Open Access. Powered by Scholars. Published by Universities.®
![Digital Commons Network](http://assets.bepress.com/20200205/img/dcn/DCsunburst.png)
Physical Sciences and Mathematics Commons™
Open Access. Powered by Scholars. Published by Universities.®
- Institution
-
- Brigham Young University (15)
- Purdue University (12)
- Old Dominion University (10)
- Utah State University (10)
- University of Montana (8)
-
- Wayne State University (8)
- Selected Works (7)
- University of Massachusetts Amherst (7)
- University of Windsor (7)
- University at Albany, State University of New York (5)
- City University of New York (CUNY) (4)
- University of South Florida (4)
- Cleveland State University (3)
- Florida International University (3)
- Stephen F. Austin State University (3)
- University of Arkansas, Fayetteville (3)
- University of Missouri, St. Louis (3)
- Clemson University (2)
- Michigan Technological University (2)
- Montclair State University (2)
- Seton Hall University (2)
- Technological University Dublin (2)
- University of Nebraska - Lincoln (2)
- University of Nevada, Las Vegas (2)
- University of Texas at El Paso (2)
- University of Wisconsin Milwaukee (2)
- California Polytechnic State University, San Luis Obispo (1)
- Central Washington University (1)
- Claremont Colleges (1)
- Gettysburg College (1)
- Keyword
-
- Mass spectrometry (3)
- Amino acid sequence (2)
- Bacteria (2)
- Biological sciences (2)
- Community structure (2)
-
- Computational chemistry (2)
- DFT (2)
- Drug delivery (2)
- Microfluidics (2)
- Monolith (2)
- Photochemistry (2)
- Pure sciences (2)
- SO2 (2)
- Supramolecular chemistry (2)
- (n=1 (1)
- 1 (1)
- 2 (1)
- 2) (1)
- 2D materials (1)
- 2′-bipyridine (1)
- 8-ANS (1)
- <p>Carnosine</p> <p>Cytology<strong> - </strong>Research</p> (1)
- <p>Cytokinesis<br />Actin<br />Actomyosin<br />Phosphorylation</p> (1)
- AFEX pretreated corn stover (1)
- APOBEC3 (1)
- APOBEC3H (1)
- APOBEC3H haplotyes (1)
- APOBEC3H purification (1)
- APOBEC3H splice variants (1)
- ATR spectroscopy (1)
- Publication
-
- Chemistry and Biochemistry Faculty Publications (18)
- Theses and Dissertations (17)
- Chemistry and Biochemistry Publications (7)
- Doctoral Dissertations (7)
- Open Access Dissertations (6)
-
- Legacy Theses & Dissertations (2009 - 2024) (5)
- Open Access Theses (5)
- Wayne State University Dissertations (5)
- Chemistry Faculty Publications (4)
- Dissertations, Theses, and Capstone Projects (4)
- Chemistry & Biochemistry Faculty Works (3)
- Computer Science Faculty Publications (3)
- Graduate Theses and Dissertations (3)
- USF Tampa Graduate Theses and Dissertations (3)
- Wayne State University Theses (3)
- All Theses (2)
- Department of Chemistry and Biochemistry (2)
- Dissertations, Master's Theses and Master's Reports - Open (2)
- Faculty Publications (2)
- Mechanical & Aerospace Engineering Faculty Publications (2)
- Open Access Theses & Dissertations (2)
- Seton Hall University Dissertations and Theses (ETDs) (2)
- Theses, Dissertations and Culminating Projects (2)
- Undergraduate Research Conference (2)
- Alexei Demchenko (1)
- All Faculty Scholarship for the College of the Sciences (1)
- Articles (1)
- Bioelectrics Publications (1)
- Biological Sciences Faculty Publications (1)
- Books/Book Chapters (1)
- Publication Type
Articles 121 - 150 of 150
Full-Text Articles in Physical Sciences and Mathematics
Substituent Effects In The Noncovalent Bonding Of So2 To Molecules Containing A Carbonyl Group. The Dominating Role Of The Chalcogen Bond, L. M. Azofra, Steve Scheiner
Substituent Effects In The Noncovalent Bonding Of So2 To Molecules Containing A Carbonyl Group. The Dominating Role Of The Chalcogen Bond, L. M. Azofra, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
