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Sample records for analysis molecular investigation

  1. Evolution & Phylogenetic Analysis: Classroom Activities for Investigating Molecular & Morphological Concepts

    Science.gov (United States)

    Franklin, Wilfred A.

    2010-01-01

    In a flexible multisession laboratory, students investigate concepts of phylogenetic analysis at both the molecular and the morphological level. Students finish by conducting their own analysis on a collection of skeletons representing the major phyla of vertebrates, a collection of primate skulls, or a collection of hominid skulls.

  2. SNR analysis: molecular investigation of an anthrax epidemic

    Directory of Open Access Journals (Sweden)

    Adone Rosanna

    2010-02-01

    Full Text Available Abstract Background In Italy, anthrax is endemic but occurs sporadically. During the summer of 2004, in the Pollino National Park, Basilicata, Southern Italy, an anthrax epidemic consisting of 41 outbreaks occurred; it claimed the lives of 124 animals belonging to different mammal species. This study is a retrospective molecular epidemiological investigation carried out on 53 isolates collected during the epidemic. A 25-loci Multiple Locus VNTR Analysis (MLVA MLVA was initially performed to define genetic relationships, followed by an investigation of genetic diversity between epidemic strains through Single Nucleotide Repeat (SNR analysis. Results 53 Bacillus anthracis strains were isolated. The 25-loci MLVA analysis identified all of them as belonging to a single genotype, while the SNR analysis was able to detect the existence of five subgenotypes (SGTs, allowing a detailed epidemic investigation. SGT-1 was the most frequent (46/53; SGTs 2 (4/53, 3 (1/53 4 (1/53 and 5 (1/53 were detected in the remaining seven isolates. Conclusions The analysis revealed the prevalent spread, during this epidemic, of a single anthrax clone. SGT-1 - widely distributed across the epidemic area and present throughout the period in question - may, thus, be the ancestral form. SGTs 2, 3 and 4 differed from SGT-1 at only one locus, suggesting that they could have evolved directly from the latter during the course of this epidemic. SGT-5 differed from the other SGTs at 2-3 loci. This isolate, thus, appears to be more distantly related to SGT-1 and may not be a direct descendant of the lineage responsible for the majority of cases in this epidemic. These data confirm the importance of molecular typing and subtyping methods for in-depth epidemiological analyses of anthrax epidemics.

  3. Structural analysis and investigation of molecular properties of Cefpodoxime acid, a third generation antibiotic

    Science.gov (United States)

    Suganthi, S.; Balu, P.; Sathyanarayanamoorthi, V.; Kannappan, V.; Kamil, M. G. Mohamed; Kumar, R.

    2016-03-01

    Extensive quantum mechanical studies are carried out on Cefpodoxime acid (CA), a new generation drug by Hartree-Fock (HF) and B3LYP methods to understand the structural and spectral characteristics of the molecule. The most stable geometry of the molecule was optimized and the bond parameters were reported. The spectroscopic properties of this pharmaceutically important compound were investigated by FT-IR, FT-Raman, UV and 1H NMR techniques. The scaled vibrational frequencies of CA in the ground state are calculated by HF and B3LYP methods with 6-311++G (d, p) basis set and compared with the observed FT-IR and FT-Raman spectra. The vibrational spectral analysis indicates the presence of two intra molecular hydrogen bonds in the molecule which is supported by theoretical study. 1H NMR chemical shifts (δ) were calculated for the CA molecule and compared with the experimental values. The theoretical electronic absorption spectral data in water and ethanol solvents were computed by TD-DFT method. UV-Vis absorption spectra of CA are recorded in these two solvents and compared with theoretical spectra. The spectral data and natural bond orbital (NBO) analysis confirm the occurrence of intra molecular interactions in CA. The electronic distribution, in conjunction with electrophilicity index of CA was used to establish the active site and type of interaction between CA and beta lactamases. Mulliken population analysis on atomic charges is also carried out and thermodynamic properties of the title compound are calculated.

  4. 3D-QSAR Investigation of Synthetic Antioxidant Chromone Derivatives by Molecular Field Analysis

    Directory of Open Access Journals (Sweden)

    Jiraporn Ungwitayatorn

    2008-02-01

    Full Text Available A series of 7-hydroxy, 8-hydroxy and 7,8-dihydroxy synthetic chromone derivatives was evaluated for their DPPH free radical scavenging activities. A training set of 30 synthetic chromone derivatives was subject to three-dimensional quantitative structure-activity relationship (3D-QSAR studies using molecular field analysis (MFA. The substitutional requirements for favorable antioxidant activity were investigated and a predictive model that could be used for the design of novel antioxidants was derived. Regression analysis was carried out using genetic partial least squares (G/PLS method. A highly predictive and statistically significant model was generated. The predictive ability of the developed model was assessed using a test set of 5 compounds (r2pred = 0.924. The analyzed MFA model demonstrated a good fit, having r2 value of 0.868 and crossvalidated coefficient r2cv value of 0.771.

  5. Investigation of the interaction of naringin palmitate with bovine serum albumin: spectroscopic analysis and molecular docking.

    Directory of Open Access Journals (Sweden)

    Xia Zhang

    Full Text Available BACKGROUND: Bovine serum albumin (BSA contains high affinity binding sites for several endogenous and exogenous compounds and has been used to replace human serum albumin (HSA, as these two compounds share a similar structure. Naringin palmitate is a modified product of naringin that is produced by an acylation reaction with palmitic acid, which is considered to be an effective substance for enhancing naringin lipophilicity. In this study, the interaction of naringin palmitate with BSA was characterised by spectroscopic and molecular docking techniques. METHODOLOGY/PRINCIPAL FINDINGS: The goal of this study was to investigate the interactions between naringin palmitate and BSA under physiological conditions, and differences in naringin and naringin palmitate affinities for BSA were further compared and analysed. The formation of naringin palmitate-BSA was revealed by fluorescence quenching, and the Stern-Volmer quenching constant (KSV was found to decrease with increasing temperature, suggesting that a static quenching mechanism was involved. The changes in enthalpy (ΔH and entropy (ΔS for the interaction were detected at -4.11 ± 0.18 kJ·mol(-1 and -76.59 ± 0.32 J·mol(-1·K(-1, respectively, which indicated that the naringin palmitate-BSA interaction occurred mainly through van der Waals forces and hydrogen bond formation. The negative free energy change (ΔG values of naringin palmitate at different temperatures suggested a spontaneous interaction. Circular dichroism studies revealed that the α-helical content of BSA decreased after interacting with naringin palmitate. Displacement studies suggested that naringin palmitate was partially bound to site I (subdomain IIA of the BSA, which was also substantiated by the molecular docking studies. CONCLUSIONS/SIGNIFICANCE: In conclusion, naringin palmitate was transported by BSA and was easily removed afterwards. As a consequence, an extension of naringin applications for use in food, cosmetic

  6. Investigating Molecular Interactions

    DEFF Research Database (Denmark)

    Clausen, Henrik Fanø

    2010-01-01

    the thesis to the two types of structures. The first chapter is a brief introduction to the theory used in this dissertation, where diffraction theory, the aspherical atom model, and the Atom in Molecules theory will be presented. Physical properties, such as thermal stability and magnetic susceptibility...... chapters concern transition metal coordination polymers and the last three describe hydroquinone co-crystals and clathrate structures. Even though, the goal of the thesis has been to give account of all the work that I have performed, I have chosen to leave out results of certain projects, and confine......, are also introduced, as a goal of the analysis of charge density distributions is to obtain further understanding of these macroscopic properties. Neutron diffraction will be used as a complementary tool to the X-ray diffraction experiment, as positional and thermal parameters of hydrogen atoms can...

  7. Techniques for Investigating Molecular Toxicology of Nanomaterials.

    Science.gov (United States)

    Wang, Yanli; Li, Chenchen; Yao, Chenjie; Ding, Lin; Lei, Zhendong; Wu, Minghong

    2016-06-01

    Nanotechnology has been a rapidly developing field in the past few decades, resulting in the more and more exposure of nanomaterials to human. The increased applications of nanomaterials for industrial, commercial and life purposes, such as fillers, catalysts, semiconductors, paints, cosmetic additives and drug carriers, have caused both obvious and potential impacts on human health and environment. Nanotoxicology is used to study the safety of nanomaterials and has grown at the historic moment. Molecular toxicology is a new subdiscipline to study the interactions and impacts of materials at the molecular level. To better understand the relationship between the molecular toxicology and nanomaterials, this review summarizes the typical techniques and methods in molecular toxicology which are applied when investigating the toxicology of nanomaterials and include six categories: namely; genetic mutation detection, gene expression analysis, DNA damage detection, chromosomal aberration analysis, proteomics, and metabolomics. Each category involves several experimental techniques and methods. PMID:27319209

  8. Investigation of allosteric modulation mechanism of metabotropic glutamate receptor 1 by molecular dynamics simulations, free energy and weak interaction analysis

    Science.gov (United States)

    Bai, Qifeng; Yao, Xiaojun

    2016-02-01

    Metabotropic glutamate receptor 1 (mGlu1), which belongs to class C G protein-coupled receptors (GPCRs), can be coupled with G protein to transfer extracellular signal by dimerization and allosteric regulation. Unraveling the dimer packing and allosteric mechanism can be of great help for understanding specific regulatory mechanism and designing more potential negative allosteric modulator (NAM). Here, we report molecular dynamics simulation studies of the modulation mechanism of FITM on the wild type, T815M and Y805A mutants of mGlu1 through weak interaction analysis and free energy calculation. The weak interaction analysis demonstrates that van der Waals (vdW) and hydrogen bonding play an important role on the dimer packing between six cholesterol molecules and mGlu1 as well as the interaction between allosteric sites T815, Y805 and FITM in wild type, T815M and Y805A mutants of mGlu1. Besides, the results of free energy calculations indicate that secondary binding pocket is mainly formed by the residues Thr748, Cys746, Lys811 and Ser735 except for FITM-bound pocket in crystal structure. Our results can not only reveal the dimer packing and allosteric regulation mechanism, but also can supply useful information for the design of potential NAM of mGlu1.

  9. Investigation of torsional potentials, molecular structure, vibrational properties, molecular characteristics and NBO analysis of some bipyridines using experimental and theoretical tools

    Science.gov (United States)

    Prashanth, J.; Reddy, B. Venkatram; Rao, G. Ramana

    2016-08-01

    The Fourier Transform Infrared (FTIR) and Fourier Transform Raman (FT-Raman) spectra of 2,2‧-bipyridine (2BPE); 4,4‧-bipyridine (4BPE); and 2,4‧-bipyridine (24BPE) were measured in the range 4000-450 cm-1 and 4000-50 cm-1, respectively. Torsional potentials were evaluated at various angles of rotation around the C-C inter-ring bond for the three molecules in order to arrive at the molecular conformation of lowest energy. This conformation was further optimized to get ground state geometry. Vibrational frequencies along with infrared and Raman intensities were computed. In the above calculations, DFT employing B3LYP functional with 6311++G(d,p) basis set was used. The rms error between observed and calculated frequencies was 10.0, 10.9 and 10.2 cm-1 for 2BPE, 4BPE and 24BPE, respectively. A 54-parameter modified valence force field was derived by solving inverse vibrational problem using Wilson's GF matrix method. The force constants were refined using 117 experimental frequencies of the three molecules in overlay least-squares technique. The average error between observed and computed frequencies was 12.44 cm-1. PED and eigen vectors calculated in the process were used to make unambiguous vibrational assignments of all the fundamental vibrations. The values of dipole moment, polarizability and hyperpolarizability were computed to determine the NLO behaviour of these molecules. The HOMO and LUMO energies, thermodynamic parameters and molecular electrostatic surface potentials (MESP) were also evaluated. Stability of the molecules arising from hyper conjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis.

  10. Theoretical investigations on the molecular structure, vibrational spectra, HOMO-LUMO and NBO analysis of 5-chloro-2-((4-chlorophenoxy)methyl)benzimidazole

    Science.gov (United States)

    Mary, Y. Shyma; Jojo, P. J.; Panicker, C. Yohannan; Van Alsenoy, Christian; Ataei, Sanaz; Yildiz, Ilkay

    2014-03-01

    The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments of 5-chloro-2-((4-chlorophenoxy)methyl)benzimidazole have been investigated experimentally and theoretically using Gaussian09 software package. The energy and oscillator strength calculated by time dependent density functional theory results almost compliments with experimental findings. Gauge-including atomic orbital 1H NMR chemical shifts calculations were carried out and compared with experimental data. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. Molecular electrostatic potential was performed by the DFT method and the infrared intensities and Raman activities are reported. Mulliken's net charges have been calculated and compared with the atomic natural charges. Fist hyperpolarizability is calculated in order to find its role in non-linear optics.

  11. Investigating the Equilibrium Melting Temperature of Polyethylene Using the Non-Linear Hoffman-Weeks Analysis: Effect of Molecular Weight

    Science.gov (United States)

    Mohammadi, Hadi; Marand, Herve

    The limiting equilibrium melting temperature for infinite molar mass linear polyethylene, Tmo , has been a point of controversy for about five decades. On one hand, Broadhurst and Flory-Vrij extrapolated melting data for short alkanes to a value of ca. 145oC. On the other hand, Wunderlich proposed a value of 141oC from melting studies of extended-chain PE crystals formed under high pressure. While a difference in Tmo by 4oC might seem superfluous, it has significant implication for the analysis of the temperature and chain length dependences of crystal growth kinetic data. In this work we estimate the equilibrium melting temperatures, Tm for three linear narrow molecular weight distribution polyethylenes using the non-linear Hoffman-Weeks treatment. The resulting Tm values thus obtained are significantly lower than these predicted by the Flory-Vrij treatment and are within experimental uncertainty indistinguishable from those reported by Wunderlich and Hikosaka et al. Our results also suggest that the constant C2 in the expression for the undercooling dependence of the initial lamellar thickness (lg*= C1/ ΔT + C2) increases linearly with chain length.

  12. Investigation of chemical modifiers for sulfur determination in diesel fuel samples by high-resolution continuum source graphite furnace molecular absorption spectrometry using direct analysis

    Energy Technology Data Exchange (ETDEWEB)

    Huber, Charles S. [Instituto Federal Sul-rio-grandense, Câmpus Pelotas, Pelotas, RS (Brazil); Universidade Federal do Rio Grande do Sul, Instituto de Química, Porto Alegre, RS (Brazil); Vale, Maria Goreti R. [Universidade Federal do Rio Grande do Sul, Instituto de Química, Porto Alegre, RS (Brazil); Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Welz, Bernhard [Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Universidade Federal de Santa Catarina, Departamento de Química, Florianópolis, SC (Brazil); Andrade, Jailson B. [Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Dessuy, Morgana B., E-mail: mbdessuy@ufrgs.br [Universidade Federal do Rio Grande do Sul, Instituto de Química, Porto Alegre, RS (Brazil); Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil)

    2015-06-01

    High-resolution continuum source graphite furnace molecular absorption spectrometry has been applied for sulfur determination in diesel fuel. The sharp rotational lines of the carbon monosulfide molecule (formed during the vaporization step) were used to measure the absorbance. The analytical line at 258.056 nm was monitored using the sum of three pixels. Different chemical modifiers were investigated and the mixture of palladium and magnesium was used as chemical modifier in combination with iridium as permanent modifier. L-Cysteine was chosen as sulfur standard and the calibration was done against aqueous standard solutions. The proposed method was applied for the analyses of four diesel samples: two S10 samples and two S500 samples. The trueness of the method was checked with a certified reference material (CRM) of sulfur in diesel fuel (NIST 2724b). Accurate results, for samples and CRM, were achieved after a dilution with propan-1-ol. The following figures of merit were obtained: characteristic mass of 17 ± 3 ng, limit of detection and limit of quantification of 1.4 mg kg{sup −1} and 4.7 mg kg{sup −1}, respectively. - Highlights: • Ir, Ru and Zr were investigated as permanent modifiers. • Ca, Mg, Pd and Pd/Mg were investigated as modifiers in solution. • Indirect determination of sulfur monitoring the molecular absorbance of the CS • Direct analysis of diesel samples using a dilution in propan-1-ol.

  13. Investigation of chemical modifiers for sulfur determination in diesel fuel samples by high-resolution continuum source graphite furnace molecular absorption spectrometry using direct analysis

    International Nuclear Information System (INIS)

    High-resolution continuum source graphite furnace molecular absorption spectrometry has been applied for sulfur determination in diesel fuel. The sharp rotational lines of the carbon monosulfide molecule (formed during the vaporization step) were used to measure the absorbance. The analytical line at 258.056 nm was monitored using the sum of three pixels. Different chemical modifiers were investigated and the mixture of palladium and magnesium was used as chemical modifier in combination with iridium as permanent modifier. L-Cysteine was chosen as sulfur standard and the calibration was done against aqueous standard solutions. The proposed method was applied for the analyses of four diesel samples: two S10 samples and two S500 samples. The trueness of the method was checked with a certified reference material (CRM) of sulfur in diesel fuel (NIST 2724b). Accurate results, for samples and CRM, were achieved after a dilution with propan-1-ol. The following figures of merit were obtained: characteristic mass of 17 ± 3 ng, limit of detection and limit of quantification of 1.4 mg kg−1 and 4.7 mg kg−1, respectively. - Highlights: • Ir, Ru and Zr were investigated as permanent modifiers. • Ca, Mg, Pd and Pd/Mg were investigated as modifiers in solution. • Indirect determination of sulfur monitoring the molecular absorbance of the CS • Direct analysis of diesel samples using a dilution in propan-1-ol

  14. Appendix II. Molecular Analysis

    Science.gov (United States)

    The study of crop evolution, origins, and conservation entails the assessment of genetic variability with and between populations and species at different genetic, evolutionary, and taxonomic hierarchical levels. Molecular biology has greatly increased the amount of data and computational intensity...

  15. Preparation, physicochemical analysis and molecular modeling investigation of 2,2‧-Bipyridine: β-Cyclodextrin inclusion complex in solution and solid state

    Science.gov (United States)

    Periasamy, R.; Kothainayaki, S.; Sivakumar, K.

    2015-11-01

    Supramolecular interaction between 2,2‧-Bipyridine (BPY) and β-Cyclodextrin (β-CD) has been investigated in solution and solid state. Non-covalent interaction between BPY and β-CD was studied in solution using absorption and fluorescence spectroscopy. Inclusion complex of BPY and β-CD was prepared in solid state by co-precipitation method and it was characterized using Fourier Transform Infra-red spectroscopy (FT-IR), Thermal analysis, Scanning Electron Microscopy (SEM), Powder X-ray diffractometry (XRD) and Atomic Force Microscopy (AFM). Binding constant values and 1:1 stoichiometry of the inclusion complex were calculated using Benesi-Hildebrand plots at 303 K. Using continuous variation method the 1:1 stoichiometry has been confirmed for BPY: β-CD complex. Thermodynamic parameter, ΔG of inclusion complex formation was determined and the negative value indicated that the inclusion process was an exergonic and spontaneous process. The most probable model of BPY: β-CD inclusion complex suggested by molecular docking studies was in good agreement with the results obtained by experimental methods.

  16. "Mini-Array" Transcriptional Analysis of the "Listeria Monocytogenes" Lecithinase Operon as a Class Project: A Student Investigative Molecular Biology Laboratory Experience

    Science.gov (United States)

    Christensen, Douglas; Jovic, Marko

    2006-01-01

    This report describes a molecular biotechnology-based laboratory curriculum developed to accompany an undergraduate genetics course. During the course of a semester, students researched the pathogen, developed a research question, designed experiments, and performed transcriptional analysis of a set of genes that confer virulence to the food-borne…

  17. Binding affinities of Schiff base Fe(II) complex with BSA and calf-thymus DNA: Spectroscopic investigations and molecular docking analysis.

    Science.gov (United States)

    Rudra, Suparna; Dasmandal, Somnath; Patra, Chiranjit; Kundu, Arjama; Mahapatra, Ambikesh

    2016-09-01

    The binding interaction of a synthesized Schiff base Fe(II) complex with biological macromolecules viz., bovine serum albumin (BSA) and calf thymus(ct)-DNA have been investigated using different spectroscopic techniques coupled with viscosity measurements at physiological pH and 298K. Regular amendments in emission intensities of BSA upon the action of the complex indicate significant interaction between them, and the binding interaction have been characterized by Stern Volmer plots and thermodynamic binding parameters. On the basis of this quenching technique one binding site with binding constant (Kb=(7.6±0.21)×10(5)) between complex and protein have been obtained at 298K. Time-resolved fluorescence studies have also been encountered to understand the mechanism of quenching induced by the complex. Binding affinities of the complex to the fluorophores of BSA namely tryptophan (Trp) and tyrosine (Tyr) have been judged by synchronous fluorescence studies. Secondary structural changes of BSA rooted by the complex has been revealed by CD spectra. On the other hand, hypochromicity of absorption spectra of the complex with the addition of ct-DNA and the gradual reduction in emission intensities of ethidium bromide bound ct-DNA in presence of the complex indicate noticeable interaction between ct-DNA and the complex with the binding constant (4.2±0.11)×10(6)M(-1). Life-time measurements have been studied to determine the relative amplitude of binding of the complex to ct-DNA base pairs. Mode of binding interaction of the complex with ct-DNA has been deciphered by viscosity measurements. CD spectra have also been used to understand the changes in ct-DNA structure upon binding with the metal complex. Density functional theory (DFT) and molecular docking analysis have been employed in highlighting the interactive phenomenon and binding location of the complex with the macromolecules. PMID:27214273

  18. RFLP Analysis and Allelic Discrimination with Real-Time PCR Using the Human Lactase Persistence Trait: A Pair of Molecular Genetic Investigations

    Science.gov (United States)

    Weinlander, Kenneth M.; Hall, David J.; De Stasio, Elizabeth A.

    2010-01-01

    We describe here two open-ended laboratory investigations for an undergraduate laboratory course that uses students' DNA as templates for quantitative real-time PCR and for traditional PCR followed by RFLP analysis. Students are captivated by the immediacy of the application and the relevance of the genotypes and traits, lactase persistence or…

  19. Molecular Contamination Investigation Facility (MCIF) Capabilities

    Science.gov (United States)

    Soules, David M.

    2013-01-01

    This facility was used to guide the development of ASTM E 1559 center dot Multiple Quartz Crystal Microbalances (QCMs), large sample and spectral effects capability center dot Several instrumented, high vacuum chamber systems are used to evaluate the molecular outgassing characteristics of materials, flight components and other sensitive surfaces. Test materials for spacecraft/instrument selection center.Test flight components for acceptable molecular outgas levels center dot Determine time/temperature vacuum bake-out requirements center. Data used to set limits for use of materials and specific components center. Provide Input Data to Contamination Transport Models -Applied to numerous flight projects over the past 20 years.

  20. Shock induced phase transition of water: Molecular dynamics investigation

    Energy Technology Data Exchange (ETDEWEB)

    Neogi, Anupam, E-mail: anupamneogi@atdc.iitkgp.ernet.in [Advanced Technology Development Center, Indian Institute of Technology Kharagpur, Kharagpur 721302 (India); Mitra, Nilanjan, E-mail: nilanjan@civil.iitkgp.ernet.in [Department of Civil Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302 (India)

    2016-02-15

    Molecular dynamics simulations were carried out using numerous force potentials to investigate the shock induced phenomenon of pure bulk liquid water. Partial phase transition was observed at single shock velocity of 4.0 km/s without requirement of any external nucleators. Change in thermodynamic variables along with radial distribution function plots and spectral analysis revealed for the first time in the literature, within the context of molecular dynamic simulations, the thermodynamic pathway leading to formation of ice VII from liquid water on shock loading. The study also revealed information for the first time in the literature about the statistical time-frame after passage of shock in which ice VII formation can be observed and variations in degree of crystallinity of the sample over the entire simulation time of 100 ns.

  1. Shock induced phase transition of water: Molecular dynamics investigation

    International Nuclear Information System (INIS)

    Molecular dynamics simulations were carried out using numerous force potentials to investigate the shock induced phenomenon of pure bulk liquid water. Partial phase transition was observed at single shock velocity of 4.0 km/s without requirement of any external nucleators. Change in thermodynamic variables along with radial distribution function plots and spectral analysis revealed for the first time in the literature, within the context of molecular dynamic simulations, the thermodynamic pathway leading to formation of ice VII from liquid water on shock loading. The study also revealed information for the first time in the literature about the statistical time-frame after passage of shock in which ice VII formation can be observed and variations in degree of crystallinity of the sample over the entire simulation time of 100 ns

  2. Molecular analysis of 11 galactosemia patients.

    OpenAIRE

    Reichardt, J K

    1991-01-01

    Galactosemia is a human inborn error of galactose metabolism due to deficiency of galactose-1-phosphate uridyl transferase. In this paper, I describe the molecular analysis of genomic DNA, mRNA and protein from 11 different galactosemic patients by Southern, Northern and Western blotting. The results of these experiments lead me to conclude that galactosemia is caused mostly by missense mutations. The unusual preponderance of missense mutations in galactosemia led me to investigate its cause....

  3. Molecular investigations applied to nontuberculous mycobacteria identification

    OpenAIRE

    Monica Pecorari; William Gennari; Anna Fabio; Antonella Grottola; Massimino Messinò; Giuliana Fabio; Nadia Nanni; Giulia Forbicini; Rita Magnani; Anna Maria Teresa Sabbatini; Fabio Rumpianesi; Chiara Casolari

    2009-01-01

    Objective. Aim of this study was molecular identification in clinical specimens of NonTuberculous Mycobacteria (NTM) with commercial methods and automated sequencing. Materials and methods. Three thousand clinical specimens were analyzed for the isolation of Mycobacteria. Forty strains of NTM were previously analyzed with GenoType Mycobacteria CM/AS kit and then with partial 16S rDNA sequencing. Results. 38/40 NMT strains were identified with GenoType Mycobacteria CM/AS kit as: M. gordonae (1...

  4. Investigation of chemical modifiers for sulfur determination in diesel fuel samples by high-resolution continuum source graphite furnace molecular absorption spectrometry using direct analysis

    Science.gov (United States)

    Huber, Charles S.; Vale, Maria Goreti R.; Welz, Bernhard; Andrade, Jailson B.; Dessuy, Morgana B.

    2015-06-01

    High-resolution continuum source graphite furnace molecular absorption spectrometry has been applied for sulfur determination in diesel fuel. The sharp rotational lines of the carbon monosulfide molecule (formed during the vaporization step) were used to measure the absorbance. The analytical line at 258.056 nm was monitored using the sum of three pixels. Different chemical modifiers were investigated and the mixture of palladium and magnesium was used as chemical modifier in combination with iridium as permanent modifier. L-Cysteine was chosen as sulfur standard and the calibration was done against aqueous standard solutions. The proposed method was applied for the analyses of four diesel samples: two S10 samples and two S500 samples. The trueness of the method was checked with a certified reference material (CRM) of sulfur in diesel fuel (NIST 2724b). Accurate results, for samples and CRM, were achieved after a dilution with propan-1-ol. The following figures of merit were obtained: characteristic mass of 17 ± 3 ng, limit of detection and limit of quantification of 1.4 mg kg- 1 and 4.7 mg kg- 1, respectively.

  5. Molecular dynamics investigation of dynamic crack stability

    International Nuclear Information System (INIS)

    A series of molecular-dynamics simulations has been performed in order to evaluate the effects of several physical factors on dynamic crack stability. These factors are the crystalline structure and the interatomic interaction modeled by various empirical potentials. For brittle crack propagation at low temperature we find that steady-state crack velocities are limited to a band of accessible values. Increasing the overload beyond KIc, the crack can propagate with a steady-state velocity, which quickly reaches the terminal velocity of about 0.4 of the Rayleigh wave speed. The magnitude of the terminal velocity can be related to the nonlinearity of the interatomic interaction. Further increasing the overload does not change the steady-state velocity dramatically, but significantly increases the amplitude of acoustic emission from the crack tip. Loading the crack even further leads to instabilities which take the form of cleavage steps, dislocation emission, or branching. The instability is closely related to the buildup of a localized coherent, phononlike field generated by the bond-breaking events. The form of the instability depends critically on crystal structure and on the crystallographic orientation of the crack system but can also be correlated with the relative ease of dislocation generation (and motion). copyright 1997 The American Physical Society

  6. Normal coordinate analysis, molecular structure, vibrational, electronic spectra and NMR investigation of 4-Amino-3-phenyl-1H-1,2,4-triazole-5(4H)-thione by ab initio HF and DFT method

    Science.gov (United States)

    Bahgat, Khaled; Fraihat, Safwan

    2015-01-01

    In the present work, the characterization of 4-Amino-3-phenyl-1H-1,2,4-triazole-5(4H)-thione (APTT) molecule was carried out by quantum chemical method and vibrational spectral techniques. The FT-IR (4000-400 cm-1) and FT-Raman (4000-100 cm-1) spectra of APTT were recorded in solid phase. The UV-Vis absorption spectrum of the APTT was recorded in the range of 200-400 nm. The molecular geometry, harmonic vibrational frequencies and bonding features of APTT in the ground state have been calculated by HF and DFT methods using 6-311++G(d,p) basis set. The complete vibrational frequency assignments were made by normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMF). The molecular stability and bond strength were investigated by applying the natural bond orbital analysis (NBO) and natural localized molecular orbital (NLMO) analysis. The electronic properties, such as excitation energies, absorption wavelength, HOMO and LUMO energies were performed by time depended DFT (TD-DFT) approach. The 1H and 13C nuclear magnetic resonance chemical shift of the molecule were calculated using the gauge-including atomic orbital (GIAO) method and compared with experimental results. Finally, the calculation results were analyzed to simulate infrared, FT-Raman and UV spectra of the title compound which shows better agreement with observed spectra.

  7. Molecular Dynamics Investigated by Neutron Scattering

    International Nuclear Information System (INIS)

    A short review of the present state of the problem of applicability of the Krieger-Nelkin theory as well as of the Griffing theory to gases is made. Then, on the basis of experiments with liquid methane, the applicability of the mass-tensor concept to molecules in condensed states is criticized. Strong arguments against the application of the Krieger-Nelkin theory to condensed states are: a shift of neutron energy distribution after scattering towards higher energies and the lack of dependence of the Inelastic part on the scattering angle. Further sections deal with the rotational dynamics of ammonium groups in ammonium compounds. Most of the experimental material is discussed in connection with ammonium halides on the basis of experiments by different authors. For some substances a freedom of rotation of NH4 groups was obtained from neutron measurements, whereas for some others the rotation goes over into torsional vibration. In this case, frequencies of torsional vibrations obtained by various authors from neutron experiments were compared with those obtained from infrared spectroscopy and specific heat measurements. The barrier-to-rotation evaluation from total neutron cross-section measurements is also discussed. Further a comparison is made of the rotational dynamics of NH4 groups in NH4CIO4 and H3O groups in H3OCIO4 on the basis of neutron inelastic scattering experiments. A free rotation of the NH4 group in ammonium perchlorate was obtained even at temperatures as low as liquid nitrogen temperature. For H3OCIO4 a torsional vibration of the H3O group with a frequency of 497 cm-1 was obtained. So in spite of the identity of the crystal lattices of NH4CIO4 and H3OCIO4 the dynamics of the NH4 and H3O groups are different. The results are compared with those known from Raman spectroscopy and nuclear magnetic resonance. Finally, a number of other substances is discussed from the point of view of molecular dynamics. (author)

  8. Generalized analysis of molecular variance.

    Directory of Open Access Journals (Sweden)

    Caroline M Nievergelt

    2007-04-01

    Full Text Available Many studies in the fields of genetic epidemiology and applied population genetics are predicated on, or require, an assessment of the genetic background diversity of the individuals chosen for study. A number of strategies have been developed for assessing genetic background diversity. These strategies typically focus on genotype data collected on the individuals in the study, based on a panel of DNA markers. However, many of these strategies are either rooted in cluster analysis techniques, and hence suffer from problems inherent to the assignment of the biological and statistical meaning to resulting clusters, or have formulations that do not permit easy and intuitive extensions. We describe a very general approach to the problem of assessing genetic background diversity that extends the analysis of molecular variance (AMOVA strategy introduced by Excoffier and colleagues some time ago. As in the original AMOVA strategy, the proposed approach, termed generalized AMOVA (GAMOVA, requires a genetic similarity matrix constructed from the allelic profiles of individuals under study and/or allele frequency summaries of the populations from which the individuals have been sampled. The proposed strategy can be used to either estimate the fraction of genetic variation explained by grouping factors such as country of origin, race, or ethnicity, or to quantify the strength of the relationship of the observed genetic background variation to quantitative measures collected on the subjects, such as blood pressure levels or anthropometric measures. Since the formulation of our test statistic is rooted in multivariate linear models, sets of variables can be related to genetic background in multiple regression-like contexts. GAMOVA can also be used to complement graphical representations of genetic diversity such as tree diagrams (dendrograms or heatmaps. We examine features, advantages, and power of the proposed procedure and showcase its flexibility by

  9. One Pot Selective Arylation of 2-Bromo-5-Chloro Thiophene; Molecular Structure Investigation via Density Functional Theory (DFT), X-ray Analysis, and Their Biological Activities

    Science.gov (United States)

    Rasool, Nasir; Kanwal, Aqsa; Rasheed, Tehmina; Ain, Quratulain; Mahmood, Tariq; Ayub, Khurshid; Zubair, Muhammad; Khan, Khalid Mohammed; Arshad, Muhammad Nadeem; M. Asiri, Abdullah; Zia-Ul-Haq, Muhammad; Jaafar, Hawa Z. E.

    2016-01-01

    Synthesis of 2,5-bisarylthiophenes was accomplished by sequential Suzuki cross coupling reaction of 2-bromo-5-chloro thiophenes. Density functional theory (DFT) studies were carried out at the B3LYP/6-31G(d, p) level of theory to compare the geometric parameters of 2,5-bisarylthiophenes with those from X-ray diffraction results. The synthesized compounds are screened for in vitro bacteria scavenging abilities. At the concentration of 50 and 100 μg/mL, compounds 2b, 2c, 2d, 3c, and 3f with IC50-values of 51.4, 52.10, 58.0, 56.2, and 56.5 μg/mL respectively, were found most potent against E. coli. Among all the synthesized compounds 2a, 2d, 3c, and 3e with the least values of IC50 77, 76.26, 79.13 μg/mL respectively showed significant antioxidant activities. Almost all of the compounds showed good antibacterial activity against Escherichia coli, whereas 2-chloro-5-(4-methoxyphenyl) thiophene (2b) was found most active among all synthesized compound with an IC50 value of 51.4 μg/mL. All of the synthesized compounds were screened for nitric oxide scavenging activity as well. Frontier molecular orbitals (FMOs) and molecular electrostatic potentials of the target compounds were also studied theoretically to account for their relative reactivity PMID:27367666

  10. One Pot Selective Arylation of 2-Bromo-5-Chloro Thiophene; Molecular Structure Investigation via Density Functional Theory (DFT, X-ray Analysis, and Their Biological Activities

    Directory of Open Access Journals (Sweden)

    Nasir Rasool

    2016-06-01

    Full Text Available Synthesis of 2,5-bisarylthiophenes was accomplished by sequential Suzuki cross coupling reaction of 2-bromo-5-chloro thiophenes. Density functional theory (DFT studies were carried out at the B3LYP/6-31G(d, p level of theory to compare the geometric parameters of 2,5-bisarylthiophenes with those from X-ray diffraction results. The synthesized compounds are screened for in vitro bacteria scavenging abilities. At the concentration of 50 and 100 μg/mL, compounds 2b, 2c, 2d, 3c, and 3f with IC50-values of 51.4, 52.10, 58.0, 56.2, and 56.5 μg/mL respectively, were found most potent against E. coli. Among all the synthesized compounds 2a, 2d, 3c, and 3e with the least values of IC50 77, 76.26, 79.13 μg/mL respectively showed significant antioxidant activities. Almost all of the compounds showed good antibacterial activity against Escherichia coli, whereas 2-chloro-5-(4-methoxyphenyl thiophene (2b was found most active among all synthesized compound with an IC50 value of 51.4 μg/mL. All of the synthesized compounds were screened for nitric oxide scavenging activity as well. Frontier molecular orbitals (FMOs and molecular electrostatic potentials of the target compounds were also studied theoretically to account for their relative reactivity

  11. Molecular analysis of Sarcoptes scabiei

    OpenAIRE

    Ljunggren, Erland L.

    2005-01-01

    The mite Sarcoptes scabiei (Acari), causes sarcoptic mange or scabies that globally affects animals and humans. Although scabies and mange are recognised as important diseases in human and veterinary medicine the amount of molecular studies of S. scabiei have been limited, which has been attributed to a shortage of parasitic material. This thesis is based on four studies that make use of molecular techniques with the aims to overcome the problems associated with a scarcity of mites, gain insi...

  12. Investigation of gamma spectra analysis

    International Nuclear Information System (INIS)

    During the investigation of radiation fingerprint comparison, it is found out that the popular gamma spectra analysis softwares are faultful, which decrease the precision of radiation fingerprint comparison. So a new analysis software is development for solving the problems. In order to display the advantage of new program, some typical simulative gamma spectra of radiation source are analyzed respectively by our software and GAMMAVISION and GENNIE2000. The software can be applied not only in nuclear warheads deep-cuts verification, but also in any radiation measurement field. (authors)

  13. Investigations on the adsorbents for uremic middle molecular toxins (II)

    Institute of Scientific and Technical Information of China (English)

    WANG; Hong

    2001-01-01

    normal and uremic urine by high-performance liquid chromatography, J. Chromatogr., 1982, 233: 107.[15]Mabuchi, H., Nakahashi, H., Analysis of middle molecular peptides in normal and uremic body fluids by high-performance gel chromatography, J. Chromatogr,, 1981,224: 322.[16]Flanagan, R. W. J., Murphy, R. F., Buchanan, K. D., Circulating forms of glucagon and related peptides in normal subjects and uraemic patients, Biochem. Soc. Transt., 1980, 8: 426.[17]Matthaei, D., Ludwig-Krln, H., Kramer, P. et al., Changes of plasma hormone levels in hemofiltration, Int. J. Artif. Organs,1983, 6: 21.[18]Ehrlich, R. W., Holland, F., Turnham, T. et al., Osmotic concentration of polypeptides from hemofiltrate of uremic patients,Clin. Nephrol., 1980, 14: 31.[19]Menyhart, J., Grof, J., Many hitherto unknown peptides are principal constituents of uremic “middle molecules”, Clin.Chem., 1981, 27: 1712.[20]Wang, S. X., Wu, J. P., Nephrology, Beijing: People's Health Publishing House, 1987, 740.[21]Chu, J. G., Investigations on the separation, characterization and toxicity of middle molecular substances, Doctoral Dissertation, Nankai University, 2000, 108.

  14. Growth mechanism, electronic spectral investigation and molecular orbital studies of L-prolinium phosphate.

    Science.gov (United States)

    Liu, Xiaojing; Sun, Xin; Xu, Xijin; Sun, Ping

    2015-11-01

    By using atomic force microscopy, birth and spread has proved to be the primary growth mechanism for L-prolinium phosphate (LPP). The phenomenon of newly formed islands expanding to the edge of the preceding terrace was observed. The optimized molecular structure and the molecular properties were calculated by density functional theory method. Natural bond orbital analysis was carried out to demonstrate the various inter and intramolecular interactions that are responsible for the stabilization of LPP leading to high NLO activity. Molecular electrostatic potential, frontier molecular orbital analysis and thermodynamic properties were investigated to get a better insight of the molecular properties. Global and local reactivity descriptors were computed to predict the reactivity and reactive sites on the molecules. Non-linear optical (NLO) properties such as the total dipole moment (μ) and first order hyperopolarizability (β) were also calculated to predict NLO behavior. PMID:26067937

  15. Rheological investigation of highly filled polymers: Effect of molecular weight

    Science.gov (United States)

    Hnatkova, Eva; Hausnerova, Berenika; Hales, Andrew; Jiranek, Lukas; Vera, Juan Miguel Alcon

    2015-04-01

    The paper deals with rheological properties of highly filled polymers used in powder injection molding. Within the experimental framework seven PIM feedstocks based on superalloy Inconel 718 powder were prepared. Each feedstock contains the fixed amount of powder loading and the same composition of binder system consisting of three components: polyethylene glycol (PEG) differing in molecular weight, poly (methyl methacrylate) (PMMA) and stearic acid (SA). The aim is to investigate the influence of PEG's molecular weight on the flow properties of feedstocks. Non-Newtonian indices, representing the shear rate sensitivity of the feedstocks, are obtained from a polynomial fit, and found to vary within measured shear rates range from 0.2 to 0.8. Temperature effect is considered via activation energies, showing decreasing trend with increasing of molecular weight of PEG (except of feedstock containing 1,500 g.mol-1 PEG).

  16. Molecular dynamics investigation of radiation damage in semiconductors

    Science.gov (United States)

    Good, Brian S.

    1991-01-01

    Results of a molecular dynamics investigation of the effects of radiation damage on the crystallographic structure of semiconductors are reported. Particular cosiderastion is given to the formation of point defects and small defect complexes in silicon at the end of a radiation-damage cascade. The calculations described make use of the equivalent crystal theory of Smith and Banerjea (1988). Results on the existence of an atomic displacement threshold, the defect formation energy, and some crystallographic information on the defects observed are reported.

  17. [Evolution and systematics of nematodes based on molecular investigation].

    Science.gov (United States)

    Okulewicz, Anna; Perec, Agnieszka

    2004-01-01

    Evolution and systematics of nematodes based on molecular investigation. The use of molecular phylogenetics to examine the interrelationships between animal parasites, free-living nematodes, and plant parasites versus traditional classification based on morphological-ecological characters was discussed and reviewed. Distinct differences were observed between parasitic nematodes and free-living ones. Within the former group, animal parasites turned out to be distinctly different from plant parasites. Using small subunit of ribosomal RNA gene sequence from a wide range of nematodes, there is a possibility to compare animal-parasitic, plant-parasitic and free-living taxa. Nowadays the parasitic nematodes expressed sequence tag (EST) project is currently generating sequence information to provide a new source of data to examine the evolutionary history of this taxonomic group. PMID:16859012

  18. Classical molecular dynamics investigations of biphenyl-based carbon nanomembranes

    Directory of Open Access Journals (Sweden)

    Andreas Mrugalla

    2014-06-01

    Full Text Available Background: Free-standing carbon nanomembranes (CNM with molecular thickness and macroscopic size are fascinating objects both for fundamental reasons and for applications in nanotechnology. Although being made from simple and identical precursors their internal structure is not fully known and hard to simulate due to the large system size that is necessary to draw definite conclusions.Results: We performed large-scale classical molecular dynamics investigations of biphenyl-based carbon nanomembranes. We show that one-dimensional graphene-like stripes constitute a highly symmetric quasi one-dimensional energetically favorable ground state. This state does not cross-link. Instead cross-linked structures are formed from highly excited precursors with a sufficient amount of broken phenyls.Conclusion: The internal structure of the CNM is very likely described by a disordered metastable state which is formed in the energetic initial process of electron irradiation and depends on the process of relaxation into the sheet phase.

  19. Investigation of glassy state molecular motions in thermoset polymers

    Science.gov (United States)

    Tu, Jianwei

    This dissertation presents the investigation of the glassy state molecular motions in isomeric thermoset epoxies by means of solid-state deuterium (2H) NMR spectroscopy technique. The network structure of crosslinked epoxies was altered through monomer isomerism; specifically, diglycidyl ether of bisphenol A (DGEBA) was cured with isomeric amine curatives, i.e., the meta-substituted diaminodiphenylsulfone (33DDS) and para-substituted diaminodiphenylsulfone (44DDS). The use of structural isomerism provided a path way for altering macroscopic material properties while maintaining identical chemical composition within the crosslinked networks. The effects of structural isomerism on the glassy state molecular motions were studied using solid-state 2H NMR spectroscopy, which offers unrivaled power to monitor site-specific molecular motions. Three distinctive molecular groups on each isomeric network, i.e., the phenylene rings in the bisphenol A structure (BPA), the phenylene rings in the diaminodiphenylsulfone structure (DDS), and the hydroxypropoyl ether group (HPE) have been selectively deuterated for a comprehensive study of the structure-dynamics- property relationships in thermoset epoxies. Quadrupolar echo experiments and line shape simulations were employed as the main research approach to gain both qualitative and quantitative motional information of the epoxy networks in the glassy state. Quantitative information on the geometry and rate of the molecular motions allows the elucidation of the relationship between molecular motions and macro physical properties and the role of these motions in the mechanical relaxation. Specifically, it is revealed that both the BPA and HPE moieties in the isomeric networks have almost identical behaviors in the deep glassy state, which indicates that the molecular motions in the glassy state are localized, and the correlation length of the motions does not exceed the length of the DGEBA repeat unit. BPA ring motions contribute

  20. Turcot syndrome confirmed with molecular analysis.

    Science.gov (United States)

    Lebrun, C; Olschwang, S; Jeannin, S; Vandenbos, F; Sobol, H; Frenay, M

    2007-04-01

    Turcot syndrome is clinically characterized by the occurrence of primary brain tumor and colorectal tumor and has, in previous reports, been shown associated with germline mutations in the genes APC, MLH1, MHS6, and PMS2. To date, only few families have been documented by molecular analysis. We report two new families with Turcot syndrome to illustrate and review its characteristics and facilitate diagnosis. Molecular analysis revealed two germline mutations, one in the MLH1 gene and one in MSH2. The latter has never been describe in the literature. Personal and familial relevant anamnestic data from patients with glioma might aid in the diagnosis of genetic disorders. The subsequent molecular characterization may contribute to the appropriate care of affected patients and asymptomatic gene carriers. PMID:17389002

  1. Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

    Science.gov (United States)

    Asafi, M. S.; Yildirim, A.; Tekpinar, M.

    2016-04-01

    Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.

  2. A molecular investigation of adsorption onto mineral pigments

    Science.gov (United States)

    Ninness, Brian J.

    Pigment suspensions are important in several processes such as ceramics, paints, inks, and coatings. In the wet state, pigments are combined with a variety of chemical species such as polymers, surfactants, and polyelectrolytes which produce a complex colloidal system. The adsorption, desorption, and redistribution of these species at the pigment-aqueous solution interface can have an impact on the behavior in both the wet state or its final dried state. The goal of this work is to establish a molecular picture of the adsorption properties of these pigmented systems. A novel in situ infrared technique has been developed which allows the detection of adsorbed surface species on pigment particles in an aqueous environment. The technique involves the use of a polymeric binder to anchor the colloidal pigment particles to the surface of an internal reflection element (IRE). The binder only weakly perturbs about 25% of the reactive surface sites (hydroxyl groups) on silica. The reaction of succinic anhydride with an aminosilanized silica surface has been quantified using this technique. The adsorption dynamics of the cationic surfactant cetyltrimethylammonium bromide (C16TAB) at the TiO2-aqueous solution interface has been investigated using Fourier transform infrared-attenuated total reflection spectroscopy (FTIR-ATR) and electrokinetic analysis. At low bulk concentrations, C16TAB is shown to adsorb as isolated islands with a "defective" bilayer structure. Anionic probe molecules are shown to effectively "tune" the adsorbed surfactant microstructure. The results indicate that the structure of the adsorbed surfactant layer, and not the amount of adsorbed surfactant, dictates the subsequent adsorption behavior of the system. Atomic Layer Deposition is used to deposit a TiO2 layer onto the surfaces of silica and kaolin pigments. The process involves the cyclic reaction sequence of the vapors of TiCl4 and H2O. Three complete deposition cycles are needed before the surfaces

  3. Tumor classification: molecular analysis meets Aristotle

    International Nuclear Information System (INIS)

    Traditionally, tumors have been classified by their morphologic appearances. Unfortunately, tumors with similar histologic features often follow different clinical courses or respond differently to chemotherapy. Limitations in the clinical utility of morphology-based tumor classifications have prompted a search for a new tumor classification based on molecular analysis. Gene expression array data and proteomic data from tumor samples will provide complex data that is unobtainable from morphologic examination alone. The growing question facing cancer researchers is, 'How can we successfully integrate the molecular, morphologic and clinical characteristics of human cancer to produce a helpful tumor classification?' Current efforts to classify cancers based on molecular features ignore lessons learned from millennia of experience in biological classification. A tumor classification must include every type of tumor and must provide a unique place for each tumor within the classification. Groups within a classification inherit the properties of their ancestors and impart properties to their descendants. A classification was prepared grouping tumors according to their histogenetic development. The classification is simple (reducing the complexity of information received from the molecular analysis of tumors), comprehensive (providing a place for every tumor of man), and consistent with recent attempts to characterize tumors by cytogenetic and molecular features. The clinical and research value of this historical approach to tumor classification is discussed. This manuscript reviews tumor classification and provides a new and comprehensive classification for neoplasia that preserves traditional nomenclature while incorporating information derived from the molecular analysis of tumors. The classification is provided as an open access XML document that can be used by cancer researchers to relate tumor classes with heterogeneous experimental and clinical tumor

  4. Molecular dynamics investigation of mechanical mixing in mechanical alloying

    International Nuclear Information System (INIS)

    Molecular dynamic simulation is exploited to obtain a deep insight of atomic scale mixing and amorphization mechanisms happening during mechanical mixing. Impact-relaxation cycles are performed to simulate the mechanical alloying process. The results obtained by structural analysis shows that the final structure obtained through simulation of mechanical alloying is in an amorphous state. This analysis reveals that amorphization occurs concurrently with the attainment of a perfectly mixed alloy. The results indicate diffusion and deformation are two important mechanisms for mixing during mechanical alloying. The rate of diffusion is controlled by the temperature and by the density of defects in the structure. Deformation enhances mixing directly by sliding atomic layers on each other and increases the number of defects in the structure. The results agree with mechanical alloying experiments described in the literature

  5. Molecular dynamics investigation of mechanical mixing in mechanical alloying

    Energy Technology Data Exchange (ETDEWEB)

    Ali Nematollahi, Gh. [Department of Ceramic, Materials and Energy Research Center, Karaj, Tehran (Iran, Islamic Republic of)], E-mail: ali61gh@yahoo.com; Marzbanrad, E.; Aghaei, A.R. [Department of Ceramic, Materials and Energy Research Center, Karaj, Tehran (Iran, Islamic Republic of)

    2008-09-25

    Molecular dynamic simulation is exploited to obtain a deep insight of atomic scale mixing and amorphization mechanisms happening during mechanical mixing. Impact-relaxation cycles are performed to simulate the mechanical alloying process. The results obtained by structural analysis shows that the final structure obtained through simulation of mechanical alloying is in an amorphous state. This analysis reveals that amorphization occurs concurrently with the attainment of a perfectly mixed alloy. The results indicate diffusion and deformation are two important mechanisms for mixing during mechanical alloying. The rate of diffusion is controlled by the temperature and by the density of defects in the structure. Deformation enhances mixing directly by sliding atomic layers on each other and increases the number of defects in the structure. The results agree with mechanical alloying experiments described in the literature.

  6. Theoretical analysis of dynamic processes for interacting molecular motors

    International Nuclear Information System (INIS)

    Biological transport is supported by the collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by carrying out an analysis of a new class of totally asymmetric exclusion processes, in which interactions are accounted for in a thermodynamically consistent fashion. This allows us to explicitly connect microscopic features of motor proteins with their collective dynamic properties. A theoretical analysis that combines various mean-field calculations and computer simulations suggests that the dynamic properties of molecular motors strongly depend on the interactions, and that the correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motor transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed. (paper)

  7. Thermal and molecular investigation of laser tissue welding

    Energy Technology Data Exchange (ETDEWEB)

    Small, W., IV

    1998-06-01

    Despite the growing number of successful animal and human trials, the exact mechanisms of laser tissue welding remain unknown. Furthermore, the effects of laser heating on tissue on the molecular scale are not fully understood. To address these issues, a multi-front attack oil both extrinsic (solder/patch mediated) and intrinsic (laser only) tissue welding was launched using two-color infrared thermometry, computer modeling, weld strength assessment, biochemical assays, and vibrational spectroscopy. The coupling of experimentally measured surface temperatures with the predictive numerical simulations provided insight into the sub-surface dynamics of the laser tissue welding process. Quantification of the acute strength of the welds following the welding procedure enabled comparison among trials during an experiment, with previous experiments, and with other studies in the literature. The acute weld integrity also provided an indication of tile probability of long-term success. Molecular effects induced In the tissue by laser irradiation were investigated by measuring tile concentrations of specific collagen covalent crosslinks and characterizing the Fourier-Transform infrared (FTIR) spectra before and after the laser exposure.

  8. Molecular analysis of retinoblastoma in pediatrics

    International Nuclear Information System (INIS)

    Inactivation of RB protein produced by mutation of RB-1 gene is critical to the pathogenesis of Retinoblastoma. Since other factors besides this gene are thought to be involved in this mechanism, we performed the molecular analysis of Retinoblastoma for loss of RB-1 gene and N-myc gene amplification. Loss of RB-1 gene was found in five(56%) among nine patients with Retinoblastoma and total loss of the gene in one patient. We also found total loss of RB-1 gene in WERI cell line and a more than 100 fold amplification of N-myc in Y-79 cell line. The analysis of the relationship between molecular events and clinical characteristics such as age, sex, tumor laterality did not reveal any specific correlation. We suggest this method can be a useful tool for initially screening a large number of tumors and for genetic counseling and early detection of the tumor. (Author)

  9. Molecular dynamics investigation of tracer diffusion in a simple liquid

    International Nuclear Information System (INIS)

    Extensive Molecular-Dynamics (MD) simulations have been carried out for a model trace-solvent system made up of 100 solvent molecules and 8 tracer molecules interacting through truncated Lennard-Jones potentials. The influence of the size ratio between solute and solvent, of their mass ratio and of the solvent viscosity on the diffusivity of a small tracer were investigated. Positive deviations from a Stokes-Einstein behaviour are observed, in qualitative agreement with experimental observations. It was also observed that as tracer and solvent become increasingly dissimilar, their respective dynamics becomes decoupled. We suggest that such decouplings can be interpreted by writing their mobility of the tracer as the sum of two terms, the first one arising from a coupling between tracer dynamics and hydrodynamics modes of the solvent, and the second one describing jump motion in a locally nearly frozen environment. (author). 17 refs, 4 figs, 6 tabs

  10. Theoretical investigation of the molecular structure of the isoquercitrin molecule

    Science.gov (United States)

    Cornard, J. P.; Boudet, A. C.; Merlin, J. C.

    1999-09-01

    Isoquercitrin is a glycosilated flavonoid that has received a great deal of attention because of its numerous biological effects. We present a theoretical study on isoquercitrin using both empirical (Molecular Mechanics (MM), with MMX force field) and quantum chemical (AM1 semiempirical method) techniques. The most stable structures of the molecule obtained by MM calculations have been used as input data for the semiempirical treatment. The position and orientation of the glucose moiety with regard to the remainder of the molecule have been investigated. The flexibility of isoquercitrin principally lies in rotations around the inter-ring bond and the sugar link. In order to know the structural modifications generated by the substitution by a sugar, geometrical parameters of quercetin (aglycon) and isoquercitrin have been compared. The good accordance between theoretical and experimental electronic spectra permits to confirm the reliability of the structural model.

  11. Molecular Dynamics Investigation of Benzene in Supercritical Water

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Microscopic structure and diffusion properties of benzene in ambient water (298 K, 0.1 MPa) and super critical water (673-773 K, 25-35 MPa) are investigated by molecular dynamics simulation with site-site models. It is found that at the ambient condition, the water molecules surrounding a benzene molecule form a hydrogen bond network. The hydrogen bond interaction between supercritical water molecules decreases dramatically under supercritical conditions. The diffusion coefficients of both the solute molecule and solvent molecule at supercritical conditions increase by 30-180 times than those at the ambient condition. With the temperature approaching the critical temperature, the change of diffusion coefficient with pressure becomes pronounced.

  12. Tumor classification: molecular analysis meets Aristotle

    OpenAIRE

    Berman Jules J

    2004-01-01

    Abstract Background Traditionally, tumors have been classified by their morphologic appearances. Unfortunately, tumors with similar histologic features often follow different clinical courses or respond differently to chemotherapy. Limitations in the clinical utility of morphology-based tumor classifications have prompted a search for a new tumor classification based on molecular analysis. Gene expression array data and proteomic data from tumor samples will provide complex data that is unobt...

  13. An investigation of molecular dynamics simulation and molecular docking: interaction of citrus flavonoids and bovine β-lactoglobulin in focus.

    Science.gov (United States)

    Sahihi, M; Ghayeb, Y

    2014-08-01

    Citrus flavonoids are natural compounds with important health benefits. The study of their interaction with a transport protein, such as bovine β-lactoglobulin (BLG), at the atomic level could be a valuable factor to control their transport to biological sites. In the present study, molecular docking and molecular dynamics simulation methods were used to investigate the interaction of hesperetin, naringenin, nobiletin and tangeretin as citrus flavonoids and BLG as transport protein. The molecular docking results revealed that these flavonoids bind in the internal cavity of BLG and the BLG affinity for binding the flavonoids follows naringenin>hesperetin>tangeretin>nobiletin. The docking results also indicated that the BLG-flavonoid complexes are stabilized through hydrophobic interactions, hydrogen bond interactions and π-π stacking interactions. The analysis of molecular dynamics (MD) simulation trajectories showed that the root mean square deviation (RMSD) of various systems reaches equilibrium and fluctuates around the mean value at various times. Time evolution of the radius of gyration, total solvent accessible surface of the protein and the second structure of protein showed as well that BLG and BLG-flavonoid complexes were stable around 2500ps, and there was not any conformational change as for BLG-flavonoid complexes. Further, the profiles of atomic fluctuations indicated the rigidity of the ligand binding site during the simulation. PMID:24880994

  14. Thermal and molecular investigation of laser tissue welding

    Science.gov (United States)

    Small, Ward, IV

    Despite the growing number of successful animal and human trials, the exact mechanisms of laser tissue welding remain unknown. Furthermore, the effects of laser heating on tissue on the molecular scale are not fully understood. To address these issues, a multi-front attack on both extrinsic (solder/patch mediated) and intrinsic (laser only) tissue welding was launched using two-color infrared thermometry, computer modeling, weld strength assessment, biochemical assays, and vibrational spectroscopy. The coupling of experimentally measured surface temperatures with the predictive numerical simulations provided insight into the sub surface dynamics of the laser tissue welding process. Quantification of the acute strength of the welds following the welding procedure enabled comparison among trials during an experiment, with previous experiments, and with other studies in the literature. The acute weld integrity also provided an indication of the probability of long-term success. Molecular effects induced in the tissue by laser irradiation were investigated by measuring the concentrations of specific collagen covalent crosslinks and measuring the infrared absorption spectra before and after the laser exposure. This investigation yielded results pertaining to both the methods and mechanisms of laser tissue welding. The combination of two-color infrared thermometry to obtain accurate surface temperatures free from emissivity bias and computer modeling illustrated the importance of including evaporation in the simulations, which effectively serves as an inherent cooling mechanism during laser irradiation. Moreover, the hydration state predicted by the model was useful in assessing the role of electrostatic versus covalent bonding in the fusion. These tools also helped elicit differences between dye- enhanced liquid solders and solid-matrix patches in laser-assisted tissue welding, demonstrating the significance of repeatable energy delivery. Surprisingly, covalent bonds

  15. MOLECULAR INVESTIGATION OF GLUTARIC ACIDURIA TYPE1 IN IRAN

    Directory of Open Access Journals (Sweden)

    Massoud HOUSHMAND

    2012-03-01

    Full Text Available Glutaric Acidemia, Type I (GA I, was first described in 1975. The disease is caused by a genetic deficiency of the enzyme, Glutaryl-CoA Dehydrogenase (GCD, which leads to the buildup of Glutaric acid in the tissues and its excretion in the urine of affected patients. GCD is involved in the catabolism of the amino acids, Lysine, Hydroxylysine, and Tryptophan. Over 200 cases of GA I have been reported in the medical literature. GA I is one of the most common organic acidemias and has an estimated incidence of about 1 in 50,000 live births.Because of the initial slow progression of clinical symptoms, GA I is frequently undiagnosed until an acute metabolic crisis occurs. A total of 25 unrelated patients suspected to GA1 were investigated in our study. Genomic DNA was extracted from peripheral blood cells of the 25 probands whom were biochemically and/or clinically and/or neuro-radiologically suspected to GA1. 15 of them had elevated glutaric acid in the urine organic acid test.PCR and direct sequencing of all 11 exons and their flanking region of the GCDH gene were examined.Some of them were investigated for known mutation in the other their family members. Fifteen patients had homozygous mutations and 10 patients were normal for GCDH gene. Our Results Showed:• 60% Known mutation were found in our 15 patients• 80% can be detected by 4 exons sequencing so for molecular investigatins exon 6, 7, 8, 10 are good choice for beginning of analysis• 33% was mutation in exon 7, so because of the cost of genetic diagnosis we suggest that investigation begin with this exon.• Pro 348 Leu was most detected 20%.• 40% are new mutations wich will be investigated for phenotype Genotype Correlations.

  16. Chemical protection and sensitization to ionizing radiation:molecular investigations

    International Nuclear Information System (INIS)

    Chemical radioprotection and radiosensitization are induced by the presence of certain chemical compounds, which reduce or enhance the effect of ionizing radiation on living organisms. Such substances are either naturally present or may be artificially introduced in the living cells. Chemical radioprotectors are interesting for possible application in the health protection of both professionally exposed workers and patients treated by radiation for diagnostic and thereapeutic purposes. Interest in chemical radiosensitization has increased recently because of its potential application in the radiotherapy of tumours. Both radioprotection and radiosensitization occur by means of complicated mechanisms, which at first correspond to very fast reactions. The mechanism of the interaction between such substances and radiation-induced biological radicals has been investigated by means of pulse radiolysis and rapid mixing techniques. Examples of the application of these techniques are given to illustrate how information has been obtained on the molecular basis of radiation chemical modi-fication at the cellular level. In particular some interactions between model systems of biological interest (DNA, DNA components, enzymes, amino acids, etc.) and sulphur-containing radioprotectors (glutathione, cysteine, etc.) and/or electroaffinic radiosensitizers, are described. (H.K.)

  17. Matched molecular pair analysis in drug discovery.

    Science.gov (United States)

    Dossetter, Alexander G; Griffen, Edward J; Leach, Andrew G

    2013-08-01

    Multiple parameter optimisation in drug discovery is difficult, but Matched Molecular Pair Analysis (MMPA) can help. Computer algorithms can process data in an unbiased way to yield design rules and suggest better molecules, cutting the number of design cycles. The approach often makes more suggestions than can be processed manually and methods to deal with this are proposed. However, there is a paucity of contextually specific design rules, which would truly make the technique powerful. By combining extracted information from multiple sources there is an opportunity to solve this problem and advance medicinal chemistry in a matter of months rather than years. PMID:23557664

  18. Investigation of the Physical and Molecular Properties of Asphalt Binders Processed with Used Motor Oils

    Directory of Open Access Journals (Sweden)

    Mohyeldin Ragab

    2015-01-01

    Full Text Available In this work we investigated the performance aspects of addition of used motor oils (UMO to neat and crumb rubber modified asphalts (CRMA and related that to the change of molecular size distribution of modified asphalt’s fractions; asphaltenes, saturates, naphthene aromatics, and polar aromatics. Based on the results of temperature sweep viscoelastic tests, addition of crumb rubber modifier (CRM alone or with UMO results in the formation of internal network within the modified asphalt. Based on the results of short and long term aged asphalts, the utilization of combination of UMO and CRM enhanced the aging behavior of asphalt. Bending beam rheometer was utilized to investigate the low temperature behavior of UMO modified asphalts. Based on those tests, the utilization of the UMO and CRM enhanced the low temperature properties of asphalts. Based on the results of the asphalt separation tests and the Gel Permeation Chromatography (GPC analysis, it was found that saturates and naphthene aromatics are the two asphalt fractions that have similar molecular size fractions as those of UMO. However, UMO only shifts the molecular sizes of saturates after interaction with asphalt. Results also show that polar aromatics pose higher molecular size structures than UMO.

  19. Copromicroscopic and molecular investigations on intestinal parasites in kenneled dogs.

    Science.gov (United States)

    Simonato, Giulia; Frangipane di Regalbono, Antonio; Cassini, Rudi; Traversa, Donato; Beraldo, Paola; Tessarin, Cinzia; Pietrobelli, Mario

    2015-05-01

    Intestinal parasites are common in dogs worldwide, and their importance has recently increased for a renewed awareness on the public health relevance that some of them have. In this study, the prevalence of helminths and protozoa was evaluated by microscopy in 318 canine faecal samples collected from eight rescue shelters in the North-eastern Italy; 285 of them were also submitted to the molecular characterization of Giardia duodenalis and Cryptosporidium spp. isolates. An analysis was performed to evaluate the prevalence rates in relation to canine individual data, shelter provenance and anthelmintic treatments. Overall, 52.5% (167/318) of faecal samples were positive for at least one parasite. Trichuris vulpis showed the highest overall prevalence rate (29.2%), followed by G. duodenalis (15.1%), Toxocara canis (9.7%), ancylostomatids (8.2%) and Cystoisospora (5.7%). The prevalence of G. duodenalis, evaluated by real-time PCR, was 57.9% (165/285), and 79 isolates were characterized by nested PCR on the β-giardin gene. The assemblages found were mainly the host-specific genotypes C and D, while only one assemblage was identified as the human-specific genotype B1. Isolates of Cryptosporidium spp., recorded in 3/285 (1.1%) stool samples, were Cryptosporidium parvum based on the characterization of the Cryptosporidium oocyst wall protein (COWP) gene. Although the results describe a relatively limited risk of dog-originating zoonoses, there is the need to improve the quality of shelter practices towards better health managements for safe pet-adoption campaigns and a minimization of the environmental faecal pollution with canine intestinal parasites. PMID:25687526

  20. Synthesis, crystal structure analysis, spectral investigations, DFT computations, Biological activities and molecular docking of methyl(2E)-2-{[N-(2-formylphenyl)(4-methylbenzene) sulfonamido]methyl}-3-(4-fluorophenyl)prop-2-enoate, a potential bioactive agent

    Science.gov (United States)

    Murugavel, S.; Vetri Velan, V.; Kannan, Damodharan; Bakthadoss, Manickam

    2016-03-01

    The title compound methyl(2E)-2-{[N-(2-formylphenyl) (4-methylbenzene)sulfonamido]methyl}-3-(4-fluorophenyl) prop-2-enoate (MFMSF) has been synthesized and single crystals were grown by slow evaporation solution growth technique at room temperature. The grown crystals were characterized by FTIR, 1H NMR, 13C NMR, and single crystal X-ray diffraction. In the crystal, molecules are linked by intermolecular C-H…O hydrogen bonds forming a two-dimensional supramolecular network along [110] direction. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6-311G (d,p) basis set in ground state and compared with the experimental data. The entire vibrational assignments of wave numbers were made on the basis of potential energy distribution (PED) by VEDA 4 programme. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. In addition, NLO, MEP, Mulliken, thermodynamic properties, HOMO and LUMO energy gap were theoretically predicted. The global chemical reactivity descriptors are calculated for MFMSF and used to predict their relative stability and reactivity. The antibacterial activity of the compound was also tested against various pathogens. The molecular docking studies concede that title compound may exhibit PBP-2X inhibitor activity.

  1. Investigating Atmospheric Oxidation with Molecular Dynamics Imaging and Spectroscopy

    Science.gov (United States)

    Merrill, W. G.; Case, A. S.; Keutsch, F. N.

    2013-06-01

    Volatile organic compounds (VOCs) in the Earth's atmosphere constitute trace gas species emitted primarily from the biosphere, and are the subject of inquiry for a variety of air quality and climate studies. Reactions intiated (primarily) by the hydroxyl radical (OH) lead to a myriad of oxygenated species (OVOCs), which in turn are prone to further oxidation. Investigations of the role that VOC oxidation plays in tropospheric chemistry have brought to light two troubling scenarios: (1) VOCs are responsible in part for the production of two EPA-regulated pollutants---tropospheric ozone and organic aerosol---and (2) the mechanistic details of VOC oxidation remain convoluted and poorly understood. The latter issue hampers the implementation of near-explicit atmospheric simulations, and large discrepancies in OH reactivity exist between measurements and models at present. Such discrepancies underscore the need for a more thorough description of VOC oxidation. Time-of-flight measurements and ion-imaging techniques are viable options for resolving some of the mechanistic and energetic details of VOC oxidation. Molecular beam studies have the advantage of foregoing unwanted bimolecular reactions, allowing for the characterization of specific processes which must typically compete with the complex manifold of VOC oxidation pathways. The focus of this work is on the unimolecular channels of organic peroxy radical intermediates, which are necessarily generated during VOC oxidation. Such intermediates may isomerize and decompose into distinct chemical channels, enabling the unambiguous detection of each pathway. For instance, a (1 + 1') resonance enhanced multiphoton ionization (REMPI) scheme may be employed to detect carbon monoxide generated from a particular unimolecular process. A number of more subtle mechanistic details may be explored as well. By varying the mean free path of the peroxy radicals in a flow tube, the role of collisional quenching in these unimolecular

  2. Spectroscopic investigation (FT-IR and FT-Raman), vibrational assignments, HOMO-LUMO, NBO, MEP analysis and molecular docking study of 2-(4-hydroxyphenyl)-4,5-dimethyl-1H-imidazole 3-oxide

    Science.gov (United States)

    Benzon, K. B.; Varghese, Hema Tresa; Panicker, C. Yohannan; Pradhan, Kiran; Tiwary, Bipransh Kumar; Nanda, Ashis Kumar; Alsenoy, C. Van

    2015-07-01

    In this work, the vibrational spectral analysis was carried out using FT-IR and FT-Raman spectroscopy of 2-(4-hydroxyphenyl)-4,5-dimethyl-1H-imidazole 3-oxide. The computations were performed at DFT levels of theory to get the optimized geometry and vibrational frequencies of the normal modes of the title compound using Gaussian09 software. The complete vibrational assignments of frequencies were made on the basis of potential energy distribution. The calculated HOMO and LUMO energies show the chemical activity of the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. The hyperpolarizability values are reported and the first hyperpolarizability of the title compound is 19.61 times that of standard NLO material urea. From the MEP plot, the negative charge covers the nitro group and the positive region is over the hydroxyl group and N-H part of the imidazole ring. The calculated 1H NMR results are in good agreement with experimental data. Molecular docking study is also reported.

