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Sample records for diverse molecular substituents

  1. Molecular Transistor Based on the Biphenyl Substituents

    Directory of Open Access Journals (Sweden)

    A.G. Malashenko

    2016-11-01

    Full Text Available It was investigated the physical processes in the molecules, which have properties required in case of using as molecular switches, transistors, or other electronic elements of future computers. Studies show that in the molecules of biphenyl substituents the angle between the planes of the phenyl rings depends on the magnitude of the applied external electric field. So, the ratio of squares of cosines of the angles between the phenyl groups in the field 0.01 a.u. and without field reaches 18. It significantly changes the ability of electrons to move along the long axis of the molecule. By varying the nature of the substituents, we can obtain the molecule characteristics that make these molecules promising for future using. This effect provides the use of biphenyl substitutes as transistors in electrical circuits constructed on separate molecules.

  2. Discovery of Farnesoid X Receptor Antagonists Based on a Library of Oleanolic Acid 3-O-Esters through Diverse Substituent Design and Molecular Docking Methods

    Directory of Open Access Journals (Sweden)

    Shao-Rong Wang

    2017-04-01

    Full Text Available The pentacyclic triterpene oleanolic acid (OA, 1 with known farnesoid X receptor (FXR modulatory activity was modified at its C-3 position to find new FXR-interacting agents. A diverse substitution library of OA derivatives was constructed in silico through a 2D fingerprint similarity cluster strategy. With further docking analysis, four top-scored OA 3-O-ester derivatives were selected for synthesis. The bioassay results indicated that all four compounds 3 inhibited chenodeoxycholic acid (CDCA-induced FXR transactivation in a concentration-dependent mode. Among them 3b and 3d are more active than the parent compound OA. A molecular simulation study was performed to attempt to explain the structure-activity relationship (SAR and the antagonistic action. To the best of our knowledge, this is the first report on semi-synthetic pentacyclic triterpenoids with FXR-modulatory activities.

  3. Structural Diversity and Function of Xyloglucan Sidechain Substituents

    Directory of Open Access Journals (Sweden)

    Alex Schultink

    2014-11-01

    Full Text Available Xyloglucan (XyG is a hemicellulose found in the cell walls of all land plants including early-divergent groups such as liverworts, hornworts and mosses. The basic structure of XyG, a xylosylated glucan, is similar in all of these plants but additional substituents can vary depending on plant family, tissue, and developmental stage. A comprehensive list of known XyG sidechain substituents is assembled including their occurrence within plant families, thereby providing insight into the evolutionary origin of the various sidechains. Recent advances in DNA sequencing have enabled comparative genomics approaches for the identification of XyG biosynthetic enzymes in Arabidopsis thaliana as well as in non-model plant species. Characterization of these biosynthetic genes not only allows the determination of their substrate specificity but also provides insights into the function of the various substituents in plant growth and development.

  4. Quantification and classification of substituent effects in organic chemistry: a theoretical molecular electrostatic potential study.

    Science.gov (United States)

    Remya, Geetha S; Suresh, Cherumuttathu H

    2016-07-27

    Substituent effects in organic chemistry are generally described in terms of experimentally derived Hammett parameters whereas a convenient theoretical tool to study these effects in π-conjugated molecular systems is molecular electrostatic potential (MESP) analysis. The present study shows that the difference between MESP at the nucleus of the para carbon of substituted benzene and a carbon atom in benzene, designated as ΔVC, is very useful to quantify and classify substituent effects. On the basis of positive and negative ΔVC values, a broad classification of around 381 substituents into electron withdrawing and donating categories is made. Each category is again sorted based on the magnitude of ΔVC into subcategories such as very strong, strong, medium, and weak electron donating/withdrawing. Furthermore, the data are used to show the transferability and additivity of substituent effects in π-conjugated organic molecules such as condensed aromatic, olefinic, acetylenic, and heterocyclic systems. The transferability properties hold good for ΔVC in all these molecular systems. The additive properties of substituent effects are strongly reflected on ΔVC and the predictive power of the data to assign the total substituent effects of multi-substituted systems is verified. The ΔVC data and the present classification of substituents are very useful to design π-conjugated organic molecular systems with desired electron rich/poor character.

  5. Self-assembly of organogels via new luminol imide derivatives: diverse nanostructures and substituent chain effect

    Science.gov (United States)

    Jiao, Tifeng; Huang, Qinqin; Zhang, Qingrui; Xiao, Debao; Zhou, Jingxin; Gao, Faming

    2013-06-01

    Luminol is considered as an efficient sycpstem in electrochemiluminescence (ECL) measurements for the detection of hydrogen peroxide. In this paper, new luminol imide derivatives with different alkyl substituent chains were designed and synthesized. Their gelation behaviors in 26 solvents were tested as novel low molecular mass organic gelators. It was shown that the length and number of alkyl substituent chains linked to a benzene ring in gelators played a crucial role in the gelation behavior of all compounds in various organic solvents. Longer alkyl chains in molecular skeletons in present gelators are favorable for the gelation of organic solvents. Scanning electron microscope and atomic force microscope observations revealed that the gelator molecules self-assemble into different micro/nanoscale aggregates from a dot, flower, belt, rod, and lamella to wrinkle with change of solvents. Spectral studies indicated that there existed different H-bond formations and hydrophobic forces, depending on the alkyl substituent chains in molecular skeletons. The present work may give some insight to the design and characteristic of new versatile soft materials and potential ECL biosensors with special molecular structures.

  6. On the effect of donor and acceptor substituents on the behaviour of light-driven rotary molecular motors

    NARCIS (Netherlands)

    Pollard, Michael M.; Wesenhagen, Philana V.; Pijper, Dirk; Feringa, Ben L.

    2008-01-01

    Light-driven rotary molecular motors based on overcrowded alkenes can be substituted with electron-donating and electron-withdrawing substituents ( R = OMe, Cl and CN) in direct conjugation with the central double bond ( the axis of rotation) without having a significant influence on the rate-limiti

  7. Molecular binding thermodynamics of spherical guests by β-cyclodextrins bearing aromatic substituents

    Energy Technology Data Exchange (ETDEWEB)

    Li, Nan; Chen, Yong; Zhang, Ying-Ming; Wang, Li-Hua; Mao, Wen-Zhao; Liu, Yu, E-mail: yuliu@nankai.edu.cn

    2014-01-20

    Graphical abstract: - Highlights: • Different conformation of β-CD derivatives. • Enthalpy gain. • High binding ability. - Abstract: The molecular binding behaviors of two β-cyclodextrin (β-CD) derivatives bearing 1,2,3-triazole moieties, i.e. mono-6-deoxy-6-{4-(8-oxymethylquinolino)[1,2,3]triazolyl}-β-CD (1) and mono-6-deoxy-6-{4-(8-oxymethylnaphthol)[1,2,3]triazolyl}-β-CD (3), and their analogs without 1,2,3-triazole moieties, i.e. mono-6-deoxy-6-(8-oxymethylquinolino)-β-CD (2) and mono-6-deoxy-6-(8-oxymethylnaphthol)-β-CD (4) toward spherical guests (±)-borneol and (±)-camphor were investigated to elucidate how substituent moiety of host affects the binding abilities by 2D NMR as well as microcalorimetric titrations in aqueous phosphate buffer solution (pH 7.20) at 298.15 K. The binding modes of host–guest interactions obtained from 2D NMR displayed that host CDs without triazole moieties gave better induce-fit efficiency between hosts and guests, leading to stronger binding abilities. Thermodynamically, the inclusion complexation was driven by enthalpy with the stoichiometry of 1:1. Another factor contributed to the enhanced binding abilities was the enthalpy gain with the smaller entropy loss.

  8. Substituent effects on molecular properties of dicarba-closo-dodecarborane derivatives.

    Science.gov (United States)

    Junqueira, Georgia M A; Sato, Fernando

    2014-07-01

    In this paper we study the role played by substituent effects on reactivity and NLO properties of ortho-, meta- and para- dicarba-closo-dodecarborane derivatives at B3LYP/6-31G(d,p) level of theory. In addition correlations with Hammett parameters of the substituents were established. In accordance with obtained results the reactivity properties of derivatives have not been significantly influenced by the isomer type, however the replaced para isomers were the most sensitive to NLO calculations. Moreover, the push-pull para isomers were found to be the most reactive and displayed the largest values of β tot and dipole moment.

  9. Topological Substituent Descriptors

    Directory of Open Access Journals (Sweden)

    Mircea V. DIUDEA

    2002-12-01

    Full Text Available Motivation. Substituted 1,3,5-triazines are known as useful herbicidal substances. In view of reducing the cost of biological screening, computational methods are carried out for evaluating the biological activity of organic compounds. Often a class of bioactives differs only in the substituent attached to a basic skeleton. In such cases substituent descriptors will give the same prospecting results as in case of using the whole molecule description, but with significantly reduced computational time. Such descriptors are useful in describing steric effects involved in chemical reactions. Method. Molecular topology is the method used for substituent description and multi linear regression analysis as a statistical tool. Results. Novel topological descriptors, XLDS and Ws, based on the layer matrix of distance sums and walks in molecular graphs, respectively, are proposed for describing the topology of substituents linked on a chemical skeleton. They are tested for modeling the esterification reaction in the class of benzoic acids and herbicidal activity of 2-difluoromethylthio-4,6-bis(monoalkylamino-1,3,5-triazines. Conclusions. Ws substituent descriptor, based on walks in graph, satisfactorily describes the steric effect of alkyl substituents behaving in esterification reaction, with good correlations to the Taft and Charton steric parameters, respectively. Modeling the herbicidal activity of the seo of 1,3,5-triazines exceeded the models reported in literature, so far.

  10. Effect of metallation, substituents and inter/intra-molecular polarization on electronic couplings for hole transport in stacked porphyrin dyads.

    Science.gov (United States)

    Hernández-Fernández, F; Pavanello, M; Visscher, L

    2016-08-03

    We carried out a systematic study of the hole transport properties for a series of symmetrically stacked porphyrin dimers. In the first part of this study, we evaluated the sensitivity of electronic couplings to orbital relaxation due to molecular ionization and intermolecular interactions for a series of halogenated porphyrins. The effect of polarization was estimated by comparing electronic couplings from fragment orbital density functional theory (FODFT) and frozen density embedding electron transfer (FDE-CT). For the dimers considered, the effect of polarization was estimated to be less than 20%, in line with previous studies on different molecular dimers. Thus, we decided to employ a computationally cheaper FODFT method to continue our study of the effect of metals and substituents on the electronic couplings for hole transfer. We find that, compared to the non-metallated porphyrins, Ni, Fe and Pt significantly reduce the coupling, while Zn, Ti, Cd and Pd increase it. The effect of substituents was studied on a series of meso-substituted porphyrins (meso-tetrapyridineporphyrin, meso-tetraphenylporphyrin and derivatives) for which we could relate a reduction of the coupling to steric effects that reduce the overlap between the frontier orbitals of the monomers.

  11. Controlling the Adsorption of Aromatic Compounds on Pt(111) with Oxygenate Substituents: From DFT to Simple Molecular Descriptors.

    Science.gov (United States)

    Réocreux, Romain; Huynh, Minh; Michel, Carine; Sautet, Philippe

    2016-06-01

    Aromatic chemistry on metallic surfaces is involved in many processes within the contexts of biomass valorization, pollutant degradation, or corrosion protection. Albeit theoretically and experimentally challenging, knowing the structure and the stability of aromatic compounds on such surfaces is essential to understand their properties. To gain insights on this topic, we performed periodic ab initio calculations on Pt(111) to determine a set of simple molecular descriptors that predict both the stability and the structure of aromatic adsorbates substituted with alkyl and alkoxy (or hydroxy) groups. While the van der Waals (vdW) interaction is controlled by the molecular weight and the deformation energy by both the nature and the relative position of the substituents to the surface, the chemical bonding can be correlated to the Hard and Soft Acids and Bases (HSAB) interaction energy. This work gives general insights on the interaction of aromatic compounds with the Pt(111) surface.

  12. Substituent effect on the molecular stability, group interaction, detonation performance, and thermolysis mechanism of nitroamino-substituted cyclopentanes and cyclohexanes

    Institute of Scientific and Technical Information of China (English)

    QIU Ling; GONG XueDong; JU XueHai; XIAO HeMing

    2008-01-01

    Density functional theory (DFT) method has been employed to study the effect of nitroamino group as a substituent in cyclopentane and cyclohexane, which usually construct the polycyclic or caged nitra-mines. Molecular structures were investigated at the B3LYP/6-31G** level, and isodesmic reactions were designed for calculating the group interactions. The results show that the group interactions ac-cord with the group additivity, increasing with the increasing number of nitroamino groups. The distance between substituents influences the interactions. Detonation performances were evaluated by the Kamlet-Jacobs equations based on the predicted densities and heats of formation, while thermal stability and pyrolysis mechanism were studied by the computations of bond dissociation energy (BDE). It is found that the contributions of nitroamino groups to the detonation heat, detonation velocity, detonation pressure, and stability all deviate from the group additivity. Only 3a, 3b, and 9a-9c may be novel potential candidates of high energy density materials (HEDMs) according to the quantitative cri-teria of HEDM (ρ≈1.9 g/cm3, D≈9.0 km/s, P≈40.0 GPa). Stability decreases with the increasing number of N-NO2 groups, and homolysis of N-NO2 bond is the initial step in the thermolysis of the title com-pounds. Coupled with the demand of thermal stability (BDE > 20 kcal/mol), only 1,2,4-trinitrotriazacy-clohexane and 1,2,4,5-tetranitrotetraazacyclohexane are suggested as feasible energetic materials.These results may provide basic information for the molecular design of HEDMs.

  13. Influence of Simultaneous Tuning of Molecular Weights and Alkyl Substituents of Poly(thienoisoindigo-alt-naphthalene)s on Morphology and Change Transport Properties.

    Science.gov (United States)

    Cho, Hye Jin; Kang, Seok-Ju; Lee, Sang Myeon; Jeong, Minkyu; Kim, Gyoungsik; Noh, Yong-Young; Yang, Changduk

    2017-08-21

    To simultaneously assess the impact of molecular weight (Mn) and alkyl substituent variations of polymers on the structural and optoelectronic properties; herein, we conduct a systematic study of a series of poly(thienoisoindigo-alt-naphthalene) (PTIIG-Np)-based polymers containing different alkyl substituents (2-hexyldecyl (HD), 2-octyldodecyl (OD), and 2-decyltetradecyl (DT) chains) and Mns (low (L) and high (H)). All the polymers produce almost identical energy levels, whereas their optical spectra show a clear dependence on Mns and the alkyl substituents. Interestingly, increasing the alkyl substituent sizes of the polymers steadily increases the lamellar d-spacings (d100), ultimately leading to a densely-packed lamellar structure for PTIIGHD-Np. In addition, both H-PTIIGOD-Np and H-PTIIGDT-Np exhibit larger π-stacking crystallites than the corresponding low-Mn polymers, while for PTIIGHD-Np, their size increases in the low-Mn batch. Ultimately, L-PTIIGHD-Np shows the best hole mobility of 1.87 cm(2) V(-1) s(-1) in top gate and bottom-contact organic field-effect transistors (OFETs) with a poly(methyl methacrylate), which is nearly one order of magnitude higher than other polymers tested in this study. Our results demonstrate that the simultaneous Mn and alkyl substituent engineering of the polymers can optimize their film morphology to produce high-performance OFETs.

  14. Acylated 2-(N-arylaminomethylenebenzo[b]thiophene-3(2H-Ones: Molecular Switches with Varying Migrants and Substituents

    Directory of Open Access Journals (Sweden)

    Alexander D. Dubonosov

    2009-01-01

    Full Text Available Synthesis and properties of photochromic acylated 2-(N-arylaminomethylenebenzo[b]thiophene-3(2H-ones are described. Their structure largely depends on the nature of acyl migrant and in a less degree on N-aryl substituent.

  15. Structures and properties of molecular torsion balances to decipher the nature of substituent effects on the aromatic edge-to-face interaction.

    Science.gov (United States)

    Gardarsson, Haraldur; Schweizer, W Bernd; Trapp, Nils; Diederich, François

    2014-04-14

    Various recent computational studies initiated this systematic re-investigation of substituent effects on aromatic edge-to-face interactions. Five series of Tröger base derived molecular torsion balances (MTBs), initially introduced by Wilcox and co-workers, showing an aromatic edge-to-face interaction in the folded, but not in the unfolded form, were synthesized. A fluorine atom or a trifluoromethyl group was introduced onto the edge ring in ortho-, meta-, and para-positions to the C-H group interacting with the face component. The substituents on the face component were varied from electron-donating to electron-withdrawing. Extensive X-ray crystallographic data allowed for a discussion on the conformational behavior of the torsional balances in the solid state. While most systems adopt the folded conformation, some were found to form supramolecular intercalative dimers, lacking the intramolecular edge-to-face interaction, which is compensated by the gain of aromatic π-stacking interactions between four aryl rings of the two molecular components. This dimerization does not take place in solution. The folding free enthalpy ΔG(fold) of all torsion balances was determined by (1)H NMR measurements by using 10 mM solutions of samples in CDCl3 and C6D6. Only the ΔG(fold) values of balances bearing an edge-ring substituent in ortho-position to the interacting C-H show a steep linear correlation with the Hammett parameter (σ(meta)) of the face-component substituent. Thermodynamic analysis using van't Hoff plots revealed that the interaction is enthalpy-driven. The ΔG(fold) values of the balances, in addition to partial charge calculations, suggest that increasing the polarization of the interacting C-H group makes a favorable contribution to the edge-to-face interaction. The largest contribution, however, seems to originate from local direct interactions between the substituent in ortho-position to the edge-ring C-H and the substituted face ring.

  16. On the possibility to accelerate the thermal isomerizations of overcrowded alkene-based rotary molecular motors with electron-donating or electron-withdrawing substituents.

    Science.gov (United States)

    Oruganti, Baswanth; Durbeej, Bo

    2016-09-01

    We employ computational methods to investigate the possibility of using electron-donating or electron-withdrawing substituents to reduce the free-energy barriers of the thermal isomerizations that limit the rotational frequencies achievable by synthetic overcrowded alkene-based molecular motors. Choosing as reference systems one of the fastest motors known to date and two variants thereof, we consider six new motors obtained by introducing electron-donating methoxy and dimethylamino or electron-withdrawing nitro and cyano substituents in conjugation with the central olefinic bond connecting the two (stator and rotator) motor halves. Performing density functional theory calculations, we then show that electron-donating (but not electron-withdrawing) groups at the stator are able to reduce the already small barriers of the reference motors by up to 18 kJ mol(-1). This result outlines a possible strategy for improving the rotational frequencies of motors of this kind. Furthermore, exploring the origin of the catalytic effect, it is found that electron-donating groups exert a favorable steric influence on the thermal isomerizations, which is not manifested by electron-withdrawing groups. This finding suggests a new mechanism for controlling the critical steric interactions of these motors. Graphical Abstract The introduction of electron-donating groups in one of the fastest rotary molecular motors known to date is found to reduce the free-energy barriers of the thermal steps that limit the rotational frequencies by up to 18 kJ mol(-1).

  17. Molecular Technique to Understand Deep Microbial Diversity

    Science.gov (United States)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

    2012-01-01

    Current sequencing-based and DNA microarray techniques to study microbial diversity are based on an initial PCR (polymerase chain reaction) amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of the minor template appears to be suppressed by the exponential amplification of the more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck has overlooked the presence of the less abundant minority population, and underestimated their role in the ecosystem maintenance. To generate PCR amplicons for subsequent diversity analysis, bacterial l6S rRNA genes are amplified by PCR using universal primers. Two distinct PCR regimes are employed in parallel: one using normal and the other using biotinlabeled universal primers. PCR products obtained with biotin-labeled primers are mixed with streptavidin-labeled magnetic beads and selectively captured in the presence of a magnetic field. Less-abundant DNA templates that fail to amplify in this first round of PCR amplification are subjected to a second round of PCR using normal universal primers. These PCR products are then subjected to downstream diversity analyses such as conventional cloning and sequencing. A second round of PCR amplified the minority population and completed the deep diversity picture of the environmental sample.

  18. Substituent effect on the molecular stability,group interaction,detonation performance,and thermolysis mechanism of nitroamino-substituted cyclopentanes and cyclohexanes

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Density functional theory (DFT) method has been employed to study the effect of nitroamino group as a substituent in cyclopentane and cyclohexane, which usually construct the polycyclic or caged nitra-mines. Molecular structures were investigated at the B3LYP/6-31G** level, and isodesmic reactions were designed for calculating the group interactions. The results show that the group interactions ac-cord with the group additivity, increasing with the increasing number of nitroamino groups. The dis-tance between substituents influences the interactions. Detonation performances were evaluated by the Kamlet-Jacobs equations based on the predicted densities and heats of formation, while thermal stability and pyrolysis mechanism were studied by the computations of bond dissociation energy (BDE). It is found that the contributions of nitroamino groups to the detonation heat, detonation velocity, detonation pressure, and stability all deviate from the group additivity. Only 3a, 3b, and 9a-9c may be novel potential candidates of high energy density materials (HEDMs) according to the quantitative cri-teria of HEDM (ρ≈ 1.9 g/cm3, D ≈ 9.0 km/s, P ≈ 40.0 GPa). Stability decreases with the increasing number of N-NO2 groups, and homolysis of N-NO2 bond is the initial step in the thermolysis of the title com-pounds. Coupled with the demand of thermal stability (BDE > 20 kcal/mol), only 1,2,4-trinitrotriazacy-clohexane and 1,2,4,5-tetranitrotetraazacyclohexane are suggested as feasible energetic materials. These results may provide basic information for the molecular design of HEDMs.

  19. Molecular diversity of phospholipase D in angiosperms

    Directory of Open Access Journals (Sweden)

    Cvrčková Fatima

    2002-02-01

    Full Text Available Abstract Background The phospholipase D (PLD family has been identified in plants by recent molecular studies, fostered by the emerging importance of plant PLDs in stress physiology and signal transduction. However, the presence of multiple isoforms limits the power of conventional biochemical and pharmacological approaches, and calls for a wider application of genetic methodology. Results Taking advantage of sequence data available in public databases, we attempted to provide a prerequisite for such an approach. We made a complete inventory of the Arabidopsis thaliana PLD family, which was found to comprise 12 distinct genes. The current nomenclature of Arabidopsis PLDs was refined and expanded to include five newly described genes. To assess the degree of plant PLD diversity beyond Arabidopsis we explored data from rice (including the genome draft by Monsanto as well as cDNA and EST sequences from several other plants. Our analysis revealed two major PLD subfamilies in plants. The first, designated C2-PLD, is characterised by presence of the C2 domain and comprises previously known plant PLDs as well as new isoforms with possibly unusual features-catalytically inactive or independent on Ca2+. The second subfamily (denoted PXPH-PLD is novel in plants but is related to animal and fungal enzymes possessing the PX and PH domains. Conclusions The evolutionary dynamics, and inter-specific diversity, of plant PLDs inferred from our phylogenetic analysis, call for more plant species to be employed in PLD research. This will enable us to obtain generally valid conclusions.

  20. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

    E. SANTOS; M. MATOS; P. SILVA; A. M. FIGUEIRAS; C. BENITO; O. PINTO-CARNIDE

    2016-06-01

    The objective of this study was to quantify the molecular diversity and to determine the genetic relationships amongSecalespp. and among cultivars ofSecale cerealeusing RAPDs, ISSRs and sequence analysis of six exons ofScMATE1gene.Thirteen ryes (cultivated and wild) were genotyped using 21 RAPD and 16 ISSR primers. A total of 435 markers (242 RAPDsand 193 ISSRs) were obtained, with 293 being polymorphic (146 RAPDs and 147 ISSRs). Two RAPD and nine ISSR primersgenerated more than 80% of polymorphism. The ISSR markers were more polymorphic and informative than RAPDs. Further,69% of the ISSR primers selected achieved at least 70% of DNA polymorphism. The study of six exons of theScMATE1gene also demonstrated a high genetic variability that subsists inSecalegenus. One difference observed in exon 1 sequencesfromS. vaviloviiseems to be correlated with Al sensitivity in this species. The genetic relationships obtained using RAPDs,ISSRs and exons ofScMATE1gene were similar.S. ancestrale ,S. kuprijanoviiandS. cerealewere grouped in the same clusterandS. segetalewas in another cluster.S. vaviloviishowed evidences of not being clearly an isolate species and having greatintraspecific difference

  1. Molecular genetics of human pigmentation diversity

    National Research Council Canada - National Science Library

    Sturm, Richard A

    2009-01-01

    The genetic basis underlying normal variation in the pigmentary traits of skin, hair and eye colour has been the subject of intense research directed at understanding the diversity seen both between...

  2. Marine Fungi: Their Ecology and Molecular Diversity

    Science.gov (United States)

    Richards, Thomas A.; Jones, Meredith D. M.; Leonard, Guy; Bass, David

    2012-01-01

    Fungi appear to be rare in marine environments. There are relatively few marine isolates in culture, and fungal small subunit ribosomal DNA (SSU rDNA) sequences are rarely recovered in marine clone library experiments (i.e., culture-independent sequence surveys of eukaryotic microbial diversity from environmental DNA samples). To explore the diversity of marine fungi, we took a broad selection of SSU rDNA data sets and calculated a summary phylogeny. Bringing these data together identified a diverse collection of marine fungi, including sequences branching close to chytrids (flagellated fungi), filamentous hypha-forming fungi, and multicellular fungi. However, the majority of the sequences branched with ascomycete and basidiomycete yeasts. We discuss evidence for 36 novel marine lineages, the majority and most divergent of which branch with the chytrids. We then investigate what these data mean for the evolutionary history of the Fungi and specifically marine-terrestrial transitions. Finally, we discuss the roles of fungi in marine ecosystems.

  3. Marine fungi: their ecology and molecular diversity.

    Science.gov (United States)

    Richards, Thomas A; Jones, Meredith D M; Leonard, Guy; Bass, David

    2012-01-01

    Fungi appear to be rare in marine environments. There are relatively few marine isolates in culture, and fungal small subunit ribosomal DNA (SSU rDNA) sequences are rarely recovered in marine clone library experiments (i.e., culture-independent sequence surveys of eukaryotic microbial diversity from environmental DNA samples). To explore the diversity of marine fungi, we took a broad selection of SSU rDNA data sets and calculated a summary phylogeny. Bringing these data together identified a diverse collection of marine fungi, including sequences branching close to chytrids (flagellated fungi), filamentous hypha-forming fungi, and multicellular fungi. However, the majority of the sequences branched with ascomycete and basidiomycete yeasts. We discuss evidence for 36 novel marine lineages, the majority and most divergent of which branch with the chytrids. We then investigate what these data mean for the evolutionary history of the Fungi and specifically marine-terrestrial transitions. Finally, we discuss the roles of fungi in marine ecosystems.

  4. Morphological and molecular based diversity studies of some cassava

    African Journals Online (AJOL)

    Jane

    2011-10-17

    Oct 17, 2011 ... 2Department of Molecular Biology and Biotechnology, University of Cape ... The current study therefore investigated genetic diversity among ... application of morphological descriptors in management of ..... environment and subject to environment x cultivar .... in plants: a new class of molecular markers.

  5. Genetic diversity and molecular epidemiology of Anaplasma.

    Science.gov (United States)

    Battilani, Mara; De Arcangeli, Stefano; Balboni, Andrea; Dondi, Francesco

    2017-04-01

    Anaplasma are obligate intracellular bacteria of cells of haematopoietic origin and are aetiological agents of tick-borne diseases of both veterinary and medical interest common in both tropical and temperate regions. The recent disclosure of their zoonotic potential has greatly increased interest in the study of these bacteria, leading to the recent reorganisation of Rickettsia taxonomy and to the possible discovery of new species belonging to the genus Anaplasma. This review is particularly focused on the common and unique characteristics of Anaplasma marginale and Anaplasma phagocytophilum, with an emphasis on genetic diversity and evolution, and the main distinguishing features of the diseases caused by the different Anaplasma spp. are described as well. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Molecular markers: a potential resource for ginger genetic diversity studies.

    Science.gov (United States)

    Ismail, Nor Asiah; Rafii, M Y; Mahmud, T M M; Hanafi, M M; Miah, Gous

    2016-12-01

    Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.

  7. Morphological and molecular genetic diversity of Syrian indigenous ...

    African Journals Online (AJOL)

    Tuoyo Aghomotsegin

    2016-05-04

    May 4, 2016 ... This study aimed to assess the morphological variation, genetic diversity and population ... goat breed was well differentiated and grouped into a separate cluster that suggests its evolutionary ... research and development centers in representative ... Phenotypic and molecular characterizations have been.

  8. Assessment of morphological and molecular diversity among okra ...

    African Journals Online (AJOL)

    kamalsidhu

    2013-05-22

    May 22, 2013 ... Key words: Decamer primers, Randomly amplified polymorphic DNA (RAPD), genetic diversity, ... The development and use of molecular markers for the ..... Primer sequence(5'-3') Number of alleles Amplification polymorphic information content (PIC) .... to be monomorphic in the present investigation.

  9. Substituent effects of iron porphyrins: Structural, kinetic, and theoretical studies

    Energy Technology Data Exchange (ETDEWEB)

    Lu Xiaoquan, E-mail: luxq@nwnu.edu.c [Key Laboratory of Bioelectrochemistry and Environmental Analysis of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070 (China); Ma Junying; Sun Ruiping; Nan Mina; Meng Fanfu; Du Jie; Wang Xiaoyan; Shang Hui [Key Laboratory of Bioelectrochemistry and Environmental Analysis of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070 (China)

    2010-12-15

    Substituent effects of iron porphyrin complexes on the structures and kinetic processes have been examined for the first time. Basing on the premise that iron porphyrin is functional analogous to heme, a series of iron porphyrin derivatives bearing different substituents at the meso positions of the corrole ring are investigated as to their electrochemistry, the relationships among the electron transfer (ET) processes, their structures, and orbital energies. The good coherence between the experiment and theory indicates that the ET rate can be accelerated when electron-donating substituents are introduced to the iron porphyrin ring. Finally, the implications of the results are discussed in the influence of stability of iron porphyrin complexes on the ability to carry molecular oxygen, which may suggest it possible to dominate the biological activity of heme by selecting the appropriate substituents to iron porphyrin ring.