The SO2 molecule is paired with a number of carbonyl-containing molecules, and the properties of the resulting complexes are calculated by high-level ab initio theory. The global minimum of each pair is held together primarily by a S···O chalcogen bond wherein the lone pairs of the carbonyl O transfer charge to the π* antibonding SO orbital, supplemented by smaller contributions from weak CH···O H-bonds. The binding energies vary between 4.2 and 8.6 kcal/mol, competitive with even some of the stronger noncovalent forces such as H-bonds and halogen bonds. The geometrical arrangement places the carbonyl O atom above the plane of …
Competition Between Lone Pair-Π, Halogen Bond, And Hydrogen Bond In Adducts Of Water With Perhalogenated Alkenes C2clnf4-N (N = 0-4), U. Adhikari, Steve Scheiner
Competition Between Lone Pair-Π, Halogen Bond, And Hydrogen Bond In Adducts Of Water With Perhalogenated Alkenes C2clnf4-N (N = 0-4), U. Adhikari, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
A thorough search of the potential energy surface is carried out for heterodimers of water with C2ClnF4−n. Three different types of interactions are observed. Structures dominated by a lone pair–π interaction have the highest binding energies, and are stabilized by charge transfer from O lone pairs of H2O to the Csingle bondC π* antibonding orbital of the alkene. Halogen-bonded O⋯Cl complexes are slightly less strongly bound, followed by OH⋯X hydrogen bonds. The replacements of Cl by F atoms have only small effects upon binding energies. Inclusion of vibrational and entropic effects removes the clear energetic superiority of lp–π binding energies. …
Complexes Containing Co2 And So2. Mixed Dimers, Trimers And Tetramers, L. M. Azofra, Steve Scheiner
Complexes Containing Co2 And So2. Mixed Dimers, Trimers And Tetramers, L. M. Azofra, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
Mixed dimers, trimers and tetramers composed of SO2 and CO2 molecules are examined by ab initio calculations to identify all minimum energy structures. While AIM formalism leads to the idea of a pair of C···O bonds in the most stable heterodimer, bound by some 2 kcal mol(-1), NBO analysis describes the bonding in terms of charge transfer from O lone pairs of SO2 to the CO π* antibonding orbitals. The second minimum on the surface, just slightly less stable, is described by AIM as containing a single O···O chalcogen bond. The NBO picture is that of two transfers in opposite …
Effects Of Charge And Substituent On The S∙∙∙N Chalcogen Bond, U. Adhikari, Steve Scheiner
Effects Of Charge And Substituent On The S∙∙∙N Chalcogen Bond, U. Adhikari, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
Neutral complexes containing a S···N chalcogen bond are compared with similar systems in which a positive charge has been added to the S-containing electron acceptor, using high-level ab initio calculations. The effects on both XS···N and XS+···N bonds are evaluated for a range of different substituents X = CH3, CF3, NH2, NO2, OH, Cl, and F, using NH3 as the common electron donor. The binding energy of XMeS···NH3 varies between 2.3 and 4.3 kcal/mol, with the strongest interaction occurring for X = F. The binding is strengthened by a factor of 2–10 in charged XH2S+···NH3 complexes, reaching a maximum of …
Design And Study Of The Efflux Function Of The Egfp Fused Mexab-Oprm Membrane Transporter In Pseudomonas Aeruginosa Using Spectroscopy, Feng Ding, Kerry J. Lee, Ardeschir Vahedi-Faridi, Hiroshi Yoneyama, Christopher J. Osgood, Xiao-Hong Nancy Xu
Design And Study Of The Efflux Function Of The Egfp Fused Mexab-Oprm Membrane Transporter In Pseudomonas Aeruginosa Using Spectroscopy, Feng Ding, Kerry J. Lee, Ardeschir Vahedi-Faridi, Hiroshi Yoneyama, Christopher J. Osgood, Xiao-Hong Nancy Xu
Biological Sciences Faculty Publications
