Local hydrogen reactions of H*2 in a-Si:H

Hydrogen rearrangements at the H*2 complex are used as a model of low energy, local transitions in the two-hydrogen density of states of hydrogenated amorphous silicon (a-Si:H). These are used to account for the low activation energy motion of H observed by nuclear magnetic resonance, the low energy defect annealing of defects formed by bias stress in thin film transistors, and the elimination of hydrogen from the growth zone during the low temperature plasma deposition of a-Si:H. © 1998 Elsevier Science B.V. All rights reserved.

BipA: a tyrosine-phosphorylated GTPase that mediates interactions between enteropathogenic Escherichia coli (EPEC) and epithelial cells.

We report the functional characterization of BipA, a GTPase that undergoes tyrosine phosphorylation in an enteropathogenic Escherichia coli (EPEC) strain. BipA mutants adhere to cultured epithelial cells but fail to trigger the characteristic cytoskeletal rearrangements found in cells infected with wild-type EPEC. In contrast, increased expression of BipA enhances actin remodelling and results in the hyperformation of pseudopods. BipA appears to be the first example of a new class of virulence regulator, as it also controls flagella-mediated cell motility and resistance to the antibacterial effects of a human host defence protein. Its striking sequence similarity to ribosome-binding elongation factors suggests that it uses a novel mechanism to modulate gene expression.

Atomistic Origin Of Rate-Dependent Serrated Plastic Flow In Metallic Glasses

Nanoindentation simulations on a binary metallic glass were performed under various strain rates by using molecular dynamics. The rate-dependent serrated plastic flow was clearly observed, and the spatiotemporal behavior of its underlying irreversible atomic rearrangement was probed. Our findings clearly validate that the serration is a temporally inhomogeneous characteristic of such rearrangements and not directly dependent on the resultant shear-banding spatiality. The unique spatiotemporal distribution of shear banding during nanoindentation is highlighted in terms of the potential energy landscape (PEL) theory.

Molecular Dynamics Study Of The Mechanical Behavior Of Nickel Nanowire: Strain Rate Effects

We present the analysis of uniaxial deformation of nickel nanowires using molecular dynamics simulations, and address the strain rate effects on mechanical responses and deformation behavior. The applied strain rate is ranging from 1 x 10(8) s(-1) to 1.4 x 10(11) s(-1). The results show that two critical strain rates, i.e., 5 x 10(9) s(-1) and 8 x 10(10) s(-1), are observed to play a pivotal role in switching between plastic deformation modes. At strain rate below 5 x 10(9) s(-1), Ni nanowire maintains its crystalline structure with neck occurring at the end of loading, and the plastic deformation is characterized by {111} slippages associated with Shockley partial dislocations and rearrangements of atoms close to necking region. At strain rate above 8x10(10) s(-1), Ni nanowire transforms from a fcc crystal into a completely amorphous state once beyond the yield point, and hereafter it deforms uniformly without obvious necking until the end of simulation. For strain rate between 5 x 10(9) s(-1) and 8 x 10(10) s(-1), only part of the nanowire exhibits amorphous state after yielding while the other part remains crystalline state. Both the {111} slippages in ordered region and homogenous deformation in amorphous region contribute to the plastic deformation. (C) 2007 Published by Elsevier B.V.

Ajuste estatal sin equilibrio político : la gestión de López Murphy como ministro de economía de la Alianza en marzo de 2001