  10. Investigating Genetic Diversity of Foeniculum Vulgare Mill using Molecular Markers

    Directory of Open Access Journals (Sweden)

    Omid Jadidi

    2016-06-01

    Full Text Available Medicinal plants are considered valuable genetic resources in Iran. One of these medicinal as well as spice plants is Foeniculum Vulgare Mill from Umbellifetae family used in different industries such as food, medicine, and cosmetics. It seems that due to different climate conditions in Iran this plant represents a high and valuable genetic diversity; therefore, management of genetic resources protection and obtaining information about genetic diversity will help awareness of evolution processes as well as genetic erosion of this valuable plant. Genetic diversity in local masses of Foeniculum Vulgare Mill can be investigated using molecule markers such as AFLP, RAPD, ISSR, SRAP, RFLP, and so on. In investigation of over 30 ecotype of local Foeniculum Vulgare Mill, different markers have shown that mean polymorphic content (PIC is about 36% and mean genetic diversity is estimated about 40% in different samples. Data obtained from molecule software analyses help to categorize Foeniculum Vulgare Mill genotype in different groups based on climate and geographical conditions. Principle components analysis (PCOA has also confirmed the results of cluster analysis. Dendrogram obtained by cluster analysis based on similarity coefficient of simple matching (SM and UPGMA algorithm can also categorize population of Foeniculum Vulgare Mill in different groups. Results of molecular variance analysis (AMOVA have shown that most genetic variance between geographical groups can be seen in populations. In general, according to investigations, there is a significant genetic diversity regarding agronomic and molecular traits of Foeniculum Vulgare Mill masses in Iran and knowing this genetic diversity will help in breeding programs, complementary studies, categorization, and so on.

  11. Lewis Acid and Substituent Effects on the Molecular Mechanism for the Nazarov Reaction of Penta-1,4-dien-3-one and Derivatives. A Topological Analysis Based on the Combined Use of Electron Localization Function and Catastrophe Theory.

    Science.gov (United States)

    Polo, Victor; Andrés, Juan

    2007-05-01

    The joint use of the topological analysis provided by the electron localization function (ELF) and catastrophe theory (CT), at the B3LYP/6-31G(d) calculation level, allows us to examine the Lewis acid (protonation H(+) and presence of BH3) and the role of an electron donor substituent (-OCH3) at α and β positions along the course of the molecular mechanism for the Nazarov rearrangement of penta-1,4-dien-3-one and eight derivatives. The progress of the reaction is monitored by the changes of the ELF structural stability domains (SSDs), each change being controlled by a turning point derived from CT. These SSDs and the corresponding turning points are associated with a sequence of elementary chemical steps. Along the cyclization path of penta-1,4-diene-3-one, four SSDs as well as three turning points (cusp1-fold1-cusp2) have been characterized. The first and second SSDs correspond to a polarization of the C-O bond and electronic redistribution among the C-C bonds, respectively, and they can be associated with the formation of an oxyallyl structure. The third and fourth SSDs can be assigned to the ring closure process. Protonation of the oxygen atom shifts the reactive directly into the second SSD, greatly reducing the activation and reaction energies. The electronic effects due to Lewis acids and electron donor substituents have been rationalized in terms of calculations of mesomeric structures from ELF basin populations. The combination of Lewis acids together with α and β -OCH3 substitutions renders a cooperative and competitive effect on activation and reaction free energies, respectively.

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

    Science.gov (United States)

    Gill-Langarica, Homar R; Muruaga-Martínez, José S; Vargas-Vázquez, M L Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    2011-01-01

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

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

    Science.gov (United States)

    Gill-Langarica, Homar R.; Muruaga-Martínez, José S.; Vargas-Vázquez, M.L. Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-01-01

    A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation. PMID:22215964

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

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

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

  16. Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments.

    Science.gov (United States)

    Chaudhary, Prem Prashant; Brablcová, Lenka; Buriánková, Iva; Rulík, Martin

    2013-09-01

    Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.

  17. Connecting diverse molecular cloud environments with nascent protostars in Orion

    Science.gov (United States)

    Stutz, Amelia M.; Megeath, S.; Fischer, W. J.; Ali, B.; Furlan, E.; Tobin, J. J.; Stanke, T.; Henning, T.; Krause, O.; Manoj, P.; Osorio, M.; Robitaille, T.; HOPS Team

    2014-01-01

    Understanding how the gas environment within molecular clouds influences the properties of protostars is a key step towards understanding the physical factors that control star formation. We report on an analysis of the connection between molecular cloud environment and protostellar properties using the Herschel Orion Protostar Survey (HOPS), a large multi-observatory survey of protostars in the Orion molecular clouds. HOPS has produced well sampled 1 um to 870 um SEDs of over 300 protostars in the Orion molecular clouds using images and spectra from 2MASS, Spitzer, Herschel and APEX. Furthermore, the combination of APEX 870 um continuum observations with the HOPS/PACS 160 um data over the same area allows for a determination of the temperatures and column densities in the often filamentary dense gas surrounding the Orion protostars. Based on these data, we link the protostellar properties with their environmental properties. Utilizing the diverse environments present within the Orion molecular clouds, we show how the luminosity and spacing of protostars in Orion depends on the local gas column density. Furthermore, we report an unusual concentration of the youngest known protostars (the Herschel identified PBRS, PACS Bright Red Sources) in the Orion B cloud, and we discuss possible reasons for this concentration.

  18. Organochalcogen substituents in phenolic antioxidants.

    Science.gov (United States)

    Amorati, Riccardo; Pedulli, Gian Franco; Valgimigli, Luca; Johansson, Henrik; Engman, Lars

    2010-05-21

    Little is known about the ED/EW character of organochalcogen substituents and their contribution to the O-H bond dissociation enthalpy (BDE) in phenolic compounds. A series of ortho- and para-(S,Se,Te)R-substituted phenols were prepared and investigated by EPR, IR, and computational methods. Substituents lowered the O-H BDE by >3 kcal/mol in the para position, while the ortho-effect was modest due to hydrogen bonding ( approximately 3 kcal/mol) to the O-H group.

  19. Molecular Diversity and Genetic Structure of Durum Wheat Landraces

    Directory of Open Access Journals (Sweden)

    GULNAR SHIKHSEYIDOVA

    2015-06-01

    Full Text Available To determine the genetic diversity of durum wheat, 41 accessions from Morocco, Ethiopia, Turkey, Lebanon, Kazakhstan, China, and Mongolia were analyzed through Inter-Simple Sequence Repeats (ISSR molecular markers. Out of the used twenty primers, 15 primers that included a considerable polymorphism were selected for the analyses. Among the genotypes under study, 163 fragments (73.7% were polymorph. Several indexes were used to determine the most appropriate primers. While UBC812, UBC864, UBC840, and UBC808 primers were among those markers which produced the highest number of bands and polymorphic bands, they also dedicated the highest rate of polymorphic index content (PIC. These primers also possessed the highest amounts of effective multiplex ratio (EMR and marker index (MI. Therefore, these primers can be recommended for genetic evaluation of the durum wheat. The results of cluster analysis and principle component analysis indicated that the observed genetic diversity in wheat materials under study is geographically structured. The results also indicated that the genetic diversity index based on ISSR markers was higher for Turkey, Lebanon, Morocco, and Ethiopia accessions than for other countries. The high level of polymorphism in this collections durum wheat would agree with the suggestion that Fertile Crescent and parts of Africa are first possible diversity center of this crop.

  20. Molecular assessment of genetic diversity in mung bean germplasm

    Indian Academy of Sciences (India)

    G. Roopa Lavanya; Jyoti Srivastava; Shirish A. Ranade

    2008-04-01

    RAPD profiles were used to identify the extent of diversity among 54 accessions of mung bean that included both improved and local land races. Out of the 40 primers screened, seven primers generated 174 amplification products with an average of 24.85 bands per primer. The RAPD profiles were analysed for Jaccard’s similarity coefficients that was found to be in the range from 0 to 0.48, indicating the presence of wide range of genetic diversity at molecular level. Cluster analysis was carried out based on distances (1-similarity coefficient) using neighbour-joining method in Free Tree package. The dendrogram resolved all the accessions into two major clusters, I (with 11 accessions) and II (with 43 accessions). However, the cluster was further divided into four subclusters (II A with six, II B with nine, II C with 15 and II D with 13 accessions). The distribution of the accessions in different clusters and subclusters appeares to be related to their performance in field conditions for 10 morphological traits that were scored. This study indicated that the RAPD profiles provide an easy and simple technique for preliminary genetic diversity assessment of mung bean accessions that may reflect morphological trait differences among them.

  1. THE INFLUENCE OF SUBSTITUENTS IN METALLOCENE ON PROPYLENE POLYMERIZATION

    Institute of Scientific and Technical Information of China (English)

    Tariq Yasin; Zhi-qiang Fan; Lin-xian Feng

    1999-01-01

    Two new unbridged zirconocenes, bis(2,4,7-trimethyl indenyl)zirconium dichloride (Met-Ⅰ) and bis(2-methyl-4,7-diethyl indenyl)zirconium dichloride (Met-Ⅱ) were prepared in order to investigate the steric effects of substituents on the nature of the catalysts for the polymerization of propylene. A mixture of methyl aluminoxane (MAO) and triisobutylaluminum [Al(iBu)3] was used as cocatalyst to activate these catalysts. The decrease in steric bulkiness of substituents at 4 and 7 positions of the indenyl ring resulted in an increase of both activity and molecular weight as well as the isotacticity.

  2. Genetic diversity assessment of summer squash landraces using molecular markers.

    Science.gov (United States)

    Mady, Emad A; Helaly, Alaa Al-Din; Abu El-Hamd, Abdel Naem; Abdou, Arafa; Shanan, Shamel A; Craker, Lyle E

    2013-07-01

    Plant identification, classification, and genotyping within a germplasm collection are essential elements for establishing a breeding program that enhances the probability of plants with desirable characteristics in the market place. In this study, random amplified polymorphic DNA (RAPD) was used as a molecular tool to assess the diversity and relationship among 20 summer squash (Curcubita pepo L.) landraces traditionally used to treat hypertension and prostate hyperplasia. A total of 10 RAPD primers produced 65 reproducible bands of which 46 (70.77 %) were polymorphic, indicating a large number of genotypes within the summer squash lines. Cluster analysis divided the summer squash germplasm into two groups, one including one landrace and a second containing 19 landraces that could be divided into five sub-groups. Results of this study indicate the potential of RAPD markers for the identification and assessment of genetic variations among squash landraces and provide a number of choices for developing a successful breeding program to improve summer squash.

  3. Photochromic fulgides and spirooxazines: mechanism and substituent effect on photoreactions

    Institute of Scientific and Technical Information of China (English)

    樊美公; 明阳福; 于联合; 张新宇; 孟宪娟; 梁永超; 杨茁

    1996-01-01

    Molecular design, synthesis and photochromic properties of spirooxazines and fulgides are described. In the case of fulgides, the change of the substituents may lead to different photochromic properties and different photoreactions of the kind of compounds. In photochromic process of pyrryl-substituted fulgides, the excited singlet state is the mam species, but the excited triplet state is also involved. However, no excited triplet state has been observed in cyclization of aryl-substituted fulgides. In the case of spirooxazines, the substituents at 2’-position have great effect on the formation of photoproduct and on the mechanism of photoreaction. The increase of steric hindrance of the 2’-position substituent gives rise to the decrease of the quantum yield for the formation of photochromic merocyanine (PMC) and the increase of the relative quantum yield for the charge separated twist intermediate (CT).

  4. Molecular Cooperativity Governs Diverse and Monoallelic Olfactory Receptor Expression

    Science.gov (United States)

    Xing, Jianhua; Tian, Xiaojun; Zhang, Hang; Sannerud, Jens

    Multiple-objective optimization is common in biological systems. In the mammalian olfactory system, each sensory neuron stochastically expresses only one out of up to thousands of olfactory receptor (OR) gene alleles; at organism level the types of expressed ORs need to be maximized. The molecular mechanism of this Nobel-Prize winning puzzle remains unresolved after decades of extensive studies. Existing models focus only on monoallele activation, and cannot explain recent observations in mutants, especially the reduced global diversity of expressed ORs in G9a/GLP knockouts. In this work we integrated existing information on OR expression, and proposed an evolutionarily optimized three-layer regulation mechanism, which includes zonal segregation, epigenetic and enhancer competition coupled to a negative feedback loop. This model not only recapitulates monoallelic OR expression, but also elucidates how the olfactory system maximizes and maintains the diversity of OR expression. The model is validated by several experimental results, and particularly underscores cooperativity and synergy as a general design principle of multi-objective optimization in biology. The work is supported by the NIGMS/DMS Mathematical Biology program.

  5. Molecular approaches to diversity of populations of apicomplexan parasites.

    Science.gov (United States)

    Beck, Hans-Peter; Blake, Damer; Dardé, Marie-Laure; Felger, Ingrid; Pedraza-Díaz, Susana; Regidor-Cerrillo, Javier; Gómez-Bautista, Mercedes; Ortega-Mora, Luis Miguel; Putignani, Lorenza; Shiels, Brian; Tait, Andrew; Weir, Willie

    2009-01-01

    Apicomplexan parasites include many parasites of importance either for livestock or as causative agents of human diseases. The importance of these parasites has been recognised by the European Commission and resulted in support of the COST (Cooperation in Science and Technology) Action 857 'Apicomplexan Biology in the Post-Genomic Era'. In this review we discuss the current understanding in 'Biodiversity and Population Genetics' of the major apicomplexan parasites, namely the Eimeria spp., Cryptosporidium spp., Toxoplasma gondii, Neospora caninum, Theileria spp. and Plasmodium spp. During the past decade molecular tools for characterizing and monitoring parasite populations have been firmly established as an integral part of field studies and intervention trials. Analyses have been conducted for most apicomplexan pathogens to describe the extent of genetic diversity, infection dynamics or population structure. The underlying key question for all parasites is to understand how genetic diversity influences epidemiology and pathogenicity and its implication in therapeutic and vaccination strategies as well as disease control. Similarities in the basic biology and disease or transmission patterns among this order of parasites promote multifaceted discussions and comparison of epidemiological approaches and methodological tools. This fosters mutual learning and has the potential for cross-fertilisation of ideas and technical approaches.

  6. Virulence and molecular diversity in Colletotrichum graminicola from Brazil.

    Science.gov (United States)

    Valèrio, H M; Rèsende, M A; Weikert-Oliveira, R C B; Casela, C R

    2005-04-01

    Genetic diversity among 37 isolates of the sorghum anthracnose pathogen Colletotrichum graminicola, from four geographically distinct regions of Brazil, was evaluated by RAPD and RFLP-PCR markers and virulence characters on a set of 10 differential sorghum genotypes. Twenty-two races were identified and race 13B was the most frequent, but present in only two regions. RAPD analysis revealed 143 polymorphic bands that grouped the isolates according to their geographic origin, but not by their virulence phenotypes. RFLP with HaeIII, MspI, HinfI, HhaI, HpaII, EcoRI, HindIII, PstI, RsaI, Taq alphaI, and AluI enzymes over ITS domains and 5.8 rDNA genes of C. graminicola did not show differences among the isolates, indicating high conservation of these restriction sites. Molecular polymorphism was observed among isolates belonging to the same race. No association between virulence phenotypes and molecular profiles was observed.

  7. Molecular identification and genetic diversity among Photorhabdus and Xenorhabdus isolates.

    Science.gov (United States)

    Moghaieb, Reda E A; Abdelhadi, Abdelhadi A; El-Sadawy, Hanan A; Allam, Nesreen A T; Baiome, Baiome Abdelmaguid; Soliman, Mohamed H

    2017-05-01

    Five bacterial strains were isolated from the hemocoel of the greater wax moth larvae (Galleria mellonella) infected with the entomopathogenic nematodes: Heterorhabditis bacteriophora HP88, Heterorhabditis indicus RM1 and Heterorhabditis sp (S1), Steinernema abbasi and Steinernema sp. (S II). Strains were identified as Photorhabdus luminescens HRM1, P. luminescens HS1, P. luminescens HP88, Xenorhabdus indica and X. nematophila ATTC19061 using 16S rDNA sequence analysis. To reveal the genetic diversity among these strains, three molecular markers (RAPD, ISSR and SRAP) were employed. RAPD analysis showed 73.8 and 54.5 polymorphism percentages for the Photorhabdus and Xenorhabdus strains, respectively. ISSR analysis resulted in 70.1 and 75.2 polymorphism percentages among the Photorhabdus and Xenorhabdus strains, respectively. The SRAP analysis indicated that 75.6 and 61.2% genetic polymorphism was detected among Photorhabdus and Xenorhabdus strains, respectively. The cluster analysis grouped the three Photorhabdus strains together in one cluster and the two Xenorhabdus strains together in another cluster indicating the phylogenetic relationships among them. The genotype-specific markers detected from the three molecular markers (RAPD, ISSR and SRAP) were sufficient to distinguish between the different bacterial strains tested and can be used in the future IBM program that could be built on the use of these strains.

  8. Diversity of extrasolar planets and diversity of molecular cloud cores. I. Semimajor axes

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Liping; Li, Min, E-mail: jinlp@jlu.edu.cn, E-mail: minli09@mails.jlu.edu.cn [College of Physics, Jilin University, Changchun, Jilin 130012 (China)

    2014-03-01

    We show that the diversity of extrasolar planetary systems may be related to the diversity of molecular cloud cores. In previous studies of planet formation, artificial initial conditions of protoplanetary disks or steady state disks, such as the minimum mass nebula model, have often been used so that the influence of cloud core properties on planet formation is not realized. To specifically and quantitatively demonstrate our point, we calculate the dependence of disk properties on cloud core properties and show that the boundary of the giant planet formation region in a disk is a function of cloud core properties with the conventional core accretion model of giant planet formation. The gravitational stability of a disk depends on the properties of its progenitor cloud core. We also compare our calculations with observations of extrasolar planets. From the observational data of cloud cores, our model could infer the range and most frequent values of observed semimajor axes of extrasolar planets. Our calculations suggest that planet formation at the snowline alone could not completely explain the semimajor axis distribution. If the current observations are not biased, our calculations indicate that the planet formation at the snowline is inefficient. We suggest that there will be more observed planets with semimajor axis <9 AU than >9 AU, even with a longer duration of observations, if the planet formation at the snowline is inefficient.

  9. A molecular method to assess Phytophthora diversity in environmental samples.

    Science.gov (United States)

    Scibetta, Silvia; Schena, Leonardo; Chimento, Antonio; Cacciola, Santa O; Cooke, David E L

    2012-03-01

    Current molecular detection methods for the genus Phytophthora are specific to a few key species rather than the whole genus and this is a recognized weakness of protocols for ecological studies and international plant health legislation. In the present study a molecular approach was developed to detect Phytophthora species in soil and water samples using novel sets of genus-specific primers designed against the internal transcribed spacer (ITS) regions. Two different rDNA primer sets were tested: one assay amplified a long product including the ITS1, 5.8S and ITS2 regions (LP) and the other a shorter product including the ITS1 only (SP). Both assays specifically amplified products from Phytophthora species without cross-reaction with the related Pythium s. lato, however the SP assay proved the more sensitive and reliable. The method was validated using woodland soil and stream water from Invergowrie, Scotland. On-site use of a knapsack sprayer and in-line water filters proved more rapid and effective than centrifugation at sampling Phytophthora propagules. A total of 15 different Phytophthora phylotypes were identified which clustered within the reported ITS-clades 1, 2, 3, 6, 7 and 8. The range and type of the sequences detected varied from sample to sample and up to three and five different Phytophthora phylotypes were detected within a single sample of soil or water, respectively. The most frequently detected sequences were related to members of ITS-clade 6 (i.e. P. gonapodyides-like). The new method proved very effective at discriminating multiple species in a given sample and can also detect as yet unknown species. The reported primers and methods will prove valuable for ecological studies, biosecurity and commercial plant, soil or water (e.g. irrigation water) testing as well as the wider metagenomic sampling of this fascinating component of microbial pathogen diversity.

  10. Molecular diversity of bacteria in commercially available "Spirulina" food supplements.

    Science.gov (United States)

    Vardaka, Elisabeth; Kormas, Konstantinos A; Katsiapi, Matina; Genitsaris, Savvas; Moustaka-Gouni, Maria

    2016-01-01

    The cyanobacterium Arthrospira is among the most well-known food supplements worldwide known as "Spirulina." While it is a widely recognized health-promoting natural product, there are no reports on the molecular diversity of commercially available brands of "Spirulina" supplements and the occurrence of other cyanobacterial and heterotrophic bacterial microorganisms in these products. In this study, 454-pyrosequencing analysis of the total bacterial occurrence in 31 brands of "Spirulina" dietary supplements from the Greek market was applied for the first time. In all samples, operational taxonomic units (OTUs) of Arthrospira platensis were the predominant cyanobacteria. Some products contained additional cyanobacterial OTUs including a few known potentially toxic taxa. Moreover, 469 OTUs were detected in all 31 products collectively, with most of them being related to the Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Verrucomicrobia. All samples included heterotrophic bacterial OTUs, ranging from 9-157 per product. Among the most common OTUs were ones closely related to taxa known for causing health issues (i.e., Pseudomonas, Flavobacterium, Vibrio, Aeromonas, Clostridium, Bacillus, Fusobacterium, Enterococcus). The observed high cyanobacterial and heterotrophic bacterial OTUs richness in the final product is a point for further research on the growth and processing of Arthrospira biomass for commercial purposes.

  11. Molecular Diversity of Vaccine Candidates in Leptospira spp.

    Directory of Open Access Journals (Sweden)

    Patricia Hernández-Rodríguez

    2015-09-01

    Full Text Available The aim of this study was to determine the molecular diversity of OmpL1, LipL32, LipL41, LigA and LigB proteins and that of the genes that encode them using bioinformatic analysis in different pathogenic strains of Leptospira spp. based on the information available in databases. The amino acid sequences of OmpL1, LipL32, LipL41, LigA and LigB proteins were used, as well as the genes encoding them in strains of Leptospira spp. reported at The National Center for Biotechnology Information (NCBI. The analysis of proteins and genes were performed using the Protein, Nucleotide and Gene resources from the NCBI. The alignment of the consensus sequences was performed using the PSI-BLAST and BLASTn tools. The coverage percentage of the selected sequences of the ompL1, lipL32, lipL41, ligA and ligB genes in pathogenic strains of Leptospira spp. is 100% for ompL1, lipL32 and lipL41, 75% for ligA and 99% for ligB with identity percentages of 85, 98, 88, 90 and 80% respectively; the coverage percentage of the selected protein sequences is 100, 77, 99, 100 and 100% with identity percentages of 90, 99, 92, 63 and 60% respectively, indicating that genes and proteins, except LigA and LigB proteins, are highly conserved in various pathogenic serovars of Leptospira spp. According to these results, it is recommended that further analysis of these proteins be made in order to determine the feasibility of its use as vaccine candidates.

  12. Genetic diversity and molecular genealogy of local silkworm varieties

    Directory of Open Access Journals (Sweden)

    Zhouhe Du

    2013-03-01

    Full Text Available In order to explore the genetic diversity and systematic differentiation pattern among silkworm varieties, aiming to guide hybridization breeding, we sequenced a total of 72 Bmamy2 gene fragments from local silkworm varieties. The analysis of nucleotide sequence diversity and systematic differentiation indicated that there was rich genovariation in the sequencing region of Bmamy2 gene, and the base mutation rate is 5.6–8.2%, the haplotype diversity is 0.8294, and the nucleotide diversity is 0.0236±0.00122, suggesting Bmamy2 being a better marking gene with rich nucleotide sequence diversity, based on which the genetic diversity among different local silkworm varieties can be identified. The same heredity population structure is proclaimed by several analysis methods that every clade consisting of varieties from different geosystems and ecological types, while the varieties from the same geosystem and ecotype belong to different clades in the phylogeny. There is no population structure pattern that different varieties claded together according to geosystem or ecotype. It can be speculated that the silkworm origins from mixture of kinds of several voltinism mulberry silkworm, Bombyx mandarina, while the domestication events took place in several regions, from which the domesticated mulberry silkworms are all devoting to the domesticated silkworm population of today.

  13. Correlating substituent parameter values to electron transport properties of molecules

    Science.gov (United States)

    Vedova-Brook, Natalie; Matsunaga, Nikita; Sohlberg, Karl

    2004-03-01

    There are a vast number of organic compounds that could be considered for use in molecular electronics. Because of this, the need for efficient and economical screening tools has emerged. We demonstrate that the substituent parameter values ( σ), commonly found in advanced organic chemistry textbooks, correlate strongly with features of the charge migration process, establishing them as useful indicators of electronic properties. Specifically, we report that ab initio derived electronic charge transfer values for 16 different substituted aromatic molecules for molecular junctions correlate to the σ values with a correlation coefficient squared ( R2) of 0.863.

  14. Molecular diversity among Turkish oaks (QUERCUS) using random ...

    African Journals Online (AJOL)

    aykut

    2013-11-06

    Nov 6, 2013 ... 1Department of Molecular Biology and Genetics, Faculty of Science and Arts, Uşak University, 64200 Uşak, Turkey. 2Department ... sing and wind-pollination species. ... merase chain reaction (PCR) based technique used to.

  15. Applying Molecular Markers in Coriander Populations with Diverse Geographical Origins

    Science.gov (United States)

    Relationships between patterns of genetic diversity and geographical origins were studied in coriander by using amplified fragment length polymorphisms (AFLP) to survey coriander accessions. In 2005, 60 coriander accessions from 28 countries, from the USDA-ARS North Central Regional Plant Introduct...

  16. Morphological and molecular genetic diversity of Syrian indigenous ...

    African Journals Online (AJOL)

    This study aimed to assess the morphological variation, genetic diversity and ... questionnaire was used in recording both qualitative (coat color, eye color, horn ... these goat breeds have not yet undergone an organized breeding program. ... The Syrian goat populations had observed and expected heterozygosity values ...

  17. Diversity surveys of soil bacterial community by cultivation-based methods and molecular fingerprinting techniques

    Institute of Scientific and Technical Information of China (English)

    LUO Hai-feng; QI Hong-yan; ZHANG Hong-xun

    2004-01-01

    By combining the cultivation methods with molecular fingerprinting techniques, the diversity surveys of soil bacterial community in 13 areas of China were carried out. The cultivable heterotrophic diversity was investigated by colony morphology on solid LB medium. Genetic diversity was measured as bands on denaturing gradient gel electrophoresis(DGGE) by the extraction and purification of the total soil DNA, and amplification of bacterial 16S rDNA fragments by polymerase chain reaction ( PCR). The Shannon-Wiener indices of diversity (H), richness (S)and evenness( EH ) were employed to estimate the diversity of soil bacterial community. The results showed that there was an obvious diversification existed in soil from the different areas. However, the genetic diversity estimated by PCR-DGGE can provide more comprehensive information on bacterial community than the cultivation-based methods. Therefore, it is suggested to combine the traditional methods with genetic fingerprinting techniques to survey and estimate soil bacterial diversity.

  18. Prospects of molecular markers in Fusarium species diversity

    DEFF Research Database (Denmark)

    Nayaka, S. Chandra; Wulff, Ednar Gadelha; Udayashankar, A.C.

    2011-01-01

    focuses of various molecular-based techniques employed to study the diversity of Fusarium species causing diseases in major food crops. An introduction of fusarial diseases and their mycotoxins and molecular-marker-based methods for detection introduce the concept of marker application. Various well...

  19. Simple Sequence Repeat Polymorphisms (SSRPs for Evaluation of Molecular Diversity and Germplasm Classification of Minor Crops

    Directory of Open Access Journals (Sweden)

    Nam-Soo Kim

    2009-11-01

    Full Text Available Evaluation of the genetic diversity among populations is an essential prerequisite for the preservation of endangered species. Thousands of new accessions are introduced into germplasm institutes each year, thereby necessitating assessment of their molecular diversity before elimination of the redundant genotypes. Of the protocols that facilitate the assessment of molecular diversity, SSRPs (simple sequence repeat polymorphisms or microsatellite variation is the preferred system since it detects a large number of DNA polymorphisms with relatively simple technical complexity. The paucity of information on DNA sequences has limited their widespread utilization in the assessment of genetic diversity of minor or neglected crop species. However, recent advancements in DNA sequencing and PCR technologies in conjunction with sophisticated computer software have facilitated the development of SSRP markers in minor crops. This review examines the development and molecular nature of SSR markers, and their utilization in many aspects of plant genetics and ecology.