Multidrug membrane transporters (efflux pumps) can selectively extrude a variety of structurally and functionally diverse substrates (e.g., chemotoxics, antibiotics), leading to multidrug resistance (MDR) and ineffective treatment of a wide variety of diseases. In this study, we have designed and constructed a fusion gene (egfp-mexB) of N-terminal mexB with C-terminal egfp, inserted it into a plasmid vector (pMMB67EH), and successfully expressed it in the Δ MexB (MexB deletion) strain of Pseudomonas aeruginosato create a new strain that expresses MexA-(EGFP-MexB)-OprM. We characterized the fusion gene using gel electrophoresis and DNA sequencing, and determined its expression in live …
Vibrational Spectroscopy: Disease Diagnostics And Beyond, Hugh Byrne, Kamila Ostrowska, Haq Nawaz, Jennifer Dorney, Aidan Meade, Franck Bonnier, Fiona Lyng
Vibrational Spectroscopy: Disease Diagnostics And Beyond, Hugh Byrne, Kamila Ostrowska, Haq Nawaz, Jennifer Dorney, Aidan Meade, Franck Bonnier, Fiona Lyng
Books/Book Chapters
Summary
This chapter outlines some developments in the applications of vibrational spectroscopy for disease diagnostics and demonstrates how the applications of the spectroscopic techniques can be extended to the analysis and evaluation of disease aetiology and the mechanisms of interaction and the cellular and subcellular responses to, for example chemotherapeutic agents and nanoparticles. The primary emphasis is on Raman spectroscopy, although some examples are based on infrared absorption spectroscopy. The studies presented are chosen to illustrate how a range of multivariate analytical techniques can be employed to maximize the potential benefits of the complex spectral information obtained from tissue or …
An Exploration Of The Ozone Dimer Potential Energy Surface, L. M. Azofra, I. Alkorta, Steve Scheiner
An Exploration Of The Ozone Dimer Potential Energy Surface, L. M. Azofra, I. Alkorta, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
The (O3)2 dimer potential energy surface is thoroughly explored at the ab initio CCSD(T) computational level. Five minima are characterized with binding energies between 0.35 and 2.24 kcal/mol. The most stable may be characterized as slipped parallel, with the two O3 monomers situated in parallel planes. Partitioning of the interaction energy points to dispersion and exchange as the prime contributors to the stability, with varying contributions from electrostatic energy, which is repulsive in one case. Atoms in Molecules analysis of the wavefunction presents specific O⋯O bonding interactions, whose number is related to the overall stability of each dimer. All internal …
Dephosphorylation Of Iqg1 By Cdc14 Temporally Regulates Actin Ring Formation, Daniel Patrick Miller
Dephosphorylation Of Iqg1 By Cdc14 Temporally Regulates Actin Ring Formation, Daniel Patrick Miller
Masters Theses
"Cytokinesis is the final step in cell division when the cell separates the cytoplasm by contracting a ring composed of filamentous actin (F-actin) and type II myosin. Iqg1, an IQGAP family member, is an essential scaffolding protein in budding yeast (S. cerevisiae) required for actin recruitment to, and contraction of, the actomyosin ring. Actin is recruited by the calponin homology domain (CHD) in anaphase after Iqg1 is localized to the bud neck. Consensus sites for the cyclin-dependent kinase (CDK) Cdc28 were identified flanking the CHD. This led us to the hypothesis that phosphorylation of Iqg1 by Cdc28 negatively regulates actin …
Template-Based C8-Scorpion: A Protein 8 State Secondary Structure Prediction Method Using Structural Information And Context-Based Features, Ashraf Yaseen, Yaohang Li
Template-Based C8-Scorpion: A Protein 8 State Secondary Structure Prediction Method Using Structural Information And Context-Based Features, Ashraf Yaseen, Yaohang Li
Computer Science Faculty Publications
Background: Secondary structures prediction of proteins is important to many protein structure modeling applications. Correct prediction of secondary structures can significantly reduce the degrees of freedom in protein tertiary structure modeling and therefore reduces the difficulty of obtaining high resolution 3D models.