  3. Synchrotron based mass spectrometry to investigate the molecular properties of mineral-organic associations

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Suet Yi; Kleber, Markus; Takahashi, Lynelle K.; Nico, Peter; Keiluweit, Marco; Ahmed, Musahid

    2013-04-01

    Soil organic matter (OM) is important because its decay drives life processes in the biosphere. Analysis of organic compounds in geological systems is difficult because of their intimate association with mineral surfaces. To date there is no procedure capable of quantitatively separating organic from mineral phases without creating artifacts or mass loss. Therefore, analytical techniques that can (a) generate information about both organic and mineral phases simultaneously and (b) allow the examination of predetermined high-interest regions of the sample as opposed to conventional bulk analytical techniques are valuable. Laser Desorption Synchrotron Postionization (synchrotron-LDPI) mass spectrometry is introduced as a novel analytical tool to characterize the molecular properties of organic compounds in mineral-organic samples from terrestrial systems, and it is demonstrated that when combined with Secondary Ion Mass Spectrometry (SIMS), can provide complementary information on mineral composition. Mass spectrometry along a decomposition gradient in density fractions, verifies the consistency of our results with bulk analytical techniques. We further demonstrate that by changing laser and photoionization energies, variations in molecular stability of organic compounds associated with mineral surfaces can be determined. The combination of synchrotron-LDPI and SIMS shows that the energetic conditions involved in desorption and ionization of organic matter may be a greater determinant of mass spectral signatures than the inherent molecular structure of the organic compounds investigated. The latter has implications for molecular models of natural organic matter that are based on mass spectrometric information.

  4. Investigating Ceiling Effects in Longitudinal Data Analysis

    Science.gov (United States)

    Wang, Lijuan; Zhang, Zhiyong; McArdle, John J.; Salthouse, Timothy A.

    2008-01-01

    Score limitation at the top of a scale is commonly termed "ceiling effect." Ceiling effects can lead to serious artifactual parameter estimates in most data analysis. This study examines the consequences of ceiling effects in longitudinal data analysis and investigates several methods of dealing with ceiling effects through Monte Carlo simulations…

  5. Topological investigations of the molecular species and molecular interactions that characterize pyrrolidin-2-one + lower alkanol mixtures

    International Nuclear Information System (INIS)

    Molar excess volumes, VE, molar excess enthalpies, HE, and speeds of sound data, u, of pyrrolidin-2-one (i) + ethanol or propan-1-ol or propan-2-ol or butan-1-ol (j) binary mixtures have been determined over entire composition range at 308.15 K. The observed speeds of sound data have been utilized to predict excess isentropic compressibilities, κSE of the investigated binary mixtures. The observed excess thermodynamic properties VE, HE and κSE have been analyzed in terms of Graph theory. The analysis of VE data by the Graph theory suggests that pyrrolidin-2-one exists mainly as a mixture of cyclic and open dimer; ethanol as a mixture of dimer and trimer; butan-1-ol and propan-2-ol as mixture of monomer and dimer and propan-1-ol as a dimer in the pure state, and their mixtures contain 1:1 molecular complex. The IR studies lend additional credence to the nature and extent of interactions for the proposed molecular entities in the mixtures. Also, it has been observed that VE, HE and κSE values predicted by the Graph theory compare well to with their corresponding experimental values.

  6. Molecular forensic science analysis of nuclear materials

    Science.gov (United States)

    Reilly, Dallas David

    Concerns over the proliferation and instances of nuclear material in the environment have increased interest in the expansion of nuclear forensics analysis and attribution programs. A new related field, molecular forensic science (MFS) has helped meet this expansion by applying common scientific analyses to nuclear forensics scenarios. In this work, MFS was applied to three scenarios related to nuclear forensics analysis. In the first, uranium dioxide was synthesized and aged at four sets of static environmental conditions and studied for changes in chemical speciation. The second highlighted the importance of bulk versus particle characterizations by analyzing a heterogeneous industrially prepared sample with similar techniques. In the third, mixed uranium/plutonium hot particles were collected from the McGuire Air Force Base BOMARC Site and analyzed for chemical speciation and elemental surface composition. This work has identified new signatures and has indicated unexpected chemical behavior under various conditions. These findings have lead to an expansion of basic actinide understanding, proof of MFS as a tool for nuclear forensic science, and new areas for expansion in these fields.

  7. Molecular analysis of holoprosencephaly in South America.

    Science.gov (United States)

    Savastano, Clarice Pagani; El-Jaick, Kênia Balbi; Costa-Lima, Marcelo Aguiar; Abath, Cristina Maria Batista; Bianca, Sebastiano; Cavalcanti, Denise Pontes; Félix, Têmis Maria; Scarano, Gioacchino; Llerena, Juan Clinton; Vargas, Fernando Regla; Moreira, Miguel Ângelo Martins; Seuánez, Hector N; Castilla, Eduardo Enrique; Orioli, Iêda Maria

    2014-03-01

    Holoprosencephaly (HPE) is a spectrum of brain and facial malformations primarily reflecting genetic factors, such as chromosomal abnormalities and gene mutations. Here, we present a clinical and molecular analysis of 195 probands with HPE or microforms; approximately 72% of the patients were derived from the Latin American Collaborative Study of Congenital Malformations (ECLAMC), and 82% of the patients were newborns. Alobar HPE was the predominant brain defect in almost all facial defect categories, except for patients without oral cleft and median or lateral oral clefts. Ethmocephaly, cebocephaly, and premaxillary agenesis were primarily observed among female patients. Premaxillary agenesis occurred in six of the nine diabetic mothers. Recurrence of HPE or microform was approximately 19%. The frequency of microdeletions, detected using Multiplex Ligation-dependant Probe Amplification (MLPA) was 17% in patients with a normal karyotype. Cytogenetics or QF-PCR analyses revealed chromosomal anomalies in 27% of the probands. Mutational analyses in genes SHH, ZIC2, SIX3 and TGIF were performed in 119 patients, revealing eight mutations in SHH, two mutations in SIX3 and two mutations in ZIC2. Thus, a detailed clinical description of new HPE cases with identified genetic anomalies might establish genotypic and phenotypic correlations and contribute to the development of additional strategies for the analysis of new cases. PMID:24764759

  8. Molecular analysis of holoprosencephaly in South America

    Directory of Open Access Journals (Sweden)

    Clarice Pagani Savastano

    2014-01-01

    Full Text Available Holoprosencephaly (HPE is a spectrum of brain and facial malformations primarily reflecting genetic factors, such as chromosomal abnormalities and gene mutations. Here, we present a clinical and molecular analysis of 195 probands with HPE or microforms; approximately 72% of the patients were derived from the Latin American Collaborative Study of Congenital Malformations (ECLAMC, and 82% of the patients were newborns. Alobar HPE was the predominant brain defect in almost all facial defect categories, except for patients without oral cleft and median or lateral oral clefts. Ethmocephaly, cebocephaly, and premaxillary agenesis were primarily observed among female patients. Premaxillary agenesis occurred in six of the nine diabetic mothers. Recurrence of HPE or microform was approximately 19%. The frequency of microdeletions, detected using Multiplex Ligation-dependant Probe Amplification (MLPA was 17% in patients with a normal karyotype. Cytogenetics or QF-PCR analyses revealed chromosomal anomalies in 27% of the probands. Mutational analyses in genes SHH, ZIC2, SIX3 and TGIF were performed in 119 patients, revealing eight mutations in SHH, two mutations in SIX3 and two mutations in ZIC2. Thus, a detailed clinical description of new HPE cases with identified genetic anomalies might establish genotypic and phenotypic correlations and contribute to the development of additional strategies for the analysis of new cases.

  9. Polymer Molecular Weight Analysis by [Superscript 1]H NMR Spectroscopy

    Science.gov (United States)

    Izunobi, Josephat U.; Higginbotham, Clement L.

    2011-01-01

    The measurement and analysis of molecular weight and molecular weight distribution remain matters of fundamental importance for the characterization and physical properties of polymers. Gel permeation chromatography (GPC) is the most routinely used method for the molecular weight determination of polymers whereas matrix-assisted laser…

  10. Thermal conductivity of ZnTe investigated by molecular dynamics

    International Nuclear Information System (INIS)

    The thermal conductivity of ZnTe with zinc-blende structure has been computed by equilibrium molecular dynamics method based on Green-Kubo formalism. A Tersoff's potential is adopted in the simulation to model the atomic interactions. The calculations are performed as a function of temperature up to 800 K. The calculated thermal conductivities are in agreement with the experimental values between 150 K and 300 K, while the results above the room temperature are comparable with the Slack's equation.

  11. Investigation of nuclear multifragmentation using molecular dynamics and restructured aggregation

    International Nuclear Information System (INIS)

    We study the stability of excited 197 Au nuclei with respect to multifragmentation. For that we use a dynamical simulation based on molecular dynamics and restructured aggregation. A particular attention is paid to check the stability of the ground state nuclei generated by the simulation. Four kinds of excitations are considered: heat, compression, rotation and a geometrical instability created when a projectile drills a hole in a 197 Au nucleus

  12. Molecular-level investigation on electrochemical interfaces by Raman spectroscopy

    Institute of Scientific and Technical Information of China (English)

    TIAN, Zhong-Qun; REN, Bin

    2000-01-01

    The structure and dynamics of electrode/liquid interfaces play an increasingly important role in electrochemistry. Raman spectroscopy is capable of providing detailed structural information at molecular level and new insight into the interfacial structure, adsorption, reaction, electrocatalysis and corrosion. In this account we will summarize some progresses of surface Raman spectroscopy in the study of electrochemical interfaces, mainly based on our group's work, laying emphasis on the detection sensitivity, spectral resolution, time resolution and spatial resolution as well as the hyphenated technique.

  13. Quantitative Analysis in Multimodality Molecular Imaging

    International Nuclear Information System (INIS)

    PET offers the possibility of truly quantitative (physiological) measurements of tracer concentration in vivo. However, there are several issues limiting both visual qualitative interpretation and quantitative analysis capabilities of reconstructed PET images that must be considered in order to fully realize this potential. The major challenges to quantitative PET can be categorized in 5 classes: (i) factors related to imaging system performance and data acquisition protocols (instrumentation and measurement factors), (ii) those related to the physics of photon interaction with biologic tissues (physical factors), (iii) image reconstruction (reconstruction factors), (iv) factors related to patient motion and other physiological issues (physiological factors), and (v) Methodological factors: issues related to difficulties in developing accurate tracer kinetic models, especially at the voxel level. This paper reflects the tremendous increase in interest in quantitative molecular imaging using PET as both clinical and research imaging modality in the past decade. It offers an overview of the entire range of quantitative PET imaging from basic principles to various steps required for obtaining quantitatively accurate data from dedicated standalone PET and combined PET/CT and PET/MR systems including data collection methods and algorithms used to correct for physical degrading factors as well as image processing and analysis techniques and their clinical and research applications. Impact of physical degrading factors including attenuation of photons and contribution from photons scattered in the patient and partial volume effect on the diagnostic quality and quantitative accuracy of PET data will be discussed. Considerable advances have been made and much worthwhile research focused on the development of quantitative imaging protocols incorporating accurate data correction techniques and sophisticated image reconstruction algorithms. The fundamental concepts of

  14. Experimental investigation of molecular beam injection in HL-1 tokamak

    International Nuclear Information System (INIS)

    A new method of gas puffing is presented. The molecular beam, formed by high pressure deuterium gas through Larval nozzle and skimmer slit, is injected into the HL-1 vacuum vessel. The deuterium molecular current from the nozzle passing through the skimmer is about 3 x 1020/s. At the line average electron density of 5.2 x 1019 m-3, the beam velocity is about 100 m/s. As the plasma density and temperature increasing, the influxes of deuterium particles attenuate quickly. When the molecular beam injection (MBI) just returned to normal gas puffing, the Dα emission rapidly decreases, meanwhile, the particles move toward plasma center, the electron density is continuously peaking. The line average electron density rising lasts 45 ms. The thermal energy of plasma and confinement time for particles and energy are also increasing. the MBI is a direct and efficient gas fuelling mode, and the injected particles can reach to inside about 8 cm of plasma and q ≅ 2 confinement region. Its efficiency of injection is about 50%. After the MBI, the particle recycling coefficient R on the wall is 0.6 which is 10% lower than that of normal gas puffing

  15. Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

    Science.gov (United States)

    Mathiazhagan, S.; Anup, S.

    2016-08-01

    Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models.

  16. Molecular sieves analysis by elastic recoil detection

    International Nuclear Information System (INIS)

    The opportunity of water determination in zeolites via hydrogen detection using the elastic recoil detection analysis (ERDA) was investigated. The radiation effect upon the desorption rate of hydrogen in miscellaneous types of zeolites, e.g. Y-Faujasite, ZSM-5, SK, etc. and in a natural clay, e.g. an Algerian bentonite was discussed. Quantitative measurements were carried out in order to determine the amount and distribution shape of hydrogen in each material. Various explanations dealing with hydration and constitution water in such a crystalline framework were proposed. The experimental results are in a good agreement with the corresponding theoretical values

  17. Computational investigation of stoichiometric effects, binding site heterogeneities, and selectivities of molecularly imprinted polymers.

    Science.gov (United States)

    Terracina, Jacob J; Bergkvist, Magnus; Sharfstein, Susan T

    2016-06-01

    A series of quantum mechanical (QM) computational optimizations of molecularly imprinted polymer (MIP) systems were used to determine optimal monomer-to-target ratios. Imidazole- and xanthine-derived target molecules were studied. The investigation included both small-scale models (3-7 molecules) and larger-scale models (15-35 molecules). The optimal ratios differed between the small and larger scales. For the larger models containing multiple targets, binding-site surface area analysis was used to quantify the heterogeneity of these sites. The more fully surrounded sites had greater binding energies. No discretization of binding modes was seen, furthering arguments for continuous affinity distribution models. Molecular mechanical (MM) docking was then used to measure the selectivities of the QM-optimized binding sites. Selectivity was also shown to improve as binding sites become more fully encased by the monomers. For internal sites, docking consistently showed selectivity favoring the molecules that had been imprinted via QM geometry optimizations. The computationally imprinted sites were shown to exhibit size-, shape-, and polarity-based selectivity. Here we present a novel approach to investigate the selectivity and heterogeneity of imprinted polymer binding sites, by applying the rapid orientation screening of MM docking to the highly accurate QM-optimized geometries. Modeling schemes were designed such that no computing clusters or other specialized modeling equipment would be required. Improving the in silico analysis of MIP system properties will ultimately allow for the production of more sensitive and selective polymers. PMID:27207254

  18. Alternative Radioligands for Investigating the Molecular Pharmacology of Melatonin Receptors.

    Science.gov (United States)

    Legros, Céline; Brasseur, Chantal; Delagrange, Philippe; Ducrot, Pierre; Nosjean, Olivier; Boutin, Jean A

    2016-03-01

    Melatonin exerts a variety of physiologic activities that are mainly relayed through the melatonin receptors MT1 and MT2 Low expressions of these receptors in tissues have led to widespread experimental use of the agonist 2-[(125)I]-iodomelatonin as a substitute for melatonin. We describe three iodinated ligands: 2-(2-[(2-iodo-4,5-dimethoxyphenyl)methyl]-4,5-dimethoxy phenyl) (DIV880) and (2-iodo-N-2-[5-methoxy-2-(naphthalen-1-yl)-1H-pyrrolo[3,2-b]pyridine-3-yl])acetamide (S70254), which are specific ligands at MT2 receptors, and N-[2-(5-methoxy-1H-indol-3-yl)ethyl]iodoacetamide (SD6), an analog of 2-[(125)I]-iodomelatonin with slightly different characteristics. Here, we further characterized these new ligands with regards to their molecular pharmacology. We performed binding experiments, saturation assays, association/dissociation rate measurements, and autoradiography using sheep and rat tissues and recombinant cell lines. Our results showed that [(125)I]-S70254 is receptor, and can be used with both cells and tissue. This radioligand can be used in autoradiography. Similarly, DIV880, a partial agonist [43% of melatonin on guanosine 5'-3-O-(thio)triphosphate binding assay], selective for MT2, can be used as a tool to selectively describe the pharmacology of this receptor in tissue samples. The molecular pharmacology of both human melatonin receptors MT1 and MT2, using a series of 24 ligands at these receptors and the new radioligands, did not lead to noticeable variations in the profiles. For the first time, we described radiolabeled tools that are specific for one of the melatonin receptors (MT2). These tools are amenable to binding experiments and to autoradiography using sheep or rat tissues. These specific tools will permit better understanding of the role and implication in physiopathologic processes of the melatonin receptors. PMID:26759496

  19. Investigation of Film Curing by Dielectric Analysis.

    Science.gov (United States)

    Guma, Noemi Candelaria

    1995-01-01

    Dielectric analysis (DEA) relies on the response of molecules to a changing electric field. Permittivity (epsilon^') is a parameter obtained from DEA, which is proportional to the amount of molecular alignment (or motion). A DEA methodology was developed to evaluate and classify the degree of cure of films, and to demonstrate the mechanism of the curing phenomenon at a molecular level. The model material employed in the study was Eudragit^circler RS30D, an aqueous-based film forming polymeric material, containing 20% acetyl tributyl citrate as plasticizer. The data showed changes in the dielectric behavior of the polymer molecules in films that were subjected to accelerated stability or improper curing conditions. These dielectric changes were also manifested as changes in the permeability characteristics of the film, which ultimately influenced the final performance of the dosage form. By monitoring the dielectric behavior of the coating material during a curing cycle, a classification of three stages of curing was developed, namely undercured, optimally cured, and overcured. The changes in dielectric properties of the film reflected the changes in molecular structure, which correlated with changes in permeability and surface morphology. Based on the data, a mechanism of improper cure was proposed, which contends that the curing phenomenon is driven by two major forces, namely: the heterogenous loss and/or redistribution of plasticizer molecules during the curing process and the development of strain in the film structure during the coating process. A mathematical equation was derived to predict the epsilon^' of film-coated beads based on the epsilon^ ' data of free films cured under the same conditions. The model is based on the premise that "equal epsilon^' denotes equal mobility" for the same material, whether as free film or applied onto a substrate. The DEA technique developed and the proposed rationale of the curing phenomenon may be useful in optimizing the

  20. Investigation of the molecular relationship between breast cancer and obesity by candidate gene prioritization methods

    Directory of Open Access Journals (Sweden)

    Saba Garshasbi

    2015-10-01

    Full Text Available Background: Cancer and obesity are two major public health concerns. More than 12 million cases of cancer are reported annually. Many reports confirmed obesity as a risk factor for cancer. The molecular relationship between obesity and breast cancer has not been clear yet. The purpose of this study was to investigate priorities of effective genes in the molecular relationship between obesity and breast cancer. Methods: In this study, computer simulation method was used for prioritizing the genes that involved in the molecular links between obesity and breast cancer in laboratory of systems biology and bioinformatics (LBB, Tehran University, Tehran, Iran, from March to July 2014. In this study, ENDEAVOUR software was used for prioritizing the genes and integrating multiple data sources was used for data analysis. Training genes were selected from effective genes in obesity and/or breast cancer. Two groups of candidate genes were selected. The first group was included the existential genes in 5 common region chromosomes (between obesity and breast cancer and the second group was included the results of genes microarray data analysis of research Creighton, et al (In 2012 on patients with breast cancer. The microarray data were analyzed with GER2 software (R online software on GEO website. Finally, both training and candidate genes were entered in ENDEAVOUR software package. Results: The candidate genes were prioritized to four style and five genes in ten of the first priorities were repeated twice. In other word, the outcome of prioritizing of 72 genes (Product of microarray data analysis and genes of 5 common chromosome regions (Between obesity and breast cancer showed, 5 genes (TNFRSF10B, F2, IGFALS, NTRK3 and HSP90B1 were the priorities in the molecular connection between obesity and breast cancer. Conclusion: There are some common genes between breast cancer and obesity. So, molecular relationship is confirmed. In this study the possible effect

  1. Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods.

    Science.gov (United States)

    Gilbert, Kathleen M; Skawinski, William J; Misra, Milind; Paris, Kristina A; Naik, Neelam H; Buono, Ronald A; Deutsch, Howard M; Venanzi, Carol A

    2004-11-01

    Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte > MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the

  2. Microscopic, chemical, and molecular-biological investigation of the decayed medieval stained window glasses of two Catalonian churches

    OpenAIRE

    Piñar, Guadalupe; Garcia-Valles, Maite; Gimeno-Torrente, Domingo; Fernandez-Turiel, Jose Luis; Ettenauer, Jörg; Sterflinger, Katja

    2012-01-01

    We investigated the decayed historical church window glasses of two Catalonian churches, both under Mediterranean climate. Glass surfaces were studied by scanning electron microscopy (SEM), energy dispersive spectrometry (EDS), and X-ray diffraction (XRD). Their chemical composition was determined by wavelength-dispersive spectrometry (WDS) microprobe analysis. The biodiversity was investigated by molecular methods: DNA extraction from glass, amplification by PCR targeting the16S rRNA and ITS...

  3. Multilocus sequence analysis for Leishmania braziliensis outbreak investigation.

    Directory of Open Access Journals (Sweden)

    Mariel A Marlow

    2014-02-01

    Full Text Available With the emergence of leishmaniasis in new regions around the world, molecular epidemiological methods with adequate discriminatory power, reproducibility, high throughput and inter-laboratory comparability are needed for outbreak investigation of this complex parasitic disease. As multilocus sequence analysis (MLSA has been projected as the future gold standard technique for Leishmania species characterization, we propose a MLSA panel of six housekeeping gene loci (6pgd, mpi, icd, hsp70, mdhmt, mdhnc for investigating intraspecific genetic variation of L. (Viannia braziliensis strains and compare the resulting genetic clusters with several epidemiological factors relevant to outbreak investigation. The recent outbreak of cutaneous leishmaniasis caused by L. (V. braziliensis in the southern Brazilian state of Santa Catarina is used to demonstrate the applicability of this technique. Sequenced fragments from six genetic markers from 86 L. (V. braziliensis strains from twelve Brazilian states, including 33 strains from Santa Catarina, were used to determine clonal complexes, genetic structure, and phylogenic networks. Associations between genetic clusters and networks with epidemiological characteristics of patients were investigated. MLSA revealed epidemiological patterns among L. (V. braziliensis strains, even identifying strains from imported cases among the Santa Catarina strains that presented extensive homogeneity. Evidence presented here has demonstrated MLSA possesses adequate discriminatory power for outbreak investigation, as well as other potential uses in the molecular epidemiology of leishmaniasis.

  4. Molecular self-assembly for biological investigations and nanoscale lithography

    Science.gov (United States)

    Cheunkar, Sarawut

    Small, diffusible molecules when recognized by their binding partners, such as proteins and antibodies, trigger enzymatic activity, cell communication, and immune response. Progress in analytical methods enabling detection, characterization, and visualization of biological dynamics at the molecular level will advance our exploration of complex biological systems. In this dissertation, analytical platforms were fabricated to capture membrane-associated receptors, which are essential proteins in cell signaling pathways. The neurotransmitter serotonin and its biological precursor were immobilized on gold substrates coated with self-assembled monolayers (SAMs) of oligo(ethylene glycol)alkanethiols and their reactive derivatives. The SAM-coated substrates present the biologically selective affinity of immobilized molecules to target native membrane-associated receptors. These substrates were also tested for biospecificity using antibodies. In addition, small-molecule-functionalized platforms, expressing neurotransmitter pharmacophores, were employed to examine kinetic interactions between G-protein-coupled receptors and their associated neurotransmitters. The binding interactions were monitored using a quartz crystal microbalance equipped with liquid-flow injection. The interaction kinetics of G-protein-coupled serotonin 1A receptor and 5-hydroxytyptophan-functionalized surfaces were studied in a real-time, label-free environment. Key binding parameters, such as equilibrium dissociation constants, binding rate constants, and dissociative half-life, were extracted. These parameters are critical for understanding and comparing biomolecular interactions in modern biomedical research. By integrating self-assembly, surface functionalization, and nanofabrication, small-molecule microarrays were created for high-throughput screening. A hybrid soft-lithography, called microcontact insertion printing, was used to pattern small molecules at the dilute scales necessary for highly

  5. Molecular and immunodiagnostic investigations on bovine neosporosis in Switzerland.

    Science.gov (United States)

    Gottstein, B; Hentrich, B; Wyss, R; Thür, B; Busato, A; Stärk, K D; Müller, N

    1998-04-01

    Neospora caninum has gained considerable attention through its role in the aetiology of bovine abortion. Due to its close phylogenetic relationship with Toxoplasma gondii, respective unequivocal differential diagnosis deserves special consideration. In order to evaluate the diagnostic performance of molecular and immunodiagnostic techniques and to provide insights into the epidemiological significance of bovine neosporosis in Switzerland, we conducted a study on 83 cases of bovine abortion: of these, 24 (29%) foetal brains were positive by Neospora-PCR, six of these foetuses were simultaneously seropositive in Neospora-IFAT and/or somatic antigen-ELISA. Conversely, four (5%) foetal brains were considered positive by Toxoplasma-PCR, two of which were also seropositive in the Toxoplasma-P30-ELISA and/or direct agglutination test. The seroprevalence in 1689 cattle sera obtained from 113 diary farms was 11.5% (95% confidence interval: 9.2-13.8) by Neospora-somatic antigen-ELISA were and 10.7% (95% confidence interval: 8.3-12.6) by Toxoplasma-P30-ELISA. From the same samples, 1.1%, less than statistically expected, were positive in both ELISA. Within selected groups of cow-calf farms, the seroprevalence determined using the Neospora-somatic antigen-ELISA was 14% (95% confidence interval 5.0-23.0) for dams and 15% (95% confidence interval: 3.0-28.0) for offspring calves. Seroprevalences determined by Toxoplasma-P30-ELISA were 8% (95% confidence interval: 4.0-12.0) for dams and 3% (95% confidence interval: 0.3-6.0) for calves. None of the sera gave a positive reaction in both ELISA. Our data indicated that prenatal neosporosis appears as an important cause of bovine abortion in Switzerland. PMID:9602392

  6. Diffusometry and relaxometry : complementary approaches to investigate probe molecular mobility

    OpenAIRE

    Salami, S; Rondeau Mouro, C.; Van Duyhoven, J.; Mariette, F.

    2012-01-01

    Since several years, Pulsed-Field Gradient (PFG)-NMR diffusometry and NMR relaxometry have been used as non-invasive, selective techniques to investigate structures of porous materials through the measurement of displacements of molecules in porous systems. In this work, we used these techniques to study the diffusion and relaxation of different probe structures (dendrimers “spherical and non-flexible” and polyethyleneglycols (PEGs) “linear chain and flexible”) in susp...

  7. Investigation of small molecular weight poly(acrylic acid) adsorption on γ-alumina

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Lei; Luo, Shi-Zhong [College of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065 (China); Wang, Bin, E-mail: bin_wang@scu.edu.cn [College of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065 (China); Guo, ZhanHu [Chemical and Biomolecular Engineering Department, University of Tennessee, Knoxville, TN 37996 (United States)

    2015-08-01

    Highlights: • Small molecular weight poly(acrylic acid) incorporated on γ-alumina. • PAA adsorbed primarily on outer surface of alumina at low pH. • PAA infiltrated inside alumina pore at high pH. • Polymer chain reptation motion during the infiltration. - Abstract: The interactions between poly(acrylic acid) (PAA) and alumina have been widely investigated. In this study, the pattern of small molecular weight PAA (M{sub W} 3000) interaction with γ-alumina has been dissected. The alumina/PAA hybrids were prepared at pH 4.0, 5.5, and 7.0, respectively. Nitrogen absorption–desorption analysis, Fourier transform infrared spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy, scanning electron microscopy, and elemental analysis were conducted to illustrate the characteristics of the hybrids. At pH 4.0, the coiled PAA conformation yielded polymer adsorption primarily on alumina outer surface. At higher pH values, the more stretched PAA molecules were able to infiltrate inside the alumina pores. The phenomenon is explained by the polymer chain reptation motion model. Coiled polymer chains are not oriented enough to penetrate the oxide pore channels. In contrary, stretched polymer chains are more likely to move along the pore channels.

  8. Investigation of small molecular weight poly(acrylic acid) adsorption on γ-alumina

    International Nuclear Information System (INIS)

    Highlights: • Small molecular weight poly(acrylic acid) incorporated on γ-alumina. • PAA adsorbed primarily on outer surface of alumina at low pH. • PAA infiltrated inside alumina pore at high pH. • Polymer chain reptation motion during the infiltration. - Abstract: The interactions between poly(acrylic acid) (PAA) and alumina have been widely investigated. In this study, the pattern of small molecular weight PAA (MW 3000) interaction with γ-alumina has been dissected. The alumina/PAA hybrids were prepared at pH 4.0, 5.5, and 7.0, respectively. Nitrogen absorption–desorption analysis, Fourier transform infrared spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy, scanning electron microscopy, and elemental analysis were conducted to illustrate the characteristics of the hybrids. At pH 4.0, the coiled PAA conformation yielded polymer adsorption primarily on alumina outer surface. At higher pH values, the more stretched PAA molecules were able to infiltrate inside the alumina pores. The phenomenon is explained by the polymer chain reptation motion model. Coiled polymer chains are not oriented enough to penetrate the oxide pore channels. In contrary, stretched polymer chains are more likely to move along the pore channels

  9. Investigations on Accurate Analysis of Microstrip Reflectarrays

    DEFF Research Database (Denmark)

    Zhou, Min; Sørensen, S. B.; Kim, Oleksiy S.;

    2011-01-01

    An investigation on accurate analysis of microstrip reflectarrays is presented. Sources of error in reflectarray analysis are examined and solutions to these issues are proposed. The focus is on two sources of error, namely the determination of the equivalent currents to calculate the radiation...... pattern, and the inaccurate mutual coupling between array elements due to the lack of periodicity. To serve as reference, two offset reflectarray antennas have been designed, manufactured and measured at the DTUESA Spherical Near-Field Antenna Test Facility. Comparisons of simulated and measured data are...

  10. Cloning Yeast Actin cDNA Leads to an Investigative Approach for the Molecular Biology Laboratory

    Science.gov (United States)

    Black, Michael W.; Tuan, Alice; Jonasson, Erin

    2008-01-01

    The emergence of molecular tools in multiple disciplines has elevated the importance of undergraduate laboratory courses that train students in molecular biology techniques. Although it would also be desirable to provide students with opportunities to apply these techniques in an investigative manner, this is generally not possible in the…

  11. Investigating Actinide Molecular Adducts From Absorption Edge Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Den Auwer, C.; Conradson, S.D.; Guilbaud, P.; Moisy, P.; Mustre de Leon, J.; Simoni, E.; /SLAC, SSRL

    2006-10-27

    Although Absorption Edge Spectroscopy has been widely applied to the speciation of actinide elements, specifically at the L{sub III} edge, understanding and interpretation of actinide edge spectra are not complete. In that sense, semi-quantitative analysis is scarce. In this paper, different aspects of edge simulation are presented, including semi-quantitative approaches. Comparison is made between various actinyl (U, Np) aquo or hydroxy compounds. An excursion into transition metal osmium chemistry allows us to compare the structurally related osmyl and uranyl hydroxides. The edge shape and characteristic features are discussed within the multiple scattering picture and the role of the first coordination sphere as well as contributions from the water solvent are described.

  12. Molecular analysis of transplant rejection: marching onward

    OpenAIRE

    Lakkis, Fadi G.; Billiar, Timothy R.

    2013-01-01

    Transcriptional profiling of organ transplants is increasingly defining the biological pathways responsible for graft rejection at the molecular level and identifying gene transcripts that diagnose or predict rejection. These advances hold significant promise for the treatment of organ rejection and for improving clinical outcomes after transplantation, but hurdles remain.

  13. Molecular analysis of transplant rejection: marching onward

    Science.gov (United States)

    Lakkis, Fadi G.

    2013-01-01

    Transcriptional profiling of organ transplants is increasingly defining the biological pathways responsible for graft rejection at the molecular level and identifying gene transcripts that diagnose or predict rejection. These advances hold significant promise for the treatment of organ rejection and for improving clinical outcomes after transplantation, but hurdles remain. PMID:24145950

  14. Statistical Analysis of Hominoid Molecular Evolution

    OpenAIRE

    Barry, Daniel; Hartigan, J. A.

    1987-01-01

    The core data of molecular biology consists of DNA sequences. We will show how DNA sequences may be used to infer the evolution of the primates, human, chimpanzee, ape, orangutan and gibbon. The underlying probability models are taken to be Markov processes on trees. Some dependencies along the sequence due to the genetic code are also considered.

  15. Efficient algorithms for molecular sequence analysis.

    OpenAIRE

    Karlin, S.; Morris, M.; Ghandour, G; Leung, M Y

    1988-01-01

    Efficient (linear time) algorithms are described for identifying global molecular sequence features allowing for errors including repeats, matches between sequences, dyad symmetry pairings, and other sequence patterns. A multiple sequence alignment algorithm is also described. Specific applications are given to hepatitis B viruses and the J5-C (J, joining; C, constant) region of the immunoglobulin kappa gene.

  16. Psychometric precision in phenotype definition is a useful step in molecular genetic investigation of psychiatric disorders.

    Science.gov (United States)

    Xu, M K; Gaysina, D; Barnett, J H; Scoriels, L; van de Lagemaat, L N; Wong, A; Richards, M; Croudace, T J; Jones, P B

    2015-01-01

    Affective disorders are highly heritable, but few genetic risk variants have been consistently replicated in molecular genetic association studies. The common method of defining psychiatric phenotypes in molecular genetic research is either a summation of symptom scores or binary threshold score representing the risk of diagnosis. Psychometric latent variable methods can improve the precision of psychiatric phenotypes, especially when the data structure is not straightforward. Using data from the British 1946 birth cohort, we compared summary scores with psychometric modeling based on the General Health Questionnaire (GHQ-28) scale for affective symptoms in an association analysis of 27 candidate genes (249 single-nucleotide polymorphisms (SNPs)). The psychometric method utilized a bi-factor model that partitioned the phenotype variances into five orthogonal latent variable factors, in accordance with the multidimensional data structure of the GHQ-28 involving somatic, social, anxiety and depression domains. Results showed that, compared with the summation approach, the affective symptoms defined by the bi-factor psychometric model had a higher number of associated SNPs of larger effect sizes. These results suggest that psychometrically defined mental health phenotypes can reflect the dimensions of complex phenotypes better than summation scores, and therefore offer a useful approach in genetic association investigations. PMID:26125156

  17. Normal Mode Analysis with Molecular Geometry Restraints: Bridging Molecular Mechanics and Elastic Models

    OpenAIRE

    Lu, Mingyang; Ma, Jianpeng

    2011-01-01

    A new method for normal mode analysis is reported for all-atom structures using molecular geometry restraints (MGR). Similar to common molecular mechanics force fields, the MGR potential contains short- and long-range terms. The short-range terms are defined by molecular geometry, i.e. bond lengths, angles and dihedrals; the long-range term is similar to that in elastic network models. Each interaction term uses a single force constant parameter, and is determined by fitting against a set of ...

  18. Molecular analysis of Ku redox regulation

    Directory of Open Access Journals (Sweden)

    Shatilla Andrea

    2009-08-01

    Full Text Available Abstract Background DNA double-strand breaks (DSBs can occur in response to ionizing radiation (IR, radiomimetic agents and from endogenous DNA-damaging reactive oxygen metabolites. Unrepaired or improperly repaired DSBs are potentially the most lethal form of DNA damage and can result in chromosomal translocations and contribute to the development of cancer. The principal mechanism for the repair of DSBs in humans is non-homologous end-joining (NHEJ. Ku is a key member of the NHEJ pathway and plays an important role in the recognition step when it binds to free DNA termini. Ku then stimulates the assembly and activation of other NHEJ components. DNA binding of Ku is regulated by redox conditions and evidence from our laboratory has demonstrated that Ku undergoes structural changes when oxidized that results in a reduction in DNA binding activity. The C-terminal domain and cysteine 493 of Ku80 were investigated for their contribution to redox regulation of Ku. Results We effectively removed the C-terminal domain of Ku80 generating a truncation mutant and co-expressed this variant with wild type Ku70 in an insect cell system to create a Ku70/80ΔC heterodimer. We also generated two single amino acid variants of Cys493, replacing this amino acid with either an alanine (C493A or a serine (C493S, and over-expressed the variant proteins in SF9 insect cells in complex with wild type Ku70. Neither the truncation nor the amino acid substitutions alters protein expression or stability as determined by SDS-PAGE and Western blot analysis. We show that the C493 mutations do not alter the ability of Ku to bind duplex DNA in vitro under reduced conditions while truncation of the Ku80 C-terminus slightly reduced DNA binding affinity. Diamide oxidation of cysteines was shown to inhibit DNA binding similarly for both the wild-type and all variant proteins. Interestingly, differential DNA binding activity following re-reduction was observed for the Ku70/80

  19. Dynamical analysis of highly excited molecular spectra

    Energy Technology Data Exchange (ETDEWEB)

    Kellman, M.E. [Univ. of Oregon, Eugene (United States)

    1993-12-01

    The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.

  20. A nanostructural investigation of glassy gelatin oligomers: molecular organization and interactions with low molecular weight diluents

    International Nuclear Information System (INIS)

    The effects of low molecular weight diluents (namely water and glycerol) on the nanostructure and thermodynamic state of low water content gelatin matrices are explored systematically by combining positron annihilation lifetime spectroscopy (PALS) with calorimetric measurements. Bovine gelatin matrices with a variation in the glycerol content (0-10 wt.%) are equilibrated in a range of water activities (aw = 0.11-0.68, T = 298 K). Both water and glycerol reduce the glass transition temperature, Tg, and the temperature of dissociation of the ordered triple helical segments, Tm, while having no significant effect on the level of re-naturation of the gelatin matrices. Our PALS measurements show that over the concentration range studied, glycerol acts as a packing enhancer and in the glassy state it causes a nonlinear decrease in the average hole size, vh, of the gelatin matrices. Finally, we report complex changes in vh for the gelatin matrices as a function of the increasing level of hydration. At low water contents (Qw ∼ 0.01-0.10), water acts as a plasticizer, causing a systematic increase in vh. Conversely, for water contents higher than Qw ∼ 0.10, vh is found to decrease, as small clusters of water begin to form between the polypeptide chains. (paper)

  1. Continuous enrichment culture and molecular monitoring to investigate the microbial diversity of thermophiles inhabiting deep-sea hydrothermal ecosystems

    OpenAIRE

    POSTEC, Anne; Urios, Laurent; Lesongeur, Francoise; Ollivier, Bernard; Querellou, Joel; Godfroy, Anne

    2005-01-01

    The microflora developing during a continuous enrichment culture from a hydrothermal chimney sample was investigated by molecular methods. The culture was performed in a gas-lift bioreactor under anaerobic conditions, at 90 degrees C and pH 6.5, on a complex medium containing sulfur as the terminal electron acceptor. Archaeal and bacterial diversity was studied. Microorganisms affiliated with the genera Pyrococcus, Marinitoga, and Bacillus were detected through DGGE analysis of 16S rDNA. Addi...

  2. Molecular dynamics analysis on impact behavior of carbon nanotubes

    International Nuclear Information System (INIS)

    Graphical abstract: - Highlights: • We present an analytical solution of impact based on two degree of freedom model. • The accuracy is verified by Molecular dynamics simulations. • The effects of the small-size effects on the dynamic deflections are investigated. • The relative motion is also accounted that is due to local indentation. - Abstract: Dynamic analysis of impact of a nanoparticle on carbon nanotubes is investigated based on two degree of freedom model. The accuracy and stability of the present methods are verified by molecular dynamics (MD) simulations. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (length/diameter). Besides, the influences of velocity of impactor on the dynamic deflections are studied. It is shown that the dynamic behavior on the armchair and zigzag single-walled carbon nanotubes are almost similar. Finally, by making use of the above MD simulation and theoretical results some insight has been obtained about the dynamic characteristics of the impact problems of nanobeam structures. Nonlocal Timoshenko beam models TBT2 should be employed for an accurate prediction of the dynamic deflection rather than nonlocal Euler–Bernoulli beam models EBT2 which ignores the effects of transverse shear deformation and rotary inertia that is especially significant for short beams. The results from nonlocal EBT2 and TBT2 models demonstrated good agreement with MD simulation. The EBT2 and TBT2 models also account for the relative motion between the nanoparticle and the nanobeam that is due to local indentation as can be seen in MD simulation

  3. Molecular dynamics analysis on impact behavior of carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Seifoori, Sajjad, E-mail: sajjad.seifoori@vru.ac.ir

    2015-01-30

    Graphical abstract: - Highlights: • We present an analytical solution of impact based on two degree of freedom model. • The accuracy is verified by Molecular dynamics simulations. • The effects of the small-size effects on the dynamic deflections are investigated. • The relative motion is also accounted that is due to local indentation. - Abstract: Dynamic analysis of impact of a nanoparticle on carbon nanotubes is investigated based on two degree of freedom model. The accuracy and stability of the present methods are verified by molecular dynamics (MD) simulations. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (length/diameter). Besides, the influences of velocity of impactor on the dynamic deflections are studied. It is shown that the dynamic behavior on the armchair and zigzag single-walled carbon nanotubes are almost similar. Finally, by making use of the above MD simulation and theoretical results some insight has been obtained about the dynamic characteristics of the impact problems of nanobeam structures. Nonlocal Timoshenko beam models TBT2 should be employed for an accurate prediction of the dynamic deflection rather than nonlocal Euler–Bernoulli beam models EBT2 which ignores the effects of transverse shear deformation and rotary inertia that is especially significant for short beams. The results from nonlocal EBT2 and TBT2 models demonstrated good agreement with MD simulation. The EBT2 and TBT2 models also account for the relative motion between the nanoparticle and the nanobeam that is due to local indentation as can be seen in MD simulation.

  4. Molecular and genetics approaches for investigation of phospholipase D role in plant cells

    Directory of Open Access Journals (Sweden)

    Volotovsky I. D.

    2010-04-01

    Full Text Available The review is devoted to the analysis of publications ñoncerning the role of phospholipase D (PLD in regulation of metabolism in plant cells. Analysis of molecular and genetic studies suggest that PLD is an important component of various hormonal and stress signaling pathways

  5. Onboard functional and molecular imaging: A design investigation for robotic multipinhole SPECT

    OpenAIRE

    Bowsher, James; Yan, Susu; Roper, Justin; Giles, William; Yin, Fang-Fang

    2013-01-01

    Purpose: Onboard imaging—currently performed primarily by x-ray transmission modalities—is essential in modern radiation therapy. As radiation therapy moves toward personalized medicine, molecular imaging, which views individual gene expression, may also be important onboard. Nuclear medicine methods, such as single photon emission computed tomography (SPECT), are premier modalities for molecular imaging. The purpose of this study is to investigate a robotic multipinhole approach to onboard S...

  6. Molecular analysis of the oral microbiota of dental diseases

    OpenAIRE

    Kanasi, Eleni

    2008-01-01

    Traditionally, bacterial culture has been used for bacterial detection, allowing study of living microorganisms. Molecular methods are rapid and allow simultaneous identification of numerous species and uncultivated phylotypes. The objective of this doctoral thesis was to investigate the role of the oral microbiota, including poorly characterized and uncultivated bacteria, in dental caries and periodontitis, by comprehensive molecular, clinical, and statistical methods. The microbiota of 275 ...

  7. Cytogenetic and Molecular Investigation in Children with Possible Fragile X Syndrome

    Directory of Open Access Journals (Sweden)

    Onur Ozer

    2012-04-01

    Full Text Available Objective: Fragile X syndrome (FXS is the most common cause of inherited mental retardation and is due to a mutation in the X-linked FMR1 gene. Molecular genetic testing and chromosome analysis are indicated for this disorder. In this context, we tried to determine the frequency of the FXS, and other chro¬mosomal abnormalities of Turkish pediatric neurology outpatients. Materials and Methods: Cytogenetic and molecular screenings were performed to esti-mate the prevalence of the fragile X in 107 patients with mental retardation, language disorders, hyperactivity, develop¬mental delay or fragile X syndrome phenotype. Only 26 out of 107 patients were screened, molecularly. Results: Cytogenetically fragile X-positive cells was found in 8 cases (7.5% of 107 patients; in 4.7% of males and in 2.8% of females. The autosomal fragile sites (FS was found in 14 (13.1% cases. One (0.9% patient had pericentric inversion of chromosome 9. Molecular analysis were performed for 26 patients and all patients showed normal CGG expansion. Conclusion: In diagnosis of fragile X syndrome, chromosome analysis must be run in conjunction with the molecular studies. It is recommended that all members of the fragile X family under risk should be screened both by cytogenetic and molecular methods. Genetic counseling can be useful to patients and families considering genetic testing. [Cukurova Med J 2012; 37(2.000: 76-83

  8. Investigation of the structure of levan polysaccharide chains in water via molecular dynamics simulations

    Science.gov (United States)

    Turgut, Deniz; Coskunkan, Binnaz; Cem, Gulcin; Rende, Deniz; Arga, K. Yalcin; Bucak, Seyda; Baysal, Nihat; Toksoy-Oner, Ebru; Ozisik, Rahmi

    2014-03-01

    Levan is a biopolymer consisting of β-D-fructofuranose units with β (2-6) linkages between fructose rings. Investigation of the structure and behavior of levan in aqeous environments is necessary to understand its biological activity and its potential use in various applications such as carbohydrate-derived drug release. The use of different in vivo and in vitro bioactivity assays fail to relate the chemical structure and conformation to the observed biological activity. Therefore, considerable research has been directed on elucidating the biological activity mechanisms of polysaccharides by structure-function analysis. To overcome the inherent difficulties of experiments, molecular dynamics (MD) simulations have been used to retrieve comprehensive information regarding the conformations of polysaccharides and their dynamic properties. In the current study, the structure of levan is investigated in aqueous medium and in saline solutions via fully atomistic MD simulations at 298 and 310 K, representing room temperature and physiological temperatures, respectively. The material is partially based upon work supported by NSF under Grant Nos. 1200270 and 1003574, and TUBITAK 111M232 and 113M265.

  9. Interactive analysis of systems biology molecular expression data

    Directory of Open Access Journals (Sweden)

    Prabhakar Sunil

    2008-02-01

    Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

  10. Molecular investigation of zoonotic genotypes of Giardia intestinalis isolates in humans, dogs and cats, sheep, goats and cattle in Araçatuba (São Paulo State, Brazil) by the analysis of ß-giardin gene fragments

    OpenAIRE

    Elenir Alves Macedo de Godoy; Juares Elias Santos Junior; Marcus Vinícius Teresa Belloto; Marcus Vinícius Proença de Moraes; Gustavo Capatti Cassiano; Aline Cardoso Caseca Volotão; Maria Cecília Rui Luvizotto; Claudia Márcia Aparecida Carareto; Mônica Cristina de Moraes Silva; Ricardo Luiz Dantas Machado

    2013-01-01

    In the period from July 2009 to October 2010, fecal samples from 61 animals and 154 humans from the municipality of Aracatuba (São Paulo State, Brazil) were studied. Fecal samples from animals were collected in the Municipal Animal Shelter and the Veterinary Hospital of the Universidade Estadual Paulista. Human fecal specimens were collected in playschools in the outskirts of the city by the private network of clinical analysis laboratories of the municipal. Diagnosis was done by optical mic...

  11. Processing of Microdissected Tissue for Molecular Analysis

    OpenAIRE

    sprotocols

    2014-01-01

    Author: National Cancer Institute These methods were successful in our lab using prostate tissue and for our specific objectives. Investigators must be aware that they will need to tailor the following protocol for their own research objectives and tissue under study. **More than 10,000 Cells** If the amount of microdissected material is substantial (>10,000 cells) then any of the standard procedures for isolating DNA are acceptable. **Less than 10,000 Cells** If the n...

  12. Inhibition of acetylcholinesterase by two genistein derivatives: kinetic analysis, molecular docking and molecular dynamics simulation.

    Science.gov (United States)

    Fang, Jiansong; Wu, Ping; Yang, Ranyao; Gao, Li; Li, Chao; Wang, Dongmei; Wu, Song; Liu, Ai-Lin; Du, Guan-Hua

    2014-12-01

    In this study two genistein derivatives (G1 and G2) are reported as inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE), and differences in the inhibition of AChE are described. Although they differ in structure by a single methyl group, the inhibitory effect of G1 (IC50=264 nmol/L) on AChE was 80 times stronger than that of G2 (IC50=21,210 nmol/L). Enzyme-kinetic analysis, molecular docking and molecular dynamics (MD) simulations were conducted to better understand the molecular basis for this difference. The results obtained by kinetic analysis demonstrated that G1 can interact with both the catalytic active site and peripheral anionic site of AChE. The predicted binding free energies of two complexes calculated by the molecular mechanics/generalized born surface area (MM/GBSA) method were consistent with the experimental data. The analysis of the individual energy terms suggested that a difference between the net electrostatic contributions (ΔE ele+ΔG GB) was responsible for the binding affinities of these two inhibitors. Additionally, analysis of the molecular mechanics and MM/GBSA free energy decomposition revealed that the difference between G1 and G2 originated from interactions with Tyr124, Glu292, Val294 and Phe338 of AChE. In conclusion, the results reveal significant differences at the molecular level in the mechanism of inhibition of AChE by these structurally related compounds. PMID:26579414

  13. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

    Science.gov (United States)

    Carnevale, V.; Raugei, S.

    2009-12-01

    Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

  14. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

    International Nuclear Information System (INIS)

    Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

  15. Molecular genetic analysis of human alcohol dehydrogenase

    OpenAIRE

    Duester, G; Wesley Hatfield, G.; Smith, M.

    1985-01-01

    Human alcohol dehydrogenase (ADH) consists of a complex group of isozymes encoded by at least five non-identical genes, two of which have previously been shown through enzymatic analysis to possess polymorphic variants. Using a cDNA probe the ADH2gene encoding the β subunit of human ADH was mapped to human chromosome 4. The cDNA probe for ADH2 was also used to detect a restriction fragment length polymorphism present in human populations. This polymorphism may help establish whether certain A...

  16. Molecular analysis of phylogenetic relationships among Myrmecophytic macaranga species (Euphorbiaceae).

    Science.gov (United States)

    Blattner, F R; Weising, K; Bänfer, G; Maschwitz, U; Fiala, B

    2001-06-01

    Many species of the paleotropical pioneer tree genus Macaranga Thou. (Euphorbiaceae) live in association with ants. Various types of mutualistic interactions exist, ranging from the attraction of unspecific ant visitors to obligate myrmecophytism. In the latter, nesting space and food bodies are exchanged for protection by highly specific ant partners (mainly species of the myrmicine genus Crematogaster). As a first step toward elucidating the coevolution of ant-plant interactions in the Macaranga-Crematogaster system, we have initiated a molecular investigation of the plant partners' phylogeny. Nuclear ribosomal DNA internal transcribed spacer (ITS) sequences were analyzed for 73 accessions from 47 Macaranga species, representing 17 sections or informally described species groups. Three accessions from the putative sister taxon Mallotus Lour, were included as outgroups. Cladograms of the ITS data revealed Macaranga to be nested within Mallotus. ITS sequences are highly similar within section Pachystemon s.str., suggesting a relatively recent and rapid radiation of obligate myrmecophytes within this section. Forty-three accessions, mainly of ant-inhabited species, were additionally investigated by random amplified polymorphic DNA (RAPD) and microsatellite-primed PCR (MP-PCR) techniques. Phenetic analysis of RAPD and MP-PCR banding profiles generally confirmed the ITS results. Best resolutions for individual clades were obtained when ITS and RAPD/MP-PCR data were combined into a single matrix and analyzed phenetically. The combined analysis suggests multiple (four) rather than a single evolutionary origin of myrmecophytism, at least one reversal from obligate myrmecophytism to nonmyrmecophytism, and one loss of mutualistic specifity. PMID:11399144

  17. Molecular Eigensolution Symmetry Analysis and Fine Structure

    Directory of Open Access Journals (Sweden)

    William G. Harter

    2013-01-01

    Full Text Available Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES. Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES used in Born-Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v, then applied to families of Oh clusters in SF6 spectra and to extreme clusters.

  18. Molecular-dynamics analysis of the diffusion of molecular hydrogen in all-silica sodalite

    OpenAIRE

    Van den Berg, A.W.C.; Bromley, S.T.; Flikkema, E.; Wojdel, J.; Maschmeyer, T; Jansen, J C

    2004-01-01

    In order to investigate the technical feasibility of crystalline porous silicates as hydrogen storage materials, the self-diffusion of molecular hydrogen in all-silica sodalite is modeled using large-scale classical molecular-dynamics simulations employing full lattice flexibility. In the temperature range of 700–1200 K, the diffusion coefficient is found to range from 1.6⋅10−10 to 1.8⋅10−9 m2/s. The energy barrier for hydrogen diffusion is determined from the simulations allowing the applica...

  19. Molecular investigation of zoonotic genotypes of Giardia intestinalis isolates in humans, dogs and cats, sheep, goats and cattle in Araçatuba (São Paulo State, Brazil by the analysis of ß-giardin gene fragments

    Directory of Open Access Journals (Sweden)

    Elenir Alves Macedo de Godoy

    2013-10-01

    Full Text Available In the period from July 2009 to October 2010, fecal samples from 61 animals and 154 humans from the municipality of Aracatuba (São Paulo State, Brazil were studied. Fecal samples from animals were collected in the Municipal Animal Shelter and the Veterinary Hospital of the Universidade Estadual Paulista. Human fecal specimens were collected in playschools in the outskirts of the city by the private network of clinical analysis laboratories of the municipal. Diagnosis was done by optical microscopy using the Faust and Hoffmann, Pons and Janer techniques. The genotypes of Giardia intestinalis were characterized by PCR-RFLP and confirmed by sequencing the ß-giardin gene. Human specimens were positive in 25.3% (39/154 of the cases with 26.8% (36/134 of the specimens from children and 15% (3/20 from adults being positive. The frequency of G. intestinalis among the animals was 23.0% (14/61. A total of 32 isolates of G. intestinalis obtained from human feces and six from dogs and cats were characteristic of the A genotype (AI and AII/AIII. The results of this study in respect to frequency of giardiasis are similar to reported in most studies in Brazil. The prevalence observed in animal populations conforms to worldwide infection rates. G. intestinalis genotypes considered zoonotic were detected in both pets and humans from the city of Aractuba, suggesting a possible zoonotic transmission of the parasite in the northwestern region of São Paulo State. The absence of these genotypes in farm animals may imply that they are not involved in the chain of transmission to humans in this region.

  20. Protein analysis based on molecular beacon probes and biofunctionalized nanoparticles

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    With the completion of the human genome-sequencing project, there has been a resulting change in the focus of studies from genomics to proteomics. By utilizing the inherent advantages of molecular beacon probes and biofunctionalized nanoparticles, a series of novel principles, methods and techniques have been exploited for bioanalytical and biomedical studies. This review mainly discusses the applications of molecular beacon probes and biofunctionalized nanoparticles-based technologies for realtime, in-situ, highly sensitive and highly selective protein analysis, including the nonspecific or specific protein detection and separation, protein/DNA interaction studies, cell surface protein recognition, and antigen-antibody binding process-based bacteria assays. The introduction of molecular beacon probes and biofunctionalized nanoparticles into the protein analysis area would necessarily advance the proteomics research.

  1. Molecular analysis of deep subsurface bacteria

    International Nuclear Information System (INIS)

    Deep sediments samples from site C10a, in Appleton, and sites, P24, P28, and P29, at the Savannah River Site (SRS), near Aiken, South Carolina were studied to determine their microbial community composition, DNA homology and mol %G+C. Different geological formations with great variability in hydrogeological parameters were found across the depth profile. Phenotypic identification of deep subsurface bacteria underestimated the bacterial diversity at the three SRS sites, since bacteria with the same phenotype have different DNA composition and less than 70% DNA homology. Total DNA hybridization and mol %G+C analysis of deep sediment bacterial isolates suggested that each formation is comprised of different microbial communities. Depositional environment was more important than site and geological formation on the DNA relatedness between deep subsurface bacteria, since more 70% of bacteria with 20% or more of DNA homology came from the same depositional environments. Based on phenotypic and genotypic tests Pseudomonas spp. and Acinetobacter spp.-like bacteria were identified in 85 million years old sediments. This suggests that these microbial communities might have been adapted during a long period of time to the environmental conditions of the deep subsurface

  2. Investigation of the Cellular and Molecular Mechanisms of Radiation-induced Bystander Effects

    OpenAIRE

    Furlong, Hayley

    2014-01-01

    The overall aim of this study was to investigate the cellular and molecular mechanisms involved in radiation-induced bystander effects in HaCaT cells, predominantly at low-doses of irradiation. They do not follow the original dose-response theory and exhibit a unique cascade of signalling events, which are under intense investigation for radiation risk purposes. An in vitro system was first used to observe the bystander effect, comparing two cell viability assays while measuring apoptotic cel...

  3. A molecular cytogenetic analysis of introgression in Alstroemeria

    NARCIS (Netherlands)

    Kamstra, S.A.

    1999-01-01

    This thesis describes the results of a molecular cytogenetic investigation of the process of introgression in Alstroemeria . The aim of this study was to transfer chromosomes or genes from one Alstroemeria species into another. For this, two distantly related species, A. aurea and A. inodora , were

  4. A Molecular Iodine Spectral Data Set for Rovibronic Analysis

    Science.gov (United States)

    Williamson, J. Charles; Kuntzleman, Thomas S.; Kafader, Rachael A.

    2013-01-01

    A data set of 7,381 molecular iodine vapor rovibronic transitions between the X and B electronic states has been prepared for an advanced undergraduate spectroscopic analysis project. Students apply standard theoretical techniques to these data and determine the values of three X-state constants (image omitted) and four B-state constants (image…

  5. Identification and in silico analysis of the Citrus HSP70 molecular chaperone gene family

    OpenAIRE

    Fietto, Luciano G.; Maximiller D.L. Costa; Cosme D Cruz; De Souza, Alessandra A.; Machado, Marcos A; Fontes, Elizabeth P. B.

    2007-01-01

    The completion of the genome sequencing of the Arabidopsis thaliana model system provided a powerful molecular tool for comparative analysis of gene families present in the genome of economically relevant plant species. In this investigation, we used the sequences of the Arabidopsis Hsp70 gene family to identify and annotate the Citrus Hsp70 genes represented in the CitEST database. Based on sequence comparison analysis, we identified 18 clusters that were further divided into 5 subgroups enc...

  6. Investigation of a metal-organic interface. Realization and understanding of a molecular switch

    Energy Technology Data Exchange (ETDEWEB)

    Neucheva, Olga [Forschungszentrum Juelich (DE). Institute of Bio- and Nanosystems (IBN), Functional Nanostructures at Surfaces (IBN-3)

    2010-07-01

    The field of molecular organic electronics is an emerging and very dynamic area. The continued trend to miniaturisation, combined with increasing complexity and cost of production in conventional semiconductor electronics, forces companies to turn their attention to alternatives that promise the next levels of scale at significantly lower cost. After consumer electronic devices based on organic transistors, such as TVs and book readers, have already been presented, molecular electronics is expected to offer the next breakthrough in feature size. Unfortunately, most of the organic/metal interfaces contain intrinsic defects that break the homogeneity of the interface properties. In this thesis, the electronic and structural properties of such defects were examined in order to understand the influence of the inhomogeneities on the quality of the interface layer. However, the main focus of this work was the investigation of the local properties of a single molecule. Taking advantage of the Scanning Tunnelling Microscope's (STM's) ability to act as a local probe, a single molecular switch was realized and studied. Moreover, in close collaboration with theory groups, the underlying mechanism driving the switching process was identified and described. Besides the investigation of the switching process, the ability of the STM to build nanostructures of different shapes from large organic molecules was shown. Knowing the parameters for realization and control of the switching process and for building the molecular corrals, the results of this investigation enable the reconstruction of the studied molecular ensemble and its deployment in electric molecular circuits, constituting a next step towards further miniaturization of electronic devices. (orig.)

  7. Molecular size distribution and structure investigations of humic substances in groundwater

    International Nuclear Information System (INIS)

    A non-ionic macroporous polymeric sorbent DAX-8 was applied to the isolation of humic and fulvic acids from groundwater. This procedure was able to isolate approximately 40% of the DOC as humic solutes. For the investigation of the structure and molecular size distribution of the isolated humic solutes, the hyphenated SEC-ESIMS system with a quadrupole mass spectrometer and a UV detector were utilized. For the higher-molecular-weight humic acids, the ESI-MS loses sensitivity compared with the parallel UV detection, because of the difficulty in getting the ionized humic compounds to fly efficiently through the mass spectrometer. (orig.)

  8. Quasi- and inelastic neutron scattering to investigate the molecular dynamics of discotic molecules in the bulk

    International Nuclear Information System (INIS)

    In- and quasielastic neutron scattering is employed to investigate both the vibrational density of states and the molecular dynamics of two homologous discotic liquid crystals (DLC) with different length of the alkyl side chain based on a triphenylene derivate. For both compounds characteristic low frequency excess contributions to the vibrational density of states are found. Therefore it is concluded that these liquid crystals show a glass-like behaviour. Elastic scans further show that a rich molecular dynamics takes place in these materials. (authors)

  9. Automated tumor analysis for molecular profiling in lung cancer.

    Science.gov (United States)

    Hamilton, Peter W; Wang, Yinhai; Boyd, Clinton; James, Jacqueline A; Loughrey, Maurice B; Hougton, Joseph P; Boyle, David P; Kelly, Paul; Maxwell, Perry; McCleary, David; Diamond, James; McArt, Darragh G; Tunstall, Jonathon; Bankhead, Peter; Salto-Tellez, Manuel

    2015-09-29

    The discovery and clinical application of molecular biomarkers in solid tumors, increasingly relies on nucleic acid extraction from FFPE tissue sections and subsequent molecular profiling. This in turn requires the pathological review of haematoxylin & eosin (H&E) stained slides, to ensure sample quality, tumor DNA sufficiency by visually estimating the percentage tumor nuclei and tumor annotation for manual macrodissection. In this study on NSCLC, we demonstrate considerable variation in tumor nuclei percentage between pathologists, potentially undermining the precision of NSCLC molecular evaluation and emphasising the need for quantitative tumor evaluation. We subsequently describe the development and validation of a system called TissueMark for automated tumor annotation and percentage tumor nuclei measurement in NSCLC using computerized image analysis. Evaluation of 245 NSCLC slides showed precise automated tumor annotation of cases using Tissuemark, strong concordance with manually drawn boundaries and identical EGFR mutational status, following manual macrodissection from the image analysis generated tumor boundaries. Automated analysis of cell counts for % tumor measurements by Tissuemark showed reduced variability and significant correlation (p tissue samples for molecular profiling in discovery and diagnostics. PMID:26317646

  10. Analysis and computational dissection of molecular signature multiplicity.

    Directory of Open Access Journals (Sweden)

    Alexander Statnikov

    2010-05-01

    Full Text Available Molecular signatures are computational or mathematical models created to diagnose disease and other phenotypes and to predict clinical outcomes and response to treatment. It is widely recognized that molecular signatures constitute one of the most important translational and basic science developments enabled by recent high-throughput molecular assays. A perplexing phenomenon that characterizes high-throughput data analysis is the ubiquitous multiplicity of molecular signatures. Multiplicity is a special form of data analysis instability in which different analysis methods used on the same data, or different samples from the same population lead to different but apparently maximally predictive signatures. This phenomenon has far-reaching implications for biological discovery and development of next generation patient diagnostics and personalized treatments. Currently the causes and interpretation of signature multiplicity are unknown, and several, often contradictory, conjectures have been made to explain it. We present a formal characterization of signature multiplicity and a new efficient algorithm that offers theoretical guarantees for extracting the set of maximally predictive and non-redundant signatures independent of distribution. The new algorithm identifies exactly the set of optimal signatures in controlled experiments and yields signatures with significantly better predictivity and reproducibility than previous algorithms in human microarray gene expression datasets. Our results shed light on the causes of signature multiplicity, provide computational tools for studying it empirically and introduce a framework for in silico bioequivalence of this important new class of diagnostic and personalized medicine modalities.

  11. structural investigation of sildenafil using mass spectrometry and molecular orbital calculation

    International Nuclear Information System (INIS)

    Sildenafil (C22 H30N6O4 S) drug is very important in medicine since it is a potent and selective inhibitor of (type-5) specific phosphodiesterase (PDE-5) that is responsible for degradation of cyclic guanosine monophosphate (cGMP).The drug was investigated using electron ionization (EI) mass spectrometry (MS) at 70 eV with the aid of PM5 molecular orbital calculation . The calculation included bond length, bond order, partial charge distribution, heat of formation and many other physicochemical properties. The mass spectral fragmentation pathways were reported and interpreted from the point of molecular orbital calculation view. The importance of the present work is also due to the decision of the possible mechanisms of fragmentation and its confirmation by molecular orbital calculation

  12. An investigation of a possible molecular effect in ion atom collision using a gaseous argon target

    International Nuclear Information System (INIS)

    The present work deals with an investigation of the molecular effect, which is defined as the difference in experimental results using isotachic atomic ion and molecular ion beams in ion atom collisions. Previous studies have dealt almost exclusively with total cross section measurements. This thesis explores the idea that the molecular effect may be more pronounced in the differential ionization probability of the target atoms. Also, a gaseous argon target of sufficiently low density was used in order to ensure that the two correlated protons in the H+2 beam did not interact with two adjacent target atoms simultaneously. The author reports that, contrary to the expectations noted above, the molecular effect in the K shell differential ionization probability of argon for scattering angles up to 90 degrees appears to be no more than the molecular effect in the total ionization probability. The uncertainty in the results is statistical in nature and can be improved upon by running the experiment for a longer duration of time

  13. Investigation of coherent molecular resonances in quantum dot–metallic nanoparticle systems using their spontaneous emission

    International Nuclear Information System (INIS)

    In the presence of metallic nanoparticles the nature of the optical excitations (pumping) of semiconductor quantum dots can be determined by their molecular states and resonances formed via coherent coupling of excitons and plasmons. We show that the spontaneous emission of such quantum dots can provide key information regarding formation and characteristics of such molecular properties. This includes an ultra-fast switching process associated with optical transition between the molecular states of the quantum dot-metallic nanoparticle system or its plasmonic meta-resonance when the intensity of the laser field responsible for the exciton–plasmon coupling reaches a critical value. We also show that by varying the intensity of this laser, the spontaneous emission exhibits characteristic features indicating tunability of the molecular resonances and excitation-power dependence of plasmonic fields of the metallic nanoparticles. - Highlights: • Investigation of collective molecular properties of quantum dot-metallic nanoparticle systems. • Impact of such collective properties on the optical excitation of quantum dots. • Effects of exciton–plasmon coupling in the spontaneous emission of the quantum dots. • Signatures of plasmonic meta-resonances in the fluorescence of quantum dots

  14. Molecular epidemiological investigation of G6PD deficiency by a gene chip among Chinese Hakka of southern Jiangxi province

    OpenAIRE

    Hu, Rong; Lin, Min; Ye, Jun; Zheng, Bao-Ping; Jiang, Li-Xia; Zhu, Juan-Juan; Chen, Xiao-Hong; Lai, Mi; Zhong, Tian-Yu

    2015-01-01

    In southern China, glucose-6-phosphate dehydrogenase (G6PD) deficiency is a significant health problem, and the incidence ranged from 0.5 to 4.08% in different Chinese population. The aims of this study are to investigate the molecular epidemiological characteristic of the G6PD gene among Chinese Hakka in southern Jiangxi province. 2331 unrelated subjects were screened for G6PD deficiency by a fluorescent test. DNA from deficient individuals was analyzed by a gene chip analysis for thirteen c...

  15. Molecular conformational analysis, vibrational spectra, NBO, NLO analysis and molecular docking study of bis[(E)-anthranyl-9-acrylic]anhydride based on density functional theory calculations.

    Science.gov (United States)

    Mary, Y Sheena; Panicker, C Yohannan; Thiemann, Thies; Al-Azani, Mariam; Al-Saadi, Abdulaziz A; Van Alsenoy, C; Raju, K; War, Javeed Ahmad; Srivastava, S K

    2015-12-01

    FT-IR and FT-Raman spectra of bis[(E)-anthranyl-9-acrylic]anhydride were recorded and analyzed. The conformational behavior is also investigated. The vibrational wave numbers were calculated using density functional theory (DFT) quantum chemical calculations. The data obtained from wave number calculations are used to assign vibrational bands obtained in Infrared and Raman spectra. Potential energy distribution was done using GAR2PED program. The geometrical parameters are compared with related structures. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using Natural Bonding Orbital (NBO) analysis. The Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) analysis are used to determine the charge transfer within the molecule. Molecular Electrostatic Potential (MEP) was performed by the DFT method. The calculated first hyperpolarizability of the title compound is comparable with the reported values of similar derivatives and is 4.23 times that of the standard nonlinear optical (NLO) material urea and the title compound and its derivatives are an attractive object for future studies of nonlinear optical properties. To evaluate the in silico antitumor activity of the title compound molecular docking studies were carried out against protein Bcl-xL. The (1)H-NMR spectrum is also reported. PMID:26143327

  16. Investigating the molecular mechanisms of the interactions between Lactobacillus reuteri strains and intestinal mucus

    OpenAIRE

    Jeffers, Faye

    2012-01-01

    Mucus is the first point of contact between the gut microbiota and the host. Here we used the gut symbiont Lactobacillus reuteri to investigate the molecular mechanisms underlying the interactions between gut bacteria and mucus. Firstly, the mucus binding ability of a collection of L. reuteri strains from different vertebrate hosts was assessed in vitro against mucus extracted from mouse and porcine gastrointestinal tracts. The adhesion profile was strain-specific showing the highest bindi...

