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

Biochemistry, Biophysics, and Structural Biology Commons

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

12,655 Full-Text Articles 26,590 Authors 1,658,542 Downloads 250 Institutions

All Articles in Biochemistry, Biophysics, and Structural Biology

Faceted Search

12,655 full-text articles. Page 3 of 436.

Promotion Of Adipogenesis By Jmjd6 Requires The At Hook-Like Domain And Is Independent Of Its Catalytic Function, Pablo Reyes-Gutierrez, Jake W. Carrasquillo-Rodriguez, Anthony N. Imbalzano 2019 University of Massachusetts Medical School

Promotion Of Adipogenesis By Jmjd6 Requires The At Hook-Like Domain And Is Independent Of Its Catalytic Function, Pablo Reyes-Gutierrez, Jake W. Carrasquillo-Rodriguez, Anthony N. Imbalzano

Open Access Articles

JMJD6 is a member of the Jumonji C domain containing enzymes that demethylate and/or hydroxylate substrate proteins. It is a multi-functional protein that has been implicated in disparate aspects of transcriptional and post-transcriptional control of gene expression, including but not limited to enhancer and promoter binding, release of paused RNA polymerase II, control of splicing, and interaction with the translation machinery. JMJD6 contributes to multiple aspects of animal development, including adipogenesis modeled in culture. We mutated proposed or characterized domains in the JMJD6 protein to better understand the requirement for JMJD6 in adipogenic differentiation. Mutation of JMJD6 amino acids ...


Trophic Upgrading And Mobilization Of Wax Esters In Microzooplankton, Keyana Roohani, Brad A. Haubrich, Kai-Lou Yue, Nigel D'souza, Amanda Mantalbano, Tatiana Rynearson, Susanne Menden-Deuer, Christopher Reid 2019 University of Nevada, Reno

Trophic Upgrading And Mobilization Of Wax Esters In Microzooplankton, Keyana Roohani, Brad A. Haubrich, Kai-Lou Yue, Nigel D'Souza, Amanda Mantalbano, Tatiana Rynearson, Susanne Menden-Deuer, Christopher Reid

Science and Technology Faculty Journal Articles

Heterotrophic protists play pivotal roles in aquatic ecosystems by transferring matter and energy, including lipids, from primary producers to higher trophic predators. Using Oxyrrhis marina as a model organism, changes to the non-saponifiable protist lipids were investigated under satiation and starvation conditions. During active feeding on the alga Cryptomonas sp., the O. marina hexane soluble non-saponifiable fraction lipid profile reflected its food source with the observed presence of long chain mono-unsaturated fatty alcohols up to C25:1. Evidence of trophic upgrading in O. marina was observed with long chain mono-unsaturated fatty alcohol accumulation of up to C35:1. To the ...


Assessing The Structure-Function Relationships Of The Apolipoprotein(A) Kringle Iv Sub-Type 10 Domain, Matthew J. Borrelli 2019 The University of Western Ontario

Assessing The Structure-Function Relationships Of The Apolipoprotein(A) Kringle Iv Sub-Type 10 Domain, Matthew J. Borrelli

Electronic Thesis and Dissertation Repository

Elevated plasma lipoprotein(a) (Lp(a)) is the most prevalent heritable risk factor in the development of cardiovascular disease. The apolipoprotein(a) (apo(a)) component of Lp(a) is strongly implicated in the pathogenicity of Lp(a). It is hypothesized that the inflammatory potential of Lp(a)/apo(a) is mediated by the lysine binding ability of the apo(a) kringle IV10 (KIV10) domain, along with its covalently bound oxidized phospholipid (oxPL). Using targeted mutagenesis, two novel null alleles for the LPA gene that generate non-secretable apo(a) species have been identified, resulting from amino acid substitutions in the KIV10 ...


