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Sample records for molecular polymorphism distribution

  1. Phenotypic characterisation and molecular polymorphism of ...

    The study of the phenotypic characterisation and molecular polymorphism of local chicken populations was carried out in Benin on 326 chickens of the Forest ecological area and 316 of the Savannah ecological area, all were 7 months old at least. The collection of blood for the molecular typing was achieved on 121 ...

  2. Human butyrylcholinesterase polymorphism: Molecular modeling.

    Lushchekina, S; Delacour, H; Lockridge, O; Masson, P

    2015-01-01

    Prolonged apnoea following injection of ester-containing myoralaxants was first described in 1953. Because a large part of administered succinylcholine is shortly hydrolyzed by plasma butyrylcholinesterase (BChE) under normal conditions, prolonged apnoea was attributed to deficiency in BChE. It was found that BChE deficiency was due to genetic variations. Human BChE gene shows a large polyallelism. About 75 natural mutations of the BCHE gene have been documented so far [1]. Most of them cause alteration in BChE activity through point mutation effect on catalytic activity. Frame shifts and stop codons may also affect expression, or cause truncations in the sequence. Recently, two novel BChE "silent" variants, Val204Asp [2] and Ala34Val [3], causing prolonged neuromuscular block after administration of mivacurium, were discovered. Mutations were genetically and kinetically characterized. The aim of the current study was to understand how these mutations determine "silent" phenotype. Molecular dynamics studies were carried out with NAMD 2.9 software at the Lomonosov supercomputer. Charmm 36 force field was used, periodical boundary conditions, 1 atm pressure, 298 K. 100 ns molecular dynamics runs were performed for the wild-type BChE and its mutants Val204Asp and Ala34Val. Unlike wild-type BChE, which retained its operative catalytic triad through the whole MD simulation, the catalytic triad of mutants was disrupted, making chemical step impossible. Val204Asp mutation leads to reorganization of hydrogen bonding network around the catalytic triad, which in turn increases the distance between catalytic residue main chains. Mutation Ala34Val, located on the protein surface, leads to increased fluctuations in the Ω-loop and subsequent disruption of the gorge structure, including disruption of the catalytic triad and formation of new hydrogen bonds involving catalytic center residues. Comparative study of the "silent" Ala328Asp mutant and the catalytically active mutant

  3. Advances in molecular modeling of human cytochrome P450 polymorphism.

    Martiny, Virginie Y; Miteva, Maria A

    2013-11-01

    Cytochrome P450 (CYP) is a supergene family of metabolizing enzymes involved in the phase I metabolism of drugs and endogenous compounds. CYP oxidation often leads to inactive drug metabolites or to highly toxic or carcinogenic metabolites involved in adverse drug reactions (ADR). During the last decade, the impact of CYP polymorphism in various drug responses and ADR has been demonstrated. Of the drugs involved in ADR, 56% are metabolized by polymorphic phase I metabolizing enzymes, 86% among them being CYP. Here, we review the major CYP polymorphic forms, their impact for drug response and current advances in molecular modeling of CYP polymorphism. We focus on recent studies exploring CYP polymorphism performed by the use of sequence-based and/or protein-structure-based computational approaches. The importance of understanding the molecular mechanisms related to CYP polymorphism and drug response at the atomic level is outlined. © 2013.

  4. Molecular markers. Amplified fragment length polymorphism

    Pržulj Novo

    2005-01-01

    Full Text Available Amplified Fragment Length Polymorphism molecular markers (AFLPs has been developed combining procedures of RFLPs and RAPDs molekular markers, i.e. the first step is restriction digestion of the genomic DNA that is followed by selective amplification of the restricted fragments. The advantage of the AFLP technique is that it allows rapid generation of a large number of reproducible markers. The reproducibility of AFLPs markers is assured by the use of restriction site-specific adapters and adapter-specific primers for PCR reaction. Only fragments containing the restriction site sequence plus the additional nucleotides will be amplified and the more selected nucleotides added on the primer sequence the fewer the number of fragments amplified by PCR. The amplified products are normally separated on a sequencing gel and visualized after exposure to X-ray film or by using fluorescent labeled primers. AFLP shave proven to be extremely proficient in revealing diversity at below the species level. A disadvantage of AFLP technique is that AFLPs are essentially a dominant marker system and not able to identify heterozygotes.

  5. Polymorphic phase transitions: Macroscopic theory and molecular simulation.

    Anwar, Jamshed; Zahn, Dirk

    2017-08-01

    Transformations in the solid state are of considerable interest, both for fundamental reasons and because they underpin important technological applications. The interest spans a wide spectrum of disciplines and application domains. For pharmaceuticals, a common issue is unexpected polymorphic transformation of the drug or excipient during processing or on storage, which can result in product failure. A more ambitious goal is that of exploiting the advantages of metastable polymorphs (e.g. higher solubility and dissolution rate) while ensuring their stability with respect to solid state transformation. To address these issues and to advance technology, there is an urgent need for significant insights that can only come from a detailed molecular level understanding of the involved processes. Whilst experimental approaches at best yield time- and space-averaged structural information, molecular simulation offers unprecedented, time-resolved molecular-level resolution of the processes taking place. This review aims to provide a comprehensive and critical account of state-of-the-art methods for modelling polymorph stability and transitions between solid phases. This is flanked by revisiting the associated macroscopic theoretical framework for phase transitions, including their classification, proposed molecular mechanisms, and kinetics. The simulation methods are presented in tutorial form, focusing on their application to phase transition phenomena. We describe molecular simulation studies for crystal structure prediction and polymorph screening, phase coexistence and phase diagrams, simulations of crystal-crystal transitions of various types (displacive/martensitic, reconstructive and diffusive), effects of defects, and phase stability and transitions at the nanoscale. Our selection of literature is intended to illustrate significant insights, concepts and understanding, as well as the current scope of using molecular simulations for understanding polymorphic

  6. Molecular nucleation mechanisms and control strategies for crystal polymorph selection

    van Driessche, Alexander E. S.; van Gerven, Nani; Bomans, Paul H. H.; Joosten, Rick R. M.; Friedrich, Heiner; Gil-Carton, David; Sommerdijk, Nico A. J. M.; Sleutel, Mike

    2018-04-01

    The formation of condensed (compacted) protein phases is associated with a wide range of human disorders, such as eye cataracts, amyotrophic lateral sclerosis, sickle cell anaemia and Alzheimer’s disease. However, condensed protein phases have their uses: as crystals, they are harnessed by structural biologists to elucidate protein structures, or are used as delivery vehicles for pharmaceutical applications. The physiochemical properties of crystals can vary substantially between different forms or structures (‘polymorphs’) of the same macromolecule, and dictate their usability in a scientific or industrial context. To gain control over an emerging polymorph, one needs a molecular-level understanding of the pathways that lead to the various macroscopic states and of the mechanisms that govern pathway selection. However, it is still not clear how the embryonic seeds of a macromolecular phase are formed, or how these nuclei affect polymorph selection. Here we use time-resolved cryo-transmission electron microscopy to image the nucleation of crystals of the protein glucose isomerase, and to uncover at molecular resolution the nucleation pathways that lead to two crystalline states and one gelled state. We show that polymorph selection takes place at the earliest stages of structure formation and is based on specific building blocks for each space group. Moreover, we demonstrate control over the system by selectively forming desired polymorphs through site-directed mutagenesis, specifically tuning intermolecular bonding or gel seeding. Our results differ from the present picture of protein nucleation, in that we do not identify a metastable dense liquid as the precursor to the crystalline state. Rather, we observe nucleation events that are driven by oriented attachments between subcritical clusters that already exhibit a degree of crystallinity. These insights suggest ways of controlling macromolecular phase transitions, aiding the development of protein

  7. Molecular characterization and polymorphisms of butyrylcholinesterase in cynomolgus macaques.

    Uno, Yasuhiro; Uehara, Shotaro; Mahadhi, Hassan M D; Ohura, Kayoko; Hosokawa, Masakiyo; Imai, Teruko

    2018-06-01

    Butyrylcholinesterase (BChE), an enzyme essential for drug metabolism, has been investigated as antidotes against organophosphorus nerve agents, and the efficacy and safety have been studied in cynomolgus macaques. BChE polymorphisms partly account for variable BChE activities among individuals in humans, but have not been investigated in cynomolgus macaques. Molecular characterization was carried out by analyzing primary sequence, gene, tissue expression, and genetic variants. In cynomolgus and human BChE, phylogenetically closely related, amino acid residues important for enzyme function were conserved, and gene and genomic structure were similar. Cynomolgus BChE mRNA was most abundantly expressed in liver among the 10 tissue types analyzed. Re-sequencing found 26 non-synonymous genetic variants in 121 cynomolgus and 23 rhesus macaques, indicating that macaque BChE is polymorphic, although none of these variants corresponded to the null or defective alleles of human BChE. These results suggest molecular similarities of cynomolgus and human BChE. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  8. Molecular Identification of Date Palm Cultivars Using Random Amplified Polymorphic DNA (RAPD) Markers.

    Al-Khalifah, Nasser S; Shanavaskhan, A E

    2017-01-01

    Ambiguity in the total number of date palm cultivars across the world is pointing toward the necessity for an enumerative study using standard morphological and molecular markers. Among molecular markers, DNA markers are more suitable and ubiquitous to most applications. They are highly polymorphic in nature, frequently occurring in genomes, easy to access, and highly reproducible. Various molecular markers such as restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR), inter-simple sequence repeats (ISSR), and random amplified polymorphic DNA (RAPD) markers have been successfully used as efficient tools for analysis of genetic variation in date palm. This chapter explains a stepwise protocol for extracting total genomic DNA from date palm leaves. A user-friendly protocol for RAPD analysis and a table showing the primers used in different molecular techniques that produce polymorphisms in date palm are also provided.

  9. Mixed signals? Morphological and molecular evidence suggest a color polymorphism in some neotropical polythore damselflies.

    Melissa Sánchez Herrera

    Full Text Available The study of color polymorphisms (CP has provided profound insights into the maintenance of genetic variation in natural populations. We here offer the first evidence for an elaborate wing polymorphism in the Neotropical damselfly genus Polythore, which consists of 21 described species, distributed along the eastern slopes of the Andes in South America. These damselflies display highly complex wing colors and patterning, incorporating black, white, yellow, and orange in multiple wing bands. Wing colors, along with some components of the male genitalia, have been the primary characters used in species description; few other morphological traits vary within the group, and so there are few useful diagnostic characters. Previous research has indicated the possibility of a cryptic species existing in P. procera in Colombia, despite there being no significant differences in wing color and pattern between the populations of the two putative species. Here we analyze the complexity and diversity of wing color patterns of individuals from five described Polythore species in the Central Amazon Basin of Peru using a novel suite of morphological analyses to quantify wing color and pattern: geometric morphometrics, chromaticity analysis, and Gabor wavelet transformation. We then test whether these color patterns are good predictors of species by recovering the phylogenetic relationships among the 5 species using the barcode gene (COI. Our results suggest that, while highly distinct and discrete wing patterns exist in Polythore, these "wingforms" do not represent monophyletic clades in the recovered topology. The wingforms identified as P. victoria and P. ornata are both involved in a polymorphism with P. neopicta; also, cryptic speciation may have taking place among individuals with the P. victoria wingform. Only P. aurora and P. spateri represent monophyletic species with a single wingform in our molecular phylogeny. We discuss the implications of this

  10. Mixed signals? Morphological and molecular evidence suggest a color polymorphism in some neotropical polythore damselflies.

    Sánchez Herrera, Melissa; Kuhn, William R; Lorenzo-Carballa, Maria Olalla; Harding, Kathleen M; Ankrom, Nikole; Sherratt, Thomas N; Hoffmann, Joachim; Van Gossum, Hans; Ware, Jessica L; Cordero-Rivera, Adolfo; Beatty, Christopher D

    2015-01-01

    The study of color polymorphisms (CP) has provided profound insights into the maintenance of genetic variation in natural populations. We here offer the first evidence for an elaborate wing polymorphism in the Neotropical damselfly genus Polythore, which consists of 21 described species, distributed along the eastern slopes of the Andes in South America. These damselflies display highly complex wing colors and patterning, incorporating black, white, yellow, and orange in multiple wing bands. Wing colors, along with some components of the male genitalia, have been the primary characters used in species description; few other morphological traits vary within the group, and so there are few useful diagnostic characters. Previous research has indicated the possibility of a cryptic species existing in P. procera in Colombia, despite there being no significant differences in wing color and pattern between the populations of the two putative species. Here we analyze the complexity and diversity of wing color patterns of individuals from five described Polythore species in the Central Amazon Basin of Peru using a novel suite of morphological analyses to quantify wing color and pattern: geometric morphometrics, chromaticity analysis, and Gabor wavelet transformation. We then test whether these color patterns are good predictors of species by recovering the phylogenetic relationships among the 5 species using the barcode gene (COI). Our results suggest that, while highly distinct and discrete wing patterns exist in Polythore, these "wingforms" do not represent monophyletic clades in the recovered topology. The wingforms identified as P. victoria and P. ornata are both involved in a polymorphism with P. neopicta; also, cryptic speciation may have taking place among individuals with the P. victoria wingform. Only P. aurora and P. spateri represent monophyletic species with a single wingform in our molecular phylogeny. We discuss the implications of this polymorphism, and the

  11. Bistetracene Thin Film Polymorphic Control to Unravel the Effect of Molecular Packing on Charge Transport

    Burnett, Edmund K.

    2018-02-26

    Polymorphism, the ability for a given material to adopt multiple crystalline packing states, is a powerful approach for investigating how changes in molecular packing influence charge transport within organic semiconductors. In this study, a new

  12. Bistetracene Thin Film Polymorphic Control to Unravel the Effect of Molecular Packing on Charge Transport

    Burnett, Edmund K.; Ly, Jack; Niazi, Muhammad Rizwan; Zhang, Lei; McCuskey, Samantha R.; Amassian, Aram; Smilgies, Detlef-M.; Mannsfeld, Stefan C. B.; Briseno, Alejandro L.

    2018-01-01

    Polymorphism, the ability for a given material to adopt multiple crystalline packing states, is a powerful approach for investigating how changes in molecular packing influence charge transport within organic semiconductors. In this study, a new

  13. Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference

    Park Jongsun

    2008-01-01

    Full Text Available Abstract Background Simple sequence repeats (SSRs have been successfully used for various genetic and evolutionary studies in eukaryotic systems. The eukaryotic model organism Neurospora crassa is an excellent system to study evolution and biological function of SSRs. Results We identified and characterized 2749 SSRs of 963 SSR types in the genome of N. crassa. The distribution of tri-nucleotide (nt SSRs, the most common SSRs in N. crassa, was significantly biased in exons. We further characterized the distribution of 19 abundant SSR types (AST, which account for 71% of total SSRs in the N. crassa genome, using a Poisson log-linear model. We also characterized the size variation of SSRs among natural accessions using Polymorphic Index Content (PIC and ANOVA analyses and found that there are genome-wide, chromosome-dependent and local-specific variations. Using polymorphic SSRs, we have built linkage maps from three line-cross populations. Conclusion Taking our computational, statistical and experimental data together, we conclude that 1 the distributions of the SSRs in the sequenced N. crassa genome differ systematically between chromosomes as well as between SSR types, 2 the size variation of tri-nt SSRs in exons might be an important mechanism in generating functional variation of proteins in N. crassa, 3 there are different levels of evolutionary forces in variation of amino acid repeats, and 4 SSRs are stable molecular markers for genetic studies in N. crassa.

  14. Development and Molecular Characterization of Novel Polymorphic Genomic DNA SSR Markers in Lentinula edodes.

    Moon, Suyun; Lee, Hwa-Yong; Shim, Donghwan; Kim, Myungkil; Ka, Kang-Hyeon; Ryoo, Rhim; Ko, Han-Gyu; Koo, Chang-Duck; Chung, Jong-Wook; Ryu, Hojin

    2017-06-01

    Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.

  15. Distribution of HIV-1 resistance-conferring polymorphic alleles SDF ...

    Polymorphic allelic variants of chemokine receptors CCR2 and CCR5, as well as of stromal-derived factor-1 SDF-1, the ligand for the chemokine receptor CXCR4, are known to have protective effects against HIV-1 infection and to be involved with delay in disease progression. We have studied the DNA polymorphisms at ...

  16. Molecular weight distribution of Athabasca bitumen

    Champagne, P J; Manolakis, E; Ternan, M

    1985-03-01

    A sample of whole Athabasca bitumen has been fractionated by preparative g.p.c. The weights of the fractions have been determined and their molecular weights measured by several methods. In contras to previously published data, consistent results were obtained using different solvents (THF, benzene/water) and using different techniques (v.p.o., f.p.d. and g.c.-m.s.). This has resulted in a accurate definition of the molecular weight distribution of Athabasca bitumen.

  17. Molecular polymorphisms of the ABO locus as informative markers of ancestry in Central Argentina.

    Tavella, María Pía; García, Angelina; Pauro, Maia; Demarchi, Darío A; Nores, Rodrigo

    2017-07-08

    The aim of this study was to investigate the distribution of molecular polymorphisms of the ABO gene in four population samples from the province of Córdoba, in Central Argentina, and to compare them with other worldwide populations. A total of 110 buccal swab samples from autochthonous individuals of Córdoba were typified. Molecular characterization of the allelic variants was performed by the analysis of exons 6 and 7 of the ABO gene using PCR-RFLP analysis. Additionally, the Native American AIM O1v542 was characterized by direct sequencing. The four Córdoba populations did not show significant geographic structure, although the frequency of the O1v542 haplotype, detected in all the populations studied, ranged from 0.019 to 0.222. The principal component analysis based on O allele distribution showed that the populations from Córdoba clustered close to the admixed populations of Santiago and Mexico City, and at intermediate distances between European and Native American populations, while being distant from the African population. The results demonstrate that the analysis of the ABO system constitutes a useful tool for the study of the genetic structure and evolutionary history of human populations, reflecting accurately the relative contribution of parental continental contribution to the gene pool of admixed populations. © 2017 Wiley Periodicals, Inc.

  18. [Genetic polymorphism of flax Linum usitatissimum based on use of molecular cytogenetic markers].

    Rachinskaia, O A; Lemesh, V A; Muravenko, O V; Iurkevich, O Iu; Guzenko, E V; Bol'sheva, N L; Bogdanova, M V; Samatadze, T E; Popov, K V; Malyshev, S V; Shostak, N G; Heller, K; Khotyleva, L V; Zelenin, A V

    2011-01-01

    Using a set of approaches based on the use of molecular cytogenetic markers (DAPI/C-banding, estimation of the total area of DAPI-positive regions in prophase nuclei, FISH with 26S and 5S rDNA probes) and the microsatellite (SSR-PCR) assay, we studied genomic polymorphism in 15 flax (Linum usitatissimum L.) varieties from different geographic regions belonging to three directions of selection (oil, fiber, and intermediate flaxes) and in the k-37 x Viking hybrid. All individual chromosomes have been identified in the karyotypes of these varieties on the basis of the patterns of differential DAPI/C-banding and the distribution of 26S and 5S rDNA, and idiograms of the chromosomes have been generated. Unlike the oil flax varieties, the chromosomes in the karyotypes of the fiber flax varieties have, as a rule, pericentromeric and telomeric DAPI-positive bands of smaller size, but contain larger intercalary regions. Two chromosomal rearrangements (chromosome 3 inversions) were discovered in the variety Luna and in the k-37 x Viking hybrid. In both these forms, no colocalization of 26S rDNA and 5S rDNA on the satellite chromosome was detected. The SSR assay with the use of 20 polymorphic pairs of primers revealed 22 polymorphic loci. Based on the SSR data, we analyzed genetic similarity of the flax forms studied and constructed a genetic similarity dendrogram. The genotypes studied here form three clusters. The oil varieties comprise an independent cluster. The genetically related fiber flax varieties Vita and Luna, as well as the landrace Lipinska XIII belonging to the intermediate type, proved to be closer to the oil varieties than the remaining fiber flax varieties. The results of the molecular chromosomal analysis in the fiber and oil flaxes confirm their very close genetic similarity. In spite of this, the combined use of the chromosomal and molecular markers has opened up unique possibilities for describing the genotypes of flax varieties and creating their genetic

  19. Insertion polymorphisms of SINE200 retrotransposons within speciation islands of Anopheles gambiae molecular forms

    Tu Zhijian

    2008-08-01

    Full Text Available Abstract Background SINEs (Short INterspersed Elements are homoplasy-free and co-dominant genetic markers which are considered to represent useful tools for population genetic studies, and could help clarifying the speciation processes ongoing within the major malaria vector in Africa, Anopheles gambiae s.s. Here, we report the results of the analysis of the insertion polymorphism of a nearly 200 bp-long SINE (SINE200 within genome areas of high differentiation (i.e. "speciation islands" of M and S A. gambiae molecular forms. Methods A SINE-PCR approach was carried out on thirteen SINE200 insertions in M and S females collected along the whole range of distribution of A. gambiae s.s. in sub-Saharan Africa. Ten specimens each for Anopheles arabiensis, Anopheles melas, Anopheles quadriannulatus A and 15 M/S hybrids from laboratory crosses were also analysed. Results Eight loci were successfully amplified and were found to be specific for A. gambiae s.s.: 5 on 2L chromosome and one on X chromosome resulted monomorphic, while two loci positioned respectively on 2R (i.e. S200 2R12D and X (i.e. S200 X6.1 chromosomes were found to be polymorphic. S200 2R12D was homozygote for the insertion in most S-form samples, while intermediate levels of polymorphism were shown in M-form, resulting in an overall high degree of genetic differentiation between molecular forms (Fst = 0.46 p S200 X6.1 was found to be fixed in all M- and absent in all S-specimens. This led to develop a novel easy-to-use PCR approach to straightforwardly identify A. gambiae molecular forms. This novel approach allows to overcome the constraints associated with markers on the rDNA region commonly used for M and S identification. In fact, it is based on a single copy and irreversible SINE200 insertion and, thus, is not subjected to peculiar evolutionary patterns affecting rDNA markers, e.g. incomplete homogenization of the arrays through concerted evolution and/or mixtures of M and S IGS

  20. Molecular basis of the apolipoprotein H (beta 2-glycoprotein I) protein polymorphism

    Sanghera, Dharambir K; Kristensen, Torsten; Hamman, Richard F

    1997-01-01

    Apolipoprotein H (apoH, protein; APOH, gene) is considered to be an essential cofactor for the binding of certain antiphospholipid autoantibodies to anionic phospholipids. APOH exhibits a genetically determined structural polymorphism due to the presence of three common alleles (APOH*1, APOH*2...... was observed sporadically in blacks (0.008), it was present at a polymorphic frequency in Hispanics (0.027) and non-Hispanic whites (0.059). The identification of the molecular basis of the APOH protein polymorphism will help to elucidate the structural – functional relationship of apoH in the production...

  1. Parallel Molecular Distributed Detection With Brownian Motion.

    Rogers, Uri; Koh, Min-Sung

    2016-12-01

    This paper explores the in vivo distributed detection of an undesired biological agent's (BAs) biomarkers by a group of biological sized nanomachines in an aqueous medium under drift. The term distributed, indicates that the system information relative to the BAs presence is dispersed across the collection of nanomachines, where each nanomachine possesses limited communication, computation, and movement capabilities. Using Brownian motion with drift, a probabilistic detection and optimal data fusion framework, coined molecular distributed detection, will be introduced that combines theory from both molecular communication and distributed detection. Using the optimal data fusion framework as a guide, simulation indicates that a sub-optimal fusion method exists, allowing for a significant reduction in implementation complexity while retaining BA detection accuracy.

  2. Distribution and linkage disequilibrium analysis of polymorphisms of ...

    2Five-Star Animal Health Pharmaceutical Factory of Jilian Province, 5333 Xi'an Road, Changchun, Jilin 130062,. People's .... showed that GH peptide sequence of mature protein in. Rongjiang pig ..... 1, white. (PIC value <0.25, low polymorphism; 0.25

  3. Systematic examination of polymorphism in amyloid fibrils by molecular-dynamics simulation.

    Berryman, Joshua T; Radford, Sheena E; Harris, Sarah A

    2011-05-04

    Amyloid fibrils often exhibit polymorphism. Polymorphs are formed when proteins or peptides with identical sequences self-assemble into fibrils containing substantially different arrangements of the β-strands. We used atomistic molecular-dynamics simulation to examine the thermodynamic stability of a amyloid fibrils in different polymorphic forms by performing a systematic investigation of sequence and symmetry space for a series of peptides with a range of physicochemical properties. We show that the stability of fibrils depends on both sequence and the symmetry because these factors determine the availability of favorable interactions between the peptide strands within a sheet and in intersheet packing. By performing a detailed analysis of these interactions as a function of symmetry, we obtained a series of simple design rules that can be used to determine which polymorphs of a given sequence are most likely to form thermodynamically stable fibrils. These rules can potentially be employed to design peptide sequences that aggregate into a preferred polymorphic form for nanotechnological purposes. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. Polymorphic Ring-Shaped Molecular Clusters Made of Shape-Variable Building Blocks

    Keitel Cervantes-Salguero

    2015-02-01

    Full Text Available Self-assembling molecular building blocks able to dynamically change their shapes, is a concept that would offer a route to reconfigurable systems. Although simulation studies predict novel properties useful for applications in diverse fields, such kinds of building blocks, have not been implemented thus far with molecules. Here, we report shape-variable building blocks fabricated by DNA self-assembly. Blocks are movable enough to undergo shape transitions along geometrical ranges. Blocks connect to each other and assemble into polymorphic ring-shaped clusters via the stacking of DNA blunt-ends. Reconfiguration of the polymorphic clusters is achieved by the surface diffusion on mica substrate in response to a monovalent salt concentration. This work could inspire novel reconfigurable self-assembling systems for applications in molecular robotics.

  5. Virulence and molecular polymorphism of Prunus necrotic ringspot virus isolates.

    Hammond, R W; Crosslin, J M

    1998-07-01

    Prunus necrotic ringspot virus (PNRSV) occurs as numerous strains or isolates that vary widely in their pathogenic, biophysical and serological properties. Prior attempts to distinguish pathotypes based upon physical properties have not been successful; our approach was to examine the molecular properties that may distinguish these isolates. The nucleic acid sequence was determined from 1.65 kbp RT-PCR products derived from RNA 3 of seven distinct isolates of PNRSV that differ serologically and in pathology on sweet cherry. Sequence comparisons of ORF 3a (putative movement protein) and ORF 3b (coat protein) revealed single nucleotide and amino acid differences with strong correlations to serology and symptom types (pathotypes). Sequence differences between serotypes and pathotypes were also reflected in the overall phylogenetic relationships between the isolates.

  6. A Comprehensive Experiment for Molecular Biology: Determination of Single Nucleotide Polymorphism in Human REV3 Gene Using PCR-RFLP

    Zhang, Xu; Shao, Meng; Gao, Lu; Zhao, Yuanyuan; Sun, Zixuan; Zhou, Liping; Yan, Yongmin; Shao, Qixiang; Xu, Wenrong; Qian, Hui

    2017-01-01

    Laboratory exercise is helpful for medical students to understand the basic principles of molecular biology and to learn about the practical applications of molecular biology. We have designed a lab course on molecular biology about the determination of single nucleotide polymorphism (SNP) in human REV3 gene, the product of which is a subunit of…

  7. Polymorphic transitions in single crystals: A new molecular dynamics method

    Parrinello, M.; Rahman, A.

    1981-12-01

    A new Lagrangian formulation is introduced. It can be used to make molecular dynamics (MD) calculations on systems under the most general, externally applied, conditions of stress. In this formulation the MD cell shape and size can change according to dynamical equations given by this Lagrangian. This new MD technique is well suited to the study of structural transformations in solids under external stress and at finite temperature. As an example of the use of this technique we show how a single crystal of Ni behaves under uniform uniaxial compressive and tensile loads. This work confirms some of the results of static (i.e., zero temperature) calculations reported in the literature. We also show that some results regarding the stress-strain relation obtained by static calculations are invalid at finite temperature. We find that, under compressive loading, our model of Ni shows a bifurcation in its stress-strain relation; this bifurcation provides a link in configuration space between cubic and hexagonal close packing. It is suggested that such a transformation could perhaps be observed experimentally under extreme conditions of shock.

  8. Polymorphic transitions in single crystals: A new molecular dynamics method

    Parrinello, M.; Rahman, A.

    1981-01-01

    A new Lagrangian formulation is introduced. It can be used to make molecular dynamics (MD) calculations on systems under the most general, externally applied, conditions of stress. In this formulation the MD cell shape and size can change according to dynamical equations given by this Lagrangian. This new MD technique is well suited to the study of structural transformations in solids under external stress and at finite temperature. As an example of the use of this technique we show how a single crystal of Ni behaves under uniform uniaxial compressive and tensile loads. This work confirms some of the results of static (i.e., zero temperature) calculations reported in the literature. We also show that some results regarding the stress-strain relation obtained by static calculations are invalid at finite temperature. We find that, under compressive loading, our model of Ni shows a bifurcation in its stress-strain relation; this bifurcation provides a link in configuration space between cubic and hexagonal close packing. It is suggested that such a transformation could perhaps be observed experimentally under extreme conditions of shock

  9. Supra-molecular Association and Polymorphic Behaviour In Systems Containing Bile Acid Salts

    Camillo La Mesa

    2007-08-01

    Full Text Available A wide number of supra-molecular association modes are observed in mixtures containing water and bile salts, BS, (with, eventually, other components. Molecular or micellar solutions transform into hydrated solids, fibres, lyotropic liquid crystals and/or gels by raising the concentration, the temperature, adding electrolytes, surfactants, lipids and proteins. Amorphous or ordered phases may be formed accordingly. The forces responsible for this very rich polymorphism presumably arise from the unusual combination of electrostatic, hydrophobic and hydrogen-bond contributions to the system stability, with subsequent control of the supra-molecular organisation modes. The stabilising effect due to hydrogen bonds does not occur in almost all surfactants or lipids and is peculiar to bile acids and salts. Some supra-molecular organisation modes, supposed to be related to malfunctions and dis-metabolic diseases in vivo, are briefly reported and discussed.

  10. Molecular evolution of the Li/li chemical defence polymorphism in white clover (Trifolium repens L.).

    Olsen, K M; Sutherland, B L; Small, L L

    2007-10-01

    White clover (Trifolium repens) is naturally polymorphic for cyanogenesis (hydrogen cyanide release following tissue damage). The ecological factors favouring cyanogenic and acyanogenic plants have been examined in numerous studies over the last half century, making this one of the best-documented examples of an adaptive polymorphism in plants. White clover cyanogenesis is controlled by two, independently segregating Mendelian genes: Ac/ac controls the presence/absence of cyanogenic glucosides; and Li/li controls the presence/absence of their hydrolysing enzyme, linamarase. In this study, we examine the molecular evolution and population genetics of Li as it relates to the cyanogenesis polymorphism. We report here that Li exists as a single-copy gene in plants possessing linamarase activity, and that the absence of enzyme activity in li/li plants is correlated with the absence of much or all of the gene from the white clover genome. Consistent with this finding, we confirm by reverse transcription-polymerase chain reaction that Li gene expression is absent in plants lacking enzyme activity. In a molecular population genetic analysis of Li and three unlinked genes using a worldwide sample of clover plants, we find an absence of nucleotide variation and statistically significant deviations from neutrality at Li; these findings are consistent with recent positive directional selection at this cyanogenesis locus.

  11. Approximation to the distribution of fitness effects across functional categories in human segregating polymorphisms.

    Fernando Racimo

    2014-11-01

    Full Text Available Quantifying the proportion of polymorphic mutations that are deleterious or neutral is of fundamental importance to our understanding of evolution, disease genetics and the maintenance of variation genome-wide. Here, we develop an approximation to the distribution of fitness effects (DFE of segregating single-nucleotide mutations in humans. Unlike previous methods, we do not assume that synonymous mutations are neutral or not strongly selected, and we do not rely on fitting the DFE of all new nonsynonymous mutations to a single probability distribution, which is poorly motivated on a biological level. We rely on a previously developed method that utilizes a variety of published annotations (including conservation scores, protein deleteriousness estimates and regulatory data to score all mutations in the human genome based on how likely they are to be affected by negative selection, controlling for mutation rate. We map this and other conservation scores to a scale of fitness coefficients via maximum likelihood using diffusion theory and a Poisson random field model on SNP data. Our method serves to approximate the deleterious DFE of mutations that are segregating, regardless of their genomic consequence. We can then compare the proportion of mutations that are negatively selected or neutral across various categories, including different types of regulatory sites. We observe that the distribution of intergenic polymorphisms is highly peaked at neutrality, while the distribution of nonsynonymous polymorphisms has a second peak at [Formula: see text]. Other types of polymorphisms have shapes that fall roughly in between these two. We find that transcriptional start sites, strong CTCF-enriched elements and enhancers are the regulatory categories with the largest proportion of deleterious polymorphisms.

  12. Extensive variation in the density and distribution of DNA polymorphism in sorghum genomes.

    Joseph Evans

    Full Text Available Sorghum genotypes currently used for grain production in the United States were developed from African landraces that were imported starting in the mid-to-late 19(th century. Farmers and plant breeders selected genotypes for grain production with reduced plant height, early flowering, increased grain yield, adaptation to drought, and improved resistance to lodging, diseases and pests. DNA polymorphisms that distinguish three historically important grain sorghum genotypes, BTx623, BTx642 and Tx7000, were characterized by genome sequencing, genotyping by sequencing, genetic mapping, and pedigree-based haplotype analysis. The distribution and density of DNA polymorphisms in the sequenced genomes varied widely, in part because the lines were derived through breeding and selection from diverse Kafir, Durra, and Caudatum race accessions. Genomic DNA spanning dw1 (SBI-09 and dw3 (SBI-07 had identical haplotypes due to selection for reduced height. Lower SNP density in genes located in pericentromeric regions compared with genes located in euchromatic regions is consistent with background selection in these regions of low recombination. SNP density was higher in euchromatic DNA and varied >100-fold in contiguous intervals that spanned up to 300 Kbp. The localized variation in DNA polymorphism density occurred throughout euchromatic regions where recombination is elevated, however, polymorphism density was not correlated with gene density or DNA methylation. Overall, sorghum chromosomes contain distal euchromatic regions characterized by extensive, localized variation in DNA polymorphism density, and large pericentromeric regions of low gene density, diversity, and recombination.

  13. Polymorphisms in the endocannabinoid receptor 1 in relation to fat mass distribution

    Nielsen, Morten Frost; Nielsen, T L; Wraae, K

    2010-01-01

    OBJECTIVE: Both animal and human studies have associated the endocannabinoid system with obesity and markers of metabolic dysfunction. Blockade of the cannabinoid receptor 1 (CB1) caused weight loss and reduction in waist size in both obese and type II diabetics. Recent studies on common variants...... of the CB1 receptor gene (CNR1) and the link to obesity have been conflicting. The aim of the present study was to evaluate whether selected common variants of the CNR1 are associated with measures of obesity and fat distribution. DESIGN AND METHODS: The single nucleotide polymorphisms (SNPs) rs806381, rs......10485179 and rs1049353 were genotyped, and body fat and fat distribution were assessed by the use of dual-energy X-ray absorptiometry and magnetic resonance imaging in a population-based study comprising of 783 Danish men, aged 20-29 years. RESULTS: The rs806381 polymorphism was significantly associated...

  14. Cooling Crystallization of Indomethacin: Effect of Supersaturation, Temperature and Seeding on Polymorphism and Crystal Size Distribution

    Malwade, Chandrakant Ramkrishna; Qu, Haiyan

    2018-01-01

    In this work, effect of crystallization parameters i.e., supersaturation, seeding, and temperature on polymorphism and crystal size of a non-steroidal anti-inflammatory drug, indomethacin (IMC), was investigated. Firstly, several crystallization solvents (ethanol, methanol, ethyl acetate, acetone...... of IMC from ethanol confirmed that the supersaturation, operating temperature and seeding does affect the polymorphism as well as crystal size distribution of IMC. Fine needle shaped crystals of metastable α-IMC were obtained at 5 °C with high supersaturation even in presence of γ-IMC seeds, while...... rhombic plates like crystals of thermodynamically stable γ-IMC were obtained in remaining experiments. The amount of seed loading only marginally influenced the crystal growth rate and median particle diameter (d50). Particle size analysis of crystals obtained showed bimodal distribution in all...

  15. Sequence-Related Amplified Polymorphism (SRAP Markers: A Potential Resource for Studies in Plant Molecular Biology

    Daniel W. H. Robarts

    2014-07-01

    Full Text Available In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR, random-amplified polymorphic DNA (RAPD, and amplified fragment length polymorphism (AFLP to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use. highly variable marker with inherent biological significance.

  16. Molecular profiles of Venezuelan isolates of Trypanosoma sp. by random amplified polymorphic DNA method.

    Perrone, T M; Gonzatti, M I; Villamizar, G; Escalante, A; Aso, P M

    2009-05-12

    Nine Trypanosoma sp. Venezuelan isolates, initially presumed to be T. evansi, were collected from three different hosts, capybara (Apure state), horse (Apure state) and donkey (Guarico state) and compared by the random amplification polymorphic DNA technique (RAPD). Thirty-one to 46 reproducible fragments were obtained with 12 of the 40 primers that were used. Most of the primers detected molecular profiles with few polymorphisms between the seven horse, capybara and donkey isolates. Quantitative analyses of the RAPD profiles of these isolates revealed a high degree of genetic conservation with similarity coefficients between 85.7% and 98.5%. Ten of the primers generated polymorphic RAPD profiles with two of the three Trypanosoma sp. horse isolates, namely TeAp-N/D1 and TeGu-N/D1. The similarity coefficient between these two isolates and the rest, ranged from 57.9% to 68.4% and the corresponding dendrogram clustered TeAp-N/D1 and Te Gu-N/D1 in a genetically distinct group.

  17. Molecular polymorphism of a cell surface proteoglycan: distinct structures on simple and stratified epithelia.

    Sanderson, R D; Bernfield, M

    1988-12-01

    Epithelial cells are organized into either a single layer (simple epithelia) or multiple layers (stratified epithelia). Maintenance of these cellular organizations requires distinct adhesive mechanisms involving many cell surface molecules. One such molecule is a cell surface proteoglycan, named syndecan, that contains both heparan sulfate and chondroitin sulfate chains. This proteoglycan binds cells to fibrillar collagens and fibronectin and thus acts as a receptor for interstitial matrix. The proteoglycan is restricted to the basolateral surface of simple epithelial cells, but is located over the entire surface of stratified epithelial cells, even those surfaces not contacting matrix. We now show that the distinct localization in simple and stratified epithelia correlates with a distinct proteoglycan structure. The proteoglycan from simple epithelia (modal molecular size, 160 kDa) is larger than that from stratified epithelia (modal molecular size, 92 kDa), but their core proteins are identical in size and immunoreactivity. The proteoglycan from simple epithelia has more and larger heparan sulfate and chondroitin sulfate chains than the proteoglycan from stratified epithelia. Thus, the cell surface proteoglycan shows a tissue-specific structural polymorphism due to distinct posttranslational modifications. This polymorphism likely reflects distinct proteoglycan functions in simple and stratified epithelia, potentially meeting the different adhesive requirements of the cells in these different organizations.

  18. A molecular perspective on a complex polymorphic inversion system with cytological evidence of multiply reused breakpoints.

    Orengo, D J; Puerma, E; Papaceit, M; Segarra, C; Aguadé, M

    2015-06-01

    Genome sequence comparison across the Drosophila genus revealed that some fixed inversion breakpoints had been multiply reused at this long timescale. Cytological studies of Drosophila inversion polymorphism had previously shown that, also at this shorter timescale, some breakpoints had been multiply reused. The paucity of molecularly characterized polymorphic inversion breakpoints has so far precluded contrasting whether cytologically shared breakpoints of these relatively young inversions are actually reused at the molecular level. The E chromosome of Drosophila subobscura stands out because it presents several inversion complexes. This is the case of the E1+2+9+3 arrangement that originated from the ancestral Est arrangement through the sequential accumulation of four inversions (E1, E2, E9 and E3) sharing some breakpoints. We recently identified the breakpoints of inversions E1 and E2, which allowed establishing reuse at the molecular level of the cytologically shared breakpoint of these inversions. Here, we identified and sequenced the breakpoints of inversions E9 and E3, because they share breakpoints at sections 58D and 64C with those of inversions E1 and E2. This has allowed establishing that E9 and E3 originated through the staggered-break mechanism. Most importantly, sequence comparison has revealed the multiple reuse at the molecular level of the proximal breakpoint (section 58D), which would have been used at least by inversions E2, E9 and E3. In contrast, the distal breakpoint (section 64C) might have been only reused once by inversions E1 and E2, because the distal E3 breakpoint is displaced >70 kb from the other breakpoint limits.

  19. Allele and Genotype Distributions of DNA Repair Gene Polymorphisms in South Indian Healthy Population

    Katiboina Srinivasa Rao

    2014-01-01

    Full Text Available Various DNA repair pathways protect the structural and chemical integrity of the human genome from environmental and endogenous threats. Polymorphisms of genes encoding the proteins involved in DNA repair have been found to be associated with cancer risk and chemotherapeutic response. In this study, we aim to establish the normative frequencies of DNA repair genes in South Indian healthy population and compare with HapMap populations. Genotyping was done on 128 healthy volunteers from South India, and the allele and genotype distributions were established. The minor allele frequency of Xeroderma pigmentosum group A ( XPA G23A, Excision repair cross-complementing 2 ( ERCC2 /Xeroderma pigmentosum group D ( XPD Lys751Gln, Xeroderma pigmentosum group G ( XPG His46His, XPG Asp1104His, and X-ray repair cross-complementing group 1 ( XRCC1 Arg399Gln polymorphisms were 49.2%, 36.3%, 48.0%, 23.0%, and 34.0% respectively. Ethnic variations were observed in the frequency distribution of these polymorphisms between the South Indians and other HapMap populations. The present work forms the groundwork for cancer association studies and biomarker identification for treatment response and prognosis.

  20. Data on genotypic distribution and linkage disequilibrium of several ANRIL polymorphisms in hemodialysis patients

    A. Arbiol-Roca

    2017-04-01

    Full Text Available A long non-coding RNA called ANRIL located on chromosome 9p21.3 has been identified as a novel genetic factor associated with cardiovascular disease. Investigation of several single nucleotide polymorphisms (SNPs of Noncoding Antisense RNA in the INK4 Locus (ANRIL gene are of particular interest. This article reports data related to the research article entitled: “Association of ANRIL gene polymorphisms with major adverse cardiovascular events in hemodialysis patients” (Arbiol-Roca et al. [1]. Data presented show the genotypic distribution of four selected ANRIL SNPs: rs10757278, rs4977574, rs10757274 and rs6475606 in a cohort constituted by 284 hemodialysis patients. This article analyzes the Hardy-Weinberg disequilibrium of each studied SNP, and the linkage disequilibrium between them.

  1. The Influence of Single Nucleotide Polymorphism Microarray-Based Molecular Karyotype on Preimplantation Embryonic Development Potential.

    Gang Li

    Full Text Available In order to investigate the influence of the molecular karyotype based on single nucleotide polymorphism (SNP microarray on embryonic development potential in preimplantation genetic diagnosis (PGD, we retrospectively analyzed the clinical data generated by PGD using embryos retrieved from parents with chromosome rearrangements in our center. In total, 929 embryos from 119 couples had exact diagnosis and development status. The blastocyst formation rate of balanced molecular karyotype embryos was 56.6% (276/488, which was significantly higher than that of genetic imbalanced embryos 24.5% (108/441 (P35 respectively. Blastocyst formation rates of male and female embryos were 44.5% (183/411 and 38.8% (201/518 respectively, with no significant difference between them (P>0.05. The rates of balanced molecular karyotype embryos vary from groups of embryos with different cell numbers at 68 hours after insemination. The blastocyst formation rate of embryos with 6-8 cells (48.1% was significantly higher than that of embryos with 8 cells (42.9% (P8 cells, embryos with 6-8 blastomeres have higher rate of balanced molecular karyotype and blastocyst formation.

  2. Molecular weight and its distribution of tetrafluoroethylene and propylene copolymer

    Watanabe, Hiromasa; Okamoto, Jiro; Yamaguchi, Koichi.

    1978-04-01

    In comparison of molecular structure of tetrafluoroethylene and propylene copolymer produced by radiation and chemical initiators respectively, both were fractionated by elution method and fine structure was examined. For the fractionated sample by radiation, the relation between molecular weight anti Mn and intrinsic viscosity ( eta] is ( eta] = 3.97 x 10 -4 anti Mnsup(0.630) The result is not in agreement with that of the unfractionated sample by radiation, and similar to those of samples by chemical initiators. There is no difference, however, in the elution method of GPC between both these copolymers; the elution behavior agrees with that of standard polystyrene. Long chain branching thus exists little in the copolymer of tetrafluoroethylene and propylene. To reveal the relations between reaction conditions and molecular weight and its distribution of the copolymer produced by flow apparatus, the molecular weight distribution was measured by GPC. The method of analysis could evaluate molecular weight distribution changing constantly. (auth.)

  3. Radiation chemistry of polymer degradation processes: molecular weight distribution effects

    Viswanathan, N.S.

    1976-01-01

    The molecular weight distributions of poly(methyl methacrylate) irradiated at 15 and 25 MeV with electron beams were investigated. The experimental values for the effect of chain scissions on the dispersivity agreed well with theoretical predictions

  4. Chloroquine resistant Plasmodium vivax: in vitro characterisation and association with molecular polymorphisms.

    Rossarin Suwanarusk

    2007-10-01

    Full Text Available Treatment failure of chloroquine for P. vivax infections has reached high levels in the eastern provinces of Indonesia, however, in vitro characterization of chloroquine resistance and its associated molecular profile have yet to be determined.Using a modified schizont maturation assay we investigated the in vitro chloroquine susceptibility profile and molecular polymorphisms of P. vivax isolates collected from Papua, Indonesia, where high levels of clinical chloroquine treatment failure have been reported, and from Thailand, where chloroquine treatment is generally effective.The geometric mean chloroquine IC(50 for P. vivax isolates from Papua (n = 145 was 312 nM [95%CI: 237-411 nM] compared to 46.8 nM [95%CI: 34.7-63.1 nM] from Thailand (n = 81; p<0.001. Correlating with the known clinical efficacy of the area, a cut off for chloroquine resistance was defined as 220 nM, a level exceeded in 13.6% (11/81 of Thai isolates and 65% (94/145 of Papuan isolates; p<0.001. Several sequence polymorphisms in pvcrt-o and pvmdr1, and difference in pvmdr1 copy number were identified. A Y976F mutation in pvmdr1 was present in 96% (123/128 of Papuan isolates and 25% (17/69 of Thai isolates; p<0.001. Overall, the geometric mean chloroquine IC(50 in isolates with the Y976F mutation was 283 nM [95%CI: 211-379], compared to 44.5 nM [95%CI: 31.3-63.4] in isolates with the wild type; p< 0.001. Pvmdr1 amplification occurred in 23% (15/66 of Thai isolates compared to none (0/104 of Indonesian isolates (p<0.001, but was not associated with increased chloroquine resistance after controlling for geographical location.In vitro susceptibility testing of P. vivax discriminates between populations with differing levels of clinical efficacy of chloroquine. The pvmdr1 polymorphism at Y976F may provide a useful tool to highlight areas of emerging chloroquine resistance, although further studies defining its clinical correlates are needed.

  5. Toxocariasis in Carnivora from Argentinean Patagonia: Species molecular identification, hosts, and geographical distribution

    R.M. Vega

    2018-04-01

    Full Text Available Twenty four specimens of seven species belonging to the families Felidae, Mustelidae, and Canidae were obtained in Lanín and Nahuel Huapi National Parks from March 1996 to April 2016. Specimens were processed by necropsy in order to contribute to the knowledge of toxocariasis in wild carnivores of Argentinean Patagonia. The only Puma concolor and the seven Leopardus geoffroyi were positive for Toxocara cati. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP of the ITS-1 region from larval and adult DNA was carried out to confirm parasite species identification. This is the first molecular determination of T. cati from wild felids in Argentina and the study also fill gaps about the spatial distribution and hosts for Toxocara cati. Keywords: Toxocara cati, Puma concolor, Leopardus geoffroyi, Molecular identification, Argentina

  6. Functional analysis and molecular dynamics simulation of LOX-1 K167N polymorphism reveal alteration of receptor activity.

    Silvia Biocca

    Full Text Available The human lectin-like oxidized low density lipoprotein receptor 1 LOX-1, encoded by the ORL1 gene, is the major scavenger receptor for oxidized low density lipoprotein in endothelial cells. Here we report on the functional effects of a coding SNP, c.501G>C, which produces a single amino acid change (K>N at codon 167. Our study was aimed at elucidating whether the c.501G>C polymorphism changes the binding affinity of LOX-1 receptor altering its function. The presence of p.K167N mutation reduces ox-LDL binding and uptake. Ox-LDL activated extracellular signal-regulated kinases 1 and 2 (ERK 1/2 is inhibited. Furthermore, ox-LDL induced biosynthesis of LOX-1 receptors is dependent on the p.K167N variation. In human macrophages, derived from c.501G>C heterozygous individuals, the ox-LDL induced LOX-1 46 kDa band is markedly lower than in induced macrophages derived from c.501G>C controls. Investigation of p.K167N mutation through molecular dynamics simulation and electrostatic analysis suggests that the ox-LDL binding may be attributed to the coupling between the electrostatic potential distribution and the asymmetric flexibility of the basic spine residues. The N/N-LOX-1 mutant has either interrupted electrostatic potential and asymmetric fluctuations of the basic spine arginines.

  7. Spatial distribution of single-nucleotide polymorphisms related to fungicide resistance and implications for sampling.

    Van der Heyden, H; Dutilleul, P; Brodeur, L; Carisse, O

    2014-06-01

    Spatial distribution of single-nucleotide polymorphisms (SNPs) related to fungicide resistance was studied for Botrytis cinerea populations in vineyards and for B. squamosa populations in onion fields. Heterogeneity in this distribution was characterized by performing geostatistical analyses based on semivariograms and through the fitting of discrete probability distributions. Two SNPs known to be responsible for boscalid resistance (H272R and H272Y), both located on the B subunit of the succinate dehydrogenase gene, and one SNP known to be responsible for dicarboximide resistance (I365S) were chosen for B. cinerea in grape. For B. squamosa in onion, one SNP responsible for dicarboximide resistance (I365S homologous) was chosen. One onion field was sampled in 2009 and another one was sampled in 2010 for B. squamosa, and two vineyards were sampled in 2011 for B. cinerea, for a total of four sampled sites. Cluster sampling was carried on a 10-by-10 grid, each of the 100 nodes being the center of a 10-by-10-m quadrat. In each quadrat, 10 samples were collected and analyzed by restriction fragment length polymorphism polymerase chain reaction (PCR) or allele specific PCR. Mean SNP incidence varied from 16 to 68%, with an overall mean incidence of 43%. In the geostatistical analyses, omnidirectional variograms showed spatial autocorrelation characterized by ranges of 21 to 1 m. Various levels of anisotropy were detected, however, with variograms computed in four directions (at 0°, 45°, 90°, and 135° from the within-row direction used as reference), indicating that spatial autocorrelation was prevalent or characterized by a longer range in one direction. For all eight data sets, the β-binomial distribution was found to fit the data better than the binomial distribution. This indicates local aggregation of fungicide resistance among sampling units, as supported by estimates of the parameter θ of the β-binomial distribution of 0.09 to 0.23 (overall median value = 0

  8. Polymorphism in molecular solids: an extraordinary system of red, orange, and yellow crystals.

    Yu, Lian

    2010-09-21

    Diamond and graphite are polymorphs of each other: they have the same composition but different structures and properties. Many other substances exhibit polymorphism: inorganic and organic, natural and manmade. Polymorphs are encountered in studies of crystallization, phase transition, materials synthesis, and biomineralization and in the manufacture of specialty chemicals. Polymorphs can provide valuable insights into crystal packing and structure-property relationships. 5-Methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, known as ROY for its red, orange, and yellow crystals, has seven polymorphs with solved structures, the largest number in the Cambridge Structural Database. First synthesized by medicinal chemists, ROY has attracted attention from solid-state chemists because it demonstrates the remarkable diversity possible in organic solids. Many structures of ROY polymorphs and their thermodynamic properties are known, making ROY an important model system for testing computational models. Though not the most polymorphic substance on record, ROY is extraordinary in that many of its polymorphs can crystallize simultaneously from the same liquid and are kinetically stable under the same conditions. Studies of ROY polymorphs have revealed a new crystallization mechanism that invalidates the common view that nucleation defines the polymorph of crystallization. A slow-nucleating polymorph can still dominate the product if it grows rapidly and nucleates on another polymorph. Studies of ROY have also helped understand a new, surprisingly fast mode of crystal growth in organic liquids cooled to the glass transition temperature. This growth mode exists only for those polymorphs that have more isotropic, and perhaps more liquid-like, packing. The rich polymorphism of ROY results from a combination of favorable thermodynamics and kinetics. Not only must there be many polymorphs of comparable energies or free energies, many polymorphs must be kinetically stable and

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

    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.

  10. Molecular size distribution of Np(V)-humate

    Sakamoto, Yoshiaki; Nagao, Seiya; Tanaka, Tadao

    1996-10-01

    Molecular size distributions of humic acid and Np(V)-humate were studied as a function of pH and an ionic strength by an ultrafiltration method. Small particle (10,000-30,000 daltons) of humic acid increased slightly with increases in solution pH. The ion strength dependence of the molecular size distribution was clearly observed for humic acid. The abundance ratio of humic acid in the range from 10,000 to 30,000 daltons increased with the ionic strength from 0.015 M to 0.105 M, in place of the decreasing of that in range from 30,000 to 100,000 daltons. Most of neptunium(V) in the 200 mg/l of the humic acid solution was fractionated into 10,000-30,000 daltons. The abundance ratio of neptunium(V) in the 10,000-30,000 daltons was not clearly dependent on pH and the ionic strength of the solution, in spite of the changing in the molecular size distribution of humic acid by the ionic strength. These results imply that the molecular size distribution of Np(V)-humate does not simply obey by that of the humic acid. Stability constant of Np(V)-humate was measured as a function of the molecular size of the humic acid. The stability constant of Np(V)-humate in the range from 10,000 to 30,000 daltons was highest value comparing with the constants in the molecular size ranges of 100,000 daltons-0.45μm, 30,000-100,000, 5,000-10,000 daltons and under 5,000 daltons. These results may indicate that the Np(V) complexation with humic acid is dominated by the interaction of neptunyl ion with the humic acid in the specific molecular size range. (author)

  11. A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms.

    Guo, Qingsheng; Bai, Zhixiong; Liu, Yuqian; Sun, Qingjiang

    2016-03-15

    In this work, we report the application of streptavidin-coated quantum dot (strAV-QD) in molecular beacon (MB) microarray assays by using the strAV-QD to label the immobilized MB, avoiding target labeling and meanwhile obviating the use of amplification. The MBs are stem-loop structured oligodeoxynucleotides, modified with a thiol and a biotin at two terminals of the stem. With the strAV-QD labeling an "opened" MB rather than a "closed" MB via streptavidin-biotin reaction, a sensitive and specific detection of label-free target DNA sequence is demonstrated by the MB microarray, with a signal-to-background ratio of 8. The immobilized MBs can be perfectly regenerated, allowing the reuse of the microarray. The MB microarray also is able to detect single nucleotide polymorphisms, exhibiting genotype-dependent fluorescence signals. It is demonstrated that the MB microarray can perform as a 4-to-2 encoder, compressing the genotype information into two outputs. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Distribution of genotypes C825T polymorphism G-protein β3-subunit gene in patients with hypertension depending on body mass index

    Prystupa L.N.

    2015-09-01

    Full Text Available The aim of the study was to investigate the frequency of genotypes of C825T polymorphism G-protein β3-subunit gene (GNB3 in patients with arterial hypertension (AH, depending on body mass index (BMI. The study involved 155 patients with verified diagnosis of AH (study group and 50 healthy individuals (control group. The patients of the main group were divided into 3 groups according to BMI: I - 35 patients with normal body weight, II - 38 patients with overweight, III - 82 patients with obesity. We used general clinical, anthropometric, instrumental, molecular-genetic and statistical methods. Probability of differences in the frequency of alleles and genotypes was determined using χ² criteria. Pairwise comparison of groups was made using nonparametric Mann-Whitney test. The difference was considered statistically significant at p <0,05. Investigation of the distribution of genotypes C825T polymorphism GNB3 in patients with AH according to BMI showed statistically significant increase in the frequency of genotypes C / T and T / T and T allele in patients with overweight and obesity as compared with patients with normal body weight (χ² = 26 8; p <0.001. The risk of weight increase in AH patients with T allele carriers is 2,2 times higher than in C allele carriers. Association of C825T polymorphism of GNB3 with a tendency to obesity and overweight in patients with AH was proved.

  13. Spatial and mass distributions of molecular clouds and spiral structure

    Kwan, J.; Valdes, F.; National Optical Astronomy Observatories, Tucson, AZ)

    1987-01-01

    The growth of molecular clouds resulting from cloud-cloud collisions and coalescence in the Galactic ring between 4 and 8 kpc are modeled, taking into account the presence of a spiral potential and the mutual cloud-cloud gravitational attraction. The mean lifetime of molecular clouds is determined to be about 200 million years. The clouds are present in both spiral arm and interarm regions, but a spiral pattern in their spatial distribution is clearly discernible, with the more massive clouds showing a stronger correlation with the spiral arms. As viewed from within the Galactic disk, however, it is very difficult to ascertain that the molecular cloud distribution in longitude-velocity space has a spiral pattern. 19 references

  14. Frequency of distribution of leptin receptor gene polymorphism in obstructive sleep apnea patients.

    Popko, K; Gorska, E; Wasik, M; Stoklosa, A; Pływaczewski, R; Winiarska, M; Gorecka, D; Sliwinski, P; Demkow, U

    2007-11-01

    Leptin is an adipocyte-derived hormone regulating energy homeostasis and body weight. Leptin concentration is increased in patients with the obstructive sleep apnea syndrome (OSAS). Leptin receptor (LEPR) is a single transmembrane protein belonging to the superfamily of cytokine receptors related by a structure to the hemopoietin receptor family. The aim of the present study was to evaluate the frequency of distribution of leptin receptor gene polymorphism GLN223ARG in OSAS patients compared with healthy controls. The examined group included 179 subjects: 102 OSAS patients (74 men and 28 women) and 77 non-apneic controls (39 men and 38 women). Genomic DNA was isolated with the use of a column method and genotyping of DNA sequence variation was carried out by restriction enzyme analysis of PCR-amplified DNA. The results revealed a significant correlation between the polymorphism of LEPR and OSAS. Carriers of Arg allele in homozygotic genotype Arg/Arg and heterozygotic genotype Gln/Arg were more often obese and developed OSAS than the group of carriers of homozygotic Gln/Gln genotype. This tendency was observed in the whole examined population and in the group of obese women. We also found the highest levels of total cholesterol, LDL, HDL, and triglycerides in the group of homozygotic Arg/Arg genotype carriers, lower in heterozygotic Gln/Arg genotype carriers, and the lowest in the group of persons carring homozygotic Gln/Gln genotype. The presence of Arg allel seems linked to a higher risk of obesity and higher lipid levels in OSAS patients. OSAS may have a strong genetic basis due to the effects from a variety of genes including those for leptin receptor.

  15. Leishmania isoenzyme polymorphisms in Ecuador: Relationships with geographic distribution and clinical presentation

    Calvopina, Manuel; Armijos, Rodrigo X; Marco, Jorge D; Uezato, Hiroshi; Kato, Hirotomo; Gomez, Eduardo A; Korenaga, Masataka; Barroso, Paola A; Mimori, Tatsuyuki; Cooper, Philip J; Nonaka, Shigeo; Hashiguchi, Yoshihisa

    2006-01-01

    Background Determinants of the clinical presentation of the leishmaniases are poorly understood but Leishmania species and strain differences are important. To examine the relationship between clinical presentation, species and isoenzyme polymorphisms, 56 Leishmania isolates from distinct presentations of American tegumentary leishmaniasis (ATL) from Ecuador were analyzed. Methods Isolates were characterized by multilocus enzyme electrophoresis for polymorphisms of 11 isoenzymes. Patients were infected in four different ecologic regions: highland and lowland jungle of the Pacific coast, Amazonian lowlands and Andean highlands. Results Six Leishmania species constituting 21 zymodemes were identified: L. (Viannia) panamensis (21 isolates, 7 zymodemes), L. (V.) guyanensis (7 isolates, 4 zymodemes), L. (V.) braziliensis (5 isolates, 3 zymodemes), L. (Leishmania) mexicana (11 isolates, 4 zymodemes), L. (L.) amazonensis (10 isolates, 2 zymodemes) and L. (L.) major (2 isolates, 1 zymodeme). L. panamensis was the species most frequently identified in the Pacific region and was associated with several clinical variants of cutaneous disease (CL); eight cases of leishmaniasis recidiva cutis (LRC) found in the Pacific highlands were associated with 3 zymodemes of this species. Mucocutaneous leishmaniasis found only in the Amazonian focus was associated with 3 zymodemes of L. braziliensis. The papular variant of CL, Uta, found in the Andean highlands was related predominantly with a single zymodeme of L. mexicana. Conclusion Our data show a high degree of phenotypic variation within species, and some evidence for associations between specific variants of ATL (i.e. Uta and LRC) and specific Leishmania zymodemes. This study further defines the geographic distribution of Leishmania species and clinical variants of ATL in Ecuador. PMID:16968553

  16. Leishmania isoenzyme polymorphisms in Ecuador: Relationships with geographic distribution and clinical presentation

    Mimori Tatsuyuki

    2006-09-01

    Full Text Available Abstract Background Determinants of the clinical presentation of the leishmaniases are poorly understood but Leishmania species and strain differences are important. To examine the relationship between clinical presentation, species and isoenzyme polymorphisms, 56 Leishmania isolates from distinct presentations of American tegumentary leishmaniasis (ATL from Ecuador were analyzed. Methods Isolates were characterized by multilocus enzyme electrophoresis for polymorphisms of 11 isoenzymes. Patients were infected in four different ecologic regions: highland and lowland jungle of the Pacific coast, Amazonian lowlands and Andean highlands. Results Six Leishmania species constituting 21 zymodemes were identified: L. (Viannia panamensis (21 isolates, 7 zymodemes, L. (V. guyanensis (7 isolates, 4 zymodemes, L. (V. braziliensis (5 isolates, 3 zymodemes, L. (Leishmania mexicana (11 isolates, 4 zymodemes, L. (L. amazonensis (10 isolates, 2 zymodemes and L. (L. major (2 isolates, 1 zymodeme. L. panamensis was the species most frequently identified in the Pacific region and was associated with several clinical variants of cutaneous disease (CL; eight cases of leishmaniasis recidiva cutis (LRC found in the Pacific highlands were associated with 3 zymodemes of this species. Mucocutaneous leishmaniasis found only in the Amazonian focus was associated with 3 zymodemes of L. braziliensis. The papular variant of CL, Uta, found in the Andean highlands was related predominantly with a single zymodeme of L. mexicana. Conclusion Our data show a high degree of phenotypic variation within species, and some evidence for associations between specific variants of ATL (i.e. Uta and LRC and specific Leishmania zymodemes. This study further defines the geographic distribution of Leishmania species and clinical variants of ATL in Ecuador.

  17. Controlling silk fibroin microspheres via molecular weight distribution

    Zeng, Dong-Mei; Pan, Jue-Jing; Wang, Qun; Liu, Xin-Fang; Wang, Hui; Zhang, Ke-Qin

    2015-01-01

    Silk fibroin (SF) microspheres were produced by salting out SF solution via the addition of potassium phosphate buffer solution (K 2 HPO 4 –KH 2 PO 4 ). The morphology, size and polydispersity of SF microspheres were adjusted by changing the molecular weight (MW) distribution and concentration of SF, as well as the ionic strength and pH of the buffer solution. Changing the conditions under which the SF fiber dissolved in the Lithium Boride (LiBr) solution resulted in altering the MW distribution of SF solution. Under optimal salting-out conditions (ionic strength > 0.7 M and pH > 7) and using a smaller and narrower SF MW distribution, SF microspheres with smoother shapes and more uniform sizes were produced. Meanwhile, the size and polydispersity of the microspheres increased when the SF concentration was increased from 0.25 mg/mL to 20 mg/mL. The improved SF microspheres, obtained by altering the distribution of molecular weight, have potential in drug and gene delivery applications. - Highlights: • MW distribution was changed by applying different dissolving methods of SF fiber. • Smaller and narrower MW distribution improves the quality of SF microspheres. • Size and polydispersity of microspheres increase as SF concentration increases. • Improved SF microspheres have potential in drug and gene delivery applications

  18. Controlling silk fibroin microspheres via molecular weight distribution

    Zeng, Dong-Mei; Pan, Jue-Jing; Wang, Qun; Liu, Xin-Fang; Wang, Hui [National Engineering Laboratory for Modern Silk, College for Textile and Clothing Engineering, Soochow University, Suzhou, Jiangsu 215123 (China); Zhang, Ke-Qin, E-mail: kqzhang@suda.edu.cn [National Engineering Laboratory for Modern Silk, College for Textile and Clothing Engineering, Soochow University, Suzhou, Jiangsu 215123 (China); Research Center of Cooperative Innovation for Functional Organic/Polymer Material Micro/Nanofabrication, Soochow University, Suzhou, Jiangsu 215123 (China)

    2015-05-01

    Silk fibroin (SF) microspheres were produced by salting out SF solution via the addition of potassium phosphate buffer solution (K{sub 2}HPO{sub 4}–KH{sub 2}PO{sub 4}). The morphology, size and polydispersity of SF microspheres were adjusted by changing the molecular weight (MW) distribution and concentration of SF, as well as the ionic strength and pH of the buffer solution. Changing the conditions under which the SF fiber dissolved in the Lithium Boride (LiBr) solution resulted in altering the MW distribution of SF solution. Under optimal salting-out conditions (ionic strength > 0.7 M and pH > 7) and using a smaller and narrower SF MW distribution, SF microspheres with smoother shapes and more uniform sizes were produced. Meanwhile, the size and polydispersity of the microspheres increased when the SF concentration was increased from 0.25 mg/mL to 20 mg/mL. The improved SF microspheres, obtained by altering the distribution of molecular weight, have potential in drug and gene delivery applications. - Highlights: • MW distribution was changed by applying different dissolving methods of SF fiber. • Smaller and narrower MW distribution improves the quality of SF microspheres. • Size and polydispersity of microspheres increase as SF concentration increases. • Improved SF microspheres have potential in drug and gene delivery applications.

  19. Molecular Characterization of Yeast Strains Isolated from Different Sources by Restriction Fragment Length Polymorphism

    Ali, M. S.; Latif, Z.

    2016-01-01

    Various molecular techniques like analysis of the amplified rDNA internal transcribed spacers (ITS), intragenic spacers and total ITS region analysis by restriction fragment length polymorphism (RFLP) has been introduced for yeast identification but there are limited databases to identify yeast species on the basis of 5.8S rDNA. In this study, twenty nine yeast strains from various sources including spoiled fruits, vegetables, foodstuffs, and concentrated juices were characterized by PCR-RFLP. PCR-RFLP has been used to characterize yeasts present in different spoiled food samples after isolation of the yeasts. By using this technique, the isolated yeast strains were characterized by direct 5.8S-ITS rDNA region amplification. RFLP analysis was applied to each of the amplification products (varied from 400bp to 800bp) detected, and the corresponding yeast identifications were made according to each specific restriction patterns obtained after treatment with two endonucleases TaqI and HaeIII which yielded a specific banding pattern for each species. For further confirmation amplified products of eleven selected isolates were sequenced and blast on NCBI. Both RFLP and sequence analyses of the strains with accession nos. KF472163, KF472164, KF472165, KF472166, KF472167, KF472168, KF472169, KF472170, KF472171, KF472172, KF472173 gave significantly similar results. The isolates were found to belong five different yeast species including; Candida spp., Pichia spp., Kluyveromyces spp., Clavispora spp. and Hanseniaspora spp. This method provides a fast, easy, reliable and authentic way for determining yeast population present in different type of samples, as compared to traditional characterization technique. (author)

  20. Breed distribution of the ABCB1-1Delta (multidrug sensitivity) polymorphism among dogs undergoing ABCB1 genotyping.

    Mealey, Katrina L; Meurs, Kathryn M

    2008-09-15

    To evaluate the breed distribution of the ABCB1-1Delta polymorphism in a large number of dogs in North America, including dogs of several herding breeds in which this polymorphism has been detected and other breeds in which this polymorphism has not yet been identified. Cross-sectional study. 5,368 dogs from which buccal swab samples were collected for purposes of ABCB1 genotyping. From May 1, 2004, to September 30, 2007, DNA specimens derived from buccal swab samples collected from 5,368 dogs underwent ABCB1 genotyping. These data were reviewed, and results for each dog were recorded in a spreadsheet, along with the dog's breed. The genotypes for each breed were tallied by use of a sorting function. The ABCB1-1Delta allele was identified in 9 breeds of dogs and in many mixed-breed dogs. Breeds that had the ABCB1-1Delta allele included Collie, Longhaired Whippet, Australian Shepherd (standard and miniature), Shetland Sheepdog, Old English Sheepdog, Border Collie, Silken Windhound, and German Shepherd Dog (a breed in which this mutation had not been detected previously). The ABCB1-1Delta polymorphism is associated with increased susceptibility to many adverse drug reactions and with suppression of the hypothalamic-pituitary-adrenal axis and is present in many herding breeds of dog. Veterinarians should be familiar with the breeds that have the ABCB1-1Delta polymorphism to make appropriate pharmacologic choices for these patients.

  1. The impact of particle preparation methods and polymorphic stability of lipid excipients on protein distribution in microparticles

    Liu, Jingying; Christophersen, Philip C; Yang, Mingshi

    2017-01-01

    OBJECTIVE: The present study aimed at elucidating the influence of polymorphic stability of lipid excipients on the physicochemical characters of different solid lipid microparticles (SLM), with the focus on the alteration of protein distribution in SLM. METHODS: Labeled lysozyme was incorporated...... provides updated knowledge for rational development of lipid-based formulations for oral delivery of peptide or protein drugs.......OBJECTIVE: The present study aimed at elucidating the influence of polymorphic stability of lipid excipients on the physicochemical characters of different solid lipid microparticles (SLM), with the focus on the alteration of protein distribution in SLM. METHODS: Labeled lysozyme was incorporated...... into SLM prepared with different excipients, i.e. trimyristin (TG14), glyceryl distearate (GDS), and glyceryl monostearate (GMS), by water-oil-water (w/o/w) or solid-oil-water (s/o/w) method. The distribution of lysozyme in SLM and the release of the protein from SLM were evaluated by confocal laser...

  2. Rotational distributions of molecular photoions following resonant excitation

    Poliakoff, E.D.; Chan, J.C.K.; White, M.G.

    1986-01-01

    We demonstrate that the photoelectron energy mediates the rotational energy distribution of N + 2 ions created by photoionization, and conversely, that rotational energy determinations probe resonant excitation in molecular photoionization. Experimentally, this is accomplished by monitoring the dispersed fluorescence from N + 2 (B 2 Σ + /sub u/) photoions to determine their rotational energy distribution. These results demonstrate that while dipole selection rules constrain the total angular momentum of the electron--ion complex, the partitioning of angular momentum between the photoelectron and photoion depends on the photoejection dynamics. Implications for photoionization and electron impact ionizatin studies are discussed

  3. Global pharmacogenomics: distribution of CYP3A5 polymorphisms and phenotypes in the Brazilian population.

    Guilherme Suarez-Kurtz

    Full Text Available The influence of self-reported "race/color", geographical origin and genetic ancestry on the distribution of three functional CYP3A5 polymorphisms, their imputed haplotypes and inferred phenotypes was examined in 909 healthy, adult Brazilians, self-identified as White, Brown or Black ("race/color" categories of the Brazilian census. The cohort was genotyped for CYP3A5*3 (rs776746, CYP3A5*6 (rs10264272 and CYP3A5*7 (rs41303343, CYP3A5 haplotypes were imputed and CYP3A5 metabolizer phenotypes were inferred according to the number of defective CYP3A5 alleles. Estimates of the individual proportions of Amerindian, African and European ancestry were available for the entire cohort. Multinomial log-linear regression models were applied to infer the statistical association between the distribution of CYP3A5 alleles, haplotypes and phenotypes (response variables, and self-reported Color, geographical region and ancestry (explanatory variables. We found that Color per se or in combination with geographical region associates significantly with the distribution of CYP3A5 variant alleles and CYP3A5 metabolizer phenotypes, whereas geographical region per se influences the frequency distribution of CYP3A5 variant alleles. The odds of having the default CYP3A5*3 allele and the poor metabolizer phenotype increases continuously with the increase of European ancestry and decrease of African ancestry. The opposite trend is observed in relation to CYP3A5*6, CYP3A5*7, the default CYP3A5*1 allele, and both the extensive and intermediate phenotypes. No significant effect of Amerindian ancestry on the distribution of CYP3A5 alleles or phenotypes was observed. In conclusion, this study strongly supports the notion that the intrinsic heterogeneity of the Brazilian population must be acknowledged in the design and interpretation of pharmacogenomic studies, and dealt with as a continuous variable, rather than proportioned in arbitrary categories that do not capture the

  4. The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism.

    Salm, Maximilian P A; Horswell, Stuart D; Hutchison, Claire E; Speedy, Helen E; Yang, Xia; Liang, Liming; Schadt, Eric E; Cookson, William O; Wierzbicki, Anthony S; Naoumova, Rossi P; Shoulders, Carol C

    2012-06-01

    Genomic inversions are an increasingly recognized source of genetic variation. However, a lack of reliable high-throughput genotyping assays for these structures has precluded a full understanding of an inversion's phylogenetic, phenotypic, and population genetic properties. We characterize these properties for one of the largest polymorphic inversions in man (the ∼4.5-Mb 8p23.1 inversion), a structure that encompasses numerous signals of natural selection and disease association. We developed and validated a flexible bioinformatics tool that utilizes SNP data to enable accurate, high-throughput genotyping of the 8p23.1 inversion. This tool was applied retrospectively to diverse genome-wide data sets, revealing significant population stratification that largely follows a clinal "serial founder effect" distribution model. Phylogenetic analyses establish the inversion's ancestral origin within the Homo lineage, indicating that 8p23.1 inversion has occurred independently in the Pan lineage. The human inversion breakpoint was localized to an inverted pair of human endogenous retrovirus elements within the large, flanking low-copy repeats; experimental validation of this breakpoint confirmed these elements as the likely intermediary substrates that sponsored inversion formation. In five data sets, mRNA levels of disease-associated genes were robustly associated with inversion genotype. Moreover, a haplotype associated with systemic lupus erythematosus was restricted to the derived inversion state. We conclude that the 8p23.1 inversion is an evolutionarily dynamic structure that can now be accommodated into the understanding of human genetic and phenotypic diversity.

  5. Interethnic differences of PEPT2 (SLC15A2) polymorphism distribution and associations with cephalexin pharmacokinetics in healthy Asian subjects.

    Liu, Rui; Tang, Audrey May Yi; Tan, Yen Ling; Limenta, Lie Michael George; Lee, Edmund Jon Deoon

    2009-01-01

    The aims of this study were to characterize the population frequency of PEPT2 (SLC15A2) polymorphic variants in three Asian ethnic populations, namely Chinese, Malay and Asian Indian, and to investigate the associations of ethnicity (Chinese vs. Asian Indian), PEPT2 haplotype and cephalexin pharmacokinetics in healthy Asian subjects. PEPT2 polymorphisms were screened from a cohort of 96 Chinese, 96 Malay and 96 Asian Indian subjects. Cephalexin (1000 mg, orally) pharmacokinetics was characterized in an additional 15 Chinese and 15 Asian Indian healthy subjects. These 30 subjects were subsequently genotyped for their PEPT2 polymorphisms. In total, ten common single nucleotide polymorphisms (SNPs) were detected in the three populations, forming two PEPT2 haplotypes. There were significant ethnic differences in PEPT2 haplotype distribution: the frequencies of the *1 and *2 alleles were 0.307 and 0.693 in the Chinese population, 0.495 and 0.505 in the Malay population and 0.729 and 0.271 in Asian Indian population, respectively. The C (max) of cephalexin was significantly lower in the Chinese (29.80 +/- 4.09 microg ml(-1)) population than in the Asian Indian one (33.29 +/- 4.97 microg ml(-1); P = 0.045). This difference could be explained by the higher average body weight of the Chinese population. There was no other significant difference in cephalexin pharmacokinetics between either ethnic or PEPT2 genotype groups. PEPT2 polymorphism distributions differ significantly between Chinese, Malay and Asian Indian populations. However, cephalexin pharmacokinetics is not meaningfully different between Chinese and Asian Indians. The association between the PEPT2 haplotype and cephalexin pharmacokinetics could not be confirmed, and future studies under better controlled conditions are needed.