Methods: In this work, we investigate a template-based approach to enhance 8-state secondary structure prediction accuracy. We construct structural templates from known protein structures with certain sequence similarity. The structural templates are then incorporated as features with sequence and evolutionary information to train two-stage neural networks. In case of structural templates absence, heuristic structural information is incorporated instead. …
Automated Identification Of Cell Type Specific Genes In The Mouse Brain By Image Computing Of Expression Patterns, Rongjian Li, Wenlu Zhang, Shuiwang Ji
Automated Identification Of Cell Type Specific Genes In The Mouse Brain By Image Computing Of Expression Patterns, Rongjian Li, Wenlu Zhang, Shuiwang Ji
Computer Science Faculty Publications
Background: Differential gene expression patterns in cells of the mammalian brain result in the morphological, connectional, and functional diversity of cells. A wide variety of studies have shown that certain genes are expressed only in specific cell-types. Analysis of cell-type-specific gene expression patterns can provide insights into the relationship between genes, connectivity, brain regions, and cell-types. However, automated methods for identifying cell-type-specific genes are lacking to date.
Results: Here, we describe a set of computational methods for identifying cell-type-specific genes in the mouse brain by automated image computing of in situ hybridization (ISH) expression patterns. We applied invariant image feature …
Tracing Beta Strands Using Strandtwister From Cryo-Em Density Maps At Medium Resolutions, Dong Si, Jing He
Tracing Beta Strands Using Strandtwister From Cryo-Em Density Maps At Medium Resolutions, Dong Si, Jing He
Computer Science Faculty Publications
Major secondary structure elements such as α helices and β sheets can be computationally detected from cryoelectron microscopy (cryo-EM) density maps with medium resolutions of 5–10 A˚ . However, a critical piece of information for modeling atomic structures is missing, because there are no tools to detect β strands from cryo-EM maps at medium resolutions. We propose a method, StrandTwister, to detect the traces of β strands through the analysis of twist, an intrinsic nature of a β sheet. StrandTwister has been tested using 100 β sheets simulated at 10 A˚ resolution and 39 β sheets computationally detected from cryo-EM …
Structure And Dynamics Of The Hiv-1 Frameshift Element Rna, Kathryn Mouzakis
Structure And Dynamics Of The Hiv-1 Frameshift Element Rna, Kathryn Mouzakis
Chemistry and Biochemistry Faculty Works
The HIV-1 ribosomal frameshift element is highly structured, regulates translation of all virally encoded enzymes, and is a promising therapeutic target. The prior model for this motif contains two helices separated by a three-nucleotide bulge. Modifications to this model were suggested by SHAPE chemical probing of an entire HIV-1 RNA genome. Novel features of the SHAPE-directed model include alternate helical conformations and a larger, more complex structure. These structural elements also support the presence of a secondary frameshift site within the frameshift domain. Here, we use oligonucleotide-directed structure perturbation, probing in the presence of formamide, and in-virion experiments to examine …
Structural And Functional Characterization Of Proteins Of Unknown Function (Hp0495, Hp0100 And Hp1259) In Helicobacter Pylori, Shirin Fatma
Structural And Functional Characterization Of Proteins Of Unknown Function (Hp0495, Hp0100 And Hp1259) In Helicobacter Pylori, Shirin Fatma
Wayne State University Dissertations
H. pylori is missing the glutaminyl- and asparaginyl-tRNA synthetases (GlnRS and AsnRS, respectively). Consequently, H. pylori uses an indirect aminoacylation pathway to generate Gln-tRNAGln and Asn-tRNAAsn. Within this process, Asn-tRNAAsn is produced by misacylation of tRNAAsn with aspartate by a non-discriminating aspartyl-tRNA synthetase (ND-AspRS). Next, the heterotrimeric, glutamine-dependent amidotransferase (called AdT or GatCAB) converts the misacylated Asp-tRNAAsn into Asn-tRNAAsn. A parallel pathway exists for the synthesis of Gln-tRNAGln, wherein misacylation of tRNAGln with glutamate is catalyzed by a tRNAGln-specific glutamyl-tRNA synthetase (GluRS2) to generate Glu-tRNAGln; this misacylated intermediate is converted to Gln-tRNAGln by the same AdT. This dependence on misacylated …
Intrinsic Delocalization During The Decay Of Excitons In Polymeric Solar Cells, Thomas George, W. Chen, D. Jiang, R. Chen, S. Li
Intrinsic Delocalization During The Decay Of Excitons In Polymeric Solar Cells, Thomas George, W. Chen, D. Jiang, R. Chen, S. Li
Chemistry & Biochemistry Faculty Works
In bulk heterojunction polymer solar cells, external photoexcitation results in localized excitons in the polymer chain. After hot exciton formation and subsequent relaxation, the dipole moment drives the electron to partially transfer to extended orbitals from the original localized ones, leading to self-delocalization. Based on the dynamic fluorescence spectra, the delocalization of excitons is revealed to be an intrinsic property dominated by exciton decay, acting as a bridge for the exciton to diffuse in the polymeric solar cell. The modification of the dipole moment enhances the efficiency of polymer solar cells.
