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Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James Van Etten, Kenneth Nickerson 2016 University of Nebraska-Lincoln

Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James Van Etten, Kenneth Nickerson

Kenneth Nickerson Papers

Most animal–microbe symbiotic interactions must be advantageous to the host and provide nutritional benefits to the endosymbiont. When the host provides nutrients, it can gain the capacity to control the interaction, promote self-growth, and increase its fitness. Chlorella-like green algae engage in symbiotic relationships with certain protozoans, a partnership that significantly impacts the physiology of both organisms. Consequently, it is often challenging to grow axenic Chlorella cultures after isolation from the host because they are nutrient fastidious and often susceptible to virus infection. We hypothesize that the establishment of a symbiotic relationship resulted in natural selection for nutritional and ...


Genetic Analysis Reveals A Hierarchy Of Interactions Between Polycystin-Encoding Genes And Genes Controlling Cilia Function During Left-Right Determination, Daniel T. Grimes, Jennifer L. Keynton, Maria T. Buenavista, Xingjian Jin, Saloni H. Patel, Shinohara Kyosuke, Jennifer Vibert, Debbie J. Williams, Hiroshi Hamada, Rohana Hussain, Surya M. Nauli, Dominic P. Norris 2016 MRC Harwell

Genetic Analysis Reveals A Hierarchy Of Interactions Between Polycystin-Encoding Genes And Genes Controlling Cilia Function During Left-Right Determination, Daniel T. Grimes, Jennifer L. Keynton, Maria T. Buenavista, Xingjian Jin, Saloni H. Patel, Shinohara Kyosuke, Jennifer Vibert, Debbie J. Williams, Hiroshi Hamada, Rohana Hussain, Surya M. Nauli, Dominic P. Norris

Pharmacy Faculty Articles and Research

During mammalian development, left-right (L-R) asymmetry is established by a cilia-driven leftward fluid flow within a midline embryonic cavity called the node. This ‘nodal flow’ is detected by peripherally-located crown cells that each assemble a primary cilium which contain the putative Ca2+ channel PKD2. The interaction of flow and crown cell cilia promotes left side-specific expression of Nodal in the lateral plate mesoderm (LPM). Whilst the PKD2-interacting protein PKD1L1 has also been implicated in L-R patterning, the underlying mechanism by which flow is detected and the genetic relationship between Polycystin function and asymmetric gene expression remains unknown. Here, we ...


Identification Of Qtls For Resistance Against Rhizoctonia Solani And Phoma Glycinicola In Soybeans (Glycine Max L. Merr), Herbert Sserunkuma 2016 University of Nebraska-Lincoln

Identification Of Qtls For Resistance Against Rhizoctonia Solani And Phoma Glycinicola In Soybeans (Glycine Max L. Merr), Herbert Sserunkuma

Theses, Dissertations, and Student Research in Agronomy and Horticulture

A QTL (Quantitative trait locus) is a chromosome location of a gene controlling a specific phenotypic trait. The trait maybe governed by multiple genes. Fungal pathogens are responsible for over 50% of all soybean diseases. Rhizoctonia solani Kühn causes seedling dumping off, root and hypocotyl rots and other disease in soybeans. Phoma glycinicola de Gruyter & Boerema causes Red leaf blotch disease, predominantly in Sub-Saharan Africa. There is no reported complete resistance against these fungal pathogens in soybeans. Reaction to R.solani is reportedly a quantitative trait controlled by major and minor genes. Three QTLs contributing to reaction to R. solani ...


Characterization Of Induced Rnai Silencing Of Vaccinia Virus Essential Genes, Kewa Jiang 2016 University of Connecticut

Characterization Of Induced Rnai Silencing Of Vaccinia Virus Essential Genes, Kewa Jiang

University Scholar Projects

Vaccinia virus (VACV) is a large double-stranded DNA virus and the prototypical member of the family Poxviridae and is most notable for its use as the vaccine that eradicated smallpox (variola virus). More recently, VACV has been used to develop recombinant vaccines and immunotherapies. However, many of these processes require VACV replication to be tightly controlled. RNA interference (RNAi) is a powerful tool for in vitro silencing of mRNAs that are complimentary to 19-21 base pairs (bp) of double-stranded RNA (dsRNA). This project outlines the design and preliminary analysis of two inducible RNAi silencing constructs targeting multiple VACV essential genes ...


Social And Scientific Implications Of Genetic Testing In The Digital Age, Yaruska A. Ordinola 2016 University of Rhode Island

Social And Scientific Implications Of Genetic Testing In The Digital Age, Yaruska A. Ordinola

Senior Honors Projects

From Mendel’s law of inheritance in the 19th century through Watson and Crick’s revolutionary observations of the double helix in the 20th century, genetics has been a fascinating and continuing topic of discussion in the field of science (Collins & McKusick, 2001). Major studies like the Human Genome Project (HGP), initiated in 1990 and completed in 2003, provided a starting point from which scientists could more thoroughly investigate the human condition on a genetic level. Arising from this study, personal genomics is considered a blooming field in genetics- in which rapidly developing technological advances are able to provide easier ...


