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Biochemistry, Biophysics, and Structural Biology

2006

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Articles 1 - 30 of 206

Full-Text Articles in Life Sciences

Secis Elements In The Coding Regions Of Selenoprotein Transcripts Are Functional In Higher Eukaryotes, Heiko Mix, Alexey V. Lobanov, Vadim Gladyshev Dec 2006

Secis Elements In The Coding Regions Of Selenoprotein Transcripts Are Functional In Higher Eukaryotes, Heiko Mix, Alexey V. Lobanov, Vadim Gladyshev

Vadim Gladyshev Publications

Expression of selenocysteine (Sec)-containing proteins requires the presence of a cis-acting mRNA structure, called selenocysteine insertion sequence (SECIS) element. In bacteria, this structure is located in the coding region immediately downstream of the Sec-encoding UGA codon, whereas in eukaryotes a completely different SECIS element has evolved in the 3’-untranslated region. Here, we report that SECIS elements in the coding regions of selenoprotein mRNAs support Sec insertion in higher eukaryotes. Comprehensive computational analysis of all available viral genomes revealed a SECIS element within the ORF of a naturally occurring selenoprotein homolog of glutathione peroxidase 4 in fowlpox virus. The fowlpox …

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Functional Association Between Three Archaeal Aminoacyl-Trna Synthetases, Mette Praetorius-Ibba, Corinne D. Hausmann, Molly Paras, Theresa E. Rogers, Michael Ibba Dec 2006

Functional Association Between Three Archaeal Aminoacyl-Trna Synthetases, Mette Praetorius-Ibba, Corinne D. Hausmann, Molly Paras, Theresa E. Rogers, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Aminoacyl-tRNA synthetases (aaRSs) are responsible for attaching amino acids to their cognate tRNAs during protein synthesis. In eukaryotes aaRSs are commonly found in multi-enzyme complexes, although the role of these complexes is still not completely clear. Associations between aaRSs have also been reported in archaea, including a complex between prolyl-(ProRS) and leucyl-tRNA synthetases (LeuRS) in Methanothermobacter thermautotrophicus that enhances tRNAPro aminoacylation. Yeast two-hybrid screens suggested that lysyl-tRNA synthetase (LysRS) also associates with LeuRS in M. thermautotrophicus. Co-purification experiments confirmed that LeuRS, LysRS, and ProRS associate in cell-free extracts. LeuRS bound LysRS and ProRS with a comparable KD …

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Evidence That Talin Alternative Splice Variants From Ciona Intestinalis Have Different Roles In Cell Adhesion, Richard H. Singiser, Richard O. Mccann Dec 2006

Evidence That Talin Alternative Splice Variants From Ciona Intestinalis Have Different Roles In Cell Adhesion, Richard H. Singiser, Richard O. Mccann

Molecular and Cellular Biochemistry Faculty Publications

BACKGROUND: Talins are large, modular cytoskeletal proteins found in animals and amoebozoans such as Dictyostelium discoideum. Since the identification of a second talin gene in vertebrates, it has become increasingly clear that vertebrate Talin1 and Talin2 have non-redundant roles as essential links between integrins and the actin cytoskeleton in distinct plasma membrane-associated adhesion complexes. The conserved C-terminal I/LWEQ module is important for talin function. This structural element mediates the interaction of talins with F-actin. The I/LWEQ module also targets mammalian Talin1 to focal adhesion complexes, which are dynamic multicomponent assemblies required for cell adhesion and cell motility. Although Talin1 is …

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Synthesis And Optical Properties Of Four Oligothiophene-Ruthenium Complexes And Synthesis Of A Bidentate Ligand For C-F Bond Activation, Joseph S. Bair Dec 2006

Synthesis And Optical Properties Of Four Oligothiophene-Ruthenium Complexes And Synthesis Of A Bidentate Ligand For C-F Bond Activation, Joseph S. Bair

