Janani Subramaniam Thesis.Pdf, 2019 The University of Texas MD Anderson Cancer Center
Janani Subramaniam Thesis.Pdf, Janani Subramaniam
Parallel Multipole Expansion Algorithms And Their Biology Applications, 2019 Southern Methodist University
Parallel Multipole Expansion Algorithms And Their Biology Applications, Jiahui Chen
Mathematics Theses and Dissertations
N-body pairwise interactions are ubiquitous in scientific areas such as astrophysics, fluids mechanics, electrical engineering, molecular biology, etc. Computing these interactions using direct sum of an O(N) cost is expensive, whereas multipole expansion methods, such as the fast multipole method (FMM) or treecode, can reduce the cost to O(N) or O(N log N). This thesis focuses on developing numerical algorithms of Cartesian FMM and treecode, as well as using these algorithms to directly or implicitly solve biological problems involving pairwise interactions. This thesis consists of the following topics. 1) A cyclic parallel scheme is developed to handle ...
Investigation Of The Electrode Polarization Effect For Biosensor Applications, 2019 Southern Methodist University
Investigation Of The Electrode Polarization Effect For Biosensor Applications, Anil Koklu
Mechanical Engineering Research Theses and Dissertations
My research focuses on electrokinetic transport. Particularly, in this dissertation, we focus on fabrication and testing of micro electrodes with nanostructured surfaces to minimize the electrode polarization (EP) effects for biosensor applications. In the first study, electrochemical deposition of gold nanoparticles on to planar gold electrodes was used to generate rough surfaces. Dendritic nanostructures that reduced EP up to two orders of magnitude was obtained by optimizing the deposition conditions. These structures also enhanced dielectrophoresis (DEP) response of our bio-chips, making them usable in physiological buffers. In further studies we discovered a universal scaling of EP in the frequency domain ...
Iron-Sulfur Cluster Assembly; In Vivo Analysis Of The Methanogenic Suf System, 2019 Louisiana State University and Agricultural and Mechanical College
Iron-Sulfur Cluster Assembly; In Vivo Analysis Of The Methanogenic Suf System, Evan Dunkle
LSU Master's Theses
Iron-sulfur (Fe-S) clusters are among the most ancient and prevalent of all biological cofactors. Their assembly into associated proteins is a tightly regulated process with many organisms employing multiple cluster assembly pathways. Much is known about Fe-S cluster assembly in aerobic organisms such as Escherichia coli (E. coli) but little is known in regards to cluster assembly in more ancient organisms such as methanogens. Methanogens are members of the domain of Archaea and are defined by their ability to generate methane as a byproduct of their main energy generating pathway. Methanogens also have significantly higher Fe-S cluster content compared to ...
Effects Of Halogen, Chalcogen, Pnicogen, And Tetrel Bonds On Ir And Nmr Spectra, 2019 Utah State University
Effects Of Halogen, Chalcogen, Pnicogen, And Tetrel Bonds On Ir And Nmr Spectra, Jia Lu, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
Complexes were formed pairing FX, FHY, FH2Z, and FH3T (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) with NH3 in order to form an A⋯N noncovalent bond, where A refers to the central atom. Geometries, energetics, atomic charges, and spectroscopic characteristics of these complexes were evaluated via DFT calculations. In all cases, the A–F bond, which is located opposite the base and is responsible for the σ-hole on the A atom, elongates and its stretching frequency undergoes a shift to the red. This shift varies ...
Does Thermotolerance In Daphnia Depend On The Mitochondrial Function?, 2019 East Tennessee State University
Does Thermotolerance In Daphnia Depend On The Mitochondrial Function?, Rajib Hasan
Electronic Theses and Dissertations
Thermotolerance limit in aquatic organism is set by the ability to sustain aerobic scope to sudden temperature shifts. This study tested the genetic and plastic differences in thermotolerance of Daphnia that can be explained by the differences in the ability to retain mitochondrial integrity at high temperatures. Five genotypes with different biogeographic origins were acclimated to 18ᵒC and 25ᵒC. We developed a rhodamine 123 in-vivo assay to measure mitochondrial membrane potential and observed higher fluorescent in heat damaged tissues as the disruption of the mitochondrial membrane potential. Significant effects on temperature tolerance were observed with CCCP ...