  17. Investigation of coupling geometry and dimerization effects on thermoelectric properties of a C60 molecular transistor

    OpenAIRE

    Tagani, M. Bagheri; Golsanamlou, Z.; Izadi, S; Soleimani, H. Rahimpour

    2013-01-01

    Thermoelectric properties of a C60 molecular transistor are studied using Green function formalism in linear response regime. A tight-binding model is used to investigate the effect of the dimerization and coupling geometry on the electrical conductance, thermopower, and figure of merit. Increase of the connection points between the molecule and electrodes results in decrease of the number of the peaks of the electrical conductance owing to the interference effects. In addition, oscillation o...

  18. Osmotic Pressure of Aqueous Chondroitin Sulfate Solution: A Molecular Modeling Investigation

    OpenAIRE

    Bathe, Mark; Rutledge, Gregory C.; Grodzinsky, Alan J.; TIDOR, BRUCE

    2005-01-01

    The osmotic pressure of chondroitin sulfate (CS) solution in contact with an aqueous 1:1 salt reservoir of fixed ionic strength is studied using a recently developed coarse-grained molecular model. The effects of sulfation type (4- vs. 6-sulfation), sulfation pattern (statistical distribution of sulfate groups along a chain), ionic strength, CS intrinsic stiffness, and steric interactions on CS osmotic pressure are investigated. At physiological ionic strength (0.15 M NaCl), the sulfation typ...

  19. Investigation of variables influencing cognitive inhibition: from the behavioral to the molecular level

    OpenAIRE

    Dieler, Alica Christina

    2011-01-01

    The present work investigated the neural mechanisms underlying cognitive inhibition/thought suppression in Anderson’s and Green’s Think/No-Think paradigm (TNT), as well as different variables influencing these mechanisms at the cognitive, the neurophysiological, the electrophysiological and the molecular level. Neurophysiological data collected with fNIRS and fMRI have added up to the existing evidence of a fronto-hippocampal network interacting during the inhibition of unwanted thoughts. Som...

  20. Investigation of the Physical and Molecular Properties of Asphalt Binders Processed with Used Motor Oils

    OpenAIRE

    Mohyeldin Ragab; Magdy Abdelrahman

    2015-01-01

    In this work we investigated the performance aspects of addition of used motor oils (UMO) to neat and crumb rubber modified asphalts (CRMA) and related that to the change of molecular size distribution of modified asphalt’s fractions; asphaltenes, saturates, naphthene aromatics, and polar aromatics. Based on the results of temperature sweep viscoelastic tests, addition of crumb rubber modifier (CRM) alone or with UMO results in the formation of internal network within the modified asphalt. Ba...

  1. Ab initio investigation of molecular hydrogen physisorption on graphene and carbon nanotubes

    OpenAIRE

    Henwood, D; Carey, JD

    2007-01-01

    Density-functional theory is used to investigate hydrogen physisorption on a graphene layer and on single wall carbon nanotubes. Both external and internal adsorption sites of (9, 0) and (10, 0) carbon nanotubes have been studied with the hydrogen molecular axis oriented parallel or perpendicular to the nanotube wall. A range of hydrogen molecule binding sites has been examined and it is found that hydrogen binds weakly to each of the graphitic structures and at all adsorption sites examined....

  2. The Electronic Structure of Organic Molecular Materials : Theoretical and Spectroscopic Investigations

    OpenAIRE

    Brumboiu, Iulia Emilia

    2014-01-01

    In the present thesis the electronic properties of two organic molecules were studied by means of density functional theory (DFT) in connection to their possible applications in organic photovoltaics and molecular spintronics respectively. The first analysed system is the C60 derivative PCBM extensively used in polymer solar cells for the charge separation process. Since fullerenes have been shown to undergo modifications as a result of light exposure, investigating their electronic structure...

  3. Molecular investigations of chikungunya virus during outbreaks in Orissa, Eastern India in 2010.

    Science.gov (United States)

    Das, Biswadeep; Sahu, Abhipsa; Das, Mumani; Patra, Aparna; Dwibedi, Bhagirathi; Kar, Santanu K; Hazra, Rupenangshu K

    2012-07-01

    Chikungunya virus (CHIKV), an arthritogenic alphavirus, is transmitted to humans by mosquitoes of genus Aedes, mainly Aedes aegypti and Aedes albopictus. The resurgence of CHIKV in different parts of India is a point of major public health concern. In 2010, chikungunya outbreaks with high epidemic magnitude were recorded in coastal areas of Orissa, Eastern India, affecting more than 15,000 people coupled with severe arthralgia and prolonged morbidites. Detailed entomological, serological and molecular investigation of this unprecendented outbreak was carried out by collecting and studying 1359 mosquito samples belonging to A. albopictus, A. aegypti, A. vittatus, A. edwardsii and Culex species and 220 patients serum from the affected areas. In this study, CHIKV specific IgM capture-ELISA and reverse-transcription PCR (RT-PCR) were done to detect recent infection of CHIKV in serum samples and adult mosquitoes collected from the affected areas. The high maximum likelihood estimate (MLE) (15.2) in A. albopictus mosquitoes indicated that it was the principal vector involved in transmission of CHIKV in Orissa. Phylogenetic analysis revealed that the CHIKV strains involved in the outbreak belonged to the Indian Ocean Lineage (IOL) group within the East, Central and South African (ECSA) genotype. Genetic characterization of envelope glycoprotein (E1 and E2) genes revealed that all the CHIKV isolates from Orissa had the E1-A226V mutation that enhances viral dissemination and transmissibility by A. albopictus mosquitoes along with E2-L210Q and E2-I211T mutations, which play an epistatic role with E1-A226V mutation in adaptation of CHIKV to A. albopictus by increasing its midgut infectivity, thereby favoring its vectorial capacity. Our results showed the involvement of A. albopictus vector in the recent outbreaks in Orissa and circulation of IOL strains of ECSA genotype of CHIKV with E1-A226V, E2-L210Q and E2-I211T mutations in vectors and patients serum. PMID:22484761

  4. Controlling the sense of molecular rotation: classical vs quantum analysis

    CERN Document Server

    Khodorkovsky, Yuri; Hasegawa, Hirokazu; Ohshima, Yasuhiro; Averbukh, Ilya Sh

    2010-01-01

    Recently, it was predicted theoretically and verified experimentally that a pair of delayed and cross-polarized short laser pulses can create molecular ensembles with a well defined sense of rotation (clockwise or counterclockwise). Here we provide a comparative study of the classical and quantum aspects of the underlying mechanism for linear molecules and for symmetric tops, like benzene molecules, that were used for the first experimental demonstration of the effect. Very good quantitative agreement is found between the classical description of the process and the rigorous quantum mechanical analysis at the relevant experimental conditions. Both approaches predict the same optimal values for the delay between pulses and the angle between them, and deliver the same magnitude of the induced oriented angular momentum of the molecular ensemble. As expected, quantum and classical analysis substantially deviate when the delay between pulses is comparable with the period of quantum rotational revivals. However, ti...

  5. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

    Directory of Open Access Journals (Sweden)

    von Haeseler Arndt

    2004-06-01

    Full Text Available Abstract Background Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience. Results TREEFINDER is an easy-to-use integrative platform-independent analysis environment for molecular phylogenetics. In this paper the main features of TREEFINDER (version of April 2004 are described. TREEFINDER is written in ANSI C and Java and implements powerful statistical approaches for inferring gene tree and related analyzes. In addition, it provides a user-friendly graphical interface and a phylogenetic programming language. Conclusions TREEFINDER is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies.

  6. A molecular cytogenetic analysis of introgression in Alstroemeria

    OpenAIRE

    Kamstra, S.A.

    1999-01-01

    This thesis describes the results of a molecular cytogenetic investigation of the process of introgression in Alstroemeria . The aim of this study was to transfer chromosomes or genes from one Alstroemeria species into another. For this, two distantly related species, A. aurea and A. inodora , were hybridized and the resulting hybrids were further backcrossed with the species A. inodora . To monitor the process of introgression accurately it was necessary to identify the individual chromosome...

  7. Molecular orbital analysis of the hydrogen bonded water dimer

    OpenAIRE

    Bo Wang; Wanrun Jiang; Xin Dai; Yang Gao; Zhigang Wang; Rui-Qin Zhang

    2016-01-01

    As an essential interaction in nature, hydrogen bonding plays a crucial role in many material formations and biological processes, requiring deeper understanding. Here, using density functional theory and post-Hartree-Fock methods, we reveal two hydrogen bonding molecular orbitals crossing the hydrogen-bond’s O and H atoms in the water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. Our finding sheds light on the essential understanding of ...

  8. A Quantitative Analysis of IRAS Maps of Molecular Clouds

    OpenAIRE

    Wiseman, Jennifer J.; Adams, Fred C.

    1994-01-01

    We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps; this procedure allows us to measure quantitatively the difference bet...

  9. Discovering novel ingredient pairings in molecular gastronomy using network analysis

    OpenAIRE

    Ključevšek, Aleksander; Krapić, Luka

    2016-01-01

    Molecular gastronomy is a distinct sub-discipline of food science that takes an active role in examining chemical and physical properties of ingredients and as such lends itself to more scientific approaches to finding novel ingredient pairings. With thousands of ingredients and molecules, which participate in the creation of each ingredient's flavour, it can be difficult to find compatible flavours in an efficient manner. Existing literature is focused mainly on analysis of already establish...

  10. Organizational Climate in Police Investigative Work: A Comparative Analysis of Police Investigators and Investigative Trainers

    OpenAIRE

    2013-01-01

    The aim of this study is twofold: First, it seeks to identify organizational climate aspects that are considered important by police investigators and investigative trainers in the context of police investigation. Second, it examines how these various aspects of organizational climate are perceived by the two samples. Open-ended interviews were conducted in order to generate information about the organizational climate aspects, respectively with 51 police investigators from 16 of the 27 polic...

  11. Investigation & Analysis of Different Aluminium Alloys t

    OpenAIRE

    Nibedita Sethi*¹,; Ajit Senapati²

    2014-01-01

    Aluminium alloy LM-29, A-356 AND A-6060 was fabricated in sand casting method. Mach inability of aluminium alloy LM-29, A-356 AND A-6060 was investigated and evaluate the mach inability studying the different parameter such as cutting force, surface roughness, chip thickness, and power consumption during turning at different cutting speed and constant depth of cut and feed rate. In this paper also studies the mechanical properties means hardness, density and tensile strength o...

  12. Investigation of Terminal Group Effect on Electron Transport Through Open Molecular Structures

    International Nuclear Information System (INIS)

    The effect of terminal groups on the electron transport through metal-molecule-metal system has been investigated using nonequilibrium Green's function (NEGF) formalism combined with extended Huckel theory (EHT). Au-molecule-Au junctions are constructed with borazine and BCN unit structure as core molecule and sulphur (S), oxygen (O), selenium (Se) and cyano-group (CN) as terminal groups. The electron transport characteristics of the borazine and BCN molecular systems are analyzed through the transmission spectra and the current-voltage curve. The results demonstrate that the terminal groups modifying the transport behaviors of these systems in a controlled way. Our result shows that, selenium is the best linker to couple borazine to Au electrode and oxygen is the best one to couple BCN to Au electrode. Furthermore, the results of borazine systems are compared with that of BCN molecular systems and are discussed. Simulation results show that the conductance through BCN molecular systems is four times larger than the borazine molecular systems. Negative differential resistance behavior is observed with borazine-CN system and the saturation feature appears in BCN systems. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  13. Ligand binding to anti-cancer target CD44 investigated by molecular simulations.

    Science.gov (United States)

    Nguyen, Tin Trung; Tran, Duy Phuoc; Pham Dinh Quoc Huy; Hoang, Zung; Carloni, Paolo; Van Pham, Phuc; Nguyen, Chuong; Li, Mai Suan

    2016-07-01

    CD44 is a cell-surface glycoprotein and receptor for hyaluronan, one of the major components of the tumor extracellular matrix. There is evidence that the interaction between CD44 and hyaluronan promotes breast cancer metastasis. Recently, the molecule F-19848A was shown to inhibit hyaluronan binding to receptor CD44 in a cell-based assay. In this study, we investigated the mechanism and energetics of F-19848A binding to CD44 using molecular simulation. Using the molecular mechanics/Poisson Boltzmann surface area (MM-PBSA) method, we obtained the binding free energy and inhibition constant of the complex. The van der Waals (vdW) interaction and the extended portion of F-19848A play key roles in the binding affinity. We screened natural products from a traditional Chinese medicine database to search for CD44 inhibitors. From combining pharmaceutical requirements with docking and molecular dynamics simulations, we found ten compounds that are potentially better or equal to the F-19848A ligand at binding to CD44 receptor. Therefore, we have identified new candidates of CD44 inhibitors, based on molecular simulation, which may be effective small molecules for the therapy of breast cancer. PMID:27342250

  14. Application of atomic absorption in molecular analysis (spectrophotometry)

    International Nuclear Information System (INIS)

    The apparatus of atomic absorption has been considered by all the experts in chemical analysis as one of the most important equipments in actual utilization in such field. Among its several applications one should emphasize direct and indirect metals analyses using flame, graphite furnace, cold vapor generator,... Besides such known applications, the authors have developed at the R and D Center of CSN a patent pendent method for the utilization of such equipment for molecular analysis, in substitution of a sophisticated and specific apparatus. (Author)

  15. New Diethyl Ammonium Salt of Thiobarbituric Acid Derivative: Synthesis, Molecular Structure Investigations and Docking Studies

    Directory of Open Access Journals (Sweden)

    Assem Barakat

    2015-11-01

    Full Text Available The synthesis of the new diethyl ammonium salt of diethylammonium(E-5-(1,5-bis(4-fluorophenyl-3-oxopent-4-en-1-yl-1,3-diethyl-4,6-dioxo-2-thioxohexaydropyrimidin-5-ide 3 via a regioselective Michael addition of N,N-diethylthiobarbituric acid 1 to dienone 2 is described. In 3, the carboanion of the thiobarbituric moiety is stabilized by the strong intramolecular electron delocalization with the adjacent carbonyl groups and so the reaction proceeds without any cyclization. The molecular structure investigations of 3 were determined by single-crystal X-ray diffraction as well as DFT computations. The theoretically calculated (DFT/B3LYP geometry agrees well with the crystallographic data. The effect of fluorine replacement by chlorine atoms on the molecular structure aspects were investigated using DFT methods. Calculated electronic spectra showed a bathochromic shift of the π-π* transition when fluorine is replaced by chlorine. Charge decomposition analyses were performed to study possible interaction between the different fragments in the studied systems. Molecular docking simulations examining the inhibitory nature of the compound show an anti-diabetic activity with Pa (probability of activity value of 0.229.

  16. Investigation of the structure of molecular complexes by X ray absorption and diffraction: application to the f compound family

    International Nuclear Information System (INIS)

    After having recalled that his research thesis was dealing with 4d transition elements while investigating niobium clusters reactivity, and having outlined that he is now interested in the investigation of 4f and 5f compound behaviour, notably by using X ray absorption spectroscopy, the author describes the experimental methods he implemented. Then, he discusses the stereo-chemical structure of molecular complexes, reports the use of X ray absorption and diffraction, discusses the generation of electronic functions of chi(k) and the adjustment of the chi(k) function through geometrical parameters. He also describes the simple diffusion approach, reports a multiple diffusion analysis. He outlines the peculiarity of heavy atoms because of relativistic effects. Then, he discusses the investigation of the electronic structure of molecular complexes by means of a stereo-chemical approach, with the determination of the absorption threshold and of the oxidation degree. He discusses the attempt of a semi-empirical approach of the stereo-chemical and electronic structure

  17. X-ray diffraction and molecular-dynamics studies: Structural analysis of phases in diglyceride monolayers

    DEFF Research Database (Denmark)

    Peters, Günther H.J.; Larsen, Niels Bent; Bjørnholm, T.;

    1998-01-01

    We report a detailed structural analysis of the phases of 1,2-sn-dipalmitoylglycerol Langmuir monolayers at room temperature. Pressure-induced transitions have been investigated by combination of molecular-dynamics simulations and grazing-incidence x-ray diffraction (XRD). The diglyceride film un...... indicate that in the simulated monolayer the finite size with periodic boundary conditions imposes a higher degree of order....

  18. Molecular arrangement investigation of copper phthalocyanine grown on hydrogen passivated Si(1 1 1) surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Arbi, I.; Ben Hamada, B.; Souissi, A.; Menzli, S.; Ben Azzouz, C.; Laribi, A.; Akremi, A., E-mail: a_akremi@yahoo.fr; Chefi, C.

    2014-06-01

    Chemical, electronic and structural properties of ultra thin films of copper phthalocyanine (CuPc) grown on hydrogen passivated silicon (1 1 1) surfaces were investigated in situ by X-ray photoelectron spectroscopy (XPS), ultraviolet photoemission spectroscopy (UPS), X-ray photoelectron diffraction (XPD) and electron diffraction (LEED). The early stages of copper phthalocyanine adsorption (1–2) were characterized by the saturation of surface defects and by a flat lying disposition on the surface. Upon further CuPc coverage, the passivation of Si surfaces resulted in the molecule taking a standing position in films. The molecular packing deduced from these studies appears very close to the one in the bulk α phase of CuPc. The work function of the films was found to be decreasing during the growth and was correlated with the molecular orientation.

  19. Spectroscopic investigations on the interactions between isopropanol and trypsin at molecular level

    Science.gov (United States)

    Hu, Xinxin; Yu, Zehua; Liu, Rutao

    2013-05-01

    The toxicity of hydroxyl group of isopropanol to trypsin in aqueous solution was investigated by techniques including UV-visible absorption spectroscopy, fluorescence spectroscopy, circular dichroism (CD) spectroscopy, enzyme activity assay and molecular docking technology. The results of UV-visible absorption spectroscopy and CD spectra indicate that isopropanol could change the secondary structure of trypsin by increasing the content of α-helix and decreasing the content of β-sheet. The tertiary structure of trypsin was also changed owing to the loss of environmental asymmetry of amino acid residues. Isopropanol bound into a hydrophobic cavity on the surface of trypsin by a hydrogen bond located between the hydrogen atom on the hydroxyl of isopropanol and the oxygen atoms on SER 214 and hydrophobic interaction, as the molecular docking results showed. In addition, isopropanol could affect the function of trypsin by increasing its catalytic activity.

  20. Investigation of crack tip dislocation emission in aluminum using multiscale molecular dynamics simulation and continuum modeling

    Science.gov (United States)

    Yamakov, V. I.; Warner, D. H.; Zamora, R. J.; Saether, E.; Curtin, W. A.; Glaessgen, E. H.

    2014-04-01

    This work investigates the dislocation nucleation processes that occur at the tip of a crack in aluminum under a broad range of crystallographic orientations and temperatures. A concurrent multiscale molecular dynamics - continuum simulation framework is employed. The results are then interpreted using a Peierls continuum model that uses finite temperature material properties derived from molecular dynamics simulation. Under ramped loading, partial dislocation nucleation at the crack tip is found to lead to both full dislocation emission and twinning, depending upon the orientation, temperature, and magnitude of the applied load in the simulation. The origins of the dependencies are made apparent by the Peierls continuum model. The continuum model suggests that in many instances dislocation nucleation from the crack tip can be considered to be a strain rate independent process, yet still temperature dependent through the temperature dependence of the stacking fault energies and elastic constants.

  1. Investigation of the dislocation interaction with voids and helium bubbles in nickel using molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Simar, A.; Lee, H.J. [California Univ., Dept. NE/ERL, Berkeley, California, CA (United States); Robertson, I.M. [Illinois Univ., Dept. of Materials Science and Engineering, Urbana-Champaign, AK (United States); Wirth, B. [California Univ., Nuclear Engineering Department, UC, Berkeley, California, AK CA (United States)

    2007-07-01

    Full text of publication follows: Pressurized helium bubbles are expected to form in fusion materials. At high densities they will detrimentally impact mechanical properties. Molecular dynamics simulations of the interaction between gliding dislocations and voids or helium bubbles have been performed to investigate the effect of dislocation character, temperature, stacking fault energy, bubble size, density and helium pressure. The results clearly indicate that helium bubbles are effective obstacles to dislocation motion, and the importance of the partial dislocations in determining the obstacle strength. Low pressure bubbles are sheared, and the interaction is controlled by departure side pinning. With increasing helium pressure, the bubbles become over-pressurized and the interaction and detachment mechanism is controlled by the interaction of the dislocation with interfacial distortions (including prismatic loops) and Orowan type detachment can be observed. The molecular dynamics simulations are compared to in-situ TEM observations. (authors)

  2. The interaction between 4-aminoantipyrine and bovine serum albumin: Multiple spectroscopic and molecular docking investigations

    International Nuclear Information System (INIS)

    4-Aminoantipyrine (AAP) is widely used in the pharmaceutical industry, in biochemical experiments and in environmental monitoring. AAP as an aromatic pollutant in the environment poses a great threat to human health. To evaluate the toxicity of AAP at the protein level, the effects of AAP on bovine serum albumin (BSA) were investigated by multiple spectroscopic techniques and molecular modeling. After the inner filter effect was eliminated, the experimental results showed that AAP effectively quenched the intrinsic fluorescence of BSA via static quenching. The number of binding sites, the binding constant, the thermodynamic parameters and binding subdomain were measured, and indicated that AAP could spontaneously bind with BSA on subdomain IIIA through electrostatic forces. Molecular docking results revealed that AAP interacted with the Glu 488 and Glu 502 residues of BSA. Furthermore, the conformation of BSA was demonstrably changed in the presence of AAP. The skeletal structure of BSA loosened, exposing internal hydrophobic aromatic ring amino acids and peptide strands to the solution.

  3. Confirming an integrated pathology of diabetes and its complications by molecular biomarker-target network analysis.

    Science.gov (United States)

    Zhao, Zide; Zhang, Yingying; Gai, Fengchun; Wang, Ying

    2016-09-01

    Despite ongoing research into diabetes and its complications, the underlying molecular associations remain to be elucidated. The systematic identification of molecular interactions in associated diseases may be approached using a network analysis strategy. The biomarker-target interrelated molecules associated with diabetes and its complications were identified via the Comparative Toxicogenomics Database (CTD); the Search Tool for Recurring Instances of Neighboring Genes was utilized for network construction. Functional enrichment analysis was performed with Database for Annotation, Visualization and Integrated Discovery software to investigate connections between diabetes and its complications. A total of 142 (including 122 biomarkers, 10 therapeutic targets and 10 overlapping molecules) biomarker-target interrelated molecules associated with diabetes and its complications were identified via the CTD database, and analysis of the network yielded 1,087 biological processes and fifteen Kyoto Encyclopedia of Genes and Genomes pathways with significant P‑values. Various critical aspects of the networks were examined in the present study: a) Intermolecular horizontal and vertical combinations in biomarkers and therapeutic targets associated with diabetes and its complicationb) network topology properties associated with molecular pathological responsec) contribution of key molecules to integrated regulation; and d) crosstalk between multiple pathways. Based on a multi-dimensional analysis, it was concluded that the integrated molecular pathological development of diabetes and its complications does not proceed randomly, which suggests a requirement for integrated, multi-target intervention. PMID:27430657

  4. Investigation of hybrid molecular material prepared by ionic liquid and polyoxometalate anion

    Indian Academy of Sciences (India)

    T Rajkumar; G Ranga Rao

    2008-11-01

    A solid hybrid molecular material containing 1-butyl 3-methyl imidazolium cations and Keggin anions of phosphotungstic acid has been synthesized. It is fully characterized by CHN analysis, FTIR, XRD, UV-Vis-NIR DRS, 31P MAS NMR, TGA and SEM. The FTIR spectrum of the compound shows the fingerprint vibrational bands of both Keggin molecular anions and imidazolium cations. The aromatic C-H stretch region (2700-3250 cm-1) of imidazolium cation is split due to the interaction between the ring C-H and bulky Keggin anion. The red-shift in the UV-Vis spectra and the downfield 31P MAS NMR chemical shift also confirm the electrostatic interaction between the ions in the compound. Near IR spectral region (1000-2500 nm) shows the elimination of water in the compound which is hydrophobic.

  5. Application of molecular simulation to investigate chrome(III)-crosslinked collagen problems

    International Nuclear Information System (INIS)

    Molecular dynamics simulation with a modified CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field was carried out to investigate the properties of chrome-tanned collagen in comparison with chrome-free collagen under hydrated and dehydrated conditions. An attempt has been made to explain the microcosmic origins of the various properties of the chromium(III)-crosslinked collagen. The present simulation describes the clear crosslinking topology of polychromiums to peptide chains, identifies the linking site and the capacity of the linkage, explains why the efficiency is not 100% in a practical tanning process and provides a new viewpoint on the crosslinking of the polychromium with the side chains of the collagen. (paper)

  6. Molecular dynamics investigation into the oscillatory behavior of double-walled boron-nitride nanotubes

    Science.gov (United States)

    Ansari, R.; Ajori, S.

    2016-05-01

    In this paper, the oscillatory behavior of double-walled boron-nitride nanotubes is investigated based on the molecular dynamics (MD) simulations. The MD simulations are performed using the Lennard-Jones and Tersoff-like potential functions. The influences of friction between the walls of inner and outer tubes, flexibility, velocity and outer length-to-inner length ratio on the frequency of oscillations are studied. The results show that the flexibility increases the frequency during the simulation. Furthermore, it is observed that by increasing the initial velocity, the frequency decreases.

  7. Investigation of InN layers grown by molecular beam epitaxy on GaN templates

    Energy Technology Data Exchange (ETDEWEB)

    Vilalta-Clemente, A.; Mutta, G.R.; Chauvat, M.P.; Morales, M.; Doualan, J.L.; Ruterana, P. [CIMAP UMR 6252 CNRS-ENSICAEN-CEA-UCBN, Caen (France); Grandal, J.; Sanchez-Garcia, M.A.; Calle, F. [ISOM y Department de Ingenieria Electronica, E.T.S.I. Telecomunicacion, Universidad Politecnica de Madrid, Ciudad Universitaria (Spain); Valcheva, E.; Kirilov, K. [Faculty of Physics, Sofia University (Bulgaria)

    2010-05-15

    An investigation of InN layers grown on GaN templates by molecular beam epitaxy (MBE) has been carried out by X-ray diffraction (XRD), Raman spectroscopy (RS) and photoluminescence (PL). A good correlation is noticed between their crystalline quality and optical properties. The best samples exhibit a PL emission between 0.6 and 0.7 eV. The surface structure was quite different from one sample to the other, pointing out to a critical role of the growth conditions, which probably need to be tightly optimized for a good reproducibility. (Abstract Copyright [2010], Wiley Periodicals, Inc.)

  8. Investigations of the Formation of Molecular Hydrogen on Dust Grain Analogues

    Science.gov (United States)

    Vidali, Gianfranco; Roser, Joseph E.; Manico, Giulio; Pirronello, Valerio

    2002-01-01

    In the last four years we have been working to investigate the formation of molecular hydrogen on surfaces of materials of astrophysical interest, such as silicates, carbonaceous particles and ices, and in conditions approximating the ones present in a variety of astrophysical environments. Our experimental studies - the first of their kind and complemented with computer simulations and theoretical analyses - have given not only hydrogen recombination rates under different ISM conditions, but they have also offered new insights into this fundamental astrophysical problem. Here we summarize our experimental methods and most significant results.

  9. Protein-Protein Interaction Investigated by Steered Molecular Dynamics: The TCR-pMHC Complex

    OpenAIRE

    Cuendet, Michel A.; Michielin, Olivier

    2008-01-01

    We present a novel steered molecular dynamics scheme to induce the dissociation of large protein-protein complexes. We apply this scheme to study the interaction of a T cell receptor (TCR) with a major histocompatibility complex (MHC) presenting a peptide (p). Two TCR-pMHC complexes are considered, which only differ by the mutation of a single amino acid on the peptide; one is a strong agonist that produces T cell activation in vivo, while the other is an antagonist. We investigate the intera...

  10. Investigation of thermodynamic properties of molten rare earth trichlorides by molecular dynamics method

    International Nuclear Information System (INIS)

    The physical and thermodynamic properties of molten rare earth trichlorides were investigated by the molecular dynamics (MD) technique. In addition to a fully ionic model, partially ionic models, in which covalency was considered in the nearest unlike ion pair (cation-chloride ion), was used in the present work. The liquid structure, shear viscosity and enthalpy of molten YCl3 and LaCl3 calculated from the MD simulation were compared with the experimental data. It is concluded that the partially ionic model can better represent the experimental data than the fully ionic model. (orig.)

  11. Investigations towards multi-step laser spectroscopy of stored H3+ molecular ions

    International Nuclear Information System (INIS)

    The triatomic H3+ molecular ion plays an important role in molecular quantum dynamics through its equilateral triangular structure. Many studies of molecular reactions involving H3+ have been done thus far, among them dissociative recombination in storage ring experiments with a cold electron-beam. For these strongly energy dependent reactions, the population in individual rovibrational levels is of large importance. To determine such populations for H3+ ions inside a storage ring, an extremely sensitive state-selective method must be used, such as the Resonant- Enhanced Multi-Photon Dissociation (REMPD). In REMPD, molecules are highly excited from a low lying initial level in a first resonant step and photodissociated from these high lying states in a second step. To fully employ this method, detailed investigations are necessary. Here, an experiment is presented which determines the energy range of the highly excited vibrational states of H3+ suitable for photodissociation. Additional photodissociation experiments, using hot H3+ ions in the storage ring TSR at the Max-Planck Institute for Nuclear Physics, yield an effective lifetime of these dissociated H3+ states. Finally selective vibrational excitation of cold H3+ (the rst step of REMPD) is discussed with the aim of reaching the highly excited vibrational states suitable for photodissociation. (orig.)

  12. Role of redox centre in charge transport investigated by novel self-assembled conjugated polymer molecular junctions

    Science.gov (United States)

    Wang, Zongrui; Dong, Huanli; Li, Tao; Hviid, Rune; Zou, Ye; Wei, Zhongming; Fu, Xiaolong; Wang, Erjing; Zhen, Yonggang; Nørgaard, Kasper; Laursen, Bo W.; Hu, Wenping

    2015-06-01

    Molecular electronics describes a field that seeks to implement electronic components made of molecular building blocks. To date, few studies have used conjugated polymers in molecular junctions despite the fact that they potentially transport charge more efficiently than the extensively investigated small-molecular systems. Here we report a novel type of molecular tunnelling junction exploring the use of conjugated polymers, which are self-assembled into ultrathin films in a distinguishable `planar' manner from the traditional vertically oriented small-molecule monolayers. Electrical measurements on the junctions reveal molecular-specific characteristics of the polymeric molecules in comparison with less conjugated small molecules. More significantly, we decorate redox-active functionality into polymeric backbones, demonstrating a key role of redox centre in the modulation of charge transport behaviour via energy level engineering and external stimuli, and implying the potential of employing tailor-made polymeric components as alternatives to small molecules for future molecular-scale electronics.

  13. Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy.

    Science.gov (United States)

    Alves, Gelio; Ogurtsov, Aleksey Y; Yu, Yi-Kuo

    2014-01-01

    In this paper, we present Molecular Isotopic Distribution Analysis (MIDAs), a new software tool designed to compute molecular isotopic distributions with adjustable accuracies. MIDAs offers two algorithms, one polynomial-based and one Fourier-transform-based, both of which compute molecular isotopic distributions accurately and efficiently. The polynomial-based algorithm contains few novel aspects, whereas the Fourier-transform-based algorithm consists mainly of improvements to other existing Fourier-transform-based algorithms. We have benchmarked the performance of the two algorithms implemented in MIDAs with that of eight software packages (BRAIN, Emass, Mercury, Mercury5, NeutronCluster, Qmass, JFC, IC) using a consensus set of benchmark molecules. Under the proposed evaluation criteria, MIDAs's algorithms, JFC, and Emass compute with comparable accuracy the coarse-grained (low-resolution) isotopic distributions and are more accurate than the other software packages. For fine-grained isotopic distributions, we compared IC, MIDAs's polynomial algorithm, and MIDAs's Fourier transform algorithm. Among the three, IC and MIDAs's polynomial algorithm compute isotopic distributions that better resemble their corresponding exact fine-grained (high-resolution) isotopic distributions. MIDAs can be accessed freely through a user-friendly web-interface at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html. PMID:24254576

  14. Molecular organization in liquid crystals: A comparative computational analysis

    International Nuclear Information System (INIS)

    A comparative computational analysis of molecular organization in four-nematogenic acids (nOCAC) having two, four, six, and eight carbon atoms in the alkyl chain is carried out with respect to translatory and orientational motions. The evaluation of the atomic charge and dipole moment at each atomic center is performed through the complete neglect differential overlap (CNDO/2) method. The Rayleigh-Schroedinger perturbation theory, along with the multicentered-multipole expansion method, is employed to evaluate the long-range interactions, while the '6-exp' potential function is assumed for short-range interactions. The total interaction-energy values obtained through these computations are used to calculate the probability of each configuration at the phase transition temperature via the Maxwell-Boltzmann formula. Further, the flexibility of various configurations is studied in terms of variation of probability due to small departures from the most probable configuration. A comparative picture of molecular parameters, such as the total energy, binding energy, and total dipole moment, is given. An attempt is made to explain the nematogenic behavior of these liquid crystals in terms of their relative order and, thereby, to develop a molecular model for the liquid crystallinity.

  15. Cellular and molecular investigations of the adhesion and mechanics of Listeria monocytogenes

    Science.gov (United States)

    Eskhan, Asma Omar

    Atomic force microscopy has been used to quantify the adherence and mechanical properties of an array of L. monocytogenes strains and their surface biopolymers. First, eight L. monocytogenes strains that represented the two major lineages of the species were compared for their adherence and mechanics at cellular and molecular levels. Our results indicated that strains of lineage' II were characterized by higher adhesion and Young's moduli, longer and more rigid surface biopolymers and lower specific and nonspecific forces when compared to lineage' I strains. Additionally, adherence and mechanical properties of eight L. monocytogenes epidemic and environmental strains were probed. Our results pointed to that environmental and epidemic strains representative of a given lineage were similar in their adherence and mechanical properties when investigated at a cellular level. However, when the molecular properties of the strains were considered, epidemic strains were characterized by higher specific and nonspecific forces, shorter, denser and more flexible biopolymers compared to environmental strains. Second, the role of environmental pH conditions of growth on the adhesion and mechanics of a pathogenic L. monocytogenes EGDe was investigated. Our results pointed to a transition in the adhesion energies for cells cultured at pH 7. In addition, when the types of molecular forces that govern the adhesion were quantified using Poisson statistical approach and using a new proposed method, specific hydrogen-bond energies dominated the bacterial adhesion process. Such a finding is instrumental to researchers designing methods to control bacterial adhesion. Similarly, bacterial cells underwent a transition in their mechanical properties. We have shown that cells cultured at pH 7 were the most rigid compared to those cultured in lower or higher pH conditions of growth. Due to transitions observed in adherence and mechanics when cells were cultured at pH 7, we hypothesized that

  16. Onboard functional and molecular imaging: A design investigation for robotic multipinhole SPECT

    International Nuclear Information System (INIS)

    Purpose: Onboard imaging—currently performed primarily by x-ray transmission modalities—is essential in modern radiation therapy. As radiation therapy moves toward personalized medicine, molecular imaging, which views individual gene expression, may also be important onboard. Nuclear medicine methods, such as single photon emission computed tomography (SPECT), are premier modalities for molecular imaging. The purpose of this study is to investigate a robotic multipinhole approach to onboard SPECT. Methods: Computer-aided design (CAD) studies were performed to assess the feasibility of maneuvering a robotic SPECT system about a patient in position for radiation therapy. In order to obtain fast, high-quality SPECT images, a 49-pinhole SPECT camera was designed which provides high sensitivity to photons emitted from an imaging region of interest. This multipinhole system was investigated by computer-simulation studies. Seventeen hot spots 10 and 7 mm in diameter were placed in the breast region of a supine female phantom. Hot spot activity concentration was six times that of background. For the 49-pinhole camera and a reference, more conventional, broad field-of-view (FOV) SPECT system, projection data were computer simulated for 4-min scans and SPECT images were reconstructed. Hot-spot localization was evaluated using a nonprewhitening forced-choice numerical observer. Results: The CAD simulation studies found that robots could maneuver SPECT cameras about patients in position for radiation therapy. In the imaging studies, most hot spots were apparent in the 49-pinhole images. Average localization errors for 10-mm- and 7-mm-diameter hot spots were 0.4 and 1.7 mm, respectively, for the 49-pinhole system, and 3.1 and 5.7 mm, respectively, for the reference broad-FOV system. Conclusions: A robot could maneuver a multipinhole SPECT system about a patient in position for radiation therapy. The system could provide onboard functional and molecular imaging with 4-min

  17. Onboard functional and molecular imaging: A design investigation for robotic multipinhole SPECT

    Energy Technology Data Exchange (ETDEWEB)

    Bowsher, James, E-mail: james.bowsher@duke.edu; Giles, William; Yin, Fang-Fang [Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710 and Medical Physics Graduate Program, Duke University, Durham, North Carolina 27710 (United States); Yan, Susu [Medical Physics Graduate Program, Duke University, Durham, North Carolina 27710 (United States); Roper, Justin [Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710 (United States)

    2014-01-15

    Purpose: Onboard imaging—currently performed primarily by x-ray transmission modalities—is essential in modern radiation therapy. As radiation therapy moves toward personalized medicine, molecular imaging, which views individual gene expression, may also be important onboard. Nuclear medicine methods, such as single photon emission computed tomography (SPECT), are premier modalities for molecular imaging. The purpose of this study is to investigate a robotic multipinhole approach to onboard SPECT. Methods: Computer-aided design (CAD) studies were performed to assess the feasibility of maneuvering a robotic SPECT system about a patient in position for radiation therapy. In order to obtain fast, high-quality SPECT images, a 49-pinhole SPECT camera was designed which provides high sensitivity to photons emitted from an imaging region of interest. This multipinhole system was investigated by computer-simulation studies. Seventeen hot spots 10 and 7 mm in diameter were placed in the breast region of a supine female phantom. Hot spot activity concentration was six times that of background. For the 49-pinhole camera and a reference, more conventional, broad field-of-view (FOV) SPECT system, projection data were computer simulated for 4-min scans and SPECT images were reconstructed. Hot-spot localization was evaluated using a nonprewhitening forced-choice numerical observer. Results: The CAD simulation studies found that robots could maneuver SPECT cameras about patients in position for radiation therapy. In the imaging studies, most hot spots were apparent in the 49-pinhole images. Average localization errors for 10-mm- and 7-mm-diameter hot spots were 0.4 and 1.7 mm, respectively, for the 49-pinhole system, and 3.1 and 5.7 mm, respectively, for the reference broad-FOV system. Conclusions: A robot could maneuver a multipinhole SPECT system about a patient in position for radiation therapy. The system could provide onboard functional and molecular imaging with 4-min

  18. Spectroscopic and molecular modeling investigation on the binding of a synthesized steroidal amide to protein

    International Nuclear Information System (INIS)

    Owing to the various valuable biological activities, steroidal amides have become a hot topic in steroidal pharmaceutical chemistry. In this paper, an anti-tumor steroid derivate (DAAO) was synthesized and identified. The interaction between DAAO and human serum albumin (HSA) was studied by fluorescence spectra, circular dichroism (CD) spectra, molecular modeling and molecular probe techniques. The results suggested that DAAO had reacted with HSA through hydrogen bonds and van der Waals power. The formation of DAAO–HSA complex at ground state led to static quenching of HSA's fluorescence. The number of binding sites, binding constants, enthalpy change (ΔHθ), Gibbs free energy change (ΔGθ) and entropy change (ΔSθ) were calculated at different temperatures based on fluorescence quenching theory and classic equation. Molecular modeling investigation indicated that DAAO was more inclined to absorb on Sudlow's site I in subdomain IIA of HSA molecule on grounds of the lowest energy principle and steric hindrance effect. The binding location was further confirmed by fluorescence probe experiment using warfarin (site I probe) for displacement. Furthermore, the conformational changes of HSA in presence of DAAO were investigated by CD spectra. The results could provide new evidence explaining the relationship between the chemical structure and biological activity and may be useful for understanding the anti-cancer mechanism of steroidal drug. - Highlights: • A designed steroidal amide compound (DAAO) was synthesized by introducing amido bonds into a steroid nucleus. • DAAO binds to Sudlow's site I in HSA through hydrogen bonds and van der Waals power. • The interaction was a spontaneous and exothermic process with modest degree of reversibility. • The secondary structure of HSA and the microenvironment of TRP214 altered. • Amido bond in steroid nucleus (–NH–CO–) plays important role in stabling the structure of macromolecules

  19. Spectroscopic and molecular modeling investigation on the binding of a synthesized steroidal amide to protein

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Hua-xin, E-mail: h.x.zhang@yeah.net; Liu, E.

    2014-09-15

    Owing to the various valuable biological activities, steroidal amides have become a hot topic in steroidal pharmaceutical chemistry. In this paper, an anti-tumor steroid derivate (DAAO) was synthesized and identified. The interaction between DAAO and human serum albumin (HSA) was studied by fluorescence spectra, circular dichroism (CD) spectra, molecular modeling and molecular probe techniques. The results suggested that DAAO had reacted with HSA through hydrogen bonds and van der Waals power. The formation of DAAO–HSA complex at ground state led to static quenching of HSA's fluorescence. The number of binding sites, binding constants, enthalpy change (ΔH{sup θ}), Gibbs free energy change (ΔG{sup θ}) and entropy change (ΔS{sup θ}) were calculated at different temperatures based on fluorescence quenching theory and classic equation. Molecular modeling investigation indicated that DAAO was more inclined to absorb on Sudlow's site I in subdomain IIA of HSA molecule on grounds of the lowest energy principle and steric hindrance effect. The binding location was further confirmed by fluorescence probe experiment using warfarin (site I probe) for displacement. Furthermore, the conformational changes of HSA in presence of DAAO were investigated by CD spectra. The results could provide new evidence explaining the relationship between the chemical structure and biological activity and may be useful for understanding the anti-cancer mechanism of steroidal drug. - Highlights: • A designed steroidal amide compound (DAAO) was synthesized by introducing amido bonds into a steroid nucleus. • DAAO binds to Sudlow's site I in HSA through hydrogen bonds and van der Waals power. • The interaction was a spontaneous and exothermic process with modest degree of reversibility. • The secondary structure of HSA and the microenvironment of TRP214 altered. • Amido bond in steroid nucleus (–NH–CO–) plays important role in stabling the structure of

  20. Single Molecule Switches and Molecular Self-Assembly: Low Temperature STM Investigations and Manipulations

    International Nuclear Information System (INIS)

    This dissertation is devoted to single molecule investigations and manipulations of two porphyrin-based molecules, chlorophyll-a and Co-popphyrin. The molecules are absorbed on metallic substrates and studied at low temperatures using a scanning tunneling microscope. The electronic, structural and mechanical properties of the molecules are investigated in detail with atomic level precision. Chlorophyll-a is the key ingredient in photosynthesis processes while Co-porphyrin is a magnetic molecule that represents the recent emerging field of molecular spintronics. Using the scanning tunneling microscope tip and the substrate as electrodes, and the molecules as active ingredients, single molecule switches made of these two molecules are demonstrated. The first switch, a multiple and reversible mechanical switch, is realized by using chlorophyll-a where the energy transfer of a single tunneling electron is used to rotate a C-C bond of the molecule's tail on a Au(111) surface. Here, the det

  1. On the vibrational behavior of graphynes and its family: a molecular dynamics investigation

    Energy Technology Data Exchange (ETDEWEB)

    Rouhi, S.; Salmalian, K., E-mail: s_rouhi@iaul.ac.ir [Young Researchers Club, Langroud Branch, Islamic Azad University, Langroud, Guilan (Iran, Islamic Republic of); Ghasemi, A. [Young Researchers and Elite Club, Science and Research Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of)

    2015-10-01

    Molecular dynamics (MD) simulation is used to investigate the vibrational behavior of γ-graphyne and its family. Five different nanosheet types including graphyne, graphdiyne, 3-graphyne, 4-graphyne, and 5-graphyne are considered for investigation. The fundamental natural frequencies of armchair and zigzag nanosheets with different geometrical sizes under different boundary conditions are computed. It is shown that increasing the size of γ-graphyne results in decreasing the natural frequency. Comparing the vibrational behavior of armchair and zigzag nanosheets, it is shown that for large nanosheets, the effect of atomic structure on the fundamental natural frequency can be neglected. Besides, it is represented that increasing the number of acetylene links connecting neighboring hexagons in the structure of nanosheets leads to decreasing the frequency. (author)

  2. Investigation of the influence factors of polyethylene molecule encapsulated into carbon nanotubes by molecular dynamics simulation

    International Nuclear Information System (INIS)

    In this work, the influence factors, namely chirality, temperature, radius and surface chemical modification, of the interaction energy for polyethylene (PE) molecule encapsulated into single-walled carbon nanotubes (SWNTs) had been investigated by molecular mechanics (MM) and molecular dynamics (MD) simulation. The results showed that all these factors would influence the interaction energy between PE and SWNTs. The interaction energy between PE molecule and the armchair SWNTs is largest among eight kinds of chiral SWNTs. The interaction energy decreases with the increase of temperature or the SWNT radius. The methyl, phenyl, hydroxyl, carboxyl, -F, and amino groups, have been introduced onto the surface of the SWNTs by the simulation software and the influence of SWNT chemical modification has also been investigated. The interaction energy between PE and chemically modified SWNTs is larger than that between PE and pristine SWNTs, and increases with increasing the concentration of the modified groups monotonously. In addition, the group electronegativity and van der Waals force will affect the interaction energy between PE and chemically modified SWNTs greatly, which can be attributed to the electronic structures of the chemically modified groups. This study can provide some useful suggestions for the composite material design and drug transport.

  3. [Molecular interactions in dilute supercritical mixtures: Molecular dynamics investigation]. Final technical report, December 1, 1990--August 31, 1993

    Energy Technology Data Exchange (ETDEWEB)

    Debenedetti, P.G.

    1993-12-31

    Research was done in the following areas: computational and theoretical studies of molecular interactions in supercritical mixtures; supercooled liquids, network fluids, and glasses; and fast algorithms for simulating large systems on a vector processor.

  4. Application of Molecular Genetics to the Investigation of Inherited Bleeding Disorders

    DEFF Research Database (Denmark)

    Lethagen, Stefan Rune; Dunø, Morten; Nielsen, Lars Bo

    causative mutation is unknown. More rare bleeding disorders are generally recessively inherited, and are often caused by mutations that are specific for individual families, and mutations are scattered throughout the genes. Laboratories performing molecular genetic analyses must have validated internal......Hemophilia is an inherited bleeding disorder primarily caused by deficiency of coagulation factor (F)VIII (hemophilia A) or FIX (hemophilia B). Both conditions are X-linked. More than 2100 different F8 mutations have been described, the most common being a 500 kb inversion involving exon 1 to exon...... 22. In hemophilia B, more than 1100 unique F9 mutations have been described scattered all over the gene. Carrier analysis, genetic counseling, prenatal and pre-implantation genetic diagnosis are all based on correct identifying the disease-causing mutation. Linkage analysis can be considered when the...

  5. The pathology of familial breast cancer: Immunohistochemistry and molecular analysis

    International Nuclear Information System (INIS)

    Extensive studies of BRCA1- and BRCA2-associated breast tumours have been carried out in the few years since the identification of these familial breast cancer predisposing genes. The morphological studies suggest that BRCA1 tumours differ from BRCA2 tumours and from sporadic breast cancers. Recent progress in immunohistochemistry and molecular biology techniques has enabled in-depth investigation of molecular pathology of these tumours. Studies to date have investigated issues such as steroid hormone receptor expression, mutation status of tumour suppressor genes TP53 and c-erbB2, and expression profiles of cell cycle proteins p21, p27 and cyclin D1. Despite relative paucity of data, strong evidence of unique biological characteristics of BRCA1-associated breast cancer is accumulating. BRCA1-associated tumours appear to show an increased frequency of TP53 mutations, frequent p53 protein stabilization and absence of imunoreactivity for steroid hormone receptors. Further studies of larger number of samples of both BRCA1- and BRCA2-associated tumours are necessary to clarify and confirm these observations

  6. Molecular activation analysis for organo-halogen contaminants in yogurt

    International Nuclear Information System (INIS)

    The concentrations of total halogen (TX), extractable organo-halogen (EOX), extractable persistent organo-halogen (EPOX), organo-chlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) in 18 different yogurt specimens of 14 brands from Beijing, Tianjin, Shanghai, Guangzhou and Shijiazhuang were determined by epithermal neutron activation analysis (ENAA), molecular activation analysis (MAA) and GC-Mass Spectrometry (GC-MS), respectively. The results indicated that the halogen in yogurt mainly existed as inorganic species and non-extractable organo-halogen compounds. About 1/3 to 1/4 of EOX was EPOX. Further, EOCl and EPOCl were the main organo-halogen species in yogurt. The average concentration of the unknown organo-chlorine was 96% of the EPOCl. HCHs and DDTs were still the main contaminants of OCPs in the yogurt of interest. Also, PCB202, PCB103 and PCB208 were the main contaminants of PCBs. (authors)

  7. Molecular analysis of Boophilus spp. (Acari: Ixodidae) tick strains.

    Science.gov (United States)

    Fuente, J; García-García, J C; González, D M; Izquierdo, G; Ochagavia, M E

    2000-10-01

    Boophilus spp. (Acari: Ixodidae) parasitize cattle and other farm and wild animals in tropical and subtropical regions of the world. Ticks belonging to the genus Boophilus have undergone evolutionary processes associated with habitat adaptation following biogeographical separation, resulting in strains with marked morphological differences. We have characterized at the molecular level B. microplus strains from Latin America and Australia, employing sequences derived from the bm86 coding region, an intron located within the bm86 gene, and DNA short tandem repeats (STR). A B. annulatus strain was employed for comparison. The results indicated that variation within the bm86 coding region is higher between B. microplus strains than between some B. microplus strains and B. annulatus. The sequence of the intron was not informative for phylogenetic analysis, varying among individuals of the same strain. Two STRs were identified in B. microplus (STRs BmM1 and BmM2) and one in B. annulatus (STR Ba1). Southern hybridization experiments with STRs BmM1 and BmM2 as a probe revealed the prevalence of dispersed moderately repeated DNA in the genome of B. microplus. The analysis of polymorphism at STR locus BmM1 evidenced differences within and between populations of B. microplus. These results support at the molecular level the existing differences between B. microplus strains and suggest tools to characterize these populations. PMID:10962158

  8. Molecular genetic analysis of Dongzhou-period ancient human of Helingeer in Inner Mongolia, China

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The mtDNA hypervariable region I (HVR-I) of 10 ancient individuals from Dongzhou-period ancient human populations in Helingeer county of Inner Mongolia were amplified and sequenced to investigate the genetic structure. The relationships between the ancient population and related extant populations, as well as its possible origin at the molecular level, were also studied. Moreover, phylogenetic analysis and multi-dimensional scaling analysis were also performed based on the mtDNA data of the ancient population in Helingeer and the related Eurasian population. The results showed that the ancient population in Helingeer were closer to the northern Asian populations than to the other compared populations in matrilineal lineage. Combining the research results of archaeology and anthropology as well as molecular biology, we inferred that they were nomads who migrated from Mongolia plateau and cis-Baikal region to Helingeer in Inner Mongolia, China.

  9. Investigation of molecular mechanisms and regulatory pathways of pro-angiogenic nanorods

    Science.gov (United States)

    Nethi, Susheel Kumar; Veeriah, Vimal; Barui, Ayan Kumar; Rajendran, Saranya; Mattapally, Saidulu; Misra, Sanjay; Chatterjee, Suvro; Patra, Chitta Ranjan

    2015-05-01

    Angiogenesis, a process involving the growth of new blood vessels from the pre-existing vasculature, plays a crucial role in various pathophysiological conditions. We have previously demonstrated that europium hydroxide [EuIII(OH)3] nanorods (EHNs) exhibit pro-angiogenic properties through the generation of reactive oxygen species (ROS) and mitogen activated protein kinase (MAPK) activation. Considering the enormous implication of angiogenesis in cardiovascular diseases (CVDs) and cancer, it is essential to understand in-depth molecular mechanisms and signaling pathways in order to develop the most efficient and effective alternative treatment strategy for CVDs. However, the exact underlying mechanism and cascade signaling pathways behind the pro-angiogenic properties exhibited by EHNs still remain unclear. Herein, we report for the first time that the hydrogen peroxide (H2O2), a redox signaling molecule, generated by these EHNs activates the endothelial nitric oxide synthase (eNOS) that promotes the nitric oxide (NO) production in a PI3K (phosphoinositide 3-kinase)/Akt dependent manner, eventually triggering angiogenesis. We intensely believe that the investigation and understanding of the in-depth molecular mechanism and signaling pathways of EHNs induced angiogenesis will help us in developing an effective alternative treatment strategy for cardiovascular related and ischemic diseases where angiogenesis plays an important role.Angiogenesis, a process involving the growth of new blood vessels from the pre-existing vasculature, plays a crucial role in various pathophysiological conditions. We have previously demonstrated that europium hydroxide [EuIII(OH)3] nanorods (EHNs) exhibit pro-angiogenic properties through the generation of reactive oxygen species (ROS) and mitogen activated protein kinase (MAPK) activation. Considering the enormous implication of angiogenesis in cardiovascular diseases (CVDs) and cancer, it is essential to understand in-depth molecular

  10. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations

    Science.gov (United States)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-01

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K+ ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K+ ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K+ ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K+ ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  11. NCI-Molecular Analysis for Therapy Choice (NCI-MATCH) Trial

    Science.gov (United States)

    NCI's gateway for information about the NCI-Molecular Analysis for Therapy Choice (NCI-MATCH) trial, in which patients with advanced cancer are assigned to treatment arms based on the molecular profiles of their disease.

  12. Investigating the effects of chemistry on molecular line profiles of infalling low mass cores

    CERN Document Server

    Roberts, Julia F; Rawlings, Jonathan M C

    2010-01-01

    We have coupled a chemical model with two dynamical models of collapsing low mass star-forming cores to predict abundances across the core of the commonly used infall tracers, CS and HCO$^+$, at various stages of the collapse. The models investigated are a new ambipolar diffusion model and the `inside-out' collapse model. We have then used these results as an input to a radiative transfer model to predict the line profiles of several transitions of these molecules. For the inside-out collapse model, we predict significant molecular depletion due to freeze-out in the core centre, which prevents the formation of the blue asymmetry (believed to be the `signature' of infall) in the line profiles. Molecular depletion also occurs in the ambipolar diffusion model during the late stages of collapse, but the line profiles still exhibit a strong blue asymmetry due to extended infall. For the inside-out collapse model to exhibit the blue asymmetry it is necessary to impose a negative kinetic temperature gradient on the ...

  13. Molecular-orbital and structural descriptors in theoretical investigation of electroreduction of nitrodiazoles

    Directory of Open Access Journals (Sweden)

    BRANKO KOLARIC

    2005-07-01

    Full Text Available It is shown how a simple theoretical approach can be used for the investigation of electro-organic reactions.Mononitroimidazoles and mononitropyrazoles were studied by the semiempirical MNDO-PM3 molecular orbital method. The electrochemical reduction potentials of diazoles have been correlated with the energy of the lowest unoccupied molecular orbital (LUMO. It was found that an admirable correlation could be obtained by the introduction of simple structural descriptors as a correction to the energy of the LUMO. The interaction of a molecule with its surrounding depends on electrostatic potential and on steric hindrance. Most of these steric effects are taken into account using two parameters having a very limited set of integer values. The first (b is the position of a ring substituent regarding ring nitrogens, which accounts for the different orientations of dipole moments and for the different shape of the electrostatic potential. The second (structural parameter (t is the type of the ring, which accounts mostly for different modes of electrode approach, and for different charge polarization patterns in two diazole rings. The extended correlation with ELUMO, b and t, is very good, having a regression coefficient r = 0.991. The intrinsic importance of b and t is exemplified by their high statistical weight.

  14. Investigation of the silicon ion density during molecular beam epitaxy growth

    CERN Document Server

    Eifler, G; Ashurov, K; Morozov, S

    2002-01-01

    Ions impinging on a surface during molecular beam epitaxy influence the growth and the properties of the growing layer, for example, suppression of dopant segregation and the generation of crystal defects. The silicon electron gun in the molecular beam epitaxy (MBE) equipment is used as a source for silicon ions. To use the effect of ion bombardment the mechanism of generation and distribution of ions was investigated. A monitoring system was developed and attached at the substrate position in the MBE growth chamber to measure the ion and electron densities towards the substrate. A negative voltage was applied to the substrate to modify the ion energy and density. Furthermore the current caused by charge carriers impinging on the substrate was measured and compared with the results of the monitoring system. The electron and ion densities were measured by varying the emission current of the e-gun achieving silicon growth rates between 0.07 and 0.45 nm/s and by changing the voltage applied to the substrate betw...

  15. Molecular dynamics investigation of the ionic liquid/enzyme interface: application to engineering enzyme surface charge.

    Science.gov (United States)

    Burney, Patrick R; Nordwald, Erik M; Hickman, Katie; Kaar, Joel L; Pfaendtner, Jim

    2015-04-01

    Molecular simulations of the enzymes Candida rugosa lipase and Bos taurus α-chymotrypsin in aqueous ionic liquids 1-butyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium ethyl sulfate were used to study the change in enzyme-solvent interactions induced by modification of the enzyme surface charge. The enzymes were altered by randomly mutating lysine surface residues to glutamate, effectively decreasing the net surface charge by two for each mutation. These mutations resemble succinylation of the enzyme by chemical modification, which has been shown to enhance the stability of both enzymes in ILs. After establishing that the enzymes were stable on the simulated time scales, we focused the analysis on the organization of the ionic liquid substituents about the enzyme surface. Calculated solvent charge densities show that for both enzymes and in both solvents that changing positively charged residues to negative charge does indeed increase the charge density of the solvent near the enzyme surface. The radial distribution of IL constituents with respect to the enzyme reveals decreased interactions with the anion are prevalent in the modified systems when compared to the wild type, which is largely accompanied by an increase in cation contact. Additionally, the radial dependence of the charge density and ion distribution indicates that the effect of altering enzyme charge is confined to short range (≤1 nm) ordering of the IL. Ultimately, these results, which are consistent with that from prior experiments, provide molecular insight into the effect of enzyme surface charge on enzyme stability in ILs. PMID:25641162

  16. Investigation of molecular markers related to fecundity in local egyptian sheep

    International Nuclear Information System (INIS)

    The present experimental work aimed to investigate a number of molecular makers that influence fecundity in local Egyptian sheep. In the present study, twenty two (11 twin producing crossbred ewes, 7 single lamb producing crossbred ewes, 2 crossbred rams from twin producing ewes and 2 pure bred rams from twin producing ewes) were tested. They were carefully selected from the records of the Egyptian Nuclear Research Centre. The ewes were selected for their twin production in three repetitive production cycles while the rams were selected for being produced from prolific ewes as above. The presence of the booroola fecundity gene (FecB) (FecB mutation in bone morphogenic protein receptor gene 1B (BMPR1B)) and the Inverdale gene (FecXI) (FecXI mutation in bone morphogenic receptor gene (BMP15)) using Forced restriction PCR of the FecB and FecXI mutations, 190 base pair (bp) was amplified using specific primer which was forward (5'-CCAGAGGACAATAGCAAAGCAAA -3') and reverse (5'-CAAGATGTTTTCATGCCTCATCAACAGGTC -3' ) and designed to introduce a point mutation in the resulting PCR products with FecB carrier sheep containing an AvaII restriction site (G|GACC). The FecB DNA test showed that there were no carriers for the FecB mutation in the selected prolific sheep sample. When a specific primer which was forward (5'-GAAGTAACCAGTGTTCCCTCCACCCTTTTCT-3') and reverse (5'-CATGATTGGGAGAATTGAGACC-3') used to test the presence of FecXI mutation no amplification resulted from DNA samples of the twin producing ewes while two amplified DNA fragments of molecular size 154 bp and 120 bp resulted from the single lamb producing females and male sheep under study. Serum samples were collected from sheep under study and tested using totallab 120 computer software analyses for Native protein gel images. Gel images revealed a protein pattern in twin producing ewe samples characterized by the presence of three bands with molecular weights 679.7, 524.3, and 431.1 kd and the absence two bands with

  17. A co-axially configured submillimeter spectrometer and investigations of hydrogen bound molecular complexes

    Science.gov (United States)

    McElmurry, Blake Anthony

    The development of a co-axially configured submillimeter spectrometer is reported. The spectrometer has been constructed to observe molecular complexes that exhibit non-covalent interactions with energies much less than that of a traditional covalent bond. The structure of molecular complexes such as those formed between a rare gas and a hydrogen halide, Rg:HX where Rg is a rare gas (Rg=Ne, Ar and Kr) and HX (X=F, Cl, Br and I) can be determined directly and accurately. The center of mass interaction distance, RCM, as well as the angle of the hydrogen halide is determined, along with direct evaluation of the intermolecular vibrations as well as accurate isomerization energies between the hydrogen bound and van der Waals forms. The accuracy of the frequency determination of rovibrational transitions using the submillimeter spectrometer is also evaluated by direct comparison with the state-of-the-art pulsed nozzle Fourier transform microwave spectrometer, and this accuracy is estimated to be less than 1 kHz at 300 GHz. The tunneling or geared bending vibration of a dimer of hydrogen bromide or hydrogen iodide has been investigated. The selection rules, nuclear statistics and intensity alternation for transitions observed in these dimmers, which is a consequence of interchanging two identical nuclei in the low frequency geared bending vibration of the molecular complex, are reported. Furthermore, the rotation and quadrupole coupling constants are used to determine a vibrationally averaged structure of the complex. The energy of the low frequency bending vibration can then be compared with ab initio based potential energy surfaces. A study of the multiple isomeric forms of the molecular complex OC:HI is also presented. Multiple isotopic substitutions are used to determine the relevant ground state structures and data reported evidence for an anomalous isotope effect supporting a ground state isotopic isomerization effect. All spectroscopic data that has been reported

  18. Molecular Dynamics Investigation of Adhesion between TATB Surfaces and Amorphous Fluoropolymers

    Energy Technology Data Exchange (ETDEWEB)

    Gee, R H; Maiti, A; Bastea, S; Fried, L

    2007-01-25

    Atomistic simulations are used to study the adhesion properties of amorphous perfluoro- and fluoro-polymers onto two different crystal surfaces of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Properties of the bulk amorphous polymer melts are also investigated. The fluoropolymers studied in this article include Kel-F 800, Teflon{reg_sign} AF, Hyflon AD{reg_sign}, and Cytop{reg_sign}. Simulations of the bulk polymer melts were performed over a wide range of temperatures including the volumetric glass transition temperature, so as to validate the interaction parameters used. The computed glass transition temperatures and densities compare well with experiment. The solubility parameters for the various polymers also compare well with calculations based on group additive methods. The local molecular structure at the TATB interface, as well as the degree of adhesion varies from one polymer to another. All polymers except Hyflon show a propensity to readily wet the two TATB surfaces studied.

  19. Electron microscopy investigation of interface between carbon fiber and ultra high molecular weight polyethylene

    Energy Technology Data Exchange (ETDEWEB)

    Stepashkin, A.A.; Chukov, D.I., E-mail: dil_chukov@yahoo.com; Gorshenkov, M.V.; Tcherdyntsev, V.V.; Kaloshkin, S.D.

    2014-02-15

    Highlights: • Effect of the carbon fibers surface treatments on the adhesive interactions in UHMWPE composites was studied. • Air oxidation of carbon filler ensures most significant increase in adhesion interaction in UHMWPE based composites. • Nanosized UHMWPE fibers with 20–40 nm in diameter and with 6–10 μm in length, was observed on the surface of carbon fibers. -- Abstract: Scanning electron microscopy was used to investigate the surface of initial and modified high-strength and high-modulus carbon fibers as well as interfaces in the ultra high molecular weight polyethylene, filled with above-mentioned fibers. Effect of the fibers surface modifying method on the adhesive interactions in composites was studied. It was observed that interaction of matrix with a modified surface of fibers results in a formation of bonds with strength higher than the yield strength of the polymer. It results in a formation of long nanosized polymer wires at tensile fracture of composites.

  20. Characterisation of bacteria in ascites--reporting the potential of culture-independent, molecular analysis.

    Science.gov (United States)

    Rogers, G B; Russell, L E; Preston, P G; Marsh, P; Collins, J E; Saunders, J; Sutton, J; Fine, D; Bruce, K D; Wright, M

    2010-05-01

    Spontaneous bacterial peritonitis (SBP) is a severe complication of liver disease. A significant proportion of patients have culture-negative ascites, despite having similar signs, symptoms and mortality to those with SBP. Therefore, empirical antibiotic treatment for infection is often started without knowledge of the causative organisms. Here, we investigated the potential of molecular techniques to provide rapid and accurate characterisation of the bacteria present in ascitic fluid. Ascites samples were obtained from 29 cirrhotic patients undergoing clinically indicated therapeutic paracentesis. Bacterial content was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis, quantitative polymerase chain reaction (PCR) and 16S ribosomal clone sequence analysis. Bacterial signal was detected in all samples, compared to three out of ten using standard methods. Bacterial loads ranged from 5.5 x 10(2) to 5.4 x 10(7) cfu/ml, with a mean value of 1.9 x 10(6) cfu/ml (standard deviation +/- 9.6 x 10(6) cfu/ml). In all but one instance, bacterial species identified by culture were also confirmed by molecular analyses. Preliminary data presented here suggests that culture-independent, molecular analyses could provide rapid characterisation of the bacterial content of ascites fluid, providing a basis for the investigation of SBP development and allowing early and targeted antibiotic intervention. PMID:20238135

  1. Molecular dynamics investigation of the interaction of dislocations with carbides in BCC Fe

    Science.gov (United States)

    Granberg, F.; Terentyev, D.; Nordlund, K.

    2015-06-01

    Different types of carbides are present in many steels used as structural materials. To safely use steel in demanding environments, like nuclear power plants, it is important to know how defects will affect the mechanical properties of the material. In this study, the effect of carbide precipitates on the edge dislocation movement is investigated. Three different types of carbides were investigated by means of molecular dynamics, with a Tersoff-like bond order interatomic potential by Henriksson et al. The obstacles were 4 nm in diameter and were of Fe3C- (cementite-), Fe23C6- and Cr23C6-type. The critical unpinning stress was calculated for each type at different temperatures, to get the temperature-dependent obstacle strength. The results showed a decreasing critical stress with increasing temperature, consistent with previous studies. The critical unpinning stress was seen to be dependent on the type of carbide, but the differences were small. A difference was also observed between the obstacles with the same structure, but with different composition. This study shows the relation between the existing Cr23C6 carbide and the experimentally non-existing Fe23C6 carbide, which needs to be used as a model system for investigations with interatomic potentials not able to describe the interaction of Cr in the Fe-C-system. We found the difference to be a between 7% and 10% higher critical unpinning stress for the chromium carbide, than for the iron carbide of the same type.

  2. Molecular mechanics and microcalorimetric investigations of the effects of molecular water on the aggregation of asphaltenes in solutions

    DEFF Research Database (Denmark)

    Murgich, J.; Lira-Galeana, C.; Garcia, Daniel Merino; Andersen, Simon Ivar; del Rio-Garcia, J.M.

    2002-01-01

    The interaction of two model asphaltene molecules from the Athabasca sand oil with a water molecule in a toluene solution was studied by means of molecular mechanics calculations. It was found that water forms bridging H bonds between the heteroatoms of asphaltenes with a considerable span in ene...

  3. Compressive characteristics of single walled carbon nanotube with water interactions investigated by using molecular dynamics simulation

    International Nuclear Information System (INIS)

    The elastic properties of single walled carbon nanotube (SWCNT) with surrounding water interactions are studied using molecular dynamics simulation technique. The compressive loading characteristic of carbon nanotubes (CNTs) in a fluidic medium such as water is critical for its role in determining the lifetime and stability of CNT based nano-fluidic devices. In this paper, we conducted a comprehensive analysis on the effect of geometry, chirality and density of encapsulated water on the elastic properties of SWCNT. Our studies show that defect density and distribution can strongly impact the compressive resistance of SWCNTs in water. Further studies were conducted on capped SWCNTs with varying densities of encapsulated water, which is necessary to understand the strength of CNT as a potential drug carrier. The results obtained from this paper will help determining the potential applications of CNTs in the field of nano-electromechanical systems (NEMS) such as nano-biological and nano-fluidic devices.

  4. Compressive characteristics of single walled carbon nanotube with water interactions investigated by using molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Wong, C.H., E-mail: chwong@ntu.edu.sg; Vijayaraghavan, V.

    2014-01-24

    The elastic properties of single walled carbon nanotube (SWCNT) with surrounding water interactions are studied using molecular dynamics simulation technique. The compressive loading characteristic of carbon nanotubes (CNTs) in a fluidic medium such as water is critical for its role in determining the lifetime and stability of CNT based nano-fluidic devices. In this paper, we conducted a comprehensive analysis on the effect of geometry, chirality and density of encapsulated water on the elastic properties of SWCNT. Our studies show that defect density and distribution can strongly impact the compressive resistance of SWCNTs in water. Further studies were conducted on capped SWCNTs with varying densities of encapsulated water, which is necessary to understand the strength of CNT as a potential drug carrier. The results obtained from this paper will help determining the potential applications of CNTs in the field of nano-electromechanical systems (NEMS) such as nano-biological and nano-fluidic devices.