Theses and Dissertations

Photovoltaic cells and fluorescence sensing are two important areas of research in chemistry. The combination of photon-activated electron donors with electron acceptors provides a strong platform for the study of optical devices. A series of four oligothiophene-ruthenium complexes has been synthesized. Variation in oligothiophene length and bipyridine substitution allowed comparison of these variables on electronic properties. The longer oligothiophenes display lower energy absorption and emission compared to the shorter ones. Aromatic conjugation appears more complete with para-, rather than meta-, substitution. Oligothiophenes and Ru(bpy)32+ are highly fluorescent individually, but fluorescence is quenched when connected. Bonds of carbon to fluorine are …

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Development Of Polymer Monoliths For The Analysis Of Peptides And Proteins, Binghe Gu Dec 2006

Development Of Polymer Monoliths For The Analysis Of Peptides And Proteins, Binghe Gu

Theses and Dissertations

Several novel polymer monoliths for the analysis of peptides and proteins were synthesized using polyethylene glycol diacrylate (PEGDA) as crosslinker. Photo-initiated copolymerization of polyethylene glycol methyl ether acrylate and PEGDA yielded an inert monolith that could be used for size exclusion liquid chromatography of peptides and proteins. This macroscopically uniform monolith did not shrink or swell in either water or tetrahydrofuran. More importantly, it was found to resist adsorption of both acidic and basic proteins in aqueous buffer without any organic solvent additives. A strong cation-exchange polymer monolith was synthesized by copolymerization of 2-acrylamido-2-methyl-1-propanesulfonic acid (AMPS) and PEGDA. A ternary …

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Alternative Probeset Definitions For Combining Microarray Data Across Studies Using Different Versions Of Affymetrix Oligonucleotide Arrays, Jeffrey S. Morris, Chunlei Wu, Kevin R. Coombes, Keith A. Baggerly, Jing Wang, Li Zhang Dec 2006

Alternative Probeset Definitions For Combining Microarray Data Across Studies Using Different Versions Of Affymetrix Oligonucleotide Arrays, Jeffrey S. Morris, Chunlei Wu, Kevin R. Coombes, Keith A. Baggerly, Jing Wang, Li Zhang

Jeffrey S. Morris

Many published microarray studies have small to moderate sample sizes, and thus have low statistical power to detect significant relationships between gene expression levels and outcomes of interest. By pooling data across multiple studies, however, we can gain power, enabling us to detect new relationships. This type of pooling is complicated by the fact that gene expression measurements from different microarray platforms are not directly comparable. In this chapter, we discuss two methods for combining information across different versions of Affymetrix oligonucleotide arrays. Each involves a new approach for combining probes on the array into probesets. The first approach involves …

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Engineering Calpastatin To Develop A Sensor To Detect Active Calpain, Lisa M. Vanhooser Dec 2006

Engineering Calpastatin To Develop A Sensor To Detect Active Calpain, Lisa M. Vanhooser

Electronic Theses and Dissertations

Calpains, Ca2+-activated cysteine proteases are essential for early embryonic development and function in signal transduction, cell adhesion, and apoptosis. Calpains also contribute to cataractogenesis, myocardial infarctions, and neurodegenerative diseases such as Alzheimer's. The various methods currently available to demonstrate these roles do not directly identify spatial or temporal activation of calpain in cells. Therefore, a tool to detect active calpain in situ will be useful. Calpastatin is the ubiquitous, endogenous inhibitor that specifically binds the active conformation of the conventional calpains. Calpastatin consists of four homologous domains each containing three subdomains A, B, and C. The crystal structure …

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The Role Of Prolactin And Its Antagonist In Her2/Neu Tumorigenesis, Michele Scotti Dec 2006

The Role Of Prolactin And Its Antagonist In Her2/Neu Tumorigenesis, Michele Scotti