Resumen: Este trabajo intenta abordar desde la perspectiva de la historia política la corta gestión, de apenas diecisiete días, de López Murphy como Ministro de Economía de la Alianza en marzo de 2001 como un caso de estudio del “triángulo de gobierno” de Matus. Para esto, primero señalaremos la conformación inicial de los equilibrios políticos de la Alianza, explicando por qué se designó como primer Ministro de Economía a Machinea, enfatizando los delicados compromisos sobre los cuales debió actuar, así como su progresivo agotamiento. Luego, analizaremos cómo su reemplazo por López Murphy generó un profundo cambio de alianzas políticas, generando diversos tipos de enfrentamientos y reagrupamientos, que debilitaban la opción que representaba López Murphy. Igualmente, y a pesar de las resistencias iníciales, veremos que López Murphy decidió llevar a cabo un descomunal ajuste estatal, sin miramientos por las condiciones políticas para aplicarlo. Finalmente, nos dedicaremos a plantear el fin de la gestión de López Murphy y el cambio de condiciones que generó su reemplazo por Cavallo, cambio sobre el cual la Alianza hizo depender su suerte política.

A High Degree of LINE-1 Hypomethylation Is a Unique Feature of Early-Onset Colorectal Cancer

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The effect of the drug colchicine on the early life of fish

The alkaloid drug colchicine is a mitotic inhibitor. The results of this study show that colchicine influence the normal functioning of the mitotic process in Sarotherodon galilaeus, S. melanotheron and the hybrid S. galilaeus, X S. melanotheron leading to the production of unusual chromosomal events such as anaphase bridges, laggards and polyploid cells. These unusual events could have serious genetic implications in the area of variability of the chromosome number. The use of colchicine also produces results with consistent karyotypes and better morphology as well as providing detailed information on the behaviour of the chromosome of the early life of fish. The knowledge of such information will be of great use in cytotaxonomy, fish breeding and in studying the effects of sub-lethal levels of water pollutants on fish

Genetically engineered sensors of cell signaling

Measuring electrical activity in large numbers of cells with high spatial and temporal resolution is a fundamental problem for the study of neural development and information processing. To address this problem, we have constructed FlaSh: a novel, genetically-encoded probe that can be used to measure trans-membrane voltage in single cells. We fused a modified green fluorescent protein (GFP) into a voltage-sensitive potassium channel so that voltage dependent rearrangements in the potassium channel induce changes in the fluorescence of GFP. A voltage sensor encoded into DNA has the advantage that it may be introduced into an organism non-invasively and targeted to specific developmental stages, brain regions, cell types, and sub-cellular compartments.

We also describe modifications to FlaSh that shift its color, kinetics, and dynamic range. We used multiple green fluorescent proteins to produce variants of the FlaSh sensor that generate ratiometric signal output via fluorescence resonance energy transfer (FRET). Finally, we describe initial work toward FlaSh variants that are sensitive to G-protein coupled receptor (GPCR) activation. These sensors can be used to design functional assays for receptor activation in living cells.

Chemical-scale studies of G protein-coupled receptors and ligand-gated ion channels

This dissertation describes studies of G protein-coupled receptors (GPCRs) and ligand-gated ion channels (LGICs) using unnatural amino acid mutagenesis to gain high precision insights into the function of these important membrane proteins.

Chapter 2 considers the functional role of highly conserved proline residues within the transmembrane helices of the D2 dopamine GPCR. Through mutagenesis employing unnatural α-hydroxy acids, proline analogs, and N-methyl amino acids, we find that lack of backbone hydrogen bond donor ability is important to proline function. At one proline site we additionally find that a substituent on the proline backbone N is important to receptor function.

In Chapter 3, side chain conformation is probed by mutagenesis of GPCRs and the muscle-type nAChR. Specific side chain rearrangements of highly conserved residues have been proposed to accompany activation of these receptors. These rearrangements were probed using conformationally-biased β-substituted analogs of Trp and Phe and unnatural stereoisomers of Thr and Ile. We also modeled the conformational bias of the unnatural Trp and Phe analogs employed.

Chapters 4 and 5 examine details of ligand binding to nAChRs. Chapter 4 describes a study investigating the importance of hydrogen bonds between ligands and the complementary face of muscle-type and α4β4 nAChRs. A hydrogen bond involving the agonist appears to be important for ligand binding in the muscle-type receptor but not the α4β4 receptor.