  6. A comprehensive experiment for molecular biology: Determination of single nucleotide polymorphism in human REV3 gene using PCR-RFLP.

    Zhang, Xu; Shao, Meng; Gao, Lu; Zhao, Yuanyuan; Sun, Zixuan; Zhou, Liping; Yan, Yongmin; Shao, Qixiang; Xu, Wenrong; Qian, Hui

    2017-07-08

    Laboratory exercise is helpful for medical students to understand the basic principles of molecular biology and to learn about the practical applications of molecular biology. We have designed a lab course on molecular biology about the determination of single nucleotide polymorphism (SNP) in human REV3 gene, the product of which is a subunit of DNA polymerase ζ and SNPs in this gene are associated with altered susceptibility to cancer. This newly designed experiment is composed of three parts, including genomic DNA extraction, gene amplification by PCR, and genotyping by RFLP. By combining these activities, the students are not only able to learn a series of biotechniques in molecular biology, but also acquire the ability to link the learned knowledge with practical applications. This comprehensive experiment will help the medical students improve the conceptual understanding of SNP and the technical understanding of SNP detection. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):299-304, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  7. Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology1

    Robarts, Daniel W. H.; Wolfe, Andrea D.

    2014-01-01

    In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance. PMID:25202637

  8. Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology(1.).

    Robarts, Daniel W H; Wolfe, Andrea D

    2014-07-01

    In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance.

  9. Spatial and temporal distribution of the neutral polymorphisms in the last ZFX intron: analysis of the haplotype structure and genealogy.

    Jaruzelska, J; Zietkiewicz, E; Batzer, M; Cole, D E; Moisan, J P; Scozzari, R; Tavaré, S; Labuda, D

    1999-07-01

    With 10 segregating sites (simple nucleotide polymorphisms) in the last intron (1089 bp) of the ZFX gene we have observed 11 haplotypes in 336 chromosomes representing a worldwide array of 15 human populations. Two haplotypes representing 77% of all chromosomes were distributed almost evenly among four continents. Five of the remaining haplotypes were detected in Africa and 4 others were restricted to Eurasia and the Americas. Using the information about the ancestral state of the segregating positions (inferred from human-great ape comparisons), we applied coalescent analysis to estimate the age of the polymorphisms and the resulting haplotypes. The oldest haplotype, with the ancestral alleles at all the sites, was observed at low frequency only in two groups of African origin. Its estimated age of 740 to 1100 kyr corresponded to the time to the most recent common ancestor. The two most frequent worldwide distributed haplotypes were estimated at 550 to 840 and 260 to 400 kyr, respectively, while the age of the continentally restricted polymorphisms was 120 to 180 kyr and smaller. Comparison of spatial and temporal distribution of the ZFX haplotypes suggests that modern humans diverged from the common ancestral stock in the Middle Paleolithic era. Subsequent range expansion prevented substantial gene flow among continents, separating African groups from populations that colonized Eurasia and the New World.

  10. [Distribution of three polymorphisms of the TSLP gen in African-descendent population from San Basilio de Palenque, Colombia].

    Fang, Luis; Martínez, Beatriz; Marrugo, Javier

    2013-01-01

    Thymic stromal lymphopoietin (TSLP) has been linked as a susceptibility gene for the development of allergic diseases. It is known that the population of Cartagena is a triethnic mix, in which the component of African ancestry was significantly associated with risk of asthma and high total serum IgE levels. This component comes from African slaves brought into the continent and settled in "palenques", one of them is San Basilio de Palenque, in the Colombian Caribbean Coast. To analyze the distribution of single nucleotide polymorphisms (SNP) rs1837253, rs17551370 and rs2289276 located in TSLP gene, in the African-descendent population of San Basilio de Palenque. By real time-PCR and probes TaqMan SNP Genotyping™, we genotyped three polymorphisms in 80 individuals of African-descent aged 5 to 18 years of age. The frequency of the rs1837253 allele T was 41.9%, for the allele A, 14.3% for rs17551370, and 22.5% for the allele T of rs2289276. The rs17551370 and rs2289276 distribution remained in Hardy- Weinberg genetic equilibrium. The allele frequency of each SNP did not show statistically significant differences with those reported for other African and African-descendent populations. The three polymorphisms in the TSLP were present in the sample population of San Basilio de Palenque and its distribution is similar to that reported for African populations and African ancestry in America.

  11. High Molecular Weight Adiponectin Levels are Neither Influenced by Adiponectin Polymorphisms Nor Associated with Insulin Resistance in Mixed-Ancestry Hyperglycemic Subjects from South Africa

    Zemlin Annalise E

    2016-10-01

    Full Text Available Background: High molecular weight (HMW adiponectin has antiatherogenic, antiinflammatory and antidiabetic properties and these effects have been linked to its effect on high density lipoprotein cholesterol (HDL-c. Single nucleotide polymorphisms (SNPs in the adiponectin gene influence adiponectin levels. We examined the relationship between HMW-adiponectin levels and cardiometabolic traits in normo- and hyperglycemic mixed ancestry South Africans and correlated these levels to two common polymorphisms.

  12. Molecular identification and polymorphism determination of cutaneous and visceral leishmaniasis agents isolated from human and animal hosts in Iran.

    Hajjaran, Homa; Mohebali, Mehdi; Mamishi, Setareh; Vasigheh, Farzaneh; Oshaghi, Mohammad Ali; Naddaf, Saied Reza; Teimouri, Aref; Edrissian, Gholam Hossein; Zarei, Zabiholah

    2013-01-01

    Amplification of internal transcript spacer 1 of ribosomal RNA (ITS1-RNA) gene followed by RFLP analysis and sequencing was used to identify the causing agents of cutaneous and visceral leishmaniasis (CL and VL) in humans and animal reservoir hosts from various geographical areas in Iran. We also used random amplified polymorphic DNA (RAPD-PCR) to obtain polymorphisms among isolates of Leishmania spp. Totally, 362 suspected human and animal cases including 173 CL, 49 VL, 60 rodents, and 80 domestic dogs were examined for Leishmania infection. From 112 culture-positive samples prepared from CL cases, 75 (67%) were infected with L. major and 37 (33%) with L. tropica. Of the 60 rodents examined, 25 (41.6%) harbored the Leishmania infection; 21 were infected with L. major and 4 with L. turanica. From 49 suspected VL, 29 were positive by direct agglutination test (DAT), whereas microscopy detected parasite in bone marrow of 25 and culture in 28 of the patients. Two VL patients were infected with L. tropica and 26 with L. infantum. Of the 80 domestic dogs, 56 showed anti-Leishmania antibodies with DAT. Of these, 55 were positive by both microscopy and culture. Molecular identity, obtained only for 47 samples, revealed L. infantum in 43 and L. tropica in 4 dogs. The polymorphisms among L. tropica and L. major isolates were 3.6% and 7.3%; the rate among human and canine VL isolates was 2.8% and 9.8%, respectively. Our results showed that at least four different Leishmania species with various polymorphisms circulate among humans and animal hosts in Iran.

  13. Molecular Identification and Polymorphism Determination of Cutaneous and Visceral Leishmaniasis Agents Isolated from Human and Animal Hosts in Iran

    Homa Hajjaran

    2013-01-01

    Full Text Available Amplification of internal transcript spacer 1 of ribosomal RNA (ITS1-RNA gene followed by RFLP analysis and sequencing was used to identify the causing agents of cutaneous and visceral leishmaniasis (CL and VL in humans and animal reservoir hosts from various geographical areas in Iran. We also used random amplified polymorphic DNA (RAPD-PCR to obtain polymorphisms among isolates of Leishmania spp. Totally, 362 suspected human and animal cases including 173 CL, 49 VL, 60 rodents, and 80 domestic dogs were examined for Leishmania infection. From 112 culture-positive samples prepared from CL cases, 75 (67% were infected with L. major and 37 (33% with L. tropica. Of the 60 rodents examined, 25 (41.6% harbored the Leishmania infection; 21 were infected with L. major and 4 with L. turanica. From 49 suspected VL, 29 were positive by direct agglutination test (DAT, whereas microscopy detected parasite in bone marrow of 25 and culture in 28 of the patients. Two VL patients were infected with L. tropica and 26 with L. infantum. Of the 80 domestic dogs, 56 showed anti-Leishmania antibodies with DAT. Of these, 55 were positive by both microscopy and culture. Molecular identity, obtained only for 47 samples, revealed L. infantum in 43 and L. tropica in 4 dogs. The polymorphisms among L. tropica and L. major isolates were 3.6% and 7.3%; the rate among human and canine VL isolates was 2.8% and 9.8%, respectively. Our results showed that at least four different Leishmania species with various polymorphisms circulate among humans and animal hosts in Iran.

  14. Molecular diagnostics of catecholaminergic polymorphic ventricular tachycardia using denaturing high-performance liquid chromatography and sequencing

    Postma, Alex V.; Bhuiyan, Zahurul A.; Bikker, Hennie

    2006-01-01

    Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an arrhythmogenic disease characterized by adrenergic-induced arrhythmias in the form of bidirectional and PVT. CPVT is a distinct clinical entity associated with a high mortality rate of up to 50% by the age of 30 yr. Recently, the

  15. Molecular typing of Borrelia burgdorferi sensu lato by randomly amplified polymorphic DNA fingerprinting analysis

    Wang, G.; van Dam, A. P.; Spanjaard, L.; Dankert, J.

    1998-01-01

    To study whether pathogenic clusters of Borrelia burgdorferi sensu lato strains occur, we typed 136 isolates, cultured from specimens from patients (n = 49) with various clinical entities and from ticks (n = 83) or dogs (n = 4) from different geographic regions, by randomly amplified polymorphic DNA

  16. Temperature-mediated polymorphism in molecular crystals: The impact on crystal packing and charge transport

    Stevens, Loah A.; Goetz, Katelyn P.; Fonari, Alexandr; Shu, Ying; Williamson, Rachel M.; Bredas, Jean-Luc; Coropceanu, Veaceslav P.; Jurchescu, Oana D.; Collis, Gavin E.

    2015-01-01

    We report a novel synthesis to ultra high purity 7,14-bis((trimethylsilyl)ethynyl)dibenzo[b,def]-chrysene (TMS-DBC) and the use of this material in the growth of single crystals by solution and vapor deposition techniques. We observe that the substrate temperature has a dramatic impact on the crystal growth, producing two distinct polymorphs of TMS-DBC; low temperature (LT) fine red needles and high temperature (HT) large yellow platelets. Single crystal X-ray crystallography confirms packing structures where the LT crystals form a 1D slipped-stack structure, while the HT crystals adopt a 2D brickwork motif. These polymorphs also represent a rare example where both are extremely stable and do not interconvert to the other crystal structure upon solvent or thermal annealing. Single crystal organic field-effect transistors of the LT and HT crystals show that the HT 2D brickwork motif produces hole mobilities as high as 2.1 cm2 V-1 s-1, while the mobility of the 1D structure is significantly lower, at 0.028 cm2 V-1 s-1. Electronic-structure calculations indicate that the superior charge transport in the brickwork polymorph in comparison to the slipped-stack polymorph is due to the presence of an increased dimensionality of the charge migration pathways.

  17. Temperature-mediated polymorphism in molecular crystals: The impact on crystal packing and charge transport

    Stevens, Loah A.

    2015-01-13

    We report a novel synthesis to ultra high purity 7,14-bis((trimethylsilyl)ethynyl)dibenzo[b,def]-chrysene (TMS-DBC) and the use of this material in the growth of single crystals by solution and vapor deposition techniques. We observe that the substrate temperature has a dramatic impact on the crystal growth, producing two distinct polymorphs of TMS-DBC; low temperature (LT) fine red needles and high temperature (HT) large yellow platelets. Single crystal X-ray crystallography confirms packing structures where the LT crystals form a 1D slipped-stack structure, while the HT crystals adopt a 2D brickwork motif. These polymorphs also represent a rare example where both are extremely stable and do not interconvert to the other crystal structure upon solvent or thermal annealing. Single crystal organic field-effect transistors of the LT and HT crystals show that the HT 2D brickwork motif produces hole mobilities as high as 2.1 cm2 V-1 s-1, while the mobility of the 1D structure is significantly lower, at 0.028 cm2 V-1 s-1. Electronic-structure calculations indicate that the superior charge transport in the brickwork polymorph in comparison to the slipped-stack polymorph is due to the presence of an increased dimensionality of the charge migration pathways.

  18. Implementation of force distribution analysis for molecular dynamics simulations

    Seifert Christian

    2011-04-01

    Full Text Available Abstract Background The way mechanical stress is distributed inside and propagated by proteins and other biopolymers largely defines their function. Yet, determining the network of interactions propagating internal strain remains a challenge for both, experiment and theory. Based on molecular dynamics simulations, we developed force distribution analysis (FDA, a method that allows visualizing strain propagation in macromolecules. Results To be immediately applicable to a wide range of systems, FDA was implemented as an extension to Gromacs, a commonly used package for molecular simulations. The FDA code comes with an easy-to-use command line interface and can directly be applied to every system built using Gromacs. We provide an additional R-package providing functions for advanced statistical analysis and presentation of the FDA data. Conclusions Using FDA, we were able to explain the origin of mechanical robustness in immunoglobulin domains and silk fibers. By elucidating propagation of internal strain upon ligand binding, we previously also successfully revealed the functionality of a stiff allosteric protein. FDA thus has the potential to be a valuable tool in the investigation and rational design of mechanical properties in proteins and nano-materials.

  19. Association study of molecular polymorphisms in candidate genes related to stress responses with production and meat quality traits in pigs.

    Terenina, E; Babigumira, B M; Le Mignon, G; Bazovkina, D; Rousseau, S; Salin, F; Bendixen, C; Mormede, P

    2013-02-01

    The hypothalamic-pituitary-adrenal (HPA) axis exerts a large range of effects on metabolism, the immune system, inflammatory processes, and brain functions. Together with the sympathetic nervous system, it is also the most important stress-responsive neuroendocrine system. Both systems influence production traits, carcass composition, and meat quality. The HPA axis may be a critical target for genetic selection of more robust animals. Indeed, numerous studies in various species have demonstrated the importance of genetic factors in shaping the individual HPA axis phenotype, and genetic polymorphism can be found at each level of the axis, including hormone production by the adrenal cortices under stimulation by adrenocorticotropic hormone (ACTH), hormone bioavailability, or receptor and postreceptor mechanisms. The aim of the present experiment was to extend these findings to the brain neurochemical systems involved in stress responses. To this end, a number of candidate genes were sequenced for molecular polymorphisms and their association was studied with stress neuroendocrine and production traits in a genetically diverse population consisting of 100 female pigs from an advanced intercross (F10-F12) between 2 highly divergent breeds, Large White (LW) and Meishan (MS). The LW breed has a high production potential for lean meat and a low HPA axis activity, and the MS breed has low growth rate, fat carcasses-but large litters of highly viable piglets-and a high HPA axis activity. Candidate genes were chosen in the catecholaminergic and serotonergic pathways, in the pituitary control of cortisol production, among genes previously demonstrated to be differentially expressed in ACTH-stimulated adrenal glands from LW and MS pigs, and in cortisol receptors. Sixty new polymorphisms were found. The association study with carcass and meat quality traits and with endocrine traits showed a number of significant results, such as monoamine oxidase (MAOA) polymorphisms with

  20. Molecular Polymorphisms in Tunisian Pomegranate (Punica granatum L. as Revealed by RAPD Fingerprints

    Jemni Chibani

    2010-01-01

    Full Text Available The genetic diversity among Tunisian pomegranate cultivars has been investigated. Using universal primers, the random amplified polymorphic DNA (RAPD method was used to generate banding profiles from a set of twelve cultivars. Data was then computed with appropriate programs to construct a dendrogram illustrating the relationships between the studied cultivars. Our data proved the efficiency of the designed method to examine the DNA polymorphism in this crop since the tested primers are characterized by a collective resolving power of 12.83. In addition, the cluster analysis has exhibited a parsimonious tree branching independent from the geographic origin of the cultivars. In spite of the relatively low number of primers and cultivars, RAPD constitutes an appropriate procedure to assess the genetic diversity and to survey the phylogenetic relationships in this crop.

  1. Distribution and molecular evolution of bacillus anthracis genotypes in Namibia.

    Wolfgang Beyer

    Full Text Available The recent development of genetic markers for Bacillus anthracis has made it possible to monitor the spread and distribution of this pathogen during and between anthrax outbreaks. In Namibia, anthrax outbreaks occur annually in the Etosha National Park (ENP and on private game and livestock farms. We genotyped 384 B. anthracis isolates collected between 1983-2010 to identify the possible epidemiological correlations of anthrax outbreaks within and outside the ENP and to analyze genetic relationships between isolates from domestic and wild animals. The isolates came from 20 animal species and from the environment and were genotyped using a 31-marker multi-locus-VNTR-analysis (MLVA and, in part, by twelve single nucleotide polymorphism (SNP markers and four single nucleotide repeat (SNR markers. A total of 37 genotypes (GT were identified by MLVA, belonging to four SNP-groups. All GTs belonged to the A-branch in the cluster- and SNP-analyses. Thirteen GTs were found only outside the ENP, 18 only within the ENP and 6 both inside and outside. Genetic distances between isolates increased with increasing time between isolations. However, genetic distance between isolates at the beginning and end of the study period was relatively small, indicating that while the majority of GTs were only found sporadically, three genetically close GTs, accounting for more than four fifths of all the ENP isolates, appeared dominant throughout the study period. Genetic distances among isolates were significantly greater for isolates from different host species, but this effect was small, suggesting that while species-specific ecological factors may affect exposure processes, transmission cycles in different host species are still highly interrelated. The MLVA data were further used to establish a model of the probable evolution of GTs within the endemic region of the ENP. SNR-analysis was helpful in correlating an isolate with its source but did not elucidate

  2. Modeling of molecular weight and molecular weight distribution in slurry polymerization of propylene by Ziegler-Natta catalysts

    Khorasani, R.; Pourmahdian, S.

    2007-01-01

    The Precise prediction of polypropylene synthesized by heterogeneous Ziegler-Natta catalysts needs good knowledge of parameters affecting on polymerization. molecular weight and molecular weight distribution are among important characteristics of a polymer determining physical-mechanical properties. broadening of molecular weight distribution is an important and well known characteristic of polypropylene synthesized by heterogeneous Ziegler-Natta catalysts, So it is important to understand the origin of broad molecular weight. Two main factors in broadening molecular weight, namely mass transfer resistances and multiplicity of active sites, are discussed in this paper and a model including these factors is presented. Then we calculate molecular weight and molecular weight distribution by the model and compare our results with

  3. An alternative to the search for single polymorphisms: toward molecular personality scales for the five-factor model.

    McCrae, Robert R; Scally, Matthew; Terracciano, Antonio; Abecasis, Gonçalo R; Costa, Paul T

    2010-12-01

    There is growing evidence that personality traits are affected by many genes, all of which have very small effects. As an alternative to the largely unsuccessful search for individual polymorphisms associated with personality traits, the authors identified large sets of potentially related single nucleotide polymorphisms (SNPs) and summed them to form molecular personality scales (MPSs) with from 4 to 2,497 SNPs. Scales were derived from two thirds of a large (N = 3,972) sample of individuals from Sardinia who completed the Revised NEO Personality Inventory (P. T. Costa, Jr., & R. R. McCrae, 1992) and were assessed in a genomewide association scan. When MPSs were correlated with the phenotype in the remaining one third of the sample, very small but significant associations were found for 4 of the 5e personality factors when the longest scales were examined. These data suggest that MPSs for Neuroticism, Openness to Experience, Agreeableness, and Conscientiousness (but not Extraversion) contain genetic information that can be refined in future studies, and the procedures described here should be applicable to other quantitative traits. PsycINFO Database Record (c) 2010 APA, all rights reserved.

  4. Sequence based polymorphic (SBP marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome

    Sahu Binod B

    2012-01-01

    Full Text Available Abstract Background Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have made possible the identification of single nucleotide polymorphisms (SNPs for any genomic regions. Here a sequence based polymorphic (SBP marker technology for generating molecular markers for targeted genomic regions in Arabidopsis is described. Results A ~3X genome coverage sequence of the Arabidopsis thaliana ecotype, Niederzenz (Nd-0 was obtained by applying Illumina's sequencing by synthesis (Solexa technology. Comparison of the Nd-0 genome sequence with the assembled Columbia-0 (Col-0 genome sequence identified putative single nucleotide polymorphisms (SNPs throughout the entire genome. Multiple 75 base pair Nd-0 sequence reads containing SNPs and originating from individual genomic DNA molecules were the basis for developing co-dominant SBP markers. SNPs containing Col-0 sequences, supported by transcript sequences or sequences from multiple BAC clones, were compared to the respective Nd-0 sequences to identify possible restriction endonuclease enzyme site variations. Small amplicons, PCR amplified from both ecotypes, were digested with suitable restriction enzymes and resolved on a gel to reveal the sequence based polymorphisms. By applying this technology, 21 SBP markers for the marker poor regions of the Arabidopsis map representing polymorphisms between Col-0 and Nd-0 ecotypes were generated. Conclusions The SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for

  5. Molecular cloning, polymorphisms, and expression analysis of the RERG gene in indigenous Chinese goats.

    Sui, M X; Wang, H H; Wang, Z W

    2015-11-24

    The current study aimed to investigate the coding sequence, polymorphisms, and expression of the RERG gene in indigenous Chinese goats. cDNA of RERG, obtained through reverse transcription PCR was analyzed using bioinformatic techniques. Polymorphisms in the exon regions of the RERG gene were identified and their associations with growth traits in three varieties of indigenous Chinese goats were investigated. Expression of the RERG gene in three goat breeds of the same age was detected using real-time quantitative PCR. The results revealed that the cDNA of RERG, which contained a complete open reading frame of 20-620 bp, was 629 bp in length. The associated accession numbers in GenBank are JN672576, JQ917222, and JN580309 for the QianBei Ma goat, the GuiZhou white goat, and the GuiZhou black goat, respectively. Four consistent SNP sites were found in the exon regions of the RERG gene for the three goat breeds. mRNA expression of the RERG gene differed between different tissues in adult goats of same age. The highest expression was observed in lung and spleen tissues, while the lowest expression was recorded in thymus gland tissue. In addition, the expression of the RERG gene in the muscle of Guizhou white goat, GuiZhou black goat, and QianBei Ma goat decreased sequentially. Our results lay the foundations for further investigation into the role of the RERG gene in goat growth traits.

  6. Molecular weights and molecular weight distributions of irradiated cellulose fibers by gel permeation chromatography

    Kusama, Y.; Kageyama, E.; Shimada, M.; Nakamura, Y.

    1976-01-01

    Radiation degradation of cellulose fibers was investigated by gel permeation chromatography (GPC). Scoured cotton of Mexican variety (cellulose I), Polynosic rayon (cellulose II), and their microcrystalline celluloses obtained by hydrolysis of the original fibers were irradiated by Co-60 γ-rays under vacuum or humid conditions. The irradiated samples were then nitrated under nondegradative conditions. The molecular weights and molecular weight distributions were measured by GPC using tetrahydrofuran as solvent. The relationship between molecular weight and elution count was obtained with cellulose trinitrate standards fractionated by preparative GPC. The degree of polymerization of the fibers decreased with increasing irradiation dose, but their microcrystalline celluloses were only slightly degraded by irradiation, especially in microcrystalline cellulose from cellulose I. Degradation of the fibers irradiated under humid conditions was less than that irradiated under vacuum. It was found that the G-values for main-chain scission for the irradiated cellulose I, cellulose II, microcrystalline cellulose I, and microcrystalline cellulose II were 2.8, 2.9, less than 1, and 2.9, respectively, but the G-value for main-chain scission for the irradiated cellulose II was increased to 11.2 at irradiation doses above 3 Mrad. Consequently, it is inferred that cellulose molecules in the amorphous regions are degraded more readily, and the well-aligned molecules in crystalline regions are not as easily degraded by irradiation

  7. Distribution of Human Leukocyte Antigen alleles in Systemic Lupus Erythematosus patients with Angiotensin Converting Enzyme Insertion/Deletion Polymorphism

    Nageen Hussain

    2013-02-01

    Full Text Available Systemic Lupus Erythematosus is one of the classic examples of autoimmune diseases among human beings and is a rare disease in Pakistani population. Clinically it is a quite diverse and complicated autoimmune disease in a sense that it involves multiple organs of the body and mimics with other diseases as well. This study focused on the distribution of HLA alleles in SLE patients with ACE I/D Polymorphism. A total of 122 individuals were enrolled in this study, 61 were the SLE patients who fulfilled revised ACR criteria and 61 were the healthy controls. Mean age of SLE patients at diagnosis was 30.35 ± 1.687 years (12-68 years. ACE gene I/D polymorphism was performed by nested PCR and DNA based HLA typing technique was used. ACE gene I/D polymorphism of Intron16 was studied and found to be involved in the activity of SLE. There is high frequency of HLA-A*01, HLA-B*40, HLA-DRB1*01 alleles in SLE patients with ACE DD genotype. The distribution of HLA-A, -B, -DRB1 alleles was analyzed in SLE patients with various disease phenotypes. HLA-A*01 and HLA-B*40 was the most common allele found in SLE patients with the involvement of skin. HLA-A*01, -A*03, HLA-B*13 and -B*46 were common in SLE patients with arthritis while HLA-A*26 and -A*69 were commonly found in Lupus nephritis cases. SLE patients involving both skin and kidney had an allele HLA-DRB1*01 common in them.

  8. PPARγ Pro12Ala and ACE ID polymorphisms are associated with BMI and fat distribution, but not metabolic syndrome

    Passaro Angela

    2011-12-01

    Full Text Available Abstract Background Metabolic Syndrome (MetS results from the combined effect of environmental and genetic factors. We investigated the possible association of peroxisome proliferator-activated receptor-γ2 (PPARγ2 Pro12Ala and Angiotensin Converting Enzyme (ACE I/D polymorphisms with MetS and interaction between these genetic variants. Methods Three hundred sixty four unrelated Caucasian subjects were enrolled. Waist circumference, blood pressure, and body mass index (BMI were recorded. Body composition was estimated by impedance analysis; MetS was diagnosed by the NCEP-ATPIII criteria. A fasting blood sample was obtained for glucose, insulin, lipid profile determination, and DNA isolation for genotyping. Results The prevalence of MetS did not differ across PPARγ2 or ACE polymorphisms. Carriers of PPARγ2 Ala allele had higher BMI and fat-mass but lower systolic blood pressure compared with Pro/Pro homozygotes. A significant PPARγ2 gene-gender interaction was observed in the modulation of BMI, fat mass, and blood pressure, with significant associations found in women only. A PPARγ2-ACE risk genotype combination for BMI and fat mass was found, with ACE DD/PPARγ2 Ala subjects having a higher BMI (p = 0.002 and Fat Mass (p = 0.002. Pro12Ala was independently associated with waist circumference independent of BMI and gender. Conclusions Carriers of PPARγ2 Ala allele had higher BMI and fat-mass but not a worse metabolic profile, possibly because of a more favorable adipose tissue distribution. A gene interaction exists between Pro12Ala and ACE I/D on BMI and fat mass. Further studies are needed to assess the contribution of Pro12Ala polymorphism in adiposity distribution.

  9. Dust and gas distribution in molecular clouds: an observational approach

    Campeggio, Loretta; Elia, Davide; Maiolo, Berlinda M T; Strafella, Francesco; Cecchi-Pestellini, Cesare

    2005-01-01

    The interstellar medium (ISM), gas and dust, appears to be arranged in clouds, whose dimensions, masses and densities span a large range of scales: from giant molecular clouds to small isolated globules. The structure of these objects show a high degree of complexity appearing, in the range of the observed scales, as a non-homogeneous ('clumpy') distribution of matter. The arrangement of the ISM is clearly relevant for the study of the fragmentation of the clouds and then of the star formation processes. To quantify observationally the ISM structure, many methods have been developed and our study is focused on some of them, exploiting multiwavelength observations of IS objects. The investigations presented here have been carried out by considering both the dust absorption (in optical and near IR wavelengths) and the gas emission (in the submm-radio spectral range). We present the maps obtained from the reduction of raw data and a first tentative analysis by means of methods as the structure function, the autocorrelation, and the Δ-variance. These are appropriate tools to highlight the complex structure of the ISM with reference to the paradigm given by the supersonic turbulence. Three observational cases are briefly discussed. In order to analyse the structure of objects characterized by different sizes, we applied the above-mentioned algorithms to the extinction map of the dark globule CB 107 and to the CO(J = 1-0) integrated intensity map of Vela Molecular Ridge, D Cloud. Finally we compare the results obtained with synthetic fractal maps known as 'fractional Brownian motion' fBm images

  10. Molecular characterization and differentiation of five horse breeds raised in Algeria using polymorphic microsatellite markers.

    Berber, N; Gaouar, S; Leroy, G; Kdidi, S; Tabet Aouel, N; Saïdi Mehtar, N

    2014-10-01

    In this study, genetic analyses of diversity and differentiation were performed on five horse breeds raised in Algeria (Barb, Arab-Barb, Arabian, Thoroughbred and French Trotter). All microsatellite markers were highly polymorphic in all the breeds. A total of 123 alleles from 14 microsatellite loci were detected in 201 horses. The average number of alleles per locus was the highest in the Arab-Barb horses (7.86) and lowest in the thoroughbred breed (5.71), whereas the observed and expected heterozygosities per breed ranged from 0.71 (Thoroughbred) to 0.752 (Barb) and 0.71 (Thoroughbred) to 0.77 (Arab-Barb), respectively. The genetic differentiation between the breeds was significant (p horse populations and the other breeds. The Barb and Arab-Barb breeds seem to be the most genetically related and support the decision to consider the breeds as same population. © 2014 Blackwell Verlag GmbH.

  11. Distribution of the 3' VNTR polymorphism in the human dopamine transporter gene in world populations.

    Mitchell, R J; Howlett, S; Earl, L; White, N G; McComb, J; Schanfield, M S; Briceno, I; Papiha, S S; Osipova, L; Livshits, G; Leonard, W R; Crawford, M H

    2000-04-01

    A polymorphism with a variable number of tandem repeats (VNTR) found in the 3' untranslated region of the human dopamine transporter gene (DAT1) was scored in unrelated individuals drawn from 10 geographically widely dispersed populations in order to assess this marker's usefulness in human population genetics. The populations that were analyzed in this study included 4 indigenous groups of Siberia, natives of North and South America, as well as Caucasian and Oceanic groups, most of which represented small-scale societies. A total of 5 DAT1 alleles were seen overall, but only in one Siberian population, the Altai-Kizhi, were all 5 present, and in the Native Americans of Colombia the locus was monomorphic. The most common allele, DAT1*10, ranged in frequency from 52% in Greeks to 100% in South Americans. The high frequency of the DAT1*10 allele (approximately 90%) among Mongoloid groups of north and east Asia distinguishes them from most Caucasian groups. The presence of the rare DAT1*7 allele in relatively high frequency (approximately 5%) among all Siberian groups suggests a close affinity with north Asian groups, especially Mongolians. The presence of the even rarer DAT1*13 allele in one Siberian population, the Altai-Kizhi, reflects this group's long historical contact with Mongolians. The results demonstrated that the DAT1 VNTR polymorphism is useful in investigating population relationships, and that rare alleles at this locus may be particularly valuable in understanding the extent of genetic affinity between neighboring groups and in situations where admixture is suspected. However, because of both the association and linkage of this VNTR locus with attention-deficit hyperactivity disorder (ADHD) in children, and its highly restricted polymorphism (usually 3 alleles) in most human groups, the possibility of selection constraints on the DAT1 gene cannot be ignored.

  12. Effects of single nucleotide polymorphisms on human N-acetyltransferase 2 structure and dynamics by molecular dynamics simulation.

    M Rajasekaran

    Full Text Available BACKGROUND: Arylamine N-acetyltransferase 2 (NAT2 is an important catalytic enzyme that metabolizes the carcinogenic arylamines, hydrazine drugs and chemicals. This enzyme is highly polymorphic in different human populations. Several polymorphisms of NAT2, including the single amino acid substitutions R64Q, I114T, D122N, L137F, Q145P, R197Q, and G286E, are classified as slow acetylators, whereas the wild-type NAT2 is classified as a fast acetylator. The slow acetylators are often associated with drug toxicity and efficacy as well as cancer susceptibility. The biological functions of these 7 mutations have previously been characterized, but the structural basis behind the reduced catalytic activity and reduced protein level is not clear. METHODOLOGY/PRINCIPAL FINDINGS: We performed multiple molecular dynamics simulations of these mutants as well as NAT2 to investigate the structural and dynamical effects throughout the protein structure, specifically the catalytic triad, cofactor binding site, and the substrate binding pocket. None of these mutations induced unfolding; instead, their effects were confined to the inter-domain, domain 3 and 17-residue insert region, where the flexibility was significantly reduced relative to the wild-type. Structural effects of these mutations propagate through space and cause a change in catalytic triad conformation, cofactor binding site, substrate binding pocket size/shape and electrostatic potential. CONCLUSIONS/SIGNIFICANCE: Our results showed that the dynamical properties of all the mutant structures, especially in inter-domain, domain 3 and 17-residue insert region were affected in the same manner. Similarly, the electrostatic potential of all the mutants were altered and also the functionally important regions such as catalytic triad, cofactor binding site, and substrate binding pocket adopted different orientation and/or conformation relative to the wild-type that may affect the functions of the mutants

  13. Random Amplified Polymorphic DNA PCR in the Teaching of Molecular Epidemiology

    Reinoso, Elina B.; Bettera, Susana G.

    2016-01-01

    In this article, we describe a basic practical laboratory designed for fifth-year undergraduate students of Microbiology as part of the Epidemiology course. This practice provides the students with the tools for molecular epidemiological analysis of pathogenic microorganisms using a rapid and simple PCR technique. The aim of this work was to assay…

  14. Molecular identification of Giardia duodenalis in Ecuador by polymerase chain reaction-restriction fragment length polymorphism

    Richard Atherton

    2013-06-01

    Full Text Available The aim of this study was to determine the genetic diversity of Giardia duodenalis present in a human population living in a northern Ecuadorian rain forest. All Giardia positive samples (based on an ELISA assay were analysed using a semi-nested polymerase chain reaction-restriction fragment length polymorphism assay that targets the glutamate dehydrogenase (gdh gene; those amplified were subsequently genotyped using NlaIV and RsaI enzymes. The gdh gene was successfully amplified in 74 of 154 ELISA positive samples; 69 of the 74 samples were subsequently genotyped. Of these 69 samples, 42 (61% were classified as assemblage B (26 as BIII and 16 as BIV, 22 (32% as assemblage A (3 as AI and 19 as AII and five (7% as mixed AII and BIII types. In this study site we observe similar diversity in genotypes to other regions in Latin America, though in contrast to some previous studies, we found similar levels of diarrheal symptoms in those individuals infected with assemblage B compared with those infected with assemblage A.

  15. Differential distribution and association of FTO rs9939609 gene polymorphism with obesity: A cross-sectional study among two tribal populations of India with East-Asian ancestry.

    Ningombam, Somorjit Singh; Chhungi, Varhlun; Newmei, Masan Kambo; Rajkumari, Sunanda; Devi, Naorem Kiranmala; Mondal, Prakash Ranjan; Saraswathy, Kallur Nava

    2018-03-20

    The fat mass and obesity associated (FTO) rs9939609 gene polymorphism is most widely studied in terms of obesity in various populations. Recently, the prevalence of obesity has been reported to be very high among the North-Eastern State of India. The major aim of the present study is to understand the extent of FTO rs9939609 gene polymorphism and its association with obesity among the two North-East Indian tribal populations with similar East Asian ancestry. Somatometric data and fasting blood sample were collected from 521 tribal individuals (258 Liangmai and 263 Mizo) of Manipur after obtaining written informed consent. Genotyping of FTO rs9939609 single nucleotide polymorphism (SNP) was done using restriction fragment length polymorphism method for PCR-amplified fragments. Both the presently studied populations were not following Hardy-Weinberg law. The prevalence of obesity and minor allele frequency of FTO rs9939609 polymorphism was found to be significantly higher among the Mizo tribe compared to that of Liangmai. The selected polymorphism was found to be significantly associated with obesity (BMI) only among the Liangmai tribe (Odds ratio-3.0; 95% CI-1.4, 6.4; p-0.003), after adjusting for age and occupation. Age-cohort wise distribution and absolute fitness analysis indicated the lower fitness of minor allele in the higher age group among the Liangmai tribe. To the best of the author's knowledge this is the first study, associating FTO rs9939609 gene polymorphism and obesity in the North-eastern Indian tribal populations with East-Asian ancestry. This study revealed the FTO rs9939609 polymorphism is observed to be associated with obesity only among the Liangmai tribe not among the Mizo tribe. The differential distribution and association observed in the two selected tribes, inhabited in a similar geographical region, could be attributed to differences in their migratory histories in terms of both route and time of settlement. Copyright © 2018 Elsevier B

  16. Variability and distribution of COL1A2 (type I collagen) polymorphisms in the central-eastern Mediterranean Basin.

    Scorrano, Gabriele; Lelli, Roberta; Martínez-Labarga, Cristina; Scano, Giuseppina; Contini, Irene; Hafez, Hani S; Rudan, Pavao; Rickards, Olga

    2016-01-01

    The most abundant of the collagen protein family, type I collagen is encoded by the COL1A2 gene. The COL1A2 restriction fragment length polymorphisms (RFLPs) EcoRI, RsaI and MspI in samples from several different central-eastern Mediterranean populations were analysed and found to be potentially informative anthropogenetic markers. The objective was to define the genetic variability of COL1A2 in the central-eastern Mediterranean and to shed light on its genetic distribution in human groups over a wide geographic area. PCR-RFLP analysis of EcoRI, RsaI and MspI polymorphisms of the COL1A2 gene was performed on oral swab and blood samples from 308 individuals from the central-eastern Mediterranean Basin. The genetic similarities among these groups and other populations described in the literature were investigated through correspondence analysis. Single-marker data and haplotype frequencies seemed to suggest a genetic homogeneity within the European populations, whereas a certain degree of differentiation was noted for the Egyptians and the Turks. The genetic variability in the central-eastern Mediterranean area is probably a result of the geographical barrier of the Mediterranean Sea, which separated European and African populations over time.

  17. POLYANA-A tool for the calculation of molecular radial distribution functions based on Molecular Dynamics trajectories

    Dimitroulis, Christos; Raptis, Theophanes; Raptis, Vasilios

    2015-12-01

    We present an application for the calculation of radial distribution functions for molecular centres of mass, based on trajectories generated by molecular simulation methods (Molecular Dynamics, Monte Carlo). When designing this application, the emphasis was placed on ease of use as well as ease of further development. In its current version, the program can read trajectories generated by the well-known DL_POLY package, but it can be easily extended to handle other formats. It is also very easy to 'hack' the program so it can compute intermolecular radial distribution functions for groups of interaction sites rather than whole molecules.

  18. Molecular Typing of Borrelia burgdorferi Sensu Lato by Randomly Amplified Polymorphic DNA Fingerprinting Analysis

    Wang, Guiqing; van Dam, Alje P.; Spanjaard, Lodewijk; Dankert, Jacob

    1998-01-01

    To study whether pathogenic clusters of Borrelia burgdorferi sensu lato strains occur, we typed 136 isolates, cultured from specimens from patients (n = 49) with various clinical entities and from ticks (n = 83) or dogs (n = 4) from different geographic regions, by randomly amplified polymorphic DNA (RAPD) fingerprinting with four arbitrary primers. The RAPD patterns were reproducible up to the 95% similarity level as shown in duplicate experiments. In these experiments the purified DNAs prepared on different days, from different colonies, and after various passages were used as templates. With an intergroup difference of 55%, the 136 strains could be divided into seven genetic clusters. Six clusters comprised and corresponded to the established species B. burgdorferi sensu stricto (n = 23), Borrelia garinii (n = 39), Borrelia afzelii (n = 59), Borrelia japonica (n = 1), Borrelia valaisiana (n = 12), and genomic group DN127 (n = 1). One strain from a patient with erythema migrans (EM) did not belong to any of the species or genomic groups known up to now. The RAPD types of B. burgdorferi sensu stricto, B. garinii, and B. afzelii isolates, which may give rise to human Lyme borreliosis (LB), were associated with their geographic origins. A high degree of genetic diversity was observed among the 39 B. garinii strains, and six subgroups could be recognized. One of these comprised eight isolates from patients with disseminated LB only and no tick isolates. B. afzelii strains from patients with EM or acrodermatitis chronica atrophicans were not clustered in particular branches. Our study showed that RAPD analysis is a powerful tool for discriminating different Borrelia species as well as Borrelia isolates within species. PMID:9508310

  19. Effect of Cooling Rates on Shape and Crystal Size Distributions of Mefenamic Acid Polymorph in Ethyl Acetate

    Mudalip, S. K. Abdul; Adam, F.; Parveen, J.; Abu Bakar, M. R.; Amran, N.; Sulaiman, S. Z.; Che Man, R.; Arshad, Z. I. Mohd; Shaarani, S. Md.

    2017-06-01

    This study investigate the effect of cooling rates on mefenamic acid crystallisation in ethyl acetate. The cooling rate was varied from 0.2 to 5 °C/min. The in-line conductivity system and turbidity system were employed to detect the onset of the crystallization process. The crystals produced were analysed using optical microscopy and Fourier transform infrared spectroscopy (FTIR). It was found that the crystals produced at different cooling rates were needle-like and exhibit polymorphic form type I. However, the aspect ratio and crystal size distributions were varied with the increased of cooling rate. A high crystals aspect ratio and narrower CSD (100-900 μm) was obtained at cooling rate of 0.5 °C/min. Thus, can be suggested as the most suitable cooling rate for crystallization of mefenamic acid in ethyl acetate.

  20. Genetic diversity of pigeon pea (Cajanus cajan (l.) Millsp.) based on molecular characterization using randomly amplified polymorphic DNA (RAPD) markers

    Khoiriyah, N.; Yuniastuti, E.; Purnomo, D.

    2018-03-01

    Pigeon pea (Cajanus cajan (L.) Millsp.) is an annual leguminous crop (perennial) which has advantages over other local leguminous crops as drought resistant, hold collapsed and strong pods. The research on drought resistance plant is very important to adapt to climate change adverse impact to support food security. The potential of pigeon pie has not been supported by accurate data. To explore the potential of pigeon pea, it is necessary to record the important properties by characterization, one of which is molecular. Increasing genetic diversity can be done through mutation which widely used gamma ray for the induction. The purpose of this study was to identify the genetic diversity of pigeon pea of black, white and brown seeds type resulted by gamma-ray irradiation with a wavelength of 100, 200 and 300 grays by using RAPD method. The experiment resulted 14 bands, 12 of them are polymorphic bands and 2 of them are monomorphic with size varied from 300 bp to 1.3 kbp. The dendrogram showed from 30 accessions are divided into two main clusters, B shows clear genetical divergence from other clusters and some others split randomly. The range of similarity coefficient is from 0.43 to 1.00

  1. Transmission of tuberculosis in Havana, Cuba: a molecular epidemiological study by IS6110 restriction fragment length polymorphism typing

    Diaz R

    2001-01-01

    Full Text Available The combination of molecular and conventional epidemiological methods has improved the knowledge about the transmission of tuberculosis in urban populations. To examine transmission of tuberculosis in Havana, Cuba, with DNA fingerprinting, we studied 51 out of 92 Mycobacterium tuberculosis strains isolated from tuberculosis patients who resided in Havana and whose infection was culture-confirmed in the period from September 1997 to March 1998. Isolates from 28 patients (55% had unique IS6110 restriction fragment length polymorphism (RFLP patterns, while isolates from 23 others (45% had identical patterns and belonged to 7 clusters. Three clusters consisting of six, five and two cases were each related to small outbreaks that occurred in a closed setting. Three other clustered cases were linked to a large outbreak that occurred in another institution. Younger patients were more correlated to clustering than older ones. The finding that 45% of the isolates had clustered RFLP patterns suggests that recent transmission is a key factor in the tuberculosis cases in Havana. The IS6110 RFLP typing made it possible to define the occurrence of outbreaks in two closed institutions.

  2. Genotypic distribution of single nucleotide polymorphisms in oral cancer: global scene.

    Multani, Shaleen; Saranath, Dhananjaya

    2016-11-01

    Globocan 2012 reports the global oral cancer incidence of 300,373 new oral cancer cases annually, contributing to 2.1 % of the world cancer burden. The major well-established risk factors for oral cancer include tobacco, betel/areca nut, alcohol and high-risk oncogenic human papilloma virus (HPV) 16/18. However, only 5-10 % of individuals with high-risk lifestyle develop oral cancer. Thus, genomic variants in individuals represented as single nucleotide polymorphisms (SNPs) influence susceptibility to oral cancer. With a view to understanding the role of genomic variants in oral cancer, we reviewed SNPs in case-control studies with a minimum of 100 cases and 100 controls. PubMed and HuGE navigator search engines were used to obtain data published from 1990 to 2015, which identified 67 articles investigating the role of SNPs in oral cancer. Single publications reported 93 SNPs in 55 genes, with 34 SNPs associated with a risk of oral cancer. Meta-analysis of data in multiple studies defined nine SNPs associated with a risk of oral cancer. The genes were associated with critical functions deregulated in cancers, including cell proliferation, immune function, inflammation, transcription, DNA repair and xenobiotic metabolism.

  3. Distribution, ecology and polymorphic behaviour of the genus Oxycephalus (Hyperiidea, Oxycephalidae) in the Indian Ocean

    Nair, K.K.C.

    There have been many controversies on the number of valid, species under Oxycephalus including the studies made from Indian waters. This is the first comprehensive account on the distribution of this genus covering the entire Indian Ocean through...

  4. Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in Bacteroides coprocola.

    Chen, Yaowen; Li, Zongcheng; Hu, Shuofeng; Zhang, Jian; Wu, Jiaqi; Shao, Ningsheng; Bo, Xiaochen; Ni, Ming; Ying, Xiaomin

    2017-02-01

    Gut microbes play a critical role in human health and disease, and researchers have begun to characterize their genomes, the so-called gut metagenome. Thus far, metagenomics studies have focused on genus- or species-level composition and microbial gene sets, while strain-level composition and single-nucleotide polymorphism (SNP) have been overlooked. The gut metagenomes of type 2 diabetes (T2D) patients have been found to be enriched with butyrate-producing bacteria and sulfate reduction functions. However, it is not known whether the gut metagenomes of T2D patients have characteristic strain patterns or SNP distributions. We downloaded public gut metagenome datasets from 170 T2D patients and 174 healthy controls and performed a systematic comparative analysis of their metagenome SNPs. We found that Bacteroides coprocola, whose relative abundance did not differ between the groups, had a characteristic distribution of SNPs in the T2D patient group. We identified 65 genes, all in B. coprocola, that had remarkably different enrichment of SNPs. The first and sixth ranked genes encode glycosyl hydrolases (GenBank accession EDU99824.1 and EDV02301.1). Interestingly, alpha-glucosidase, which is also a glycosyl hydrolase located in the intestine, is an important drug target of T2D. These results suggest that different strains of B. coprocola may have different roles in human gut and a specific set of B. coprocola strains are correlated with T2D.

  5. Molecular frame and recoil frame angular distributions in dissociative photoionization of small molecules

    Lucchese, R R; Carey, R; Elkharrat, C; Houver, J C; Dowek, D

    2008-01-01

    Photoelectron angular distributions in the dipole approximation can be written with respect to several different reference frames. A brief review of the molecular frame and recoil frame are given. Experimentally, one approach for obtaining such angular distributions is through angle-resolved coincidence measurements of dissociative ionization. If the system dissociates into two heavy fragments, then the recoil frame angular distribution can be measured. Computed molecular frame and recoil frame photoelectron angular distributions are compared to experimental data for the Cl 2p ionization of CH 3 Cl.

  6. Polymorphisms in the endocannabinoid receptor 1 in relation to fat mass distribution

    Frost, M; Nielsen, T L; Wraae, K

    2010-01-01

    Both animal and human studies have associated the endocannabinoid system with obesity and markers of metabolic dysfunction. Blockade of the cannabinoid receptor 1 (CB1) caused weight loss and reduction in waist size in both obese and type II diabetics. Recent studies on common variants of the CB1...... receptor gene (CNR1) and the link to obesity have been conflicting. The aim of the present study was to evaluate whether selected common variants of the CNR1 are associated with measures of obesity and fat distribution....

  7. Geographical and Ethnic Distributions of the MTHFR C677T, A1298C and MTRR A66G Gene Polymorphisms in Chinese Populations: A Meta-Analysis.

    Xingmin Wang

    Full Text Available The geographical and ethnic distributions of the polymorphic methylenetetrahydrofolate reductase (MTHFR mutations (C677T and A1298C and methionine synthase reductase (MTRR mutation (A66G remain heterogeneous in China. The goal of this study was to estimate the pooled frequencies of the alleles and associated genotypes of these gene polymorphisms among healthy populations in Mainland China.We systematically reviewed published epidemiological studies on the distributions of 3 genetic variants in Chinese healthy populations living in Mainland China through a meta-analysis. The relevant electronic databases were searched. All of the raw data of the eligible citations were extracted. The frequency estimates were stratified by geography, ethnicity and sex.Sixty-six studies were identified with a total of 92277 study participants. The meta-analysis revealed that the frequencies of the MTHFR C677T, A1298C, and MTRR A66G gene polymorphisms varied significantly between different ethnic groups and along geographical gradients. The frequencies of the 677T allele and 677TT genotype increased along the southern-central-northern direction across Mainland China (all Pvalues≤0.001. The frequencies of the 1298C, 1298CC, 66G and 66GG genotypes decreased along the south-central-north direction across the country (all Pvalues≤0.001.Our meta-analysis strongly indicates significant geographical and ethnic variations in the frequencies of the C677T, A1298C, and A66G gene polymorphisms in the folate metabolism pathway among Chinese populations.

  8. Molecular effects of autoimmune-risk promoter polymorphisms on expression, exon choice, and translational efficiency of interferon regulatory factor 5.

    Clark, Daniel N; Lambert, Jared P; Till, Rodney E; Argueta, Lissenya B; Greenhalgh, Kathryn E; Henrie, Brandon; Bills, Trieste; Hawkley, Tyson F; Roznik, Marinya G; Sloan, Jason M; Mayhew, Vera; Woodland, Loc; Nelson, Eric P; Tsai, Meng-Hsuan; Poole, Brian D

    2014-05-01

    The rs2004640 single nucleotide polymorphism and the CGGGG copy-number variant (rs77571059) are promoter polymorphisms within interferon regulatory factor 5 (IRF5). They have been implicated as susceptibility factors for several autoimmune diseases. IRF5 uses alternative promoter splicing, where any of 4 first exons begin the mRNA. The CGGGG indel is in exon 1A's promoter; the rs2004640 allele creates a splicing recognition site, enabling usage of exon 1B. This study aimed at characterizing alterations in IRF5 mRNA due to these polymorphisms. Cells with risk polymorphisms exhibited ~2-fold higher levels of IRF5 mRNA and protein, but demonstrated no change in mRNA stability. Quantitative PCR demonstrated decreased usage of exons 1C and 1D in cell lines with the risk polymorphisms. RNA folding analysis revealed a hairpin in exon 1B; mutational analysis showed that the hairpin shape decreased translation 5-fold. Although translation of mRNA that uses exon 1B is low due to a hairpin, increased IRF5 mRNA levels in individuals with the rs2004640 risk allele lead to higher overall protein expression. In addition, several new splice variants of IRF5 were sequenced. IRF5's promoter polymorphisms alter first exon usage and increase transcription levels. High levels of IRF5 may bias the immune system toward autoimmunity.

  9. Cloning of soluble alkaline phosphatase cDNA and molecular basis of the polymorphic nature in alkaline phosphatase isozymes of Bombyx mori midgut.

    Itoh, M; Kanamori, Y; Takao, M; Eguchi, M

    1999-02-01

    A cDNA coding for soluble type alkaline phosphatase (sALP) of Bombyx mori was isolated. Deduced amino acid sequence showed high identities to various ALPs and partial similarities to ATPase of Manduca sexta. Using this cDNA sequence as a probe, the molecular basis of electrophoretic polymorphism in sALP and membrane-bound type ALP (mALP) was studied. As for mALP, the result suggested that post-translational modification was important for the proteins to express activity and to represent their extensive polymorphic nature, whereas the magnitude of activities was mainly regulated by transcription. On the other hand, sALP zymogram showed poor polymorphism, but one exception was the null mutant, in which the sALP gene was largely lost. Interestingly, the sALP gene was shown to be transcribed into two mRNAs of different sizes, 2.0 and 2.4 Kb. In addition to the null mutant of sALP, we found a null mutant for mALP. Both of these mutants seem phenotypically silent, suggesting that the functional differentiation between these isozymes is not perfect, so that they can still work mutually and complement each other as an indispensable enzyme for B. mori.

  10. Historical distribution and molecular diversity of Bacillus anthracis, Kazakhstan.

    Aikembayev, Alim M; Lukhnova, Larissa; Temiraliyeva, Gulnara; Meka-Mechenko, Tatyana; Pazylov, Yerlan; Zakaryan, Sarkis; Denissov, Georgiy; Easterday, W Ryan; Van Ert, Matthew N; Keim, Paul; Francesconi, Stephen C; Blackburn, Jason K; Hugh-Jones, Martin; Hadfield, Ted

    2010-05-01

    To map the distribution of anthrax outbreaks and strain subtypes in Kazakhstan during 1937-2005, we combined geographic information system technology and genetic analysis by using archived cultures and data. Biochemical and genetic tests confirmed the identity of 93 archived cultures in the Kazakhstan National Culture Collection as Bacillus anthracis. Multilocus variable number tandem repeat analysis genotyping identified 12 genotypes. Cluster analysis comparing these genotypes with previously published genotypes indicated that most (n = 78) isolates belonged to the previously described A1.a genetic cluster, 6 isolates belonged to the A3.b cluster, and 2 belonged to the A4 cluster. Two genotypes in the collection appeared to represent novel genetic sublineages; 1 of these isolates was from Krygystan. Our data provide a description of the historical, geographic, and genetic diversity of B. anthracis in this Central Asian region.

  11. Reconciling in vivo and in vitro kinetics of the polymorphic transformation in zirconia-toughened alumina for hip joints: III. Molecular scale mechanisms

    Pezzotti, Giuseppe, E-mail: pezzotti@kit.ac.jp [Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, 606-8126 Kyoto (Japan); Bal, B. Sonny [Department of Orthopaedic Surgery, University of Missouri, Columbia, MO 65212 (United States); Amedica Corporation, 1885 West 2100 South, Salt Lake City, UT 84119 (United States); Zanocco, Matteo; Marin, Elia [Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, 606-8126 Kyoto (Japan); Sugano, Nobuhiko [Department of Medical Engineering for Treatment of Bone and Joint Disorders, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0854 (Japan); McEntire, Bryan J. [Amedica Corporation, 1885 West 2100 South, Salt Lake City, UT 84119 (United States); Zhu, Wenliang, E-mail: wlzhu2002@hotmail.com [Department of Medical Engineering for Treatment of Bone and Joint Disorders, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0854 (Japan)

    2017-02-01

    Understanding the intrinsic reason(s) for the enhanced tetragonal to monoclinic (t → m) polymorphic phase transformation observed on metal-stained surfaces of zirconia-toughened alumina (ZTA) requires detailed knowledge of off-stoichiometry reactions at the molecular scale. In this context, knowledge of the mechanism(s) for oxygen vacancy creation or annihilation at the material surface is a necessary prerequisite. The crucial aspect of the surface destabilization phenomenon, namely the availability of electrons and holes that allow for vacancy creation/annihilation, is elucidated in this paper. Metal-enhanced alterations of the oxygen sublattice in both Al{sub 2}O{sub 3} and ZrO{sub 2} of the ZTA composite play a decisive role in accelerating the polymorphic transformation. According to spectroscopic evidences obtained through nanometer-scale analyses, enhanced annihilation of oxygen vacancies triggers polymorphic transformation in ZrO{sub 2} near the metal stain, while the overall Al{sub 2}O{sub 3} lattice tends to dehydroxylate by forming oxygen vacancies. A mechanism for chemically driven “reactive metastability” is suggested, which results in accelerating the polymorphic transformation. The Al{sub 2}O{sub 3} matrix is found to play a key-role in the ZrO{sub 2} transformation process, with unambiguous confirmation of oxygen and hydrogen transport at the material surface. It is postulated that this transport is mediated by migration of dissociated O and H elements at the surface of the stained transition metal as they become readily available by the thermally activated surrounding. - Graphical abstract: Metal-enhanced alterations of the oxygen sublattice in both Al{sub 2}O{sub 3} and ZrO{sub 2} of the ZTA composite play a decisive role in the polymorphic transformation. According to spectroscopic evidence obtained through nanometer-scale analyses, enhanced annihilation of oxygen vacancies in Al{sub 2}O{sub 3} and ZrO{sub 2} occurs near the metal stain

  12. Detailed analysis of inversions predicted between two human genomes: errors, real polymorphisms, and their origin and population distribution.

    Vicente-Salvador, David; Puig, Marta; Gayà-Vidal, Magdalena; Pacheco, Sarai; Giner-Delgado, Carla; Noguera, Isaac; Izquierdo, David; Martínez-Fundichely, Alexander; Ruiz-Herrera, Aurora; Estivill, Xavier; Aguado, Cristina; Lucas-Lledó, José Ignacio; Cáceres, Mario

    2017-02-01

    The growing catalogue of structural variants in humans often overlooks inversions as one of the most difficult types of variation to study, even though they affect phenotypic traits in diverse organisms. Here, we have analysed in detail 90 inversions predicted from the comparison of two independently assembled human genomes: the reference genome (NCBI36/HG18) and HuRef. Surprisingly, we found that two thirds of these predictions (62) represent errors either in assembly comparison or in one of the assemblies, including 27 misassembled regions in HG18. Next, we validated 22 of the remaining 28 potential polymorphic inversions using different PCR techniques and characterized their breakpoints and ancestral state. In addition, we determined experimentally the derived allele frequency in Europeans for 17 inversions (DAF = 0.01-0.80), as well as the distribution in 14 worldwide populations for 12 of them based on the 1000 Genomes Project data. Among the validated inversions, nine have inverted repeats (IRs) at their breakpoints, and two show nucleotide variation patterns consistent with a recurrent origin. Conversely, inversions without IRs have a unique origin and almost all of them show deletions or insertions at the breakpoints in the derived allele mediated by microhomology sequences, which highlights the importance of mechanisms like FoSTeS/MMBIR in the generation of complex rearrangements in the human genome. Finally, we found several inversions located within genes and at least one candidate to be positively selected in Africa. Thus, our study emphasizes the importance of careful analysis and validation of large-scale genomic predictions to extract reliable biological conclusions. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  13. Molecular Effects of Polymorphism in the 3'UTR of Unc-5 homolog C Associated with Conception Rate in Holsteins.

    Mayumi Sugimoto

    Full Text Available Conception rates among dairy cows in Japan have declined in recent decades. To enhance our understanding of the genes involved in conception rates, we conducted a genome-wide association study (GWAS using 822 Holsteins and identified a single-nucleotide polymorphism (SNP associated with conception rate: A+169G in the 3' untranslated region (UTR of unc-5 homolog C (UNC5C. Cows with higher conception rates carried the A polymorphism in the UNC5C 3'UTR. Luciferase assays and quantitative analysis of allele ratios revealed that UNC5C transcripts with the A polymorphism were expressed at higher levels than those carrying the G polymorphism. UNC5C transmits either pro- or anti-apoptotic signals depending on the availability of its ligand, Netrin-1. UNC5C expression is negatively regulated by reproductive homeobox X-linked 5 (Rhox5, and the Rhox5 locus is methylated by G9a methyltransferase. G9a-knockout mice have previously been demonstrated to be subfertile, and we found that UNC5C, G9a, and Netrin-1 expression levels increased from the 4-cell stage to the blastocyst stage in fertilized murine embryos, whereas Rhox5 expression decreased. Repression of UNC5C, G9a, or Netrin-1 or forced expression of Rhox5 in the anterior nucleus stage inhibited development to the blastocyst stage, suggesting that cows carrying the G polymorphism in UNC5C might have lower conception rates because of the poor development of preimplantation embryos. This study provides novel insights into the role of UNC5C during embryonic development.

  14. Molecular epidemiology of HFE gene polymorphic variants (C282Y, H63D and S65C) in the population of Espírito Santo, Brazil.

    Alves, L N R; Santos, E V W; Stur, E; Silva Conforti, A M A; Louro, I D

    2016-04-27

    Hereditary hemochromatosis (HH) is an autosomal recessive disorder that leads to progressive iron accumulation and may cause cirrhosis, hepatocellular carcinoma, diabetes, and heart failure. Most cases of HH have been linked to mutations in genes associated with iron homeostasis. There have been three major variants in the high Fe (HFE) gene associated with the disease: C282Y, H63D and S65C. In this context, we aimed to evaluate the prevalence of the polymorphic variants (C282Y, H63D and S65C) of the HFE gene in the population of the Espírito Santo State (ES), Brazil by analyzing three different groups: general population (N = 120), Pomeranian descendants (N = 59), and patients with HH (N = 20). Using genomic DNA extracted from peripheral blood, polymorphic variant identification was performed by polymerase chain reaction-restriction fragment length polymorphism. Statistically significant differences were observed for genotype distribution of C282Y (P HFE gene allele frequencies for the general population, Pomeranian subpopulation, and patients with HH of ES, Brazil.

  15. Role of Molecular Weight Distribution on Charge Transport in Semiconducting Polymers

    Himmelberger, Scott

    2014-10-28

    © 2014 American Chemical Society. Model semiconducting polymer blends of well-controlled molecular weight distributions are fabricated and demonstrated to be a simple method to control intermolecular disorder without affecting intramolecular order or degree of aggregation. Mobility measurements exhibit that even small amounts of low molecular weight material are detrimental to charge transport. Trends in charge carrier mobility can be reproduced by a simple analytical model which indicates that carriers have no preference for high or low molecular weight chains and that charge transport is limited by interchain hopping. These results quantify the role of long polymer tie-chains and demonstrate the need for controlled polydispersity for achieving high carrier mobilities.

  16. Molecular frame photoelectron angular distribution for oxygen 1s photoemission from CO2 molecules

    Saito, N; Ueda, K; De Fanis, A

    2005-01-01

    We have measured photoelectron angular distributions in the molecular frame (MF-PADs) for O 1s photoemission from CO 2 , using photoelectron-O + -CO + coincidence momentum imaging. Results for the molecular axis at 0, 45 and 90 0 to the electric vector of the light are reported. The major features of the MF-PADs are fairly well reproduced by calculations employing a relaxed-core Hartree-Fock approach. Weak asymmetric features are seen through a plane perpendicular to the molecular axis and attributed to symmetry lowering by anti-symmetric stretching motion. (letter to the editor)

  17. Genetic and clinical characteristics of primary and secondary glioblastoma is associated with differential molecular subtype distribution

    Li, Rui; Li, Hailin; Yan, Wei; Yang, Pei; Bao, Zhaoshi; Zhang, Chuanbao; Jiang, Tao; You, Yongping

    2015-01-01

    Glioblastoma multiforme (GBM) is classified into primary (pGBM) or secondary (sGBM) based on clinical progression. However, there are some limits to this classification for insight into genetically and clinically distinction between pGBM and sGBM. The aim of this study is to characterize pGBM and sGBM associating with differential molecular subtype distribution. Whole transcriptome sequencing data was used to assess the distribution of molecular subtypes and genetic alterations in 88 pGBM and...

  18. Projection methods for the analysis of molecular-frame photoelectron angular distributions

    Grum-Grzhimailo, A.N.; Lucchese, R.R.; Liu, X.-J.; Pruemper, G.; Morishita, Y.; Saito, N.; Ueda, K.

    2007-01-01

    A projection method is developed for extracting the nondipole contribution from the molecular frame photoelectron angular distributions of linear molecules. A corresponding convenient parametric form for the angular distributions is derived. The analysis was performed for the N 1s photoionization of the NO molecule a few eV above the ionization threshold. No detectable nondipole contribution was found for the photon energy of 412 eV

  19. The distribution of 14C-chitosan by different molecular weight in mice

    Kim, Kwang Yoon; Kim, Young Ho; Bom, Hee Seung; Kim, Ji Yeul; Kim, Hee Kyung; Roh, Young Bok; Nishimura, Yoshikazu

    1998-01-01

    Chitosan is a nontoxic natural chealtor which was made by chitin, and reduced a contamination of radiostrontium in animals. In this experiment, a different molecular weight of C-14 chitosan was intravenously administered to mice, and then the distribution of C-14 chitosan in the body was observed. Male mice (8 to 10 weeks, body weight of 30 to 35g) of ICR strain were used. C-14 chitosan, mice was sacrificed at the 6th hour, 1st, 3rd, 5th, and 7th day. Beta radioactivities in the blood, liver, kidney, liver, muscle, testis, and urine was measured using a liquid scintillation analyzer. Most of the C-14 chitosan was excreted through urine within 6 hours. Biodistribution of C-14 chitosan was similar despite the difference of molecular weight. Higher distributions of radioactivities were found in the liver, kidney, spleen. The relative concentration in tissue increased for the 6 hours and then decreased. In conclusion, most of C-14 chitosan was excreted through urine despite the difference of molecular weight. and, low molecular weight of C-14 chitosan showed higher distribution than high molecular weight of C-14 chitosan in tissues

  20. The allelic distribution of -308 Tumor Necrosis Factor-alpha gene polymorphism in South African women with cervical cancer and control women

    Govan, Vandana A; Constant, Debbie; Hoffman, Margaret; Williamson, Anna-Lise

    2006-01-01

    Cervical cancer is due to infection with specific high-risk types of human papillomavirus (HPV). Although the incidence of genital HPV infection in various population groups is high, most of these regress without intervention. Investigating genetic host factors and cellular immune responses, particularly cytokines, could help to understand the association between genital HPV infection and carcinogenesis. The tumor necrosis factor alpha (TNF-α) cytokine plays an important role in all stages of cervical cancer and has the ability to induce the regression of human tumors. Therefore the aim of the study was to investigate the allelic distribution of -308 TNF-α gene polymorphism in South African women with cervical cancer compared to control women. Included in our study were women with histologically proven cancer of the cervix (n = 244) and hospital-based controls (n = 228). All patients and controls were from mixed race and black population groups in South Africa. The detection of a bi-allelic -308 (A/G) polymorphism in the promoter region of TNF-α was investigated using the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) technique. The distributions of the allelic frequencies were stratified in both patients and controls into two South African ethnic population groups. In this study we observed no association between the distribution of -308 TNF-α polymorphism and the risk of developing cervical cancer even after combining the data from the two ethnic populations (X 2 = 2.26). In addition, using the chi-squared test we found no significant association between the known risk factors for cervical cancer and the allele distribution of -308 TNF-α. However, the frequency of the rare high-producing allele -308A of TNF-α was significantly lower in the South African population when compared to Caucasians and Chinese population groups. We demonstrated no association between -308 TNF-α polymorphism and the risk of cervical cancer among two

  1. Accessing the molecular frame through strong-field alignment of distributions of gas phase molecules

    Reid, Katharine L.

    2018-03-01

    A rationale for creating highly aligned distributions of molecules is that it enables vector properties referenced to molecule-fixed axes (the molecular frame) to be determined. In the present work, the degree of alignment that is necessary for this to be achieved in practice is explored. Alignment is commonly parametrized in experiments by a single parameter, ?, which is insufficient to enable predictive calculations to be performed. Here, it is shown that, if the full distribution of molecular axes takes a Gaussian form, this single parameter can be used to determine the complete set of alignment moments needed to characterize the distribution. In order to demonstrate the degree of alignment that is required to approach the molecular frame, the alignment moments corresponding to a few chosen values of ? are used to project a model molecular frame photoelectron angular distribution into the laboratory frame. These calculations show that ? needs to approach 0.9 in order to avoid significant blurring to be caused by averaging. This article is part of the theme issue `Modern theoretical chemistry'.

  2. Projection methods for the analysis of molecular-frame photoelectron angular distributions

    Lucchese, R.R.; Montuoro, R.; Grum-Grzhimailo, A.N.; Liu, X.-J.; Pruemper, G.; Morishita, Y.; Saito, N.; Ueda, K.

    2007-01-01

    The analysis of the molecular-frame photoelectron angular distributions (MFPADs) is discussed within the dipole approximation. The general expressions are reviewed and strategies for extracting the maximum amount of information from different types of experimental measurements are considered. The analysis of the N 1s photoionization of NO is given to illustrate the method

  3. Distribution and kinematics of atomic and molecular gas inside the solar circle

    Marasco, A.; Fraternali, F.; van der Hulst, J. M.; Oosterloo, T.

    2017-01-01

    The detailed distribution and kinematics of the atomic and the CO-bright molecular hydrogen in the disc of the Milky Way inside the solar circle are derived under the assumptions of axisymmetry and pure circular motions. We divide the Galactic disc into a series of rings, and assume that the gas in

  4. Effects of Fat Polymorphic Transformation and Nonfat Particle Size Distribution on the Surface Changes of Untempered Model Chocolate, Based on Solid Cocoa Mass.

    Zhao, Huanhuan; Young, Ashley K; James, Bryony J

    2018-04-01

    This study aims to understand the bloom process in untempered chocolate by investigating the polymorphic transformation of cocoa butter and changes in chocolate surface. Cocoa mass with varying particle size distributions (PSD) were used to produce untempered model chocolate. Optical microscopy showed that during 25 d of storage, the chocolate surface gradually became honeycombed in appearance with dark spots surrounded by white sandy bloom areas. In conjunction with X-ray diffraction this indicates that the polymorphic transformation of form IV cocoa butter to more stable form V crystals caused the observed surface changes with the most significant changes occurring within 6 d. As bloom developed the surface whiteness increased, but the PSD of nonfat particles showed limited impact on the changes in whiteness. Moreover, scanning electron microscopy showed separated fat crystals on fat-rich dark spots and empty spaces between particles in bloom areas suggesting redistribution of fat in the chocolate matrix. The results reported in this work can facilitate the understanding of fat bloom formation in untempered chocolate with respect to the changes in microstructure and surface appearances. It also contributes to show the details of IV-to-V polymorphic transformation in the fat phase as time went by. © 2018 Institute of Food Technologists®.

  5. Distribution of Angiotensin-1 Converting Enzyme Insertion/Deletion and α-Actinin-3 Codon 577 Polymorphisms in Turkish Male Soccer Players

    Korkut Ulucan

    2015-01-01

    Full Text Available Angiotensin-1 converting enzyme (ACE gene and α-actinin-3 (ACTN3 gene polymorphisms are considered to be the most important candidate genes for genetic predisposition to human athletic performance. In the present study, we aimed to analyze the distribution of ACE and ACTN3 polymorphisms for the first time in male Turkish soccer players. In this prospective study, our cohort consisted of 25 professional players, all with Turkish ancestry. Polymerase chain reaction (PCR-restriction length polymorphism was used for the characterization of the genotype of ACTN3 and single PCR for ACE . For ACE genotype, 16%, 44%, and 40% of the players had insertion/insertion (II, insertion/deletion (ID, and deletion/deletion (DD genotypes, respectively, whereas 20% had XX, 36% had RX, and 44% had RR genotypes for ACTN3 . When we examined the allelic percentages, for ACE , D allele was recorded as 62 and I as 38, and for ACTN3 , R allele was 62 and X was 38. Our results were in agreement with the previous reports, indicating the presence of ACTN3 D and ACE X allele in soccer players. We suggest that ACE and ACTN3 genotypes are important biomarkers for genetic counseling for the individuals who are prone to be successful soccer players.

  6. How does the preparation of rye porridge affect molecular weight distribution of extractable dietary fibers?

    Rakha, Allah; Aman, Per; Andersson, Roger

    2011-01-01

    Extractable dietary fiber (DF) plays an important role in nutrition. This study on porridge making with whole grain rye investigated the effect of rest time of flour slurries at room temperature before cooking and amount of flour and salt in the recipe on the content of DF components and molecular weight distribution of extractable fructan, mixed linkage (1→3)(1→4)-β-d-glucan (β-glucan) and arabinoxylan (AX) in the porridge. The content of total DF was increased (from about 20% to 23% of dry matter) during porridge making due to formation of insoluble resistant starch. A small but significant increase in the extractability of β-glucan (P = 0.016) and AX (P = 0.002) due to rest time was also noted. The molecular weight of extractable fructan and AX remained stable during porridge making. However, incubation of the rye flour slurries at increased temperature resulted in a significant decrease in extractable AX molecular weight. The molecular weight of extractable β-glucan decreased greatly during a rest time before cooking, most likely by the action of endogenous enzymes. The amount of salt and flour used in the recipe had small but significant effects on the molecular weight of β-glucan. These results show that whole grain rye porridge made without a rest time before cooking contains extractable DF components maintaining high molecular weights. High molecular weight is most likely of nutritional importance.

  7. How Does the Preparation of Rye Porridge Affect Molecular Weight Distribution of Extractable Dietary Fibers?

    Roger Andersson

    2011-05-01

    Full Text Available Extractable dietary fiber (DF plays an important role in nutrition. This study on porridge making with whole grain rye investigated the effect of rest time of flour slurries at room temperature before cooking and amount of flour and salt in the recipe on the content of DF components and molecular weight distribution of extractable fructan, mixed linkage (1→3(1→4-β-D-glucan (β-glucan and arabinoxylan (AX in the porridge. The content of total DF was increased (from about 20% to 23% of dry matter during porridge making due to formation of insoluble resistant starch. A small but significant increase in the extractability of β-glucan (P = 0.016 and AX (P = 0.002 due to rest time was also noted. The molecular weight of extractable fructan and AX remained stable during porridge making. However, incubation of the rye flour slurries at increased temperature resulted in a significant decrease in extractable AX molecular weight. The molecular weight of extractable β-glucan decreased greatly during a rest time before cooking, most likely by the action of endogenous enzymes. The amount of salt and flour used in the recipe had small but significant effects on the molecular weight of β-glucan. These results show that whole grain rye porridge made without a rest time before cooking contains extractable DF components maintaining high molecular weights. High molecular weight is most likely of nutritional importance.

  8. Molecular Characterization of Colombian Yam Germoplasm by "Selective Amplificaron of M i c rósate l lite Polymorphic Loci" (SAMPL

    Silvia Bustamante R.

    2006-07-01

    Full Text Available In Colombia, yam (Dioscoreu spp. has been a basic and traditional crop for small-and medium-scale farmers. It has been an important source of family employment in the Colombian Atlantic Coast for the past several centuries. However, yam is the most fragüe crop regarding market issues and disease susceptibility (e.g. to anthracnose and viruses. At present, the crop is under progressive recovery from a previous drastic reduction in área and production, and apparently allows high profits. Is imperative for the future of the crop, that the rural farmers are supplied with selected varieties, thereby increasing their sustainability and economic yield. However, such varieties are not available, but have to be bred. Breeding of yam in turn is difficult, and presupposes knowledge about the genetic diversity in the breeding germplasm, which is not known. For these reasons, we characterized the Colombian yam varieties used in the fields as well as wild relatives with a molecular marker technique: SAMPL (Selective Amplification of Microsatellite Polymorphic Loci. Positions of 160 unequivocally scorable bands (of which 56 were monomorphic, 35% of total, with an average of 2.8 polymorphic bands per assay were transformed into a binary character matrix and analyzed. The resulting similarity matrix was transformed into a dendrogram with the UPGMA algorithm. The diversity of the collections with this technique was 0.0471 with a mean similarity of 0.9529. Key Words: Dioscorea spp, microsatellites, DNA

  9. Molecular diagnosis of Prader-Willi syndrome: Parent-of-origin dependent methylation sites and non-isotopic detection of (CA){sub n} dinucleotide repeat polymorphisms

    Lerer, I.; Meiner, V.; Pashut-Lavon, I.; Abeliovich, D.

    1994-08-01

    We describe our experience in the molecular diagnosis of 22 patients suspected of Prader-Willi syndrome (PWS) using a DNA probe PW71 (D15S63) which detects a parent-of-origin specific methylated site in the PWS critical region. The cause of the syndrome was determined as deletion or uniparental disomy according to the segregation of (CA){sub n} dinucleotide repeat polymorphisms of the PWS/AS region and more distal markers of chromosome 15. In 10 patients the clinical diagnosis was confirmed by the segregation of (CA){sub n}, probably due to paternal microdeletion in the PWs critical region which did not include the loci D15S97, D15S113, GABRB3, and GABRA5. This case demonstrates the advantage of the DNA probe PW71 in the diagnosis of PWS. 31 refs., 2 figs., 3 tabs.