Elements Of An Effectiveresearch Presentation, 2019 South Dakota State University
Elements Of An Effectiveresearch Presentation, Rachel Willand Charnley
Chemistry and Biochemistry Faculty Presentations and Other Materials
No abstract provided.
Ipsc Based Gene Correction And Disease Model Of A New Class Of Lgmd Due To Poglut1 Mutation, 2019 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
Ipsc Based Gene Correction And Disease Model Of A New Class Of Lgmd Due To Poglut1 Mutation, Jose Ortiz-Vitali
UT GSBS Dissertations and Theses (Open Access)
Recently, a novel class of muscular dystrophy has been discovered in a family due to autosomal recessive missense mutation in POGLUT1. Mutation of this enzyme leads to decreased O-glucosyltransferase activity and impaired Notch signaling, the pathways important for skeletal muscle stem cell (satellite cells) quiescence and activation. We hypothesize that reduced POGLUT1 activity and impaired Notch signaling is causative of this limb girdle muscular dystrophy through dysfunction of muscle stem cells and myogenic progenitors.
To test this, we have used iPSCs for disease modeling and rescue experiments. Using a CRISPR based gene targeting method, we aimed to correct the point ...
Electronic Transmutation: An Aid For The Rational Design Of New Chemical Materials Using The Knowledge Of Bonding And Structure Of Neighboring Elements, Katie A. Lundell
All Graduate Theses and Dissertations
Everything in the universe is made up of elements from the periodic table. Each element has its own role that it plays in the formation of things it makes up. For instance, pencil lead is graphite. A series of honeycomb-like structures made up of carbon stacked on top of one another. Carbon’s neighbor to the left, boron doesn’t like to form such stacked honeycomb-like structures. But, what if there was a way to make boron act like carbon so it did like to form such structures? That question is the basis of the electronic transmutation concept presented in ...
High-Fat Diet In A Mouse Insulin-Resistant Model Induces Widespread Rewiring Of The Phosphotyrosine Signaling Network, 2019 Massachusetts Institute of Technology
High-Fat Diet In A Mouse Insulin-Resistant Model Induces Widespread Rewiring Of The Phosphotyrosine Signaling Network, Antje Dittmann, Norman J. Kennedy, Nina L. Soltero, Nader Morshed, Miyeko D. Mana, Omer H. Yilmaz, Roger J. Davis, Forest M. White
Open Access Articles
Obesity-associated type 2 diabetes and accompanying diseases have developed into a leading human health risk across industrialized and developing countries. The complex molecular underpinnings of how lipid overload and lipid metabolites lead to the deregulation of metabolic processes are incompletely understood. We assessed hepatic post-translational alterations in response to treatment of cells with saturated and unsaturated free fatty acids and the consumption of a high-fat diet by mice. These data revealed widespread tyrosine phosphorylation changes affecting a large number of enzymes involved in metabolic processes as well as canonical receptor-mediated signal transduction networks. Targeting two of the most prominently affected ...
Intron And Small Rna Localization In Mammalian Neurons, 2019 University of Massachusetts Medical School
Intron And Small Rna Localization In Mammalian Neurons, Harleen Saini
GSBS Dissertations and Theses
RNA molecules are diverse in form and function. They include messenger RNAs (mRNAs) that are templates for proteins, splice products such as introns that can generate functional noncoding RNAs, and a slew of smaller RNAs such as transfer RNAs (tRNAs) that help decode mRNAs into proteins. RNAs can show distinct patterns of subcellular localization that play an important role in protein localization. However, RNA distribution in cells is incompletely understood, with prior studies focusing primarily on RNAs that are long (>200 nucleotides), fully processed, and polyadenylated. We examined the distribution of RNAs in neurons. Neuronal compartments can be separated by ...