All Dissertations

Purpose: To study the role of prolactin (PRL) and its antagonist, G129R, in HER2/Neu tumorigenesis. Specifically, to investigate the interaction between the oncogene HER2 and the PRL receptor (PRLR) signaling pathways for designing effective combinational therapeutics for breast cancer.
Experimental Design: The combination effects of G129R and an anti-HER2 antibody, Herceptin, were tested against HER2-overexpressing human breast cancer cell lines, T-47D and BT-474, using cell based assays and xenografts established in athymic mice. Furthermore, four different bitransgenic mouse lines co-expressing the murine version of HER2 and PRL or G129R were generated. The mammary tumor incidence, characterization of mammary gland development, …

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Development Of Methods For The Study Of Phosphoproteins, Zhaoyuan Chen Dec 2006

Development Of Methods For The Study Of Phosphoproteins, Zhaoyuan Chen

Theses and Dissertations

Characterization of phosphoproteins-including detection, identification of phosphoproteins and identification of phosphorylation sites-is mostly done with radiolabeling and proteomic techniques. Three main topics related to phosphoprotein characterization are included in this dissertation. First, large-scale characterization of the CHO (Chinese hamster ovary) cell phosphoproteome was done using two dimensional gel electrophoresis (2DE) separation, visualization of phosphoproteins by radiolabeling or a phosphoprotein specific dye, followed by MALDI-TOF identification. Because radiolabeling of phosphoproteins is very sensitive and straightforward to quantify, such analysis can give a clear picture of the relative phosphosphorylation of proteins present in a sample. But there are also limitations to this …

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Organochlorine Levels In Seawater And Sediment From The Florida Gulf Coast, If Present, Are Low. , Richard B. Philp Nov 2006

Organochlorine Levels In Seawater And Sediment From The Florida Gulf Coast, If Present, Are Low. , Richard B. Philp

Richard B. Philp

Seawater and sediment from the Florida panhandle coast were assayed for a panel of 28 organochlorine insecticides and PCBs. No samples exeeded the detection limits of the analytical technique, which were well below levels reported for other ocean locales. Organochlorine levels in this area of the Gulf must be very low. This does not preclude their biomagnificatioon up the food web.

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Capillary Electrophoresis Of Proteins With Selective On-Line Affinity Monoliths, Jenny Marcela Armenta Blanco Nov 2006

Capillary Electrophoresis Of Proteins With Selective On-Line Affinity Monoliths, Jenny Marcela Armenta Blanco

Theses and Dissertations

The analysis of proteins in biological fluids by capillary electrophoresis (CE) is of interest in clinical chemistry. However, due to low analyte concentrations and poor concentration limits of detection (CLOD), protein analysis by this technique is frequently challenging. Coupling preconcentration techniques with CE greatly improves the CLOD. An on-line preconcentration-CE method that can selectively preconcentrate any protein for which an antibody is available would be very useful for the analysis of low abundance proteins and would establish CE as a major tool in biomarker discovery. To accomplish this, an on-line protein G monolithic preconcentrator CE system for enrichment and separation …

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Physical And Structural Basis For The Strong Interactions Of The -Impy- Central Pairing Motif In The Polyamide F-Impyim, K. Buchmueller, S. Bailey, D. Matthews, Z. Taherbhai, J. Register, Z. Davis, Chrystal Bruce, C. O'Hare, J. Hartley, M. Lee Nov 2006

Physical And Structural Basis For The Strong Interactions Of The -Impy- Central Pairing Motif In The Polyamide F-Impyim, K. Buchmueller, S. Bailey, D. Matthews, Z. Taherbhai, J. Register, Z. Davis, Chrystal Bruce, C. O'Hare, J. Hartley, M. Lee

