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Organelle Genome Evolution Within The Green Algal Genus Dunaliella, Michael Del Vasto 2015 The University of Western Ontario

Organelle Genome Evolution Within The Green Algal Genus Dunaliella, Michael Del Vasto

Electronic Thesis and Dissertation Repository

A large amount of diversity in genomic size and content exists within the mitochondrial and plastid genomes of green algae. However, there are still many un-sequenced green algal organelle genomes. In Smith et al. 2010, the green algal species Dunaliella salina, isolated from Western Australia (strain CCAP 19/18), had its organelle genomes fully sequenced. The genomes of this organism were found to contain large amounts of noncoding DNA. The lack of sequenced organelle genomes of green algae prevented the comparison of genomic architectures in other closely related species. In this study, I expanded on the information from the 2010 ...


Genetic Analysis Of A Non-Germinating Mutant Of Arabidopsis Thaliana, Md Jakir Hossan 2015 The University of Western Ontario

Genetic Analysis Of A Non-Germinating Mutant Of Arabidopsis Thaliana, Md Jakir Hossan

Electronic Thesis and Dissertation Repository

Seed germination is partially controlled by plant hormone gibberellins (GAs). Chemical mutagenesis yielded an Arabidopsis thaliana mutant gm11, which has an absolute gibberellin requirement for seed germination. This mutant exhibited phenotypes of GA-rescuable dwarfs, including dark-green leaves, and reduced fertility. However, with repeated GA treatment, gm11 develops into fertile plants with a nearly wild type phenotype. Bulked-segregant analysis mapped gm11 to the bottom arm of chromosome 1, and subsequent next-generation mapping revealed that the mutation is a G → A transition in At1g79460 (GA2), creating a premature stop codon. This gene encodes an ent-kaurene synthase (KS) which catalyzes the conversion of ...


Determination Of The Phylogenetic Range Of Sex Combs Reduced Activity In Drosophila Melanogaster, Laura E. Garofalo 2015 The University of Western Ontario

Determination Of The Phylogenetic Range Of Sex Combs Reduced Activity In Drosophila Melanogaster, Laura E. Garofalo

Electronic Thesis and Dissertation Repository

The homeotic selector (Hox) genes are required for body patterning in bilaterians. Sex combs reduced (SCR) is a HOX protein in Drosophila melanogaster with two activities: SCRT1 and SCRlab activity required for patterning the prothorax (T1) and labia, respectively. SCRT1 is proposed to be conserved throughout bilaterians while the phylogenetic range of functional conservation of SCRlab is comparatively unknown. The goal of this work was to elucidate the evolutionary time point at which SCR activity changed. CRISPR/Cas9 transgenesis was used to incorporate ɸC31 integrase recombination sites in Drosophila Scr. The ɸC31 integrase could then be ...


Dna Methylation In Genomically Imprinted Genes Of Mice, Ethan Scott, Katherine Teeter 2015 University of Michigan - Ann Arbor

Dna Methylation In Genomically Imprinted Genes Of Mice, Ethan Scott, Katherine Teeter

McNair Scholars

Many questions in genetics are raised toward the causes and effects of imprinted genes. A major exception to Mendel’s laws, imprinted genes possibly have effects in the speciation of mammals and in biomedical phenomena like mental disorders and cancers. A common explanation for the silencing for one parental allele but not the other is differential methylation in regions of imprinted genes called imprinting control regions (ICR). A loss of this methylation in the cytosine residues of cytosine-guanine dinucleotides (CpG) can perhaps explain the hybrid inviability and disorders mammals experience. This investigation examined the ICRs of four known imprinted genes ...


Hemochromatosis: Niche Construction And The Genetic Domino Effect In The European Neolithic, John M. McCullough, Kathleen M. Heath, Alexis M. Smith 2015 University of Utah

Hemochromatosis: Niche Construction And The Genetic Domino Effect In The European Neolithic, John M. Mccullough, Kathleen M. Heath, Alexis M. Smith

Human Biology Open Access Pre-Prints

Hereditary hemochromatosis (HH) is caused by a potentially lethal recessive gene (HFE, C282Y allele) that increases iron absorption and reaches polymorphic levels in Northern European populations. Because persons carrying the allele absorb iron more readily than non-carriers, it has often been suggested HFE is an adaptation to anemia. We hypothesize positive selection for HFE began during or after the European Neolithic with the adoption of an iron-deficient high grain and dairying diet and consequent anemia, a finding confirmed in Neolithic and later European skeletons. HFE frequency compared with rate of lactase persistence in Eurasia yields a positive linear correlation coefficient ...