  10. Segmental distribution of some common molecular markers for colorectal cancer (CRC): influencing factors and potential implications.

    Papagiorgis, Petros Christakis

    2016-05-01

    Proximal and distal colorectal cancers (CRCs) are regarded as distinct disease entities, evolving through different genetic pathways and showing multiple clinicopathological and molecular differences. Segmental distribution of some common markers (e.g., KRAS, EGFR, Ki-67, Bcl-2, COX-2) is clinically important, potentially affecting their prognostic or predictive value. However, this distribution is influenced by a variety of factors such as the anatomical overlap of tumorigenic molecular events, associations of some markers with other clinicopathological features (stage and/or grade), and wide methodological variability in markers' assessment. All these factors represent principal influences followed by intratumoral heterogeneity and geographic variation in the frequency of detection of particular markers, whereas the role of other potential influences (e.g., pre-adjuvant treatment, interaction between markers) remains rather unclear. Better understanding and elucidation of the various influences may provide a more accurate picture of the segmental distribution of molecular markers in CRC, potentially allowing the application of a novel patient stratification for treatment, based on particular molecular profiles in combination with tumor location.

  11. Novel approach of molecular genetic understanding of iridology: relationship between iris constitution and angiotensin converting enzyme gene polymorphism.

    Um, Jae-Young; An, Nyeon-Hyoung; Yang, Gui-Bi; Lee, Geon-Mok; Cho, Ju-Jang; Cho, Jae-Woon; Hwang, Woo-Jun; Chae, Han-Jung; Kim, Hyung-Ryong; Hong, Seung-Heon; Kim, Hyung-Min

    2005-01-01

    Iridology is the study of the iris of the eye to detect the conditions of the body and its organs, genetic strengths and weaknesses, etc. Although iridology is not widely used as a scientific tool for healthcare professionals to get to the source of people's health conditions, it has been used as a supplementary source to help the diagnosis of medical conditions by noting irregularities of the pigmentation in the iris among some Korean Oriental medical doctors. Angiotensin converting enzyme (ACE) gene polymorphism is one of the most well studied genetic markers of vascular disease. We investigated the relationship between iridological constitution and ACE polymorphism in hypertensives. We classified 87 hypertensives and 79 controls according to iris constitution and determined the ACE genotype of each individual. DD genotype was more prevalent in patients with a neurogenic constitution than in controls. This finding supports the hypothesis that D allele is a candidate gene for hypertension and demonstrates the association among ACE genotype, Korean hypertensives and iris constitution.

  12. Effect of molecular weight distribution on e-beam exposure properties of polystyrene

    Dey, Ripon Kumar; Cui Bo

    2013-01-01

    Polystyrene is a negative electron beam resist whose exposure properties can be tuned simply by using different molecular weights (Mw). Most previous studies have used monodisperse polystyrene with a polydispersity index (PDI) of less than 1.1 in order to avoid any uncertainties. Here we show that despite the fact that polystyrene’s sensitivity is inversely proportional to its Mw, no noticeable effect of very broad molecular weight distribution on sensitivity, contrast and achievable resolution is observed. It is thus unnecessary to use the costly monodisperse polystyrene for electron beam lithography. Since the polydispersity is unknown for general purpose polystyrene, we simulated a high PDI polystyrene by mixing in a 1:1 weight ratio two polystyrene samples with Mw of 170 and 900 kg mol −1 for the high Mw range, and 2.5 and 13 kg mol −1 for the low Mw range. The exposure property of the mixture resembles that of a monodisperse polystyrene with similar number averaged molecular weight (Mn)-bar, which indicates that it is (Mn)-bar rather than (Mw)-bar (weight averaged molecular weight) that dominates the exposure properties of polystyrene resist. This also implies that polystyrene of a certain molecular weight can be simulated by a mixture of two polystyrenes having different molecular weights. (paper)

  13. Semiempirical equations for modeling solid-state kinetics based on a Maxwell-Boltzmann distribution of activation energies: applications to a polymorphic transformation under crystallization slurry conditions and to the thermal decomposition of AgMnO4 crystals.

    Skrdla, Peter J; Robertson, Rebecca T

    2005-06-02

    Many solid-state reactions and phase transformations performed under isothermal conditions give rise to asymmetric, sigmoidally shaped conversion-time (x-t) profiles. The mathematical treatment of such curves, as well as their physical interpretation, is often challenging. In this work, the functional form of a Maxwell-Boltzmann (M-B) distribution is used to describe the distribution of activation energies for the reagent solids, which, when coupled with an integrated first-order rate expression, yields a novel semiempirical equation that may offer better success in the modeling of solid-state kinetics. In this approach, the Arrhenius equation is used to relate the distribution of activation energies to a corresponding distribution of rate constants for the individual molecules in the reagent solids. This distribution of molecular rate constants is then correlated to the (observable) reaction time in the derivation of the model equation. In addition to providing a versatile treatment for asymmetric, sigmoidal reaction curves, another key advantage of our equation over other models is that the start time of conversion is uniquely defined at t = 0. We demonstrate the ability of our simple, two-parameter equation to successfully model the experimental x-t data for the polymorphic transformation of a pharmaceutical compound under crystallization slurry (i.e., heterogeneous) conditions. Additionally, we use a modification of this equation to model the kinetics of a historically significant, homogeneous solid-state reaction: the thermal decomposition of AgMnO4 crystals. The potential broad applicability of our statistical (i.e., dispersive) kinetic approach makes it a potentially attractive alternative to existing models/approaches.

  14. Genetic ancestry effects on the distribution of toll-like receptors (TLRs) gene polymorphisms in a population of the Atlantic Forest, São Paulo, Brazil.

    Guimarães, Lilian O; Bajay, Miklos Maximiliano; Monteiro, Eliana F; Wunderlich, Gerhard; Santos, Sidney E; Kirchgatter, Karin

    2018-02-01

    The innate immune system governed by toll-like receptors (TLRs) provides the first line of defense against pathogens. Surface-localized TLR1 and TLR6 are known to detect parasite components. TLR encoding genes were shown to display signatures of recent positive selection in Europeans and might be involved in local adaptation at immune-related genes. To verify the influence of Brazilian population admixture on the distribution of polymorphisms in TLRs, we analyzed the genotype frequencies of 24 polymorphisms distributed across five TLR genes in a Southeastern Brazilian population where autochthonous cases of malaria occur in small foci of transmission. The estimation of ancestry showed mainly European ancestry (63%) followed by African ancestry (22%). Mean proportions of European ancestry differed significantly between the genotypes of the TLR1 (I602S) gene and in the TLR6 (P249S) gene. The chance of having the G allele in TLR1 gene increases as European ancestry increases as well as the chance of having the T allele in the TLR6 gene. The 602S allele is related to a ''hypo-responsiveness'' possibly explaining the high prevalence of asymptomatic malaria cases in areas of Southeastern Brazil. Our results underline the necessity to include informative ancestry markers in genetic association studies in order to avoid biased results. Copyright © 2017 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

  15. Control of molecular weight distribution in synthesis of poly(2-hydroxyethyl methacrylate) using ultrasonic irradiation.

    Kubo, Masaki; Kondo, Takayuki; Matsui, Hideki; Shibasaki-Kitakawa, Naomi; Yonemoto, Toshikuni

    2018-01-01

    Poly(2-hydroxyethyl methacrylate) (PHEMA) was synthesized using ultrasonic irradiation without any chemical initiator. The effect of the ultrasonic power intensity on the time course of the conversion to polymer, the number average molecular weight, and the polydispersity were investigated in order to synthesize a polymer with a low molecular weight distribution (i.e., low polydispersity). The conversion to polymer increased with time. A higher ultrasonic power intensity resulted in a faster reaction rate. The number average molecular weight increased during the early stage of the reaction and then gradually decreased with time. A higher ultrasonic intensity resulted in a faster degradation rate of the polymer. The polydispersity decreased with time. This was because the degradation rate of a polymer with a higher molecular weight was faster than that of a polymer with a lower molecular weight. A polydispersity below 1.3 was obtained under ultrasonic irradiation. By changing the ultrasonic power intensity during the reaction, the number average molecular weight can be controlled while maintaining low polydispersity. When the ultrasonic irradiation was halted, the reactions stopped and the number average molecular weight and polydispersity did not change. On the basis of the experimental results, a kinetic model for synthesis of PHEMA under ultrasonic irradiation was constructed considering both polymerization and polymer degradation. The kinetic model was in good agreement with the experimental results for the time courses of the conversion to polymer, the number average molecular weight, and the polydispersity for various ultrasonic power intensities. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Ozonation of humic substances: Effects on molecular weight distributions of organic carbon and trihalomethane formation potential

    Amy, G.L.; Kuo, C.J.; Sierka, R.A.

    1988-01-01

    Four different sources of humic substances were studied to determine the effects of ozonation on molecular weight distributions, based on dissolved organic carbon (DOC) and trihalomethane formation potential (THMFP). Solutions of two soil-derived fulvic acids and a one soil-derived humic acid, as well as dissolved organic matter (DOM) associated with a natural water source were studied. Both gel permeation chromatography (GPC) and ultrafiltration (UF) were employed to define apparent molecular weight (AMW). Applied ozone doses ranged from 2.0 to 2.5 mg O 3 /mg DOC. Overall samples of untreated and ozonated waters, as well as individual molecular weight fractions, were characterized according to DOC, uv absorbance, and THMFP. Ozonation resulted in a significant disappearance of higher AMW material with a corresponding increase in lower AMW material. Although little overall reduction in DOC concentration was observed, significant overall reductions in UV absorbance and THMFP levels were observed

  17. Observation of the Distribution of Molecular Spin States by Resonant Quantum Tunneling of the Magnetization

    Wernsdorfer, W.; Ohm, T.; Sangregorio, C.; Sessoli, R.; Mailly, D.; Paulsen, C.

    1999-05-01

    Below 360 mK, Fe8 magnetic molecular clusters are in the pure quantum relaxation regime and we show that the predicted ``square-root time'' relaxation is obeyed, allowing us to develop a new method for watching the evolution of the distribution of molecular spin states in the sample. We measure as a function of applied field H the statistical distribution P\\(ξH\\) of magnetic energy bias ξH acting on the molecules. Tunneling initially causes rapid transitions of molecules, thereby ``digging a hole'' in P\\(ξH\\) (around the resonant condition ξH = 0). For small initial magnetization values, the hole width shows an intrinsic broadening which may be due to nuclear spins.

  18. Stable Flocking of Multiple Agents Based on Molecular Potential Field and Distributed Receding Horizon Control

    Zhang Yun-Peng; Duan Hai-Bin; Zhang Xiang-Yin

    2011-01-01

    A novel distributed control scheme to generate stable flocking motion for a group of agents is proposed. In this control scheme, a molecular potential field model is applied as the potential field function because of its smoothness and unique shape. The approach of distributed receding horizon control is adopted to drive each agent to find its optimal control input to lower its potential at every step. Experimental results show that this proposed control scheme can ensure that all agents eventually converge to a stable flocking formation with a common velocity and the collisions can also be avoided at the same time. (general)

  19. Channel-facilitated molecular transport: The role of strength and spatial distribution of interactions

    Uppulury, Karthik, E-mail: karthik.uppulury@gmail.com [Department of Chemistry, Texas Tech University, Lubbock, TX 79409 (United States); Kolomeisky, Anatoly B. [Department of Chemistry, Department of Chemical and Biomolecular Engineering, Center for Theoretical Biological Physics, Rice University, Houston, TX 77005 (United States)

    2016-12-20

    Highlights: • Molecular flux strongly depends on the strength of the molecule-pore interactions. • There exists an optimal molecule-pore interaction potential for maximal flux. • Volume of interactions depends inversely on the strength for maximal flux. • Stronger interactions need more number of attractive sites for maximal flux. • Channels with few special sites need more attractive sites for higher flux. - Abstract: Molecular transport across channels and pores is critically important for multiple natural and industrial processes. Recent advances in single-molecule techniques have allowed researchers to probe translocation through nanopores with unprecedented spatial and temporal resolution. However, our understanding of the mechanisms of channel-facilitated molecular transport is still not complete. We present a theoretical approach that investigates the role of molecular interactions in the transport through channels. It is based on the discrete-state stochastic analysis that provides a fully analytical description of this complex process. It is found that a spatial distribution of the interactions strongly influences the translocation dynamics. We predict that there is the optimal distribution that leads to the maximal flux through the channel. It is also argued that the channel transport depends on the strength of the molecule-pore interactions, on the shape of interaction potentials and on the relative contributions of entrance and diffusion processes in the system. These observations are discussed using simple physical-chemical arguments.

  20. Channel-facilitated molecular transport: The role of strength and spatial distribution of interactions

    Uppulury, Karthik; Kolomeisky, Anatoly B.

    2016-01-01

    Highlights: • Molecular flux strongly depends on the strength of the molecule-pore interactions. • There exists an optimal molecule-pore interaction potential for maximal flux. • Volume of interactions depends inversely on the strength for maximal flux. • Stronger interactions need more number of attractive sites for maximal flux. • Channels with few special sites need more attractive sites for higher flux. - Abstract: Molecular transport across channels and pores is critically important for multiple natural and industrial processes. Recent advances in single-molecule techniques have allowed researchers to probe translocation through nanopores with unprecedented spatial and temporal resolution. However, our understanding of the mechanisms of channel-facilitated molecular transport is still not complete. We present a theoretical approach that investigates the role of molecular interactions in the transport through channels. It is based on the discrete-state stochastic analysis that provides a fully analytical description of this complex process. It is found that a spatial distribution of the interactions strongly influences the translocation dynamics. We predict that there is the optimal distribution that leads to the maximal flux through the channel. It is also argued that the channel transport depends on the strength of the molecule-pore interactions, on the shape of interaction potentials and on the relative contributions of entrance and diffusion processes in the system. These observations are discussed using simple physical-chemical arguments.

  1. Propulsion of a Molecular Machine by Asymmetric Distribution of Reaction Products

    Golestanian, Ramin; Liverpool, Tanniemola B.; Ajdari, Armand

    2005-06-01

    A simple model for the reaction-driven propulsion of a small device is proposed as a model for (part of) a molecular machine in aqueous media. The motion of the device is driven by an asymmetric distribution of reaction products. The propulsive velocity of the device is calculated as well as the scale of the velocity fluctuations. The effects of hydrodynamic flow as well as a number of different scenarios for the kinetics of the reaction are addressed.

  2. A nanojet: propulsion of a molecular machine by an asymmetric distribution of reaction--products

    Liverpool, Tanniemola; Golestanian, Ramin; Ajdari, Armand

    2006-03-01

    A simple model for the reaction-driven propulsion of a small device is proposed as a model for (part of) a molecular machine in aqueous media. Motion of the device is driven by an asymmetric distribution of reaction products. We calculate the propulsive velocity of the device as well as the scale of the velocity fluctuations. We also consider the effects of hydrodynamic flow as well as a number of different scenarios for the kinetics of the reaction.

  3. Molecular analysis of Leptospira spp. isolated from humans by restriction fragment length polymorphism, real-time PCR and pulsed-field gel electrophoresis.

    Turk, Nenad; Milas, Zoran; Mojcec, Vesna; Ruzic-Sabljic, Eva; Staresina, Vilim; Stritof, Zrinka; Habus, Josipa; Postic, Daniele

    2009-11-01

    A total of 17 Leptospira clinical strains isolated from humans in Croatia were serologically and genetically analysed. For serovar identification, the microscopic agglutination test (MAT) and pulsed-field gel electrophoresis (PFGE) were used. To identify isolates on genomic species level, PCR-based restriction fragment length polymorphism (RFLP) and real-time PCR were performed. MAT revealed the following serogroup affinities: Grippotyphosa (seven isolates), Icterohaemorrhagiae (eight isolates) and Javanica (two isolates). RFLP of PCR products from a 331-bp-long fragment of rrs (16S rRNA gene) digested with endonucleases MnlI and DdeI and real-time PCR revealed three Leptospira genomic species. Grippotyphosa isolates belonged to Leptospira kirschneri, Icterohaemorrhagiae isolates to Leptospira interrogans and Javanica isolates to Leptospira borgpetersenii. Genomic DNA from 17 leptospiral isolates was digested with NotI and SgrAI restriction enzymes and analysed by PFGE. Results showed that seven isolates have the same binding pattern to serovar Grippotyphosa, eight isolates to serovar Icterohaemorrhagiae and two isolates to serovar Poi. Results demonstrate the diversity of leptospires circulating in Croatia. We point out the usefulness of a combination of PFGE, RFLP and real-time PCR as appropriate molecular methods in molecular analysis of leptospires.

  4. Single-Nucleotide Polymorphisms of the MSH2 and MLH1 Genes, Potential Molecular Markers for Susceptibility to the Development of Basal Cell Carcinoma in the Brazilian Population.

    da Silva Calixto, Poliane; Lopes, Otávio Sérgio; Dos Santos Maia, Mayara; Herrero, Sylvia Satomi Takeno; Longui, Carlos Alberto; Melo, Cynthia Germoglio Farias; de Carvalho Filho, Ivan Rodrigues; Soares, Leonardo Ferreira; de Medeiros, Arnaldo Correia; Delatorre, Plínio; Khayat, André Salim; Burbano, Rommel Rodriguez; Lima, Eleonidas Moura

    2018-07-01

    Basal cell carcinoma - BCC is considered a multifactorial neoplasm involving genetic, epigenetic and environmental factors. Where UVB radiation is considered the main physical agent involved in BCC carcinogenesis. The Brazil and state of Paraíba are exposed to high levels of UVB rays. The mismatch repair - MMR is important DNA repair mechanisms to maintain replication fidelity. Therefore, single nucleotide polymorphisms (SNPs) in genes encoding proteins involved in MMR may be potential molecular markers of susceptibility to BCC. The objective of this study was to evaluate and describe for the first time the SNPs rs560246973, rs2303425 and rs565410865 and risk of developing BCC. The present study analyzed 100 samples of paraffin-embedded tissue from patients with histopathological diagnosis of BCC and 100 control samples. The results were obtained by genotyping method, Dideoxy Unique Allele Specific - PCR (DSASP). The SNPs rs2303425 were not associated with Basal Cell Carcinoma. However, the SNPs rs560246973 and rs565410865 was shown to be associated with the development of BCC when compared to control samples (P molecular markers for BCC.

  5. A Semester-Long Project for Teaching Basic Techniques in Molecular Biology Such as Restriction Fragment Length Polymorphism Analysis to Undergraduate and Graduate Students

    DiBartolomeis, Susan M.

    2011-01-01

    Several reports on science education suggest that students at all levels learn better if they are immersed in a project that is long term, yielding results that require analysis and interpretation. I describe a 12-wk laboratory project suitable for upper-level undergraduates and first-year graduate students, in which the students molecularly locate and map a gene from Drosophila melanogaster called dusky and one of dusky's mutant alleles. The mapping strategy uses restriction fragment length polymorphism analysis; hence, students perform most of the basic techniques of molecular biology (DNA isolation, restriction enzyme digestion and mapping, plasmid vector subcloning, agarose and polyacrylamide gel electrophoresis, DNA labeling, and Southern hybridization) toward the single goal of characterizing dusky and the mutant allele dusky73. Students work as individuals, pairs, or in groups of up to four students. Some exercises require multitasking and collaboration between groups. Finally, results from everyone in the class are required for the final analysis. Results of pre- and postquizzes and surveys indicate that student knowledge of appropriate topics and skills increased significantly, students felt more confident in the laboratory, and students found the laboratory project interesting and challenging. Former students report that the lab was useful in their careers. PMID:21364104

  6. Distribution and linkage disequilibrium analysis of polymorphisms of GH1 gene in different populations of pigs associated with body size.

    Cheng, Yunyun; Liu, Songcai; Su, Dan; Lu, Chao; Zhang, Xin; Wu, Qingyan; Li, Siming; Fu, Haoyu; Yu, Hao; Hao, Linlin

    2016-03-01

    Growth hormone (GH) has been considered as a candidate gene for growth and body size in pigs. In this study, polymorphisms of the GH1 gene were evaluated for associations with body size traits in 190 pig individuals. Seventeen single-nucleotide polymorphisms (SNPs) were identified in GH1 gene of the large pig breeds and miniature pig breeds using direct sequencing and genotyped by allele-specific PCR approach. Notably, six (g.237A>G, g.283T>C, g.309A>G, g.318A>G, g.540A>G and g.544A>G) of them were significantly associated with body size, of which three loci (g.283T>C, g.309A>G, g.318A>G) located in the signal-peptide coding region of GH1 gene compose a CGG haplotype for large pigs and TAA haplotype for miniature pigs (P G and g.544A>G) located in the second intron of GH1 gene compose a GG haplotype for large pigs and AA haplotype for miniature pigs (P body size of pigs providing genetic basis for pig breeding with the improved economic benefits.

  7. Breast cancer in Ethiopia: evidence for geographic difference in the distribution of molecular subtypes in Africa.

    Hadgu, Endale; Seifu, Daniel; Tigneh, Wondemagegnhu; Bokretsion, Yonas; Bekele, Abebe; Abebe, Markos; Sollie, Thomas; Merajver, Sofia D; Karlsson, Christina; Karlsson, Mats G

    2018-02-14

    Breast cancer is a heterogeneous disease with several morphological and molecular subtypes. Widely accepted molecular classification system uses assessment of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and proliferation marker Ki67. Few studies have been conducted on the incidence and molecular types of breast cancer in Sub-Saharan Africa. Previous studies mainly from Western and Central Africa, showed breast cancer to occur at younger ages and to present with aggressive features, such as high-grade, advanced stage and triple-negative phenotype (negative for ER, PR and HER2). Limited data from East Africa including Ethiopia however shows hormone receptor negative tumors to account for a lower proportion of all breast cancers than has been reported from elsewhere in Africa. In this study from Tikur Anbessa Specialized Hospital, 114 breast cancer patients diagnosed between 2012 and 2015 were enrolled. ER, PR, Ki67 and HER2 receptor status were assessed using immunohistochemistry from tissue microarrays. FISH was used for assessment of gene amplification in all equivocal tumor samples and for confirmation in HER2-enriched cases. The distribution of molecular subtypes was: Luminal A: 40%; Luminal B: 26%; HER2-enriched: 10%; TNBC: 23%. ER were positive in 65% of all tumors and 43% the cases were positive for PR. There was statistically significant difference in median age at diagnosis between the molecular subtypes (P molecular subtypes in different age ranges with Luminal B subtype being more common at younger ages (median = 36) and Luminal A subtype more prevalent at older ages (median = 42). There were no statistically significant differences in tumor grade, histology, and stage between the molecular subtypes of breast cancer. The present study detected Luminal A breast cancer to be the most common subtype and reveals a relatively low rate of hormone receptor negative and TNBC. Our findings and

  8. Phenotyping polyclonal kappa and lambda light chain molecular mass distributions in patient serum using mass spectrometry.

    Barnidge, David R; Dasari, Surendra; Ramirez-Alvarado, Marina; Fontan, Adrian; Willrich, Maria A V; Tschumper, Renee C; Jelinek, Diane F; Snyder, Melissa R; Dispenzieri, Angela; Katzmann, Jerry A; Murray, David L

    2014-11-07

    We previously described a microLC-ESI-Q-TOF MS method for identifying monoclonal immunoglobulins in serum and then tracking them over time using their accurate molecular mass. Here we demonstrate how the same methodology can be used to identify and characterize polyclonal immunoglobulins in serum. We establish that two molecular mass distributions observed by microLC-ESI-Q-TOF MS are from polyclonal kappa and lambda light chains using a combination of theoretical molecular masses from gene sequence data and the analysis of commercially available purified polyclonal IgG kappa and IgG lambda from normal human serum. A linear regression comparison of kappa/lambda ratios for 74 serum samples (25 hypergammaglobulinemia, 24 hypogammaglobulinemia, 25 normal) determined by microflowLC-ESI-Q-TOF MS and immunonephelometry had a slope of 1.37 and a correlation coefficient of 0.639. In addition to providing kappa/lambda ratios, the same microLC-ESI-Q-TOF MS analysis can determine the molecular mass for oligoclonal light chains observed above the polyclonal background in patient samples. In 2 patients with immune disorders and hypergammaglobulinemia, we observed a skewed polyclonal molecular mass distribution which translated into biased kappa/lambda ratios. Mass spectrometry provides a rapid and simple way to combine the polyclonal kappa/lambda light chain abundance ratios with the identification of dominant monoclonal as well as oligoclonal light chain immunoglobulins. We anticipate that this approach to evaluating immunoglobulin light chains will lead to improved understanding of immune deficiencies, autoimmune diseases, and antibody responses.

  9. Determination of nanoparticle size distribution together with density or molecular weight by 2D analytical ultracentrifugation

    Carney, Randy P.; Kim, Jin Young; Qian, Huifeng; Jin, Rongchao; Mehenni, Hakim; Stellacci, Francesco; Bakr, Osman

    2011-01-01

    Nanoparticles are finding many research and industrial applications, yet their characterization remains a challenge. Their cores are often polydisperse and coated by a stabilizing shell that varies in size and composition. No single technique can characterize both the size distribution and the nature of the shell. Advances in analytical ultracentrifugation allow for the extraction of the sedimentation (s) and diffusion coefficients (D). Here we report an approach to transform the s and D distributions of nanoparticles in solution into precise molecular weight (M), density (?P) and particle diameter (dp) distributions. M for mixtures of discrete nanocrystals is found within 4% of the known quantities. The accuracy and the density information we achieve on nanoparticles are unparalleled. A single experimental run is sufficient for full nanoparticle characterization, without the need for standards or other auxiliary measurements. We believe that our method is of general applicability and we discuss its limitations. 2011 Macmillan Publishers Limited. All rights reserved.

  10. Quantifying Multistate Cytoplasmic Molecular Diffusion in Bacterial Cells via Inverse Transform of Confined Displacement Distribution.

    Chen, Tai-Yen; Jung, Won; Santiago, Ace George; Yang, Feng; Krzemiński, Łukasz; Chen, Peng

    2015-11-12

    Single-molecule tracking (SMT) of fluorescently tagged cytoplasmic proteins can provide valuable information on the underlying biological processes in living cells via subsequent analysis of the displacement distributions; however, the confinement effect originated from the small size of a bacterial cell skews the protein's displacement distribution and complicates the quantification of the intrinsic diffusive behaviors. Using the inverse transformation method, we convert the skewed displacement distribution (for both 2D and 3D imaging conditions) back to that in free space for systems containing one or multiple (non)interconverting Brownian diffusion states, from which we can reliably extract the number of diffusion states as well as their intrinsic diffusion coefficients and respective fractional populations. We further demonstrate a successful application to experimental SMT data of a transcription factor in living E. coli cells. This work allows a direct quantitative connection between cytoplasmic SMT data with diffusion theory for analyzing molecular diffusive behavior in live bacteria.

  11. Determination of nanoparticle size distribution together with density or molecular weight by 2D analytical ultracentrifugation

    Carney, Randy P.

    2011-06-07

    Nanoparticles are finding many research and industrial applications, yet their characterization remains a challenge. Their cores are often polydisperse and coated by a stabilizing shell that varies in size and composition. No single technique can characterize both the size distribution and the nature of the shell. Advances in analytical ultracentrifugation allow for the extraction of the sedimentation (s) and diffusion coefficients (D). Here we report an approach to transform the s and D distributions of nanoparticles in solution into precise molecular weight (M), density (?P) and particle diameter (dp) distributions. M for mixtures of discrete nanocrystals is found within 4% of the known quantities. The accuracy and the density information we achieve on nanoparticles are unparalleled. A single experimental run is sufficient for full nanoparticle characterization, without the need for standards or other auxiliary measurements. We believe that our method is of general applicability and we discuss its limitations. 2011 Macmillan Publishers Limited. All rights reserved.

  12. Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions.

    Miyoshi, Daisuke; Nakamura, Kaori; Tateishi-Karimata, Hisae; Ohmichi, Tatsuo; Sugimoto, Naoki

    2009-03-18

    It has been revealed recently that molecular crowding, which is one of the largest differences between in vivo and in vitro conditions, is a critical factor determining the structure, stability, and function of nucleic acids. However, the effects of molecular crowding on Watson-Crick and Hoogsteen base pairs remain unclear. In order to investigate directly and quantitatively the molecular crowding effects on base pair types in nucleic acids, we designed intramolecular parallel- and antiparallel-stranded DNA duplexes consisting of Hoogsteen and Watson-Crick base pairs, respectively, as well as an intramolecular parallel-stranded triplex containing both types of base pairs. Thermodynamic analyses demonstrated that the values of free energy change at 25 degrees C for Hoogsteen base-pair formations decreased from +1.45 +/- 0.15 to +1.09 +/- 0.13 kcal mol(-1), and from -1.89 +/- 0.13 to -2.71 +/- 0.11 kcal mol(-1) in the intramolecular duplex and triplex, respectively, when the concentration of PEG 200 (polyethylene glycol with average molecular weight 200) increased from 0 to 20 wt %. However, corresponding values for Watson-Crick formation in the duplex and triplex increased from -10.2 +/- 0.2 to -8.7 +/- 0.1 kcal mol(-1), and from -10.8 +/- 0.2 to -9.2 +/- 0.2 kcal mol(-1), respectively. Furthermore, it was revealed that the opposing effects of molecular crowding on the Hoogsteen and Watson-Crick base pairs were due to different behaviors of water molecules binding to the DNA strands.

  13. Molecular Diversity Analysis of Two in vitro and Irradiated Potato Varieties Expressed by Random Amplified Polymorphic DNA

    Ayman El-FIKI

    2018-03-01

    Full Text Available Potato buds cvs. ҅Valor’ and ‘Spunta’ were cultured in vitro on MS solid medium with 0.2 mg -1 BAP. The resulting plantlets were irradiated with gamma radiation doses 10, 20, 30, 40 and 50 Gy. Irradiated segments were transferred onto fresh MS with BAP and plantlets survival percentage was calculated after eight weeks. Gamma radiation caused the death of 3.8% to 81% in cv. ҅Spunta’ and 2.9% to 83.9% in cv. ҅Valor’. Microtubers produced from irradiated plantlets were decreased with increasing gamma radiation doses, with notable changes in shape, size and numbers. The proline contents in irradiated plantlets were steady increase with gamma radiation doses. The genomic DNA of the two cultivars and ten radiation treatments was amplified with 10 RAPD primers that generated 53 polymorphic bands. The highest number of genetic identity was 0.9672 showed between irradiated plantlets with 20 and 30 Gy in cv. ҅Valor’. However, the highest genetic distance was 0.3995 observed between irradiated plantlets with dose 20 Gy in cv. ҅Valor’ and 30 Gy in cv. ҅Spunta’. The dendrogram generated by cluster analysis distinguished the irradiated plantlets genetically.

  14. Toward Measuring Galactic Dense Molecular Gas Properties and 3D Distribution with Hi-GAL

    Zetterlund, Erika; Glenn, Jason; Maloney, Phil

    2016-01-01

    The Herschel Space Observatory's submillimeter dust continuum survey Hi-GAL provides a powerful new dataset for characterizing the structure of the dense interstellar medium of the Milky Way. Hi-GAL observed a 2° wide strip covering the entire 360° of the Galactic plane in broad bands centered at 70, 160, 250, 350, and 500 μm, with angular resolution ranging from 10 to 40 arcseconds. We are adapting a molecular cloud clump-finding algorithm and a distance probability density function distance-determination method developed for the Bolocam Galactic Plane Survey (BGPS) to the Hi-GAL data. Using these methods we expect to generate a database of 105 cloud clumps, derive distance information for roughly half the clumps, and derive precise distances for approximately 20% of them. With five-color photometry and distances, we will measure the cloud clump properties, such as luminosities, physical sizes, and masses, and construct a three-dimensional map of the Milky Way's dense molecular gas distribution.The cloud clump properties and the dense gas distribution will provide critical ground truths for comparison to theoretical models of molecular cloud structure formation and galaxy evolution models that seek to emulate spiral galaxies. For example, such models cannot resolve star formation and use prescriptive recipes, such as converting a fixed fraction of interstellar gas to stars at a specified interstellar medium density threshold. The models should be compared to observed dense molecular gas properties and galactic distributions.As a pilot survey to refine the clump-finding and distance measurement algorithms developed for BGPS, we have identified molecular cloud clumps in six 2° × 2° patches of the Galactic plane, including one in the inner Galaxy along the line of sight through the Molecular Ring and the termination of the Galactic bar and one toward the outer Galaxy. Distances have been derived for the inner Galaxy clumps and compared to Bolocam Galactic Plane

  15. Molecular-weight distributions of coal and petroleum asphaltenes from laser desorption/ionization experiments

    Ana R. Hortal; Paola Hurtado; Bruno Martinez-Haya; Oliver C. Mullins [Universidad Pablo de Olavide, Seville (Spain). Departamento de Sistemas Fisicos, Quimicos y Naturales

    2007-09-15

    Molecular-weight distributions (MWDs) of asphaltenes extracted from coal and petroleum have been measured in laser desorption/ionization (LDI) mass spectrometric experiments. The dried-droplet and solvent-free sample preparation methods are compared. The coal asphaltenes have a relatively narrow MWD (full width 150 amu) with an average molecular weight of 340 amu. The petroleum asphaltenes display a broader MWD (full width 300 amu) and are heavier on average (680 amu). The LDI spectra also provide evidence for the formation of noncovalent clusters of the two types of asphaltenes during the desorption process. Petroleum and coal asphaltenes exhibit aggregation as do large model polycyclic aromatic hydrocarbons (PAHs) with five or more fused rings also included in the study. Smaller PAHs (pyrene) exhibit less aggregation, especially when alkane-chain substituents are incorporated to the molecular structure. This indicates that asphaltenes possess large PAHs and, according to the relatively small molecular weights observed, that there is a preponderance of asphaltene molecules with only a single fused ring system. The coal asphaltenes present a significantly smaller propensity toward aggregation than their crude oil counterparts. This finding, coupled with the fact that (1) alkanes inhibit aggregation in LDI and (2) petroleum asphaltenes possess much more alkane carbon, indicates that coal asphaltenes have smaller PAHs on average than petroleum asphaltenes. This is further corroborated by the stronger ultraviolet absorbance of the coal asphaltenes at wavelengths shorter than 400 nm. 32 refs., 8 figs.

  16. Effect of thermal treatment on potato starch evidenced by EPR, XRD and molecular weight distribution.

    Bidzińska, Ewa; Michalec, Marek; Pawcenis, Dominika

    2015-12-01

    Effect of heating of the potato starch on damages of its structure was investigated by quantitative electron paramagnetic resonance (EPR) spectroscopy, X-ray diffraction and determination of the molecular weight distribution. The measurements were performed in the temperature range commonly used for starch modifications optimizing properties important for industrial applications. Upon thermal treatment, because of breaking of the polymer chains, diminishing of the average molecular weights occurred, which significantly influences generation of radicals, evidenced by EPR. For the relatively mild conditions, with heating parameters not exceeding temperature 230 °C and time of heating equal to 30 min a moderate changes of both the number of thermally generated radicals and the mean molecular weight of the starch were observed. After more drastic thermal treatment (e.g. 2 h at 230 °C), a rapid increase in the radical amount occurred, which was accompanied by significant reduction of the starch molecular size and crystallinity. Experimentally established threshold values of heating parameters should not be exceeded in order to avoid excessive damages of the starch structure accompanied by the formation of the redundant amount of radicals. This requirement is important for industrial applications, because significant destruction of the starch matrix might annihilate the positive influence of the previously performed intentional starch modification. Copyright © 2015 John Wiley & Sons, Ltd.

  17. Aegilops tauschii Accessions with Geographically Diverse Origin Show Differences in Chromosome Organization and Polymorphism of Molecular Markers Linked to Leaf Rust and Powdery Mildew Resistance Genes.

    Majka, Maciej; Kwiatek, Michał T; Majka, Joanna; Wiśniewska, Halina

    2017-01-01

    Aegilops tauschii (2n = 2x = 14) is a diploid wild species which is reported as a donor of the D-genome of cultivated bread wheat. The main goal of this study was to examine the differences and similarities in chromosomes organization among accessions of Ae. tauschii with geographically diversed origin, which is believed as a potential source of genes, especially determining resistance to fungal diseases (i.e., leaf rust and powdery mildew) for breeding of cereals. We established and compared the fluorescence in situ hybridization patterns of 21 accessions of Ae. tauschii using various repetitive sequences mainly from the BAC library of wheat cultivar Chinese Spring. Results obtained for Ae. tauschii chromosomes revealed many similarities between analyzed accessions, however, some hybridization patterns were specific for accessions, which become from cognate regions of the World. The most noticeable differences were observed for accessions from China which were characterized by presence of distinct signals of pTa-535 in the interstitial region of chromosome 3D, less intensity of pTa-86 signals in chromosome 2D, as well as lack of additional signals of pTa-86 in chromosomes 1D, 5D, or 6D. Ae. tauschii of Chinese origin appeared homogeneous and separate from landraces that originated in western Asia. Ae. tauschii chromosomes showed similar hybridization patterns to wheat D-genome chromosomes, but some differences were also observed among both species. What is more, we identified reciprocal translocation between short arm of chromosome 1D and long arm of chromosome 7D in accession with Iranian origin. High polymorphism between analyzed accessions and extensive allelic variation were revealed using molecular markers associated with resistance genes. Majority of the markers localized in chromosomes 1D and 2D showed the diversity of banding patterns between accessions. Obtained results imply, that there is a moderate or high level of polymorphism in the genome of Ae

  18. Molecular characterization of Mycobacterium tuberculosis isolates from Tehran, Iran by restriction fragment length polymorphism analysis and spoligotyping

    Seifu Gizaw Feyisa

    2016-04-01

    Full Text Available Abstract: INTRODUCTION Characterization of Mycobacterium tuberculosis (MTB isolates by DNA fingerprinting has contributed to tuberculosis (TB control. The aim of this study was to determine the genetic diversity of MTB isolates from Tehran province in Iran. METHODS MTB isolates from 60 Iranian and 10 Afghan TB patients were fingerprinted by standard IS6110-restriction fragment length polymorphism (RFLP analysis and spoligotyping. RESULTS The copy number of IS6110 ranged from 10-24 per isolate. The isolates were classified into 22 clusters showing ≥ 80% similarity by RFLP analysis. Fourteen multidrug-resistant (MDR isolates were grouped into 4 IS6110-RFLP clusters, with 10 isolates [71% (95% CI: 45-89%] in 1 cluster, suggesting a possible epidemiological linkage. Eighteen Iranian isolates showed ≥ 80% similarity with Afghan isolates. There were no strains with identical fingerprints. Spoligotyping of 70 isolates produced 23 distinct patterns. Sixty (85.7% isolates were grouped into 13 clusters, while the remaining 10 isolates (14.2% were not clustered. Ural (formerly Haarlem4 (n = 22, 31.4% was the most common family followed by Central Asian strain (CAS (n = 18, 25.7% and T (n = 9, 12.8% families. Only 1strain was characterized as having the Beijing genotype. Among 60 Iranian and 10 Afghan MTB isolates, 25% (95% CI: 16-37 and 70% (95% CI: 39-89 were categorized as Ural lineage, respectively. CONCLUSIONS A higher prevalence of Ural family MTB isolates among Afghan patients than among Iranian patients suggests the possible transmission of this lineage following the immigration of Afghans to Iran.

  19. Frequency of distribution of inflammatory cytokines IL-1, IL-6 and TNF-alpha gene polymorphism in patients with obstructive sleep apnea.

    Popko, K; Gorska, E; Potapinska, O; Wasik, M; Stoklosa, A; Plywaczewski, R; Winiarska, M; Gorecka, D; Sliwinski, P; Popko, M; Szwed, T; Demkow, U

    2008-12-01

    Obesity is one of the most commonly identified factors for the obstructive sleep apnea syndrome (OSAS). Adipose tissue is the source of many cytokines, among them there are IL-6, IL-1, and TNF-alpha. The level of inflammatory cytokines increases in people with OSAS and obesity. The aim of this study was to evaluate the distribution of genotypes in inflammatory cytokine genes in people with obesity-related OSAS. The examined group consisted of 102 person with obesity related-OSAS and 77 normal weight person without OSAS. Genotyping of DNA sequence variation was carried out by restriction enzyme (IL-1: Taq I, IL-6: Lwe I, TNF-alpha: Nco I) analysis of PCR amplified DNA. The study revealed a significant correlation between polymorphism located in the promoter region of inflammatory cytokine genes and obesity-related OSAS.

  20. AFD: an application for bi-molecular interaction using axial frequency distribution.

    Raza, Saad; Azam, Syed Sikander

    2018-03-06

    Conformational flexibility and generalized structural features are responsible for specific phenomena existing in biological pathways. With advancements in computational chemistry, novel approaches and new methods are required to compare the dynamic nature of biomolecules, which are crucial not only to address dynamic functional relationships but also to gain detailed insights into the disturbance and positional fluctuation responsible for functional shifts. Keeping this in mind, axial frequency distribution (AFD) has been developed, designed, and implemented. AFD can profoundly represent distribution and density of ligand atom around a particular atom or set of atoms. It enabled us to obtain an explanation of local movements and rotations, which are not significantly highlighted by any other structural and dynamical parameters. AFD can be implemented on biological models representing ligand and protein interactions. It shows a comprehensive view of the binding pattern of ligand by exploring the distribution of atoms relative to the x-y plane of the system. By taking a relative centroid on protein or ligand, molecular interactions like hydrogen bonds, van der Waals, polar or ionic interaction can be analyzed to cater the ligand movement, stabilization or flexibility with respect to the protein. The AFD graph resulted in the residual depiction of bi-molecular interaction in gradient form which can yield specific information depending upon the system of interest.

  1. Relationship of molecular weight distribution profile of unreduced gluten protein extracts with quality characteristics of bread.

    Chaudhary, Nisha; Dangi, Priya; Khatkar, B S

    2016-11-01

    A statistical correlation was established among the molecular weight distribution patterns of unreduced gluten proteins and physicochemical, rheological and bread-making quality characteristics of wheat varieties. Size exclusion chromatography fractionated the gluten proteins apparently into five peaks. Peak I signified glutenins (30-130kDa), peak II as gliadins (20-55kDa), peak III as very low molecular weight monomeric gliadins (10-28kDa), peak IV and V, collectively, as albumins and globulins (bread loaf volume (r=0.848(∗∗)); however, peak II had negative (r=-0.818(∗∗)) impact. Bread firmness increased with increment in peak II (r=0.625(∗∗)), and decreased with accretion in peak I (r=-0.623(∗∗)). Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Effect of pH on molecular constitution and distribution of hemoglobin in living erythrocyte.

    Wu, Yue; Huang, Yao-Xiong; Kang, Li-Li; Wu, Zheng-Jie; Luo, Man

    2010-04-01

    The molecular constitution of in situ hemoglobin (Hb) and their distribution in living erythrocyte were investigated versus pH using the technique of confocal Raman microscopy. Both Raman point spectra and line mapping measurements were performed on living erythrocytes in suspensions with pH values from 4.82 to 9.70. It was found that the Hb inside a living erythrocyte would dissociate into monomer/dimer when the cells are in low and high pH environments. In contrast to the homogeneous distribution of the Hbs in the cells in neutral suspension, there are more Hbs distributing around the cell membrane or binding to the membrane as pH increases. While in low pH, as the cell become spherical, most of the Hbs distribute to the central part of the cell. In summary, our investigation suggests that the variation of the external pH not only brings changes in the morphology and membrane structure of an erythrocyte, but also affects the constitution and distribution of its intracellular Hbs, thereby the flexibility of the cell membrane and the oxygenation ability of the Hb.

  3. Family Polymorphism

    Ernst, Erik

    2001-01-01

    safety and flexibility at the level of multi-object systems. We are granted the flexibility of using different families of kinds of objects, and we are guaranteed the safety of the combination. This paper highlights the inability of traditional polymorphism to handle multiple objects, and presents family...... polymorphism as a way to overcome this problem. Family polymorphism has been implemented in the programming language gbeta, a generalized version of Beta, and the source code of this implementation is available under GPL....

  4. Effects of volumetric expansion in molecular crystals: A quantum mechanical investigation on aspirin and paracetamol most stable polymorphs

    Adhikari, Kapil; Flurchick, Kenneth M.; Valenzano, Loredana

    2015-02-01

    This work reports a study performed at hybrid semi-empirical density functional level (B3LYP-D2*) of the physico-chemical properties of aspirin (acetylsalicylic acid) and paracetamol (acetaminophen) in their most stable crystalline forms. It is shown how effects arising from volumetric expansions influence the properties of the materials. Structural, energetic, and vibrational properties are in good agreement with experimental values reported at temperatures far from 0 K. Results show that the proposed approach is reliable enough to reproduce effects of volumetric expansion on lattice energies and other measurable physico-chemical observables related to inter-molecular forces.

  5. Polymorphs of Pridopidine Hydrochloride

    Zimmermann, A.; Frostrup, B.; Bond, A. D.

    2012-01-01

    of both polymorphs contain N+-H center dot center dot center dot Cl-center dot center dot center dot N+-H center dot center dot center dot interactions, and the polymorphism can be viewed as alternative orientations (parallel or antiparallel) of comparable molecular columns while retaining the center dot...... center dot center dot N+-H center dot center dot center dot Cl-center dot center dot center dot N+-H center dot center dot center dot motif between columns. Forms I and II have melting points of 199 and 210 degrees C, respectively. Following melting of form I, a kinetically controlled crystallization...

  6. Unusual polymorphism in new bent-shaped liquid crystals based on biphenyl as a central molecular core

    Anna Kovářová

    2014-04-01

    Full Text Available Bent-shaped mesogens possessing a biphenyl as a central core have been synthesized and the role of the terminal chain and the orientation of the ester as a linkage group have been investigated. For the studied molecular core we have established that both parameters play an important role for the mesomorphic properties. The polyfluoroalkyl terminal chain supports the formation of mesophases, and the introduction of a chiral lactate terminal chain destabilizes mesophases for the first type of mutual orientation of ester groups, attached to the central core. On the contrary, for the opposite orientation of esters, the terminal chain has no effect on the mesomorphic properties, and columnar phases have been found for all compounds. A unique phase sequence has been found for the mesogen with the fluorinated chain. A generalized tilted smectics, SmCG, have been observed in a temperature interval between two different lamellar SmCP phases and characterized by X-ray and dielectric measurements. The dielectric spectroscopy data are unique and presented for the first time in the SmCG phase providing new information about the molecular dynamics.

  7. Molecular dynamics simulations of electrostatics and hydration distributions around RNA and DNA motifs

    Marlowe, Ashley E.; Singh, Abhishek; Semichaevsky, Andrey V.; Yingling, Yaroslava G.

    2009-03-01

    Nucleic acid nanoparticles can self-assembly through the formation of complementary loop-loop interactions or stem-stem interactions. Presence and concentration of ions can significantly affect the self-assembly process and the stability of the nanostructure. In this presentation we use explicit molecular dynamics simulations to examine the variations in cationic distributions and hydration environment around DNA and RNA helices and loop-loop interactions. Our simulations show that the potassium and sodium ionic distributions are different around RNA and DNA motifs which could be indicative of ion mediated relative stability of loop-loop complexes. Moreover in RNA loop-loop motifs ions are consistently present and exchanged through a distinct electronegative channel. We will also show how we used the specific RNA loop-loop motif to design a RNA hexagonal nanoparticle.

  8. Molecular identification of similar species of the genus Biomphalaria (Mollusca: Planorbidae determined by a polymerase chain reaction-restriction fragment length polymorphism

    Caldeira Roberta Lima

    1998-01-01

    Full Text Available The freshwater snails Biomphalaria straminea, B. intermedia, B. kuhniana and B. peregrina, are morphologically similar; based on this similarity the first three species were therefore grouped in the complex B. straminea. The morphological identification of these species is based on characters such as vaginal wrinkling, relation between prepuce: penial sheath:deferens vas and number of muscle layers in the penis wall. In this study the polymerase chain reaction restriction fragment length polymorphism technique was used for molecular identification of these molluscs. This technique is based on the amplification of the internal transcribed spacer regions ITS1 e ITS2 of the ribosomal RNA gene and subsequent digestion of these fragments by restriction enzymes. Six enzymes were tested: Dde I, Mnl I, Hae III, Rsa I, Hpa II e Alu I. The restriction patterns obtained with DdeI presented the best profile for separation of the four species of Biomphalaria. The profiles obtained with all the enzymes were used to estimate the genetic distances among the species through analysis of common banding patterns.

  9. THE 'TRUE' COLUMN DENSITY DISTRIBUTION IN STAR-FORMING MOLECULAR CLOUDS

    Goodman, Alyssa A.; Pineda, Jaime E.; Schnee, Scott L.

    2009-01-01

    We use the COMPLETE Survey's observations of the Perseus star-forming region to assess and intercompare the three methods used for measuring column density in molecular clouds: near-infrared (NIR) extinction mapping; thermal emission mapping in the far-IR; and mapping the intensity of CO isotopologues. Overall, the structures shown by all three tracers are morphologically similar, but important differences exist among the tracers. We find that the dust-based measures (NIR extinction and thermal emission) give similar, log-normal, distributions for the full (∼20 pc scale) Perseus region, once careful calibration corrections are made. We also compare dust- and gas-based column density distributions for physically meaningful subregions of Perseus, and we find significant variations in the distributions for those (smaller, ∼few pc scale) regions. Even though we have used 12 CO data to estimate excitation temperatures, and we have corrected for opacity, the 13 CO maps seem unable to give column distributions that consistently resemble those from dust measures. We have edited out the effects of the shell around the B-star HD 278942 from the column density distribution comparisons. In that shell's interior and in the parts where it overlaps the molecular cloud, there appears to be a dearth of 13 CO, which is likely due either to 13 CO not yet having had time to form in this young structure and/or destruction of 13 CO in the molecular cloud by the HD 278942's wind and/or radiation. We conclude that the use of either dust or gas measures of column density without extreme attention to calibration (e.g., of thermal emission zero-levels) and artifacts (e.g., the shell) is more perilous than even experts might normally admit. And, the use of 13 CO data to trace total column density in detail, even after proper calibration, is unavoidably limited in utility due to threshold, depletion, and opacity effects. If one's main aim is to map column density (rather than temperature

  10. Molecular polymorphism as a tool for differentiating ground beetles (Carabus species): application of ubiquitin PCR/SSCP analysis.

    Boge, A; Gerstmeier, R; Einspanier, R

    1994-11-01

    Differentiation between Carabus species (ground beetle) and subspecies is difficult, although there have been extensive studies. To address this problem we have applied PCR in combination with SSCP analysis focussing on the evolutionally conservative ubiquitin gene to elaborate a new approach to molecular differentiation between species. We report that Carabidae possess an ubiquitin gene and that its gene has a multimeric structure. Differential SSCP analysis was performed with the monomeric form of the gene to generate a clear SSCP pattern. Such PCR/SSCP resulted in reproducible patterns throughout our experiments. Comparing different Carabus species (Carabus granulatus, C. irregularis, C. violaceus and C. auronitens) we could observe clear interspecies differences but no differences between genders. Some species showed some remarkable differences between the individuals. We suggest that the ubiquitin PCR-SSCP technique might be an additional tool for the differentiation of ground beetles.

  11. An Intronic Polymorphism in couch potato Is Not Distributed Clinally in European Drosophila melanogaster Populations nor Does It Affect Diapause Inducibility.

    Zonato, Valeria; Fedele, Giorgio; Kyriacou, Charalambos P

    2016-01-01

    couch potato (cpo) encodes an RNA binding protein that has been reported to be expressed in the peripheral and central nervous system of embryos, larvae and adults, including the major endocrine organ, the ring gland. A polymorphism in the D. melanogaster cpo gene coding region displays a latitudinal cline in frequency in North American populations, but as cpo lies within the inversion In(3R)Payne, which is at high frequencies and itself shows a strong cline on this continent, interpretation of the cpo cline is not straightforward. A second downstream SNP in strong linkage disequilibrium with the first has been claimed to be primarily responsible for the latitudinal cline in diapause incidence in USA populations.Here, we investigate the frequencies of these two cpo SNPs in populations of Drosophila throughout continental Europe. The advantage of studying cpo variation in Europe is the very low frequency of In(3R)Payne, which we reveal here, does not appear to be clinally distributed. We observe a very different geographical scenario for cpo variation from the one in North America, suggesting that the downstream SNP does not play a role in diapause. In an attempt to verify whether the SNPs influence diapause we subsequently generated lines with different combinations of the two cpo SNPs on known timeless (tim) genetic backgrounds, because polymorphism in the clock gene tim plays a significant role in diapause inducibility. Our results reveal that the downstream cpo SNP does not seem to play any role in diapause induction in European populations in contrast to the upstream coding cpo SNP. Consequently, all future diapause studies on strains of D. melanogaster should initially determine their tim and cpo status.

  12. Molecular insight into systematics, host associations, life cycles and geographic distribution of the nematode family Rhabdiasidae.

    Tkach, Vasyl V; Kuzmin, Yuriy; Snyder, Scott D

    2014-04-01

    Rhabdiasidae Railliet, 1915 is a globally distributed group of up to 100 known species of nematodes parasitic in amphibians and reptiles. This work presents the results of a molecular phylogenetic analysis of 36 species of Rhabdiasidae from reptiles and amphibians from six continents. New DNA sequences encompassing partial 18S rDNA, ITS1, 5.8S rDNA, ITS2 and partial 28S rDNA regions of nuclear ribosomal DNA were obtained from 27 species and pre-existing sequences for nine species were incorporated. The broad taxonomic, host and geographical coverage of the specimens allowed us to address long-standing questions in rhabdiasid systematics, evolution, geographic distribution, and patterns of host association. Our analysis demonstrated that rhabdiasids parasitic in snakes are an independent genus sister to the rest of the Rhabdiasidae, a status supported by life cycle data. Based on the combined evidence of molecular phylogeny, morphology and life cycle characteristics, a new genus Serpentirhabdias gen. nov. with the type species Serpentirhabdias elaphe (Sharpilo, 1976) comb. nov. is established. The phylogeny supports the monophyly of Entomelas Travassos, 1930, Pneumonema Johnston, 1916 and the largest genus of the family, Rhabdias Stiles and Hassall, 1905. DNA sequence comparisons demonstrate the presence of more than one species in the previously monotypic Pneumonema from Australian scincid lizards. The distribution of some morphological characters in the genus Rhabdias shows little consistency within the phylogenetic tree topology, in particular the apical structures widely used in rhabdiasid systematics. Our data suggest that some of the characters, while valuable for species differentiation, are not appropriate for differentiation among higher taxa and are of limited phylogenetic utility. Rhabdias is the only genus with a cosmopolitan distribution, but some of the lineages within Rhabdias are distributed on a single continent or a group of adjacent

  13. Studies on cellular distribution of elements in human hepatocellular carcinoma samples by molecular activation analysis

    Deng Guilong; Chen Chunying; Zhang Peiqun; Zhao Jiujiang; Chai Zhifang

    2005-01-01

    The distribution patterns of 17 elements in the subcellular fractions of nuclei, mitochondria, lysosome, microsome and cytosol of human hepatocellular carcinoma (HCC) and normal liver samples were investigated by using molecular activation analysis (MAA) and differential centrifugation. Their significant difference was checked by the Studient's t-test. These elements exhibit inhomogeneous distributions in each subcellular fraction. Some elements have no significant difference between hepatocellular carcinoma and normal liver samples. However, the concentrations of Br, Ca, Cd and Cs are significantly higher in each component of hepatocarcinoma than in normal liver. The content of Fe in microsome of HCC is significantly lower, almost half of normal liver samples, but higher in other subcellular fractions than in those of normal tissues. The rare earth elements of La and Ce have the patterns similar to Fe. The concentrations of Sb and Zn in nuclei of HCC are obviously lower (P<0.05, P<0.05). The contents of K and Na are higher in cytosol of HCC (P<0.05). The distributions of Ba and Rb show no significant difference between two groups. The relationships of Fe, Cd and K with HCC were also discussed. The levels of some elements in subcellular fractions of tumor were quite different from those of normal liver, which suggested that trace elements might play important roles in the occurrence and development of hepatocellular carcinoma. (authors)

  14. Studies on cellular distribution of elements in human hepatocellular carcinoma samples by molecular activation analysis

    Guilong, Deng [Chinese Academy of Sciences, Beijing (China). Inst. of High Energy Physics, Key Laboratory of Nuclear Analytical Techniques; Department of General Surgery, the Second Affiliated Hospital, School of Medicine, Zhejiang Univ., Hangzhou (China); Chunying, Chen; Peiqun, Zhang; Jiujiang, Zhao; Zhifang, Chai [Chinese Academy of Sciences, Beijing (China). Inst. of High Energy Physics, Key Laboratory of Nuclear Analytical Techniques; Yingbin, Liu; Jianwei, Wang; Bin, Xu; Shuyou, Peng [Department of General Surgery, the Second Affiliated Hospital, School of Medicine, Zhejiang Univ., Hangzhou (China)

    2005-07-15

    The distribution patterns of 17 elements in the subcellular fractions of nuclei, mitochondria, lysosome, microsome and cytosol of human hepatocellular carcinoma (HCC) and normal liver samples were investigated by using molecular activation analysis (MAA) and differential centrifugation. Their significant difference was checked by the Studient's t-test. These elements exhibit inhomogeneous distributions in each subcellular fraction. Some elements have no significant difference between hepatocellular carcinoma and normal liver samples. However, the concentrations of Br, Ca, Cd and Cs are significantly higher in each component of hepatocarcinoma than in normal liver. The content of Fe in microsome of HCC is significantly lower, almost half of normal liver samples, but higher in other subcellular fractions than in those of normal tissues. The rare earth elements of La and Ce have the patterns similar to Fe. The concentrations of Sb and Zn in nuclei of HCC are obviously lower (P<0.05, P<0.05). The contents of K and Na are higher in cytosol of HCC (P<0.05). The distributions of Ba and Rb show no significant difference between two groups. The relationships of Fe, Cd and K with HCC were also discussed. The levels of some elements in subcellular fractions of tumor were quite different from those of normal liver, which suggested that trace elements might play important roles in the occurrence and development of hepatocellular carcinoma. (authors)

  15. New results in the relation between intensity distribution of reflected molecular beams and spatial distribution of elementary crystal cells in solids

    Nikuradse, A.; Weidner, J.

    1974-01-01

    Analytic expressions for the intensity distribution of a molecular beam reflected by a solid surface which consists of face centered cubic elementary cells have been studied. One has also tried to study the influence of the spatial distribution of the elementary crystal cells on the intensity of reflection. Some curves which had been evaluated and designed by a computer are now published. The Kratzer potential of interaction has alway been supposed [fr

  16. Single nucleotide polymorphism-based molecular typing of M. leprae from multicase families of leprosy patients and their surroundings to understand the transmission of leprosy.

    Turankar, R P; Lavania, M; Chaitanya, V S; Sengupta, U; Darlong, J; Darlong, F; Siva Sai, K S R; Jadhav, R S

    2014-03-01

    The exact mode of transmission of leprosy is not clearly understood; however, many studies have demonstrated active transmission of leprosy around a source case. Families of five active leprosy cases and their household contacts were chosen from a high endemic area in Purulia. Fifty-two soil samples were also collected from different areas of their houses. DNA was extracted from slit-skin smears (SSS) and soil samples and the Mycobacterium leprae-specific RLEP (129 bp) region was amplified using PCR. Molecular typing of M. leprae was performed for all RLEP PCR-positive samples by single nucleotide polymorphism (SNP) typing and confirmation by DNA sequencing. SSS of these five patients and six out of the total 28 contacts were PCR positive for RLEP whereas 17 soil samples out of 52 showed the presence of M. leprae DNA. SNP typing of M. leprae from all RLEP PCR-positive subjects (patients and smear-positive contacts) and 10 soil samples showed the SNP type 1 genotype. M. leprae DNA from the five leprosy patients and the six contacts was further subtyped and the D subtype was noted in all patients and contacts, except for one contact where the C subtype was identified. Typing followed by subtyping of M. leprae clearly revealed that either the contacts were infected by the patients or both patients and contacts had the same source of infection. It also revealed that the type of M. leprae in the soil in the inhabited areas where patients resided was also of the same type as that found in patients. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

  17. Molecular assessment of artemisinin resistance markers, polymorphisms in the k13 propeller, and a multidrug-resistance gene in the eastern and western border areas of Myanmar.

    Nyunt, Myat Htut; Hlaing, Thaung; Oo, Htet Wai; Tin-Oo, Lu-Lu Kyaw; Phway, Hnin Phyu; Wang, Bo; Zaw, Ni Ni; Han, Soe Soe; Tun, Thurein; San, Kyaw Kyaw; Kyaw, Myat Phone; Han, Eun-Taek

    2015-04-15

    As K13 propeller mutations have been recently reported to serve as molecular markers, assessment of K13 propeller polymorphisms in multidrug-resistant gene in isolates from Myanmar, especially the eastern and western border areas, is crucial if we are to understand the spread of artemisinin resistance. A 3-day surveillance study was conducted in the eastern and western border areas in Myanmar, and K13 propeller and Plasmodium falciparum multidrug resistance-associated protein 1 (pfmrp1) mutations were analyzed. Among the 1761 suspected malaria cases screened, a total of 42 uncomplicated falciparum cases from the eastern border and 49 from the western border were subjected to 3 days of surveillance after artemether-lumefantrine treatment. No parasitemic case showing positivity on day 3 was noted from the western border, but 26.2% (11/42) of cases were positive in the eastern border. Although we found no marked difference in the prevalence of the pfmrp1 mutation in the eastern and western borders (36% vs 31%, respectively), K13 mutations were more frequent in the eastern border area (where the 3-day persistent cases were detected; 48% vs 14%). C580Y, M476I, A481V, N458Y, R539T, and R516Y accounted for 68.9% of all K13 mutations significantly associated with day 3 parasitaemia. The K13 mutations were significantly associated with day 3 parasitaemia, emphasizing the importance of K13 surveillance. The low prevalence of K13 mutations and the absence of day 3 parasitaemic cases indicate that artemisinin resistance may not have spread to the western Myanmar border region. Although analysis of multiple K13 mutations is challenging, it should be done at various sentinel sites in Myanmar. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. Concholepas concholepas Ferritin H-like subunit (CcFer): Molecular characterization and single nucleotide polymorphism associated to innate immune response.

    Chávez-Mardones, Jacqueline; Valenzuela-Muñoz, Valentina; Núñez-Acuña, Gustavo; Maldonado-Aguayo, Waleska; Gallardo-Escárate, Cristian

    2013-09-01

    Ferritin has been identified as the principal protein of iron storage and iron detoxification, playing a pivotal role for the cellular homeostasis in living organisms. However, recent studies in marine invertebrates have suggested its association with innate immune system. In the present study, one Ferritin subunit was identified from the gastropod Concholepas concholepas (CcFer), which was fully characterized by Rapid Amplification of cDNA Ends technique. Simultaneously, a challenge test was performed to evaluate the immune response against Vibrio anguillarum. The full length of cDNA Ccfer was 1030 bp, containing 513 bp of open reading frame that encodes to 170 amino acid peptide, which was similar to the Ferritin H subunit described in vertebrates. Untranslated Regions (UTRs) were identified with a 5'UTR of 244 bp that contains iron responsive element (IRE), and a 3'UTR of 273 bp. The predicted molecular mass of deduced amino acid of CcFer was 19.66 kDa and isoelectric point of 4.92. Gene transcription analysis revealed that CcFer increases against infections with V. anguillarum, showing a peak expression at 6 h post-infection. Moreover, a single nucleotide polymorphism was detected at -64 downstream 5'UTR sequence (SNP-64). Quantitative real time analysis showed that homozygous mutant allele (TT) was significantly associated with higher expression levels of the challenged group compared to wild (CC) and heterozygous (CT) variants. Our findings suggest that CcFer is associated to innate immune response in C. concholepas and that the presence of SNPs may involve differential transcriptional expression of CcFer. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Molecular systematics and biogeography of the circumglobally distributed genus Seriola (Pisces: Carangidae).

    Swart, Belinda L; von der Heyden, Sophie; Bester-van der Merwe, Aletta; Roodt-Wilding, Rouvay

    2015-12-01

    The genus Seriola includes several important commercially exploited species and has a disjunct distribution globally; yet phylogenetic relationships within this genus have not been thoroughly investigated. This study reports the first comprehensive molecular phylogeny for this genus based on mitochondrial (Cytb) and nuclear gene (RAG1 and Rhod) DNA sequence data for all extant Seriola species (nine species, n=27). All species were found to be monophyletic based on Maximum parsimony, Maximum likelihood and Bayesian inference. The closure of the Tethys Sea (12-20 MYA) coincides with the divergence of a clade containing ((S. fasciata and S. peruana), S. carpenteri) from the rest of the Seriola species, while the formation of the Isthmus of Panama (±3 MYA) played an important role in the divergence of S. fasciata and S. peruana. Furthermore, factors such as climate and water temperature fluctuations during the Pliocene played important roles during the divergence of the remaining Seriola species. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Exploiting Molecular Weight Distribution Shape to Tune Domain Spacing in Block Copolymer Thin Films.

    Gentekos, Dillon T; Jia, Junteng; Tirado, Erika S; Barteau, Katherine P; Smilgies, Detlef-M; DiStasio, Robert A; Fors, Brett P

    2018-04-04

    We report a method for tuning the domain spacing ( D sp ) of self-assembled block copolymer thin films of poly(styrene- block-methyl methacrylate) (PS- b-PMMA) over a large range of lamellar periods. By modifying the molecular weight distribution (MWD) shape (including both the breadth and skew) of the PS block via temporal control of polymer chain initiation in anionic polymerization, we observe increases of up to 41% in D sp for polymers with the same overall molecular weight ( M n ≈ 125 kg mol -1 ) without significantly changing the overall morphology or chemical composition of the final material. In conjunction with our experimental efforts, we have utilized concepts from population statistics and least-squares analysis to develop a model for predicting D sp based on the first three moments of the MWDs. This statistical model reproduces experimental D sp values with high fidelity (with mean absolute errors of 1.2 nm or 1.8%) and provides novel physical insight into the individual and collective roles played by the MWD moments in determining this property of interest. This work demonstrates that both MWD breadth and skew have a profound influence over D sp , thereby providing an experimental and conceptual platform for exploiting MWD shape as a simple and modular handle for fine-tuning D sp in block copolymer thin films.

  1. A Molecular Investigation of Soil Organic Carbon Composition, Variability, and Spatial Distribution Across an Alpine Catchment

    Hsu, H. T.; Lawrence, C. R.; Winnick, M.; Druhan, J. L.; Williams, K. H.; Maher, K.; Rainaldi, G. R.; McCormick, M. E.

    2016-12-01

    The cycling of carbon through soils is one of the least understood aspects of the global carbon cycle and represents a key uncertainty in the prediction of land-surface response to global warming. Thus, there is an urgent need for advanced characterization of soil organic carbon (SOC) to develop and evaluate a new generation of soil carbon models. We hypothesize that shifts in SOC composition and spatial distribution as a function of soil depth can be used to constrain rates of transformation between the litter layer and the deeper subsoil (extending to a depth of approximately 1 m). To evaluate the composition and distribution of SOC, we collected soil samples from East River, a shale-dominated watershed near Crested Butte, CO, and characterized relative changes in SOC species as a function of depth using elemental analysis (EA), Fourier transform infrared spectroscopy (FT-IR) and bulk C X-ray absorption spectroscopy (XAS). Our results show that total organic carbon (TOC) decreases with depth, and high total inorganic carbon (TIC) content was found in deeper soils (after 75 cm), a characteristic of the bedrock (shale). The distribution of aliphatic C relative to the parent material generally decreases with depth and that polysaccharide can be a substantial component of SOC at various depths. On the other hand, the relative distribution of aromatic C, traditionally viewed as recalcitrant, only makes up a very small part of SOC regardless of depth. These observations confirm that molecular structure is not the only determinant of SOC turnover rate. To study other contributors to SOC decomposition, we studied changes in the spatial correlation of SOC and minerals using X-ray fluorescence spectroscopy (XRF) and scanning transmission X-ray microscopy (STXM). We found that aromatics mostly locate on the surface of small soil aggregates (1-10 μm). Polysaccharides and proteins, both viewed as labile traditionally, are more evenly distributed over the interior of the

  2. Unlike twins: an NMR comparison of two α-synuclein polymorphs featuring different toxicity.

    Julia Gath

    Full Text Available We structurally compare, using solid-state NMR, two different polymorphs of α-synuclein which, as established recently, display contrasting biochemical properties, toxicity, and tropism for cells. We show that both forms, which can each be produced as a pure polymorph, are greatly different in secondary structure. While β-sheets are the dominating secondary structure elements for both polymorphs, they are markedly divergent in terms of number of elements, as well as their distribution. We demonstrate that all identified β-sheets feature an in-register parallel stacking for both polymorphs. The two forms show a different molecular arrangement in the unit cell and distinct dynamic features, while sharing a highly flexible C-terminal domain. The use of reproducible, well-identified conditions for sample preparation and the recording of identical NMR experiments allows for a direct comparison of the results.

  3. MODELING THE ATOMIC-TO-MOLECULAR TRANSITION AND CHEMICAL DISTRIBUTIONS OF TURBULENT STAR-FORMING CLOUDS

    Offner, Stella S. R. [Department of Astronomy, Yale University, New Haven, CT 06511 (United States); Bisbas, Thomas G.; Viti, Serena [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6B (United Kingdom); Bell, Tom A., E-mail: stella.offner@yale.edu [Centro de Astrobiologia (CSIC-INTA), Carretera de Ajalvir, km 4, E-28850 Madrid (Spain)

    2013-06-10

    We use 3D-PDR, a three-dimensional astrochemistry code for modeling photodissociation regions (PDRs), to post-process hydrodynamic simulations of turbulent, star-forming clouds. We focus on the transition from atomic to molecular gas, with specific attention to the formation and distribution of H, C{sup +}, C, H{sub 2}, and CO. First, we demonstrate that the details of the cloud chemistry and our conclusions are insensitive to the simulation spatial resolution, to the resolution at the cloud edge, and to the ray angular resolution. We then investigate the effect of geometry and simulation parameters on chemical abundances and find weak dependence on cloud morphology as dictated by gravity and turbulent Mach number. For a uniform external radiation field, we find similar distributions to those derived using a one-dimensional PDR code. However, we demonstrate that a three-dimensional treatment is necessary for a spatially varying external field, and we caution against using one-dimensional treatments for non-symmetric problems. We compare our results with the work of Glover et al., who self-consistently followed the time evolution of molecule formation in hydrodynamic simulations using a reduced chemical network. In general, we find good agreement with this in situ approach for C and CO abundances. However, the temperature and H{sub 2} abundances are discrepant in the boundary regions (A{sub v} {<=} 5), which is due to the different number of rays used by the two approaches.

  4. The formation of molecular hydrogen on silicate dust analogs: The rotational distribution

    Gavilan, L.; Lemaire, J. L. [LERMA, UMR 8112 du CNRS, de l' Observatoire de Paris et de l' Université de Cergy Pontoise, 5 mail Gay Lussac, F-95000 Cergy Pontoise Cedex (France); Vidali, G. [Visiting Professor. Permanent address: Syracuse University, Physics Department, Syracuse, NY 13244-1320, USA. (United States); Sabri, T.; Jæger, C., E-mail: lisseth.gavilan@obspm.fr [Laboratory Astrophysics and Cluster Physics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena (Germany)

    2014-02-01

    Our laboratory experiments continue to explore how the formation of molecular hydrogen is influenced by dust and how dust thereby affects hydrogen molecules adsorbed on its surface. In Sabri et al., we present the preparation of nanometer-sized silicate grain analogs via laser ablation. These analogs illustrate extremes in structure (fully crystalline or fully amorphous grains), and stoichiometry (the forsterite and fayalite end-members of the olivine family). These were inserted in FORMOLISM, an ultra-high vacuum setup where they can be cooled down to ∼5 K. Atomic beams are directed at these surfaces and the formation of new molecules is studied via REMPI(2+1) spectroscopy. We explored the rotational distribution (0 ≤ J'' ≤ 5) of v'' = 0 of the ground electronic state of H{sub 2}. The results of these measurements are reported here. Surprisingly, molecules formed and ejected from crystalline silicates have a cold (T {sub rot} ∼ 120 K) rotational energy distribution, while for molecules formed on and ejected from amorphous silicate films, the rotational temperature is ∼310 K. These results are compared to previous experiments on metallic surfaces and theoretical simulations. Solid-state surface analysis suggests that flatter grains could hinder the 'cartwheel' rotation mode. A search for hot hydrogen, predicted as a result of H{sub 2} formation, hints at its production. For the first time, the rotational distribution of hydrogen molecules formed on silicate dust is reported. These results are essential to understanding the chemistry of astrophysical media containing bare dust grains.

  5. Genetic diversity analysis among male and female Jojoba genotypes employing gene targeted molecular markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) markers.

    Heikrujam, Monika; Kumar, Jatin; Agrawal, Veena

    2015-09-01

    To detect genetic variations among different Simmondsia chinensis genotypes, two gene targeted markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) were employed in terms of their informativeness and efficiency in analyzing genetic relationships among different genotypes. A total of 15 SCoT and 17 CBDP primers detected genetic polymorphism among 39 Jojoba genotypes (22 females and 17 males). Comparatively, CBDP markers proved to be more effective than SCoT markers in terms of percentage polymorphism as the former detecting an average of 53.4% and the latter as 49.4%. The Polymorphic information content (PIC) value and marker index (MI) of CBPD were 0.43 and 1.10, respectively which were higher than those of SCoT where the respective values of PIC and MI were 0.38 and 1.09. While comparing male and female genotype populations, the former showed higher variation in respect of polymorphic percentage and PIC, MI and Rp values over female populations. Nei's diversity (h) and Shannon index (I) were calculated for each genotype and found that the genotype "MS F" (in both markers) was highly diverse and genotypes "Q104 F" (SCoT) and "82-18 F" (CBDP) were least diverse among the female genotype populations. Among male genotypes, "32 M" (CBDP) and "MS M" (SCoT) revealed highest h and I values while "58-5 M" (both markers) was the least diverse. Jaccard's similarity co-efficient of SCoT markers ranged from 0.733 to 0.922 in female genotypes and 0.941 to 0.746 in male genotype population. Likewise, CBDP data analysis also revealed similarity ranging from 0.751 to 0.958 within female genotypes and 0.754 to 0.976 within male genotype populations thereby, indicating genetically diverse Jojoba population. Employing the NTSYS (Numerical taxonomy and multivariate analysis system) Version 2.1 software, both the markers generated dendrograms which revealed that all the Jojoba genotypes were clustered into two major groups, one group consisting of

  6. Spatial and energy distributions of the fragments resulting from the dissociation of swift molecular ions in solids

    Heredia-Avalos, Santiago; Garcia-Molina, Rafael; Abril, Isabel

    2002-01-01

    We have simulated the spatial evolution and energy loss of the fragments that result when swift molecular ions dissociate inside solid targets. In our calculations we have considered that these fragments undergo the following interactions: Coulomb repulsion (among like charged particles), stopping and wake forces (due to electronic excitations induced in the target), and nuclear scattering (with the target nuclei). We study the case of silicon targets irradiated with boron molecular or atomic ions; our results show that the main differences in the energy and spatial distributions of molecular fragments or atomic ions appear at shallow regions, and these tend to disappear at deeper depths

  7. Clock gene polymorphism, migratory behaviour and geographic distribution: a comparative study of trans-Saharan migratory birds.

    Bazzi, Gaia; Cecere, Jacopo G; Caprioli, Manuela; Gatti, Emanuele; Gianfranceschi, Luca; Podofillini, Stefano; Possenti, Cristina D; Ambrosini, Roberto; Saino, Nicola; Spina, Fernando; Rubolini, Diego

    2016-12-01

    Migratory behaviour is controlled by endogenous circannual rhythms that are synchronized by external cues, such as photoperiod. Investigations on the genetic basis of circannual rhythmicity in vertebrates have highlighted that variation at candidate 'circadian clock' genes may play a major role in regulating photoperiodic responses and timing of life cycle events, such as reproduction and migration. In this comparative study of 23 trans-Saharan migratory bird species, we investigated the relationships between species-level genetic variation at two candidate genes, Clock and Adcyap1, and species' traits related to migration and geographic distribution, including timing of spring migration across the Mediterranean Sea, migration distance and breeding latitude. Consistently with previous evidence showing latitudinal clines in 'circadian clock' genotype frequencies, Clock allele size increased with breeding latitude across species. However, early- and late-migrating species had similar Clock allele size. Species migrating over longer distances, showing delayed spring migration and smaller phenotypic variance in spring migration timing, had significantly reduced Clock (but not Adcyap1) gene diversity. Phylogenetic confirmatory path analysis suggested that migration date and distance were the most important variables directly affecting Clock gene diversity. Hence, our study supports the hypothesis that Clock allele size increases poleward as a consequence of adaptation to the photoperiodic regime of the breeding areas. Moreover, we show that long-distance migration is associated with lower Clock diversity, coherently with strong stabilizing selection acting on timing of life cycle events in long-distance migratory species, likely resulting from the time constraints imposed by late spring migration. © 2016 John Wiley & Sons Ltd.

