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Maize Breeding, J. S. C. Smith, O. S. Smith, Kendall R. Lamkey 2017 Pioneer Hi-Bred International, Inc.

Maize Breeding, J. S. C. Smith, O. S. Smith, Kendall R. Lamkey

Kendall R Lamkey

Maize (Zea mays L.) is a remarkable plant. Human societies depend upon maize for food, health, scientific knowledge, economic growth, culture and spirituality. Maize breeders have improved productivity through selection on phenotype. Future improvements in maize productivity will require more effective utilization of genetic resources including direct selection upon genotype. Success will require a greater understanding of the complex biology of quantitative traits and a more thorough evaluation of the broader genetic base of maize. Maize breeders are fortunate and privileged to work with a species that encompasses a broad array of diversity and which provides a rich source of ...


Body Size Regulation Via Bmp Signaling In Caenorhabditis Elegans, Uday Madaan 2017 The Graduate Center, City University of New York

Body Size Regulation Via Bmp Signaling In Caenorhabditis Elegans, Uday Madaan

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

The body size of an organism can be a crucial determinant of access to nutrition, reproductive success and overall survival in the wild. However, how body size of an individual is determined is incompletely understood. Body size is a complex trait determined by multiple pathways and genes, making it difficult to understand the role of individual genes and pathways in determining overall size. In Caenorhabditis elegans, a homolog of Bone Morphogenetic Proteins (BMP) is a major regulator of body size; functional loss of DBL-1 leads to a small body size. Due to a drastic change in body size in dbl-1 ...


Genome, Transcriptome And Methylome Sequencing Of A Primitively Eusocial Wasp Reveal A Greatly Reduced Dna Methylation System In A Social Insect, Daniel S. Standage, Ali J. Berens, Karl M. Glastad, Andrew J. Severin, Volker P. Brendel, Amy L. Toth 2017 Indiana University

Genome, Transcriptome And Methylome Sequencing Of A Primitively Eusocial Wasp Reveal A Greatly Reduced Dna Methylation System In A Social Insect, Daniel S. Standage, Ali J. Berens, Karl M. Glastad, Andrew J. Severin, Volker P. Brendel, Amy L. Toth

Amy Toth

Comparative genomics of social insects has been intensely pursued in recent years with the goal of providing insights into the evolution of social behaviour and its underlying genomic and epigenomic basis. However, the comparative approach has been hampered by a paucity of data on some of the most informative social forms (e.g. incipiently and primitively social) and taxa (especially members of the wasp family Vespidae) for studying social evolution. Here, we provide a draft genome of the primitively eusocial model insect Polistes dominula, accompanied by analysis of caste-related transcriptome and methylome sequence data for adult queens and workers. Polistes ...


Isolation And Comparative Genomic Analysis Of Final Third Of Satis Genome, Kelly Hartigan, Nicole Curnutt, Matthew McDermut 2017 Washington University in St. Louis

Isolation And Comparative Genomic Analysis Of Final Third Of Satis Genome, Kelly Hartigan, Nicole Curnutt, Matthew Mcdermut

Undergraduate Research Symposium Posters

A highly novel Streptomyces phage, Satis, was isolated from a direct environmental sample collected from outside Danforth House on the Washington University campus. Satis infects bacterial species Streptomyces lividans producing pinpoint, cloudy plaques less than 1mm in diameter. Electron microscope data shows rare atypical physical features. Rather than the common octahedral capsid shape, Satis has a prolate head with visible cross-linked hexagonal protein structure and average measurements of 285 nm by 47 nm with a long, flexible tail measuring 268 nm. Upon sequencing, it was found that Satis contains the longest phage genome discovered to date through the SEA-PHAGE program ...


Characterization Of Zic2 As An Oncoprotein In Prostate Cancer, Keira C. Davis 2017 Clark Atlanta University

Characterization Of Zic2 As An Oncoprotein In Prostate Cancer, Keira C. Davis

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

The field of prostate cancer research is in need of biological markers that predict which cancers do not need treatment, those that can be treated successfully with a localized treatment and more specific cases in which patients are likely to have an aggressive form of cancer that will require more aggressive surgical and chemotherapeutic treatments. ZIC2 is one of five members of a family of proteins that play critical roles in neural crest and mesoderm growth in normal embryonic brain development and in the adult cerebellum of vertebrates. Found throughout the animal kingdom, ZIC1-5 genes encode five distinct ZIC proteins ...