Natural Phenomena As Potential Influence On Social And Political Behavior: The Earth’S Magnetic Field, Jackie R. East
Natural Phenomena As Potential Influence On Social And Political Behavior: The Earth’S Magnetic Field, Jackie R. East
Theses and Dissertations--Political Science
Researchers use natural phenomena in a number of disciplines to help explain human behavioral outcomes. Research regarding the potential effects of magnetic fields on animal and human behavior indicates that fields could influence outcomes of interest to social scientists. Tests so far have been limited in scope. This work is a preliminary evaluation of whether the earth’s magnetic field influences human behavior it examines the baseline relationship exhibited between geomagnetic readings and a host of social and political outcomes. The emphasis on breadth of topical coverage in these statistical trials, rather than on depth of development for any one model, …
Strongly Bound Noncovalent (So3)N:H2co Complexes (N = 1, 2), L. M. Azofra, I. Alkorta, Steve Scheiner
Strongly Bound Noncovalent (So3)N:H2co Complexes (N = 1, 2), L. M. Azofra, I. Alkorta, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
The potential energy surfaces (PES) for the SO3:H2CO and (SO3)2:H2CO complexes were thoroughly examined at the MP2/aug-cc-pVDZ computational level. Heterodimers and trimers are held together primarily by SO chalcogen bonds, supplemented by weaker CHO and/or OC bonds. The nature of the interactions is probed by a variety of means, including electrostatic potentials, AIM, NBO, energy decomposition, and electron density redistribution maps. The most stable dimer is strongly bound, with an interaction energy exceeding 10 kcal mol(-1). Trimers adopt the geometry of the most stable dimer, with an added SO3 molecule situated so as to interact with both of the original …
Monitoring Ligand-Induced Nucleic Acid Conformational Changes Using Ion Mobility Spectrometry-Mass Spectrometry, Bill Kenneth Redick
Monitoring Ligand-Induced Nucleic Acid Conformational Changes Using Ion Mobility Spectrometry-Mass Spectrometry, Bill Kenneth Redick
Legacy Theses & Dissertations (2009 - 2024)
Three-dimensional structures of biopolymers frequently dictate the biological role those molecules play. As such, investigation into structure of nucleic acids can provide important information pertaining to how those nucleic acids work. Many nucleic acid species, especially single-stranded RNA, fold into unique structures that allow them to function properly. Metals, and other cationic species, are often bound to the nucleic acid to make folding into the proper structure more favorable by neutralizing the negative charge on the nucleic acid imparted by the phosphate group. This investigation explores tertiary structure of nucleic acids that have been folded in the presence of ligands …
Raman Spectroscopy Of Blood Serum And Cerebrospinal Fluid And Multivariate Data Analysis For Alzheimer's Disease Diagnostics, Elena Ryzhikova
Raman Spectroscopy Of Blood Serum And Cerebrospinal Fluid And Multivariate Data Analysis For Alzheimer's Disease Diagnostics, Elena Ryzhikova
Legacy Theses & Dissertations (2009 - 2024)
The efficient and accurate diagnosis at the early stages of dementia is a key moment for effective treatment and productive research to find a new ways to combat the disease. It is especially true for Alzheimer's disease (AD) for which there is no effective cure, but several treatments are known to allow slowing down the degenerative processes. Alzheimer's disease (AD) displays only non-specific clinical symptoms of mental decline for decades after the initiation and is very challenging to differentiate even at the later stages when it becomes very aggressive. Despite the great need, current diagnostic tests are unable to diagnose …
Modeling The Early, Aging-Related Changes In Human Recombinant Gammas-Crystallin In Vitro, Christiana Oluwaseun Salami
Modeling The Early, Aging-Related Changes In Human Recombinant Gammas-Crystallin In Vitro, Christiana Oluwaseun Salami
Legacy Theses & Dissertations (2009 - 2024)