  20. Genetic Diversity and Molecular Evolution of Chinese Waxy Maize Germplasm

    Science.gov (United States)

    Zheng, Hongjian; Wang, Hui; Yang, Hua; Wu, Jinhong; Shi, Biao; Cai, Run; Xu, Yunbi; Wu, Aizhong; Luo, Lijun

    2013-01-01

    Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima’s D and Fu and Li’s F*) were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection. PMID:23818949

  1. Molecular Diversity of Ralstonia solanacearum Isolated from Ginger in Hawaii.

    Science.gov (United States)

    Yu, Q; Alvarez, A M; Moore, P H; Zee, F; Kim, M S; de Silva, A; Hepperly, P R; Ming, R

    2003-09-01

    ABSTRACT The genetic diversity of Ralstonia solanacearum strains isolated from ginger (Zingiber officinale) growing on the island of Hawaii was determined by analysis of amplified fragment length polymorphisms (AFLPs). Initially 28 strains of R. solanacearum collected from five host plant species worldwide were analyzed by AFLP. A second analysis was conducted on 55 R. solanacearum strains collected from three ginger farms along the Hamakua Coast of Hawaii, the principle area of ginger cultivation in the state. From the initial analysis, R. solanacearum strains from ginger in Hawaii showed a high degree of similarity at 0.853. In contrast, the average genetic similarity between R. solanacearum strains from heliconia and ginger was only 0.165, and strains from ginger showed little similarity with strains from all other hosts. The second analysis of 55 strains from ginger on different Hawaiian farms confirmed that they were distinct from race 1 strains from tomato. Strains from ginger also showed greater diversity among themselves in the second analysis, and the greatest diversity occurred among strains from a farm where ginger is frequently imported and maintained. Our results provide evidence that R. solanacearum strains from ginger in Hawaii are genetically distinct from local strains from tomato (race 1) and heliconia (race 2).

  2. Genetic diversity and molecular evolution of Chinese waxy maize germplasm.

    Directory of Open Access Journals (Sweden)

    Hongjian Zheng

    Full Text Available Waxy maize (Zea mays L. var. certaina Kulesh, with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima's D and Fu and Li's F* were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection.

  3. Photoswitchable fluorescent diheteroarylethenes: substituent effects on photochromic and solvatochromic properties.

    Science.gov (United States)

    Gillanders, Florencia; Giordano, Luciana; Díaz, Sebastián A; Jovin, Thomas M; Jares-Erijman, Elizabeth A

    2014-03-01

    Photoswitchable fluorescent diheteroarylethenes are promising candidates for applications in super-resolution molecular localization fluorescence microscopy thanks to their high quantum yields and fatigue-resistant photoswitching characteristics. We have studied the effect of varying substituents on the photophysical properties of six sulfone derivatives of diheteroarylethenes, which display fluorescence in one (closed form) of two thermally stable photochromic states. Electron-donating substituents displace the absorption and emission spectra towards the red without substantially affecting the fluorescence quantum yields. Furthermore, ethoxybromo, a very electron-donating substituent, stabilizes the excited state of the closed isomer to the extent of almost entirely inhibiting its cycloreversion. Multi-parameter Hammett correlations indicate a relationship between the emission maxima and electron-donating character, providing a useful tool in the design of future photochromic molecules. Most of the synthesized compounds exhibit small bathochromic shifts and shorter fluorescence lifetimes with an increase in solvent polarity. However, the ethoxybromo-substituted fluorescent photochrome is unique in its strong solvatochromic behaviour, constituting a photoactivatable (photochromic), fluorescent and highly solvatochromic small organic compound. The Catalán formalism identified solvent dipolarity as the principal basis of the solvatochromism, reflecting the highly polarized nature of this molecule.

  4. Molecular markers to study competition and diversity of Rhizobium

    NARCIS (Netherlands)

    Sessitsch, A.

    1997-01-01

    The research described in this thesis was directed to the development of molecular identification and detection techniques for studying the ecology of Rhizobium, a nitrogen- fixing bacterium of agricultural importance. Competition of inoculant strains with indigenous mi

  5. Genetic Diversity and Molecular evolution of Hepatitis C Virus

    NARCIS (Netherlands)

    S. Noppornpanth (Suwanna)

    2008-01-01

    textabstractHepatitis C virus (HCV), an enveloped positive stranded RNA virus, is the causative agent of non-A, non-B (NANB) hepatitis (27). The virus was identified and characterized by molecular cloning techniques using serum from a NANB hepatitis virus infected chimpanzee (15) and based on the si

  6. Molecular markers to study competition and diversity of Rhizobium.

    NARCIS (Netherlands)

    Sessitsch, A.

    1997-01-01

    The research described in this thesis was directed to the development of molecular identification and detection techniques for studying the ecology of Rhizobium, a nitrogen- fixing bacterium of agricultural importance. Competition of inoculant strains with indigenous microbes is a serious problem in

  7. A DFT study of substituent effects in corannulene dimers.

    Science.gov (United States)

    Josa, Daniela; Rodríguez Otero, Jesús; Cabaleiro Lago, Enrique M

    2011-12-21

    Corannulene dimers made up of corannulene monomers with different curvature and substituents were studied using M06-2X, B97D and ωB97XD functionals and 6-31+G* basis set. Corannulene molecules were substituted with five alternating Br, Cl, CH(3), C(2)H or CN units. Geometric results showed that substituents gave rise to small changes in the curvature of corannulene bowls. So, there was not a clear relationship between the curvature of bowls and the changes on interaction energy generated by addition of substituents in the bowl. Electron withdrawing substituents gave rise to a more positive molecular electrostatic potential (MEP) of the bowl, which was able to get a strong interaction with the negative MEP at the surface of a fullerene. Substitution with CN caused the largest effect, giving rise to the most positive MEP and to a large interaction energy of -24.64 kcal mol(-1), at the ωB97XD/6-31+G* level. Dispersive effects must be taken into account to explain the catching ability of the different substituted corannulenes. For unsubstituted dimers, calculations with DFT-D methods employing ωB97XD and B97D functionals led to similar results to those previously reported at the SCS-MP2/cc-pVTZ level for corannulene dimers (A. Sygula and S. Saebø, Int. J. Quant. Chem., 2009, 109, 65). In particular, the ωB97XD functional led to a difference of only 0.35 kcal mol(-1), regarding MP2 interaction energy for corannulene dimers. On the other hand, the M06-2X functional showed a general considerable underestimation of interaction energies. This functional worked quite well to study trends, but not to obtain absolute interaction energies.

  8. Molecular diversity of bovine viral diarrhea virus in uruguay.

    Science.gov (United States)

    Maya, L; Puentes, R; Reolón, E; Acuña, P; Riet, F; Rivero, R; Cristina, J; Colina, R

    2016-03-01

    Bovine viral diarrhea (BVD) affects bovine production and reproduction causing significant economic losses all over the world. Two viral species has been recognized: BVDV-1 and BVDV-2, both distributed worldwide. Recently, novel specie of BVDV named HoBi-like pestivirus was discovered. The presence of BVDV was confirmed in 1996 in Uruguay, however, does not exist until today a schedule of compulsory vaccination along the country. Serological studies with samples from all Uruguayan herds were performed during 2000 and 2001 demonstrating that all of them were seropositive to BVDV with a mean prevalence of 69%. In addition, there have been no new studies done since those previously described and it is important to mention that the genetic diversity of BVD has never been described in Uruguay. Nowadays, there is strongly suspect that BVDV is one of the most important causes of reproductive failures in our herds. The aim of this study was to describe for the first time in Uruguay the genetic diversity of BVDV with samples collected from different regions along the country. Serological status of 390 non-vaccinated animals against BVDV with reproductive problems from farms of Rivera, Tacuarembó and Florida departments of Uruguay were studied. All herds were seropositive to BVDV and high proportion of animals were positive (298/390), while 4.1% (16/390) of the animals were positive to Antigen Capture ELISA test and Real Time PCR. Phylogenetic analysis performed with concatenated sequences from the 5'UTR and Npro genomic regions revealed that BVDV-1 and BVDV-2 are infecting our herds, being BVDV-1 the most frequently found. The major subtype was BVDV-1a, followed by BVDV-1i and BVDV-2b. This is the first study that describes the genetic diversity of BVDV in Uruguay and it will contribute to the elaboration of sanitization programs.

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

    Directory of Open Access Journals (Sweden)

    Juliana Morini Küpper Cardoso Perseguini

    2011-01-01

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

  10. Molecular diversity of avian schistosomes in Danish freshwater snails

    DEFF Research Database (Denmark)

    Christiansen, Anne Ø.; Olsen, Annette; Buchmann, Kurt

    2016-01-01

    Avian schistosomes are widespread parasites of snails and waterfowl and may cause cercarial dermatitis (swimmer's itch) in humans, a disease that is frequently reported in European countries. These parasites are known to occur in Denmark, but here, we applied a new approach using molecular tools...... to identify the parasites at species level. In order to do that, 499 pulmonate freshwater snails (Radix sp., Lymnaea stagnalis, Stagnicola sp. and Planorbarius corneus) were sampled from 12 lakes, ponds, and marshes in the greater Copenhagen area. Avian schistosome cercariae were identified by microscopy...... and subjected to molecular investigation by sequencing and phylogenetic analysis of the 5.8S and ITS2 ribosomal DNA for species identification. Additionally, snail hosts belonging to the genus Radix were identified by sequencing and phylogenetic analysis of partial ITS2 ribosomal DNA. Three out of 499 snails...

  11. Molecular diversity at the plant-pathogen interface.

    Science.gov (United States)

    McDowell, John M; Simon, Stacey A

    2008-01-01

    Plants have evolved a robust innate immune system that exhibits striking similarities as well as significant differences with various metazoan innate immune systems. For example, plants are capable of perceiving pathogen-associated molecular patterns through pattern recognition receptors that bear structural similarities to animal Toll-like receptors. In addition, plants have evolved a second surveillance system based on cytoplasmic "NB-LRR" proteins (nucleotide-binding, leucine-rich repeat) that are structurally similar to animal nucleotide-binding and oligomerization domain (NOD)-like receptors. Plant NB-LRR proteins do not detect PAMPs; rather, they perceive effector proteins that pathogens secrete into plant cells to promote virulence. This review summarizes the current state of knowledge about the molecular functionality and evolution of these immune surveillance genes.

  12. Molecular diversity of diazotrophs in oligotrophic tropical seagrass bed communities.

    Science.gov (United States)

    Bagwell, Christopher E; Rocque, Jeannine R; Smith, Garriett W; Polson, Shawn W; Friez, Michael J; Longshore, John W; Lovell, Charles R

    2002-02-01

    Denaturing gradient gel electrophoresis (DGGE) was employed to resolve PCR-amplified nifH sequences from vegetated and unvegetated sediments from two oligotrophic seagrass bed sites on San Salvador Island, Bahamas, in order to assess diazotroph species composition. All DGGE profiles from these sites showed the same prominent bands. These bands were sequenced, yielding 67 different nifH sequences, which were used in phylogenetic reconstructions. Most sequences were from anaerobes, but some were affiliated with the alpha- and (gamma-+beta-) Proteobacteria. Several NifH sequences were nearly identical to those from Azospirillum brasilense and Vibrio diazotrophicus. These seagrass bed sediments support a diverse diazotroph assemblage that is, at least superficially, similar to that associated with an intertidal grass (Spartina alterniflora).

  13. Predicting phenotypic diversity and the underlying quantitative molecular transitions.

    Directory of Open Access Journals (Sweden)

    Claudiu A Giurumescu

    2009-04-01

    Full Text Available During development, signaling networks control the formation of multicellular patterns. To what extent quantitative fluctuations in these complex networks may affect multicellular phenotype remains unclear. Here, we describe a computational approach to predict and analyze the phenotypic diversity that is accessible to a developmental signaling network. Applying this framework to vulval development in C. elegans, we demonstrate that quantitative changes in the regulatory network can render approximately 500 multicellular phenotypes. This phenotypic capacity is an order-of-magnitude below the theoretical upper limit for this system but yet is large enough to demonstrate that the system is not restricted to a select few outcomes. Using metrics to gauge the robustness of these phenotypes to parameter perturbations, we identify a select subset of novel phenotypes that are the most promising for experimental validation. In addition, our model calculations provide a layout of these phenotypes in network parameter space. Analyzing this landscape of multicellular phenotypes yielded two significant insights. First, we show that experimentally well-established mutant phenotypes may be rendered using non-canonical network perturbations. Second, we show that the predicted multicellular patterns include not only those observed in C. elegans, but also those occurring exclusively in other species of the Caenorhabditis genus. This result demonstrates that quantitative diversification of a common regulatory network is indeed demonstrably sufficient to generate the phenotypic differences observed across three major species within the Caenorhabditis genus. Using our computational framework, we systematically identify the quantitative changes that may have occurred in the regulatory network during the evolution of these species. Our model predictions show that significant phenotypic diversity may be sampled through quantitative variations in the regulatory network

  14. Molecular diversity of avian schistosomes in Danish freshwater snails.

    Science.gov (United States)

    Christiansen, Anne Ø; Olsen, Annette; Buchmann, Kurt; Kania, Per W; Nejsum, Peter; Vennervald, Birgitte J

    2016-03-01

    Avian schistosomes are widespread parasites of snails and waterfowl and may cause cercarial dermatitis (swimmer's itch) in humans, a disease that is frequently reported in European countries. These parasites are known to occur in Denmark, but here, we applied a new approach using molecular tools to identify the parasites at species level. In order to do that, 499 pulmonate freshwater snails (Radix sp., Lymnaea stagnalis, Stagnicola sp. and Planorbarius corneus) were sampled from 12 lakes, ponds, and marshes in the greater Copenhagen area. Avian schistosome cercariae were identified by microscopy and subjected to molecular investigation by sequencing and phylogenetic analysis of the 5.8S and ITS2 ribosomal DNA for species identification. Additionally, snail hosts belonging to the genus Radix were identified by sequencing and phylogenetic analysis of partial ITS2 ribosomal DNA. Three out of 499 snails shed different species of Trichobilharzia cercariae: Trichobilharzia szidati was isolated from L. stagnalis, Trichobilharzia franki from Radix auricularia and Trichobilharzia regenti from Radix peregra. In the light of the public health risk represented by bird schistosomes, these findings are of concern and, particularly, the presence of the potentially neuro-pathogenic species, T. regenti, in Danish freshwaters calls for attention.

  15. Molecular diversity of Mycobacterium tuberculosis strains indifferent provinces of Iran.

    Directory of Open Access Journals (Sweden)

    Mohadese Mozafari

    2013-12-01

    Full Text Available Molecular epidemiology tools are widely used in determining epidemiology of tuberculosis. Spoligotyping is a molecular epidemiology method that is used for characterization and typing of Mycobacterium tuberculosis complex strains. The method is based on polymorphism of the chromosomal DR locus consisting of identical 36-bp DRs alternating with 35-41 unique spacers. The objective of this study was to investigate the prevalence of M. tuberculosis spoligotypes in different provinces of Iran.M. tuberculosis strains were isolated from TB patients of Mycobacteriology Research center (MRC. DNA was extracted from patient's clinical samples. PCR was performed by using of specific primers for DR region. The amplified DNA was hybridized to the spoligotyping Membrane. Hybridized DNA was detected with ECL detection kit and by exposing ECL Hyperfilm to the membrane. The obtained result was entered to a binary format and was analyzed using SpolDB4 database.Spoligotyping resulted in 136 different patterns. Out of 1242 M. tuberculosis strains, 1165 strains (93.8% were classified into 59 clusters and the remaining strains (6.2 % were singleton.The results of present study showed that strains of CAS family were more prevalent than other strains in Iran. Other prevalent families were Haarlem, T and Beijing, respectively.

  16. European molecular epidemiology and strain diversity of feline calicivirus.

    Science.gov (United States)

    Hou, J; Sánchez-Vizcaíno, F; McGahie, D; Lesbros, C; Almeras, T; Howarth, D; O'Hara, V; Dawson, S; Radford, A D

    2016-01-30

    Feline calicivirus (FCV) causes a variable syndrome of upper respiratory tract disease, mouth ulcers and lameness. A convenience-based prospective sample of oropharyngeal swabs (n=426) was obtained from five countries (France, Germany, Greece, Portugal and the UK). The prevalence of FCV by virus isolation was 22.2 per cent. Multivariable analysis found that animals presenting with lymphoplasmacytic gingivitis stomatitis complex were more likely to test positive for FCV infection. Furthermore, vaccinated cats up to 48 months of age were significantly less likely to be infected with FCV than unvaccinated animals of similar ages. Phylogenetic analysis based on consensus sequences for the immunodominant region of the capsid gene from 72 FCV isolates identified 46 strains. Thirteen of the 14 strains with more than one sequence were restricted to individual regions or sites in individual countries; the exception was a strain present in two sites close to each other in France. Four strains were present in more than one household. Five colonies, four of which were rescue shelters, had multiple strains within them. Polymerase sequence suggested possible rare recombination events. These locally, nationally and internationally diverse FCV populations maintain a continuous challenge to the control of FCV infection and disease.

  17. High molecular diversity of extraterrestrial organic matter in Murchison meteorite revealed 40 years after its fall.

    Science.gov (United States)

    Schmitt-Kopplin, Philippe; Gabelica, Zelimir; Gougeon, Régis D; Fekete, Agnes; Kanawati, Basem; Harir, Mourad; Gebefuegi, Istvan; Eckel, Gerhard; Hertkorn, Norbert

    2010-02-16

    Numerous descriptions of organic molecules present in the Murchison meteorite have improved our understanding of the early interstellar chemistry that operated at or just before the birth of our solar system. However, all molecular analyses were so far targeted toward selected classes of compounds with a particular emphasis on biologically active components in the context of prebiotic chemistry. Here we demonstrate that a nontargeted ultrahigh-resolution molecular analysis of the solvent-accessible organic fraction of Murchison extracted under mild conditions allows one to extend its indigenous chemical diversity to tens of thousands of different molecular compositions and likely millions of diverse structures. This molecular complexity, which provides hints on heteroatoms chronological assembly, suggests that the extraterrestrial chemodiversity is high compared to terrestrial relevant biological- and biogeochemical-driven chemical space.

  18. Structural and Substituent Group Effects on Multielectron Standard Reduction Potentials of Aromatic N-Heterocycles.

    Science.gov (United States)

    Groenenboom, Mitchell C; Saravanan, Karthikeyan; Zhu, Yaqun; Carr, Jeffrey M; Marjolin, Aude; Faura, Gabriel G; Yu, Eric C; Dominey, Raymond N; Keith, John A

    2016-09-01

    Aromatic N-heterocycles have been used in electrochemical CO2 reduction, but their precise role is not yet fully understood. We used first-principles quantum chemistry to determine how the molecular sizes and substituent groups of these molecules affect their standard redox potentials involving various proton and electron transfers. We then use that data to generate molecular Pourbaix diagrams to find the electrochemical conditions at which the aromatic N-heterocycle molecules could participate in multiproton and electron shuttling in accordance with the Sabatier principle. While one-electron standard redox potentials for aromatic N-heterocycles can vary significantly with molecule size and the presence of substituent groups, the two-electron and two-proton standard redox potentials depend much less on structural modifications and substituent groups. This indicates that a wide variety of aromatic N-heterocycles can participate in proton, electron, and/or hydride shuttling under suitable electrochemical conditions.

  19. Molecular diversity of L-type Ca2+ channel transcripts in human fibroblasts.

    Science.gov (United States)

    Soldatov, N M

    1992-05-15

    The nucleotide sequence of cDNA encoding the human fibroblast Ca2+ channel of L type (HFCC) has been determined. It is highly homologous to L-type channels previously cloned from rabbit lung and heart as well as from rat brain. At least four sites of molecular diversity were identified in the nucleotide sequence of HFCC. Three of these include regions encoding the transmembrane segments IIS6, IIIS2, and IVS3, which are known to be important for channel gating properties. The positions of these sites correlate with RNA splice sites, indicating that the molecular diversity of the transcripts is a result of alternative splicing. The fourth diversity region is located at the C-terminal region and comprises insertions and deletions. It is suggested that these variations may give rise to multiple subforms of HFCC with altered electrophysiological properties.

  20. Morphological and molecular diversity of Unionidae (Mollusca, Bivalvia from Portugal

    Directory of Open Access Journals (Sweden)

    Reis, J.

    2013-06-01

    Full Text Available Freshwater mussels from the family Unionidae are known to exhibit a high level of ecological phenotypic plasticity that is reflected in their shell shape. This variation has caused uncertainty on systematics and taxonomy of the group. Several naiad populations from nine river basins from Portugal were analyzed genetically, using two mitochondrial gene fragments (16SrRNA and Cytochrome Oxidase I and morphologically, using ANOVA analyses of shell dimmensions. Molecular phylogenetic analyses were used to revise the systematics and to infer an evolutionary hypothesis for the family at the western-most Atlantic Iberian Peninsula. Genetic and morphological data were in agreement and supported the occurrence of 5 species in the region: Anodonta anatina, Anodonta cygnea, Potomida littoralis, Unio tumidiformis and Unio delphinus. The differentiation of all these species, except A. cygnea, is thought to have taken place during the isolation of the Iberian Peninsula and formation of the current river basins in the Tertiary. The possibility of A. cygnea being a relatively recent introduction is discussed. Basic morphometric measures of the shell proved to be useful to separate Unio species, but also seem to be strongly affected by environmental conditions. The high intra-specific morphologic variation was partially related to the species’ high level of phenotypic plasticity, but seems to have an important role in evolutionary processes.Las náyades de la familia Unionidae tienen gran plasticidad fenotípica, lo que se refleja en la forma de su concha. Esta variabilidad morfológica ha sido causa de gran confusión en la taxonomía y sistemática del grupo. Se han estudiado, genética y morfológicamente, numerosas poblaciones de náyades provenientes de nueve cuencas hidrográficas portuguesas. Para ello se han analizando dos fragmentos de genes mitocondriales (ARNr 16S y Citocromo Oxidasa I así como diferentes variables morfológicas de la concha. Se

  1. Assessment of the Genetic Diversity in Forest Tree Populations Using Molecular Markers

    Directory of Open Access Journals (Sweden)

    Ilga Porth

    2014-04-01

    Full Text Available Molecular markers have proven to be invaluable tools for assessing plants’ genetic resources by improving our understanding with regards to the distribution and the extent of genetic variation within and among species. Recently developed marker technologies allow the uncovering of the extent of the genetic variation in an unprecedented way through increased coverage of the genome. Markers have diverse applications in plant sciences, but certain marker types, due to their inherent characteristics, have also shown their limitations. A combination of diverse marker types is usually recommended to provide an accurate assessment of the extent of intra- and inter-population genetic diversity of naturally distributed plant species on which proper conservation directives for species that are at risk of decline can be issued. Here, specifically, natural populations of forest trees are reviewed by summarizing published reports in terms of the status of genetic variation in the pure species. In general, for outbred forest tree species, the genetic diversity within populations is larger than among populations of the same species, indicative of a negligible local spatial structure. Additionally, as is the case for plants in general, the diversity at the phenotypic level is also much larger than at the marker level, as selectively neutral markers are commonly used to capture the extent of genetic variation. However, more and more, nucleotide diversity within candidate genes underlying adaptive traits are studied for signatures of selection at single sites. This adaptive genetic diversity constitutes important potential for future forest management and conservation purposes.

  2. Fusarium diversity in soil using a specific molecular approach and a cultural approach.

    Science.gov (United States)

    Edel-Hermann, Véronique; Gautheron, Nadine; Mounier, Arnaud; Steinberg, Christian

    2015-04-01

    Fusarium species are ubiquitous in soil. They cause plant and human diseases and can produce mycotoxins. Surveys of Fusarium species diversity in environmental samples usually rely on laborious culture-based methods. In the present study, we have developed a molecular method to analyze Fusarium diversity directly from soil DNA. We designed primers targeting the translation elongation factor 1-alpha (EF-1α) gene and demonstrated their specificity toward Fusarium using a large collection of fungi. We used the specific primers to construct a clone library from three contrasting soils. Sequence analysis confirmed the specificity of the assay, with 750 clones identified as Fusarium and distributed among eight species or species complexes. The Fusarium oxysporum species complex (FOSC) was the most abundant one in the three soils, followed by the Fusarium solani species complex (FSSC). We then compared our molecular approach results with those obtained by isolating Fusarium colonies on two culture media and identifying species by sequencing part of the EF-1α gene. The 750 isolates were distributed into eight species or species complexes, with the same dominant species as with the cloning method. Sequence diversity was much higher in the clone library than in the isolate collection. The molecular approach proved to be a valuable tool to assess Fusarium diversity in environmental samples. Combined with high throughput sequencing, it will allow for in-depth analysis of large numbers of samples.

  3. Estimating genetic diversity and sampling strategy for a wild soybean (Glycine soja) population based on different molecular markers

    Institute of Scientific and Technical Information of China (English)

    CHEN Zhong; ZHAO Ru; GU Senchang; YAN Wen; CHENG Zhou; CHEN Muhong; LU Weifeng; WANG Shuhong; LU Baorong; LU Jun; ZHANG Fan; XIANG Rong; XIAO Shangbin; YAN Pin

    2006-01-01

    Genetic diversity is the basic and most important component of biodiversity. It is essential for the effective conservation and utilization of genetic resources to accurately estimate genetic diversity of the targeted species and populations. This paper reports analyses of genetic diversity of a wild soybean population using three molecular marker technologies (AFLP, ISSR and SSR), and computer simulation studies of randomly selected subsets with different sample size (5-90 individuals) drawn 50 times from a total of 100 wild soybean individuals. The variation patterns of genetic diversity indices, including expected heterozygosity (He), Shannon diversity index (/), and percentage of polymorphic loci (P), were analyzed to evaluate changes of genetic diversity associated with the increase of individuals in each subset. The results demonstrated that (1) values of genetic diversity indices of the same wild soybean population were considerably different when estimated by different molecular marker techniques; (2) genetic diversity indices obtained from subsets with different sample sizes also diverged considerably; (3) P values were relatively more reliable for comparing genetic diversity detected by different molecular marker techniques; and (4) different diversity indices reached 90% of the total genetic diversity of the soybean population quite differently in terms of the sample size (number of individuals) analyzed.When using the P value as a determinator, 30-40individuals could capture over 90% of the total genetic diversity of the wild soybean population. Results from this study provide a strong scientific basis for estimating genetic diversity and for strategic conservation of plant species.

  4. Substituent effects on hydrogen bonding of aromatic amide-carboxylate

    Science.gov (United States)

    Sen, Ibrahim; Kara, Hulya; Azizoglu, Akın

    2016-10-01

    N-(p-benzoyl)-anthranilic acid (BAA) derivatives have been synthesized with different substituents (X: Br, Cl, OCH3, CH3), and their crystal structures have been analyzed in order to understand the variations in their molecular geometries with respect to the substituents by using 1H NMR, 13C NMR, IR and X-ray single-crystal diffraction. The carboxylic acid group forms classic Osbnd H ⋯ O hydrogen bonded dimers in a centrosymmetric R22(8) ring motifs for BAA-Br and BAA-Cl. However, no carboxylic acid group forms classic Osbnd H ⋯ O hydrogen bonded dimers in BAA-OCH3 and BAA-CH3. The asymmetric unit consists of two crystallographically independent molecules in BAA-OCH3. DFT computations show that the interaction energies between monomer and dimer are in the range of 0.5-3.8 kcal/mol with the B3LYP/6-31 + G*, B3LYP/6-31 ++G*, B3LYP/6-31 ++G**, and B3LYP/AUG-cc-pVDZ levels of theory. The presence of different hydrogen bond patterns is also governed by the substrate. For monomeric compounds studied herein, theoretical calculations lead to two low-energy conformers; trans (a) and cis (b). Former one is more stable than latter by about 4 kcal/mol.

  5. Hydroxypropyl methylcellulose substituent analysis and rheological properties.

    Science.gov (United States)

    Akinosho, Hannah; Hawkins, Samantha; Wicker, Louise

    2013-10-15

    The methyl and hydroxypropyl substituents in hydroxypropyl methylcellulose (HPMC) affect the resulting gel properties. These substituents in five HPMC gels were characterized using Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy, small-amplitude oscillatory shear measurements, and differential scanning calorimetry (DSC). In FT-IR spectra, the most intense peak appeared at 1053 cm(-1), denoting the presence of the glucose ring. The ratio of peak intensities at 1452 cm(-1), which represents -C-H absorptions, and at 1053 cm(-1) (I1452/I1053) and percent methylation from gas chromatography exhibited a linear association (r(2)=0.6296). The broadening of the Raman spectra indicated that the relative crystallinity of HPMC decreases with increasing hydroxypropyl contents. DSC showed no linear relationship between the percent hydroxypropylation in HPMC and the percentage of free water in an HPMC gel. Small-amplitude oscillatory shear measurements revealed that the formation of an entanglements networks and/or weak gel depends on substituent contents.

  6. Electrochemiluminescent Detection of Hydrogen Peroxide via Some Luminol Imide Derivatives with Different Substituent Groups

    Directory of Open Access Journals (Sweden)

    Tifeng Jiao

    2013-01-01

    Full Text Available Some luminol imide derivatives with different substituent groups have been designed and synthesized. Their electrochemiluminescence properties have been measured with a view to developing new biosensors. The ECL response to hydrogen peroxide in the presence of these luminescent derivatives has been investigated taking into account crucial factors such as the applied potential value, injection volume of hydrogen peroxide, and the substituent groups in molecular structures. The experimental data demonstrated that the substituent groups in these imide derivatives can have a profound effect upon the ECL abilities of these studied compounds. The present research work affords new and useful exploration for the design and development of new soft matter for ECL biosensors with luminol functional groups.

  7. Cross-interaction effects of substituents on N-benzylideneanilines conformation: A DFT investigation

    Science.gov (United States)

    Wu, Feng; Fang, Zhengjun; Yi, Bing; Au, Chaktong; Cao, Chenzhong; Huang, Linjie; Xie, Xin

    2017-08-01

    The conformations of N-benzylideneanilines (X-PhPhCH = NPh-Y) were explored by the B3LYP density functional theory (DFT) hybrid method in combination with the 6-31G* split valence basis set. The crystal structure information of PhPhCH = NPh-OMe was obtained experimentally to assess the accuracy of this DFT approach. It was observed that the twist angle of the benzylidene ring or aniline ring with respect to the rest of the molecule (τ1 or τ2) estimated by the DFT method are highly reliable, and τ2 can be systematically regulated through X and Y substitution. The substituent effects on τ2 obtained from DFT calculations were investigated. The results show that when substituent Y becomes more electron-withdrawing, there is decrease of τ2 (i.e. increase in the distortion of aniline ring with respect to the rest of the molecule). However, substituent X has an opposite effect on τ2. It is demonstrated that substituent cross-interaction has a certain influence on τ2, and a quantitative model is proposed to express such an effect. The findings of the present study illustrate a practical method for expressing the relationship between substituents and molecular conformation of the X-PhPhCH = NPh-Y compounds.