Using Mathematical Models Of Biological Processes In Genome-Wide Association Studies Of Psychiatric Disorders, Amy Cochran 2017 University of Michigan-Ann Arbor

Using Mathematical Models Of Biological Processes In Genome-Wide Association Studies Of Psychiatric Disorders, Amy Cochran

Biology and Medicine Through Mathematics Conference

No abstract provided.


Method For Solid State Genome Analysis, Eric Henderson, Michael P. Lynch 2017 Iowa State University

Method For Solid State Genome Analysis, Eric Henderson, Michael P. Lynch

Eric Henderson

The invention is a solid state process for analyzing genomes by visualizing sequence specific markers (e.g., proteins that bind a defined DNA sequence elements) by scanning probe microscopy. The method includes linear display of the nucleic acid on a solid surface, image acquisition by the scanning probe microscope, and digital data analysis. The acts of the method result in a bar code type display of each fragment of the DNA sample. These bar codes are then used to place the fragments in the order they appear on the original DNA sample.


Evolutionary Genetic Aspects Of Host Association In Generalist Ectoparasites, Benoit Talbot 2017 The University of Western Ontario

Evolutionary Genetic Aspects Of Host Association In Generalist Ectoparasites, Benoit Talbot

Electronic Thesis and Dissertation Repository

Despite the use of the host for dispersal by most parasite species, the extremely loose relationship typical between highly mobile hosts and generalist ectoparasites may lead to very different gene flow patterns between the two, leading in turn to different spatial genetic structure, and potentially different demographic history. I examined how similar gene flow patterns are between Cimex adjunctus, a generalist ectoparasite of bats present throughout North America, and two of its key bat hosts. I first analyzed the continent-scale genetic structure and demographic history of C. adjunctus and compared it to that of two of its hosts, the little ...


Purification, Characterization And Molecular Cloning Of Tgp1, A Novel G-Dna Binding Protein From Tetrahymena Thermophila, Quan Lu, Ted Schierer, Sang-Gu Kang, Eric Henderson 2017 Iowa State University

Purification, Characterization And Molecular Cloning Of Tgp1, A Novel G-Dna Binding Protein From Tetrahymena Thermophila, Quan Lu, Ted Schierer, Sang-Gu Kang, Eric Henderson

Eric Henderson

G-DNA, a polymorphic family of four-stranded DNA structures, has been proposed to play roles in a variety of biological processes including telomere function, meiotic recombination and gene regulation. Here we report the purification and cloning of TGP1, a G-DNA specific binding protein from Tetrahymena thermophila. TGP1 was purified by three-column chromatographies, including a G-DNA affinity column. Two major proteins (∼80 and ∼40 kDa) were present in the most highly purified column fraction. Renaturation experiments showed that the ∼80 kDa protein contains TGP1 activity. Biochemical characterization showed that TGP1 is a G-DNA specific binding protein with a preference for parallel G-DNAs ...


Formation Of Novel Hairpin Structures By Telemeric C-Strand Oligonucleotides, Shawn Ahmed, Eric Henderson 2017 Iowa State University

Formation Of Novel Hairpin Structures By Telemeric C-Strand Oligonucleotides, Shawn Ahmed, Eric Henderson

Eric Henderson

Telomeres are specialized structures at the ends of chromosomes that are required for long term chromosome stability and replication of the chromosomal terminus. Telomeric DNA consists of simple repetitive sequences with one strand G-rich relative to the other, C-rich, strand. Evolutionary conservation of this feature of telomeric repeat sequences suggests that they have specific structural characteristics involved in telomere function. Absorbance thermal denaturation, chemical modification and non-denaturing gel electrophoretic analyses showed that telomeric C-strand oligonucIeotides form stable non-Watson-Crick hairpin structures containing C.C + base pairs.Formation of such hairpins may facilitate previously reported G-strand exclusive interactions.


An Overhanging 3' Terminus Is A Conserved Feature Of Telomeres, Eric R. Henderson, Elizabeth H. Blackburn 2017 Iowa State University

An Overhanging 3' Terminus Is A Conserved Feature Of Telomeres, Eric R. Henderson, Elizabeth H. Blackburn

Eric Henderson

The reactivity of single-stranded thymidines with osmium tetraoxide was used to demonstrate the existence of a terminal overhang of the G-rich strand of telomeres from two distantly related eucaryotes, the ciliated protozoan Tetrahymena spp. and the acellular slime mold Didymium spp. Conservation of a G-strand overhang at the molecular terminus of telomeres is consistent with our suggestion that an unusual DNA structure formed by the G-strand overhang is important for telomere function (E. Henderson, C. C. Hardin, S. K. Wolk, I. Tinoco Jr., and E. H. Blackburn, Cell 51:899-908, 1987).