Cataract is the leading cause of blindness in the world. Cataractous lenses scatter a significant part of the light entering the eye. Cataract can be of several types: Age-related cataract, secondary cataract, traumatic cataract, congenital cataract, and radiation cataract. Age-related cataract is the most common type of cataract. Several factors contribute to age-onset cataract; among them are the Post-Translational Modifications (PTMs) to the major lens proteins or crystallins, which constitute about 80-90% of the protein content of the lens. Predominant PTMs of the crystallins are oxidation, deamidation, phosphorylation, glycation, and disulfide crosslinking, which tend to increase as the lens ages.
Probing Secondary And Tertiary Rna Folding Using Force And Temperature, William Stephenson
Probing Secondary And Tertiary Rna Folding Using Force And Temperature, William Stephenson
Legacy Theses & Dissertations (2009 - 2024)
RNA folding is the process whereby a single stranded RNA molecule assumes its three-dimensional functional conformation. Along with the protein folding problem, the RNA folding problem remains as one of the great unsolved problems in biophysics. Generally RNA folding occurs in a hierarchical manner whereby the sequence of an RNA (primary structure) determines which regions will form helical segments (secondary structure) before further rearrangement and base pairing of secondary structure motifs (tertiary structure). Due to the intimate connection between structure and function within molecular biology, increased familiarity with the thermodynamic and kinetic factors that govern RNA folding will permit the …
Improving The Microbial Source Tracking Toolbox : Evaluating The Use Of Selective Enrichments And Artificial Sweeteners In A Multi-Tiered Approach, Stacey A. Helming
Improving The Microbial Source Tracking Toolbox : Evaluating The Use Of Selective Enrichments And Artificial Sweeteners In A Multi-Tiered Approach, Stacey A. Helming
Legacy Theses & Dissertations (2009 - 2024)
Microbial contamination of surface waters is a public health concern world-wide, with non-point source fecal input contributing to millions of cases of waterborne illness annually. Numerous techniques have been proposed to monitor for non-point source fecal contamination, but few studies have explored the correlation of multiple chemical and microbial fecal source tracking markers in ambient waters. Therefore, the purpose of these studies was to evaluate the use of multiple "ideal" markers of fecal contamination and improve upon any analytical techniques required to identify species-specific fecal contamination in surface waters. The use of selective enrichments to improve the sensitivity of end-point …
Effects Of Statin Drugs And Tocotrienol Rich Fraction Supplementation In Chronic Hemodialysis Patients And Metabolomic Profile, Eno Latifi
Wayne State University Theses
Chronic kidney disease (CKD) is known as a heterogeneous disorder which currently is on the rise and lately has been classified as a public health issues in the United State and worldwide. CKD is an irreversible and progressive disease which can lead to kidney failure, and this is depicted by the advanced stage of the disorder when it reaches the point, that is classified as end stage of renal disease (ESRD) (Stage 5 of CKD) (eGRF <15 mL/min/ 1.73 m2 working capacity), where both organs are in a total or permanent kidney failure. End-Stage renal disease patients, on hemodialysis have been associated to experience an accelerated form of atherosclerosis, which is induced by inflammation, impairment of antioxidant system and elevated oxidative stress. Since the problem effecting ESRD patients is multifactorial, the objective of this investigation is to explore and look at the effects of supplementing with vitamin E-tocotrienol rich fraction (TRF), a micronutrient which has anti-inflammatory, antioxidant, and lipid lower capabilities into tackling these comorbid conditions experienced by this population. Therefore the aims of this investigation will be to explore changes in lipid profiles, inflammatory markers, and oxidative status, as well as look at any changes in metabolomic profiles. It was hypothesized that by supplementing with TRF a vitamin E, for 16 weeks in ESRD patients undergoing hemodialysis, it may help reverse and/or improve, oxidative status, inflammatory markers, increase antioxidants status and improve lipid profiles.