Impact Of Obesity On Ovotoxicity Induced By 7,12-Dimethylbenz[A]Anthracene In Mice, 2019 Iowa State University
Impact Of Obesity On Ovotoxicity Induced By 7,12-Dimethylbenz[A]Anthracene In Mice, Jackson Nteeba, Shanthi Ganesan, Aileen F. Keating
Insulin, elevated during obesity, regulates xenobiotic biotransformation enzymes, potentially through phosphatidylinositol 3-kinase (PI3K) signaling, in extraovarian tissues. PI3K regulates oocyte viability, follicular activation, and ovarian chemical biotransformation. 7,12-Dimethylbenz[a]anthracene (DMBA), a carcinogen and ovotoxicant, destroys all stages of follicles, leading to premature ovarian failure. Obesity has been reported to promote DMBA-induced tumors, but it remains unknown whether obesity affects ovarian xenobiotic metabolism. Therefore, we investigated ovarian expression of xenobiotic metabolism genes—microsomal epoxide hydrolase (Ephx1), glutathione S-transferase (GST) class Pi (Gstp1) and class mu 1 (Gstm1), and PI3K-signaling members (protein kinase B [AKT] alpha [Akt1], beta [Akt2], and ...
Effective Mismatch Repair Depends On Timely Control Of Pcna Retention On Dna By The Elg1 Complex, 2019 University of Aberdeen
Effective Mismatch Repair Depends On Timely Control Of Pcna Retention On Dna By The Elg1 Complex, Lovely Jael Paul Solomon Devakumar, Christl Gaubitz, Victoria Lundblad, Brian A. Kelch, Takashi Kubota
Open Access Articles
Proliferating cell nuclear antigen (PCNA) is a sliding clamp that acts as a central co-ordinator for mismatch repair (MMR) as well as DNA replication. Loss of Elg1, the major subunit of the PCNA unloader complex, causes over-accumulation of PCNA on DNA and also increases mutation rate, but it has been unclear if the two effects are linked. Here we show that timely removal of PCNA from DNA by the Elg1 complex is important to prevent mutations. Although premature unloading of PCNA generally increases mutation rate, the mutator phenotype of elg1Delta is attenuated by PCNA mutants PCNA-R14E and PCNA-D150E that spontaneously ...
Glutathione S-Transferase Class Mu Regulation Of Apoptosis Signal-Regulating Kinase 1 Protein During Vcd-Induced Ovotoxicity In Neonatal Rat Ovaries, Poulomi Bhattacharya, Jill A. Madden, Nivedita Sen, Patricia B. Hoyer, Aileen F. Keating
4-vinylcyclohexene diepoxide (VCD) destroys ovarian primordial and small primary follicles via apoptosis. In mice, VCD exposure induces ovarian mRNA expression of glutathione S-transferase (GST) family members, including isoform mu (Gstm). Extra-ovarian GSTM negatively regulates pro-apoptotic apoptosis signal-related kinase 1 (ASK1) through protein complex formation, which dissociates during stress, thereby initiating ASK1-induced apoptosis. The present study investigated the ovarian response of Gstm mRNA and protein to VCD. Induction of Ask1 mRNA at VCD-induced follicle loss onset was determined. Ovarian GSTM:ASK1 protein complex formation was investigated and VCD exposure effects thereon evaluated. Phosphatidylinositol-3 kinase (PI3K) regulation of GSTM protein was also ...
Science, Physiology, And Nutrition For The Nonscientist, 2019 San Jose State University
Science, Physiology, And Nutrition For The Nonscientist, Judi S. Morrill
Open Educational Resources
A wonderful blend of physiology, nutrition, biochemistry, genetics, biology, evolution, chemistry--what we all need to know as informed citizens. A basic knowledge of the life sciences and how our bodies work--to promote our own good health, especially as we're bombarded with misleading advertisements, soundbites, and the like. DNA fingerprinting, calorie requirements, dietary advice, genetic engineering (including gene editing with CRISPR cas9)--all in an easy-to understand book.
Nonnative Structure In A Peptide Model Of The Unfolded State Of Sod1: Implications For Als-Linked Aggregation, 2019 University of Massachusetts Medical School
Nonnative Structure In A Peptide Model Of The Unfolded State Of Sod1: Implications For Als-Linked Aggregation, Noah R. Cohen, Jill A. Zitzewitz, Osman Bilsel, C. Robert Matthews
Open Access Articles
Dozens of mutations throughout the sequence of the gene encoding superoxide dismutase 1 (SOD1) have been linked to toxic protein aggregation in the neurodegenerative disease amyotrophic lateral sclerosis (ALS). A parsimonious explanation for numerous genotypes resulting in a common phenotype would be mutation-induced perturbation of the folding free-energy surface that increases the populations of high-energy states prone to aggregation. The absence of intermediates in the folding of monomeric SOD1 suggests that the unfolded ensemble is a potential source of aggregation. To test this hypothesis, here we dissected SOD1 into a set of peptides end-labeled with FRET probes to model the ...