The Utilization Of Polymerase Chain Reaction, Dna Barcoding And Bioinformatics In Identifying Plant Species, Lindee J. Triplett, Ryan Foo, Ronald W. Strohmeyer (Mentor) 2015 Northwest Nazarene University

The Utilization Of Polymerase Chain Reaction, Dna Barcoding And Bioinformatics In Identifying Plant Species, Lindee J. Triplett, Ryan Foo, Ronald W. Strohmeyer (Mentor)

Idaho Conference on Undergraduate Research

Bioinformatics and DNA barcoding is a process used to identify plants, animals, and fungi. DNA barcoding in plants utilizes a key variable region in the genome, the RuBisCo large subunit (RbcL) on Chloroplast DNA. Once the DNA is extracted, Polymerase Chain Reaction (PCR) amplifies that region and that sample is sent off for sequencing. Bioinformatics and DNA barcoding helps taxonomists determine the sequence of the RbcL gene as well as obtain a unique barcode that can be used to identify plants. Several plant species from our local campus were sequenced and identified using the previously described methods.


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 ...


Beyond Bivariate Correlations: Three-Block Partial Least Squares Illustrated With Vegetation, Soil, And Topography, Daehyun Kim, Thomas J. DeWitt, César S. B. Costa, John A. Kupfer, Ryan W. McEwan, J. Anthony Stallins 2015 University of Kentucky

Beyond Bivariate Correlations: Three-Block Partial Least Squares Illustrated With Vegetation, Soil, And Topography, Daehyun Kim, Thomas J. Dewitt, César S. B. Costa, John A. Kupfer, Ryan W. Mcewan, J. Anthony Stallins

Biology Faculty Publications

Ecologists, particularly those engaged in biogeomorphic studies, often seek to connect data from three or more domains. Using three-block partial least squares regression, we present a procedure to quantify and define bi-variance and tri-variance of data blocks related to plant communities, their soil parameters, and topography. Bi-variance indicates the total amount of covariation between these three domains taken in pairs, whereas tri-variance refers to the common variance shared by all domains. We characterized relationships among three domains (plant communities, soil properties, topography) for a salt marsh, four coastal dunes, and two temperate forests spanning several regions in the world. We ...


A Search For Parent-Of-Origin Effects On Honey Bee Gene Expression, Sarah D. Kocher, Jennifer M. Tsuruda, Joshua D. Gibson, Christine M. Emore, Miguel E. Arechavaleta-Velasco, David C. Queller, Joan E. Strassmann, Christina M. Grozinger, Michael R. Gribskov, Phillip San Miguel, Rick Westerman, Greg J. Hunt 2015 Washington University in St Louis

A Search For Parent-Of-Origin Effects On Honey Bee Gene Expression, Sarah D. Kocher, Jennifer M. Tsuruda, Joshua D. Gibson, Christine M. Emore, Miguel E. Arechavaleta-Velasco, David C. Queller, Joan E. Strassmann, Christina M. Grozinger, Michael R. Gribskov, Phillip San Miguel, Rick Westerman, Greg J. Hunt

Biology Faculty Publications

Parent-specific gene expression (PSGE) is little known outside of mammals and plants. PSGE occurs when the expression level of a gene depends on whether an allele was inherited from the mother or the father. Kin selection theory predicts that there should be extensive PSGE in social insects because social insect parents can gain inclusive fitness benefits by silencing parental alleles in female offspring. We searched for evidence of PSGE in honey bees using transcriptomes from reciprocal crosses between European and Africanized strains. We found 46 transcripts with significant parent-of-origin effects on gene expression, many of which overexpressed the maternal allele ...


Characterization Of Putative Wnt3a-Inducible Enhancers, Katelynn C. Lee, Nicholas Hum, Aimy Sebastian, Gabriela Loots 2015 California Polytechnic State University - San Luis Obispo

Characterization Of Putative Wnt3a-Inducible Enhancers, Katelynn C. Lee, Nicholas Hum, Aimy Sebastian, Gabriela Loots

STAR (STEM Teacher and Researcher) Program Posters

The Wnt signaling pathway has been previously shown to play a major role in regulating bone metabolism and it is emerging as a target for the therapeutic intervention of bone thinning disorders such as osteoporosis. Several Wnt proteins have been shown to be expressed in bone and mutations in Wnt pathway members such as Wnt co-receptor Lrp5 and Wnt inhibitor Sost have been shown to be associated with low or high bone mass disorders, however, very little is known about specific roles played by different Wnt ligands in bone development, repair and remodeling. To identify downstream targets of Wnt signaling ...