  8. The evolutionary diversity of insect retinal mosaics: common design principles and emerging molecular logic.

    Science.gov (United States)

    Wernet, Mathias F; Perry, Michael W; Desplan, Claude

    2015-06-01

    Independent evolution has resulted in a vast diversity of eyes. Despite the lack of a common Bauplan or ancestral structure, similar developmental strategies are used. For instance, different classes of photoreceptor cells (PRs) are distributed stochastically and/or localized in different regions of the retina. Here, we focus on recent progress made towards understanding the molecular principles behind patterning retinal mosaics of insects, one of the most diverse groups of animals adapted to life on land, in the air, under water, or on the water surface. Morphological, physiological, and behavioral studies from many species provide detailed descriptions of the vast variation in retinal design and function. By integrating this knowledge with recent progress in the characterization of insect Rhodopsins as well as insight from the model organism Drosophila melanogaster, we seek to identify the molecular logic behind the adaptation of retinal mosaics to the habitat and way of life of an animal. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Morphological and molecular diversity of Lake Baikal candonid ostracods, with description of a new genus

    Directory of Open Access Journals (Sweden)

    Ivana Karanovic

    2017-07-01

    Full Text Available Uncoupling between molecular and morphological evolution is common in many animal and plant lineages. This is especially frequent among groups living in ancient deep lakes, because these ecosystems promote rapid morphological diversification, and has already been demonstrated for Tanganyika cychlid fishes and Baikal amphipods. Ostracods are also very diverse in these ecosystems, with 107 candonid species described so far from Baikal, majority of them in the genera Candona Baird, 1845 and Pseudocandona Kaufmann, 1900. Here we study their morphological and molecular diversity based on four genes (two nuclear and two mitochondrial, 10 species from the lake, and 28 other species from around the world. The results of our phylogenetic analysis based on a concatenated data set, along with sequence diversity, support only two genetic lineages in the lake and indicate that a majority of the Baikal Candona and Pseudocandona species should be excluded from these genera. We describe a new genus, Mazepovacandona gen. n., to include five Baikal species, all redescribed here. We also amend the diagnosis for the endemic genus Baicalocandona Mazepova, 1972 and redescribe two species. Our study confirms an exceptional morphological diversity of Lake Baikal candonids and shows that both Baikal lineages are closely related to Candona, but only distantly to Pseudocandona.

  10. Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake

    Science.gov (United States)

    Soldánová, Miroslava; Georgieva, Simona; Roháčováa, Jana; Knudsen, Rune; Kuhn, Jesper A.; Henriksen, Eirik H.; Siwertsson, Anna; Shaw, Jenny C.; Kuris, Armand M.; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D.; Kostadinova, Aneta

    2017-01-01

    To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem, and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages.

  11. Nanostructures and Self-Assembly of Organogels via Benzimidazole/Benzothiazole Imide Derivatives with Different Alkyl Substituent Chains

    Directory of Open Access Journals (Sweden)

    Xihai Shen

    2013-01-01

    Full Text Available New benzimidazole/benzothiazole imide derivatives with different alkyl substituent chains were designed and synthesized. Their gelation behaviors in 22 solvents were tested as novel low-molecular-mass organic gelators. The test showed that the alkyl substituent chains and headgroups of benzimidazole/benzothiazole residues in gelators played a crucial role in the gelation behavior of all compounds in various organic solvents. More alkyl chains in molecular skeletons in present gelators are favorable for the gelation of organic solvents. SEM and AFM observations revealed that the gelator molecules self-assemble into different aggregates from wrinkle, lamella and belt to dot with change of solvents. Spectral studies indicated that there existed different H-bond formation between imide groups and hydrophobic force of alkyl substituent chains in molecular skeletons. The present work may give some insights into design and character of new organogelators and soft materials with special molecular structures.

  12. Detecting shifts in diversity limits from molecular phylogenies: what can we know?

    Science.gov (United States)

    McInnes, Lynsey; Orme, C David L; Purvis, A

    2011-11-01

    Large complete species-level molecular phylogenies can provide the most direct information about the macroevolutionary history of clades having poor fossil records. However, extinction will ultimately erode evidence of pulses of rapid speciation in the deep past. Assessment of how well, and for how long, phylogenies retain the signature of such pulses has hitherto been based on a--probably untenable--model of ongoing diversity-independent diversification. Here, we develop two new tests for changes in diversification 'rules' and evaluate their power to detect sudden increases in equilibrium diversity in clades simulated with diversity-dependent speciation and extinction rates. Pulses of diversification are only detected easily if they occurred recently and if the rate of species turnover at equilibrium is low; rates reported for fossil mammals suggest that the power to detect a doubling of species diversity falls to 50 per cent after less than 50 Myr even with a perfect phylogeny of extant species. Extinction does eventually draw a veil over past dynamics, suggesting that some questions are beyond the limits of inference, but sudden clade-wide pulses of speciation can be detected after many millions of years, even when overall diversity is constrained. Applying our methods to existing phylogenies of mammals and angiosperms identifies intervals of elevated diversification in each.

  13. Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula

    KAUST Repository

    Ziegler, Maren

    2017-01-02

    Aim: Coral reefs rely on the symbiosis between scleractinian corals and intracellular, photosynthetic dinoflagellates of the genus Symbiodinium making the assessment of symbiont diversity critical to our understanding of ecological resilience of these ecosystems. This study characterizes Symbiodinium diversity around the Arabian Peninsula, which contains some of the most thermally diverse and understudied reefs on Earth. Location: Shallow water coral reefs throughout the Red Sea (RS), Sea of Oman (SO), and Persian/Arabian Gulf (PAG). Methods: Next-generation sequencing of the ITS2 marker gene was used to assess Symbiodinium community composition and diversity comprising 892 samples from 46 hard and soft coral genera. Results: Corals were associated with a large diversity of Symbiodinium, which usually consisted of one or two prevalent symbiont types and many types at low abundance. Symbiodinium communities were strongly structured according to geographical region and to a lesser extent by coral host identity. Overall symbiont communities were composed primarily of species from clade A and C in the RS, clade A, C, and D in the SO, and clade C and D in the PAG, representing a gradual shift from C- to D-dominated coral hosts. The analysis of symbiont diversity in an Operational Taxonomic Unit (OTU)-based framework allowed the identification of differences in symbiont taxon richness over geographical regions and host genera. Main conclusions: Our study represents a comprehensive overview over biogeography and molecular diversity of Symbiodinium in the Arabian Seas, where coral reefs thrive in one of the most extreme environmental settings on the planet. As such our data will serve as a baseline for further exploration into the effects of environmental change on host-symbiont pairings and the identification and ecological significance of Symbiodinium types from regions already experiencing \\'Future Ocean\\' conditions.

  14. Molecular Insights into the Genetic Diversity of Garcinia cambogia Germplasm Accessions

    Directory of Open Access Journals (Sweden)

    C Tharachand

    2015-10-01

    Full Text Available ABSTRACTIn this work, the genetic relationship among twelveGarcinia cambogia (Gaertn. Desr. accessions were evaluated using Random Amplified Polymorphic DNA markers. The samples were part of the germplasm collected and maintained at NBPGR Regional station, Thrissur, India. Out of thirty RAPD primers used for screening, seven primers produced a total of 128 polymorphic markers in twelve accessions. The Polymorphic Information Content (PIC ranged from 0.28 (OPA18 to 0.37 (OPA9 and Marker Index (MI ranged between 3.61 (OPA12 and 5.93 (OPA3 among the primers used. Jaccard's coefficient of genetic similarity ranged between 0.07 and 0.64. The dendrogram constructed based on the similarity matrix generated from the molecular and morphological data showed the genetic relationship among the sampled accessions. Mantel matrix test showed a positive correlation (r = 0.49 between the cluster analysis of RAPD data and morphological data. The clustering pattern in the molecular dendrogram and Principle Coordinate Analysis (PCoA showed that the genotypes were diverse, which was in congruence with the similarity index values and morphological dendrogram. High frequency of similarity values in the range of 0.11 to 0.17 suggested the existence of high genetic diversity among the accessions. The high level of genetic diversity among the studied accessions ofG.cambogia was also supported by the large variation in the morphological characters observed in the flowers, leaves, fruits and seeds of these sampled accessions. This is the first report for the molecular based genetic diversity studies for these accessions.

  15. N-Salicylideneamine Derivatives with TEMPO Substituents

    Directory of Open Access Journals (Sweden)

    Shin’ichi Nakatsuji

    2004-08-01

    Full Text Available Three N-salicylideneamine derivatives bearing TEMPO (2,2,6,6-tetra- methyl-1-piperidinyloxy substituents were prepared in order to study their structure and property relationships and to investigate the possibilities of the existence of heat and/or light responsive magnetic properties. Curie-Weiss behavior with weak ferromagnetic intermolecular spin-spin interactions was observed in one of the radicals, while antiferromagnetic interactions were predominant for the other radicals and the structure-property relationships were investigated for the radical compounds from their crystal structures obtained by X-ray analyses. Preliminary results of the examination of their responses towards light and heat are also described.

  16. Mesogenic benzothiazole derivatives with methoxy substituents

    Indian Academy of Sciences (India)

    A K Prajapati; N L Bonde

    2006-03-01

    Two new mesogenic homologous series containing 6-methoxybenzothiazole ring at the terminus of the molecule, viz. 2-(4'--alkoxyphenylazo)-6-methoxybenzothiazoles and 2-[4'-(4"--alkoxybenzoyloxy) phenylazo]-6-methoxybenzothiazoles were synthesized. In series I, -butyloxy to -tetradecyloxy derivatives exhibit nematic mesophase. Smectic A mesophase commences from the -dodecyloxy derivative as a monotropic phase and is retained up to the last member synthesized. All the members of series II exhibit enantiotropic nematic mesophase. The mesomorphic properties of the present series are compared with other structurally related series to evaluate the effect of the benzothiazole ring and the methoxy substituent on mesomorphism.

  17. Maximal use of minimal libraries through the adaptive substituent reordering algorithm.

    Science.gov (United States)

    Liang, Fan; Feng, Xiao-jiang; Lowry, Michael; Rabitz, Herschel

    2005-03-31

    This paper describes an adaptive algorithm for interpolation over a library of molecules subjected to synthesis and property assaying. Starting with a coarse sampling of the library compounds, the algorithm finds the optimal substituent orderings on all of the functionalized scaffold sites to allow for accurate property interpolation over all remaining compounds in the full library space. A previous paper introduced the concept of substituent reordering and a smoothness-based criterion to search for optimal orderings (Shenvi, N.; Geremia, J. M.; Rabitz, H. J. Phys. Chem. A 2003, 107, 2066). Here, we propose a data-driven root-mean-squared (RMS) criteria and a combined RMS/smoothness criteria as alternative methods for the discovery of optimal substituent orderings. Error propagation from the property measurements of the sampled compounds is determined to provide confidence intervals on the interpolated molecular property values, and a substituent rescaling technique is introduced to manage poorly designed/sampled libraries. Finally, various factors are explored that can influence the applicability and interpolation quality of the algorithm. An adaptive methodology is proposed to iteratively and efficiently use laboratory experiments to optimize these algorithmic factors, so that the accuracy of property predictions is maximized. The enhanced algorithm is tested on copolymer and transition metal complex libraries, and the results demonstrate the capability of the algorithm to accurately interpolate various properties of both molecular libraries.

  18. Mutagenic influences of colchicine on phenological and molecular diversity of Calendula officinalis L.

    Science.gov (United States)

    El-Nashar, Y I; Ammar, M H

    2016-04-26

    Six different colchicine concentrations: 0, 400, 800, 1200, 1600, and 2000 ppm, in combination with four soaking time treatments (1, 2, 3, and 4 h), were selected to assess the effects on germination, vegetative growth, and flower yield components in calendula plants. The molecular diversity among the treatments was assessed using ten SRAP marker combinations. Seed soaking in colchicine significantly enhanced both the fresh and the dry shoot and root masses, flowering date, number of flowers per plant, and flower diameter. At 1200-ppm colchicine combined with a 4-h soaking time, a superior effect on seed germination was observed, whereas 800 ppm for 4 h produced the highest number of flowers and the largest flower diameter. The earliest flowering time was found at 800 ppm combined with a short soaking time (1 h), while the 4-h soaking time with 800 ppm, is recommended for growing calendula outdoors, since it enhances flower development. At the molecular level, 752 fragments were successfully amplified using the SRAP primers, with 280 genetic loci found throughout the calendula genome. The polymorphism percentage ranged from 79 to 100% and the polymorphic information content (PIC) values ranged between 0.85 and 0.97. The high number of detected loci and PIC values suggests a great power of SRAP markers in detecting mutant molecular diversity. Our results clearly show the existence of genetic variation among colchicine treated calendula plants and the clustering of the studied mutants was concordant with the colchicine concentration used.

  19. Molecular diversity of corticotropin-releasing hormone mRNA-containing neurons in the hypothalamus.

    Science.gov (United States)

    Romanov, Roman A; Alpár, Alán; Hökfelt, Tomas; Harkany, Tibor

    2017-03-01

    Hormonal responses to acute stress rely on the rapid induction of corticotropin-releasing hormone (CRH) production in the mammalian hypothalamus, with subsequent instructive steps culminating in corticosterone release at the periphery. Hypothalamic CRH neurons in the paraventricular nucleus of the hypothalamus are therefore considered as 'stress neurons'. However, significant morphological and functional diversity among neurons that can transiently produce CRH in other hypothalamic nuclei has been proposed, particularly as histochemical and molecular biology evidence associates CRH to both GABA and glutamate neurotransmission. Here, we review recent advances through single-cell RNA sequencing and circuit mapping to suggest that CRH production reflects a state switch in hypothalamic neurons and thus confers functional competence rather than being an identity mark of phenotypically segregated neurons. We show that CRH mRNA transcripts can therefore be seen in GABAergic, glutamatergic and dopaminergic neuronal contingents in the hypothalamus. We then distinguish 'stress neurons' of the paraventricular nucleus that constitutively express secretagogin, a Ca(2+) sensor critical for the stimulus-driven assembly of the molecular machinery underpinning the fast regulated exocytosis of CRH at the median eminence. Cumulatively, we infer that CRH neurons are functionally and molecularly more diverse than previously thought. © 2017 Society for Endocrinology.

  20. Molecular diversity of Enteromorpha from the coast of Yantai: a dual-marker assessment

    Science.gov (United States)

    Liu, Haiyan; Liu, Zhengyi; Wang, Yinchu; Zhao, Yushan; Qin, Song

    2013-11-01

    We collected nine Enteromorpha specimens from the coast of Yantai and evaluated their diversity based on analyses of their ITS (internal transcribed spacer) and 5S rDNA NTS (non-transcribed spacer) sequences. The ITS sequences showed slight nucleotide divergences between Enteromorpha linza and Enteromorpha prolifera. In contrast, multiple highly variable regions were found in the ITS region of Enteromorpha flexuosa. In general, there were more variable sites in the NTS region than in the ITS region in the three species. The variations in 5S rDNA NTS sequences indicated that the molecular diversity of Enteromorpha from the coast of Yantai is very high. However, a phylogenetic tree constructed using 5S rDNA NTS sequence data indicated that genetic differences were not directly related to geographical distribution.

  1. Prospects of molecular markers in Fusarium species diversity

    DEFF Research Database (Denmark)

    Nayaka, S. Chandra; Wulff, Ednar Gadelha; Udayashankar, A.C.

    2011-01-01

    that negatively affect animal and human health. The identification of Fusarium species still remains one of the most critical issues in fungal taxonomy, given that the number of species recognized in the genus has been constantly changing in the last century due to the different taxonomic systems. This review......Recent developments in genomics have opened up for newer opportunities to study the diversity and classification of fungi. The genus Fusarium contains many plant pathogens that attack diverse agricultural crops. Fusarium spp. are not only pathogenic to plants but are also known as toxin producers......-known molecular techniques such as random amplified polymorphic DNA, amplification fragment length polymorphism, etc. to more modern ones such as DNA microarrays, DNA barcoding, and pyrosequencing and their application form the core of the review. Target regions in the genome which can be potential candidates...

  2. Molecular diversity at the major cluster of disease resistance genes in cultivated and wild Lactuca spp.

    Science.gov (United States)

    Sicard, D; Woo, S S; Arroyo-Garcia, R; Ochoa, O; Nguyen, D; Korol, A; Nevo, E; Michelmore, R

    1999-08-01

    Diversity was analyzed in wild and cultivated Lactuca germplasm using molecular markers derived from resistance genes of the NBS-LRR type. Three molecular markers, one microsatellite marker and two SCAR markers that amplified LRR-encoding regions, were developed from sequences of resistance gene homologs at the main resistance gene cluster in lettuce. Variation for these markers were assessed in germplasm including accessions of cultivated lettuce, Lactuca sativa L. and three wild Lactuca spp., L. serriola L., L. saligna and L. virosa L. Diversity was also studied within and between natural populations of L. serriola from Israel and California; the former is close to the center of diversity for Lactuca spp. while the latter is an area of more recent colonization. Large numbers of haplotypes were detected indicating the presence of numerous resistance genes in wild species. The diversity in haplotypes provided evidence for gene duplication and unequal crossing-over during the evolution of this cluster of resistance genes. However, there was no evidence for duplications and deletions within the LRR-encoding regions studied. The three markers were highly correlated with resistance phenotypes in L. sativa. They were able to discriminate between accessions that had previously been shown to be resistant to all known isolates of Bremia lactucae. Therefore, these markers will be highly informative for the establishment of core collections and marker-aided selection. A hierarchical analysis of the population structure of L. serriola showed that countries, as well as locations, were significantly differentiated. These differences may reflect local founder effects and/or divergent selection.

  3. Protein change in plant evolution: tracing one thread connecting molecular and phenotypic diversity

    Directory of Open Access Journals (Sweden)

    Madelaine eBartlett

    2013-10-01

    Full Text Available Proteins change over the course of evolutionary time. New protein-coding genes and gene families emerge and diversify, ultimately affecting an organism’s phenotype and interactions with its environment. Here we survey the range of structural protein change observed in plants and review the role these changes have had in the evolution of plant form and function. Verified examples tying evolutionary change in protein structure to phenotypic change remain scarce. We will review the existing examples, as well as draw from investigations into domestication, and quantitative trait locus (QTL cloning studies searching for the molecular underpinnings of natural variation. The evolutionary significance of many cloned QTL has not been assessed, but all the examples identified so far have begun to reveal the extent of protein structural diversity tolerated in natural systems. This molecular (and phenotypic diversity could come to represent part of natural selection’s source material in the adaptive evolution of novel traits. Protein structure and function can change in many distinct ways, but the changes we identified in studies of natural diversity and protein evolution were predicted to fall primarily into one of six categories: altered active and binding sites; hypomorphic and hypermorphic alleles; altered protein-protein interactions; altered domain content; altered protein stability; and altered activity as an activator or repressor. Variability was also observed in the evolutionary scale at which particular changes were observed. Some changes were detected at both micro- and macroevolutionary timescales, while others were observed primarily at deep or shallow phylogenetic levels. This variation might be used to determine the trajectory of future investigations in structural molecular evolution.

  4. Protein change in plant evolution: tracing one thread connecting molecular and phenotypic diversity.

    Science.gov (United States)

    Bartlett, Madelaine E; Whipple, Clinton J

    2013-10-10

    Proteins change over the course of evolutionary time. New protein-coding genes and gene families emerge and diversify, ultimately affecting an organism's phenotype and interactions with its environment. Here we survey the range of structural protein change observed in plants and review the role these changes have had in the evolution of plant form and function. Verified examples tying evolutionary change in protein structure to phenotypic change remain scarce. We will review the existing examples, as well as draw from investigations into domestication, and quantitative trait locus (QTL) cloning studies searching for the molecular underpinnings of natural variation. The evolutionary significance of many cloned QTL has not been assessed, but all the examples identified so far have begun to reveal the extent of protein structural diversity tolerated in natural systems. This molecular (and phenotypic) diversity could come to represent part of natural selection's source material in the adaptive evolution of novel traits. Protein structure and function can change in many distinct ways, but the changes we identified in studies of natural diversity and protein evolution were predicted to fall primarily into one of six categories: altered active and binding sites; altered protein-protein interactions; altered domain content; altered activity as an activator or repressor; altered protein stability; and hypomorphic and hypermorphic alleles. There was also variability in the evolutionary scale at which particular changes were observed. Some changes were detected at both micro- and macroevolutionary timescales, while others were observed primarily at deep or shallow phylogenetic levels. This variation might be used to determine the trajectory of future investigations in structural molecular evolution.

  5. Propargyl Vinyl Ethers and Tertiary Skipped Diynes: Two Pluripotent Molecular Platforms for Diversity-Oriented Synthesis.

    Science.gov (United States)

    Tejedor, David; López-Tosco, Sara; Méndez-Abt, Gabriela; Cotos, Leandro; García-Tellado, Fernando

    2016-04-19

    During the last years, we have been involved in the development of a diversity-oriented synthetic strategy aimed at transforming simple, linear, and densely functionalized molecular platforms into collections of topologically diverse scaffolds incorporating biologically relevant structural motifs such as N- and O- heterocycles, multifunctionalized aromatic rings, fused macrocycles, etc. The strategy merges the concepts of pluripotency (the property of an array of chemical functionalities to express different chemical outcomes under different chemical environments) and domino chemistry (chemistry based on processes involving two or more bond-forming transformations that take place while the initial reaction conditions are maintained, with the subsequent reaction resulting as a consequence of the functionality installed in the previous one) to transform common multifunctional substrates into complex and diverse molecular frameworks. This design concept constitutes the ethos of the so-called branching cascade strategy, a branch of diversity-oriented synthesis focused on scaffold diversity generation. Two pluripotent molecular platforms have been extensively studied under this merging (branching) paradigm: C4-O-C3 propargyl vinyl ethers (PVEs) and C7 tertiary skipped diynes (TSDs). These are conveniently constructed from simple and commercially available raw materials (alkyl propiolates, ketones, aldehydes, acid chlorides) through multicomponent manifolds (ABB' three-component reaction for PVEs; A2BB' four-component reaction for TSDs) or a simple two-step procedure (for PVEs). Their modular origin facilitates their structural/functional diversification without increasing the number of synthetic steps for their assembly. These two pluripotent molecular platforms accommodate a well-defined and dense array of through-bond/through-space interrelated functionalities on their structures, which defines their primary reactivity principles and establishes the reactivity profile

  6. Molecular Technique to Reduce PCR Bias for Deeper Understanding of Microbial Diversity

    Science.gov (United States)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

    2012-01-01

    Current planetary protection policies require that spacecraft targeted to sensitive solar system bodies be assembled and readied for launch in controlled cleanroom environments. A better understanding of the distribution and frequency at which high-risk contaminant microbes are encountered on spacecraft surfaces would significantly aid in assessing the threat of forward contamination. However, despite a growing understanding of the diverse microbial populations present in cleanrooms, less abundant microbial populations are probably not adequately taken into account due to technological limitations. This novel approach encompasses a wide spectrum of microbial species and will represent the true picture of spacecraft cleanroom-associated microbial diversity. All of the current microbial diversity assessment techniques are based on an initial PCR amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of a minor template appears to be suppressed by the amplification of a more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck overlooks the presence of the less abundant minority population and may underestimate their role in the ecosystem maintenance. DNA intercalating agents such as propidium monoazide (PMA) covalently bind with DNA molecules upon photolysis using visible light, and make it unavailable for DNA polymerase enzyme during polymerase chain reaction (PCR). Environmental DNA samples will be treated with suboptimum PMA concentration, enough to intercalate with 90 99% of the total DNA. The probability of PMA binding with DNA from abundant bacterial species will be much higher than binding with DNA from less abundant species. This will increase the relative DNA concentration of

  7. Molecular diversity of L-type Ca2+ channel transcripts in human fibroblasts.

    OpenAIRE

    Soldatov, N M

    1992-01-01

    The nucleotide sequence of cDNA encoding the human fibroblast Ca2+ channel of L type (HFCC) has been determined. It is highly homologous to L-type channels previously cloned from rabbit lung and heart as well as from rat brain. At least four sites of molecular diversity were identified in the nucleotide sequence of HFCC. Three of these include regions encoding the transmembrane segments IIS6, IIIS2, and IVS3, which are known to be important for channel gating properties. The positions of thes...

  8. The importance of molecular analyses for understanding the genetic diversity of Histoplasma capsulatum: an overview.

    Science.gov (United States)

    Vite-Garín, Tania; Estrada-Bárcenas, Daniel Alfonso; Cifuentes, Joaquín; Taylor, Maria Lucia

    2014-01-01

    Advances in the classification of the human pathogen Histoplasma capsulatum (H. capsulatum) (ascomycete) are sustained by the results of several genetic analyses that support the high diversity of this dimorphic fungus. The present mini-review highlights the great genetic plasticity of H. capsulatum. Important records with different molecular tools, mainly single- or multi-locus sequence analyses developed with this fungus, are discussed. Recent phylogenetic data with a multi-locus sequence analysis using 5 polymorphic loci support a new clade and/or phylogenetic species of H. capsulatum for the Americas, which was associated with fungal isolates obtained from the migratory bat Tadarida brasiliensis. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  9. Effect of bulky substituents on thiopyrylium polymethine aggregation in the solid state: A theoretical evaluation of the implications for all-optical switching applications

    KAUST Repository

    Gieseking, Rebecca L.

    2014-11-25

    Polymethine dyes in dilute solutions display many of the optical properties required for all-optical switching applications. However, in thin films, aggregation and polymethine-counterion interactions can substantially modify their properties and limit their utility. Here, we examine the impact of a series of bulky substituents on the solid-state molecular packing of thiopyrylium polymethines by using a theoretical approach combining molecular-dynamics simulations and quantum-chemical calculations. Importantly, it is found that the positions of the substituents near the center and/or ends of the dye determine the extent to which aggregation is reduced; in particular, substituents near the polymethine center primarily modify the type of aggregation that is observed, while substituents near the polymethine ends reduce aggregation and aid in maintaining solution-like properties in the solid state. Our theoretical study elucidates relationships between molecular structure and bulk optical properties and provides design guidelines for all-optical switching materials.

  10. Inferring Diversity and Evolution in Fish by Means of Integrative Molecular Cytogenetics.

    Science.gov (United States)

    Artoni, Roberto Ferreira; Castro, Jonathan Pena; Jacobina, Uedson Pereira; Lima-Filho, Paulo Augusto; da Costa, Gideão Wagner Werneck Félix; Molina, Wagner Franco

    2015-01-01

    Fish constitute a paraphyletic and profusely diversified group that has historically puzzled ichthyologists. Hard efforts are necessary to better understand this group, due to its extensive diversity. New species are often identified and it leads to questions about their phylogenetic aspects. Cytogenetics is becoming an important biodiversity-detection tool also used to measure biodiversity evolutionary aspects. Molecular cytogenetics by fluorescence in situ hybridization (FISH) allowed integrating quantitative and qualitative data from DNA sequences and their physical location in chromosomes and genomes. Although there is no intention on presenting a broader review, the current study presents some evidences on the need of integrating molecular cytogenetic data to other evolutionary biology tools to more precisely infer cryptic species detection, population structuring in marine environments, intra- and interspecific karyoevolutionary aspects of freshwater groups, evolutionary dynamics of marine fish chromosomes, and the origin and differentiation of sexual and B chromosomes. The new cytogenetic field, called cytogenomics, is spreading due to its capacity to give resolute answers to countless questions that cannot be answered by traditional methodologies. Indeed, the association between chromosomal markers and DNA sequencing as well as between biological diversity analysis methodologies and phylogenetics triggers the will to search for answers about fish evolutionary, taxonomic, and structural features.

  11. Molecular evidence shows low species diversity of coral-associated hydroids in Acropora corals.

    Directory of Open Access Journals (Sweden)

    Silvia Fontana

    Full Text Available A novel symbiosis between scleractinians and hydroids (Zanclea spp. was recently discovered using taxonomic approaches for hydroid species identification. In this study, we address the question whether this is a species-specific symbiosis or a cosmopolitan association between Zanclea and its coral hosts. Three molecular markers, including mitochondrial 16S and nuclear 28S ribosomal genes, and internal transcribed spacer (ITS, were utilized to examine the existence of Zanclea species from 14 Acropora species and 4 other Acroporidae genera including 142 coral samples collected from reefs in Kenting and the Penghu Islands, Taiwan, Togian Island, Indonesia, and Osprey Reef and Orpheus Island on the Great Barrier Reef, Australia. Molecular phylogenetic analyses of the 16S and 28S genes showed that Acropora-associated Zanclea was monophyletic, but the genus Zanclea was not. Analysis of the ITS, and 16S and 28S genes showed either identical or extremely low genetic diversity (with mean pairwise distances of 0.009 and 0.006 base substitutions per site for the 16S and 28S genes, respectively among Zanclea spp. collected from diverse Acropora hosts in different geographic locations, suggesting that a cosmopolitan and probably genus-specific association occurs between Zanclea hydroids and their coral hosts.

  12. Comparative Estimation of Genetic Diversity in Population Studies using Molecular Sampling and Traditional Sampling Methods.