The study was double-blinded, randomized, parallel, placebo-controlled design trial, of 81 adult patients undergoing chronic hemodialysis at Great Lake Dialysis Clinic, Detroit MI, where …
15>Biophysical Studies Of Mutant H69 Rna Constructs, Daya Nidhi Kharel
Biophysical Studies Of Mutant H69 Rna Constructs, Daya Nidhi Kharel
Wayne State University Theses
The importance of helix 69 (H69) of the large ribosomal subunit is emphasized by its location in the ribosome and key contacts with protein factors and tRNAs during different steps of protein synthesis. The presence of three highly conserved pseudouridine modifications in H69 has a significant impact on modulation of the ribosome conformations. Specific nucleotides of H69 may be necessary for the function of this helix-loop RNA, as some mutations are deleterious to bacterial growth. In this study, we investigated the effects of single nucleotide mutations in a 19-nucleotide H69 construct with and without pseudouridines on the RNA stability and …
Genetic And Biochemical Studies Of Human Apobec3h Enzyme, Thisari Sachithra Aluthgama Guruge
Genetic And Biochemical Studies Of Human Apobec3h Enzyme, Thisari Sachithra Aluthgama Guruge
Wayne State University Theses
The AID/APOBEC enzymes are DNA/RNA cytosine deaminases with important functions in innate and adaptive immunity. APOBEC3 enzymes play a crucial role in restricting the replication of exogenous retroviruses such HIV-1 and endogenous retrotransposition events. In particular, APOBEC3 enzymes have evolved in humans by gene duplication to compose seven members. APOBEC3H is highly diverse in its allelic sequence and the distribution is population-specific. It has evolved under strong positive selection over millions of years. To study the catalytic mechanism, structure, function and the underlying cause of its high diversity, a high resolution crystal or NMR structure is required are not yet …
A Loose Domain Swapping Organization Confers A Remarkable Stability To The Dimeric Structure Of The Arginine Binding Protein From Thermotoga Maritima, Alessia Ruggiero, Jonathan D. Dattelbaum, Maria Staiano, Rita Berisio, Sabato D'Auria, Luigi Vitagliano
A Loose Domain Swapping Organization Confers A Remarkable Stability To The Dimeric Structure Of The Arginine Binding Protein From Thermotoga Maritima, Alessia Ruggiero, Jonathan D. Dattelbaum, Maria Staiano, Rita Berisio, Sabato D'Auria, Luigi Vitagliano
Chemistry Faculty Publications
The arginine binding protein from Thermatoga maritima (TmArgBP), a substrate binding protein (SBP) involved in the ABC system of solute transport, presents a number of remarkable properties. These include an extraordinary stability to temperature and chemical denaturants and the tendency to form multimeric structures, an uncommon feature among SBPs involved in solute transport. Here we report a biophysical and structural characterization of the TmArgBP dimer. Our data indicate that the dimer of the protein is endowed with a remarkable stability since its full dissociation requires high temperature as well as SDS and urea at high concentrations. In order to elucidate …
Microfluidic Electrical Sorting Of Particles Based On Shape In A Spiral Microchannel, John Dubose, Xinyu Lu, Saurin Patel, Shizhi Qian, Sang Woo Joo
Microfluidic Electrical Sorting Of Particles Based On Shape In A Spiral Microchannel, John Dubose, Xinyu Lu, Saurin Patel, Shizhi Qian, Sang Woo Joo
Mechanical & Aerospace Engineering Faculty Publications