Chrystal D. Bruce

The polyamide f-ImPyIm has a higher affinity for its cognate DNA than either the parent analogue, distamycin A (10-fold), or the structural isomer, f-PyImIm (250-fold), has for its respective cognate DNA sequence. These findings have led to the formulation of a two-letter polyamide “language” in which the -ImPy- central pairings associate more strongly with Watson−Crick DNA than -PyPy-, -PyIm-, and -ImIm-. Herein, we further characterize f-ImPyIm and f-PyImIm, and we report thermodynamic and structural differences between -ImPy- (f-ImPyIm) and -PyIm- (f-PyImIm) central pairings. DNase I footprinting studies confirmed that f-ImPyIm is a stronger binder than distamycin A and f-PyImIm and …

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Biochemical Investigations Of Macular Degeneration: The Significance Of Protein Oxidation Including Novel Methods For Its Study, Sarah Warburton Nov 2006

Biochemical Investigations Of Macular Degeneration: The Significance Of Protein Oxidation Including Novel Methods For Its Study, Sarah Warburton

Theses and Dissertations

The retinal pigment epithelium (RPE) is a monolayer of cells located directly behind the photoreceptor cells in the retina. These cells are involved in a variety of functions that support the visual process in the eye, namely 1) they form a blood-retina barrier which separates the neural retina from the choroid's blood supply, 2) the apical processes of RPE cells diurnally phagocytose the outer segments of photoreceptor cells, and 3) they participate in the renewal of the photopigment 11-cis retinal. Age-related macular degneration (AMD) is the leading cause of blindness in people over the age of 50 years in North …

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Sub-Typing Of Prrsv Isolates By Means Of Measurement Of Cross-Neutralization Reactions, Fernando A. Osorio Nov 2006

Sub-Typing Of Prrsv Isolates By Means Of Measurement Of Cross-Neutralization Reactions, Fernando A. Osorio

School of Veterinary and Biomedical Sciences: Faculty Publications

The degree of similitude or closeness between two different isolates or strains of PRRSV is very important for deciding which strains should be used for immunization, by either vaccinating with commercial vaccines or attempting to stabilize a herd with planned wt PRRSV infection. As previously known for certain important viral diseases, such as in Foot and Mouth Disease, the reciprocal (cross-) neutralization titers between two strains may be of utmost importance to establish the degree of similarity or difference between these. There is currently a void of methods that would allow distinguishing or grouping strains of PRRSV in a manner …

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Characterization Of Cucurbituril Complex Ions In The Gas Phase Using Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Haizhen Zhang Nov 2006

Characterization Of Cucurbituril Complex Ions In The Gas Phase Using Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Haizhen Zhang

Theses and Dissertations

Host-guest interactions have been well studied in the new century to obtain fundamental insights into supramolecular chemistry. Most of the pioneering works have been done using techniques such as NMR, X-ray crystallography, IR spectroscopy and so on. However, none of these techniques is universal for the investigation of all types of supramolecules, and usually they have one or more limiting factors such as relatively large sample consumption, matrix effects from solvents, etc. Electrospray mass spectrometry has been widely used to investigate host-guest interactions in the gas phase. A particular advantage of gas phase host-guest research is that the experimental results …

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Prepms: Tof Ms Data Graphical Preprocessing Tool, Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, Jonas S. Almeida Nov 2006

Prepms: Tof Ms Data Graphical Preprocessing Tool, Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, Jonas S. Almeida

Jeffrey S. Morris

We introduce a simple-to-use graphical tool that enables researchers to easily prepare time-of-flight mass spectrometry data for analysis. For ease of use, the graphical executable provides default parameter settings experimentally determined to work well in most situations. These values can be changed by the user if desired. PrepMS is a stand-alone application made freely available (open source), and is under the General Public License (GPL). Its graphical user interface, default parameter settings, and display plots allow PrepMS to be used effectively for data preprocessing, peak detection, and visual data quality assessment.