Using High Throughput Genomic Sequencing To Predict Ecological Impacts On Sea Turtle Populations, Lesley Anderson 2015 California Polytechnic State University

Using High Throughput Genomic Sequencing To Predict Ecological Impacts On Sea Turtle Populations, Lesley Anderson

STAR (STEM Teacher and Researcher) Program Posters

Marine turtles are long-lived, migratory vertebrates that encounter a variety of human and natural stressors throughout their lives. Understanding the biology and threats of these animals is challenging because they are hard to observe, and can migrate across whole ocean basins. Minimally invasive sampling techniques (e.g., blood samples) allow us to learn about their physiology, genetics, and the environmental conditions they have experienced. In this project, we developed a novel method to extract the RNA from whole green and loggerhead turtle blood from animals inhabiting a variety of sites across the Pacific Ocean. Some habitats are more pristine, while ...


Development Of A Comprehensive Massively Parallel Sequencing Panel Of Single Nucleotide Polymorphism And Short Tandem Repeat Markers For Human Identification, David H. Warshauer B.S., M.S. 2015 University of North Texas Health Science Center at Fort Worth

Development Of A Comprehensive Massively Parallel Sequencing Panel Of Single Nucleotide Polymorphism And Short Tandem Repeat Markers For Human Identification, David H. Warshauer B.S., M.S.

Theses and Dissertations

Massively parallel sequencing (MPS) technologies allow for the detection of an unparalleled amount of genetic information with unprecedented speed and relative ease. These qualities make the technology desirable for generating DNA profiles that may be uploaded into forensic offender, arrestee, and family reference database files. This doctoral dissertation research was conducted under the hypothesis that MPS, with its exquisitely high throughput, can provide a system whereby reference samples can be typed for a large battery of markers, providing more discrimination power for forensic DNA typing and offering increased opportunities to develop investigative leads. The design and implementation of large marker ...


Genetic Modification Of Switchgrass (Panicum Virgatum L.) For Improvement Of Plant Architecture, Biomass Productivity And Sugar Release Efficiency For Biofuel, Wegi Aberra Wuddineh 2015 University of Tennessee - Knoxville

Genetic Modification Of Switchgrass (Panicum Virgatum L.) For Improvement Of Plant Architecture, Biomass Productivity And Sugar Release Efficiency For Biofuel, Wegi Aberra Wuddineh

Doctoral Dissertations

Switchgrass (Panicum virgatum L.) is a leading candidate bioenergy crop for sustainable biofuel production. To ensure its economic viability, tremendous improvements in switchgrass biomass productivity and recalcitrance to enzymatic saccharification are needed. Genetic manipulation of lignin biosynthesis by targeting transcriptional regulators of higher level domains of lignin biosynthesis and other complex traits could alter several bioenergy-desirable traits at once. A three-pronged approach was made in the dissertation research to target one plant growth regulator and transcription factors to alter plant architecture and cell wall biosynthesis.

Gibberellin (GA) catabolic enzymes, GA 2-oxidases (GA2oxs), were utilized to alternatively modify the lignin biosynthesis ...


Evolution And Phylogeny Of The Parasitoid Subfamily Phasiinae (Diptera: Tachinidae), Jeremy Daniel Blaschke 2015 University of Tennessee - Knoxville

Evolution And Phylogeny Of The Parasitoid Subfamily Phasiinae (Diptera: Tachinidae), Jeremy Daniel Blaschke

Doctoral Dissertations

The first molecular phylogenetic analysis of the agriculturally important parasitoid subfamily Phasiinae (Diptera: Tachinidae) is presented, estimated from 128 worldwide taxa (80 genera) and approximately 7.6 kilobases of nuclear data. Special emphasis is placed on taxa with controversial taxonomic placement. The resultant phylogenetic tree is used to reconstruct ancestral character states, trace the evolution of significant adaptive traits within the Tachinidae, and test hypotheses about the classification of Phasiinae. Subfamily placements of the taxa Eutherini, Epigrimyiini, Litophasia, Strongygastrini, and Parerigonini are confidently resolved, the former three within Dexiinae and the latter two within Phasiinae. Due to sparse molecular evidence ...


Spectroscopic Characterization Of Chloramphenicol And Tetracycline: An Impact Of Biofield Treatment, Mahendra Kumar Trivedi 2015 Trivedi Global Inc.