  5. Investigation of Localized States in GaAsSb Epilayers Grown by Molecular Beam Epitaxy

    Science.gov (United States)

    Gao, Xian; Wei, Zhipeng; Zhao, Fenghuan; Yang, Yahui; Chen, Rui; Fang, Xuan; Tang, Jilong; Fang, Dan; Wang, Dengkui; Li, Ruixue; Ge, Xiaotian; Ma, Xiaohui; Wang, Xiaohua

    2016-01-01

    We report the carrier dynamics in GaAsSb ternary alloy grown by molecular beam epitaxy through comprehensive spectroscopic characterization over a wide temperature range. A detailed analysis of the experimental data reveals a complex carrier relaxation process involving both localized and delocalized states. At low temperature, the localized degree shows linear relationship with the increase of Sb component. The existence of localized states is also confirmed by the temperature dependence of peak position and band width of the emission. At temperature higher than 60 K, emissions related to localized states are quenched while the band to band transition dominates the whole spectrum. This study indicates that the localized states are related to the Sb component in the GaAsSb alloy, while it leads to the poor crystal quality of the material, and the application of GaAsSb alloy would be limited by this deterioration. PMID:27381641

  6. Gene Expression Profiling as a Tool to Investigate the Molecular Machinery Activated during Hippocampal Neurodegeneration Induced by Trimethyltin (TMT Administration

    Directory of Open Access Journals (Sweden)

    Maria Concetta Geloso

    2013-08-01

    Full Text Available Trimethyltin (TMT is an organotin compound exhibiting neurotoxicant effects selectively localized in the limbic system and especially marked in the hippocampus, in both experimental animal models and accidentally exposed humans. TMT administration causes selective neuronal death involving either the granular neurons of the dentate gyrus or the pyramidal cells of the Cornu Ammonis, with a different pattern of localization depending on the different species studied or the dosage schedule. TMT is broadly used to realize experimental models of hippocampal neurodegeneration associated with cognitive impairment and temporal lobe epilepsy, though the molecular mechanisms underlying the associated selective neuronal death are still not conclusively clarified. Experimental evidence indicates that TMT-induced neurodegeneration is a complex event involving different pathogenetic mechanisms, probably acting differently in animal and cell models, which include neuroinflammation, intracellular calcium overload, and oxidative stress. Microarray-based, genome-wide expression analysis has been used to investigate the molecular scenario occurring in the TMT-injured brain in different in vivo and in vitro models, producing an overwhelming amount of data. The aim of this review is to discuss and rationalize the state-of-the-art on TMT-associated genome wide expression profiles in order to identify comparable and reproducible data that may allow focusing on significantly involved pathways.

  7. Investigation of vital pathogenic target orotate phosphoribosyltransferases (OPRTase) from Thermus thermophilus HB8: Phylogenetic and molecular modeling approach.

    Science.gov (United States)

    Surekha, Kanagarajan; Prabhu, Damodharan; Richard, Mariadasse; Nachiappan, Mutharasappan; Biswal, Jayashree; Jeyakanthan, Jeyaraman

    2016-06-01

    Biosynthesis pathways of pyrimidine and purine are shown to play an important role in regular cellular activities. The biosynthesis can occur either through de novo or salvage pathways based on the requirement of the cell. The pyrimidine biosynthesis pathway has been linked to several disorders and various autoimmune diseases. Orotate phosphoribosyl transferase (OPRTase) is an important enzyme which catalyzes the conversion of orotate to orotate monophosphate in the fifth step of pyrimidine biosynthesis. Phylogenetic analysis of 228 OPRTase sequences shows the distribution of proteins across different living forms of life. High structural similarities between Thermusthermophilus and other organisms kindled us to concentrate on OPRTase as an anti-pathogenic target. In this study, a homology model of OPRTase was constructed using 2P1Z as a template. About 100ns molecular dynamics simulation was performed to investigate the conformational stability and dynamic patterns of the protein. The amino acid residues (Met1, Asp2, Glu43, Ala44, Glu47, Lys51, Ala157 and Leu158) lining in the binding site were predicted using SiteMap. Further, structure based virtual screening was performed on the predicted binding site using ChemBridge, Asinex, Binding, NCI, TosLab and Zinc databases. Compounds retrieved from the screening collections were manually clustered. The resultant protein-ligand complexes were subjected to molecular dynamics simulations, which further validates the binding modes of the hits. The study may provide better insight for designing potent anti-pathogenic agent. PMID:26861612

  8. Human cell culture models for investigating molecular and cytogenetic changes in radiation carcinogenesis

    International Nuclear Information System (INIS)

    Primary cultures of human epithelial cells have proved difficult to transform because of the inherent short duration that these cells can be cultured. However, primary cultures of human cells can be immortalised using the catalytic sub-unit of telomerase (hTERT). Radiation carcinogenesis has been investigated using a human retinal pigment epithelial cell line (340RPE-T53 hTERT). Transformants can be selected using anchorage independent growth and cell lines derived from these are tumourigenic in immunosupressed mice. Molecular cytogenetic changes using CGH, SKY and FISH with breakpoint-specific YAC- and BAC- probes revealed a high level amplification on 10p11.2 in several clones which has been identified as an atypical protein kinase C binding protein using FISH gene-specific PCR products. Patterns of gene expression were studied using HuGen Human cDNA arrays using indirect labelling. The control parent RPE cell line could then be compared with cloned radiation-induced tumour cell lines derived from it following fractionated doses of gamma irradiation. Osteonectin was down regulated in 4 different tumour lines. This gene maps to a region of chromosome 5q that is commonly deleted in leukaemia. Nexin and p105 were down regulated in 3 lines and tumour suppressing subtransferable candidate 1 in I line. Further hTERT immortalised cell lines have been derived from primary cultures of human mammary epithelial cells. The breast epithelium contains a number of different cell types and the lines have been characterised using immunocytochemical techniques. The cells are cytokeratin 19 negative but CD10, cytokeratin 5 and p63 positive indicating a basal cell phenotype. Following exposure to fractionated doses of gamma irradiation anchorage independent colonies are formed. Thus human cell lines immortalised with hTERT are providing a useful model system for investigating radiation carcinogenesis and the molecular and cytogenetic changes induced. Supported by EC Nuclear Fission

  9. STRUCTURAL ANALYSIS AND MOLECULAR DYNAMICS STUDY OF PHB SYNTHASE

    Directory of Open Access Journals (Sweden)

    T. Femlin Blessia

    2012-02-01

    Full Text Available Polyhydroxybutyrate (PHB is a polyhydroxyalkanoate (PHA, a polymer belonging to polyesters class and is composed of hydroxy fatty acids. PHB is produced by microorganisms apparently in response to conditions of physiological stress. PHB synthases are the key enzymes of PHB biosynthesis. The PHB synthases obtained from Chromobacterium violaceum, belongs to the class I PHA synthases. Due to the limited structural information of PHB synthase, its functional properties including catalysis are unknown. Therefore, this study seeks to investigate the structural and functional properties of PHB synthase (phaC by predicting its three dimensional structure using bioinformatics methods. Present 15 ns molecular dynamics study provides an overall insight about some of the parameters such as energy, RMSD (Root Mean Square Deviation, SASA (Solvent Accessible Surface Area, hydrogen bonds, etc., Protein-protein docking reveals the binding mode of the protein in the active dimer state.

  10. Genetic diversity analysis of common beans based on molecular markers

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    2011-01-01

    Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  11. Genetic diversity of popcorn genotypes using molecular analysis.

    Science.gov (United States)

    Resh, F S; Scapim, C A; Mangolin, C A; Machado, M F P S; do Amaral, A T; Ramos, H C C; Vivas, M

    2015-01-01

    In this study, we analyzed dominant molecular markers to estimate the genetic divergence of 26 popcorn genotypes and evaluate whether using various dissimilarity coefficients with these dominant markers influences the results of cluster analysis. Fifteen random amplification of polymorphic DNA primers produced 157 amplified fragments, of which 65 were monomorphic and 92 were polymorphic. To calculate the genetic distances among the 26 genotypes, the complements of the Jaccard, Dice, and Rogers and Tanimoto similarity coefficients were used. A matrix of Dij values (dissimilarity matrix) was constructed, from which the genetic distances among genotypes were represented in a more simplified manner as a dendrogram generated using the unweighted pair-group method with arithmetic average. Clusters determined by molecular analysis generally did not group material from the same parental origin together. The largest genetic distance was between varieties 17 (UNB-2) and 18 (PA-091). In the identification of genotypes with the smallest genetic distance, the 3 coefficients showed no agreement. The 3 dissimilarity coefficients showed no major differences among their grouping patterns because agreement in determining the genotypes with large, medium, and small genetic distances was high. The largest genetic distances were observed for the Rogers and Tanimoto dissimilarity coefficient (0.74), followed by the Jaccard coefficient (0.65) and the Dice coefficient (0.48). The 3 coefficients showed similar estimations for the cophenetic correlation coefficient. Correlations among the matrices generated using the 3 coefficients were positive and had high magnitudes, reflecting strong agreement among the results obtained using the 3 evaluated dissimilarity coefficients. PMID:26345916

  12. Investigating the Molecular Basis of Retinal Degeneration in a Familial Cohort of Pakistani Decent by Exome Sequencing.

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    Bruno Maranhao

    Full Text Available To define the molecular basis of retinal degeneration in consanguineous Pakistani pedigrees with early onset retinal degeneration.A cohort of 277 individuals representing 26 pedigrees from the Punjab province of Pakistan was analyzed. Exomes were captured with commercial kits and sequenced on an Illumina HiSeq 2500. Candidate variants were identified using standard tools and analyzed using exomeSuite to detect all potentially pathogenic changes in genes implicated in retinal degeneration. Segregation analysis was performed by dideoxy sequencing and novel variants were additionally investigated for their presence in ethnicity-matched controls.We identified a total of nine causal mutations, including six novel variants in RPE65, LCA5, USH2A, CNGB1, FAM161A, CERKL and GUCY2D as the underlying cause of inherited retinal degenerations in 13 of 26 pedigrees. In addition to the causal variants, a total of 200 variants each observed in five or more unrelated pedigrees investigated in this study that were absent from the dbSNP, HapMap, 1000 Genomes, NHLBI ESP6500, and ExAC databases were identified, suggesting that they are common in, and unique to the Pakistani population.We identified causal mutations associated with retinal degeneration in nearly half of the pedigrees investigated in this study through next generation whole exome sequencing. All novel variants detected in this study through exome sequencing have been cataloged providing a reference database of variants common in, and unique to the Pakistani population.

  13. Nutritional Proteomics: Investigating molecular mechanisms underlying the health beneficial effect of functional foods

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    Yusuke Kawashima

    2013-07-01

    Full Text Available ABSTRACTObjective: We introduce a new technical and conceptual term “nutritional proteomics” by identifying and quantifying the proteins and their changes in a certain organ or tissue dependent on the food intake by utilizing a mass spectrometry-based proteomics technique.Purpose: Food intake is essentially important for every life on earth to sustain the physical as well as mental functions. The outcome of food intake will be manifested in the health state and its dysfunction. The molecular information about the protein expression change caused by diets will assist us to understand the significance of functional foods. We wish to develop nutritional proteomics to promote a new area in functional food studies for a better understanding of the role of functional foods in health and disease.Methods: We chose two classes of food ingredients to show the feasibility of nutritional proteomics, omega-3 polyunsaturated fatty acids and omega-6 polyunsaturated fatty acids both of which are involved in the inflammation/anti-inflammation axis. Each class of the polyunsaturated fatty acids was mixed in mouse chow respectively. The liver tissue of mice fed with omega-3 diet or omega-3 diet was analyzed by the state-of-the-art shotgun proteomics using nano-HPLC-ESI-MS/MS. The data were analyzed by the number of differentially expressed proteins that were guaranteed by 1% false discovery rate for protein identification and by the statistical significance of variance evaluated by p-value in two-tailed distribution analysis better than 0.05 (n=4. The differential pattern of protein expression was characterized with Gene Ontology designation.Results: The data analysis of the shotgun nutritional proteomics identified 2,810 proteins that are validated with 1% FDR. Among these 2,810 proteins, 125 were characterized with statistical significance of variance (p<0.05; n=4 between the omega-3 diet and the omega-6 diet by twotailed distribution analysis. The results

  14. Using molecular docking to investigate the anti-breast cancer activity of low molecular weight compounds present on wild mushrooms.

    OpenAIRE

    Froufe, Hugo J. C.; Abreu, Rui M. V.; Ferreira, Isabel C. F. R.

    2011-01-01

    Mushrooms represent an unlimited source of compounds with antitumor and immunostimulating properties and mushroom intake as been shown to reduce the risk of breast cancer. A large number of LMW (low molecular weight) compounds present in mushrooms have been identified including: phenolic acids, flavonoids, tocopherols, carotenoids, sugars and fatty acids. In order to evaluate which wild mushroom LMW compounds may be involved in anti-breast cancer activity we selected a representative dataset ...

  15. Experimental and computational study on molecular structure and vibrational analysis of an antihyperglycemic biomolecule: Gliclazide

    Science.gov (United States)

    Karakaya, Mustafa; Kürekçi, Mehmet; Eskiyurt, Buse; Sert, Yusuf; Çırak, Çağrı

    2015-01-01

    In present study, the experimental and theoretical harmonic vibrational frequencies of gliclazide molecule have been investigated. The experimental FT-IR (400-4000 cm-1) and Laser-Raman spectra (100-4000 cm-1) of the molecule in the solid phase were recorded. Theoretical vibrational frequencies and geometric parameters (bond lengths and bond angles) have been calculated using ab initio Hartree Fock (HF), density functional theory (B3LYP hybrid function) methods with 6-311++G(d,p) and 6-31G(d,p) basis sets by Gaussian 09W program. The assignments of the vibrational frequencies were performed by potential energy distribution (PED) analysis by using VEDA 4 program. Theoretical optimized geometric parameters and vibrational frequencies have been compared with the corresponding experimental data, and they have been shown to be in a good agreement with each other. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies have been found.

  16. Molecular analysis of microbial diversity in corrosion samples from energy transmission towers.

    Science.gov (United States)

    Oliveira, Valéria M; Lopes-Oliveira, Patrícia F; Passarini, Michel R Z; Menezes, Claudia B A; Oliveira, Walter R C; Rocha, Adriano J; Sette, Lara D

    2011-04-01

    Microbial diversity in corrosion samples from energy transmission towers was investigated using molecular methods. Ribosomal DNA fragments were used to assemble gene libraries. Sequence analysis indicated 10 bacterial genera within the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. In the two libraries generated from corroded screw-derived samples, the genus Acinetobacter was the most abundant. Acinetobacter and Clostridium spp. dominated, with similar percentages, in the libraries derived from corrosion scrapings. Fungal clones were affiliated with 14 genera belonging to the phyla Ascomycota and Basidiomycota; of these, Capnobotryella and Fellomyces were the most abundant fungi observed. Several of the microorganisms had not previously been associated with biofilms and corrosion, reinforcing the need to use molecular techniques to achieve a more comprehensive assessment of microbial diversity in environmental samples. PMID:21563009

  17. Investigation of Molecular Marker Lipids in Alpine Ice Cores Via Stir Bar Sorptive Extraction

    Science.gov (United States)

    Makou, M. C.; Eglinton, T. I.; Thompson, L. G.; Hughen, K. A.

    2005-12-01

    Recently developed analytical techniques were employed to identify and quantify organic molecular markers trapped in high-altitude ice. While various compounds represent potentially useful proxies for biomass burning, vegetation type, atmospheric circulation, and anthropogenic activity, prior attempts to measure organic compounds in ice cores have typically required large volumes of sample material that are incompatible with generation of high-resolution paleoclimate records. We employed stir bar sorptive extraction (SBSE) and thermal desorption (TD), coupled with gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS), to examine the organic content of small quantities (≤ 30 ml) of ice. To test the utility of the approach, post-industrial ice core samples from the Huascarán and Sajama sites (Andes), the Dasuopu and Puruogangri sites (Tibetan Plateau), and Mt. Kilimanjaro (east Africa) were tested. n-Alkanes, n-alkanoic acids, n-alkyl amides and nitriles, polycyclic aromatic hydrocarbons (PAHs), and various diterpenoids were identified in this suite of cores. These marker compounds suggest inputs from biomass burning, fresh vascular plant material, and anthropogenic activities such as fossil fuel combustion. Differences in distributions of the alkyl amide and nitrile homologues between the different sites suggest a predominantly local or regional supply of organic matter. Pre-industrial samples from the Sajama and Puruogangri ice cores were also analyzed in order to assess the character of biomarker assemblages in the absence of anthropogenic contributions and investigate changes in inputs over time. PAHs and diterpenoids, which may result from biomass burning and were observed in the modern Sajama samples, occurred in two Holocene Sajama samples, but not in a last glacial sample. Enhanced inputs of terrestrial vegetation combustion biomarkers were consistent with periods of enhanced aridity in both cores. This study demonstrates the utility of SBSE, TD

  18. Low energy Cu clusters slow deposition on a Fe (001) surface investigated by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Highlights: • We study the deposition of low energy Cu clusters on Fe (001) surface by molecular dynamics. • The interaction between low energy cluster and substrate can be divided to the landing and the thermal diffusion phases. • The phenomenon of contact epitaxy of cluster occurred. • The thermal diffusion of cluster atoms was analyzed. - Abstract: The slow deposition of low energy Cu clusters on a Fe (001) surface was investigated by molecular dynamics simulation. A many-body potential based on Finnis–Sinclair model was used to describe the interactions among atoms. Three clusters comprising of 13, 55 and 147 atoms, respectively, were deposited with incident energies ranging from 0.0 to 1.0 eV/atom at various substrate temperatures (0, 300 and 800 K). The rearrangement and the diffusion of cluster can occur, only when the cluster atoms are activated and obtained enough migration energy. The interaction between low energy cluster and substrate can be divided to the landing and the thermal diffusion phases. In the former, the migration energy originates from the latent heat of binding energy for the soft deposition regime and primarily comes from the incident energy of cluster for the energetic cluster deposition regime. In the latter, the thermal vibration would result in some cluster atoms activated again at medium and high substrate temperatures. Also, the effects of incident energy, cluster size and substrate temperature on the interaction potential energy between cluster and substrate, the final deposition morphology of cluster, the spreading index and the structure parameter of cluster are analyzed

  19. Investigation of the silicon ion density during molecular beam epitaxy growth

    International Nuclear Information System (INIS)

    Ions impinging on a surface during molecular beam epitaxy influence the growth and the properties of the growing layer, for example, suppression of dopant segregation and the generation of crystal defects. The silicon electron gun in the molecular beam epitaxy (MBE) equipment is used as a source for silicon ions. To use the effect of ion bombardment the mechanism of generation and distribution of ions was investigated. A monitoring system was developed and attached at the substrate position in the MBE growth chamber to measure the ion and electron densities towards the substrate. A negative voltage was applied to the substrate to modify the ion energy and density. Furthermore the current caused by charge carriers impinging on the substrate was measured and compared with the results of the monitoring system. The electron and ion densities were measured by varying the emission current of the e-gun achieving silicon growth rates between 0.07 and 0.45 nm/s and by changing the voltage applied to the substrate between 0 to -1000 V. The dependencies of ion and electron densities were shown and discussed within the framework of a simple model. The charged carrier densities measured with the monitoring system enable to separate the ion part of the substrate current and show its correlation to the generation rate. Comparing the ion density on the whole substrate and in the center gives a hint to the ion beam focusing effect. The maximum ion and electron current densities obtained were 0.40 and 0.61 μA/cm2, respectively

  20. Linking healthcare associated norovirus outbreaks: a molecular epidemiologic method for investigating transmission

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    Andrews Nick

    2006-07-01

    Full Text Available Abstract Background Noroviruses are highly infectious pathogens that cause gastroenteritis in the community and in semi-closed institutions such as hospitals. During outbreaks, multiple units within a hospital are often affected, and a major question for control programs is: are the affected units part of the same outbreak or are they unrelated transmission events? In practice, investigators often assume a transmission link based on epidemiological observations, rather than a systematic approach to tracing transmission. Here, we present a combined molecular and statistical method for assessing: 1 whether observed clusters provide evidence of local transmission and 2 the probability that anecdotally|linked outbreaks truly shared a transmission event. Methods 76 healthcare associated outbreaks were observed in an active and prospective surveillance scheme of 15 hospitals in the county of Avon, England from April 2002 to March 2003. Viral RNA from 64 out of 76 specimens from distinct outbreaks was amplified by reverse transcription-PCR and was sequenced in the polymerase (ORF 1 and capsid (ORF 2 regions. The genetic diversity, at the nucleotide level, was analysed in relation to the epidemiological patterns. Results Two out of four genetic and epidemiological clusters of outbreaks were unlikely to have occurred by chance alone, thus suggesting local transmission. There was anecdotal epidemiological evidence of a transmission link among 5 outbreaks pairs. By combining this epidemiological observation with viral sequence data, the evidence of a link remained convincing in 3 of these pairs. These results are sensitive to prior beliefs of the strength of epidemiological evidence especially when the outbreak strains are common in the background population. Conclusion The evidence suggests that transmission between hospitals units does occur. Using the proposed criteria, certain hypothesized transmission links between outbreaks were supported while

  1. Molecular dynamics investigations of BioH protein substrate specificity for biotin synthesis.

    Science.gov (United States)

    Xue, Qiao; Cui, Ying-Lu; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2016-05-01

    BioH, an enzyme of biotin synthesis, plays an important role in fatty acid synthesis which assembles the pimelate moiety. Pimeloyl-acyl carrier protein (ACP) methyl ester, which is long known to be a biotin precursor, is the physiological substrate of BioH. Azelayl methyl ester, which has a longer chain than pimeloyl methyl ester, conjugated to ACP is also indeed accepted by BioH with very low rate of hydrolysis. To date, the substrate specificity for BioH and the molecular origin for the experimentally observed rate changes of hydrolysis by the chain elongation have remained elusive. To this end, we have investigated chain elongation effects on the structures by using the fully atomistic molecular dynamics simulations combined with binding free energy calculations. The results indicate that the substrate specificity is determined by BioH together with ACP. The added two methylenes would increase the structural flexibility by protein motions at the interface of ACP and BioH, instead of making steric clashes with the side chains of the BioH hydrophobic cavity. On the other hand, the slower hydrolysis of azelayl substrate is suggested to be associated with the loose of contacts between BioH and ACP, and with the lost electrostatic interactions of two ionic/hydrogen bonding networks at the interface of the two proteins. The present study provides important insights into the structure-function relationships of the complex of BioH with pimeloyl-ACP methyl ester, which could contribute to further understanding about the mechanism of the biotin synthetic pathway, including the catalytic role of BioH. PMID:26132538

  2. Relationships of Campanian olive cultivars: comparative analysis of molecular and phenotypic data.

    Science.gov (United States)

    Corrado, Giandomenico; La Mura, Maurizio; Ambrosino, Orsola; Pugliano, Giuseppe; Varricchio, Paola; Rao, Rosa

    2009-08-01

    Estimation of the genetic relatedness of traditional olive cultivars with genetic markers and phenotypic data enables progress in plant breeding, management of genetic resources, and protection of both breeders' rights and certified premium products. We used amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), and quantitative and qualitative morphological traits, including characteristics recommended for variety registration, to study genetic diversity and relationships in the olive at different levels. The 14 varieties analyzed, which are used for the production of Protected Denomination of Origin extra-virgin olive oil, represent the most important cultivars in the Campania region of Italy and typify a regional diversity characteristic of traditional olive cultivation. The genetic distances obtained with the two DNA marker systems were significantly correlated, as were those obtained by quantitative and qualitative traits. A lower but significant correlation was also observed between distances based on molecular markers and quantitative traits, but qualitative traits, even if sampled in high numbers, failed to describe the pattern of molecular similarity. Our data imply that the type and the number of phenotypic traits scored can greatly influence the outcome of the analysis, and care should be taken when qualitative and quantitative data are combined. Furthermore, the data indicate that the two molecular marker systems are useful for investigating genetic relationships, but they may also be used to complement and assist the traditional registration of varieties. We propose that since the information provided by molecular and morphological marker systems in olive is different, they should serve different purposes. PMID:19767899

  3. Investigations on the usefulness of CEACAMs as potential imaging targets for molecular imaging purposes.

    Directory of Open Access Journals (Sweden)

    Markus Heine

    Full Text Available Members of the carcinoembryonic antigen cell adhesion molecules (CEACAMs family are the prototype of tumour markers. Classically they are used as serum markers, however, CEACAMs could serve as targets for molecular imaging as well.In order to test the anti CEACAM monoclonal antibody T84.1 for imaging purposes, CEACAM expression was analysed using this antibody. Twelve human cancer cell lines from different entities were screened for their CEACAM expression using qPCR, Western Blot and FACS analysis. In addition, CEACAM expression was analyzed in primary tumour xenografts of these cells. Nine of 12 tumour cell lines expressed CEACAM mRNA and protein when grown in vitro. Pancreatic and colon cancer cell lines showed the highest expression levels with good correlation of mRNA and protein level. However, when grown in vivo, the CEACAM expression was generally downregulated except for the melanoma cell lines. As the CEACAM expression showed pronounced expression in FemX-1 primary tumours, this model system was used for further experiments. As the accessibility of the antibody after i.v. application is critical for its use in molecular imaging, the binding of the T84.1 monoclonal antibody was assessed after i.v. injection into SCID mice harbouring a FemX-1 primary tumour. When applied i.v., the CEACAM specific T84.1 antibody bound to tumour cells in the vicinity of blood vessels. This binding pattern was particularly pronounced in the periphery of the tumour xenograft, however, some antibody binding was also observed in the central areas of the tumour around blood vessels. Still, a general penetration of the tumour by i.v. application of the anti CEACAM antibody could not be achieved despite homogenous CEACAM expression of all melanoma cells when analysed in tissue sections. This lack of penetration is probably due to the increased interstitial fluid pressure in tumours caused by the absence of functional lymphatic vessels.

  4. Investigation of flap flexibility of β-secretase using molecular dynamic simulations.

    Science.gov (United States)

    Kumalo, Hezekiel M; Bhakat, Soumendranath; Soliman, Mahmoud E

    2016-05-01

    Flap motif and its dynamics were extensively reported in aspartate proteases, e.g. HIV proteases and plasmepsins. Herein, we report the first account of flap dynamics amongst different conformations of β-secretase using molecular dynamics simulation. Various parameters were proposed and a selected few were picked which could appropriately describe the flap motion. Three systems were studied, namely Free (BACEFree) and two ligand-bound conformations, which belonged to space groups P6122 (BACEBound1) and C2221 (BACEBound2), respectively and four parameters (distance between the flaps tip residue, Thr72 and Ser325, d1; dihedral angle, ϕ (Thr72-Asp32-Asp228-Ser325); TriCα angles, θ1 (Thr72-Asp32-Ser325), and θ2 (Thr72-Asp228-Ser325)) were proposed to understand the change in dynamics of flap domain and the extent of flap opening and closing. Analysis of, θ2, d1, θ1 and ϕ confirmed that the BACEFree adopted semi-open, open and closed conformations with slight twisting during flap opening. However, BACEBound1 (P6122) showed an adaptation to open conformation due to lack of hydrogen bond interaction between the ligand and flap tip residue. A slight flap twisting, ϕ (lateral twisting) was observed for BACEBound1 during flap opening which correlates with the opening of BACEFree. Contradictory to the BACEBound1, the BACEBound2 locked the flap in a closed conformation throughout the simulation due to formation of a stable hydrogen bond interaction between the flap tip residue and ligand. Analyses of all three systems highlight that d1, θ2 and ϕ can be precisely used to describe the extent of flap opening and closing concurrently with snapshots along the molecular dynamics trajectory across several conformations of β-secretase. PMID:26208540

  5. In silico analysis of the molecular mechanism of postmenopausal osteoporosis.

    Science.gov (United States)

    Liu, Yanqing; Wang, Yueqiu; Yang, Nailong; Wu, Suning; Lv, Yanhua; Xu, Lili

    2015-11-01

    Postmenopausal osteoporosis (PO) is a common disease in females >50 years of age worldwide and is becoming an increasing burden to society. The present study aimed to assess the molecular mechanism of PO using bioinformatic methods. The gene expression data from patients with PO and normal controls were downloaded from the ArrayExpress database provided by European Bioinformatics Institute. Following the screening of the differentially expressed genes (DEGs) using the Limma package in R language, Kyoto Encyclopedia of Genes and Genomes pathways enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery online tools. Sequentially, modulators of the DEGs, including transcription factors (TFs) and microRNAs, were predicted by the ChIP Enrichment Analysis databases and WEB‑based GEne SeT AnaLysis Toolkit system, respectively. In addition, the protein‑protein interaction network of DEGs was constructed via the search tool for the retrieval of interacting genes and then the functional modules were further analyzed via the clusterMaker package and The Biological Networks Gene Ontology package within the Cytoscape software. A total of 482 DEGs, including 279 upregulated and 203 downregulated DEGs, were screened out. DEGs were predominantly enriched in the pathways of fatty acid metabolism, cardiac muscle contraction and DNA replication. TFs, including SMAD4, in addition to microRNAs, including the microRNA‑125 (miR‑125) family, miR‑331 and miR‑24, may be the modulators of the DEGs in PO. In addition, the five largest modules were identified with TTN, L1G1, ACADM, UQCRC2 and TRIM63 as the hub proteins, and they were associated with the biological processes of muscle contraction, DNA replication initiation, lipid modification, generation of precursor metabolites and energy, and regulation of acetyl‑CoA biosynthetic process, respectively. SMAD4, CACNG1 and TRIM63 are suggested to be important factors in the

  6. Molecular analysis of radiation-induced experimental tumors in mice

    International Nuclear Information System (INIS)

    Molecular analysis was made on mouse tumors induced by radiation and chemicals. Expression of oncogenes was studied in 12 types of 178 mouse tumors. Southern blotting was done on tumors in which overexpression of oncogenes was noted. Amplification of the myc oncogene was found in chemically induced sarcomas, but not those induced by radiations. Radiogenic thymomas were studied in detail. These thymomas were induced in two different ways. The first was thymomas induced by direct irradiation of F1 mice between C57BL/6NxC3H/He. Southern analysis of DNA revealed deletion of specific minisatellite bands in these tumors. DNA from directly induced thymomas induced focus formation when transfected into normal Golden hamster cells. The mouse K-ras oncogene was detected in these transformants. The second type of thymomas was induced by X-irradiation of thymectomized B10.thy1.2 mice in which normal thymus from congenic B10,thy1.1. mice was grafted. Thymomas of the donor origin was analysed by transfection and the transformants by DNA from those indirectly induced thymomas did not contain activated ras oncogenes. (author)

  7. Investigating the influence of effective parameters on molecular characteristics of bovine serum albumin nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Rohiwal, S.S.; Satvekar, R.K.; Tiwari, A.P.; Raut, A.V.; Kumbhar, S.G.; Pawar, S.H., E-mail: pawar_s_h@yahoo.com

    2015-04-15

    Graphical abstract: The physiochemical properties of nanoparticles provide the basic aspects about the conformational transitions which could have a strong bearing on the bioavailability for bioactive molecules such as peptides and hormones. - Highlights: • Synthesis and surface and structural properties of Bovine Serum Albumin nanoparticles (BSANPs). • Study of conformational transitions of BSANPs by spectroscopic techniques. • Studies on the effect of pH and protein concentration on formulation of BSANPs. - Abstract: The protein nanoparticles formulation is a challenging task as they are prone to undergo conformational transitions while processing which may affect bioavailability for bioactive compounds. Herein, a modified desolvation method is employed to prepare Bovine Serum Albumin nanoparticles, with controllable particle size ranging from 100 to 300 nm and low polydispersity index. The factors influencing the size and structure of BSA NPs viz. protein concentration, pH and the conditions for purification are well investigated. The structure of BSA NPs is altered due to processing, and may affect the effective binding ability with drugs and bioactive compounds. With that aims, investigations of molecular characteristics of BSA NPs are carried out in detail by using spectroscopic techniques. UV–visible absorption and Fourier Transform Infrared demonstrate the alteration in protein structure of BSA NPs whereas the FT-Raman spectroscopy investigates changes in the secondary and tertiary structures of the protein. The conformational changes of BSA NPs are observed by change in fluorescence intensity and emission maximum wavelength of tryptophan residue by fluorescence spectroscopy. The field emission scanning electron and atomic force microscopy micrographs confirm the size and semi-spherical morphology of the BSA NPs. The effect of concentration and pH on particle size distribution is studied by particle size analyzer.

  8. Molecular dynamics investigation of the interaction of dislocations with carbides in BCC Fe

    Energy Technology Data Exchange (ETDEWEB)

    Granberg, F., E-mail: fredric.granberg@helsinki.fi [Department of Physics, P.O. Box 43, FIN-00014 University of Helsinki (Finland); Terentyev, D. [Nuclear Materials Science Institute, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Nordlund, K. [Department of Physics, P.O. Box 43, FIN-00014 University of Helsinki (Finland)

    2015-06-01

    Different types of carbides are present in many steels used as structural materials. To safely use steel in demanding environments, like nuclear power plants, it is important to know how defects will affect the mechanical properties of the material. In this study, the effect of carbide precipitates on the edge dislocation movement is investigated. Three different types of carbides were investigated by means of molecular dynamics, with a Tersoff-like bond order interatomic potential by Henriksson et al. The obstacles were 4 nm in diameter and were of Fe{sub 3}C- (cementite-), Fe{sub 23}C{sub 6}- and Cr{sub 23}C{sub 6}-type. The critical unpinning stress was calculated for each type at different temperatures, to get the temperature-dependent obstacle strength. The results showed a decreasing critical stress with increasing temperature, consistent with previous studies. The critical unpinning stress was seen to be dependent on the type of carbide, but the differences were small. A difference was also observed between the obstacles with the same structure, but with different composition. This study shows the relation between the existing Cr{sub 23}C{sub 6} carbide and the experimentally non-existing Fe{sub 23}C{sub 6} carbide, which needs to be used as a model system for investigations with interatomic potentials not able to describe the interaction of Cr in the Fe–C-system. We found the difference to be a between 7% and 10% higher critical unpinning stress for the chromium carbide, than for the iron carbide of the same type.

  9. Investigating the influence of effective parameters on molecular characteristics of bovine serum albumin nanoparticles

    International Nuclear Information System (INIS)

    Graphical abstract: The physiochemical properties of nanoparticles provide the basic aspects about the conformational transitions which could have a strong bearing on the bioavailability for bioactive molecules such as peptides and hormones. - Highlights: • Synthesis and surface and structural properties of Bovine Serum Albumin nanoparticles (BSANPs). • Study of conformational transitions of BSANPs by spectroscopic techniques. • Studies on the effect of pH and protein concentration on formulation of BSANPs. - Abstract: The protein nanoparticles formulation is a challenging task as they are prone to undergo conformational transitions while processing which may affect bioavailability for bioactive compounds. Herein, a modified desolvation method is employed to prepare Bovine Serum Albumin nanoparticles, with controllable particle size ranging from 100 to 300 nm and low polydispersity index. The factors influencing the size and structure of BSA NPs viz. protein concentration, pH and the conditions for purification are well investigated. The structure of BSA NPs is altered due to processing, and may affect the effective binding ability with drugs and bioactive compounds. With that aims, investigations of molecular characteristics of BSA NPs are carried out in detail by using spectroscopic techniques. UV–visible absorption and Fourier Transform Infrared demonstrate the alteration in protein structure of BSA NPs whereas the FT-Raman spectroscopy investigates changes in the secondary and tertiary structures of the protein. The conformational changes of BSA NPs are observed by change in fluorescence intensity and emission maximum wavelength of tryptophan residue by fluorescence spectroscopy. The field emission scanning electron and atomic force microscopy micrographs confirm the size and semi-spherical morphology of the BSA NPs. The effect of concentration and pH on particle size distribution is studied by particle size analyzer

  10. Mathematical analysis of compressive/tensile molecular and nuclear structures

    Science.gov (United States)

    Wang, Dayu

    Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

  11. Thermal behaviour of molecular sieves (SAPO-11/AIPO-11 type) investigated by synchrotron radiation X-ray diffraction (SRXD)

    International Nuclear Information System (INIS)

    The structure of molecular sieves is important for a successful application as a catalyzer. The final structure of the synthetic product depends on the technological steps. This process was investigated by in-situ Synchrotron radiation X-ray diffraction. Structural changes in the molecular sieves exist not only during the heating process but also during the following cooling process. (author) 3 figs., 2 refs

  12. Use of an in vitro muscle model to investigate cellular and molecular aspects of exercise physiology: Answering the key questions

    OpenAIRE

    Player, D. J.; Martin, N. R. W.; Davies, P; Sculthorpe, N.; Castle, P. C.; Passey, S.; Mudera, V.; Ferguson, R.; Lewis, M. P.

    2011-01-01

    Research within exercise physiology has traditionally focused upon measurements of gross physiological function of skeletal muscle. However, in order to develop a greater understanding of the exact mechanisms that contribute to skeletal muscle in response to exercise, the cellular and molecular determinants need to be investigated. There is a growing body of in vivo research utilising methods of molecular biology, which has led to the establishment of proposed genes and proteins involved in t...

  13. Investigating Molecular Inheritance of Carbon in Star-forming Regions along a Galactic Gradient

    KAUST Repository

    Smith, Rachel L.

    2015-04-01

    Observations of CO isotopologues taken at high spectral resolution toward young stellar objects (YSOs) are valuable tools for investigating protoplanetary chemical reservoirs, and enable robust comparisons between YSOs and solar system material (meteorites and the Sun). Investigating a range of YSO environments also helps parameterize variations in the distribution and evolution of carbon-based molecules, furthering an understanding of prebiotic chemistry. We have begun a wide survey of massive YSOs using Keck-NIRSPEC at high spectral resolution (R=25,000). Fundamental and first-overtone near-IR CO rovibrational absorption spectra have thus far been obtained toward 14 massive, luminous YSOs at Galactocentric radii (RGC) ranging from ~4.5 to 9.7 kpc. From these data we can obtain precise [12CO]/[13CO] gas-phase abundance ratios along a Galactic gradient, and [12CO]/[13CO]Gas can be further evaluated against published [12CO2]/[13CO2]Ice and [12CO]/[13CO]Ice because all observations are in absorption, a robust study of molecular inheritance is possible by virtue of comparing 12C/13C along the same lines-of-sight. Initial results for cold CO gas at RGC ~ 6.1 kpc and 9.4 kpc reveal [12C16O]/[13C16O] of 59+/‑8 and 74+/‑3, respectively, roughly following an expected 12C/13C Galactic gradient. Thus far, we find [12CO]/[13CO] in the cold CO gas to be lower than [12CO2]/[13CO2]Ice, suggesting that CO2 may not originate from CO reservoirs as often assumed. While very high-resolution observations of CO gas toward low-mass YSOs observed with VLT-CRIRES show significant heterogeneity in [12CO]/[13CO] at RGC ~ 8 kpc, this dispersion is not found for the massive YSOs. Both the low-mass and massive YSOs have higher [12CO]/[13CO] in warm vs. cold gas, and both show signatures suggesting possible interplay between CO ice and gas reservoirs. Overall, our results indicate that carbon isotopic evolution in massive YSO environments may follow different paths compared to low-mass YSOs

  14. Using molecular docking to investigate the anti-breast cancer activity of low molecular weight compounds present on wild mushrooms.

    Science.gov (United States)

    Froufe, H J C; Abreu, R M V; Ferreira, I C F R

    2011-06-01

    Mushrooms represent an unlimited source of compounds with anti-tumour and immunostimulating properties, and their intake has been shown to reduce the risk of breast cancer. A large number of low molecular weight (LMW) compounds present in mushrooms have been identified, including phenolic acids, flavonoids, tocopherols, carotenoids, sugars and fatty acids. In order to evaluate which wild mushroom LMW compounds may be involved in anti-breast cancer activity we selected a representative dataset of 43 LMW compounds and performed molecular docking against three known protein targets involved in breast cancer (aromatase, estrone sulfatase and 17β-HSD-1) using AutoDock4 as docking software. The estimated inhibition constants for all LMW compounds were determined, and the potential structure-activity relationships for the compounds with the best estimated inhibition constants are discussed for each compound family. 4-O-caffeoylquinic, naringin and lycopene stand out as the top-ranked potential inhibitors for aromatase, estrone sulfatase and 17β-HSD1, respectively, and the 3-D docked conformations for these compounds are discussed in detail. This information provides several interesting starting points for further development of aromatase, estrone sulfatase and 17β-HSD1 inhibitors. PMID:21598196

  15. Can molecular projected density of states (PDOS be systematically used in electronic conductance analysis?

    Directory of Open Access Journals (Sweden)

    Tonatiuh Rangel

    2015-06-01

    Full Text Available Using benzenediamine and benzenedithiol molecular junctions as benchmarks, we investigate the widespread analysis of the quantum transport conductance in terms of the projected density of states (PDOS onto molecular orbitals (MOs. We first consider two different methods for identifying the relevant MOs: (1 diagonalization of the Hamiltonian of the isolated molecule and (2 diagonalization of a submatrix of the junction Hamiltonian constructed by considering only basis elements localized on the molecule. We find that these two methods can lead to substantially different MOs and hence PDOS. Furthermore, within Method 1, the PDOS can differ depending on the isolated molecule chosen to represent the molecular junction (e.g., with or without dangling bonds; within Method 2, the PDOS depends on the chosen basis set. We show that these differences can be critical when the PDOS is used to provide a physical interpretation of the conductance (especially when its value is small, as it happens typically at zero bias. In this work, we propose a new approach in an attempt to reconcile the two traditional methods. Although some improvements were achieved, the main problems remain unsolved. Our results raise more general questions and doubts on a PDOS-based analysis of the conductance.

  16. Optical, vibrational, NBO, first-order molecular hyperpolarizability and Hirshfeld surface analysis of a nonlinear optical chalcone.

    Science.gov (United States)

    Aditya Prasad, A; Muthu, K; Meenatchi, V; Rajasekar, M; Agilandeshwari, R; Meena, K; Vijila Manonmoni, J; Meenakshisundaram, S P

    2015-04-01

    The synthesis of (1E,4E)-1,5-di-p-tolylpenta-1,4-dien-3-one (DTDO) was done and its single crystals were grown by slow evaporation solution technique from 4-methylbenzaldehyde, acetone solution at room temperature. Crystal structure is determined by single crystal X-ray diffraction analysis and reveals that it belongs to the monoclinic system with four molecules in the unit cell (space group C2). The emission of green light from the sample confirms the second harmonic generation (SHG) of the specimen responsible for nonlinear optical property. The various vibration patterns of the specimen have been investigated by Fourier transform infrared and Fourier transform Raman spectroscopy. Optimized molecular geometry, vibrational patterns of DTDO are derived from density functional theory (DFT) calculations and the results are compared with experimental one. The molecular stability and bond strengths were investigated by applying the natural bond orbital analysis. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density with molecular electrostatic potential (MEP). Highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy gaps were calculated. The other molecular properties like charge transfer are explained using Mulliken population analysis and the first-order molecular hyperpolarizability (β) of the specimen is also estimated and SHG efficiency of DTDO was found to be 3.9 times that of KDP. Fingerprint plots and Hirshfeld surfaces were used to locate and analyze the molecular surface and bonding interactions in various methodologies utilized in the establishment of the relative energies. PMID:25615677

  17. Optical, vibrational, NBO, first-order molecular hyperpolarizability and Hirshfeld surface analysis of a nonlinear optical chalcone

    Science.gov (United States)

    Aditya Prasad, A.; Muthu, K.; Meenatchi, V.; Rajasekar, M.; Agilandeshwari, R.; Meena, K.; Vijila Manonmoni, J.; Meenakshisundaram, S. P.

    2015-04-01

    The synthesis of (1E,4E)-1,5-di-p-tolylpenta-1,4-dien-3-one (DTDO) was done and its single crystals were grown by slow evaporation solution technique from 4-methylbenzaldehyde, acetone solution at room temperature. Crystal structure is determined by single crystal X-ray diffraction analysis and reveals that it belongs to the monoclinic system with four molecules in the unit cell (space group C2). The emission of green light from the sample confirms the second harmonic generation (SHG) of the specimen responsible for nonlinear optical property. The various vibration patterns of the specimen have been investigated by Fourier transform infrared and Fourier transform Raman spectroscopy. Optimized molecular geometry, vibrational patterns of DTDO are derived from density functional theory (DFT) calculations and the results are compared with experimental one. The molecular stability and bond strengths were investigated by applying the natural bond orbital analysis. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density with molecular electrostatic potential (MEP). Highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy gaps were calculated. The other molecular properties like charge transfer are explained using Mulliken population analysis and the first-order molecular hyperpolarizability (β) of the specimen is also estimated and SHG efficiency of DTDO was found to be 3.9 times that of KDP. Fingerprint plots and Hirshfeld surfaces were used to locate and analyze the molecular surface and bonding interactions in various methodologies utilized in the establishment of the relative energies.

  18. PET/SPECT molecular imaging in clinical neuroscience: recent advances in the investigation of CNS diseases

    OpenAIRE

    Lu, Feng-Mei; Yuan, Zhen

    2015-01-01

    Molecular imaging is an attractive technology widely used in clinical practice that greatly enhances our understanding of the pathophysiology and treatment in central nervous system (CNS) diseases. It is a novel multidisciplinary technique that can be defined as real-time visualization, in vivo characterization and qualification of biological processes at the molecular and cellular level. It involves the imaging modalities and the corresponding imaging agents. Nowadays, molecular imaging in n...

  19. Low-dose laulimalide represents a novel molecular probe for investigating microtubule organization.

    Science.gov (United States)

    Bennett, Melissa J; Chan, Gordon K; Rattner, J B; Schriemer, David C

    2012-08-15

    Laulimalide is a natural product that has strong taxoid-like properties but binds to a distinct site on β-tubulin in the microtubule (MT) lattice. At elevated concentrations, it generates MTs that are resistant to depolymerization, and it induces a conformational state indistinguishable from taxoid-treated MTs. In this study, we describe the effect of low-dose laulimalide on various stages of the cell cycle and compare these effects to docetaxel as a representative of taxoid stabilizers. No evidence of MT bundling in interphase was observed with laulimalide, in spite of the fact that MTs are stabilized at low dose. Cells treated with laulimalide enter mitosis but arrest at prometaphase by generating multiple asters that coalesce into supernumerary poles and interfere with the integrity of the metaphase plate. Cells with a preformed bipolar spindle exist under heightened tension under laulimalide treatment, and chromosomes rapidly shear from the plate, even though the bipolar spindle is well-preserved. Docetaxel generates a similar phenotype for HeLa cells entering mitosis, but when treated at metaphase, cells undergo chromosomal fragmentation and demonstrate reduced centromere dynamics, as expected for a taxoid. Our results suggest that laulimalide represents a new class of molecular probe for investigating MT-mediated events, such as kinetochore-MT interactions, which may reflect the location of the ligand binding site within the interprotofilament groove. PMID:22871740

  20. Experimental investigation of generalized self-filtering unstable resonator in longitudinally excited molecular nitrogen laser

    International Nuclear Information System (INIS)

    In this research work the application of the generalized self-filtering unstable resonator (GSFUR) in a longitudinally excited molecular nitrogen laser has been investigated and compared with the plane-paral let resonator. In a typical design of magnification M=-5, the beam divergence of 0.33 mrad, and the brightness of 1.3x109 W divided to cm2.Sr have been obtained. For a plane-paral led resonator of equivalent length these figures are∼1 mrad and 2.3x107 W divided to cm2.SR respectively, where it is shown that in the GSFUR design there is a reduction in the beam divergence by a factor of 3 and enhancement in measured brightness by a factor of 56, as compared with the plane-paral led design. Using a field limiting aperture as an output coupler, the beam profile in the far-field and near-field were Gaussian and donut shape, respectively. A mathematical model based on the rate equations for the gain medium and equation for the electric circuit is introduced and the results are consistent with the experimental measurements

  1. A molecular dynamics investigation on the crizotinib resistance mechanism of C1156Y mutation in ALK

    International Nuclear Information System (INIS)

    Highlights: ► The study revealed the detailed resistance mechanism of the non-active mutation C1156Y in ALK. ► C1156Y leads to crizotinib displacement and conformational changes in the binding cavity. ► The conformations cause a decline in the vdW and electrostatic energy between crizotinib and ALK. -- Abstract: Crizotinib is an anaplastic lymphoma kinase (ALK) inhibitor that has recently been approved in the US for the treatment of non-small cell lung carcinoma (NSCLC). Despite its outstanding safety and efficacy, several resistant mutations against crizotinib have been detected in the treatment of NSCLC. However, in contrast to the widely accepted mechanism of steric hindrance by mutations at the active site, the mechanism by which the C1156Y non-active site mutation confers resistance against crizotinib remains unclear. In the present study, the resistance mechanism of C1156Y in ALK was investigated using molecular dynamics simulations. The results suggest that despite the non-active site mutation, C1156Y causes the dislocation of crizotinib as well as the indirect conformational changes in the binding cavity, which results in a marked decrease in the van der Waals and electrostatic interactions between crizotinib and ALK. The obtained results provide a detailed explanation of the resistance caused by C1156Y and may give a vital clue for the design of drugs to combat crizotinib resistance.

  2. Molecular dynamics investigation of structure and high-temperature mechanical properties of SiBCO ceramics

    International Nuclear Information System (INIS)

    Highlights: • The nano-domain structure of SiBCO is reproduced by large-scale atomistic simulations. • Calculated pair and angular distribution functions consist with experiments and DFT calculation. • Silicon atoms form mixed bonds tetrahedron with carbon and oxygen at domains interfaces. • Change in slope of temperature-dependent Young’s moduli indicates glass transition temperature. - Abstract: SiCO ceramics present excellent properties at high temperatures, the addition of boron for SiCO leads to enhanced performance on thermal stability and creep temperature. Investigating atomic structure and its influence on material property are essential for further study. In this study, large-scale molecular dynamics simulations were used to study amorphous SiBCO structures with different carbon contents. Phase separation and free carbon structures were successfully reproduced by melt-quench simulation. The calculated pair distribution functions of SiBCO are comparable to those of SiCO in experiments, the C–C–C angular distribution indicates strong sp2 carbon character together with a sp3 character. Si-centered tetrahedrons present in amorphous SiBCO and the most popular case is Si–C/O tetrahedron. Si3BC7O3 presents the largest Young’s modulus for all the temperatures due to the network structure of free carbon. A change in the slope of temperature-dependent Young’s moduli at 1300 K–1700 K for Si3BC3O3 indicates the glass transition temperature

  3. Ab initio investigation of the adsorption of atomic and molecular hydrogen on AlN nanotubes

    International Nuclear Information System (INIS)

    Highlights: • The adsorption characteristics of hydrogen inside the zigzag and armchair AlN nanotubes are explored. • The AlN nanotubes can store hydrogen up to 8.89 wt% with the average binding energies of 0.2–0.4 eV/H-2. - Abstract: The adsorption of atomic and molecular hydrogen on zigzag and armchair AlN nanotubes is investigated within the ab initio density functional theory. The adsorption configurations are magnetic when the H atom is adsorbed on the Al atom and the center of a hexagon. The total magnetic moment is 1.00 μB which comes from the H atom and the nearest neighbor N atoms. The barrier height of various adsorption configurations is very low, indicating that the adsorbed H atom can easily transform into other forms. The adsorption energies of hydrogen atoms to the zigzag and armchair AlN nanotubes are calculated at 25%, 50%, 75%, 100%, 133%, and 200% coverages, the most favorable adsorption configurations are 100% hydrogen coverages. The adsorption configuration of hydrogen molecule adsorbed on the Al atom is the most energetically favorable. Each Al atom is capable of binding one hydrogen molecule, corresponding to the hydrogen gravimetric density to 8.89 wt%. Our theoretical study demonstrates that AlN nanotube can be a potential candidate for the hydrogen storage materials

  4. Mechanistic investigations and molecular medicine applications of gold nanoparticle mediated (GNOME) laser transfection

    Science.gov (United States)

    Schomaker, M.; Heinemann, D.; Kalies, S.; Willenbrock, S.; Murua Escobar, H.; Buch, A.; Sodeik, B.; Ripken, T.; Meyer, H.

    2014-03-01

    Alternative high throughput transfection methods are required to understand the molecular network of the cell, which is linked to the evaluation of target genes as therapeutic agents. Besides diagnostic purposes, the transfection of primary- and stem cells is of high interest for therapeutic use. Here, the cell release of trans- or exogene proteins is used to develop immune cancer therapies. The basic requirement to accomplish manipulation of cells is an efficient and gentle transfection method. Therefore, we developed an automatized cell manipulation platform providing high throughput by using GNOME laser transfection. Herein, the interaction of moderately focused laser pulses with gold nanoparticles in close vicinity to the cell membrane mediate transient membrane permeabilization. The exact nature of the involved permeabilization effects depends on the applied particles and laser parameters. Hereinafter, we describe investigations considering the parameter regime, the permeabilization mechanism and the safety profile of GNOME laser transfection. The experimental and calculated results imply a combined permeabilization mechanism consisting of both photochemical and photothermal effects. Furthermore, paramount spatial control achieved either by laser illumination with micrometer precision or targeted gold nanoparticle binding to the cells was demonstrated, allowing selective cell manipulation and destruction. Additionally, the possibility to manipulate difficult to transfect primary cells (neurons) is shown. These results give insights in the basic mechanisms involved in GNOME laser transfection and serve as a strong basis to deliver different molecules for therapeutic (e.g. proteins) and diagnostic (siRNA) use.

  5. Investigation of the molecular similarity in closely related protein systems: The PrP case study.

    Science.gov (United States)

    Storchi, Loriano; Paciotti, Roberto; Re, Nazzareno; Marrone, Alessandro

    2015-10-01

    The amyloid conversion is a massive detrimental modification affecting several proteins upon specific physical or chemical stimuli characterizing a plethora of diseases. In many cases, the amyloidogenic stimuli induce specific structural features to the protein conferring the propensity to misfold and form amyloid deposits. The investigation of mutants, structurally similar to their native isoform but inherently prone to amyloid conversion, may be a viable strategy to elucidate the structural features connected with amyloidogenesis. In this article, we present a computational protocol based on the combination of molecular dynamics (MD) and grid-based approaches suited for the pairwise comparison of closely related protein structures. This method was applied on the cellular prion protein (PrP(C)) as a case study and, in particular, addressed to the quali/quantification of the structural features conferred by either E200K mutations and treatment with CaCl(2), both able to induce the scrapie conversion of PrP. Several schemes of comparison were developed and applied to this case study, and made up suitable of application to other protein systems. At this purpose an in-house python codes has been implemented that, together with the parallelization of the GRID force fields program, will spread the applicability of the proposed computational procedure. PMID:26018750

  6. First Principles Investigation of the C3 Coefficients for Molecular Adsorption on Transition Metal Surfaces

    Science.gov (United States)

    Kara, Abdelkader; Matos, Jeronimo; Yildirim, Handan

    2015-03-01

    C6 coefficients are used to investigate the strength of the long-range interactions for weakly interacting dimers as a function of separation distance. These coefficients are useful both as a measure for the accuracy of the various van der Waals (vdW) inclusive methods as well as reference for use in large-scale molecular dynamics simulations. In the case of molecule-surface interaction, the C3 coefficient is the counterpart to the C6 coefficient that is used for testing the interaction of dimers. We will present the results of the vdW inclusive density functional theory (DFT) calculations evaluating the C3 coefficients for the adsorption of M/X(110) and X(111), with X: Ag, Au, Cu, Pt, Pd, Ni, Rh and M: Benzene, Thiophene, Sexithiophene, Pentacene and Olympicene, as described by the PBE exchange-correlation functional and the self-consistent vdW-DF, optimized vdW-DFs and vdW-DF2 functionals. Work supported by the U.S. Department of Energy Basic Energy Science under Contract No. DE-FG02-11ER16243.

  7. Molecular dynamics investigation of the effect of copper nanoparticle on the solid contact between friction surfaces

    Science.gov (United States)

    Hu, Chengzhi; Bai, Minli; Lv, Jizu; Liu, Hao; Li, Xiaojie

    2014-12-01

    This study investigated the effect of copper (Cu) nanoparticles on the solid contact between friction surfaces by applying a molecular dynamics method to reveal the mechanisms responsible for the favorable friction properties of nanoparticles. Two models were built, which were named model A (without Cu) and model B (with Cu), respectively. The differences in the mechanical properties between these two models were compared. The simulation results demonstrated that the improvement in friction properties by Cu nanoparticles was more obvious at low velocity than at high velocity. At low velocity, a Cu nano-film was formed on the friction surface, which accommodated the velocity gradient and plastic deformation. Due to the good lubrication effect of the nano-film, the plastic deformation, defect structures and friction force of model B were improved compared with model A. Under high velocity conditions, a transfer layer appeared adjacent to the interface in both models. Because of this, the friction forces of the two models decreased with increased velocity. The fluid mechanics theory was used to explain why the friction force in model B was lower than that in model A at high velocity. The effect of the load on friction properties was also analyzed and the results showed that the mechanisms of anti-wear and friction reduction by Cu nanoparticles under a low load were the same as those under a high load.

  8. Investigation of ethanol infiltration into demineralized dentin collagen fibrils using molecular dynamics simulations.

    Science.gov (United States)

    Jee, Sang Eun; Zhou, Jienfeng; Tan, Jianquo; Breschi, Lorenzo; Tay, Franklin R; Grégoire, Geneviève; Pashley, David H; Jang, Seung Soon

    2016-05-01

    The purpose of this study is to investigate the interaction of neat ethanol with bound and non-bound water in completely demineralized dentin that is fully hydrated, using molecular dynamics (MD) simulation method. The key to creating ideal resin-dentin bonds is the removal of residual free water layers and its replacement by ethanol solvent in which resin monomers are soluble, using the ethanol wet-bonding technique. The test null hypotheses were that ethanol cannot remove any collagen-bound water, and that ethanol cannot infiltrate into the spacing between collagen triple helix due to narrow interlayer spacing. Collagen fibrillar structures of overlap and gap regions were constructed by aligning the collagen triple helix of infinite length in hexagonal packing. Three layers of the water molecules were specified as the layers of 0.15-0.22nm, 0.22-0.43nm and 0.43-0.63nm from collagen atoms by investigating the water distribution surrounding collagen molecules. Our simulation results show that ethanol molecules infiltrated into the intermolecular spacing in the gap region, which increased due to the lateral shrinkage of the collagen structures in contact with ethanol solution, while there was no ethanol infiltration observed in the overlap region. Infiltrated ethanol molecules in the gap region removed residual water molecules via modifying mostly the third water layer (50% decrease), which would be considered as a loosely-bound water layer. The first and second hydration layers, which would be considered as tightly bound water layers, were not removed by the ethanol molecules, thus maintaining the helical structures of the collagen molecules. PMID:26969524

  9. Performance Analysis on Molecular Dynamics Simulation of Protein Using GROMACS

    OpenAIRE

    Astuti, A. D.; Mutiara, A. B.

    2009-01-01

    Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example of molecular dynamics application developed by Groningen University. This application is a non-commercial and able to work in the operating system Linux. The main ability of Gromacs is to perform molecular dynamics simulation and minimization energy. In this...

  10. Molecular Modeling and Structural Analysis of Arylesterase of Ancylostoma Duodenale

    Science.gov (United States)

    Panda, Subhamay; Panda, Santamay; Kumari, Leena

    2016-01-01

    Parasitic worm infection of humans is one of the most commonly prevalent helminth infection that has imposed great impact on society and public health in the developing world. The two species of hookworm, namely Ancylostoma duodenale and Necator americanus may be primarily responsible for causing parasitic infections in human beings. The highly prevalent areas for Ancylostoma duodenale infections are mainly India, Middle East, Australia, northern Africa and other parts of the world. The serum arylesterases/paraoxonases are family of enzymes that is involved in the hydrolysis of a number of organophosphorus insecticides to the nontoxic products. The participation of the enzymes in the breakdown of a variety of organophosphate substrates that is generally made up of paraoxon and numerous aromatic carboxylic acid esters (e.g., phenyl acetate), and hence combats the toxic effect of organophosphates. The aim of the present investigation is to evaluate the arylesterases of Ancylostoma duodenale giving special importance to structure generation, validation of the generated models, distribution of secondary structural elements and positive charge distribution over the structure. By the implementation of comparative modeling approach we propose the first molecular model structure of arylesterases of Ancylostoma duodenale.

  11. Molecular analysis of mutants of the Neurospora adenylosuccinate synthetase locus

    Indian Academy of Sciences (India)

    A. Wiest; A. J. McCarthy; R. Schnittker; K. McCluskey

    2012-08-01

    The ad-8 gene of Neurospora crassa, in addition to being used for the study of purine biology, has been extensively studied as a model for gene structure, mutagenesis and intralocus recombination. Because of this there is an extensive collection of well-characterized N. crassa ad-8 mutants in the Fungal Genetics Stock Center collection. Among these are spontaneous mutants and mutants induced with X-ray, UV or chemical mutagens. The specific lesions in these mutants have been genetically mapped at high resolution. We have sequenced the ad-8 locus from 13 of these mutants and identified the molecular nature of the mutation in each strain. We compare the historical fine-structure map to the DNA and amino acid sequence of each allele. The placement of the individual lesions in the fine-structure map was more accurate at the 5′ end of the gene and no mutants were identified in the 3′ untranslated region of this gene. We additionally analysed ad-8+ alleles in 18 N. crassa strains subjected to whole-genome sequence analysis and describe the variability among Neurospora strains and among fungi and other organisms.

  12. Molecular genetic analysis of tumor suppressor genes in ovarian cancer

    International Nuclear Information System (INIS)

    To examine the loci of putative tumor suppressor genes in ovarian cancers, we performed the molecular genetic analysis with fresh human ovarian cancers and observed the following data. Frequent allelic losses were observed on chromosomes 4p(42%), 6p(50%), 7p(43%), 8q(31%), 12p(38%), 12q(33%), 16p(33%), 16q(37%), and 19p(34%) in addition to the previously reported 6q, 11p, and 17p in ovarian caroinomas. we have used an additional probe, TCP10 to narrow down the deleted region on chromosome 6q. TCP10 was reported to be mapped to 6q 25-27. Allelic loss was found to be 40% in epithelial ovarian caroinomas. This finding suggests that chromosome 6q 24-27 is one of putative region haboring the tumor suppressor gene of epithelial ovarian cancer (particularly serous type). To examine the association between FAL(Fractional Allelic Loss) and histopathological features, the FAL value on each phenotypically different tumor was calculated as the ratio of the number of allelic losses versus the number of cases informative in each chromosomal arm. The average FALs for each phenotypically different tumor were: serous cystoadenocarcinomas. FAL=0.31 : mucinous 0.12 : and clear cell carcinoma. FAL=0.20. (Author)

  13. Circumscribed sebaceous neoplasms: a morphological, immunohistochemical and molecular analysis.

    Science.gov (United States)

    Harvey, Nathan Tobias; Tabone, Tania; Erber, Wendy; Wood, Benjamin Andrew

    2016-08-01

    Sebaceous neoplasms encompass a range of lesions, including benign entities such as sebaceous adenoma and sebaceoma, as well as sebaceous carcinoma. The distinction of sebaceous carcinoma from benign lesions relies on histological identification of architectural or cytological features of malignancy. In this study we have assessed the diagnostic discriminatory ability of mitotic rate and immunohistochemical markers (p53, bcl-2 and p16) in a selected group of well circumscribed sebaceous neoplasms, incorporating examples of sebaceous adenoma, sebaceoma and sebaceous carcinoma. We found that mitotic rate was significantly higher in malignant lesions as compared to benign lesions, but none of the immunohistochemical markers showed a discriminatory expression pattern. In addition, we performed a mutational analysis on the same group of lesions using next generation sequencing (NGS) technology. The most commonly mutated gene was TP53, although there was no correlation between the p53 immunohistochemical results and number or type of TP53 mutation detected. CDKN2A, EGFR, CTNNB1 and KRAS were also commonly mutated across all lesions. No particular gene, mutation profile or individual mutation could be identified which directly correlated with the consensus histological diagnosis. In conclusion, within this diagnostically challenging group of lesions, mitotic activity, but not immunohistochemical labelling for p16 or bcl-2, correlates with diagnostic category. While a number of genes potentially involved in the genesis of sebaceous neoplasia were uncovered, any molecular differences between the histological diagnostic categories remain unclear. PMID:27311873

  14. Molecular analysis of mucopolysaccharidosis IVA: Common mutations and racial difference

    Energy Technology Data Exchange (ETDEWEB)

    Tomatsu, S.; Hori, T.; Nakashima, Y. [Gifu Univ. (Japan)] [and others

    1994-09-01

    Mucopolysaccharidosis IVA (MPS IVA) is an autosomal recessive disorder caused by a deficiency in N-acetylgalactosamine -6-sulfate sulfatase (GALNS). Studies on the molecular basis of MPS IVA have been facilitated following cloning of the full-length cDNA and genomic DNA. In this study we detected mutations from 20 Caucasian and 19 Japanese MPS IVA patients using SSCP system and compared mutations of Caucasian origin with those of Japanese origin. The results showed the presence of 16 various mutations (3 small, deletions, 2 nonsense and 11 missense mutations) for Caucasian patients and 15 (1 deletion, 1 large alteration and 13 missense mutations) for Japanese. Moreover, two common mutations existed; one is double gene deletion characteristic for Japanese (6 alleles; 15%) and the other is a point mutation (1113F A{yields}T transition) characteristic for Caucasian (9 alleles; 22.5%). And the clear genotype/phenotype relationship among 1342delCA, IVS1(-2), P151S, Q148X, R386C, I113F, Q473X, W220G, P151L, A291T, R90W, and P77R, for a severe type, G96B N204K and V138A for a milder type, was observed. Only R386 mutation was seen in both of the populations. Further, the precise DNA analysis for double gene deletion of a common double gene deletion has been performed by defining the breakpoints and the results showed that one deletion was caused by homologous recombination due to Alu repetitive sequences and the other was due to nonhomologous recombination of short direct repeat. Haplotype analysis for six alleles with double deletion were different, indicating the different origin of this mutation or the frequent recombination events before a mutational event. Thus the mutations in GALNS gene are very heterogeneous and the racial difference is characteristic.

  15. Investigation of total reflection X-ray fluorescence analysis technique

    International Nuclear Information System (INIS)

    Total-Reflection X-ray Fluorescence spectrometry (TRXF) is known for its high sensitivity down to Pg-level or sub ppb level, respectively. Therefore the spectrometry is considered as a most competitive tool in the application of trace element analysis. The technique of TRXF was investigated in the laboratory. But small isotope X-γ source is chosen as an exciting source instead of general X-ray tube. From the primitive experiment the conclusion proved that the condition of total reflection can be built and the analysis sensitivity of TRXF is higher than that of normal x-ray analysis

  16. PROGRAMA DE CALIDAD PARA LAS INVESTIGACIONES BÁSICAS DEL CENTRO DE INMUNOLOGÍA MOLECULAR / PROGRAM OF QUALITY FOR THE BASIC INVESTIGATIONS OF THE CENTER OF MOLECULAR IMMUNOLOGY

    Directory of Open Access Journals (Sweden)

    Dainerys Infante-Santana

    2011-09-01

    Full Text Available

    El artículo describe el Programa de calidad para las investigaciones del Centro de Inmunología Molecular. Este programa incorpora el cumplimiento de las Buenas Prácticas de Laboratorio con una gestión basada en el comportamiento, el análisis de los riesgos, el enfoque a procesos y la evaluación a través de indicadores. La aplicación del nuevo programa de calidad en el proceso de la actividad científica, permitió disminuir los incumplimientos de las mencionadas prácticas, mejorar los indicadores de productividad científica y lograr una mayor cultura de calidad en el área de investigaciones del Centro de Inmunología Molecular.

    Abstract

    The paper describes the Program of quality for the investigations of the Center of Molecular Immunology. This program incorporates the execution of the Good Practices of Laboratory with a behaviour-based management, the analysis of the risks, the process approach and the assessment through indicators. The application of the new quality program in the process of the scientific activity, allowed to decrease the nonfulfillments of the above mentioned practices, to improve the scientific productivity indicators and to achieve a greater quality culture in the area of investigations of the Center of Molecular Immunology.

  17. Integrative network analysis unveils convergent molecular pathways in Parkinson's disease and diabetes.

    Directory of Open Access Journals (Sweden)

    Jose A Santiago

    Full Text Available BACKGROUND: Shared dysregulated pathways may contribute to Parkinson's disease and type 2 diabetes, chronic diseases that afflict millions of people worldwide. Despite the evidence provided by epidemiological and gene profiling studies, the molecular and functional networks implicated in both diseases, have not been fully explored. In this study, we used an integrated network approach to investigate the extent to which Parkinson's disease and type 2 diabetes are linked at the molecular level. METHODS AND FINDINGS: Using a random walk algorithm within the human functional linkage network we identified a molecular cluster of 478 neighboring genes closely associated with confirmed Parkinson's disease and type 2 diabetes genes. Biological and functional analysis identified the protein serine-threonine kinase activity, MAPK cascade, activation of the immune response, and insulin receptor and lipid signaling as convergent pathways. Integration of results from microarrays studies identified a blood signature comprising seven genes whose expression is dysregulated in Parkinson's disease and type 2 diabetes. Among this group of genes, is the amyloid precursor protein (APP, previously associated with neurodegeneration and insulin regulation. Quantification of RNA from whole blood of 192 samples from two independent clinical trials, the Harvard Biomarker Study (HBS and the Prognostic Biomarker Study (PROBE, revealed that expression of APP is significantly upregulated in Parkinson's disease patients compared to healthy controls. Assessment of biomarker performance revealed that expression of APP could distinguish Parkinson's disease from healthy individuals with a diagnostic accuracy of 80% in both cohorts of patients. CONCLUSIONS: These results provide the first evidence that Parkinson's disease and diabetes are strongly linked at the molecular level and that shared molecular networks provide an additional source for identifying highly sensitive biomarkers

  18. Investigating the dopaminergic synapse in vivo. II. Molecular imaging studies in small laboratory animals.

    Science.gov (United States)

    Nikolaus, Susanne; Larisch, Rolf; Beu, Markus; Antke, Christina; Kley, Konstantin; Forutan, Farhad; Wirrwar, Andreas; Müller, Hans-Wilhelm

    2007-01-01

    Dopaminergic synaptic function may be assessed either at the presynaptic terminal or at the postsynaptic binding sites using molecular in vivo imaging methods. Apart from the density of binding sites, parameters such as alterations in dopamine synthesis, dopamine storage or dopamine release can be quantified either by application of specific radiotracers or by assessing the competition between the exogenous radioligand and endogenous dopamine. The performance of animal studies allows the induction of specific short-term or long-term synaptic conditions via pharmacological challenges or infliction of neurotoxic lesions. Therefore, small laboratory animals such as rats and mice have become invaluable models for a variety of human disorders. This article gives an overview of those small animal studies which have been performed so far on dopaminergic neurotransmission using in vivo imaging methods, with a special focus on the relevance of findings within the functional entity of the dopaminergic synapse. Taken together, in vivo investigations on animal models of Parkinson's disease showed decreases of dopamine storage, dopamine release and dopamine transporter binding, no alterations of dopamine synthesis and DA release, and either increases or no alterations of D2 receptor binding, while in vivo investigations of animal models of Huntington's disease. showed decreases of DAT and D1 receptor binding. For D2 receptor binding, both decreases and increases have been reported, dependent on the radioligand employed. Substances of abuse, such as alcohol, amphetamine and methylphenidate, led to an increase of dopamine release in striatal regions. This held for the acute application of substances to both healthy animals and animal models of drug abuse. Findings also showed that chronic application of cocaine induced long-term reductions of both D1 and D2 receptor binding, which disappeared after several weeks of withdrawal. Finally, preliminary results yielded the first

  19. The investigation of molecular mixing and segregation in opv materials and devices

    Science.gov (United States)

    Rochester, Christopher W.