    Science.gov (United States)

    Saeb, Amr Tm; David, Satish Kumar

    2014-01-01

    Entomopathogenic nematodes (EPN) are efficient biological pest control agents. Population genetics studies on EPN are seldom known. Therefore, it is of interest to evaluate the significance of molecular sampling method (MSM) for accuracy, time needed, and cost effectiveness over traditional sampling method (TSM). The study was conducted at the Mohican Hills golf course at the state of Ohio where the EPN H. bacteriophora has been monitored for 18 years. The nematode population occupies an area of approximately 3700 m(2) with density range from 0.25-2 per gram soil. Genetic diversity of EPN was studied by molecular sampling method (MSM) and traditional sampling method (TSM) using the mitochondrial gene pcox1. The MSM picked 88% in compared to TSM with only 30% of sequenced cox 1 gene. All studied genetic polymorphism measures (sequence and haplotype) showed high levels of genetic diversity of MSM over TSM. MSM minimizes the chance of mitochondrial genes amplification from non target organisms (insect or other contaminating microorganisms). Moreover, it allows the sampling of more individuals with a reliable and credible representative sample size. Thus, we show that MSM supersedes TSM in labour intensity, time consumption and requirement of no special experience and efficiency.

  13. Inferring Diversity and Evolution in Fish by Means of Integrative Molecular Cytogenetics

    Directory of Open Access Journals (Sweden)

    Roberto Ferreira Artoni

    2015-01-01

    Full Text Available Fish constitute a paraphyletic and profusely diversified group that has historically puzzled ichthyologists. Hard efforts are necessary to better understand this group, due to its extensive diversity. New species are often identified and it leads to questions about their phylogenetic aspects. Cytogenetics is becoming an important biodiversity-detection tool also used to measure biodiversity evolutionary aspects. Molecular cytogenetics by fluorescence in situ hybridization (FISH allowed integrating quantitative and qualitative data from DNA sequences and their physical location in chromosomes and genomes. Although there is no intention on presenting a broader review, the current study presents some evidences on the need of integrating molecular cytogenetic data to other evolutionary biology tools to more precisely infer cryptic species detection, population structuring in marine environments, intra- and interspecific karyoevolutionary aspects of freshwater groups, evolutionary dynamics of marine fish chromosomes, and the origin and differentiation of sexual and B chromosomes. The new cytogenetic field, called cytogenomics, is spreading due to its capacity to give resolute answers to countless questions that cannot be answered by traditional methodologies. Indeed, the association between chromosomal markers and DNA sequencing as well as between biological diversity analysis methodologies and phylogenetics triggers the will to search for answers about fish evolutionary, taxonomic, and structural features.

  14. Spatial variations in the molecular diversity of dissolved organic matter in water moving through a boreal forest in eastern Finland

    Science.gov (United States)

    Ide, Jun’ichiro; Ohashi, Mizue; Takahashi, Katsutoshi; Sugiyama, Yuko; Piirainen, Sirpa; Kortelainen, Pirkko; Fujitake, Nobuhide; Yamase, Keitaro; Ohte, Nobuhito; Moritani, Mina; Hara, Miyako; Finér, Leena

    2017-01-01

    Dissolved organic matter (DOM) strongly affects water quality within boreal forest ecosystems. However, how the quality of DOM itself changes spatially is not well understood. In this study, to examine how the diversity of DOM molecules varies in water moving through a boreal forest, the number of DOM molecules in different water samples, i.e., rainwater, throughfall, soil water, groundwater, and stream water was determined using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in Norway spruce and Scots pine stands in eastern Finland during May and June 2010. The number of molecular compounds identified by FT-ICR MS (molecular diversity) ranged from 865 to 2,194, revealing large DOM molecular diversity in the water samples. Additionally, some of the molecular compounds were shared between different water samples. The DOM molecular diversity linearly correlated with the number of low-biodegradable molecules, such as, lignin-like molecules (lignins), but not with dissolved organic carbon concentration. The number of lignins shared between different sampling locations was larger than that of any other biomolecular class. Our results suggest that low-biodegradable molecules, especially lignins, regulate spatial variations in DOM molecular diversity in boreal forests. PMID:28186141

  15. Sequence diversity in three tomato species: SNPs, markers, and molecular evolution.

    Science.gov (United States)

    Jiménez-Gómez, José M; Maloof, Julin N

    2009-07-03

    Tomato species are of significant agricultural and ecological interest, with cultivated tomato being among the most common vegetable crops grown. Wild tomato species are native to diverse habitats in South America and show great morphological and ecological diversity that has proven useful in breeding programs. However, relatively little is known about nucleotide diversity between tomato species. Until recently limited sequence information was available for tomato, preventing genome-wide evolutionary analyses. Now, an extensive collection of tomato expressed sequence tags (ESTs) is available at the SOL Genomics Network (SGN). This database holds sequences from several species, annotated with quality values, assembled into unigenes, and tested for homology against other genomes. Despite the importance of polymorphism detection for breeding and natural variation studies, such analyses in tomato have mostly been restricted to cultivated accessions. Importantly, previous polymorphisms surveys mostly ignored the linked meta-information, limiting functional and evolutionary analyses. The current data in SGN is thus an under-exploited resource. Here we describe a cross-species analysis taking full-advantage of available information. We mined 20,000 interspecific polymorphisms between Solanum lycopersicum and S. habrochaites or S. pennellii and 28,800 intraspecific polymorphisms within S. lycopersicum. Using the available meta-information we classified genes into functional categories and obtained estimations of single nucleotide polymorphisms (SNP) quality, position in the gene, and effect on the encoded proteins, allowing us to perform evolutionary analyses. Finally, we developed a set of more than 10,000 between-species molecular markers optimized by sequence quality and predicted intron position. Experimental validation of 491 of these molecular markers resulted in confirmation of 413 polymorphisms. We present a new analysis of the extensive tomato EST sequences

  16. Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity.

    Science.gov (United States)

    Dols, Joke A M; Molenaar, Douwe; van der Helm, Jannie J; Caspers, Martien P M; de Kat Angelino-Bart, Alie; Schuren, Frank H J; Speksnijder, Adrianus G C L; Westerhoff, Hans V; Richardus, Jan Hendrik; Boon, Mathilde E; Reid, Gregor; de Vries, Henry J C; Kort, Remco

    2016-04-23

    To date, women are most often diagnosed with bacterial vaginosis (BV) using microscopy based Nugent scoring or Amsel criteria. However, the accuracy is less than optimal. The aim of the present study was to confirm the identity of known BV-associated composition profiles and evaluate indicators for BV using three molecular methods. Evaluation of indicators for BV was carried out by 16S rRNA amplicon sequencing of the V5-V7 region, a tailor-made 16S rRNA oligonucleotide-based microarray, and a PCR-based profiling technique termed IS-profiling, which is based on fragment variability of the 16S-23S rRNA intergenic spacer region. An inventory of vaginal bacterial species was obtained from 40 females attending a Dutch sexually transmitted infection outpatient clinic, of which 20 diagnosed with BV (Nugent score 7-10), and 20 BV negative (Nugent score 0-3). Analysis of the bacterial communities by 16S rRNA amplicon sequencing revealed two clusters in the BV negative women, dominated by either Lactobacillus iners or Lactobacillus crispatus and three distinct clusters in the BV positive women. In the former, there was a virtually complete, negative correlation between L. crispatus and L. iners. BV positive subjects showed cluster profiles that were relatively high in bacterial species diversity and dominated by anaerobic species, including Gardnerella vaginalis, and those belonging to the Families of Lachnospiraceae and Leptotrichiaceae. Accordingly, the Gini-Simpson index of species diversity, and the relative abundance Lactobacillus species appeared consistent indicators for BV. Under the conditions used, only the 16S rRNA amplicon sequencing method was suitable to assess species diversity, while all three molecular composition profiling methods were able to indicate Lactobacillus abundance in the vaginal microbiota. An affordable and simple molecular test showing a depletion of the genus Lactobacillus in combination with an increased species diversity of vaginal

  17. Molecular diversity of the foregut bacteria community in the dromedary camel (Camelus dromedarius).

    Science.gov (United States)

    Samsudin, Anjas A; Evans, Paul N; Wright, André-Denis G; Al Jassim, Rafat

    2011-11-01

    The molecular diversity of the foregut bacterial community in the dromedary camel (Camelus dromedarius) in Central Australia was investigated through comparative analyses of 16S rRNA gene sequences prepared from the foregut contents of 12 adult feral camels fed on native vegetation. A total of 267 full-length 16S rRNA gene clones were examined, with 151 operational taxonomic units (OTUs) identified at a 99% species-level identity cut-off criterion. The prediction of actual diversity in the foregut of the dromedary camel using the Chaol approach was 238 OTUs, while the richness and evenness of the diversity estimated using Shannon index was 4.84. The majority of bacteria in the current study were affiliated with the bacterial phylum Firmicutes (67% of total clones) and were related to the classes Clostridia, Bacilli and Mollicutes, followed by the Bacteroidetes (25%) that were mostly represented by the family Prevotellaceae. The remaining phyla were represented by Actinobacteria, Chloroflexi, Cynophyta, Lentisphaerae, Planctomycetes, Proteobacteria and Sphirochaetes. Moreover, 11 clones of cultivated bacteria were identified as Brevundimonas sp., Butyrivibrio fibrisolvens, Prevotella sp. and Ruminococcus flavefaciens. The novelty in this foregut environment is remarkable where 97% of the OTUs were distantly related to any known sequence in the public database.

  18. Molecular diversity of fungal and bacterial communities in the marine sponge Dragmacidon reticulatum.

    Science.gov (United States)

    Passarini, Michel R Z; Miqueletto, Paula B; de Oliveira, Valéria M; Sette, Lara D

    2015-02-01

    The present work aimed to investigate the diversity of bacteria and filamentous fungi of southern Atlantic Ocean marine sponge Dragmacidon reticulatum using cultivation-independent approaches. Fungal ITS rDNA and 18S gene analyses (DGGE and direct sequencing approaches) showed the presence of representatives of three order (Polyporales, Malasseziales, and Agaricales) from the phylum Basidiomycota and seven orders belonging to the phylum Ascomycota (Arthoniales, Capnodiales, Dothideales, Eurotiales, Hypocreales, Pleosporales, and Saccharomycetales). On the other hand, bacterial 16S rDNA gene analyses by direct sequencing approach revealed the presence of representatives of seven bacterial phyla (Cyanobacteria, Proteobacteria, Actinobacteria, Bacteroidetes, Lentisphaerae, Chloroflexi, and Planctomycetes). Results from statistical analyses (rarefaction curves) suggested that the sampled clones covered the fungal diversity in the sponge samples studied, while for the bacterial community additional sampling would be necessary for saturation. This is the first report related to the molecular analyses of fungal and bacterial communities by cultivation-independent approaches in the marine sponges D. reticulatum. Additionally, the present work broadening the knowledge of microbial diversity associated to marine sponges and reports innovative data on the presence of some fungal genera in marine samples. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Molecular fingerprinting of lacustrian cyanobacterial communities: regional patterns in summer diversity.

    Science.gov (United States)

    Touzet, Nicolas; McCarthy, David; Fleming, Gerard T A

    2013-12-01

    The assessment of lacustrian water quality is necessary to comply with environmental regulations. At the regional scale, difficulties reside in the selection of representative lakes. Given the risks towards water quality associated with phytoplankton blooms, a mesoscale survey was carried out in Irish lakes to identify patterns in the distribution and diversity of planktonic cyanobacteria. A stratified sampling strategy was carried out via geographic information systems (GIS) analysis of river catchment attributes due to the range of hydrogeomorphological features and the high number of lakes within the study area. 16S rRNA gene denaturing gradient gel electrophoresis analysis showed variation between the cyanobacterial communities sampled, with lower occurrence of cyanobacteria in August concomitant to increased wind and precipitation regimes. Multivariate analysis delineated three ecoregions based on land cover typology and revealed significant patterns in the distribution of cyanobacterial diversity. A majority of filamentous cyanobacteria genotypes occurred in larger lakes contained river catchments with substantial forest cover. In contrast, higher diversity of spherical cyanobacteria genotypes was observed in lakes of lesser trophic state. In the context of aquatic resource management, the combined use of GIS-based sampling strategy and molecular methods offers promising prospects for assessing microbial community structure at varying scales of space and time.

  20. Pharmacological investigations of N-substituent variation in morphine and oxymorphone: opioid receptor binding, signaling and antinociceptive activity.

    Science.gov (United States)

    Ben Haddou, Tanila; Béni, Szabolcs; Hosztafi, Sándor; Malfacini, Davide; Calo, Girolamo; Schmidhammer, Helmut; Spetea, Mariana

    2014-01-01

    Morphine and structurally related derivatives are highly effective analgesics, and the mainstay in the medical management of moderate to severe pain. Pharmacological actions of opioid analgesics are primarily mediated through agonism at the µ opioid peptide (MOP) receptor, a G protein-coupled receptor. Position 17 in morphine has been one of the most manipulated sites on the scaffold and intensive research has focused on replacements of the 17-methyl group with other substituents. Structural variations at the N-17 of the morphinan skeleton led to a diversity of molecules appraised as valuable and potential therapeutics and important research probes. Discovery of therapeutically useful morphine-like drugs has also targeted the C-6 hydroxyl group, with oxymorphone as one of the clinically relevant opioid analgesics, where a carbonyl instead of a hydroxyl group is present at position 6. Herein, we describe the effect of N-substituent variation in morphine and oxymorphone on in vitro and in vivo biological properties and the emerging structure-activity relationships. We show that the presence of a N-phenethyl group in position 17 is highly favorable in terms of improved affinity and selectivity at the MOP receptor, potent agonism and antinociceptive efficacy. The N-phenethyl derivatives of morphine and oxymorphone were very potent in stimulating G protein coupling and intracellular calcium release through the MOP receptor. In vivo, they were highly effective against acute thermal nociception in mice with marked increased antinociceptive potency compared to the lead molecules. It was also demonstrated that a carbonyl group at position 6 is preferable to a hydroxyl function in these N-phenethyl derivatives, enhancing MOP receptor affinity and agonist potency in vitro and in vivo. These results expand the understanding of the impact of different moieties at the morphinan nitrogen on ligand-receptor interaction, molecular mode of action and signaling, and may be

  1. Pharmacological investigations of N-substituent variation in morphine and oxymorphone: opioid receptor binding, signaling and antinociceptive activity.

    Directory of Open Access Journals (Sweden)

    Tanila Ben Haddou

    Full Text Available Morphine and structurally related derivatives are highly effective analgesics, and the mainstay in the medical management of moderate to severe pain. Pharmacological actions of opioid analgesics are primarily mediated through agonism at the µ opioid peptide (MOP receptor, a G protein-coupled receptor. Position 17 in morphine has been one of the most manipulated sites on the scaffold and intensive research has focused on replacements of the 17-methyl group with other substituents. Structural variations at the N-17 of the morphinan skeleton led to a diversity of molecules appraised as valuable and potential therapeutics and important research probes. Discovery of therapeutically useful morphine-like drugs has also targeted the C-6 hydroxyl group, with oxymorphone as one of the clinically relevant opioid analgesics, where a carbonyl instead of a hydroxyl group is present at position 6. Herein, we describe the effect of N-substituent variation in morphine and oxymorphone on in vitro and in vivo biological properties and the emerging structure-activity relationships. We show that the presence of a N-phenethyl group in position 17 is highly favorable in terms of improved affinity and selectivity at the MOP receptor, potent agonism and antinociceptive efficacy. The N-phenethyl derivatives of morphine and oxymorphone were very potent in stimulating G protein coupling and intracellular calcium release through the MOP receptor. In vivo, they were highly effective against acute thermal nociception in mice with marked increased antinociceptive potency compared to the lead molecules. It was also demonstrated that a carbonyl group at position 6 is preferable to a hydroxyl function in these N-phenethyl derivatives, enhancing MOP receptor affinity and agonist potency in vitro and in vivo. These results expand the understanding of the impact of different moieties at the morphinan nitrogen on ligand-receptor interaction, molecular mode of action and signaling

  2. Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus

    Directory of Open Access Journals (Sweden)

    Timms Peter

    2011-04-01

    Full Text Available Abstract Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58, we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. OmpA and incA were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the tarP and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala C. pecorum. Furthermore, the concatenation of ompA, incA and ORF663 sequences highlighted the monophyletic nature of koala C. pecorum infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts. Conclusions While the continued use of

  3. Molecular characterization and genetic diversity of insecticidal crystal protein genes in native Bacillus thuringiensis isolates.

    Science.gov (United States)

    Mahadeva Swamy, H M; Asokan, R; Mahmood, Riaz; Nagesha, S N

    2013-04-01

    The Western Ghats of Karnataka natural ecosystem are among the most diverse and is one of the eight hottest hotspots of biological diversity in the world, that runs along the western part of India through four states including Karnataka. Bacillus thuringiensis (Bt) strains were isolated from soils of Western Ghats of Karnataka and characterized by molecular and analytical methods as a result of which 28 new Bt-like isolates were identified. Bt strains were isolated from soil samples using sodium acetate selection method. The morphology of crystals was studied using light and phase contrast microscopy. Isolates were further characterized for insecticidal cry gene by PCR, composition of toxins in bacterial crystals by SDS-PAGE cloning, sequencing and evaluation of toxicity was done. As a result 28 new Bt-like isolates were identified. Majority of the isolates showed the presence of a 55 kDa protein bands on SDS-PAGE while the rest showed 130, 73, 34, and 25 kDa bands. PCR analysis revealed predominance of Coleopteran-active cry genes in these isolates. The variations in the nucleotide sequences, crystal morphology, and mass of crystal protein(s) purified from the Bt isolates revealed genetic and molecular diversity. Three strains containing Coleopteran-active cry genes showed higher activity against larvae Myllocerus undecimpustulatus undatus Marshall (Coleoptera: Curculionidae) than B. thuringiensis subsp. Morrisoni. Results indicated that Bt isolates could be utilized for bioinsecticide production, aiming to reduce the use of chemical insecticide which could be useful to use in integrated pest management to control agriculturally important pests for sustainable crop production.

  4. Molecular diversity and evolutionary processes of Alternaria solani in Brazil inferred using genealogical and coalescent approaches.

    Science.gov (United States)

    Lourenço, Valdir; Moya, Andrés; González-Candelas, Fernando; Carbone, Ignazio; Maffia, Luiz A; Mizubuti, Eduardo S G

    2009-06-01

    Alternaria spp. form a heterogeneous group of saprophytic and plant-pathogenic fungi widespread in temperate and tropical regions. However, the relationship between evolutionary processes and genetic diversity with epidemics is unknown for several plant-pathogenic Alternaria spp. The interaction of Alternaria solani populations with potato and tomato plants is an interesting case study for addressing questions related to molecular evolution of an asexual fungus. Gene genealogies based on the coalescent process were used to infer evolutionary processes that shape the A. solani population. Sequences of the rDNA internal transcribed spacer (ITS) region and the genes which encode the allergenic protein alt a 1 (Alt a 1) and glyceraldehyde-3-phosphate dehydrogenase (Gpd) were used to estimate haplotype and nucleotide diversity as well as for the coalescent analyses. The highest number of parsimony informative sites (n = 14), nucleotide diversity (0.007), and the average number of nucleotide differences (3.20) were obtained for Alt a 1. Although the highest number of haplotypes (n = 7) was generated for ITS, haplotype diversity was the lowest (0.148) for this region. Recombination was not detected. Subdivision was inferred from populations associated with hosts but there was no evidence of geographic subdivision, and gene flow is occurring among subpopulations. In the analysis of the Alt a 1, balancing selection and population expansion or purifying selection could have occurred in A. solani subpopulations associated with potato and tomato plants, respectively. There is strong evidence that the subpopulation of A. solani that causes early blight in potato is genetically distinct from the subpopulation that causes early blight in tomato. The population of A. solani is clonal, and gene flow and mutation are the main evolutionary processes shaping its genetic structure.

  5. Molecular analysis of the bacterial diversity in a specialized consortium for diesel oil degradation

    Energy Technology Data Exchange (ETDEWEB)

    Paixao, Douglas Antonio Alvaredo; Accorsini, Fabio Raphael; Vidotti, Maria Benincasa; Lemos, Eliana Gertrudes de Macedo [Universidade Estadual Paulista (FCAV/UNESP), Jaboticabal, SP (Brazil). Fac. de Ciencias Agrarias e Veterinarias], Emails: douglas_unespfcav@yahoo.com.br, vidotti@netsite.com.bregerle@fcav.unesp.br; Dimitrov, Mauricio Rocha [Universidade de Sao Paulo (USP), SP (Brazil)], Email: mau_dimitrov@yahoo.com.br; Pereira, Rodrigo Matheus [EMBRAPARA Soybean - Empresa Brasileira de Pesquisa Agropecuaria (EMBRAPA - Soja), Londrina, PR (Brazil)], Email: poetbr@gmail.com

    2010-05-15

    Diesel oil is a compound derived from petroleum, consisting primarily of hydrocarbons. Poor conditions in transportation and storage of this product can contribute significantly to accidental spills causing serious ecological problems in soil and water and affecting the diversity of the microbial environment. The cloning and sequencing of the 16S rRNA gene is one of the molecular techniques that allows estimation and comparison of the microbial diversity in different environmental samples. The aim of this work was to estimate the diversity of microorganisms from the Bacteria domain in a consortium specialized in diesel oil degradation through partial sequencing of the 16S rRNA gene. After the extraction of DNA metagenomics, the material was amplified by PCR reaction using specific oligonucleotide primers for the 16S rRNA gene. The PCR products were cloned into a pGEM-T-Easy vector (Promega), and Escherichia coli was used as the host cell for recombinant DNAs. The partial clone sequencing was obtained using universal oligonucleotide primers from the vector. The genetic library obtained generated 431 clones. All the sequenced clones presented similarity to phylum Proteobacteria, with Gammaproteobacteria the most present group (49.8 % of the clones), followed by Alphaproteobacteira (44.8 %) and Betaproteobacteria (5.4 %). The Pseudomonas genus was the most abundant in the metagenomics library, followed by the Parvibaculum and the Sphingobium genus, respectively. After partial sequencing of the 16S rRNA, the diversity of the bacterial consortium was estimated using DOTUR software. When comparing these sequences to the database from the National Center for Biotechnology Information (NCBI), a strong correlation was found between the data generated by the software used and the data deposited in NCBI. (author)

  6. Exploring occurrence and molecular diversity of betaine lipids across taxonomy of marine microalgae.

    Science.gov (United States)

    Cañavate, José Pedro; Armada, Isabel; Ríos, José Luis; Hachero-Cruzado, Ismael

    2016-04-01

    Betaine lipids (BL) from ten microalgae species of the kingdoms Plantae and Chromista were identified and quantified by HPLC/ESI-TOF-MS. Diacylgyceryl-N-trimethylhomoserine (DGTS) was detected in Trebouxiophyceae and Eustigmatophyceae species, whereas Tetraselmis suecica was described as the first green algae containing diacylglyceryl-hydroxymethyl-N,N,N-trimethyl-beta-alanine (DGTA). DGTA molecular species where also characterized in Cryptophyceae species as well as in the Bacillariophyceae diatom Phaeodactylum tricornutum. The Mediophyceae diatom Chaetoceros gracilis had no DGTA, but contained diacylglyceryl-carboxyhydroxymethylcholine (DGCC). A principal coordinate (PCO) analysis of microalgae species revealed the existence of three main clusters around each BL type. The first PCO axis (43.9% of total variation) grouped Chlorophyceae, Trebouxiophyceae and Eustigmatophyceae species and positively correlated with DGTS. The second PCO axis (27.8% of total variation) segregated DGTA from DGCC containing species. Cryptophyceae, Bacillariophyceae and Chlorodendrophyceae were the more closely associated species to DGTA. Mediophyceae and Dinophyceae species contained DGCC as the only BL. Molecular diversity varied from the simplest DGCC composition in Gyrodinium dorsum to the highest spectrum of ten different molecular species detected for DGTA (Rhodomonas baltica) and DGCC (C. gracilis). The fatty acid profile of DGTS was very dissimilar to that of the whole lipid cell content. DGTS from Nannochloropsis gaditana was highly unsaturated respecting to total lipids, whereas in Picochlorum atomus DGTS unsaturation was nearly one half to that of total lipids. Dissimilarity between DGTA and total lipid fatty acid profile was minimum among all BL and DGTA fatty acid unsaturation was the maximum observed in the study. New DGCC molecular species enriched in 20:5 were described in Mediophyceae diatoms. Multivariate microalgae ordination using BL as descriptors revealed a higher

  7. Molecular diversity of Mycobacterium tuberculosis strains in a slum area of Rio de Janeiro, Brazil.

    Science.gov (United States)

    Mendes, Joycenea Matsuda; Machado, Silvia Maria Almeida; Lourenço, Maria Cristina; Ferreira, Rosa Maria Carvalho; Fonseca, Leila de Souza; Saad, Maria Helena Feres

    2008-12-01

    This retrospective molecular study involving restriction fragment length polymorphism, using insertion sequence 6110 as a marker, was conducted in order to provide an initial insight into the genetic diversity of Mycobacterium tuberculosis strains isolated in the slums of the Complexo de Manguinhos, located in the city of Rio de Janeiro, Brazil. Of the 67 strains evaluated, 23 (34.3%) were found to belong to clusters (total clusters, 10). Household and social chains of transmission were associated with clustering, in 20% and 60%, respectively. Living in the Conjunto Habitacional Programado 2 slum was associated with clustering. Although not significant, it is relevant that 26% of the clustered strains presented primary resistance. These findings, although possibly underestimating the prevalence due to the failure to analyze all strains, could help improve the local tuberculosis control program.

  8. Allelic diversity and molecular characterization of puroindoline genes in five diploid species of the Aegilops genus.

    Science.gov (United States)

    Cuesta, Susana; Guzmán, Carlos; Alvarez, Juan B

    2013-11-01

    Grain hardness is an important quality trait in wheat. This trait is related to the variation in, and the presence of, puroindolines (PINA and PINB). This variation can be increased by the allelic polymorphism present in the Aegilops species that are related to wheat. This study evaluated allelic Pina and Pinb gene variability in five diploid species of the Aegilops genus, along with the molecular characterization of the main allelic variants found in each species. This polymorphism resulted in 16 alleles for the Pina gene and 24 alleles for the Pinb gene, of which 10 and 17, respectively, were novel. Diverse mutations were detected in the deduced mature proteins of these alleles, which could influence the hardness characteristics of these proteins. This study shows that the diploid species of the Aegilops genus could be a good source of genetic variability for both Pina and Pinb genes, which could be used in breeding programmes to extend the range of different textures in wheat.

  9. GENETIC DIVERSITY IN ACCESSIONS OF Passiflora cincinnata Mast. BASED ON MORPHOAGRONOMIC DESCRIPTORS AND MOLECULAR MARKERS

    Directory of Open Access Journals (Sweden)

    TIAGO VINÍCIUS BATISTA DO CARMO

    2017-01-01

    Full Text Available Passiflora cincinnata Mast. has become more popular in the market because the unusual flavor of its fruits and natural beauty of its flowers, and has great potential for breeding programs of Passiflora edulis f. flavicarpa, because its resistance to diseases and drought. The objective of this work was to evaluate seven wild passion fruit (P. cincinnata accessions, using morphological and agronomic descriptors and molecular markers type ISSR, to identify their morphoagronomic and genetic variabilities and potential for use in breeding programs. A randomized block experimental design was used with five replications and two plants per plot. Thirteen qualitative and twenty-one quantitative, vegetative and floral characteristics were used for morphoagronomic characterization. Twelve ISSR primers were evaluated for molecular characterization. Among the qualitative characteristics, only the color variations were significantly different between the accessions. According to the mean squares of the quantitative characteristics evaluated, obtained from analysis of variance, the means of accessions showed significant differences (p<0.01 for all characteristics. The IAL (internode average length was the morphological descriptor that most contributed to diversity, with 43.12%, followed by DH5 (stem diameter at 5 cm height and SW (sepal width. The average genetic similarity found was 68%. Despite the low genetic variability found among accessions, the primers UBC-887 and UBC-841 stood out with high percentage of polymorphism with 14 and 11 polymorphic fragments, respectively, and higher values of polymorphism information content (PIC, resolving power (RP and marker index (MI, denoting suitability for use in diversity studies of P. cincinnata. Low variability was found among accessions evaluated.

  10. Molecular marker development and genetic diversity exploration by RNA-seq in Platycodon grandiflorum.

    Science.gov (United States)

    Kim, Hyun Jung; Jung, Jungsu; Kim, Myung-Shin; Lee, Je Min; Choi, Doil; Yeam, Inhwa

    2015-10-01

    Platycodon grandiflorum, generally known as the bellflower or balloon flower, is the only species in the genus Platycodon of the family Campanulaceae. Platycodon plants have been traditionally used as a medicinal crop in East Asia for their antiphlogistic, antitussive, and expectorant properties. Despite these practical uses, marker-assisted selection and molecular breeding in platycodons have lagged due to the lack of genetic information on this genus. In this study, we performed RNA-seq analysis of three platycodon accessions to develop molecular markers and explore genetic diversity. First, genic simple sequence repeats (SSRs) were retrieved and compared; dinucleotide motifs were the most abundant repeats (39%-40%) followed by trinucleotide (25%-31%), tetranucleotide (1.5%-1.9%), and pentanucleotide (0.3%-1.0%) repeats. The result of in silico SSR analysis, three SSR markers were detected and showed possibility to distinguish three platycodon accessions. After several filtering procedures, 180 single nucleotide polymorphisms (SNPs) were used to design 40 cleaved amplified polymorphic sequence (CAPS) markers. Twelve of these PCR-based markers were validated as highly polymorphic and utilized to investigate genetic diversity in 21 platycodon accessions collected from various regions of South Korea. Collectively, the 12 markers yielded 35 alleles, with an average of 3 alleles per locus. Polymorphism information content (PIC) values ranged from 0.087 to 0.693, averaging 0.373 per locus. Since platycodon genetics have not been actively studied, the sequence information and the DNA markers generated from our research have the potential to contribute to further genetic improvements, genomic studies, and gene discovery in this genus.