Shape is an intrinsic marker of cell cycle, an important factor for identifying a bioparticle, and also a useful indicator of cell state for disease diagnostics. Therefore, shape can be a specific marker in label-free particle and cell separation for various chemical and biological applications. We demonstrate in this work a continuous-flow electrical sorting of spherical and peanut-shaped particles of similar volumes in an asymmetric double-spiral microchannel. It exploits curvature-induced dielectrophoresis to focus particles to a tight stream in the first spiral without any sheath flow and subsequently displace them to shape-dependent flow paths in the second spiral without any …
An Unexpected Particle Oscillation For Electrophoresis In Viscoelastic Fluids Through A Microchannel Constriction, Xinyu Lu, Saurin Patel, Meng Zhang, Sang Woo Joo, Shizhi Qian, Amod Ogale, Xiangchun Xuan
An Unexpected Particle Oscillation For Electrophoresis In Viscoelastic Fluids Through A Microchannel Constriction, Xinyu Lu, Saurin Patel, Meng Zhang, Sang Woo Joo, Shizhi Qian, Amod Ogale, Xiangchun Xuan
Mechanical & Aerospace Engineering Faculty Publications
Electrophoresis plays an important role in many applications, which, however, has so far been extensively studied in Newtonian fluids only. This work presents the first experimental investigation of particle electrophoresis in viscoelastic polyethylene oxide (PEO) solutions through a microchannel constriction under pure DC electric fields. An oscillatory particle motion is observed in the constriction region, which is distinctly different from the particle behavior in a polymer-free Newtonian fluid. This stream-wise particle oscillation continues until a sufficient number of particles form a chain to pass through the constriction completely. It is speculated that such an unexpected particle oscillating phenomenon is a …
Assembly And Function Of Macromolecular Complexes For Accurate Trna Aminoacylation In Helicobacter Pylori, Gayathri Niroshani Silva
Assembly And Function Of Macromolecular Complexes For Accurate Trna Aminoacylation In Helicobacter Pylori, Gayathri Niroshani Silva
Wayne State University Dissertations
ABSTRACT
ASSEMBLY AND FUNCTION OF MACROMOLECULAR COMPLEXES FOR ACCURATE TRNA AMINOACYLATION IN HELICOBACTER PYLORI
by
GAYATHRI SILVA
January 2014
Advisor: Dr. Tamara L. Hendrickson
Major: Chemistry (Biochemistry)
Degree: Doctor of Philosophy
Abstract
The aminoacylation of tRNA is a critical step in maintaining the accuracy of the genetic code. Many microorganisms are missing one or more aminoacyl tRNA synthetases (aaRSs) and rely on indirect pathways to produce certain aa–tRNAs. In Helicobacter pylori (H. pylori), the genes encoding both asparaginyl tRNA synthetase (AsnRS) and glutaminyl tRNA synthetase (GlnRS) are missing and the organism consequently relies on the indirect pathway for …
Basic Features Of A Cell Electroporation Model: Illustrative Behavior For Two Very Different Pulses, Reuben S. Son, Kyle C. Smith, Thiruvallur R. Gowrishankar, P. Thomas Vernier, James C. Weaver
Basic Features Of A Cell Electroporation Model: Illustrative Behavior For Two Very Different Pulses, Reuben S. Son, Kyle C. Smith, Thiruvallur R. Gowrishankar, P. Thomas Vernier, James C. Weaver
Bioelectrics Publications
Science increasingly involves complex modeling. Here we describe a model for cell electroporation in which membrane properties are dynamically modified by poration. Spatial scales range from cell membrane thickness (5 nm) to a typical mammalian cell radius (10 μm), and can be used with idealized and experimental pulse waveforms. The model consists of traditional passive components and additional active components representing nonequilibrium processes. Model responses include measurable quantities: transmembrane voltage, membrane electrical conductance, and solute transport rates and amounts for the representative "long" and "short" pulses. The long pulse-1.5 kV/cm, 100 μs-evolves two pore subpopulations with a valley at ~5 …
Intrinsic Delocalization During The Decay Of Excitons In Polymeric Solar Cells, Thomas F. George, W. Chen, D. Jiang, R. Chen, S. Li