Open Access. Powered by Scholars. Published by Universities.®

Molecular Genetics Commons

Open Access. Powered by Scholars. Published by Universities.®

1189 Full-Text Articles 3103 Authors 119169 Downloads 102 Institutions

All Articles in Molecular Genetics

Faceted Search

1189 full-text articles. Page 1 of 44.

Pirna Biogenesis And Transposon Silencing In Drosophila: A Dissertation, Zhao Zhang 2017 University of Massachusetts Medical School

Pirna Biogenesis And Transposon Silencing In Drosophila: A Dissertation, Zhao Zhang

Zhao Zhang

piRNAs guide PIWI proteins to silence transposons in animal germ cells. In Drosophila, the heterochromatic piRNA clusters transcribe piRNA precursors to be transported into nuage, a perinuclear structure for piRNA production and transposon silencing. At nuage, reciprocal cycles of piRNA-directed RNA cleavage—catalyzed by the PIWI proteins Aubergine (Aub) and Argonaute3 (Ago3) in Drosophila—destroy the sense transposon mRNA and expand the population of antisense piRNAs in response to transposon expression, a process called the Ping-Pong cycle. Heterotypic Ping-Pong between Aub and Ago3 ensures that antisense piRNAs predominate. My thesis research mainly focuses on two fundamental questions about the piRNA ...


Engineering And Verifying Requirements For Programmable Self-Assembling Nanomachines, Robyn Lutz, Jack Lutz, James Lathrop, Titus Klinge, Eric Henderson, Davita Mathur, Dalia Abo Sheasha 2017 Iowa State University

Engineering And Verifying Requirements For Programmable Self-Assembling Nanomachines, Robyn Lutz, Jack Lutz, James Lathrop, Titus Klinge, Eric Henderson, Davita Mathur, Dalia Abo Sheasha

Robyn Lutz

We propose an extension of van Lamsweerde's goal-oriented requirements engineering to the domain of programmable DNA nanotechnology. This is a domain in which individual devices (agents) are at most a few dozen nanometers in diameter. These devices are programmed to assemble themselves from molecular components and perform their assigned tasks. The devices carry out their tasks in the probabilistic world of chemical kinetics, so they are individually error-prone. However, the number of devices deployed is roughly on the order of a nanomole (a 6 followed by fourteen 0s), and some goals are achieved when enough of these agents achieve ...


Cellular/Molecular Analysis Of Interspecies Sterile Male Hybrids In Drosophila, Rachelle L. Kanippayoor 2017 The Unviersity of Western Ontario

Cellular/Molecular Analysis Of Interspecies Sterile Male Hybrids In Drosophila, Rachelle L. Kanippayoor

Electronic Thesis and Dissertation Repository

Over time, genetic differences can accumulate between populations that are geographically separated. This genetic divergence can lead to the evolution of reproductive isolating mechanisms that reduce gene flow between the populations and, upon secondary contact, result in distinct species. The process of speciation is, thus, what accounts for the multitude of species that contribute to the rich biodiversity on Earth. Interspecies hybrid sterility is a postzygotic isolating mechanism that affects the development of hybrids, rendering them sterile. A notable trend, known as Haldane's Rule, describes that heterogametic individual (e.g. males in Drosophila) are more susceptible to sterility than ...


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 ...


The 'Pseudomonas Aeruginosa' Psl Polysaccharide Is A Social But Noncheatable Trait In Biofilms, Yasuhiko Irie, Aled E. Roberts, Kasper N. Kragh, Vernita D. Gordon, Jaime B. Hutchison, Rosalind J. Allen, Gavin Melaugh, Thomas Bjarnsholt, Stuart A. West, Stephen P. Diggle 2017 University of Dayton

The 'Pseudomonas Aeruginosa' Psl Polysaccharide Is A Social But Noncheatable Trait In Biofilms, Yasuhiko Irie, Aled E. Roberts, Kasper N. Kragh, Vernita D. Gordon, Jaime B. Hutchison, Rosalind J. Allen, Gavin Melaugh, Thomas Bjarnsholt, Stuart A. West, Stephen P. Diggle

Biology Faculty Publications

Extracellular polysaccharides are compounds secreted by microorganisms into the surrounding environment, and they are important for surface attachment and maintaining structural integrity within biofilms. The social nature of many extracellular polysaccharides remains unclear, and it has been suggested that they could function as either cooperative public goods or as traits that provide a competitive advantage. Here, we empirically tested the cooperative nature of the PSL polysaccharide, which is crucial for the formation of biofilms in Pseudomonas aeruginosa. We show that (i) PSL is not metabolically costly to produce; (ii) PSL provides populationlevel benefits in biofilms, for both growth and antibiotic ...