  11. The Hidden Diversity of Zanclea Associated with Scleractinians Revealed by Molecular Data.

    Directory of Open Access Journals (Sweden)

    Simone Montano

    Full Text Available Scleractinian reef corals have recently been acknowledged as the most numerous host group found in association with hydroids belonging to the Zanclea genus. However, knowledge of the molecular phylogenetic relationships among Zanclea species associated with scleractinians is just beginning. This study, using the nuclear 28S rDNA region and the fast-evolving mitochondrial 16S rRNA and COI genes, provides the most comprehensive phylogenetic reconstruction of the genus Zanclea with a particular focus on the genetic diversity among Zanclea specimens associated with 13 scleractinian genera. The monophyly of Zanclea associated with scleractinians was strongly supported in all nuclear and mitochondrial phylogenetic reconstructions. Furthermore, a combined mitochondrial 16S and COI phylogenetic tree revealed a multitude of hidden molecular lineages within this group (Clades I, II, III, V, VI, VII, and VIII, suggesting the existence of both host-generalist and genus-specific lineages of Zanclea associated with scleractinians. In addition to Z. gallii living in association with the genus Acropora, we discovered four well-supported lineages (Clades I, II, III, and VII, each one forming a strict association with a single scleractinian genus, including sequences of Zanclea associated with Montipora from two geographically separated areas (Maldives and Taiwan. Two host-generalist Zanclea lineages were also observed, and one of them was formed by Zanclea specimens symbiotic with seven scleractinian genera (Clade VIII. We also found that the COI gene allows the recognition of separated hidden lineages in agreement with the commonly recommended mitochondrial 16S as a DNA barcoding gene for Hydrozoa and shows reasonable potential for phylogenetic and evolutionary analyses in the genus Zanclea. Finally, as no DNA sequences are available for the majority of the nominal Zanclea species known, we note that they will be necessary to elucidate the diversity of the

  12. The Hidden Diversity of Zanclea Associated with Scleractinians Revealed by Molecular Data.

    Science.gov (United States)

    Montano, Simone; Maggioni, Davide; Arrigoni, Roberto; Seveso, Davide; Puce, Stefania; Galli, Paolo

    2015-01-01

    Scleractinian reef corals have recently been acknowledged as the most numerous host group found in association with hydroids belonging to the Zanclea genus. However, knowledge of the molecular phylogenetic relationships among Zanclea species associated with scleractinians is just beginning. This study, using the nuclear 28S rDNA region and the fast-evolving mitochondrial 16S rRNA and COI genes, provides the most comprehensive phylogenetic reconstruction of the genus Zanclea with a particular focus on the genetic diversity among Zanclea specimens associated with 13 scleractinian genera. The monophyly of Zanclea associated with scleractinians was strongly supported in all nuclear and mitochondrial phylogenetic reconstructions. Furthermore, a combined mitochondrial 16S and COI phylogenetic tree revealed a multitude of hidden molecular lineages within this group (Clades I, II, III, V, VI, VII, and VIII), suggesting the existence of both host-generalist and genus-specific lineages of Zanclea associated with scleractinians. In addition to Z. gallii living in association with the genus Acropora, we discovered four well-supported lineages (Clades I, II, III, and VII), each one forming a strict association with a single scleractinian genus, including sequences of Zanclea associated with Montipora from two geographically separated areas (Maldives and Taiwan). Two host-generalist Zanclea lineages were also observed, and one of them was formed by Zanclea specimens symbiotic with seven scleractinian genera (Clade VIII). We also found that the COI gene allows the recognition of separated hidden lineages in agreement with the commonly recommended mitochondrial 16S as a DNA barcoding gene for Hydrozoa and shows reasonable potential for phylogenetic and evolutionary analyses in the genus Zanclea. Finally, as no DNA sequences are available for the majority of the nominal Zanclea species known, we note that they will be necessary to elucidate the diversity of the Zanclea

  13. The Hidden Diversity of Zanclea Associated with Scleractinians Revealed by Molecular Data

    KAUST Repository

    Montano, Simone

    2015-07-24

    Scleractinian reef corals have recently been acknowledged as the most numerous host group found in association with hydroids belonging to the Zanclea genus. However, knowledge of the molecular phylogenetic relationships among Zanclea species associated with scleractinians is just beginning. This study, using the nuclear 28S rDNA region and the fast-evolving mitochondrial 16S rRNA and COI genes, provides the most comprehensive phylogenetic reconstruction of the genus Zanclea with a particular focus on the genetic diversity among Zanclea specimens associated with 13 scleractinian genera. The monophyly of Zanclea associated with scleractinians was strongly supported in all nuclear and mitochondrial phylogenetic reconstructions. Furthermore, a combined mitochondrial 16S and COI phylogenetic tree revealed a multitude of hidden molecular lineages within this group (Clades I, II, III, V, VI, VII, and VIII), suggesting the existence of both host-generalist and genus-specific lineages of Zanclea associated with scleractinians. In addition to Z. gallii living in association with the genus Acropora, we discovered four well-supported lineages (Clades I, II, III, and VII), each one forming a strict association with a single scleractinian genus, including sequences of Zanclea associated with Montipora from two geographically separated areas (Maldives and Taiwan). Two host-generalist Zanclea lineages were also observed, and one of them was formed by Zanclea specimens symbiotic with seven scleractinian genera (Clade VIII). We also found that the COI gene allows the recognition of separated hidden lineages in agreement with the commonly recommended mitochondrial 16S as a DNA barcoding gene for Hydrozoa and shows reasonable potential for phylogenetic and evolutionary analyses in the genus Zanclea. Finally, as no DNA sequences are available for the majority of the nominal Zanclea species known, we note that they will be necessary to elucidate the diversity of the Zanclea

  14. Molecular diversity of arbuscular mycorrhizal fungi in relation to soil chemical properties and heavy metal contamination

    Energy Technology Data Exchange (ETDEWEB)

    Zarei, Mehdi [Department of Soil Science, College of Agriculture, University of Shiraz, Shiraz (Iran, Islamic Republic of); Hempel, Stefan, E-mail: hempel.stefan@googlemail.co [UFZ Helmholtz Centre for Environmental Research Leipzig-Halle, Department of Soil Ecology, Theodor-Lieser-Strasse 4, 06120 Halle (Germany); Freie Universitaet Berlin, Institut fuer Biologie, Okologie der Pflanzen, Altensteinstrasse 6, 14195 Berlin (Germany); Wubet, Tesfaye; Schaefer, Tina [UFZ Helmholtz Centre for Environmental Research Leipzig-Halle, Department of Soil Ecology, Theodor-Lieser-Strasse 4, 06120 Halle (Germany); Savaghebi, Gholamreza [Department of Soil Science Engineering, University College of Agriculture and Natural Resources, University of Tehran, Karaj (Iran, Islamic Republic of); Jouzani, Gholamreza Salehi; Nekouei, Mojtaba Khayam [Agricultural Biotechnology Research Institute of Iran (ABRII), P.O. Box 31535-1897, Karaj (Iran, Islamic Republic of); Buscot, Francois [UFZ Helmholtz Centre for Environmental Research Leipzig-Halle, Department of Soil Ecology, Theodor-Lieser-Strasse 4, 06120 Halle (Germany)

    2010-08-15

    Abundance and diversity of arbuscular mycorrhizal fungi (AMF) associated with dominant plant species were studied along a transect from highly lead (Pb) and zinc (Zn) polluted to non-polluted soil at the Anguran open pit mine in Iran. Using an established primer set for AMF in the internal transcribed spacer (ITS) region of rDNA, nine different AMF sequence types were distinguished after phylogenetic analyses, showing remarkable differences in their distribution patterns along the transect. With decreasing Pb and Zn concentration, the number of AMF sequence types increased, however one sequence type was only found in the highly contaminated area. Multivariate statistical analysis revealed that further factors than HM soil concentration affect the AMF community at contaminated sites. Specifically, the soils' calcium carbonate equivalent and available P proved to be of importance, which illustrates that field studies on AMF distribution should also consider important environmental factors and their possible interactions. - The molecular diversity of AMF was found to be influenced by a combination of soil heavy metal and other soil chemical parameters.

  15. Molecular diversity of myxomycetes associated with decaying wood and forest floor leaf litter.

    Science.gov (United States)

    Ko, Thida Win Ko; Stephenson, Steven L; Jeewon, Rajesh; Lumyong, Saisamorn; Hyde, Kevin D

    2009-01-01

    Denaturing gradient gel electrophoresis (DGGE) fingerprinting was used to assess the molecular diversity of myxomycetes from environmental samples (decaying wood and forest floor litter) collected at the Mushroom Research Centre in northern Thailand. Total genomic DNA was extracted directly from environmental samples on which myxomycetes were not apparent. Part of the small subunit ribosomal RNA gene (SSU rDNA) was amplified and DNA sequences analyzed. DGGE gels revealed up to 17 operational taxonomic units (OTU) from decaying wood and 10 OTU from forest floor litter samples, but only seven (wood) and six (litter) OTU could be re-amplified and/or sequenced. Based on results obtained with the BLAST analysis program, the species involved appeared to correspond most closely to Diderma saundersii, Didymium iridis, Stemonitis flavogenita and Hyperamoeba sp. strain W2i on decaying wood and to Diderma saundersii and Physarum didermoides on forest floor litter. Our results suggest that then PCR-DGGE can be used to obtain data on the presence of myxomycetes in their primary microhabitats without the need to observe the sporocarps of these organisms. As such the technique would seem to have considerable potential for contributing to a more complete understanding of myxomycete diversity and ecology in terrestrial ecosystems.

  16. The application of rarefaction techniques to molecular inventories of microbial diversity.

    Science.gov (United States)

    Hughes, Jennifer B; Hellmann, Jessica J

    2005-01-01

    With the growing capacity to inventory microbial community diversity, the need for statistical methods to compare community inventories is also growing. Several approaches have been proposed for comparing the diversity of microbial communities: some adapted from traditional ecology and others designed specifically for molecular inventories of microbes. Rarefaction is one statistical method that is commonly applied in microbial studies, and this chapter discusses the procedure and its advantages and disadvantages. Rarefaction compares observed taxon richness at a standardized sampling effort using confidence intervals. Special emphasis is placed here on the need for precise, rather than unbiased, estimation methods in microbial ecology, but precision can be judged only with a very large sample or with multiple samples drawn from a single community. With low sample sizes, rarefaction curves also have the potential to lead to incorrect rankings of relative species richness, but this chapter discusses a new method with the potential to address this problem. Finally, this chapter shows how rarefaction can be applied to the comparison of the taxonomic similarity of microbial communities.

  17. Design of a multi-purpose fragment screening library using molecular complexity and orthogonal diversity metrics.

    Science.gov (United States)

    Lau, Wan F; Withka, Jane M; Hepworth, David; Magee, Thomas V; Du, Yuhua J; Bakken, Gregory A; Miller, Michael D; Hendsch, Zachary S; Thanabal, Venkataraman; Kolodziej, Steve A; Xing, Li; Hu, Qiyue; Narasimhan, Lakshmi S; Love, Robert; Charlton, Maura E; Hughes, Samantha; van Hoorn, Willem P; Mills, James E

    2011-07-01

    Fragment Based Drug Discovery (FBDD) continues to advance as an efficient and alternative screening paradigm for the identification and optimization of novel chemical matter. To enable FBDD across a wide range of pharmaceutical targets, a fragment screening library is required to be chemically diverse and synthetically expandable to enable critical decision making for chemical follow-up and assessing new target druggability. In this manuscript, the Pfizer fragment library design strategy which utilized multiple and orthogonal metrics to incorporate structure, pharmacophore and pharmacological space diversity is described. Appropriate measures of molecular complexity were also employed to maximize the probability of detection of fragment hits using a variety of biophysical and biochemical screening methods. In addition, structural integrity, purity, solubility, fragment and analog availability as well as cost were important considerations in the selection process. Preliminary analysis of primary screening results for 13 targets using NMR Saturation Transfer Difference (STD) indicates the identification of uM-mM hits and the uniqueness of hits at weak binding affinities for these targets.

  18. Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica

    Directory of Open Access Journals (Sweden)

    Marcela Vásquez-Mayorga

    2017-02-01

    Full Text Available We estimated the genetic diversity of 50 Jatropha curcas samples from the Costa Rican germplasm bank using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ tree and a Maximum Likelihood (ML tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346, but considerable compared to worldwide values for J. curcas. The PIC (PIC = 0.274 and inbreeding coefficient (f =  − 0.102 were both low. Clustering was not related to the geographical origin of accessions. International accessions clustered independently of collection sites, suggesting a lack of genetic structure, probably due to the wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24 from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of the Jatropha curcas germplasm bank in Costa Rica.

  19. Planarian (Platyhelminthes, Tricladida Diversity and Molecular Markers: A New View of an Old Group

    Directory of Open Access Journals (Sweden)

    Marta Álvarez-Presas

    2014-04-01

    Full Text Available Planarians are a group of free-living platyhelminths (triclads best-known largely due to long-standing regeneration and pattern formation research. However, the group’s diversity and evolutionary history has been mostly overlooked. A few taxonomists have focused on certain groups, resulting in the description of many species and the establishment of higher-level groups within the Tricladida. However, the scarcity of morphological features precludes inference of phylogenetic relationships among these taxa. The incorporation of molecular markers to study their diversity and phylogenetic relationships has facilitated disentangling many conundrums related to planarians and even allowed their use as phylogeographic model organisms. Here, we present some case examples ranging from delimiting species in an integrative style, and barcoding them, to analysing their evolutionary history on a lower scale to infer processes affecting biodiversity origin, or on a higher scale to understand the genus level or even higher relationships. In many cases, these studies have allowed proposing better classifications and resulted in taxonomical changes. We also explain shortcomings resulting in a lack of resolution or power to apply the most up-to-date data analyses. Next-generation sequencing methodologies may help improve this situation and accelerate their use as model organisms.

  20. Molecular epidemiology and genetic diversity of hepatitis B virus in Ethiopia.

    Science.gov (United States)

    Hundie, Gadissa Bedada; Raj, V Stalin; Michael, Daniel Gebre; Pas, Suzan D; Osterhaus, Albert D M E; Koopmans, Marion P; Smits, Saskia L; Haagmans, Bart L

    2016-06-01

    Although hepatitis B virus (HBV) infection is hyperendemic in Ethiopia and constitutes a major public health problem, little is known about its genetic diversity, genotypes, and circulation. The aim of this study was to determine the molecular epidemiology and genetic diversity of HBV in Ethiopia, using 391 serum samples collected from HBsAg-positive blood donors living in five different geographic regions. The HBV S/pol gene was amplified, sequenced, and HBV genotypes, subgenotypes, serotypes, and major hydrophilic region (MHR) variants were determined. Phylogenetic analysis of 371 samples (95%) revealed the distribution of genotypes A (78%) and D (22%) in Ethiopia. Further phylogenetic analysis identified one subgenotype (A1) within genotype A, and 4 subgenotypes within genotype D (D1; 1.3%, D2; 55%, D4; 2.5%, and D6; 8.8%). Importantly, 24 isolates (30%) of genotype D formed a novel phylogenetic cluster, distinct from any known D subgenotypes, and two A/D recombinants. Analysis of predicted amino-acid sequences within the HBsAg revealed four serotypes: adw2 (79%), ayw1 (3.1%), ayw2 (7.8%), and ayw3 (11.6%). Subsequent examination of sequences showed that 51 HBV isolates (14%) had mutations in the MHR and 8 isolates (2.2%) in the reverse transcriptase known to confer antiviral resistance. This study provides the first description of HBV genetic diversity in Ethiopia with a predominance of subgenotypes A1 and D2, and also identified HBV isolates that could represent a novel subgenotype. Furthermore, a significant prevalence of HBsAg variants in Ethiopian population is revealed.

  1. Self-Assembly and Drug Release Capacities of Organogels via Some Amide Compounds with Aromatic Substituent Headgroups

    Directory of Open Access Journals (Sweden)

    Lexin Zhang

    2016-07-01

    Full Text Available In this work, some amide compounds with different aromatic substituent headgroups were synthesized and their gelation self-assembly behaviors in 22 solvents were characterized as new gelators. The obtained results indicated that the size of aromatic substituent headgroups in molecular skeletons in gelators showed crucial effect in the gel formation and self-assembly behavior of all compounds in the solvents used. Larger aromatic headgroups in molecular structures in the synthesized gelator molecules are helpful to form various gel nanostructures. Morphological investigations showed that the gelator molecules can self-assembly and stack into various organized aggregates with solvent change, such as wrinkle, belt, rod, and lamella-like structures. Spectral characterizations suggested that there existed various weak interactions including π-π stacking, hydrogen bonding, and hydrophobic forces due to aromatic substituent headgroups and alkyl substituent chains in molecular structures. In addition, the drug release capacities experiments demonstrated that the drug release rate in present obtained gels can be tuned by adjusting the concentrations of dye. The present work would open up enormous insight to design and investigate new kind of soft materials with designed molecular structures and tunable drug release performance.

  2. Morphological and sequence-related amplified polymorphism-based molecular diversity of local and exotic wheat genotypes.

    Science.gov (United States)

    Abdelkhalik, S M; Salem, A K M; Abdelaziz, A R; Ammar, M H

    2016-04-28

    Assessing genetic diversity is a prerequisite for the genetic improvement of wheat. Molecular markers offer accurate and reproducible means for assessing genetic diversity. Field performance and sequence-related amplified polymorphism (SRAP)-based assessment of molecular diversity was carried out on a set of 10 local and introduced bread wheat (Triticum sativum L.) genotypes grown in the middle arid region of Saudi Arabia. The results revealed highly significant differences among the studied phenological traits and revealed a significant amount of genetic diversity across the tested genotypes. The overall performance revealed the superiority of KSU 102 in terms of yield and its components, with a yield potential of 8.7 tons/ha. Highly significant and positive correlations were observed among grain yield and biological yield, and also, spike length and spike weight. Thirteen SRAP primer combinations successfully amplified 954 fragments. The total number of genetic loci analyzed was 312. The overall polymorphism ratio was 99.67%, ranging from 98 to 100%. The polymorphic information content values ranged from 0.67 for ME11 x EM5 to 0.97 for ME9 x EM4 and ME11 x EM6, respectively. The wheat genotypes were clustered based on their genetic constitution and origin. The results demonstrate the power of SRAP primers for detecting molecular diversity and for varietal discrimination. The results show that high levels of genetic diversity exist, and suggest the potential of the tested materials for wheat crop improvement in the arid central region of Saudi Arabia.

  3. Hidden Mediterranean diversity: assessing species taxa by molecular phylogeny within the opilionid family Trogulidae (Arachnida, Opiliones).

    Science.gov (United States)

    Schönhofer, Axel L; Martens, Jochen

    2010-01-01

    This is the first comprehensive study to evaluate the relationships between the western palearctic harvestman families Dicranolasmatidae, Trogulidae and Nemastomatidae with focus on the phylogeny and systematics of Trogulidae, using combined sequence data of the nuclear 28S rRNA and the mitochondrial cytochrome b gene. Bayesian analysis and Maximum parsimony do not reliably resolve Dicranolasma as distinct family but place it on a similar phylogenetic level as several lineages of Trogulidae. Nemastomatidae and Trogulidae turned out to be monophyletic, as did genera Anelasmocephalus and Trogulus within the Trogulidae. The genera Calathocratus, Platybessobius and Trogulocratus each appeared para or polyphyletic, respectively and are synonymized with Calathocratus. The monotypic genus Kofiniotis is well supported. We show molecular data to be in general concordance with taxa characterized by morphology. Molecular data are especially useful to calibrate morphological characters for systematic purposes within homogeneous taxa. In the majority of closely related valid species we show the lowest level of genetic distance to be not lower than 5%. By this threshold in terms of traditionally accepted species the estimated number of species turns out to be 1.5-2.4 times higher than previously believed. With respect to European fauna cryptic diversity in Trogulidae is obviously extraordinarily high and hitherto largely underestimated.

  4. The diverse heterogeneity of molecular alterations in prostate cancer identified through next-generation sequencing

    Institute of Scientific and Technical Information of China (English)

    Alexander W Wyatt; Fan Mo; Yuzhuo Wang; Colin C Collins

    2013-01-01

    Prostate cancer is a leading cause of global cancer-related death but attempts to improve diagnoses and develop novel therapies have been confounded by significant patient heterogeneity.In recent years,the application of next-generation sequencing to hundreds of prostate tumours has defined novel molecular subtypes and characterized extensive genomic aberration underlying disease initiation and progression.It is now clear that the heterogeneity observed in the clinic is underpinned by a molecular landscape rife with complexity,where genomic rearrangements and rare mutations combine to amplify transcriptomic diversity.This review dissects our current understanding of prostate cancer ‘omics',including the sentinel role of copy number variation,the growing spectrum of oncogenic fusion genes,the potential influence of chromothripsis,and breakthroughs in defining mutation-associated subtypes.Increasing evidence suggests that genomic lesions frequently converge on specific cellular functions and signalling pathways,yet recurrent gene aberration appears rare.Therefore,it is critical that we continue to define individual tumour genomes,especially in the context of their expressed transcriptome.Only through improved characterisation of tumour to tumour variability can we advance to an age of precision therapy and personalized oncology.

  5. Application of molecular techniques for the assessment of microorganism diversity on cultural heritage objects.

    Science.gov (United States)

    Otlewska, Anna; Adamiak, Justyna; Gutarowska, Beata

    2014-01-01

    As a result of their unpredictable ability to adapt to varying environmental conditions, microorganisms inhabit different types of biological niches on Earth. Owing to the key role of microorganisms in many biogeochemical processes, trends in modern microbiology emphasize the need to know and understand the structure and function of complex microbial communities. This is particularly important if the strategy relates to microbial communities that cause biodeterioration of materials that constitute our cultural heritage. Until recently, the detection and identification of microorganisms inhabiting objects of cultural value was based only on cultivation-dependent methods. In spite of many advantages, these methods provide limited information because they identify only viable organisms capable of growth under standard laboratory conditions. However, in order to carry out proper conservation and renovation, it is necessary to know the complete composition of microbial communities and their activity. This paper presents and characterizes modern techniques such as genetic fingerprinting and clone library construction for the assessment of microbial diversity based on molecular biology. Molecular methods represent a favourable alternative to culture-dependent methods and make it possible to assess the biodiversity of microorganisms inhabiting technical materials and cultural heritage objects.

  6. Assessing diversity among traditional Greek and foreign eggplant cultivars using molecular markers and morphometrical descriptors

    Directory of Open Access Journals (Sweden)

    Antonios A. Augustinos

    2016-12-01

    Full Text Available Eggplant is a widely cultivated vegetable crop of great economic importance. Its long lasting history of domestication, selection and breeding has led to the development of numerous cultivars with variable traits. In the present study, we assessed the diversity levels within and among eleven Greek and foreign cultivars, using 22 morphological descriptors and two different classes of molecular markers (retrotransposon microsatellite amplified polymorphism-REMAP markers and nuclear microsatellites. Our results, in accordance with other studies in the field showed: a the limited levels of genetic polymorphism within the cultivars; b the high morphological and genetic divergence existing among them as indicated by the genetic distance values calculated, which could be attributed to selection, inbreeding and bottleneck effects; and c the lack of concordance among morphological descriptors and molecular markers. Despite these, our analysis showed that the utilization of combinations of markers is an effective method for the characterization of plant material providing also useful diagnostic tools for the identification and authentication of the selected Greek cultivars.

  7. Virulence and Molecular Diversity in Colletotrichum lindemuthianum from South, Central, and North America.

    Science.gov (United States)

    Balardin, R S; Jarosz, A M; Kelly, J D

    1997-12-01

    ABSTRACT Isolates of Colletotrichum lindemuthianum (138 total) from Argentina, Brazil, the Dominican Republic, Honduras, Mexico, and the United States were characterized into 41 races based on virulence to 12 differential cultivars of Phaseolus vulgaris. These 41 races were categorized into two groups: those found over a wide geographic area and those restricted to a single country. Races 7, 65, and 73 were widespread. Race 73 was the most common (28%). Race 7 was found once in Argentina and Mexico but at a higher frequency in the United States. Race 65 was found repeatedly in Brazil and the United States. Although 39% of the races were detected repeatedly and three races were widespread, no race was isolated from both P. vulgaris gene pools. Phenetic analyses showed no obvious patterns correlated with virulence clusters. No geographic pattern was evident. Molecular polymorphism generated by random amplified polymorphic DNA confirmed the extensive variability in virulence of C. lindemuthianum. Virulence phenotypes were grouped into 15 clusters. The two largest clusters contained isolates from all the geographic regions sampled. Molecular polymorphism was observed among isolates from races 65 and 73 within and among countries, except among Bra-zilian isolates of race 65. The genetic diversity of C. lindemuthianum was greatest in Mexico and Honduras. Our data suggest that C. lindemuthianum may not be highly structured to specific Phaseolus gene pools.

  8. Molecular characterization of chemical mutagenesis induced diversity in elite maize germplasm

    Directory of Open Access Journals (Sweden)

    Christov Nikolai K.

    2004-01-01

    Full Text Available Three classical breeding Iowa Super Stiff Stalk (SSS inbred lines B37, B73 and B84, one Lancaster inbred Oh43 and mutant lines obtained by chemical mutagenesis followed by mutation breeding as follows: two of B37 and four of Oh43 were selected for molecular characterization. The mutant inbred lines were chosen because in addition to the improved GCA and SCA for grain yield, proven by their predominance in the Bulgarian breeding programs, they showed shifts in the flowering time as compared to the initial inbreds. Molecular markers (micro satellites and other PCR-based DNA markers were used for characterization of maize genotypes and determination of the induced by chemical mutagenesis genetic variability in maize germplasm. The tested nine SSR markers (umc 1001, umclO14, umcl057, umcll81, umcl0lS, umc 1029. umcl003, umc 1033 and umcl035 can discriminate between the initial classical breeding inbred lines and the originating mutant inbreds. Allelic diversity was also studied by PCR amplification with specifically de-signed primers in the coding regions and flanking sequence of two genes: dwarf8 (d&: chromosome 1, 198.5 cM, and indeterminate l (id1; chromosome 1. 175.0 cM. These are considered candidate genes for variation in plant height and/or flowering time, based on mutant phenotypes and chromosomal locations near major QTLs. Single nucleotide polymorphisms and indels were detected in the region flanking the SH2 domain of dwarf8 gene in some of the mutant inbreds as a result of SSCP and sequencing analyses. However, these polymorphisms could not be associated with the observed variations in flowering time. PCR analysis of the promoter region dwarf8 showed a variant fragment of about 1 kb in the inbred line Oh43 that was not present in any other initial and mutant in-bred lines included in the study. PCR amplification of the 5' end of the Id1 coding sequence revealed polymorphic bands in the mutant lines XM535, XM521, XM250-l, XM98-8 and XM85

  9. Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis.

    Science.gov (United States)

    Ling, Zongxin; Kong, Jianming; Liu, Fang; Zhu, Haibin; Chen, Xiaoyi; Wang, Yuezhu; Li, Lanjuan; Nelson, Karen E; Xia, Yaxian; Xiang, Charlie

    2010-09-07

    markers and could be used as targets for clinical BV diagnosis by molecular approaches. The data presented here have clearly profiled the overall structure of vaginal communities and clearly demonstrated that BV is associated with a dramatic increase in the taxonomic richness and diversity of vaginal microbiota. The study also provides the most comprehensive picture of the vaginal community structure and the bacterial ecosystem, and significantly contributes to the current understanding of the etiology of BV.

  10. Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm.

    Science.gov (United States)

    Abdurakhmonov, I Y; Kohel, R J; Yu, J Z; Pepper, A E; Abdullaev, A A; Kushanov, F N; Salakhutdinov, I B; Buriev, Z T; Saha, S; Scheffler, B E; Jenkins, J N; Abdukarimov, A

    2008-12-01

    The narrow genetic base of cultivated cotton germplasm is hindering the cotton productivity worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely 'underutilized' due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of linkage disequilibrium (LD)-based association mapping is an alternative powerful molecular tool to dissect and exploit the natural genetic diversity conserved within cotton germplasm collections, greatly accelerating still 'lagging' cotton marker-assisted selection (MAS) programs. However, the extent of genome-wide linkage disequilibrium (LD) has not been determined in cotton. We report the extent of genome-wide LD and association mapping of fiber quality traits by using a 95 core set of microsatellite markers in a total of 285 exotic Gossypium hirsutum accessions, comprising of 208 landrace stocks and 77 photoperiodic variety accessions. We demonstrated the existence of useful genetic diversity within exotic cotton germplasm. In this germplasm set, 11-12% of SSR loci pairs revealed a significant LD. At the significance threshold (r(2)>/=0.1), a genome-wide average of LD declines within the genetic distance at 30 cM in variety germplasm. Genome wide LD at r(2)>/=0.2 was reduced on average to approximately 1-2 cM in the landrace stock germplasm and 6-8 cM in variety germplasm, providing evidence of the potential for association mapping of agronomically important traits in cotton. We observed significant population structure and relatedness in assayed germplasm. Consequently, the application of the mixed liner model (MLM), considering both kinship (K) and population structure (Q) detected between 6% and 13% of SSR markers associated with the main fiber quality traits in cotton. Our results highlight for the first time the feasibility and potential of association mapping, with consideration of the population structure and stratification existing in cotton germplasm

  11. Electronic properties of amino acid side chains: quantum mechanics calculation of substituent effects

    Directory of Open Access Journals (Sweden)

    Dwyer Donard S

    2005-08-01

    Full Text Available Abstract Background Electronic properties of amino acid side chains such as inductive and field effects have not been characterized in any detail. Quantum mechanics (QM calculations and fundamental equations that account for substituent effects may provide insight into these important properties. PM3 analysis of electron distribution and polarizability was used to derive quantitative scales that describe steric factors, inductive effects, resonance effects, and field effects of amino acid side chains. Results These studies revealed that: (1 different semiempirical QM methods yield similar results for the electronic effects of side chain groups, (2 polarizability, which reflects molecular deformability, represents steric factors in electronic terms, and (3 inductive effects contribute to the propensity of an amino acid for α-helices. Conclusion The data provide initial characterization of the substituent effects of amino acid side chains and suggest that these properties affect electron density along the peptide backbone.