Studying The Needles In The Haystack: A Qualitative Study Of African-American And Latino Genetic Counselors, Amanda Kass, Larissa Veres 2016 Sarah Lawrence College

Studying The Needles In The Haystack: A Qualitative Study Of African-American And Latino Genetic Counselors, Amanda Kass, Larissa Veres

Human Genetics Theses and Capstones

The field of genetic counseling as a whole significantly lacks ethnic diversity within the ranks of their prospective students and trained professionals. This article describes the importance of understanding underrepresented minorities’ (URM’s) experiences and how their stories can be used to better implement recruitment techniques. In this qualitative study, five practicing genetic counselors and three genetic counseling students who identified as African-American and/or Latino participated in a structured phone interview. These interviews were aimed at better understanding their introduction into the field, their experiences in their training program, and their experiences in the profession. Themes that were explored ...


Assessing Tumor Genomic Profiling Reports For Genetic Counseling Referral Indications, Margaret McDuffee, Michelle Ning 2016 Sarah Lawrence College

Assessing Tumor Genomic Profiling Reports For Genetic Counseling Referral Indications, Margaret Mcduffee, Michelle Ning

Human Genetics Theses and Capstones

Our purpose is two-fold: (1) to identify patients who may benefit from referrals to cancer genetic counseling by characterizing the alterations reported in tumor profiling reports without matched germline control, and (2) to assess the utility of public database ClinVar in providing further information on these alterations. We assessed 160 reports across 66 tumor types. 127 (79%) reports had a mutation in 1 of 86 selected cancer predisposition genes. Of these, 29 (23%) did not meet ACMG/NSGC criteria for referral based on tumor type alone. 19% of mutations in selected genes were found in ClinVar, with 15% reported as ...


The Utility Of Genomic Variant Databases In Genetic Counseling, Colleen Ahern, Elly Brokamp 2016 Sarah Lawrence College

The Utility Of Genomic Variant Databases In Genetic Counseling, Colleen Ahern, Elly Brokamp

Human Genetics Theses and Capstones

Organizations such as the American College of Medical Genetics (ACMG) and the National Society of Genetic Counselors (NSGC) are in agreement that public genomic data sharing will benefit patient care. Despite these recommendations, not all clinical laboratories share their variant data onto public databases. As the amount of genetic material being analyzed for patient care continues to increase, more variants of unknown significance (VUS) are reported as well. Genetic counselors need to properly interpret VUS results in order to aid patients in making educated health decisions. For this paper, genetic counselors were asked about genomic data sharing and how they ...


Examining Psychological Outcomes Associated With Genetic Testing For Primary Arrhythmic Disorders In Adult Patients, Samantha Colaiacovo, Erin Kelter 2016 Sarah Lawrence College

Examining Psychological Outcomes Associated With Genetic Testing For Primary Arrhythmic Disorders In Adult Patients, Samantha Colaiacovo, Erin Kelter

Human Genetics Theses and Capstones

The psychological impact of genetic testing for an inherited arrhythmia and its influence on future well-being is highly variable and has not been well studied. Thirty-seven participants completed a survey which included questions from the Multidimensional Impact of Cancer Risk Assessment (MICRA) questionnaire, Impact of Events Scale (IES) and Satisfaction with Decision Scale (SWDS) to provide more information on their genetic testing experience and to allow the authors to search for trends that may improve the genetic counseling experience moving forward. Trends were seen upon the comparison of those who had positive versus negative genetic testing results. Those with positive ...


Exploring The Role Of Genetic Counselors In Tumor Genomic Sequencing : A Survey Of Genetic Counselors, Michelle Weinberg 2016 Sarah Lawrence College

Exploring The Role Of Genetic Counselors In Tumor Genomic Sequencing : A Survey Of Genetic Counselors, Michelle Weinberg

Human Genetics Theses and Capstones

In the emerging era of genomics-driven medicine, tumor genomic profiling in particular has begun to revolutionize the field of oncology. As the integration of such technologies evolves and affects the management and treatment of cancer, questions arise with regards to the changing roles of healthcare professionals involved in cancer care. One hundred and twenty-eight members of the National Society of Genetic Counselors (NSGC) responded to a survey to assess the current roles of genetic counselors in oncology and the perceived roles that genetic counselors will have in the clinical use of tumor genomic profiling. With regards to current roles in ...