The Santa Ana Speckled Dace (Rhinichthys Osculus): Phylogeography And Molecular Evolution Of The Mitochondrial Dna Control Region, James Jay VanMeter 2017 California State University San Bernardino

The Santa Ana Speckled Dace (Rhinichthys Osculus): Phylogeography And Molecular Evolution Of The Mitochondrial Dna Control Region, James Jay Vanmeter

Electronic Theses, Projects, and Dissertations

The purpose of this genetic study of the Santa Ana Speckled Dace Rhinichthys osculus was three-fold. The first goal was to characterize the molecular structure of the mtDNA control region of R. osculus. An 1143 base-pair region of the mitochondrial DNA genome, which included the complete control region was sequenced for all individuals. Analysis of the sequence data revealed that the molecular structure of the speckled dace control region was similar to the molecular structure described for other vertebrate taxa. The speckled dace control region contains three major domains, which vary in base frequency as well as in the frequency ...


Nanoscale Molecular Arrayer, Eric Henderson, Curtis Mosher 2017 Iowa State University

Nanoscale Molecular Arrayer, Eric Henderson, Curtis Mosher

Eric Henderson

The present invention is a dedicated apparatus for the formation of array that includes one or more deposition domains comprised of one or more deposition materials. The present invention may include an X, Y controller, an X, Y translation stage, a loading substrate, a deposition substrate, a Z controller, and a deposition probe. A computer controls all of the relative positions of each of the components. Furthermore, the present invention utilizes a humidity control system to create a capillary bridge between the probe and the substrate for transferring the deposition material between the loading substrate, the deposition probe, and the ...


Method And Apparatus For Solid State Molecular Analysis, Eric Henderson, Curtis Mosher, Michael P. Lynch 2017 Iowa State University

Method And Apparatus For Solid State Molecular Analysis, Eric Henderson, Curtis Mosher, Michael P. Lynch

Eric Henderson

The invention is a method for the formation and analysis of novel miniature deposition domains. These deposition domains are placed on a surface to form a molecular array. The molecular array is scanned with an AFM to analyze molecular recognition events and the effect of introduced agents on defined molecular interactions. This approach can be carried out in a high throughput format, allowing rapid screening of thousands of molecular species in a solid state array. The procedures described here have the added benefit of allowing the measurement of changes in molecular binding events resulting from changes in the analysis environment ...


Method And Apparatus For Solid State Molecular Analysis, Eric Henderson, Curtis Mosher, Michael P. Lynch 2017 Iowa State University

Method And Apparatus For Solid State Molecular Analysis, Eric Henderson, Curtis Mosher, Michael P. Lynch

Eric Henderson

The invention is a method for the formation and analysis of novel miniature deposition domains. These deposition domains are placed on a surface to form a molecular array. The molecular array is scanned with an AFM to analyze molecular recognition events and the effect of introduced agents on defined molecular interactions. this approach can be carried out in a high throughput format, allowing rapid screening of thousands of molecular species in a sold state array. The procedures described here have the added benefit of allowing the measurement of changes in the analysis environment or introduction of additional effector molecules to ...


Risk Assessment In Crispr Transgenic Organisms, Jeffrey B. Warner 2017 Murray State University

Risk Assessment In Crispr Transgenic Organisms, Jeffrey B. Warner

Honors College Theses

CRISPR/Cas, a gene editing tool modified from an antiviral response in bacteria, has been demonstrated to faithfully and precisely introduce double strand breaks (DSB’s) in DNA at sites designated by guide RNA’s (gRNA’s). The system is applicable to many model organisms and shows promise in the study of gene function, creation of model organisms, and, importantly, treatment of heritable disease. However, the specificity of the Cas endonuclease is such that DSB’s are often introduced at sites similar to the target sequence, called off-target sites. Minimization of off-target DNA cleavage is important to prevent unknown and ...