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A Genomic Approach To Identify Regulatory Nodes In The Transcriptional Network Of Systemic Acquired Resistance In Plants, Dong Wang, Nita Amornsiripanitch, Xinnian Dong Nov 2006

A Genomic Approach To Identify Regulatory Nodes In The Transcriptional Network Of Systemic Acquired Resistance In Plants, Dong Wang, Nita Amornsiripanitch, Xinnian Dong

Dong Wang

Many biological processes are controlled by intricate networks of transcriptional regulators. With the development of microarray technology, transcriptional changes can be examined at the whole-genome level. However, such analysis often lacks information on the hierarchical relationship between components of a given system. Systemic acquired resistance (SAR) is an inducible plant defense response involving a cascade of transcriptional events induced by salicylic acid through the transcription cofactor NPR1. To identify additional regulatory nodes in the SAR network, we performed microarray analysis on Arabidopsis plants expressing the NPR1-GR (glucocorticoid receptor) fusion protein. Since nuclear translocation of NPR1-GR requires dexamethasone, we were able …

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The Allantois And Chorion, When Isolated Before Circulation Or Chorio-Allantoic Fusion, Have Hematopoietic Potential, Brandon M. Zeigler, Daisuke Sugiyama, Michael Chen, Yalin Guo, K. M. Downs, N. A. Speck Nov 2006

The Allantois And Chorion, When Isolated Before Circulation Or Chorio-Allantoic Fusion, Have Hematopoietic Potential, Brandon M. Zeigler, Daisuke Sugiyama, Michael Chen, Yalin Guo, K. M. Downs, N. A. Speck

Dartmouth Scholarship

The chorio-allantoic placenta forms through the fusion of the allantois (progenitor tissue of the umbilical cord), with the chorionic plate. The murine placenta contains high levels of hematopoietic stem cells, and is therefore a stem cell niche. However, it is not known whether the placenta is a site of hematopoietic cell emergence, or whether hematopoietic cells originate from other sites in the conceptus and then colonize the placenta. Here, we show that the allantois and chorion, isolated prior to the establishment of circulation, have the potential to give rise to myeloid and definitive erythroid cells following explant culture. We further …

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Characterization Of Host Cell Death Induced By Chlamydia Trachomatis, Songmin Ying, Silke F. Fischer, Matthew A. Pettengill, Debye Conte, Stefan A. Paschen, David M. Ojcius, Georg Hacker Nov 2006

Characterization Of Host Cell Death Induced By Chlamydia Trachomatis, Songmin Ying, Silke F. Fischer, Matthew A. Pettengill, Debye Conte, Stefan A. Paschen, David M. Ojcius, Georg Hacker

All Dugoni School of Dentistry Faculty Articles

Chlamydia are obligate intracellular bacteria that modulate apoptosis of the host cell. Strikingly, chlamydial infection has been reported both to inhibit and to induce apoptosis. Although the ability to inhibit apoptosis has been corroborated by the identification of cellular targets, confirmation of cell death induction has been complicated by a mixture of apoptotic features and atypical cell death during infection, as well as by differences in the experimental techniques used to measure cell death. Here we use a panel of well-established approaches in the study of apoptosis to define the form of cell death induced by Chlamydia trachomatis infection. Infected …

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The Role Of A Conserved Serine Residue Within Hydrogen Bonding Distance Of Fad In Redox Properties And The Modulation Of Catalysis By Ca2+/Calmodulin Of Constitutive Nitric-Oxide Synthases, Satya Prakash Panda, Ying Tong Gao, Linda J. Roman, Pavel Marta´Sek, John C. Salerno, Bettie Masters Nov 2006

The Role Of A Conserved Serine Residue Within Hydrogen Bonding Distance Of Fad In Redox Properties And The Modulation Of Catalysis By Ca2+/Calmodulin Of Constitutive Nitric-Oxide Synthases, Satya Prakash Panda, Ying Tong Gao, Linda J. Roman, Pavel Marta´Sek, John C. Salerno, Bettie Masters