  12. Aromatic substituents for prohibiting side-chain packing and π-π stacking in tin-cored tetrahedral stilbenoids

    Science.gov (United States)

    Kim, Cheolmin; Yoon, Min-Ju; Hong, Seok Hee; Park, Minjoon; Park, Kwangyong; Kim, Soo Young

    2016-05-01

    Tetrahedral structures comprising Sn-cored materials with five different types of substituents were synthesized. For the substituents, we employed methyl and tert-butyl as aliphatic groups, and naphthyl and phenyl as aromatic groups. The bandgap is in the range of 3.28 - 3.56 eV. The All the compounds with substituents showed bathochromical photoluminescence characteristics and exhibited aggregation-induced emission characteristics. Specifically, the compounds with aromatic substituents prohibited side-chain packing and π-π stacking. The energy levels of the highest occupied and lowest unoccupied molecular orbitals were measured to be 5.5 - 5.75 and 2.0 - 2.37 eV, respectively. The maximum luminance efficiencies and power efficiencies of the Sn-cored compound-based organic light-emitting diodes (OLEDs) were 0.38 - 0.71 cd/A and 0.15 - 0.28 lm/W. Therefore, it is expected that Sn-cored compounds with a tetrahedral structure, especially those containing aromatic substituents, can be used as an active material in blue OLEDs for prohibiting side-chain packing and π-π stacking. [Figure not available: see fulltext.

  13. Genetic diversity and molecular characterization of several Heliconia species in Colombia.

    Science.gov (United States)

    Isaza, L; Marulanda, M L; López, A M

    2012-12-19

    Researchers have classified the Heliconia genus as a group of highly variable and diverse plants. Species and cultivars are visually differentiated primarily on the basis of the color and size of inflorescence bracts. At taxonomic level, flower type (parabolic, sigmoid, or erect) and size are taken into account. The vast morphological diversity of heliconias at intra-specific, intra-population, and varietal levels in central-west Colombia prompted the present study. We characterized the genetic variability of 67 genotypes of cultivated heliconias belonging to Heliconia caribaea Lamarck, H. bihai (L.) L., H. orthotricha L. Andersson, H. stricta Huber, H. wagneriana Petersen, and H. psittacorum L. f., as well as that of several interspecific hybrids such as H. psittacorum L. f. x H. spathocircinata Aristeguieta and H. caribaea Lamarck x H. bihai (L.) L. We also created an approximation to their phylogenetic analysis. Molecular analysis using amplified fragment length polymorphism (AFLP) markers revealed a total of 170 bands. Two large, well-defined groups resulted: the first grouped cultivars of the very closely related H. caribaea and H. bihai species with those of H. orthotricha and H. psittacorum, and the second grouped H. stricta and H. wagneriana cultivars. The lowest percentage of polymorphism was found in H. psittacorum (17.65%) and the highest was in H. stricta (55.88%). Using AFLP, phylogenetic analysis of the species studied revealed the monophyletic origin of the Heliconiaceae family, and identified the Heliconia subgenus as monophyletic while providing evidence of the polyphyletic origin of several representatives of the Stenochlamys subgenus.

  14. Subtracted diversity array identifies novel molecular markers including retrotransposons for fingerprinting Echinacea species.

    Directory of Open Access Journals (Sweden)

    Alexandra Olarte

    Full Text Available Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationship within the species of this genus is unclear, making the authentication of the species used for the medicinal industry more difficult. We report the construction of a novel Subtracted Diversity Array (SDA for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences. In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA fragments were amplified and arrayed. Twenty-seven Echinacea genotypes including four that were not used in the array construction could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic retrotransposon sequences. Five out of the eleven most discriminatory features matched to known retrotransposons. This is the first time retrotransposon sequences have been used to fingerprint Echinacea, highlighting the potential of retrotransposons as based molecular markers useful for fingerprinting and studying diversity patterns in Echinacea.

  15. Subtracted Diversity Array Identifies Novel Molecular Markers Including Retrotransposons for Fingerprinting Echinacea Species

    Science.gov (United States)

    Olarte, Alexandra; Mantri, Nitin; Nugent, Gregory; Pang, Edwin C. K.

    2013-01-01

    Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationship within the species of this genus is unclear, making the authentication of the species used for the medicinal industry more difficult. We report the construction of a novel Subtracted Diversity Array (SDA) for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences. In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH) was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. Twenty-seven Echinacea genotypes including four that were not used in the array construction could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic retrotransposon sequences. Five out of the eleven most discriminatory features matched to known retrotransposons. This is the first time retrotransposon sequences have been used to fingerprint Echinacea, highlighting the potential of retrotransposons as based molecular markers useful for fingerprinting and studying diversity patterns in Echinacea. PMID:23940565

  16. Molecular and morphological diversity of fungi and the associated functions in three European nearby lakes.

    Science.gov (United States)

    Jobard, Marlène; Rasconi, Serena; Solinhac, Laurent; Cauchie, Henry-Michel; Sime-Ngando, Télesphore

    2012-09-01

    This study presents an original rDNA PCR and microscopic survey of pelagic freshwater fungal communities, and was designed to unveil the diversity of true Fungi (i.e. the kingdom Eumycota) in three contrasting lake ecosystems (Lakes Pavin, Aydat and Vassivière) located in the French Massif Central. Three clone libraries were constructed from samples collected in the euphotic layers of the lakes during spring 2007. Phylogenetic analysis of the combined data from the three lakes clustered our sequences into thee divisions: Chytridiomycota (50% of total sequences), Ascomycota (40%) and Basidiomycota (10% in Pavin and Aydat only). Several sequences were assigned to a novel Chytridiomycota clade first recovered in Lake Pavin in 2005. Most of the sequences retrieved in the investigated lakes were affiliated with known fungal species, most of which were apparently well adapted to thrive in the pelagic realm. Their main functions (i.e. parasitism and saprophytism), putatively inferred from the closest relatives of the retrieved molecular sequences, were confirmed by microscopic approaches and by enrichment experiments with pollen grains. The occurrence of three fungal forms (zoosporic, yeast and mycelial) was associated with different trophic modes, establishing fungi as strong potential competitors for various niches in pelagic ecosystems, primarily in relation to the processing of particulate organic matter and the production of propagule food sources for grazers. For the first time, this study provides insight into the diversity and the associated functions of all members of the Kingdom Eumycota investigated in the whole plankton fraction of aquatic ecosystems. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  17. Tuning Conductance in Aromatic Molecules: Constructive and Counteractive Substituent Effects

    DEFF Research Database (Denmark)

    Garner, Marc H.; Solomon, Gemma C.; Strange, Mikkel

    2016-01-01

    Destructive quantum interference in aromatic hydrocarbons can be tuned using chemical substituents; however, classical chemical intuition is not enough to explain the effects on electron transport. Using Huckel theory and density functional theory calculations, in combination with the Landauer....... This insight should be useful when substituents are to be used for tuning destructive quantum interference features in the transmission relative to the Fermi energy of the electrodes....

  18. Substituent Effects on the Stability and Antioxidant Activity of Spirodiazaselenuranes

    Directory of Open Access Journals (Sweden)

    Devappa S. Lamani

    2015-07-01

    Full Text Available Spirodiazaselenuranes are structurally interesting compounds and the stability of these compounds depends highly on the nature of the substituents attached to the nitrogen atoms. Aromatic substituents are known to play important roles in stabilizing the Se-N bonds in spiro compounds. In this study, several spirodiazaselenuranes are synthesized by introducing benzylic and aliphatic substituents to understand their effect on the stability of the Se-N bonds and the antioxidant activity. Replacement of phenyl substituent by benzyl/alkyl groups significantly reduces the stability of the spirodiazaselenuranes and slows down the oxidative cyclization process. The selenium centre in the spiro compounds undergoes further oxidation to produce the corresponding selenurane oxides, which are stable at room temperature. Comparison of the glutathione peroxidase (GPx mimetic activity of the compounds showed that the diaryl selenides having heterocyclic rings are significantly more active due to the facile oxidation of the selenium centre. However, the activity is reduced significantly for compounds having aliphatic substituents. In addition to GPx activity, the compounds also inhibit peroxynitrite-mediated nitration and oxidation reaction of protein and small molecules, respectively. The experimental observations suggest that the antioxidant activity is increased considerably upon substitution of the aromatic group with the benzylic/aliphatic substituents on the nitrogen atoms.

  19. Diversity of Molecular Mechanisms Conferring Carbapenem Resistance to Pseudomonas aeruginosa Isolates from Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Mohamed H. Al-Agamy

    2016-01-01

    Full Text Available Background. This study described various molecular and epidemiological characters determining antibiotic resistance patterns in Pseudomonas aeruginosa isolates. Methods. A total of 34 carbapenem-resistant P. aeruginosa clinical isolates were isolated from samples collected at a tertiary hospital in Riyadh, Saudi Arabia, from January to December 2011. Susceptibility testing, serotyping, molecular characterization of carbapenem resistance, and pulsed-field gel electrophoresis (PFGE were performed. Results. All isolates were resistant to ceftazidime, and more than half were highly resistant (minimum inhibitory concentration (MIC > 256 mg/L. Fifteen isolates had MIC values ≥64 mg/L for any of the carbapenems examined. Vietnamese extended-spectrum β-lactamase (VEB-1 (n=16/34 and oxacillinase (OXA-10 (n=14/34 were the most prevalent extended-spectrum β-lactamase and penicillinase, respectively. Verona imipenemase (VIM-1, VIM-2, VIM-4, VIM-11, and VIM-28 and imipenemase (IMP-7 variants were found in metallo-β-lactamase producers. A decrease in outer membrane porin gene (oprD expression was seen in nine isolates, and an increase in efflux pump gene (MexAB expression was detected in five isolates. Six serotypes (O:1, O:4, O:7, O:10, O:11, and O:15 were found among the 34 isolates. The predominant serotype was O:11 (16 isolates, followed by O:15 (nine isolates. PFGE analysis of the 34 carbapenem-resistant P. aeruginosa isolates revealed 14 different pulsotypes. Conclusions. These results revealed diverse mechanisms conferring carbapenem resistance to P. aeruginosa isolates from Saudi Arabia.

  20. A molecular survey of Campylobacter jejuni and Campylobacter coli virulence and diversity.

    Science.gov (United States)

    Ghorbanalizadgan, Mahdi; Bakhshi, Bita; Kazemnejad Lili, Anoshirvan; Najar-Peerayeh, Shahin; Nikmanesh, Bahram

    2014-07-01

    The aim of this study was to determine the prevalence of virulence-associated genes and enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) analysis of Campylobacter spp. isolated from children with diarrhea in Iran. A total of 200 stool specimens were obtained from children under 5 years during July 2012 to July 2013. Detection of C. jejuni and C. coli was performed by standard biochemical and molecular methods. The presence of virulence-associated genes and genetic diversity of isolates was examined using PCR and ERIC-PCR analyses. A total of 12 (6%) Campylobacter spp. were isolated from patients including 10 (4.5%) C. jejuni and 2 (1.5%) C.coli. The flaA, cadF and ciaB genes were present in 100% of isolates, while no plasmid of virB11 gene was present in their genome. The prevalence of invasion-associated marker was 100% among C. coli and was not detected in C. jejuni isolates. The distribution of both pldA and the genes associated with cytolethal distending toxin (CDT) was 58.3% in C. jejuni isolates. Seven distinct ERIC-PCR profiles were distinguished in three clusters using ERIC-PCR analysis. Genotyping analysis showed a relative correlation with geographic location of patients and virulence gene content of isolates. To our knowledge, this is the first molecular survey of Campylobacter spp. in Iran concerning genotyping and virulence gene content of both C. jejuni and C. coli. ERIC-PCR revealed appropriate discriminatory power for clustering C. jejuni isolates with identical virulence gene content. However, more studies are needed to clearly understand the pathogenesis properties of specific genotypes.

  1. Harnessing Nature's Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins.

    Science.gov (United States)

    Jacob, Reed B; Michaels, Kenan C; Anderson, Cathy J; Fay, James M; Dokholyan, Nikolay V

    2016-11-15

    Organophosphate poisoning can occur from exposure to agricultural pesticides or chemical weapons. This exposure inhibits acetylcholinesterase resulting in increased acetylcholine levels within the synaptic cleft causing loss of muscle control, seizures, and death. Mitigating the effects of organophosphates in our bodies is critical and yet an unsolved challenge. Here, we present a computational strategy that integrates structure mining and modeling approaches, using which we identify novel candidates capable of interacting with a serine hydrolase probe (with equilibrium binding constants ranging from 4 to 120 μM). One candidate Smu. 1393c catalyzes the hydrolysis of the organophosphate omethoate (kcat/Km of (2.0 ± 1.3) × 10(-1) M(-1)s(-1)) and paraoxon (kcat/Km of (4.6 ± 0.8) × 10(3) M(-1)s(-1)), V- and G-agent analogs respectively. In addition, Smu. 1393c protects acetylcholinesterase activity from being inhibited by two organophosphate simulants. We demonstrate that the utilized approach is an efficient and highly-extendable framework for the development of prophylactic therapeutics against organophosphate poisoning and other important targets. Our findings further suggest currently unknown molecular evolutionary rules governing natural diversity of the protein universe, which make it capable of recognizing previously unseen ligands.

  2. GEOGRAPHIC DISTRIBUTION AND MOLECULAR DIVERSITY OF BARTONELLA SPP. INFECTIONS IN MOOSE (ALCES ALCES) IN FINLAND.

    Science.gov (United States)

    Pérez Vera, Cristina; Aaltonen, Kirsi; Spillmann, Thomas; Vapalahti, Olli; Sironen, Tarja

    2016-04-28

    Moose, Alces alces (Artiodactyla: Cervidae) in Finland are heavily infested with deer keds, Lipoptena cervi (Diptera: Hippoboschidae). The deer ked, which carries species of the genus Bartonella, has been proposed as a vector for the transmission of bartonellae to animals and humans. Previously, bartonella DNA was found in deer keds as well as in moose blood collected in Finland. We investigated the prevalence and molecular diversity of Bartonella spp. infection from blood samples collected from free-ranging moose. Given that the deer ked is not present in northernmost Finland, we also investigated whether there were geographic differences in the prevalence of bartonella infection in moose. The overall prevalence of bartonella infection was 72.9% (108/148). Geographically, the prevalence was highest in the south (90.6%) and lowest in the north (55.9%). At least two species of bartonellae were identified by multilocus sequence analysis. Based on logistic regression analysis, there was no significant association between bartonella infection and either age or sex; however, moose from outside the deer ked zone were significantly less likely to be infected (Pmoose hunted within the deer ked zone.

  3. Molecular Diversity of Sapovirus Infection in Outpatients Living in Nanjing, China (2011–2013)

    Science.gov (United States)

    Wang, Xuan

    2016-01-01

    Aim. To gain insight into the molecular diversity of sapovirus in outpatients with acute gastroenteritis in Nanjing, China. Methods. The specimens from outpatients clinically diagnosed as acute gastroenteritis were detected by real-time PCR; RT-PCR was then performed to amplify part of VP1 sequences. The PCR products were cloned into pGEM-T Easy vector and bidirectionally sequenced. All sequences were edited and analyzed. A phylogenetic tree was drawn with the MEGA 5.0 software. Results. Between 2011 and 2013, 16 sapovirus positive cases were confirmed by real-time PCR. The infected cases increased from two in 2011 and six in 2012 to eight in 2013. The majority was children and the elderly (15, 93.75%) and single infections (15, 93.75%). Of the 16 real-time positive specimens, 14 specimens had PCR products and the analysis data of the 14 nucleic sequences showed that there was one GI genogroup with four genotypes, two GI.2 in 2011, three GI.2, and one GI.1 in 2012 and one GI.2, three GI.1, two GI.3, and two GI.5 in 2013. Conclusion. Our data confirmed continuous existing of GI genogroup and GI.2 genotype from 2011 to 2013 in Nanjing and the successive appearance of different genotypes from outpatients with gastroenteritis. PMID:27656204

  4. Molecular Diversity of Sapovirus Infection in Outpatients Living in Nanjing, China (2011–2013

    Directory of Open Access Journals (Sweden)

    Hong-ying Zhang

    2016-01-01

    Full Text Available Aim. To gain insight into the molecular diversity of sapovirus in outpatients with acute gastroenteritis in Nanjing, China. Methods. The specimens from outpatients clinically diagnosed as acute gastroenteritis were detected by real-time PCR; RT-PCR was then performed to amplify part of VP1 sequences. The PCR products were cloned into pGEM-T Easy vector and bidirectionally sequenced. All sequences were edited and analyzed. A phylogenetic tree was drawn with the MEGA 5.0 software. Results. Between 2011 and 2013, 16 sapovirus positive cases were confirmed by real-time PCR. The infected cases increased from two in 2011 and six in 2012 to eight in 2013. The majority was children and the elderly (15, 93.75% and single infections (15, 93.75%. Of the 16 real-time positive specimens, 14 specimens had PCR products and the analysis data of the 14 nucleic sequences showed that there was one GI genogroup with four genotypes, two GI.2 in 2011, three GI.2, and one GI.1 in 2012 and one GI.2, three GI.1, two GI.3, and two GI.5 in 2013. Conclusion. Our data confirmed continuous existing of GI genogroup and GI.2 genotype from 2011 to 2013 in Nanjing and the successive appearance of different genotypes from outpatients with gastroenteritis.

  5. Molecular diversity of brinjal (Solanum melongena L. and S. aethiopicum L. genotypes revealed by SSR markers

    Directory of Open Access Journals (Sweden)

    Abdul Majid Ansari, and Y. V. Singh

    2014-12-01

    Full Text Available In the present study, simple sequence repeat (SSR markers were used to study the genetic diversity among 14 genotypes of brinjal. A total of 14 polymorphic SSR primer pairs were used. Amplification of genomic DNA of 14 genotypes yielded 50 fragments, of which 43 were polymorphic. A clear cut differentiation was exhibited among the genotypes. The range of similarity coefficient varied from 17.8% [between S. aethiopicum L. (2n=2x=24 and Pant Rituraj (S. melongena L., 2n=2x=24] to 94.1% [between PB-71 and NDB-1] followed by 88.9% [between SMB-115 and KS-331] and 88.6% [between BARI and PB-67]. SAHN cluster analysis using UPGMA method separated the genotypes into six cluster groups. Solanum aethiopicum and PB-67 were positioned as single genotype in separate groups i.e., cluster-I & II, SMB-115 and KS-331 in cluster-III, BARI, PB-66 and Pant Rituraj in cluster-IV, WB-1, PB-4, PB-70 and LC-7 in cluster-V and PB-71, Pant Samrat and NDB-1 in cluster-VI. Morphological characters viz., shape, size and peel colour of brinjal fruits and plant type showed a positive relationship with the DNA based molecular analysis through SSR markers.

  6. Assessment of genetic diversity in glandless cotton germplasm resources by using agronomic traits and molecular markers

    Institute of Scientific and Technical Information of China (English)

    Zhikun LI; Xingfen WANG; Yan ZHANG; Guiyin ZHANG; Liqiang WU; Jina CHI; Zhiying MA

    2008-01-01

    Seventy-one glandless cotton germplasm resources were firstly evaluated genetically by using nine agronomic traits,33 simple sequence repeat (SSR) primers and ten amplified fragment length polymorphism (AFLP)primer combinations.Principal component analysis (PCA) of the agronomic traits showed that the first six principal components (PCs) explained a total of 86.352% of the phenotypic variation.A total of 329 alleles were amplified for 33 SSR primers,and 232 polymorphic bands in a total of 389 bands were obtained by using ten AFLP primer combinations.The average polymorphic information content (PIC) value was 0.80 and 0.18 for SSR primers and AFLP primer combinations,respectively.The DIST (average taxonomic distance) and DICE (Nei and Li's pairwise distance) coefficients ranged from 0.373 to 3.164 and 0.786 to 0.948,respectively,for agronomic traits and SSR & AFLP data based on UPGMA analysis.This suggested that there was a higher diversity in the evaluated population for both agronomic traits and molecular markers.The Mantel's test showed that the correlation between the dendrograms based on agronomic traits and SSR & AFLP data was non-significant.

  7. Molecular evaluation of genetic diversity and association studies in rice (Oryza sativa L.)

    Indian Academy of Sciences (India)

    C. Vanniarajan; K. K. Vinod; Andy Pereira

    2011-04-01

    In the present study, we tested rice genotypes that included un(der)exploited landraces of Tamil Nadu along with indica and japonica test cultivars to ascertain their genetic diversity structure. Highly polymorphic microsatellite markers were used for generating marker segregation data. A novel measure, allele discrimination index, was used to determine subpopulation differentiation power of each marker. Phenotypic data were collected for yield and component traits. Pattern of molecular differentiation separated indica and japonica genotypes; indica genotypes had two subpopulations within. Landraces were found to have indica genome, but formed a separate subgroup with low linkage disequilibrium. The landraces further separated into distinct group in both hierarchical clustering analysis using neighbour-joining method as well as in the model based population structure analysis. Japonica and the remaining indica cultivars formed two other distinct groups. Linkage disequilibrium observed in the whole population was considerably reduced in subpopulations. Low linkage disequilibrium of landforms suggests their narrow adaptation in local geographical niche. Many population specific alleles could be identified particularly for japonica cultivars and landraces. Association analysis revealed nine marker–trait associations with three agronomic traits, of which 67% were previously reported. Although the testing landraces together with known cultivars had permitted genomewide association mapping, the experiment offers scope to study more landraces collected from the entire geographical region for drawing more reliable information.

  8. Diversity of Clonostachys species assessed by molecular phylogenetics and MALDI-TOF mass spectrometry.

    Science.gov (United States)

    Abreu, Lucas M; Moreira, Gláucia M; Ferreira, Douglas; Rodrigues-Filho, Edson; Pfenning, Ludwig H

    2014-12-01

    We assessed the species diversity among 45 strains of Clonostachys from different substrates and localities in Brazil using molecular phylogenetics, and compared the results with the phenotypic classification of strains obtained from matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Phylogenetic analyses were based on beta tubulin (Tub), ITS-LSU rDNA, and a combined Tub-ITS DNA dataset. MALDI-TOF MS analyses were performed using intact conidia and conidiophores of strains cultivated on oatmeal agar and 4% malt extract agar. Six known species were identified: Clonostachys byssicola, Clonostachys candelabrum, Clonostachys pseudochroleuca, Clonostachys rhizophaga, Clonostachys rogersoniana, and Clonostachys rosea. Two clades and two singleton lineages did not correspond to known species represented in the reference DNA dataset and were identified as Clonostachys sp. 1-4. Multivariate cluster analyses of MALDI-TOF MS data classified the strains into eight clusters and three singletons, corresponding to the ten identified species plus one additional cluster containing two strains of C. rogersoniana that split from the other co-specific strains. The consistent results of MALDI-TOF MS supported the identification of strains assigned to C. byssicola and C. pseudochroleuca, which did not form well supported clades in all phylogenetic analyses, but formed distinct clusters in the MALDI-TOF dendrograms.

  9. Molecular diversity of bacteria in commercially available “Spirulina” food supplements

    Directory of Open Access Journals (Sweden)

    Elisabeth Vardaka

    2016-01-01

    Full Text Available The cyanobacterium Arthrospira is among the most well-known food supplements worldwide known as “Spirulina.” While it is a widely recognized health-promoting natural product, there are no reports on the molecular diversity of commercially available brands of “Spirulina” supplements and the occurrence of other cyanobacterial and heterotrophic bacterial microorganisms in these products. In this study, 454-pyrosequencing analysis of the total bacterial occurrence in 31 brands of “Spirulina” dietary supplements from the Greek market was applied for the first time. In all samples, operational taxonomic units (OTUs of Arthrospira platensis were the predominant cyanobacteria. Some products contained additional cyanobacterial OTUs including a few known potentially toxic taxa. Moreover, 469 OTUs were detected in all 31 products collectively, with most of them being related to the Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Verrucomicrobia. All samples included heterotrophic bacterial OTUs, ranging from 9–157 per product. Among the most common OTUs were ones closely related to taxa known for causing health issues (i.e., Pseudomonas, Flavobacterium, Vibrio, Aeromonas, Clostridium, Bacillus, Fusobacterium, Enterococcus. The observed high cyanobacterial and heterotrophic bacterial OTUs richness in the final product is a point for further research on the growth and processing of Arthrospira biomass for commercial purposes.

  10. Molecular diversity of native rhizobia trapped by five field pea genotypes in Indian soils.

    Science.gov (United States)

    Wadhwa, K; Dudeja, S S; Yadav, R K

    2011-02-01

    Five pea cultivars; HFP 4, HVP 3-5, HFP 9426, Jayanti and Hariyal, being grown in CCS Haryana Agricultural University farm were used to isolate native rhizobia. Selected 54 rhizobia, from all cultivars, were authenticated as rhizobia by plant infectivity test. Along with nodulation, symbiotic effectiveness in terms of symbiotic ratios showed wide range of effectiveness of pea rhizobia from 1.11 to 5.0. DNA of all the 54 rhizobia was extracted and amplified by PCR, using ERIC and 16S rDNA primers. Dendrogram based on ERIC profiles of these 54 rhizobia showed the formation of 13 subclusters at 80% level of similarity. Dendrogram based on RFLP of 16S rDNA by three restriction endonucleases; Msp I, Csp 6I and Rsa I; also formed 13 subclusters at 80% level of similarity. However, positioning of subclusters was different from that of ERIC based dendrogram. Majority of the isolates i.e. 64.8% by ERIC profiles and 44.4% by RFLP of 16S rDNA formed one cluster. Isolates from same nodule were not 100% similar. Considering each cluster representing a rhizobial genotype, both techniques used to assess molecular diversity indicated the presence of 13 genotypes of field pea rhizobia in CCS Haryana Agricultural University farm soil. Two pea rhizobial genotypes were able to nodulate all the five pea cultivars. Furthermore, high strain richness index (0.43-0.5) of field pea rhizobia was observed by both the techniques.

  11. At Baltic crossroads: a molecular snapshot of Mycobacterium tuberculosis population diversity in Kaliningrad, Russia.

    Science.gov (United States)

    Mokrousov, Igor; Otten, Tatiana; Zozio, Thierry; Turkin, Eugeni; Nazemtseva, Vera; Sheremet, Aleksandra; Vishnevsky, Boris; Narvskaya, Olga; Rastogi, Nalin

    2009-01-01

    The Kaliningrad region is the westernmost part of the Russian Federation; it includes an enclave on the Baltic Sea inside the European Union separated from mainland Russia by Lithuania and Poland. The incidence of tuberculosis in Kaliningrad has shown a steady and dramatic increase from 83/100,000 in 2000 to 134/100,000 in 2006; the rate of multidrug-resistant tuberculosis (MDR-tuberculosis) in the Kaliningrad region was reported to be 30.5% among newly diagnosed tuberculosis patients. This study presents a first molecular snapshot of the population diversity of Mycobacterium tuberculosis in this region. A total of 90 drug-resistant and susceptible M. tuberculosis strains from Kaliningrad were subjected to spoligotyping, 12-locus MIRU typing and mutation analysis of the drug resistance genes rpoB and katG. A comparison with international databases showed that the M. tuberculosis population in this region shares a joint pool of strains with the European part of Russia, and also exhibits a certain affinity with those of its northern European neighbours, such as Poland and Germany. Comparison of the genotyping and drug resistance data emphasized that the high prevalence of the MDR Beijing genotype strains is a major cause of the adverse epidemiological situation of MDR-tuberculosis in the Kaliningrad region.

  12. Molecular systematics and undescribed diversity of Madagascan scolecophidian snakes (Squamata: Serpentes).

    Science.gov (United States)

    Nagy, Zoltán T; Marion, Angela B; Glaw, Frank; Miralles, Aurélien; Nopper, Joachim; Vences, Miguel; Hedges, S Blair

    2015-11-10

    We provide an updated molecular phylogenetic analysis of global diversity of typhlopid and xenotyphlopid blindsnakes, adding a set of Madagascan samples and sequences of an additional mitochondrial gene to an existing supermatrix of nuclear and mitochondrial gene segments. Our data suggest monophyly of Madagascan typhlopids, exclusive of introduced Indotyphlops braminus. The Madagascar-endemic typhlopid clade includes two species previously assigned to the genus Lemuriatyphlops (in the subfamily Asiatyphlopinae), which were not each others closest relatives. This contradicts a previous study that described Lemuriatyphlops based on a sequence of the cytochrome oxidase subunit 1 gene from a single species and found this species not forming a clade with the other Malagasy species included. Based on our novel phylogenetic assessment we include all species in this endemic typhlopid clade in the genus Madatyphlops and in the subfamily Madatyphlopinae and consider Lemuriatyphlops as junior synonym. Within Madatyphlops, we identify several candidate species. For some of these (those in the M. arenarius complex), our preliminary data suggest sympatric occurrence and morphological differentiation, thus the existence of undescribed species. We also comment on the genus-level classification of several non-Madagascan typhlopids. We suggest that African species included in Madatyphlops (Afrotyphlops calabresii, A. cuneirostris, A. platyrhynchus, and Rhinotyphlops leucocephalus) should not be included in this genus. We furthermore argue that recent claims of Sundatyphlops, Antillotyphlops, and Cubatyphlops being "undiagnosable" or "not monophyletic" were based on errors in tree reconstruction and failure to notice diagnostic characters, and thus regard these three genera as valid.