Genetic Factors Affecting Hybrid Male Sterility Leading To Speciation, Patrick Opperman, Colin D. Meiklejohn 2016 University of Nebraska - Lincoln

Genetic Factors Affecting Hybrid Male Sterility Leading To Speciation, Patrick Opperman, Colin D. Meiklejohn

UCARE Research Products

The process whereby speciation occurs can come about through the evolution of barriers to gene flow. One of these barriers to gene flow can be an incompatibility, which leaves hybrids dead or sterile. Two theories underlie the work of this experiment, Haldane’s Rule and the large X effect. Haldane’s Rule is the observation that unisexual inviability or sterility among species’ hybrids is almost always found in the heterogametic sex. The large X effect is the observation that substitution of one species’ X-chromosome for another’s has a disproportionately large effect on hybrid fitness compared to similar substitution of ...


Turn Me On Or Off: A Study On Epigenetics And Merleau-Ponty In Angela Carter’S “The Lady Of The House Of Love”, Solsiree Lynn Skarlinsky 2016 Florida International University

Turn Me On Or Off: A Study On Epigenetics And Merleau-Ponty In Angela Carter’S “The Lady Of The House Of Love”, Solsiree Lynn Skarlinsky

FIU Electronic Theses and Dissertations

This study aims to trace points of intersection between the too often divorced disciplines of literature, continental philosophy, and the hard sciences in Angela Carter’s “The Lady of the House of Love.” In short, this thesis will not only explore how such conversations surface within the short story, but will also serve as an explication of Maurice Merleau-Ponty’s philosophy of body and space, and the theory of epigenetics. Through these explications, the thesis itself will also gear one discipline towards the other as both theories intimately bind the environment with the body, and the body with the environment ...


The Association Between Adolescent Marijuana Use And Early Adulthood Depression, Madeline L. Fritz 2016 University of Colorado Boulder

The Association Between Adolescent Marijuana Use And Early Adulthood Depression, Madeline L. Fritz

Undergraduate Honors Theses

Marijuana is one of the most widely used drugs in the United States, and the consequences of its use are mostly unknown. As marijuana becomes legalized and more widely available, it is important to investigate possible cognitive and mental health consequences of its use. The present study examined the associations between childhood internalizing behavior, adolescent marijuana use and early adulthood depression. A twin study was conducted to examine two alternative hypotheses regarding the association between adolescent marijuana use and early adulthood depression: 1. the association between marijuana use and depression is due to common genes or shared environmental influences, 2 ...


Evidence For The Fixation Of Gene Duplications By Positive Selection In Drosophila, Margarida Cardoso-Moreira, J. Roman Arguello, Srikanth Gottipati, Lawrence G. Harshman, Jennifer K. Grenier, Andrew G. Clark 2016 Cornell University

Evidence For The Fixation Of Gene Duplications By Positive Selection In Drosophila, Margarida Cardoso-Moreira, J. Roman Arguello, Srikanth Gottipati, Lawrence G. Harshman, Jennifer K. Grenier, Andrew G. Clark

Lawrence G. Harshman Publications

Gene duplications play a key role in the emergence of novel traits and in adaptation. But despite their centrality to evolutionary processes, it is still largely unknown how new gene duplicates are initially fixed within populations and later maintained in genomes. Long-standing debates on the evolution of gene duplications could be settled by determining the relative importance of genetic drift vs. positive selection in the fixation of new gene duplicates. Using the Drosophila Global Diversity Lines (GDL), we have combined genome-wide SNP polymorphism data with a novel set of copy number variant calls and gene expression profiles to characterize the ...


The Role Of Rapgap1 In Sxl Activation In Drosophila Melanogaster, Katherine M. Barnes 2016 University of Kentucky

The Role Of Rapgap1 In Sxl Activation In Drosophila Melanogaster, Katherine M. Barnes

Honors Program Senior Capstone Collection

The master switch of the sexual differentiation and dosage compensation pathway in Drosophila is the sex lethal gene, Sxl. The early promoter, SxlPe, is activated in females, resulting in female-specific splicing of later transcripts (notably the late Sxl transcript SxlPm), while inactive in males. Chromatin immunoprecipitation (ChIP) assays have previously shown association of two conventionally heterochromatin-localized proteins, HOAP and HP1, at SxlPe, and in situ hybridization as well as RT-PCR assays have confirmed a repressive role for HOAP and both repressive and activating roles for HP1. The mechanism for the activity shift of HP1 is currently unknown. Deletions in the ...