Inactivating Mutations And X-Ray Crystal Structure Of The Tumor Suppressor Opcml Reveal Cancer-Associated Functions, 2019 University of Massachusetts Medical School
Inactivating Mutations And X-Ray Crystal Structure Of The Tumor Suppressor Opcml Reveal Cancer-Associated Functions, James R. Birtley, Zachary Maben, Grant C. Weaver, Mollie M. Jurewicz, Lawrence J. Stern, Chiara Recchi, Hani Gabra
Open Access Articles
OPCML, a tumor suppressor gene, is frequently silenced epigenetically in ovarian and other cancers. Here we report, by analysis of databases of tumor sequences, the observation of OPCML somatic missense mutations from various tumor types and the impact of these mutations on OPCML function, by solving the X-ray crystal structure of this glycoprotein to 2.65 A resolution. OPCML consists of an extended arrangement of three immunoglobulin-like domains and homodimerizes via a network of contacts between membrane-distal domains. We report the generation of a panel of OPCML variants with representative clinical mutations and demonstrate clear phenotypic effects in vitro and ...
Calcineurin Broadly Regulates The Initiation Of Skeletal Muscle-Specific Gene Expression By Binding Target Promoters And Facilitating The Interaction Of The Swi/Snf Chromatin Remodeling Enzyme, 2019 University of Massachusetts Medical School
Calcineurin Broadly Regulates The Initiation Of Skeletal Muscle-Specific Gene Expression By Binding Target Promoters And Facilitating The Interaction Of The Swi/Snf Chromatin Remodeling Enzyme, Hanna Witwicka, Jumpei Nogami, Sabriya A. Syed, Kazumitsu Maehara, Teresita Padilla-Benavides, Yasuyuki Ohkawa, Anthony N. Imbalzano
Open Access Articles
Calcineurin (Cn) is a calcium-activated serine/threonine protein phosphatase that is broadly implicated in diverse cellular processes, including the regulation of gene expression. During skeletal muscle differentiation, Cn activates the NFAT transcription factor but also promotes differentiation by counteracting the negative influences of protein kinase C beta (PKCbeta) via dephosphorylation and activation of BRG1, an enzymatic subunit of the mammalian SWI/SNF ATP-dependent chromatin remodeling enzyme. Here we identified four major temporal patterns of Cn-dependent gene expression in differentiating myoblasts and determined that Cn is broadly required for the activation of the myogenic gene expression program. Mechanistically, Cn promotes gene ...
Histone H2a Repression Domain Regulates Cell-Cycle Progression In Saccaromyces Cerevisea, 2019 Susquehanna University
Histone H2a Repression Domain Regulates Cell-Cycle Progression In Saccaromyces Cerevisea, Taylor Nattress
Landmark Conference Summer Research Symposium
This study researched the histone H2A's N-terminal tail amino acid sequence, focusing on amino acids 16-20 known as the histone H2A repression, HAR, domain. This study found a sensitivity within the deletion of the HAR domain to hydroxyurea, a genotoxin known to show defects in DNA replication. A spotting assay concluded that the HAR domain has an important regulator of the DNA replication process. The RNR1-4 genes were studied through reverse transcriptase polymerase chain reactions in order to see the difference in wild type gene expression compared to the deletion of the HAR domain. The deletion of the HAR ...
Synthesis Of An Amide-Based Extended Heterocyclic System Capable Of Hydrogen Bonding To Both The Adenine And Uracil In Dsrna For Rna Recognition Using Pna, John M. Talbott, Aubrey L. Maryniak
Landmark Conference Summer Research Symposium
The majority of information known about RNA is centered around coding RNA for its role in synthesizing proteins from DNA. However, noncoding RNA is also biologically relevant, showing importance in gene expression and catalyzing reactions. Peptide Nucleic Acids, or PNAs, are a promising tool that can be used to study noncoding RNA. PNAs can bind to double-stranded RNA forming a triple helix and are highly selective for specific sequences of dsRNA. A current limitation of PNA as a ligand is that traditional nucleobases only bind with high affinity to single purine residues on the RNA, as triplex formation relies on ...