  8. Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming

    Levine, Benjamin G.; Stone, John E.; Kohlmeyer, Axel

    2011-01-01

    The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU's memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm are presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 s per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis.

  9. Molecular research on the genetic diversity of Tunisian date palm ...

    Molecular research on the genetic diversity of Tunisian date palm ( Phoenix dactylifera L.) using the random amplified microsatellite polymorphism (RAMPO) and amplified fragment length polymorphism (AFLP) methods.

  10. Electronic structure and partial charge distribution of Doxorubicin in different molecular environments.

    Poudel, Lokendra; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Podgornik, Rudolf; Steinmetz, Nicole F; Ching, Wai-Yim

    2015-05-18

    The electronic structure and partial charge of doxorubicin (DOX) in three different molecular environments-isolated, solvated, and intercalated in a DNA complex-are studied by first-principles density functional methods. It is shown that the addition of solvating water molecules to DOX, together with the proximity to and interaction with DNA, has a significant impact on the electronic structure as well as on the partial charge distribution. Significant improvement in estimating the DOX-DNA interaction energy is achieved. The results are further elucidated by resolving the total density of states and surface charge density into different functional groups. It is concluded that the presence of the solvent and the details of the interaction geometry matter greatly in determining the stability of DOX complexation. Ab initio calculations on realistic models are an important step toward a more accurate description of the long-range interactions in biomolecular systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Formulation of state projected centroid molecular dynamics: Microcanonical ensemble and connection to the Wigner distribution

    Orr, Lindsay; Hernández de la Peña, Lisandro; Roy, Pierre-Nicholas

    2017-06-01

    A derivation of quantum statistical mechanics based on the concept of a Feynman path centroid is presented for the case of generalized density operators using the projected density operator formalism of Blinov and Roy [J. Chem. Phys. 115, 7822-7831 (2001)]. The resulting centroid densities, centroid symbols, and centroid correlation functions are formulated and analyzed in the context of the canonical equilibrium picture of Jang and Voth [J. Chem. Phys. 111, 2357-2370 (1999)]. The case where the density operator projects onto a particular energy eigenstate of the system is discussed, and it is shown that one can extract microcanonical dynamical information from double Kubo transformed correlation functions. It is also shown that the proposed projection operator approach can be used to formally connect the centroid and Wigner phase-space distributions in the zero reciprocal temperature β limit. A Centroid Molecular Dynamics (CMD) approximation to the state-projected exact quantum dynamics is proposed and proven to be exact in the harmonic limit. The state projected CMD method is also tested numerically for a quartic oscillator and a double-well potential and found to be more accurate than canonical CMD. In the case of a ground state projection, this method can resolve tunnelling splittings of the double well problem in the higher barrier regime where canonical CMD fails. Finally, the state-projected CMD framework is cast in a path integral form.

  12. Formulation of state projected centroid molecular dynamics: Microcanonical ensemble and connection to the Wigner distribution.

    Orr, Lindsay; Hernández de la Peña, Lisandro; Roy, Pierre-Nicholas

    2017-06-07

    A derivation of quantum statistical mechanics based on the concept of a Feynman path centroid is presented for the case of generalized density operators using the projected density operator formalism of Blinov and Roy [J. Chem. Phys. 115, 7822-7831 (2001)]. The resulting centroid densities, centroid symbols, and centroid correlation functions are formulated and analyzed in the context of the canonical equilibrium picture of Jang and Voth [J. Chem. Phys. 111, 2357-2370 (1999)]. The case where the density operator projects onto a particular energy eigenstate of the system is discussed, and it is shown that one can extract microcanonical dynamical information from double Kubo transformed correlation functions. It is also shown that the proposed projection operator approach can be used to formally connect the centroid and Wigner phase-space distributions in the zero reciprocal temperature β limit. A Centroid Molecular Dynamics (CMD) approximation to the state-projected exact quantum dynamics is proposed and proven to be exact in the harmonic limit. The state projected CMD method is also tested numerically for a quartic oscillator and a double-well potential and found to be more accurate than canonical CMD. In the case of a ground state projection, this method can resolve tunnelling splittings of the double well problem in the higher barrier regime where canonical CMD fails. Finally, the state-projected CMD framework is cast in a path integral form.

  13. Molecular and biometric assessment of Myzodium mimulicola (Hemiptera: Aphididae), with new synonymy and host and distributional data

    Molecular and biometric assessment and redescription of Myzodium mimulicola (Drew & Sampson) are provided. New host and distributional data for North America are presented, including the first record from Alaska. Myzodium knowltoni (Smith & Robinson) is found to be a junior subjective synonym of M....

  14. Molecular and biometric assessment of Myzodium mimulicola (Drew & Sampson) (Hemiptera, Aphididae), new synonymy, host, and distributional data

    Molecular and biometric assessment and subsequent redescription of Myzodium mimulicola (Drew & Sampson) is provided. New host and distributional data for North America are presented, including the first record from Alaska. The current study determined that Myzodium knowltoni (Smith & Robinson) is a ...

  15. Removal of Anabaena spiroides by potassium permanganate pre-oxidation: effect on photosynthetic capacity and molecular weight distribution.

    Qiao, Junlian; Zhang, Xiaodong; Lv, Liping

    2017-11-01

    Bench scale tests were conducted to investigate the effect of potassium permanganate pre-oxidation on the photosynthetic activity and molecular weight distribution of Anabaena spiroides. Different concentrations of potassium permanganate were added into the suspension of Anabaena spiroides, one of the dominant algae in water bloom, and after pre-oxidation of permanganate for 1 h, the results show that the removal rate significantly increases by 33.99~36.35% compared to direct coagulation. Then, the algal characteristics, including photosynthetic ability, the changes in extracellular organic matter three-dimensional fluorescence, and the distribution of molecular weight were conducted and the results show that along with increasing concentration of potassium permanganate, the photosynthetic ability of algae decreases, more extracellular organic matter is secreted, and large molecular weight matter (humic-like and fulvic-like substances) are generated. Therefore, this study demonstrates that potassium permanganate could be used in addressing the algae-rich water.

  16. Toxic polyacetylenes in the genus Bupleurum (Apiaceae) - Distribution, toxicity, molecular mechanism and analysis.

    Lin, Meiyu; Zhang, Weidong; Su, Juan

    2016-12-04

    The genus Bupleurum includes approximately 200 species that are widely distributed in the Northern Hemisphere, Eurasia and North Africa. Certain species of this genus have long been used as antiphlogistic, antipyretic and analgesic agents in traditional folk medicine. As described in the Chinese Pharmacopoeia, the roots of Bupleurum chinense DC. and B. scorzonerifolium Willd. are the herbal materials that compose Chaihu (Radix Bupleuri), a well-known TCM herb. This review aims to provide up-to-date and comprehensive information regarding the distribution, toxicity, molecular mechanism and relatively new methods for the qualitative and quantitative determination of polyacetylenes in different Bupleurum species. The information needed for this paper were sourced from publishing sites such as Elsevier, science Direct, PubMed; electronic search engines such as Scopus and Web of Science, Google scholar; other scientific database sites for chemicals such as ChemSpider, PubChem, SciFinder, and also from on line books. Polyacetylenes, which are widely distributed in genus Bupleurum of the Apiaceae family, have high toxicity. Among polyacetylenes, bupleurotoxin, acetylbupleurotoxin and oenanthotoxin have strong neurotoxicity. Through previous research, it was found that the toxicity of Bupleurum polyacetylenes manifested as epileptic seizures, with the target of toxicity being the brain. The neurotoxicity of polyacetylenes exhibits a relationship with the γ-aminobutyric acid (GABA) receptor pathway, and polyacetylenes have been shown to inhibit GABA-induced currents (I GABA ) in a competitive manner. The plants of genus Bupleurum have been used in traditional medicine for thousands of years. However, certain species of this genus are poisonous, and it was attributed to the high content of polyacetylenes. The present review indicates that certain polyacetylenes in the genus Bupleurum have highly neurotoxic effects. The major challenge with regard to toxic polyacetylenes is

  17. Genotype distribution of estrogen receptor-alpha, catechol-O-methyltransferase, and cytochrome P450 17 gene polymorphisms in Caucasian women with uterine leiomyomas.

    Denschlag, Dominik; Bentz, Eva-Katrin; Hefler, Lukas; Pietrowski, Detlef; Zeillinger, Robert; Tempfer, Clemens; Tong, Dan

    2006-02-01

    To evaluate the association between the presence of uterine leiomyomas and three functional single nucleotide polymorphisms (SNPs) of the estrogen receptor alpha (ESR1), catechol-O-methyltransferase (COMT), and cytochrom P450 17 (CYP17A) genes, which have been described to modify the estrogen metabolism. Prospective case control study. Academic research institution. One hundred thirty women with clinically and surgically diagnosed uterine leiomyomas and 139 population controls. Peripheral venous puncture. Polymerase chain reaction and pyrosequencing were performed to genotype women with respect to the ESR1 IVS1-397 T/C (PvuII), COMT G158A, and the CYP17A 34T-->C SNPs. Comparing women with uterine leiomyomas and controls, no statistically significant differences with respect to allele frequency and genotype distribution were ascertained for ESR1 IVS 1-397 T/C (PvuII) (P=0.9 and P=0.6, respectively), COMT G158A (P=0.3 and P=0.6, respectively), and CYP17A 34T-->C (P=0.1 and P=0.5, respectively). When all two-way interactions of investigated SNPs were ascertained, no significant interactions were observed. In a multivariate model, no SNP was significantly associated with leiomyomas. Carriage of the ESR1 IVS1-397 T/C (PvuII), COMT G158A, and the CYP17A 34T-->C SNPs is not associated with the susceptibility to uterine leiomyoma in a Caucasian population.

  18. Carbon K-shell photoionization of CO: Molecular frame angular distributions of normal and conjugate shakeup satellites

    Jahnke, T.; Titze, J.; Foucar, L.; Wallauer, R.; Osipov, T.; Benis, E.P.; Jagutzki, O.; Arnold, W.; Czasch, A.; Staudte, A.; Schoeffler, M.; Alnaser, A.; Weber, T.; Prior, M.H.; Schmidt-Boecking, H.; Doerner, R.

    2011-01-01

    We have measured the molecular frame angular distributions of photoelectrons emitted from the Carbon K-shell of fixed-in-space CO molecules for the case of simultaneous excitation of the remaining molecular ion. Normal and conjugate shakeup states are observed. Photoelectrons belonging to normal Σ-satellite lines show an angular distribution resembling that observed for the main photoline at the same electron energy. Surprisingly a similar shape is found for conjugate shakeup states with Π-symmetry. In our data we identify shake rather than electron scattering (PEVE) as the mechanism producing the conjugate lines. The angular distributions clearly show the presence of a Σ shape resonance for all of the satellite lines.

  19. Molecular evaluation of genetic diversity and association studies in ...

    Molecular evaluation of genetic diversity and association studies in rice. (Oryza sativa L.) C. Vanniarajan, K. K. Vinod and Andy Pereira. J. Genet. 91, 9–19. Table 1. Chromosome-wise distribution of SSR alleles and their number (k), polymorphic information content (PIC) and allele discrimination index (Dm). Chromosome.

  20. LOW MOLECULAR MASS POLYPEPTIDE AND TRANSPORTER ANTIGEN PEPTIDE GENES POLYMORPHISM AS THE RISK FACTORS OF CERVICAL CANCER WHICH CAUSED BY HUMAN PAPILLOMAVIRUS TYPE-16 INFECTION IN BALI

    I N. B. Mahendra

    2015-12-01

    Full Text Available Background: Until recently, cervical cancer is one of the major problem in women’s health issue related to its high incidence and mortality rate. The etiology of cervical cancer is the high risk oncogenic group of Human Papillomavirus (HPV, especially HPV-16 and 18 and its phylogenies. Meanwhile in Bali, more than 50% of infection are caused by HPV-16 infection. The main objective of this study was to investigate the role of LMP-2, LMP-7, TAP-1 and TAP-2 gene polymorphism as the risk factor in the cervical cancer carcinogenesis that is caused by HPV-16 infection. Method: A nested non-paired case-control study was conducted at Obstetric and Gynecologic Department Sanglah General Hospital, Bali-Indonesia from March 1 until August 31, 2013. Laboratory testing was carried out at Laboratory of Histopathology Leiden University Medical Centre, Netherlands,. Results: A total of 40 samples were collected, consist of 20epithelial cervical cancer patients with positive HPV-16 infection as the case group and 20 non-cervical cancer patients with positive HPV-16 infection as the control group. Women infected by HPV-16 with LMP-7 gene polymorphism had a higher risk (OR=7.36, CI 95%=1.38-40.55, p=0.013 to be diagnosed with cervical cancer. Balinese women who were infected by HPV-16 with TAP-2 gene polymorphism had a higher risk (OR= 9.33, CI 95%=2.18-39.96, p=0.001 to be diagnosed with cervical cancer. Meanwhile, Balinese women who were infected by HPV-16 with LMP-7 and TAP-2 genes polymorphism had a higher risk (OR=12.67, CI 95%=1.40-114.42, p=0.020 to be diagnosed with cervical cancer. As the result, it was shown that both of this gene polymorphism was working synergistically. Conclusion: TAP-2 and LMP-7 genes polymorphism play a role in the carcinogenesis mechanism of cervical cancer that is caused by HPV-16 infection in Bali. Meanwhile, LMP-2 and TAP-1 genes polymorphism were not found to play a role in the immunology pathway of cervical cancer that is

  1. Distribution and kinematics of atomic and molecular gas inside the solar circle

    Marasco, A.; Fraternali, F.; van der Hulst, J. M.; Oosterloo, T.

    2017-11-01

    The detailed distribution and kinematics of the atomic and the CO-bright molecular hydrogen in the disc of the Milky Way inside the solar circle are derived under the assumptions of axisymmetry and pure circular motions. We divide the Galactic disc into a series of rings, and assume that the gas in each ring is described by four parameters: its rotation velocity, velocity dispersion, midplane density and its scale height. We fit these parameters to the Galactic H I and 12CO (J = 1-0) data by producing artificial H I and CO line-profiles and comparing them with the observations. Our approach allows us to fit all parameters to the data simultaneously without assuming a-priori a radial profile for one of the parameters. We present the distribution and kinematics of the H I and H2 in both the approaching (QIV) and the receding (QI) regions of the Galaxy. Our best-fit models reproduces remarkably well the observed H I and CO longitude-velocity diagrams up to a few degrees of distance from the midplane. With the exception of the innermost 2.5 kpc, QI and QIV show very similar kinematics. The rotation curves traced by the H I and H2 follow each other closely, flattening beyond R = 6.5 kpc. Both the H I and the H2 surface densities show a) a deep depression at 0.5 < R < 2.5 kpc, analogous to that shown by some nearby barred galaxies, b) local overdensities that can be interpreted in terms of spiral arms or ring-like features in the disc. The H I (H2) properties are fairly constant in the region outside the depression, with typical velocity dispersion of 8.9 ± 1.1 (4.4 ± 1.2) km s-1, density of 0.43 ± 0.11 (0.42 ± 0.22) cm-3 and HWHM scale height of 202 ± 28 (64 ± 12) pc. We also show that the H I opacity in the LAB data can be accounted for by using an "effective" spin temperature of 150 K: assuming an optically thin regime leads to an underestimate of the H I mass by about 30%.

  2. Na(+)-D-glucose cotransporter in the kidney of Squalus acanthias: molecular identification and intrarenal distribution.

    Althoff, Thorsten; Hentschel, Hartmut; Luig, Jutta; Schütz, Hendrike; Kasch, Myriam; Kinne, Rolf K-H

    2006-04-01

    Using primers against conserved regions of mammalian Na(+)-d-glucose cotransporters (SGLT), a cDNA was cloned from the kidney of spiny dogfish shark (Squalus acanthias). On the basis of comparison of amino acid sequence, membrane topology, and putative glycosylation and phosphorylation sites, the cDNA could be shown to belong to the family of sglt genes. Indeed, Na(+)-dependent d-glucose uptake could be demonstrated after expression of the gene in Xenopus laevis oocytes. In a dendrogram, the SGLT from shark kidney has a high homology to the mammalian SGLT2. Computer analysis revealed that the elasmobranch protein is most similar to the mammalian proteins in the transmembrane regions and contains already all the amino acids identified to be functionally important, suggesting early conservation during evolution. Extramembraneous loops show larger variations. This holds especially for loop 13, which has been implied as a phlorizin-binding domain. Antibodies were generated and the intrarenal distribution of the SGLT was studied in cryosections. In parallel, the nephron segments were identified by lectins. Positive immunoreactions were found in the proximal tubule in the early parts PIa and PIb and the late segment PIIb. The large PIIa segment of the proximal tubule showed no reaction. In contrast to the mammalian kidney also the late distal tubule, the collecting tubule, and the collecting duct showed immunoreactivity. The molecular information confirms previous vesicle studies in which a low affinity SGLT with a low stoichiometry has been observed and supports the notion of a similarity of the shark kidney SGLT to the mammalian SGLT2. Despite its presence in the late parts of the nephron, the absence of SGLT in the major part of the proximal tubule, the relatively low affinity, and in particular the low stoichiometry might explain the lack of a T(m) for d-glucose in the shark kidney.

  3. Distribution and molecular diversity of three cucurbit-infecting poleroviruses in China.

    Shang, Qiao-xia; Xiang, Hai-ying; Han, Cheng-gui; Li, Da-wei; Yu, Jia-lin

    2009-11-01

    Cucurbit aphid-borne yellows virus (CABYV) and Melon aphid-borne yellows virus (MABYV) have been found to be associated with cucurbit yellowing disease in China. Our report identifies for the first time a third distinct polerovirus, tentatively named Suakwa aphid-borne yellows virus (SABYV), infecting Suakwa vegetable sponge. To better understand the distribution and molecular diversity of these three poleroviruses infecting cucurbits, a total of 214 cucurbitaceous crop samples were collected from 25 provinces in China, and were investigated by RT-PCR and sequencing. Of these, 108 samples tested positive for CABYV, while 40 samples from five provinces were positive for MABYV, and SABYV was detected in only 4 samples which were collected in the southern part of China. Forty-one PCR-amplified fragments containing a portion of the RdRp gene, intergenic NCR and CP gene were cloned and sequenced. Sequence comparisons showed that CABYV isolates shared 78.0-79.2% nucleotide sequence identity with MABYV isolates, and 69.7-70.8% with SABYV. Sequence identity between MABYV and SABYV was 73.3-76.5%. In contrast, the nucleotide identities within each species were 93.2-98.7% (CABYV), 98.1-99.9% (MABYV), and 96.1-98.6% (SABYV). Phylogenetic analyses revealed that the polerovirus isolates fit into three distinct groups, corresponding to the three species. The CABYV group could be further divided into two subgroups: the Asia subgroup and the Mediterranean subgroup, based on CP gene and partial RdRp gene sequences. Recombination analysis suggested that MABYV may be a recombinant virus.

  4. EDF: Computing electron number probability distribution functions in real space from molecular wave functions

    Francisco, E.; Pendás, A. Martín; Blanco, M. A.

    2008-04-01

    Given an N-electron molecule and an exhaustive partition of the real space ( R) into m arbitrary regions Ω,Ω,…,Ω ( ⋃i=1mΩ=R), the edf program computes all the probabilities P(n,n,…,n) of having exactly n electrons in Ω, n electrons in Ω,…, and n electrons ( n+n+⋯+n=N) in Ω. Each Ω may correspond to a single basin (atomic domain) or several such basins (functional group). In the later case, each atomic domain must belong to a single Ω. The program can manage both single- and multi-determinant wave functions which are read in from an aimpac-like wave function description ( .wfn) file (T.A. Keith et al., The AIMPAC95 programs, http://www.chemistry.mcmaster.ca/aimpac, 1995). For multi-determinantal wave functions a generalization of the original .wfn file has been introduced. The new format is completely backwards compatible, adding to the previous structure a description of the configuration interaction (CI) coefficients and the determinants of correlated wave functions. Besides the .wfn file, edf only needs the overlap integrals over all the atomic domains between the molecular orbitals (MO). After the P(n,n,…,n) probabilities are computed, edf obtains from them several magnitudes relevant to chemical bonding theory, such as average electronic populations and localization/delocalization indices. Regarding spin, edf may be used in two ways: with or without a splitting of the P(n,n,…,n) probabilities into α and β spin components. Program summaryProgram title: edf Catalogue identifier: AEAJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAJ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 5387 No. of bytes in distributed program, including test data, etc.: 52 381 Distribution format: tar.gz Programming language: Fortran 77 Computer

  5. Genetic Polymorphisms in Glutathione (GSH- Related Genes Affect the Plasmatic Hg/Whole Blood Hg Partitioning and the Distribution between Inorganic and Methylmercury Levels in Plasma Collected from a Fish-Eating Population

    Andréia Ávila Soares de Oliveira

    2014-01-01

    Full Text Available This study aims to evaluate the effects of polymorphisms in glutathione (GSH- related genes (GSTM1, GSTT1, GSTP1, GCLM, and GCLC in the distribution of Hg in the blood compartments in humans exposed to methylmercury (MeHg. Subjects (n=88, exposed to MeHg from fish consumption, were enrolled in the study. Hg species in the plasma compartment were determined by LC-ICP-MS, whereas genotyping was performed by PCR assays. Mean total Hg levels in plasma (THgP and whole blood (THgB were 10±4.2 and 37±21, whereas mean evels of plasmatic MeHg (MeHgP, inorganic Hg (IHgP, and HgP/HgB were 4.3±2.9, 5.8±2.3 µg/L, and 0.33±0.15, respectively. GSTM1 and GCLC polymorphisms influence THgP and MeHgP (multivariate analyses, P<0.050. Null homozygotes for GSTM1 showed higher THgP and MeHgP levels compared to subjects with GSTM1 (THgP β=0.22, P=0.035; MeHgP β=0.30, P=0.050 and persons carrying at least one T allele for GCLC had significant higher MeHgP (β=0.59, P=0.046. Also, polymorphic GCLM subjects had lower THgP/THgB than those with the nonvariant genotype. Taken together, data of this study suggest that GSH-related polymorphisms may change the metabolism of MeHg by modifying the distribution of mercury species iin plasma compartment and the HgP/HgB partitioning.

  6. Polymorphic Contracts

    Belo, João Filipe; Greenberg, Michael; Igarashi, Atsushi; Pierce, Benjamin C.

    Manifest contracts track precise properties by refining types with predicates - e.g., {x : Int |x > 0 } denotes the positive integers. Contracts and polymorphism make a natural combination: programmers can give strong contracts to abstract types, precisely stating pre- and post-conditions while hiding implementation details - for example, an abstract type of stacks might specify that the pop operation has input type {x :α Stack |not ( empty x )} . We formalize this combination by defining FH, a polymorphic calculus with manifest contracts, and establishing fundamental properties including type soundness and relational parametricity. Our development relies on a significant technical improvement over earlier presentations of contracts: instead of introducing a denotational model to break a problematic circularity between typing, subtyping, and evaluation, we develop the metatheory of contracts in a completely syntactic fashion, omitting subtyping from the core system and recovering it post facto as a derived property.

  7. A Molecular Case-Control Study on the Association of Melatonin Hormone and rs#10830963 Single Nucleotide Polymorphism in its Receptor MTNR1B Gene with Breast Cancer

    Nadia A Abd El Moneim

    2015-01-01

    Full Text Available Background: The main function of the pineal hormone melatonin which is mediated via its two receptors, MTNR1A and MTNR1B, is to mediate dark signals in addition to anti-oxidation, immune system enhancement, protection from radiation, and anti-cancer functions. A common single nucleotide polymorphism in the MTNR1B gene is rs#10830963, which is well known as a risk factor for type 2 diabetes mellitus. This study intends to figure out the role of melatonin and its receptor MTNR1B gene rs#10830963 polymorphism in breast cancer incidence, diagnosis and prognosis. Methods: This study included 43 females with breast cancer and 45 apparently normal healthy females. Restriction fragment length polymorphism-PCR was used for amplification and genotyping of the MTNR1B gene rs#10830963 polymorphism in whole blood. Serum melatonin levels were measured using a ready-for-use radioimmunoassay kit. Results: For the MTNR1B gene rs#10830963 polymorphism, we observed a significantly higher GG genotype frequency among cases (72.1% than controls (13.3%, with a diagnostic sensitivity of 83.78% and specificity of 76.47%. The cases had a frequency of 11.6% for the CC genotype and 16.3% for the CG genotype which was significantly lower compared to controls that had a 44.4% frequency of the CC genotype and 42.2% frequency of the CG genotype. The GG genotype had a significant association with larger tumor volume (P=0.048. Serum melatonin levels were significantly lower among breast cancer patients than controls. Using the ROC curve analysis, serum melatonin showed a significant AUC (72.6%, P39.5 pg/ml. Conclusion: The risk for breast cancer incidence increased as the serum levels of melatonin decreased and in females homozygous for the G allele (GG genotype of the MTNR1B gene rs#10830963 polymorphism. The GG genotype was found to be associated with increased breast tumor volume as a marker of a poor prognosis breast cancer.

  8. Molecular dynamics equation designed for realizing arbitrary density: Application to sampling method utilizing the Tsallis generalized distribution

    Fukuda, Ikuo; Nakamura, Haruki

    2010-01-01

    Several molecular dynamics techniques applying the Tsallis generalized distribution are presented. We have developed a deterministic dynamics to generate an arbitrary smooth density function ρ. It creates a measure-preserving flow with respect to the measure ρdω and realizes the density ρ under the assumption of the ergodicity. It can thus be used to investigate physical systems that obey such distribution density. Using this technique, the Tsallis distribution density based on a full energy function form along with the Tsallis index q ≥ 1 can be created. From the fact that an effective support of the Tsallis distribution in the phase space is broad, compared with that of the conventional Boltzmann-Gibbs (BG) distribution, and the fact that the corresponding energy-surface deformation does not change energy minimum points, the dynamics enhances the physical state sampling, in particular for a rugged energy surface spanned by a complicated system. Other feature of the Tsallis distribution is that it provides more degree of the nonlinearity, compared with the case of the BG distribution, in the deterministic dynamics equation, which is very useful to effectively gain the ergodicity of the dynamical system constructed according to the scheme. Combining such methods with the reconstruction technique of the BG distribution, we can obtain the information consistent with the BG ensemble and create the corresponding free energy surface. We demonstrate several sampling results obtained from the systems typical for benchmark tests in MD and from biomolecular systems.

  9. Microbial quality and molecular identification of cultivable microorganisms isolated from an urban drinking water distribution system (Limassol, Cyprus).

    Botsaris, George; Kanetis, Loukas; Slaný, Michal; Parpouna, Christiana; Makris, Konstantinos C

    2015-12-01

    Microorganisms can survive and multiply in aged urban drinking water distribution systems, leading to potential health risks. The objective of this work was to investigate the microbial quality of tap water and molecularly identify its predominant cultivable microorganisms. Tap water samples collected from 24 different households scattered in the urban area of Limassol, Cyprus, were microbiologically tested following standard protocols for coliforms, E. coli, Pseudomonas spp., Enterococcus spp., and total viable count at 22 and 37 °C. Molecular identification was performed on isolated predominant single colonies using 16SrRNA sequencing. Approximately 85% of the household water samples were contaminated with one or more microorganisms belonging to the genera of Pseudomonas, Corynebacterium, Agrobacterium, Staphylococcus, Bacillus, Delftia, Acinetobacter, Enterococcus, Enterobacter, and Aeromonas. However, all samples tested were free from E. coli. This is the first report in Cyprus molecularly confirming specific genera of relevant microbial communities in tap water.

  10. Direct assignment of molecular vibrations via normal mode analysis of the neutron dynamic pair distribution function technique

    Fry-Petit, A. M.; Sheckelton, J. P.; McQueen, T. M.; Rebola, A. F.; Fennie, C. J.; Mourigal, M.; Valentine, M.; Drichko, N.

    2015-01-01

    For over a century, vibrational spectroscopy has enhanced the study of materials. Yet, assignment of particular molecular motions to vibrational excitations has relied on indirect methods. Here, we demonstrate that applying group theoretical methods to the dynamic pair distribution function analysis of neutron scattering data provides direct access to the individual atomic displacements responsible for these excitations. Applied to the molecule-based frustrated magnet with a potential magnetic valence-bond state, LiZn 2 Mo 3 O 8 , this approach allows direct assignment of the constrained rotational mode of Mo 3 O 13 clusters and internal modes of MoO 6 polyhedra. We anticipate that coupling this well known data analysis technique with dynamic pair distribution function analysis will have broad application in connecting structural dynamics to physical properties in a wide range of molecular and solid state systems

  11. Comparable investigation of the molecular size distribution and the amount of humic substances isolated from ONKALO, Olkiluoto, 2010

    Vilhunen, S.; Manninen, P.

    2010-11-01

    The humic substances at groundwater from Onkalo, Olkiluoto were studied in order to determine the molecular size distribution and the amount of humic substances. Humic substances were isolated from the water sample using DAX-8 resin and eluted with 0.1 M NaOH. The molecular size distribution was defined using high performance size exclusion chromatography (HPSEC) and ultraviolet (UV) or reflactive index (RI) detector. Two calibration standard sets (poly(styrene sulfonate) sodium salt (PSS) or polyethylene glycol (PEG) standards) with distinct structures as well as two eluents (0.05 M NaNO3 or 0.01 M Na-acetate) were studied and the results were compared with the previous ones. The calibration standards and eluents were found to have major effect on the measured parameters. The amount of humic substances was determined using total organic carbon (TOC) measurements. (orig.)

  12. A measurement of the turbulence-driven density distribution in a non-star-forming molecular cloud

    Ginsburg, Adam; Darling, Jeremy [CASA, University of Colorado, 389-UCB, Boulder, CO 80309 (United States); Federrath, Christoph, E-mail: Adam.G.Ginsburg@gmail.com [Monash Centre for Astrophysics, School of Mathematical Sciences, Monash University, Vic 3800 (Australia)

    2013-12-10

    Molecular clouds are supersonically turbulent. This turbulence governs the initial mass function and the star formation rate. In order to understand the details of star formation, it is therefore essential to understand the properties of turbulence, in particular the probability distribution of density in turbulent clouds. We present H{sub 2}CO volume density measurements of a non-star-forming cloud along the line of sight toward W49A. We use these measurements in conjunction with total mass estimates from {sup 13}CO to infer the shape of the density probability distribution function. This method is complementary to measurements of turbulence via the column density distribution and should be applicable to any molecular cloud with detected CO. We show that turbulence in this cloud is probably compressively driven, with a compressive-to-total Mach number ratio b=M{sub C}/M>0.4. We measure the standard deviation of the density distribution, constraining it to the range 1.5 < σ {sub s} < 1.9, assuming that the density is lognormally distributed. This measurement represents an essential input into star formation laws. The method of averaging over different excitation conditions to produce a model of emission from a turbulent cloud is generally applicable to optically thin line observations.

  13. Inulin in Medicinal Plants (IV) : Reversed-Phase High-Performance Liquid Chromatography of Inulin after Acetylation : Molecular-Weight Distribution of Inulin in Medicinal Plants

    三野, 芳紀; 筒井, 聡美; 太田, 長世; YOSHIKI, MINO; SATOMI, TSUTSUI; NAGAYO, OTA; 大阪薬科大学; 大阪薬科大学; 大阪薬科大学; Osaka College of Pharmacy; Osaka College of Pharmacy; Osaka College of Pharmacy

    1985-01-01

    Reversed-phase high-performance liquid chromatography coupled with pre-acetylation enabled acculate molecular-weight assay of inulin in medicinal plants to be conducted. The results clearly showed that the molecular-weight distribution of inulin varied depending on the stage of growth: Small molecular weight inulin polymers were detected in large quantity in the earlier growth stage whereas large molecular weight inulin polymers at the flowering and post flowering period.

  14. Presence and Distribution of Oilseed Pumpkin Viruses and Molecular Detection of Zucchini Yellow Mosaic Virus

    Ana Vučurović

    2009-01-01

    Full Text Available Over the past decade, intensive spread of virus infections of oilseed pumpkin has resulted in significant economic losses in pumpkin crop production, which is currently expanding in our country. In 2007 and 2008, a survey for the presence and distribution of oilseed pumpkin viruses was carried out in order to identify viruses responsible for epidemics and incidences of very destructive symptoms on cucurbit leaves and fruits. Monitoring andcollecting samples of oil pumpkin, as well as other species such as winter and butternut squash and buffalo and bottle gourd with viral infection symptoms, was conducted in several localities of Vojvodina Province. The collected plant samples were tested by DAS-ELISA using polyclonal antisera specific for the detection of six most economically harmful pumpkin viruses: Cucumber mosaic virus (CMV, Zucchini yellow mosaic virus (ZYMV, Watermelon mosaic virus (WMW, Squash mosaic virus (SqMV, Papaya ringspot virus (PRSV and Tobaccoringspot virus (TRSV that are included in A1 quarantine list of harmful organisms in Serbia.Identification of viruses in the collected samples indicated the presence of three viruses, ZYMV, WMV and CMV, in individual and mixed infections. Frequency of the identified viruses varied depending on locality and year of investigations. In 2007, WMV was the most frequent virus (94.2%, while ZYMV was prevalent (98.04% in 2008. High frequency of ZYMV determined in both years of investigation indicated the need for its rapid and reliable molecular detection. During this investigation, a protocol for ZYMVdetection was developed and optimized using specific primers CPfwd/Cprev and commercial kits for total RNA extraction, as well as for RT-PCR. In RT-PCR reaction using these primers, a DNA fragment of approximately 1100 bp, which included coat protein gene, was amplified in the samples of infected pumkin leaves. Although serological methods are still useful for large-scale testing of a great number of

  15. Comparable investigation of the molecular size distribution and the amount of humic substances isolated from ONKALO, Olkiluoto, 2011

    Luste, S.; Maekelae, J.; Manninen, P.

    2012-06-01

    The humic substances (HS) at groundwater from ONKALO, Olkiluoto were studied in order to determine the apparent molecular size distribution and the amount of humic substances. Humic substances were isolated from the water sample using DAX-8 resin and eluted with 0.1 M NaOH. The molecular size distribution was defined using high performance size exclusion chromatography (HPSEC) and ultraviolet (UV) and refractive index (RI) detector. In the SEC calibration (polystyrene sulfonate) sodium salts (PSS) were employed. Different eluents (NaNO 3 , Na-acetate and asetonitrile) with phosphate buffer and distinct ionic strengths were studied in order to optimize the determination method. The amount of humic substances was determined using total organic carbon (TOC) measurements. The results were compared with the previous ones in order to find out the variation of different methods (HPSEC) and to follow up the HS quantity (TOC). The method developed during the study is considered to be suitable for the HS molecular size distribution follow up, although the method development is suggested to be continued. (orig.)

  16. Comparable investigation of the molecular size distribution and the amount of humic substances isolated from ONKALO, Olkiluoto, 2011

    Luste, S.; Maekelae, J.; Manninen, P. [Ramboll Finland Oy, Espoo (Finland)

    2012-06-15

    The humic substances (HS) at groundwater from ONKALO, Olkiluoto were studied in order to determine the apparent molecular size distribution and the amount of humic substances. Humic substances were isolated from the water sample using DAX-8 resin and eluted with 0.1 M NaOH. The molecular size distribution was defined using high performance size exclusion chromatography (HPSEC) and ultraviolet (UV) and refractive index (RI) detector. In the SEC calibration (polystyrene sulfonate) sodium salts (PSS) were employed. Different eluents (NaNO{sub 3}, Na-acetate and asetonitrile) with phosphate buffer and distinct ionic strengths were studied in order to optimize the determination method. The amount of humic substances was determined using total organic carbon (TOC) measurements. The results were compared with the previous ones in order to find out the variation of different methods (HPSEC) and to follow up the HS quantity (TOC). The method developed during the study is considered to be suitable for the HS molecular size distribution follow up, although the method development is suggested to be continued. (orig.)

  17. Distribution of polymorphisms IL4-590 C/T and IL4 RP2 in the human populations of Madeira, Azores, Portugal, Cape Verde and Guinea-Bissau.

    Berenguer, Anabela G; Câmara, Rita A; Brehm, António D; Oliveira, Susana; Fernandes, Ana T

    2012-01-01

    The IL4 gene is located on chromosome 5q23.3-31.2. Polymorphisms within this cytokine gene, like the derivative allele T of IL4-590, have been reported as being associated to elevated IgE serum levels and asthma. In the present work, the allelic and genotypic frequency of the IL4-590 and IL4 RP2 polymorphisms was carried out in 599 individuals from Madeira, Azores, Portugal mainland, Cape Verde and Guinea-Bissau and in a sample of 101 asthmatics from Madeira population. In all populations the polymorphisms were in LD and presented a significant dissimilar allelic and genotypic distribution (pMadeira when compared to Azores. Significant differences regarding both loci were found between Madeira population and the group of asthmatics. Genotype 183183TT frequency is higher for African populations while 253253CC prevails in Caucasian populations. The existence of a Hardy-Weinberg Disequilibrium in Guinea-Bissau population not observed in neutral markers leads to the hypothesis of natural selection occurring in these loci probably associated to a rapid population growth an hypothesis strengthened by neutral STRs D5S818 and CSF1PO gene diversity.

  18. Detection of irradiated food by the changes in protein molecular mass distribution

    Niciforovic, A.; Radojcic, M.; Milosavljevic, B.H.

    1998-01-01

    Complete text of publication follows. The present work deals with the radiation-induced damage of proteins, which is followed by the change in the molecular mass. The phenomenon was studied on protein rich samples, i.e., chicken meat and dehydrated egg white. The radiation dose applied was in the range of the ones used for food microbial control. Chicken drumstick and chicken white meat proteins were separated according to their molecular mass. The protein profile was compared to the meat samples irradiated in the frozen state with 5 kGy at 60 Co source. In the case of chicken white meat, irradiation produces both nonselective protein scission (e.g. the amount of proteins of molecular mass larger than 30 kDa decreases, while the amount of proteins of molecular mass smaller than 30 kDa increases), and selective protein scission (e.g. appearance of a protein fragment of molecular mass equal to 18 kDa). In the case of chicken drumstick proteins the irradiation induces both the protein scission and the aggregation. The changes are nonspecific as well as specific and the generation of Mm = 18 kDa protein fragment was observed again. Irradiation of aerated dehydrated egg white proteins produces only nonselective protein scission. The results are discussed in view of the routine application of SDS-PAGE method for the detection of irradiated foodstuff

  19. Comparison of semi-automated commercial rep-PCR fingerprinting, spoligotyping, 12-locus MIRU-VNTR typing and single nucleotide polymorphism analysis of the embB gene as molecular typing tools for Mycobacterium bovis.

    Armas, Federica; Camperio, Cristina; Coltella, Luana; Selvaggini, Serena; Boniotti, Maria Beatrice; Pacciarini, Maria Lodovica; Di Marco Lo Presti, Vincenzo; Marianelli, Cinzia

    2017-08-04

    Highly discriminatory genotyping strategies are essential in molecular epidemiological studies of tuberculosis. In this study we evaluated, for the first time, the efficacy of the repetitive sequence-based PCR (rep-PCR) DiversiLab Mycobacterium typing kit over spoligotyping, 12-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and embB single nucleotide polymorphism (SNP) analysis for Mycobacterium bovis typing. A total of 49 M. bovis animal isolates were used. DNA was extracted and genomic DNA was amplified using the DiversiLab Mycobacterium typing kit. The amplified fragments were separated and detected using a microfluidics chip with Agilent 2100. The resulting rep-PCR-based DNA fingerprints were uploaded to and analysed using web-based DiversiLab software through Pearson's correlation coefficient. Rep-PCR DiversiLab grouped M. bovis isolates into ten different clusters. Most isolates sharing identical spoligotype, MIRU-VNTR profile or embB gene polymorphism were grouped into different rep-PCR clusters. Rep-PCR DiversiLab displayed greater discriminatory power than spoligotyping and embB SNP analysis but a lower resolution power than the 12-locus MIRU-VNTR analysis. MIRU-VNTR confirmed that it is superior to the other PCR-based methods tested here. In combination with spoligotyping and 12-locus MIRU-VNTR analysis, rep-PCR improved the discriminatory power for M. bovis typing.

  20. Wild common bean in the Central Valley of Costa Rica: ecological distribution and molecular characterization

    Rosa In\\u00E9s Gonz\\u00E1lez Torres

    2004-01-01

    Full Text Available Frijol silvestre en el Valle Central de Costa Rica: distribución ecológica y caracterización molecular. Este trabajo presenta una actualización sobre la distribución de las formas silvestres de fríjol común en Costa Rica, su ecología y su caracterización molecular. Ala fecha 22 poblaciones fueron encontradas en cuatro cuencas alrededor del Valle Central, generalmente en vegetaciones ruderales (frecuentemente bordes de cafetales, con estatuto de conservación variable (desde protegido a amenazado. Su caracterización molecular indica su pertenencia al acervo genético mesoamericano. Varios marcadores indican una variabilidad aumentada en las formas silvestres y permiten inferir la presencia de un fenómeno de flujo genético e introgresión desde materiales cultivados.

  1. Molecular weights distribution and temperature effects in the styrene polymerization initiated with gamma rays

    Burillo, G.; Martinez, R.

    1979-01-01

    The polymerization of styrene irradiated in a 60 CO source to 18 0 C temperature and to 70 0 C temperature was studied, in order to reduce the irradiation time raising the polymerization rate and looking for a highest molecular weight. The radiation doses used were from 0.2 to 33.26 Mrad, at the rate of 56 rad/sec, the percent of polymerization and the molecular weight formed were determined, the results indicate one highest molecular weight of 132,700 when the radiation dose of 20 Mrad and the temperature of 20 0 C were used, and one of 395,000 when the irradiation is carried out to 70 0 C. (author)

  2. Proximal Region of the Gene Encoding Cytadherence-Related Protein Permits Molecular Typing of Mycoplasma genitalium Clinical Strains by PCR-Restriction Fragment Length Polymorphism

    Musatovova, Oxana; Herrera, Caleb; Baseman, Joel B.

    2006-01-01

    Restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified proximal region of the gene encoding cytadherence accessory protein P110 (MG192) revealed DNA sequence divergences among 54 Mycoplasma genitalium clinical strains isolated from the genitourinary tracts of women attending a sexually transmitted disease-related health clinic, plus one from the respiratory tract and one from synovial fluid. Seven of 56 (12.5%) strains exhibited RFLPs following digestion of the proximal region with restriction endonuclease MboI or RsaI, or both. No sequence variability was detected in the distal portion of the gene. PMID:16455921

  3. Photoelectron angular distributions for states of any mixed character: An experiment-friendly model for atomic, molecular, and cluster anions

    Khuseynov, Dmitry; Blackstone, Christopher C.; Culberson, Lori M.; Sanov, Andrei

    2014-01-01

    We present a model for laboratory-frame photoelectron angular distributions in direct photodetachment from (in principle) any molecular orbital using linearly polarized light. A transparent mathematical approach is used to generalize the Cooper-Zare central-potential model to anionic states of any mixed character. In the limit of atomic-anion photodetachment, the model reproduces the Cooper-Zare formula. In the case of an initial orbital described as a superposition of s and p-type functions, the model yields the previously obtained s-p mixing formula. The formalism is further advanced using the Hanstorp approximation, whereas the relative scaling of the partial-wave cross-sections is assumed to follow the Wigner threshold law. The resulting model describes the energy dependence of photoelectron anisotropy for any atomic, molecular, or cluster anions, usually without requiring a direct calculation of the transition dipole matrix elements. As a benchmark case, we apply the p-d variant of the model to the experimental results for NO − photodetachment and show that the observed anisotropy trend is described well using physically meaningful values of the model parameters. Overall, the presented formalism delivers insight into the photodetachment process and affords a new quantitative strategy for analyzing the photoelectron angular distributions and characterizing mixed-character molecular orbitals using photoelectron imaging spectroscopy of negative ions

  4. Photoelectron angular distributions for states of any mixed character: An experiment-friendly model for atomic, molecular, and cluster anions

    Khuseynov, Dmitry; Blackstone, Christopher C.; Culberson, Lori M.; Sanov, Andrei

    2014-09-01

    We present a model for laboratory-frame photoelectron angular distributions in direct photodetachment from (in principle) any molecular orbital using linearly polarized light. A transparent mathematical approach is used to generalize the Cooper-Zare central-potential model to anionic states of any mixed character. In the limit of atomic-anion photodetachment, the model reproduces the Cooper-Zare formula. In the case of an initial orbital described as a superposition of s and p-type functions, the model yields the previously obtained s-p mixing formula. The formalism is further advanced using the Hanstorp approximation, whereas the relative scaling of the partial-wave cross-sections is assumed to follow the Wigner threshold law. The resulting model describes the energy dependence of photoelectron anisotropy for any atomic, molecular, or cluster anions, usually without requiring a direct calculation of the transition dipole matrix elements. As a benchmark case, we apply the p-d variant of the model to the experimental results for NO- photodetachment and show that the observed anisotropy trend is described well using physically meaningful values of the model parameters. Overall, the presented formalism delivers insight into the photodetachment process and affords a new quantitative strategy for analyzing the photoelectron angular distributions and characterizing mixed-character molecular orbitals using photoelectron imaging spectroscopy of negative ions.

  5. Anacroneuria flintorum Froehlich 2002 (Plecoptera: Perlidae): Notes, distribution, and life stages association using molecular tools.

    Almeida, Lucas Henrique de; GonÇalves, MaÍsa de Carvalho; Novaes, Marcos Carneiro; Paresqui, Rayner Constantino; Bispo, PitÁgoras da conceiÇÃo

    2018-01-12

    Specimens of the perlid stonefly Anacroneuria flintorum from different regions of the Brazilian Atlantic Forest along the Atlantic coast of Brazil were studied. In this paper, the nymph of A. flintorum is described based on reared specimens and molecular associations. Additionally, we provide new locality records and comments about variation of the species.

  6. A single nucleotide polymorphism in cBIM is associated with a slower achievement of major molecular response in chronic myeloid leukaemia treated with imatinib.

    Vanessa Augis

    Full Text Available BIM is essential for the response to tyrosine-kinase inhibitors (TKI in chronic myeloid leukaemia (CML patients. Recently, a deletion polymorphism in intron 2 of the BIM gene was demonstrated to confer an intrinsic TKI resistance in Asian patients. The present study aimed at identifying mutations in the BIM sequence that could lead to imatinib resistance independently of BCR-ABL mutations.BIM coding sequence analysis was performed in 72 imatinib-treated CML patients from a French population of our centre and in 29 healthy controls (reference population as a case-control study. Real-time quantitative PCR (RT qPCR was performed to assess Bim expression in our reference population.No mutation with amino-acid change was found in the BIM coding sequence. However, we observed a silent single nucleotide polymorphism (SNP c465C>T (rs724710. A strong statistical link was found between the presence of the T allele and the high Sokal risk group (p = 0.0065. T allele frequency was higher in non responsive patients than in the reference population (p = 0.0049. Similarly, this T allele was associated with the mutation frequency on the tyrosine kinase domain of BCR-ABL (pT SNP of BIM could be useful for predicting the outcome of imatinib-treated CML patients.

  7. Molecular distribution in the comae of H2O-comets: an analytic model

    Yamamoto, T.

    1981-01-01

    Density distribution in cometary comae resulting from photodissociation, ionization and ion-molecule reaction of H 2 O is investigated in an analytic manner. It is assumed that particles expand isotropically around the nucleus, and that each species has its own constant radial velocity. Formulae for the density distribution of photochemical products are presented throughout the coma, and approximate formulae are given for the distribution of ion-molecule reaction products in the inner coma. Characteristics of the density profile are discussed on the basis of these analytic formulae. (Auth.)

  8. Seeing the Forest Through the Trees: The Distribution and Properties of Dense Molecular Gas in the Milky Way Galaxy

    Ellsworth-Bowers, Timothy P.

    The Milky Way Galaxy serves as a vast laboratory for studying the dynamics and evolution of the dense interstellar medium and the processes of and surrounding massive star formation. From our vantage point within the Galactic plane, however, it has been extremely difficult to construct a coherent picture of Galactic structure; we cannot see the forest for the trees. The principal difficulties in studying the structure of the Galactic disk have been obscuration by the ubiquitous dust and molecular gas and confusion between objects along a line of sight. Recent technological advances have led to large-scale blind surveys of the Galactic plane at (sub-)millimeter wavelengths, where Galactic dust is generally optically thin, and have opened a new avenue for studying the forest. The Bolocam Galactic Plane Survey (BGPS) observed over 190 deg 2 of the Galactic plane in dust continuum emission near lambda = 1.1 mm, producing a catalog of over 8,000 dense molecular cloud structures across a wide swath of the Galactic disk. Deriving the spatial distribution and physical properties of these objects requires knowledge of distance, a component lacking in the data themselves. This thesis presents a generalized Bayesian probabilistic distance estimation method for dense molecular cloud structures, and demonstrates it with the BGPS data set. Distance probability density functions (DPDFs) are computed from kinematic distance likelihoods (which may be double- peaked for objects in the inner Galaxy) and an expandable suite of prior information to produce a comprehensive tally of our knowledge (and ignorance) of the distances to dense molecular cloud structures. As part of the DPDF formalism, this thesis derives several prior DPDFs for resolving the kinematic distance ambiguity in the inner Galaxy. From the collection of posterior DPDFs, a set of objects with well-constrained distance estimates is produced for deriving Galactic structure and the physical properties of dense molecular

  9. The incubation period distribution of tuberculosis estimated with a molecular epidemiological approach.

    Borgdorff, M.W.; Sebek, M.; Geskus, R.B.; Kremer, K.; Kalisvaart, N.; Soolingen, D. van

    2011-01-01

    BACKGROUND: There is limited information on the distribution of incubation periods of tuberculosis (TB). METHODS: In The Netherlands, patients whose Mycobacterium tuberculosis isolates have identical DNA fingerprints in the period 1993-2007 were interviewed to identify epidemiological links between

  10. (Al)MCM-41 Molecular Sieves. Aluminium Distribution, Uniformity and Structure of Inner Surface

    Dědeček, Jiří; Žilková, Naděžda; Kotrla, Josef; Čejka, Jiří

    2003-01-01

    Roč. 68, č. 10 (2003), s. 1998-2018 ISSN 0010-0765 R&D Projects: GA ČR GA104/02/0571; GA AV ČR IAA4040001; GA AV ČR IBS4040017 Grant - others:Volkswagen Stiftung(DE) I/75886 Institutional research plan: CEZ:AV0Z4040901 Keywords : molecular sieves * mesoporous materials * Vis spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.041, year: 2003

  11. Mapping molecular orientational distributions for biological sample in 3D (Conference Presentation)

    HE, Wei; Ferrand, Patrick; Richter, Benjamin; Bastmeyer, Martin; Brasselet, Sophie

    2016-04-01

    Measuring molecular orientation properties is very appealing for scientists in molecular and cell biology, as well as biomedical research. Orientational organization at the molecular scale is indeed an important brick to cells and tissues morphology, mechanics, functions and pathologies. Recent work has shown that polarized fluorescence imaging, based on excitation polarization tuning in the sample plane, is able to probe molecular orientational order in biological samples; however this applies only to information in 2D, projected in the sample plane. To surpass this limitation, we extended this approach to excitation polarization tuning in 3D. The principle is based on the decomposition of any arbitrary 3D linear excitation in a polarization along the longitudinal z-axis, and a polarization in the transverse xy-sample plane. We designed an interferometer with one arm generating radial polarization light (thus producing longitudinal polarization under high numerical aperture focusing), the other arm controlling a linear polarization in the transverse plane. The amplitude ratio between the two arms can vary so as to get any linear polarized excitation in 3D at the focus of a high NA objective. This technique has been characterized by polarimetry imaging at the back focal plane of the focusing objective, and modeled theoretically. 3D polarized fluorescence microscopy is demonstrated on actin stress fibers in non-flat cells suspended on synthetic polymer structures forming supporting pillars, for which heterogeneous actin orientational order could be identified. This technique shows a great potential in structural investigations in 3D biological systems, such as cell spheroids and tissues.

  12. Molecular orbital calculations of the unpaired electron distribution and electric field gradients in divalent paramagnetic Ir complexes

    Nogueira, S.R.; Vugman, N.V.; Guenzburger, D.

    1988-01-01

    Semi-empirical Molecular Orbital calculations were performed for the paramagnetic complex ions [Ir(CN) 5 ] 3- , [Ir(CN) 5 Cl] 4- and [Ir(CN) 4 Cl 2 ] 4- . Energy levels schemes and Mulliken-type populations were obtained. The distribution of the unpaired spin over the atoms in the complexes was derived, and compared to data obtained from Electron Paramagnetic Resonance spectra with the aid of a Ligand Field model. The electric field gradients at the Ir nucleus were calculated and compared to experiment. The results are discussed in terms of the chemical bonds formed by Ir and the ligands. (author) [pt

  13. Spatial Distribution and Kinematics of the Molecular Material Associated with eta Carinae

    Loinard, Laurent; Kamiński, Tomasz; Serra, Paolo; Menten, Karl M.; Zapata, Luis A.; Rodríguez, Luis F.

    2016-12-01

    Single-dish submillimeter observations have recently revealed the existence of a substantial, chemically peculiar molecular gas component located in the innermost circumstellar environment of the very massive luminous blue variable star, η Carinae. Here, we present 5″-resolution interferometric observations of the 1\\to 0 rotational transition of hydrogen cyanide (HCN) toward this star obtained with the Australia Telescope Compact Array. The emission is concentrated in the central few arcseconds around η Carinae and shows a clear 150 km s-1 velocity gradient running from west-north-west (blue) to east-south-east (red). Given the extent, location, and kinematics of this molecular material, we associate it with the complex of dusty arcs and knots seen in mid-infrared emission near the center of the Homunculus nebula. Indeed, the shielding provided by this dust could help explain how molecules survive in the presence of the intense UV radiation field produced by η Carinae. The dust located in the central few arcseconds around η Carinae and the molecular component described here most likely formed in situ and out of material expelled by the massive interacting binary system. Thus, η Carinae offers us a rare glimpse of the processes that lead to the formation of dust and molecules around massive stars, which are relevant to the interpretation of dust and molecule detections at high redshifts.

  14. Molecular identification and distribution profile of Candida species isolated from Iranian patients.

    Mohammadi, Rasoul; Mirhendi, Hossein; Rezaei-Matehkolaei, Ali; Ghahri, Mohammad; Shidfar, Mohammad Reza; Jalalizand, Nilufar; Makimura, Koichi

    2013-08-01

    A total of 855 yeast strains isolated from different clinical specimens, mainly nail (42%) and vulva-vagina (25%) were identified by a set of polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP). Genomic DNA was extracted from fresh colonies using Whatman FTA Card technology. PCR assays were performed on the complete ribosomal DNA internal transcribed spacer (rDNA-ITS) region for all isolates and species identification was carried out through their specific electrophoretic profiles after digestion with the enzyme MspI. Those isolates suspected as Candida parapsilosis group were then subjected to amplification of the secondary alcohol dehydrogenase (SADH) gene and restriction digestion with NlaIII enzyme. In total, 71.1% of the strains were obtained from females and 28.9% from males. The age group of 31-40 years consisted of the highest frequency of patients with candidiasis. Candida albicans was the predominant species (58.6%) followed by C. parapsilosis (11.0%), C. glabrata (8.3%), C. tropicalis (7.0%), C. kefyr (5.8%), C. krusei (4.4%), C. orthopsilosis (2.1%), and C. guilliermondii (0.6%). A few strains of C. lusitaniae, C. rugosa, C. intermedia, C. inconspicua, C. neoformans and S. cerevisiae were isolated. We could not identify 8 (0.9%) isolates. Candida albicans remains the most frequently species isolated from Iranian patients; however, the number of non-C. albicans Candida species looks to be increasing. The simple and reliable PCR-RFLP system used in the study has the potential to identify most clinically isolated yeasts.

  15. Investigation of haemoglobin polymorphism in Ogaden cattle

    Sanjoy Kumar Pal

    2014-04-01

    Full Text Available Background and Aim: The Ogaden cattle is one among the tropical cattle breeds (Bos indicus widely distributed in eastern and south eastern part of Ethiopia. The breed has been evolved in arid and semi arid agro-ecological setup, but later on distributed and adapted to the wide agro-ecological zones. Because of its multi-purpose role, the Ogaden cattle have been used for milk, beef, and income generation. Information on the inherent genetic diversity is important in the design of breeding improvement programmes, making rational decisions on sustainable utilization and conservation of Animal Genetic Resources. Limited information is available about genetic variation of Ogaden breed at molecular level. The present investigation was aimed to study the biochemical polymorphism at the Hemoglobin (Hb locus. Materials and Methods: Blood samples collected from 105 Ogaden cattle maintained at Haramaya beef farm by jugular vein puncture were subjected to agarose gel electrophoresis [pH range 8.4-8.5] to study the polymorphic activities of haemoglobin. Results: Three types of phenotypes were detected i.e. a slow moving (AA band, fast moving (BB band and a combination of slow + fast moving bands (AB. The frequency of the fast moving band was less [13 (12.3%] than the slow moving band [57 (54.2%]. Both slow & fast moving phenotype was observed in 35 (33.3% animals. The gene frequency of HBA allele was 0.709 and that of HBB allele 0.291. Conclusion: The distribution of phenotypes was in agreement with codominant single gene inheritance. The Chi-square (χ2 test revealed that the population is under Hardy-Weinberg equilibrium.

  16. Asymptotic behavior of a rotational population distribution in a molecular quantum-kicked rotor with ideal quantum resonance

    Matsuoka, Leo, E-mail: leo-matsuoka@hiroshima-u.ac.jp [Graduate School of Engineering, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8527 (Japan); Segawa, Etsuo [Graduate School of Information Sciences, Tohoku University, Aoba, Sendai 980-8579 (Japan); Yuki, Kenta [Graduate School of Engineering, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8527 (Japan); Konno, Norio [Department of Applied Mathematics, Faculty of Engineering, Yokohama National University, Hodogaya, Yokohama 240-8501 (Japan); Obata, Nobuaki [Graduate School of Information Sciences, Tohoku University, Aoba, Sendai 980-8579 (Japan)

    2017-06-09

    We performed a mathematical analysis of the time-dependent dynamics of a quantum-kicked rotor implemented in a diatomic molecule under the condition of ideal quantum resonance. We examined a model system featuring a diatomic molecule in a periodic train of terahertz pulses, regarding the molecule as a rigid rotor with the state-dependent transition moment and including the effect of the magnetic quantum number M. We derived the explicit expression for the asymptotic distribution of a rotational population by making the transition matrix correspondent with a sequence of ultraspherical polynomials. The mathematical results obtained were validated by numerical simulations. - Highlights: • The behavior of the molecular quantum-kicked rotor was mathematically investigated. • The matrix elements were made correspondent with the ultraspherical polynomials. • The explicit formula for asymptotic distribution was obtained. • Complete agreement with the numerical simulation was verified.

  17. The embedded young stars in the Taurus-Auriga molecular cloud. I - Models for spectral energy distributions

    Kenyon, Scott J.; Calvet, Nuria; Hartmann, Lee

    1993-01-01

    We describe radiative transfer calculations of infalling, dusty envelopes surrounding pre-main-sequence stars and use these models to derive physical properties for a sample of 21 heavily reddened young stars in the Taurus-Auriga molecular cloud. The density distributions needed to match the FIR peaks in the spectral energy distributions of these embedded sources suggest mass infall rates similar to those predicted for simple thermally supported clouds with temperatures about 10 K. Unless the dust opacities are badly in error, our models require substantial departures from spherical symmetry in the envelopes of all sources. These flattened envelopes may be produced by a combination of rotation and cavities excavated by bipolar flows. The rotating infall models of Terebey et al. (1984) models indicate a centrifugal radius of about 70 AU for many objects if rotation is the only important physical effect, and this radius is reasonably consistent with typical estimates for the sizes of circumstellar disks around T Tauri stars.

  18. The use of Gauss-Hermite quadrature in the determination of the molecular weight distribution of linear polymers by rheometry

    T. M. Farias

    2013-12-01

    Full Text Available The molecular weight distribution (MWD and its parameters are of the fundamental importance in the characterization of polymers. Therefore, the development of techniques for faster MWD determination is a relevant issue. This paper aims at implementing one of the relaxation models from double reptation theory proposed in the literature and analyzing the numeric strategy for the evaluation of the integrals appearing in the relaxation model. The inverse problem, i.e., the determination of the MWD from rheological data using a specified relaxation model and an imposed distribution function was approximated. Concerning the numerical strategy for the evaluation of the integrals appearing in the relaxation models, the use of Gauss-Hermite quadrature using a new change of variables was proposed. In the test of samples of polyethylene with polydispersities less than 10, the application of this methodology led to MWD curves which provided a good fit of the experimental SEC data.

  19. Biological monitoring and the influence of genetic polymorphism of As3MT and GSTs on distribution of urinary arsenic species in occupational exposure workers.

    Janasik, Beata; Reszka, Edyta; Stanislawska, Magdalena; Wieczorek, Edyta; Fendler, Wojciech; Wasowicz, Wojciech

    2015-08-01

    To examine the differences in urinary arsenic metabolism patterns in men affected by occupational exposure, we performed a study on 149 participants—workers of a copper mill and 52 healthy controls without occupational exposure. To elucidate the role of genetic factors in arsenic (As) metabolism, we studied the associations of six polymorphisms: As3MT Met287Thr (T>C) in exon 9; As3MT A>G in 5'UTR; As3MT C>G in intron 6; As3MT T>G in intron 1; GSTP1 Ile105Val and GSTO2 T>C. Air samples were collected using individual samplers during work shift. Urine samples were analyzed for total arsenic and arsenic chemical forms (As(III); As(V), MMA, DMA, AsB) using HPLC-ICP-MS. A specific polymerase chain reaction was done for the amplification of exons and flanking regions of As3MT and GSTs. The geometric mean arsenic concentrations in the air were 27.6 ± 4.9 µg/m(3). A significant correlation (p iAs +MMA and iAs. As3MT (rs3740400) GG homozygotes showed significantly (p iAs (21.8 ± 2.0) in urine than GC+CC heterozygotes (16.0 ± 2.1). A strong association between the gene variants and As species in urine was observed for GSTO2 (rs156697) polymorphism. The findings of the study point out that the concentration of iAs or the sum of iAs + MMA in urine can be a reliable biological indicator of occupational exposure to arsenic. This study demonstrates that As3MT and/or GSTs genotype may influence As metabolism. Nevertheless, further studies investigating genetic polymorphism in occupational conditions are required.

  20. Molecular Diversity of Antagonistic Streptomyces spp. against Botrytis allii, the agent of onion gray mold using Random Amplified Polymorphic DNA (RAPD Markers

    M. Jorjandi

    2014-08-01

    Full Text Available As an aim in sustainable agriculture, biological control of plant diseases has received intensive attention mainly as a response to public concern about the use of chemical fungicides in the environment. Soil Actinomycetes particularly Streptomyces spp. enhance soil fertility and have antagonistic activity against wide range of plant pathogens. To investigate for biocontrol means against the pathogen, 30 isolates of Actinomycetes have been isolated from agricultural soils of Kerman province of Iran and assayed for antagonistic activity against Botrytis allii, the agent of onion gray mold. RAPD DNA analysis has been used to determine the relatedness of active and non-active isolates based on their RAPD-PCR fingerprints. PCR amplifiable DNA samples have been isolated using the CTAB method and amplified fragments have been obtained from 5 random 10-mer primers. Different DNA fingerprinting patterns have been obtained for all of the isolates. Electrophoretic and cluster analysis of the amplification products has revealed incidence of polymorphism among the isolates. A total of 138 bands, ranging in size from 150-2800 bp, have been amplified from primers which 63.7% of the observed bands have been polymorphic. Genetic distances among different varieties have been analyzed with a UPGMA (Unweighted pair-group method, arithmetic average-derived dendrogram. Resulting dendrogram has showed from 0.65 to 0.91 similarities among varieties and divided the isolates into five major groups. Isolates which haven’t had any antagonistic activity against B. allii have been separated into a group and other isolates classified into four groups. The results indicate that RAPD is an efficient method for discriminating and studying genetic diversity of Streptomyces isolates.

  1. Prevalence, distribution and functional significance of the -237C to T polymorphism in the IL-12Rβ2 promoter in Indian tuberculosis patients.

    Vikas Kumar Verma

    Full Text Available Cytokine/cytokine receptor gene polymorphisms related to structure/expression could impact immune response. Hence, the -237 polymorphic site in the 5' promoter region of the IL-12Rβ2 (SNP ID: rs11810249 gene associated with the AP-4 transcription motif GAGCTG, was examined. Amplicons encompassing the polymorphism were generated from 46 pulmonary tuberculosis patients, 35 family contacts and 28 miscellaneous volunteers and sequenced. The C allele predominated among patients, (93.4%, 43/46, and in all volunteers and contacts screened, but the T allele was exclusively limited to patients, (6.5%, 3/46. The functional impact of this polymorphism on transcriptional activity was assessed by Luciferase-reporter and electrophoretic mobility shift assays (EMSA. Luciferase-reporter assays showed a significant reduction in transcriptional efficiency with T compared to C allele. The reduction in transcriptional efficiency with the T allele construct (pGIL-12Rb2-T, in U-87MG, THP-1 and Jurkat cell lines, were 53, 37.6, and 49.8% respectively, compared to the C allele construct (pGIL-12Rb2-C. Similarly, densitometric analysis of the EMSA assay showed reduced binding of the AP-4 transcription factor, to T compared to the C nucleotide probe. Reduced mRNA expression in all patients (3/3 harboring the T allele was seen, whereas individuals with the C allele exhibited high mRNA expression (17/25; 68%, p = 0.05. These observations were in agreement with the in vitro assessment of the promoter activity by Luciferase-reporter and EMSA assays. The reduced expression of IL-12Rβ2 transcripts in 8 patients despite having the C allele was attributed to the predominant over expression of the suppressors (IL-4 and GATA-3 and reduced expression of enhancers (IFN-α of IL-12Rβ2 transcripts. The 17 high IL-12Rβ2 mRNA expressers had significantly elevated IFN-α mRNA levels compared to low expressers and volunteers. Notwithstanding the presence of high levels of IL-12R

  2. GEOGRAPHIC DISTRIBUTION OF MOLECULAR VARIANCE WITHIN THE BLUE MARLIN (MAKAIRA NIGRICANS): A HIERARCHICAL ANALYSIS OF ALLOZYME, SINGLE-COPY NUCLEAR DNA, AND MITOCHONDRIAL DNA MARKERS.

    Buonaccorsi, Vincent P; Reece, Kimberly S; Morgan, Lee W; Graves, John E

    1999-04-01

    This study presents a comparative hierarchical analysis of variance applied to three classes of molecular markers within the blue marlin (Makaira nigricans). Results are reported from analyses of four polymorphic allozyme loci, four polymorphic anonymously chosen single-copy nuclear DNA (scnDNA) loci, and previously reported restriction fragment length polymorphisms (RFLPs) of mitochondrial DNA (mtDNA). Samples were collected within and among the Atlantic and Pacific Oceans over a period of several years. Although moderate levels of genetic variation were detected at both polymorphic allozyme (H = 0.30) and scnDNA loci (H = 0.37), mtDNA markers were much more diverse (h = 0.85). Allele frequencies were significantly different between Atlantic and Pacific Ocean samples at three of four allozyme loci and three of four scnDNA loci. Estimates of allozyme genetic differentiation (θ O ) ranged from 0.00 to 0.15, with a mean of 0.08. The θ O values for scnDNA loci were similar to those of allozymes, ranging from 0.00 to 0.12 with a mean of 0.09. MtDNA RFLP divergence between oceans (θ O = 0.39) was significantly greater than divergence detected at nuclear loci (95% nuclear confidence interval = 0.04-0.11). The fourfold smaller effective population size of mtDNA and male-mediated gene flow may account for the difference observed between nuclear and mitochondrial divergence estimates. © 1999 The Society for the Study of Evolution.

  3. Colocalization coefficients evaluating the distribution of molecular targets in microscopy methods based on pointed patterns

    Pastorek, Lukáš; Sobol, Margaryta; Hozák, Pavel

    2016-01-01

    Roč. 146, č. 4 (2016), s. 391-406 ISSN 0948-6143 R&D Projects: GA TA ČR(CZ) TE01020118; GA ČR GA15-08738S; GA MŠk(CZ) ED1.1.00/02.0109; GA MŠk(CZ) LM2015062 Grant - others:Human Frontier Science Program(FR) RGP0017/2013 Institutional support: RVO:68378050 Keywords : Colocalization * Quantitative analysis * Pointed patterns * Transmission electron microscopy * Manders' coefficients * Immunohistochemistry Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.553, year: 2016

  4. The incubation period distribution of tuberculosis estimated with a molecular epidemiological approach

    Borgdorff, Martien W.; Sebek, Maruschka; Geskus, Ronald B.; Kremer, Kristin; Kalisvaart, Nico; van Soolingen, Dick

    2011-01-01

    There is limited information on the distribution of incubation periods of tuberculosis (TB). In The Netherlands, patients whose Mycobacterium tuberculosis isolates have identical DNA fingerprints in the period 1993-2007 were interviewed to identify epidemiological links between cases. We determined

  5. Geographic distribution of Staphylococcus aureus causing invasive infections in Europe : A molecular-epidemiological analysis

    Grundmann, Hajo; Aanensen, David M; van den Wijngaard, Cees C; Spratt, Brian G; Harmsen, Dag; Friedrich, Alexander W; Tami, Adriana

    Background: Staphylococcus aureus is one of the most important human pathogens and methicillin-resistant variants (MRSAs) are a major cause of hospital and community-acquired infection. We aimed to map the geographic distribution of the dominant clones that cause invasive infections in Europe.

  6. TWO MASS DISTRIBUTIONS IN THE L 1641 MOLECULAR CLOUDS: THE HERSCHEL CONNECTION OF DENSE CORES AND FILAMENTS IN ORION A

    Polychroni, D.; Schisano, E.; Elia, D.; Molinari, S.; Turrini, D.; Rygl, K. L. J.; Benedettini, M.; Busquet, G.; Di Giorgio, A. M.; Pestalozzi, M.; Pezzuto, S.; Roy, A.; André, Ph.; Hennemann, M.; Hill, T.; Könyves, V.; Martin, P.; Di Francesco, J.; Arzoumanian, D.; Bontemps, S.

    2013-01-01

    We present Herschel survey maps of the L 1641 molecular clouds in Orion A. We extracted both the filaments and dense cores in the region. We identified which of the dense sources are proto- or pre-stellar, and studied their association with the identified filaments. We find that although most (71%) of the pre-stellar sources are located on filaments there, is still a significant fraction of sources not associated with such structures. We find that these two populations (on and off the identified filaments) have distinctly different mass distributions. The mass distribution of the sources on the filaments is found to peak at 4 M ☉ and drives the shape of the core mass function (CMF) at higher masses, which we fit with a power law of the form dN/dlogM∝M –1.4±0.4 . The mass distribution of the sources off the filaments, on the other hand, peaks at 0.8 M ☉ and leads to a flattening of the CMF at masses lower than ∼4 M ☉ . We postulate that this difference between the mass distributions is due to the higher proportion of gas that is available in the filaments, rather than in the diffuse cloud

  7. TWO MASS DISTRIBUTIONS IN THE L 1641 MOLECULAR CLOUDS: THE HERSCHEL CONNECTION OF DENSE CORES AND FILAMENTS IN ORION A

    Polychroni, D. [Department of Astrophysics, University of Athens, Astronomy and Mechanics, Faculty of Physics, Panepistimiopolis, 15784 Zografos, Athens (Greece); Schisano, E.; Elia, D.; Molinari, S.; Turrini, D.; Rygl, K. L. J.; Benedettini, M.; Busquet, G.; Di Giorgio, A. M.; Pestalozzi, M.; Pezzuto, S. [Istituto di Astrofisica e Planetologia Spaziali (INAF-IAPS), via del Fosso del Cavaliere 100, I-00133 Roma (Italy); Roy, A.; André, Ph.; Hennemann, M.; Hill, T.; Könyves, V. [Laboratoire AIM, CEA/IRFU CNRS/INSU Université Paris Diderot, Paris-Saclay, F-91191 Gif-sur-Yvette (France); Martin, P. [Canadian Institute for Theoretical Astrophysics, University of Toronto, 60 St. George Street, Toronto, ON M5S 3H8 (Canada); Di Francesco, J. [National Research Council Canada, 5071 West Saanich Road, Victoria, BC V9E 2E7 (Canada); Arzoumanian, D. [IAS, CNRS (UMR 8617), Université Paris-Sud, Bâtiment 121, F-91400 Orsay (France); Bontemps, S., E-mail: dpolychroni@phys.uoa.gr [Université de Bordeaux, Laboratoire d' Astrophysique de Bordeaux, CNRS/INSU, UMR 5804, BP 89, F-33271, Floirac Cedex (France); and others

    2013-11-10

    We present Herschel survey maps of the L 1641 molecular clouds in Orion A. We extracted both the filaments and dense cores in the region. We identified which of the dense sources are proto- or pre-stellar, and studied their association with the identified filaments. We find that although most (71%) of the pre-stellar sources are located on filaments there, is still a significant fraction of sources not associated with such structures. We find that these two populations (on and off the identified filaments) have distinctly different mass distributions. The mass distribution of the sources on the filaments is found to peak at 4 M {sub ☉} and drives the shape of the core mass function (CMF) at higher masses, which we fit with a power law of the form dN/dlogM∝M {sup –1.4±0.4}. The mass distribution of the sources off the filaments, on the other hand, peaks at 0.8 M {sub ☉} and leads to a flattening of the CMF at masses lower than ∼4 M {sub ☉}. We postulate that this difference between the mass distributions is due to the higher proportion of gas that is available in the filaments, rather than in the diffuse cloud.

  8. Crystallography and Molecular Arrangement of Polymorphic Monolayer J-Aggregates of a Cyanine Dye: Multiangle Polarized Light Fluorescence Optical Microscopy Study.

    Prokhorov, Valery V; Pozin, Sergey I; Perelygina, Olga M; Mal'tsev, Eugene I

    2018-04-24

    The molecular orientation in monolayer J-aggregates of 3,3-di(γ-sulfopropyl)-5,5-dichlorotiamonomethinecyanine dye has been precisely estimated using improved linear polarization measurements in the fluorescence microscope in which a multiangle set of polarization data is obtained using sample rotation. The estimated molecular orientation supplemented with the previously established crystallographic constraints based on the analysis of the well-developed two-dimensional J-aggregate shapes unambiguously indicate the staircase type of molecular arrangement for striplike J-aggregates with the staircases oriented along strips. The molecular transition dipoles are inclined at an angle of ∼25° to the strip direction, whereas the characteristic strip vertex angle ∼45° is formed by the [100] and [1-10] directions of the monoclinic unit cell. Measurements of the geometry of partially unwound tubes and their polarization properties support the model of tube formation by close-packed helical winding of flexible monolayer strips. In the tubes, the long molecular axes are oriented at a small angle in the range of 5-15° to the normal to the tube axis providing low bending energy. At a nanoscale, high-resolution atomic force microscopy imaging of J-aggregate monolayers reveals a complex quasi-one-dimensional organization.

  9. Amino Acid Composition, Molecular Weight Distribution and Gel Electrophoresis of Walnut (Juglans regia L. Proteins and Protein Fractionations

    Xiaoying Mao

    2014-01-01

    Full Text Available As a by-product of oil production, walnut proteins are considered as an additional source of plant protein for human food. To make full use of the protein resource, a comprehensive understanding of composition and characteristics of walnut proteins are required. Walnut proteins have been fractionated and characterized in this study. Amino acid composition, molecular weight distribution and gel electrophoresis of walnut proteins and protein fractionations were analyzed. The proteins were sequentially separated into four fractions according to their solubility. Glutelin was the main component of the protein extract. The content of glutelin, albumin, globulin and prolamin was about 72.06%, 7.54%, 15.67% and 4.73% respectively. Glutelin, albumin and globulin have a balanced content of essential amino acids, except for methionine, with respect to the FAO pattern recommended for adults. SDS-PAGE patterns of albumin, globulin and glutelin showed several polypeptides with molecular weights 14.4 to 66.2 kDa. The pattern of walnut proteins in two-dimension electrophoresis (2-DE showed that the isoelectric point was mainly in the range of 4.8–6.8. The results of size exclusion chromatogram indicated molecular weight of the major components of walnut proteins were between 3.54 and 81.76 kDa.