    With the growing energy demand and the threat of global warming caused by our excessive use of fossil fuels, it is imperative that we search for and develop alternative ways to generate energy. Using photovoltaic technologies to produce energy is a good way to supplement our current energy supplies. The problem with conventional PV technology is that it is too expensive to compete with cheap fossil fuels. Polymer solar cells have the potential to be a much cheaper alternative to conventional PV technology, as they can easily be manufactured using simple roll-to-roll printing methods, are light-weight, and are flexible. Polymer solar cells consist of layered organic materials that are deposited using solution deposition methods. The organic layers often consist of mixtures of organic molecules, that may be composed of polymer and small molecules. The behavior of these organic materials are not always predictable as they have been found to often diffuse, causing material segregation and mixing within layers and at interfaces. These processes are measured and observed using a combination of experimental techniques. P3HT/PCBM bilayer samples were fabricated by spin coating PCBM dissolved in CH2Cl 2 onto P3HT films. We show using steady-state spectroscopy, neutron reflectometry, and current-voltage measurements that substantial mixing occurs between the P3HT and PCBM during the PCBM deposition. We conclude that the PCBM mixes with amorphous P3HT and does not disrupt the existing crystalline domains. A PCBM loading of 25-30 wt% into the P3HT layer was determined, which explains why reported photovoltaic performances of these solution processed bilayer structures are comparable to that of bulk-heterojunctions. The use of F4-TCNQ as a molecular dopant for the polymeric hole transport layer, S-P3MEET, for use in organic photovoltaic devices was investigated. It is shown that F4-TCNQ effectively oxidized the S-P3MEET polymer, and that even for low doping concentrations

  20. Investigating Convergence Patterns for Numerical Methods Using Data Analysis

    Science.gov (United States)

    Gordon, Sheldon P.

    2013-01-01

    The article investigates the patterns that arise in the convergence of numerical methods, particularly those in the errors involved in successive iterations, using data analysis and curve fitting methods. In particular, the results obtained are used to convey a deeper level of understanding of the concepts of linear, quadratic, and cubic…

  1. Analysis of Musa genome using flow cytometry and molecular cytogenetics

    Czech Academy of Sciences Publication Activity Database

    Doležel, Jaroslav; Valárik, Miroslav; Vrána, Jan; Šafář, Jan; Hřibová, Eva; Gasmanová, Nikol; Van den Howe, I.; Doleželová, Marie; Swennen, R.; Šimková, Hana

    2002. s. 16-17. [ FAO /IAEA Research Co-ordination Meeting on Cellular Biology and Biotechnology Including Mutation Techniques for Creation of New Useful Banana Genotypes /4./. 24.09.2002-28.09.2002, Leuven] Institutional research plan: CEZ:AV0Z5038910 Keywords : flow cytometry * molecular cytogenetics * Musa spp Subject RIV: EB - Genetics ; Molecular Biology

  2. Image analysis used for aluminium alloy microstructure investigation

    Directory of Open Access Journals (Sweden)

    M. Krupiński

    2010-09-01

    Full Text Available Purpose: In this work the metallographic microstructure analysis of the investigated AlSi7Cu3Mg aluminium cast alloy was performed for samples cooled with different cooling rate settings. The preformed investigations are subjected to the analysis of cooling rate influence on the phase morphology.Design/methodology/approach: The solidification process itself is analysed using the UMSA device by appliance of the Derivative Thermo Analysis. The influence of the cooling rate on the alloy microstructure was investigated using computer aided image analysis, in this work also the content of particular phases was analysed, as well the percentage of pinholes compared to the chosen cooling rate.Findings: The treated sample is without holes, cracks and defects as well as has a slightly higher hardness value compared to the as-cast material.Research limitations/implications: The investigated samples were made of the cylindrical shape and were cooled in the range of 0.2°C/s to 1.25°C/s. In this work also the derivative thermoanalysis was performed to determine the correlation between the chosen cooling rate and the microstructure as well changes in the derivative curve shape. For alloy cooling with chosen cooling rate as well for the derivative thermo-analysis the UMSA analysator was applied.Practical implications: The investigated material can find its use in the foundry industry; an improvement of component quality depends mainly on better control over the production parameters.Originality/value: The originality of this work is based on applying of regulated cooling rate of aluminium alloy for structure and mechanical properties changes. As an effect of this study it will be possible to understand and to influence the mechanism of structure forming, refinement and nucleation. Also a better understanding of the thermal characteristics will be provided to achieve a desirable phase morphology required for application of this material under production

  3. Investigation of the molecular epidemiology of Acinetobacter baumannii isolated from patients and environmental contamination.

    Science.gov (United States)

    Ying, Chunmei; Li, Yongli; Wang, Yaping; Zheng, Bing; Yang, Chengde

    2015-09-01

    The objective of this work was to investigate correlations between Acinetobacter baumannii isolates from neurosurgical intensive care unit patients and its environment. This is a prospective, observational study. The minimal inhibitory concentrations of antimicrobial agents against 27 clinical and 28 environmental isolates were determined by the agar dilution method. Molecular genotyping was performed by enterobacterial repetitive intergenic consensus PCR (ERIC-PCR), pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The presence of carbapenemase and metallo-β-lactamase genes were analyzed by specific PCRs and DNA sequencing. From the clinical A. baumannii isolates, 25.9% were found resistant to minocycline, 51.9% to cefoperazone-sulbactam, 59.3% to imipenem and 70% resistant to other antimicrobial agents. Environmental isolates were more sensitive compared with clinical isolates (P<0.05). Twenty-seven clinical isolates comprised three ERIC-PCR genotypes, four major PFGE pulsotypes and five distinct MLST sequence types (STs) (ST208, ST368, ST191, ST195, ST540), all belonging to CC92 with only one locus (gpi) difference among them. Twenty-eight environmental isolates showed more diverse genetic types than clinical isolates and comprised six ERIC-PCR groups, nine PFGE groups and two main STs (ST208, ST229). Four clinical and 15 environmental isolates could not be identified by MLST and were assigned to non-clonal STs. We identified the presence of the blaOXA-23 carbapenemase encoding gene in most of the clinical (21/27) but fewer in the environmental isolates (3/28). The A. baumannii strains isolated from patients were genetically similar to the environmental strains, with CC92 members as the major fraction but with different antibiotic susceptibilities. PMID:25873322

  4. Molecular dynamics investigation of the structure of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer.

    Science.gov (United States)

    Tu, K; Tobias, D J; Blasie, J K; Klein, M L

    1996-02-01

    We report the results of a constant pressure and temperature molecular dynamics simulation of a gel-phase dipalmitoylphosphatidylcholine bilayer with nw = 11.8 water molecules/lipid at 19 degrees C. The results of the simulation were compared in detail with a variety of x-ray and neutron diffraction data. The average positions of specific carbon atoms along the bilayer normal and the interlamellar spacing and electron density profile were in very good agreement with neutron and x-ray diffraction results. The area per lipid and the details of the in-plane hydrocarbon chain structure were in excellent agreement with wide-angle x-ray diffraction results. The only significant deviation is that the chains met in a pleated arrangement at the bilayer center, although they should be parallel. Novel discoveries made in the present work include the observation of a bimodal headgroup orientational distribution. Furthermore, we found that there are a significant number of gauche conformations near the ends of the hydrocarbon chains and, in addition to verifying a previous suggestion that there is partial rotational ordering in the hydrocarbon chains, that the two chains in a given molecule are inequivalent with respect to rotations. Finally, we have investigated the lipid/water interface and found that the water penetrates beneath the headgroups, but not as far as the carbonyl groups, that the phosphates are strongly hydrated almost exclusively at the nonesterified oxygen atoms, and that the hydration of the ammonium groups is more diffuse, with some water molecules concentrated in the grooves between the methyl groups. PMID:8789079

  5. Investigation of cation self-diffusion mechanisms in UO2±x using molecular dynamics

    International Nuclear Information System (INIS)

    This article is devoted to investigation of cation self-diffusion mechanisms, taking place in UO2, UO2+x, and UO2−x crystals simulated under periodic (PBC) and isolated (IBC) boundary conditions using the method of molecular dynamics in the approximation of rigid ions and pair interactions. It is shown that under PBC the cations diffuse via an exchange mechanism (with the formation of Frenkel defects) with activation energy of 15–22 eV, while under IBC there is competition between the exchange and vacancy (via Schottky defects) diffusion mechanisms, which give the effective activation energy of 11–13 eV near the melting temperature of the simulated UO2.00 nanocrystals. Vacancy diffusion with lower activation energy of 6–7 eV was dominant in the non-stoichiometric crystals UO2.10, UO2.15 and UO1.85. Observations showed that a cation vacancy is accompanied by different number of anion vacancies depending on the deviation from stoichiometry: no vacancies in UO2.15, single vacancy in UO2.00 and four vacancies in UO1.85. The corresponding law of mass action formulas derived within the Lidiard–Matzke model allowed explaining the obtained activation energies and predicting a change in the activation energy within the temperature range of the superionic phase transition. The diffusion of cations on the surface of nanocrystals had activation energy of 3.1–3.6 eV

  6. 2D IR spectra of cyanide in water investigated by molecular dynamics simulations

    Science.gov (United States)

    Lee, Myung Won; Carr, Joshua K.; Göllner, Michael; Hamm, Peter; Meuwly, Markus

    2013-01-01

    Using classical molecular dynamics simulations, the 2D infrared (IR) spectroscopy of CN− solvated in D2O is investigated. Depending on the force field parametrizations, most of which are based on multipolar interactions for the CN− molecule, the frequency-frequency correlation function and observables computed from it differ. Most notably, models based on multipoles for CN− and TIP3P for water yield quantitatively correct results when compared with experiments. Furthermore, the recent finding that T 1 times are sensitive to the van der Waals ranges on the CN− is confirmed in the present study. For the linear IR spectrum, the best model reproduces the full widths at half maximum almost quantitatively (13.0 cm−1 vs. 14.9 cm−1) if the rotational contribution to the linewidth is included. Without the rotational contribution, the lines are too narrow by about a factor of two, which agrees with Raman and IR experiments. The computed and experimental tilt angles (or nodal slopes) α as a function of the 2D IR waiting time compare favorably with the measured ones and the frequency fluctuation correlation function is invariably found to contain three time scales: a sub-ps, 1 ps, and one on the 10-ps time scale. These time scales are discussed in terms of the structural dynamics of the surrounding solvent and it is found that the longest time scale (≈10 ps) most likely corresponds to solvent exchange between the first and second solvation shell, in agreement with interpretations from nuclear magnetic resonance measurements.

  7. Development and evaluation of double locus sequence typing for molecular epidemiological investigations of Clostridium difficile.

    Science.gov (United States)

    Stojanov, M; Magalhaes, B; Terletsky, V; Basset, P; Prod'hom, G; Greub, G; Senn, L; Blanc, D S

    2016-02-01

    Despite the development of novel typing methods based on whole genome sequencing, most laboratories still rely on classical molecular methods for outbreak investigation or surveillance. Reference methods for Clostridium difficile include ribotyping and pulsed-field gel electrophoresis, which are band-comparing methods often difficult to establish and which require reference strain collections. Here, we present the double locus sequence typing (DLST) scheme as a tool to analyse C. difficile isolates. Using a collection of clinical C. difficile isolates recovered during a 1-year period, we evaluated the performance of DLST and compared the results to multilocus sequence typing (MLST), a sequence-based method that has been used to study the structure of bacterial populations and highlight major clones. DLST had a higher discriminatory power compared to MLST (Simpson's index of diversity of 0.979 versus 0.965) and successfully identified all isolates of the study (100 % typeability). Previous studies showed that the discriminatory power of ribotyping was comparable to that of MLST; thus, DLST might be more discriminatory than ribotyping. DLST is easy to establish and provides several advantages, including absence of DNA extraction [polymerase chain reaction (PCR) is performed on colonies], no specific instrumentation, low cost and unambiguous definition of types. Moreover, the implementation of a DLST typing scheme on an Internet database, such as that previously done for Staphylococcus aureus and Pseudomonas aeruginosa ( http://www.dlst.org ), will allow users to easily obtain the DLST type by submitting directly sequencing files and will avoid problems associated with multiple databases. PMID:26581425

  8. Molecular polymorphism: microwave spectra, equilibrium structures, and an astronomical investigation of the HNCS isomeric family.

    Science.gov (United States)

    McGuire, Brett A; Martin-Drumel, Marie-Aline; Thorwirth, Sven; Brünken, Sandra; Lattanzi, Valerio; Neill, Justin L; Spezzano, Silvia; Yu, Zhenhong; Zaleski, Daniel P; Remijan, Anthony J; Pate, Brooks H; McCarthy, Michael C

    2016-08-10

    The rotational spectra of thioisocyanic acid (HNCS), and its three energetic isomers (HSCN, HCNS, and HSNC) have been observed at high spectral resolution by a combination of chirped-pulse and Fabry-Pérot Fourier-transform microwave spectroscopy between 6 and 40 GHz in a pulsed-jet discharge expansion. Two isomers, thiofulminic acid (HCNS) and isothiofulminic acid (HSNC), calculated here to be 35-37 kcal mol(-1) less stable than the ground state isomer HNCS, have been detected for the first time. Precise rotational, centrifugal distortion, and nitrogen hyperfine coupling constants have been determined for the normal and rare isotopic species of both molecules; all are in good agreement with theoretical predictions obtained at the coupled cluster level of theory. On the basis of isotopic spectroscopy, precise molecular structures have been derived for all four isomers by correcting experimental rotational constants for the effects of rotation-vibration interaction calculated theoretically. Formation and isomerization pathways have also been investigated; the high abundance of HSCN relative to ground state HNCS, and the detection of strong lines of SH using CH3CN and H2S, suggest that HSCN is preferentially produced by the radical-radical reaction HS + CN. A radio astronomical search for HSCN and its isomers has been undertaken toward the high-mass star-forming region Sgr B2(N) in the Galactic Center with the 100 m Green Bank Telescope. While we find clear evidence for HSCN, only a tentative detection of HNCS is proposed, and there is no indication of HCNS or HSNC at the same rms noise level. HSCN, and tentatively HNCS, displays clear deviations from a single-excitation temperature model, suggesting weak masing may be occurring in some transitions in this source. PMID:27478937

  9. Circulating tumor cells (CTCs) in breast cancer: a diagnostic tool for prognosis and molecular analysis

    Institute of Scientific and Technical Information of China (English)

    Xiaoshen Dong; R.Katherine Alpaugh; Massimo Cristofanilli

    2012-01-01

    Metastatic breast cancer (MBC) is characterized by a combination of tumor growth,proliferation and metastatic progression and is typically managed with palliative intent.The benefit of standard systemic therapies is relatively limited and the disease is considered incurable suggesting the need to investigate the biological drivers of the various phases of the metastatic process in order to improve the selection of molecularly driven therapies.The detection,enumeration and molecular analysis of circulating tumor cells (CTCs) provide an intriguing opportunity to advance this knowledge.CTCs enumerated by the Food and Drugs Administration-cleared CellSearchTM system are an independent prognostic factor of progression-free survival (PFS) and overall survival (OS) in MBC patients.Several published papers demonstrated the poor prognosis for MBC patients that presented basal CTC count ≥5 in 7.5 mL of blood.Therefore,the enumeration of CTCs during treatment for MBC provides a tool with the ability to predict progression of disease earlier than standard timing of anatomical assessment using conventional radiological tests.During the metastatic process cancer cells exhibit morphological and phenotypic plasticity undergoing epithelial-mesenchymal transition (EMT).This important phenomenon is associated with down regulation of epithelial marker (e.g.,EpCAM) with potential limitations in the applicability of current CTCs enrichment methods.Such observations translated in a number of investigations aimed at improving our capabilities to enumerate and perform molecular characterization of CTCs.Theoretically,the phenotypic analysis of CTCs can represent a "liquid" biopsy of breast tumor that is able to identify a new potential target against the metastatic disease and advance the development and monitoring of personalized therapies.

  10. Classical and quantum analysis of a hetero-triatomic molecular Bose-Einstein condensate model

    Energy Technology Data Exchange (ETDEWEB)

    Tonel, A.P. [CCET da Universidade Federal do Pampa/Unipampa, Bag´e, RS (Brazil); Kuhn, C.C.N.; Foerster, A. [Instituto de F´ısica da UFRGS, Porto Alegre, RS (Brazil); Santos, G. [Departamento de Físi a - UFS, São Cristóvão, SE (Brazil); Roditi, I.; Santos, Z.V.T. [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil)

    2014-11-15

    We investigate an integrable Hamiltonian modelling a hetero-triatomic-molecular Bose-Einstein condensate. This model describes a mixture of two species of atoms in different proportions, which can combine to form a triatomic molecule. Beginning with a classical analysis, we determine the fixed points of the system. Bifurcations of these points separate the parameter space into different regions. Three distinct scenarios are found, varying with the atomic population imbalance. This result suggests the ground state properties of the quantum model exhibits a sensitivity on the atomic population imbalance, which is confirmed by a quantum analysis using different approaches, such as the ground-state expectation values, the behaviour of the quantum dynamics, the energy gap and the ground state fidelity. (author)

  11. HMW glutenin subunits in multiploid Aegilops species: composition analysis and molecular cloning of coding sequences

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The Aegilops genus contains species closely related to wheat. Incommon with wheat, Aegilops species accumulate high molecular weight (HMW) glutenin subunits in their endospermic tissue. In this study, we investigated the composition of HMW glutenin subunits in four multiploid Aegilops species using SDS-PAGE analysis. Furthermore, by working with Ae. ventricosa, we established an efficient genomic PCR condition for simultaneous amplification of DNA sequences coding for either x-ory-type HMW glutenin subunits from polyploid Aegilops species. Using the genomic PCR condition, we amplified and subsequently cloned two DNA fragments that may code for HMW glutenin subunits in Ae. ventricosa. Based on an analysis of the deduced amino acid sequences, we concluded that the two cloned sequences encode one x- and one y-type of HMW glutenin subunit, respectively.

  12. Investigating the dopaminergic synapse in vivo. I. Molecular imaging studies in humans.

    Science.gov (United States)

    Nikolaus, Susanne; Antke, Christina; Kley, Konstantin; Poeppel, Thorsten D; Hautzel, Hubertus; Schmidt, Daniela; Müller, Hans-Wilhelm

    2007-01-01

    Dopaminergic synaptic function may be assessed either at the presynaptic terminal or at the postsynaptic binding sites using molecular in vivo imaging methods. Apart from the density of binding sites, parameters such as alterations in dopamine synthesis, dopamine storage or dopamine release can be quantified either by application of specific radiotracers or by assessing the competition between the exogenous radioligand and endogenous dopamine. Investigations of humans in both clinical and experimental settings have yielded evidence that disturbances of dopaminergic function may be associated with numerous neurological and psychiatric conditions, among which are movement disorders, schizophrenia, attention-deficit hyperactivity disorder, depression and drug abuse. This article gives an overview of those studies, which so far have been performed on dopaminergic neurotransmission in humans using in vivo imaging methods. We focus on disease-related deficiencies within the functional entity of the dopaminergic synapse. Taken together, in vivo findings yield evidence of presynaptic dysfunctions in Parkinson's disease with decreases in striatal dopamine synthesis, dopamine storage, dopamine release and dopamine transporter binding. In contrast, 'Parkinson plus' syndromes (multiple system atrophy, progressive supranuclear palsy, corticobasal degeneration, dementia with Lewy bodies) are characterized by both pre- and postsynaptic deficiencies with reductions in striatal dopamine synthesis, dopamine storage, dopamine release, and dopamine transporter, as well as D, and D, receptor binding. In patients with Huntington's disease, postsynaptic dysfunctions with reductions of striatal D1 and D2 receptor binding have become apparent, whereas attention-deficit/ hyperactivity disorder is mainly characterized by presynaptic deficits with increases in dopamine transporter binding. Interestingly, findings are also consistent with respect to drug abuse: cocaine, amphetamine

  13. Molecular analysis of the bacterial diversity in uranium mill tailings

    International Nuclear Information System (INIS)

    A culture-independent molecular approach has been applied to investigate the bacterial diversity in three uranium contaminated sites. The three analysed soil samples have been collected from the uranium waste pile Haberland near Johanngeorgenstadt (Germany), from the uranium mill tailings in Gunnison, Colorado (USA) and from the uranium mill tailings in Shiprock, New Mexico (USA). The 16S rDNA fragments which has been isolated through direct lysis of the whole-DNA were amplified by the use of the universal primers 16S43f and 16S1404r and cloned. With restriction fragment length polymorphismus (RFLP) were the clones screened and one representative of all RFLP types that occurred more than once in the clone library was sequenced and analysed. In spite of the contamination a considerable diversity and significant differences in the composition of the natural bacterial communities in these three sites have been found. In the sample collected from the waste pile Haberland near Johanngeorgenstadt α-Proteobacteria and representatives of the Holophaga/Acidobacterium were numerically predominant. The distribution of bacteria in the sample collected from uranium mill tailings Gunnison was very similar to those found in the Haberland waste pile, but there were found besides α-Proteobacteria and representatives of Holophaga/Acidobacterium a lot of γ-Proteobacteria. The structure of the bacterial community in the sample collected from the uranium mill tailings Shiprock was significantly different. Only some representatives of the Holophaga/Acidobacterium and α-Proteobacteria were represented. Large populations of Bacilli, γ-Proteobacteria and green non sulfur bacteria were dominant in this sample. (orig.)

  14. The molecular turn in psychiatry: a philosophical analysis.

    Science.gov (United States)

    Rudnick, Abraham

    2002-06-01

    Biological psychiatry has been dominated by a psychopharmacologically-driven neurotransmitter dysfunction paradigm. The objective of this paper is to explore a reductionist assumption underlying this paradigm, and to suggest an improvement on it. The methods used are conceptual analysis with a comparative approach, particularly using illustrations from the history of both biological psychiatry and molecular biology. The results are that complete reduction to physicochemical explanations is not fruitful, at least in the initial stages of research in the medical and life sciences, and that an appropriate (non-reducible) integrative principle--addressing a property of the whole system under study--is required for each domain of research. This is illustrated in Pauling's use of a topological integrative principle for the discovery of the functioning of proteins and in Watson and Crick's use of the notion of a genetic code as an integrative principle for the discovery of the structure of genes. The neurotransmitter dysfunction paradigm addresses single molecules and their neural pathways, yet their interactions within the CNS as a whole seem most pertinent to mental disorders such as schizophrenia. The lack within biological psychiatry of an integrative principle addressing a property of the CNS as a whole may be responsible for the empirical failure of orthomolecular psychiatry, as well as for the central role that serendipity has played in the study of mental disorders, which is dominated by the neurotransmitter paradigm. The conclusion is that research in biological psychiatry may benefit from using, at least initially, some integrative principle(s) addressing a property of the CNS as a whole, such as connectionism or a hierarchical notion. PMID:12187435

  15. Molecular parentage analysis is essential in breeding Asian seabass.

    Directory of Open Access Journals (Sweden)

    Peng Liu

    Full Text Available In aquaculture species, maintaining pedigree information and genetic variation in each generation is essential, but very difficult. In this study, we used nine microsatellites to genotype 2,520 offspring from four independent full-factorial crosses (10 males × 10 females of Asian seabass to reconstruct pedigree and monitor the change of genetic variations. In all four crosses, over 96.8% of the offspring could be assigned to their parents, indicating the high power of the nine microsatellites for parentage assignment. This study revealed several interesting results: (1. In all four crosses, the contribution of parents to offspring was significantly uneven, and some dominant breeding fishes (i.e. brooders were found; (2. In two mass crosses where the brooders were carefully checked for reproductive status, a majority (≥ 90% of brooders contributed to offspring, whereas in another two crosses, where the brooders were randomly picked without checking reproductive status, only a few brooders (40.0-45.0% produced offspring; (3. Females had more problems in successful spawning compared to males; and (4. In the two crosses where a few brooders produced offspring, there was a substantial loss in allelic (24.1-34.3% and gene (20.5-25.7% diversities in offspring, while in the other two crosses, the majority of allelic (96.8-97.0% and gene diversities (94.8-97.1% were maintained. These observations suggest that a routine molecular parentage analysis is required to maintain both allelic and gene diversity in breeding Asian seabass.

  16. Genetic diversity in cultivated carioca common beans based on molecular marker analysis

    Directory of Open Access Journals (Sweden)

    Juliana Morini Küpper Cardoso Perseguini

    2011-01-01

    Full Text Available A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.

  17. Psychometric precision in phenotype definition is a useful step in molecular genetic investigation of psychiatric disorders

    OpenAIRE

    Xu, M. K.; Gaysina, D; Barnett, J H; Scoriels, L; van de Lagemaat, L. N.; Wong, A.; M. Richards; Croudace, T.J.; Jones, P. B.

    2015-01-01

    Affective disorders are highly heritable, but few genetic risk variants have been consistently replicated in molecular genetic association studies. The common method of defining psychiatric phenotypes in molecular genetic research is either a summation of symptom scores or binary threshold score representing the risk of diagnosis. Psychometric latent variable methods can improve the precision of psychiatric phenotypes, especially when the data structure is not straightforward. Using data from...

  18. Investigating the composition of organic aerosol resulting from cyclohexene ozonolysis: low molecular weight and heterogeneous reaction products

    Directory of Open Access Journals (Sweden)

    J. F. Hamilton

    2006-01-01

    Full Text Available The composition of organic aerosol formed from the gas phase ozonolysis of cyclohexene has been investigated in a smog chamber experiment. Comprehensive gas chromatography with time of flight mass spectrometric detection was used to determine that dicarboxylic acids and corresponding cyclic anhydrides dominated the small gas phase reaction products found in aerosol sampled during the first hour after initial aerosol formation. Structural analysis of larger more polar molecules was performed using liquid chromatography with ion trap tandem mass spectrometry. This indicated that the majority of identified organic mass was in dimer form, built up from combinations of the most abundant small acid molecules, with frequent indication of the inclusion of adipic acid. Trimers and tetramers potentially formed via similar acid combinations were also observed in lower abundances. Tandem mass spectral data indicated dimers with either acid anhydride or ester functionalities as the linkage between monomers. High-resolution mass spectrometry identified the molecular formulae of the most abundant dimer species to be C10H16O6, C11H18O6, C10H14O8 and C11H16O8 and could be used in some cases to reduce uncertainty in exact chemical structure determination by tandem MS.

  19. Molecular Epidemiological Investigation of Porcine kobuvirus and Its Coinfection Rate with PEDV and SaV in Northwest China.

    Science.gov (United States)

    Wang, Chen; Lan, Xi; Yang, Bin

    2016-01-01

    Porcine kobuvirus (PKV) has circulated throughout China in recent years. Although many studies have detected it throughout the world, its molecular epidemiology has not been characterized in northwest China. To understand its prevalence, 203 fecal samples were collected from different regions of Gansu Province and tested with reverse transcription-polymerase chain reaction. In this study, we tested these samples for PKV, porcine epidemic diarrhea virus (PEDV), and sapovirus and analyzed the amplified 2C gene fragments of PKV. Overall, 126 (62.1%) samples were positive for PKV. Of the 74 piglets samples among the 203 fecal samples, 65 (87.8%) were positive for PKV. PKV infection was often accompanied by PEDV, but the relationship between the two viruses must be confirmed. A phylogenetic analysis indicated that the PKV strains isolated from the same regions clustered on the same branches. This investigation shows that PKV infections are highly prevalent in pigs in northwest China, especially in piglets with symptoms of diarrhea. PMID:27294133

  20. Molecular Epidemiological Investigation of Porcine kobuvirus and Its Coinfection Rate with PEDV and SaV in Northwest China

    Directory of Open Access Journals (Sweden)

    Chen Wang

    2016-01-01

    Full Text Available Porcine kobuvirus (PKV has circulated throughout China in recent years. Although many studies have detected it throughout the world, its molecular epidemiology has not been characterized in northwest China. To understand its prevalence, 203 fecal samples were collected from different regions of Gansu Province and tested with reverse transcription-polymerase chain reaction. In this study, we tested these samples for PKV, porcine epidemic diarrhea virus (PEDV, and sapovirus and analyzed the amplified 2C gene fragments of PKV. Overall, 126 (62.1% samples were positive for PKV. Of the 74 piglets samples among the 203 fecal samples, 65 (87.8% were positive for PKV. PKV infection was often accompanied by PEDV, but the relationship between the two viruses must be confirmed. A phylogenetic analysis indicated that the PKV strains isolated from the same regions clustered on the same branches. This investigation shows that PKV infections are highly prevalent in pigs in northwest China, especially in piglets with symptoms of diarrhea.

  1. Molecular investigation of a fungemia outbreak due to Candida parapsilosis in an intensive care unit

    Directory of Open Access Journals (Sweden)

    Murat Dizbay

    2008-10-01

    Full Text Available We investigated a nosocomial cluster of four Candida parapsilosis fungemia episodes that occurred in a neurological intensive care unit over a two-week period. The four infected patients had received parenteral nutrition through central lines, and all four had catheter-related candidemia. All of the isolates were susceptible to all of the antifungals tested, including amphotericin B, fluconazole, voriconazole, and caspofungin. They had strictly related fingerprints, based on randomly amplified polymorphic DNA analysis. Additional DNA sequencing data revealed that they were same strain. Although no isolate of Candida parapsilosis was recovered from other clinical, surveillance, or environmental samples, nosocomial spread of this yeast ceased, following the reinforcement of infection-control measures. Candida parapsilosis may require an intravascular foreign body to cause fungemia, but this outbreak shows that it can be transmitted nosocomially and can cause epidemics.

  2. Dengue virus. Fast Diagnosis of dengue virus by molecular analysis

    International Nuclear Information System (INIS)

    This article is about a regional project in the assurance and quality control of molecular diagnosis. It allows the identification of parasites genotypes that infect humans, particularly dengue that is a viral disease transmitted by mosquitoes

  3. Analysis of the Time Reversible Born-Oppenheimer Molecular Dynamics

    CERN Document Server

    Lin, Lin; Shao, Sihong

    2013-01-01

    We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD) scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition as well as the accuracy of TRBOMD for computing physical properties such as the phonon frequency obtained from the molecular dynamic simulation. We connect and compare TRBOMD with the Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one dimensional model for Kohn-Sham density functional theory.

  4. Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Lin Lin

    2013-12-01

    Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.

  5. Northern blot analysis to investigate the abundance of microorganisms

    International Nuclear Information System (INIS)

    Modern molecular microbial ecology has its origins in the analysis of informative macromolecules. Zuckerkandl and Pauling proposed that certain macromolecules are relatively free from evolutionary pressure and may be considered a molecular document of the evolutionary history of the organism that carries the molecule. In their paper, they proposed that the sequence difference of a molecule is proportional to the evolutionary distance between the organisms; the greater the sequence differences the greater the evolutionary distance. A significant breakthrough with this approach in microbial systematics resulted from the work of Woese and Fox who used oligonucleotide cataloguing of 16S-rRNA to delineate the phylogenetic relationships between microorganisms. By using this approach, it was possible to demonstrate that all life on earth could be divided into three kingdoms: eukarya, procarya and archaea. The unique findings of this research was that the archaea, made up of many methanogenic and thermophilic microorganisms, were probably the most ancient life forms on earth and were not bacteria at all. One of the first applications of rRNA genes was the recovery of unique 5S-rRNA sequences from the Yellowstone hot spring. Even though the statistical utility of the short 5S sequences was limited, it demonstrated that there was a great deal of uncultured diversity within the ecosystem. This uncultured diversity was demonstrated to be highly significant when clone libraries were constructed from the Yellowstone hot spring. Universal PCR primers were used to amplify 16S-rDNA from the microbial community, and these mixed amplicons were cloned into a vector. Each insert, potentially representing a different species, was sequenced giving a snapshot of microbial diversity in the sample. A unique feature of the rRNAs is that they are hierarchical molecules. This means that there are regions where the molecules is highly conserved, others where the sequence is variable, and even

  6. Investigation of a medieval sword using photon activation analysis

    International Nuclear Information System (INIS)

    An ancient sword was examined for indications of forgery or, if authentic, any later processing or changes, e.g. replacement of parts of the weapon. Radiochemical as well as non-destructive analyses using high energy photon activation were used as analytical techniques. Metal parts of the hilt were analysed radiochemically and instrumentally whereas the blade was analysed non-destructively. Metallurgical investigations (hardness measurements, microstructure analysis) performed in parallel are also briefly described. No evidence of non-authenticity was found, which agrees well with the results of stylistical and weapon-scientific investigation carried out by an expert of ancient weaponry. (author) 20 refs.; 1 fig.; 2 tabs

  7. Interactive analysis of systems biology molecular expression data

    OpenAIRE

    Prabhakar Sunil; Salt David E; Kane Michael D; Stephenson Alan; Ouyang Qi; Zhang Mingwu; Burgner John; Buck Charles; Zhang Xiang

    2008-01-01

    Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferr...

  8. Molecular Analysis of Bacterial Species Associated with Childhood Caries

    OpenAIRE

    Becker, Mitzi R.; Paster, Bruce J.; Leys, Eugene J.; Moeschberger, Melvin L.; Kenyon, Sarah G.; Galvin, Jamie L.; Boches, Susan K.; Dewhirst, Floyd E.; Griffen, Ann L.

    2002-01-01

    Although substantial epidemiologic evidence links Streptococcus mutans to caries, the pathobiology of caries may involve more complex communities of bacterial species. Molecular methods for bacterial identification and enumeration now make it possible to more precisely study the microbiota associated with dental caries. The purpose of this study was to compare the bacteria found in early childhood caries (ECC) to those found in caries-free children by using molecular identification methods. C...

  9. Molecular Analysis of the Microflora Associated with Dental Caries

    OpenAIRE

    Munson, M A; Banerjee, A.; Watson, T.F.; Wade, W. G.

    2004-01-01

    Molecular techniques have revealed many novel, presumed unculturable, taxa in oral infections. The aim of this study was to characterize the bacterial community of the middle and advancing front of carious dental lesions by cultural and molecular analyses. Samples were collected with a hand excavator from five teeth with carious lesions involving dentine. Samples were cultured on blood agar and Rogosa agar incubated in air plus 5% CO2 and on fastidious anaerobe agar anaerobically. DNA was als...

  10. Molecular Hydrogen Optical Depth Templates for FUSE Data Analysis

    OpenAIRE

    McCandliss, S. R.

    2003-01-01

    The calculation and use of molecular hydrogen optical depth templates to quickly identify and model molecular hydrogen absorption features longward of the Lyman edge at 912 Angstroms are described. Such features are commonly encountered in spectra obtained by the Far Ultraviolet Spectroscopic Explorer and also in spectra obtained by the Space Telescope Imaging Spectrograph, albeit less commonly. Individual templates are calculated containing all the Lyman and Werner transitions originating fr...

  11. Using molecular-scale tracers to investigate transport of agricultural pollutants in soil and water

    Science.gov (United States)

    Lloyd, C.; Michaelides, K.; Chadwick, D.; Dungait, J.; Evershed, R. P.

    2012-12-01

    We explore the use of molecular-scale tracers to investigate the transport of potential pollutants due to the application of slurry to soil. The molecular-scale approach allows us to separate the pollutants which are moved to water bodies through sediment-bound and dissolved transport pathways. Slurry is applied to agricultural land to as a soil-improver across a wide-range of topographic and climatic regimes, hence a set of experiments were designed to assess the effect of changing slope gradient and rainfall intensity on the transport of pollutants. The experiments were carried out using University of Bristol's TRACE (Test Rig for Advancing Connectivity Experiments) facility. The facility includes a dual axis soil slope (6 x 2.5 x 0.3 m3) and 6-nozzle rainfall simulator, which enables the manipulation of the slope to simulate different slope gradient and rainfall scenarios. Cattle slurry was applied to the top 1 metre strip of the experimental soil slope followed by four rainfall simulations, where the gradient (5° & 10°) and the rainfall intensity (60 & 120 mm hr-1) were co-varied. Leachate was sampled from different flow pathways (surface, subsurface and percolated) via multiple outlets on the slope throughout the experiments and soil cores were taken from the slope after each experiment. Novel tracers were used to trace the pollutants in both dissolved and sediment-bound forms. Fluorescence spectroscopy was used to trace dissolved slurry-derived material via water flow pathways, as the slurry was found to have a distinct signature compared with the soil. The fluorescence signatures of the leachates were compared with those of many organic compounds in order to characterise the origin of the signal. This allowed the assessment of the longevity of the signal in the environment to establish if it could be used as a robust long-term tracer of slurry material in water or if would be subject to transform processes through time. 5-βstanols, organic compounds

  12. Investigation of proton pump inhibitors binding with bovine serum albumin and their relationship to molecular structure

    International Nuclear Information System (INIS)

    The interactions of three proton pump inhibitors (PPIs), omeprazole, pantoprazole and ilaprazole with bovine serum albumin (BSA) have been investigated by fluorescence, synchronous fluorescence, ultraviolet–visible (UV–vis) and circular dichroism (CD). Various binding parameters have been calculated at various temperatures. The results indicated that omeprazole, pantoprazole and ilaprazole had a strong ability to quench the intrinsic fluorescence of BSA with static quenching mechanism, and the binding affinities were significantly affected by different substituents and polarities as the order ilaprazole>pantoprazole>omeprazole. The site marker competitive experiments indicated that the binding of omeprazole, pantoprazole and ilaprazole to BSA primarily took place in subdomain IIA. The results of thermodynamic parameters ΔG, ΔH and ΔS indicated that electrostatic interaction played a major role for PPIs–BSA association. The distance r between PPIs and BSA was evaluated according to the theory of Förster's energy transfer. The quantitative analysis of synchronous fluorescence and CD spectra showed the change in secondary structure of the BSA upon interaction with PPIs by a reduction of α-helix. All the above results many have relevant insight into the PPIs' availability and distribution. - Highlights: ► The interactions of three PPIs with BSA have been investigated. ► The fluorescence quenching mechanism is static quenching. ► Binding affinities were greatly affected by the substituents and polarities. ► The binding of three PPIs to BSA primarily took place in subdomain IIA.

  13. Using the Singular Spectrum Analysis for Investigation of Troposphere Parameters

    CERN Document Server

    Miller, Natalia

    2009-01-01

    In this paper, the method of Singular Spectrum Analysis (SSA) is applied for investigation of the zenith troposphere delay time-series derived from VLBI observations. With the help of this method we can analyze the structure of time-series and separate the harmonic and irregular (trend) components. Combined IVS time-series of zenith wet and total troposphere delays obtained in IGG were used for analysis. For this study, several VLBI stations with the most long time series of troposphere zenith delays were selected, also taking into consideration the geographic region where the station is located. The investigations were carried out using SSA mode. As a result, trends and seasonal components (with annual and semiannual periods) were obtained for all the stations. Using of SSA enabled us to determine nonlinear trends in zenith delay, and also to study variations in the amplitude and the phase of the seasonal components with time.

  14. Investigation of molecular interactions in the complex formation of tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The molecular interactions in the complex formation of two tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid are investigated. The complex formation with a 1:1 stoichiometry between tartaric acid derivatives and D2EHPA can be obtained through UV-Vis titration, NMR chemical shifts and molecular dynamic simulations. Furthermore, the differences of the two complexes on the binding constants and strength of hydrogen bonds can also be determined. Such research will ideally provide insight into ways of regulating the complex forming properties of tartaric acid derivatives for composing or syn- thesizing new chiral resolving agents.

  15. Investigation of molecular interactions in the complex formation of tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid

    Institute of Scientific and Technical Information of China (English)

    TAN Bin; ZHAI Zheng; LUO GuangSheng; WANG JiaDing

    2008-01-01

    The molecular interactions in the complex formation of two tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid are investigated. The complex formation with a 1:1 stoichiometry between tartaric acid derivatives and D2EHPA can be obtained through UV-Vis titration, NMR chemical shifts and molecular dynamic simulations. Furthermore, the differences of the two complexes on the binding constants and strength of hydrogen bonds can also be determined. Such research will ideally provide insight into ways of regulating the complex forming properties of tartaric acid derivatives for composing or syn-thesizing new chiral resolving agents.

  16. Holographic investigations of azobenzene-containing low-molecular-weight compounds in pure materials and binary blends with polystyrene.

    Science.gov (United States)

    Audorff, Hubert; Walker, Roland; Kador, Lothar; Schmidt, Hans-Werner

    2011-11-01

    This paper reports on the synthesis and the thermal and optical properties of photochromic low-molecular-weight compounds, especially with respect to the formation of holographic volume gratings in the pure materials and in binary blends with polystyrene. Its aim is to provide a basic understanding of the holographic response with regard to the molecular structure, and thus to show a way to obtain suitable rewritable materials with high sensitivity for holographic data storage. The photoactive low-molecular-weight compounds consist of a central core with three or four azobenzene-based arms attached through esterification. Four different cores were investigated that influence the glass transition temperature and the glass-forming properties. Additional structural variations were introduced by the polar terminal substituent at the azobenzene chromophore to fine-tune the optical properties and the holographic response. Films of the neat compounds were investigated in holographic experiments, especially with regard to the material sensitivity. In binary blends of the low-molecular-weight compounds with polystyrene, the influence of a polymer matrix on the behavior in holographic experiments was studied. The most promising material combination was also investigated at elevated temperatures, at which the holographic recording sensitivity is even higher. PMID:21956207

  17. Investigations of the CLOCK and BMAL1 Proteins Binding to DNA: A Molecular Dynamics Simulation Study

    Science.gov (United States)

    Xue, Tuo; Song, Chunnian; Wang, Qing; Wang, Yan; Chen, Guangju

    2016-01-01

    The circadian locomotor output cycles kaput (CLOCK), and brain and muscle ARNT-like 1 (BMAL1) proteins are important transcriptional factors of the endogenous circadian clock. The CLOCK and BMAL1 proteins can regulate the transcription-translation activities of the clock-related genes through the DNA binding. The hetero-/homo-dimerization and DNA combination of the CLOCK and BMAL1 proteins play a key role in the positive and negative transcriptional feedback processes. In the present work, we constructed a series of binary and ternary models for the bHLH/bHLH-PAS domains of the CLOCK and BMAL1 proteins, and the DNA molecule, and carried out molecular dynamics simulations, free energy calculations and conformational analysis to explore the interaction properties of the CLOCK and BMAL1 proteins with DNA. The results show that the bHLH domains of CLOCK and BMAL1 can favorably form the heterodimer of the bHLH domains of CLOCK and BMAL1 and the homodimer of the bHLH domains of BMAL1. And both dimers could respectively bind to DNA at its H1-H1 interface. The DNA bindings of the H1 helices in the hetero- and homo-bHLH dimers present the rectangular and diagonal binding modes, respectively. Due to the function of the α-helical forceps in these dimers, the tight gripping of the H1 helices to the major groove of DNA would cause the decrease of interactions at the H1-H2 interfaces in the CLOCK and BMAL1 proteins. The additional PAS domains in the CLOCK and BMAL1 proteins affect insignificantly the interactions of the CLOCK and BMAL1 proteins with the DNA molecule due to the flexible and long loop linkers located at the middle of the PAS and bHLH domains. The present work theoretically explains the interaction mechanisms of the bHLH domains of the CLOCK and BMAL1 proteins with DNA. PMID:27153104

  18. Doses in radiation accidents investigated by chromosome aberration analysis

    International Nuclear Information System (INIS)

    Results from cytogenetic investigations into 55 cases of suspected over-exposure to radiation during 1977 are reviewed. This report is the seventh in an annual series (previous results were published in NRPB-R5, R10, R23, R35, R41 and R57) which together contain data on 327 studies. Results from all investigations have been pooled for general analysis. Brief accounts are given in an appendix of the circumstances behind the past year's investigations and, where possible, physical estimates of dose have been included for comparison. Two cases are described in more detail: the first concerned a non-classified worker who put an iridium-192 source in his pocket and took it home; and the second involved the accidental contamination of two people with tritium gas. In a second appendix, the confidence limits on cytogenetic dosimetry for X- and γ-ray over-exposures are given and the derivation of these limits is discussed. (author)

  19. The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis.

    Science.gov (United States)

    Ghanbari, Z; Housaindokht, M R; Bozorgmehr, M R; Izadyar, M

    2016-09-01

    Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure. PMID:27235585

  20. Laser spectroscopies for elemental and molecular analysis in art and archaeology

    Science.gov (United States)

    Nevin, Austin; Spoto, Giuseppe; Anglos, Demetrios

    2012-02-01

    Spectroscopic methods using laser sources have significantly improved our capacity to unravel the chemical composition of works of art and archaeological remains. Lasers enhance the performance of spectroscopic techniques which require intense light sources and specific analytical protocols assuring a microanalytical approach for analysis has been established. This review focuses on laser spectroscopic methods used in the field of cultural heritage diagnostics. Emphasis in this work is given to the analytical capabilities of laser-based techniques for elemental and/or molecular analysis and in-situ use, spatial resolution and microanalysis. Analytical methods are classified according to the elemental (LIBS, LA-ICP-MS) and molecular (LIF/LIDAR, time-resolved absorption spectroscopy, laser desorption ionization mass spectrometry) information they yield. For non-destructive laser-induced fluorescence (LIF/LIDAR) and time-resolved fluorescence spectroscopy, imaging applications are described. The advantages provided by combined complementary techniques including but not limited to LIBS-LIF-Raman and LIBS-XRF are presented, as are recent improvements in terms of chemical imaging. Advances and applications of THz spectroscopy, non-linear spectroscopy and imaging are outlined. Finally, laser spectroscopies are described for investigations of different materials and works of art which include Bronze Age ceramics, Minoan archaeological remains, Ancient Roman buildings, Renaissance wall paintings and sculptures, and manuscripts containing iron gall inks and colorants.

  1. STM investigation of imine-based molecular switches on Au(111)

    Energy Technology Data Exchange (ETDEWEB)

    Mielke, Johannes; Grill, Leonhard [Institut fuer Experimentalphysik, Freie Universitaet Berlin (Germany); Luo, Ying; Haag, Rainer [Institut fuer Chemie und Biochemie - Organische Chemie, Freie Universitaet Berlin (Germany)

    2009-07-01

    In the field of molecular electronics, molecular switches are highly relevant because they can control the conductance. Switches based on azobenzene molecules have attracted large interest in the last years. A very similar molecular switch can be created by replacing the functional azo group by an imine group, which does not considerably alter the electronic structure of the molecule and conserves the capability of undergoing a reversible trans-cis isomerisation. Such processes have already been studied in solution and the gas phase but not on surfaces. In this work, imine molecules with four tert-butyl groups were adsorbed on Au(111) and their adsorption and switching behaviour were studied using a low temperature STM. The molecules were found to form two types of ordered islands and an interesting irreversible switching behaviour was observed when looking at their temperature dependence, because the number of trans isomers was reduced upon heating of the sample.

  2. Ab initio analysis of electron-phonon coupling in molecular devices

    OpenAIRE

    Sergueev, N.; Roubtsov, D.; Guo, Hong

    2005-01-01

    We report first principles analysis of electron-phonon coupling in molecular devices under external bias voltage and during current flow. Our theory and computational framework are based carrying out density functional theory within the Keldysh nonequilibrium Green's function formalism. We analyze which molecular vibrational modes are most relevant to charge transport under nonequilibrium conditions. For a molecular tunnel junction of a 1,4-benzenedithiolate molecule contacted by two leads, t...

  3. Molecular Analysis in the differentiation of Colletotrichum gloeosporioides isolates from the cashew and mango trees

    OpenAIRE

    Ilka Márcia Ribeiro de Souza Serra; Maria Menezes; Rildo Sartori Barbosa Coelho; Gabriela Moraes Guerra Ferraz; Angélica Virginia Valois Montarroyos; Luiza Suely Semem Martins

    2011-01-01

    The aim of the present work was to analyze the molecular methods in the differentiation of Colletotrichum gloeosporioides isolates obtained from the cashew and mango trees. The different molecular taxonomic methods used proved to be efficient regarding intraspecific characterization. Similarly, molecular methods also proved to be efficient in differentiation of the C. gloeosporioides isolates in relation to host specificity. In the analysis of the ITS sequence of the ribosomal DNA, all the is...

  4. Correlation between smoking history and molecular pathways in sporadic colorectal cancer: a meta-analysis

    OpenAIRE

    Chen, Ke; Xia, Guanggai; Zhang, Changhua; Sun, Yunwei

    2015-01-01

    Background: Epidemiological studies have shown that smoking increases the risk for colorectal cancer (CRC). Evidence of the guiding significance of smoking history for molecular classification and molecular targeted anti-tumor therapy is not well established. Aims: To provide indirectly evidence, we conducted a systematic meta-analysis of association between smoking history and different molecular classification. Methods: We searched in multiple databases up to January 2014, and identified 27...

  5. Analysis and investigation to draw up design method by inelastic analysis

    International Nuclear Information System (INIS)

    To realize small simple plant equipment, FBR design by inelastic analysis was studied. With the constitutive equation and analysis procedure proposed as the design method by inelastic analysis, effects of loading history on the results of inelastic analysis was investigated using a simple model. It was confirmed that estimation by the classical inelastic constitutive equation belonged to the safe site of loading history of the real reactor. The problems of application of the detailed constitutive equation to design were investigated. The creep fatigue damage evaluation logic in the intermediate retaining state, which is problem of estimation of strength on the basis of inelastic analysis, is studied. (S.Y.)

  6. Structure based investigation on the binding interaction of transport proteins in leishmaniasis: insights from molecular simulation.

    Science.gov (United States)

    Singh, Shailza; Mandlik, Vineetha

    2015-05-01

    Leishmania major is the causative agent of cutaneous leishmaniasis which affects over 1 million people in 88 different countries. The incidence of this disease is on the rise due to the current problems associated with the present chemotherapeutics. In addition, Leishmania confronts resistance to the traditional drugs like sodium stibogluconate and newer repurposed drugs like miltefosine. ABC transporters are involved in the development of drug resistance. Miltefosine, the drug used for the treatment of leishmaniasis, is effluxed by P4 ATPase and ABC transporter, which is the prime focus of our study in this paper. P4 ATPase (MDR1) along with an unnamed protein (cdc50) translocates miltefosine from the outer to the inner leaflet by the process of flipping which is ATP driven. In contrast, miltefosine also escapes from the cells by an energy dependent mechanism that involves the ABC transporter protein (ABC). It is known that certain genes in the parasite amplify the portions of a gene which encodes ABC transporter and P4 ATPase involved in translocating phospholipids and hence resistance to miltefosine. We observed the ABC and P4 ATPase genes, 39 T-box elements were observed in the ABC transporter protein and three elements were observed in the P4 ATPase gene suggesting its role in transcription regulation. To the best of our knowledge, there are no structural and regulatory reports on these two proteins in L. major. Computational structural biology tools may aid in understanding the interaction of miltefosine with the P4-ATPase-cdc50 complex and the ABC transporter. This can be achieved by modeling the target protein structures, studying the dynamics associated with the different domains of the protein and later using activators and inhibitors to alter the functioning of the protein. Molecular dynamics simulation with a lipid bilayer is performed to investigate the conformational changes and structure-activity relationship. As transporters are difficult to model

  7. Investigation of tensile response and thermal conductivity of boron-nitride nanosheets using molecular dynamics simulations

    Science.gov (United States)

    Mortazavi, Bohayra; Rémond, Yves

    2012-06-01

    In this paper, we employed classical molecular dynamics simulations using the Tersoff potential for the evaluation of thermal conductivity and tensile response of single-layer boron-nitride sheets (SBNS). By carrying out uniaxial tension simulations, the elastic moduli of SBNS structures are predicted to be close to those of boron-nitride nanotubes in a range between 0.8 and 0.85 TPa for different chirality directions. Performing non-equilibrium molecular dynamics simulations, the thermal conductivity of SBNS is predicted to be around 80 W/m-K, which is shown to be independent of chirality directions.

  8. Investigating the Fundamentals of Molecular Depth Profiling Using Strong-field Photoionization of Sputtered Neutrals

    OpenAIRE

    Willingham, D.; Brenes, D. A.; Winograd, N.; Wucher, A

    2011-01-01

    Molecular depth profiles of model organic thin films were performed using a 40 keV C60+ cluster ion source in concert with TOF-SIMS. Strong-field photoionization of intact neutral molecules sputtered by 40 keV C60+ primary ions was used to analyze changes in the chemical environment of the guanine thin films as a function of ion fluence. Direct comparison of the secondary ion and neutral components of the molecular depth profiles yields valuable information about chemical damage accumulation ...

  9. The molecular properties of humic substances isolated from a UK upland peat system: a temporal investigation.

    Science.gov (United States)

    Scott, M J; Jones, M N; Woof, C; Simon, B; Tipping, E

    2001-12-01

    The study concerns the possible changes in the molecular characteristics of humic materials isolated from the same source as a function of time. A great deal of data has been reported concerning the contrast in molecular characteristics of humic substances isolated from different environments. This has primarily been an attempt to identify source-specific molecular characteristics. However, data presented in this paper suggests that humic substances isolated from a single catchment have significant changes in molecular characteristics over time. Two naturally occurring peat pools (X and Y) situated upon a small organic catchment on Great Dun Fell, Cumbria, UK were sampled monthly between November 1994 and November 1996. Dissolved organic matter (DOM) from the pool water samples was fractionated using macroporous nonionic resins (XAD8 and 4), and the humic, fulvic and hydrophilic acids were collected. These fractions were analysed for elemental composition (C, H and N), weight average molecular weight, functional group content and adsorption (340 nm) of a 1 g l(-1) solution measured in a 1-cm spectrophotometer cell. The molecular characteristics were compared to those of natural DOM described by Scott et al. (1998). Scott et al. reported that drought conditions and seasonal climatic changes could have appreciable effects upon molecular characteristics of natural DOM. Results showed that the atomic H/C ratio of the humic substances increased immediately after strong drought conditions experienced in the summer of 1995. This change was temporary with atomic H/C ratio decreasing gradually over the following months. A similar decrease was observed in the carboxyl group content of the isolated compounds. The data set suggested that atomic H/C ratio in the fulvic and hydrophilic fractions exhibited seasonal characteristics of higher ratios during the late summer/early autumn months. This was not observed in the humic fraction. Humic acids exhibited a seasonal pattern of

  10. Molecular Typing of Treponema pallidum: A Systematic Review and Meta-Analysis

    Science.gov (United States)

    Peng, Rui-Rui; Wang, Alberta L.; Li, Jing; Tucker, Joseph D.; Yin, Yue-Ping; Chen, Xiang-Sheng

    2011-01-01

    Background Syphilis is resurgent in many regions of the world. Molecular typing is a robust tool for investigating strain diversity and epidemiology. This study aimed to review original research on molecular typing of Treponema pallidum (T. pallidum) with three objectives: (1) to determine specimen types most suitable for molecular typing; (2) to determine T. pallidum subtype distribution across geographic areas; and (3) to summarize available information on subtypes associated with neurosyphilis and macrolide resistance. Methodology/Principal Findings Two researchers independently searched five databases from 1998 through 2010, assessed for eligibility and study quality, and extracted data. Search terms included “Treponema pallidum,” or “syphilis,” combined with the subject headings “molecular,” “subtyping,” “typing,” “genotype,” and “epidemiology.” Sixteen eligible studies were included. Publication bias was not statistically significant by the Begg rank correlation test. Medians, inter-quartile ranges, and 95% confidence intervals were determined for DNA extraction and full typing efficiency. A random-effects model was used to perform subgroup analyses to reduce obvious between-study heterogeneity. Primary and secondary lesions and ear lobe blood specimens had an average higher yield of T. pallidum DNA (83.0% vs. 28.2%, χ2 = 247.6, p<0.001) and an average higher efficiency of full molecular typing (80.9% vs. 43.1%, χ2 = 102.3, p<0.001) compared to plasma, whole blood, and cerebrospinal fluid. A pooled analysis of subtype distribution based on country location showed that 14d was the most common subtype, and subtype distribution varied across geographic areas. Subtype data associated with macrolide resistance and neurosyphilis were limited. Conclusions/Significance Primary lesion was a better specimen for obtaining T. pallidum DNA than blood. There was wide geographic variation in T. pallidum subtypes. More research is needed

  11. Molecular typing of Treponema pallidum: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Rui-Rui Peng

    2011-11-01

    Full Text Available BACKGROUND: Syphilis is resurgent in many regions of the world. Molecular typing is a robust tool for investigating strain diversity and epidemiology. This study aimed to review original research on molecular typing of Treponema pallidum (T. pallidum with three objectives: (1 to determine specimen types most suitable for molecular typing; (2 to determine T. pallidum subtype distribution across geographic areas; and (3 to summarize available information on subtypes associated with neurosyphilis and macrolide resistance. METHODOLOGY/PRINCIPAL FINDINGS: Two researchers independently searched five databases from 1998 through 2010, assessed for eligibility and study quality, and extracted data. Search terms included "Treponema pallidum," or "syphilis," combined with the subject headings "molecular," "subtyping," "typing," "genotype," and "epidemiology." Sixteen eligible studies were included. Publication bias was not statistically significant by the Begg rank correlation test. Medians, inter-quartile ranges, and 95% confidence intervals were determined for DNA extraction and full typing efficiency. A random-effects model was used to perform subgroup analyses to reduce obvious between-study heterogeneity. Primary and secondary lesions and ear lobe blood specimens had an average higher yield of T. pallidum DNA (83.0% vs. 28.2%, χ(2 = 247.6, p<0.001 and an average higher efficiency of full molecular typing (80.9% vs. 43.1%, χ(2 = 102.3, p<0.001 compared to plasma, whole blood, and cerebrospinal fluid. A pooled analysis of subtype distribution based on country location showed that 14d was the most common subtype, and subtype distribution varied across geographic areas. Subtype data associated with macrolide resistance and neurosyphilis were limited. CONCLUSIONS/SIGNIFICANCE: Primary lesion was a better specimen for obtaining T. pallidum DNA than blood. There was wide geographic variation in T. pallidum subtypes. More research is needed on the

  12. Ampelographic Characteristics and Molecular Investigation of Azerbaijani Local Grape Varieties by Microsatellites

    Directory of Open Access Journals (Sweden)

    VUGAR SALIMOV

    2015-12-01

    Full Text Available The article aims at introducing of some local grapevine varieties cultivated in different areas of Azerbaijan. The cultivars are grown in the ampelographic collection of the Azerbaijani Scientific Research Institute of Viticulture and Wine-making. The description of their ampelographic specifications was based on the OIV list. Comparing cultivars, it has been found that, although there are similarities in various descriptor traits, most of the characteristics are distinctive of specific cultivars. A considerable polymorphism was found concerning the botanical features of leaves, clusters, berries, as well as considering some biological and technological characteristics. In more details, these genotypes differ each other by the morphological features of leaves; the shape, size and structure of clusters; the shape, color and flavor of berries; the productivity indices; the resistance to pests and diseases; the duration of their vegetative period; the sugar and acid contents; and the number of seeds in the berry. This study was carried out on nine grape cultivars grown in region Garabagh, Nakhchyvan and Absheron in 2008- 2012. Analyses of the ampelographic features of the studied grape varieties showed that the genotypes considerably differ by their main morphological, biological and technological characteristics. 42 Azerbaijani grape varieties (including above mentioned have been investigated comparatively with Caucasian countries` and European grape varieties. Based on the descriptive statistics Azerbaijani samples appeared having the highest genetic diversity. The first two coordinates of the PCoA differentiated the samples into two main clusters, despite the presence of overlapping zones: i the group clusterizing the most part of cultivars from Azerbaijan; ii the other Caucasian and European varieties. STRUCTURE analysis revealed the optimal K value equal to 3, highlighting 3 groups: i Central European group; ii an admixed group, containing

  13. Numerical analysis and output characteristics of molecular nitrigen laser

    International Nuclear Information System (INIS)

    Molecular nitrogen lasers have proved to be one of the most versatile lasers. Their strong, fast pulsed output in the near ultraviolet is ideally suited for pumping organic dye lasers, for flourescence studies and for Raman spectroscopy. The design and construction of a transversely excited molecular nitrogen laser are described in detail. Using the time dependent rate equations, the threshold conditions are given. The output peak power and pulse width as a function of length and initial inversion density are shown. The theoretical results derived are compared with experimental data and are found to be in good agreement. (Author)

  14. New molecular analysis of differential gene expressions to evaluate new exposure markers and radioresistance

    International Nuclear Information System (INIS)

    Molecular techniques, such as macro array and representation difference analysis (RDA) (1), allow to detect subtle variations into complex biological processes induced by exposure to ionising radiation. One of the most reliable method to investigate radioresistance in vitro is to select a clone with acquired or intrinsic resistant phenotype by delivering repeated fractions of low-dose X-irradiation to a parent cell line. The resulting isolated resistant clone is then suitable for molecular techniques to analyse differential genes which expressions are important in characterising response and resistance to radiation. The cDNA expression arrays allow to perform the analysis of hundreds of known genes while RDA permits the comparison of genomic cDNA also from higher eukaryotes. The aim of the present work was to verify the suitable of these new molecular approaches to recognize the expression of genes hypothetically useful as radioprotection markers. To this end, a relatively high dose of X-rays was used (2 Gy), differentially expressed genes were isolated, and new experiments based on high sensitive and reproducible RT-PCR are foreseen for lower doses. Human neuroblastoma cell lines IMR32 and its resistant clone (Clone F), previously isolated by repeated 2 Gy X-irradiation( 2), were irradiated with a single 2 Gy X-rays. Six hours later, cells were monitored for surviving fraction, index of apoptosis and RNAs were extracted, purified and analysed either by human macro array with 205 cDNA of apoptosis genes related spiked on and either by RDA methodology. Human apoptosis macro array confirmed higher expression of genes related both to apoptosis regulator (Bax) and apoptosis effectors (caspase-2) in IMR32 cell line. RDA showed several differentially expressed genes in the resistant clone. Among these genes, two unknown forms of a protein with a putative enzymatic activity are cloned and transfected in the sensitive cell line to understand their role in radioresistance

  15. The Silica-Water Interface from the Analysis of Molecular Dynamic Simulations

    KAUST Repository

    Lardhi, Sheikha F.

    2013-05-01

    Surface chemistry is an emerging field that can give detailed insight about the elec- tronic properties and the interaction of complex material surfaces with their neigh- bors. This is for both solid-solid and solid-liquid interfaces. Among the latter class, the silica-water interface plays a major role in nature. Silica is among the most abundant materials on earth, as well in advanced technological applications such as catalysis and nanotechnology. This immediately indicates the relevance of a detailed understanding of the silica-water interface. In this study, we investigate the details of this interaction at microscopic level by analyzing trajectories obtained with ab initio molecular dynamic simulations. The system we consider consists of bulk liquid water confined between two β-cristobalite silica surfaces. The molecular dynamics were generated with the CP2K, an ab initio molecular dynamic simulation tool. The simulations are 25 picoseconds long, and the CP2K program was run on 64 cores on a supercomputer cluster. During the simulations the program integrates Newton’s equations of motion for the system and generates the trajectory for analysis. For analysis, we focused on the following properties that characterize the silica water interface. We calculated the density profile of the water layers from the silica surface, and we also calculated the radial distribution function (RDF) of the hydrogen bond at the silanols on the silica surface. The main focus of this thesis is to write the programs for calculating the atom density profile and the RDF from the generated MD trajectories. The atomic probability density profile shows that water is strongly adsorbed on the (001) cristobalite surface, while the RDF indicates differently ad- sorbed water molecules in the first adsorption layer. As final remark, the protocol and the tools developed in this thesis can be applied to the study of basically any crystal-water interface.

  16. AB INITIO HF AND DFT STUDIES ON MOLECULAR STRUCTURE AND VIBRATIONAL ANALYSIS OF 2,5-DIBROMOPYRIDINE

    OpenAIRE

    ÇIRAK, Çağrı; KOÇ, Nurettin

    2014-01-01

    Theoretical study on molecular structure and vibrational spectra of 2,5-dibromopyridine (2,5-DBP) have been investigated. The optimized geometry, theoretical vibration frequencies and intensities were calculated by using ab initio Hartree-Fock and density functional B3LYP method with 6-31G(d,p) basis sets. The vibrational analysis of title molecule was done and its optimized geometry parameters (bond lengths and bond angles) were given. Scaled theoretical frequencies have been compared with e...

  17. Teaching Structure-Property Relationships: Investigating Molecular Structure and Boiling Point

    Science.gov (United States)

    Murphy, Peter M.

    2007-01-01

    A concise, well-organized table of the boiling points of 392 organic compounds has facilitated inquiry-based instruction in multiple scientific principles. Many individual or group learning activities can be derived from the tabulated data of molecular structure and boiling point based on the instructor's education objectives and the students'…

  18. Investigation on the protein-binding properties of icotinib by spectroscopic and molecular modeling method.

    Science.gov (United States)

    Zhang, Hua-Xin; Xiong, Hang-Xing; Li, Li-Wei

    2016-05-15

    Icotinib is a highly-selective epidermal growth factor receptor tyrosine kinase inhibitor with preclinical and clinical activity in non-small cell lung cancer, which has been developed as a new targeted anti-tumor drug in China. In this work, the interaction of icotinib and human serum albumin (HSA) were studied by three-dimensional fluorescence spectra, ultraviolet spectra, circular dichroism (CD) spectra, molecular probe and molecular modeling methods. The results showed that icotinib binds to Sudlow's site I in subdomain IIA of HSA molecule, resulting in icotinib-HSA complexes formed at ground state. The number of binding sites, equilibrium constants, and thermodynamic parameters of the reaction were calculated at different temperatures. The negative enthalpy change (ΔH(θ)) and entropy change (ΔS(θ)) indicated that the structure of new complexes was stabilized by hydrogen bonds and van der Waals power. The distance between donor and acceptor was calculated according to Förster's non-radiation resonance energy transfer theory. The structural changes of HSA caused by icotinib binding were detected by synchronous spectra and circular dichroism (CD) spectra. Molecular modeling method was employed to unfold full details of the interaction at molecular level, most of which could be supported by experimental results. The study analyzed the probability that serum albumins act as carriers for this new anticarcinogen and provided fundamental information on the process of delivering icotinib to its target tissues, which might be helpful in understanding the mechanism of icotinib in cancer therapy. PMID:26963729

  19. Investigation of the Hydroxylation Mechanism of Noncoupled Copper Oxygenases by Ab Initio Molecular Dynamics Simulations

    Czech Academy of Sciences Publication Activity Database

    Meliá, C.; Ferrer, S.; Řezáč, Jan; Parisel, O.; Reinaud, O.; Moliner, V.; de la Lande, A.

    2013-01-01

    Roč. 19, č. 51 (2013), s. 17328-17337. ISSN 0947-6539 Institutional support: RVO:61388963 Keywords : ab initio calculations * copper * electron transfer * enzymes * molecular dynamics * reaction mechanisms Subject RIV: CC - Organic Chemistry Impact factor: 5.696, year: 2013

  20. Metal-amyloid-β peptide interactions: a preliminary investigation of molecular mechanisms for Alzheimer's disease

    Institute of Scientific and Technical Information of China (English)

    JIAO Yong; YANG Pin

    2007-01-01

    Although humans have spent exactly 100 years combating Alzheimer's disease (AD), the molecular mechanisms of AD remain unclear. Owing to the rapid growth of the oldest age groups of the population and the continuous increase of the incidence of AD, it has become one of the crucial problems to modern sciences. It would be impossible to prevent or reverse AD at the root without elucidating its molecular mechanisms. From the point of view of metal-amyloid-β peptide (Aβ) interactions, we review the molecular mechanisms of AD, mainly including Cu2+ and Zn2+ inducing the aggregation of Aβ, catalysing the production of active oxygen species from Aβ, as well as interacting with the ion-channel-like structures of Aβ. Moreover, the development of therapeutic drugs on the basis of metal-Aβ interactions is also briefly introduced. With the increasingly rapid progress of the molecular mechanisms of AD, we are now entering a new dawn that promises the delivery of revolutionary developments for the control of dementias.

  1. Molecular Investigation of the Aum Shinrikyo Anthrax Release in Kameido, Japan

    OpenAIRE

    Keim, Paul; Smith, Kimothy L; Keys, Christine; Takahashi, Hiroshi; Kurata, Takeshi; Kaufmann, Arnold

    2001-01-01

    In 1993, the Aum Shinrikyo cult aerosolized Bacillus anthracis spores over Kameido, Japan. Spore samples were obtained from the release site, cultured, and characterized by molecular genetic typing. The isolates were consistent with strain Sterne 34F2, which is used in Japan for animal prophylaxis against anthrax.