Monocyte Mri Relaxation Rates Are Regulated By Extracellular Iron And Hepcidin, Praveen S.B Dassanayake 2019 The University of Western Ontario

Monocyte Mri Relaxation Rates Are Regulated By Extracellular Iron And Hepcidin, Praveen S.B Dassanayake

Electronic Thesis and Dissertation Repository

Monocytes are an important immune cell type in chronic inflammatory conditions like atherosclerosis and heart failure. The increase in number of monocytes released to the peripheral blood circulation, the differentiation of monocytes to macrophages, and the presence of different macrophage subpopulations during pro- and anti-inflammatory stages of tissue injury may provide markers for monitoring inflammation. In particular, changes in monocyte iron metabolism during an inflammatory response may increase the possibility of tracking these immune cells non-invasively using magnetic resonance imaging (MRI). When secretion of the polypeptide hormone hepcidin is stimulated during inflammation, it binds the iron export protein ferroportin (FPN ...


Structural And Functional Characterization Of Deinococcal Dna Damage Response A (Ddra), Filip Todorovic 2019 The University of Western Ontario

Structural And Functional Characterization Of Deinococcal Dna Damage Response A (Ddra), Filip Todorovic

Electronic Thesis and Dissertation Repository

Deinococci exhibit a remarkable resilience toward DNA damage through the actions of several unique proteins, including DdrA. Although DdrA is critical for damage resistance, little is known about its mechanism of action. Despite sharing sequence similarity with Rad52, DdrA has been reported to lack single-stranded DNA annealing activity. In order to better characterize DdrA, structural studies were undertaken with the primary objective of gaining insight into the mechanism by which DdrA functions. Significant progress was made toward elucidating the X-ray crystal structure; in particular, identifying suitable DdrA domain boundaries for successful expression, purification and crystallization. In addition, we demonstrate for ...


An Attenuated Zika Virus Encoding Non-Glycosylated Envelope (E) And Non-Structural Protein 1 (Ns1) Confers Complete Protection Against Lethal Challenge In A Mouse Model, Arun S. Annamalai, Aryamav Pattnaik, Bikash R. Sahoo, Zack P. Guinn, Brianna L. Bullard, Eric A. Weaver, David J. Steffen, Sathish Kumar Natarajan, Thomas M. Petro, Asit K. Pattnaik 2019 University of Nebraska-Lincoln

An Attenuated Zika Virus Encoding Non-Glycosylated Envelope (E) And Non-Structural Protein 1 (Ns1) Confers Complete Protection Against Lethal Challenge In A Mouse Model, Arun S. Annamalai, Aryamav Pattnaik, Bikash R. Sahoo, Zack P. Guinn, Brianna L. Bullard, Eric A. Weaver, David J. Steffen, Sathish Kumar Natarajan, Thomas M. Petro, Asit K. Pattnaik

Papers in Veterinary and Biomedical Science

Zika virus (ZIKV), a mosquito-transmitted flavivirus, emerged in the last decade causing serious human diseases, including congenital microcephaly in newborns and Guillain-Barré syndrome in adults. Although many vaccine platforms are at various stages of development, no licensed vaccines are currently available. Previously, we described a mutant MR766 ZIKV (m2MR) bearing an E protein mutation (N154A) that prevented its glycosylation, resulting in attenuation and defective neuroinvasion. To further attenuate m2MR for its potential use as a live viral vaccine, we incorporated additional mutations into m2MR by substituting the asparagine residues in the glycosylation sites (N130 and N207) of NS1 with alanine ...


Janani Subramaniam Thesis.Pdf, Janani Subramaniam 2019 The University of Texas MD Anderson Cancer Center

Janani Subramaniam Thesis.Pdf, Janani Subramaniam

Janani Subramaniam

Distinctly organized domains of receptors, ion channels, transporters, signaling molecules, cell adhesion molecules, and contractile proteins are crucial to cardiac function. Interactions between adaptor proteins such as ankyrins and cytoskeletal proteins such as obscurin play a pivotal role in organizing these functional domains in cardiomyocytes. Therefore, dysfunction of both ankyrin as well as obscurin lead to a host of cardiovascular diseases such as arrhythmias and cardiomyopathies. Alternative splicing of ankyrin yields numerous isoforms that interact with obscurin at various sub-cellular domains. And while some of these obscurin-ankyrin complexes have been studied, many others have not been characterized. Further, previous studies ...