Identification And Characterization Of A Putative Telomere End-Binding Protein From Tetrahymena Thermophila, Hong Sheng, Zhen Hou, Ted Schierer, Drena L. Dobbs, Eric Henderson 2017 Iowa State University

Identification And Characterization Of A Putative Telomere End-Binding Protein From Tetrahymena Thermophila, Hong Sheng, Zhen Hou, Ted Schierer, Drena L. Dobbs, Eric Henderson

Eric Henderson

Telomeric DNA of Tetrahymena thermophila consists of a long stretch of (TTGGGG)n double-stranded repeats with a single-stranded (TTGGGG)2 3' overhang at the end of the chromosome. We have identified and characterized a protein that specifically binds to a synthetic telomeric substrate consisting of duplex DNA and the 3' telomeric repeat overhang. This protein is called TEP (telomere end-binding protein). A change from G to A in the third position of the TTGGGG overhang repeat converts the substrate to a human telomere analog and reduces the binding affinity approximately threefold. Changing two G's to C's in the ...


Denoising Tandem Mass Spectrometry Data, Felix Offei 2017 East Tennessee State Universtiy

Denoising Tandem Mass Spectrometry Data, Felix Offei

Electronic Theses and Dissertations

Protein identification using tandem mass spectrometry (MS/MS) has proven to be an effective way to identify proteins in a biological sample. An observed spectrum is constructed from the data produced by the tandem mass spectrometer. A protein can be identified if the observed spectrum aligns with the theoretical spectrum. However, data generated by the tandem mass spectrometer are affected by errors thus making protein identification challenging in the field of proteomics. Some of these errors include wrong calibration of the instrument, instrument distortion and noise. In this thesis, we present a pre-processing method, which focuses on the removal of ...


Hybridization Dynamics Of A Newly Discovered Parrotfish Swarm In The Tropical Eastern Pacific, Robert Barron 2017 Bowdoin College

Hybridization Dynamics Of A Newly Discovered Parrotfish Swarm In The Tropical Eastern Pacific, Robert Barron

Honors Projects

Hybrid zones and their dynamics are important in the understanding of the genetic basis of reproductive isolation and speciation. This study seeks to investigate the hybridization dynamics of a Scarus hybrid swarm within the Tropical Eastern Pacific (TEP) that includes four phenotypically distinct species: S. perrico, S. ghobban, S. rubroviolaceus, and S. compressus. Genetic and population structure analyses of four nuclear loci and a mitochondrial locus revealed that one of the four species, S. compressus, was the result of two different hybrid crosses: S. perricoS. rubroviolaceus and S. perricoS. ghobban. A NewHybrids model indicated that most of the ...


A Novel Method For Quantifying Spatial Patterns In Plants, Logan H. George 2017 College of William and Mary

A Novel Method For Quantifying Spatial Patterns In Plants, Logan H. George

Undergraduate Honors Theses

Color patterns are found in a plethora of organisms, from vertebrates to flowering plants. While many studies have examined the mechanisms that produce these diverse patterns in animals, little research has investigated the mechanisms by which plants create color patterns. The conclusions drawn from animal studies may not accurately translate to plants due to early divergence in the evolution of life. Characterization of plant patterning mechanisms would have widespread impacts on developmental and evolutionary biology. To unravel the mystery behind pattern formation, we suggest an experimental framework to understand pattern evolution and development at a phenotypic, genotypic, and quantitative level ...


