance, which also depends on location and management practices. Climate change is projected to increase temperature globally. As a result, climate change will most likely aggravate the pressure from different sources of stressors on the current agricultural production system in general and in livestock specifically. Environmental conditions, such as changes in ambient temperature, can cause changes in animal behavior and performance. In general, it is believed that as ambient temperature increases, dry matter intake (DMI) of beef cattle decreases. However ...


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 ...


Determining Bioindicators For Coastal Tidal Marsh Health Using The Food Web Of Larvae Of The Greenhead Horse Fly (Tabanus Nigrovittatus), Devika Rajeev Bhalerao 2018 Louisiana State University and Agricultural and Mechanical College

Determining Bioindicators For Coastal Tidal Marsh Health Using The Food Web Of Larvae Of The Greenhead Horse Fly (Tabanus Nigrovittatus), Devika Rajeev Bhalerao

LSU Master's Theses

The greenhead horse fly Tabanus nigrovittatus Macquart is native to coastal marshlands from Texas to Nova Scotia. The larvae are apex invertebrate predators and their development is dependent on the food web in the soil. Surveillance of T. nigrovittatus after the 2010 Deepwater Horizon oil spill in the Gulf of Mexico showed population crashes of adults in the coastal marshes of East Louisiana near places where oil made landfall, but not in West Louisiana where the oil did not reach. Sediment collection in 2011 from West and East Louisiana revealed larval population crashes in the Eastern coastal region. We hypothesized ...


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 ...


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