Analyzing Chromosomes, Ion Channels And Novel Nucleic Acid Structures By Afm, Eric Henderson, Linda Ambrosio, Curtis Mosher, Daniel Jondle, Elis Stanley, Philip Haydon, Thomas Marsh, James Vesenka 2017 Iowa State University

Analyzing Chromosomes, Ion Channels And Novel Nucleic Acid Structures By Afm, Eric Henderson, Linda Ambrosio, Curtis Mosher, Daniel Jondle, Elis Stanley, Philip Haydon, Thomas Marsh, James Vesenka

Eric Henderson

The atomic force microscope (AFM) is proving to be a powerful tool for analysis of biological samples. We provide three examples of the application of AFM to the study of biological questions. First, polytene chromosomes from Drosophila are imaged and manipulated by the AFM. Second, the localization of calcium channels on the release face of a nerve terminal is described. Finally, analyses of a new form of DNA, the G-wire, is presented. These examples illustrate the wide variety of biological questions to which AFM can contribute.


Telomere G-Strand Structure And Function Analyzed By Chemical Protection, Base Analog Substitution, And Utilization By Telomerase In Vitro, Eric R. Henderson, Michael Moore, Bruce A. Malcolm 2017 Iowa State University

Telomere G-Strand Structure And Function Analyzed By Chemical Protection, Base Analog Substitution, And Utilization By Telomerase In Vitro, Eric R. Henderson, Michael Moore, Bruce A. Malcolm

Eric Henderson

Eukaryotic telomeres have a 12-1 6 nucleotide long deoxyguanosine (dG) rich single-stranded overhang at their molecular termini. Some of the unique features of telomeres are probably attributable to a specialized structure formed by this overhang. In the ciliated protozoan Tetrahymena thermophila, the dG-rich overhang is comprised of approximately two repeats of the sequence d(TTGGGG). Previous work has shown that the synthetic oligonucleotide d(TTGGGG),, can form an unusual non-Watson-Crick base-paired structure (the "G-strand structure") containing G-G base pairs and syn-guanines. We have tested the susceptibility of various dGs in this structure to methylation by DMS. At 0-10 "C one ...


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 ...


Monovalent Cation Induced Structural Transitions In Telomeric Dnas: G-Dna Folding Intermediates, Charles C. Hardin, Eric Henderson, Thomas Watson, Joyce K. Prosser 2017 North Carolina State University

Monovalent Cation Induced Structural Transitions In Telomeric Dnas: G-Dna Folding Intermediates, Charles C. Hardin, Eric Henderson, Thomas Watson, Joyce K. Prosser

Eric Henderson

Telomeric DNA consists of G- and C-rich strands that are always polarized such that the G-rich strand extends past the 3’ end of the duplex to form a 12-16-base overhang. These overhanging strands can self-associate in vitro to form intramolecular structures that have several unusual physical properties and at least one common feature, the presence of non-Watson-Crick G-G base pairs. The term “G-DNA” was coined for this class of structures (Cech, 1988). On the basis of gel electrophoresis, imino proton NMR, and circular dichroism (CD) results, we find that changing the counterions from sodium to potassium (in 20 mM phosphate ...


Engineering And Verifying Requirements For Programmable Self-Assembling Nanomachines, Robyn Lutz, Jack Lutz, James Lathrop, Titus Klinge, Eric Henderson, Davita Mathur, Dalia Abo Sheasha 2017 Iowa State University

Engineering And Verifying Requirements For Programmable Self-Assembling Nanomachines, Robyn Lutz, Jack Lutz, James Lathrop, Titus Klinge, Eric Henderson, Davita Mathur, Dalia Abo Sheasha

Eric Henderson

We propose an extension of van Lamsweerde's goal-oriented requirements engineering to the domain of programmable DNA nanotechnology. This is a domain in which individual devices (agents) are at most a few dozen nanometers in diameter. These devices are programmed to assemble themselves from molecular components and perform their assigned tasks. The devices carry out their tasks in the probabilistic world of chemical kinetics, so they are individually error-prone. However, the number of devices deployed is roughly on the order of a nanomole (a 6 followed by fourteen 0s), and some goals are achieved when enough of these agents achieve ...