Systematic Analysis Of Whole Exome Sequencing Determines Ret G691s Polymorphism As Germline Variant In Melanoma, Brent J. Smith Jr, Jennifer D. Hintzsche, Carol M. Amato, Aik-Choon Tan, Keith R. Wells, Allison J. Applegate, Rita T. Gonzalez, Jodie R. Barr, William A. Robinson 2017 Marshall University Joan C. Edwards School of Medicine

Systematic Analysis Of Whole Exome Sequencing Determines Ret G691s Polymorphism As Germline Variant In Melanoma, Brent J. Smith Jr, Jennifer D. Hintzsche, Carol M. Amato, Aik-Choon Tan, Keith R. Wells, Allison J. Applegate, Rita T. Gonzalez, Jodie R. Barr, William A. Robinson

Marshall Journal of Medicine

Abstract

The RET proto-oncogene encodes a receptor tyrosine kinase that is activated by glial cell derived neutrotrophic factor (GDNF). Previous studies have found that a single nucleotide polymorphism (SNP), RETp (G691S), in the juxtamembrane domain enhances the signaling pathway and promotes tumor growth by GDNF in pancreatic and thyroid cancer in addition to melanoma. It is uncertain however whether this SNP is a germline variant or somatic mutation. A prior study reported that the RETp variant was a germline SNP in desmoplastic and non-desmoplastic melanomas. In the present study, we examined both melanoma tissue samples and matching peripheral blood DNA ...


Accumulation And Expression Of Multiple Antibiotic Resistance Genes In That Thrives In Sewage, Jess A. Millar, Rahul Raghavan 2017 Portland State University

Accumulation And Expression Of Multiple Antibiotic Resistance Genes In That Thrives In Sewage, Jess A. Millar, Rahul Raghavan

Biology Faculty Publications and Presentations

We explored the bacterial diversity of untreated sewage influent samples of a wastewater treatment plant in Tucson, AZ and discovered that Arcobacter cryaerophilus, an emerging human pathogen of animal origin, was the most dominant bacterium. The other highly prevalent bacteria were members of the phyla Bacteroidetes and Firmicutes, which are major constituents of human gut microbiome, indicating that bacteria of human and animal origin intermingle in sewage. By assembling a near-complete genome of A. cryaerophilus, we show that the bacterium has accumulated a large number of antibiotic resistance genes (ARGs) probably enabling it to thrive in the wastewater. We also ...


Hippocampal Epigenetic Changes In A Mouse Model Of Fetal Alcohol Spectrum Disorders, Eric J. Chater-Diehl 2017 The University of Western Ontario

Hippocampal Epigenetic Changes In A Mouse Model Of Fetal Alcohol Spectrum Disorders, Eric J. Chater-Diehl

Electronic Thesis and Dissertation Repository

Fetal alcohol spectrum disorders (FASD) refers to the neurological, developmental, and behavioural abnormalities arising from in utero ethanol exposure. These abnormities included attention deficit, anxiety, and learning and memory impairment persisting into adulthood. The molecular mechanisms of such persistent behavioural changes remain unknown and are an area of intense research. In this thesis, mice were exposed to ethanol during the third trimester equivalent, the peak of synaptic development. Following this exposure, genome-wide epigenetic and gene expression and changes in the hippocampus were assessed in adult (70 day old) mice.

In the first experiment, genome-wide trimethylation of histone H3 at histone ...


Using Imputation As A Method Of Improving Genetic Data Analysis, Kimberly Diaz Perez 2017 Georgia State University

Using Imputation As A Method Of Improving Genetic Data Analysis, Kimberly Diaz Perez

Georgia State Undergraduate Research Conference

No abstract provided.


Genomic Analysis Of Factors Associated With Low Prevalence Of Antibiotic Resistance In Extraintestinal Pathogenic Escherichia Coli Sequence Type 95 Strains, Craig M. Stephens, Sheila Adams-Sapper, Manraj Sekhon, James R. Johnson, Lee W. Riley 2017 Santa Clara University

Genomic Analysis Of Factors Associated With Low Prevalence Of Antibiotic Resistance In Extraintestinal Pathogenic Escherichia Coli Sequence Type 95 Strains, Craig M. Stephens, Sheila Adams-Sapper, Manraj Sekhon, James R. Johnson, Lee W. Riley

Biology

Extraintestinal pathogenic Escherichia coli (ExPEC) strains belonging to multilocus sequence type 95 (ST95) are globally distributed and a common cause of infections in humans and domestic fowl. ST95 isolates generally show a lower prevalence of acquired antimicrobial resistance than other pandemic ExPEC lineages. We took a genomic approach to identify factors that may underlie reduced resistance. We fully assembled genomes for four ST95 isolates representing the four major fimH-based lineages within ST95 and also analyzed draft-level genomes from another 82 ST95 isolates, largely from the western United States. The fully assembled genomes of antibiotic-resistant isolates carried resistance genes exclusively on ...


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