Faculty and Research Publications

The crystal structure of the neuronal nitric-oxide synthase (nNOS) NADPH/FAD binding domain indicated that Ser-1176 is within hydrogen bonding distance of Asp-1393 and the O4 atom of FAD and is also near the N5 atom of FAD (3.7Å). This serine residue is conserved in most of the ferredoxin-NADP+ reductase family of proteins and is important in electron transfer. In the present study, the homologous serines of both nNOS (Ser-1176) and endothelial nitric-oxide synthase (eNOS) (Ser-942) were mutated to threonine and alanine. Both substitutions yielded proteins that exhibited decreased rates of electron transfer through the flavin domains, in the presence …

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An Ascorbate-Reducible Cytochrome B561 Is Localized In Macrophage Lysosomes, De-Liang Zhang, Dan Su, Alajos Berczi , Amy Vargas , Han H. Asard Oct 2006

An Ascorbate-Reducible Cytochrome B561 Is Localized In Macrophage Lysosomes, De-Liang Zhang, Dan Su, Alajos Berczi , Amy Vargas , Han H. Asard

Department of Biochemistry: Faculty Publications

Cytochromes b561 (Cyts b561) are a family of intrinsic membrane proteins involved in ascorbate-mediated transmembrane electron transport. The chromaffin granule Cyt b561 (CGCytb) is believed to transport electrons donated by extravesicular ascorbate (ASC) across the membrane to intravesicular monodehydroascorbate (MDA) supporting catecholamine synthesis in neuroendocrine tissues. Another isoform, the duodenal Cyt b561 (Dcytb), was reported to have ferric reductase activity, possibly facilitating intestinal iron uptake. Herein, a new Cyt b561 homologue, LCytb (for lysosomal Cytb561) was found expressed in the late endosomal–lysosomal membrane. LCytb shared high sequence similarity with CGCytb (45% identity) and Dcytb (42% identity). Moreover, four heme-coordinating His …

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The Role Of Mapks In B Cell Receptor-Induced Down-Regulation Of Egr-1 In Immature B Lymphoma Cells, Jiyuan Ke, Murali Gururajan, Anupam Kumar, Alan Simmons, Lilia Turcios, Ralph Lakshman Chelvarajan, David M. Cohen, David L. Wiest, John G. Monroe, Subbarao Bondada Oct 2006

The Role Of Mapks In B Cell Receptor-Induced Down-Regulation Of Egr-1 In Immature B Lymphoma Cells, Jiyuan Ke, Murali Gururajan, Anupam Kumar, Alan Simmons, Lilia Turcios, Ralph Lakshman Chelvarajan, David M. Cohen, David L. Wiest, John G. Monroe, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Cross-linking of the B cell receptor (BCR) on the immature B lymphoma cell line BKS-2 induces growth inhibition and apoptosis accompanied by rapid down-regulation of the immediate-early gene egr-1. In these lymphoma cells, egr-1 is expressed constitutively and has a prosurvival role, as Egr-1-specific antisense oligonucleotides or expression of a dominant-negative inhibitor of Egr-1 also prevented the growth of BKS-2 cells. Moreover, enhancement of Egr-1 protein with phorbol 12-myristate 13-acetate or an egr-1 expression vector rescued BKS-2 cells from BCR signal-induced growth inhibition. Nuclear run-on and mRNA stability assays indicated that BCR-derived signals act at the transcriptional level to …

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Periodic Boundary Condition Induced Breakdown Of The Equipartition Principle And Other Kinetic Effects Of Finite Sample Size In Classical Hard-Sphere Molecular Dynamics Simulation, Randall B. Shirts, Scott R. Burt, Aaron M. Johnson Oct 2006

Periodic Boundary Condition Induced Breakdown Of The Equipartition Principle And Other Kinetic Effects Of Finite Sample Size In Classical Hard-Sphere Molecular Dynamics Simulation, Randall B. Shirts, Scott R. Burt, Aaron M. Johnson