  2. Investigation on the protein-binding properties of icotinib by spectroscopic and molecular modeling method

    Science.gov (United States)

    Zhang, Hua-xin; Xiong, Hang-xing; Li, Li-wei

    2016-05-01

    Icotinib is a highly-selective epidermal growth factor receptor tyrosine kinase inhibitor with preclinical and clinical activity in non-small cell lung cancer, which has been developed as a new targeted anti-tumor drug in China. In this work, the interaction of icotinib and human serum albumin (HSA) were studied by three-dimensional fluorescence spectra, ultraviolet spectra, circular dichroism (CD) spectra, molecular probe and molecular modeling methods. The results showed that icotinib binds to Sudlow's site I in subdomain IIA of HSA molecule, resulting in icotinib-HSA complexes formed at ground state. The number of binding sites, equilibrium constants, and thermodynamic parameters of the reaction were calculated at different temperatures. The negative enthalpy change (ΔHθ) and entropy change (ΔSθ) indicated that the structure of new complexes was stabilized by hydrogen bonds and van der Waals power. The distance between donor and acceptor was calculated according to Förster's non-radiation resonance energy transfer theory. The structural changes of HSA caused by icotinib binding were detected by synchronous spectra and circular dichroism (CD) spectra. Molecular modeling method was employed to unfold full details of the interaction at molecular level, most of which could be supported by experimental results. The study analyzed the probability that serum albumins act as carriers for this new anticarcinogen and provided fundamental information on the process of delivering icotinib to its target tissues, which might be helpful in understanding the mechanism of icotinib in cancer therapy.

  3. Structural investigation of bistrifluron using x-ray crystallography, NMR spectroscopy, and molecular modeling

    CERN Document Server

    Moon, J K; Rhee, S K; Kim, G B; Yun, H S; Chung, B J; Lee, S S; Lim, Y H

    2002-01-01

    A new insecticide, bistrifluron acts as an inhibitor of insect development and interferes with the cuticle formation of insects. Since it shows low acute oral and dermal toxicities, it can be one of potent insecticides. Based on X-ray crystallography, NMR spectroscopy and molecular modeling, the structural studies of bistrifluron have been carried out.

  4. In silico investigation of molecular effects caused by missense mutations in creatine transporter protein

    Science.gov (United States)

    Zhang, Zhe; Schwatz, Charles; Alexov, Emil

    2011-03-01

    Creatine transporter (CT) protein, which is encoded by SLC6A8 gene, is essential for taking up the creatine in the cell, which in turn plays a key role in the spatial and temporal maintenance of energy in skeletal and cardiac muscle cells. It was shown that some missense mutations in CT cause mental retardation, while others are harmless non-synonymous single nucleoside polymorphism (nsSNP). Currently fifteen missense mutations in CT are known, among which twelve are disease-causing. Sequence analysis reveals that there is no clear trend distinguishing disease-causing from harmless missense mutations. Because of that, we built 3D model of the CT using highly homologous template and use the model to investigate the effects of mutations of CT stability and hydrogen bond network. It is demonstrated that disease-causing mutations affect the folding free energy and ionization states of titratable group in much greater extend as compared with harmless mutations. Supported by grants from NLM, NIH, grant numbers 1R03LM009748 and 1R03LM009748-S1.

  5. Thermodynamic Models from Fluctuation Solution Theory Analysis of Molecular Simulations

    DEFF Research Database (Denmark)

    Christensen, Steen; Peters, Günther H.j.; Hansen, Flemming Yssing;

    2007-01-01

    Fluctuation solution theory (FST) is employed to analyze results of molecular dynamics (MD) simulations of liquid mixtures. The objective is to generate parameters for macroscopic GE-models, here the modified Margules model. We present a strategy for choosing the number of parameters included in ...

  6. Molecular Laser Spectroscopy as a Tool for Gas Analysis Applications

    OpenAIRE

    Javis Anyangwe Nwaboh; Thibault Desbois; Daniele Romanini; Detlef Schiel; Olav Werhahn

    2011-01-01

    We have used the traceable infrared laser spectrometric amount fraction measurement (TILSAM) method to perform absolute concentration measurements of molecular species using three laser spectroscopic techniques. We report results performed by tunable diode laser absorption spectroscopy (TDLAS), quantum cascade laser absorption spectroscopy (QCLAS), and cavity ring down spectroscopy (CRDS), all based on the TILSAM methodology. The measured results of the different spectroscopic techniques are ...

  7. Influence of out-of-plane defects on vibration analysis of graphene: Molecular Dynamics and Non-local Elasticity approaches

    Science.gov (United States)

    Jalali, S. K.; Jomehzadeh, E.; Pugno, N. M.

    2016-03-01

    Out-of-plane defects may exist in graphene inevitably or purposely. The present study aims at investigating the influence of out-of-plane defects on vibrational analysis of single layered graphene sheets (SLGSs) implementing both nonlocal elasticity and molecular dynamics (MD) simulations. In nonlocal elasticity analysis, the defect is considered as an initial curvature which is modeled by an analytical function having controllable parameters for the amplitude, extension, and location. In molecular dynamics analysis, defects are simulated by inserting inverse Stone-Wales defects in the perfect structure of SLGSs. Both nonlocal continuum and MD simulation results reveal that the defects increase the vibrational frequency. It is shown that classical elasticity overestimates frequencies with a considerable error while the nonlocal plate model can fit MD results by implementing a proper small scale parameter.

  8. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces

    Directory of Open Access Journals (Sweden)

    Tairacan Augusto Pereira da Fonseca

    2015-10-01

    Full Text Available Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$ notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or “feiras” in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  9. Investigation, experiment and analysis on PWR sump screen clogging issue

    International Nuclear Information System (INIS)

    JNES has been conducting experimental and analytical study to develop an evaluation method concerning the downstream effect of the sump screen clogging issue during LOCA in PWR plants. Flow clogging characteristics were investigated based on data for the relation of pressure loss and flow velocity during flow clogging due to debris accumulation. Deposition of chemical precipitates on the fuel cladding using an electrically heated rod was investigated. A test shows chemical precipitates deposited on the cladding and the deposit was mainly analyzed to be calcium compounds. The analysis with a thermal-hydraulic code on the downstream effect has shown that the core could be cooled because the core inlet flow compensates a evaporation of coolant due to the decay-heat even if core inlet was 99% clogged just after the ECCS recirculation operation started during the cold-leg break LOCA in PWR plants. (author)

  10. Molecular diversity of Renibacterium salmoninarum isolates determined by randomly amplified polymorphic DNA analysis.

    Science.gov (United States)

    Grayson, T H; Atienzar, F A; Alexander, S M; Cooper, L F; Gilpin, M L

    2000-01-01

    The molecular diversity among 60 isolates of Renibacterium salmoninarum which differ in place and date of isolation was investigated by using randomly amplified polymorphic DNA (RAPD) analysis. Isolates were grouped into 21 banding patterns which did not reflect the biological source. Four 16S-23S rRNA intergenic spacer (ITS1) sequence variations and two alleles of an exact tandem repeat locus, ETR-A, were the bases for formation of distinct groups within the RAPD clusters. This study provides evidence that the most common ITS1 sequence variant, SV1, possesses two copies of a 51-bp repeat unit at ETR-A and has been widely dispersed among countries which are associated with mainstream intensive salmonid culture. PMID:10618262

  11. Genomic analysis to define molecular basis of aggressiveness in a mouse model of oral cancer

    Directory of Open Access Journals (Sweden)

    Varun Chalivendra

    2015-03-01

    Full Text Available To investigate the molecular basis underlying aggressive behavior in oral squamous cell carcinoma (OSCC, our laboratory developed a carcinogen-induced mouse oral cancer (MOC cell line model that encompasses the growth and metastasis spectrum of its human counterpart. We performed next-generation sequencing (NGS and gene expression microarray profiles to explore the genomic and transcriptional backgrounds of the differential MOC line phenotypes, as well as, the cross-species relevance of the model. Here we describe the comparative analysis of NGS (www.ncbi.nlm.nih.gov/biosample?LinkName=bioproject_biosample_all&from_uid=247825 and expression microarray (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50041 data from the MOC lines and corresponding human data, as described in our recent publication [1].

  12. Investigating Research Streams of Conjoint Analysis: A Bibliometric Study

    Directory of Open Access Journals (Sweden)

    Thorsten Teichert

    2010-05-01

    Full Text Available Conjoint analysis (CA is one of the most important methods for preference elicitation. In this paper we investigate the intellectual structure within the conjoint analytical research community. Analyses based on single papers provide a method-based overview of streams of conjoint research. By using novel bibliometric techniques in this field we complement findings of existing reviews. We use co-citation and factor analysis of the most cited articles in SSCI to identify the most important articles and research streams. Seven research streams are revealed which are visualized by means of multidimensional scaling. Tables and graphics reveal the disciplinary affiliations of contributors to CA, the special structure within the classes as well as links between them.

  13. Molecular Analysis of Endolithic Microbial Communities in Volcanic Glasses

    Science.gov (United States)

    di Meo, C. A.; Giovannoni, S.; Fisk, M.

    2002-12-01

    Terrestrial and marine volcanic glasses become mineralogically and chemically altered, and in many cases this alteration has been attributed to microbial activity. We have used molecular techniques to study the resident microbial communities from three different volcanic environments that may be responsible for this crustal alteration. Total microbial DNA was extracted from rhyolite glass of the 7 million year old Rattlesnake Tuff in eastern Oregon. The DNA was amplified using the polymerase chain reaction (PCR) with bacterial primers targeting the 16S rRNA gene. This 16S rDNA was cloned and screened with restriction fragment length polymorphism (RFLP). Out of 89 total clones screened, 46 belonged to 13 different clone families containing two or more members, while 43 clones were unique. Sequences of eight clones representing the most dominant clone families in the library were 92 to 97% similar to soil bacterial species. In a separate study, young pillow basalts (microbial life. Total DNA was extracted from the basalt glass and screened for the presence of both bacteria and archaea using the PCR. Repeated attempts with different primer sets yielded no bacterial genes, whereas archaeal genes were quite abundant. A genetic fingerprinting technique, terminal restriction fragment length polymorphism (T-RFLP), was used to compare the archaeal community compositions among the six different basalts. Filtered deep-sea water samples (~15 L) were examined in parallel to identify any overlap between rock- and seawater-associated archaea. The six rock community profiles were quite similar to each other, and the background water communities were also similar, respectively. Both the rock and water communities shared the same dominant peak. To identify the T-RFLP peaks corresponding to the individual members of the rock and seawater communities, clone libraries of the archaeal 16S rDNA for one basalt sample (Dive 3718) and its corresponding background water sample were

  14. Investigation of shielding analysis method for fusion reactors

    International Nuclear Information System (INIS)

    An investigation has been made, at the shielding laboratory, into the status of shielding analysis method for fusion reactor based on conceptual designs of a variety of fusion power reactors and fusion experimental facilities, in cooperation with the Fusion Reactor Shielding Working Group in the Research Committee on Fast Neutron Shielding of the Atomic Energy Society of Japan. The reactors and facilities considered are CULHAM MKII(U.K), SPTR (Japan), TFTR(U.S.A.), STARFIRE(U.S.A.) and INTOR-USA(U.S.A.). (author)

  15. Neutron activation analysis for investigation of chosen food products

    International Nuclear Information System (INIS)

    In this work neutron activation analysis is applied for investigation of the elemental composition of Amaranths seeds. The characterization by multi-elemental instrumental NAA is enriched by the results of radiochemical NAA for cobalt, molybdenum and uranium content. The comparison of the results, for three sorts of edible flour, commercially available: soya Flour, Corn Bean Flour and Amaranths Flour, is presented. The validation of the analytical methods used was carried out on the basis of participation in the interlaboratory comparison organised by INCT and NIST. (author)

  16. Symbiosis between hydra and chlorella: molecular phylogenetic analysis and experimental study provide insight into its origin and evolution.

    Science.gov (United States)

    Kawaida, Hitomi; Ohba, Kohki; Koutake, Yuhki; Shimizu, Hiroshi; Tachida, Hidenori; Kobayakawa, Yoshitaka

    2013-03-01

    Although many physiological studies have been reported on the symbiosis between hydra and green algae, very little information from a molecular phylogenetic aspect of symbiosis is available. In order to understand the origin and evolution of symbiosis between the two organisms, we compared the phylogenetic relationships among symbiotic green algae with the phylogenetic relationships among host hydra strains. To do so, we reconstructed molecular phylogenetic trees of several strains of symbiotic chlorella harbored in the endodermal epithelial cells of viridissima group hydra strains and investigated their congruence with the molecular phylogenetic trees of the host hydra strains. To examine the species specificity between the host and the symbiont with respect to the genetic distance, we also tried to introduce chlorella strains into two aposymbiotic strains of viridissima group hydra in which symbiotic chlorella had been eliminated in advance. We discussed the origin and history of symbiosis between hydra and green algae based on the analysis. PMID:23219706

  17. Statistical Properties of the Dense Hydrogen Plasma an ab initio Molecular Dynamics Investigation

    CERN Document Server

    Kohanoff, J J; Kohanoff, Jorge; Hansen, Jean-Pierre

    1996-01-01

    The metallic regime of the hydrogen plasma is studied by ab initio Molecular Dynamics simulations, for classical protons and fully degenerate electrons, in the strong coupling regime of the protons. The breakdown of linear screening observed for decreasing density gives rise to a surprisingly rich low-temperature phase diagram, showing in particular a dramatic drop of the melting temperature of the proton crystal. Extensive dynamical simulations reveal the remarkable persistence of a weakly damped high-frequency ion acoustic mode (plasmon-like), even under conditions of strong electron screening. This collective mode should disappear in the molecular phase, thus providing a probe for the metal-insulator transition in a region of parameters where experiment is difficult to achieve. Finite-size effects arising in the simulation of liquid metals are discussed. The status of the dense Hydrogen matter is extensively reviewed in the introduction.

  18. HULIS in nanoaerosol clusters; investigations of surface tension and aggregate formation using molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    T. Hede

    2011-03-01

    Full Text Available Cloud condensation nuclei act as cores for water vapor condensation, and their composition and chemical properties may enhance or depress the ability for droplet growth. In this study we use molecular dynamics simulations to show that humic-like substances of larger systems (8.6 nm in diameter mimic experimental data well referring to reduction of surface tension. The structural properties examined show the ability for the humic-like substances to aggregate inside the nanoaerosol clusters.

  19. Investigations into the molecular evolution of plant terpene, alkaloid, and urushiol biosynthetic enzymes

    OpenAIRE

    Weisberg, Alexandra Jamie

    2014-01-01

    Plants produce a vast number of low-molecular-weight chemicals (so called secondary or specialized metabolites) that confer a selective advantage to the plant, such as defense against herbivory or protection from changing environmental conditions. Many of these specialized metabolites are used for their medicinal properties, as lead compounds in drug discovery, or to impart our food with different tastes and scents. These chemicals are produced by various pathways of enzyme-mediated reactions...

  20. Experimental investigation of molecular solids and vanadium at high pressure and temperature

    OpenAIRE

    Jenei, Zsolt

    2009-01-01

    Understanding high pressure effects on simple molecular system is of great interest for condensed matter science and geophysics. Accessing the static pressure and temperature regions found in planetary interiors is made possible by the development of the Diamond Anvil Cell technique. We developed a double sided resistive heating method for the membrane DAC operating in low pressure (<0.5 mTorr) pressure environment requiring only 175 W input power to reach sample temperatures up to 1300 K....

  1. Investigation of Combining Plant Genotypic Values and Molecular Marker Information for Constructing Core Subsets

    Institute of Scientific and Technical Information of China (English)

    Jian-Cheng Wang; Jin Hu; Ning-Ning Liu; Hai-Ming Xu; Sheng Zhang

    2006-01-01

    In the present study, a strategy was proposed for constructing plant core subsets by clusters based on the combination of continuous data for genotypic values and discrete data for molecular marker information. A mixed linear model approach was used to predict genotypic values for eliminating the environment effect.The "mixed genetic distance" was designed to solve the difficult problem of combining continuous and discrete data to construct a core subset by cluster. Four commonly used genetic distances for continuous data (Euclidean distance, standardized Euclidean distance, city block distance, and Mahalanobis distance)were used to assess the validity of the continuous data part of the mixed genetic distance; three commonly used genetic distances for discrete data (cosine distance, correlation distance, and Jaccard distance) were used to assess the validity of the discrete data part of the mixed genetic distance. A rice germplasm group with eight quantitative traits and information for 60 molecular markers was used to evaluate the validity of the new strategy. The results suggest that the validity of both parts of the mixed genetic distance are equal to or higher than the common genetic distance. The core subset constructed on the basis of a combination of data for genotypic values and molecular marker information was more representative than that constructed on the basis of data from genotypic values or molecular marker information alone. Moreover, the strategy of using combined data was able to treat dominant marker information and could combine any other continuous data and discrete data together to perform cluster to construct a plant core subset.

  2. Ultrasonic Investigations of Molecular Interaction in Binary Mixtures of Benzyl Benzoate with Acetonitrile and Benzonitrile

    OpenAIRE

    N. Jaya Madhuri; Naidu, P S; Glory, J.; K. Ravindra Prasad

    2011-01-01

    Ultrasonic velocity, density and viscosity have been measured in the binary mixtures of benzyl benzoate with acetonitrile, benzonitrile at three temperatures 30, 40 and 50 °C. From the experimental data, thermodynamic parameters like adiabatic compressibility, internal pressure, enthalpy, activation energy etc., were computed and the molecular interactions were predicted based on the variation of excess parameters in the mixture. Also theoretical evaluation of velocities was made employing th...

  3. Raman spectroscopy in investigations of mechanism of binding of human serum albumin to molecular probe fluorescein

    International Nuclear Information System (INIS)

    The mechanism of binding of molecular probe fluorescein to molecules of human serum albumin was studied by the Raman spectroscopy method. The position of binding Center on human serum albumin molecule for fluorescein is determined. The amino acid residues of albumin molecule, participating in binding of fluorescein at different pH values of solution, are established. The conformation rearrangements of globules of human serum albumin, taking place at binding of fluorescein at different pH values of solution, are registered

  4. Adsorption mechanisms of microcystin variant conformations at water-mineral interfaces: A molecular modeling investigation.

    Science.gov (United States)

    Pochodylo, Amy L; Aoki, Thalia G; Aristilde, Ludmilla

    2016-10-15

    Microcystins (MCs) are potent toxins released during cyanobacterial blooms. Clay minerals are implicated in trapping MCs within soil particles in surface waters and sediments. In the absence of molecular characterization, the relevance of previously proposed adsorption mechanisms is lacking. Towards obtaining this characterization, we conducted Monte Carlo simulations combined with molecular dynamics relaxation of two MC variants, MC-leucine-arginine (MC-LR) and MC-leucine-alanine (MC-LA), adsorbed on hydrated montmorillonite with different electrolytes. The resulting adsorbate structures revealed how MC conformations and aqueous conditions dictate binding interactions at the mineral surface. Electrostatic coupling between the arginine residue and a carboxylate in MC-LR excluded the participation of arginine in mediating adsorption on montmorillonite in a NaCl solution. However, in a CaCl2 solution, the complexation of Ca by two carboxylate moieties in MC-LR changed the MC conformation, which allowed arginine to mediate electrostatic interaction with the mineral. By contrast, due to the lack of arginine in MC-LA, complexation of Ca by only one carboxylate in MC-LA was required to favor Ca-bridging interaction with the mineral. Multiple water-bridged H-bonding interactions were also important in anchoring MCs at the mineral surface. Our modeling results offer molecular insights into the structural and chemical factors that can control the fate of MCs at water-mineral interfaces. PMID:27433998

  5. Investigation of indazole unbinding pathways in CYP2E1 by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Zhonghua Shen

    Full Text Available Human microsomal cytochrome P450 2E1 (CYP2E1 can oxidize not only low molecular weight xenobiotic compounds such as ethanol, but also many endogenous fatty acids. The crystal structure of CYP2E1 in complex with indazole reveals that the active site is deeply buried into the protein center. Thus, the unbinding pathways and associated unbinding mechanisms remain elusive. In this study, random acceleration molecular dynamics simulations combined with steered molecular dynamics and potential of mean force calculations were performed to identify the possible unbinding pathways in CYP2E1. The results show that channel 2c and 2a are most likely the unbinding channels of CYP2E1. The former channel is located between helices G and I and the B-C loop, and the latter resides between the region formed by the F-G loop, the B-C loop and the β1 sheet. Phe298 and Phe478 act as the gate keeper during indazole unbinding along channel 2c and 2a, respectively. Previous site-directed mutagenesis experiments also supported these findings.

  6. Molecular investigations of protriptyline as a multi-target directed ligand in Alzheimer's disease.

    Directory of Open Access Journals (Sweden)

    Sneha B Bansode

    Full Text Available Alzheimer's disease (AD is a complex neurodegenerative disorder involving multiple cellular and molecular processes. The discovery of drug molecules capable of targeting multiple factors involved in AD pathogenesis would greatly facilitate in improving therapeutic strategies. The repositioning of existing non-toxic drugs could dramatically reduce the time and costs involved in developmental and clinical trial stages. In this study, preliminary screening of 140 FDA approved nervous system drugs by docking suggested the viability of the tricyclic group of antidepressants against three major AD targets, viz. Acetylcholinesterase (AChE, β-secretase (BACE-1, and amyloid β (Aβ aggregation, with one member, protriptyline, showing highest inhibitory activity. Detailed biophysical assays, together with isothermal calorimetry, fluorescence quenching experiments, kinetic studies and atomic force microscopy established the strong inhibitory activity of protriptyline against all three major targets. The molecular basis of inhibition was supported with comprehensive molecular dynamics simulations. Further, the drug inhibited glycation induced amyloid aggregation, another important causal factor in AD progression. This study has led to the discovery of protriptyline as a potent multi target directed ligand and established its viability as a promising candidate for AD treatment.

  7. Systematic pharmacognostical study on Panax drugs and Curcuma drugs : Phylogenetic analysis, molecular authentication and quality evaluation

    OpenAIRE

    Komatsu, Katsuko; Zhu, Shu; Sasaki, Yohei

    2004-01-01

    We proposed pharmacognostical studies in the prime of molecular biology, citing the systematic studies of Panax drugs and Curcuma drugs. Each study was composed of three approaches, phylogenetic analysis of plants based on nuclear 18S rRNA and chloroplast trnK gene sequences, molecular authentication of herbal drugs, and quality evaluation on bioactive chemical constituents or pharmacological effect. Parsimony analysis of the combined trnK-18S rRNA gene sequence data yielded a well-resolved p...

  8. Molecular structure and DFT investigations on new cobalt(II) chloride complex with superbase guanidine type ligand

    Indian Academy of Sciences (India)

    Saied M Soliman; Morsy A M Abu-Youssef; Jörg Albering; Ayman El-Faham

    2015-12-01

    The new [Co(btmgn)Cl2] complex and the 1,8-bis(tetramethylguanidino)naphthalene (btmgn) ligand were synthesized and characterized. The X-ray single crystal investigation showed distorted tetrahedral geometry around the Co(II) ion. The geometry of the btmgn and [Co(btmgn)Cl2] complex was optimized using the B3LYP/6–311G(d,p) method. The calculated geometric parameters at the optimized structure of the [Co(btmgn)Cl2] complex showed good agreement with our reported X-ray structure. The two tetramethylguanidino groups are in a cis-type position to the naphthalene ring plane both in the free and coordinated btmgn. The large red shift of the C=N mode upon coordination indicates the strong ligand–metal interactions. The calculated natural charges using natural bond orbital (NBO) analysis at the two coordinated Cl-atoms are not equivalent. Also the two LP(4)Cl → LP*(3)Co intramolecular charge transfer interaction energies (E(2)) are 29.00 and 39.17 kcal/mol, respectively. The two Co-Cl bonds are not equivalent where the longer Co-Cl bond has more electronegative chlorine atom than the shorter one. Molecular electrostatic potential (MEP) study of the btmgn ligand showed that the N4 and N7 atoms are the most reactive nucleophilic centers for the coordination with the Co2+ ion. The [Co(btmgn)Cl2] complex has higher polarizability (0), first hyperpolarizability (0) and lower energy gap (E) than the free ligand. The TD-DFT calculations predicted the transition bands at 337.2 nm (f=0.2299, H→L) and 342.6 nm (f=0.1465, H-2/H→L) for the btmgn and [Co(btmgn)Cl2], respectively.

  9. [Investigation of molecular-genetic heterogeneity of clematis plants (Clematis L.) obtained by organogenesis and somatic embryogenesis in vitro].

    Science.gov (United States)

    Mitrofanova, I V; Galaev, A V; Sivolap, Iu M

    2003-01-01

    Genome variability of in vitro micropropagated Clematis plants was established. The optimum concentrations of BAP and zeatin in the culture medium regulating in vitro morphogenetic processes in clematis explants cv. Serenada Kryma were determined. Molecular-genetic analysis of Clematis plants obtained via in vitro somatic embryogenesis and organogenesis was carried out. Using ISSR primers 105 amplicons have been revealed, six of them were polymorphic. The mean index of heterogeneity of clematis plants was 5.7%. PMID:15067940

  10. Investigation of the interaction between isomeric derivatives and human serum albumin by fluorescence spectroscopy and molecular modeling

    International Nuclear Information System (INIS)

    In this paper, we have synthesized 9H-pyrrolo[1,2-a]indol-9-ones and the isomeric indeno[2,1-b]pyrrol-8-ones. The interactions of human serum albumin with series of isomeric derivatives have been studied by spectrophotometric methods. Results show the intrinsic fluorescence is quenched by the derivatives with a static quenching procedure. The thermodynamics parameters indicate that van der Waals forces and hydrogen bonds play a major role in the interactions. The results of synchronous fluorescence spectra demonstrate that the microenvironments of Trp residue of human serum albumin are disturbed by most derivatives. Thermodynamic results showed that the 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers and bind to human serum albumin with the higher affinity than isomeric indeno[2,1-b]pyrrol-8-ones. The influence of molecular structure on the binding aspects has been investigated. - Highlights: • The interactions between isomeric derivatives and HSA have been investigated. • Results reveal that 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers for HSA. • Hydrogen bonds and van der Waals forces play major role in the binding process. • The influence of molecular structure on the binding aspects has been investigated. • The binding study was also modeled by molecular docking

  11. A Modiifed Molecular Structure Mechanics Method for Analysis of Graphene

    Institute of Scientific and Technical Information of China (English)

    HUA Jun; LI Dongbo; ZHAO Dong; LIANG Shengwei; LIU Qinlong; JIA Ruiyan

    2015-01-01

    Based on molecular mechanics and the deformation characteristics of the atomic lattice structure of graphene, a modiifed molecular structure mechanics method was developed to improve the original one, that is, the semi-rigid connections were used to model the bond angle variations between the C-C bonds in graphene. The simulated results show that the equivalent space frame model with semi-rigid connections for graphene proposed in this article is a simple, efifcient, and accurate model to evaluate the equivalent elastic properties of graphene. Though the present computational model of the semi-rigid connected space frame is only applied to characterize the mechanical behaviors of the space lattices of graphene, it has more potential applications in the static and dynamic analyses of graphene and other nanomaterials.

  12. Time Resolved Analysis of Molecular Interactions Using Nanomechanical Cantilever Sensors

    Energy Technology Data Exchange (ETDEWEB)

    Koeser, J [University of Applied Sciences Northwestern Switzerland, Basel/Muttenz (Switzerland); Shahgaldian, P [University of Applied Sciences Northwestern Switzerland, Basel/Muttenz (Switzerland); Bammerlin, M [Concentris GmbH, Basel (Switzerland); Battiston, F M [Concentris GmbH, Basel (Switzerland); Pieles, U [University of Applied Sciences Northwestern Switzerland, Basel/Muttenz (Switzerland)

    2007-03-15

    Cantilever sensors have created a widespread interest in recent years due to their unique nanomechanical signal generation mechanism. Their applications range from sensing of small molecules, chemicals and biomolecules to on-line monitoring of surface-associated phenomena, such as molecular reorganization and formation of self assembled monolayers (SAMs). Cantilever sensors allow real-time monitoring, which is the basis for the kinetic description of interactions at the sensor surface. In this paper, we present examples of cantilever sensor measurements in continuous liquid flow using a commercially available instrument (Cantisens (registered) Research, Concentris GmbH, Switzerland) and demonstrate successful approaches for a) the description of molecular interaction kinetics, b) the improvement of calibration curves of cantilever biosensors and c) the study of SAM formation, protein immobilization and surface-related conformational changes.

  13. Molecular Hydrogen Optical Depth Templates for FUSE Data Analysis

    CERN Document Server

    McCandliss, S R

    2003-01-01

    The calculation and use of molecular hydrogen optical depth templates to quickly identify and model molecular hydrogen absorption features longward of the Lyman edge at 912 Angstroms are described. Such features are commonly encountered in spectra obtained by the Far Ultraviolet Spectroscopic Explorer and also in spectra obtained by the Space Telescope Imaging Spectrograph, albeit less commonly. Individual templates are calculated containing all the Lyman and Werner transitions originating from a single rotational state (J'') of the 0th vibrational level (v'') of the ground electronic state. Templates are provided with 0.01 Angstrom sampling for doppler parameters ranging from 2 <= b <= 20 km s^-1 and rotational states 0 <= J'' <= 15. Optical depth templates for excited vibrational states are also available for select doppler parameters. Each template is calculated for a fiducial column density of log[N(cm^-2)] = 21 and may be scaled to any column less than this value without loss of accuracy. The...

  14. Molecular weight analysis by size exclusion chromatography with multiple detection

    Czech Academy of Sciences Publication Activity Database

    Netopilík, Miloš

    Bangalore : Central Power Research Institute, 2007, s. 1-6. [International Conference on Polymeric Materials in Power Engineering. Bangalore (IN), 04.10.2007-06.10.2007] R&D Projects: GA AV ČR IAA400500703; GA ČR GA203/07/0659 Institutional research plan: CEZ:AV0Z40500505 Keywords : size exclusion chromatography * viscometric detection * number- average molecular weight Subject RIV: CF - Physical ; Theoretical Chemistry

  15. Molecular analysis of carnitine palmitoyltransferase II deficiency with hepatocardiomuscular expression.

    OpenAIRE

    Bonnefont, J P; Taroni, F; P. Cavadini; Cepanec, C.; Brivet, M.; Saudubray, J M; Leroux, J P; Demaugre, F.

    1996-01-01

    Carnitine palmitoyltransferase (CPT) II deficiency, an inherited disorder of mitochondrial long-chain fatty-acid (LCFA) oxidation, results in two distinct clinical phenotypes, namely, an adult (muscular) form and an infantile (hepatocardiomuscular) form. The rationale of this phenotypic heterogeneity is poorly understood. The adult form of the disease is commonly ascribed to the Ser-113-Leu substitution in CPT II. Only few data are available regarding the molecular basis of the infantile form...

  16. A molecular propeller effect for chiral separation and analysis

    OpenAIRE

    Clemens, Jonathon B.; Kibar, Osman; Chachisvilis, Mirianas

    2015-01-01

    Enantiomers share nearly identical physical properties but have different chiral geometries, making their identification and separation difficult. Here we show that when exposed to a rotating electric field, the left- and right-handed chiral molecules rotate with the field and act as microscopic propellers; moreover, owing to their opposite handedness, they propel along the axis of field rotation in opposite directions. We introduce a new molecular parameter called hydrodynamic chirality to c...

  17. Neutron activation analysis: a powerful tool in provenance investigations

    International Nuclear Information System (INIS)

    It is well known that neutron activation analysis (NAA), both instrumental and destructive, allows the simultaneous determination of a number of elements, mostly trace elements, with high levels of precision and accuracy. These peculiar properties of NAA are very useful when applied to provenance studies, i.e. to the identification of the origin of raw materials with which artifacts had been manufactured in ancient times. Data reduction by statistical procedures, especially multivariate analysis techniques, provides a statistical 'fingerprint' of investigated materials, both raw materials and archaeological artifacts, that, upon comparison, allows the identification of the provenance of prime matters used for artifact manufacturing. Thus information on quarries and flows exploitation in the antiquity, on technological raw materials processing, on trade routes and about the circulation of fakes, can be obtained. In the present paper two case studies are reported. The first one deals with the identification of the provenance of clay used to make ceramic materials, mostly bricks and tiles, recovered from the excavation of a Roman 'villa' in Lomello (Roman name Laumellum) and of Roman settlings in Casteggio (Roman name Clastidium). Both sites are located in the Province of Pavia in areas called Lomellina and Oltrepo respectively. The second one investigates the origin of the white marble used to build medieval arks, Carolingian age, located in the church of San Felice, now property of the University of Pavia. Experimental set-up, analytical results and data reduction procedures are presented and discussed. (author)

  18. Simulated, Emulated, and Physical Investigative Analysis (SEPIA) of networked systems.

    Energy Technology Data Exchange (ETDEWEB)

    Burton, David P.; Van Leeuwen, Brian P.; McDonald, Michael James; Onunkwo, Uzoma A.; Tarman, Thomas David; Urias, Vincent E.

    2009-09-01

    This report describes recent progress made in developing and utilizing hybrid Simulated, Emulated, and Physical Investigative Analysis (SEPIA) environments. Many organizations require advanced tools to analyze their information system's security, reliability, and resilience against cyber attack. Today's security analysis utilize real systems such as computers, network routers and other network equipment, computer emulations (e.g., virtual machines) and simulation models separately to analyze interplay between threats and safeguards. In contrast, this work developed new methods to combine these three approaches to provide integrated hybrid SEPIA environments. Our SEPIA environments enable an analyst to rapidly configure hybrid environments to pass network traffic and perform, from the outside, like real networks. This provides higher fidelity representations of key network nodes while still leveraging the scalability and cost advantages of simulation tools. The result is to rapidly produce large yet relatively low-cost multi-fidelity SEPIA networks of computers and routers that let analysts quickly investigate threats and test protection approaches.

  19. Investigating product development strategy in beverage industry using factor analysis

    Directory of Open Access Journals (Sweden)

    Naser Azad

    2013-03-01

    Full Text Available Selecting a product development strategy that is associated with the company's current service or product innovation, based on customers’ needs and changing environment, plays an important role in increasing demand, increasing market share, increasing sales and profits. Therefore, it is important to extract effective variables associated with product development to improve performance measurement of firms. This paper investigates important factors influencing product development strategies using factor analysis. The proposed model of this paper investigates 36 factors and, using factor analysis, we extract six most influential factors including information sharing, intelligence information, exposure strategy, differentiation, research and development strategy and market survey. The first strategy, partnership, includes five sub-factor including product development partnership, partnership with foreign firms, customers’ perception from competitors’ products, Customer involvement in product development, inter-agency coordination, customer-oriented approach to innovation and transmission of product development change where inter-agency coordination has been considered the most important factor. Internal strengths are the most influential factors impacting the second strategy, intelligence information. The third factor, introducing strategy, introducing strategy, includes four sub criteria and consumer buying behavior is the most influencing factor. Differentiation is the next important factor with five components where knowledge and expertise in product innovation is the most important one. Research and development strategy with four sub-criteria where reducing product development cycle plays the most influential factor and finally, market survey strategy is the last important factor with three factors and finding new market plays the most important role.

  20. Structural modeling and molecular simulation analysis of HvAP2/EREBP from barley.

    Science.gov (United States)

    Pandey, Bharati; Sharma, Pradeep; Tyagi, Chetna; Goyal, Sukriti; Grover, Abhinav; Sharma, Indu

    2016-06-01

    AP2/ERF transcription factors play a critical role in plant development and stress adaptation. This study reports the three-dimensional ab initio-based model of AP2/EREBP protein of barley and its interaction with DNA. Full-length coding sequence of HvAP2/EREBP gene isolated from two Indian barley cultivars, RD 2503 and RD 31, was used to model the protein. Of five protein models obtained, the one with lowest C-score was chosen for further analysis. The N- and C-terminal regions of HvAP2 protein were found to be highly disordered. The dynamic properties of AP2/EREBP and its interaction with DNA were investigated by molecular dynamics simulation. Analysis of trajectories from simulation yielded the equilibrated conformation between 2-10ns for protein and 7-15ns for protein-DNA complex. We established relationship between DNA having GCC box and DNA-binding domain of HvAP2/EREBP was established by modeling 11-base-pair-long nucleotide sequence and HvAP2/EREBP protein using ab initio method. Analysis of protein-DNA interaction showed that a β-sheet motif constituting amino acid residues THR105, ARG100, ARG93, and ARG83 seems to play important role in stabilizing the complex as they form strong hydrogen bond interactions with the DNA motif. Taken together, this study provides first-hand comprehensive information detailing structural conformation and interactions of HvAP2/EREBP proteins in barley. The study intensifies the role of computational approaches for preliminary examination of unknown proteins in the absence of experimental information. It also provides molecular insight into protein-DNA binding for understanding and enhancing abiotic stress resistance for improving the water use efficiency in crop plants. PMID:26198402

  1. Ancestry analysis in the 11-M Madrid bomb attack investigation.

    Directory of Open Access Journals (Sweden)

    Christopher Phillips

    Full Text Available The 11-M Madrid commuter train bombings of 2004 constituted the second biggest terrorist attack to occur in Europe after Lockerbie, while the subsequent investigation became the most complex and wide-ranging forensic case in Spain. Standard short tandem repeat (STR profiling of 600 exhibits left certain key incriminatory samples unmatched to any of the apprehended suspects. A judicial order to perform analyses of unmatched samples to differentiate European and North African ancestry became a critical part of the investigation and was instigated to help refine the search for further suspects. Although mitochondrial DNA (mtDNA and Y-chromosome markers routinely demonstrate informative geographic differentiation, the populations compared in this analysis were known to show a proportion of shared mtDNA and Y haplotypes as a result of recent gene-flow across the western Mediterranean, while any two loci can be unrepresentative of the ancestry of an individual as a whole. We based our principal analysis on a validated 34plex autosomal ancestry-informative-marker single nucleotide polymorphism (AIM-SNP assay to make an assignment of ancestry for DNA from seven unmatched case samples including a handprint from a bag containing undetonated explosives together with personal items recovered from various locations in Madrid associated with the suspects. To assess marker informativeness before genotyping, we predicted the probable classification success for the 34plex assay with standard error estimators for a naïve Bayesian classifier using Moroccan and Spanish training sets (each n = 48. Once misclassification error was found to be sufficiently low, genotyping yielded seven near-complete profiles (33 of 34 AIM-SNPs that in four cases gave probabilities providing a clear assignment of ancestry. One of the suspects predicted to be North African by AIM-SNP analysis of DNA from a toothbrush was identified late in the investigation as Algerian in origin. The

  2. A conformational analysis of mouse Nalp3 domain structures by molecular dynamics simulations, and binding site analysis.

    Science.gov (United States)

    Sahoo, Bikash R; Maharana, Jitendra; Bhoi, Gopal K; Lenka, Santosh K; Patra, Mahesh C; Dikhit, Manas R; Dubey, Praveen K; Pradhan, Sukanta K; Behera, Bijay K

    2014-05-01

    Scrutinizing various nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) genes in higher eukaryotes is very important for understanding the intriguing mechanism of the host defense against pathogens. The nucleotide-binding domain (NACHT), leucine-rich repeat (LRR), and pyrin domains (PYD)-containing protein 3 (Nalp3), is an intracellular innate immune receptor and is associated with several immune system related disorders. Despite Nalp3's protective role during a pathogenic invasion, the molecular features and structural organization of this crucial protein is poorly understood. Using comparative modeling and molecular dynamics simulations, we have studied the structural architecture of Nalp3 domains, and characterized the dynamic and energetic parameters of adenosine triphosphate (ATP) binding in NACHT, and pathogen-derived ligands muramyl dipeptide (MDP) and imidazoquinoline with LRR domains. The results suggested that walker A, B and extended walker B motifs were the key ATP binding regions in NACHT that mediate self-oligomerization. The analysis of the binding sites of MDP and imidazoquinoline revealed LRR 7-9 to be the most energetically favored site for imidazoquinoline interaction. However, the binding free energy calculations using the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method indicated that MDP is incompatible for activating the Nalp3 molecule in its monomeric form, and suggest its complex interaction with NOD2 or other NLRs accounts for MDP recognition. The high binding affinity of ATP with NACHT was correlated to the experimental data for human NLRs. Our binding site prediction for imidazoquinoline in LRR warrants further investigation via in vivo models. This is the first study that provides ligand recognition in mouse Nalp3 and its spatial structural arrangements. PMID:24595807

  3. Probing the Interaction of a Therapeutic Flavonoid, Pinostrobin with Human Serum Albumin: Multiple Spectroscopic and Molecular Modeling Investigations

    OpenAIRE

    Feroz, Shevin R.; Saharuddin B. Mohamad; Bakri, Zarith S. D.; Sri N A Malek; Tayyab, Saad

    2013-01-01

    Interaction of a pharmacologically important flavonoid, pinostrobin (PS) with the major transport protein of human blood circulation, human serum albumin (HSA) has been examined using a multitude of spectroscopic techniques and molecular docking studies. Analysis of the fluorescence quenching data showed a moderate binding affinity (1.03 × 105 M−1 at 25°C) between PS and HSA with a 1∶1 stoichiometry. Thermodynamic analysis of the binding data (ΔS = +44.06 J mol−1 K−1 and ΔH = −15.48 kJ mol−1)...

  4. Crystallographic and Molecular Dynamics Simulation Analysis of Escherichia Coli Dihydroneopterin Aldolase

    Energy Technology Data Exchange (ETDEWEB)

    Blaszczyk, Jaroslaw [National Cancer Inst., Frederick, MD (United States); Michigan State Univ., East Lansing, MI (United States); Lu, Zhenwei [Michigan State Univ., East Lansing, MI (United States); Li, Yue [Michigan State Univ., East Lansing, MI (United States); Yan, Honggao [Michigan State Univ., East Lansing, MI (United States); Ji, Xinhua [National Cancer Inst., Frederick, MD (United States)

    2014-09-01

    To understand the structural basis for the biochemical differences and further investigate the catalytic mechanism of DHNA, we have determined the structure of EcDHNA complexed with NP at 1.07-Å resolution [PDB:2O90], built an atomic model of EcDHNA complexed with the substrate DHNP, and performed molecular dynamics (MD) simulation analysis of the substrate complex. EcDHNA has the same fold as SaDHNA and also forms an octamer that consists of two tetramers, but the packing of one tetramer with the other is significantly different between the two enzymes. Furthermore, the structures reveal significant differences in the vicinity of the active site, particularly in the loop that connects strands β3 and β4, mainly due to the substitution of nearby residues. The building of an atomic model of the complex of EcDHNA and the substrate DHNP and the MD simulation of the complex show that some of the hydrogen bonds between the substrate and the enzyme are persistent, whereas others are transient. The substrate binding model and MD simulation provide the molecular basis for the biochemical behaviors of the enzyme, including noncooperative substrate binding, indiscrimination of a pair of epimers as the substrates, proton wire switching during catalysis, and formation of epimerization product.

  5. Experimental investigation of thermal neutron analysis based landmine detection technology

    International Nuclear Information System (INIS)

    Background: Recently, the prompt gamma-rays neutron activation analysis method is wildly used in coal analysis and explosive detection, however there were less application about landmine detection using neutron method especially in the domestic research. Purpose: In order to verify the feasibility of Thermal Neutron Analysis (TNA) method used in landmine detection, and explore the characteristic of this technology. Methods: An experimental system of TNA landmine detection was built based on LaBr3 (Ce) fast scintillator detector and 252Cf isotope neutron source. The system is comprised of the thermal neutron transition system, the shield system, and the detector system. Results: On the basis of the TNA, the wide energy area calibration method especially to the high energy area was investigated, and the least detection time for a typical mine was defined. In this study, the 72-type anti-tank mine, the 500 g TNT sample and several interferential objects are tested in loess, red soil, magnetic soil and sand respectively. Conclusions: The experimental results indicate that TNA is a reliable demining method, and it can be used to confirm the existence of Anti-Tank Mines (ATM) and large Anti-Personnel Mines (APM) in complicated condition. (authors)

  6. Investigation of Eigenvalue Behavior in the Asymptotic Analysis of PCMI

    International Nuclear Information System (INIS)

    As a result, two eigenvalues, associated with the stress singularity at the contact edge, were produced. A finite element analysis technique to calculate the generalized stress intensity factors was also presented in these papers, which would be used as the calibration factors to evaluate the actual stresses when the pellet fragments expand the cladding in the PCMI. This analysis is further extended in this paper to accommodate a more realistic condition of the PCMI such as a frictional contact between two adjacent pellet fragments and a cladding tube. However, this yields a sophisticated behavior of the eigenvalues depending on the coefficient of friction (incorporating the direction of slipping of each fragment) as well as the angle of the pellet crack. Since the stress field of the cladding is directly determined from the eigenvalues, it is crucial to evalutae and investigate them to analyze the PCMI problem mechanistically, which is pursed in this paper. In the sequel to the previous work of an asymptotic analysis of a bonded contact between a wedge and a half plane (two bodies in contact), a frictional contact problem of three bodies mutually contacted is considered here to simulate a further actual contact configuration of a cracked pellet and a cladding tube in PCMI. The results are summarized as follows

  7. Molecular Dynamics Investigation of Bond Ordering of Unsaturated Lipids in Monolayers

    OpenAIRE

    Rabinovich, Alexander L.; Ripatti, Pauli O.; Balabaev, Nikolay K.

    1999-01-01

    Molecular dynamics simulations of three model lipid monolayers of 2,3-diacyl-D-glycerolipids, that contained stearoyl (18:0) in the position 3 and oleoyl (18:ω9cis), linoleoyl (18:2ω6cis), or linolenoyl (18:3ω3cis) in the position 2, have been carried out. The simulation systems consisted of 24 lipid molecules arranged in a rectangular simulation cell, with periodic boundary conditions in the surface plane. 1 nanosecond simulations were performed at T = 295 K. C-C and C-H bond order parameter...

  8. Radical damage in lipids investigated with the fragment molecular orbital method

    Science.gov (United States)

    Green, Mandy C.; Nakata, Hiroya; Fedorov, Dmitri G.; Slipchenko, Lyudmila V.

    2016-05-01

    To quantify the thermodynamics for hydrogen abstraction lipids, the fragment molecular orbital method (FMO) is used to calculate structures and energies of the reactants and products. The analytic second derivative is developed for the open-shell Hartree-Fock formulation of FMO and used to calculate zero point energy corrections. The accuracy of FMO is evaluated for a lipid model and the errors in reaction energies are found not to exceed 0.5 kcal/mol. The reaction energies determined for multiple sites in two lipids are used to discuss likely sites and pathways of radical initiation in membranes.

  9. Molecular dynamics investigation of the structure of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer.

    OpenAIRE

    Tu, K; Tobias, D J; Blasie, J K; Klein, M.L.

    1996-01-01

    We report the results of a constant pressure and temperature molecular dynamics simulation of a gel-phase dipalmitoylphosphatidylcholine bilayer with nw = 11.8 water molecules/lipid at 19 degrees C. The results of the simulation were compared in detail with a variety of x-ray and neutron diffraction data. The average positions of specific carbon atoms along the bilayer normal and the interlamellar spacing and electron density profile were in very good agreement with neutron and x-ray diffract...

  10. Methodologies and Application of New Target Identification, Drug Action Mechanism Investigation and New Molecular Entity Discovery

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    @@ The group, headed by Prof.JIANG Hualiang with the CAS Shanghai Institute of Materia Medica, has been centering on the basic research of pharmaceutical science, including identifying new targets, studying new drug action mechanisms and discovering new drug candidates.On the basis of new methodology development, an effective multi-disciplinary research platform for drug research and discovery has been established through the integration of different disciplines of computational chemistry, organic synthesis, molecular and cellular biology.A bunch of creative results have been achieved in these areas.

  11. Investigating molecular interactions and surface morphology of wax-doped asphaltenes.

    Science.gov (United States)

    Pahlavan, Farideh; Mousavi, Masoumeh; Hung, Albert; Fini, Ellie H

    2016-04-01

    The nature and origin of bee-like microstructures (bees) in asphalt binders and their impact on asphalt oxidation have been the subject of extensive discussions in recent years. While several studies refer to the bees as solely surface features, some others consider them to be bulk microcrystalline components that are formed due to co-precipitation of wax and asphaltene molecules. In this study, we use a rigorous theoretical and experimental approach to investigate the interplay of asphalt components (mainly asphaltene and wax) and their impact on bee formation. In the theoretical section, quantum-mechanical calculations using density functional theory (DFT) are used to evaluate the strength of interactions between asphaltene unit sheets in the presence and absence of a wax component, as well as the mutual interactions between asphaltene molecules (monomers and dimers) and paraffin wax. The results of this section reveal that paraffin waxes not only do not reinforce the interaction between the asphaltene unit sheets, they destabilize asphaltene assembly and dimerization. AIM (Atom in Molecules) analysis shows the destabilizing effect of wax on asphaltene assembly as a reduction in the number of cage and bond critical points between asphaltenes. This destabilization effect among interacting systems (asphaltene-asphaltene and wax-asphaltene) does not support the hypothesis that interaction between paraffin waxes and non-wax components, such as asphaltene, is responsible for their co-precipitation and bee formation. To further examine the effect of wax component on asphalt microstructure experimentally, we used atomic force microscopy (AFM) to study the surface morphology of an asphalt sample doped with 1% to 25% paraffin wax. In agreement with the conclusions drawn from the DFT approach, our experiments indicate that paraffin wax tends to crystallize separately and form lamellar paraffin wax crystal inclusions with 10 nm thickness. Moreover, the addition of 3% wax

  12. Molecular Laser Spectroscopy as a Tool for Gas Analysis Applications

    Directory of Open Access Journals (Sweden)

    Javis Anyangwe Nwaboh

    2011-01-01

    Full Text Available We have used the traceable infrared laser spectrometric amount fraction measurement (TILSAM method to perform absolute concentration measurements of molecular species using three laser spectroscopic techniques. We report results performed by tunable diode laser absorption spectroscopy (TDLAS, quantum cascade laser absorption spectroscopy (QCLAS, and cavity ring down spectroscopy (CRDS, all based on the TILSAM methodology. The measured results of the different spectroscopic techniques are in agreement with respective gravimetric values, showing that the TILSAM method is feasible with all different techniques. We emphasize the data quality objectives given by traceability issues and uncertainty analyses.

  13. Molecular Laser Spectroscopy as a Tool for Gas Analysis Applications

    International Nuclear Information System (INIS)

    We have used the traceable infrared laser spectrometric amount fraction measurement (TILSAM) method to perform absolute concentration measurements of molecular species using three laser spectroscopic techniques. We report results performed by tunable diode laser absorption spectroscopy (TDLAS), quantum cascade laser absorption spectroscopy (QCLAS), and cavity ring down spectroscopy (CRDS), all based on the TILSAM methodology. The measured results of the different spectroscopic techniques are in agreement with respective gravimetric values, showing that the TILSAM method is feasible with all different techniques. We emphasize the data quality objectives given by traceability issues and uncertainty analyses.

  14. Analysis of the Offspring Sex Ratio of Chicken by Using Molecular Sexing

    Institute of Scientific and Technical Information of China (English)

    FENG Yan-ping; GONG Yan-zhang; Nabeel Ahmed Affara; PENG Xiu-li; YUAN Jin-feng; ZHAO Rui-xia; Mohammed Yusuf; Osman Jeffer; ZHANG Shu-jun

    2006-01-01

    The overall sex ratio of offspring (dead embryos and hatch chicks) from all the fertilized eggs of 140 hens collected for30 days was studied using duplex PCR of certain fragments of sex chromosomes. Additional 894 dead embryos over a period of 21 days of incubation were also investigated to verify the sex ratio of the dead embryos. The sex of the early dead embryos was identified using this molecular sexing technique. The sex ratio of the hatch chicks and the total offspring of the hens investigated in this experiment did not differ from the expected sex ratio (i.e., 1:1). However, the number of female dead embryos was significantly more than that of males. The data indicated that the different physiologic function of males and females contributed to female-biased mortality during incubation. It was also found by further analysis that the sex ratios of the offspring of some hens were significantly biased to female or male over the period investigated, which suggested that the sex ratio of offspring might be influenced by the maternal condition to some degrees.

  15. First principles investigations of vinazene molecule and molecular crystal: a prospective candidate for organic photovoltaic applications.

    Science.gov (United States)

    Mohamad, Mazmira; Ahmed, Rashid; Shaari, Amirudin; Goumri-Said, Souraya

    2015-02-01

    Escalating demand for sustainable energy resources, because of the rapid exhaustion of conventional energy resources as well as to maintain the environmental level of carbon dioxide (CO2) to avoid its adverse effect on the climate, has led to the exploitation of photovoltaic technology manifold more than ever. In this regard organic materials have attracted great attention on account of demonstrating their potential to harvest solar energy at an affordable rate for photovoltaic technology. 2-vinyl-4,5-dicyanoimidazole (vinazene) is considered as a suitable material over the fullerenes for photovoltaic applications because of its particular chemical and physical nature. In the present study, DFT approaches are employed to provide an exposition of optoelectronic properties of vinazene molecule and molecular crystal. To gain insight into its properties, different forms of exchange correlation energy functional/potential such as LDA, GGA, BLYP, and BL3YP are used. Calculated electronic structure of vinazene molecule has been displayed via HOMO-LUMO isosurfaces, whereas electronic structure of the vinazene molecular crystal, via electronic band structure, is presented. The calculated electronic and optical properties were analyzed and compared as well. Our results endorse vinazene as a suitable material for organic photovoltaic applications. PMID:25631921

  16. Solution Structure of Molecular Associations Investigated Using NMR for Polysaccharides: Xanthan/Galactomannan Mixtures.

    Science.gov (United States)

    Takemasa, Makoto; Nishinari, Katsuyoshi

    2016-03-31

    Although the intermolecular nuclear Overhauser effect (NOE) signal was valuable to elucidate molecular association structure, it could not always be observed for associated molecules due to the short spin-spin relaxation time T2 in NMR measurements, especially for high molar mass systems. While almost no study has been reported for high molar mass polymers (>1 × 10(6)), especially for polysaccharide-polysaccharide interactions, NOE signals were observed for the first time between two different types of polysaccharides, xanthan and galactomannan (locust bean gum), forming a synergistic gel, as a direct evidence of intermolecular binding of polysaccharides. The NOE peak was found between pyruvic acid in xanthan and anomeric proton of mannose of galactomannan. This NOE signal was observed only when mixing time >0.5 s, indicating indirect NOEs caused by spin diffusion. Therefore, this NOE could not be used to construct the molecular models. However, it is a direct evidence for the binding between two different types of polysaccharide to elucidate the synergistic gelation. This NOE signal was observed only for low molar mass galactomannans (1.4 × 10(4)). T2 of pyruvate methyl drastically decreased at low temperatures in the presence of synergistic interaction, suggesting that pyruvate group at terminal end of side chain in xanthan plays an essential role in synergistic interaction. PMID:26943259

  17. Low molecular weight heparin for the treatment of retinal vein occlusion: a systematic review and meta-analysis of randomized trials

    OpenAIRE

    Lazo-Langner, Alejandro; Hawel, Jeff; Ageno, Walter; Kovacs, Michael J

    2010-01-01

    Retinal vein occlusion is a frequent cause of visual loss for which few effective therapies are available. Anticoagulation with low molecular weight heparin might be of value in its treatment. We conducted a systematic review and meta analysis of randomized trials evaluating the effect of low molecular weight heparin in patients with retinal vein occlusion. Data sources included MEDLINE, EMBASE, HealthSTAR, the Cochrane Library, Lilacs, the Investigative Ophthalmology and Visual Science datab...

  18. O6-methylguanine-DNA methyltransferase in equine sarcoids: molecular and epigenetic analysis

    Directory of Open Access Journals (Sweden)

    Altamura Gennaro

    2012-11-01

    Full Text Available Abstract Background Bovine papillomaviruses (BPVs types 1 and 2 are the only known papillomaviruses able to jump the species. In fact, BPVs 1/2 induce neoplasia in their natural bovine host but infection is also associated to neoplastic skin lesions in equids termed sarcoids. The equine sarcoid is considered to be the most common equine cutaneous tumour worldwide for which no effective therapy is available. Very little is known about the molecular mechanisms underlying tumourigenesis, although genes contributing to sarcoid development have been identified. Several studies associate the development of cancer to the loss of function of a number of oncosuppressor genes. In this study the putative role of O6-methylguanine-DNA methyltrasferase (MGMT was investigated for sarcoids. The expression of the oncosuppressor protein was assessed in normal and sarcoid cells and tissues. In addition, the DNA methylation profile was analysed to assess the role of epigenetic mechanism in regulation of MGMT expression. Results A group of 15 equine sarcoids and two primary sarcoid cell lines (fibroblasts were analyzed for the expression of MGMT protein by immunohistochemistry, immunofluorescence and Western blotting techniques. The sarcoid cell line EqSO4b and the tumour samples showed a reduction or absence of MGMT expression. To investigate the causes of deregulated MGMT expression, ten samples were analyzed for the DNA methylation profile of the CpG island associated to the MGMT promoter. The analysis of 73 CpGs encompassing the region of interest showed in 1 out of 10 (10% sarcoids a pronouncedly altered methylation profile when compared to the control epidermal sample. Similarily the EqSO4b cell line showed an altered MGMT methylation pattern in comparison to normal fibroblasts. Conclusion As previously demonstrated for the oncosuppressor gene FHIT, analysis of MGMT expression in sarcoid tissues and a sarcoid-derived fibroblast cell line further suggests that

  19. Molecular Investigation of Francisella-Like Endosymbiont in Ticks and Francisella tularensis in Ixodid Ticks and Mosquitoes in Turkey.

    Science.gov (United States)

    Duzlu, Onder; Yildirim, Alparslan; Inci, Abdullah; Gumussoy, Kadir Semih; Ciloglu, Arif; Onder, Zuhal

    2016-01-01

    This study was carried out to investigate the molecular prevalence of Francisella-like endosymbionts (FLEs) and Francisella tularensis in ticks (Acari: Ixodidae) and mosquitoes in Turkey. Genomic DNA pools were constructed from a total of 1477 adult hard ticks of Rhipicephalus (Rh.) annulatus, Rh. turanicus, Rh. sanguineus, Rh. bursa, Haemaphysalis (Hae.) parva, Hae. sulcata, Hyalomma marginatum marginatum, H. anatolicum anatolicum, H. anatolicum excavatum, H. detritum detritum, H. dromedarii, Dermacentor marginatus, and Ixodes ricinus species, which were collected from several barns, cattle, and people. Genomic DNA was also extracted from pools consisting of 6203 adult female mosquito species belonging to Aedes vexans, Culex (Cx.) pipiens, Cx. hortensis, Cx. theileri, Culiseta annulata, and Anopheles maculipennis species. Conventional PCR and TaqMan probe-based real- time PCR targeting the 16S rRNA gene for FLEs and the lpnA gene for F. tularensis, respectively, were performed on the DNA isolates obtained. FLEs and F. tularensis were not found in any genomic DNA pools constructed from ixodid ticks and mosquitos. This study represents the first investigation of F. tularensis and FLEs in potential vector ticks and mosquitoes by molecular methods in Turkey. The present study provides useful insights into the molecular epidemiology of F. tularensis and FLEs. One of the major conclusions of the study is that tularemia outbreaks may be essentially due to direct transmission from the environment (especially from water) in Turkey and not to vector-borne transmission. PMID:26741324

  20. Molecular structure, conformational preferences and vibrational analysis of 2-hydroxystyrene: A computational and spectroscopic research

    International Nuclear Information System (INIS)

    Graphical abstract: The torsion barriers of 2-hydroxy-styrene are analyzed. Intramolecular contacts have been dealt theoretically and using IR/Raman spectroscopy. Some conclusions about the conformational preferences are given. - Abstract: The molecular structure of 2-hydroxy-styrene has been investigated at DFT (B3LYP, mPW1PW91) and MP2 levels with an assortment of Pople's and Dunning's basis sets within the isolated molecule approximation. The presence of intramolecular hydrogen bonds has been theoretically characterized through a topological analysis of the electron density according to the Atom-In-Molecules, AIM, theory. The conformational equilibrium has been pursued by means of an analysis of the hydroxyl-phenyl and vinyl-phenyl internal rotation barriers. This analysis also allowed getting an insight into the effects governing the torsion barriers and the preferred conformations. A twofold scheme has been used for this goal, i.e. the total electronic energy changes and the natural bonding orbital, NBO, schemes. The vibrational spectrum was recorded and then calculated at DFT-B3LYP/6-31G* and cc-pVTZ levels. Two scaling methods, SQMFF and linear scaling, have been applied on the theoretical spectrum in order to analyse the experimental one. The results point out that at least three different conformers coexist at room temperature.

  1. Probing the interaction of a therapeutic flavonoid, pinostrobin with human serum albumin: multiple spectroscopic and molecular modeling investigations.

    Directory of Open Access Journals (Sweden)

    Shevin R Feroz

    Full Text Available Interaction of a pharmacologically important flavonoid, pinostrobin (PS with the major transport protein of human blood circulation, human serum albumin (HSA has been examined using a multitude of spectroscopic techniques and molecular docking studies. Analysis of the fluorescence quenching data showed a moderate binding affinity (1.03 × 10(5 M(-1 at 25°C between PS and HSA with a 1∶1 stoichiometry. Thermodynamic analysis of the binding data (ΔS = +44.06 J mol(-1 K(-1 and ΔH = -15.48 kJ mol(-1 and molecular simulation results suggested the involvement of hydrophobic and van der Waals forces, as well as hydrogen bonding in the complex formation. Both secondary and tertiary structural perturbations in HSA were observed upon PS binding, as revealed by intrinsic, synchronous, and three-dimensional fluorescence results. Far-UV circular dichroism data revealed increased thermal stability of the protein upon complexation with PS. Competitive drug displacement results suggested the binding site of PS on HSA as Sudlow's site I, located at subdomain IIA, and was well supported by the molecular modelling data.

  2. Probing the interaction of a therapeutic flavonoid, pinostrobin with human serum albumin: multiple spectroscopic and molecular modeling investigations.

    Science.gov (United States)

    Feroz, Shevin R; Mohamad, Saharuddin B; Bakri, Zarith S D; Malek, Sri N A; Tayyab, Saad

    2013-01-01

    Interaction of a pharmacologically important flavonoid, pinostrobin (PS) with the major transport protein of human blood circulation, human serum albumin (HSA) has been examined using a multitude of spectroscopic techniques and molecular docking studies. Analysis of the fluorescence quenching data showed a moderate binding affinity (1.03 × 10(5) M(-1) at 25°C) between PS and HSA with a 1∶1 stoichiometry. Thermodynamic analysis of the binding data (ΔS = +44.06 J mol(-1) K(-1) and ΔH = -15.48 kJ mol(-1)) and molecular simulation results suggested the involvement of hydrophobic and van der Waals forces, as well as hydrogen bonding in the complex formation. Both secondary and tertiary structural perturbations in HSA were observed upon PS binding, as revealed by intrinsic, synchronous, and three-dimensional fluorescence results. Far-UV circular dichroism data revealed increased thermal stability of the protein upon complexation with PS. Competitive drug displacement results suggested the binding site of PS on HSA as Sudlow's site I, located at subdomain IIA, and was well supported by the molecular modelling data. PMID:24116089

  3. Equilibrium analysis of the efficiency of an autonomous molecular computer

    Science.gov (United States)

    Rose, John A.; Deaton, Russell J.; Hagiya, Masami; Suyama, Akira

    2002-02-01

    In the whiplash polymerase chain reaction (WPCR), autonomous molecular computation is implemented in vitro by the recursive, self-directed polymerase extension of a mixture of DNA hairpins. Although computational efficiency is known to be reduced by a tendency for DNAs to self-inhibit by backhybridization, both the magnitude of this effect and its dependence on the reaction conditions have remained open questions. In this paper, the impact of backhybridization on WPCR efficiency is addressed by modeling the recursive extension of each strand as a Markov chain. The extension efficiency per effective polymerase-DNA encounter is then estimated within the framework of a statistical thermodynamic model. Model predictions are shown to provide close agreement with the premature halting of computation reported in a recent in vitro WPCR implementation, a particularly significant result, given that backhybridization had been discounted as the dominant error process. The scaling behavior further indicates completion times to be sufficiently long to render WPCR-based massive parallelism infeasible. A modified architecture, PNA-mediated WPCR (PWPCR) is then proposed in which the occupancy of backhybridized hairpins is reduced by targeted PNA2/DNA triplex formation. The efficiency of PWPCR is discussed using a modified form of the model developed for WPCR. Predictions indicate the PWPCR efficiency is sufficient to allow the implementation of autonomous molecular computation on a massive scale.

  4. Genetic, molecular, and morphological analysis of compound leaf development.

    Science.gov (United States)

    Goliber, T; Kessler, S; Chen, J J; Bharathan, G; Sinha, N

    1999-01-01

    Leaves, the plant organs responsible for capturing and converting most of the 170 billion metric tons of carbon fixed globally each year, can be broadly grouped into two morphological categories: simple and compound. Although simple-leaved species such as corn and Arabidopsis have traditionally been favored model systems for studying leaf development, recent years have seen an increase in genetic and molecular studies of compound leaf development. Two compound-leaved species in particular have emerged as model systems: tomato and pea. A variety of mutations which alter leaf morphology in these species have been described, and analyses of these mutations have allowed the construction of testable models of leaf development. Also, the knotted-like homeobox (KNOX) genes, which were originally discovered as regulators of meristem function, now appear to have a role in compound leaf development. In addition to the recent genetic and molecular analyses of tomato and pea, insight into the nature of compound leaf development may be gained through the study of (a) heteroblasty and heterophylly, phenomena in which a range of leaf forms can be produced by a single shoot, and (b) the evolutionary origins of compound leaves. PMID:9891889

  5. Investigation on Nodalization for Analysis of SFR Channel Blockage Accidents

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Won Pyo; Kwon, Young Min; Ha, Ki Suk; Lee, Kwi Lim; Jeong, Hae Yong [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2011-05-15

    The present paper demonstrates nodalization analysis results obtained in application of the MATRA-LMR/FB to channel blockage accidents for a SFR (Sodium cooled Fast Reactor), KALIMER-150. In the earlier study, a uniform node size over the total sub-channel length in a subassembly was used. The study was carried out not only for the radially different positions, i.e. central, medium between the center and the duct wall, and edge sub-channels in the assembly, but also for larger blockage sizes larger than 6 sub-channels, the blockage size of which was classified into a DBE(Design Basis Event) in the KALIMER-150 design. The present investigation focuses mainly on the identification of conservatism as well as consistency in the analyses of the maximum coolant temperature for the 6 sub-channels blockage accidents

  6. Investigation, experiment and analysis on PWR sump screen clogging issue

    International Nuclear Information System (INIS)

    JNES has been conducting experimental and analytical study to develop an evaluation method concerning the chemical effect and the downstream effect of the sump screen clogging issue during LOCA in PWR plants. Chemical effect tests show that corrosion of carbon steel and galvanized steal may come to be important in domestic plants, in addition to corrosion of aluminum and insulator which has been considered dominant in the chemical effect. With respect to the downstream effect, deposition of chemical precipitates on the fuel cladding using an electrically heated rod is investigated. A test shows chemical precipitates deposited on the cladding and the deposit was mainly analyzed to be calcium compounds. The analysis on the downstream effect has shown that even if core inlet was completely clogged just after the recirculation operation started during LOCA in PWR plants, although upper part of core may be uncovered temporary and cladding temperature increased, core could be cooled by coolant injection through the hot-leg. (author)

  7. Binding of molecular oxygen by an artificial heme analogue: investigation on the formation of an Fe-tetracarbene superoxo complex.

    Science.gov (United States)

    Anneser, Markus R; Haslinger, Stefan; Pöthig, Alexander; Cokoja, Mirza; D'Elia, Valerio; Högerl, Manuel P; Basset, Jean-Marie; Kühn, Fritz E

    2016-04-12

    The dioxygen reactivity of a cyclic iron(ii) tetra-NHC-complex (NHC: N-heterocyclic carbene) is investigated. Divergent oxidation behavior is observed depending on the choice of the solvent (acetonitrile or acetone). In the first case, exposure to molecular oxygen leads to an oxygen free Fe(iii) whereas in the latter case an oxide bridged Fe(iii) dimer is formed. In acetone, an Fe(iii)-superoxide can be trapped, isolated and characterized as intermediate at low temperatures. An Fe(iii)-O-Fe(iii) dimer is formed from the Fe(iii) superoxide in acetone upon warming and the molecular structure has been revealed by single crystal X-ray diffraction. It is shown that the oxidation of the Fe(ii) complex in both solvents is a reversible process. For the regeneration of the initial Fe(ii) complex both organic and inorganic reducing agents can be used. PMID:26952651

  8. Binding of molecular oxygen by an artificial heme analogue: investigation on the formation of an Fe–tetracarbene superoxo complex

    KAUST Repository

    Anneser, Markus R.

    2016-02-26

    The dioxygen reactivity of a cyclic iron(II) tetra–NHC-complex (NHC: N-heterocyclic carbene) is investigated. Divergent oxidation behavior is observed depending on the choice of the solvent (acetonitrile or acetone). In the first case, exposure to molecular oxygen leads to an oxygen free Fe(III) whereas in the latter case an oxide bridged Fe(III) dimer is formed. In acetone, an Fe(III)-superoxide can be trapped, isolated and characterized as intermediate at low temperatures. An Fe(III)–O–Fe(III) dimer is formed from the Fe(III) superoxide in acetone upon warming and the molecular structure has been revealed by single crystal X-ray diffraction. It is shown that the oxidation of the Fe(II) complex in both solvents is a reversible process. For the regeneration of the initial Fe(II) complex both organic and inorganic reducing agents can be used.