  10. Spatial distribution of intra-molecular water and polymeric components in polyelectrolyte dendrimers revealed by small angle scattering investigations

    Wu, Bin; Li, Xin; Do, Changwoo; Kim, Tae-Hwan; Shew, Chwen-Yang; Liu, Yun; Yang, Jun; Hong, Kunlun; Porcar, Lionel; Chen, Chun-Yu; Liu, Emily L.; Smith, Gregory S.; Herwig, Kenneth W.; Chen, Wei-Ren

    2011-10-01

    An experimental scheme using contrast variation small angle neutron scattering technique is developed to investigate the structural characteristics of amine-terminated poly(amidoamine) dendrimers solutions. Using this methodology, we present the dependence of both the intra-dendrimer water and the polymer distribution on molecular protonation, which can be precisely adjusted by tuning the pH of the solution. Assuming spherical symmetry of the spatial arrangement of the constituent components of dendrimer, and that the atomic ratio of hydrogen-to-deuterium for the solvent residing within the cavities of dendrimer is identical to that for the solvent outside the dendrimer, the intra-dendrimer water distribution along the radial direction is determined. Our result clearly reveals an outward relocation of the peripheral groups, as well as enhanced intra-dendrimer hydration, upon increasing the molecular protonation and, therefore, allows the determination of segmental backfolding in a quantitative manner. The connection between these charge-induced structural changes and our recently observed progressively active segmental dynamics is also discussed.

  11. Vicinage forces between molecular and atomic fragments dissociated from small hydrogen clusters and their effects on energy distributions

    Barriga-Carrasco, Manuel D.; Garcia-Molina, Rafael

    2003-01-01

    In this paper we analyze the dynamic evolution of molecular and atomic fragments of small hydrogen clusters interacting with thin solid foils. We compare the vicinage forces, calculated within the dielectric formalism, for H + , H 0 , and H 2 + fragments. Using a molecular dynamics numerical code we determine the energy distribution of the fragments after interacting with the target. This distribution is compared to experimental results for protons coming from the fragmentation of v=2.02 a.u. H 2 + ions impinging on an aluminum foil; a fraction of neutral H 0 is needed to be included in the simulation to get a good agreement with the experimental results. The H 2 + energy spectra for v=5.42 a.u. H 3 + interacting with amorphous carbon is also determined. The asymmetry in the Coulomb peaks appearing in the energy spectra both experimentally and in our calculation is opposite for H 2 + than in H + ; kinematic effects and differences in the electronic stopping are enough to reproduce the difference in the alignment of H 2 + and H + fragments

  12. Dynamical Timescale of Pre-collapse Evolution Inferred from Chemical Distribution in the Taurus Molecular Cloud-1 (TMC-1) Filament

    Choi, Yunhee; Lee, Jeong-Eun [School of Space Research, Kyung Hee University, 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104 (Korea, Republic of); Bourke, Tyler L. [Square Kilometre Array Organisation, Jodrell Bank Observatory, Lower Withington, Cheshire SK11 9DL (United Kingdom); II, Neal J. Evans, E-mail: yunhee.choi@khu.ac.kr, E-mail: jeongeun.lee@khu.ac.kr [Department of Astronomy, University of Texas at Austin, 2515 Speedway, Stop C1400, Austin, TX 78712-1205 (United States)

    2017-04-01

    We present observations and analyses of the low-mass star-forming region, Taurus Molecular Cloud-1 (TMC-1). CS ( J = 2–1)/N{sub 2}H{sup +} ( J = 1–0) and C{sup 17}O ( J = 2–1)/C{sup 18}O ( J = 2–1) were observed with the Five College Radio Astronomy Observatory and the Seoul Radio Astronomy Observatory, respectively. In addition, Spitzer infrared data and 1.2 mm continuum data observed with Max-Planck Millimetre Bolometer are used. We also perform chemical modeling to investigate the relative molecular distributions of the TMC-1 filament. Based on Spitzer observations, there is no young stellar object along the TMC-1 filament, while five Class II and one Class I young stellar objects are identified outside the filament. The comparison between column densities calculated from dust continuum and C{sup 17}O 2–1 line emission shows that CO is depleted much more significantly in the ammonia peak than in the cyanopolyyne peak, while the column densities calculated from the dust continuum are similar at the two peaks. N{sub 2}H{sup +} is not depleted much in either peak. According to our chemical calculation, the differential chemical distribution in the two peaks can be explained by different timescales required to reach the same density, i.e., by different dynamical processes.

  13. Molecular variation and distribution of Anopheles fluviatilis (Diptera: Culicidae) complex in Iran.

    Naddaf, Saied Reza; Razavi, Mohammad Reza; Bahramali, Golnaz

    2010-09-01

    Anopheles fluviatilis James (Diptera: Culicidae) is one of the known malaria vectors in south and southeastern Iran. Earlier ITS2 sequences analysis of specimens from Iran demonstrated only a single genotype that was identical to species Y in India, which is also the same as species T. We identified 2 haplotypes in the An. fluviatilis populations of Iran based on differences in nucleotide sequences of D3 domain of the 28S locus of ribosomal DNA (rDNA). Comparison of sequence data from 44 Iranian specimens with those publicly available in the Genbank database showed that all of the 28S-D3 sequences from Kazeroun and Khesht regions in Fars Province were identical to the database entry representing species U in India. In other regions, all the individuals showed heterozygosity at the single nucleotide position, which identifies species U and T. It is argued that the 2 species may co-occur in some regions and hybridize; however, the heterozygosity in the 28S-D3 locus was not reflected in ITS2 sequences and this locus for all individuals was identical to species T. This study shows that in a newly diverged species, like members of An. fluviatilis complex, a single molecular marker may not be sufficiently discriminatory to identify all the taxa over a vast geographical area. In addition, other molecular markers may provide more reliable information for species discrimination.

  14. Effect of ablation photon energy on the distribution of molecular species in laser-induced plasma from polymer in air

    Lei, W.Q. [State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai (China); Universite de Lyon, F-69622, Lyon, France, Universite Lyon 1, Villeurbanne, CNRS, UMR5579, LASIM (France); Ma, Q.L.; Motto-Ros, V.; Bai, X.S. [Universite de Lyon, F-69622, Lyon, France, Universite Lyon 1, Villeurbanne, CNRS, UMR5579, LASIM (France); Zheng, L.J. [State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai (China); Zeng, H.P., E-mail: hpzeng@phy.ecnu.edu.cn [State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai (China); Yu, J., E-mail: Jin.Yu@lasim.univ-lyon1.fr [Universite de Lyon, F-69622, Lyon, France, Universite Lyon 1, Villeurbanne, CNRS, UMR5579, LASIM (France)

    2012-07-15

    Distribution of molecular species, C{sub 2} and CN, in laser-induced plasma from a polymer target (polyvinyl chloride: PVC) was observed for ablation with 266 nm and 355 nm pulses. The influence of ablation photon energy on the distribution of molecular species in the plasma has been thus studied. Time- and space-resolved emission spectroscopy was used for the observation which led to the determination of emission intensity profiles of C{sub 2} molecule and CN radical for different delays after the impact of the laser pulse on the target. The profiles of related elements, C, N, and excitation temperature in the plasma were further determined to correlate with those of molecular emission intensity. Different behaviors were clearly observed between plasmas induced by pulses with the two different wavelengths chosen to be close each other in the near ultraviolet (UV). A closer analysis shows the photon energy corresponding to 266 nm pulse of 4.66 eV is larger than bond energies of all the chemical bonds in the studied polymer, while that of 355 nm radiation of 3.49 eV is smaller than or in the same range of the involved bond energies. Observed different behaviors suggest therefore different ablation mechanisms of polymer by laser radiation, and consequently different channels of molecule formation in the plasma. Observation of the morphology of the craters on the target surface left by laser ablation confirmed further different ablation mechanisms with the two used wavelengths. - Highlights: Black-Right-Pointing-Pointer The profiles of C{sub 2} and CN in a plasma induced from a PVC target were determined. Black-Right-Pointing-Pointer Different behaviors were observed for ablation with 266 nm and 355 nm pulses. Black-Right-Pointing-Pointer Different molecule formation channels were used to interpret such behaviors. Black-Right-Pointing-Pointer The morphology of the craters confirmed further the different ablation mechanisms.

  15. Directing filtration to narrow molecular weight distribution of oligodextran in an enzymatic membrane reactor

    Su, Ziran; Luo, Jianquan; Pinelo, Manuel

    2018-01-01

    ) should be minimized to reduce accumulation of large oligodextran molecules on the membrane surface, which might diffuse through the membrane and thus broaden the Mw distribution of the products in the permeate. Both dextranase and dextran caused membrane irreversible fouling. The fouling caused...... product, hypersaline wastewater discharge and potential safety hazards. In this work, a novel enzymatic membrane reactor (EMR) system to produce oligodextran is proposed, whereby in-situ product recovery can be manipulated to control the Mw distribution of the resulting products. Results showed...... that the membrane material played an important role in the permeate flux and transmission of oligodextran. Among the tested membranes, a 20kDa polyethersulfone (PES) membrane was found to be optimal for building up the EMR, as it successfully controlled the oligodextran Mw within the desired range with a relatively...

  16. Orbital momentum distributions and binding energies for the complete valence shell of molecular iodine

    Grisogono, A.M.; Pascual, R.; Weigold, E.

    1988-03-01

    The complete valence shell binding energy spectrum (8-43eV) of I 2 has been measured by using electron momentum spectroscopy at 1000eV. The complete inner valence region, corresponding to ionization from the 10 σ u and 10 σ g orbitals, has been measured for the first time and shows extensive splitting of the ionization strength due to electron correlation effects in the ion. Many-body calculations using the Green's function method have been carried out and are compared with the data. Momentum distributions, measured in both the outer and inner valence regions, are compared with those given by SCF orbital wave functions calculated with a number of different basis sets. Computed orbital position and momentum density maps for oriented I 2 molecules are discussed in comparison with the measured and calculated spherically averaged momentum distributions

  17. Presence and Distribution of Oilseed Pumpkin Viruses and Molecular Detection of Zucchini Yellow Mosaic Virus

    Ana Vučurović; Aleksandra Bulajić; Ivana Đekić; Danijela Ristić; Janoš Berenji; Branka Krstić

    2009-01-01

    Over the past decade, intensive spread of virus infections of oilseed pumpkin has resulted in significant economic losses in pumpkin crop production, which is currently expanding in our country. In 2007 and 2008, a survey for the presence and distribution of oilseed pumpkin viruses was carried out in order to identify viruses responsible for epidemics and incidences of very destructive symptoms on cucurbit leaves and fruits. Monitoring and collecting samples of oil pumpkin, as well as other s...

  18. Molecular determinants of Guanylate Cyclase Activating Protein subcellular distribution in photoreceptor cells of the retina.

    López-Begines, Santiago; Plana-Bonamaisó, Anna; Méndez, Ana

    2018-02-13

    Retinal guanylate cyclase (RetGC) and guanylate cyclase activating proteins (GCAPs) play an important role during the light response in photoreceptor cells. Mutations in these proteins are linked to distinct forms of blindness. RetGC and GCAPs exert their role at the ciliary outer segment where phototransduction takes place. We investigated the mechanisms governing GCAP1 and GCAP2 distribution to rod outer segments by expressing selected GCAP1 and GCAP2 mutants as transient transgenes in the rods of GCAP1/2 double knockout mice. We show that precluding GCAP1 direct binding to RetGC (K23D/GCAP1) prevented its distribution to rod outer segments, while preventing GCAP1 activation of RetGC post-binding (W94A/GCAP1) did not. We infer that GCAP1 translocation to the outer segment strongly depends on GCAP1 binding affinity for RetGC, which points to GCAP1 requirement to bind to RetGC to be transported. We gain further insight into the distinctive regulatory steps of GCAP2 distribution, by showing that a phosphomimic at position 201 is sufficient to retain GCAP2 at proximal compartments; and that the bovine equivalent to blindness-causative mutation G157R/GCAP2 results in enhanced phosphorylation in vitro and significant retention at the inner segment in vivo, as likely contributing factors to the pathophysiology.

  19. An equal force theory for network models of soft materials with arbitrary molecular weight distribution

    Verron, E.; Gros, A.

    2017-09-01

    Most network models for soft materials, e.g. elastomers and gels, are dedicated to idealized materials: all chains admit the same number of Kuhn segments. Nevertheless, such standard models are not appropriate for materials involving multiple networks, and some specific constitutive equations devoted to these materials have been derived in the last few years. In nearly all cases, idealized networks of different chain lengths are assembled following an equal strain assumption; only few papers adopt an equal stress assumption, although some authors argue that such hypothesis would reflect the equilibrium of the different networks in contact. In this work, a full-network model with an arbitrary chain length distribution is derived by considering that chains of different lengths satisfy the equal force assumption in each direction of the unit sphere. The derivation is restricted to non-Gaussian freely jointed chains and to affine deformation of the sphere. Firstly, after a proper definition of the undeformed configuration of the network, we demonstrate that the equal force assumption leads to the equality of a normalized stretch in chains of different lengths. Secondly, we establish that the network with chain length distribution behaves as an idealized full-network of which both chain length and density of are provided by the chain length distribution. This approach is finally illustrated with two examples: the derivation of a new expression for the Young modulus of bimodal interpenetrated polymer networks, and the prediction of the change in fluorescence during deformation of mechanochemically responsive elastomers.

  20. Molecular biology in a distributed world. A Kantian perspective on scientific practices and the human mind

    Mariagrazia Portera

    2016-01-01

    Full Text Available In recent years the number of scholarly publications devoted to Kant's theory of biology has rapidly growing, with particular attention being given to Kant's thoughts about the concepts of teleology, function, organism, and their respective roles in scientific practice. Moving from these recent studies, and distancing itself from their mostly evolutionary background, the main aim of the present paper is to suggest an original "cognitive turn" in the interpretation of Kant's theory of biology. More specifically, the Authors will trace a connection between some Kantian theses about the “peculiar” or special nature of the human mind (intellectus ectypus, advanced in the Critique of the Power of Judgement (§ 76, 77, and some specific epistemological issues pertaining to the research practice of contemporary molecular biology.

  1. Molecular diversity and body distribution of saponins in the sea star Asterias rubens by mass spectrometry.

    Demeyer, Marie; De Winter, Julien; Caulier, Guillaume; Eeckhaut, Igor; Flammang, Patrick; Gerbaux, Pascal

    2014-02-01

    Saponins are natural molecules that the common sea star Asterias rubens produces in the form of steroid glycosides bearing a sulfate group attached on the aglycone part. In order to highlight the inter-organ and inter-individual variability, the saponin contents of five distinct body components, namely the aboral body wall, the oral body wall, the stomach, the pyloric caeca and the gonads, from different individuals were separately analyzed by mass spectrometry. MALDI-ToF experiments were selected as the primary tool for a rapid screening of the saponin mixtures, whereas LC-MS and LC-MS/MS techniques were used to achieve chromatographic separation of isomers. First of all, our analyses demonstrated that the diversity of saponins is higher than previously reported. Indeed, nine new congeners were observed in addition to the 17 saponins already described in this species. On the basis of all the collected MS/MS data, we also identified collision-induced key-fragmentations that could be used to reconstruct the molecular structure of both known and unknown saponin ions. Secondly, the comparison of the saponin contents from the five different body components revealed that each organ is characterized by a specific mixture of saponins and that between animals there are also qualitative and quantitative variability of the saponin contents which could be linked to the sex or to the collecting season. Therefore, the observed high variability unambiguously confirms that saponins probably fulfill several biological functions in A. rubens. The current results will pave the way for our future studies that will be devoted to the clarification of the biological roles of saponins in A. rubens at a molecular level. © 2013.

  2. Molecular weight​/branching distribution modeling of low-​density-​polyethylene accounting for topological scission and combination termination in continuous stirred tank reactor

    Yaghini, N.; Iedema, P.D.

    2014-01-01

    We present a comprehensive model to predict the molecular weight distribution (MWD),(1) and branching distribution of low-density polyethylene (IdPE),(2) for free radical polymerization system in a continuous stirred tank reactor (CSTR).(3) The model accounts for branching, by branching moment or

  3. Theory for site-site pair distribution functions of molecular fluids. II. Approximations for the Percus--Yevick site-site direct correlation functions

    Johnson, E.

    1977-01-01

    A theory for site-site pair distribution functions of molecular fluids is derived from the Ornstein-Zernike equation. Atom-atom pair distribution functions of this theory which were obtained by using different approximations for the Percus-Yevick site-site direct correlation functions are compared

  4. Molecular taxonomy of cupped oysters (Crassostrea, Saccostrea, and Striostrea) in Thailand based on COI, 16S, and 18S rDNA polymorphism.

    Klinbunga, S; Khamnamtong, B; Puanglarp, N; Jarayabhand, P; Yoosukh, W; Menasveta, P

    2005-01-01

    Genetic diversity of oysters Crassostrea belcheri (Sowerby, 1871), C. iredalei (Faustino, 1932), Saccostrea cucullata (Born, 1778), S. forskali (Gmelin, 1791), and Striostrea (Parastriostrea) mytiloides (Lamarck, 1819) (Ostreoida, Mollusca) was analyzed by polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) of 16S ribosomal DNA with AcsI, AluI, DdeI, DraI, RsaI, and TaqI, 18S ribosomal DNA with HinfI, and cytochrome oxidase subunit I with AcsI, DdeI and MboI. A total of 54 composite haplotypes were observed. Species-diagnostic markers were specifically found in C. belcheri, C. iredalei, and S. cucullata, but not in S. forskali and Striostrea mytiloides, which shared common composite haplotypes. Neighbor-joining trees constructed from genetic distances between pairs of composite haplotypes and species indicated large genetic differences between Crassostrea and Saccostrea (including Striostrea mytiloides), but closer relationships were observed within each genus. Four groups of unidentified oysters (Crassostrea sp. and Saccostrea sp. groups 1, 2, and 3) were also genetically analyzed. Fixed RFLP markers were found in Crassostrea sp. and Saccostrea sp. group 2, but not in Saccostrea sp. groups 1 and 3. Phylogenetic and genetic heterogeneity analyses indicated that Crassostrea sp. and Saccostrea sp. group 2 should be considered as newly unidentified oyster species in Thailand.

  5. Molecular identification of Candida species isolated from cases of neonatal candidemia using polymerase chain reaction-restriction fragment length polymorphism in a tertiary care hospital

    Akeela Fatima

    2017-01-01

    Full Text Available Context: Candida spp. is an emerging cause of bloodstream infections worldwide. Delay in speciation of Candida isolates by conventional methods and resistance to antifungal drugs in various Candida species are responsible for the increase in morbidity and mortality due to candidemia. Hence, the rapid identification of Candida isolates is very important for the proper management of patients with candidemia. Aims: The aim was to re-evaluate the identification of various Candida spp. by polymerase chain reaction (PCR-restriction fragment length polymorphism (RFLP and to evaluate the accuracy, speed, and cost of phenotypic methodology versus PCR-RFLP. Settings and Design: Hospital-based cross-sectional study. Materials and Methods: Ninety consecutive clinical isolates of seven Candida species, isolated from blood of neonates and identified by routine phenotypic methods, were re-evaluated using universal primers internal transcribed spacer 1 (ITS1 and ITS4 for PCR amplification and Msp I restriction enzyme for RFLP. Statistical Analysis Used: Kappa test for agreement. Results: The results of PCR-RFLP were 100% in agreement with those obtained using conventional phenotypic methods. Identification could be achieved within 3 work days by both the methods. Our routine methods proved to be cost effective than PCR-RFLP. Conclusions: We can continue with our routine phenotypic methods and PCR-RFLP can be used for periodic quality control or when conventional methods fail to identify a species.

  6. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    Anantachaisilp, Suranan; Smith, Siwaporn Meejoo [Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400 (Thailand); Treetong, Alongkot; Ruktanonchai, Uracha Rungsardthong [National Nanotechnology Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120 (Thailand); Pratontep, Sirapat [College of KMITL Nanotechnology, King Mongkut' s Institute of Technology Ladkrabang, Bangkok (Thailand); Puttipipatkhachorn, Satit, E-mail: uracha@nanotec.or.th [Department of Manufacturing Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok 10400 (Thailand)

    2010-03-26

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of {gamma}-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812 as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the {gamma}-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance ({sup 1}H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the {sup 1}H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of {gamma}-oryzanol inside the lipid nanoparticles, the {sup 1}H-NMR revealed that the chemical shifts of the liquid lipid in {gamma}-oryzanol loaded systems were found at rather higher field than those in {gamma}-oryzanol free systems, suggesting incorporation of {gamma}-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of {gamma}-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models

  7. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    Anantachaisilp, Suranan; Meejoo Smith, Siwaporn; Treetong, Alongkot; Pratontep, Sirapat; Puttipipatkhachorn, Satit; Rungsardthong Ruktanonchai, Uracha

    2010-03-01

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of γ-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812® as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the γ-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance (1H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the 1H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of γ-oryzanol inside the lipid nanoparticles, the 1H-NMR revealed that the chemical shifts of the liquid lipid in γ-oryzanol loaded systems were found at rather higher field than those in γ-oryzanol free systems, suggesting incorporation of γ-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of γ-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of γ-oryzanol and

  8. Geographic distribution of Staphylococcus aureus causing invasive infections in Europe: a molecular-epidemiological analysis.

    Hajo Grundmann

    2010-01-01

    Full Text Available Staphylococcus aureus is one of the most important human pathogens and methicillin-resistant variants (MRSAs are a major cause of hospital and community-acquired infection. We aimed to map the geographic distribution of the dominant clones that cause invasive infections in Europe.In each country, staphylococcal reference laboratories secured the participation of a sufficient number of hospital laboratories to achieve national geo-demographic representation. Participating laboratories collected successive methicillin-susceptible (MSSA and MRSA isolates from patients with invasive S. aureus infection using an agreed protocol. All isolates were sent to the respective national reference laboratories and characterised by quality-controlled sequence typing of the variable region of the staphylococcal spa gene (spa typing, and data were uploaded to a central database. Relevant genetic and phenotypic information was assembled for interactive interrogation by a purpose-built Web-based mapping application. Between September 2006 and February 2007, 357 laboratories serving 450 hospitals in 26 countries collected 2,890 MSSA and MRSA isolates from patients with invasive S. aureus infection. A wide geographical distribution of spa types was found with some prevalent in all European countries. MSSA were more diverse than MRSA. Genetic diversity of MRSA differed considerably between countries with dominant MRSA spa types forming distinctive geographical clusters. We provide evidence that a network approach consisting of decentralised typing and visualisation of aggregated data using an interactive mapping tool can provide important information on the dynamics of MRSA populations such as early signalling of emerging strains, cross border spread, and importation by travel.In contrast to MSSA, MRSA spa types have a predominantly regional distribution in Europe. This finding is indicative of the selection and spread of a limited number of clones within health care

  9. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    Anantachaisilp, Suranan; Smith, Siwaporn Meejoo; Treetong, Alongkot; Ruktanonchai, Uracha Rungsardthong; Pratontep, Sirapat; Puttipipatkhachorn, Satit

    2010-01-01

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of γ-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812 as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the γ-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance ( 1 H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the 1 H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of γ-oryzanol inside the lipid nanoparticles, the 1 H-NMR revealed that the chemical shifts of the liquid lipid in γ-oryzanol loaded systems were found at rather higher field than those in γ-oryzanol free systems, suggesting incorporation of γ-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of γ-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of γ-oryzanol and

  10. Density distribution function of a self-gravitating isothermal compressible turbulent fluid in the context of molecular clouds ensembles

    Donkov, Sava; Stefanov, Ivan Z.

    2018-03-01

    We have set ourselves the task of obtaining the probability distribution function of the mass density of a self-gravitating isothermal compressible turbulent fluid from its physics. We have done this in the context of a new notion: the molecular clouds ensemble. We have applied a new approach that takes into account the fractal nature of the fluid. Using the medium equations, under the assumption of steady state, we show that the total energy per unit mass is an invariant with respect to the fractal scales. As a next step we obtain a non-linear integral equation for the dimensionless scale Q which is the third root of the integral of the probability distribution function. It is solved approximately up to the leading-order term in the series expansion. We obtain two solutions. They are power-law distributions with different slopes: the first one is -1.5 at low densities, corresponding to an equilibrium between all energies at a given scale, and the second one is -2 at high densities, corresponding to a free fall at small scales.

  11. Dependence of hotspot initiation on void distribution in high explosive crystals simulated with molecular dynamics

    Herring, Stuart Davis

    Microscopic defects may dramatically affect the susceptibility of high explosives to shock initiation. Such defects redirect the shock's energy and become hotspots (concentrations of stress and heat) that can initiate chemical reactions. Sufficiently large or numerous defects may produce a self-sustaining deflagration or even detonation from a shock notably too weak to detonate defect-free samples. The effects of circular or spherical voids on the shock sensitivity of a model (two- or three-dimensional) high explosive crystal are considered. We simulate a piston impact using molecular dynamics with a Reactive Empirical Bond Order (REBO) model potential for a sub-micron, sub-ns exothermic reaction in a diatomic molecular solid. In both dimensionalities, the probability of initiating chemical reactions rises more suddenly with increasing piston velocity for larger voids that collapse more deterministically. A void of even 10 nm radius (˜39 interatomic spacings) reduces the minimum initiating velocity by a factor of 4 (8 in 3D). The transition at larger velocities to detonation is studied in micron-long samples with a single void (and its periodic images). Reactions during the shock traversal increase rapidly with velocity, then become a reliable detonation. In 2D, a void of radius 2.5 nm reduces the critical velocity by 10% from the perfect crystal; a Pop plot of the detonation delays at higher velocities shows a characteristic pressure dependence. 3D samples are more likely to react but less to detonate. In square lattices of voids, reducing the (common) void radius or increasing the porosity without changing the other parameter causes the hotspots to consume the material faster and detonation to occur sooner and at lower velocities. Early behavior is seen to follow a very simple ignition and growth model; the pressure exponents are more realistic than with single voids. The hotspots collectively develop a broad pressure wave (a sonic, diffuse deflagration front

  12. Molecular identification, phylogeny and geographic distribution of Brazilian mangrove oysters (Crassostrea

    Aline Grasielle Costa de Melo

    2010-01-01

    Full Text Available Oysters (Ostreidae manifest a high degree of phenotypic plasticity, whereby morphology is of limited value for species identification and taxonomy. By using molecular data, the aim was to genetically characterize the species of Crassostrea occurring along the Brazilian coast, and phylogenetically relate these to other Crassostrea from different parts of the world. Sequencing of the partial cytochrome oxidase c subunit I gene (COI, revealed a total of three species of Crassostrea at 16 locations along the Brazilian coast. C. gasar was found from Curuçá (Pará state to Santos (São Paulo state, and C. rhizophorae from Fortim (Ceará state to Florianópolis (Santa Catarina state, although small individuals of the latter species were also found at Ajuruteua beach (municipality of Bragança, Pará state. An unidentified Crassostrea species was found only on Canela Island, Bragança. Crassostrea gasar and C. rhizophorae grouped with C. virginica, thereby forming a monophyletic Atlantic group, whereas Crassostrea sp. from Canela Island was shown to be more similar to Indo-Pacific oysters, and either arrived in the Atlantic Ocean before the convergence of the Isthmus of Panama or was accidentally brought to Brazil by ship.

  13. Molecular identification, phylogeny and geographic distribution of Brazilian mangrove oysters (Crassostrea)

    2010-01-01

    Oysters (Ostreidae) manifest a high degree of phenotypic plasticity, whereby morphology is of limited value for species identification and taxonomy. By using molecular data, the aim was to genetically characterize the species of Crassostrea occurring along the Brazilian coast, and phylogenetically relate these to other Crassostrea from different parts of the world. Sequencing of the partial cytochrome oxidase c subunit I gene (COI), revealed a total of three species of Crassostrea at 16 locations along the Brazilian coast. C. gasar was found from Curuçá (Pará state) to Santos (São Paulo state), and C. rhizophorae from Fortim (Ceará state) to Florianópolis (Santa Catarina state), although small individuals of the latter species were also found at Ajuruteua beach (municipality of Bragança, Pará state). An unidentified Crassostrea species was found only on Canela Island, Bragança. Crassostrea gasar and C. rhizophorae grouped with C. virginica, thereby forming a monophyletic Atlantic group, whereas Crassostrea sp. from Canela Island was shown to be more similar to Indo-Pacific oysters, and either arrived in the Atlantic Ocean before the convergence of the Isthmus of Panama or was accidentally brought to Brazil by ship. PMID:21637433

  14. Molecular distribution of deafness loci in variou ethnic groups of the punjab, pakistan

    Ullah, S.; Aslam, K.M.

    2015-01-01

    To determine the existence of autosomal recessive deafness loci in different ethnic tribes of the Punjab. Study Design: Descriptive observational study. Place and Duration of Study: Department of Human Genetics and Centre of Excellence in Molecular Biology, University of Health Sciences, Lahore, from July 2009 to March 2012. Methodology: Healthy willing subjects with autosomal recessive deafness loci were studied for selected deafness loci. Those who were unhealthy and gave history of infectious disease were excluded. DNA extraction was carried out using the inorganic method. Fluorescently labeled microsatellite markers were used for amplification of desired regions by PCR (Polymerase Chain Reaction). Automated allele assignment was performed using the ABI PRISM GeneScan Analysis Software Version 3.7 for Windows NT Platform. Two-point LOD scores were calculated using the FASTLINK computer package (Schaffer 1996) and MLINK was used for calculation and 95% CI (confidence intervals) were calculated. Results: One hundred and thirty two individuals of 8 families were analyzed. Three families (SAPun-03, SAPun-10 and SAPun-15) were found linked to DFNB12; two families (SAPun-05 and SAPun-17) were found linked to DFNB8/10, while three families (SAPun-06, SAPun-13 and SAPun-19) were found linked to DFNB29, DFNB36 and DFNB37 respectively. Conclusion: The genotyping results revealed that DFNB12 locus was the most common followed by DFNB8/10 locus, while the Loci DFNB29, DFNB36 and DFNB37 were less common. (author)

  15. Molecular characterization of sympatrically distributed Neotricula aperta-like snails in the Mekong River, Kratie, Cambodia.

    Wang, Chennan; Saijuntha, Weerachai; Kirinoki, Masashi; Hayashi, Naoko; Chigusa, Yuichi; Muth, Sinuon; Meng, Chuor Char; Ai, Yingchun; Agatsuma, Takeshi

    2016-01-01

    Fifty-six samples of Neotricula aperta-like snails were collected from six locations in Cambodia. Their mitochondrial cytochrome c oxidase subunit 1 (cox1) sequences were examined using haplotype network and neighbor-joining (NJ) tree analysis. Twenty-seven haplotypes (H1-H27) were observed and were divided into two different groups/lineages. Of 27, 17 haplotypes (H11-H27) were clustered with the reference samples of the γ-race N. aperta. The remaining 10 haplotypes (H1-H10) were clustered in a separate group/lineage, differing from the reference samples of the α-, β-, and γ-race N. aperta, suggesting a new lineage belonging the genus Neotricula. Our results show that both the γ-race and a new lineage were sympatrically present approximately 60 km upstream of the Mekong River near the Kratie port, Cambodia. Further morphological and molecular studies are required to confirm the taxonomic status of this new, unidentified lineage.

  16. Orbital momentum distribution and binding energies for the complete valence shell of molecular bromine

    Frost, L.; Grisogono, A.M.; Weigold, E.

    1987-08-01

    The binding energy spectrum of Br 2 has been recorded in both the outer and inner valence regions using electron momentum spectroscopy. The measurements are compared with the results of several Green's function calculations using different approximations and based on both polarized and unpolarized wave functions. The inner valence region, observed for the first time, is found to exhibit complex structure that is shown to be due to many-body effects, thus indicating a breakdown of the simple MO picture for ionization in this region. Momentum distributions for the three outer valence orbitals are also measured and compared with spherically averaged calculations using the target Hartree-Fock and plane wave impulse approximations. The effect of polarization functions in the basis set is investigated. Orbital density maps in both momentum and position space have been calculated and compared with the experimental measurements

  17. Biochemical and molecular study on interleukin-1β gene expression and relation of single nucleotide polymorphism in promoter region with Type 2 diabetes mellitus.

    Tayel, Safaa I; Fouda, Eman A M; Elshayeb, Elsayed I; Eldakamawy, Asmaa R A; El-Kousy, Salah M

    2018-01-11

    Interleukin-1β (IL-1β) assumes a centric role in the regulation of immune and inflammatory responses and thus has been recognized in immune mediated diseases like type 2 diabetes mellitus (T2DM). We aimed to investigate expressed level of IL-1β and its relation with IL-1β -511T>C polymorphism in T2DM patients. This study enrolled 80 subjects (50 patients with T2DM and 30 healthy control subjects). Laboratory investigations included fasting (FBG) and 2 h postprandial blood sugar (2 h PBG), HBA1c, lipid profile, and renal function tests. Genotyping of IL-1β -511T>C (rs16944) SNP assay by real-time PCR and relative quantitation of IL-1β gene expression transcript by real-time PCR. T2DM patients had significantly higher FBG and 2 h PBG, HBA1c, LDLc, TC, TG, systolic, and diastolic BP while lower HDLc compared with control group. IL 1- β -511 T>C, CC genotype and C allele were significantly associated with risk of T2DM with odds ratio (OR) 4.73, 95%CI (1.21-18.39) and OR 2.27, 95%CI (1.72-4.40), respectively. Moreover, diabetic patients had significantly higher IL 1- β gene transcript compared with control group (P  C had the highest significant level of IL 1- β gene transcript demonstrated compared with C/T and T/T genotypes (P C could be considered risk factor contributor to T2DM and excess level of IL-1 β transcript may disclose to some degree the inflammatory role of cytokines in T2DM. © 2018 Wiley Periodicals, Inc.

  18. Towards the molecular characterisation of parasitic nematode assemblages: an evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis.

    Lott, M J; Hose, G C; Power, M L

    2014-09-01

    Identifying factors which regulate temporal and regional structuring within parasite assemblages requires the development of non-invasive techniques which facilitate both the rapid discrimination of individual parasites and the capacity to monitor entire parasite communities across time and space. To this end, we have developed and evaluated a rapid fluorescence-based method, terminal restriction fragment length polymorphism (T-RFLP) analysis, for the characterisation of parasitic nematode assemblages in macropodid marsupials. The accuracy with which T-RFLP was capable of distinguishing between the constituent taxa of a parasite community was assessed by comparing sequence data from two loci (the ITS+ region of nuclear ribosomal DNA and the mitochondrial CO1) across ∼20 species of nematodes (suborder Strongylida). Our results demonstrate that with fluorescent labelling of the forward and reverse terminal restriction fragments (T-RFs) of the ITS+ region, the restriction enzyme Hinf1 was capable of generating species specific T-RFLP profiles. A notable exception was within the genus Cloacina, in which closely related species often shared identical T-RFs. This may be a consequence of the group's comparatively recent evolutionary radiation. While the CO1 displayed higher sequence diversity than the ITS+, the subsequent T-RFLP profiles were taxonomically inconsistent and could not be used to further differentiate species within Cloacina. Additionally, several of the ITS+ derived T-RFLP profiles exhibited unexpected secondary peaks, possibly as a consequence of the restriction enzymes inability to cleave partially single stranded amplicons. These data suggest that the question of T-RFLPs utility in monitoring parasite communities cannot be addressed without considering the ecology and unique evolutionary history of the constituent taxa. Copyright © 2014 Elsevier Inc. All rights reserved.

  19. Isotopic and molecular distributions of biochemicals from fresh and buried Rhizophora mangle leaves†

    Smallwood, Barbara J; Wooller, Matthew J; Jacobson, Myrna E; Fogel, Marilyn L

    2003-01-01

    Rhizophora mangle L. (red mangrove) is the dominant species of mangrove in the Americas. At Twin Cays, Belize (BZ) red mangroves are present in a variety of stand structures (tall >5 m in height, transition ~2–4 m and dwarf ~1–1.5 m). These height differences are coupled with very different stable carbon and nitrogen isotopic values[1] (mean tall δ13C = -28.3‰, δ15N = 0‰; mean tall δ13C = -25.3‰, δ15N = -10‰). To determine the utility of using these distinct isotopic compositions as 'biomarkers' for paleoenvironmental reconstruction of mangrove ecosystems and nutrient availability, we investigated the distribution and isotopic (δ13C and δ15N) composition of different biochemical fractions (water soluble compounds, free lipids, acid hydrolysable compounds, individual amino acids, and the residual un-extractable compounds) in fresh and preserved red mangrove leaves from dwarf and tall trees. The distribution of biochemicals are similar in dwarf and tall red mangrove leaves, suggesting that, regardless of stand structure, red mangroves use nutrients for biosynthesis and metabolism in a similar manner. However, the δ13C and δ15N of the bulk leaf, the biochemical fractions, and seven amino acids can be used to distinguish dwarf and tall trees at Twin Cays, BZ. The data support the theory that the fractionation of carbon and nitrogen occurs prior to or during uptake in dwarf and tall red mangrove trees. Stable carbon and nitrogen isotopes could, therefore, be powerful tools for predicting levels of nutrient limitation at Twin Cays. The δ13C and δ15N of biochemical fractions within preserved leaves, reflect sedimentary cycling and nitrogen immobilization. The δ15N of the immobilized fraction reveals the overlying stand structure at the time of leaf deposition. The isotopic composition of preserved mangrove leaves could yield significant information about changes in ecosystem dynamics, nutrient limitation and past stand structure in mangrove

  20. Isotopic and molecular distributions of biochemicals from fresh and buried Rhizophora mangle leaves†

    Jacobson Myrna E

    2003-12-01

    Full Text Available Rhizophora mangle L. (red mangrove is the dominant species of mangrove in the Americas. At Twin Cays, Belize (BZ red mangroves are present in a variety of stand structures (tall >5 m in height, transition ~2–4 m and dwarf ~1–1.5 m. These height differences are coupled with very different stable carbon and nitrogen isotopic values1 (mean tall δ13C = -28.3‰, δ15N = 0‰; mean tall δ13C = -25.3‰, δ15N = -10‰. To determine the utility of using these distinct isotopic compositions as 'biomarkers' for paleoenvironmental reconstruction of mangrove ecosystems and nutrient availability, we investigated the distribution and isotopic (δ13C and δ15N composition of different biochemical fractions (water soluble compounds, free lipids, acid hydrolysable compounds, individual amino acids, and the residual un-extractable compounds in fresh and preserved red mangrove leaves from dwarf and tall trees. The distribution of biochemicals are similar in dwarf and tall red mangrove leaves, suggesting that, regardless of stand structure, red mangroves use nutrients for biosynthesis and metabolism in a similar manner. However, the δ13C and δ15N of the bulk leaf, the biochemical fractions, and seven amino acids can be used to distinguish dwarf and tall trees at Twin Cays, BZ. The data support the theory that the fractionation of carbon and nitrogen occurs prior to or during uptake in dwarf and tall red mangrove trees. Stable carbon and nitrogen isotopes could, therefore, be powerful tools for predicting levels of nutrient limitation at Twin Cays. The δ13C and δ15N of biochemical fractions within preserved leaves, reflect sedimentary cycling and nitrogen immobilization. The δ15N of the immobilized fraction reveals the overlying stand structure at the time of leaf deposition. The isotopic composition of preserved mangrove leaves could yield significant information about changes in ecosystem dynamics, nutrient limitation and past stand structure in

  1. Molecular typing of Sarcocystis neurona: current status and future trends.

    Elsheikha, Hany M; Mansfield, Linda S

    2007-10-21

    Sarcocystis neurona is an important protozoal pathogen because it causes the serious neurological disease equine protozoal myeloencephalitis (EPM). The capacity of this organism to cause a wide spectrum of neurological signs in horses and the broad geographic distribution of observed cases in the Americas drive the need for sensitive, reliable and rapid typing methods to characterize strains. Various molecular methods have been developed and used to diagnose EPM due to S. neurona, to identify S. neurona isolates and to determine the heterogeneity and evolutionary relatedness within this species and related Sarcocystis spp. These methods included sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), immuno-fluorescent assay (IFA), slide agglutination test (SAT), SnSAG-specific ELISA, random amplified polymorphic DNA (RAPD), PCR-based restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP) fingerprinting, and sequence analysis of surface protein genes, ribosomal genes, microsatellite alleles and other molecular markers. Here, the utility of these molecular methods is reviewed and evaluated with respect to the need for molecular approaches that utilize well-characterized polymorphic, simple, independent, and stable genetic markers. These tools have the potential to add to knowledge of the genetic population structure of S. neurona and to provide new insights into the pathogenesis of EPM and S. neurona epidemiology. In particular, these methods provide new tools to address the hypothesis that particular genetic variants are associated with adverse clinical outcomes (severe pathotypes). The ultimate goal is to utilize them in future studies to improve treatment and prevention strategies.

  2. Distribution of PON1 polymorphisms PON1Q192R and PON1L55M among Chinese, Malay and Indian males in Singapore and possible susceptibility to organophosphate exposure.

    Chia, Sin Eng; Mohamed Ali, Safiyya; Yap, Peng Huat Eric; Gan, Linda; Ong, Yeong Bing; Chia, Kee Seng

    2009-03-01

    Organophosphate (OP)-containing pesticides are widely used worldwide for domestic and industrial purposes. Studies on acute and chronic exposure to OPs have revealed numerous health effects attributed mainly to acetylcholinesterase (AChE) inhibition. The enzyme human serum paraoxonase (PON1) is involved in the detoxification of OP compounds. PON1 polymorphisms have been shown to affect susceptibility to OP exposure. We studied the effect of OP exposure on pest control workers and assessed the distribution of two common PON1 polymorphisms in our local population. The exposed group consisted of 103 workers from various pest control companies under the Singapore Pest Management Association while the 91 unexposed workers were from a lead stabilizer factory. For all workers, the mean age was 36.9 (20-70) years and the ethnic distribution was 38.1% Chinese, 44.3% Malay and 17.5% Indian. The mean+/-S.D. exposure duration among the pesticide workers was 10.4+/-8.4 years. The mean+/-S.D. RBC cholinesterase level was 18436.2+/-2078U/L and 18079.6+/-1576U/L for the exposed and unexposed groups, respectively (p=0.216). The mean+/-S.D. serum pseudocholinesterase was 11028.4+/-2867.4U/L and 9433.6+/-2022.6U/L in the exposed and unexposed groups, respectively (pChinese and Malays (266.5 and 266.3U/L, respectively) whereas that of the Indians was significantly lower (165.6U/L). Our study showed that cholinesterase levels among the exposed were not lower than those in the unexposed group. PON1 polymorphisms differed among ethnic groups, implying that ethnicity could be an important surrogate for identifying susceptible groups in case of OP exposure. Although OP poisoning is rare among occupationally exposed workers in Singapore, this information is useful for other developing countries that have large populations of Chinese, Malays and Indians where OP exposure could be very high especially in agricultural settings.

  3. Genotype Distribution and Molecular Epidemiology of Hepatitis C Virus in Hubei, Central China.

    Jing Peng

    Full Text Available Little is known about the molecular epidemiology of hepatitis C virus (HCV infection in Central China.A total of 570 patients from Hubei Province in central China were enrolled. These patients were tested positive for HCV antibody prior to blood transfusion. Among them, 177 were characterized by partial NS5B and/or Core-E1 sequences and classified into five subtypes: 1b, 83.0% (147/177; 2a, 13.0% (23/177; 3b, 2.3% (4/177; 6a, 1.1% (2/177; 3a, 0.6% (1/177. Analysis of genotype-associated risk factors revealed that paid blood donation and transfusion before 1997 were strongly associated with subtypes 1b and 2a, while some subtype 2a cases were also found in individuals with high risk sexual behaviors; subtypes 3b, 6a, and 3a were detected only in intravenous drug users. Phylogeographic analyses based on the coalescent datasets demonstrated that 1b, 2a, 3b, and 6a were locally epidemic in Hubei Province. Among them, subtype 1b Hubei strains may have served as the origins of this subtype in China, and 2a and 3b Hubei strains may have descended from the northwest and southwest of China, respectively, while 6a Hubei strains may have been imported from the central south and southwest.The results suggest that the migration patterns of HCV in Hubei are complex and variable among different subtypes. Implementation of mandatory HCV screening before donation has significantly decreased the incidence of transfusion-associated HCV infection since 1997. More attention should be paid to intravenous drug use and unsafe sexual contact, which may have become new risk factors for HCV infection in Hubei Province.

  4. Subarcsecond observations of NGC 7538 IRS 1: Continuum distribution and dynamics of molecular gas

    Zhu, Lei; Shi, Hui [National Astronomical Observatories, Chinese Academy of Sciences, A20 Datun Road, Chaoyang District, Beijing 100012 (China); Zhao, Jun-Hui [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Wright, M. C. H. [Department of Astronomy, University of California, Berkeley, Berkeley, CA 94720 (United States); Sandell, Göran [SOFIA-USRA, NASA Ames Research Center, MS 232-12, Building N232, Rm. 146, P.O. Box 1, Moffett Field, CA 94035-0001 (United States); Wu, Yue-Fang [Department of Astronomy, Peking University, Beijing 100871 (China); Brogan, Crystal; Corder, Stuartt, E-mail: lzhu@nao.cas.cn [NRAO, 520 Edgemont Road, Charlottesville, VA 22903 (United States)

    2013-12-10

    We report new results based on the analysis of the Submillimeter Array (SMA) and Combined Array for Research in Millimeter-wave Astronomy (CARMA) observations of NGC 7538 IRS 1 at 1.3 and 3.4 mm with subarcsecond resolutions. With angular resolutions ∼0.''7, the SMA and CARMA observations show that the continuum emission at 1.3 and 3.4 mm from the hyper-compact H II region IRS 1 is dominated by a compact source with a tail-like extended structure to the southwest of IRS 1. With a CARMA B-array image at 1.3 mm convolved to 0.''1, we resolve the hyper-compact H II region into two components: an unresolved hyper-compact core, and a north-south extension with linear sizes of <270 AU and ∼2000 AU, respectively. The fine structure observed with CARMA is in good agreement with the previous Very Large Array results at centimeter wavelengths, suggesting that the hyper-compact H II region at the center of IRS 1 is associated with an ionized bipolar outflow. We image the molecular lines OCS(19-18) and CH{sub 3}CN(12-11) as well as {sup 13}CO(2-1) surrounding IRS 1, showing a velocity gradient along the southwest-northeast direction. The spectral line profiles in {sup 13}CO(2-1), CO(2-1), and HCN(1-0) observed toward IRS 1 show broad redshifted absorption, providing evidence for gas infall with rates in the range of 3-10 × 10{sup –3} M {sub ☉} yr{sup –1} inferred from our observations.

  5. Distribution and Molecular Characterization of Acinetobacter baumannii International Clone II Lineage in Japan.

    Matsui, Mari; Suzuki, Masato; Suzuki, Masahiro; Yatsuyanagi, Jun; Watahiki, Masanori; Hiraki, Yoichi; Kawano, Fumio; Tsutsui, Atsuko; Shibayama, Keigo; Suzuki, Satowa

    2018-02-01

    Multidrug-resistant (MDR) Acinetobacter spp. have been globally disseminated in association with the successful clonal lineage Acinetobacter baumannii international clone II (IC II). Because the prevalence of MDR Acinetobacter spp. in Japan remains very low, we characterized all Acinetobacter spp. ( n = 866) from 76 hospitals between October 2012 and March 2013 to describe the entire molecular epidemiology of Acinetobacter spp. The most prevalent species was A. baumannii ( n = 645; 74.5%), with A. baumannii IC II ( n = 245) accounting for 28.3% of the total. Meropenem-resistant isolates accounted for 2.0% ( n = 17) and carried IS Aba1-bla OXA-23-like ( n = 10), bla IMP ( n = 4), or IS Aba1-bla OXA-51-like ( n = 3). Multilocus sequence typing of 110 representative A. baumannii isolates revealed the considerable prevalence of domestic sequence types (STs). A. baumannii IC II isolates were divided into the domestic sequence type 469 (ST469) ( n = 18) and the globally disseminated STs ST208 ( n = 14) and ST219 ( n = 4). ST469 isolates were susceptible to more antimicrobial agents, while ST208 and ST219 overproduced the intrinsic AmpC β-lactamase. A. baumannii IC II and some A. baumannii non-IC II STs (e.g., ST149 and ST246) were associated with fluoroquinolone resistance. This study revealed that carbapenem-susceptible A. baumannii IC II was moderately disseminated in Japan. The low prevalence of acquired carbapenemase genes and presence of domestic STs could contribute to the low prevalence of MDR A. baumannii A similar epidemiology might have appeared before the global dissemination of MDR epidemic lineages. In addition, fluoroquinolone resistance associated with A. baumannii IC II may provide insight into the significance of A. baumannii epidemic clones. Copyright © 2018 American Society for Microbiology.

  6. Molecular Identification of Paramecium bursaria Syngens and Studies on Geographic Distribution using Mitochondrial Cytochrome C Oxidase Subunit I (COI).

    Zagata, Patrycja; Greczek-Stachura, Magdalena; Tarcz, Sebastian; Rautian, Maria

    2015-01-01

    Paramecium bursaria is composed of five syngens that are morphologically indistinguishable but sexually isolated. The aim of the present study was to confirm by molecular methods (analyses of mitochondrial COI) the identification of P. bursaria syngens originating from different geographical locations. Phylograms constructed using both the neighbor-joining and maximum-likelihood methods based on a comparison of 34 sequences of P. bursaria strains and P. multimicronucleatum, P. caudatum and P.calkinsi strains used as outgroups revealed five clusters which correspond to results obtained previously by mating reaction. Our analysis shows the existence of 24 haplotypes for the COI gene sequence in the studied strains. The interspecies haplotype diversity was Hd = 0.967. We confirmed genetic differentiation between strains of P. bursaria and the occurrence of a correlation between geographical distribution and the correspondent syngen.

  7. Defect distribution in low-temperature molecular beam epitaxy grown Si/Si(100), improved depth profiling with monoenergetic positrons

    Szeles, C.; Asoka-Kumar, P.; Lynn, K.G.; Gossmann, H.; Unterwald, F.C.; Boone, T.

    1995-01-01

    The depth distribution of open-volume defects has been studied in Si(100) crystals grown by molecular beam epitaxy at 300 degree C by the variable-energy monoenergetic positron beam technique combined with well-controlled chemical etching. This procedure gave a 10 nm depth resolution which is a significant improvement over the inherent depth resolving power of the positron beam technique. The epitaxial layer was found to grow defect-free up to 80 nm, from the interface, where small vacancy clusters, larger than divacancies, appear. The defect density then sharply increases toward the film surface. The result clearly shows that the nucleation of small open-volume defects is a precursor state to the breakdown of epitaxy and to the evolution of an amorphous film

  8. Size-exclusion chromatography (HPLC-SEC) technique optimization by simplex method to estimate molecular weight distribution of agave fructans.

    Moreno-Vilet, Lorena; Bostyn, Stéphane; Flores-Montaño, Jose-Luis; Camacho-Ruiz, Rosa-María

    2017-12-15

    Agave fructans are increasingly important in food industry and nutrition sciences as a potential ingredient of functional food, thus practical analysis tools to characterize them are needed. In view of the importance of the molecular weight on the functional properties of agave fructans, this study has the purpose to optimize a method to determine their molecular weight distribution by HPLC-SEC for industrial application. The optimization was carried out using a simplex method. The optimum conditions obtained were at column temperature of 61.7°C using tri-distilled water without salt, adjusted pH of 5.4 and a flow rate of 0.36mL/min. The exclusion range is from 1 to 49 of polymerization degree (180-7966Da). This proposed method represents an accurate and fast alternative to standard methods involving multiple-detection or hydrolysis of fructans. The industrial applications of this technique might be for quality control, study of fractionation processes and determination of purity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Distribution and molecular characterization of β-glucans from hull-less barley bran, shorts and flour.

    Zheng, Xueling; Li, Limin; Wang, Qi

    2011-01-01

    Six hull-less barley cultivars widely grown in China were roller-milled to produce bran, shorts and flour fractions. The distribution and molecular characteristics of β-glucans from the three roller-milled fractions were investigated. The β-glucan contents in the six hull-less barley cultivars varied from 4.96% to 7.62%. For all the six cultivars, the shorts fraction contained the highest concentration of β-glucan (8.12-13.01%), followed by bran (6.15-7.58%) and flour (2.48-2.95%). Crude β-glucans were prepared from the three roller-milled fractions using aqueous sodium carbonate (pH 10). These preparations contained 45.38-71.41% β-glucan, 10.81-17.26% arabinoxylan, 2.6-9.6% protein, 2.7-9.0% starch, and 5.23-9.68% ash. Purification using α-amylase and β-xylanase in combination with pH adjustment and dialysis produced high purity β-glucan preparations (91-95%). The molecular weight (Mw) of β-glucan preparations from roller-milled fractions ranged from 117,600 to 852,400 g/mol. β-Glucan from flour had higher Mw than those from shorts and bran within the same cultivar, and β-glucan preparations from bran had the lowest Mw.

  10. Sensitivity of ion-induced sputtering to the radial distribution of energy transfers: A molecular dynamics study

    Mookerjee, S.; Khan, S. A.; Roy, A.; Beuve, M.; Toulemonde, M.

    2008-01-01

    Using different models for the deposition of energy on the lattice and a classical molecular dynamics approach to the subsequent transport, we evaluate how the details of the energy deposition model influence sputtering yield from a Lennard-Jones target irradiated with a MeV/u ion beam. Two energy deposition models are considered: a uniform, instantaneous deposition into a cylinder of fixed radius around the projectile ion track, used in earlier molecular dynamics and fluid dynamics simulations of sputtering yields; and an energy deposition distributed in time and space based on the formalism developed in the thermal spike model. The dependence of the sputtering yield on the total energy deposited on the target atoms is very sensitive to the energy deposition model. To clarify the origin of this strong dependence, we explore the role of the radial expansion of the electronic system prior to the transfer of its energy to the lattice. The results imply that observables such as the sputtering yield may be used as signatures of the fast electron-lattice energy transfer in the electronic energy-loss regime, and indicate the need for more experimental and theoretical investigations of these processes

  11. Genetic analyses place most Spanish isolates of Beauveria bassiana in a molecular group with word-wide distribution

    2011-01-01

    Background The entomopathogenic anamorphic fungus Beauveria bassiana is currently used as a biocontrol agent (BCA) of insects. Fifty-seven Beauveria bassiana isolates -53 from Spain- were characterized, integrating group I intron insertion patterns at the 3'-end of the nuclear large subunit ribosomal gene (LSU rDNA) and elongation factor 1-alpha (EF1-α) phylogenetic information, in order to assess the genetic structure and diversity of this Spanish collection of B. bassiana. Results Group I intron genotype analysis was based on the four highly conserved insertion sites of the LSU (Ec2653, Ec2449, Ec2066, Ec1921). Of the 16 possible combinations/genotypes, only four were detected, two of which were predominant, containing 44 and 9 members out of 57 isolates, respectively. Interestingly, the members of the latter two genotypes showed unique differences in their growth temperatures. In follow, EF1-α phylogeny served to classify most of the strains in the B. bassiana s.s. (sensu stricto) group and separate them into 5 molecular subgroups, all of which contained a group I intron belonging to the IC1 subtype at the Ec1921 position. A number of parameters such as thermal growth or origin (host, geographic location and climatic conditions) were also examined but in general no association could be found. Conclusion Most Spanish B. bassiana isolates (77.2%) are grouped into a major phylogenetic subgroup with word-wide distribution. However, high phylogenetic diversity was also detected among Spanish isolates from close geographic zones with low climatic variation. In general, no correlation was observed between the molecular distribution and geographic origin or climatic characteristics where the Spanish B. bassiana isolates were sampled. PMID:21521527

  12. Spatial distributions of and diurnal variations in low molecular weight carbonyl compounds in coastal seawater, and the controlling factors

    Takeda, Kazuhiko, E-mail: takedaq@hiroshima-u.ac.jp [Graduate School of Biosphere Science, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521 (Japan); Katoh, Shinya; Mitsui, Yumi; Nakano, Shinichi [Graduate School of Biosphere Science, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521 (Japan); Nakatani, Nobutake [Graduate School of Biosphere Science, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521 (Japan); Department of Environmental and Symbiotic Sciences, Rakuno Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido 069-8501 (Japan); Sakugawa, Hiroshi [Graduate School of Biosphere Science, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521 (Japan)

    2014-09-15

    We studied the spatial distributions of and the diurnal variations in four low molecular weight (LMW) carbonyl compounds, formaldehyde, acetaldehyde, propionaldehyde, and glyoxal, in coastal seawater. The samples were taken from the coastal areas of Hiroshima Bay, the Iyo Nada, and the Bungo Channel, western Japan. The formaldehyde, acetaldehyde, and glyoxal concentrations were higher in the northern part of Hiroshima Bay than at offshore sampling points in the Iyo Nada and the Bungo Channel. These three compounds were found at much higher concentrations in the surface water than in deeper water layers in Hiroshima Bay. It is noteworthy that propionaldehyde was not detected in any of the seawater samples, the concentrations present being lower than the detection limit (1 nanomole per liter (nM)) of the high performance liquid chromatography (HPLC) system we used. Photochemical and biological experiments were performed in the laboratory to help understand the characteristic distributions and fates of the LMW carbonyl compounds. The primary process controlling their fate in the coastal environment appears to be their biological consumption. The direct photo degradation of propionaldehyde, initiated by ultraviolet (UV) absorption, was observed, although formaldehyde and acetaldehyde were not degraded by UV irradiation. Our results suggest that the degradation of the LMW carbonyl compounds by photochemically formed hydroxyl radicals is relatively insignificant in the study area. Atmospheric deposition is a possible source of soluble carbonyl compounds in coastal surface seawater, but it may not influence the carbonyl concentrations in offshore waters. - Highlights: • Low molecular weight (LMW) carbonyl compounds in coastal seawater were determined. • Photochemical productions of LMW carbonyl compounds in seawater were observed. • LMW carbonyl compounds were largely consumed biologically. • Photochemical degradation was relatively insignificant in the study area.

  13. Spatial distributions of and diurnal variations in low molecular weight carbonyl compounds in coastal seawater, and the controlling factors

    Takeda, Kazuhiko; Katoh, Shinya; Mitsui, Yumi; Nakano, Shinichi; Nakatani, Nobutake; Sakugawa, Hiroshi

    2014-01-01

    We studied the spatial distributions of and the diurnal variations in four low molecular weight (LMW) carbonyl compounds, formaldehyde, acetaldehyde, propionaldehyde, and glyoxal, in coastal seawater. The samples were taken from the coastal areas of Hiroshima Bay, the Iyo Nada, and the Bungo Channel, western Japan. The formaldehyde, acetaldehyde, and glyoxal concentrations were higher in the northern part of Hiroshima Bay than at offshore sampling points in the Iyo Nada and the Bungo Channel. These three compounds were found at much higher concentrations in the surface water than in deeper water layers in Hiroshima Bay. It is noteworthy that propionaldehyde was not detected in any of the seawater samples, the concentrations present being lower than the detection limit (1 nanomole per liter (nM)) of the high performance liquid chromatography (HPLC) system we used. Photochemical and biological experiments were performed in the laboratory to help understand the characteristic distributions and fates of the LMW carbonyl compounds. The primary process controlling their fate in the coastal environment appears to be their biological consumption. The direct photo degradation of propionaldehyde, initiated by ultraviolet (UV) absorption, was observed, although formaldehyde and acetaldehyde were not degraded by UV irradiation. Our results suggest that the degradation of the LMW carbonyl compounds by photochemically formed hydroxyl radicals is relatively insignificant in the study area. Atmospheric deposition is a possible source of soluble carbonyl compounds in coastal surface seawater, but it may not influence the carbonyl concentrations in offshore waters. - Highlights: • Low molecular weight (LMW) carbonyl compounds in coastal seawater were determined. • Photochemical productions of LMW carbonyl compounds in seawater were observed. • LMW carbonyl compounds were largely consumed biologically. • Photochemical degradation was relatively insignificant in the study area

  14. Molecular mass distribution and epitopes of the beta lactoglobulin submitted to hydrolysis pre-transglutaminase treatment

    Villas-Boas, M.B.; Zollner, R.L.; Netto, F.M.; Paes Leme, A.F.; Benede, S.; Molina, E.

    2012-01-01

    Full text: The β-Lactoglobulin (β-Lg) is a whey protein with important nutritional proper ties but very resistant to pepsin digestion and consequently highly antigenic. This protein can be modified by transglutaminase (TG) although it is required a pretreatment to increase their susceptibility to the TG action. In the present study the hydrolysis pre-TG treatment was used to improve the TG accessibility on β-Lg and the MM distribution and antigenic fragments were evaluated. For pre-TG treatment, the β-Lg (Davisco Inc.) was hydrolyzed with bromelain (3% of β-Lg w/w in distilled water; 25 U enzyme g 1 of substrate, pH 7.5, 240 min) and then polymerized by TG (7% hydrolysate, 10U TG g 1 protein, 50 C/180 min). The samples were evaluated by SDS-PAGE/tricine and by RP-nanoUPLC (nanoAcquity UPLC, Waters) coupled with nano-electrospray tandem mass spectrometry on a Q-Tof Ultima API mass spectrometer (MicroMass/Waters) at LNBio. The products were also submitted to pepsin digestion and the peptide identification was performed by RP-HPLC-tandem mass spectrometry (RP-HPLC-MS/MS, Brucker) with support from CIAL. The β-Lg hydrolysed by bromelain and polymerized by TG had a broad MM distribution. The intact mass analysis indicated that the non modified βLg -A showed 18.362 Da and the non modified βLg -B 18.274 Da, which is in agreement with the theoretical corresponding masses. The use of bromelain pre-TG treatment resulted in polymers with MM from 61.052 to 67.654 Da, although some non modified protein was still present. In addition, the non modified β-Lg showed fragments that present high antigenicity (such as Leu 95 - Leu 104 , Asp 95 - Phe 105 , Tyr 42 - Leu 54 , lle 29 - Val 41 ), previously identified as IgE-binding epitopes. After hydrolysis following by TG treatment the fragment Tyr 42 - Leu 54 was still present, however the other fragments that were observed in the non modified β-Lg were not detected by LC-MS/MS, suggesting that structural change occurred in

  15. Molecular mass distribution and epitopes of the beta lactoglobulin submitted to hydrolysis pre-transglutaminase treatment

    Villas-Boas, M.B.; Zollner, R.L.; Netto, F.M. [Universidade Estadual de Campinas (UNICAMP), SP (Brazil); Paes Leme, A.F. [Laboratorio Nacional de Luz Sincrotron (LNLS), Campinas, SP (Brazil); Benede, S.; Molina, E. [Universidad Autonoma de Madrid (Spain)

    2012-07-01

    Full text: The {beta}-Lactoglobulin ({beta}-Lg) is a whey protein with important nutritional proper ties but very resistant to pepsin digestion and consequently highly antigenic. This protein can be modified by transglutaminase (TG) although it is required a pretreatment to increase their susceptibility to the TG action. In the present study the hydrolysis pre-TG treatment was used to improve the TG accessibility on {beta}-Lg and the MM distribution and antigenic fragments were evaluated. For pre-TG treatment, the {beta}-Lg (Davisco Inc.) was hydrolyzed with bromelain (3% of {beta}-Lg w/w in distilled water; 25 U enzyme g{sup 1} of substrate, pH 7.5, 240 min) and then polymerized by TG (7% hydrolysate, 10U TG g{sup 1} protein, 50 C/180 min). The samples were evaluated by SDS-PAGE/tricine and by RP-nanoUPLC (nanoAcquity UPLC, Waters) coupled with nano-electrospray tandem mass spectrometry on a Q-Tof Ultima API mass spectrometer (MicroMass/Waters) at LNBio. The products were also submitted to pepsin digestion and the peptide identification was performed by RP-HPLC-tandem mass spectrometry (RP-HPLC-MS/MS, Brucker) with support from CIAL. The {beta}-Lg hydrolysed by bromelain and polymerized by TG had a broad MM distribution. The intact mass analysis indicated that the non modified {beta}Lg -A showed 18.362 Da and the non modified {beta}Lg -B 18.274 Da, which is in agreement with the theoretical corresponding masses. The use of bromelain pre-TG treatment resulted in polymers with MM from 61.052 to 67.654 Da, although some non modified protein was still present. In addition, the non modified {beta}-Lg showed fragments that present high antigenicity (such as Leu{sub 95} - Leu{sub 104}, Asp{sub 95} - Phe{sub 105}, Tyr{sub 42} - Leu{sub 54}, lle{sub 29} - Val{sub 41}), previously identified as IgE-binding epitopes. After hydrolysis following by TG treatment the fragment Tyr{sub 42} - Leu{sub 54} was still present, however the other fragments that were observed in the non

  16. Distribution

    John R. Jones

    1985-01-01

    Quaking aspen is the most widely distributed native North American tree species (Little 1971, Sargent 1890). It grows in a great diversity of regions, environments, and communities (Harshberger 1911). Only one deciduous tree species in the world, the closely related Eurasian aspen (Populus tremula), has a wider range (Weigle and Frothingham 1911)....

  17. Cockroach GABAB receptor subtypes: molecular characterization, pharmacological properties and tissue distribution.

    Blankenburg, S; Balfanz, S; Hayashi, Y; Shigenobu, S; Miura, T; Baumann, O; Baumann, A; Blenau, W

    2015-01-01

    γ-aminobutyric acid (GABA) is the predominant inhibitory neurotransmitter in the central nervous system (CNS). Its effects are mediated by either ionotropic GABAA receptors or metabotropic GABAB receptors. GABAB receptors regulate, via Gi/o G-proteins, ion channels, and adenylyl cyclases. In humans, GABAB receptor subtypes are involved in the etiology of neurologic and psychiatric disorders. In arthropods, however, these members of the G-protein-coupled receptor family are only inadequately characterized. Interestingly, physiological data have revealed important functions of GABAB receptors in the American cockroach, Periplaneta americana. We have cloned cDNAs coding for putative GABAB receptor subtypes 1 and 2 of P. americana (PeaGB1 and PeaGB2). When both receptor proteins are co-expressed in mammalian cells, activation of the receptor heteromer with GABA leads to a dose-dependent decrease in cAMP production. The pharmacological profile differs from that of mammalian and Drosophila GABAB receptors. Western blot analyses with polyclonal antibodies have revealed the expression of PeaGB1 and PeaGB2 in the CNS of the American cockroach. In addition to the widespread distribution in the brain, PeaGB1 is expressed in salivary glands and male accessory glands. Notably, PeaGB1-like immunoreactivity has been detected in the GABAergic salivary neuron 2, suggesting that GABAB receptors act as autoreceptors in this neuron. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Polymorphic Embedding of DSLs

    Hofer, Christian; Ostermann, Klaus; Rendel, Tillmann

    2008-01-01

    propose polymorphic embedding of DSLs, where many different interpretations of a DSL can be provided as reusable components, and show how polymorphic embedding can be realized in the programming language Scala. With polymorphic embedding, the static type-safety, modularity, composability and rapid...

  19. Zooming into Molecular Biomarker Distribution through Spatially Resolved Mass Spectrometry on Intact Sediment Sections

    Wörmer, L.; Fuchser, J.; Alfken, S.; Elvert, M.; Schimmelmann, A.; Hinrichs, K. U.

    2016-02-01

    Marine microorganisms adapt to their habitat by structural modification of their membrane lipids. After sedimentation, and due to their persistence in the sedimentary record, the information archived in them remains available on geological time-scales. Thereby sedimentary lipid biomarkers become important informants of past environments. Conventional biomarker analysis is labor-intensive and requires cm-sized samples, temporal resolution is consequently low. We here present an approach, based on laser desorption ionization (LDI) coupled to ultra high resolution mass spectrometry, that avoids wet-chemical sample preparation and enables analysis directly on sediment sections at sub-mm spatial resolution. Our initial study targeted archaeal glycerol dialkyl glycerol tetraethers (GDGTs). GDGTS are ubiquitous and persistent components in marine sediments, and used in several, widely recognized paleoenvironmental proxies. Applied to an Eastern Mediterranean Sapropel layer, GDGT-profiles with previously unachieved temporal resolution were obtained, and pointed to a strong influence of high frequency cycles on sea-surface temperature and planktonic archaeal ecology. Spatial information furthermore revealed a new view on the fine-scale patchiness of lipid distribution. Following these pioneering studies, major developments are under way. A dedicated facility has been set up at MARUM/University of Bremen, which combines lipid biomarker and elemental analysis at sub-mm resolution (down to 50 µm). We present methods for other comprehensive lipid biomarkers (e.g. alkenones or sterols) that are currently being targeted; and the application of spatially resolved biomarker analysis to recent laminated sediments (Santa Barbara Basin), yielding informative profiles with subannual resolution. We also discuss criteria for analyte and sample selection, as well as the main potentialities and constraints of this new approach.

  20. Distributed Physical and Molecular Separations for Selective Harvest of Higher Value Wheat Straw Components Project

    N/A

    2004-09-30

    Wheat straw (Triticum aestivum L.) is an abundant source of plant fiber. It is regenerated, in large quantities, every year. At present, this potentially valuable resource is greatly under-exploited. Most of the excess straw biomass (i.e., tonnage above that required for agronomic cropping system sustainability) is managed through expensive chopping/tillage operations and/or burnt in the field following harvest, resulting in air pollution and associated health problems. Potential applications for wheat straw investigated within this project include energy and composites manufacture. Other methods of straw utilization that will potentially benefit from the findings of this research project include housing and building, pulp and paper, thermal insulation, fuels, and chemicals. This project focused on components of the feedstock assembly system for supplying a higher value small grains straw residue for (1) gasification/combustion and (2) straw-thermoplastic composites. This project was an integrated effort to solve the technological, infrastructural, and economic challenges associated with using straw residue for these bioenergy and bioproducts applications. The objective of the research is to contribute to the development of a low-capital distributed harvesting and engineered storage system for upgrading wheat straw to more desirable feedstocks for combustion and for straw-plastic composites. They investigated two processes for upgrading wheat straw to a more desirable feedstock: (1) an efficient combine-based threshing system for separating the intermodal stems from the leaves, sheaths, nodes, and chaff. (2) An inexpensive biological process using white-rot fungi to improve the composition of the mechanically processed straw stems.

  1. Distributed Physical and Molecular Separations for Selective Harvest of Higher Value Wheat Straw Components Project

    Hess, J.R

    2005-01-31

    Wheat straw (Triticum aestivum L.) is an abundant source of plant fiber. It is regenerated, in large quantities, every year. At present, this potentially valuable resource is greatly under-exploited. Most of the excess straw biomass (i.e., tonnage above that required for agronomic cropping system sustainability) is managed through expensive chopping/tillage operations and/or burnt in the field following harvest, resulting in air pollution and associated health problems. Potential applications for wheat straw investigated within this project include energy and composites manufacture. Other methods of straw utilization that will potentially benefit from the findings of this research project include housing and building, pulp and paper, thermal insulation, fuels, and chemicals. This project focused on components of the feedstock assembly system for supplying a higher value small grains straw residue for (1) gasification/combustion and (2) straw-thermoplastic composites. This project was an integrated effort to solve the technological, infrastructural, and economic challenges associated with using straw residue for these bioenergy and bioproducts applications. The objective of the research is to contribute to the development of a low-capital distributed harvesting and engineered storage system for upgrading wheat straw to more desirable feedstocks for combustion and for straw-plastic composites. We investigated two processes for upgrading wheat straw to a more desirable feedstock: (1) An efficient combine-based threshing system for separating the internodal stems from the leaves, sheaths, nodes, and chaff. (2) An inexpensive biological process using white-rot fungi to improve the composition of the mechanically processed straw stems.

  2. Molecular characterization, genomic distribution and evolutionary dynamics of Short INterspersed Elements in the termite genome.

    Luchetti, Andrea; Mantovani, Barbara

    2011-02-01

    Short INterspersed Elements (SINEs) in invertebrates, and especially in animal inbred genomes such that of termites, are poorly known; in this paper we characterize three new SINE families (Talub, Taluc and Talud) through the analyses of 341 sequences, either isolated from the Reticulitermes lucifugus genome or drawn from EST Genbank collection. We further add new data to the only isopteran element known so far, Talua. These SINEs are tRNA-derived elements, with an average length ranging from 258 to 372 bp. The tails are made up by poly(A) or microsatellite motifs. Their copy number varies from 7.9 × 10(3) to 10(5) copies, well within the range observed for other metazoan genomes. Species distribution, age and target site duplication analysis indicate Talud as the oldest, possibly inactive SINE originated before the onset of Isoptera (~150 Myr ago). Taluc underwent to substantial sequence changes throughout the evolution of termites and data suggest it was silenced and then re-activated in the R. lucifugus lineage. Moreover, Taluc shares a conserved sequence block with other unrelated SINEs, as observed for some vertebrate and cephalopod elements. The study of genomic environment showed that insertions are mainly surrounded by microsatellites and other SINEs, indicating a biased accumulation within non-coding regions. The evolutionary dynamics of Talu~ elements is explained through selective mechanisms acting in an inbred genome; in this respect, the study of termites' SINEs activity may provide an interesting framework to address the (co)evolution of mobile elements and the host genome.

  3. Distinct distribution and prognostic significance of molecular subtypes of breast cancer in Chinese women: a population-based cohort study

    Cai Qiuyin

    2011-07-01

    Full Text Available Abstract Background Molecular classification of breast cancer is an important prognostic factor. The distribution of molecular subtypes of breast cancer and their prognostic value has not been well documented in Asians. Methods A total of 2,791 breast cancer patients recruited for a population-based cohort study were evaluated for molecular subtypes of breast cancer by immunohistochemical assays. Data on clinicopathological characteristics were confirmed by centralized pathology review. The average follow-up of the patients was 53.4 months. Overall and disease-free survival by molecular subtypes of breast cancer were evaluated. Results The prevalence of the luminal A, luminal B, human epidermal growth factor receptor 2 (HER2, and triple-negative subtypes were 48.6%, 16.7%, 13.7%, and 12.9%, respectively. The luminal A subtype was more likely to be diagnosed in older women (P = 0.03 and had a stronger correlation with favorable clinicopathological factors (smaller tumor size, lower histologic grade, and earlier TNM stage than the triple-negative or HER2 subtypes. Women with triple-negative breast cancer had a higher frequency of family history of breast cancer than women with other subtypes (P = 0.048. The 5-year overall/disease-free survival percentages for the luminal A, luminal B, HER2, and triple-negative subtypes were 92.9%/88.6%, 88.6%/85.1%, 83.2%/79.1%, and 80.7%/76.0%, respectively. A similar pattern was observed in multivariate analyses. Immunotherapy was associated with improved overall and disease-free survival for luminal A breast cancer, but reduced disease-free survival (HR = 2.21, 95% CI, 1.09-4.48 for the HER2 subtype of breast cancer. Conclusions The triple-negative and HER2 subtypes were associated with poorer outcomes compared with the luminal A subtype among these Chinese women. The HER2 subtype was more prevalent in this Chinese population compared with Western populations, suggesting the importance of standardized HER2

  4. Molecular simulation workflows as parallel algorithms: the execution engine of Copernicus, a distributed high-performance computing platform.

    Pronk, Sander; Pouya, Iman; Lundborg, Magnus; Rotskoff, Grant; Wesén, Björn; Kasson, Peter M; Lindahl, Erik

    2015-06-09

    Computational chemistry and other simulation fields are critically dependent on computing resources, but few problems scale efficiently to the hundreds of thousands of processors available in current supercomputers-particularly for molecular dynamics. This has turned into a bottleneck as new hardware generations primarily provide more processing units rather than making individual units much faster, which simulation applications are addressing by increasingly focusing on sampling with algorithms such as free-energy perturbation, Markov state modeling, metadynamics, or milestoning. All these rely on combining results from multiple simulations into a single observation. They are potentially powerful approaches that aim to predict experimental observables directly, but this comes at the expense of added complexity in selecting sampling strategies and keeping track of dozens to thousands of simulations and their dependencies. Here, we describe how the distributed execution framework Copernicus allows the expression of such algorithms in generic workflows: dataflow programs. Because dataflow algorithms explicitly state dependencies of each constituent part, algorithms only need to be described on conceptual level, after which the execution is maximally parallel. The fully automated execution facilitates the optimization of these algorithms with adaptive sampling, where undersampled regions are automatically detected and targeted without user intervention. We show how several such algorithms can be formulated for computational chemistry problems, and how they are executed efficiently with many loosely coupled simulations using either distributed or parallel resources with Copernicus.