Chapter 5 describes a study characterizing the binding of varenicline, an actively prescribed smoking cessation therapeutic, to the α7 nAChR. Additionally, binding interactions to the complementary face of the α7 binding site were examined for a small panel of agonists. We identified side chains important for binding large agonists such as varenicline, but dispensable for binding the small agonist ACh.

Chapter 6 describes efforts to image nAChRs site-specifically modified with a fluorophore by unnatural amino acid mutagenesis. While progress was hampered by high levels of fluorescent background, improvements to sample preparation and alternative strategies for fluorophore incorporation are described.

Chapter 7 describes efforts toward a fluorescence assay for G protein association with a GPCR, with the ultimate goal of probing key protein-protein interactions along the G protein/receptor interface. A wide range of fluorescent protein fusions were generated, expressed in Xenopus oocytes, and evaluated for their ability to associate with each other.

Gene enrichment using antibodies to DNA/RNA hybrids : mapping the ribosomal DNA of slime mold and rat

A novel method for gene enrichment has been developed and applied to mapping the rRNA genes of two eucaryotic organisms. The method makes use of antibodies to DNA/RNA hybrids prepared by injecting rabbits with the synthetic hybrid poly(rA)•poly(dT). Antibodies which cross-react with non-hybrid nucleic acids were removed from the purified IgG fraction by adsorption on columns of DNA-Sepharose, oligo(dT)-cellulose, and poly(rA)-Sepharose. Subsequent purification of the specific DNA/RNA hybrid antibody was carried out on a column of oligo(dT)-cellulose to which poly(rA) was hybridized. Attachment of these antibodies to CNBr-activated Sepharose produced an affinity resin which specifically binds DNA/RNA hybrids.

In order to map the rDNA of the slime mold Dictyostelium discoideum, R-loops were formed using unsheared nuclear DNA and the 178 and 268 rRNAs of this organism. This mixture was passed through a column containing the affinity resin, and bound molecules containing R- loops were eluted by high salt. This purified rDN A was observed directly in the electron microscope. Evidence was obtained that there is a physical end to Dictyostelium rDN A molecules approximately 10 kilobase pairs (kbp) from the region which codes for the 268 rRNA. This finding is consistent with reports of other investigators that the rRNA genes exist as inverse repeats on extra-chromosomal molecules of DNA unattached to the remainder of the nuclear DNA in this organism.

The same general procedure was used to map the rRNA genes of the rat. Molecules of DNA which contained R-loops formed with the 188 and 288 rRNAs were enriched approximately 150- fold from total genomal rat DNA by two cycles of purification on the affinity column. Electron microscopic measurements of these molecules enabled the construction of an R-loop map of rat rDNA. Eleven of the observed molecules contained three or four R-loops or else two R-loops separated by a long spacer. These observations indicated that the rat rRNA genes are arranged as tandem repeats. The mean length of the repeating units was 37.2 kbp with a standard deviation of 1.3 kbp. These eleven molecules may represent repeating units of exactly the same length within the errors of the measurements, although a certain degree of length heterogeneity cannot be ruled out. If significantly shorter or longer repeating units exist, they are probably much less common than the 37.2 kbp unit.

The last section of the thesis describes the production of antibodies to non-histone chromosomal proteins which have been exposed to the ionic detergent sodium dodecyl sulfate (SDS). The presence of low concentrations of SDS did not seem to affect either production of antibodies or their general specificity. Also, a technique is described for the in situ immunofluorescent detection of protein antigens in polyacrylamide gels.