  9. Investigation, Analysis, and Testing of Self-contained Oxygen Generators

    Science.gov (United States)

    Keddy, Christopher P.; Haas, Jon P.; Starritt, Larry

    2008-01-01

    Self Contained Oxygen Generators (SCOGs) have widespread use in providing emergency breathing oxygen in a variety of environments including mines, submarines, spacecraft, and aircraft. These devices have definite advantages over storing of gaseous or liquid oxygen. The oxygen is not generated until a chemical briquette containing a chlorate or perchlorate oxidizer and a solid metallic fuel such as iron is ignited starting a thermal decomposition process allowing gaseous oxygen to be produced. These devices are typically very safe to store, easy to operate, and have primarily only a thermal hazard to the operator that can be controlled by barriers or furnaces. Tens of thousands of these devices are operated worldwide every year without major incident. This report examines the rare case of a SCOG whose behavior was both abnormal and lethal. This particular type of SCOG reviewed is nearly identical to a flight qualified version of SCOG slated for use on manned space vehicles. This Investigative Report is a compilation of a NASA effort in conjunction with other interested parties including military and aerospace to understand the causes of the particular SCOG accident and what preventative measures can be taken to ensure this incident is not repeated. This report details the incident and examines the root causes of the observed SCOG behavior from forensic evidence. A summary of chemical and numerical analysis is provided as a background to physical testing of identical SCOG devices. The results and findings of both small scale and full scale testing are documented on a test-by-test basis along with observations and summaries. Finally, conclusions are presented on the findings of this investigation, analysis, and testing along with suggestions on preventative measures for any entity interested in the safe use of these devices.

  10. Synthesis, in vitro evaluation, and molecular modeling investigation of benzenesulfonimide peroxisome proliferator-activated receptors α antagonists.

    Science.gov (United States)

    Ammazzalorso, Alessandra; Carrieri, Antonio; Verginelli, Fabio; Bruno, Isabella; Carbonara, Giuseppe; D'Angelo, Alessandra; De Filippis, Barbara; Fantacuzzi, Marialuigia; Florio, Rosalba; Fracchiolla, Giuseppe; Giampietro, Letizia; Giancristofaro, Antonella; Maccallini, Cristina; Cama, Alessandro; Amoroso, Rosa

    2016-05-23

    Recent evidences suggest a moderate activation of Peroxisome Proliferator-Activated Receptors (PPARs) could be favorable in metabolic diseases, reducing side effects given from full agonists. PPAR partial agonists and antagonists represent, to date, interesting tools to better elucidate biological processes modulated by these receptors. In this work are reported new benzenesulfonimide compounds able to block PPARα, synthesized and tested by transactivation assays and gene expression analysis. Some of these compounds showed a dose-dependent antagonistic behavior on PPARα, submicromolar potency, different profiles of selectivity versus PPARγ, and a repressive effect on CPT1A expression. Dockings and molecular dynamics on properly selected benzenesulfonimide derivatives furnished fresh insights into the molecular determinant most likely responsible for PPARα antagonism. PMID:26974385

  11. Morphological and molecular investigations of a microsporidium infecting the European grape vine moth, Lobesia botrana Den. et Schiff., and its taxonomic determination as Cystosporogenes legeri nov. comb.

    Science.gov (United States)

    Kleespies, Regina G; Vossbrinck, Charles R; Lange, Martin; Jehle, Johannes A

    2003-07-01

    We have isolated a microsporidium from a laboratory stock of the European grape vine moth, Lobesia botrana Den. et Schiff. (Lepidoptera, Tortricidae). Screening of this stock showed an infection rate of more than 90%, whereas field collected larvae from three different locations in Rhineland-Palatinate (Germany) did not demonstrate any signs of infection. Light and electron microscopic investigations of infected insects showed that gross pathology, morphology, and ultrastructure of the microsporidium are similar to those described earlier for Pleistophora legeri. Comparative phylogenetic analysis of the small subunit rDNA using maximum likelihood, maximum parsimony, and neighbour joining distance methods showed that our isolate was closely related to Cystosporogenes operophterae. Based on our morphological and molecular investigations we propose to rename this species Cystosporogenes legeri nov. comb. PMID:12877831

  12. Molecular Polymorphism: Microwave Spectra, Equilibrium Structures, and an Astronomical Investigation of the HNCS Isomeric Family

    CERN Document Server

    McGuire, Brett A; Thorwirth, Sven; Brünken, Sandra; Lattanzi, Valerio; Neill, Justin L; Spezzano, Silvia; Yu, Zhenhong; Zaleski, Daniel P; Remijan, Anthony J; Pate, Brooks H; McCarthy, Michael C

    2016-01-01

    The rotational spectra of thioisocyanic acid (HNCS), and its three energetic isomers (HSCN, HCNS, and HSNC) have been observed at high spectral resolution by a combination of chirped-pulse and Fabry-P\\'{e}rot Fourier-transform microwave spectroscopy between 6 and 40~GHz in a pulsed-jet discharge expansion. Two isomers, thiofulminic acid (HCNS) and isothiofulminic acid (HSNC), calculated here to be 35-37~kcal/mol less stable than the ground state isomer HNCS, have been detected for the first time. Precise rotational, centrifugal distortion, and nitrogen hyperfine coupling constants have been determined for the normal and rare isotopic species of both molecules; all are in good agreement with theoretical predictions obtained at the coupled cluster level of theory. On the basis of isotopic spectroscopy, precise molecular structures have been derived for all four isomers by correcting experimental rotational constants for the effects of rotation-vibration calculated theoretically. Formation and isomerization path...

  13. Investigation of the intermediate LK molecular orbital radiation in heavy ion-atom collisions

    International Nuclear Information System (INIS)

    The continuum consisting of an intensive low-energy and a high-energy components in heavy-ion atom collision systems with atomic numbers Z1, Z2 > 28 is studied. The aim of the study is to prove that the C1 continuum cannot be caused by ridiative electron capture (REC) being molecular orbital (MO) radiation to the 2ptau level. It is shown that the comparison of the C1 yields obtained in Kr+Nb asymmetric collisions in gas and solid targets is associated with the formation of vacancies in the lower-Z collision partner and can be interpreted as quasimolecular radiation to the 2ptau orbital level. The strong suppression of the C2 component in the gas target experimets indicates that the MO radiation to the 1stau orbit is emitted preferentially in the two-collision process in symmetric and near-symmetric systems with Z1, Z2 <= 41

  14. Structural Effects of Small Molecules on Phospholipid Bilayers Investigated by Molecular Simulations

    CERN Document Server

    Lee, B W; Sum, A K; Vattulainen, I; Patra, M; Karttunen, M; Lee, Bryan W; Faller, Roland; Sum, Amadeu K; Vattulainen, Ilpo; Patra, Michael; Karttunen, Mikko

    2004-01-01

    We summarize and compare recent Molecular Dynamics simulations on the interactions of dipalmitoylphosphatidylcholine (DPPC) bilayers in the liquid crystalline phase with a number of small molecules including trehalose, a disaccharide of glucose, alcohols, and dimethylsulfoxide (DMSO). The sugar molecules tend to stabilize the structure of the bilayer as they bridge adjacent lipid headgroups. They do not strongly change the structure of the bilayer. Alcohols and DMSO destabilize the bilayer as they increase its area per molecule in the bilayer plane and decrease the order parameter. Alcohols have a stronger detrimental effect than DMSO. The observables which we compare are the area per molecule in the plane of the bilayer, the membrane thickness, and the NMR order parameter of DPPC hydrocarbon tails. The area per molecule and the order parameter are very well correlated whereas the bilayer thickness is not necessarily correlated with them.

  15. Molecular dynamics investigation of carbon nanotube junctions in non-aqueous solutions

    KAUST Repository

    Gkionis, Konstantinos

    2014-07-23

    The properties of liquids in a confined environment are known to differ from those in the bulk. Extending this knowledge to geometries defined by two metallic layers in contact with the ends of a carbon nanotube is important for describing a large class of nanodevices that operate in non-aqueous environments. Here we report a series of classical molecular dynamics simulations for gold-electrode junctions in acetone, cyclohexane and N,N-dimethylformamide solutions and analyze the structure and the dynamics of the solvents in different regions of the nanojunction. The presence of the nanotube has little effect on the ordering of the solvents along its axis, while in the transversal direction deviations are observed. Importantly, the orientational dynamics of the solvents at the electrode-nanotube interface differ dramatically from that found when only the electrodes are present.

  16. Synthesis and computational investigation of molecularly imprinted nanospheres for selective recognition of alpha-tocopherol succinate

    Science.gov (United States)

    Piacham, Theeraphon; Nantasenamat, Chanin; Isarankura-Na-Ayudhya, Chartchalerm; Prachayasittikul, Virapong

    2013-01-01

    Molecularly imprinted polymers (MIPs) are macromolecular matrices that can mimic the functional properties of antibodies, receptors and enzymes while possessing higher durability. As such, these polymers are interesting materials for applications in biomimetic sensor, drug synthesis, drug delivery and separation. In this study, we prepared MIPs and molecularly imprinted nanospheres (MINs) as receptors with specific recognition properties toward tocopherol succinate (TPS) in comparison to tocopherol (TP) and tocopherol nicotinate (TPN). MIPs were synthesized using methacrylic acid (MAA) as functional monomer, ethylene glycol dimethacrylate (EGDMA) as crosslinking agent and dichloromethane or acetronitrile as porogenic solvent under thermal-induced polymerization condition. Results indicated that imprinted polymers of TPS-MIP, TP-MIP and TPN-MIP all bound specifically to their template molecules at 2 folds greater than the non-imprinted polymers. The calculated binding capacity of all MIP was approximately 2 mg per gram of polymer when using the optimal rebinding solvent EtOH:H2O (3:2, v/v). Furthermore, the MINs toward TPS and TP were prepared by precipitation polymerization that yielded particles that are 200-400 nm in size. The binding capacities of MINs to their templates were greater than that of the non-imprinted nanospheres when using the optimal rebinding solvent EtOH:H2O (4:1, v/v). Computer simulation was performed to provide mechanistic insights on the binding modalities of template-monomer complexes. In conclusion, we had successful prepared MIPs and MINs for binding specifically to TP and TPS. Such MIPs and MINs have great potential for industrial and medical applications, particularly for the selective separation of TP and TPS. PMID:26622214

  17. The Sample Analysis at Mars Investigation and Instrument Suite

    Science.gov (United States)

    Mahaffy, Paul; Webster, Chris R.; Cabane, M.; Conrad, Pamela G.; Coll, Patrice; Atreya, Sushil K.; Arvey, Robert; Barciniak, Michael; Benna, Mehdi; Bleacher, L.; Brinckerhoff, William B.; Eigenbrode, Jennifer L.; Carignan, Daniel; Cascia, Mark; Chalmers, Robert A.; Dworkin, Jason P.; Errigo, Therese; Everson, Paula; Franz, Heather; Farley, Rodger; Feng, Steven; Frazier, Gregory; Freissinet, Caroline; Glavin, Daniel P.; Harpold, Daniel N.

    2012-01-01

    The Sample Analysis at Mars (SAM) investigation of the Mars Science Laboratory(MSL) addresses the chemical and isotopic composition of the atmosphere and volatilesextracted from solid samples. The SAM investigation is designed to contribute substantiallyto the mission goal of quantitatively assessing the habitability of Mars as an essentialstep in the search for past or present life on Mars. SAM is a 40 kg instrument suite locatedin the interior of MSLs Curiosity rover. The SAM instruments are a quadrupole massspectrometer, a tunable laser spectrometer, and a 6-column gas chromatograph all coupledthrough solid and gas processing systems to provide complementary information on thesame samples. The SAM suite is able to measure a suite of light isotopes and to analyzevolatiles directly from the atmosphere or thermally released from solid samples. In additionto measurements of simple inorganic compounds and noble gases SAM will conducta sensitive search for organic compounds with either thermal or chemical extraction fromsieved samples delivered by the sample processing system on the Curiosity rovers roboticarm.

  18. Investigating echo state networks dynamics by means of recurrence analysis

    CERN Document Server

    Bianchi, Filippo Maria; Alippi, Cesare

    2016-01-01

    In this paper, we elaborate over the well-known interpretability issue in echo state networks. The idea is to investigate the dynamics of reservoir neurons with time-series analysis techniques taken from research on complex systems. Notably, we analyze time-series of neuron activations with Recurrence Plots (RPs) and Recurrence Quantification Analysis (RQA), which permit to visualize and characterize high-dimensional dynamical systems. We show that this approach is useful in a number of ways. First, the two-dimensional representation offered by RPs provides a way for visualizing the high-dimensional dynamics of a reservoir. Our results suggest that, if the network is stable, reservoir and input denote similar line patterns in the respective RPs. Conversely, the more unstable the ESN, the more the RP of the reservoir presents instability patterns. As a second result, we show that the $\\mathrm{L_{max}}$ measure is highly correlated with the well-established maximal local Lyapunov exponent. This suggests that co...

  19. Induction of autoimmune disease by radiation exposure. Analysis of molecular structure of myeloperoxidase in neutrophil

    International Nuclear Information System (INIS)

    Recently, antineutrophil cytoplasmic antibody (ANCA) that is one of autoimmune antibodies has been paid attention since the antibody was found in patients with articular rheumatism. Molecular structure of myeloperoxidase (MPO), which has been regarded as the antigen of ANCA was investigated in this study. Peripheral neutrophil was exposed to γ-ray at 10 and 30 Gy followed by addition of cytochalasin B. The extracellular and intracellular activities of MPO were determined to estimate the effects of the radiation. Moreover, MPO released to the culture medium was purified from the crude extract of the medium and investigated by Western blot analysis to confirm the occurrence of molecular cleavage in MPO. The releasing activity of MPO was decreased by γ-ray exposure at a dose ranging from 0.1 to 1.0 Gy and it tended to increase with 10 or 30 Gy. On the other hand, the activity of the released enzyme was increased by exposure at 0.1-3.0 Gy and became the normal level with 10 or 30 Gy. There were no changes in the SDS-PAGE pattern for the proteins from neutrophils. Western blotting revealed that 30 kDa fragment was included in the proteins released from neutrophils exposed to 0.1-0.3 Gy. The evidence that a low dose exposure induced such fragmentation of MPO molecule would be utilized to evaluate the effects of low-dose radiation. These results suggested that the MPO molecule fragmented by radiation exposure is highly reactive with the autoantibody in neutrophils, but correlation between MPO and its ANCA- related autoimmune disease has not yet demonstrated. (M.N.)

  20. Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps

    Directory of Open Access Journals (Sweden)

    Stella Fabio

    2011-05-01

    Full Text Available Abstract Background Molecular dynamics (MD simulations are powerful tools to investigate the conformational dynamics of proteins that is often a critical element of their function. Identification of functionally relevant conformations is generally done clustering the large ensemble of structures that are generated. Recently, Self-Organising Maps (SOMs were reported performing more accurately and providing more consistent results than traditional clustering algorithms in various data mining problems. We present a novel strategy to analyse and compare conformational ensembles of protein domains using a two-level approach that combines SOMs and hierarchical clustering. Results The conformational dynamics of the α-spectrin SH3 protein domain and six single mutants were analysed by MD simulations. The Cα's Cartesian coordinates of conformations sampled in the essential space were used as input data vectors for SOM training, then complete linkage clustering was performed on the SOM prototype vectors. A specific protocol to optimize a SOM for structural ensembles was proposed: the optimal SOM was selected by means of a Taguchi experimental design plan applied to different data sets, and the optimal sampling rate of the MD trajectory was selected. The proposed two-level approach was applied to single trajectories of the SH3 domain independently as well as to groups of them at the same time. The results demonstrated the potential of this approach in the analysis of large ensembles of molecular structures: the possibility of producing a topological mapping of the conformational space in a simple 2D visualisation, as well as of effectively highlighting differences in the conformational dynamics directly related to biological functions. Conclusions The use of a two-level approach combining SOMs and hierarchical clustering for conformational analysis of structural ensembles of proteins was proposed. It can easily be extended to other study cases and to

  1. Atmospheric pressure plasma analysis by modulated molecular beam mass spectrometry

    International Nuclear Information System (INIS)

    Fractional number density measurements for a rf plasma 'needle' operating at atmospheric pressure have been obtained using a molecular beam mass spectrometer (MBMS) system designed for diagnostics of atmospheric plasmas. The MBMS system comprises three differentially pumped stages and a mass/energy analyzer and includes an automated beam-to-background measurement facility in the form of a software-controlled chopper mechanism. The automation of the beam modulation allows the neutral components in the plasma to be rapidly and accurately measured using the mass spectrometer by threshold ionization techniques. Data are reported for plasma generated by a needle plasma source operated using a helium/air mixture. In particular, data for the conversion of atmospheric oxygen and nitrogen into nitric oxide are discussed with reference to its significance for medical applications such as disinfecting wounds and dental cavities and for microsurgery

  2. iBarcode.org: web-based molecular biodiversity analysis

    OpenAIRE

    Hajibabaei Mehrdad; Singer Gregory AC

    2009-01-01

    Abstract Background DNA sequences have become a primary source of information in biodiversity analysis. For example, short standardized species-specific genomic regions, DNA barcodes, are being used as a global standard for species identification and biodiversity studies. Most DNA barcodes are being generated by laboratories that have an expertise in DNA sequencing but not in bioinformatics data analysis. Therefore, we have developed a web-based suite of tools to help the DNA barcode research...

  3. Comparative molecular field analysis and comparative molecular similarity index analysis studies on 1H NMR chemical shift of NH group of diaryl triazene derivatives.

    Science.gov (United States)

    Rofouie, M K; Salahinejad, M; Ghasemi, J B; Aghaei, A

    2013-05-01

    Comparative molecular field analysis (CoMFA), comparative molecular field analysis region focusing (CoMFA-RF) for optimizing the region for the final partial least square analysis, and comparative molecular similarity indices analysis (CoMSIA) methods were employed to develop three-dimensional quantitative structure-activity relationship (3D-QSAR) models of (1)H NMR chemical shift of NH proton of diaryl triazene derivatives. The best orientation was searched by all-orientation search (AOS) strategy to minimize the effect of the initial orientation of the structures. The predictive abilities of CoMFA-RF and CoMSIA models were determined using a test set of ten compounds affording predictive correlation coefficients of 0.721 and 0.754, respectively, indicating good predictive power. For further model validation, cross validation (leave one out), progressive scrambling, and bootstrapping were also applied. The accuracy and speed of obtained 3D-QSAR models for the prediction of (1)H NMR chemical shifts of NH group of diaryl triazene derivatives were greater compared to some computational well-known procedures. PMID:23456682

  4. Using Molecular Modeling in Teaching Group Theory Analysis of the Infrared Spectra of Organometallic Compounds

    Science.gov (United States)

    Wang, Lihua

    2012-01-01

    A new method is introduced for teaching group theory analysis of the infrared spectra of organometallic compounds using molecular modeling. The main focus of this method is to enhance student understanding of the symmetry properties of vibrational modes and of the group theory analysis of infrared (IR) spectra by using visual aids provided by…

  5. Direct investigation of viscosity of an atypical inner membrane of Bacillus spores: a molecular rotor/FLIM study.

    Science.gov (United States)

    Loison, Pauline; Hosny, Neveen A; Gervais, Patrick; Champion, Dominique; Kuimova, Marina K; Perrier-Cornet, Jean-Marie

    2013-11-01

    We utilize the fluorescent molecular rotor Bodipy-C12 to investigate the viscoelastic properties of hydrophobic layers of bacterial spores Bacillus subtilis. The molecular rotor shows a marked increase in fluorescence lifetime, from 0.3 to 4ns, upon viscosity increase from 1 to 1500cP and can be incorporated into the hydrophobic layers within the spores from dormant state through to germination. We use fluorescence lifetime imaging microscopy to visualize the viscosity inside different compartments of the bacterial spore in order to investigate the inner membrane and relate its compaction to the extreme resistance observed during exposure of spores to toxic chemicals. We demonstrate that the bacterial spores possess an inner membrane that is characterized by a very high viscosity, exceeding 1000cP, where the lipid bilayer is likely in a gel state. We also show that this membrane evolves during germination to reach a viscosity value close to that of a vegetative cell membrane, ca. 600cP. The present study demonstrates quantitative imaging of the microscopic viscosity in hydrophobic layers of bacterial spores Bacillus subtilis and shows the potential for further investigation of spore membranes under environmental stress. PMID:23831602

  6. Retrospective analysis of the efficacy of chemotherapy and molecular targeted therapy for advanced pulmonary pleomorphic carcinoma

    OpenAIRE

    Tamura, Yosuke; Fujiwara, Yutaka; Yamamoto, Noboru; Nokihara, Hiroshi; Horinouchi, Hidehito; Kanda, Shintaro; Goto, Yasushi; Kubo, Emi; Kitahara, Shinsuke; Tsuruoka, Kenjiro; Tsuta, Koji; Ohe, Yuichiro

    2015-01-01

    Background Pulmonary pleomorphic carcinoma (PPC) follows an aggressive clinical course and outcomes are disappointing. Due to its rarity, however, the clinicopathological and molecular characteristics of this disease remain unclear. Methods We retrospectively evaluated the efficacy of chemotherapy and molecular targeted therapy in 16 patients with PPC who received chemotherapy or EGFR-TKI. We also investigated the status of EGFR mutation, KRAS mutation and ALK expression. Results On histologi...

  7. Investigating the Molecular Mechanism of TSO1 Function in Arabidopsis cell division and meristem development

    Energy Technology Data Exchange (ETDEWEB)

    Zhongchi Liu

    2004-10-01

    Unlike animals, plants are constantly exposed to environmental mutagens including ultraviolet light and reactive oxygen species. Further, plant cells are totipotent with highly plastic developmental programs. An understanding of molecular mechanisms underlying the ability of plants to monitor and repair its DNA and to eliminate damaged cells are of great importance. Previously we have identified two genes, TSO1 and TSO2, from a flowering plant Arabidopsis thaliana. Mutations in these two genes cause callus-like flowers, fasciated shoot apical meristems, and abnormal cell division, indicating that TSO1 and TSO2 may encode important cell cycle regulators. Previous funding from DOE led to the molecular cloning of TSO1, which was shown to encode a novel nuclear protein with two CXC domains suspected to bind DNA. This DOE grant has allowed us to characterize and isolate TSO2 that encodes the small subunit of the ribonucleotide reductase (RNR). RNR comprises two large subunits (R1) an d two small subunits (R2), catalyzes a rate-limiting step in the production of deoxyribonucleotides needed for DNA replication and repair. Previous studies in yeast and mammals indicated that defective RNR often led to cell cycle arrest, growth retardation and p53-dependent apoptosis while abnormally elevated RNR activities led to higher mutation rates. Subsequently, we identified two additional R2 genes, R2A and R2B in the Arabidopsis genome. Using reverse genetics, mutations in R2A and R2B were isolated, and double and triple mutants among the three R2 genes (TSO2, R2A and R2B) were constructed and analyzed. We showed that Arabidopsis tso2 mutants, with reduced dNTP levels, were more sensitive to UV-C. While r2a or r2b single mutants did not exhibit any phenotypes, tso2 r2b double mutants were embryonic lethal and tso2 r2a double mutants were seedling lethal indicating redundant functions among the three R2 genes. Furthermore, tso2 r2a double mutants exhibited increased DNA dam age

  8. Statistical properties of the dense hydrogen plasma: An ab initio molecular dynamics investigation

    International Nuclear Information System (INIS)

    The hydrogen plasma is studied in the very high density (atomic and metallic) regime by extensive ab initio Molecular Dynamics simulations. Protons are treated classically, and electrons in the Born-Oppenheimer framework, within the local density approximation (LDA). Densities and temperatures studied fall within the strong coupling regime of the protons. We address the question of the validity of linear screening, and we find it to yield a reasonably good description up to rs approx. 0.5, but already too crude for rs = 1 (with rs = (3/4πρ)1/3 the ion sphere radius). Finite-size and Brillouin zone sampling effects in metallic systems are studied and shown to be very delicate also in the fluid (liquid metal) phase. We analyse the low-temperature phase diagram and the melting transition. A remarkably fast decrease of the melting temperature with decreasing density is found, up to a point when it becomes comparable to the Fermi temperature of the protons. The possible vicinity of a triple point bcc-hcp(fcc)- liquid is discussed in the region of rs approx. 1.1 and T approx. 100 - 200K. The fluid phase is studied in detail for several temperatures. Proton-electron correlations show a weak temperature dependence, and proton-proton correlations exhibit a well-defined first coordination shell, thus characterizing fluid H in this regime as an atomic liquid. Diffusion coefficients are compared to the values for the one-component plasma. Vibrational densities of states (VDOS) show a plasmon renormalization due to electron screening, and the presence of a plasmon-coupled single-particle mode up to very high temperatures. Collective modes are studied through dynamical structure factors. In close relationship with the VDOS, the simulations reveal the remarkable persistent of a weakly damped high-frequency ion acoustic mode, even under conditions of strong electron screening. The possibility of using this observation as a diagnostic for the plasma phase transition to the fluid

  9. Molecular tools for epidemiological investigations into Legionella pneumophila environmental diffusion: applications for the prevention

    Directory of Open Access Journals (Sweden)

    Stefania Boccia

    2004-12-01

    Full Text Available

    Microbiological typing is a useful tool in the epidemiological investigations of infectious diseases, given that it allows for the identification of specific clones among a set of isolates.

     In the last ten years several studies have demonstrated how genotyping methods can be useful in Legionella spp investigations in hospital setting (e.g., epidemic events. Pulsed field gel electrophoresis and amplified fragment length polymorphisms are the current typing methods of choice, even though multilocus sequence typing will probably be the gold standard of the future.

  10. Molecular analysis of the 18q- syndrome--and correlation with phenotype.

    OpenAIRE

    Kline, A D; White, M E; Wapner, R; Rojas, K; Biesecker, L G; Kamholz, J; Zackai, E. H.; Muenke, M; Scott, C I; Overhauser, J

    1993-01-01

    Seven individuals with deletions of the distal long arm of chromosome 18 were evaluated at the clinical, cytogenetic, and molecular levels. The patients had varying degrees of typical clinical findings associated with the 18q- syndrome. Cytogenetic analysis revealed deletions from 18q21.3 or 18q22.2 to qter. Somatic cell hybrids derived from the patients were molecularly characterized using ordered groups of probes isolated from a chromosome 18-specific library. In general, the size of the de...

  11. Transcriptome Analysis and Development of SSR Molecular Markers in Glycyrrhiza uralensis Fisch.

    OpenAIRE

    Yaling Liu; Pengfei Zhang; Meiling Song; Junling Hou; Mei Qing; Wenquan Wang; Chunsheng Liu

    2015-01-01

    Licorice is an important traditional Chinese medicine with clinical and industrial applications. Genetic resources of licorice are insufficient for analysis of molecular biology and genetic functions; as such, transcriptome sequencing must be conducted for functional characterization and development of molecular markers. In this study, transcriptome sequencing on the Illumina HiSeq 2500 sequencing platform generated a total of 5.41 Gb clean data. De novo assembly yielded a total of 46,641 uni...

  12. Model HULIS compounds in nanoaerosol clusters – investigations of surface tension and aggregate formation using molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    T. Hede

    2011-07-01

    Full Text Available Cloud condensation nuclei act as cores for water vapour condensation, and their composition and chemical properties may enhance or depress the ability for droplet growth. In this study we use molecular dynamics simulations to show that model humic-like substances (HULIS in systems containing 10 000 water molecules mimic experimental data well referring to reduction of surface tension. The model HULIS compounds investigated in this study are cis-pinonic acid (CPA, pinic acid (PAD and pinonaldehyde (PAL. The structural properties examined show the ability for the model HULIS compounds to aggregate inside the nanoaerosol clusters.

  13. Investigation of molecular mechanism of CNS symptoms induced by DDVP poisoning

    Institute of Scientific and Technical Information of China (English)

    ZHAOZanmei; WANGHanbin

    2005-01-01

    Objective To Screen differentially expressed genes related to dichlorphos(DDVP) poisoning from rat's hippocampus using oligonucleotide microarray technology in order to elucidate the mechanism of DDVP poisoning. Methods We composed probes of 40 genes of our interest. The probes were retrotranscribed on plata glass and oligonucleotide microarray was formed. 0.5 ml DDVP was given to the rats in experimental group and 0.Sml-pumping brine was given to the rats in control group by hypodermic injection, twenty minutes after convulsion, all hippocampus were collected for total RNA extraction, cDNAs were marked with Cy3 and Cy5 for control group and experiment group respectively, and hybridized with loligonucleotide microarray. Hybridization signals were collected and analyzed following scanning by laser co-focal scanner. Results There were 8 differentially expressed genes identified. Conclusion Many genes expressing changed by DDVP poisoning could be analyzed in a time period by using oligonucleotide microarray, which provides a powerful method for further studies on the molecular mechanism of DDVP poisoning.

  14. Molecular triads composed of ferrocene, C60, and nitroaromatic entities: electrochemical, computational, and photochemical investigations.

    Science.gov (United States)

    Zandler, Melvin E; Smith, Phillip M; Fujitsuka, Mamoru; Ito, Osamu; D'Souza, Francis

    2002-12-27

    Synthesis and physicochemical characterization of a series of molecular triads composed of ferrocene, C(60), and nitroaromatic entities are reported. Electrochemical studies revealed multiple redox processes involving all three redox active ferrocene, C(60), and nitrobenzene entities. Up to eight redox couples within the accessible potential window of o-dichlorobenzene containing 0.1 M (TBA)ClO(4) are observed. A comparison between the measured redox potentials with those of the starting compounds revealed absence of any significant electronic interactions between the different redox entities. The geometric and electronic structure of the triads are elucidated by using ab initio B3LYP/3-21G methods. In the energy-optimized structures, as predicted by electrochemical studies, the first HOMO orbitals are found to be located on the ferrocene entity, while the first LUMO orbitals are mainly on the C(60) entity. The coefficients of the subsequent LUMO orbitals track the observed site of electrochemical reductions of the triads. The photochemical events of the triads are probed by both steady-state and time-resolved techniques. The steady-state emission intensities of the triads and the starting dyad, 2-(ferrocenyl)fulleropyrrolidine, are found to be completely quenched compared to fulleropyrrolidine bearing no redox active substituents. The subpicosecond and nanosecond transient absorption spectral studies revealed efficient charge separation (and rapid charge recombination) in the triads, and this has been attributed to the close spacing of the redox entities of the triad to one another. PMID:12492311

  15. On the Quest of Dioxygen by Monomeric Sarcosine Oxidase. A Molecular Dynamics Investigation.

    Science.gov (United States)

    Pietra, Francesco

    2015-08-01

    It is reported here on random acceleration molecular dynamics (RAMD) simulations with the 2GF3 bacterial monomeric sarcosine oxidase (MSOX), O2 , and furoic acid in place of sarcosine, solvated by TIP3 H2 O in a periodic box. An external tiny force, acting randomly on O2 , accelerated its relocation, from the center of activation between residue K265 and the si face of the flavin ring of the flavin adenine dinucleotide cofactor, to the surrounding solvent. Only three of the four O2 gates previously described for this system along a composite method technique were identified, while two more major O2 gates were found. The RAMD simulations also revealed that the same gate can be reached by O2 along different pathways, often involving traps for O2 . Both the residence time of O2 in the traps, and the total trajectory time for O2 getting to the solvent, could be evaluated. The new quick pathways discovered here suggest that O2 exploits all nearby interstices created by the thermal fluctuations of the protein, not having necessarily to look for the permanent large channel used for uptake of the FADH cofactor. To this regard, MSOX resembles closely KijD3 N-oxygenase. These observations solicit experimental substantiation, in a long term aim at discovering whether gates and pathways for the small gaseous ligands inside the proteins are under Darwinian functional evolution or merely stochastic control operates. PMID:26265568

  16. Investigation of the effect of glycosylation on human prion protein by molecular dynamics.

    Science.gov (United States)

    Zhong, Linghao; Xie, Jimin

    2009-04-01

    Prion protein conformational isomerization, PrP(C)-->PrP(Sc), has been attributed as the cause of TSE diseases such as mad-cow disease. The mechanism of such isomerization, however, is little known due the experimental difficulties in studying the scrapie form. Among factors that affect PrP isomerization, the role which glycosylation plays remains vague. The number of innumerous glycan species, together with their high flexibility, leads to ineffective structural characterization. In this research, we studied the effect of chitobiose glycosylation on human PrP, in both monomeric (huPrP(mono)) and dimeric (huPrP(dimer)) forms, by molecular dynamics (MD) simulations. Our results show that this glycosylation has minimal impact on the structure of huPrP(mono). However, it affects the secondary structure of dimeric protein. An additional beta-sheet strand is found while the glycosylation is absent in the huPrP(dimer). Comparatively, when the protein is glycosylated with chitobiose, such beta-sheet addition is not observed. PMID:19236103

  17. Wetting and evaporation of salt-water nanodroplets: A molecular dynamics investigation.

    Science.gov (United States)

    Zhang, Jun; Borg, Matthew K; Sefiane, Khellil; Reese, Jason M

    2015-11-01

    We employ molecular dynamics simulations to study the wetting and evaporation of salt-water nanodroplets on platinum surfaces. Our results show that the contact angle of the droplets increases with the salt concentration. To verify this, a second simulation system of a thin salt-water film on a platinum surface is used to calculate the various surface tensions. We find that both the solid-liquid and liquid-vapor surface tensions increase with salt concentration and as a result these cause an increase in the contact angle. However, the evaporation rate of salt-water droplets decreases as the salt concentration increases, due to the hydration of salt ions. When the water molecules have all evaporated from the droplet, two forms of salt crystals are deposited, clump and ringlike, depending on the solid-liquid interaction strength and the evaporation rate. To form salt crystals in a ring, it is crucial that there is a pinned stage in the evaporation process, during which salt ions can move from the center to the rim of the droplets. With a stronger solid-liquid interaction strength, a slower evaporation rate, and a higher salt concentration, a complete salt crystal ring can be deposited on the surface. PMID:26651708

  18. Synthesis of focused library of novel aryloxyacids and pyrazoline derivatives: Molecular docking studies and antimicrobial investigation

    Directory of Open Access Journals (Sweden)

    Shubhalaxmi

    2016-12-01

    Full Text Available Infectious diseases are on the rise due to development of multidrug-resistant strains, and this renders the search for newer antimicrobials. Hybrid compounds of different scaffolds are expected to enhance the bioactivity by improved affinity to target proteins while retaining the biological efficacy of each of the components. In view of this, a series of pyrazolines with aryloxy acid in the side chain are synthesized and evaluated for their antimicrobial potential. Pyrazoline-substituted aryloxy acids were synthesized in very good yields, starting from chalcones. Synthetic method is adopted in such a way that the use of any solvents is avoided. The structures of these compounds were confirmed using FTIR, NMR, and Mass spectrometry. The potential of these molecules as antimicrobial agents was predicted using molecular docking studies. The activities were also assessed using zone of inhibition and minimum inhibitory concentration (MIC measurement against tuberculosis variant bacteria, Mycobacterium smegmatis; Gram-positive pathogen, Staphylococcus aureus; Gram-negative Escherichia coli; and fungi, Candida albicans. The positional isomers with the electron-withdrawing group farthest from the acid function showed the best activity in both chalcone acids as well as pyrazoline acids. Many of the compounds exhibited zones of inhibition comparable with the standard drugs, ciprofloxacin and fluconazole, considered for the study. Although many compounds exhibited significant zones of inhibition, their minimum inhibitory concentrations established by broth assay were higher, suggesting these molecules are not potent at lower concentrations.

  19. Wetting and evaporation of salt-water nanodroplets: A molecular dynamics investigation

    Science.gov (United States)

    Zhang, Jun; Borg, Matthew K.; Sefiane, Khellil; Reese, Jason M.

    2015-11-01

    We employ molecular dynamics simulations to study the wetting and evaporation of salt-water nanodroplets on platinum surfaces. Our results show that the contact angle of the droplets increases with the salt concentration. To verify this, a second simulation system of a thin salt-water film on a platinum surface is used to calculate the various surface tensions. We find that both the solid-liquid and liquid-vapor surface tensions increase with salt concentration and as a result these cause an increase in the contact angle. However, the evaporation rate of salt-water droplets decreases as the salt concentration increases, due to the hydration of salt ions. When the water molecules have all evaporated from the droplet, two forms of salt crystals are deposited, clump and ringlike, depending on the solid-liquid interaction strength and the evaporation rate. To form salt crystals in a ring, it is crucial that there is a pinned stage in the evaporation process, during which salt ions can move from the center to the rim of the droplets. With a stronger solid-liquid interaction strength, a slower evaporation rate, and a higher salt concentration, a complete salt crystal ring can be deposited on the surface.

  20. Ultrafast two-dimensional NMR relaxometry for investigating molecular processes in real time.

    Science.gov (United States)

    Ahola, Susanna; Telkki, Ville-Veikko

    2014-06-01

    Nuclear spin-lattice (T1) and spin-spin (T2) relaxation times provide versatile information about the dynamics and structure of substances, such as proteins, polymers, porous media, and so forth. Multidimensional experiments increase the information content and resolution of NMR relaxometry, but they also multiply the measurement time. To overcome this issue, we present an efficient strategy for a single-scan measurement of a 2D T1-T2 correlation map. The method shortens the experimental time by one to three orders of magnitude as compared to the conventional method, offering an unprecedented opportunity to study molecular processes in real-time. We demonstrate that, despite the tremendous speed-up, the T1-T2 correlation maps determined by the single-scan method are in good agreement with the maps measured by the conventional method. The concept of the single-scan T1-T2 correlation experiment is applicable to a broad range of other multidimensional relaxation and diffusion experiments. PMID:24634359

  1. Investigation of the impact of annealing on global molecular mobility in glasses: optimization for stabilization of amorphous pharmaceuticals.

    Science.gov (United States)

    Luthra, Suman A; Hodge, Ian M; Pikal, Michael J

    2008-09-01

    The purpose of this research was to investigate the effect of annealing on the molecular mobility in lyophilized glasses using differential scanning calorimetry (DSC) and isothermal microcalorimetry (IMC) techniques. A second objective that emerged was a systematic study of the unusual pre-T(g) thermal events that were observed during DSC warming scans after annealing. Aspartame lyophilized with three different excipients; sucrose, trehalose and poly vinyl pyrrolidone (PVP) was studied. The aim of this work was to quantify the decrease in mobility in amorphous lyophilized aspartame formulations upon systematic postlyophilization annealing. DSC scans of aspartame:sucrose formulation (T(g) = 73 degrees C) showed the presence of a pre-T(g) endotherm which disappeared upon annealing. Aspartame:trehalose (T(g) = 112 degrees C) and aspartame:PVP (T(g) = 100 degrees C) showed a broad exotherm before T(g) and annealing caused appearance of endothermic peaks before T(g). This work also employed IMC to measure the global molecular mobility represented by structural relaxation time (tau(beta)) in both un-annealed and annealed formulations. The effect of annealing on the enthalpy relaxation of lyophilized glasses, as measured by DSC and IMC, was consistent with the behavior predicted using the Tool-Narayanaswamy-Moynihan (TNM) phenomenology (Luthra et al., 2007, in press). The results show that the systems annealed at T(g) -15 degrees C to T(g) -20 degrees C have the lowest molecular mobility. PMID:18200533

  2. Molecular Dynamics Simulations to Investigate the Binding Mode of the Natural Product Liphagal with Phosphoinositide 3-Kinase α

    Directory of Open Access Journals (Sweden)

    Yanjuan Gao

    2016-06-01

    Full Text Available Phosphatidylinositol 3-kinase α (PI3Kα is an attractive target for anticancer drug design. Liphagal, isolated from the marine sponge Aka coralliphaga, possesses the special “liphagane” meroterpenoid carbon skeleton and has been demonstrated as a PI3Kα inhibitor. Molecular docking and molecular dynamics simulations were performed to explore the dynamic behaviors of PI3Kα binding with liphagal, and free energy calculations and energy decomposition analysis were carried out by use of molecular mechanics/Poisson-Boltzmann (generalized Born surface area (MM/PB(GBSA methods. The results reveal that the heteroatom rich aromatic D-ring of liphagal extends towards the polar region of the binding site, and the D-ring 15-hydroxyl and 16-hydroxyl form three hydrogen bonds with Asp810 and Tyr836. The cyclohexyl A-ring projects up into the upper pocket of the lipophilic region, and the hydrophobic/van der Waals interactions with the residues Met772, Trp780, Ile800, Ile848, Val850, Met922, Phe930, Ile932 could be the key interactions for the affinity of liphagal to PI3Kα. Thus, a new strategy for the rational design of more potent analogs of liphagal against PI3Kα is provided. Our proposed PI3Kα/liphagal binding mode would be beneficial for the discovery of new active analogs of liphagal against PI3Kα.

  3. The prognostic value of molecular marker analysis in patients treated with trimodality therapy for esophageal cancer.

    Science.gov (United States)

    Harpole, D H; Moore, M B; Herndon, J E; Aloia, T; D'Amico, T A; Sporn, T; Parr, A; Linoila, I; Allegra, C

    2001-03-01

    The purpose of this study was to define the prognostic value of a group of molecular tumor markers in a well-staged population of patients treated with trimodality therapy for esophageal cancer. The original pretreatment paraffin-embedded endoscopic esophageal tumor biopsy material was obtained from 118 patients treated with concurrent cisplatin + 5-fluorouracil (5-FU) + 45 Gy radiation followed by resection from 1986 until 1997 at the Duke University Comprehensive Cancer Center. Three markers of possible platinum chemotherapy association [metallothionein (MT), glutathione S-transferase-pi (GST-pi), P-glycoprotein (P-gp or multidrug resistance)] and one marker of possible 5-FU association [thymidylate synthase (TS)] were measured using immunohistochemistry. The median cancer-free survival was 25.0 months, with a significantly improved survival for the 38 patients who had a complete response (P GST-pi, P-gp, and TS were associated with a decreased survival. MT was not significant in this population. Multivariate analysis identified high-level expression in two of the platinum markers (GST-pi and P-gp) and the 5-FU marker TS as independent predictors of early recurrence and death. In conclusion, this investigation measured three possible markers associated with platinum and one possible marker associated with 5-FU in a cohort of esophageal cancer patients. Independent prognostic significance was observed, which suggests that it may be possible to predict which patients may benefit most from trimodality therapy. These data need to be reproduced in a prospective investigation. PMID:11297249

  4. Molecular dynamics simulation of polyhedron analysis of Cu–Ag alloy under rapid quenching conditions

    International Nuclear Information System (INIS)

    In this study, the formation mechanism of polyhedron clusters in Cu50Ag50 binary alloy system consisting of 50 000 atoms has been investigated by using molecular dynamics simulations based on embedded atom method (EAM) during the rapid cooling processes. The cluster-type index method (CTIM) has been used to describe the evaluation properties of clusters and the structural development has been investigated by using radial distribution function (RDF). The simulation results show that the amorphous phase is formed by the main bonded pairs of 1551, 1541 and 1431 in the system, and ideal icosahedral (icos) cluster (12 0 12 0) and other basic polyhedron clusters, such as defective icos, Frank–Kasper, Bernal polyhedron, play a critical role under the rapid cooling conditions. The results of our simulations that have been disclosed show that high cooling rate favors the icos and defective icos clusters for model alloy system. - Highlights: • The different polyhedron types are determined of model alloy system for different cooling rates. • FK and Bernal polyhedrons have been increased with increasing cooling rate. • HA pair analysis method has been analyzed in order to detect icosahedral order

  5. LiDAR Vegetation Investigation and Signature Analysis System (LVISA)

    Science.gov (United States)

    Höfle, Bernhard; Koenig, Kristina; Griesbaum, Luisa; Kiefer, Andreas; Hämmerle, Martin; Eitel, Jan; Koma, Zsófia

    2015-04-01

    lacks behind. We propose a novel concept, the LiDAR Vegetation Investigation and Signature Analysis System (LVISA), which shall enhance sharing of i) reference datasets of single vegetation objects with rich reference data (e.g., plant species, basic plant morphometric information) and ii) approaches for information extraction (e.g., single tree detection, tree species classification based on waveform LiDAR features). We will build an extensive LiDAR data repository for supporting the development and benchmarking of LiDAR-based object information extraction. The LiDAR Vegetation Investigation and Signature Analysis System (LVISA) uses international web service standards (Open Geospatial Consortium, OGC) for geospatial data access and also analysis (e.g., OGC Web Processing Services). This will allow the research community identifying plant object specific vegetation features from LiDAR data, while accounting for differences in LiDAR systems (e.g., beam divergence), settings (e.g., point spacing), and calibration techniques. It is the goal of LVISA to develop generic 3D information extraction approaches, which can be seamlessly transferred to other datasets, timestamps and also extraction tasks. The current prototype of LVISA can be visited and tested online via http://uni-heidelberg.de/lvisa. Video tutorials provide a quick overview and entry into the functionality of LVISA. We will present the current advances of LVISA and we will highlight future research and extension of LVISA, such as integrating low-cost LiDAR data and datasets acquired by highly temporal scanning of vegetation (e.g., continuous measurements). Everybody is invited to join the LVISA development and share datasets and analysis approaches in an interoperable way via the web-based LVISA geoportal.

  6. Molecular and mass spectroscopic analysis of isotopically labeled organic residues

    International Nuclear Information System (INIS)

    Experimental studies aimed at understanding the evolution of complex organic molecules on interstellar grains were performed. The photolysis of frozen gas mixtures of various compositions containing H2O, CO, NH3, and CH4 was studied. These species were chosen because of their astrophysical importance as deducted from observational as well as theoretical studies of ice mantles on interstellar grains. These ultraviolet photolyzed ices were warmed up in order to produce refractory organic molecules like the ones formed in molecular clouds when the icy mantles are being irradiated and warmed up either by a nearby stellar source or impulsive heating. The laboratory studies give estimates of the efficiency of production of such organic material under interstellar conditions. It is shown that the gradual carbonization of organic mantles in the diffuse cloud phase leads to higher and higher visual absorptivity - yellow residues become brown in the laboratory. The obtained results can be applied to explaining the organic components of comets and their relevance to the origin of life

  7. Molecular analysis of carnitine palmitoyltransferase II deficiency with hepatocardiomuscular expression.

    Science.gov (United States)

    Bonnefont, J. P.; Taroni, F.; Cavadini, P.; Cepanec, C.; Brivet, M.; Saudubray, J. M.; Leroux, J. P.; Demaugre, F.

    1996-01-01

    Carnitine palmitoyltransferase (CPT) II deficiency, an inherited disorder of mitochondrial long-chain fatty-acid (LCFA) oxidation, results in two distinct clinical phenotypes, namely, an adult (muscular) form and an infantile (hepatocardiomuscular) form. The rationale of this phenotypic heterogeneity is poorly understood. The adult form of the disease is commonly ascribed to the Ser-113-Leu substitution in CPT II. Only few data are available regarding the molecular basis of the infantile form of the disease. We report herein a homozygous A-2399-C transversion predicting a Tyr-628-Ser substitution in a CPT II-deficient infant. In vitro expression of mutant cDNA in COS-1 cells demonstrated the responsibility of this mutation for the disease. Metabolic consequences of the SER-113-Leu and Tyr-628-Ser substitutions were studied in fibroblasts. The Tyr-628-Ser substitution (infantile form) resulted in a 10% CPT II residual activity, markedly impairing LCFA oxidation, whereas the Ser-113-Leu substitution (adult form) resulted in a 20% CPT II residual activity, with out consequence on LCFA oxidation. These data show that CPT II activity has to be reduced below a critical threshold in order for LCFA oxidation in fibroblasts to be impaired. The hypothesis that this critical threshold differs among tissues could provide a basis to explain phenotypic heterogeneity of CPT II deficiency. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:8651281

  8. Molecular analysis of genome instability in barley (Hordeum vulgare)

    International Nuclear Information System (INIS)

    A reliable protocol for regenerating barley from seedling explants, including leaf bases with a complete apical meristem, has been developed at the Institute of Genetic Engineering. The system was established with Bulgarian barley cultivars (Ruen, Karnobat, Obzor and Yubilei) and reconstructed genotypes (K. Gecheff IG). Pretreatment of the mature embryos with a high concentration of 2.4D generated valuable and stable genetic deviations in the regenerants. The brewery cultivar Ruen was selected as the model genotype. It has been demonstrated that genetic variations, such as higher yield, earlier maturation and lower protein content, have been induced and maintained for 5 years. Comparative experiments, including treatment of barley mature seeds with 60Co gamma rays (10 and 20 krad) and sodium azide (1.10-3 M and 5 x 10-4 M), were also carried out. The results obtained showed that both treatments stimulated calusogenesis and regeneration of the plants. Molecular markers such as proteins, restriction fragment length polymorphisms (RFLPs) and random amplified polymorphic DNAs (RAPDs) were applied in studies on the mutagenic effects of 2.4D, gamma rays and sodium azide, and a combination threof, on the quality and quantity of the genetic diversification generated in tissue culture of the Bulgarian barley cultivars Ruen, Karnobat, Obzor and Yubilei and the reconstructed genotypes

  9. Molecular analysis of carnitine palmitoyltransferase II deficiency with hepatocardiomuscular expression

    Energy Technology Data Exchange (ETDEWEB)

    Bonnefont, J.P.; Cepanec, C.; Leroux, J.P. [Unite INSERM, Paris (France)] [and others

    1996-05-01

    Carnitine palmitoyltransferase (CPT) II deficiency, an inherited disorder of mitochondrial long-chain fatty-acid (LCFA) oxidation, results in two distinct clinical act phenotypes, namely, an adult (muscular) form and an infantile (hepatocardiomuscular) form. The rationale of this phenotypic heterogeneity is poorly understood. The adult form of the disease is commonly ascribed to the Ser-113-Leu substitution in CPT II. Only few data are available regarding the molecular basis of the infantile form of the disease. We report herein a homozygous A-2399-C transversion predicting a Tyr-628-Ser substitution in a CPT II-deficient infant. In vitro expression of mutant cDNA in COS-1 cells demonstrated the responsibility of this mutation for the disease. Metabolic consequences of the Ser-113-Leu and Tyr-628-Ser substitutions were studied in fibroblasts. The Tyr-628-Ser substitution (infantile form) resulted in a 10% CPT II residual activity, markedly impairing LCFA oxidation, whereas the Ser-113-Leu substitution (adult form) resulted in a 20% CPT II residual activity, without consequence on LCFA oxidation. These data show that CPT II activity has to be reduced below a critical threshold in order for LCFA oxidation in fibroblasts to be impaired. The hypothesis that this critical threshold differs among tissues could provide a basis to explain phenotypic heterogeneity of CPT II deficiency. 32 refs., 5 figs.

  10. A molecular phylogenetic analysis of strombid gastropod morphological diversity.

    Science.gov (United States)

    Latiolais, Jared M; Taylor, Michael S; Roy, Kaustuv; Hellberg, Michael E

    2006-11-01

    The shells of strombid gastropods show a wide variety of forms, ranging from small and fusiform to large and elaborately ornamented with a strongly flared outer lip. Here, we present the first species-level molecular phylogeny for strombids and use the resulting phylogenetic framework to explore relationships between species richness and morphological diversity. We use portions of one nuclear (325 bp of histone H3) and one mitochondrial (640 bp of cytochrome oxidase I, COI) gene to infer relationships within the two most species-rich genera in the Strombidae: Strombus and Lambis. We include 32 species of Strombus, representing 10 of 11 extant subgenera, and 3 of the 9 species of Lambis, representing 2 of 3 extant subgenera. Maximum likelihood and Bayesian analyses of COI and of H3 and COI combined suggest Lambis is nested within a paraphyletic Strombus. Eastern Pacific and western Atlantic species of Strombus form a relatively recent monophyletic radiation within an older, paraphyletic Indo-West Pacific grade. Morphological diversity of subclades scales positively with species richness but does not show evidence of strong phylogenetic constraints. PMID:16839783

  11. Molecular analysis of fragile X syndrome in Antalya Province

    Directory of Open Access Journals (Sweden)

    Bilgen T

    2005-04-01

    Full Text Available Background: Detection of the (CGGn repeats in the FMR1 gene that cause the fragile X syndrome (FXS, has become a milestone for phenotype-genotype correlation in FXS. Aims: To screen the FMR1 gene CGG repeats in index cases with FXS and their family members in the Antalya Province. Setting and design: This study was prospectively conducted between January 200and March 2005 in Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz University, Antalya. Materials and Methods: A series of 132 cases from three hospitals in Antalya Province were studied. All cases were molecularly screened using non-radioactive Expand Long PCR method that was confirmed by Southern blotting. Results: Seventeen out of 132 cases were found to have a full mutation, including three that were mosaic for premutations/full mutations. Of the 132 cases, eight were found to have the premutation size of the CGG repeats. The remaining 107 cases were identified as normal. Conclusions: Due to premature ovarian failure and Fragile X premutation Tremor/Ataxia Syndrome related with the premutation, the detection of the premutation will provide valuable information both for clinical follow-up and genetic counseling. In conclusion, our data suggest that expansion of CGG repeats in the FMR1 gene can be analyzed by Expand Long PCR, an efficient and non-radioactive method that can be used to monitor the expansion of premutation to full mutation, which would eventually lead to reduce the FXS prevalence.

  12. Molecular analysis of manufactured gas plant soils for naphthalene mineralization

    International Nuclear Information System (INIS)

    New molecular tools are being developed and tested to ascertain the biodegradability of hazardous wastes by soil bacterial population. The potential for manufactured gas plant (MGP) soil bacterial populations to degrade naphthalene, as a component mixture of polynuclear aromatic hydrocarbons, was evaluated by the detection of a naphthalene biodegradative genotype by DNA probe hybridization with DNA extracts and colonies of cultured bacteria of the MGP soils. The activity of the naphthalene-degrading populations was evaluated by mineralization assays, 14CO2 production from 14C-naphthalene. Direct messenger RNA (mRNA) extraction from MGP soil was evaluated as an instantaneous measure of naphthalene catabolic gene expression in MGP soil. The bioavailability of naphthalene for bacterial degradation within the MGP soils was assessed by measuring the bioluminescent response of a naphthalene-lux catabolic reporter strain Pseudomonas fluorescens HK44 (pUTK21). DNA extracted from 5 MGP soils and 1 creosote-contaminated soil and hybridized with a nahA gene probe indicated that the naphthalene degradative genes were present in all samples in the range of 0.06 to 0.95 ng/100 μl DNA extract which was calculated to represent 3.58 x 108 to 1.05 x 1010 nahA positive cells/g soil. Phenanthrene, anthracene, and benzo(a)pyrene were mineralized also by some of the soils. NAH7 homologous messenger RNA transcripts were detectable in one MGP soil and in the creosote-contaminated soil

  13. Molecular analysis of childhood primitive neuroectodermal tumors defines markers associated with poor outcome

    DEFF Research Database (Denmark)

    Scheurlen, W G; Schwabe, G C; Joos, S; Mollenhauer, J; Sörensen, N; Kühl, J

    1998-01-01

    PURPOSE: The diagnostic and prognostic significance of well-defined molecular markers was investigated in childhood primitive neuroectodermal tumors (PNET). MATERIALS AND METHODS: Using microsatellite analysis, Southern blot analysis, and fluorescence in situ hybridization (FISH), 30 primary tumors...... and six CSF metastasis specimens were analyzed for loss of heterozygosity (LOH) of chromosomes 1q31, 6q, 9q22, 10q, 11, 16q22, and 17p13.1 and/or high-level amplification of the c-myc gene. Experimental data were compared with clinical stage and outcome. RESULTS: LOH of chromosome 17p13.1 was found...... most frequently (14 of 30 tumors, six of six CSF metastasis specimens); LOH of chromosomes 10q, 16q22, 11, 6, 9q22, and 1q31 was observed in 20.6%, 20%, 14.3%, 12%, 10%, and 0%, respectively. Eight of 32 tumors and CSF specimens showed amplification of c-myc. All tumors with amplification of c-myc were...

  14. Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations.

    Science.gov (United States)

    Heidari, Zahra; Roe, Daniel R; Galindo-Murillo, Rodrigo; Ghasemi, Jahan B; Cheatham, Thomas E

    2016-07-25

    Long time scale molecular dynamics (MD) simulations of biological systems are becoming increasingly commonplace due to the availability of both large-scale computational resources and significant advances in the underlying simulation methodologies. Therefore, it is useful to investigate and develop data mining and analysis techniques to quickly and efficiently extract the biologically relevant information from the incredible amount of generated data. Wavelet analysis (WA) is a technique that can quickly reveal significant motions during an MD simulation. Here, the application of WA on well-converged long time scale (tens of μs) simulations of a DNA helix is described. We show how WA combined with a simple clustering method can be used to identify both the physical and temporal locations of events with significant motion in MD trajectories. We also show that WA can not only distinguish and quantify the locations and time scales of significant motions, but by changing the maximum time scale of WA a more complete characterization of these motions can be obtained. This allows motions of different time scales to be identified or ignored as desired. PMID:27286268

  15. Molecular cytogenetic analysis of human blastocysts andcytotrophoblasts by multi-color FISH and Spectra Imaging analyses

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Jingly F.; Ferlatte, Christy; Baumgartner, Adolf; Jung,Christine J.; Nguyen, Ha-Nam; Chu, Lisa W.; Pedersen, Roger A.; Fisher,Susan J.; Weier, Heinz-Ulrich G.

    2006-02-08

    Numerical chromosome aberrations in gametes typically lead to failed fertilization, spontaneous abortion or a chromosomally abnormal fetus. By means of preimplantation genetic diagnosis (PGD), we now can screen human embryos in vitro for aneuploidy before transferring the embryos to the uterus. PGD allows us to select unaffected embryos for transfer and increases the implantation rate in in vitro fertilization programs. Molecular cytogenetic analyses using multi-color fluorescence in situ hybridization (FISH) of blastomeres have become the major tool for preimplantation genetic screening of aneuploidy. However, current FISH technology can test for only a small number of chromosome abnormalities and hitherto failed to increase the pregnancy rates as expected. We are in the process of developing technologies to score all 24 chromosomes in single cells within a 3 day time limit, which we believe is vital to the clinical setting. Also, human placental cytotrophoblasts (CTBs) at the fetal-maternal interface acquire aneuploidies as they differentiate to an invasive phenotype. About 20-50% of invasive CTB cells from uncomplicated pregnancies were found aneuploidy, suggesting that the acquisition of aneuploidy is an important component of normal placentation, perhaps limiting the proliferative and invasive potential of CTBs. Since most invasive CTBs are interphase cells and possess extreme heterogeneity, we applied multi-color FISH and repeated hybridizations to investigate individual CTBs. In summary, this study demonstrates the strength of Spectral Imaging analysis and repeated hybridizations, which provides a basis for full karyotype analysis of single interphase cells.

  16. Molecular genetic analysis of X-linked hypogammaglobulinemia and isolated growth hormone deficiency

    Energy Technology Data Exchange (ETDEWEB)

    Stewart, D.M.; Kurman, C.C.; Staudt, L.M. [Univ. of Brescia (Italy)] [and others

    1995-09-01

    In 1980 the clinical syndrome of X-linked hypogammaglobulinemia and isolated growth hormone deficiency (XLA/GHD) was described. XLA/GHD patients have reduced serum levels of Ig and normal cell-mediated immunity, and thus resemble patients with Bruton`s X-linked agammaglobulinemia (XLA). However, XLA/GHD patients also have isolated GHD. Mutations and deletions in the Bruton`s tyrosine kinase gene (BTK) are responsible for Bruton`s XLA. We investigated BTK gene expression in an XLA/GHD patient from the family originally described by Northern analysis, cDNA sequencing, and Western analysis of protein production using mAb to BTK. BTK mRNA was normal in size and abundance, and the mRNA sequence was normal over the coding region, except for a single silent mutation. BTK protein was present in normal amounts in PBMC of this patient. Thus, at the molecular level, XLA/GHD is a different disease entity from Bruton`s XLA. These results suggest that undescribed genes critical for B cell development and growth hormone production exist on the X chromosome. 17 refs., 4 figs.

  17. Productivity Analysis of Public and Private Airports: A Causal Investigation

    Science.gov (United States)

    Vasigh, Bijan; Gorjidooz, Javad

    2007-01-01

    Around the world, airports are being viewed as enterprises, rather than public services, which are expected to be managed efficiently and provide passengers with courteous customer services. Governments are, increasingly, turning to the private sectors for their efficiency in managing the operation, financing, and development, as well as providing security for airports. Operational and financial performance evaluation has become increasingly important to airport operators due to recent trends in airport privatization. Assessing performance allows the airport operators to plan for human resources and capital investment as efficiently as possible. Productivity measurements may be used as comparisons and guidelines in strategic planning, in the internal analysis of operational efficiency and effectiveness, and in assessing the competitive position of an airport in transportation industry. The primary purpose of this paper is to investigate the operational and financial efficiencies of 22 major airports in the United States and Europe. These airports are divided into three groups based on private ownership (7 British Airport Authority airports), public ownership (8 major United States airports), and a mix of private and public ownership (7 major European Union airports. The detail ownership structures of these airports are presented in Appendix A. Total factor productivity (TFP) model was utilized to measure airport performance in terms of financial and operational efficiencies and to develop a benchmarking tool to identify the areas of strength and weakness. A regression model was then employed to measure the relationship between TFP and ownership structure. Finally a Granger causality test was performed to determine whether ownership structure is a Granger cause of TFP. The results of the analysis presented in this paper demonstrate that there is not a significant relationship between airport TFP and ownership structure. Airport productivity and efficiency is

  18. Detachment of semiflexible polymer chains from a substrate: A molecular dynamics investigation

    Energy Technology Data Exchange (ETDEWEB)

    Paturej, J. [Leibniz-Institut of Poslymer Research Dresden, 01069 Dresden (Germany); Institute of Physics, University of Szczecin, Wielkopolska 15, 70451 Szczecin (Poland); Erbas, A. [Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208 (United States); Milchev, A. [Institute for Physical Chemistry, Bulgarian Academy of Sciences, 1113 Sofia (Bulgaria); Rostiashvili, V. G. [Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany)

    2014-12-07

    Using Molecular Dynamics simulations, we study the force-induced detachment of a coarse-grained model polymer chain from an adhesive substrate. One of the chain ends is thereby pulled at constant speed off the attractive substrate and the resulting saw-tooth profile of the measured mean force 〈f〉 vs height D of the end-segment over the plane is analyzed for a broad variety of parameters. It is shown that the observed characteristic oscillations in the 〈f〉-D profile depend on the bending and not on the torsional stiffness of the detached chains. Allowing for the presence of hydrodynamic interactions (HI) in a setup with explicit solvent and dissipative particle dynamics-thermostat, rather than the case of Langevin thermostat, one finds that HI have little effect on the 〈f〉-D profile. Also the change of substrate affinity with respect to the solvent from solvophilic to solvophobic is found to play negligible role in the desorption process. In contrast, a changing ratio ε{sub s}{sup B}/ε{sub s}{sup A} of the binding energies of A- and B-segments in the detachment of an AB-copolymer from adhesive surface strongly changes the 〈f〉-D profile whereby the B-spikes vanish when ε{sub s}{sup B}/ε{sub s}{sup A}<0.15. Eventually, performing an atomistic simulation of (bio)-polymers, we demonstrate that the simulation results, derived from our coarse-grained model, comply favorably with those from the all-atom simulation.

  19. Dynamic features of carboxy cytoglobin distal mutants investigated by molecular dynamics simulations.

    Science.gov (United States)

    Zhao, Cong; Du, Weihong

    2016-04-01

    Cytoglobin (Cgb) is a member of hemoprotein family with roles in NO metabolism, fibrosis, and tumourigenesis. Similar to other hemoproteins, Cgb structure and functions are markedly influenced by distal key residues. The sixth ligand His(81) (E7) is crucial to exogenous ligand binding, heme pocket conformation, and physiological roles of this protein. However, the effects of other key residues on heme pocket and protein biological functions are not well known. In this work, a molecular dynamics (MD) simulation study of two single mutants in CO-ligated Cgb (L46FCgbCO and L46VCgbCO) and two double mutants (L46FH81QCgbCO and L46VH81QCgbCO) was conducted to explore the effects of the key distal residues Leu(46)(B10) and His(81)(E7) on Cgb structure and functions. Results indicated that the distal mutation of B10 and E7 affected CgbCO dynamic properties on loop region fluctuation, internal cavity rearrangement, and heme motion. The distal conformation change was reflected by the distal key residues Gln(62) (CD3) and Arg(84)(E10). The hydrogen bond between heme propionates with CD3 or E10 residues were evidently influenced by B10/E7 mutation. Furthermore, heme pocket rearrangement was also observed based on the distal pocket volume and occurrence rate of inner cavities. The mutual effects of B10 and E7 residues on protein conformational rearrangement and other dynamic features were expressed in current MD studies of CgbCO and its distal mutants, suggesting their crucial role in heme pocket stabilization, ligand binding, and Cgb biological functions. The mutation of distal B10 and E7 residues affects the dynamic features of carboxy cytoglobin. PMID:26841790

  20. Using the fragment molecular orbital method to investigate agonist-orexin-2 receptor interactions.

    Science.gov (United States)

    Heifetz, Alexander; Aldeghi, Matteo; Chudyk, Ewa I; Fedorov, Dmitri G; Bodkin, Mike J; Biggin, Philip C

    2016-04-15

    The understanding of binding interactions between any protein and a small molecule plays a key role in the rationalization of affinity and selectivity and is essential for an efficient structure-based drug discovery (SBDD) process. Clearly, to begin SBDD, a structure is needed, and although there has been fantastic progress in solving G-protein-coupled receptor (GPCR) crystal structures, the process remains quite slow and is not currently feasible for every GPCR or GPCR-ligand complex. This situation significantly limits the ability of X-ray crystallography to impact the drug discovery process for GPCR targets in 'real-time' and hence there is still a need for other practical and cost-efficient alternatives. We present here an approach that integrates our previously described hierarchical GPCR modelling protocol (HGMP) and the fragment molecular orbital (FMO) quantum mechanics (QM) method to explore the interactions and selectivity of the human orexin-2 receptor (OX2R) and its recently discovered nonpeptidic agonists. HGMP generates a 3D model of GPCR structures and its complexes with small molecules by applying a set of computational methods. FMO allowsab initioapproaches to be applied to systems that conventional QM methods would find challenging. The key advantage of FMO is that it can reveal information on the individual contribution and chemical nature of each residue and water molecule to the ligand binding that normally would be difficult to detect without QM. We illustrate how the combination of both techniques provides a practical and efficient approach that can be used to analyse the existing structure-function relationships (SAR) and to drive forward SBDD in a real-world example for which there is no crystal structure of the complex available. PMID:27068972

  1. Spectroscopic Investigation of the Origin of Magnetic Bistability in Molecular Nanomagnets

    Science.gov (United States)

    van Slageren, Joris

    Molecular nanomagnets (MNMs) are coordination complexes consisting of one of more transition metal and/or f-element ions bridged and surrounded by organic ligands. Some of these can be magnetized in a magnetic field, and remain magnetized after the field is switched off. Because of this, MNMs have been proposed for magnetic data storage applications, where up to 1000 times higher data densities than currently possible can be obtained. Other MNMs were shown to display quantum coherence, and, as a consequence, are suitable as quantum bits. Quantum bits are the building blocks of a quantum computer, which will be able to carry out calculations that will never be possible with a conventional computer. The magnetic bistability of MNMs originates from the magnetic anisotropy of the magnetic ions, which creates an energy barrier between up and down orientations of the magnetic moment. Currently, most work in the area focuses on complexes of either lanthanide ions or low-coordinate transition metal ions. Synthetic chemical efforts have led to a large number of novel materials, but the rate of improvement has been slow. Therefore a better understanding of the origin of the magnetic anisotropy is clearly necessary. To this end we have applied a wide range of advanced spectroscopic techniques, ranging from different electron spin resonance techniques at frequencies up to the terahertz domain to optical techniques, including luminescence and magnetic circular dichroism spectroscopy. We will discuss two examples, one from the area of lanthanide MNMs, one a transition metal MNM (unpublished). This work was financially supported by DFG, DAAD and COST CM1006 EUFEN.

  2. Investigating Protoplanetary Carbon Reservoirs and Molecular Inheritance along a Galactic Gradient

    OpenAIRE

    Smith, R.L.; Blake, G. A.; Boogert, A. C. A.; Pontoppidan, K. M.; Lockwood, A. C.

    2015-01-01

    High-resolution observations of CO gas toward young stellar objcts (YSOs) enable valuable comparisons between forming protoplanetry systems and solar system material, as well as robust evaluation of early protoplanetry chemical reservoirs [1-7]. Precise isotopic observations of carbon and oxygen in the gas-phase have largely targeted low-mass YSOs in our local solar neighborhood [1,2]. Yet, precise investigations of YSOs ranging in size, luminosity, and Galactic locati...

  3. Chromosomal Rearrangements in Salmonella enterica Serotype Typhi Affecting Molecular Typing in Outbreak Investigations

    OpenAIRE

    Echeita, M. A.; Usera, M A

    1998-01-01

    Salmonella enterica serotype Typhi strains belonging to eight different outbreaks of typhoid fever that occurred in Spain between 1989 and 1994 were analyzed by ribotyping and pulsed-field gel electrophoresis. For three outbreaks, two different patterns were detected for each outbreak. The partial digestion analysis by the intron-encoded endonuclease I-CeuI of the two different strains from each outbreak provided an excellent tool for examining the organization of the genomes of epidemiologic...

  4. Spectroscopic investigations and molecular docking study of 3-(1H-imidazol-1-yl)-1-phenylpropan-1-one, a potential precursor to bioactive agents

    Science.gov (United States)

    Al-Alshaikh, Monirah A.; Mary Y, Sheena; Panicker, C. Yohannan; Attia, Mohamed I.; El-Emam, Ali A.; Alsenoy, C. Van

    2016-04-01

    The optimized molecular structure, vibrational wavenumbers, corresponding vibrational assignments of 3-(1H-imidazol-1-yl)-1-phenylpropan-1-one have been investigated theoretically and experimentally. The calculated geometrical parameters of the title compound are in agreement with the reported XRD data. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. Molecular electrostatic potential was performed by the DFT method and from the MEP plot, it is evident that the negative charge covers the carbonyl group and the nitrogen atom N3 of the imidazole ring and the positive region is over the remaining portions of the molecule. The first and second hyperpolarizabilities are calculated and the first hyperpolarizability of the title compound is 16.99 times that of standard NLO material urea and the title compound and its derivatives are good object for further studies in nonlinear optics. The docked ligand title compound forms a stable complex with plasmodium falciparum and gives a binding affinity value of -5.5 kcal/mol and the preliminary results suggest that the compound might exhibit antimalarial activity against plasmodium falciparum.