  5. A molecular dynamics study on the oxygen diffusion in doped fluorites: the effect of the dopant distribution

    Tarancon, A. [M2E/XaRMAE/IREC, Department of Advanced Materials for Energy Applications, Catalonia Institute for Energy Research (IREC), Josep Pla 2, Torre 2, B2, 08019 Barcelona (Spain); Morata, A.; Peiro, F. [MIND/XaRMAE/IN2UB, Department of Electronics, University of Barcelona, Marti i Franques 1, 08028 Barcelona (Spain); Dezanneau, G. [Laboratoire Structures, Proprietes et Modelisation des Solides, Grande Voie des Vignes, Ecole Centrale Paris, F-92295 Chatenay-Malabry Cedex (France)

    2011-02-15

    The effect of the dopant distribution on the oxygen diffusion in doped fluorites typically used for solid oxide fuel cells electrolyte applications has been analysed by using molecular dynamics simulations. The oxygen mass transport in both yttria-stabilized zirconia (YSZ) and gadolinia-doped ceria has been studied and compared in the range of temperatures between 1,159 and 1,959 K. A new methodology based on the analysis of local environments is used to describe the diffusion process at an atomic scale. Preferred vacancy migration pathways, most suitable conduction models, energy landscapes and jump efficiency have been detailed for each material. Finally, a particular case of non-random distribution of dopants in YSZ is presented in order to quantitatively evaluate the effect of the dopant pattern on the mass transport properties and the potential of the methodology developed here for understanding and foreseeing real configurations at the nanoscale. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  6. Cytokine gene polymorphisms and their association with cervical ...

    Maneesh Kumar Gupta

    2015-11-17

    Nov 17, 2015 ... gene polymorphisms with cervical cancer in a north Indian population. Genotyping of ... diseases like coronary heart disease, breast cancer, cervical cancer etc ...... Environmental risk factors for prevention and molecular inter-.

  7. Role of nuclear dynamics in the asymmetric molecular-frame photoelectron angular distributions for C 1s photoejection from CO2

    Miyabe, S.; Haxton, D. J.; Rescigno, T. N.; McCurdy, C. W.

    2011-01-01

    We report the results of semiclassical calculations of the asymmetric molecular-frame photoelectron angular distributions for C 1s ionization of CO 2 measured with respect to the CO + and O + ions produced by subsequent Auger decay, and show how the decay event can be used to probe ultrafast molecular dynamics of the transient cation. The fixed-nuclei photoionization amplitudes were constructed using variationally obtained electron-molecular-ion scattering wave functions. The amplitudes are then used in a semiclassical manner to investigate their dependence on the nuclear dynamics of the cation. The method introduced here can be used to study other core-level ionization events.

  8. The influence of the rs6295 gene polymorphism on serotonin-1A receptor distribution investigated with PET in patients with major depression applying machine learning.

    Kautzky, A; James, G M; Philippe, C; Baldinger-Melich, P; Kraus, C; Kranz, G S; Vanicek, T; Gryglewski, G; Wadsak, W; Mitterhauser, M; Rujescu, D; Kasper, S; Lanzenberger, R

    2017-06-13

    Major depressive disorder (MDD) is the most common neuropsychiatric disease and despite extensive research, its genetic substrate is still not sufficiently understood. The common polymorphism rs6295 of the serotonin-1A receptor gene (HTR1A) is affecting the transcriptional regulation of the 5-HT 1A receptor and has been closely linked to MDD. Here, we used positron emission tomography (PET) exploiting advances in data mining and statistics by using machine learning in 62 healthy subjects and 19 patients with MDD, which were scanned with PET using the radioligand [carbonyl- 11 C]WAY-100635. All the subjects were genotyped for rs6295 and genotype was grouped in GG vs C allele carriers. Mixed model was applied in a ROI-based (region of interest) approach. ROI binding potential (BP ND ) was divided by dorsal raphe BP ND as a specific measure to highlight rs6295 effects (BP Div ). Mixed model produced an interaction effect of ROI and genotype in the patients' group but no effects in healthy controls. Differences of BP Div was demonstrated in seven ROIs; parahippocampus, hippocampus, fusiform gyrus, gyrus rectus, supplementary motor area, inferior frontal occipital gyrus and lingual gyrus. For classification of genotype, 'RandomForest' and Support Vector Machines were used, however, no model with sufficient predictive capability could be computed. Our results are in line with preclinical data, mouse model knockout studies as well as previous clinical analyses, demonstrating the two-pronged effect of the G allele on 5-HT 1A BP ND for, we believe, the first time. Future endeavors should address epigenetic effects and allosteric heteroreceptor complexes. Replication in larger samples of MDD patients is necessary to substantiate our findings.

  9. C2H6 scattering from LiF(0 0 1): Influence of the molecular anisotropy on rainbow scattering in both intensity and speed distributions

    Kondo, Takahiro; Tomii, Takashi; Yamamoto, Shigehiko

    2006-01-01

    We have measured the angle-resolved intensity and speed distributions of C 2 H 6 scattered from LiF(0 0 1) along the [1 0 0] azimuthal direction, the largest structural corrugation direction, to investigate the effect of the molecular anisotropy on the gas-surface interaction at the corrugated surface. While clear rainbow feature is observed in the mean energy angular distribution, no rainbow feature is detected in the intensity angular distribution. From the comparisons of the obtained results to the calculated predictions based on the simple classical theory of the ellipsoid-washboard model, the effect of the molecular anisotropy is found to play a crucial role in the rainbow feature. With an increase in the extent of the molecular anisotropy such as that of C 2 H 6 as compared with rare gas atoms, the integration of the intensity angular distributions for various molecular orientations results in the smearing of the rainbow feature on the corrugated surface. The rainbow scattering in the mean energy angular distribution, however, is not completely smeared out

  10. Effects of Abiotic Factors on the Geographic Distribution of Body Size Variation and Chromosomal Polymorphisms in Two Neotropical Grasshopper Species (Dichroplus: Melanoplinae: Acrididae

    Claudio J. Bidau

    2012-01-01

    Full Text Available We review the effects of abiotic factors on body size in two grasshopper species with large geographical distributions: Dichroplus pratensis and D. vittatus, inhabiting Argentina in diverse natural habitats. Geographical spans for both species provide an opportunity to study the effects of changes in abiotic factors on body size. The analyses of body size distribution in both species revealed a converse Bergmannian pattern: body size is positively correlated with latitude, altitude, and seasonality that influences time available for development and growth. Allen’s rule is also inverted. Morphological variability increases towards the ends of the Bergmannian clines and, in D. pratensis, is related with a central-marginal distribution of chromosomal variants that influence recombination. The converse Bergmannian patterns influence sexual size dimorphism in both species but in different fashions. Body size variation at a microspatial scale in D. pratensis is extremely sensitive to microclimatic clines. We finally compare our results with those for other Orthopteran species.

  11. Analytical and molecular dynamical investigations of the influence of molecular vibrations upon the (e,2e) electron momentum distributions of furan

    Morini, F; Deleuze, M S; Watanabe, N; Takahashi, M

    2015-01-01

    The role of molecular vibrations has been theoretically investigated in the electronic ground state on the (e, 2e) valence orbital momentum profiles of furan by means of two complementary approaches. The first one relies upon the principles of Born-Oppenheimer Molecular Dynamics (BOMD), whereas the second one, referred as Harmonic Analytical Quantum Mechanical (HAQM) approach, includes on quantum-mechanical (paper)

  12. Distribution of Brugia malayi larvae and DNA in vector and non-vector mosquitoes: implications for molecular diagnostics

    Christensen Bruce M

    2009-11-01

    Full Text Available Abstract Background The purpose of this study was to extend prior studies of molecular detection of Brugia malayi DNA in vector (Aedes aegypti- Liverpool and non-vector (Culex pipiens mosquitoes at different times after ingestion of infected blood. Results Parasite DNA was detected over a two week time course in 96% of pooled thoraces of vector mosquitoes. In contrast, parasite DNA was detected in only 24% of thorax pools from non-vectors; parasite DNA was detected in 56% of midgut pools and 47% of abdomen pools from non-vectors. Parasite DNA was detected in vectors in the head immediately after the blood meal and after 14 days. Parasite DNA was also detected in feces and excreta of the vector and non-vector mosquitoes which could potentially confound results obtained with field samples. However, co-housing experiments failed to demonstrate transfer of parasite DNA from infected to non-infected mosquitoes. Parasites were also visualized in mosquito tissues by immunohistololgy using an antibody to the recombinant filarial antigen Bm14. Parasite larvae were detected consistently after mf ingestion in Ae. aegypti- Liverpool. Infectious L3s were seen in the head, thorax and abdomen of vector mosquitoes 14 days after Mf ingestion. In contrast, parasites were only detected by histology shortly after the blood meal in Cx. pipiens, and these were not labeled by the antibody. Conclusion This study provides new information on the distribution of filarial parasites and parasite DNA in vector and non-vector mosquitoes. This information should be useful for those involved in designing and interpreting molecular xenomonitoring studies.

  13. DNA Repair Gene (XRCC1 Polymorphism (Arg399Gln Associated with Schizophrenia in South Indian Population: A Genotypic and Molecular Dynamics Study.

    S P Sujitha

    Full Text Available This paper depicts the first report from an Indian population on the association between the variant Arg399Gln of XRCC1 locus in the DNA repair system and schizophrenia, the debilitating disease that affects 1% of the world population. Genotypic analysis of a total of 523 subjects (260 patients and 263 controls revealed an overwhelming presence of Gln399Gln in the case subjects against the controls (P < 0.0068, indicating significant level of association of this nsSNP with schizophrenia; the Gln399 allele frequency was also perceptibly more in cases than in controls (p < 0.003; OR = 1.448. The results of the genotypic studies were further validated using pathogenicity and stability prediction analysis employing computational tools [I-Mutant Suite, iStable, PolyPhen2, SNAP, and PROVEAN], with a view toassess the magnitude of deleteriousness of the mutation. The pathogenicity analysis reveals that the nsSNP could be deleterious inasmuch as it could affect the functionality of the gene, and interfere with protein function. Molecular dynamics simulation of 60ns was performed using GROMACS to analyse structural change due to a mutation (Arg399Gln that was never examined before. RMSD, RMSF, hydrogen bonds, radius of gyration and SASA analysis showedthe existence of asignificant difference between the native and the mutant protein. The present study gives astrong indication that the XRCC1 locus deserves serious attention, as it could be a potential candidatecontributing to the etio-pathogenesis of the disease.

  14. Physical Selectivity of Molecularly Imprinted polymers evaluated through free volume size distributions derived from Positron Lifetime Spectroscopy

    Pasang, T.; Ranganathaiah, C.

    2015-06-01

    The technique of imprinting molecules of various sizes in a stable structure of polymer matrix has derived multitudes of applications. Once the template molecule is extracted from the polymer matrix, it leaves behind a cavity which is physically (size and shape) and chemically (functional binding site) compatible to the particular template molecule. Positron Annihilation Lifetime Spectroscopy (PALS) is a well known technique to measure cavity sizes precisely in the nanoscale and is not being used in the field of MIPs effectively. This method is capable of measuring nanopores and hence suitable to understand the physical selectivity of the MIPs better. With this idea in mind, we have prepared molecular imprinted polymers (MIPs) with methacrylicacid (MAA) as monomer and EGDMA as cross linker in different molar ratio for three different size template molecules, viz. 4-Chlorophenol (4CP)(2.29 Å), 2-Nephthol (2NP) (3.36 Å) and Phenolphthalein (PP) (4.47Å). FTIR and the dye chemical reactions are used to confirm the complete extraction of the template molecules from the polymer matrix. The free volume size and its distribution have been derived from the measured o-Ps lifetime spectra. Based on the free volume distribution analysis, the percentage of functional cavities for the three template molecules are determined. Percentage of functional binding cavities for 4-CP molecules has been found out to be 70.2% and the rest are native cavities. Similarly for 2NP it is 81.5% and nearly 100% for PP. Therefore, PALS method proves to be very precise and accurate for determining the physical selectivity of MIPs.

  15. THE HERSCHEL EXPLOITATION OF LOCAL GALAXY ANDROMEDA (HELGA). VI. THE DISTRIBUTION AND PROPERTIES OF MOLECULAR CLOUD ASSOCIATIONS IN M31

    Kirk, J. M. [Jeremiah Horrocks Institute, University of Central Lancashire, Preston PR1 2HE (United Kingdom); Gear, W. K.; Smith, M. W. L.; Ford, G.; Eales, S. A.; Gomez, H. L. [School of Physics and Astronomy, Cardiff University, Queens Buildings, The Parade, Cardiff, Wales CF24 3AA (United Kingdom); Fritz, J.; Baes, M.; De Looze, I.; Gentile, G.; Gordon, K.; Verstappen, J.; Viaene, S. [Sterrenkundig Observatorium, Universiteit Gent, Krijgslaan 281 S9, B-9000 Gent (Belgium); Bendo, G. J. [UK ALMA Regional Centre Node, Jodrell Bank Centre for Astrophysics, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL (United Kingdom); O' Halloran, B. [Astrophysics Group, Imperial College, Blackett Laboratory, Prince Consort Road, London SW7 2AZ (United Kingdom); Madden, S. C.; Lebouteiller, V. [Laboratoire AIM, CEA/DSM-CNRS-Université Paris Diderot, Irfu/Service, Paris, F-91190 Gif-sur-Yvette (France); Roman-Duval, J. [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Boselli, A. [Laboratoire d' Astrophysique de Marseille, UMR 7326 CNRS, 38 rue F. Joliot-Curie, F-13388 Marseille (France); Cooray, A. [Department of Physics and Astronomy, University of California, Irvine, CA 92697 (United States); and others

    2015-01-01

    In this paper we present a catalog of giant molecular clouds (GMCs) in the Andromeda (M31) galaxy extracted from the Herschel Exploitation of Local Galaxy Andromeda (HELGA) data set. GMCs are identified from the Herschel maps using a hierarchical source extraction algorithm. We present the results of this new catalog and characterize the spatial distribution and spectral energy properties of its clouds based on the radial dust/gas properties found by Smith et al. A total of 326 GMCs in the mass range 10{sup 4}-10{sup 7} M {sub ☉} are identified; their cumulative mass distribution is found to be proportional to M {sup –2.34}, in agreement with earlier studies. The GMCs appear to follow the same correlation of cloud mass to L {sub CO} observed in the Milky Way. However, comparison between this catalog and interferometry studies also shows that the GMCs are substructured below the Herschel resolution limit, suggesting that we are observing associations of GMCs. Following Gordon et al., we study the spatial structure of M31 by splitting the observed structure into a set of spiral arms and offset rings. We fit radii of 10.3 and 15.5 kpc to the two most prominent rings. We then fit a logarithmic spiral with a pitch angle of 8.°9 to the GMCs not associated with either ring. Last, we comment on the effects of deprojection on our results and investigate the effect different models for M31's inclination will have on the projection of an unperturbed spiral arm system.

  16. Amino Acid Profile, Group of Functional and Molecular Weight Distribution of Goat Skin Gelatin That Produced Through Acid Process

    Muhammad Irfan Said

    2012-02-01

    Full Text Available Gelatin is a product of hydrolysis of collagen protein from animals that are partially processed.  Gelatin used in food and non food industries.  Gelatin is produced when many import of raw skins and bones of pigs and cows.  Goat skins potential as a raw material substitution that still doubt its halal. Process production of gelatin determine the properties of gelatin. The objectives of this research were to determine amino acid profile, group of functional and molecular weight distribution of gelatin made from goat skins which was produced through a process of acid. The skin of male Bligon goat, 1.5 to 2.5 year old was used as raw materials. Process production of gelatin was using acid type acetic acid (CH3COOH 0.5 M (v/v as curing material. The experimental design applied in this study and commercial gelatin was used as control. The results showed that gelatin produced from goat skin through the process of acid had properties identical with commercial gelatin. It can be concluded that the gelatin has the potential substitute product of commercial gelatin. Keywords: collagen, gelatin, goat skin, curing, acid process

  17. Molecular and morphological systematics of the Ellisellidae (Coelenterata: Octocorallia): Parallel evolution in a globally distributed family of octocorals

    Bilewitch, Jaret P.

    2014-04-01

    The octocorals of the Ellisellidae constitute a diverse and widely distributed family with subdivisions into genera based on colonial growth forms. Branching patterns are repeated in several genera and congeners often display region-specific variations in a given growth form. We examined the systematic patterns of ellisellid genera and the evolution of branching form diversity using molecular phylogenetic and ancestral morphological reconstructions. Six of eight included genera were found to be polyphyletic due to biogeographical incompatibility with current taxonomic assignments and the creation of at least six new genera plus several reassignments among existing genera is necessary. Phylogenetic patterns of diversification of colony branching morphology displayed a similar transformation order in each of the two primary ellisellid clades, with a sea fan form estimated as the most-probable common ancestor with likely origins in the Indo-Pacific region. The observed parallelism in evolution indicates the existence of a constraint on the genetic elements determining ellisellid colonial morphology. However, the lack of correspondence between levels of genetic divergence and morphological diversity among genera suggests that future octocoral studies should focus on the role of changes in gene regulation in the evolution of branching patterns. © 2014 Elsevier Inc.

  18. Molecular and morphological systematics of the Ellisellidae (Coelenterata: Octocorallia): Parallel evolution in a globally distributed family of octocorals

    Bilewitch, Jaret P.; Ekins, Merrick; Hooper, John; Degnan, Sandie M.

    2014-01-01

    The octocorals of the Ellisellidae constitute a diverse and widely distributed family with subdivisions into genera based on colonial growth forms. Branching patterns are repeated in several genera and congeners often display region-specific variations in a given growth form. We examined the systematic patterns of ellisellid genera and the evolution of branching form diversity using molecular phylogenetic and ancestral morphological reconstructions. Six of eight included genera were found to be polyphyletic due to biogeographical incompatibility with current taxonomic assignments and the creation of at least six new genera plus several reassignments among existing genera is necessary. Phylogenetic patterns of diversification of colony branching morphology displayed a similar transformation order in each of the two primary ellisellid clades, with a sea fan form estimated as the most-probable common ancestor with likely origins in the Indo-Pacific region. The observed parallelism in evolution indicates the existence of a constraint on the genetic elements determining ellisellid colonial morphology. However, the lack of correspondence between levels of genetic divergence and morphological diversity among genera suggests that future octocoral studies should focus on the role of changes in gene regulation in the evolution of branching patterns. © 2014 Elsevier Inc.

  19. The Dirac Equation in the algebraic approximation. VII. A comparison of molecular finite difference and finite basis set calculations using distributed Gaussian basis sets

    Quiney, H. M.; Glushkov, V. N.; Wilson, S.; Sabin,; Brandas, E

    2001-01-01

    A comparison is made of the accuracy achieved in finite difference and finite basis set approximations to the Dirac equation for the ground state of the hydrogen molecular ion. The finite basis set calculations are carried out using a distributed basis set of Gaussian functions the exponents and

  20. Characterization of the molecular distribution of drugs in glassy solid dispersions at the nano-meter scale, using differential scanning calorimetry and gravimetric water vapour sorption techniques

    van Drooge, D J; Hinrichs, W L J; Visser, M R; Frijlink, H W

    2006-01-01

    The molecular distribution in fully amorphous solid dispersions consisting of poly(vinylpyrrolidone) (PVP)-diazepam and inulin-diazepam was studied. One glass transition temperature (T-g), as determined by temperature modulated differential scanning calorimetry (TMDSC), was observed in PVP-diazepam

  1. A revised mechanism for the activation of complement C3 to C3b: a molecular explanation of a disease-associated polymorphism.

    Rodriguez, Elizabeth; Nan, Ruodan; Li, Keying; Gor, Jayesh; Perkins, Stephen J

    2015-01-23

    The solution structure of complement C3b is crucial for the understanding of complement activation and regulation. C3b is generated by the removal of C3a from C3. Hydrolysis of the C3 thioester produces C3u, an analog of C3b. C3b cleavage results in C3c and C3d (thioester-containing domain; TED). To resolve functional questions in relation to C3b and C3u, analytical ultracentrifugation and x-ray and neutron scattering studies were used with C3, C3b, C3u, C3c, and C3d, using the wild-type allotype with Arg(102). In 50 mm NaCl buffer, atomistic scattering modeling showed that both C3b and C3u adopted a compact structure, similar to the C3b crystal structure in which its TED and macroglobulin 1 (MG1) domains were connected through the Arg(102)-Glu(1032) salt bridge. In physiological 137 mm NaCl, scattering modeling showed that C3b and C3u were both extended in structure, with the TED and MG1 domains now separated by up to 6 nm. The importance of the Arg(102)-Glu(1032) salt bridge was determined using surface plasmon resonance to monitor the binding of wild-type C3d(E1032) and mutant C3d(A1032) to immobilized C3c. The mutant did not bind, whereas the wild-type form did. The high conformational variability of TED in C3b in physiological buffer showed that C3b is more reactive than previously thought. Because the Arg(102)-Glu(1032) salt bridge is essential for the C3b-Factor H complex during the regulatory control of C3b, the known clinical associations of the major C3S (Arg(102)) and disease-linked C3F (Gly(102)) allotypes of C3b were experimentally explained for the first time. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Comparative distribution of Lysyl Oxidase (G473A and NQO1 (C609T polymorphism among tea-garden workers (habitual chewers of betel quid of Darjeeling district and Kolkata city of West Bengal

    Jay Gopal Ray

    2013-01-01

    Full Text Available Context: Chewing of processed arecanut products with tobacco and betel quid has been attributed to many oral pathological conditions. These products are very popular among the youngsters of lower economic groups. Genetic predisposition has been now identified as a major risk factor for increasing the susceptibility toward the disease among these chewers. Aims: Our study mainly aims to find out the predisposition of LOX (G473A and NQO1 (C609T polymorphisms and present a comparison between the population (habitually exposed to processed arecanut and smokeless tobacco products of a metro-city Kolkata and the tea-garden workers of Darjeeling district of West Bengal. Settings and Design: Subjects for the study was recruited from various oral health check-up camps organized in the tea-gardens of Darjeeling district and Kolkata city. Materials and Methods: Genotyping analysis was done through a Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP-based approach. Statistical Analysis Used: A two-way contingency table analysis software (JAVASTAT: http://statpages.org/ctab2 × 2.html using 95% confidence interval was used to study the distribution of genotypes among the populations. A P T (609 was found to be significantly higher among the north Bengal tea-garden workers [OR 0.480 (0.280-0.82 P = 0.01; 0.218 (0.091-0.524 P = 0.0001], respectively. Interestingly CT (21% in both and TT (8% and 7%, respectively were found to be equally distributed in the two populations. For LOX G > A (473 a significantly higher number of Kolkata individuals were found to carry the heterozygous GA allele in individuals aged <30 years [OR 3.779 (1.684-6.547 P = 0.001]. However, none were carrier of heterozygous GA allele of Kolkata population as compared with 29% north Bengal tea-garden workers aged above 31 years. Conclusions: A close observation of occurrence of oral diseases over time among such a population will be helpful to identify risk

  3. Simple, Low-Cost Detection of Candida parapsilosis Complex Isolates and Molecular Fingerprinting of Candida orthopsilosis Strains in Kuwait by ITS Region Sequencing and Amplified Fragment Length Polymorphism Analysis.

    Asadzadeh, Mohammad; Ahmad, Suhail; Hagen, Ferry; Meis, Jacques F; Al-Sweih, Noura; Khan, Ziauddin

    2015-01-01

    Candida parapsilosis has now emerged as the second or third most important cause of healthcare-associated Candida infections. Molecular studies have shown that phenotypically identified C. parapsilosis isolates represent a complex of three species, namely, C. parapsilosis, C. orthopsilosis and C. metapsilosis. Lodderomyces elongisporus is another species phenotypically closely related to the C. parapsilosis-complex. The aim of this study was to develop a simple, low cost multiplex (m) PCR assay for species-specific identification of C. parapsilosis complex isolates and to study genetic relatedness of C. orthopsilosis isolates in Kuwait. Species-specific amplicons from C. parapsilosis (171 bp), C. orthopsilosis (109 bp), C. metapsilosis (217 bp) and L. elongisporus (258 bp) were obtained in mPCR. Clinical isolates identified as C. parapsilosis (n = 380) by Vitek2 in Kuwait and an international collection of 27 C. parapsilosis complex and L. elongisporus isolates previously characterized by rDNA sequencing were analyzed to evaluate mPCR. Species-specific PCR and DNA sequencing of internal transcribed spacer (ITS) region of rDNA were performed to validate the results of mPCR. Fingerprinting of 19 clinical C. orthopsilosis isolates (including 4 isolates from a previous study) was performed by amplified fragment length polymorphism (AFLP) analysis. Phenotypically identified C. parapsilosis isolates (n = 380) were identified as C. parapsilosis sensu stricto (n = 361), C. orthopsilosis (n = 15), C. metapsilosis (n = 1) and L. elongisporus (n = 3) by mPCR. The mPCR also accurately detected all epidemiologically unrelated C. parapsilosis complex and L. elongisporus isolates. The 19 C. orthopsilosis isolates obtained from 16 patients were divided into 3 haplotypes based on ITS region sequence data. Seven distinct genotypes were identified among the 19 C. orthopsilosis isolates by AFLP including a dominant genotype (AFLP1) comprising 11 isolates recovered from 10 patients. A

  4. Polymorphous computing fabric

    Wolinski, Christophe Czeslaw [Los Alamos, NM; Gokhale, Maya B [Los Alamos, NM; McCabe, Kevin Peter [Los Alamos, NM

    2011-01-18

    Fabric-based computing systems and methods are disclosed. A fabric-based computing system can include a polymorphous computing fabric that can be customized on a per application basis and a host processor in communication with said polymorphous computing fabric. The polymorphous computing fabric includes a cellular architecture that can be highly parameterized to enable a customized synthesis of fabric instances for a variety of enhanced application performances thereof. A global memory concept can also be included that provides the host processor random access to all variables and instructions associated with the polymorphous computing fabric.

  5. Distribution of knock-down resistance mutations in Anopheles gambiae molecular forms in west and west-central Africa

    Caccone Adalgisa

    2008-04-01

    Full Text Available Abstract Background Knock-down resistance (kdr to DDT and pyrethroids in the major Afrotropical vector species, Anopheles gambiae sensu stricto, is associated with two alternative point mutations at amino acid position 1014 of the voltage-gated sodium channel gene, resulting in either a leucine-phenylalanine (L1014F, or a leucine-serine (L1014S substitution. In An. gambiae S-form populations, the former mutation appears to be widespread in west Africa and has been recently reported from Uganda, while the latter, originally recorded in Kenya, has been recently found in Gabon, Cameroon and Equatorial Guinea. In M-form populations surveyed to date, only the L1014F mutation has been found, although less widespread and at lower frequencies than in sympatric S-form populations. Methods Anopheles gambiae M- and S-form specimens from 19 sites from 11 west and west-central African countries were identified to molecular form and genotyped at the kdr locus either by Hot Oligonucleotide Ligation Assay (HOLA or allele-specific PCR (AS-PCR. Results The kdr genotype was determined for about 1,000 An. gambiae specimens. The L1014F allele was found at frequencies ranging from 6% to 100% in all S-form samples (N = 628, with the exception of two samples from Angola, where it was absent, and coexisted with the L1014S allele in samples from Cameroon, Gabon and north-western Angola. The L1014F allele was present in M-form samples (N = 354 from Benin, Nigeria, and Cameroon, where both M- and S-forms were sympatric. Conclusion The results represent the most comprehensive effort to analyse the overall distribution of the L1014F and L1014S mutations in An. gambiae molecular forms, and will serve as baseline data for resistance monitoring. The overall picture shows that the emergence and spread of kdr alleles in An. gambiae is a dynamic process and that there is marked intra- and inter-form heterogeneity in resistance allele frequencies. Further studies are needed to

  6. Polymorphs and polymorphic cocrystals of temozolomide.

    Babu, N Jagadeesh; Reddy, L Sreenivas; Aitipamula, Srinivasulu; Nangia, Ashwini

    2008-07-07

    Crystal polymorphism in the antitumor drug temozolomide (TMZ), cocrystals of TMZ with 4,4'-bipyridine-N,N'-dioxide (BPNO), and solid-state stability were studied. Apart from a known X-ray crystal structure of TMZ (form 1), two new crystalline modifications, forms 2 and 3, were obtained during attempted cocrystallization with carbamazepine and 3-hydroxypyridine-N-oxide. Conformers A and B of the drug molecule are stabilized by intramolecular amide N--HN(imidazole) and N--HN(tetrazine) interactions. The stable conformer A is present in forms 1 and 2, whereas both conformers crystallized in form 3. Preparation of polymorphic cocrystals I and II (TMZBPNO 1:0.5 and 2:1) were optimized by using solution crystallization and grinding methods. The metastable nature of polymorph 2 and cocrystal II is ascribed to unused hydrogen-bond donors/acceptors in the crystal structure. The intramolecularly bonded amide N-H donor in the less stable structure makes additional intermolecular bonds with the tetrazine C==O group and the imidazole N atom in stable polymorph 1 and cocrystal I, respectively. All available hydrogen-bond donors and acceptors are used to make intermolecular hydrogen bonds in the stable crystalline form. Synthon polymorphism and crystal stability are discussed in terms of hydrogen-bond reorganization.

  7. Molecular dynamics study of the role of symmetric tilt grain boundaries on the helium distribution in nickel

    Torres, E.; Pencer, J.

    2018-04-01

    Helium impurities, from either direct implantation or transmutation reactions, have been associated with embrittlement in nickel-based alloys. Helium has very low solubility in nickel, and has been found to aggregate at lattice defects such as vacancies, dislocations, and grain boundaries. The retention and precipitation of helium in nickel-based alloys have deleterious effects on the material mechanical properties. However, the underlying mechanisms that lead to helium effects in the host metal are not fully understood. In the present work, we investigate the role of symmetric tilt grain boundary (STGB) structures on the distribution of helium in nickel using molecular dynamics simulations. We investigate the family of STGBs specific to the 〈 110 〉 tilt axis. The present results indicate that accumulation of helium at the grain boundary may be modulated by details of grain boundary geometry. A plausible correlation between the grain boundary energy and misorientation with the accumulation and mobility of helium is proposed. Small clusters with up to 6 helium atoms show significant interstitial mobility in the nickel bulk, but also become sites for nucleation and grow of more stable helium clusters. High-energy GBs are found mainly populated with small helium clusters. The high mobility of small clusters along the GBs indicates the role of these GBs as fast two-dimensional channels for diffusion. In contrast, the accumulation of helium in large helium clusters at low-energy STGB creates a favorable environment for the formation of large helium bubbles, indicating a potential role for low-energy STGB in promoting helium-induced GB embrittlement.

  8. Association of ACE and MDR1 Gene Polymorphisms with Steroid Resistance in Children with Idiopathic Nephrotic Syndrome.

    Dhandapani, Mohanapriya Chinambedu; Venkatesan, Vettriselvi; Rengaswamy, Nammalwar Bollam; Gowrishankar, Kalpana; Nageswaran, Prahlad; Perumal, Venkatachalam

    2015-08-01

    The purpose of the study was to investigate the distribution of insertion/deletion (I/D) polymorphisms of the angiotensin-converting enzyme (ACE) gene and three exonic polymorphisms of the multidrug resistance 1 (MDR1) gene (C3435T, C1236T, and G2677T) in children diagnosed with idiopathic nephrotic syndrome (INS). The study group consisted of 100 healthy controls and 150 INS patients, of which 50 were steroid resistant. Genomic DNA from blood samples was isolated from both of these groups and genotyping of the ACE and MDR1 genes was performed by polymerase chain reaction (PCR) using specific primers. There was no significant difference observed in the genotypic distribution and D allele frequency of the ACE gene. The two single-nucleotide polymorphisms (SNPs), C1236T and C3435T, of the MDR1 gene showed no significance, whereas the SNP G2677T/A was significantly associated with the genotypes GT and GA of the MDR1 gene, indicating it may be a potential marker to detect drug resistance. Screening these polymorphisms will pave the way to better understand the molecular mechanisms of the disease, which may be useful in developing targeted therapies for INS patients.

  9. IS6110 restriction fragment length polymorphism of Mycobacterium tuberculosis isolated from patients with pulmonary tuberculosis in Campinas, Brazil: evidence of intercontinental distribution of strains

    Ana Lucia Roscani Calusni

    2003-07-01

    Full Text Available Tuberculosis (TB is a major concern in developing countries. In Brazil, few genotyping studies have been conducted to verify the number of IS6110 copies present in local prevalent strains of Mycobacterium tuberculosis, the distribution and clustering of strains. IS6110 DNA fingerprinting was performed on a sample of M. tuberculosis isolates from patients with AFB smear-positive pulmonary TB, at a hospital in Brazil. The IS6110 profiles were analyzed and compared to a M. tuberculosis database of the Houston Tuberculosis Initiative, Houston, US. Seventy-six fingerprints were obtained from 98 patients. All M. tuberculosis strains had an IS6110 copy number between 5-21 allowing for differentiation of the isolates. Human immunodeficiency virus infection was confirmed in nearly half the patients of whom data was available. Fifty-eight strains had unique patterns, while 17 strains were grouped in 7 clusters (2 to 6 strains. When compared to the HTI database, 6 strains matched isolates from El Paso, Ciudad de Juarez, Houston, and New York. Recently acquired infections were documented in 19% of cases. The community transmission of infection is intense, since some clustered strains were recovered during the four-year study period. The intercontinental dissemination of M. tuberculosis strains is suspected by demonstration of identical fingerprints in a distant country.

  10. The Atmospheric Distribution of Molecular Hydrogen (H2) and Related Species During HIPPO and Other Recent Airborne Missions

    Hintsa, E. J.; Moore, F. L.; Dutton, G. S.; Hall, B. D.; Nance, J. D.; Hurst, D. F.; Novelli, P. C.; Elkins, J. W.; Daube, B.; Kort, E. A.; Pittman, J. V.; Santoni, G. W.; Wofsy, S. C.; Jaegle, L.

    2012-12-01

    focus here is on the distribution of molecular hydrogen (H2), which has a diverse set of atmospheric and terrestrial sources, and a sink term that is dominated by soil uptake. The data show a slight maximum in the southern hemisphere and much greater variability with altitude in the northern hemisphere, broadly consistent with previous studies. Results from the GEOS-Chem model will be presented to allow greater insight into the distribution of H2 and related molecules. Tracer-tracer correlation plots of H2 with methane and CO will also be used to examine the details of the H2 distribution. HIPPO results show a local maximum in H2 at northern hemisphere midlatitudes in spring and early summer, and persistent low values of hydrogen at high northern latitudes long after the soil sink should have decreased with the onset of winter.

  11. The pattern of polymorphism in Arabidopsis thaliana.

    2005-07-01

    Full Text Available We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics.

  12. Phenotypic characterisation and molecular polymorphism of ...

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    2010-01-18

    Jan 18, 2010 ... The genetic resources of poultry in West Africa are mainly represented ... The Forest area of Benin has a subequatorial climate with 2 dry seasons and 2 ...... African, Asian and South American local chickens. Anim. Genet. 31:.

  13. Phenotypic characterisation and molecular polymorphism of ...

    PRECIOUS

    2010-01-18

    Jan 18, 2010 ... tance, the local production of poultry meat is below the needs expressed by the .... cultivated land per farmer was also greater on average in ...... 1st Conference of the UAC of Sciences, Cultures and Technologies, from the 25 ...

  14. Molecular characterization, polymorphism of growth differentiation ...

    USER

    2010-08-16

    Aug 16, 2010 ... Growth differentiation factor 5 (GDF5), involved in the development and maintenance of bone and cartilage ... mice playing a crucial role in the morphogenesis of .... using a Wizard Prep PCR purification kit (Shanghai Bioasia.

  15. The spectral distribution of intermediate L-K molecular-orbital radiation in symmetric heavy-ion collisions

    Heinig, K.-H.; Jager, H.-U.; Richter, H.; Woittennek, H.; Frank, W.; Gippener, P.; Kaun, K.-H.; Manfrass, P.

    1977-01-01

    Two distinct x-ray continua C1 and C2 above the characteristic lines are observed in high-energy collisions between atoms with atomic numbers of 28 to 57. This structure is explained by a superposition of K molecular-orbital (KMO) radiation and of an intermediate L-K molecular-orbital (ILKMO) radiation of high intensity which is due to 2psigma vacancies. In the framework of the dynamical theory of intermediate molecular phenomena and using a scaling of the H 2 + correlation diagram with screened state-dependent charges good agreement between the shapes of the measured and calculated spectra is obtained. (author)

  16. Peroxisome proliferator activated receptor gamma polymorphism Pro12Ala in polycystic ovary syndrome (PCOS of South Indian Population

    Raichel Jacob

    2016-05-01

    Conclusion: PPARγ2 gene Pro12Ala polymorphism was supposed to be susceptible genes in PCOS. The present study demonstrated that there is a statistical difference between the distributions of PPAR gamma Pro12Ala polymorphism in South Indian Population.

  17. An ancestral human genetic variant linked to an ancient disease: A novel association of FMO2 polymorphisms with tuberculosis (TB in Ethiopian populations provides new insight into the differential ethno-geographic distribution of FMO2*1.

    Ephrem Mekonnen

    Full Text Available The human FMO2 (flavin-containing monooxygenase 2 gene has been shown to be involved in innate immunity against microbial infections, including tuberculosis (TB, via the modulation of oxidative stress levels. It has also been found to possess a curious loss-of-function mutation (FMO2*1/FMO2*2 that demonstrates a distinctive differentiation in expression, function and ethno-geographic distribution. However, despite evidences of ethnic-specific genetic associations in the inflammatory profile of TB, no studies were done to investigate whether these patterns of variations correlate with evidences for the involvement of FMO2 in antimicrobial immune responses and ethnic differences in the distribution of FMO2 polymorphisms except for some pharmacogenetic data that suggest a potentially deleterious role for the functional variant (FMO2*1. This genetic epidemiological study was designed to investigate whether there is an association between FMO2 polymorphisms and TB, an ancient malady that remains a modern global health concern, in a sub-Saharan Africa setting where there is not only a relatively high co-prevalence of the disease and the ancestral FMO2*1 variant but also where both Mycobcaterium and Homo sapiens are considered to have originated and co-evolved. Blood samples and TB related clinical data were collected from ascertained TB cases and unrelated household controls (n = 292 from 3 different ethnic groups in Ethiopia. Latent Mtb infection was determined using Quantiferon to develop reliable TB progression phenotypes. We sequenced exonic regions of FMO2.We identified for the first time an association between FMO2 and TB both at the SNP and haplotype level. Two novel SNPs achieved a study-wide significance [chr1:171181877(A, p = 3.15E-07, OR = 4.644 and chr1:171165749(T, p = 3.32E-06, OR = 6.825] while multiple SNPs (22 showed nominal signals. The pattern of association suggested a protective effect of FMO2 against both active and latent TB

  18. Evolution of finger millet: evidence from random amplified polymorphic DNA.

    Hilu, K W

    1995-04-01

    Finger millet (Eleusine coracana ssp. coracana) is an annual tetraploid member of a predominantly African genus. The crop is believed to have been domesticated from the tetraploid E. coracana ssp. africana. Cytogenetic and isozyme data point to the allopolyploid nature of the species and molecular information has shown E. indica to be one of the genomic donors. A recent isozyme study questioned the proposed phylogenetic relationship between finger millet and its direct ancestor subspecies africana. An approach using random amplified polymorphic DNA (RAPD) was employed in this study to examine genetic diversity and to evaluate hypotheses concerning the evolution of domesticated and wild annual species of Eleusine. Unlike previous molecular approaches, the RAPD study revealed genetic diversity in the crop. The pattern of genetic variation was loosely correlated to geographic distribution. The allotetraploid nature of the crop was confirmed and molecular markers that can possibly identify the other genomic donor were proposed. Genotypes of subspecies africana did not group closely with those of the crop but showed higher affinities to E. indica, reflecting the pattern of similarity revealed by the isozyme study. The multiple origin of subspecies africana could explain the discrepancy between the isozyme-RAPD evidence and previous information. The RAPD study showed the close genetic affinity of E. tristachya to the E. coracana--E. indica group and understood the distinctness of E. multiflora.

  19. Characterization of the molecular distribution of drugs in glassy solid dispersions at the nano-meter scale, using differential scanning calorimetry and gravimetric water vapour sorption techniques.

    van Drooge, D J; Hinrichs, W L J; Visser, M R; Frijlink, H W

    2006-03-09

    The molecular distribution in fully amorphous solid dispersions consisting of poly(vinylpyrrolidone) (PVP)-diazepam and inulin-diazepam was studied. One glass transition temperature (T(g)), as determined by temperature modulated differential scanning calorimetry (TMDSC), was observed in PVP-diazepam solid dispersions prepared by fusion for all drug loads tested (10-80 wt.%). The T(g) of these solid dispersions gradually changed with composition and decreased from 177 degrees C for pure PVP to 46 degrees C for diazepam. These observations indicate that diazepam was dispersed in PVP on a molecular level. However, in PVP-diazepam solid dispersions prepared by freeze drying, two T(g)'s were observed for drug loads above 35 wt.% indicating phase separation. One T(g) indicated the presence of amorphous diazepam clusters, the other T(g) was attributed to a PVP-rich phase in which diazepam was dispersed on a molecular level. With both the value of the latter T(g) and the DeltaC(p) of the diazepam glass transition the concentrations of molecular dispersed diazepam could be calculated (27-35 wt.%). Both methods gave similar results. Water vapour sorption (DVS) experiments revealed that the PVP-matrix was hydrophobised by the incorporated diazepam. TMDSC and DVS results were used to estimate the size of diazepam clusters in freeze dried PVP-diazepam solid dispersions, which appeared to be in the nano-meter range. The inulin-diazepam solid dispersions prepared by spray freeze drying showed one T(g) for drug loads up to 35 wt.% indicating homogeneous distribution on a molecular level. However, this T(g) was independent of the drug load, which is unexpected because diazepam has a lower T(g) than inulin (46 and 155 degrees C, respectively). For higher drug loads, a T(g) of diazepam as well as a T(g) of the inulin-rich phase was observed, indicating the formation of amorphous diazepam clusters. From the DeltaC(p) of the diazepam glass transition the amount of molecularly dispersed

  20. Molecular epidemiology of Blastocystis

    Fadime Eroğlu

    2015-12-01

    Full Text Available Blastocystis pathogenicity and classification was newly illuminated with molecular genetic studies and recently the parasite was found in the focus of many researchers. Several molecular methods such as; polymerase chain reaction (PCR, PCR-restriction fragment length polymorphism, random amplified polymorphic DNA, real-time polymerase chain reaction and DNA sequencing analyses can be used in genotyping of Blastocystis. Blastocystis parasites may cause diarrhea, abdominal pain, bloating, gas, irritability, anorexia, cramps, vomiting, dehydration, insomnia, nausea, loss of appetite, weight loss, fatigue symptoms and also could be asymptomatic cases. In this review, it was aimed to summarize the associations between Blastocystis subtypes and pathogenicity.

  1. Understanding polymorphism in organic semiconductor thin films through nanoconfinement.

    Diao, Ying; Lenn, Kristina M; Lee, Wen-Ya; Blood-Forsythe, Martin A; Xu, Jie; Mao, Yisha; Kim, Yeongin; Reinspach, Julia A; Park, Steve; Aspuru-Guzik, Alán; Xue, Gi; Clancy, Paulette; Bao, Zhenan; Mannsfeld, Stefan C B

    2014-12-10

    Understanding crystal polymorphism is a long-standing challenge relevant to many fields, such as pharmaceuticals, organic semiconductors, pigments, food, and explosives. Controlling polymorphism of organic semiconductors (OSCs) in thin films is particularly important given that such films form the active layer in most organic electronics devices and that dramatic changes in the electronic properties can be induced even by small changes in the molecular packing. However, there are very few polymorphic OSCs for which the structure-property relationships have been elucidated so far. The major challenges lie in the transient nature of metastable forms and the preparation of phase-pure, highly crystalline thin films for resolving the crystal structures and evaluating the charge transport properties. Here we demonstrate that the nanoconfinement effect combined with the flow-enhanced crystal engineering technique is a powerful and likely material-agnostic method to identify existing polymorphs in OSC materials and to prepare the individual pure forms in thin films at ambient conditions. With this method we prepared high quality crystal polymorphs and resolved crystal structures of 6,13-bis(triisopropylsilylethynyl)pentacene (TIPS-pentacene), including a new polymorph discovered via in situ grazing incidence X-ray diffraction and confirmed by molecular mechanic simulations. We further correlated molecular packing with charge transport properties using quantum chemical calculations and charge carrier mobility measurements. In addition, we applied our methodology to a [1]benzothieno[3,2-b][1]1benzothiophene (BTBT) derivative and successfully stabilized its metastable form.

  2. Cystathionine β-synthase T833C/844INS68 polymorphism: a family-based study on mentally retarded children

    Mukhopadhyay Jotideb

    2005-12-01

    Full Text Available Abstract Background Cystathionine β-synthase (CBS mediates conversion of homocysteine to cystathionine and deficiency in enzyme activity may lead to hyperhomocysteinemia/homocystinuria, which are often associated with mental retardation (MR. A large number of polymorphisms have been reported in the CBS gene, some of which impair its activity and among these, a T833C polymorphism in cis with a 68 bp insertion at 844 in the exon 8 is found to be associated with mild hyperhomocysteinemia in different ethnic groups. Methods The present study is aimed at investigating the association between T833C/844ins68 polymorphism and MR. One hundred and ninety MR cases were recruited after psychometric evaluation. Hundred and thirty-eight control subjects, two hundred and sixty-seven parents of MR probands and thirty cardiovascular disorder (CVD patients were included for comparison. Peripheral blood was collected after obtaining informed written consent. The T833C/844ins68 polymorphism was investigated by PCR amplification of genomic DNA and restriction fragment length polymorphism analysis, followed by statistical analysis. Results The genotypic distribution of the polymorphism was within the Hardy-Weinberg equilibrium. A slightly increased genotypic frequency was observed in the Indian control population as compared to other Asian populations. Both haplotype-based haplotype relative risk analysis and transmission disequilibrium test reveled lack of association of the T833C/844ins68 polymorphism with MR; nevertheless, the relative risk calculated was higher (>1 and in a limited number of informative MR families, preferential transmission of the double mutant from heterozygous mothers to the MR probands was noticed (χ2 = 4.00, P Conclusion This is the first molecular genetic study of CBS gene dealing with T833C/844ins68 double mutation in MR subjects. Our preliminary data indicate lack of association between T833C/844ins68 polymorphism with MR. However

  3. The spatial distribution and velocity field of the molecular hydrogen line emission from the centre of the Galaxy

    Gatley, I.; Krisciunas, K.; Jones, T.J.; Hyland, A.R.; Geballe, T.R.; Rijksuniversiteit Groningen

    1986-01-01

    In an earlier paper the existence of a ring of molecular hydrogen-line emission surrounding the nucleus of the Galaxy was demonstrated. Here are presented the first detailed maps of the surface brightness and the velocity field, made in the upsilon=1-0 S(1) line of molecular hydrogen with a spatial resolution of 18 arcsec and a velocity resolution of 130 km s -1 . It is found that the molecular ring is tilted approximately 20 0 out of the plane of the Galaxy, has a broken and clumpy appearance, rotates at 100 km s -1 in the sense of galactic rotation, and exhibits radial motion at a velocity of 50 km s -1 . (author)

  4. The one-sample PARAFAC approach reveals molecular size distributions of fluorescent components in dissolved organic matter

    Wünsch, Urban; Murphy, Kathleen R.; Stedmon, Colin

    2017-01-01

    Molecular size plays an important role in dissolved organic matter (DOM) biogeochemistry, but its relationship with the fluorescent fraction of DOM (FDOM) remains poorly resolved. Here high-performance size exclusion chromatography (HPSEC) was coupled to fluorescence emission-excitation (EEM...... but not their spectral properties. Thus, in contrast to absorption measurements, bulk fluorescence is unlikely to reliably indicate the average molecular size of DOM. The one-sample approach enables robust and independent cross-site comparisons without large-scale sampling efforts and introduces new analytical...... opportunities for elucidating the origins and biogeochemical properties of FDOM...

  5. Linguistic grammar learning and DRD2-TAQ-IA polymorphism.

    Wong, Patrick C M; Ettlinger, Marc; Zheng, Jing

    2013-01-01

    As research into the neurobiology of language has focused primarily on the systems level, fewer studies have examined the link between molecular genetics and normal variations in language functions. Because the ability to learn a language varies in adults and our genetic codes also vary, research linking the two provides a unique window into the molecular neurobiology of language. We consider a candidate association between the dopamine receptor D2 gene (DRD2) and linguistic grammar learning. DRD2-TAQ-IA polymorphism (rs1800497) is associated with dopamine receptor D2 distribution and dopamine impact in the human striatum, such that A1 allele carriers show reduction in D2 receptor binding relative to carriers who are homozygous for the A2 allele. The individual differences in grammatical rule learning that are particularly prevalent in adulthood are also associated with striatal function and its role in domain-general procedural memory. Therefore, we reasoned that procedurally-based grammar learning could be associated with DRD2-TAQ-IA polymorphism. Here, English-speaking adults learned artificial concatenative and analogical grammars, which have been respectively associated with procedural and declarative memory. Language learning capabilities were tested while learners' neural hemodynamic responses were simultaneously measured by fMRI. Behavioral learning and brain activation data were subsequently compared with the learners' DRD2 (rs1800497) genotype. Learners who were homozygous for the A2 allele were better at concatenative (but not analogical) grammar learning and had higher striatal responses relative to those who have at least one A1 allele. These results provide preliminary evidence for the neurogenetic basis of normal variations in linguistic grammar learning and its link to domain-general functions.

  6. Linguistic grammar learning and DRD2-TAQ-IA polymorphism.

    Patrick C M Wong

    Full Text Available As research into the neurobiology of language has focused primarily on the systems level, fewer studies have examined the link between molecular genetics and normal variations in language functions. Because the ability to learn a language varies in adults and our genetic codes also vary, research linking the two provides a unique window into the molecular neurobiology of language. We consider a candidate association between the dopamine receptor D2 gene (DRD2 and linguistic grammar learning. DRD2-TAQ-IA polymorphism (rs1800497 is associated with dopamine receptor D2 distribution and dopamine impact in the human striatum, such that A1 allele carriers show reduction in D2 receptor binding relative to carriers who are homozygous for the A2 allele. The individual differences in grammatical rule learning that are particularly prevalent in adulthood are also associated with striatal function and its role in domain-general procedural memory. Therefore, we reasoned that procedurally-based grammar learning could be associated with DRD2-TAQ-IA polymorphism. Here, English-speaking adults learned artificial concatenative and analogical grammars, which have been respectively associated with procedural and declarative memory. Language learning capabilities were tested while learners' neural hemodynamic responses were simultaneously measured by fMRI. Behavioral learning and brain activation data were subsequently compared with the learners' DRD2 (rs1800497 genotype. Learners who were homozygous for the A2 allele were better at concatenative (but not analogical grammar learning and had higher striatal responses relative to those who have at least one A1 allele. These results provide preliminary evidence for the neurogenetic basis of normal variations in linguistic grammar learning and its link to domain-general functions.

  7. The molecular electron density distribution meeting place of X-ray diffraction and quantum chemistry intermediate - between theory and experiment

    Feil, D.; Feil, Dirk

    1992-01-01

    Quantum chemistry and the concepts used daily in chemistry are increasingly growing apart. Among the concepts that are able to bridge the gap between theory and experimental practice, electron density distribution has an important place. The study of this distribution has led to new developments in

  8. Role of the 2 adenine (g.11293_11294insAA) insertion polymorphism in the 3' untranslated region of the factor VII (FVII) gene: molecular characterization of a patient with severe FVII deficiency.

    Peyvandi, F; Garagiola, I; Palla, R; Marziliano, N; Mannucci, P M

    2005-11-01

    Polymorphic variants in the gene encoding factor VII (F7) affect the plasma levels of this coagulation protein and modify the clinical phenotype of FVII deficiency in some patients. In this study we report the in vitro functional analysis of a novel polymorphic variant located in the 3' untranslated region of F7: g.11293_11294insAA. To determine whether this variant regulates FVII expression, we initially compared an expression vector containing FVII cDNA with g.11293_11294insAA with the FVII wild-type (WT) construct. The kinetics of mRNA production showed that the insertion decreases the steady-state FVII mRNA levels. To assess whether the insertion influences the phenotype of FVII-deficient patients, we evaluated its effect on the expression of FVII in a patient with severe FVII deficiency (undetectable FVII activity and antigen) carrying two additional homozygous missense variations (p.Arg277Cys and p.Arg353Gln). The two substitutions alone reduced the expression of FVII activity and antigen in vitro, but with the insertion polymorphism in our expression vector the patient's phenotype of undetectable plasma FVII was recapitulated. The insertion polymorphism in the 3' untranslated region of F7 is another modifier of FVII expression that might explain the poor genotype-phenotype correlation in some FVII-deficient patients. Copyright 2005 Wiley-Liss, Inc.

  9. [Determination of the distribution of relative molecular mass of organic matter by high pressure size exclusion chromatography with UV and TOC detectors].

    Zhang, Han; Dong, Bing-Zhi

    2012-09-01

    An on-line high pressure size exclusion chromatography (HPSEC) with UV and TOC detectors was adapted to examine the distribution of relative molecular mass of natural organic matter (NOM). Through synchronous determination of UV254 and TOC responses in a wide range of relative molecular mass, it was possible to accurately characterize the structure of NOM, especially for some non-aromatic and non-conjugated double bond organics which have low response to UV. It was found that, TOC detector was capable of detecting all kinds of organic matters, including sucrose, sodium alginate and other hydrophilic organic compounds. The sample volume had a positively linear correlation with the TOC response, indicating that the larger volume would produce stronger responses. The effect of ion strength was relatively low, shown by the small decrease of peak area (1.2% ) from none to 0.2 mol x L(-1) NaCl. The pH value of tested samples should be adjusted to neutral or acidic because when the samples were alkaline, the results might be inaccurate. Compared to the sample solvents adopted as ultrapure water, the samples prepared by mobile phase solvents had less interference to salt boundary peak. The on-line HPSEC-UV-TOC can be used accurately to characterize the distribution of relative molecular mass and its four fractions in River Xiang.

  10. Effects of BDNF polymorphisms on antidepressant action.

    Tsai, Shih-Jen; Hong, Chen-Jee; Liou, Ying-Jay

    2010-12-01

    Evidence suggests that the down-regulation of the signaling pathway involving brain-derived neurotrophic factor (BDNF), a molecular element known to regulate neuronal plasticity and survival, plays an important role in the pathogenesis of major depression. The restoration of BDNF activity induced by antidepressant treatment has been implicated in the antidepressant therapeutic mechanism. Because there is variability among patients with major depressive disorder in terms of response to antidepressant treatment and since genetic factors may contribute to this inter-individual variability in antidepressant response, pharmacogenetic studies have tested the associations between genetic polymorphisms in candidate genes related to antidepressant therapeutic action. In human BDNF gene, there is a common functional polymorphism (Val66Met) in the pro-region of BDNF, which affects the intracellular trafficking of proBDNF. Because of the potentially important role of BDNF in the antidepressant mechanism, many pharmacogenetic studies have tested the association between this polymorphism and the antidepressant therapeutic response, but they have produced inconsistent results. A recent meta-analysis of eight studies, which included data from 1,115 subjects, suggested that the Val/Met carriers have increased antidepressant response in comparison to Val/Val homozygotes, particularly in the Asian population. The positive molecular heterosis effect (subjects heterozygous for a specific genetic polymorphism show a significantly greater effect) is compatible with animal studies showing that, although BDNF exerts an antidepressant effect, too much BDNF may have a detrimental effect on mood. Several recommendations are proposed for future antidepressant pharmacogenetic studies of BDNF, including the consideration of multiple polymorphisms and a haplotype approach, gene-gene interaction, a single antidepressant regimen, controlling for age and gender interactions, and pharmacogenetic

  11. Entropy and chemical change. 1: Characterization of product (and reactant) energy distributions in reactive molecular collisions: Information and enthropy deficiency

    Bernstein, R. B.; Levine, R. D.

    1972-01-01

    Optimal means of characterizing the distribution of product energy states resulting from reactive collisions of molecules with restricted distributions of initial states are considered, along with those for characterizing the particular reactant state distribution which yields a given set of product states at a specified total energy. It is suggested to represent the energy-dependence of global-type results in the form of square-faced bar plots, and of data for specific-type experiments as triangular-faced prismatic plots. The essential parameters defining the internal state distribution are isolated, and the information content of such a distribution is put on a quantitative basis. The relationship between the information content, the surprisal, and the entropy of the continuous distribution is established. The concept of an entropy deficiency, which characterizes the specificity of product state formation, is suggested as a useful measure of the deviance from statistical behavior. The degradation of information by experimental averaging is considered, leading to bounds on the entropy deficiency.

  12. A study of molecular correlations observed in the small-angle photon scattering distributions of 60 KeV photons interacting with low-atomic-number media

    Bradley, D.A.

    1988-01-01

    A variant of the multisection filter and annular target geometry, with a designed angular acceptance of +-0.5 0 , has been utilised in measuring accurate, O(5%), absolute total differential scattering cross sections of 60 KeV photons for H 2 O, methyl methacrylate (C 5 H 8 O 2 ) n and nylon-6 (C 12 H 22 O 3 N 2 ) n in the angular scattering range of 2 0 -10 0 . The effects of molecular correlations manifest, to varying degree, in strong forward peaking of the scattered photon distribution. Comparison is made with available experiment and theory [pt

  13. A simple scaling law for the equation of state and the radial distribution functions calculated by density-functional theory molecular dynamics

    Danel, J.-F.; Kazandjian, L.

    2018-06-01

    It is shown that the equation of state (EOS) and the radial distribution functions obtained by density-functional theory molecular dynamics (DFT-MD) obey a simple scaling law. At given temperature, the thermodynamic properties and the radial distribution functions given by a DFT-MD simulation remain unchanged if the mole fractions of nuclei of given charge and the average volume per atom remain unchanged. A practical interest of this scaling law is to obtain an EOS table for a fluid from that already obtained for another fluid if it has the right characteristics. Another practical interest of this result is that an asymmetric mixture made up of light and heavy atoms requiring very different time steps can be replaced by a mixture of atoms of equal mass, which facilitates the exploration of the configuration space in a DFT-MD simulation. The scaling law is illustrated by numerical results.

  14. Distribution of HLA-G extended haplotypes and one HLA-E polymorphism in a large-scale study of mother-child dyads with and without severe preeclampsia and eclampsia

    Nilsson, L. L.; Djurisic, S; Andersen, A.-M. N.

    2016-01-01

    was not associated with severe preeclampsia. Furthermore, the polymorphism (rs1264457) defining the two nonsynonymous HLA-E alleles, HLA-E*01:01:xx:xx and HLA-E*01:03:xx:xx, were not associated with severe preeclampsia. Finally, no specific HLA-G haplotypes were significantly associated with increased risk...

  15. Molecular organization in bacterial cell membranes. Specific labelling and topological distribution of glycoproteins and proteins in Streptomyces albus membranes

    Larraga, V; Munoz, E [Consejo Superior de Investigaciones Cientificas, Madrid (Spain). Instituto de Biologia Celular

    1975-05-01

    The paper reports about an investigation into the question of the specific labelling and topological distribution of glycoproteins and proteins in Streptomyces albus membranes. The method of sample preparation is described: Tritium labelling of glycoproteins in protoplasts and membranes, iodination of proteins, trypsin treatment and polyacrylamide gel electrophoresis. The findings suggest an asymmetrical distribution of the glycoproteins in membranes and a weak accessibility to iodine label. A structural model of the plasma membranes of Streptomyces albus is proposed similar to the general 'fluid mosaic' model of Singer and Nicholson.

  16. Plasma Temperature Determination of Hydrogen Containing High-Frequency Electrodeless Lamps by Intensity Distribution Measurements of Hydrogen Molecular Band

    Gavare, Zanda; Revalde, Gita; Skudra, Atis

    2010-01-01

    The goal of the present work was the investigation of the possibility to use intensity distribution of the Q-branch lines of the hydrogen Fulcher-α diagonal band (d3Πu−→a3∑g+ electronic transition; Q-branch with v=v′=2) to determine the temperature of hydrogen containing high-frequency electrodeless lamps (HFEDLs). The values of the rotational temperatures have been obtained from the relative intensity distributions for hydrogen-helium and hydrogen-argon HFEDLs depending on the applied curren...

  17. Influence of shock induced polymorphic transition on penetration in steel

    Hereil, P.L.; Fanget, A.

    1994-01-01

    The effects of polymorphic transition for the impact of a 27NCD10 steel projectile on a 27NCD10 steel target at 1280 m/s is presented. Comparisons between results of 2D numerical calculations performed with and without polymorphic transition show the influence of this phenomenon on stress distribution and tension zones in the target and in the projectile. Good agreement between experimental and calculated free surface velocity profiles is obtained with polymorphic transition and damage models taken into account. (orig.)

  18. Specific Reaction Patterns to Distinct Positive Emotional Cues Related to Incentive Motivation in Dependence of the Taq1A-Polymorphism: Molecular Genetic Associations of Early and Late Event-Related Potentials.

    Munk, Aisha J L; Wielpuetz, Catrin; Osinsky, Roman; Müller, Erik M; Grant, Phillip; Hennig, Jürgen

    2016-01-01

    Early and late event-related potential (ERP) responses, representing early subconscious and late motivational processes, were recorded for positive emotional words related to 'wanting' and 'liking', in dependence of the dopamine-related Taq1A genotype (ANKK1/DRD2). Research suggests that 'wanting' as opposed to 'liking' is related to dopaminergic processes. Therefore, it was hypothesized that risk allele carriers of the Taq1A polymorphism exhibit late ERP changes in reaction to words representing incentive motivation, i.e. 'wanting' (word categories 'lust' and 'anticipation'), but not to words representing 'liking' ('closeness'). Seventy-two male participants performed an emotional-word Stroop task during EEG recording and were genotyped according to the Taq1A polymorphism of ANKK1/DRD2. Positive emotional words related to anticipation and lust revealed blunted responses in the late positive potential (LPP) in carriers of the A1 allele, an effect absent in response to 'liking'-related words. These differences were not evident in the earlier posterior negativity (EPN). As no differences in dependence of the Taq1A genotype were observed in reaction to 'wanting'- and 'liking'-related words in the EPN, but merely in the LPP, it can be assumed that incentive-motivational stimuli only modify motivation-related ERP responses in carriers of the A1 allele of the Taq1A polymorphism, indicating the role of dopamine in late ERP components. © 2016 S. Karger AG, Basel.

  19. Absorption spectroscopy of colored dissolved organic carbon in Georgia (USA rivers: the impact of molecular size distribution

    Michelle McELVAINE

    2003-02-01

    Full Text Available Dissolved organic carbon (DOC was collected in six rivers that transect the coastal plain of Georgia in July 1999 and February 2000. DOC concentrations ranged from 4.9 to 40.7 g m-3 and from 7.1 to 40.5 g m-3, respectively. The absorption coefficient at 440 nm was highly correlated with DOC concentration, suggesting that the optical parameter may be utilized for rapid estimation of DOC in these waters. The isolated DOC was separated into fractions of operationally defined molecular size, using an ultrafiltration technique that yielded three fractions: 50 ("large" kilodalton. The smallest fraction was the most abundant (>50% in 4 rivers in July and in all rivers in February, and considerably more abundant than in previous years. The wavelength-dependent absorption of the total DOC and its fractions showed approximately uniform shape of a curve declining exponentially with the increase of wavelength. The average slope of logarithmically transformed curves was 0.0151 and 0.0159 nm-1, for the material collected in July and February, respectively and showed a dependence on DOC molecular size. In unfractionated DOC samples, the mass-specific light absorption determined at 440 nm was on average 0.33 m2 g-1 in July, and 0.26 m2 g-1 in February. The mass-specific absorption coefficient in all fractions ranged between 0.085 and 1.347 m2 g-1 in July and between 0.085 and 1.877 m2 g-1 in February, and was positively correlated with the molecular size of the measured samples. The results of the reported study clearly suggest that the specific absorption coefficient of the yellow substance is an outcome of the relative contribution of its different size fractions.

  20. MOLECULAR COMPARISON OF MYCOBACTERIUM AVIUM ISOLATED FROM A FRINKING WATER DISTRIBUTION SYSTEM AND FROM THE POPULATION SERVED BY THE SYSTEM

    There is evidence that drinking water, soil, and produce may be sources of Mycobacterium avium infections, a pathogen not known to be transmitted person-to-person. We sampled water from a large municipal drinking water distribution system in which surface source water is used. M...

  1. Sugar Composition and Molecular Weight Distribution of Cell Wall Polysaccharides in Outer and Inner Tissues from Segments of Dark Grown Squash (Cucurbita maxima Duch.) Hypocotyls.

    Wakabayashi, K; Sakurai, N; Kuraishi, S

    1990-07-01

    The elongation growth of stem segments is determined by the outer cell layers (epidermis and collenchyma). We measured the sugar composition and molecular weight distribution of pectin and hemicellulose fractions obtained from inner and outer tissues of squash (Cucurbita maxima Duch.) hypocotyls. In addition, we studied the changes in these parameters after a 9 hour period of incubation of the segments. The results show that outer tissues have higher molecular weight pectin and hemicellulose compared to inner tissues (2-3 times higher). Incubation results in a 13 to 25% decrease in the amount of pectin and hemicellulose in inner tissues and an increase of 11 to 32% in the outer tissues. This increase in the outer tissues is accompanied by a decrease in the molecular weight of some of the components. These results clearly show that cell wall metabolism during elongation growth differs markedly in inner and outer tissues, and that future studies on the effect of auxin need to take these differences into account.

  2. Sugar Composition and Molecular Weight Distribution of Cell Wall Polysaccharides in Outer and Inner Tissues from Segments of Dark Grown Squash (Cucurbita maxima Duch.) Hypocotyls 1

    Wakabayashi, Kazuyuki; Sakurai, Naoki; Kuraishi, Susumu

    1990-01-01

    The elongation growth of stem segments is determined by the outer cell layers (epidermis and collenchyma). We measured the sugar composition and molecular weight distribution of pectin and hemicellulose fractions obtained from inner and outer tissues of squash (Cucurbita maxima Duch.) hypocotyls. In addition, we studied the changes in these parameters after a 9 hour period of incubation of the segments. The results show that outer tissues have higher molecular weight pectin and hemicellulose compared to inner tissues (2-3 times higher). Incubation results in a 13 to 25% decrease in the amount of pectin and hemicellulose in inner tissues and an increase of 11 to 32% in the outer tissues. This increase in the outer tissues is accompanied by a decrease in the molecular weight of some of the components. These results clearly show that cell wall metabolism during elongation growth differs markedly in inner and outer tissues, and that future studies on the effect of auxin need to take these differences into account. PMID:16667612

  3. Diabat Interpolation for Polymorph Free-Energy Differences.

    Kamat, Kartik; Peters, Baron

    2017-02-02

    Existing methods to compute free-energy differences between polymorphs use harmonic approximations, advanced non-Boltzmann bias sampling techniques, and/or multistage free-energy perturbations. This work demonstrates how Bennett's diabat interpolation method ( J. Comput. Phys. 1976, 22, 245 ) can be combined with energy gaps from lattice-switch Monte Carlo techniques ( Phys. Rev. E 2000, 61, 906 ) to swiftly estimate polymorph free-energy differences. The new method requires only two unbiased molecular dynamics simulations, one for each polymorph. To illustrate the new method, we compute the free-energy difference between face-centered cubic and body-centered cubic polymorphs for a Gaussian core solid. We discuss the justification for parabolic models of the free-energy diabats and similarities to methods that have been used in studies of electron transfer.

  4. Glucocorticoid receptor polymorphism in obesity and glucose homeostasis.

    Majer-Łobodzińska, Agnieszka; Adamiec-Mroczek, Joanna

    2017-01-01

    Glucocorticoid receptor (GR) activity plays a significant role in the etiology of obesity and is essential for glucose homeostasis, the development of hyperinsulinaemia and subsequent increased fat deposition. Several polymorphisms in the GR gene have been described, and at least three of them seem to be associated with altered glucocorticoid sensitivity and changes in glucose homeostasis, and other metabolic parameters. The N363S polymorphism has been associated with increased sensitivity to glucocorticoides, increased insulin response to dexamethasone and increased plasma glucose level. BclI polymorphism is associated with increased abdominal obesity, hyperinsulinaemia and increased insulin resistance. Another polymorphism, ER22/23EK, in contrast to the others, is associated with relative resistance to glucocoricides actions and more beneficial metabolic profile-lower insulin resistance level, decreased lower cardiovascular risk and subseuent prolongation of life time. More research is still needed to understand the mechanisms behind these associations at the molecular level.

  5. Hemorrhagic shock and surgical stress alter distribution of labile zinc within high- and low-molecular-weight plasma fractions.

    Kelly, Edward; Mathew, Jeff; Kohler, Jonathan E; Blass, Amy L; Soybel, And David I

    2012-08-01

    Zinc ions (Zn) are essential for tissue repair following injury or stress. We hypothesize that during such stresses Zn is redistributed to labile pools in plasma components. Here we tested this hypothesis using a novel assay to monitor labile Zn in plasma in hemorrhagic shock. Adult rats in the shock group (S group) underwent hemorrhage and resuscitation. Blood samples were drawn at baseline and at 1, 4, and 24 h. The surgical control group (SC group) was anesthetized and instrumented, but not bled. Albumin, total Zn, and labile Zn levels were assayed in plasma. Binding capacity for Zn was assessed in high- and low-molecular-weight pools. Significant decreases in total Zn were observed by 24 h, in both S and SC groups. Albumin levels were significantly reduced in the S group at 1 and 4 h but restored at 24 h; significant changes were not observed in other groups. In whole plasma, labile Zn levels were stable initially in the S and SC groups, but declined at 24 h. In the high-molecular-weight pool, marked and significant impairment of binding was noted throughout all time periods following the shock period in the S group. Such changes were observed in the SC group of less intensity and duration. These experiments suggest that shock alters affinity of plasma proteins for Zn, promoting delivery to peripheral tissues during periods of increased Zn utilization.

  6. Raman Identification of Polymorphs in Pentacene Films

    Alberto Girlando

    2016-04-01

    Full Text Available We use Raman spectroscopy to characterize thin films of pentacene grown on Si/SiO x by Supersonic Molecular Beam Deposition (SuMBD. We find that films up to a thickness of about 781 Å (∼ 52 monolayers all belong to the so-called thin-film (TF phase. The appearance with strong intensity of some lattice phonons suggests that the films are characterized by good intra-layer order. A comparison of the Raman spectra in the lattice and CH bending spectral regions of the TF polymorph with the corresponding ones of the high-temperature (HT and low-temperature (LT bulk pentacene polymorphs provides a quick and nondestructive method to identify the different phases.

  7. Teaching polymorphism early

    2005-01-01

    Is it possible to teach dynamic polymorphism early? What techniques could facilitate teaching it in Java. This panel will bring together people who have considered this question and attempted to implement it in various ways, some more completely than others. It will also give participants...

  8. Orbital momentum distribution and binding energies for the complete valence shell of molecular chlorine by electron momentum spectroscopy

    Frost, L.; Grisogono, A.M.; McCarthy, I.E.

    1986-10-01

    The complete valence shell binding energy spectrum (10-50 eV) of Cl 2 has been determined using electron momentum (binary (e,2e)) spectroscopy. The inner valence region, corresponding to 4σ u and 4σ g ionization, has been measured for the first time and shows extensive splitting of the ionization strength due to electron correlation effects. These measurements are compared with the results of many-body calculations using Green's function and CI methods employing unpolarised as well as polarised wave functions. Momentum distributions, measured in both the outer and inner valence regions, are compared with calculations using a range of unpolarised and polarised wave functions. Computed orbital density maps in momentum and position space for oriented Cl 2 molecules are discussed in comparison with the measured and calculated spherically averaged momentum distributions

  9. DISTRIBUTION OF THE MIXTURE THROUGH THE REACTORS CASCADE IN THE PRODUCTION OF LOW MOLECULAR COPOLYMERS OF BUTADIENE WITH STYRENE

    V. F. Lebedev

    2014-01-01

    Full Text Available Summary. In the polymerization of butadiene with styrene heat removal is the main factor limiting the output of the cascade reactor. Thus the residence time of the monomers in the reactor exceeds significantly the time necessary to complete the process on the basis of kinetic regularities. To increase the output of the mixture the distribution in the reactor cascade is made. It is necessary to distribute the flow of mixture through the reactor of the cascade to have the resulting polymer of the same viscosity at the outlet of each reactor. The algorithm of distribution of the mixture in the reactor cascade with regard to the synthesis parameters (temperature in the reactor and the feed rate of the mixture, the ratio of the modifier and the initiator in the complex, the number of reactors and a determined dynamic viscosity is developed. In accordance with the developed algorithm the calculation of the velocity of the mixture feed in each reactor of the cascade is made. It is shown that the flow of mixture in each polymerization unit depends on the overall output of the installation and the number of reactors in the cascade. The algorithm for the distribution of the initial mixture in the reactor cascade is developed to provide maximum output of the installation and set the quality of the obtained polymer. To determine the degree of conversion of monomers and temperature conditions of the process of polymerization under the calculated speed of the feed mixture in the first polymerization cascade the basic technological parameters of the polymerization process in real time mode, the calculation using a mathematical model is made. The analysis of the simulation results shows that during the first hour, the concentration of monomers does not exceed of 0.085 mol/l, which corresponds to the degree of conversion of monomer to 99 %, while the temperature in the reactor corresponds to the optimal mode - from 65 to 85 0C.

  10. Plasma Temperature Determination of Hydrogen Containing High-Frequency Electrode less Lamps by Intensity Distribution Measurements of Hydrogen Molecular Band

    Gavare, Z.; Revalde, G.; Skudra, A.

    2011-01-01

    The goal of the present work was the investigation of the possibility to use intensity distribution of the Q-branch lines of the hydrogen Fulcher-a diagonal band (d3η u- a3Σg + electronic transition; Q-branch with ν=ν=2) to determine the temperature of hydrogen containing high-frequency electrode less lamps (HFEDLs). The values of the rotational temperatures have been obtained from the relative intensity distributions for hydrogen-helium and hydrogen-argon HFEDLs depending on the applied current. The results have been compared with the method of temperature derivation from Doppler profiles of He 667.8 nm and Ar 772.4 nm lines. The results of both methods are in good agreement, showing that the method of gas temperature determination from the intensity distribution in the hydrogen Fulcher-a (2-2)Q band can be used for the hydrogen containing HFEDLs. It was observed that the admixture of 10% hydrogen in the argon HFEDLs significantly reduces the gas temperature

  11. Methylation-sensitive amplification polymorphism in date palms (Phoenix dactylifera L.) and their off-shoots.

    Fang, J-G; Chao, C T

    2007-07-01

    DNA methylation plays an important role in the regulation of gene expression in eukaryotes. In this study, the extent and patterns of DNA methylation were assessed in date palm mother-plants and their off-shoots using the methylation-sensitive amplified polymorphism (MSAP) technique. Three types of bands were generated using 12 pairs of primers. Type I were present in both ECOR I + HPA II and ECOR I + MSP I lanes; type II were present in ECOR I + HPA II lanes, but not in ECOR I + MSP I lanes; and type III bands were present in ECOR I + MSP I lanes, but not in ECOR I + HPA II lanes. The total numbers of these three types of bands were 782, 55, and 34, respectively. Among these three types of bands, the polymorphic bands were, respectively, 37, 10, and 0. The distribution of polymorphic bands among mother-plants and off-shoots suggests the methylation variation was present in both the mother-plants and off-shoots. Forty- four out of these 47 polymorphic bands show clear difference between mother-plant and off-shoots: 38 were present only in off-shoots and 6 in both mother-plants and off-shoots. Compared to methylation status in mother-plants, the methylation variation during off-shoot growth of date palm can be characterized as a process involving primarily de-methylation. Hypomethylation of DNA in off-shoots, compared with mother-plants, reflects the marked expression of this molecular feature, which may be related to gene expression during off-shoot development. The methylation or de-methylation status of specific loci in the mother-plants and their off-shoots were probably random events.

  12. Synaptosomal-associated protein 25 gene polymorphisms and antisocial personality disorder: association with temperament and psychopathy.