Synthetic, kinetic and mechanistic studies in early transition metal systems. I. α- and β-hydrogen elimination reactions in derivatives of permethyltitanocene, -zirconocene, and -hafnocene. II. The reactions of aluminum alkyls with derivatives of permethylniobocene

The thermal decomposition of Cp*Ti(CH_3)_2 (Cp*≡ ƞ^5-C_5Me_5) toluene solution follows cleanly first-order kinetics and produces a single titanium product Cp*(C_5Me_4CH_2)Ti(CH_3) concurrent with the evolution of one equivalent of methane. Labeling studies using Cp*_2Ti- (CD_3)_2 and (Cp*-d_(15))_2Ti(CH_3)_2 show the decomposition to be intramolecular and the methane to be produced by the coupling of a methyl group with a hydrogen from the other TiCH_3 group. Activation parameters, ΔH^‡ and ΔS^‡, and kinetic deuterium isotope effects have been measured. The alternative decomposition pathways of α-hydrogen abstraction and a-hydrogen elimination, both leading to a titanium-methylidene intermediate, are discussed.

The insertion of unactivated acetylenes into the metal-hydride bonds of Cp*_2MH_2 (M = Zr, Hf) proceeds rapidly at low temperature to form monoand/ or bisinsertion products, dependent upon the steric bulk of the acetylene substituents. Cp*_2M(H)(C(Me)=CHMe), Cp*_2M(H)(CH=CHCMe_3), Cp*_2M(H)-(CH=CHPh), Cp*_2M(CH=CHPh)_2, Cp*_2M(CH=CHCH_3)_2 and Cp*_2Zr- (CH=CHCH_2CH_3)_2 have been isolated and characterized. To extend the study of unsaturated-carbon ligands, Cp*_2M(C≡CCH_3)_2 have been prepared by treating Cp*_2MCl_2 with LiC≡CCH_3. The reactivity of many of these complexes with carbon monoxide and dihydrogen is surveyed. The mono(2- butenyl) complexes Cp*_2M(H)(C(Me)=CHMe) rearrange at room temperature, forming the crotyl-hydride species Cp*_2M(H)(ƞ^3-C_4H_7). The bis(propenyl) and bis(l-butenyl) zirconium complexes Cp*_2Zr(CH=CHR)_2 (R = CH_3, CH_2CH_3) also rearrange, forming zirconacyclopentenes. Labeling studies, reaction chemistry, and kinetic measurements, including deuterium isotope effects, demonstrate that the unusual 6-hydrogen elimination from an sp^2-hybridized carbon is the first step in these latter rearrangements but is not observed in the former. Details of these mechanisms and the differences in reactivity of the zirconium and hafnium complexes are discussed.

The reactions of hydride- and alkyl-carbonyl derivatives of permethylniobocene with equimolar amounts of trialkylaluminum reagents occur rapidly producing the carbonyl adducts Cp*_2Nb(R)(COAlR'_3) (R = H, CH_3, CH_2CH_3, CH_2CH_2Ph, C(Me)=CHMe; R' = Me, Et). The hydride adduct Cp*_2NbH_3•AlEt_3 has also been formed. In solution, each of these compounds exists in equilibrium with the uncomplexed species. The formation constants for Cp*_2Nb(H)(COA1R'_R) have been measured. They indicate the steric bulk of the Cp* ligands plays a deciding factor in the isolation of the first example of an aluminum Lewis acid bound to a carbonyl-oxygen in preference to a metalhydride. Reactions of Cp*_2Nb(H)CO with other Lewis acids and of the one:one adducts with H_2, CO and C_2H_4 are also discussed.

Cp*_2Nb(H)(C_2H_4) also reacts with equimolar amounts of trialkylaluminum reagents, forming a one:one complex that ^1H NMR spectroscopy indicates contains a Nb-CH_2CH_2-Al bridge. This adduct also exists in equilibrium with the uncomplexed species in solution. The formation constant for Cp*_2N+/b(H)(CH_2CH_2ĀlEt_3) has been measured. Reactions of Cp*_2Nb(H)(C_2H_4) with other Lewis acids and the reactions of Cp*_2N+b(H)- (CH_2CH_2ĀlEt_3) with CO and C_2H_4 are described, as are the reactions of Cp_*2Nb(H)(CH_2=CHR) (R = Me, Ph), Cp*_2Nb(H)(CH_3C≡CCH_3) and Cp*_2Ti-(C_2H_4) with AlEt_3.