Two Tetrahymena G-Dna-Binding Proteins, Tgp1 And Tgp3, Share Novel Motifs And May Play A Role In Micronuclear Division, Quan Lu, Eric Henderson 2017 Iowa State University

Two Tetrahymena G-Dna-Binding Proteins, Tgp1 And Tgp3, Share Novel Motifs And May Play A Role In Micronuclear Division, Quan Lu, Eric Henderson

Eric Henderson

G-DNA is a four-stranded DNA structure with diverse putative biological roles. We have previously purified and cloned a novel G-DNA-binding protein TGP1 from the ciliate Tetrahymena thermophila. Here we report the molecular cloning of TGP3, an additional G-DNA-binding protein from the same organism. The TGP3 cDNA encodes a 365 amino acid protein that is homologous to TGP1 (34% identity and 44% similarity). The proteins share a sequence pattern that contains two novel repetitive and homologous motifs flanking an extensively hydrophilic and basic region. A nuclear fractionation experiment showed that TGP1 and TGP3 activities are localized predominantly in the nuclear fraction ...


Monitoring Transfected Cells Without Selection Agents By Using The Dual-Cassette Expression Egfp Vectors, Sang-Gu Kang, Eunkyung Lee, Scott Schaus, Eric Henderson 2017 Yeungnam University

Monitoring Transfected Cells Without Selection Agents By Using The Dual-Cassette Expression Egfp Vectors, Sang-Gu Kang, Eunkyung Lee, Scott Schaus, Eric Henderson

Eric Henderson

Conventional methods of selecting gene transfected cells by toxic agents may yield ambiguous results. It is difficult to determine whether cell death is due to selection agents or gene transfection, owing to the substantial overlap of the time-courses for both effects. Therefore, to determine transfection-induced cell toxicity, the mammalian expression vector pEGFP-N1 (CLONTECH Lab., Palo Alto, CA, USA) has been modified to the dual-cassette expression vectors named pEGFP-Ks by the relocation of its EGFP expression cassette. We have precisely monitored the cells transfected with this vector on our custom culture dishes, thereby bypassing the need for selection agent or fluorescent ...


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.


Does Genotype Correlate With Phenotype? Evaluating Ruffed Lemur (Varecia Spp.) Color Vision Using Subject Mediated Automatic Remote Testing Apparatus (Smarta), Raymond Vagell 2017 CUNY Hunter College

Does Genotype Correlate With Phenotype? Evaluating Ruffed Lemur (Varecia Spp.) Color Vision Using Subject Mediated Automatic Remote Testing Apparatus (Smarta), Raymond Vagell

School of Arts & Sciences Theses

Ruffed lemur (Varecia spp.) color vision research was conducted using a multidisciplinary approach: psychophysics, genetic analysis, technology, and animal training. The behavioral manifestation of Varecia spp. trichromacy was shown using a touchscreen apparatus (SMARTA). Trichromats performed better than dichromats when discriminating red from green (G2 = 78.10, p < 0.001).


Visualization Of Circular Dna Molecules Labeled With Colloidal Gold Spheres Using Atomic Force Microscopy, Wen-Ling Shaiu, James Vesenka, Daniel Jondle, Eric Henderson, Drena D. Larson 2017 Iowa State University

Visualization Of Circular Dna Molecules Labeled With Colloidal Gold Spheres Using Atomic Force Microscopy, Wen-Ling Shaiu, James Vesenka, Daniel Jondle, Eric Henderson, Drena D. Larson

Eric Henderson

We have imaged gold‐labeled DNA molecules with the atomic force microscope(AFM). Circular plasmid DNA was labeled at internal positions by nick‐translation using biotinylated dUTP. For visualization, the biotinylated DNA was linked to streptavidin‐coated colloidal gold spheres (nominally 5 nm diam) prior to AFM imaging. Reproducible images of the labeled DNA were obtained both in dry air and under propanol. Height measurements of the DNA and colloidal gold made under both conditions are presented. The stability of the DNA‐streptavidin colloidal gold complexes observed even under propanol suggests that this labeling procedure could be exploited to map ...


Digital Commons powered by bepress