    Basoglu, Cengiz; Oner, Ozgur; Ates, Alpay; Algul, Ayhan; Bez, Yasin; Cetin, Mesut; Herken, Hasan; Erdal, Mehmet Emin; Munir, Kerim M

    2011-06-01

    The molecular genetic of personality disorders has been investigated in several studies; however, the association of antisocial behaviours with synaptosomal-associated protein 25 (SNAP25) gene polymorphisms has not. This association is of interest as SNAP25 gene polymorphism has been associated with attention-deficit hyperactivity disorder and personality. We compared the distribution of DdeI and MnII polymorphisms in 91 young male offenders and in 38 sex-matched healthy control subjects. We also investigated the association of SNAP25 gene polymorphisms with severity of psychopathy and with temperament traits: novelty seeking, harm avoidance, and reward dependence. The MnII T/T and DdeI T/T genotypes were more frequently present in male subjects with antisocial personality disorder (APD) than in sex-matched healthy control subjects. The association was stronger when the frequency of both DdeI and MnII T/T were taken into account. In the APD group, the genotype was not significantly associated with the Psychopathy Checklist-Revised scores, measuring the severity of psychopathy. However, the APD subjects with the MnII T/T genotype had higher novelty seeking scores; whereas, subjects with the DdeI T/T genotype had lower reward dependence scores. Again, the association between genotype and novelty seeking was stronger when both DdeI and MnII genotypes were taken into account. DdeI and MnII T/T genotypes may be a risk factor for antisocial behaviours. The association of the SNAP25 DdeI T/T and MnII T/T genotypes with lower reward dependence and higher novelty seeking suggested that SNAP25 genotype might influence other personality disorders, as well.

  13. THE SPITZER SPACE TELESCOPE SURVEY OF THE ORION A AND B MOLECULAR CLOUDS. II. THE SPATIAL DISTRIBUTION AND DEMOGRAPHICS OF DUSTY YOUNG STELLAR OBJECTS

    Megeath, S. T.; Kryukova, E.; Gutermuth, R.; Muzerolle, J.; Hora, J. L.; Myers, P. C.; Fazio, G. G.; Allen, L. E.; Flaherty, K.; Hartmann, L.; Pipher, J. L.; Stauffer, J.; Young, E. T.

    2016-01-01

    We analyze the spatial distribution of dusty young stellar objects (YSOs) identified in the Spitzer Survey of the Orion Molecular clouds, augmenting these data with Chandra X-ray observations to correct for incompleteness in dense clustered regions. We also devise a scheme to correct for spatially varying incompleteness when X-ray data are not available. The local surface densities of the YSOs range from 1 pc −2 to over 10,000 pc −2 , with protostars tending to be in higher density regions. This range of densities is similar to other surveyed molecular clouds with clusters, but broader than clouds without clusters. By identifying clusters and groups as continuous regions with surface densities ≥10 pc −2 , we find that 59% of the YSOs are in the largest cluster, the Orion Nebula Cluster (ONC), while 13% of the YSOs are found in a distributed population. A lower fraction of protostars in the distributed population is evidence that it is somewhat older than the groups and clusters. An examination of the structural properties of the clusters and groups shows that the peak surface densities of the clusters increase approximately linearly with the number of members. Furthermore, all clusters with more than 70 members exhibit asymmetric and/or highly elongated structures. The ONC becomes azimuthally symmetric in the inner 0.1 pc, suggesting that the cluster is only ∼2 Myr in age. We find that the star formation efficiency (SFE) of the Orion B cloud is unusually low, and that the SFEs of individual groups and clusters are an order of magnitude higher than those of the clouds. Finally, we discuss the relationship between the young low mass stars in the Orion clouds and the Orion OB 1 association, and we determine upper limits to the fraction of disks that may be affected by UV radiation from OB stars or dynamical interactions in dense, clustered regions

  14. Polymorphism in vkorc1 Gene of Natal Multimammate Mice, Mastomys natalensis in Tanzania

    Gryseels, S.; Leirs, H.; Makundi, R.; Goüy de Bellocq, Joëlle

    2015-01-01

    Roč. 106, č. 5 (2015), s. 637-643 ISSN 0022-1503 Institutional support: RVO:68081766 Keywords : Anticoagulants * Bromadiolone * Polymorphism * Poison resistance * Rodent Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.075, year: 2015

  15. Distribution of HLA-G extended haplotypes and one HLA-E polymorphism in a large-scale study of mother-child dyads with and without severe preeclampsia and eclampsia.

    Nilsson, L L; Djurisic, S; Andersen, A-M N; Melbye, M; Bjerre, D; Ferrero-Miliani, L; Hackmon, R; Geraghty, D E; Hviid, T V F

    2016-10-01

    The etiological pathways and pathogenesis of preeclampsia have rendered difficult to disentangle. Accumulating evidence points toward a maladapted maternal immune system, which may involve aberrant placental expression of immunomodulatory human leukocyte antigen (HLA) class Ib molecules during pregnancy. Several studies have shown aberrant or reduced expression of HLA-G in the placenta and in maternal blood in cases of preeclampsia compared with controls. Unlike classical HLA class Ia loci, the nonclassical HLA-G has limited polymorphic variants. Most nucleotide variations are clustered in the 5'-upstream regulatory region (5'URR) and 3'-untranslated regulatory region (3'UTR) of HLA-G and reflect a stringent expressional control. Based on genotyping and full gene sequencing of HLA-G in a large number of cases and controls (n > 900), the present study, which to our knowledge is the largest and most comprehensive performed, investigated the association between the HLA-G 14-bp ins/del (rs66554220) and HLA-E polymorphisms in mother and newborn dyads from pregnancies complicated by severe preeclampsia/eclampsia and from uncomplicated pregnancies. Furthermore, results from extended HLA-G haplotyping in the newborns are presented in order to assess whether a combined contribution of nucleotide variations spanning the 5'URR, coding region, and 3'UTR of HLA-G describes the genetic association with severe preeclampsia more closely. In contrast to earlier findings, the HLA-G 14-bp ins/del polymorphism was not associated with severe preeclampsia. Furthermore, the polymorphism (rs1264457) defining the two nonsynonymous HLA-E alleles, HLA-E*01:01:xx:xx and HLA-E*01:03:xx:xx, were not associated with severe preeclampsia. Finally, no specific HLA-G haplotypes were significantly associated with increased risk of developing severe preeclampsia/eclampsia. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. Association of PPARG Pro12Ala polymorphism with insulin sensitivity and body mass index in patients with polycystic ovary syndrome.

    Baldani, Dinka Pavicic; Skrgatic, Lana; Cerne, Jasmina Z; Ferk, Polonca; Simunic, Velimir; Gersak, Ksenija

    2014-03-01

    Insulin resistance is one of the key factors in the pathogenesis of polycystic ovary syndrome (PCOS). The peroxisome proliferator-activated receptor gamma (PPARG) plays a role in the regulation of insulin sensitivity. The aim of the present study was to establish a possible association of the PPARG Pro12Ala polymorphism with PCOS and its effect on family and personal history, as well as on the metabolic and endocrine parameters in PCOS patients. A total of 151 PCOS patients and 179 healthy women of reproductive age were enrolled. History, body mass index (BMI), waist-to-hip ratio and the presence of phenotypic hyperandrogenism were recorded. Hormonal, metabolic and biochemical profiles were assessed. A molecular analysis for the genetic polymorphism was performed. One third (29.8%) of the PCOS patients were found to be carriers of at least one variant of the Ala allele (X/Ala), while 70.2% carried two wild-type Pro alleles (Pro/Pro), with an equal distribution observed in the control group. The PCOS patients carrying the X/Ala alleles exhibited lower serum fasting insulin levels, homeostatic model assessment of insulin resistance (HOMA-IR) and BMI compared to Pro/Pro carriers. This finding was significant only in the lean PCOS group. The polymorphic genotype exerted no effect on history, hormonal and clinical hyperandrogenism, lipid status or C-reactive protein, leptin, adiponectin, resistin and ghrelin serum levels in women with PCOS. In conclusion, although the PPARG Pro12Ala polymorphism is not a major determinant of PCOS in the Croatian population, it may exert a positive effect on insulin sensitivity and BMI. As these associations were recorded exclusively in the lean group of patients with PCOS, this polymorphism potentially contributes to a protective role against hyperinsulinemia and obesity.

  17. Microprobing the Molecular Spatial Distribution and Structural Architecture of Feed-type Sorghum Seed Tissue (Sorghum Bicolor L.) using the Synchrotron Radiation Infrared Microspectroscopy Technique

    Yu, P.

    2011-01-01

    Sorghum seed (Sorghum bicolor L.) has unique degradation and fermentation behaviours compared with other cereal grains such as wheat, barley and corn. This may be related to its cell and cell-wall architecture. The advanced synchrotron radiation infrared microspectroscopy (SR-IMS) technique enables the study of cell or living cell biochemistry within cellular dimensions. The objective of this study was to use the SR-IMS imaging technique to microprobe molecular spatial distribution and cell architecture of the sorghum seed tissue comprehensively. High-density mapping was carried out using SR-IMS on beamline U2B at the National Synchrotron Light Source (Brookhaven National Laboratory, NY, USA). Molecular images were systematically recorded from the outside to the inside of the seed tissue under various chemical functional groups and their ratios [peaks at ∼1725 (carbonyl C=O ester), 1650 (amide I), 1657 (protein secondary structure α-helix), 1628 (protein secondary structure β-sheet), 1550 (amide II), 1515 (aromatic compounds of lignin), 1428, 1371, 1245 (cellulosic compounds in plant seed tissue), 1025 (non-structural CHO, starch granules), 1246 (cellulosic material), 1160 (CHO), 1150 (CHO), 1080 (CHO), 930 (CHO), 860 (CHO), 3350 (OH and NH stretching), 2960 (CH 3 anti-symmetric), 2929 (CH 2 anti-symmetric), 2877 (CH 3 symmetric) and 2848 cm -1 (CH 2 asymmetric)]. The relative protein secondary structure α-helix to β-sheet ratio image, protein amide I to starch granule ratio image, and anti-symmetric CH 3 to CH 2 ratio image were also investigated within the intact sorghum seed tissue. The results showed unique cell architecture, and the molecular spatial distribution and intensity in the sorghum seed tissue (which were analyzed through microprobe molecular imaging) were generated using SR-IMS. This imaging technique and methodology has high potential and could be used for scientists to develop specific cereal grain varieties with targeted food and feed

  18. Ultra-stable long distance optical frequency distribution using the Internet fiber network and application to high-precision molecular spectroscopy

    Lopez, O; Chanteau, B; Bercy, A; Argence, B; Darquié, B; Chardonnet, C; Amy-Klein, A; Nicolodi, D; Zhang, W; Abgrall, M; Haboucha, A; Kanj, A; Rovera, D; Achkar, J; Pottie, P-E; Coq, Y Le; Santarelli, G

    2013-01-01

    We report an optical link of 540 km for ultrastable frequency distribution over the Internet fiber network. The phase-noise compensated link shows a fractional frequency instability in full bandwidth of 3×10 −14 at one second measurement time and 2×10 −18 at 30 000 s. This work is a significant step towards a sustainable wide area ultrastable optical frequency distribution and comparison network. Time transfer was demonstrated simultaneously on the same link and led to an absolute time accuracy (250 ps) and long-term timing stability (20 ps) which outperform the conventional satellite transfer methods by one order of magnitude. Current development addresses the question of multiple users distribution in the same metropolitan area. We demonstrate on-line extraction and first results show frequency stability at the same level as with conventional link. We also report an application to coherent frequency transfer to the mid-infrared. We demonstrate the frequency stabilisation of a mid-infrared laser to the near-infrared frequency reference transferred through the optical link. Fractional stability better than 4×10 −14 at 1 s averaging time was obtained, opening the way to ultrahigh resolution spectroscopy of molecular rovibrational transitions

  19. Article Molecular analysis of three FUT3 gene single nucleotide polymorphisms and their relationship with the lewis erythrocytary phenotype in a human population of japanese-ancestry living in Tomé Açu, a town in the Brazilian Amazon

    Pablo Abdon da Costa Francez

    2007-03-01

    Full Text Available The Lewis blood group system involves two major antigens, Leª and Le b. Their antigenic determinants are not primary gene products but are synthesized by the transfer of sugar subunits to a precursory chain by a specific enzyme which is the product of the FUT3 gene (Lewis gene. The presence of three FUT3 gene single nucleotide polymorphisms (SNPs (59T > G; 508G > A and 1067T > A was related to the Lewis phenotype of erythrocytes from 185 individuals of Japanese ancestry living in the town of Tomé-Açu in the Brazilian Amazon region. This relationship was detected using a serological hemagglutination test and the Dot-ELISA assay along with the molecular technique PCR-RFLP. We found that the three SNPs investigated in this study only accounted for a proportion of the Lewis-negative phenotype of the erythrocytes.

  20. Molecular diversity and genetic relationships in Secale

    2001); and molecular methods such as amplified fragment length polymorphism ... to the maintenance and rational use of germplasm resources in the improvement of ... study of diversity of ScMATE1 gene in different species of. Secale genus.

  1. Application of random amplified polymorphic DNA (RAPD) markers ...

    The random amplified polymorphic DNA (RAPD) technique has been widely applied to identify different varieties of plants for molecular breeding. However, application of RAPD markers to identify parthenogenesis in plants has not been reported. In this investigation, we used pedigree and RAPD markers to differentiate ...

  2. Relationship of status of polymorphic rapd bands with genotypic ...

    Relationship of status of polymorphic rapd bands with genotypic adaptation in early finger millet genotypes. S Das, RC Misra, GR Rout, MC Pattanaik, S Aparajita. Abstract. Molecular characterisation of the 15 early duration finger millet (Eleusine coracana G) genotypes was done through RAPD markers. Twenty-five ...

  3. Trichostrongylus colubriformis rDNA polymorphism associated with arrested development

    Langrová, I.; Zouhar, M.; Vadlejch, J.; Borovský, M.; Jankovská, I.; Lytvynets, Andrej

    2008-01-01

    Roč. 103, č. 2 (2008), s. 401-403 ISSN 0932-0113 Institutional research plan: CEZ:AV0Z50110509 Keywords : arrested development * polymorphism * rDNA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.473, year: 2008

  4. Polymorphism of the simple sequence repeat (AAC)5 in the ...

    2013-12-04

    Dec 4, 2013 ... SSRs could be present in coding and noncoding regions, contributing to genome dynamics and evolution. Previous studies by our research group detected molecular and cytogenetic riboso- mal DNA (rDNA) polymorphisms in Old Portuguese bread and durum wheat cultivars. Considering the rRNA genes.

  5. Evaluation of distribution and sources of sewage molecular marker (LABs) in selected rivers and estuaries of Peninsular Malaysia.

    Magam, Sami M; Zakaria, Mohamad Pauzi; Halimoon, Normala; Aris, Ahmad Zaharin; Kannan, Narayanan; Masood, Najat; Mustafa, Shuhaimi; Alkhadher, Sadeq; Keshavarzifard, Mehrzad; Vaezzadeh, Vahab; Sani, Muhamad S A; Latif, Mohd Talib

    2016-03-01

    This is the first extensive report on linear alkylbenzenes (LABs) as sewage molecular markers in surface sediments collected from the Perlis, Kedah, Merbok, Prai, and Perak Rivers and Estuaries in the west of Peninsular Malaysia. Sediment samples were extracted, fractionated, and analyzed using gas chromatography mass spectrometry (GC-MS). The concentrations of total LABs ranged from 68 to 154 (Perlis River), 103 to 314 (Kedah River), 242 to 1062 (Merbok River), 1985 to 2910 (Prai River), and 217 to 329 ng g(-1) (Perak River) dry weight (dw). The highest levels of LABs were found at PI3 (Prai Estuary) due to the rapid industrialization and population growth in this region, while the lowest concentrations of LABs were found at PS1 (upstream of Perlis River). The LABs ratio of internal to external isomers (I/E) in this study ranged from 0.56 at KH1 (upstream of Kedah River) to 1.35 at MK3 (Merbok Estuary) indicating that the rivers receive raw sewage and primary treatment effluents in the study area. In general, the results of this paper highlighted the necessity of continuation of water treatment system improvement in Malaysia.

  6. Molecular weight distribution of electron and γ-ray irradiated PEEK measured by very high temperature GPC

    Nakahara, H.

    1996-01-01

    Poly(ether ether ketone)(PEEK) films were irradiated with electron beam in air and in helium. Gel fractions of the PEEK samples were determined as the ratio of the weight of insoluble fraction/total weigh by extracting the samples with 1-chloronaphthalene (1-CN) at 260degC. While unirradiated PEEK samples were dissolved in 1-CN completely, PEEK samples highly (10 - 50 MGy) irradiated in air were almost insoluble in the solvent. The weight-average molecular weight M w of soluble fractions of the samples were measured by very high temperature gel permeation chromatography (VHTGPC): it was found that the M w decreases with increasing dose. On the other hand, PEEK samples irradiated in helium gave gel fractions at lower doses (0 - 5 MGy) than in air. The PEEK films were also irradiated with 60 Co γ-rays in the dose range, i.e. from 0 to 5 MGy. The γ-irradiated PEEK samples were completely dissolved in 1-CN at 260degC. Their M w measured by VHTGPC decreases with increasing dose. (author)

  7. Highly Cross-Linked Polyethylene in Total Hip and Knee Replacement: Spatial Distribution of Molecular Orientation and Shape Recovery Behavior

    Yasuhito Takahashi

    2014-01-01

    Full Text Available The present study investigated effects of processing procedures on morphology of highly cross-linked and re-melted UHMWPE (XLPE in total hip and knee arthroplasty (THA, TKA. The shape recovery behavior was also monitored via uniaxial compression test at room temperature after non-destructive characterizations of the in-depth microstructure by confocal/polarized Raman spectroscopy. The goal of this study was to relate the manufacturing-induced morphology to the in vivo micromechanical performance, and ultimately to explore an optimal structure in each alternative joint bearing. It was clearly confirmed that the investigated XLPE hip and knee implants, which were produced from different orthopaedic grade resins (GUR 1050 and GUR 1020, consisted of two structural regions in the as-received states: the near-surface transitional anisotropic layer (≈100 μm thickness and the bulk isotropic structural region. These XLPEs exhibited a different crystalline anisotropy and molecular texture within the near-surface layers. In addition, the knee insert showed a slightly higher efficiency of shape recovery against the applied strain over the hip liner owing to a markedly higher percentage of the bulk amorphous phase with intermolecular cross-linking. The quantitative data presented in this study might contribute to construct manufacturing strategies for further rationalized structures as alternative bearings in THA and TKA.

  8. Hemorrhagic Shock and Surgical Stress Alter Distribution of Labile Zinc within High and Low Molecular Weight Plasma Fractions

    Kelly, Edward; Mathew, Jeff; Kohler, Jonathan E.; Blass, Amy L.; Soybel, David I.

    2012-01-01

    Zinc ions (Zn2+) are essential for tissue repair following injury or stress. We hypothesize that during such stresses Zn2+ is redistributed to labile pools in plasma components. Here we tested this hypothesis utilizing a novel assay to monitor labile Zn2+ in plasma in hemorrhagic shock. Adult rats in the Shock (S) group underwent hemorrhage and resuscitation. Blood samples were drawn at baseline, 1 hr, 4 hrs and 24 hrs. The Surgical Control (SC) group was anesthetized and instrumented, but not bled. Albumin, total Zn2+, and labile Zn2+ levels were assayed in plasma. Binding capacity for Zn2+ was assessed in high (HMW) and low (LMW) molecular weight pools. Significant decreases in total Zn2+ were observed by 24 hrs, in both S and SC groups. Albumin levels were significantly reduced in the S group at 1 hr and 4 hr but restored at 24 hrs; significant changes were not observed in other groups. In whole plasma, labile Zn2+ levels were stable initially in the S and SC groups, but declined at 24 hrs. In the HMW pool, marked and significant impairment of binding was noted throughout all time periods following the shock period in the S group. Such changes were observed in the SC group of less intensity and duration. These experiments suggest that Shock alters affinity of plasma proteins for Zn2+, promoting delivery to peripheral tissues during periods of increased Zn2+ utilization. PMID:22744307

  9. Discrepancies between conformational distributions of a polyalanine peptide in solution obtained from molecular dynamics force fields and amide I' band profiles.

    Verbaro, Daniel; Ghosh, Indrajit; Nau, Werner M; Schweitzer-Stenner, Reinhard

    2010-12-30

    Structural preferences in the unfolded state of peptides determined by molecular dynamics still contradict experimental data. A remedy in this regard has been suggested by MD simulations with an optimized Amber force field ff03* ( Best, R. Hummer, G. J. Phys. Chem. B 2009 , 113 , 9004 - 9015 ). The simulations yielded a statistical coil distribution for alanine which is at variance with recent experimental results. To check the validity of this distribution, we investigated the peptide H-A(5)W-OH, which with the exception of the additional terminal tryptophan is analogous to the peptide used to optimize the force fields ff03*. Electronic circular dichroism, vibrational circular dichroism, and infrared spectroscopy as well as J-coupling constants obtained from NMR experiments were used to derive the peptide's conformational ensemble. Additionally, Förster resonance energy transfer between the terminal chromophores of the fluorescently labeled peptide analogue H-Dbo-A(5)W-OH was used to determine its average length, from which the end-to-end distance of the unlabeled peptide was estimated. Qualitatively, the experimental (3)J(H(N),C(α)), VCD, and ECD indicated a preference of alanine for polyproline II-like conformations. The experimental (3)J(H(N),C(α)) for A(5)W closely resembles the constants obtained for A(5). In order to quantitatively relate the conformational distribution of A(5) obtained with the optimized AMBER ff03* force field to experimental data, the former was used to derive a distribution function which expressed the conformational ensemble as a mixture of polyproline II, β-strand, helical, and turn conformations. This model was found to satisfactorily reproduce all experimental J-coupling constants. We employed the model to calculate the amide I' profiles of the IR and vibrational circular dichroism spectrum of A(5)W, as well as the distance between the two terminal peptide carbonyls. This led to an underestimated negative VCD couplet and an

  10. Assessing Date Palm Genetic Diversity Using Different Molecular Markers.

    Atia, Mohamed A M; Sakr, Mahmoud M; Adawy, Sami S

    2017-01-01

    Molecular marker technologies which rely on DNA analysis provide powerful tools to assess biodiversity at different levels, i.e., among and within species. A range of different molecular marker techniques have been developed and extensively applied for detecting variability in date palm at the DNA level. Recently, the employment of gene-targeting molecular marker approaches to study biodiversity and genetic variations in many plant species has increased the attention of researchers interested in date palm to carry out phylogenetic studies using these novel marker systems. Molecular markers are good indicators of genetic distances among accessions, because DNA-based markers are neutral in the face of selection. Here we describe the employment of multidisciplinary molecular marker approaches: amplified fragment length polymorphism (AFLP), start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), simple sequence repeats (SSR), and random amplified polymorphic DNA (RAPD) to assess genetic diversity in date palm.

  11. Molecular markers for tracking the origin and worldwide distribution of invasive strains of Puccinia striiformis

    Walter, Stephanie; Ali, Sajid; Kemen, Eric

    2016-01-01

    .g., the spreading of two aggressive and high temperature adapted strains to three continents since 2000. The combination of sequence-characterized amplified region (SCAR) markers, which were developed from two specific AFLP fragments, differentiated the two invasive strains, PstS1 and PstS2 from all other P....... striiformis strains investigated at a worldwide level. The application of the SCAR markers on 566 isolates showed that PstS1 was present in East Africa in the early 1980s and then detected in the Americas in 2000 and in Australia in 2002. PstS2 which evolved from PstS1 became widespread in the Middle East...... as the most plausible origin of the two invasive strains. The SCAR markers developed in the present study provide a rapid, inexpensive, and efficient tool to track the distribution of P. striiformis invasive strains, PstS1 and PstS2....

  12. Molecular analysis of the distribution of chromosomal breakpoints: characterization of a 'hot' region for breaks in human chromosome 11

    Vannais, D.B.; Hirai, Y.; Cologne, J.B.; Waldren, C.A.; Ueno, A.

    2003-01-01

    Full text: Ionizing radiation randomly damages DNA and chromosomes whereas subsequent chromosome breaks are non-random. Assuming, as an ideal and naive but useful proposition, that breaks are equally likely anywhere in the chromosome and that a deletion always occurs between two breaks, the frequency of fragments would decrease linearly with increasing fragment size. This simple distribution is not, however, observed. To shed light on the 'real' situation of break formation we mapped breakpoints in the human chromosome no. 11 of 353 independent CD59- mutants isolated from human/hamster hybrid AL cells exposed to radiations (high and low dose-rate gamma rays, high LET carbon or nitrogen ions, protons) or chemicals (arsenic or irradiated, mutagenic histidine) or unexposed. The number of breaks per unit length of DNA differed significantly in different regions of chromosome 11.The highest level of breaks (140/mbp) were in the 0.8 mbp segment between CD59 and Catalase (CAT). Finer mapping of break points was carried out using 26 PCR primer pairs spread across this interval in 15 independent mutants. In two mutants, the break point was in a 107 bp fragment; in the other 13 the breaks were in a single 35 mbp fragment, but not all were at exactly the same site; 4 of 13 occurred in 3 different 3 mbp sub-segments. We are sequencing these fragments to look for such features as repeats: 'colder' regions like that between CD59 and WT will also be analyzed. But, since at least some breaks occurred at different sites and the frequency and distribution of breaks was about the same for all treatments, our we postulate that hot (and cold spots) may be due more to structural features or specific repair than to sequence or type of damage

  13. Multiple glacial refugia of the low-dispersal ground beetle Carabus irregularis: molecular data support predictions of species distribution models.

    Katharina Homburg

    Full Text Available Classical glacial refugia such as the southern European peninsulas were important for species survival during glacial periods and acted as sources of post-glacial colonisation processes. Only recently, some studies have provided evidence for glacial refugia north of the southern European peninsulas. In the present study, we combined species distribution models (SDMs with phylogeographic analyses (using mitochondrial DNA = mtDNA to investigate if the cold-adapted, stenotopic and flightless ground beetle species, Carabus irregularis, survived the Last Glacial Maximum (LGM in classical and/or other refugia. SDMs (for both a western European and for a Carpathian subgroup were calculated with MAXENT on the basis of 645 species records to predict current and past distribution patterns. Two mtDNA loci (CO1 and ND5, concatenated sequence length: 1785 bp were analyzed from 91 C. irregularis specimens to reconstruct the phylogeography of Central and eastern European populations and to estimate divergence times of the given lineages. Strong intra-specific genetic differentiation (inter-clade ΦST values ranged from 0.92 to 0.99 implied long-term isolation of major clades and subsclades. The high divergence between the nominate subspecies and the Carpathian subspecies C. i. montandoni points to two independent species rather than subspecies (K-2P distance 0.042 ± 0.004; supposed divergence of the maternal lineages dated back 1.6 to 2.5 million years BP differing not only morphologically but also genetically and ecologically from each other. The SDMs also inferred classical as well as other refugia for C. irregularis, especially north of the Alps, in southeastern Europe and in the Carpathians. The coincidences between the results of both methods confirm the assumption of multiple glacial refugia for the studied species and the usefulness of combining methodological approaches for the understanding of the history of low-dispersal insect species.

  14. Molecular phylogeny and biogeographic diversification of linnaeoideae (caprifoliaceae s. L.) disjunctly distributed in Eurasia, North America and Mexico.

    Wang, Hua-Feng; Landrein, Sven; Dong, Wen-Pan; Nie, Ze-Long; Kondo, Katsuhiko; Funamoto, Tsuneo; Wen, Jun; Zhou, Shi-Liang

    2015-01-01

    Linnaeoideae is a small subfamily of erect or creeping shrubs to small trees in Caprifoliaceae that exhibits a wide disjunct distribution in Eurasia, North America and Mexico. Most taxa of the subfamily occur in eastern Asia and Mexico but the monospecific genus Linnaea has a circumboreal to north temperate distribution. In this study, we conducted phylogenetic and biogeographic analyses for Linnaeoideae and its close relatives based on sequences of the nuclear ribosomal ITS and nine plastid (rbcL, trnS-G, matK, trnL-F, ndhA, trnD-psbM, petB-D, trnL-rpl32 and trnH-psbA) markers. Our results support that Linnaeoideae is monophyletic, consisting of four eastern Asian lineages (Abelia, Diabelia, Dipelta and Kolkwitzia), the Mexican Vesalea, and Linnaea. The Mexican Vesalea was formerly placed in Abelia, but it did not form a clade with the eastern Asian Abelia; instead Vesalea and Linnaea are sisters. The divergence time between the eastern Asian lineages and the Mexican Vesalea plus the Linnaea clade was dated to be 50.86 Ma, with a 95% highest posterior density of 42.8 Ma (middle Eocene) to 60.19 Ma (early Paleocene) using the Bayesian relaxed clock estimation. Reconstructed ancestral areas indicated that the common ancestor of Linnaea plus Vesalea may have been widespread in eastern Asia and Mexico or originated in eastern Asia during the Eocene and likely migrated across continents in the Northern Hemisphere via the North Atlantic Land Bridges or the Bering Land Bridge. The Qinling Mountains of eastern Asia are the modern-day center of diversity of Kolkwitzia-Dipelta-Diabelia clade. The Diabeliaclade became highly diversified in Japan and eastern China. Populations of Diabelia serrata in Japan and eastern China were found to be genetically identical in this study, suggesting a recent disjunction across the East China Sea, following the last glacial event.

  15. Distribution of genes encoding virulence factors and molecular analysis of Shigella spp. isolated from patients with diarrhea in Kerman, Iran.

    Hosseini Nave, Hossein; Mansouri, Shahla; Emaneini, Mohammad; Moradi, Mohammad

    2016-03-01

    Shigella is one of the important causes of diarrhea worldwide. Shigella has several virulence factors contributing in colonization and invasion of epithelial cells and eventually death of host cells. The present study was performed in order to investigate the distribution of virulence factors genes in Shigella spp. isolated from patients with acute diarrhea in Kerman, Iran as well as the genetic relationship of these isolates. A total of 56 isolates including 31 S. flexneri, 18 S. sonnei and 7 S. boydii were evaluated by polymerase chain reaction (PCR) for the presence of 11 virulence genes (ipaH, ial, set1A, set1B, sen, virF, invE, sat, sigA, pic and sepA). Then, the clonal relationship of these strains was analyzed by multilocus variable-number tandem repeat analysis (MLVA) method. All isolates were positive for ipaH gene. The other genes include ial, invE and virF were found in 80.4%, 60.7% and 67.9% of the isolates, respectively. Both set1A and set1B were detected in 32.3% of S. flexneri isolates, whereas 66.1% of the isolates belonging to different serogroup carried sen gene. The sat gene was present in all S. flexneri isolates, but not in the S. sonnei and S. boydii isolates. The result showed, 30.4% of isolates were simultaneously positive and the rest of the isolates were negative for sepA and pic genes. The Shigella isolates were divided into 29 MLVA types. This study, for the first time, investigated distribution of 11 virulence genes in Shigella spp. Our results revealed heterogeneity of virulence genes in different Shigella serogroups. Furthermore, the strains belonging to the same species had little diversity. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Diffuse Scattering as an Aid to the Understanding of Polymorphism in Pharmaceuticals

    Welberry, T.R.; Chan, E.J.; Goossens, D.J.; Heerdegen, A.P. (ANU)

    2012-04-30

    Polymorphism occurs when the same molecular compound can crystallize in more than one distinct crystal structure. Its study is a field of great interest and activity. This is largely driven by its importance in the pharmaceutical industry, but polymorphism is also an issue in the pigments, dyes, and explosives industries. The polymorph formed by a compound generally exerts a strong influence on its solid-state properties. The polymorphic form of a drug molecule may affect the ease of manufacture and processing, shelf life, and most significantly the rate of uptake of the molecule by the human body. They can even vary in toxicity; one polymorph may be safe, while a second may be toxic. In this review of recently published work, we show how diffuse scattering experiments coupled with Monte Carlo (MC) computer modeling can aid in the understanding of polymorphism. Examples of the two common pharmaceuticals, benzocaine and aspirin, both of which are bimorphic, at ambient temperatures, are discussed.

  17. Exploring the diversity and distribution of neotropical avian malaria parasites--a molecular survey from Southeast Brazil.

    Gustavo A Lacorte

    Full Text Available Southeast Brazil is a neotropical region composed of a mosaic of different tropical habitats and mountain chains, which allowed for the formation of bird-rich communities with distinct ecological niches. Although this region has the potential to harbor a remarkable variety of avian parasites, there is a lack of information about the diversity of malarial parasites. We used molecular approaches to characterize the lineage diversity of Plasmodium and Haemoproteus in bird communities from three different habitats in southeast Brazil based on the prevalence, richness and composition of lineages. We observed an overall prevalence of 35.3%, with a local prevalence ranging from 17.2% to 54.8%. Moreover, no significant association between prevalence and habitat type could be verified (p>0.05. We identified 89 Plasmodium and 22 Haemoproteus lineages, with 86% of them described for the first time here, including an unusual infection of a non-columbiform host by a Haemoproteus (Haemoproteus parasite. The composition analyses of the parasite communities showed that the lineage composition from Brazilian savannah and tropical dry forest was similar, but it was different from the lineage composition of Atlantic rainforest, reflecting the greater likeness of the former habitats with respect to seasonality and forest density. No significant effects of habitat type on lineage richness were observed based on GLM analyses. We also found that sites whose samples had a greater diversity of bird species showed a greater diversity of parasite lineages, providing evidence that areas with high bird richness also have high parasite richness. Our findings point to the importance of the neotropical region (southeast Brazil as a major reservoir of new haemosporidian lineages.

  18. HERC1 polymorphisms: population-specific variations in haplotype composition.

    Yuasa, Isao; Umetsu, Kazuo; Nishimukai, Hiroaki; Fukumori, Yasuo; Harihara, Shinji; Saitou, Naruya; Jin, Feng; Chattopadhyay, Prasanta K; Henke, Lotte; Henke, Jürgen

    2009-08-01

    Human HERC1 is one of six HERC proteins and may play an important role in intracellular membrane trafficking. The human HERC1 gene is suggested to have been affected by local positive selection. To assess the global frequency distributions of coding and non-coding single nucleotide polymorphisms (SNPs) in the HERC1 gene, we developed a new simultaneous genotyping method for four SNPs, and applied this method to investigate 1213 individuals from 12 global populations. The results confirmed remarked differences in the allele and haplotype frequencies between East Asian and non-East Asian populations. One of the three common haplotypes observed was found to be characteristic of East Asians, who showed a relatively uniform distribution of haplotypes. Information on haplotypes would be useful for testing the function of polymorphisms in the HERC1 gene. This is the first study to investigate the distribution of HERC1 polymorphisms in various populations. (c) 2009 John Wiley & Sons, Ltd.

  19. A combined molecular dynamics and Monte Carlo simulation of the spatial distribution of energy deposition by proton beams in liquid water

    Garcia-Molina, Rafael [Departamento de Fisica, Centro de Investigacion en Optica y Nanofisica (CIOyN), Universidad de Murcia, E-30100 Murcia (Spain); Abril, Isabel [Departament de Fisica Aplicada, Universitat d' Alacant, E-03080 Alacant (Spain); Heredia-Avalos, Santiago [Departament de Fisica, Enginyeria de Sistemes i Teoria del Senyal, Universitat d' Alacant, E-03080 Alacant (Spain); Kyriakou, Ioanna; Emfietzoglou, Dimitris, E-mail: rgm@um.es [Medical Physics Laboratory, University of Ioannina Medical School, GR-45110 Ioannina (Greece)

    2011-10-07

    We have evaluated the spatial distribution of energy deposition by proton beams in liquid water using the simulation code SEICS (Simulation of Energetic Ions and Clusters through Solids), which combines molecular dynamics and Monte Carlo techniques and includes the main interaction phenomena between the projectile and the target constituents: (i) the electronic stopping force due to energy loss to target electronic excitations, including fluctuations due to the energy-loss straggling, (ii) the elastic scattering with the target nuclei, with their corresponding energy loss and (iii) the dynamical changes in projectile charge state due to electronic capture and loss processes. An important feature of SEICS is the accurate account of the excitation spectrum of liquid water, based on a consistent solid-state description of its energy-loss-function over the whole energy and momentum space. We analyse how the above-mentioned interactions affect the depth distribution of the energy delivered in liquid water by proton beams with incident energies of the order of several MeV. Our simulations show that the position of the Bragg peak is determined mainly by the stopping power, whereas its width can be attributed to the energy-loss straggling. Multiple elastic scattering processes contribute slightly only at the distal part of the Bragg peak. The charge state of the projectiles only changes when approaching the end of their trajectories, i.e. near the Bragg peak. We have also simulated the proton-beam energy distribution at several depths in the liquid water target, and found that it is determined mainly by the fluctuation in the energy loss of the projectile, evaluated through the energy-loss straggling. We conclude that a proper description of the target excitation spectrum as well as the inclusion of the energy-loss straggling is essential in the calculation of the proton beam depth-dose distribution.

  20. A combined molecular dynamics and Monte Carlo simulation of the spatial distribution of energy deposition by proton beams in liquid water

    Garcia-Molina, Rafael; Abril, Isabel; Heredia-Avalos, Santiago; Kyriakou, Ioanna; Emfietzoglou, Dimitris

    2011-01-01

    We have evaluated the spatial distribution of energy deposition by proton beams in liquid water using the simulation code SEICS (Simulation of Energetic Ions and Clusters through Solids), which combines molecular dynamics and Monte Carlo techniques and includes the main interaction phenomena between the projectile and the target constituents: (i) the electronic stopping force due to energy loss to target electronic excitations, including fluctuations due to the energy-loss straggling, (ii) the elastic scattering with the target nuclei, with their corresponding energy loss and (iii) the dynamical changes in projectile charge state due to electronic capture and loss processes. An important feature of SEICS is the accurate account of the excitation spectrum of liquid water, based on a consistent solid-state description of its energy-loss-function over the whole energy and momentum space. We analyse how the above-mentioned interactions affect the depth distribution of the energy delivered in liquid water by proton beams with incident energies of the order of several MeV. Our simulations show that the position of the Bragg peak is determined mainly by the stopping power, whereas its width can be attributed to the energy-loss straggling. Multiple elastic scattering processes contribute slightly only at the distal part of the Bragg peak. The charge state of the projectiles only changes when approaching the end of their trajectories, i.e. near the Bragg peak. We have also simulated the proton-beam energy distribution at several depths in the liquid water target, and found that it is determined mainly by the fluctuation in the energy loss of the projectile, evaluated through the energy-loss straggling. We conclude that a proper description of the target excitation spectrum as well as the inclusion of the energy-loss straggling is essential in the calculation of the proton beam depth-dose distribution.

  1. Single Nucleotide Polymorphism

    Børsting, Claus; Pereira, Vania; Andersen, Jeppe Dyrberg

    2014-01-01

    Single nucleotide polymorphisms (SNPs) are the most frequent DNA sequence variations in the genome. They have been studied extensively in the last decade with various purposes in mind. In this chapter, we will discuss the advantages and disadvantages of using SNPs for human identification...... of SNPs. This will allow acquisition of more information from the sample materials and open up for new possibilities as well as new challenges....

  2. Distribuição de massa molecular de ácidos húmicos e promoção do crescimento radicular Molecular weight distribution of humic acids and root growth promotion

    Natália de Oliveira Aguiar

    2009-12-01

    mais relacionada com a estrutura química das substâncias húmicas do que com a distribuição de massa molecular dos agregados húmicos.Humic acids (HA directly stimulate several physiological processes that promote plant growth, particularly of the root system. Knowledge about the chemical nature and the role of HA in the effects observed under biofertilization and biostimulation is essential to develop HA-based biological resources. The aim of this study was to evaluate a possible relationship between the distribution of the apparent molecular weight of HA isolated from vermicompost and the response in root growth promotion. HA sub-fractions were obtained through preparative chromatography by size exclusion using Sephadex gel G-50 gel (CGE. The preparative process was validated by high-performance size-exclusion chromatography (HPSEC. The five sub-fractions were tested at different concentrations (0; 0.0001; 0.001; 0.003; 0.005; and 0.001 mol L-1 C for their capacity to stimulate root growth of Arabidopisis thaliana (ecotype col 4 seedlings. For maize seedlings (Zea mays hybrid UENF 506-6 a rate of 0.002 mol L-1 C was used. The quadratic model described the relationship between root growth induction and HA dose in Arabidopsis; 0.00511 mol L-1 C was the average inflection point. At the optimum concentration, a significant negative correlation between molecular weight distribution and the number of lateral roots induced in A. thaliana was observed. However, other root traits, e.g., area and length, were not influenced by the apparent molecular weight of fractions. An increase in the number of mitotic and lateral root emission was observed for maize seedlings, both for the treatment with HA as well as with the sub-fractions. The H+-ATPase activity of plasma membrane was significantly affected by HA, although differently in the sub-fractions. The stimulating activity of root growth seems to be more related to the chemical structure of humic substances than to the

  3. The geographic distribution of Argas (Persicargas) miniatus and Argas (Persicargas) persicus (Acari: Argasidae) in America, with morphological and molecular diagnoses from Brazil, Chile and Cuba.

    Muñoz-Leal, Sebastián; Venzal, José M; Nava, Santiago; Reyes, Mercedes; Martins, Thiago F; Leite, Romário C; Vilela, Vinicius L R; Benatti, Hector R; Ríos-Rosas, Daniela; Barros-Battesti, Darci M; González-Acuña, Daniel; Labruna, Marcelo B

    2018-01-01

    High similarity of morphological traits has historically overshadowed the identities and distributions of poultry-associated soft ticks Argas (Persicargas) miniatus and Argas (Persicargas) persicus in America. In order to model the occurrence of both parasites in the continent, in the current study we performed morphological and molecular analyses to identify ticks collected in hen houses from Brazil and northern Chile. Combining these results with literature data, and the examination of Argas allotments deposited in the tick collections "Coleção Nacional de Carrapatos Danilo Gonçalves Saraiva" (Brazil), the "Coleção Acarológica do Instituto Butantan São Paulo" (Brazil), and the "Colección Zoológica de la Academia de Ciencia de Cuba" (Cuba), we present a critical list with the localities where A. (P.) miniatus and A. (P.) persicus have been reported in the American continent. Our results confirmed the presence of A. (P.) miniatus in Brazil and Cuba, and A. (P.) persicus in Chile, which in particular, constitutes the first molecularly confirmed report of the later species for South America. Although A. (P.) miniatus and A. (P.) persicus have been documented in 21 American countries, the identity of some reports must still be considered as uncertain until detailed morphological and/or molecular studies are performed. When contrasted to a Köppen-Geiger climate classification, A. (P.) miniatus predominantly occurs in equatorial and A. (P.) persicus in arid climates. However, until undetermined reports of both species are correctly identified, any conclusion on their geo-climatological occurrence throughout the American continent would be rather speculative. Copyright © 2017 Elsevier GmbH. All rights reserved.

  4. The -271 G>A polymorphism of kinase insert domain-containing receptor gene regulates its transcription level in patients with non-small cell lung cancer

    An, She-Juan; Chen, Zhi-Hong; Lin, Qiu-Xiong; Su, Jian; Chen, Hua-Jun; Lin, Jia-Ying; Wu, Yi-Long

    2009-01-01

    Kinase insert domain-containing receptor (KDR) plays a critical role in the metastasis of cancer and is used as a molecular target in cancer therapy. We investigated the characteristics of the -271 G>A polymorphism of the KDR gene to gain information that may benefit the development of individualized therapies for patients with non-small cell lung cancer (NSCLC). The -271 G>A polymorphism of the KDR gene in 106 lung cancer patients and 203 healthy control individuals was analyzed by polymerase chain reaction (PCR) and DNA sequencing methods. Real-time quantitative PCR and immunohistochemical methods were used to evaluate KDR mRNA and protein expression levels, respectively, in frozen tumor specimens. The -271 G>A polymorphism was associated with the mRNA expression level of the KDR gene in tumor tissues (t = 2.178, P = 0.032, independent samples t-test). Compared with the AG/GG genotype, the AA genotype was associated with higher KDR mRNA expression in tumor tissues. We found no relationship between the genotype and the KDR protein expression level and no significant difference in the distribution of the KDR gene polymorphism genotypes between lung cancer patients and the control group (χ 2 = 1.269, P = 0.264, Fisher's exact test). This study is the first to show that the -271 G>A polymorphism of the KDR gene may be a functional polymorphism related to the regulation of gene transcription. These findings may have important implications for therapies targeting KDR in patients with NSCLC

  5. Contributions of molecular size, charge distribution, and specific amino acids to the iron-binding capacity of sea cucumber (Stichopus japonicus) ovum hydrolysates.

    Sun, Na; Cui, Pengbo; Jin, Ziqi; Wu, Haitao; Wang, Yixing; Lin, Songyi

    2017-09-01

    This study investigated the contributions of molecular size, charge distribution and specific amino acids to the iron-binding capacity of sea cucumber (Stichopus japonicus) ovum hydrolysates (SCOHs), and further explored their iron-binding sites. It was demonstrated that enzyme type and degree of hydrolysis (DH) significantly influenced the iron-binding capacity of the SCOHs. The SCOHs produced by alcalase at a DH of 25.9% possessed the highest iron-binding capacity at 92.1%. As the hydrolysis time increased, the molecular size of the SCOHs decreased, the negative charges increased, and the hydrophilic amino acids were exposed to the surface, facilitating iron binding. Furthermore, the Fourier transform infrared spectra, combined with amino acid composition analysis, revealed that iron bound to the SCOHs primarily through interactions with carboxyl oxygen of Asp, guanidine nitrogen of Arg or nitrogen atoms in imidazole group of His. The formed SCOHs-iron complexes exhibited a fold and crystal structure with spherical particles. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Molecular technique reveals high variability of 18S rDNA distribution in harvestmen (Opiliones, Phalangiidae) from South Africa.

    Šťáhlavský, František; Opatova, Vera; Just, Pavel; Lotz, Leon N; Haddad, Charles R

    2018-01-01

    The knowledge of cytogenetics in the harvestmen family Phalangiidae has been based on taxa from the Northern Hemisphere. We performed cytogenetic analysis on Guruia africana (Karsch, 1878) (2n=24) and four species of the genus Rhampsinitus Simon, 1879 (2n=24, 26, 34) from South Africa. Fluorescence in situ hybridization with an 18S rDNA probe was used to analyze the number and the distribution of this cluster in the family Phalangiidae for the first time. The results support the cytogenetic characteristics typical for the majority of harvestmen taxa, i.e. the predominance of small biarmed chromosomes and the absence of morphologically well-differentiated sex chromosomes as an ancestral state. We identified the number of 18S rDNA sites ranging from two in R. qachasneki Kauri, 1962 to seven in one population of R. leighi Pocock, 1903. Moreover, we found differences in the number and localization of 18S rDNA sites in R. leighi between populations from two localities and between sexes of R. capensis (Loman, 1898). The heterozygous states of the 18S rDNA sites in these species may indicate the presence of XX/XY and ZZ/ZW sex chromosomes, and the possible existence of these systems in harvestmen is discussed. The variability of the 18S rDNA sites indicates intensive chromosomal changes during the differentiation of the karyotypes, which is in contrast to the usual uniformity in chromosomal morphology known from harvestmen so far.

  7. Abcb1 in Pigs: Molecular cloning, tissues distribution, functional analysis, and its effect on pharmacokinetics of enrofloxacin

    Guo, Tingting; Huang, Jinhu; Zhang, Hongyu; Dong, Lingling; Guo, Dawei; Guo, Li; He, Fang; Bhutto, Zohaib Ahmed; Wang, Liping

    2016-01-01

    P-glycoprotein (P-gp) is one of the best-known ATP-dependent efflux transporters, contributing to differences in pharmacokinetics and drug-drug interactions. Until now, studies on pig P-gp have been scarce. In our studies, the full-length porcine P-gp cDNA was cloned and expressed in a Madin-Darby Canine Kidney (MDCK) cell line. P-gp expression was then determined in tissues and its role in the pharmacokinetics of oral enrofloxacin in pigs was studied. The coding region of pig Abcb1 gene was 3,861 bp, encoding 1,286 amino acid residues (Mw = 141,966). Phylogenetic analysis indicated a close evolutionary relationship between porcine P-gp and those of cow and sheep. Pig P-gp was successfully stably overexpressed in MDCK cells and had efflux activity for rhodamine 123, a substrate of P-gp. Tissue distribution analysis indicated that P-gp was highly expressed in brain capillaries, small intestine, and liver. In MDCK-pAbcb1 cells, enrofloxacin was transported by P-gp with net efflux ratio of 2.48 and the efflux function was blocked by P-gp inhibitor verapamil. High expression of P-gp in the small intestine could modify the pharmacokinetics of orally administrated enrofloxacin by increasing the Cmax, AUC and Ka, which was demonstrated using verapamil, an inhibitor of P-gp. PMID:27572343

  8. CLASS 0 PROTOSTARS IN THE PERSEUS MOLECULAR CLOUD: A CORRELATION BETWEEN THE YOUNGEST PROTOSTARS AND THE DENSE GAS DISTRIBUTION

    Sadavoy, S. I.; Di Francesco, J. [Department of Physics and Astronomy, University of Victoria, P.O. Box 355, STN CSC, Victoria, BC, V8W 3P6 (Canada); André, Ph.; Maury, A.; Men' shchikov, A.; Motte, F.; Hennemann, M.; Könyves, V.; Louvet, F.; Roy, A. [Laboratoire AIM, CEA/DSM-CNRS-Université Paris Diderot, IRFU/Service dAstrophysique, Saclay, F-91191 Gif-sur-Yvette (France); Pezzuto, S.; Benedettini, M.; Elia, D. [Istituto di Astrofisica e Planetologia Spaziali, Via Fosso del Cavaliere 100, I-00133 Rome (Italy); Bernard, J.-P. [CNRS, IRAP, 9 Av. Colonel Roche, BP 44346, F-31028 Toulouse Cedex 4 (France); Nguyên-Lu' o' ng, Q. [Canadian Institute for Theoretical Astrophysics, University of Toronto, Toronto, ON, M5S 3H8 (Canada); Schneider, N.; Bontemps, S. [Université de Bordeaux, LAB, UMR 5804, F-33270 Floirac (France); Arzoumanian, D. [IAS, CNRS (UMR 8617), Université Paris-Sud 11, Bâtiment 121, F-91400 Orsay (France); Hill, T. [Joint ALMA Observatory, Alonso de Cordova 3107, Vitacura 763-0355, Santiago (Chile); Peretto, N., E-mail: sadavoy@mpia.de [School of Physics and Astronomy, Cardiff University, Cardiff CF24 3AA (United Kingdom); and others

    2014-06-01

    We use PACS and SPIRE continuum data at 160 μm, 250 μm, 350 μm, and 500 μm from the Herschel Gould Belt Survey to sample seven clumps in Perseus: B1, B1-E, B5, IC 348, L1448, L1455, and NGC 1333. Additionally, we identify and characterize the embedded Class 0 protostars using detections of compact Herschel sources at 70 μm as well as archival Spitzer catalogs and SCUBA 850 μm photometric data. We identify 28 candidate Class 0 protostars, four of which are newly discovered sources not identified with Spitzer. We find that the star formation efficiency of clumps, as traced by Class 0 protostars, correlates strongly with the flatness of their respective column density distributions at high values. This correlation suggests that the fraction of high column density material in a clump reflects only its youngest protostellar population rather than its entire source population. We propose that feedback from either the formation or evolution of protostars changes the local density structure of clumps.

  9. Molecular epidemiology and genotype distribution of Human Papillomavirus (HPV) among Arab women in the State of Qatar.

    Bansal, Devendra; Elmi, Asha A; Skariah, Sini; Haddad, Pascale; Abu-Raddad, Laith J; Al Hamadi, Aysha H; Mohamed-Nady, Nady; Affifi, Nahla M; Ghedira, Randa; Hassen, Elham; Al-Thani, Asma A J; Al-Ansari, Afaf A H M; Sultan, Ali A

    2014-11-26

    Human Papilloma Virus (HPV) infection is the major cause of cervical cancer worldwide. With limited data available on HPV prevalence in the Arab countries, this study aimed to identify the prevalence and genotypic distribution of HPV in the State of Qatar. 3008 cervical samples, exclusively of women with Arabic origin residing in Qatar were collected from the Women's Hospital and Primary Health Care Corporation in Doha, State of Qatar. HPV DNA detection was done using GP5+/6+ primers based real time-polymerase chain reaction (RT-PCR) assay followed by the usage of HPV type specific primers based RT- PCR reactions and Sanger sequencing for genotype identification. Similar prevalence rates of HPV infection was identified in both Qatari and non-Qatari women at 6.2% and 5.9% respectively. HPV prevalence rate of 5.8% and 18.4% was identified in women with normal cytology and in women with abnormal cytology respectively. HPV 81, 11 and 16, in decreasing order were the most commonly identified genotypes. HPV 81 was the most frequent low-risk genotype among women with both normal (74.0%) and abnormal (33.3%) cytology. HPV 16 (4.6%) was identified as the predominant high-risk HPV genotype among women with normal cytology and HPV 16, HPV 18, and HPV 56 (22.2% each) were the most common identified high-risk genotypes in women with abnormal cytology. The overall HPV prevalence in Arab women in Qatar was identified as 6.1% with an increased HPV prevalence seen in women with abnormal cytology results and no significant trends seen with age. In contrast to Western countries, we report a varied genotypic profile of HPV with a high prevalence of low-risk HPV genotype 81 among the Arab women residing in Qatar.

  10. Novel fluorescent sequence-related amplified polymorphism(FSRAP markers for the construction of a genetic linkage map of wheat(Triticum aestivum L.

    Zhao Lingbo

    2017-01-01

    Full Text Available Novel fluorescent sequence-related amplified polymorphism (FSRAP markers were developed based on the SRAP molecular marker. Then, the FSRAP markers were used to construct the genetic map of a wheat (Triticum aestivumL. recombinant inbred line population derived from a Chuanmai 42×Chuannong 16 cross. Reproducibility and polymorphism tests indicated that the FSRAP markers have repeatability and better reflect the polymorphism of wheat varieties compared with SRAP markers. A total of 430 polymorphic loci between Chuanmai 42 and Chuannong 16 were detected with 189 FSRAP primer combinations. A total of 281 FSARP markers and 39 SSR markers re classified into 20 linkage groups. The maps spanned a total length of 2499.3cM with an average distance of 7.81cM between markers. A total of 201 markers were mapped on the B genome and covered a distance of 1013cM. On the A genome, 84 markers were mapped and covered a distance of 849.6cM. On the D genome, however, only 35 markers were mapped and covered a distance of 636.7cM. No FSRAP markers were distributed on the 7D chromosome. The results of the present study revealed that the novel FSRAP markers can be used to generate dense, uniform genetic maps of wheat.

  11. Genetic Diversity Analysis of the Natural Populations of Mediterra­nean Mussels [Mytilus galloprovincialis (Lmk.] in Agadir Bay: Assess­ment of the Molecular Polymorphism and Environmental Impact

    Amal Korrida

    2010-07-01

    Full Text Available Mediterranean mussel (Mytilus galloprovincialis Lmk has a great environmental and economic importance for Morocco. This work studies the genetic structure and impact of chemical pollution on three different marine populations of Mytilus galloprovincialis that live within Agadir bay. Three collections were made at two clean sites (Cape Ghir and Cape Aglou and at an impacted site exposed to intense boating and industrial activities (Anza. A 300-bp portion of the mitochondrial DNA coding-region Cytochrome C Oxidase subunit 1 (COI was studied by polymerase chain reaction (PCR and DNA sequencing reactions to assess and evaluate amounts of polymorphism in each site. Genetic analysis using COI for 64 individuals showed no significant differentiation between the three subpopulations. AMOVA demonstrated that only 2.83% of variation exists between populations. Besides the genetic evidence presented herein, mussel’s adaptation mechanisms and strategies to marine pollution are also discussed.

  12. Neurons of the dentate molecular layer in the rabbit hippocampus.

    Francisco J Sancho-Bielsa

    Full Text Available The molecular layer of the dentate gyrus appears as the main entrance gate for information into the hippocampus, i.e., where the perforant path axons from the entorhinal cortex synapse onto the spines and dendrites of granule cells. A few dispersed neuronal somata appear intermingled in between and probably control the flow of information in this area. In rabbits, the number of neurons in the molecular layer increases in the first week of postnatal life and then stabilizes to appear permanent and heterogeneous over the individuals' life span, including old animals. By means of Golgi impregnations, NADPH histochemistry, immunocytochemical stainings and intracellular labelings (lucifer yellow and biocytin injections, eight neuronal morphological types have been detected in the molecular layer of developing adult and old rabbits. Six of them appear as interneurons displaying smooth dendrites and GABA immunoreactivity: those here called as globoid, vertical, small horizontal, large horizontal, inverted pyramidal and polymorphic. Additionally there are two GABA negative types: the sarmentous and ectopic granular neurons. The distribution of the somata and dendritic trees of these neurons shows preferences for a definite sublayer of the molecular layer: small horizontal, sarmentous and inverted pyramidal neurons are preferably found in the outer third of the molecular layer; vertical, globoid and polymorph neurons locate the intermediate third, while large horizontal and ectopic granular neurons occupy the inner third or the juxtagranular molecular layer. Our results reveal substantial differences in the morphology and electrophysiological behaviour between each neuronal archetype in the dentate molecular layer, allowing us to propose a new classification for this neural population.

  13. Tumor necrosis factor-α and -β genetic polymorphisms as a risk factor in Saudi patients with schizophrenia

    Kadasah S

    2017-04-01

    Full Text Available Saeed Kadasah,1 Misbahul Arfin,2 Sadaf Rizvi,2 Mohammed Al-Asmari,2 Abdulrahman Al-Asmari2 1Department of Psychiatry, 2Division of Molecular Biology & Genetics, Scientific Research Center, Prince Sultan Military Medical City, Riyadh, Saudi Arabia Background: Schizophrenia is one of the most common devastating psychiatric disorders that negatively affects the quality of life and psychosocial functions. Its etiology involves the interplay of complex polygenic influences and environmental risk factors. Inflammatory markers are well-known etiological factors for psychiatric disorders, including schizophrenia. Objective: The aim of this study was to investigate the association of proinflammatory cytokine genes, tumor necrosis factor (TNF-α (-308G/A and TNF-β (+252A/G polymorphisms with schizophrenia susceptibility. Subjects and methods: TNF-α and TNF-β genes were amplified using amplification refractory mutation system primers in 180 schizophrenia patients and 200 healthy matched controls recruited from the Psychiatry Clinic of Prince Sultan Military Medical City, Riyadh. The frequencies of alleles and genotypes of TNF-α (-308G/A and TNF-β (+252A/G polymorphisms in patients were compared with those in controls. Results: The frequencies of TNF-α (-308 allele A and genotype GA were significantly higher, while those of allele G and genotype GG were lower in schizophrenia patients as compared to controls, indicating that genotype GA and allele A of TNF-α (-308G/A may increase susceptibility to schizophrenia, while genotype GG and allele G may reduce it. On the other hand, the distribution of alleles and genotypes of TNF-β (+252A/G polymorphism does not differ significantly in patients from controls; however, the frequency of genotype GG of TNF-β (+252A/G was significantly higher in male patients than in female patients. The distribution of TNF-α (-308G/A and TNF-β (+252A/G polymorphisms was almost similar in schizophrenia patients with

  14. Gliadin and glutenin polymorphism in durum wheat landraces and breeding varieties of Azerbaijan

    Sadigov-Baykishi Hamlet

    2015-01-01

    Full Text Available Durum wheat genotypes including 7 landraces and 17 breeding varieties were studied. Polyacrylamide gel electrophoresis under acidic conditions of pH 3.1 was used to study gliadin and glutenin polymorphisms. In total, 32 gliadin and 8 high molecular weight glutenin alleles were identified. The contribution of B genome (58.5% to the allelic variation of durum wheat varieties was higher than of A genome. The cluster analysis delineated genotypes into four main clusters. According to cluster analysis, legitimacy identifying the distribution of botanical varieties through the tree was observed. The study confirms the suitability of biochemical markers for cultivar identification and genetic relation study in durum wheat genotypes.

  15. Polymorphism of terthiophene with surface confinement

    Roland Resel

    2018-05-01

    Full Text Available The origin of unknown polymorphic phases within thin films is still not well understood. This work reports on crystals of the molecule terthiophene which were grown by thermal gradient crystallization using glass-plate substrates. The crystalline domains displayed a plate-like morphology with an extended lateral size of about 100 µm, but a thickness of only a few µm. Specular X-ray diffraction patterns confirmed the presence of a new polymorph of terthiophene. Crystal structure solution from a single crystal peeled from the film revealed a structure with an extremely large unit-cell volume containing 42 independent molecules. In contrast to the previously determined crystal structure of terthiophene, a herringbone packing motif was observed where the terminal ends of the molecules are arranged within one plane (i.e. the molecular packing conforms to the flat substrate surface. This type of molecular packing is obtained by 180° flipped molecules combined with partially random (disordered occupation. A densely packed interface between terthiophene crystallites and the substrate surface is obtained, this confirms that the new packing motif has adapted to the flat substrate surface.

  16. Thermal and single frequency counter-current ultrasound pretreatments of sodium caseinate: enzymolysis kinetics and thermodynamics, amino acids composition, molecular weight distribution and antioxidant peptides.

    Abdualrahman, Mohammed Adam Y; Ma, Haile; Zhou, Cunshan; Yagoub, Abu ElGasim A; Hu, Jiali; Yang, Xue

    2016-12-01

    Due to the disadvantages of traditional enzymolysis, pretreatments are crucial to enhance protein enzymolysis. Enzymolysis kinetics and thermodynamics, amino acids composition, molecular weight distribution, fluorescence spectroscopy and antioxidant activity of thermal (HT) and single frequency counter-current ultrasound (SCFU) pretreated sodium caseinate (NaCas) were studied. Enzymolysis of untreated NaCas (control) improved significantly (P < 0.05) by SFCU and followed by HT. Values of the Michaelis-Menten constant (K M ) of SFCU and HT were 0.0212 and 0.0250, respectively. HT and SFCU increased (P < 0.05) the reaction rate constant (k) by 38.64 and 90.91%, respectively at 298 K. k values decreased with increasing temperature. The initial activation energy (46.39 kJ mol -1 ) reduced (P < 0.05) by HT (39.66 kJ mol -1 ) and further by SFCU (33.42 kJ mol -1 ). SFCU-pretreated NaCas hydrolysates had the highest contents of hydrophobic, aromatic, positively and negatively charged amino acids. Medium-sized peptides (5000-1000 Da) are higher in SFCU (78.11%) than HT and the control. SFCU induced molecular unfolding of NaCas proteins. Accordingly, SFCU-pretreated NaCas hydrolysate exhibited the highest scavenging activity on DPPH and hydroxyl radicals, reducing power, and iron chelating ability. SFCU pretreatment would be a useful tool for production of bioactive peptides from NaCas hydrolysate. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  17. Prediction of molecular crystal structures

    Beyer, Theresa

    2001-01-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol -1 of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  18. Prediction of molecular crystal structures

    Beyer, Theresa

    2001-07-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  19. Molecular characterization, tissue distribution and feeding related changes of NUCB2A/nesfatin-1 in Ya-fish (Schizothorax prenanti).

    Lin, Fangjun; Zhou, Chaowei; Chen, Hu; Wu, Hongwei; Xin, Zhiming; Liu, Ju; Gao, Yundi; Yuan, Dengyue; Wang, Tao; Wei, Rongbin; Chen, Defang; Yang, Shiyong; Wang, Yan; Pu, Yundan; Li, Zhiqiong

    2014-02-25

    The protein nucleobindin-2 (NUCB2) was identified over a decade ago and recently raised great interest as its derived peptide nesfatin-1 was shown to reduce food intake and body weight in rodents. However, the involvement of NUCB2 in feeding behavior has not well been studied in fish. In the present study, we characterized the structure, distribution, and meal responsive of NUCB2A/nesfatin-1 in Ya-fish (Schizothorax prenanti) for the first time. The full length cDNA of Ya-fish was 2140base pair (bp), which encoded a polypeptide of 487 amino acid residues including a 23 amino acid signal peptide. A high conservation in NUCB2 sequences was found in vertebrates, however the proposed propeptide cleavage site (Arg-Arg) conserved among other species is not present in Ya-fish NUCB2A sequence. Tissue distribution analysis revealed that Ya-fish NUCB2A mRNA was ubiquitously expressed in all test tissues, and abundant expression was detected in several regions including the hypothalamus, hepatopancreas, ovary and intestines. NUCB2A mRNA expression respond to feeding status change may vary and be tissue specific. NUCB2A mRNA levels significantly increased (P<0.05) in the hypothalamus and intestines after feeding and substantially decreased (P<0.01) during a week food deprivation in the hypothalamus. Meanwhile, NUCB2A mRNA in the hepatopancreas was significantly elevated (P<0.001) during food deprivation, and a similar increase was also found after short-time fasting. This points toward a potential hepatopancreas specific local role for NUCB2A in the regulation of metabolism during food deprivation. Collectively, these results provide the molecular and functional evidence to support potential anorectic and metabolic roles for NUCB2A in Ya-fish. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. Preprohypocretin polymorphisms in Parkinson disease patients reporting "sleep attacks".

    Rissling, Ida; Körner, Yvonne; Geller, Frank; Stiasny-Kolster, Karin; Oertel, Wolfgang H; Möller, J Carsten

    2005-07-01

    Previously, we found a significant association between the dopamine D2 receptor gene polymorphism Taq IA and sudden onset of sleep in patients with Parkinson disease. Here we evaluated the association between the preprohypocretin (-909T/C), (-22C/T), and (-20C/A) polymorphisms and sudden onset of sleep in the same population of patients with Parkinson disease. We conducted an association study analyzing the distribution of preprohypocretin polymorphisms in Germanic, caucasian Parkinson disease patients with and without sudden onset of sleep, matched according to drug therapy, disease duration, sex, and age. Movement disorders section at a university hospital. 132 Parkinson disease patients with sudden onset of sleep and 132 Parkinson disease patients without sudden onset of sleep. Blood samples were taken from each participant and used for DNA extraction. Polymorphisms were analyzed by established polymerase chain reaction protocols or direct sequencing. The variant allele T of the (-909T/C) preprohypocretin polymorphism was more commonly found in Parkinson disease patients with sudden onset of sleep. Statistical analysis showed that there were significant differences in the genotype (P = .024) and allele (P = .018) distribution between both groups. For heterozygous and homozygous carriers of allele T, the genotype relative-risk estimates for the presence of sudden onset of sleep were 2.01 (95% confidence interval: 0.76-5.34) and 2.81 (95% confidence interval: 1.09-7.25), respectively. Our results show a significant association between the (-909T/C) preprohypocretin polymorphism and sudden onset of sleep in Parkinson disease. However, we could not demonstrate any interaction between the Taq IA and (-909T/C) polymorphisms with respect to the occurrence of sudden onset of sleep, suggesting that multiple genetic factors may contribute to the pathogenesis of this phenomenon.

  1. Relationship between the fluidity of heat-treated coals and molecular weight distributions of their solvent-soluble component; Netsushoritan no yobai kayo seibun no bunshiryo bunpu to ryudosei no kanren

    Yoshida, T.; Takanohashi, T.; Iino, M. [Tohoku University, Sendai (Japan). Institute for Chemical Reaction Science; Kato, K. [Nippon Steel Co. Ltd., Tokyo (Japan); Fukada, K. [NKK Corp., Tokyo (Japan)

    1996-10-28

    In order to improve the coke manufacturing process, considerations were given on fluidity manifestation mechanism of heat-treated coals from molecular weight distributions of extracts of a solvent mixed with CS2-N-methyl-2-pyrrolidinone (CS2-NMP). The heat treatment was performed in an autoclave under nitrogen atmosphere at a rate of 3{degree}C/min to settings of 200 to 550{degree}C. The resultant heat-treated coal was quenched, and then extracted by using the CS2-NMP mixed solvent. The fluidity was measured by using a Gieseler plastometer. Maximum extraction rate and the highest fluidity are in linear relationship, which suggests that the extracts govern the fluidity. Since heavy caking coal has no difference in the extraction rates due to heat treatment temperature, and its molecular weight distribution trend does not change, the extracted components which have existed primarily in the original coal govern the fluidity. In semi-caking coals, polymer molecular components are extracted in a large quantity at the softening starting temperature, but the quantity decreases as the temperature rises. However, low-molecular components present no quantitative change, while polymer molecular components decompose, decrease in molecular weight, get solubilized with rising temperature, and act as a binder to cause a flow. 7 figs., 1 tab.

  2. Genetic structure of Bemisia tabaci Med populations from home-range countries, inferred by nuclear and cytoplasmic markers : impact on the distribution of the insecticide resistance genes

    Gauthier, Nathalie; Clouet, C.; Perrakis, A.; Kapantaidaki, D.; Peterschmitt, M.; Tsagkarakou, A.

    2014-01-01

    BACKGROUND: Insecticide resistance management in Bemisia tabaci is one of the main issues facing agricultural production today. An extensive survey was undertaken in five Mediterranean countries to examine the resistance status of Med B. tabaci species in its range of geographic origin and the relationship between population genetic structure and the distribution of resistance genes. The investigation combined molecular diagnostic tests, sequence and microsatellite polymorphism studies and mo...

  3. Impact of mixed low-molecular-weight organic acids on uranium accumulation and distribution in a variant of mustard (Brassica juncea var. tumida)

    Fangfang Qi; Dingna Wang; Lijian Ma; Yongdong Jin; Liang Du; Dong Zhang; Chuanqin Xia; Sichuan University, Chengdu

    2014-01-01

    The impact of a mixture of low-molecular-weight organic acids (LMWOAs) composed of CA/MA/OA/LA with a molar ratio of 2.5:2.31:1.15:0.044 on uranium (U) accumulation and distribution in mustard (Brassica juncea var. tumida) was studied in this paper in order to understand the mechanism of rhizosphere-exudation assisted phytoremediation by hydroponic and pot culture experiments. The impact of the mixture of LWMOAs (Mix) on U accumulation showed that in hydroponic conditions Mix could enhance U translocation from root-to-shoot in mustard, but inhibit U uptake in root. In pot experiments, Mix enhanced both root and shoot U accumulation in mustard. The time-dependent kinetics of U uptake in mustard on Mix treatment showed that U content in plant shoots and roots increased with time increasing, and the steady state conditions were obtained at the 8th and 5th day with the U content of 1,528 and 2,300 mg/kg, respectively. Transmission electron microscope and energy dispersive X-ray spectrometry analysis for mustard roots showed that U was mainly observed on cell membrane of mustard roots on Mix treatment. This study would provide new insights for the mixture of LWMOAs-assisted phytoremediation of U-contaminated soil. (author)

  4. High-Throughput Sequencing and Linkage Mapping of a Clownfish Genome Provide Insights on the Distribution of Molecular Players Involved in Sex Change.

    Casas, Laura; Saenz-Agudelo, Pablo; Irigoien, Xabier

    2018-03-06

    Clownfishes are an excellent model system for investigating the genetic mechanism governing hermaphroditism and socially-controlled sex change in their natural environment because they are broadly distributed and strongly site-attached. Genomic tools, such as genetic linkage maps, allow fine-mapping of loci involved in molecular pathways underlying these reproductive processes. In this study, a high-density genetic map of Amphiprion bicinctus was constructed with 3146 RAD markers in a full-sib family organized in 24 robust linkage groups which correspond to the haploid chromosome number of the species. The length of the map was 4294.71 cM, with an average marker interval of 1.38 cM. The clownfish linkage map showed various levels of conserved synteny and collinearity with the genomes of Asian and European seabass, Nile tilapia and stickleback. The map provided a platform to investigate the genomic position of genes with differential expression during sex change in A. bicinctus. This study aims to bridge the gap of genome-scale information for this iconic group of species to facilitate the study of the main gene regulatory networks governing social sex change and gonadal restructuring in protandrous hermaphrodites.

  5. Spontaneous core–shell elemental distribution in In-rich InxGa1−xN nanowires grown by molecular beam epitaxy

    Gómez-Gómez, M; Garro, N; Cantarero, A; Mengistu, H T; García-Cristóbal, A; Murcia-Mascarós, S; Segura-Ruiz, J; Martinez-Criado, G; Denker, C; Malindretos, J; Rizzi, A

    2014-01-01

    The elemental distribution of self-organized In-rich In x Ga 1−x N nanowires grown by plasma-assisted molecular beam epitaxy has been investigated using three different techniques with spatial resolution on the nanoscale. Two-dimensional images and elemental profiles of single nanowires obtained by x-ray fluorescence and energy-dispersive x-ray spectroscopy, respectively, have revealed a radial gradient in the alloy composition of each individual nanowire. The spectral selectivity of resonant Raman scattering has been used to enhance the signal from very small volumes with different elemental composition within single nanowires. The combination of the three techniques has provided sufficient sensitivity and spatial resolution to prove the spontaneous formation of a core–shell nanowire and to quantify the thicknesses and alloy compositions of the core and shell regions. A theoretical model based on continuum elastic theory has been used to estimate the strain fields present in such inhomogeneous nanowires. These results suggest new strategies for achieving high quality non-polar heterostructures. (paper)

  6. Spontaneous core-shell elemental distribution in In-rich InxGa1-xN nanowires grown by molecular beam epitaxy

    Gómez-Gómez, M.; Garro, N.; Segura-Ruiz, J.; Martinez-Criado, G.; Cantarero, A.; Mengistu, H. T.; García-Cristóbal, A.; Murcia-Mascarós, S.; Denker, C.; Malindretos, J.; Rizzi, A.

    2014-02-01

    The elemental distribution of self-organized In-rich InxGa1-xN nanowires grown by plasma-assisted molecular beam epitaxy has been investigated using three different techniques with spatial resolution on the nanoscale. Two-dimensional images and elemental profiles of single nanowires obtained by x-ray fluorescence and energy-dispersive x-ray spectroscopy, respectively, have revealed a radial gradient in the alloy composition of each individual nanowire. The spectral selectivity of resonant Raman scattering has been used to enhance the signal from very small volumes with different elemental composition within single nanowires. The combination of the three techniques has provided sufficient sensitivity and spatial resolution to prove the spontaneous formation of a core-shell nanowire and to quantify the thicknesses and alloy compositions of the core and shell regions. A theoretical model based on continuum elastic theory has been used to estimate the strain fields present in such inhomogeneous nanowires. These results suggest new strategies for achieving high quality non-polar heterostructures.

  7. Spontaneous core–shell elemental distribution in In-rich In(x)Ga1-xN nanowires grown by molecular beam epitaxy.

    Gómez-Gómez, M; Garro, N; Segura-Ruiz, J; Martinez-Criado, G; Cantarero, A; Mengistu, H T; García-Cristóbal, A; Murcia-Mascarós, S; Denker, C; Malindretos, J; Rizzi, A

    2014-02-21

    The elemental distribution of self-organized In-rich In(x)Ga1-xN nanowires grown by plasma-assisted molecular beam epitaxy has been investigated using three different techniques with spatial resolution on the nanoscale. Two-dimensional images and elemental profiles of single nanowires obtained by x-ray fluorescence and energy-dispersive x-ray spectroscopy, respectively, have revealed a radial gradient in the alloy composition of each individual nanowire. The spectral selectivity of resonant Raman scattering has been used to enhance the signal from very small volumes with different elemental composition within single nanowires. The combination of the three techniques has provided sufficient sensitivity and spatial resolution to prove the spontaneous formation of a core–shell nanowire and to quantify the thicknesses and alloy compositions of the core and shell regions. A theoretical model based on continuum elastic theory has been used to estimate the strain fields present in such inhomogeneous nanowires. These results suggest new strategies for achieving high quality nonpolar heterostructures.

  8. High-Throughput Sequencing and Linkage Mapping of a Clownfish Genome Provide Insights on the Distribution of Molecular Players Involved in Sex Change

    Casas, Laura

    2018-02-28

    Clownfishes are an excellent model system for investigating the genetic mechanism governing hermaphroditism and socially-controlled sex change in their natural environment because they are broadly distributed and strongly site-attached. Genomic tools, such as genetic linkage maps, allow fine-mapping of loci involved in molecular pathways underlying these reproductive processes. In this study, a high-density genetic map of Amphiprion bicinctus was constructed with 3146 RAD markers in a full-sib family organized in 24 robust linkage groups which correspond to the haploid chromosome number of the species. The length of the map was 4294.71 cM, with an average marker interval of 1.38 cM. The clownfish linkage map showed various levels of conserved synteny and collinearity with the genomes of Asian and European seabass, Nile tilapia and stickleback. The map provided a platform to investigate the genomic position of genes with differential expression during sex change in A. bicinctus. This study aims to bridge the gap of genome-scale information for this iconic group of species to facilitate the study of the main gene regulatory networks governing social sex change and gonadal restructuring in protandrous hermaphrodites.