Next-Generation Sequencing Of A Multi-Drug Resistance Plasmid Captured From Stream Sediment, kevin G. libuit 2016 James Madison University

Next-Generation Sequencing Of A Multi-Drug Resistance Plasmid Captured From Stream Sediment, Kevin G. Libuit

Masters Theses

Plasmids in agriculturally-impacted bodies of water may play a significant role in the dissemination of antibiotic resistance. Previously, Erika Gehr, as part of her M.S. thesis work in our laboratory, captured environmental plasmids without cultivation of host bacteria from stream sediment into Escherichia coli. Individual plasmids were capable of conferring resistance to a surprising array of antibiotics including aminoglycosides and extended-spectrum β-lactams. In this study, we developed a method to sequence multi-drug resistance plasmids using both Oxford Nanopore MinION and Ion Torrent Personal Genome Machine sequencers. Plasmid pEG1-1 was sequenced on both platforms and a hybrid assembly utilizing data ...


Genomic And Transcriptomic Analyses Of Microbotryum Lychnidis-Dioicae Provide Insights Into The Biology Of A Fascinating Fungal Phytopathogen., Su San Toh 2015 University of Louisville

Genomic And Transcriptomic Analyses Of Microbotryum Lychnidis-Dioicae Provide Insights Into The Biology Of A Fascinating Fungal Phytopathogen., Su San Toh

Electronic Theses and Dissertations

This study made use of the Silene latifolia/Microbotryum lychnidis-dioicae phytopathogen system as the focal system to establish the first reference genome for Microbotryum violaceum sensu lato. In silico analysis was performed on the genome assembly to identify various characteristics of the genome. Using RNA-Sequencing technologies on the Illumina platform, we collected transcriptomic data for both in vitro and in planta life stages of the fungus, providing the most comprehensive look at the gene expression and regulation of this fungus. Due to a lack of identifiable domains on the predicted genes, gene set enrichment analysis was done in context, by ...


Evidence Of Field-Evolved Resistance To Bifenthrin In Western Corn Rootworm (Diabrotica Virgifera Virgifera Leconte) Populations In Western Nebraska And Kansas, Adriano E. Pereira, Haichuan Wang, Sarah N. Zukoff, Lance Meinke, B. Wade French, Blair Siegfried 2015 University of Nebraska-Lincoln

Evidence Of Field-Evolved Resistance To Bifenthrin In Western Corn Rootworm (Diabrotica Virgifera Virgifera Leconte) Populations In Western Nebraska And Kansas, Adriano E. Pereira, Haichuan Wang, Sarah N. Zukoff, Lance Meinke, B. Wade French, Blair Siegfried

Faculty Publications: Department of Entomology

Pyrethroid insecticides have been used to control larvae or adults of the western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte, a key pest of field corn in the United States. In response to reports of reduced efficacy of pyrethroids in WCR management programs in southwestern areas of Nebraska and Kansas the present research was designed to establish a baseline of susceptibility to the pyrethroid insecticide, bifenthrin, using susceptible laboratory populations and to compare this baseline with susceptibility of field populations. Concentration-response bioassays were performed to estimate the baseline susceptibility. From the baseline data, a diagnostic concentration (LC99) was determined and ...


Odorant Receptor-Based Discovery Of Natural Repellents Of Human Lice, Julien Pelletier, Pingxi Xu, Kyong-Sup Yoon, John M. Clark, Walter S. Leal 2015 University of California-Davis

Odorant Receptor-Based Discovery Of Natural Repellents Of Human Lice, Julien Pelletier, Pingxi Xu, Kyong-Sup Yoon, John M. Clark, Walter S. Leal

SIUE Faculty Research, Scholarship, and Creative Activity

The body louse, Pediculus humanus humanus, is an obligate blood-feeding ectoparasite and an important insect vector that mediates the transmission of diseases to humans. The analysis of the body louse genome revealed a drastic reduction of the chemosensory gene repertoires when compared to other insects, suggesting specific olfactory adaptations to host specialization and permanent parasitic lifestyle. Here, we present for the first time functional evidence for the role of odorant receptors (ORs) in this insect, with the objective to gain insight into the chemical ecology of this vector. We identified seven putative full-length ORs, in addition to the odorant receptor ...


Ordinal Probit Wavelet-Based Functional Models For Eqtl Analysis, Mark Meyer, Jeffrey Morris, Craig Hersh, Jarrett Morrow, Christoph Lange, Brent Coull 2015 Bucknell University

Ordinal Probit Wavelet-Based Functional Models For Eqtl Analysis, Mark Meyer, Jeffrey Morris, Craig Hersh, Jarrett Morrow, Christoph Lange, Brent Coull

Mark J Meyer

Current methods for conducting expression Quantitative Trait Loci (eQTL) analysis are limited in scope to a pairwise association testing between a single nucleotide polymorphism (SNPs) and expression probe set in a region around a gene of interest, thus ignoring the inherent between-SNP correlation. To determine association, p-values are then typically adjusted using Plug-in False Discovery Rate. As many SNPs are interrogated in the region and multiple probe-sets taken, the current approach requires the fitting of a large number of models. We propose to remedy this by introducing a flexible function-on-scalar regression that models the genome as a functional outcome. The ...


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