The Mechanical Genome in Regulation and Infection

Biological information storage and retrieval is a dynamic process that requires the genome to undergo dramatic structural rearrangements. Recent advances in single-molecule techniques have allowed precise quantification of the nano-mechanical properties of DNA [1, 2], and direct in vivo observation of molecules in action [3]. In this work, we will examine elasticity in protein-mediated DNA looping, whose structural rearrangement is essential for transcriptional regulation in both prokaryotes and eukaryotes. We will look at hydrodynamics in the process of viral DNA ejection, which mediates information transfer and exchange and has prominent implications in evolution. As in the case of Kepler's laws of planetary motion leading to Newton's gravitational theory, and the allometric scaling laws in biology revealing the organizing principles of complex networks [4], experimental data collapse in these biological phenomena has guided much of our studies and urged us to find the underlying physical principles.

Organization and function of the phage Lambda chromosome

The process of prophage integration by phage λ and the function and structure of the chromosomal elements required for λ integration have been studied with the use of λ deletion mutants. Since att^φ, the substrate of the integration enzymes, is not essential for λ growth, and since att^φ resides in a portion of the λ chromosome which is not necessary for vegetative growth, viable λ deletion mutants were isolated and examined to dissect the structure of att^φ.

Deletion mutants were selected from wild type populations by treating the phage under conditions where phage are inactivated at a rate dependent on the DNA content of the particles. A number of deletion mutants were obtained in this way, and many of these mutants proved to have defects in integration. These defects were defined by analyzing the properties of Int-promoted recombination in these att mutants.

The types of mutants found and their properties indicated that att^φ has three components: a cross-over point which is bordered on either side by recognition elements whose sequence is specifically required for normal integration. The interactions of the recognition elements in Int-promoted recombination between att mutants was examined and proved to be quite complex. In general, however, it appears that the λ integration system can function with a diverse array of mutant att sites.

The structure of att^φ was examined by comparing the genetic properties of various att mutants with their location in the λ chromosome. To map these mutants, the techniques of heteroduplex DNA formation and electron microscopy were employed. It was found that integration cross-overs occur at only one point in att^φ and that the recognition sequences that direct the integration enzymes to their site of action are quite small, less than 2000 nucleotides each. Furthermore, no base pair homology was detected between att^φ and its bacterial analog, att^B. This result clearly demonstrates that λ integration can occur between chromosomes which have little, if any, homology. In this respect, λ integration is unique as a system of recombination since most forms of generalized recombination require extensive base pair homology.

An additional study on the genetic and physical distances in the left arm of the λ genome was described. Here, a large number of conditional lethal nonsense mutants were isolated and mapped, and a genetic map of the entire left arm, comprising a total of 18 genes, was constructed. Four of these genes were discovered in this study. A series of λdg transducing phages was mapped by heteroduplex electron microscopy and the relationship between physical and genetic distances in the left arm was determined. The results indicate that recombination frequency in the left arm is an accurate reflection of physical distances, and moreover, there do not appear to be any undiscovered genes in this segment of the genome.

Expressão de fatores de virulência, mecanismos de resistência aos agentes antimicrobianos e análise molecular da resistência aos beta-lactâmicos de enterobactérias isoladas de bolsas periodontais