  9. Distributions of low molecular weight dicarboxylic acids, ketoacids and α-dicarbonyls in the marine aerosols collected over the Arctic Ocean during late summer

    K. Kawamura

    2012-11-01

    Full Text Available Oxalic and other small dicarboxylic acids have been reported as important water-soluble organic constituents of atmospheric aerosols from different environments. Their molecular distributions are generally characterized by the predominance of oxalic acid (C2 followed by malonic (C3 and/or succinic (C4 acids. In this study, we collected marine aerosols from the Arctic Ocean during late summer in 2009 when sea ice was retreating. The marine aerosols were analyzed for the molecular distributions of dicarboxylic acids as well as ketocarboxylic acids and α-dicarbonyls to better understand the source of water-soluble organics and their photochemical processes in the high Arctic marine atmosphere. We found that diacids are more abundant than ketoacids and α-dicarbonyls, but their concentrations are generally low (< 30 ng m−3, except for one sample (up to 70 ng m−3 that was collected near the mouth of Mackenzie River during clear sky condition. Although the molecular compositions of diacids are in general characterized by the predominance of oxalic acid, a depletion of C2 was found in two samples in which C4 became the most abundant. Similar depletion of oxalic acid has previously been reported in the Arctic aerosols collected at Alert after polar sunrise and in the summer aerosols from the coast of Antarctica. Because the marine aerosols that showed a depletion of C2 were collected under the overcast and/or foggy conditions, we suggest that a photochemical decomposition of oxalic acid may have occurred in aqueous phase of aerosols over the Arctic Ocean via the photo dissociation of oxalate-Fe (III complex. We also determined stable carbon isotopic compositions (δ13C of bulk aerosol carbon and individual diacids. The δ13C of bulk aerosols showed −26.5‰ (range: −29.7 to −24.7‰, suggesting that marine aerosol carbon is derived

  10. Association of IL-6 and MMP-3 gene polymorphisms with ...

    comprehensively and systematically performed this meta-analysis to detect whether the two gene polymorphisms are corre- .... control studies; (ii) 'failure to provide the genes' distribution details ..... biological activity of corresponding proteins such as IL-6 .... pathic scoliosis is related to inadequate calcium intake and weight.

  11. Interleukin Gene Polymorphisms and Susceptibility to HIV Infection

    Chrysa

    vaccines, and with almost 36.7 million HIV-infected individuals worldwide .... The allelic and genotypic distribution of the IL genes SNPs are presented in .... polymorphism using the genetic model-free bivariate approach produced, as in ... Through its immuno-inhibitory and anti-inflammatory activities and, in particular, by.

  12. Serotonin transporter (SERT gene polymorphism in Parkinson’s disease

    Mahmut Özkaya

    2004-06-01

    Full Text Available Background: Parkinson disease (PD is the second most common neurodegenerative disorder with a prevalence of about 2% in persons older than 65 years of age. Neurodegenerative process in PD is not restricted to the dopaminergic neurons of the substantia nigra but also affects serotoninergic neurons. It has been shown that PD brains with Lewy bodies in the substantia nigra also had Lewy bodies in the raphe nuclei. The re-uptake of 5HT released into the synaptic cleft is mediated by the 5HT transporter (SERT. The SERT gene has been mapped to the chromosome of 17q11.1-q12 and has two main polymorphisms: intron two VNTR polymorphism and promoter region 44 bp insertion/deletion polymorphism. Objective: In this study we investigated whether two polymorphic regions in the serotonin transporter gene are associated with PD. Material and Method: After obtaining informed consent, blood samples were collected from 76 patients and 54 healthy volunteers. Genomic DNA was extracted from peripheral leucocytes using standard methods. The SERT gene genotypes were determined using polymerase chain reaction (PCR method. Results: Based on the intron 2 VNTR polymorphism of SERT gene, the distribution of 12/12, 12/10 and 10/10 genotypes were found as, 56.6 %, 35.5 %, 7.9 % in patients whereas this genotype distribution in control group was 40.7 %, 46.3 % and 13 %, respectively. According to 5-HTTLPR polymorphism, the distribution of L/L, L/S and S/S genotypes were found as 27.6 % 51.3 % and 21.1 % in patients whereas this genotype distribution in control group was 33.4 %, 50.0 % and 16.6 %, respectively. Despite the fact that the genotype distribution of SERT gene polymorphism in patients and control group seemed to be different from each other, this difference was not found to be statistically significant. Conclusion: This finding suggests that polymorphisms within the SERT gene do not play a major role in PD susceptibility in the Turkish population.

  13. Energy barriers and mechanisms in solid-solid polymorphic transitions exhibiting cooperative motion

    van den Ende, J.A.; Ensing, B.; Cuppen, H.M.

    2016-01-01

    Understanding solid–solid polymorphic transitions within molecular crystals on the molecular scale is a challenging task. It is, however, crucial for the understanding of transitions that are thought to occur through cooperative motion, which offer an interesting perspective for future applications.

  14. Period3 VNTR polymorphism influences the time-of-day pain onset of acute myocardial infarction with ST elevation.

    Lipkova, Jolana; Splichal, Zbynek; Bienertova-Vasku, Julie Anna; Jurajda, Michal; Parenica, Jiri; Vasku, Anna; Goldbergova, Monika Pavkova

    2014-10-01

    It is well established that the incidence and infarct size in acute myocardial infarction (AMI) is subject to circadian variations. At the molecular level, circadian clocks in distinct cells, including cardiomyocytes, generate 24-h cycles of biochemical processes. Possible imbalance or impairment in the cell clock mechanism may alter the cardiac metabolism and function and increase the susceptibility of cardiovascular diseases. One of the key components of the human clock system PERIOD3 (PER3) has been recently demonstrated to affect circadian expression of various genes in different tissues, including the heart. The variable number tandem repeat (VNTR) polymorphism (rs57875989) in gene Period3 (Per3) is related to multiple phenotypic parameters, including diurnal preference, sleep homeostasis, infection and cancer. The aim of our study was to investigate the effect of this polymorphism in AMI with ST elevation (STEMI). The study subjects (314 patients of Caucasian origin with STEMI, and 332 healthy controls) were genotyped for Per3 VNTR polymorphism using an allele-specific polymerase chain reaction. A gender difference in circadian rhythmicity of pain onset was observed with significant circadian pattern in men. Furthermore, the Per3(5/5) variant carriers were associated with higher levels of interleukin-6, B-type natriuretic peptide and lower vitamin A levels. By using cosinor analysis we observed different circadian distribution patterns of AMI onset at the level of genotype and allelic frequencies. Genotypes with at least one 4-repeat allele (Per3(4/5) and Per3(4/4)) (N = 264) showed remarkable circadian activity in comparison with Per3(5/5) (N = 50), especially in men. No significant differences in genotype and/or allele frequencies of Per3 VNTR polymorphism were observed when comparing STEMI cases and controls. Our results indicate that the Per3 VNTR may contribute to modulation of cardiac functions and interindividual differences in development and

  15. Polymorphic Evolutionary Games.

    Fishman, Michael A

    2016-06-07

    In this paper, I present an analytical framework for polymorphic evolutionary games suitable for explicitly modeling evolutionary processes in diploid populations with sexual reproduction. The principal aspect of the proposed approach is adding diploid genetics cum sexual recombination to a traditional evolutionary game, and switching from phenotypes to haplotypes as the new game׳s pure strategies. Here, the relevant pure strategy׳s payoffs derived by summing the payoffs of all the phenotypes capable of producing gametes containing that particular haplotype weighted by the pertinent probabilities. The resulting game is structurally identical to the familiar Evolutionary Games with non-linear pure strategy payoffs (Hofbauer and Sigmund, 1998. Cambridge University Press), and can be analyzed in terms of an established analytical framework for such games. And these results can be translated into the terms of genotypic, and whence, phenotypic evolutionary stability pertinent to the original game. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Yam ( Dioscorea spp.) molecular breeding

    Some progress has been made in recent years in germplasm characterization and the development of molecular markers for genome analysis. A genetic linkage map based on amplified fragment length polymorphism (AFLP) markers has been constructed for Guinea and water yams. These linkage maps were used to scan ...

  17. Major single nucleotide polymorphisms in polypoidal choroidal vasculopathy: a comparative analysis between Thai and other Asian populations

    Chantaren P

    2012-03-01

    Full Text Available Patchima Chantaren1, Paisan Ruamviboonsuk1, Mathurose Ponglikitmongkol2, Montip Tiensuwan3, Somying Promso41Department of Ophthalmology, Rajavithi Hospital, Bangkok, 2Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 3Department of Mathematics, Faculty of Science, Mahidol University, Bangkok, 4Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, ThailandPurpose: To investigate the association in a Thai population between the major age-related macular degeneration (AMD susceptibility loci, Y402H and I62V in the complement factor H (CFH and A69S in the age-related maculopathy susceptibility 2 (ARMS2 genes, and polypoidal choroidal vasculopathy (PCV.Methods: A case-control study included 97 PCV cases and 102 age- and gender-matched controls without any retinopathy. The genotypic profiles of the three polymorphisms were obtained using a real-time polymerase chain reaction assay. The allelic and genotypic association between the polymorphisms and PCV were compared with those from the compiled data of other Asian populations reported previously.Results: Strong associations between the Y402H, I62V, and A69S polymorphisms and PCV were observed in the present study (P = 0.002, 0.003, and 0.0008 respectively and in the compiled data (P < 0.0001 for all three polymorphisms. The risk allele frequencies of the polymorphisms in PCVs and in controls from the present study (15.0% and 5.4% for Y402H, 71.7% and 57.4% for I62V, and 54.1% and 37.3% for A69S respectively were also comparable with the frequencies from the compiled data (10.3% and 6.4% for Y402H, 75.2% and 58.3% for I62V, and 56.8% and 36.8% for A69S respectively. The genotype distribution for each polymorphism was also comparable in both datasets.Conclusion: The findings of this study support a significant genetic association between the major AMD susceptibility genes and PCV across Asian

  18. [Polymorphism of vitamin D receptor gene Fok I in Mongolian population of China].

    Xing, Shao-ji; Zhou, Li-she; Xu, Xiu-ju

    2006-04-01

    To investigate the polymorphism distribution of vitamin D receptor (VDR) gene Fok I in Mongolian population of China. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used to analyze three genotypes FF, Ff and ff in the start codon of VDR gene (Fok I) in unrelated normal healthy Mongolian individuals of China. In the population, we obtained the allelic frequencies of 57% and 43% for (F) and (f) allele and the percentage of genotypes FF, Ff and ff to be 31%, 52%, and 17% respectively. The polymorphism frequency and distribution of this VDR gene Fok I in Mongolian population of China exhibit its own characteristics.

  19. Sequencing and annotation of the chloroplast DNAs and identification of polymorphisms distinguishing normal male-fertile and male-sterile cytoplasms of onion.

    von Kohn, Christopher; Kiełkowska, Agnieszka; Havey, Michael J

    2013-12-01

    Male-sterile (S) cytoplasm of onion is an alien cytoplasm introgressed into onion in antiquity and is widely used for hybrid seed production. Owing to the biennial generation time of onion, classical crossing takes at least 4 years to classify cytoplasms as S or normal (N) male-fertile. Molecular markers in the organellar DNAs that distinguish N and S cytoplasms are useful to reduce the time required to classify onion cytoplasms. In this research, we completed next-generation sequencing of the chloroplast DNAs of N- and S-cytoplasmic onions; we assembled and annotated the genomes in addition to identifying polymorphisms that distinguish these cytoplasms. The sizes (153 538 and 153 355 base pairs) and GC contents (36.8%) were very similar for the chloroplast DNAs of N and S cytoplasms, respectively, as expected given their close phylogenetic relationship. The size difference was primarily due to small indels in intergenic regions and a deletion in the accD gene of N-cytoplasmic onion. The structures of the onion chloroplast DNAs were similar to those of most land plants with large and small single copy regions separated by inverted repeats. Twenty-eight single nucleotide polymorphisms, two polymorphic restriction-enzyme sites, and one indel distributed across 20 chloroplast genes in the large and small single copy regions were selected and validated using diverse onion populations previously classified as N or S cytoplasmic using restriction fragment length polymorphisms. Although cytoplasmic male sterility is likely associated with the mitochondrial DNA, maternal transmission of the mitochondrial and chloroplast DNAs allows for polymorphisms in either genome to be useful for classifying onion cytoplasms to aid the development of hybrid onion cultivars.

  20. Polytene chromosome map and inversion polymorphism in Drosophila mediopunctata

    Galina Ananina

    2002-07-01

    Full Text Available Drosophila mediopunctata belongs to the tripunctata group, and is one of the commonest Drosophila species collected in some places in Brazil, especially in the winter. A standard map of the polytene chromosomes is presented. The breakpoints of the naturally occurring chromosomal rearrangements are marked on the map. The distribution of breaking points through the chromosomes of D. mediopunctata is apparently non-random. Chromosomes X, II and IV show inversion polymorphisms. Chromosome II is the most polymorphic, with 17 inversions, 8 inversions in the distal region and 9 in the proximal region. Chromosome X has four different gene arrangements, while chromosome IV has only two.

  1. Molecular mechanisms for protein-encoded inheritance

    Wiltzius, Jed J. W.; Landau, Meytal; Nelson, Rebecca; Sawaya, Michael R.; Apostol, Marcin I.; Goldschmidt, Lukasz; Soriaga, Angela B.; Cascio, Duilio; Rajashankar, Kanagalaghatta; Eisenberg, David

    2013-01-01

    Strains are phenotypic variants, encoded by nucleic acid sequences in chromosomal inheritance and by protein “conformations” in prion inheritance and transmission. But how is a protein “conformation” stable enough to endure transmission between cells or organisms? Here new polymorphic crystal structures of segments of prion and other amyloid proteins offer structural mechanisms for prion strains. In packing polymorphism, prion strains are encoded by alternative packings (polymorphs) of β-sheets formed by the same segment of a protein; in a second mechanism, segmental polymorphism, prion strains are encoded by distinct β-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring “conformations,” capable of encoding strains. These molecular mechanisms for transfer of information into prion strains share features with the familiar mechanism for transfer of information by nucleic acid inheritance, including sequence specificity and recognition by non-covalent bonds. PMID:19684598

  2. Polymorphisms in Isoniazid and Prothionamide Resistance Genes of the Mycobacterium tuberculosis Complex

    Projahn, M.; Koser, C. U.; Homolka, S.; Summers, D. K.; Archer, John A.C.; Niemann, S.

    2011-01-01

    Sequence analyses of 74 strains that encompassed major phylogenetic lineages of the Mycobacterium tuberculosis complex revealed 10 polymorphisms in mshA (Rv0486) and four polymorphisms in inhA (Rv1484) that were not responsible for isoniazid or prothionamide resistance. Instead, some of these mutations were phylogenetically informative. This genetic diversity must be taken into consideration for drug development and for the design of molecular tests for drug resistance.

  3. Polymorphisms in Isoniazid and Prothionamide Resistance Genes of the Mycobacterium tuberculosis Complex

    Projahn, M.

    2011-06-27

    Sequence analyses of 74 strains that encompassed major phylogenetic lineages of the Mycobacterium tuberculosis complex revealed 10 polymorphisms in mshA (Rv0486) and four polymorphisms in inhA (Rv1484) that were not responsible for isoniazid or prothionamide resistance. Instead, some of these mutations were phylogenetically informative. This genetic diversity must be taken into consideration for drug development and for the design of molecular tests for drug resistance.

  4. [Recent advances of amplified fragment length polymorphism and its applications in forensic botany].

    Li, Cheng-Tao; Li, Li

    2008-10-01

    Amplified fragment length polymorphism (AFLP) is a new molecular marker to detect genomic polymorphism. This new technology has advantages of high resolution, good stability, and reproducibility. Great achievements have been derived in recent years in AFLP related technologies with several AFLP expanded methodologies available. AFLP technology has been widely used in the fields of plant, animal, and microbes. It has become one of the hotspots in Forensic Botany. This review focuses on the recent advances of AFLP and its applications in forensic biology.

  5. A monoclinic polymorph of theophylline

    Shuo Zhang

    2011-12-01

    Full Text Available A monoclinic polymorph of theophylline, C7H8N4O2, has been obtained from a chloroform/methanol mixture by evaporation under ambient conditions. The new polymorph crystallizes with two molecules in the asymmetric unit. The structure features intermolecular N—H...O hydrogen bonds, resulting in the formation of dimers between two crystallographically different molecules; each molecule acts as both donor and acceptor.

  6. Direct Determination of Molecular Weight Distribution of Calf-Thymus DNAs and Study of Their Fragmentation under Ultrasonic and Low-Energy IR Irradiations. A Charge Detection Mass Spectrometry Investigation.

    Halim, Mohammad A; Bertorelle, Franck; Doussineau, Tristan; Antoine, Rodolphe

    2018-06-09

    Calf-thymus (CT-DNA) is widely used as binding agent. The commercial samples are known to be "highly polymerized DNA" samples. CT-DNA is known to be fragile in particular upon ultrasonic wave irradiation. Degradation products might have dramatic consequence on its bio-sensing activity, and an accurate determination of the molecular weight distribution and stability of commercial samples is highly demanded. We investigated the sensitivity of charge detection mass spectrometry (CDMS), a single-molecule MS method, both with single-pass and ion trap CDMS ("Benner" trap) modes to the determination of the composition and stability (under multiphoton IR irradiation) of calf-thymus DNAs. We also investigated the changes of molecular weight distributions in the course of sonication by irradiating ultrasonic wave to CT-DNA. We report for the first time, the direct molecular weight (MW) distribution of DNA sodium salt from calf-thymus revealing two populations at high (~10 MDa) and low (~3 MDa) molecular weights. We evidence a transition between the high-MW to the low-MW distribution, confirming that the low-MW distribution results from degradation of CT-DNA. Finally, we report also IRMPD experiments carried out on trapped single-stranded linear DNAs from calf-thymus allowing to extract their activation energy for unimolecular dissociation. We show that single-pass CDMS is a direct, efficient and accurate MS-based approach to determine the composition of calf-thymus DNAs. Furthermore, ion trap CDMS allows us to evaluate the stability (both under multiphoton IR irradiation and in the course of sonication by irradiating ultrasonic wave) of calf-thymus DNAs. This article is protected by copyright. All rights reserved.

  7. Fitness consequences of polymorphic inversions in the zebra finch genome.

    Knief, Ulrich; Hemmrich-Stanisak, Georg; Wittig, Michael; Franke, Andre; Griffith, Simon C; Kempenaers, Bart; Forstmeier, Wolfgang

    2016-09-29

    Inversion polymorphisms constitute an evolutionary puzzle: they should increase embryo mortality in heterokaryotypic individuals but still they are widespread in some taxa. Some insect species have evolved mechanisms to reduce the cost of embryo mortality but humans have not. In birds, a detailed analysis is missing although intraspecific inversion polymorphisms are regarded as common. In Australian zebra finches (Taeniopygia guttata), two polymorphic inversions are known cytogenetically and we set out to detect these two and potentially additional inversions using genomic tools and study their effects on embryo mortality and other fitness-related and morphological traits. Using whole-genome SNP data, we screened 948 wild zebra finches for polymorphic inversions and describe four large (12-63 Mb) intraspecific inversion polymorphisms with allele frequencies close to 50 %. Using additional data from 5229 birds and 9764 eggs from wild and three captive zebra finch populations, we show that only the largest inversions increase embryo mortality in heterokaryotypic males, with surprisingly small effect sizes. We test for a heterozygote advantage on other fitness components but find no evidence for heterosis for any of the inversions. Yet, we find strong additive effects on several morphological traits. The mechanism that has carried the derived inversion haplotypes to such high allele frequencies remains elusive. It appears that selection has effectively minimized the costs associated with inversions in zebra finches. The highly skewed distribution of recombination events towards the chromosome ends in zebra finches and other estrildid species may function to minimize crossovers in the inverted regions.

  8. Micro-Evolution in Grasshoppers Mediated by Polymorphic Robertsonian Translocations

    Colombo, Pablo C.

    2013-01-01

    This review focuses on grasshoppers that are polymorphic for Robertsonian translocations because in these organisms the clarity of meiotic figures allows the study of both chiasma distribution and the orientation of trivalents and multivalents in metaphase I. Only five species of such grasshoppers were found in the literature, and all of them were from the New World: Oedaleonotus enigma (Scudder) (Orthoptera: Acrididae), Leptysma argentina Bruner, Dichroplus pratensis Bruner, Sinipta dalmani Stål, and Cornops aquaticum Bruner. A general feature of these species (except O. enigma) is that fusion carriers suffer a marked reduction of proximal and interstitial (with respect to the centromere) chiasma frequency; this fact, along with the reduction in the number of linkage groups with the consequent loss of independent segregation, produces a marked decrease of recombination in fusion carriers. This reduction in recombination has led to the conclusion that Robertsonian polymorphic grasshopper species share some properties with inversion polymorphic species of Drosophila, such as the central-marginal pattern (marginal populations are monomorphic, central populations are highly polymorphic). This pattern might be present in D. pratensis, which is certainly the most complex Robertsonian polymorphism system in the present study. However, L. argentina and C. aquaticum do not display this pattern. This issue is open to further research. Since C. aquaticum is soon to be released in South Africa as a biological control, the latitudinal pattern found in South America may repeat there. This experiment's outcome is open and deserves to be followed. PMID:23909914

  9. New polymorphous computing fabric

    Wolinski, Christophe; Gokhale, Maya; McCabe, Kevin P.

    2002-01-01

    This paper introduces a new polymorphous computing Fabric well suited to DSP and Image Processing and describes its implementation on a Configurable System on a Chip (CSOC). The architecture is highly parameterized and enables customization of the synthesized Fabric to achieve high performance for a specific class of application. For this reason it can be considered to be a generic model for hardware accelerator synthesis from a high level specification. Another important innovation is the Fabric uses a global memory concept, which gives the host processor random access to all the variables and instructions on the Fabric. The Fabric supports different computing models including MIMD, SPMD and systolic flow and permits dynamic reconfiguration. We present a specific implementation of a bank of FIR filters on a Fabric composed of 52 cells on the Altera Excalibur ARM running at 33 MHz. The theoretical performance of this Fabric is 1.8 GMACh. For the FIR application we obtain 1.6 GMAC/s real performance. Some automatic tools have been developed like the tool to provide a host access utility and assembler.

  10. ACE I/D Gene Polymorphism Can't Predict the Steroid Responsiveness in Asian Children with Idiopathic Nephrotic Syndrome: A Meta-Analysis

    Su, Li-Na; Lei, Feng-Ying; Huang, Wei-Fang; Zhao, Yan-Jun

    2011-01-01

    Background The results from the published studies on the association between angiotensin-converting enzyme (ACE) insertion/deletion (I/D) gene polymorphism and the treatment response to steroid in Asian children with idiopathic nephrotic syndrome (INS) is still conflicting. This meta-analysis was performed to evaluate the relation between ACE I/D gene polymorphism and treatment response to steroid in Asian children and to explore whether ACE D allele or DD genotype could become a predictive marker for steroid responsiveness. Methodology/Principal Findings Association studies were identified from the databases of PubMed, Embase, Cochrane Library and CBM-disc (China Biological Medicine Database) as of September 1, 2010, and eligible investigations were synthesized using meta-analysis method. Five investigations were identified for the analysis of association between ACE I/D gene polymorphism and steroid-resistant nephrotic syndrome (SRNS) risk in Asian children and seven studies were included to explore the relationship between ACE I/D gene polymorphism and steroid-sensitive nephrotic syndrome (SSNS) susceptibility. Five investigations were recruited to explore the difference of ACE I/D gene distribution between SRNS and SSNS. There was no a markedly association between D allele or DD genotype and SRNS susceptibility or SSNS risk, and the gene distribution differences of ACE between SRNS and SSNS were not statistically significant. II genotype might play a positive role against SRNS onset but not for SSNS (OR = 0.51, P = 0.02; OR = 0.95, P = 0.85; respectively), however, the result for the association of II genotype with SRNS risk was not stable. Conclusions/Significance Our results indicate that D allele or DD homozygous can't become a significant genetic molecular marker to predict the treatment response to steroid in Asian children with INS. PMID:21611163

  11. Molecular diversity among Turkish oaks (QUERCUS) using random ...

    aykut

    2013-11-06

    Nov 6, 2013 ... using random amplified polymorphic DNA (RAPD) ... 1Department of Molecular Biology and Genetics, Faculty of Science and Arts, Uşak University, 64200 Uşak, Turkey. ..... University Directorate of Scientific Research Projects.

  12. Association study between the Taq1A (rs1800497 polymorphism and schizophrenia in a Brazilian sample

    Quirino Cordeiro

    2014-08-01

    Full Text Available Schizophrenia is a severe psychotic disorder with recurrent relapse and functional impairment. It results from a poorly understood gene-environment interaction. The Taq1A polymorphism (located in the gene cluster NTAD is a likely candidate for schizophrenia. Its rs1800497 polymorphism was shown to be associated with DRD2 gene expression. Therefore the present work aims to investigate a possible association between schizophrenia and such polymorphism. The compared distribution of the alleles and genotypes of the studied polymorphism was investigated in a Brazilian sample of 235 patients and 834 controls. Genotypic frequencies were in Hardy-Weinberg equilibrium. There was a trend of allelic association between the Taq1A polymorphism (rs1800497 with schizophrenia in the studied sample. However no statistically differences were found between cases and controls when analyzed by gender or schizophrenia subtypes.

  13. An overview of molecular marker methods for plants | Semagn ...

    The development and use of molecular markers for the detection and exploitation of DNA polymorphism is one of the most significant developments in the field of molecular genetics. The presence of various types of molecular markers, and differences in their principles, methodologies, and applications require careful ...

  14. Molecular dynamics of CYP2D6 polymorphisms in the absence and presence of a mechanism-based inactivator reveals changes in local flexibility and dominant substrate access channels.

    Parker W de Waal

    Full Text Available Cytochrome P450 enzymes (CYPs represent an important enzyme superfamily involved in metabolism of many endogenous and exogenous small molecules. CYP2D6 is responsible for ∼ 15% of CYP-mediated drug metabolism and exhibits large phenotypic diversity within CYPs with over 100 different allelic variants. Many of these variants lead to functional changes in enzyme activity and substrate selectivity. Herein, a molecular dynamics comparative analysis of four different variants of CYP2D6 was performed. The comparative analysis included simulations with and without SCH 66712, a ligand that is also a mechanism-based inactivator, in order to investigate the possible structural basis of CYP2D6 inactivation. Analysis of protein stability highlighted significantly altered flexibility in both proximal and distal residues from the variant residues. In the absence of SCH 66712, *34, *17-2, and *17-3 displayed more flexibility than *1, and *53 displayed more rigidity. SCH 66712 binding reversed flexibility in *17-2 and *17-3, through *53 remained largely rigid. Throughout simulations with docked SCH 66712, ligand orientation within the heme-binding pocket was consistent with previously identified sites of metabolism and measured binding energies. Subsequent tunnel analysis of substrate access, egress, and solvent channels displayed varied bottle-neck radii. Taken together, our results indicate that SCH 66712 should inactivate these allelic variants, although varied flexibility and substrate binding-pocket accessibility may alter its interaction abilities.

  15. Association of ADIPOQ +45T>G polymorphism with body fat mass and blood levels of soluble adiponectin and inflammation markers in a Mexican-Mestizo population

    Guzman-Ornelas MO

    2012-10-01

    Full Text Available Milton-Omar Guzman-Ornelas,1 Efrain Chavarria-Avila,1 Jose-Francisco Munoz-Valle,1,2 Laura-Elizabeth Armas-Ramos,3 Jorge Castro-Albarran,3,4 Maria Elena Aguilar Aldrete,1,5 Edith Oregon-Romero,2 Monica Vazquez-Del Mercado,2 Rosa-Elena Navarro-Hernandez1–31Biomedical Sciences Doctorate Program, 2Department of Molecular Biology and Genomics, 3Master of Human Nutrition Program, University of Guadalajara, Guadalajara, Jalisco, México; 4HMIELM, Secretaria de Salud Jalisco, Guadalajara, Jalisco, Mexico; 5Department of Public Health, University of Guadalajara, Jalisco, MéxicoPurpose: Obesity is a disease with genetic susceptibility characterized by an increase in storage and irregular distribution of body fat. In obese patients, the decrease in the Adiponectin gene (ADIPOQ expression has been associated with a systemic low-grade inflammatory state. Our aim was to investigate the relationship between ADIPOQ +45T>G gene simple nucleotide polymorphism (SNP rs2241766 with serum adiponectin (sAdiponectin, distribution of body fat storage, and inflammation markers.Subjects and methods: In this cross-sectional study, 242 individuals from Western Mexico characterized as Mexican-Mestizo and classified by body mass index (BMI, were included. Anthropometrics, body composition, body fat distribution, and inflammation markers were measured by routine methods. Genotypes were characterized using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP technique and sAdiponectin by the ELISA method. A P-value <0.05 was considered the statistically significant threshold.Results: sAdiponectin is associated with BMI (P < 0.001 and the genotypes (P < 0.001 to 0.0046 GG (8169 ± 1162 ng/mL, TG (5189 ± 501 ng/mL, and TT (3741 ± 323 ng/mL, but the SNP ADIPOQ +45T.G is not associated with BMI. However, the detailed analysis showed association of this SNP with a pattern of fat distribution and correlations (P < 0.05 with inflammation markers and

  16. Valence and inner-valence shell dissociative photoionization of CO in the 26-33 eV range. II. Molecular-frame and recoil-frame photoelectron angular distributions

    Lebech, M.; Houver, J.C.; Raseev, G.

    2012-01-01

    Experimental and theoretical results for molecular-frame photoemission are presented for inner-valence shell photoionization of the CO molecule induced by linearly and circularly polarized light. The experimental recoil frame photoelectron angular distributions (RFPADs) obtained from dissociative...... photoionization measurements where the velocities of the ionic fragment and photoelectron were detected in coincidence, are compared to RFPADs computed using the multichannel Schwinger configuration interaction method. The formalism for including a finite lifetime of the predissociative ion state is presented...... for the case of general elliptically polarized light, to obtain the RFPAD rather than the molecular frame photoelectron angular distribution (MFPAD), which would be obtained with the assumption of instantaneous dissociation. We have considered photoionization of CO for the photon energies of 26.0 eV, 29.5 e...

  17. Tuning polymorphism and orientation in organic semiconductor thin films via post-deposition processing.

    Hiszpanski, Anna M; Baur, Robin M; Kim, Bumjung; Tremblay, Noah J; Nuckolls, Colin; Woll, Arthur R; Loo, Yueh-Lin

    2014-11-05

    Though both the crystal structure and molecular orientation of organic semiconductors are known to impact charge transport in thin-film devices, separately accessing different polymorphs and varying the out-of-plane molecular orientation is challenging, typically requiring stringent control over film deposition conditions, film thickness, and substrate chemistry. Here we demonstrate independent tuning of the crystalline polymorph and molecular orientation in thin films of contorted hexabenzocoronene, c-HBC, during post-deposition processing without the need to adjust deposition conditions. Three polymorphs are observed, two of which have not been previously reported. Using our ability to independently tune the crystal structure and out-of-plane molecular orientation in thin films of c-HBC, we have decoupled and evaluated the effects that molecular packing and orientation have on device performance in thin-film transistors (TFTs). In the case of TFTs comprising c-HBC, polymorphism and molecular orientation are equally important; independently changing either one affects the field-effect mobility by an order of magnitude.

  18. Lung Cancer Susceptibility and hOGG1 Ser326Cys Polymorphism: A Meta-Analysis

    Kiyohara, Chikako; Takayama, Koichi; Nakanishi, Yoichi

    2010-01-01

    Recent lung cancer studies have focused on identifying the effects of single nucleotide polymorphisms (SNPs) in candidate genes, among which DNA repair genes are increasingly being studied. Genetic variations in DNA repair genes are thought to modulate DNA repair capacity and are suggested to be related to lung cancer risk. In this study, we tried to assess reported studies of association between polymorphism of human 8-oxoguanine DNA glycosylase 1 (hOGG1) Ser326Cys and lung cancer. We conducted MEDLINE, Current Contents and Web of Science searches using 'hOGG1', 'lung cancer' and 'polymorphism' as keywords to search for papers published (from January 1995 through August 2010). Data were combined using both a fixed effects (the inverse variance-weighted method) and a random effects (DerSimonian and Laird method) models. The Cochran Q test was used for the assessment of heterogeneity. Publication bias was assessed by both Begg’s and Egger’s tests. We identified 20 case-control studies in 21 different ethnic populations. As two studies were not in the Hardy-Weinberg equilibrium, 18 case-control studies in 19 different ethnic populations (7,792 cases and 9,358 controls) were included in our meta-analysis. Summary frequencies of the Cys allele among Caucasians and Asians based on the random effects model were 20.9% (95% confidence interval (CI) = 18.9–22.9) and 46.1% (95% CI = 40.2–52.0), respectively. The distribution of the Cys allele was significantly different between Asians and Caucasians (P < 0.001). The Cys/Cys genotype was significantly associated with lung cancer risk in Asian populations (odds ratio = 1.27, 95% CI = 1.09–1.48) but not in Caucasian populations. This ethnic difference in lung cancer risk may be due to environmental factors such as cigarette smoking and dietary factors. Although the summary risk for developing lung cancer may not be large, lung cancer is such a common malignancy that even a small increase

  19. Lung Cancer Susceptibility and hOGG1 Ser326Cys Polymorphism: A Meta-Analysis

    Kiyohara, Chikako, E-mail: chikako@phealth.med.kyushu-u.ac.jp [Department of Preventive Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan); Takayama, Koichi; Nakanishi, Yoichi [Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan)

    2010-10-28

    Recent lung cancer studies have focused on identifying the effects of single nucleotide polymorphisms (SNPs) in candidate genes, among which DNA repair genes are increasingly being studied. Genetic variations in DNA repair genes are thought to modulate DNA repair capacity and are suggested to be related to lung cancer risk. In this study, we tried to assess reported studies of association between polymorphism of human 8-oxoguanine DNA glycosylase 1 (hOGG1) Ser326Cys and lung cancer. We conducted MEDLINE, Current Contents and Web of Science searches using 'hOGG1', 'lung cancer' and 'polymorphism' as keywords to search for papers published (from January 1995 through August 2010). Data were combined using both a fixed effects (the inverse variance-weighted method) and a random effects (DerSimonian and Laird method) models. The Cochran Q test was used for the assessment of heterogeneity. Publication bias was assessed by both Begg’s and Egger’s tests. We identified 20 case-control studies in 21 different ethnic populations. As two studies were not in the Hardy-Weinberg equilibrium, 18 case-control studies in 19 different ethnic populations (7,792 cases and 9,358 controls) were included in our meta-analysis. Summary frequencies of the Cys allele among Caucasians and Asians based on the random effects model were 20.9% (95% confidence interval (CI) = 18.9–22.9) and 46.1% (95% CI = 40.2–52.0), respectively. The distribution of the Cys allele was significantly different between Asians and Caucasians (P < 0.001). The Cys/Cys genotype was significantly associated with lung cancer risk in Asian populations (odds ratio = 1.27, 95% CI = 1.09–1.48) but not in Caucasian populations. This ethnic difference in lung cancer risk may be due to environmental factors such as cigarette smoking and dietary factors. Although the summary risk for developing lung cancer may not be large, lung cancer is such a common malignancy that even a small increase

  20. Molecular distribution and compound-specific stable carbon isotopic composition of dicarboxylic acids, oxocarboxylic acids and α-dicarbonyls in PM2.5 from Beijing, China

    W. Zhao

    2018-02-01

    Full Text Available This study investigates the seasonal variation, molecular distribution and stable carbon isotopic composition of diacids, oxocarboxylic acids and α-dicarbonyls to better understand the sources and formation processes of fine aerosols (PM2.5 in Beijing. The concentrations of total dicarboxylic acids varied from 110 to 2580 ng m−3, whereas oxoacids (9.50–353 ng m−3 and dicarbonyls (1.50–85.9 ng m−3 were less abundant. Oxalic acid was found to be the most abundant individual species, followed by succinic acid or occasionally by terephthalic acid (tPh, a plastic waste burning tracer. Ambient concentrations of phthalic acid (37.9 ± 27.3 ng m−3 and tPh (48.7 ± 51.1 ng m−3 were larger in winter than in other seasons, illustrating that fossil fuel combustion and plastic waste incineration contribute more to wintertime aerosols. The year-round mass concentration ratios of malonic acid to succinic acid (C3 ∕ C4 were relatively low by comparison with those in other urban aerosols and remote marine aerosols. The values were less than or equal to unity in Beijing, implying that the degree of photochemical formation of diacids in Beijing is insignificant. Moreover, strong correlation coefficients of major oxocarboxylic acids and α-dicarbonyls with nss-K+ suggest that biomass burning contributes significantly to these organic acids and related precursors. The mean δ13C value of succinic acid is the highest among all species, with values of −17.1 ± 3.9 ‰ (winter and −17.1 ± 2.0 ‰ (spring, while malonic acid is more enriched in 13C than others in autumn (−17.6 ± 4.6 ‰ and summer (−18.7 ± 4.0 ‰. The δ13C values of major species in Beijing aerosols are generally lower than those in the western North Pacific atmosphere, the downwind region, which indicates that stable carbon isotopic compositions of diacids depend on their precursor sources in Beijing. Therefore, our

  1. Molecular distribution and compound-specific stable carbon isotopic composition of dicarboxylic acids, oxocarboxylic acids and α-dicarbonyls in PM2.5 from Beijing, China

    Zhao, Wanyu; Kawamura, Kimitaka; Yue, Siyao; Wei, Lianfang; Ren, Hong; Yan, Yu; Kang, Mingjie; Li, Linjie; Ren, Lujie; Lai, Senchao; Li, Jie; Sun, Yele; Wang, Zifa; Fu, Pingqing

    2018-02-01

    This study investigates the seasonal variation, molecular distribution and stable carbon isotopic composition of diacids, oxocarboxylic acids and α-dicarbonyls to better understand the sources and formation processes of fine aerosols (PM2.5) in Beijing. The concentrations of total dicarboxylic acids varied from 110 to 2580 ng m-3, whereas oxoacids (9.50-353 ng m-3) and dicarbonyls (1.50-85.9 ng m-3) were less abundant. Oxalic acid was found to be the most abundant individual species, followed by succinic acid or occasionally by terephthalic acid (tPh), a plastic waste burning tracer. Ambient concentrations of phthalic acid (37.9 ± 27.3 ng m-3) and tPh (48.7 ± 51.1 ng m-3) were larger in winter than in other seasons, illustrating that fossil fuel combustion and plastic waste incineration contribute more to wintertime aerosols. The year-round mass concentration ratios of malonic acid to succinic acid (C3 / C4) were relatively low by comparison with those in other urban aerosols and remote marine aerosols. The values were less than or equal to unity in Beijing, implying that the degree of photochemical formation of diacids in Beijing is insignificant. Moreover, strong correlation coefficients of major oxocarboxylic acids and α-dicarbonyls with nss-K+ suggest that biomass burning contributes significantly to these organic acids and related precursors. The mean δ13C value of succinic acid is the highest among all species, with values of -17.1 ± 3.9 ‰ (winter) and -17.1 ± 2.0 ‰ (spring), while malonic acid is more enriched in 13C than others in autumn (-17.6 ± 4.6 ‰) and summer (-18.7 ± 4.0 ‰). The δ13C values of major species in Beijing aerosols are generally lower than those in the western North Pacific atmosphere, the downwind region, which indicates that stable carbon isotopic compositions of diacids depend on their precursor sources in Beijing. Therefore, our study demonstrates that in addition to photochemical oxidation, high abundances of diacids

  2. Preparation and evaluation of famotidine polymorphs.

    Nagaraju, Ravouru; Prathusha, Ande Penchala; Subhash Chandra Bose, Penjury; Kaza, Rajesh; Bharathi, Koganti

    2010-06-01

    The main objective of this study was to compare the behaviour of drug release among the famotidine polymorphs prepared by using various additives and solvents, by solvent evaporation method. The famotidine polyvinyl pyrrolidone polymorphs with different concentrations (0.5, 1 and 1.5%) were prepared by using solvent evaporation method. In these polymorphs of different concentrations 1% w/v polymorphs showed better release. Similarly, famotidine polymorphs of Tween 80 with different concentrations, polyethylene glycol 1% w/v and methanol was prepared. Famotidine polymorphs prepared the PVP (1% w/v) showed better drug release and solubility. DSC, FTIR, SEM and XRD studies were carried out. DSC studies revealed that PVP polymorphs were found to stable compared to other polymorphs. FTIR studies of the polymorphs prepared indicated that there was an interaction found in all polymorphs except PVP polymorphs indicating the absence of drug-additive interaction. SEM studies of PVP and methanol polymorphs revealed that they are tabular and prismatic and columnar respectively. These changes in morphology were due to variations in face dimensions and also properties of additives and solvent used in the preparation. XRD studies revealed that there is an increase in crystallinity in methanol polymorphs when compared to PVP polymorphs and pure drug. The mechanism of drug release was determined using zero order, first order and Hixon-Crowel equations. From the drug release kinetics these polymorphs followed first order and Hixon-Crowel release kinetics, exhibited fair linearity in their dissolution data. Further, in vivo studies were carried out for the evaluation of antiulcer activity. Based upon the drug release pattern and its kinetics only two of the prepared polymorphs of famotidine i.e. famotidine PVP polymorphs and famotidine methanol polymorphs were selected for animal studies. Antiulcer studies were carried out using pylorus ligation model and estimation of antioxidant

  3. Genome-wide divergence and linkage disequilibrium analyses for Capsicum baccatum revealed by genome-anchored single nucleotide polymorphisms

    Principal component analysis (PCA) with 36,621 polymorphic genome-anchored single nucleotide polymorphisms (SNPs) identified collectively for Capsicum annuum and Capsicum baccatum was used to show the distribution of these 2 important incompatible cultivated pepper species. Estimated mean nucleotide...

  4. A lack of association between polymorphisms of three positional candidate genes (CLASP2 , UBP1, and FBXL2) and canine disorder of sexual development (78,XX; SRY -negative).

    Salamon, Sylwia; Nowacka-Woszuk, Joanna; Szczerbal, Izabela; Dzimira, Stanisław; Nizanski, Wojciech; Ochota, Malgorzata; Switonski, Marek

    2014-01-01

    A disorder of sexual development (DSD) of dogs with a female karyotype, missing SRY gene, and presence of testicles or ovotestes is quite commonly diagnosed. It is suggested that this disorder is caused by an autosomal recessive mutation; however, other models of inheritance have not been definitely ruled out. In an earlier study it was hypothesized that the mutation may reside in a pericentromeric region of canine chromosome 23 (CFA23). Three positional candidate genes (CLASP2, UBP1, and FBXL2) were selected in silico in the search for polymorphisms in 7 testicular or ovotesticular XX DSD dogs, 8 XX DSD dogs of unknown cause (SRY-negative, with enlarged clitoris and unknown histology of gonads), and 29 normal female dogs as a control group. Among the 15 molecularly studied dogs with enlarged clitoris there were 3 new cases of testicular or ovotesticular XX DSD and 4 new cases of XX DSD with unknown cause (histology of the gonads unknown). Altogether, 11 (including 10 novel) polymorphisms in 5'- and 3'-flanking regions of the studied genes were found. The distribution analysis of these polymorphisms showed no association with the DSD phenotypes. Thus, it was concluded that the presence of the causative mutation for testicular or ovotesticular XX DSD in the pericentromeric region of CFA23 is unlikely. © 2014 S. Karger AG, Basel.

  5. Modeling and molecular dynamics of HPA-1a and -1b polymorphisms: effects on the structure of the β3 subunit of the αIIbβ3 integrin.

    Vincent Jallu

    Full Text Available The HPA-1 alloimmune system carried by the platelet integrin αIIbβ3 is the primary cause of alloimmune thrombocytopenia in Caucasians and the HPA-1b allele might be a risk factor for thrombosis. HPA-1a and -1b alleles are defined by a leucine and a proline, respectively, at position 33 in the β3 subunit. Although the structure of αIIbβ3 is available, little is known about structural effects of the L33P substitution and its consequences on immune response and integrin functions.A complete 3D model of the L33-β3 extracellular domain was built and a P33 model was obtained by in silico mutagenesis. We then performed molecular dynamics simulations. Analyses focused on the PSI, I-EGF-1, and I-EGF-2 domains and confirmed higher exposure of residue 33 in the L33 β3 form. These analyses also showed major structural flexibility of all three domains in both forms, but increased flexibility in the P33 β3 form. The L33P substitution does not alter the local structure (residues 33 to 35 of the PSI domain, but modifies the structural equilibrium of the three domains.These results provide a better understanding of HPA-1 epitopes complexity and alloimmunization prevalence of HPA-1a. P33 gain of structure flexibility in the β3 knee may explain the increased adhesion capacity of HPA-1b platelets and the associated thrombotic risk. Our study provides important new insights into the relationship between HPA-1 variants and β3 structure that suggest possible effects on the alloimmune response and platelet function.

  6. PARP1 Val762Ala polymorphism reduces enzymatic activity

    Wang Xiaogan; Wang Zhaoqi; Tong Weimin; Shen Yan

    2007-01-01

    Poly(ADP-ribose) polymerase 1 (PARP1) modifies a variety of nuclear proteins by poly(ADP-ribosyl)ation, and plays diverse roles in molecular and cellular processes. A common PARP1 single nucleotide polymorphism (SNP) at codon 762, resulting in the substitution of alanine (Ala) for valine (Val) in the catalytic domain has been implicated in susceptibility to cancer. To characterize the functional effect of this polymorphism on PARP1, we performed in vitro enzymatic analysis on PARP1-Ala762 and PARP1-Val762. We found that PARP1-Ala762 displayed 57.2% of the activity of PARP1-Val762 for auto-poly(ADP-ribosyl)ation and 61.9% of the activity of PARP1-Val762 for trans-poly(ADP-ribosyl)ation of histone H1. The kinetic characterization revealed that the K m of PARP1-Ala762 was increased to a 1.2-fold of the K m of PARP1-Val762 for trans-poly(ADP-ribosyl)ation. Thus, the PARP1 Val762Ala polymorphism reduces the enzymatic activity of PARP1 by increasing K m . This finding suggests that different levels of poly(ADP-ribosyl)ation by PARP1 might aid in understanding Cancer risk of carriers of the PARP1 Val762Ala polymorphism

  7. Study of the HFE gene common polymorphisms in French patients with sporadic amyotrophic lateral sclerosis.

    Praline, Julien; Blasco, Hélène; Vourc'h, Patrick; Rat, Valérian; Gendrot, Chantal; Camu, William; Andres, Christian R

    2012-06-15

    Our objective was to investigate whether the C282Y (p.Cys 282 Tyr) and H63D (p. His 63 Asp) HFE polymorphisms were associated with sporadic amyotrophic lateral sclerosis (SALS) in the French population. We searched for a relation of HFE polymorphisms with the clinical characteristics of the disease. The HFE polymorphisms were studied in 824 patients with SALS and 583 controls. We compared the frequency of the polymorphisms between SALS and controls groups by univariate and multivariate statistics, taking into account gender, site, age-at-onset and survival. We did not observe significant difference in the frequency of H63D polymorphism between SALS and control group. We observed a significant difference for C282Y between patients and controls with a low frequency of the Y allele in patients (3.2%) compared to our control group (5.9%). Disease duration, distribution of gender, site-of-onset, age-at-onset did not differ between groups taking into account genotypes of each polymorphism. Our results in this large cohort of ALS patients indicate that H63D polymorphism is not associated with SALS in the French population. This conclusion does not exclude a weak effect of the HFE gene polymorphisms in certain ALS populations, or an effect of other rare HFE gene variants. Copyright © 2012 Elsevier B.V. All rights reserved.

  8. Association study of interleukin-4 polymorphisms with paranoid schizophrenia in the Polish population: a critical approach.

    Fila-Danilow, Anna; Kucia, Krzysztof; Kowalczyk, Malgorzata; Owczarek, Aleksander; Paul-Samojedny, Monika; Borkowska, Paulina; Suchanek, Renata; Kowalski, Jan

    2012-08-01

    Changes in immunological system are one of dysfunctions reported in schizophrenia. Some changes based on an imbalance between Th1 and Th2 cytokines results from cytokine gene polymorphisms. Interleukin-4 gene (IL4) is considered as a potential candidate gene in schizophrenia association studies. The aim of the current case-control study was to examine whether the -590C/T (rs2243250) and -33C/T (rs2070874) IL4 gene polymorphisms are implicated in paranoid schizophrenia development in the Polish population. Genotyping of polymorphisms was performed by using PCR-RFLP technique. The genotypes and alleles distribution of both SNPs were analysed in patients (n = 182) and healthy individuals constituted the control group (n = 215). The connection between some clinical variables and studied polymorphisms has been examined as well. We did not revealed any association between the -590C/T and -33C/T polymorphisms and paranoid schizophrenia. In case of both SNPs the homozygous TT genotype was extremely rare. Both polymorphic sites of the IL4 gene were found to be in a very strong linkage disequilibrium. However we did not identify a haplotype predispose to paranoid schizophrenia. No associations were also observed between the clinical course and psychopathology of the disease and the genotypes of both analysed polymorphisms. Our results suggest that the polymorphisms -590C/T in IL4 gene promoter region and -33C/T in the 5'-UTR are not involved in the pathophysiology of paranoid schizophrenia in Polish residents.

  9. Polyploidy creates higher diversity among Cynodon accessions as assessed by molecular markers.

    Gulsen, Osman; Sever-Mutlu, Songul; Mutlu, Nedim; Tuna, Metin; Karaguzel, Osman; Shearman, Robert C; Riordan, Terrance P; Heng-Moss, Tiffany M

    2009-05-01

    Developing a better understanding of associations among ploidy level, geographic distribution, and genetic diversity of Cynodon accessions could be beneficial to bermudagrass breeding programs, and would enhance our understanding of the evolutionary biology of this warm season grass species. This study was initiated to: (1) determine ploidy analysis of Cynodon accessions collected from Turkey, (2) investigate associations between ploidy level and diversity, (3) determine whether geographic and ploidy distribution are related to nuclear genome variation, and (4) correlate among four nuclear molecular marker systems for Cynodon accessions' genetic analyses. One hundred and eighty-two Cynodon accessions collected in Turkey from an area south of the Taurus Mountains along the Mediterranean cost and ten known genotypes were genotyped using sequence related amplified polymorphism (SRAP), peroxidase gene polymorphism (POGP), inter-simple sequence repeat (ISSR), and random amplified polymorphic DNA (RAPD). The diploids, triploids, tetraploids, pentaploids, and hexaploids revealed by flow cytometry had a linear present band frequency of 0.36, 0.47, 0.49, 0.52, and 0.54, respectively. Regression analysis explained that quadratic relationship between ploidy level and band frequency was the most explanatory (r = 0.62, P Cynodon accessions' genetic structure can aid to enhance breeding programs and broaden genetic base of commercial cultivars.

  10. The Genealogical Consequences of Fecundity Variance Polymorphism

    Taylor, Jesse E.

    2009-01-01

    The genealogical consequences of within-generation fecundity variance polymorphism are studied using coalescent processes structured by genetic backgrounds. I show that these processes have three distinctive features. The first is that the coalescent rates within backgrounds are not jointly proportional to the infinitesimal variance, but instead depend only on the frequencies and traits of genotypes containing each allele. Second, the coalescent processes at unlinked loci are correlated with the genealogy at the selected locus; i.e., fecundity variance polymorphism has a genomewide impact on genealogies. Third, in diploid models, there are infinitely many combinations of fecundity distributions that have the same diffusion approximation but distinct coalescent processes; i.e., in this class of models, ancestral processes and allele frequency dynamics are not in one-to-one correspondence. Similar properties are expected to hold in models that allow for heritable variation in other traits that affect the coalescent effective population size, such as sex ratio or fecundity and survival schedules. PMID:19433628

  11. Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans).

    Buonaccorsi, V P; McDowell, J R; Graves, J E

    2001-05-01

    Different classes of molecular markers occasionally yield discordant views of population structure within a species. Here, we examine the distribution of molecular variance from 14 polymorphic loci comprising four classes of molecular markers within approximately 400 blue marlin individuals (Makaira nigricans). Samples were collected from the Atlantic and Pacific Oceans over 5 years. Data from five hypervariable tetranucleotide microsatellite loci and restriction fragment length polymorphism (RFLP) analysis of whole molecule mitochondrial DNA (mtDNA) were reported and compared with previous analyses of allozyme and single-copy nuclear DNA (scnDNA) loci. Temporal variance in allele frequencies was nonsignificant in nearly all cases. Mitochondrial and microsatellite loci revealed striking phylogeographic partitioning among Atlantic and Pacific Ocean samples. A large cluster of alleles was present almost exclusively in Atlantic individuals at one microsatellite locus and for mtDNA, suggesting that, if gene flow occurs, it is likely to be unidirectional from Pacific to Atlantic oceans. Mitochondrial DNA inter-ocean divergence (FST) was almost four times greater than microsatellite or combined nuclear divergences including allozyme and scnDNA markers. Estimates of Neu varied by five orders of magnitude among marker classes. Using mathematical and computer simulation approaches, we show that substantially different distributions of FST are expected from marker classes that differ in mode of inheritance and rate of mutation, without influence of natural selection or sex-biased dispersal. Furthermore, divergent FST values can be reconciled by quantifying the balance between genetic drift, mutation and migration. These results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci.

  12. Restriction Fragment Length Polymorphisms of Virulence Plasmids in Rhodococcus equi

    Takai, Shinji; Shoda, Masato; Sasaki, Yukako; Tsubaki, Shiro; Fortier, Guillaume; Pronost, Stephane; Rahal, Karim; Becu, Teotimo; Begg, Angela; Browning, Glenn; Nicholson, Vivian M.; Prescott, John F.

    1999-01-01

    Virulent Rhodococcus equi, which is a well-known cause of pyogranulomatous pneumonia in foals, possesses a large plasmid encoding virulence-associated 15- to 17-kDa antigens. Foal and soil isolates from five countries—Argentina, Australia, Canada, France, and Japan—were investigated for the presence of 15- to 17-kDa antigens by colony blotting, using the monoclonal antibody 10G5, and the gene coding for 15- to 17-kDa antigens by PCR. Plasmid DNAs extracted from positive isolates were digested with restriction endonucleases BamHI, EcoRI, EcoT22I, and HindIII, and the digestion patterns that resulted divided the plasmids of virulent isolates into five closely related types. Three of the five types had already been reported in Canadian and Japanese isolates, and the two new types had been found in French and Japanese isolates. Therefore, we tentatively designated these five types 85-kb type I (pREAT701), 85-kb type II (a new type), 87-kb type I (EcoRI and BamHI type 2 [V. M. Nicholson and J. F. Prescott, J. Clin. Microbiol. 35:738–740, 1997]), 87-kb type II (a new type), and 90-kb (pREL1) plasmids. The 85-kb type I plasmid was found in isolates from Argentina, Australia, Canada, and France. Plasmid 87-kb type I was isolated in specimens from Argentina, Canada, and France. The 85-kb type II plasmid appeared in isolates from France. On the other hand, plasmids 87-kb type II and 90-kb were found only in isolates from Japan. These results revealed geographic differences in the distribution of the virulence plasmids found in the five countries and suggested that the restriction fragment length polymorphism of virulence plasmids might be useful to elucidate the molecular epidemiology of virulent R. equi in the world. PMID:10488224

  13. Telomerase reverse transcriptase locus polymorphisms and cancer risk: a field synopsis and meta-analysis.

    Mocellin, Simone; Verdi, Daunia; Pooley, Karen A; Landi, Maria T; Egan, Kathleen M; Baird, Duncan M; Prescott, Jennifer; De Vivo, Immaculata; Nitti, Donato

    2012-06-06

    Several recent studies have provided evidence that polymorphisms in the telomerase reverse transcriptase (TERT) gene sequence are associated with cancer development, but a comprehensive synopsis is not available. We conducted a systematic review and meta-analysis of the available molecular epidemiology data regarding the association between TERT locus polymorphisms and predisposition to cancer. A systematic review of the English literature was conducted by searching PubMed, Embase, Cancerlit, Google Scholar, and ISI Web of Knowledge databases for studies on associations between TERT locus polymorphisms and cancer risk. Random-effects meta-analysis was performed to pool per-allele odds ratios for TERT locus polymorphisms and risk of cancer, and between-study heterogeneity and potential bias sources (eg, publication and chasing bias) were assessed. Because the TERT locus includes the cleft lip and palate transmembrane 1-like (CLPTM1L) gene, which is in linkage disequilibrium with TERT, CLPTM1L polymorphisms were also analyzed. Cumulative evidence for polymorphisms with statistically significant associations was graded as "strong," "moderate," and "weak" according to the Venice criteria. The joint population attributable risk was calculated for polymorphisms with strong evidence of association. Eighty-five studies enrolling 490 901 subjects and reporting on 494 allelic contrasts were retrieved. Data were available on 67 TERT locus polymorphisms and 24 tumor types, for a total of 221 unique combinations of polymorphisms and cancer types. Upon meta-analysis, a statistically significant association with the risk of any cancer type was found for 22 polymorphisms. Strong, moderate, and weak cumulative evidence for association with at least one tumor type was demonstrated for 11, 9, and 14 polymorphisms, respectively. For lung cancer, which was the most studied tumor type, the estimated joint population attributable risk for three polymorphisms (TERT rs2736100, intergenic

  14. Depressive symptoms in schizophrenia and dopamine and serotonin gene polymorphisms.

    Peitl, Vjekoslav; Štefanović, Mario; Karlović, Dalibor

    2017-07-03

    Although depressive symptoms seem to be frequent in schizophrenia they have received significantly less attention than other symptom domains. As impaired serotonergic and dopaminergic neurotransmission is implicated in the pathogenesis of depression and schizophrenia this study sought to investigate the putative association between several functional gene polymorphisms (SERT 5-HTTLPR, MAO-A VNTR, COMT Val158Met and DAT VNTR) and schizophrenia. Other objectives of this study were to closely examine schizophrenia symptom domains by performing factor analysis of the two most used instruments in this setting (Positive and negative syndrome scale - PANSS and Calgary depression rating scale - CDSS) and to examine the influence of investigated gene polymorphisms on the schizophrenia symptom domains, focusing on depressive scores. A total of 591 participants were included in the study (300 schizophrenic patients and 291 healthy volunteers). 192 (64%) of schizophrenic patients had significant depressive symptoms. Genotype distribution revealed no significant differences regarding all investigated polymorphisms except the separate gender analysis for MAO-A gene polymorphism which revealed significantly more allele 3 carriers in schizophrenic males. Factor analysis of the PANSS scale revealed the existence of five separate factors (symptom domains), while the CDSS scale revealed two distinct factors. Several investigated gene polymorphisms (mostly SERT and MAO-A, but also COMT) significantly influenced two factors from the PANSS (aggressive/impulsive and negative symptoms) and one from the CDSS scale (suicidality), respectively. Depressive symptoms in schizophrenic patients may be influenced by functional gene polymorphisms, especially those implicated in serotonergic neurotransmission. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. [Prevalence of gene polymorphisms associated with immune-dependent diseases in the populations of North Eurasia].

    Cherednichenko, A A; Trifonova, E A; Vagaitseva, K V; Bocharova, A V; Varzari, A M; Radzhabov, M O; Stepanov, V A

    2015-01-01

    The data on distribution of genetic diversity in gene polymorphisms associated with autoimmune and allergic diseases and with regulation of immunoglobulin E and cytokines levels in 26 populations of the Northern Eurasia is presented. Substantial correlation between the values of average expected heterozygosity by 44 gene polymorphisms with climatic and geographical factors has not been revealed. Clustering of population groups in correspondence with their geographic locations is observed. The degree of gene differentiation among populations and the selective neutrality of gene polymorphisms have been assessed. The results of our work evidence the substantial genetic diversity and differentiation of human populations by studied genes.

  16. A comparative study of two polymorphs of L-aspartic acid hydrochloride.

    Benali-Cherif, Rim; Takouachet, Radhwane; Bendeif, El-Eulmi; Benali-Cherif, Nourredine

    2014-07-01

    Two polymorphs of L-aspartic acid hydrochloride, C4H8NO4(+)·Cl(-), were obtained from the same aqueous solution. Their crystal structures have been determined from single-crystal data collected at 100 K. The crystal structures revealed three- and two-dimensional hydrogen-bonding networks for the triclinic and orthorhombic polymorphs, respectively. The cations and anions are connected to one another via N-H···Cl and O-H···Cl interactions and form alternating cation-anion layer-like structures. The two polymorphs share common structural features; however, the conformations of the L-aspartate cations and the crystal packings are different. Furthermore, the molecular packing of the orthorhombic polymorph contains more interesting interactions which seems to be a favourable factor for more efficient charge transfer within the crystal.

  17. Personalized Medicine Digoxin Theraphy in Individuals with MDR Gene Polymorphism

    Em Sutrisna

    2015-06-01

    Full Text Available Digoxin is one of digitalis drugs. Wider applicability to heart failure and arrhythmias (supraventricular requires fairly strict scrutiny because of its narrow therapeutic index. Digoxin is a substrate of P-glycoprotein (P-gp encoded by multi drugs resistance-1 (MDR1. MDR-1 gen located on chromosome 7q21.1. This gene contains 28 exons that encoded a protein of 1280 amino acids. This gene plays an important role in the absorption, distribution and elimination of many drugs. MDR1C3435T polymorphism occurs in exon 26. There are three types of MDR1C3435T gene namely MDR1C3435T CC, MDR1C3435T CT and MDR1C3435T TT. These polymorphisms will affect to the formation of P-gp and consequently to change the kinetic profile of digoxin. The change of kinetic profile causes changes in the digoxin blood levels. The method used in this review is data search based on pubmed, medline, and embase with keywords MDR and digoxin. There are several different studies of the influence of polymorphisms MDR1C3435T on blood digoxin levels. Increased levels of digoxin in the blood due to polymorphism of MDR1C3435T will be at risk of digitalis intoxication. Long-term digoxin treatment or large dose should consider the patient’s genetic profile. Distribution of polymorphism of MDR1C3435T in Javanese population is approximately TT (0,10, CT (0,52, and CC(0, 38.

  18. How to interpret Methylation Sensitive Amplified Polymorphism (MSAP) profiles?

    Fulneček, Jaroslav; Kovařík, Aleš

    2014-01-01

    Background DNA methylation plays a key role in development, contributes to genome stability, and may also respond to external factors supporting adaptation and evolution. To connect different types of stimuli with particular biological processes, identifying genome regions with altered 5-methylcytosine distribution at a genome-wide scale is important. Many researchers are using the simple, reliable, and relatively inexpensive Methylation Sensitive Amplified Polymorphism (MSAP) method that is ...

  19. Polymorphism of nickel sulfate hexahydrate

    Angel, R.J.; Finger, L.W.

    1988-01-01

    NiSO 4 .6H 2 O, M r =262.85; data collections with Mo Kα radiation, λ=0.7093 A, room temperature. Monoclinic polymorph: C2/c, a=9.880(3), b=7.228(2), c=24.130(3) A, β=98.38(2) 0 , V=1704.7(6) A 3 , Z=8, D x =2.05 g cm -3 , μ=25.54 cm -1 , F(000)=1088, R=0.031 (wR=0.038) for 2176 observed reflections. Tetragonal polymorph: P4 1 2 1 2, a=6.780 (1), c=18.285 (2) A, V=840.5 (3) A 3 , Z=4, D x =2.07 g cm -3 , μ=25.81 cm -1 , F(000)=544, R=0.045 (wR=0.050) for 2102 observed reflections. The structure of the tetragonal polymorph originally determined (without H positions) by Beevers and Lipson and refined by O'Connor and Dale and Stadnicka, Glazer and Koralewski, is confirmed by refinement of X-ray diffraction data. The structure of the monoclinic polymorph is confirmed as being isostructural with NiSO 4 .6D 2 O, and a number of other hexahydrate sulfates, e.g. MgSO 4 .6H 2 O. Both structures contain isolated [Ni(H 2 O 6 ] octahedra and [SO 4 ] tetrahedra linked by hydrogen bonding. (orig.)

  20. Gene polymorphisms in chronic periodontitis

    Laine, M.L.; Loos, B.G.; Crielaard, W.

    2010-01-01

    We aimed to conduct a review of the literature for gene polymorphisms associated with chronic periodontitis (CP) susceptibility. A comprehensive search of the literature in English was performed using the keywords: periodontitis, periodontal disease, combined with the words genes, mutation, or

  1. Genetic polymorphisms of multidrug and toxin extrusion proteins (MATE1 and MATE2 in South Indian population

    Gerard Marshall Raj

    2017-02-01

    Conclusion: Thus, the allele and genotype distributions of SLC47A1 and SLC47A2 gene polymorphisms were established in South Indian population and were found to be different from the frequencies of other ethnicities.

  2. Single Cystosorus Isolate Production and Restriction Fragment Length Polymorphism Characterization of the Obligate Biotroph Spongospora subterranea f. sp. subterranea.

    Qu, Xinshun; Christ, Barbara J

    2006-10-01

    ABSTRACT Spongospora subterranea f. sp. subterranea causes powdery scab in potatoes and is distributed worldwide. Genetic studies of this pathogen have been hampered due, in part, to its obligate parasitism and the lack of molecular markers for this pathogen. In this investigation, a single cystosorus inoculation technique was developed to produce large amounts of S. subterranea f. sp. subterranea plasmodia or zoosporangia in eastern black nightshade (Solanum ptycanthum) roots from which DNA was extracted. Cryopreservation of zoosporangia was used for long-term storage of the isolates. S. subterranea f. sp. subterranea-specific restriction fragment length polymorphism (RFLP) markers were developed from randomly amplified polymorphic DNA (RAPD) fragments. Cystosori of S. subterranea f. sp. subterranea were used for RAPD assays and putative pathogen-specific RAPD fragments were cloned and sequenced. The fragments were screened for specificity by Southern hybridization and subsequent DNA sequence BLAST search. Four polymorphic S. subterranea f. sp. subterranea-specific probes containing repetitive elements, and one containing single copy DNA were identified. These RFLP probes were then used to analyze 24 single cystosorus isolates derived from eight geographic locations in the United States and Canada. Genetic variation was recorded among, but not within, geographic locations. Cluster analysis separated the isolates into two major groups: group I included isolates originating from western North America, with the exception of those from Colorado, and group II included isolates originating from eastern North America and from Colorado. The techniques developed in this study, i.e., production of single cystosorus isolates of S. subterranea f. sp. subterranea and development of RFLP markers for this pathogen, provide methods to further study the genetic structure of S. subterranea f. sp. subterranea.

  3. Molecular cloning, functional expression, and tissue distribution of a novel human gap junction-forming protein, connexin-31.9. Interaction with zona occludens protein-1

    Nielsen, Peter A; Beahm, Derek L; Giepmans, Ben N G; Baruch, Amos; Hall, James E; Kumar, Nalin M

    2002-01-01

    A novel human connexin gene (GJA11) was cloned from a genomic library. The open reading frame encoded a hypothetical protein of 294 amino acid residues with a predicted molecular mass of 31,933, hence referred to as connexin-31.9 (Cx31.9) or alpha 11 connexin. A clone in GenBank containing the

  4. On the representation of the electric charge distribution in ethane for calculations of the molecular quadrupole moment and intermolecular electrostatic energy

    Hansen, Flemming Yssing; Alldredge, G. P.; Bruch, L. W.

    1985-01-01

    and gives a repulsive rather than an attractive electrostatic interaction at typical intermolecular distances. In the local multipole model, the atom-site dipoles give the largest contribution to both the molecular quadrupole moment and the intermolecular interaction. The Journal of Chemical Physics...

  5. Association study of ghrelin receptor gene polymorphisms in rheumatoid arthritis.

    Robledo, G; Rueda, B; Gonzalez-Gay, M A; Fernández, B; Lamas, J R; Balsa, A; Pascual-Salcedo, D; García, A; Raya, E; Martín, J

    2010-01-01

    Ghrelin is a newly characterised growth hormone (GH) releasing peptide widely distributed that may play an important role in the regulation of metabolic balance in inflammatory diseases such as rheumatoid arthritis (RA) by decreasing the pro-inflammatory Th1 responses. In this study we investigated the possible contribution of several polymorphisms in the functional Ghrelin receptor to RA susceptibility. A screening of 3 single nucleotide polymorphisms (SNPs) was performed in a total of 950 RA patients and 990 healthy controls of Spanish Caucasian origin. Genotyping of all 3 SNPs was performed by real-time polymerase chain reaction technology, using the TaqMan 5'-allele discrimination assay. We observed no statistically significant deviation between RA patients and controls for the GHSR SNPs analysed. In addition, we performed a haplotype analysis that did not reveal an association with RA susceptibility. The stratification analysis for the presence of shared epitope (SE), rheumatoid factor (RF) or antibodies anti cyclic citrullinated peptide (anti-CCP) did not detect significant association of the GHSR polymorphisms with RA. These findings suggest that the GHSR gene polymorphisms do not appear to play a major role in RA genetic predisposition in our population.

  6. Angiotensinogen gene polymorphisms in IDDM patients with diabetic nephropathy

    Tarnow, L; Cambien, Francois; Rossing, P

    1996-01-01

    Genotypic abnormalities of the renin-ANG system have been suggested as a risk factor for the development of diabetic nephropathy. Cleavage of angiotensinogen is the rate-limiting step in the activation of the renin-ANG system. The TT genotype of a polymorphism encoding threonine instead of methio......Genotypic abnormalities of the renin-ANG system have been suggested as a risk factor for the development of diabetic nephropathy. Cleavage of angiotensinogen is the rate-limiting step in the activation of the renin-ANG system. The TT genotype of a polymorphism encoding threonine instead...... of methionine (M235T) has been associated not only with increased plasma angiotensinogen concentration but also with essential hypertension. In addition, a polymorphism in the angiotensinogen gene substituting methionine for threonine (T174M) has been associated with hypertension in nondiabetic populations. We...... studied the relationship between these polymorphisms in the angiotensinogen gene in IDDM patients with diabetic nephropathy (121 men, 74 women, age 40.9 +/- 10 years, diabetes duration 27 +/- 8 years). There was no difference in M235T genotype distribution between IDDM patients with diabetic nephropathy...

  7. Insertion/deletion polymorphism of the angiotensin-converting enzyme gene and the risk of hypertension among residents of two cities, South-South Nigeria

    Mary Esien Kooffreh

    2014-01-01

    Conclusion: The I/D polymorphism of the angiotensin-converting enzyme gene was a risk factor for hypertension in the sample population of Calabar and Uyo. This research will form baseline information for subsequent molecular studies in this population.

  8. [The use of RAPD and ITE molecular markers to study genetical structure of the Crimean population of Triticum boeoticum Boiss].

    Mallabaeva, D Sh; Ignatov, A N; Sheĭko, I A; Isikov, V P; Geliuta, V P; Boĭko, N G; Seriapin, A A; Dorokhov, D B

    2007-01-01

    Wild wheat Triticum boeoticum Boiss. is the rare species are included in the Red Book of Ukraine. This species are reducing the magnitude of population and the area of distribution under anthropogenic activity. We studied genetic structure of two populations of T. boeoticum, located on Sapun Mountain and in Baidar Valley in Crimea. According RAPD and ITE molecular analysis we have estimated that the population of T. boeoticum on Sapun Mountain is genetically more impoverished than a population from the Baidar Valley. For preservation of maximal natural genetic polymorphism of the rare species it is recommended to direct efforts to preservations of a population of T. boeoticum from the Baidar Valley.

  9. High-Throughput Sequencing and Linkage Mapping of a Clownfish Genome Provide Insights on the Distribution of Molecular Players Involved in Sex Change

    Casas, Laura; Saenz Agudelo, Pablo; Irigoien, Xabier

    2018-01-01

    Clownfishes are an excellent model system for investigating the genetic mechanism governing hermaphroditism and socially-controlled sex change in their natural environment because they are broadly distributed and strongly site-attached. Genomic

  10. Association between perilipin gene polymorphisms and body weight traits in Jinmao Hua chickens

    T. Li

    2017-09-01

    Full Text Available The perilipin gene (PLIN plays a crucial role in lipid metabolism and fat deposition. In order to reveal the genetic effects of PLIN polymorphisms on body weight (BW traits in chickens, PLIN gene polymorphisms in 322 Jinmao Hua chickens were detected by PCR-SSCP and DNA sequencing methods. For PLIN primer pair 1, five genotypes (AA, AB, BB, JJ and JL were detected in the Jinmao Hua chicken population and three mutations (g.1889C > T, g.1904T > C and g.1922C > T were revealed by gene sequencing. For PLIN primer pair 2, three genotypes (CC, CD and DD were detected in the same population and two mutations (g.2014A > G and g.2020C > T were revealed by gene sequencing. Least squares analysis showed that individuals with the JJ and CD genotypes performed better than the other Jinmao Hua chicken genotypes. Based on the five SNPs, the frequency distributions of the eight haplotypes were estimated with PHASE2.1 software. C-T-C-G-T was the major haplotype with a frequency of 58.6957 %, while the frequency of C-C-C-A-C was less than 1 %. Fourteen diplotypes were obtained from the eight haplotypes. H1H1 was the dominant diplotype with a frequency of 47.205 %. Least squares analysis indicated that BW with the H3H3 diplotype was the lowest, while the H2H2 diplotype was the highest, suggesting that selecting for the H3H3 diplotype improved the BW traits of Jinmao Hua chickens. The findings of this study should be useful to expand the theoretical basis of the role the PLIN in poultry molecular breeding of poultry.

  11. Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae).

    Weitemier, Kevin; Straub, Shannon C K; Fishbein, Mark; Liston, Aaron

    2015-01-01

    Despite knowledge that concerted evolution of high-copy loci is often imperfect, studies that investigate the extent of intragenomic polymorphisms and comparisons across a large number of species are rarely made. We present a bioinformatic pipeline for characterizing polymorphisms within an individual among copies of a high-copy locus. Results are presented for nuclear ribosomal DNA (nrDNA) across the milkweed genus, Asclepias. The 18S-26S portion of the nrDNA cistron of Asclepias syriaca served as a reference for assembly of the region from 124 samples representing 90 species of Asclepias. Reads were mapped back to each individual's consensus and at each position reads differing from the consensus were tallied using a custom perl script. Low frequency polymorphisms existed in all individuals (mean = 5.8%). Most nrDNA positions (91%) were polymorphic in at least one individual, with polymorphic sites being less frequent in subunit regions and loops. Highly polymorphic sites existed in each individual, with highest abundance in the "noncoding" ITS regions. Phylogenetic signal was present in the distribution of intragenomic polymorphisms across the genus. Intragenomic polymorphisms in nrDNA are common in Asclepias, being found at higher frequency than any other study to date. The high and variable frequency of polymorphisms across species highlights concerns that phylogenetic applications of nrDNA may be error-prone. The new analytical approach provided here is applicable to other taxa and other high-copy regions characterized by low coverage genome sequencing (genome skimming).

  12. Porcine insulin receptor substrate 4 (IRS4) gene: cloning, polymorphism and association study

    Masopust, Martin; Vykoukalová, Z.; Knoll, Aleš; Bartenschlager, H.; Mileham, A.; Deeb, N.; Rohrer, G. A.; Čepica, Stanislav

    2010-01-01

    Roč. 38, - (2010), 2611-2617 ISSN 0301-4851 R&D Projects: GA ČR GA523/07/0353; GA ČR GAP502/10/1216 Institutional research plan: CEZ:AV0Z50450515 Keywords : PCR cloning * Polymorphism * IRS4 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.875, year: 2010

  13. Polymorphism versus species richness - systematics of large Dendrobates from the eastern Guiana Shield (Amphibia: Dendrobatidae)

    Wollenberg, K.; Veith, M.K.H.; Noonan, B.P.; Lötters, S.

    2006-01-01

    Abstract A molecular phylogeny based on a fragment of the mitochondrial 16S rRNA gene and morphological comparisons suggest that only one polymorphic species of large Dendrobates, commonly assigned to D. tinctorius, occurs on the eastern Guiana Shield and its vicinities. The oldest available name

  14. Genetic polymorphism within the Leishmania donovani complex: correlation with geographic origin

    Zemanová, Eva; Jirků, Milan; Mauricio, I. L.; Miles, M. A.; Lukeš, Julius

    2004-01-01

    Roč. 70, č. 6 (2004), s. 613-617 ISSN 0002-9637 Grant - others:European Community(XE) QLK2-CT-2001-01810 Institutional research plan: CEZ:AV0Z6022909 Keywords : genetic polymorphism * Leishmania donovani * RAPD Subject RIV: EB - Genetics ;