  5. The experimental investigation and thermodynamic analysis of vortex tubes

    Science.gov (United States)

    Celik, Adem; Yilmaz, Mehmet; Kaya, Mehmet; Karagoz, Sendogan

    2016-05-01

    In the present study, it was aimed to produce a fundamental i nformation and to investigate the effects of various design parameters on tube performance characteristics by setting up vortex tube experimental system in order to study the parameters predetermined for the design of vortex tubes and by conducting thermodynamic analysis. According to the findings of experiments, as the mass flow rate of cold flow increases (yc) temperature of cold flow also increases, while the temperature of warm flow increases approximately to yc = 0.6 and then decreases. Increases in inlet pressure, inlet nozzle surface and diameter of the cold outlet orifice increased temperature differences between cold and warm flows. Tube with L/D = 10 showed better performance than with L/D = 20. The finding that irreversibility parameter is very close to critical threshold of irreversibility proved that process in vortex tube is considerably irreversible. Coefficient of performance (COP) values in vortex tube were much lower than other heating and cooling systems. This situation may show that vortex tubes are convenient in the processes where productivity is at the second rate compared to other factors.

  6. Investigation and risk factor analysis of hyperuricemia in pilots

    Directory of Open Access Journals (Sweden)

    Hong-yu MA

    2012-01-01

    Full Text Available Objective  To investigate the incidence of hyperuricemia in military pilots and the relationship between hyperuricemia and other related risk factors of cardiovascular diseases. Methods  A total of 2563 pilots, who had undergone a regular physical examination in the Air Force General Hospital from 2005 to 2010, participated in the current study. The participants were divided into high serum uric acid (UA group (hyperuricemia group, UA >420µmol/L, n=294 and normal UA group (n=2269. The incidence rates of hypertension, hyperglycemia, and hyperlipemia were compared between these two groups. The dependent variable was serum UA level of the pilots. Other indices included the total cholesterol (CHO, triglycerides (TG, high density lipoprotein (HDL, low density lipoprotein (LDL, fasting blood glucose (FBG, systolic blood pressure (SBP, diastolic blood pressure (DBP, smoking, body weight, and flight time as independent variable. Logistic multivariate regression analysis was conducted to determine the relationship between UA level and these indexes. Results  The incidence rates of hypertension, hypercholesterolemia, hypertriglyceridemia, low HDL, and high LDL were significantly higher in hyperuricemia group than in normal UA group (POR=1.637, POR=1.025, POR=1.046, PConclusion  The serum UA of pilots is closely related to the risk factors of other cardiovascular diseases.

  7. Elemental investigation of Syrian medicinal plants using PIXE analysis

    International Nuclear Information System (INIS)

    Particle induced X-ray emission (PIXE) technique has been employed to perform elemental analysis of K, Ca, Mn, Fe, Cu, Zn, Br and Sr for Syrian medicinal plants used traditionally to enhance the body immunity. Plant samples were prepared in a simple dried base. The results were verified by comparing with those obtained from both IAEA-359 and IAEA-V10 reference materials. Relative standard deviations are mostly within ±5-10% suggest good precision. A correlation between the elemental content in each medicinal plant with its traditional remedial usage has been proposed. Both K and Ca are found to be the major elements in the samples. Fe, Mn and Zn have been detected in good levels in most of these plants clarifying their possible contribution to keep the body immune system in good condition. The contribution of the elements in these plants to the dietary recommended intakes (DRI) has been evaluated. Advantages and limitations of PIXE analytical technique in this investigation have been reviewed.

  8. Pharmacognostical Investigation and Physicochemical Analysis of Celastrus paniculatus Willd. Leaves

    Institute of Scientific and Technical Information of China (English)

    Kalaskar Mohan G.; Saner Sachin Y.; Pawar Manohar V.; Rokade Dipak L; Surana Sanjay J

    2012-01-01

    Objective: Celastrus paniculatus Willd. is an important Indian medicinal plant and widely used in the treatment of the verity of disease and well explored scientifically for their pharmacological properties. The current study was therefore carried out to provide requisite pharmacognostic details about the plant. Methods: Pharmacognostic investigation of the fresh, powdered and anatomical sections of the leaves of Celastrus paniculatus Willd. was carried out to determine its morphological, anatomical, and phytochemical diagnostic features. Quantitative diagnostic characteristics, physicochemical properties and quantitative phytochemical measures were established. Results: The morphology of leave reveled, leaves are alternate, acute, acuminate or obtuse, rounded with cuncate base,; margin is finely crenate, venation is reticulate. The microscopy reveals the dorsiventral type of leave, with anomocytic stomata, covering (lower epidermis) and glandular (upper epidermis) trichomes. The collateral vascular bundle crowned with sclerenchymatous fiber, ideoblast of calcium oxalate. The Quantitative diagnostic characteristics such as leaf constant were measured. Physicochemical properties such as ash, extractive values and fluorescence analysis were established. Quantitative phytochemical revealed presence of carbohydrates, fixed oil, glycosides, cumarines, tannins, flavonoids, saponins, steroids and triterpenoids. Conclusion: The results of the study could be useful in setting some diagnostic indices for the identification and preparation of a monograph of the plant.

  9. Elemental investigation of Syrian medicinal plants using PIXE analysis

    Science.gov (United States)

    Rihawy, M. S.; Bakraji, E. H.; Aref, S.; Shaban, R.

    2010-09-01

    Particle induced X-ray emission (PIXE) technique has been employed to perform elemental analysis of K, Ca, Mn, Fe, Cu, Zn, Br and Sr for Syrian medicinal plants used traditionally to enhance the body immunity. Plant samples were prepared in a simple dried base. The results were verified by comparing with those obtained from both IAEA-359 and IAEA-V10 reference materials. Relative standard deviations are mostly within ±5-10% suggest good precision. A correlation between the elemental content in each medicinal plant with its traditional remedial usage has been proposed. Both K and Ca are found to be the major elements in the samples. Fe, Mn and Zn have been detected in good levels in most of these plants clarifying their possible contribution to keep the body immune system in good condition. The contribution of the elements in these plants to the dietary recommended intakes (DRI) has been evaluated. Advantages and limitations of PIXE analytical technique in this investigation have been reviewed.

  10. Investigation and analysis on fatigue status of military pilots

    Directory of Open Access Journals (Sweden)

    Jian-sheng GUO

    2012-03-01

    Full Text Available Objective To investigate the fatigue status and its characteristics and influential factors of military pilots. Methods Questionnaire survey was conducted on 924 military pilots by using Fatigue Assessment Instrument (FAI and Fatigue Scale (FS-14, χ2 test and Pearson correlation analysis were performed on the data results with SPSS 17.0 software. Results The findings of fatigue status indicated 343 subjects (37.1% with positive fatigue symptoms and 581 subjects (62.9% with negative fatigue symptoms. FAI factor 1 (severity of fatigue, factor 2 (mental fatigue factor, factor 3 (consequence of fatique and the total score, FS-14 factor 1 (physical fatigue factor and the total score in fatigue-positive group were all higher than those in fatiguenegative group, and the differences were all statistically significant (P 0.05 in the possibility of developing fatigue symptoms between subjects with different aircraft types. Age and flight time were positively correlated with factor 1 and total score in FAI and factor 1, factor 2 and total score in FS-14. However, the aircraft type was associated with neither the individual factors and total score in FAI nor the individual factors and total score in FS-14. Conclusion It is common for military pilots to develop fatigue symptoms, characterized by obvious manifestations of severity, environmental specificity, consequences of fatigue and physical fatigue, and the possibilities of developing fatigue symptoms for different ages and flight time were different.

  11. Molecular cloning and expression analysis on LPL of Coilia nasus.

    Science.gov (United States)

    Wang, Meiyao; Xu, Dongpo; Liu, Kai; Yang, Jian; Xu, Pao

    2016-06-01

    Coilia nasus is one important commercial anadromous species which mainly distributed in the Yangtze River in China. At present, it has been on the "National Key Protective Species List" because of its severe resource damage. Lipid metabolism is very important during its long-distance migration. To make further research on lipid metabolism of C.nasus, we cloned lipoprotein lipase gene with homologous cloning method. A full-length cDNA of LPL of C.nasus was cloned from liver which covered 3537bp with a 1519bp open reading frame encoding 505 deduced amino acids whose molecular mass was 57.5kDa and theoretical isoelectric point was 7.58. The deduced amino acids had high similarity with the reported LPL sequence of other species. It had typical conserved domain of LPL protein containing catalytic triad, N-linked glycosylation sites and conserved heparin-binding site, etc. We adopted quantitative real-time RT-PCR method to detect the mRNA expression of LPL of C.nasus in ten tissues including mesenteric adipose, liver, muscle, stomach, spleen, heart, head kidney, trunk kidney, gill and brain with β-actin as internal reference. LPL expressed in all the detected tissues. The highest expression was in mesenteric adipose, and followed by liver, muscle, stomach. Lipid expressed lowly in spleen, heart, head kidney, trunk kidney, gill and brain. The research on the cloning and differential expression of LPL of C.nasus will lay foundation for further research on lipid metabolism of C.nasus. PMID:26877109

  12. Conventional and molecular investigation of Shigella isolates in relation to an outbreak in the area of Isfahan, Iran.

    Directory of Open Access Journals (Sweden)

    Ramin Dibaj

    2013-12-01

    Full Text Available Over 165 million cases of shigellosis occur in the world each year, mostly in developing countries. Outbreaks of shigellosis are associated with poor sanitation, natural calamities, contaminated food and crowded living conditions. In late summer 2006, during the final stage of an outbreak of shigellosis at a vast region of Isfahan province, Naein & Ardestan, our laboratory was assigned to investigate the outbreak in order to determine the causative agent.A total of 146 rectal swabs which had been collected from the patients by local laboratories on separate days were screened using a battery of conventional and molecular tests.Thirteen specimens tested positive for Shigella spp. They were identified as S. sonnei (6, 46.1%, S. dysenteriae (4, 30.8%, S. flexneri (2, 15.4% and Shigella spp (1, 7.7% by conventional and molecular microbiological tests. According to ribotyping results the isolates were grouped into 3 distinct clusters encompassing the majority of isolates and a single line of descent representing isolate S122 which was nonreactive with any Shigella polyvalent antisera.This diarrheal outbreak appeared to be the result of shigellosis. Despite the fact that Shigella sonnei was the predominant organism isolated from patients, the causative agent of outbreak diarrhea remains obscure, since other Shigella species were also involved. The serologic testing supports this conclusion, as do the molecular patterns of the Shigella isolates. Having considered the time of investigation which was in the late stage of the outbreak, it was very likely that a collection of endemic and epidemic clinical samples was screened resulting in isolation of various Shigella species.

  13. Computational investigation of locked nucleic acid (LNA) nucleotides in the active sites of DNA polymerases by molecular docking simulations.

    Science.gov (United States)

    Poongavanam, Vasanthanathan; Madala, Praveen K; Højland, Torben; Veedu, Rakesh N

    2014-01-01

    Aptamers constitute a potential class of therapeutic molecules typically selected from a large pool of oligonucleotides against a specific target. With a scope of developing unique shorter aptamers with very high biostability and affinity, locked nucleic acid (LNA) nucleotides have been investigated as a substrate for various polymerases. Various reports showed that some thermophilic B-family DNA polymerases, particularly KOD and Phusion DNA polymerases, accepted LNA-nucleoside 5'-triphosphates as substrates. In this study, we investigated the docking of LNA nucleotides in the active sites of RB69 and KOD DNA polymerases by molecular docking simulations. The study revealed that the incoming LNA-TTP is bound in the active site of the RB69 and KOD DNA polymerases in a manner similar to that seen in the case of dTTP, and with LNA structure, there is no other option than the locked C3'-endo conformation which in fact helps better orienting within the active site. PMID:25036012

  14. Molecular diagnostic analysis for Huntington's disease: a prospective evaluation.

    OpenAIRE

    MacMillan, J C; Davies, P; P.S. Harper

    1995-01-01

    The availability of mutation analysis for the CAG repeat expansion associated with Huntington's disease has prompted clinicians in various specialties to request testing of samples from patients displaying clinical features that might be attributable to Huntington's disease. A series of 38 cases presenting with clinical features thought possibly to be due to Huntington's disease were analysed prospectively. In 53% of such cases presenting initially with chorea and 62.5% with psychiatric sympt...

  15. Employing Power Graph Analysis to Facilitate Modeling Molecular Interaction Networks

    Directory of Open Access Journals (Sweden)

    Momchil Nenov

    2015-04-01

    Full Text Available Mathematical modeling is used to explore and understand complex systems ranging from weather patterns to social networks to gene-expression regulatory mechanisms. There is an upper limit to the amount of details that can be reflected in a model imposed by finite computational resources. Thus, there are methods to reduce the complexity of the modeled system to its most significant parameters. We discuss the suitability of clustering techniques, in particular Power Graph Analysis as an intermediate step of modeling.

  16. Tracking fetal development through molecular analysis of maternal biofluids☆

    OpenAIRE

    Edlow, Andrea G; Bianchi, Diana W.

    2012-01-01

    Current monitoring of fetal development includes fetal ultrasonography, chorionic villus sampling or amniocentesis for chromosome analysis, and maternal serum biochemical screening for analytes associated with aneuploidy and open neural tube defects. Over the last 15 years, significant advances in noninvasive prenatal diagnosis (NIPD) via cell-free fetal (cff) nucleic acids in maternal plasma have resulted in the ability to determine fetal sex, RhD genotype, and aneuploidy. Cff nucleic acids ...

  17. A hardware investigation of robotic SPECT for functional and molecular imaging onboard radiation therapy systems

    International Nuclear Information System (INIS)

    Purpose: To construct a robotic SPECT system and to demonstrate its capability to image a thorax phantom on a radiation therapy flat-top couch, as a step toward onboard functional and molecular imaging in radiation therapy. Methods: A robotic SPECT imaging system was constructed utilizing a gamma camera detector (Digirad 2020tc) and a robot (KUKA KR150 L110 robot). An imaging study was performed with a phantom (PET CT PhantomTM), which includes five spheres of 10, 13, 17, 22, and 28 mm diameters. The phantom was placed on a flat-top couch. SPECT projections were acquired either with a parallel-hole collimator or a single-pinhole collimator, both without background in the phantom and with background at 1/10th the sphere activity concentration. The imaging trajectories of parallel-hole and pinhole collimated detectors spanned 180° and 228°, respectively. The pinhole detector viewed an off-centered spherical common volume which encompassed the 28 and 22 mm spheres. The common volume for parallel-hole system was centered at the phantom which encompassed all five spheres in the phantom. The maneuverability of the robotic system was tested by navigating the detector to trace the phantom and flat-top table while avoiding collision and maintaining the closest possible proximity to the common volume. The robot base and tool coordinates were used for image reconstruction. Results: The robotic SPECT system was able to maneuver parallel-hole and pinhole collimated SPECT detectors in close proximity to the phantom, minimizing impact of the flat-top couch on detector radius of rotation. Without background, all five spheres were visible in the reconstructed parallel-hole image, while four spheres, all except the smallest one, were visible in the reconstructed pinhole image. With background, three spheres of 17, 22, and 28 mm diameters were readily observed with the parallel-hole imaging, and the targeted spheres (22 and 28 mm diameters) were readily observed in the pinhole

  18. A hardware investigation of robotic SPECT for functional and molecular imaging onboard radiation therapy systems

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Susu, E-mail: susu.yan@duke.edu; Tough, MengHeng [Medical Physics Graduate Program, Duke University, Durham, North Carolina 27710 (United States); Bowsher, James; Yin, Fang-Fang [Medical Physics Graduate Program, Duke University, Durham, North Carolina 27710 and Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710 (United States); Cheng, Lin [Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710 (United States)

    2014-11-01

    Purpose: To construct a robotic SPECT system and to demonstrate its capability to image a thorax phantom on a radiation therapy flat-top couch, as a step toward onboard functional and molecular imaging in radiation therapy. Methods: A robotic SPECT imaging system was constructed utilizing a gamma camera detector (Digirad 2020tc) and a robot (KUKA KR150 L110 robot). An imaging study was performed with a phantom (PET CT Phantom{sup TM}), which includes five spheres of 10, 13, 17, 22, and 28 mm diameters. The phantom was placed on a flat-top couch. SPECT projections were acquired either with a parallel-hole collimator or a single-pinhole collimator, both without background in the phantom and with background at 1/10th the sphere activity concentration. The imaging trajectories of parallel-hole and pinhole collimated detectors spanned 180° and 228°, respectively. The pinhole detector viewed an off-centered spherical common volume which encompassed the 28 and 22 mm spheres. The common volume for parallel-hole system was centered at the phantom which encompassed all five spheres in the phantom. The maneuverability of the robotic system was tested by navigating the detector to trace the phantom and flat-top table while avoiding collision and maintaining the closest possible proximity to the common volume. The robot base and tool coordinates were used for image reconstruction. Results: The robotic SPECT system was able to maneuver parallel-hole and pinhole collimated SPECT detectors in close proximity to the phantom, minimizing impact of the flat-top couch on detector radius of rotation. Without background, all five spheres were visible in the reconstructed parallel-hole image, while four spheres, all except the smallest one, were visible in the reconstructed pinhole image. With background, three spheres of 17, 22, and 28 mm diameters were readily observed with the parallel-hole imaging, and the targeted spheres (22 and 28 mm diameters) were readily observed in the

  19. Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation.

    Science.gov (United States)

    Feng, Yuan; Huang, Jing; Kim, Seongheun; Shim, Ji Hyun; MacKerell, Alexander D; Ge, Nien-Hui

    2016-06-23

    We have studied the structure of (Ala)5, a model unfolded peptide, using a combination of 2D IR spectroscopy and molecular dynamics (MD) simulation. Two different isotopomers, each bis-labeled with (13)C═O and (13)C═(18)O, were strategically designed to shift individual site frequencies and uncouple neighboring amide-I' modes. 2D IR spectra taken under the double-crossed ⟨π/4, -π/4, Y, Z⟩ polarization show that the labeled four-oscillator systems can be approximated by three two-oscillator systems. By utilizing the different polarization dependence of diagonal and cross peaks, we extracted the coupling constants and angles between three pairs of amide-I' transition dipoles through spectral fitting. These parameters were related to the peptide backbone dihedral angles through DFT calculated maps. The derived dihedral angles are all located in the polyproline-II (ppII) region of the Ramachandran plot. These results were compared to the conformations sampled by Hamiltonian replica-exchange MD simulations with three different CHARMM force fields. The C36 force field predicted that ppII is the dominant conformation, consistent with the experimental findings, whereas C22/CMAP predicted similar population for α+, β, and ppII, and the polarizable Drude-2013 predicted dominating β structure. Spectral simulation based on MD representative conformations and structure ensembles demonstrated the need to include multiple 2D spectral features, especially the cross-peak intensity ratio and shape, in structure determination. Using 2D reference spectra defined by the C36 structure ensemble, the best spectral simulation is achieved with nearly 100% ppII population, although the agreement with the experimental cross-peak intensity ratio is still insufficient. The dependence of population determination on the choice of reference structures/spectra and the current limitations on theoretical modeling relating peptide structures to spectral parameters are discussed. Compared

  20. Molecular genetic investigations on Balantidium ctenopharyngodoni Chen, 1955, a parasite of the grass carp (Ctenopharyngodon idella).

    Science.gov (United States)

    Marton, Szilvia; Bányai, Krisztián; Forró, Barbara; Lengyel, György; Székely, Csaba; Varga, Ádám; Molnár, Kálmán

    2016-06-01

    Balantidium ctenopharyngodoni is a common ciliate in Hungary, infecting the hindgut of grass carp (Ctenopharyngodon idella), a cyprinid fish of Chinese origin. Although data have already been presented on its occasional pathogenic effect on the endothelium of the host, generally it is a harmless inhabitant of the gut. Phylogenetic analysis of the 18S rDNA and ITS fragments of this protozoan proved that it is in the closest phylogenetic relationship with endocommensalist and symbiont ciliates of mammals feeding on large volumes of green forage, in a similar way as Balantidium spp. known from algae-eating marine fishes. PMID:27342092

  1. Molecular Investigations of Rickettsia helvetica Infection in Dogs, Foxes, Humans, and Ixodes Ticks▿

    OpenAIRE

    Boretti, F S; Perreten, A; Meli, M. L.; Cattori, V; Willi, B; Wengi, N; Hornok, S.; Honegger, H; Hegglin, D; Woelfel, R.; Reusch, C E; Lutz, H.; Hofmann-Lehmann, R.

    2009-01-01

    Rickettsia helvetica, a tick-borne member of the spotted-fever-group rickettsiae, is a suspected pathogen in humans; however, its role in animals is unknown. The aims of this study were to establish a R. helvetica-specific real-time TaqMan PCR assay and apply it to the analysis of tick vectors (to determine potential exposure risk) and blood samples from Canidae and humans (to determine prevalence of infection). The newly designed 23S rRNA gene assay for R. helvetica was more sensitive than a...

  2. Molecular mobility in Medicago truncatula seed during early stage of germination: Neutron scattering and NMR investigations

    International Nuclear Information System (INIS)

    Highlights: • Neutron scattering and NMR approaches were used to characterize seed germination. • A parallel between macromolecular motions and water dynamics was established. • Freezing/thawing cycle revealed a hysteresis connected to the seed hydration level. - Abstract: First hours of Medicago truncatula (MT) seeds germination were investigated using elastic incoherent neutron scattering (EINS) and nuclear magnetic resonance (NMR), to follow respectively how macromolecular motions and water mobility evolve when water permeates into the seed. From EINS results, it was shown that there is an increase in macromolecular mobility with the water uptake. Changes in NMR relaxation parameters reflected microstructural changes associated with the recovery of the metabolic processes. The EINS investigation of the effect of temperature on macromolecular motions showed that there is a relationship between the amount of water in the seeds and the effect of freezing–thawing cycle. The NMR relaxometry results obtained at 253 K allowed establishing possible link between the freezing of water molecules tightly bound to macromolecules and their drastic motion restriction around 250 K, as observed with EINS at the highest water content

  3. Molecular mobility in Medicago truncatula seed during early stage of germination: Neutron scattering and NMR investigations

    Energy Technology Data Exchange (ETDEWEB)

    Falourd, Xavier [UR1268 Biopolymères Interactions Assemblages, INRA, F-44316 Nantes (France); Natali, Francesca [CNR-IOM-OGG, c/o Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9 (France); Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9 (France); Peters, Judith [Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9 (France); Université Joseph Fourier UFR PhITEM, BP 53, 38041 Grenoble Cedex 9 (France); Institut de Biologie Structurale, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1 (France); Foucat, Loïc, E-mail: Loic.Foucat@nantes.inra.fr [UR1268 Biopolymères Interactions Assemblages, INRA, F-44316 Nantes (France)

    2014-01-15

    Highlights: • Neutron scattering and NMR approaches were used to characterize seed germination. • A parallel between macromolecular motions and water dynamics was established. • Freezing/thawing cycle revealed a hysteresis connected to the seed hydration level. - Abstract: First hours of Medicago truncatula (MT) seeds germination were investigated using elastic incoherent neutron scattering (EINS) and nuclear magnetic resonance (NMR), to follow respectively how macromolecular motions and water mobility evolve when water permeates into the seed. From EINS results, it was shown that there is an increase in macromolecular mobility with the water uptake. Changes in NMR relaxation parameters reflected microstructural changes associated with the recovery of the metabolic processes. The EINS investigation of the effect of temperature on macromolecular motions showed that there is a relationship between the amount of water in the seeds and the effect of freezing–thawing cycle. The NMR relaxometry results obtained at 253 K allowed establishing possible link between the freezing of water molecules tightly bound to macromolecules and their drastic motion restriction around 250 K, as observed with EINS at the highest water content.

  4. Functional and Structural Analyses of CYP1B1 Variants Linked to Congenital and Adult-Onset Glaucoma to Investigate the Molecular Basis of These Diseases.

    Science.gov (United States)

    Banerjee, Antara; Chakraborty, Subhadip; Chakraborty, Abhijit; Chakrabarti, Saikat; Ray, Kunal

    2016-01-01

    Glaucoma, the leading cause of irreversible blindness, appears in various forms. Mutations in CYP1B1 result in primary congenital glaucoma (PCG) by an autosomal recessive mode of inheritance while it acts as a modifier locus for primary open angle glaucoma (POAG). We investigated the molecular basis of the variable phenotypes resulting from the defects in CYP1B1 by using subclones of 23 CYP1B1 mutants reported in glaucoma patients, in a cell based system by measuring the dual activity of the enzyme to metabolize both retinol and 17β-estradiol. Most variants linked to POAG showed low steroid metabolism while null or very high retinol metabolism was observed in variants identified in PCG. We examined the translational turnover rates of mutant proteins after the addition of cycloheximide and observed that the levels of enzyme activity mostly corroborated the translational turnover rate. We performed extensive normal mode analysis and molecular-dynamics-simulations-based structural analyses and observed significant variation of fluctuation in certain segmental parts of the mutant proteins, especially at the B-C and F-G loops, which were previously shown to affect the dynamic behavior and ligand entry/exit properties of the cytochrome P450 family of proteins. Our molecular study corroborates the structural analysis, and suggests that the pathologic state of the carrier of CYP1B1 mutations is determined by the allelic state of the gene. To our knowledge, this is the first attempt to dissect biological activities of CYP1B1 for correlation with congenital and adult onset glaucomas. PMID:27243976

  5. Topological analysis of third-row main group dicarbides with molecular oxygen: A theoretical study

    International Nuclear Information System (INIS)

    Topological analysis of third-row main group dicarbides with molecular oxygen is calculated using density functional theory (DFT). In addition, Bader topological analysis show large electron density at the bond critical point (BCP) between carbon of C2X cluster and oxygen (of molecular oxygen), inferring that the C–O bonding to be more shared-type as compared to that of X - O bonding. This fact is also confirmed by larger positive value of electron density (ρ) and negative ∇2ρ. Similar conclusion is also obtained from the delocalization index (δ) which, in the case of C-O is found to be comparatively large

  6. Analysis of molecular aberrations of Wnt pathway gladiators in colorectal cancer in the Kashmiri population

    Directory of Open Access Journals (Sweden)

    Sameer A

    2011-07-01

    Full Text Available Abstract The development and progression of colorectal cancer (CRC is a multi-step process, and the Wnt pathways with its two molecular gladiators adenomatous polyposis coli (APC and β-catenin plays an important role in transforming a normal tissue into a malignant one. In this study, we aimed to investigate the role of aberrations in the APC and β-catenin genes in the pathogenesis of CRC in the Kashmir valley, and to correlate it with various clinicopathological variables. We examined the paired tumour and normal-tissue specimens of 86 CRC patients for the occurrence of aberrations in the mutation cluster region (MCR of the APC gene and exon 3 of the β-catenin gene by polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP and/or PCR-direct sequencing. Analysis of promoter hypermethylation of the APC gene was also carried out using methylation-specific PCR (MS-PCR. The overall mutation rate of the MCR of the APC gene among 86 CRC cases was 12.8 per cent (11 of 86. Promoter hypermethylation of APC was observed in 54.65 per cent (47 of 86 of cases. Furthermore, we found a significant association between tumour location, tumour grade and node status and the methylation status of the APC gene (p ≤ 0.05. Although the number of mutations in the APC and β-catenin genes in our CRC cases was very low, the study confirms the role of epigenetic gene silencing of the pivotal molecular gladiator, APC, of the Wnt pathway in the development of CRC in the Kashmiri population.

  7. Molecular characterization and association analysis of porcine PANE1 gene

    DEFF Research Database (Denmark)

    Huang, Honggang; Deng, Hong; Yang, Yiling;

    2010-01-01

    PANE1, allele frequencies determination in different pig breeds and association analysis were performed on this SNP BssHII by PCR-restriction fragment length polymorphism assay. Allele frequencies varied greatly among different pig breeds, and the association results indicated that piglet individuals......-polymerase chain reaction revealed that porcine PANE1 gene was differently expressed in seven diverse tissues, showed highest expression level in lymph node, but lowest in kidney. A single nucleotide polymorphism (SNP) (C>A) which can be digested by restriction enzyme BssHII was identified in intron 1 of porcine...

  8. Molecular analysis of the Noggin (NOG) gene in holoprosencephaly patients.

    Science.gov (United States)

    Srivastava, Kshitij; Hu, Ping; Solomon, Benjamin D; Ming, Jeffrey E; Roessler, Erich; Muenke, Maximilian

    2012-06-01

    Holoprosencephaly (HPE) is the most common structural anomaly of the human forebrain. Various genetic and teratogenic causes have been implicated in its pathogenesis. A recent report in mice described Noggin (NOG) as a candidate gene involved in the etiogenesis of microform HPE. Here, we present for the first time genetic analysis of a large HPE cohort for sequence variations in NOG. On the basis of our study, we conclude that mutations in the coding region of NOG are rare, and play at most an uncommon role in human HPE. PMID:22503063

  9. Molecular Analysis of the Noggin (NOG) Gene in Holoprosencephaly Patients

    OpenAIRE

    Srivastava, Kshitij; Hu, Ping; Solomon, Benjamin D.; Ming, Jeffrey E.; Roessler, Erich; Muenke, Maximilian

    2012-01-01

    Holoprosencephaly (HPE) is the most common structural anomaly of the human forebrain. Various genetic and teratogenic causes have been implicated in its pathogenesis. A recent report in mice described Noggin (NOG) as a candidate gene involved in the etiogenesis of microform HPE. Here, we present for the first time genetic analysis of a large HPE cohort for sequence variations in NOG. On the basis of our study, we conclude that mutations in the coding region of NOG are rare, and play at most a...

  10. Identification and in silico analysis of the Citrus HSP70 molecular chaperone gene family

    Directory of Open Access Journals (Sweden)

    Luciano G. Fietto

    2007-01-01

    Full Text Available The completion of the genome sequencing of the Arabidopsis thaliana model system provided a powerful molecular tool for comparative analysis of gene families present in the genome of economically relevant plant species. In this investigation, we used the sequences of the Arabidopsis Hsp70 gene family to identify and annotate the Citrus Hsp70 genes represented in the CitEST database. Based on sequence comparison analysis, we identified 18 clusters that were further divided into 5 subgroups encoding four mitochondrial mtHsp70s, three plastid csHsp70s, one ER luminal Hsp70 BiP, two HSP110/SSE-related proteins and eight cytosolic Hsp/Hsc70s. We also analyzed the expression profile by digital Northern of each Hsp70 transcript in different organs and in response to stress conditions. The EST database revealed a distinct population distribution of Hsp70 ESTs among isoforms and across the organs surveyed. The Hsp70-5 isoform was highly expressed in seeds, whereas BiP, mitochondrial and plastid HSp70 mRNAs displayed a similar expression profile in the organs analyzed, and were predominantly represented in flowers. Distinct Hsp70 mRNAs were also differentially expressed during Xylella infection and Citrus tristeza viral infection as well as during water deficit. This in silico study sets the groundwork for future investigations to fully characterize functionally the Citrus Hsp70 family and underscores the relevance of Hsp70s in response to abiotic and biotic stresses in Citrus.

  11. Molecular monolayer structures formed on vicinal surfaces as investigated by scanning tunneling microscopy

    Science.gov (United States)

    Avila-Bront, Lynna Gabriela

    The increasing demand for efficient cancer treatment inspired the researchers for new investigations about an alternative treatment of cancer. Microwave ablation is the newest ablation technique to cure cancer. This method is minimally noninvasive and inexpensive compared to the other methods. However, current microwave ablation systems suffer due to narrow band nature of the antenna (dipole or slot) placed at the tip of the probe. Therefore, this study developed an ultra-wide band ablation probe that operates from 300 MHz to 10 GHz. For this purpose, a small wide band antenna is designed to place at the tip of the probe and fabricated. These probes are tested at ISM frequencies (2.4 GHz and 5.8 GHz) in skin mimicking gels and pig liver. Microwave ablation probe design, simulation results, and experiment results are provided in this thesis.

  12. Pteros 2.0: Evolution of the fast parallel molecular analysis library for C++ and python.

    Science.gov (United States)

    Yesylevskyy, Semen O

    2015-07-15

    Pteros is the high-performance open-source library for molecular modeling and analysis of molecular dynamics trajectories. Starting from version 2.0 Pteros is available for C++ and Python programming languages with very similar interfaces. This makes it suitable for writing complex reusable programs in C++ and simple interactive scripts in Python alike. New version improves the facilities for asynchronous trajectory reading and parallel execution of analysis tasks by introducing analysis plugins which could be written in either C++ or Python in completely uniform way. The high level of abstraction provided by analysis plugins greatly simplifies prototyping and implementation of complex analysis algorithms. Pteros is available for free under Artistic License from http://sourceforge.net/projects/pteros/. PMID:25974373

  13. Plant and fungal diversity in gut microbiota as revealed by molecular and culture investigations.

    Directory of Open Access Journals (Sweden)

    Nina Gouba

    Full Text Available BACKGROUND: Few studies describing eukaryotic communities in the human gut microbiota have been published. The objective of this study was to investigate comprehensively the repertoire of plant and fungal species in the gut microbiota of an obese patient. METHODOLOGY/PRINCIPAL FINDINGS: A stool specimen was collected from a 27-year-old Caucasian woman with a body mass index of 48.9 who was living in Marseille, France. Plant and fungal species were identified using a PCR-based method incorporating 25 primer pairs specific for each eukaryotic phylum and universal eukaryotic primers targeting 18S rRNA, internal transcribed spacer (ITS and a chloroplast gene. The PCR products amplified using these primers were cloned and sequenced. Three different culture media were used to isolate fungi, and these cultured fungi were further identified by ITS sequencing. A total of 37 eukaryotic species were identified, including a Diatoms (Blastocystis sp. species, 18 plant species from the Streptophyta phylum and 18 fungal species from the Ascomycota, Basidiomycota and Chytridiocomycota phyla. Cultures yielded 16 fungal species, while PCR-sequencing identified 7 fungal species. Of these 7 species of fungi, 5 were also identified by culture. Twenty-one eukaryotic species were discovered for the first time in human gut microbiota, including 8 fungi (Aspergillus flavipes, Beauveria bassiana, Isaria farinosa, Penicillium brevicompactum, Penicillium dipodomyicola, Penicillium camemberti, Climacocystis sp. and Malassezia restricta. Many fungal species apparently originated from food, as did 11 plant species. However, four plant species (Atractylodes japonica, Fibraurea tinctoria, Angelica anomala, Mitella nuda are used as medicinal plants. CONCLUSIONS/SIGNIFICANCE: Investigating the eukaryotic components of gut microbiota may help us to understand their role in human health.

  14. Genomic analysis and selected molecular pathways in rare cancers

    International Nuclear Information System (INIS)

    It is widely accepted that many cancers arise as a result of an acquired genomic instability and the subsequent evolution of tumor cells with variable patterns of selected and background aberrations. The presence and behaviors of distinct neoplastic cell populations within a patient's tumor may underlie multiple clinical phenotypes in cancers. A goal of many current cancer genome studies is the identification of recurring selected driver events that can be advanced for the development of personalized therapies. Unfortunately, in the majority of rare tumors, this type of analysis can be particularly challenging. Large series of specimens for analysis are simply not available, allowing recurring patterns to remain hidden. In this paper, we highlight the use of DNA content-based flow sorting to identify and isolate DNA-diploid and DNA-aneuploid populations from tumor biopsies as a strategy to comprehensively study the genomic composition and behaviors of individual cancers in a series of rare solid tumors: intrahepatic cholangiocarcinoma, anal carcinoma, adrenal leiomyosarcoma, and pancreatic neuroendocrine tumors. We propose that the identification of highly selected genomic events in distinct tumor populations within each tumor can identify candidate driver events that can facilitate the development of novel, personalized treatment strategies for patients with cancer. (paper)

  15. Pairing preferences of the model mono-valence mono-atomic ions investigated by molecular simulation

    International Nuclear Information System (INIS)

    We carried out a series of potential of mean force calculations to study the pairing preferences of a series of model mono-atomic 1:1 ions with evenly varied sizes. The probabilities of forming the contact ion pair (CIP) and the single water separate ion pair (SIP) were presented in the two-dimensional plots with respect to the ion sizes. The pairing preferences reflected in these plots largely agree with the empirical rule of matching ion sizes in the small and big size regions. In the region that the ion sizes are close to the size of the water molecule; however, a significant deviation from this conventional rule is observed. Our further analysis indicated that this deviation originates from the competition between CIP and the water bridging SIP state. The competition is mainly an enthalpy modulated phenomenon in which the existing of the water bridging plays a significant role

  16. Experimental and modelling investigation of surface EMG spike analysis.

    Science.gov (United States)

    Gabriel, David A; Christie, Anita; Inglis, J Greig; Kamen, Gary

    2011-05-01

    A pattern classification method based on five measures extracted from the surface electromyographic (sEMG) signal is used to provide a unique characterization of the interference pattern for different motor unit behaviours. This study investigated the sensitivity of the five sEMG measures during the force gradation process. Tissue and electrode filtering effects were further evaluated using a sEMG model. Subjects (N=8) performed isometric elbow flexion contractions from 0 to 100% MVC. The sEMG signals from the biceps brachii were recorded simultaneously with force. The basic building block of the sEMG model was the detection of single fibre action potentials (SFAPs) through a homogeneous, equivalent isotropic, infinite volume conduction medium. The SFAPs were summed to generate single motor unit action potentials. The physiologic properties from a well-known muscle model and motor unit recruitment and firing rate schemes were combined to generate synthetic sEMG signals. The following pattern classification measures were calculated: mean spike amplitude, mean spike frequency, mean spike slope, mean spike duration, and the mean number of peaks per spike. Root-mean-square amplitude and mean power frequency were also calculated. Taken together, the experimental data and modelling analysis showed that below 50% MVC, the pattern classification measures were more sensitive to changes in force than traditional time and frequency measures. However, there are additional limitations associated with electrode distance from the source that must be explored further. Future experimental work should ensure that the inter-electrode distance is no greater than 1cm to mitigate the effects of tissue filtering. PMID:21146442

  17. Molecular analysis of Kaposi's sarcoma occurring during haemodialysis.

    Science.gov (United States)

    Metaxa-Mariatou, V; Chiras, T; Loli, A; Gazouli, M; Vallis, D; Nasioulas, G

    2004-03-01

    Human Herpesvirus 8 (HHV-8) has been implicated in the pathogenesis of Kaposi's sarcoma (KS). In this paper we attempted to confirm the connection between dialysis, HHV-8, and KS by examining the case of an elderly haemodialysis nonimmunosuppressed male patient with end-stage renal disease, who developed KS. By using PCR we have verified the presence of DNA from two different genomic regions (ORF 26 and ORF K1) of HHV-8. In addition, our RT-PCR results suggest active replication of HHV-8 in blood and KS lesions of the patient. Phylogenetic analysis revealed identical DNA sequence to ORF K1, and a close relation to its C1 variant. In conclusion, we document the case of KS and HHV-8 coexistence in a Greek elderly patient undergoing regular haemodialysis. Furthermore, our results indicate that factors other than immunosuppression could lead to KS development possibly due to activation of HHV-8. PMID:14987280

  18. Experimental investigation and characterization of a compact pulsed tea molecular nitrogen laser

    International Nuclear Information System (INIS)

    A locally assembled compact nitrogen laser with a Blumlein configuration is investigated. Parameters unique to the laser such as laser tube inductance, spark gap inductance, the characteristic impedance of the transmission line, the charging voltage, the laser optical pulse width, the electrical peak power input into the laser, and the optical peak power from the laser pulse are measured. To initiate the discharge, a compact high-voltage 13-25 kilovolt switching power supply was constructed. A 45 kilovolt pulse generator was necessary, so a trigerring device was also made. For high voltage measurements, a 300 turn Rogowski coil was used. Similarly a high voltage magnetic probe consisting of number 30 AWG wire wound around a 1mm bobbin and encapsulated in glass was constructed. Calibration of the probe was done using an 18-turn Helmholtz coil driven by pulses with peak voltages from 10-15kV. A fast photodiode (FND-100) with a rise time factor of 1kV/s was used for optical measurements. The fast signals were captured by a 250 Mhz storage digitizing oscilloscope. Results of the investigation show that the constructed model operates at an underdamped discharge mode. The spark gap resistance was measured at ≅ 0.5 Ω. The spark gap inductance was of the order of ≅ 1.7 nH. The peak electrical input power was placed ≅ 50 MW. The peak optical power was measured at 111mW. Finally, the laser pulse full-width was determined at 10 ns. Parametric studies on the nitrogen laser have been done to determine its optimum operating conditions. The nitrogen laser performance is usually obtained by determining the laser channel inductance and resistance. Lg and rg. These values subsequently give the laser channel current discharge and the electrical power absorbed by the laser channel. The determination of the quantities Lg and rg have been the object of many studies, but it is more desirable to have a direct measure of these quantities. This study aims to measure these constants

  19. Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers

    Directory of Open Access Journals (Sweden)

    Allender Charlotte J

    2010-03-01

    Full Text Available Abstract Background The amphiploid species Brassica napus (oilseed rape, Canola is a globally important oil crop yielding food, biofuels and industrial compounds such as lubricants and surfactants. Identification of the likely ancestors of each of the two genomes (designated A and C found in B. napus would facilitate incorporation of novel alleles from the wider Brassica genepool in oilseed rape crop genetic improvement programmes. Knowledge of the closest extant relatives of the genotypes involved in the initial formation of B. napus would also allow further investigation of the genetic factors required for the formation of a stable amphiploid and permit the more efficient creation of fully fertile re-synthesised B. napus. We have used a combination of chloroplast and nuclear genetic markers to investigate the closest extant relatives of the original maternal progenitors of B. napus. This was based on a comprehensive sampling of the relevant genepools, including 83 accessions of A genome B. rapa L. (both wild and cultivated types, 94 accessions of B. napus and 181 accessions of C genome wild and cultivated B. oleracea L. and related species. Results Three chloroplast haplotypes occurred in B. napus. The most prevalent haplotype (found in 79% of accessions was not present within the C genome accessions but was found at low frequencies in B. rapa. Chloroplast haplotypes characteristic of B. napus were found in a small number of wild and weedy B. rapa populations, and also in two accessions of cultivated B. rapa 'brocoletto'. Whilst introgression of the B. napus chloroplast type in the wild and weedy B. rapa populations has been proposed by other studies, the presence of this haplotype within the two brocoletto accessions is unexplained. Conclusions The distribution of chloroplast haplotypes eliminate any of the C genome species as being the maternal ancestor of the majority of the B. napus accessions. The presence of multiple chloroplast

  20. First principles investigations of electronic structure and transport properties of graphitic structures and single molecular junctions

    Science.gov (United States)

    Owens, Jonathan R.

    properties of the IV curves of single molecule nano-junctions. Specifically, these systems consist of a zinc-porphyrin molecule coupled between two gold electrodes, i.e., a nano-gap. The first observation we want to explain is the asymmetric nature of the experimental IV curve for this porphyrin system, where the IV curve is skewed heavily to the negative bias region. Using a plane-wave DFT calculation, we present the density of states of the porphyrin molecule (both in the presence and absence of the electrodes) and indeed see highly delocalized states (as confirmed by site-projection of the DOS) only in the negative bias region, meaning that the channels with high transmission probability reside there, in agreement with experimental observation. The next problem studied pertains to observed switching in an experimentally-measured IV curve, this time of a longer zinc porphyrin molecule, still within a gold nano-gap. The switching behavior is observed only at 300K, not at 4.2K. The temperature-dependance of this problem renders our previous toolset of DFT calculations void; DFT is a ground-state theory. Instead, we employ a density functional-based tight-binding (DFTB) approach in a molecular dynamics simulation. Basically, the structural configuration evaluated at each time step is based on a tight-binding electronic structure calculation, instead of a typical MD force field. Trajectories are presented at varying temperatures and electric field strengths. Indeed, we observe a conformation of the porphyrin molecule between two configurations of the dihedral angle of the central nitrogen ring, ±15. {o} at 300K, but not 4.2K. These confirmations are equally likely, i.e., the structure assumes these configurations an equal number of teams, meaning the average structure has an angle of 0. {o}. After computing the DOS of all three aforementioned configurations (0. {text{o}} and ±15. {text{o}}), we indeed see a difference between the DOS curves at ±15. {text{o}} (which are

  1. Comparative molecular and antibody typing during the investigation of an outbreak of Legionnaires' disease.

    Science.gov (United States)

    Garcia-Nuñez, Marian; Quero, Sara; Catini, Stella; Pedro-Botet, Maria Lluisa; Mateu, Lourdes; Sopena, Nieves; Sabria, Miguel

    2013-10-01

    An outbreak of Legionnaires' disease with 113 confirmed cases was reported in the town of Mataró, Spain, in August 2002. In this study, we compared three different typing methods and characterized the clinical isolates by comparing them with other clinical isolates with the same ST from our own database to further characterize the outbreak. In the outbreak, a total of 16 clinical (nine patients) and 32 environmental (from four environmental sources) Legionella pneumophila isolates were analyzed by pulsed-field electrophoresis (PFGE), sequence-based typing (SBT), and monoclonal antibody typing (MAb). We compared the MAb and SBT profiles of the outbreak clinical isolates and other unrelated clinical isolates showing the same ST profile. We obtained seven different PFGE and SBT profiles and six MAb patterns from the outbreak isolates. PFGE and SBT showed 100% concordance during the outbreak. SBT proved to be highly discriminatory, particularly with the addition of the new neuA gene. One PFGE, SBT (ST-37), and Philadelphia profile was observed among the clinical isolates. Using PFGE, this ST37 Philadelphia profile was closely related to other unrelated clinical isolates. These findings suggest that the ST37 Philadelphia profile could be a virulence marker in our area. The combination of the three methodologies was useful to further characterize and obtain additional information on a very explosive outbreak. Despite the minor discrimination of PFGE versus SBT, the two genetic methods are recommended in outbreak investigations. Further studies are currently underway in this area to obtain more definitive conclusions. PMID:23572275

  2. Molecular Dynamics Investigation of Ion Sorption and Permeation in Desalination Membranes.

    Science.gov (United States)

    Kolev, Vesselin; Freger, Viatcheslav

    2015-11-01

    With the purpose of gaining insights into the mechanisms of ion uptake and permeation in desalination membranes, MD investigation of a model polyamide membrane was carried out. A relatively large membrane (45K atoms) was assembled, which closely matched real desalination membrane in terms of chemistry and water permeability. Simulations demonstrate that the mechanism of ion uptake distinctly differs from mean-field approaches assuming a smeared excluding Donnan potential. Ion sorption on charged sites in the membrane phase appears to be highly localized, due to electrostatic forces dominating over translational entropy. Moreover, sorption on partial atomic charges becomes possible as well, which greatly enhances salt (co-ion) uptake and weakens the effect of fixed charges on salt exclusion. This could explain high ion uptake measured in polyamide membranes for both co- and counterions and variations of ion sorption and permeation at low salt concentrations. On the other hand, present simulations greatly overestimate ion permeability, which could be explained by a more open structure than in real membranes, in which dense polyamide fragments may efficiently block ion permeation. Unfortunately, MD cannot analyze ion uptake and permeation in dense fragments containing too few ions, which calls for new approaches to studying barrier properties of polyamide. PMID:26451495

  3. HIV-1 integrase strand-transfer inhibitors: design, synthesis and molecular modeling investigation.

    Science.gov (United States)

    De Luca, Laura; De Grazia, Sara; Ferro, Stefania; Gitto, Rosaria; Christ, Frauke; Debyser, Zeger; Chimirri, Alba

    2011-02-01

    This study is focused on a new series of benzylindole derivatives with various substituents at the benzene-fused ring, suggested by our 3D pharmacophore model developed for HIV-1 integrase inhibitors (INIs). All synthesized compounds proved to be active in the nanomolar range (6-35 nM) on the strand-transfer step (ST). In particular, derivative 4-[1-(4-fluorobenzyl)-5,7-dimethoxy-1H-indol-3-yl]-2-hydroxy-4-oxobut-2-enoic acid (8e), presenting the highest best-fit value on pharmacophore model, showed a potency comparable to that of clinical INSTIs GS 9137 (1) and MK-0518 (2). The binding mode of our molecules has been investigated using the recently published crystal structure of the complex of full-length integrase from the prototype foamy virus in complex with its cognate DNA (PFV-IN/DNA). The results highlighted the ability of derivative 8e to assume the same binding mode of MK-0518 and GS 9137. PMID:21227550

  4. Investigations of Protostellar Outflow Launching and Gas Entrainment: Hydrodynamic Simulations and Molecular Emission

    CERN Document Server

    Offner, S S R

    2013-01-01

    We investigate protostellar outflow evolution, gas entrainment, and star formation efficiency using radiation-hydrodynamic simulations of isolated, turbulent low-mass cores. We adopt an X-wind launching model, in which the outflow rate is coupled to the instantaneous protostellar accretion rate and evolution. We vary the outflow collimation angle from $\\theta$=0.01-0.1 and find that even well collimated outflows effectively sweep up and entrain significant core mass. The Stage 0 lifetime ranges from 0.14-0.19 Myr, which is similar to the observed Class 0 lifetime. The star formation efficiency of the cores spans 0.41-0.51. In all cases, the outflows drive strong turbulence in the surrounding material. Although the initial core turbulence is purely solenoidal by construction, the simulations converge to approximate equipartition between solenoidal and compressive motions due to a combination of outflow driving and collapse. When compared to a simulation of a cluster of protostars, which is not gravitationally ...

  5. Mass spectrometric investigation of molecular variability of grass pollen group 1 allergens.

    Science.gov (United States)

    Fenaille, François; Nony, Emmanuel; Chabre, Henri; Lautrette, Aurélie; Couret, Marie-Noëlle; Batard, Thierry; Moingeon, Philippe; Ezan, Eric

    2009-08-01

    Natural grass pollen allergens exhibit a wide variety of isoforms. Precise characterization of such microheterogeneity is essential to improve diagnosis and design appropriate immunotherapies. Moreover, standardization of allergen vaccine production is a prerequisite for product safety and efficiency. Both qualitative and quantitative analytical methods are thus required to monitor and control the huge natural variability of pollens, as well as final product quality. A proteomic approach has been set up to investigate in depth the structural variability of five group 1 allergens originating from distinct grass species (Ant o 1, Dac g 1, Lol p 1, Phl p 1, and Poa p 1). Whereas group 1 is the most conserved grass pollen allergen, great variations were shown between the various isoforms found in these five species using mass spectrometry, with many amino acid exchanges, as well as variations in proline hydroxylation level and in main N-glycan motifs. The presence of O-linked pentose residues was also demonstrated, with up to three consecutive units on the first hydroxyproline of Ant o 1. In addition, species-specific peptides were identified that might be used for product authentication or individual allergen quantification. Lastly, natural or process-induced modifications (deamidation, oxidation, glycation) were evidenced, which might constitute useful indicators of product degradation. PMID:19572759

  6. The first Korean case of HDR syndrome confirmed by clinical and molecular investigation.

    Science.gov (United States)

    Cheon, Chong Kun; Kim, Gu Hwan; Yoo, Han Wook

    2015-01-01

    Hypoparathyroidism, deafness, and renal dysplasia (HDR) syndrome is a rare condition inherited as autosomal dominant trait and characterized by hypoparathyroidism, sensorineural deafness, and renal dysplasia. HDR syndrome is caused by haploinsufficiency of the GATA3 gene located on chromosome 10p15. Here, we report the case of a 32-day-old Korean male with HDR syndrome. He was presented due to repeated seizures over previous 3 days. The patient was born after 40 weeks of gestation with birth weight of 2930 g, and was the first-born baby of healthy Korean parents. Hypoparathyroidism was first noticed due to seizure. A multicystic left dysplastic kidney and vesicoureteral reflux were detected by ultrasound after birth. Auditory brainstem response (ABR) testing revealed that the patient had moderate sensorineural deafness, with hearing losses of 80 dB at the mid and higher frequencies for both ears. Echocardiography finding revealed secundum atrial septal deftect. Based on biochemical results and clinical findings, a presumptive diagnosis of HDR syndrome was made. GATA3 mutation analysis identified a heterozygous deletion, c.153del (p.Phe51Leufs*144) in exon 1 causing a frameshift mutation, which is a novel de novo mutation. Therefore, we suggest that HDR syndrome should be considered in the differential diagnosis in symptomatic or asymptomatic patients with hypoparathyroidism, and that renal ultrasound or ABR testing be performed to prevent a missed diagnosis. This is the first report on Korean patient with confirmed HDR syndrome with novel mutation. PMID:25510779

  7. Interaction of human chymase with ginkgolides, terpene trilactones of Ginkgo biloba investigated by molecular docking simulations.

    Science.gov (United States)

    Dubey, Amit; Marabotti, Anna; Ramteke, Pramod W; Facchiano, Angelo

    2016-04-29

    The search for natural chymase inhibitors has a good potential to provide a novel therapeutic approach against the cardiovascular diseases and other heart ailments. We selected from literature 20 promising Ginkgo biloba compounds, and tested them for their potential ability to bind chymase enzyme using docking and a deep analysis of surface pocket features. Docking results indicated that the compounds may interact with the active site of human chymase, with favorable distinct interactions with important residues Lys40, His57, Lys192, Phe191, Val146, Ser218, Gly216, and Ser195. In particular, proanthocyanidin is the one with the best-predicted binding energy, with seven hydrogen bonds. Interestingly, all active G. biloba compounds have formed the hydrogen bond interactions with the positively charged Lys192 residue at the active site, involved in the mechanism of pH enhancement for the cleavage of angiotensin I site. Ginkgolic acid and proanthocyanidin have better predicted binding energy towards chymase than other serine proteases, i.e kallikrein, tryptase and elastase, suggesting specificity for chymase inhibition. Our study suggests these G. biloba compounds are a promising starting point for developing chymase inhibitors for the potential development of future drugs. PMID:26975469

  8. Monte Carlo simulation to investigate the formation of molecular hydrogen and its deuterated forms

    Science.gov (United States)

    Sahu, Dipen; Das, Ankan; Majumdar, Liton; Chakrabarti, Sandip K.

    2015-07-01

    H2 is the most abundant interstellar species, and its deuterated forms (HD and D2) are also present in high abundance. The high abundance of these molecules could be explained by considering the chemistry that occurs on interstellar dust. Because of its simplicity, the rate equation method is widely used to study the formation of grain-surface species. However, because the recombination efficiency for the formation of any surface species is highly dependent on various physical and chemical parameters, the Monte Carlo method is best suited for addressing the randomness of the processes. We perform Monte Carlo simulations to study the formation of H2, HD and D2 on interstellar ice. The adsorption energies of surface species are the key inputs for the formation of any species on interstellar dusts, but the binding energies of deuterated species have yet to be determined with certainty. A zero-point energy correction exists between hydrogenated and deuterated species, which should be considered during modeling of the chemistry on interstellar dusts. Following some previous studies, we consider various sets of adsorption energies to investigate the formation of these species under diverse physical conditions. As expected, notable differences in these two approaches (rate equation method and Monte Carlo method) are observed for the production of these simple molecules on interstellar ice. We introduce two factors, namely, Sf and β , to explain these discrepancies: Sf is a scaling factor, which can be used to correlate the discrepancies between the rate equation and Monte Carlo methods, and β indicates the formation efficiency under various conditions. Higher values of β indicate a lower production efficiency. We observed that β increases with a decrease in the rate of accretion from the gas phase to the grain phase.

  9. Molecular characterization and phylogenetic analysis of Fasciola hepatica from Peru.

    Science.gov (United States)

    Ichikawa-Seki, Madoka; Ortiz, Pedro; Cabrera, Maria; Hobán, Cristian; Itagaki, Tadashi

    2016-06-01

    The causative agent of fasciolosis in South America is thought to be Fasciola hepatica. In this study, Fasciola flukes from Peru were analyzed to investigate their genetic structure and phylogenetic relationships with those from other countries. Fasciola flukes were collected from the three definitive host species: cattle, sheep, and pigs. They were identified as F. hepatica because mature sperms were observed in their seminal vesicles, and also they displayed Fh type, which has an identical fragment pattern to F. hepatica in the nuclear internal transcribed spacer 1. Eight haplotypes were obtained from the mitochondrial NADH dehydrogenase subunit 1 (nad1) sequences of Peruvian F. hepatica; however, no special difference in genetic structure was observed between the three host species. Its extremely low genetic diversity suggests that the Peruvian population was introduced from other regions. Nad1 haplotypes identical to those of Peruvian F. hepatica were detected in China, Uruguay, Italy, Iran, and Australia. Our results indicate that F. hepatica rapidly expanded its range due to human migration. Future studies are required to elucidate dispersal route of F. hepatica from Europe, its probable origin, to other areas, including Peru. PMID:26657243

  10. Molecular Investigations of Rickettsia helvetica Infection in Dogs, Foxes, Humans, and Ixodes Ticks▿

    Science.gov (United States)

    Boretti, Felicitas S.; Perreten, Andrea; Meli, Marina L.; Cattori, Valentino; Willi, Barbara; Wengi, Nicole; Hornok, Sándor; Honegger, Hanspeter; Hegglin, Daniel; Woelfel, Roman; Reusch, Claudia E.; Lutz, Hans; Hofmann-Lehmann, Regina

    2009-01-01

    Rickettsia helvetica, a tick-borne member of the spotted-fever-group rickettsiae, is a suspected pathogen in humans; however, its role in animals is unknown. The aims of this study were to establish a R. helvetica-specific real-time TaqMan PCR assay and apply it to the analysis of tick vectors (to determine potential exposure risk) and blood samples from Canidae and humans (to determine prevalence of infection). The newly designed 23S rRNA gene assay for R. helvetica was more sensitive than a published citrate synthase gene (gltA) assay for several rickettsiae. Blood samples from 884 dogs, 58 foxes, and 214 human patients and 2,073 ticks (Ixodes spp.) collected from either vegetation or animals were analyzed. Although the maximal likelihood estimate of prevalence was 12% in unfed ticks and 36% in ticks collected from animals, none of the 1,156 blood samples tested PCR positive. Ticks from cats were more frequently PCR positive than ticks from dogs. Sequencing of the 23S rRNA and/or the gltA gene of 17 tick pools confirmed the presence of R. helvetica. Additionally, Rickettsia monacensis, which has not been previously found in Switzerland, was identified. In conclusion, R. helvetica was frequently detected in the tick population but not in blood samples. Nevertheless, due to the broad host range of Ixodes ticks and the high rate of infestation with this agent (i.e., R. helvetica was 13 times more frequent in unfed ticks than the tick-borne encephalitis virus), many mammals may be exposed to R. helvetica. The PCR assay described here represents an important tool for studying this topic. PMID:19329665

  11. Molecular Investigations of Rickettsia helvetica infection in dogs, foxes, humans, and Ixodes ticks.

    Science.gov (United States)

    Boretti, Felicitas S; Perreten, Andrea; Meli, Marina L; Cattori, Valentino; Willi, Barbara; Wengi, Nicole; Hornok, Sándor; Honegger, Hanspeter; Hegglin, Daniel; Woelfel, Roman; Reusch, Claudia E; Lutz, Hans; Hofmann-Lehmann, Regina

    2009-05-01

    Rickettsia helvetica, a tick-borne member of the spotted-fever-group rickettsiae, is a suspected pathogen in humans; however, its role in animals is unknown. The aims of this study were to establish a R. helvetica-specific real-time TaqMan PCR assay and apply it to the analysis of tick vectors (to determine potential exposure risk) and blood samples from Canidae and humans (to determine prevalence of infection). The newly designed 23S rRNA gene assay for R. helvetica was more sensitive than a published citrate synthase gene (gltA) assay for several rickettsiae. Blood samples from 884 dogs, 58 foxes, and 214 human patients and 2,073 ticks (Ixodes spp.) collected from either vegetation or animals were analyzed. Although the maximal likelihood estimate of prevalence was 12% in unfed ticks and 36% in ticks collected from animals, none of the 1,156 blood samples tested PCR positive. Ticks from cats were more frequently PCR positive than ticks from dogs. Sequencing of the 23S rRNA and/or the gltA gene of 17 tick pools confirmed the presence of R. helvetica. Additionally, Rickettsia monacensis, which has not been previously found in Switzerland, was identified. In conclusion, R. helvetica was frequently detected in the tick population but not in blood samples. Nevertheless, due to the broad host range of Ixodes ticks and the high rate of infestation with this agent (i.e., R. helvetica was 13 times more frequent in unfed ticks than the tick-borne encephalitis virus), many mammals may be exposed to R. helvetica. The PCR assay described here represents an important tool for studying this topic. PMID:19329665

  12. Molecular Analysis in the differentiation of Colletotrichum gloeosporioides isolates from the cashew and mango trees

    Directory of Open Access Journals (Sweden)

    Ilka Márcia Ribeiro de Souza Serra

    2011-12-01

    Full Text Available The aim of the present work was to analyze the molecular methods in the differentiation of Colletotrichum gloeosporioides isolates obtained from the cashew and mango trees. The different molecular taxonomic methods used proved to be efficient regarding intraspecific characterization. Similarly, molecular methods also proved to be efficient in differentiation of the C. gloeosporioides isolates in relation to host specificity. In the analysis of the ITS sequence of the ribosomal DNA, all the isolates amplified with the CgInt and ITS4 primers, confirming that they pertained to C. gloeosporioides. The results from this study suggested that methods based on the pathogenicity, isozyme analysis and RAPD were effective in differentiating C. gloeosporioides isolates from the cashew and mango trees.

  13. Molecular analysis of gut microbiota in obesity among Indian individuals

    Indian Academy of Sciences (India)

    Deepak P Patil; Dhiraj P Dhotre; Sachin G Chavan; Armiya Sultan; Dhawal S Jain; Vikram B Lanjekar; Jayshree Gangawani; Poonam S Shah; Jayshree S Todkar; Shashank Shah; Dilip R Ranade; Milind S Patole; Yogesh S Shouche

    2012-09-01

    Obesity is a consequence of a complex interplay between the host genome and the prevalent obesogenic factors among the modern communities. The role of gut microbiota in the pathogenesis of the disorder was recently discovered; however, 16S-rRNA-based surveys revealed compelling but community-specific data. Considering this, despite unique diets, dietary habits and an uprising trend in obesity, the Indian counterparts are poorly studied. Here, we report a comparative analysis and quantification of dominant gut microbiota of lean, normal, obese and surgically treated obese individuals of Indian origin. Representative gut microbial diversity was assessed by sequencing fecal 16S rRNA libraries for each group (n=5) with a total of over 3000 sequences. We detected no evident trend in the distribution of the predominant bacterial phyla, Bacteroidetes and Firmicutes. At the genus level, the bacteria of genus Bacteroides were prominent among the obese individuals, which was further confirmed by qPCR ( > 0.05). In addition, a remarkably high archaeal density with elevated fecal SCFA levels was also noted in the obese group. On the contrary, the treated-obese individuals exhibited comparatively reduced Bacteroides and archaeal counts along with reduced fecal SCFAs. In conclusion, the study successfully identified a representative microbial diversity in the Indian subjects and demonstrated the prominence of certain bacterial groups in obese individuals; nevertheless, further studies are essential to understand their role in obesity.

  14. Molecular analysis of HLA-B in the Malaysian aborigines.

    Science.gov (United States)

    Hirayama, K; Zaidi, A S; Lokman Hakim, S; Kimura, A; Ong, K J; Kikuchi, M; Nasuruddin, H A; Kojima, S; Mak, J W

    1996-12-01

    We have examined 56 unrelated individuals from Malaysian aborigines for their DNA polymorphism of the HLA-B gene by sequence specific oligonucleotide probe (SSO) method. Using the SSO hybridization, we found that one specific DNA allele with a B*1513 like pattern of epitope combination (ECB1513) was dominant among the Melayu Asli (Af = 41.9%) and the Senoi (Af = 24%). To determine the nucleotide sequences of ECB1513, a DNA fragment spanning from the beginning of exon 1 to the middle of exon 4 of the HLA-B gene was amplified by polymerase chain reaction (PCR) from two ECB1513 positive individuals, and the PCR products were cloned and sequenced. This sequencing analysis confirmed that ECB1513 was identical to HLA-B*1513 in exon 1, 2, 3, and 4. Amino acid sequence of this major allele, HLA-B*1513, in the aborigines especially around the peptide binding groove (B and F pockets), was compared with that of African B*5301 that had been suggested to confer resistance to malaria infection in Africa. The amino acid residues composing of the F pocket were completely identical in B*1513 and B*5301. These observations suggest that a common environmental factor, the malaria infection, might have independently enhanced the selection of functional change in the polymorphic portion of HLA-B gene in Africa and in South-East Asia. PMID:9008312

  15. Molecular analysis of the muscle protein projectin in Lepidoptera.

    Science.gov (United States)

    Ayme-Southgate, A J; Turner, L; Southgate, R J

    2013-01-01

    Striated muscles of both vertebrates and insects contain a third filament composed of the giant proteins, namely kettin and projectin (insects) and titin (vertebrates). All three proteins have been shown to contain several domains implicated in conferring elasticity, in particular a PEVK segment. In this study, the characterization of the projectin protein in the silkmoth, Bombyx mori L. (Lepidoptera: Bombycidae), and the monarch butterfly, Danaus plexippus L. (Lepidoptera: Nymphalidae), as well as a partial characterization in the Carolina sphinx, Manduca sexta L. (Lepidoptera: Sphingidae), are presented. This study showed that, similar to other insects, projectin's overall modular organization was conserved, but in contrast, the PEVK region had a highly divergent sequence. The analysis of alternative splicing in the PEVK region revealed a small number of possible isoforms and the lack of a flight-muscle specific variant, both characteristics being in sharp contrast with findings from other insects. The possible correlation with difference in flight muscle stiffness and physiology between Lepidoptera and other insect orders is discussed. PMID:24206568

  16. Statistical investigation of the length-dependent deviations in the electrical characteristics of molecular electronic junctions fabricated using the direct metal transfer method

    Science.gov (United States)

    Jeong, Hyunhak; Kim, Dongku; Kwon, Hyukwoo; Hwang, Wang-Taek; Jang, Yeonsik; Min, Misook; Char, Kookrin; Xiang, Dong; Jeong, Heejun; Lee, Takhee

    2016-03-01

    We fabricated and analyzed the electrical transport characteristics of vertical type alkanethiolate molecular junctions using the high-yield fabrication method that we previously reported. The electrical characteristics of the molecular electronic junctions were statistically collected and investigated in terms of current density and transport parameters based on the Simmons tunneling model, and we determined representative current-voltage characteristics of the molecular junctions. In particular, we examined the statistical variations in the length-dependent electrical characteristics, especially the Gaussian standard deviation σ of the current density histogram. From the results, we found that the magnitude of the σ value can be dependent on the individual molecular length due to specific microscopic structures in the molecular junctions. The probable origin of the molecular length-dependent deviation of the electrical characteristics is discussed.

  17. Statistical investigation of the length-dependent deviations in the electrical characteristics of molecular electronic junctions fabricated using the direct metal transfer method

    International Nuclear Information System (INIS)

    We fabricated and analyzed the electrical transport characteristics of vertical type alkanethiolate molecular junctions using the high-yield fabrication method that we previously reported. The electrical characteristics of the molecular electronic junctions were statistically collected and investigated in terms of current density and transport parameters based on the Simmons tunneling model, and we determined representative current–voltage characteristics of the molecular junctions. In particular, we examined the statistical variations in the length-dependent electrical characteristics, especially the Gaussian standard deviation σ of the current density histogram. From the results, we found that the magnitude of the σ value can be dependent on the individual molecular length due to specific microscopic structures in the molecular junctions. The probable origin of the molecular length-dependent deviation of the electrical characteristics is discussed. (paper)

  18. Investigations into the molecular mechanism of chromatid breakage in the G2-phase of mammalian cells

    International Nuclear Information System (INIS)

    Chromatid breakage following irradiation of cells in the G2-phase of the cell cycle results from the induction of DNA double-strand breaks (dsb). The conversion of dsb into chromatid breaks (cb) has a genetic basis, seemingly different from that of dsb rejoining. The variation in extent of this conversion is exemplified by the stiking variation in frequency of cb in irradiated cycling T-lymphocytes between different normal individuals. Elevated cb frequency in lymphocytes of around 40% of breast cancer patients and their first-degree relatives suggests the presence of mutations in low penetrance cancer predisposing genes that also affect conversion of dsb to cb. Investigation of the mechanism of chromatid radiosensitivity using genetically engineered rodent cell lines containing unique dsb break sites indicate that a single isolated dsb is sufficient to cause a cb. The single-event nature of chromatid breakage is confirmed by the fact that cb are induced as a linear function of radiation dose. Moreover, we have recently shown that ultrasoft carbon-K X-rays also induce chromatid breakage. In this case the energy of the secondary electrons produced by carbon-K X-rays is too low to span more than one DNA double helix, thus further supporting our conclusion that a single dsb is responsible for the formation of a cb. Chromatid breakage is thought to involve a rearrangement between DNA strands at the crossover points of chromatin loop(s) triggered by the presence of a dsb within the loop structure. The occasional observation of 'looped-out' sections of chromatin at cb sites supports this hypothesis. The occurrence of 'colour-switches' between FPG stained chromatids at a proportion of break sites (e.g. about 16% in CHO cells) shows that a significant proportion of cb definitely result from chromatin rearrangements. Measurements of altered colour-switch ratio (csr) in mutant rodent and human cells (irs1 and AT cells respectively) also indicate a genetic basis for the

  19. Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

    OpenAIRE

    Rangel-Figueiredo Teresa; Neves Dina; Borges Carla; Sobral Maria F; Matos José; Penedo Maria CT; Ginja Catarina; Cravador Alfredo

    2010-01-01

    Abstract Background Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed. ...

  20. Etiological and molecular-epidemiological analysis on enterovirus associated encephalitis in Zhejiang,2008-2012

    Institute of Scientific and Technical Information of China (English)

    严菊英

    2014-01-01

    Objective In order to investigate etiology and molecular-epidemiological characteristics of enterovirus associated encephalitis(EAE)in Zhejiang,2008—2012.Methods Cerebrospinal fluid and stool specimens were collected from suspected EAE patients,who were admitted to our hospitals.RD and Hep-2 cell lines were used to isolate