Em estudo anterior, as espécies de enterobactérias apresentando perfis variados de resistência aos antimicrobianos foram detectadas em 20% dos sítios com lesões periodontais de pacientes sadios do ponto de vista sistêmico. Tais cepas microbianas foram submetidas a investigações com o intuito de determinar à expressão de enzimas hidrolíticas para substratos diversos, a multirresistência aos agentes antimicrobianos e os mecanismos de resistência aos antimicrobianos da classe dos β lactâmicos. A maioria das amostras expressou atividade de gelatinase (65%), caseinase (30%) e elastase (10%). Lipase, lecitinase e DNase foram observadas apenas para Serratia marcescens. A multirresistência (considerado como a resistência a pelo menos dois agentes antimicrobianos de famílias diferentes) foi observada em 56% das amostras isoladas. A maioria das cepas foi resistentes à ampicilina (93,75%) e amoxicilina/ácido clavulânico (81,25%). Investigações sobre a resistência aos antibióticos β-lactâmicos mostraram que três amostras resistentes à cefalosporinas de 2 geração, apresentaram perfis plasmidiais de diferentes pesos moleculares. A expressão fenotípica de β-lacatamases, foi detectada nas cepas de Enterobacter cloacae (PcOM46 e PcOM5) e S. marcescens (PcOM63). No entanto, na análise molecular, não foi possível confirmar a expressão fenotípica de diferentes β-lactamases, com exceção do E. cloacae PcOM46, que apresentou amplificação para AmpC e blaTEM. Embora sensível à maioria dos antibióticos β-lactâmicos (exceção feita à ampicilina e amoxicilina / ácido clavulânico), amostra de S. marcescens PcOM68 apresentou amplificação para o gene blaSHV. Os experimentos de conjugação não detectaram a transferência de plasmídios para uma cepa de Escherichia coli K12 sensívei aos β-lactâmicos, o mesmo ocorreu nos procedimentos de transformação por eletroporação e por CaCl2, sugerindo uma resistência dependente de genes cromossomiais. A expressão de diferentes atividades enzimáticas, juntamente com a resistência aos antimicrobianos, aponta estes grupos de bactérias como agentes patogênicos potenciais capazes de contribuir para a patogênese e resposta à quimioterapia antimicrobiana nas doenças periodontais, além da disseminação sistêmica para outros locais do corpo, especialmente em indivíduos imunocomprometidos. A colonização prévia de lesões periodontais por espécies resistentes aos β-lactâmicos, pode contribuir para a disseminação destes genes relacionados à resistência aos antimicrobianos em ambientes hospitalares.

Análise da mortalidade perinatal na região do Médio Paraíba, Estado do Rio de Janeiro, de 2005 a 2009

A taxa de mortalidade perinatal (TMP) é um dos importantes indicadores de saúde que refletem a qualidade da assistência prestada durante a gestação, o parto e ao recém nascido. A TMP possui dois componentes: a taxa e mortalidade fetal e a taxa de mortalidade infantil neonatal precoce. O objetivo do presente estudo foi analisar a mortalidade perinatal na região do Médio Paraíba, estado do Rio de Janeiro, Brasil no período de 2005 a 2009, segundo causa básica dos óbitos, componentes do período perinatal e critérios de evitabilidade. Foram utilizados os dados referentes aos óbitos fetais e infantis neonatais precoces e de nascidos vivos, registrados, respectivamente, nos Sistemas de Informações sobre Mortalidade (SIM) e Nascidos Vivos (SINASC). A TMP na região foi de 18,4 óbitos por mil nascimentos totais. As taxas de mortalidade fetal e infantil neonatal precoce no período alcançaram, espectivamente 10,7 óbitos por mil nascimentos totais e 7,7 óbitos por mil nascidos vivos. A TMP apresentou redução ao longo do quinquênio analisado associada à queda do componente neonatal precoce, mantendo-se estável o componente fetal. As principais causas básicas dos óbitos perinatais, segundo a lista de mortalidade CID BR, foram as afecções originadas no período perinatal (89%) e as malformações congênitas, deformidades e anomalias cromossômicas (10,5%). Utilizando os critérios de evitabilidade segundo Ortiz, para os óbitos infantis neonatais precoces foi observado que mais de 41% eram reduzíveis por diagnósticos e tratamento precoces. Ressalta-se a necessidade da implementação de ações de assistência à saúde da gestante e de cuidados com o recémnascido com vistas à redução da mortalidade perinatal na região do Médio Paraíba.