Insulin Receptor Substrate-1 (Irs-1) And Irs-2 Expression Levels Are Associated With Prognosis In Non-Small Cell Lung Cancer (Nsclc), Andrew J. Piper, Jennifer L. Clark, Jose R. Mercado-Matos, Asia N. Matthew-Onabanjo, Chung-Cheng Hsieh, Ali Akalin, Leslie M. Shaw 2019 University of Massachusetts Medical School

Insulin Receptor Substrate-1 (Irs-1) And Irs-2 Expression Levels Are Associated With Prognosis In Non-Small Cell Lung Cancer (Nsclc), Andrew J. Piper, Jennifer L. Clark, Jose R. Mercado-Matos, Asia N. Matthew-Onabanjo, Chung-Cheng Hsieh, Ali Akalin, Leslie M. Shaw

Open Access Articles

The insulin-like growth factor-1 (IGF-1) signaling pathway has been implicated in non-small cell lung cancer (NSCLC) outcomes and resistance to targeted therapies. However, little is known regarding the molecular mechanisms by which this pathway contributes to the biology of NSCLC. The insulin receptor substrate (IRS) proteins are cytoplasmic adaptor proteins that signal downstream of the IGF-1R and determine the functional outcomes of this signaling pathway. In this study, we assessed the expression patterns of IRS-1 and IRS-2 in NSCLC to identify associations between IRS-1 and IRS-2 expression levels and survival outcomes in the two major histological subtypes of NSCLC, adenocarcinoma ...


Parallel Multipole Expansion Algorithms And Their Biology Applications, Jiahui Chen 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, Anil Koklu 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, Evan Dunkle 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, Jia Lu, Steve Scheiner 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?, Rajib Hasan 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 18C and 25C. 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, Rachel Willand Charnley 2019 South Dakota State University

Elements Of An Effectiveresearch Presentation, Rachel Willand Charnley

Chemistry and Biochemistry Faculty Presentations and Other Materials

No abstract provided.


Temporal Gene Expression Of Mesenchymal Cells In The Pediatric Lung, Quinlen F. Marshall, Soumyaroop Bhattacharya, Gautam Bandyopadhyay, Ravi Misra, Thomas Mariani, Gloria Pryhuber 2019 College of Saint Benedict/Saint John's University

Temporal Gene Expression Of Mesenchymal Cells In The Pediatric Lung, Quinlen F. Marshall, Soumyaroop Bhattacharya, Gautam Bandyopadhyay, Ravi Misra, Thomas Mariani, Gloria Pryhuber

Chemistry Student Work

INTRODUCTION: The newborn lung undergoes vast biochemical and physiological changes during adaptation from the intrauterine to the extrauterine environment. Lung morphogenesis continues from birth into early childhood, mediated by dynamic gene expression and a diversity of pulmonary cell types (Whitsett, JA. et al. Physiol. Rev, 2019). Murine models demonstrate that pulmonary mesenchymal cells exhibit remarkable heterogeneity in function and morphology during development, however, confirmation of their role is lacking in human neonates and early childhood (Guo, M. et al. Nat. Comm, 2019). In addition, many current human genomic studies of lung maturation suffer from limited sample size, limiting their applicability ...


Ipsc Based Gene Correction And Disease Model Of A New Class Of Lgmd Due To Poglut1 Mutation, Jose Ortiz-Vitali 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 2019 Utah State University

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, Antje Dittmann, Norman J. Kennedy, Nina L. Soltero, Nader Morshed, Miyeko D. Mana, Omer H. Yilmaz, Roger J. Davis, Forest M. White 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, Harleen Saini 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, Jackson Nteeba, Shanthi Ganesan, Aileen F. Keating 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

Aileen 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 ...


Digital Commons powered by bepress