Faculty Publications

We examine consequences of the non-Boltzmann nature of probability distributions for one-particle kinetic energy, momentum, and velocity for finite systems of classical hard spheres with constant total energy and nonidentical masses. By comparing two cases, reflecting walls (NVE or microcanonical ensemble) and periodic boundaries (NVEPG or molecular dynamics ensemble), we describe three consequences of the center-of-mass constraint in periodic boundary conditions: the equipartition theorem no longer holds for unequal masses, the ratio of the average relative velocity to the average velocity is increased by a factor of [N/(N–1)]^1/2, and the ratio of average collision energy to average kinetic energy is …

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Reconstitution Of Protein Targeting To The Inner Envelope Membrane Of Chloroplasts, Ming Li, Danny Schnell Oct 2006

Reconstitution Of Protein Targeting To The Inner Envelope Membrane Of Chloroplasts, Ming Li, Danny Schnell

Danny Schnell

The chloroplast envelope plays critical roles in the synthesis and regulated transport of key metabolites, including intermediates in photosynthesis and lipid metabolism. Despite this importance, the biogenesis of the envelope membranes has not been investigated in detail. To identify the determinants of protein targeting to the inner envelope membrane (IM), we investigated the targeting of the nucleus-encoded integral IM protein, atTic40. We found that pre-atTic40 is imported into chloroplasts and processed to an intermediate size (int-atTic40) before insertion into the IM. Int-atTic40 is soluble and inserts into the IM from the internal stromal compartment. We also show that atTic40 and …

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Dynamic Evolution Of Selenocysteine Utilization In Bacteria: A Balance Between Selenoprotein Loss And Evolution Of Selenocysteine From Redox Active Cysteine Residues, Yan Zhang, Hector Romero, Gustavo Salinas, Vadim Gladyshev Oct 2006

Dynamic Evolution Of Selenocysteine Utilization In Bacteria: A Balance Between Selenoprotein Loss And Evolution Of Selenocysteine From Redox Active Cysteine Residues, Yan Zhang, Hector Romero, Gustavo Salinas, Vadim Gladyshev

Vadim Gladyshev Publications

Background: Selenocysteine (Sec) is co-translationally inserted into protein in response to UGA codons. It occurs in oxidoreductase active sites and often is catalytically superior to cysteine (Cys). However, Sec is used very selectively in proteins and organisms. The wide distribution of Sec and its restricted use have not been explained.
Results: We conducted comparative genomics and phylogenetic analyses to examine dynamics of Sec decoding in bacteria at both selenium utilization trait and selenoproteome levels. These searches revealed that 21.5% of sequenced bacteria utilize Sec, their selenoproteomes have 1 to 31 selenoproteins, and selenoprotein-rich organisms are mostly Deltaproteobacteria or Firmicutes/ Clostridia …

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Dictyostelium Myosin-Ie Is A Fast Molecular Motor Involved In Phagocytosis, Ulrike Durrwang, Setsuko Fujita-Becker, Muriel Erent, F. Jon Kull Oct 2006

Dictyostelium Myosin-Ie Is A Fast Molecular Motor Involved In Phagocytosis, Ulrike Durrwang, Setsuko Fujita-Becker, Muriel Erent, F. Jon Kull

Dartmouth Scholarship

Class I myosins are single-headed motor proteins, implicated in various motile processes including organelle translocation, ion-channel gating, and cytoskeleton reorganization. Here we describe the cellular localization of myosin-IE and its role in the phagocytic uptake of solid particles and cells. A complete analysis of the kinetic and motor properties of Dictyostelium discoideum myosin-IE was achieved by the use of motor domain constructs with artificial lever arms. Class I myosins belonging to subclass IC like myosin-IE are thought to be tuned for tension maintenance or stress sensing. In contrast to this prediction, our results show myosin-IE to be a fast motor. …

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Single Molecule Detection Systems And Methods, John G. K. Williams, Gregory R. Bashford Oct 2006

Single Molecule Detection Systems And Methods, John G. K. Williams, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

A micofluidic system is provided that includes a substrate, a first microchannel disposed in the substrate for providing a reactant to a reaction zone, a second microchannel disposed in the substrate, the third microchannel providing fluid communication between the first and second microchannels. The system also typically includes first and second electrodes, positioned at opposite ends of the second microchannel, for providing an electric field within the second microchannel. In operation, when the reactant is in the reaction zone, a reaction product is produced having a net electric charge different from the electric of the reactant.