Spectroscopic Characterization Of Chloramphenicol And Tetracycline: An Impact Of Biofield Treatment, Mahendra Kumar Trivedi

Mahendra Kumar Trivedi

Objective: Chloramphenicol and tetracycline are broad-spectrum antibiotics and widely used against variety of microbial infections. Nowadays, several microbes have acquired resistance to chloramphenicol and tetracycline. The present study was aimed to evaluate the impact of biofield treatment for spectroscopic characterization of chloramphenicol and tetracycline using FT-IR and UV-Vis spectroscopy. Methods:The study was performed in two groups (control and treatment) of each antibiotic. The control groups remained as untreated, and biofield treatment was given to treatment groups. Results: FT-IR spectrum of treated chloramphenicol exhibited the decrease in wavenumber of NO2 from 1521 cm-1 to 1512 cm-1 and increase in wavenumber ...


Assessment Of Genome-Wide Genetic And Epigenetic De Novo Variation In Families With Monozygotic Twins Discordant For Schizophrenia, Christina A. Castellani 2015 The University of Western Ontario

Assessment Of Genome-Wide Genetic And Epigenetic De Novo Variation In Families With Monozygotic Twins Discordant For Schizophrenia, Christina A. Castellani

Electronic Thesis and Dissertation Repository

Schizophrenia (OMIM: 181500) is a common, debilitating and life-altering disorder. It affects 1% of the population worldwide and most often presents in early adulthood leading to devastating effects for patients, their families and society. Despite thousands of studies performed on the underlying mechanisms of schizophrenia, the causes of the disease remain unknown. However, what is known is that environmental, genetic and epigenetic factors contribute to the development of this complex disorder. Although a genetic role in schizophrenia is well established, the search for schizophrenia genes using traditional approaches has remained challenging. Interestingly, monozygotic twins show concordance for schizophrenia only 50 ...


The Yeast Genome Undergoes Significant Topological Reorganization In Quiescence, Mark T. Rutledge, Mariano Russo, Jon-Matthew Belton, Job Dekker, James R. Broach 2015 Pennsylvania State College of Medicine

The Yeast Genome Undergoes Significant Topological Reorganization In Quiescence, Mark T. Rutledge, Mariano Russo, Jon-Matthew Belton, Job Dekker, James R. Broach

Program in Systems Biology Publications and Presentations

We have examined the three-dimensional organization of the yeast genome during quiescence by a chromosome capture technique as a means of understanding how genome organization changes during development. For exponentially growing cells we observe high levels of inter-centromeric interaction but otherwise a predominance of intrachromosomal interactions over interchromosomal interactions, consistent with aggregation of centromeres at the spindle pole body and compartmentalization of individual chromosomes within the nucleoplasm. Three major changes occur in the organization of the quiescent cell genome. First, intrachromosomal associations increase at longer distances in quiescence as compared to growing cells. This suggests that chromosomes undergo condensation in ...


An Effect Of Biofield Treatment On Multidrug-Resistant Burkholderia Cepacia: A Multihost Pathogen, Mahendra Kumar Trivedi 2015 Trivedi Global Inc.

An Effect Of Biofield Treatment On Multidrug-Resistant Burkholderia Cepacia: A Multihost Pathogen, Mahendra Kumar Trivedi

Mahendra Kumar Trivedi

Burkholderia cepacia (B. cepacia) is an opportunistic, Gram negative pathogen which causes infection mainly in immunocompromised population and associated with high rate of morbidity and mortality in cystic fibrosis patients. Aim of the present study was to analyze the impact of biofield treatment on multidrug resistant B. cepacia. Clinical sample of B. cepacia was divided into two groups i.e. control and biofield treated. The analysis was done after 10 days of treatment and compared with control group. Control and treated group were analyzed for susceptibility pattern, MIC value, biochemical studies and biotype number using MicroScan Walk-Away® system.Sensitivity assay ...


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 ...


Bio-Field Treatment: An Effective Strategy To Improve The Quality Of Beef Extract And Meat Infusion Powder, Mahendra Kumar Trivedi 2015 Trivedi Global Inc.

Bio-Field Treatment: An Effective Strategy To Improve The Quality Of Beef Extract And Meat Infusion Powder, Mahendra Kumar Trivedi

Mahendra Kumar Trivedi

The present research work investigated the influence of bio-field treatment on two common flavoring agents used in food industries namely beef extract powder (BEP) and meat infusion powder (MIP). The treated powders were characterized by Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), particle size analysis, surface area analysis, differential scanning calorimetry (DSC), and thermogravimetric analysis (TGA). The FT-IR results showed disappearance of triglycerides peaks in both the treated powders as compared to control. XRD results corroborated the amorphous nature of both control and treated samples. The BEP showed enhanced average particle size (d50) and d99 (size exhibited by 99 ...


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