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Microfabrication And Evaluation Of Planar Thin-Film Microfluidic Devices, Bridget Ann Peeni Oct 2006

Microfabrication And Evaluation Of Planar Thin-Film Microfluidic Devices, Bridget Ann Peeni

Theses and Dissertations

Over the past 15 years, research in the field of microfluidics has rapidly gained popularity. By seeking to miniaturize and automate separation-based analysis, microfluidic research seeks to improve current methods through decreased cost, analysis time, and sources of contamination. My work has focused on developing a novel fabrication method, based on standard microfabrication techniques, to create thin-film microfluidic devices. This microfabrication format makes it possible to generate devices that provide high efficiencies, enable mass fabrication, and provide a platform capable of integrating the microfluidic and electronic components necessary for a micro-total analysis system (μ-TAS). Device fabrication combines the processes of …

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The Structure And Function Of Frataxin, Krisztina Z. Bencze, Kalyan C. Kondapalli, Jeremy D. Cook, Stephen Mcmahon, César Millán-Pacheco, Nina Pastor, Timothy L. Stemmler Oct 2006

The Structure And Function Of Frataxin, Krisztina Z. Bencze, Kalyan C. Kondapalli, Jeremy D. Cook, Stephen Mcmahon, César Millán-Pacheco, Nina Pastor, Timothy L. Stemmler

Biochemistry and Molecular Biology Faculty Publications

Frataxin, a highly conserved protein found in prokaryotes and eukaryotes, is required for efficient regulation of cellular iron homeostasis. Humans with a frataxin deficiency have the cardio- and neurodegenerative disorder Friedreich’s ataxia, commonly resulting from a GAA trinucleotide repeat expansion in the frataxin gene. While frataxin’s specific function remains a point of controversy, a general consensus is the protein assists in controlling cellular iron homeostasis by directly binding iron. This review focuses on the structural and biochemical aspects of iron binding by the frataxin orthologs and outlines molecular attributes that may help explain the protein’s role in different cellular pathways.

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Polymorphism Of Hla-Dr And Hla-Dq In Rheumatoid Arthritis Patients And Clinical Response To Methotrexate--A Hospital-Based Study, Azra Arif I Ali, Tariq Moatter, Jawed Altaf Baig, Ahmed Iqbal, Azmat Hussain, Mohammad Perwaiz Iqbal Oct 2006

Polymorphism Of Hla-Dr And Hla-Dq In Rheumatoid Arthritis Patients And Clinical Response To Methotrexate--A Hospital-Based Study, Azra Arif I Ali, Tariq Moatter, Jawed Altaf Baig, Ahmed Iqbal, Azmat Hussain, Mohammad Perwaiz Iqbal

Department of Biological & Biomedical Sciences

Objective: To investigate the frequency and distribution of DRB1 and DQB1 alleles in Patients with rheumatoid arthritis (RA) and analyze the relationship between clinical response to methotrexate (MTX) and the HLA-DR and HLA-DQ genotypes in these patients.
Methods: In this case-control study, the HLA-DRB1 and HLA-DQB1 polymorphism in 91 RA patients and 91 healthy controls was done using polymerase chain reaction and sequence specific primers.
Results: There was no statistical difference in frequencies of HLA-DRB1*03, DRB1*04, DRB1*07, DRB1*10, DRB1*11, DRB1*12, DRB1*13, DRB1*14, DRB1*15 and DRB1*16 genotypes between patients and controls. However, DRB1*01 was found to be significantly more common (p=0.015) …

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