  13. Molecular Diversity of Sea Spray Aerosol Particles: Impact of Ocean Biology on Particle Composition and Hygroscopicity

    Energy Technology Data Exchange (ETDEWEB)

    Cochran, Richard E.; Laskina, Olga; Trueblood, Jonathan; Estillore, Armando D.; Morris, Holly S.; Jayarathne, Thilina; Sultana, Camile M.; Lee, Christopher; Lin, Peng; Laskin, Julia; Laskin, Alexander; Dowling, Jackie; Qin, Zhen; Cappa, Christopher; Bertram, Timothy; Tivanski, Alexei V.; Stone, Elizabeth; Prather, Kimberly; Grassian, Vicki H.

    2017-05-01

    The impact of sea spray aerosol (SSA) on climate depends on the size and chemical composition of individual particles that make-up the total SSA ensemble. While the organic fraction of SSA has been characterized from a bulk perspective, there remains a lack of understanding as to the composition of individual particles within the SSA ensemble. To better understand the molecular components within SSA particles and how SSA composition changes with ocean biology, simultaneous measurements of seawater and SSA were made during a month-long mesocosm experiment performed in an ocean-atmosphere facility. Herein, we deconvolute the composition of freshly emitted SSA devoid of anthropogenic and terrestrial influences by characterizing classes of organic compounds as well as specific molecules within individual SSA particles. Analysis of SSA particles show that the diversity of molecules within the organic fraction varies between two size fractions (submicron and supermicron) with contributions from fatty acids, monosaccharides, polysaccharides and siliceous material. Significant changes in the distribution of these compounds within individual particles are observed to coincide with the rise and fall of phytoplankton and bacterial populations within the seawater. Furthermore, water uptake is impacted as shown by hygroscopicity measurements of model systems composed of representative organic compounds. Thus, the how changes in the hygroscopic growth of SSA evolves with composition can be elucidated. Overall, this study provides an important connection between biological processes that control the composition of seawater and changes in single particle composition which will enhances our ability to predict the impact of SSA on climate.

  14. Genetic diversity and molecular evolution of the major human metapneumovirus surface glycoproteins over a decade.

    Science.gov (United States)

    Papenburg, Jesse; Carbonneau, Julie; Isabel, Sandra; Bergeron, Michel G; Williams, John V; De Serres, Gaston; Hamelin, Marie-Ève; Boivin, Guy

    2013-11-01

    Human metapneumovirus (HMPV) is a recently discovered paramyxovirus that is a major cause of respiratory infections worldwide. We aim to describe the molecular evolution of the HMPV F (fusion) and G (attachment) surface glycoproteins because they are targets for vaccines, monoclonal antibodies and antivirals currently in development. Nasopharyngeal aspirates were collected in children genetic lineages (A1, A2a, A2b, B1 and B2). Multiple lineages circulated each year in Quebec City. With the exception of B1, each of the 5 subgroups was the predominant lineage during ≥1 season. The A1 lineage was not detected since 2002-2003 in our local cohort. There was no evidence of inter- or intragenic recombination. HMPV-F was highly conserved, whereas HMPV-G exhibited greater diversity. HMPV-F demonstrated strong evidence of purifying selection, both overall and in an abundance of negatively selected amino acid sites. In contrast, sites under diversifying selection were detected in all HMPV-G lineages (range, 4-15), all of which were located in the ectodomain. Predominant circulating HMPV lineages vary by year. HMPV-F is highly constrained and undergoes significant purifying selection. Given its high genetic variability, we found a modest number of positively selected sites in HMPV-G. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Diversity and molecular characterization of novel hemoplasmas infecting wild rodents from different Brazilian biomes.

    Science.gov (United States)

    Gonçalves, Luiz Ricardo; Roque, André Luiz Rodrigues; Matos, Carlos Antonio; Fernandes, Simone de Jesus; Olmos, Isabella Delamain Fernandez; Machado, Rosangela Zacarias; André, Marcos Rogério

    2015-12-01

    Although hemoplasma infection in domestic animals has been well documented, little is known about the prevalence and genetic diversity of these bacteria in wild rodents. The present work aimed to investigate the occurrence of hemotrophic mycoplasmas in wild rodents from five Brazilian biomes, assessing the 16S rRNA phylogenetic position of hemoplasma species by molecular approach. Spleen tissues were obtained from 500 rodents, comprising 52 different rodent species trapped between 2000 and 2011. DNA samples were submitted to previously described PCR protocols for amplifying Mycoplasma spp. based on 16S rRNA, followed by sequencing and phylogenetic inferences. Among 457 rodent spleen samples showing absence of inhibitors, 100 (21.9%) were PCR positive to Mycoplasma spp. The occurrence of hemotropic mycoplasmas among all sampled rodents was demonstrated in all five biomes and ranged from 9.3% (7/75) to 26.2% (38/145). The Blastn analysis showed that amplified sequences had a percentage of identity ranging from 86 to 99% with other murine hemoplasmas. The ML phylogenetic analysis of 16S rRNA gene of 24 positive randomly selected samples showed the presence of ten distinct groups, all clustering within the Mycoplasma haemofelis. The phylogenetic assessment suggests the circulation of novel hemoplasma species in rodents from different biomes in Brazil. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Molecular diversity of bacteria in commercially available “Spirulina” food supplements

    Science.gov (United States)

    Kormas, Konstantinos A.; Katsiapi, Matina; Genitsaris, Savvas; Moustaka-Gouni, Maria

    2016-01-01

    The cyanobacterium Arthrospira is among the most well-known food supplements worldwide known as “Spirulina.” While it is a widely recognized health-promoting natural product, there are no reports on the molecular diversity of commercially available brands of “Spirulina” supplements and the occurrence of other cyanobacterial and heterotrophic bacterial microorganisms in these products. In this study, 454-pyrosequencing analysis of the total bacterial occurrence in 31 brands of “Spirulina” dietary supplements from the Greek market was applied for the first time. In all samples, operational taxonomic units (OTUs) of Arthrospira platensis were the predominant cyanobacteria. Some products contained additional cyanobacterial OTUs including a few known potentially toxic taxa. Moreover, 469 OTUs were detected in all 31 products collectively, with most of them being related to the Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Verrucomicrobia. All samples included heterotrophic bacterial OTUs, ranging from 9–157 per product. Among the most common OTUs were ones closely related to taxa known for causing health issues (i.e., Pseudomonas, Flavobacterium, Vibrio, Aeromonas, Clostridium, Bacillus, Fusobacterium, Enterococcus). The observed high cyanobacterial and heterotrophic bacterial OTUs richness in the final product is a point for further research on the growth and processing of Arthrospira biomass for commercial purposes. PMID:26819852

  17. Genetic diversity analysis of Croton antisyphiliticus Mart. using AFLP molecular markers.

    Science.gov (United States)

    Oliveira, T G; Pereira, A M S; Coppede, J S; França, S C; Ming, L C; Bertoni, B W

    2016-02-19

    Croton antisyphiliticus Mart. is a medicinal plant native to Cerrado vegetation in Brazil, and it is popularly used to treat urogenital tract infections. The objective of the present study was to assess the genetic variability of natural C. antisyphiliticus populations using AFLP molecular markers. Accessions were collected in the states of Minas Gerais, São Paulo, and Goiás. The genotyping of individuals was performed using a LI-COR® DNA Analyzer 4300. The variability within populations was found to be greater than the variability between them. The F(ST) value was 0.3830, which indicated that the populations were highly structured. A higher percentage of polymorphic loci (92.16%) and greater genetic diversity were found in the population accessions from Pratinha-MG. Gene flow was considered restricted (N(m) = 1.18), and there was no correlation between genetic and geographic distances. The populations of C. antisyphiliticus exhibited an island-model structure, which demonstrates the vulnerability of the species.

  18. Molecular phylogeny and diversity of Fusarium endophytes isolated from tomato stems.

    Science.gov (United States)

    Imazaki, Iori; Kadota, Ikuo

    2015-09-01

    Plant tissues are a known habitat for two types of Fusarium species: plant pathogens and endophytes. Here, we investigated the molecular phylogeny and diversity of endophytic fusaria, because endophytes are not as well studied as pathogens. A total of 543 Fusarium isolates were obtained from the inside of tomato stems cultivated in soils mainly obtained from agricultural fields. We then determined partial nucleotide sequences of the translation elongation factor-1 alpha (EF-1α) genes of the isolates. Among the isolates from tomato, 24 EF-1α gene sequence types (EFST) were found: nine were classified as being from the Fusarium oxysporum species complex and its sister taxa (FOSC, 332 isolates), seven from the F. fujikuroi species complex (FFSC, 75 isolates) and eight from the F. solani species complex (FSSC, 136 isolates). To determine more characteristic details of the tomato isolates, we isolated 180 fusaria directly from soils and found 95% of them were nested within the FOSC (82 isolates; five EFSTs), FFSC (21 isolates; six FESTs) and FSSC (68 isolates; 11 EFSTs). These results suggested that the dominant Fusarium endophytes within tomato stems were members of the same three species complexes, which were also the dominant fusaria in the soils. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. Genetic diversity analyses of Lasiodiplodia theobromae on Morus alba and Agave sisalana based on RAPD and ISSR molecular markers

    Directory of Open Access Journals (Sweden)

    Hong-hui Xie

    2016-10-01

    Full Text Available Genetic diversity of 23 Lasiodiplodia theobromae isolates on Morus alba and 6 isolates on Agave sisalana in Guangxi province, China, was studied by using random amplified polymorphic DNA and inter-simple sequence repeat molecular markers. Results of two molecular markers showed that the average percentage of polymorphic loci of all isolates was more than 93%. Both dendrograms of two molecular markers showed obvious relationship between groups and the geographical locations where those strains were collected, among which, the 23 isolates on M. alba were divided into 4 populations and the 6 isolates on A. sisalana were separated as a independent population. The average genetic identity and genetic distance of 5 populations were 0.7215, 0.3284 and 0.7915, 0.2347, respectively, which indicated that the genetic identity was high and the genetic distance was short in the 5 populations. Average value of the gene diversity index (H and the Shannon’s information index (I of 29 isolates were significantly higher than 5 populations which showed that genetic diversity of those isolates was richer than the populations and the degree of genetic differentiation of the isolates was higher. The Gst and Nm of 29 isolates were 0.4411, 0.6335 and 0.4756, 0.5513, respectively, which showed that the genetic diversity was rich in those isolates.

  20. Regulation of substituent groups on morphologies and self-assembly of organogels based on some azobenzene imide derivatives

    Science.gov (United States)

    Jiao, Tifeng; Wang, Yujin; Zhang, Qingrui; Zhou, Jingxin; Gao, Faming

    2013-04-01

    In this paper, new azobenzene imide derivatives with different substituent groups were designed and synthesized. Their gelation behaviors in 21 solvents were tested as novel low-molecular-mass organic gelators. It was shown that the alkyl substituent chains and headgroups of azobenzene residues in gelators played a crucial role in the gelation behavior of all compounds in various organic solvents. More alkyl chains in molecular skeletons in present gelators are favorable for the gelation of organic solvents. Scanning electron microscopy and atomic force microscopy observations revealed that the gelator molecules self-assemble into different aggregates, from wrinkle, lamella, and belt to fiber with the change of solvents. Spectral studies indicated that there existed different H-bond formations between amide groups and conformations of methyl chains. The present work may give some insight to the design and character of new organogelators and soft materials with special molecular structures.

  1. Molecular Diversity of Trypanosoma cruzi Detected in the Vector Triatoma protracta from California, USA.

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    Lisa A Shender

    2016-01-01

    Full Text Available Trypanosoma cruzi, causative agent of Chagas disease in humans and dogs, is a vector-borne zoonotic protozoan parasite that can cause fatal cardiac disease. While recognized as the most economically important parasitic infection in Latin America, the incidence of Chagas disease in the United States of America (US may be underreported and even increasing. The extensive genetic diversity of T. cruzi in Latin America is well-documented and likely influences disease progression, severity and treatment efficacy; however, little is known regarding T. cruzi strains endemic to the US. It is therefore important to expand our knowledge on US T. cruzi strains, to improve upon the recognition of and response to locally acquired infections.We conducted a study of T. cruzi molecular diversity in California, augmenting sparse genetic data from southern California and for the first time investigating genetic sequences from northern California. The vector Triatoma protracta was collected from southern (Escondido and Los Angeles and northern (Vallecito California regions. Samples were initially screened via sensitive nuclear repetitive DNA and kinetoplast minicircle DNA PCR assays, yielding an overall prevalence of approximately 28% and 55% for southern and northern California regions, respectively. Positive samples were further processed to identify discrete typing units (DTUs, revealing both TcI and TcIV lineages in southern California, but only TcI in northern California. Phylogenetic analyses (targeting COII-ND1, TR and RB19 genes were performed on a subset of positive samples to compare Californian T. cruzi samples to strains from other US regions and Latin America. Results indicated that within the TcI DTU, California sequences were similar to those from the southeastern US, as well as to several isolates from Latin America responsible for causing Chagas disease in humans.Triatoma protracta populations in California are frequently infected with T. cruzi

  2. Effects of heterocyclic aromatic substituents on binding affinities at two distinct sites of somatostatin receptors. Correlation with the electrostatic potential of the substituents.

    Science.gov (United States)

    Prasad, Vidya; Birzin, Elizabeth T; McVaugh, Cheryl T; Van Rijn, Rachel D; Rohrer, Susan P; Chicchi, Gary; Underwood, Dennis J; Thornton, Edward R; Smith, Amos B; Hirschmann, Ralph

    2003-05-08

    In our continuing program exploring glucose-based peptidomimetics of somatostatin (SRIF-14), we sought to improve the water solubility of our glycosides. This led to insights into the nature of the ligand binding sites at the SRIF receptor. Replacement of the C4 benzyl substituent in glucoside (+)-2 with pyridinylmethyl or pyrazin-2-ylmethyl congeners increased water solubility and enhanced affinity for the human SRIF subtype receptor 4 (sst4). We attribute this effect to hydrogen bond formation. The pyridin-3-ylmethyl substituent at C4, when combined with the imidazol-4-ylmethyl group at C2, generated (-)-19, which has the highest affinity of a glucose-based peptidomimetic at a human SRIF receptor to date (K(i) 53 +/- 23 nM, n = 6 at sst4). The C4 heterocyclic congeners of glucosides bearing a 1-methoxy substituent rather than an indole side chain at the anomeric carbon, such as (+)-16, also provided information about the Trp(8) binding pocket. We correlated the SARs at both the C4 and the Trp(8) binding pockets with calculations of the electrostatic potentials of the diverse C4 aromatic substituents using Spartan 3-21G(*) MO analysis. These calculations provide an approximate analysis of a molecule's ability to interact within a receptor binding site. Our binding studies show that benzene and indole rings, but not pyridinylmethyl nor pyrazin-2-ylmethyl rings, can bind the hydrophobic Trp(8) binding pocket of sst4. The Spartan 3-21G(*) MO analysis reveals significant negative electrostatic potential in the region of the pi-clouds for the benzene and indole rings but not for the pyridinylmethyl or pyrazin-2-ylmethyl congeners. Our data further demonstrate that the replacement of benzene or indole side chains by heterocyclic aromatic rings typified by pyridine and pyrazine not only enhances water solubility and hydrogen bonding capacity as expected, but can also profoundly diminish the ability of the pi-cloud of the aromatic substituent to interact with side chains

  3. The catalytic diversity of zeolites: confinement and solvation effects within voids of molecular dimensions.

    Science.gov (United States)

    Gounder, Rajamani; Iglesia, Enrique

    2013-05-01

    The ability of molecular sieves to control the access and egress of certain reactants and products and to preferentially contain certain transition states while excluding others based on size were captured as shape selectivity concepts early in the history of zeolite catalysis. The marked consequences for reactivity and selectivity, specifically in acid catalysis, have since inspired and sustained many discoveries of novel silicate frameworks and driven the engineering of hierarchical structures and void size to influence catalysis. The catalytic diversity of microporous voids is explored and extended here in the context of their solvating environments, wherein voids act as hosts and stabilize guests, whether reactive intermediates or transition states, by van der Waals forces. We use specific examples from acid catalysis, including activation of C-C and C-H bonds in alkanes, alkylation and hydrogenation of alkenes, carbonylation of dimethyl ether, and elimination and homologation reactions of alkanols and ethers, which involve transition states and adsorbed precursors of varying size and composition. Mechanistic interpretations of measured turnover rates enable us to assign precise chemical origins to kinetic and thermodynamic constants in rate equations and, in turn, to identify specific steps and intermediates that determine the free energy differences responsible for chemical reactivity and selectivity. These free energy differences reflect the stabilization of transition states and their relevant precursors via electrostatic interactions that depend on acid strength and van der Waals interactions that depend on confinement within voids. Their respective contributions to activation free energies are examined by Born-Haber thermochemical cycles by considering plausible transition states and the relevant precursors. These examples show that zeolite voids solvate transition states and precursors differently, and markedly so for guest moieties of different size and

  4. Molecular diversity of Mycobacterium tuberculosis isolates from patients with tuberculosis in Honduras

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    Ghebremichael Solomon

    2010-08-01

    Full Text Available Abstract Background Tuberculosis persists as a public health problem in Honduras. A better knowledge of the molecular characteristics of Mycobacterium tuberculosis strains will contribute to understand the transmission dynamics of the disease within the country. The aim of this study was to provide an insight of the genetic biodiversity of M. tuberculosis clinical isolates collected in Honduras between 1994 and 2002. Genotyping was performed using spoligotyping and RFLP. The spoligotypes obtained were compared with the SITVIT2 proprietary database of the Pasteur Institute of Guadeloupe. Results Spoligotyping grouped 84% of the isolates into 27 clusters (2 to 43 strains per cluster. Of the 44 shared international types (SITs identified among the Honduran stains, 8 SITs were newly identified either within the present study or after match with an orphan type previously identified in the SITVIT2 database. In addition, 16 patterns corresponded to orphan, previously unreported isolates. The Latin American Mediterranean (LAM lineage was the most common in this study; 55% of the strains belonged to this family. Other genotypes found were Haarlem (16%, T (16%, X-clade (6%, Unknown signature (5% and S (1%. Only one Beijing strain was identified (0.5%. We observed a high degree of diversity after characterizing the 43 isolates belonging to the main spoligotyping cluster (SIT 33, LAM3 with IS6110-RFLP. A total of 35 different RFLP-fingerprints were detected, of which 6 patterns corresponded to the same number of clusters comprising 14 strains. Conclusions The findings obtained in this study show that tuberculosis transmission in Honduras is due to modern M. tuberculosis lineages with high level of biodiversity.

  5. Molecular epidemiology and genetic diversity of Blastocystis infection in humans in Italy.

    Science.gov (United States)

    Mattiucci, S; Crisafi, B; Gabrielli, S; Paoletti, M; Cancrini, G

    2016-02-01

    In order to describe the molecular epidemiology of Blastocystis infection in Italy, 189 isolates, which had been collected during the years 2012-2014 from mildly symptomatic patients, or those affected by inflammatory bowel disease (IBD), irritable bowel syndrome (IBS) or chronic diarrhoea, or otherwise immunosuppressed, were subtyped by sequence analysis of the SSU rRNA gene (536 bp). Six subtypes (STs) were detected: ST1 (15·3%), ST2 (13·8%), ST3 (46·0%), ST4 (21·7%), ST6 (3·2%) and ST8 (0·5%). They clustered in distinct clades, as inferred from Bayesian inference phylogenetic and median joining network analyses. A high genetic differentiation was found at the inter-subtype level; it ranged from Jukes-Cantor (JC) distance = 0·02 (between ST1 and ST4) to JC = 0·11 (between ST6 and ST2). At the intra-ST level, a high genetic homogeneity was registered in ST4, whereas higher genetic variation was found in isolates corresponding to ST1 and ST2. Accordingly, high values of haplotype and nucleotide diversity were observed in ST1, ST2 and ST3. No association was found between patient gender and ST, whereas ST3 and ST1 were significantly more prevalent in patients aged 15-50 years. A significant occurrence of Blastocystis ST4 in patients suffering from IBS, IBD or chronic diarrhoea was observed; in addition, a slight significant association between ST1 and ST3 and IBS patients was found. Multiple correspondence analysis showed some significant contribution of different variables (subtypes, haplotypes, age) in the observed pattern of ordination of the 189 patients in the symptom categories.

  6. Molecular structure and diversity of PBAN/Pyrokinin family peptides in ants

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    Man-Yeon eChoi

    2012-02-01

    Full Text Available Neuropeptides are the largest group of insect hormones. They are produced in the central and peripheral nervous systems and affect insect development, reproduction, feeding and behavior. A variety of neuropeptide families have been identified in insects. One of these families is the PBAN/pyrokinin family defined by a common FXPRLamide or similar amino acid fragment at the C-terminal end. These peptides, found in all insects studied thus far, have been conserved throughout evolution. The most well studied physiological function is regulation of moth sex pheromone biosynthesis through the Pheromone Biosynthesis Activating Neurohormone (PBAN, although several developmental functions have also been reported. Over the past years we have extended knowledge of the PBAN/pyrokinin family of peptides to ants, focusing mainly on the fire ant, Solenopsis invicta. The fire ant is one of the most studied social insects and over the last 60 years a great deal has been learned about many aspects of this ant, including the behaviors and chemistry of pheromone communication. However, virtually nothing is known about the regulation of these pheromone systems. Recently, we demonstrated the presence of PBAN/pyrokinin immunoreactive neurons in the fire ant, and identified and characterized PBAN and additional neuropeptides. We have mapped the fire ant PBAN gene structure and determined the tissue expression level in the central nervous system of the ant. We review here our research to date on the molecular structure and diversity of ant PBAN/pyrokinin peptides in preparation for determining the function of the neuropeptides in ants and other social insects.

  7. Molecular epidemiology and genetic diversity of hepatitis B virus in Mar del Plata city, Argentina.

    Science.gov (United States)

    Barbini, Luciana; Elizalde, Mercedes; Torres, Carolina; Campos, Rodolfo

    2013-10-01

    The aim of this work was to describe the current molecular epidemiology and genetic diversity of HBV in Mar del Plata, an important Argentinean touristic city. The phylogenetic analysis of 29 HBV DNA positive serum samples showed that F1b was the predominant subgenotype (sgt, 62.1%), followed by sgt A2 (13.8%) and sgt F4, gt D and gt G (6.9% each). Among anti-HBc IgM positive samples, 75.0% were sgt F1b, followed by sgt F4 (12.5%), sgt A2 (6.25%) and sgt D (6.25%). Three recombinant full length genomes were found: two G/F1b (some of the first gt G detected in Argentina) and one F4/D2. The circulation of clinical important mutations in the city was described. Mutations at the HBsAg were detected in 34.5% of the analyzed samples, associated with laboratory diagnosis and antiviral treatment failures, immune escape and hepatocellular carcinoma. Most of the samples presented wild type BCP/PC sequences. Coalescence analysis for the most prevalent sgt F1b estimated that the diversification mainly occured during mid '90s and the tMRCA was estimated in 1987. Finally, the high presence of the autochthonous sgt F1b, associated with the anti-HBc IgM positive infection and its present-day diversification process, shows the strong impact of internal human migratory movements into the current population of Mar del Plata.

  8. The halo-substituent effect on Pseudomonas cepacia lipase-mediated regioselective acylation of nucleosides: A comparative investigation.

    Science.gov (United States)

    Wang, Zhao-Yu; Bi, Yan-Hong; Yang, Rong-Ling; Duan, Zhang-Qun; Nie, Ling-Hong; Li, Xiang-Qian; Zong, Min-Hua; Wu, Jie

    2015-10-20

    In this work, comparative experiments were explored to investigate the substrate specificity of Pseudomonas cepacia lipase in regioselective acylation of nucleosides carrying various substituents (such as the H, F, Cl, Br, I) at 2'- and 5-positions. Experimental data indicated that the catalytic performance of the enzyme depended very much on the halo-substituents in nucleosides. The increased bulk of 2'-substituents in ribose moiety of the nucleoside might contribute to the improved 3'-regioselectivity (90-98%, nucleosides a-d) in enzymatic decanoylation, while the enhancement of regioselectivity (93-99%) in 3'-O-acylated nucleosides e-h could be attributable to the increasing hydrophobicity of the halogen atoms at 5-positions. With regard to the chain-length selectivity, P. cepacia lipase displayed the highest 3'-regioselectivity toward the longer chain (C14) as compared to shorter (C6 and C10) ones. The position, orientation and property of the substituent, specific structure of the lipase's active site, and acyl structure could account for the diverse results.

  9. Unlocking the black box of feather louse diversity: A molecular phylogeny of the hyper-diverse genus Brueelia.

    Science.gov (United States)

    Bush, Sarah E; Weckstein, Jason D; Gustafsson, Daniel R; Allen, Julie; DiBlasi, Emily; Shreve, Scott M; Boldt, Rachel; Skeen, Heather R; Johnson, Kevin P

    2016-01-01

    Songbirds host one of the largest, and most poorly understood, groups of lice: the Brueelia-complex. The Brueelia-complex contains nearly one-tenth of all known louse species (Phthiraptera), and the genus Brueelia has over 300 species. To date, revisions have been confounded by extreme morphological variation, convergent evolution, and periodic movement of lice between unrelated hosts. Here we use Bayesian inference based on mitochondrial (COI) and nuclear (EF-1α) gene fragments to analyze the phylogenetic relationships among 333 individuals within the Brueelia-complex. We show that the genus Brueelia, as it is currently recognized, is paraphyletic. Many well-supported and morphologically unified clades within our phylogenetic reconstruction of Brueelia were previously described as genera. These genera should be recognized, and the erection of several new genera should be explored. We show that four distinct ecomorphs have evolved repeatedly within the Brueelia-complex, mirroring the evolutionary history of feather-lice across the entire order. We show that lice in the Brueelia-complex, with some notable exceptions, are extremely host specific and that the host family associations and geographic distributions of these lice are significantly correlated with our understanding of their phylogenetic history. Several ecological phenomena, including phoresis, may be responsible for the macroevolutionary patterns in this diverse group.

  10. Molecular Recognition Studies on Modified Cyclodextrins

    Institute of Scientific and Technical Information of China (English)

    LIU,Yu; YOU,Chang-Cheng

    2001-01-01

    This account deacribes our research progress in recent years in the areas of the molecular recognition studies on modified cy clodextrins, including positively charged cyclodextrins, cy clodextrin derivatives with hydrophobic substituent, and dimeric cyclodextrins. Calorimetric titration and various spec trometric techniques were employed to determine the complex stability constants, as well as the thermodynamic parameters, for their inclusion complexation with diverse guest molecules. The results obtained have heen discussed from the viewpoint of size/shape-matching, induced-fit, geometric compensation, and multiple recognition. Thermodynamically, the compen satory relationship between △H and T△S was found to be ex hibited in the inclusion complexation of modified cyclodextrin.

  11. Comparison of genetic diversity structure analyses of SSR molecular marker data within apple (Malus×domestica) genetic resources.

    Science.gov (United States)

    Patzak, Josef; Paprštein, František; Henychová, Alena; Sedlák, Jiří

    2012-09-01

    The aim of this study was to compare traditional hierarchical clustering techniques and principal coordinate analysis (PCoA) with the model-based Bayesian cluster analyses in relation to subpopulation differentiation based on breeding history and geographical origin of apple (Malus×domestica Borkh.) cultivars and landraces. We presented the use of a set of 10 microsatellite (SSR) loci for genetic diversity structure analyses of 273 apple accessions from national genetic resources. These SSR loci yielded a total of 113 polymorphic SSR alleles, with 5-18 alleles per locus. SSR molecular data were successfully used in binary and allelic input format for all genetic diversity analyses, but allelic molecular data did not reveal reliable results with the NTSYS-pc and BAPS softwares. A traditional cluster analysis still provided an easy and effective way for determining genetic diversity structure in the apple germplasm collection. A model-based Bayesian analysis also provided the clustering results in accordance to traditional cluster analysis, but the analyses were distorted by the presence of a dominant group of apple genetic resources owing to the narrow origin of the apple genome. PCoA confirmed that there were no noticeable differences in genetic diversity structure of apple genetic resources during the breeding history. The results of our analyses are useful in the context of enhancing apple collection management, sampling of core collections, and improving breeding processes.

  12. Seasonality in molecular and cytometric diversity of marine bacterioplankton: the reshuffling of bacterial taxa by vertical mixing

    KAUST Repository

    García, Francisca C.

    2015-07-17

    The ’cytometric diversity’ of phytoplankton communities has been studied based on single-cell properties, but the applicability of this method to characterize bacterioplankton has been unexplored. Here, we analysed seasonal changes in cytometric diversity of marine bacterioplankton along a decadal time-series at three coastal stations in the Southern Bay of Biscay. Shannon-Weaver diversity estimates and Bray-Curtis similarities obtained by cytometric and molecular (16S rRNA tag sequencing) methods were significantly correlated in samples from a 3.5-year monthly time-series. Both methods showed a consistent cyclical pattern in the diversity of surface bacterial communities with maximal values in winter. The analysis of the highly resolved flow cytometry time-series across the vertical profile showed that water column mixing was a key factor explaining the seasonal changes in bacterial composition and the winter increase in bacterial diversity in coastal surface waters. Due to its low cost and short processing time as compared to genetic methods, the cytometric diversity approach represents a useful complementary tool in the macroecology of aquatic microbes.

  13. Molecular diversity and relationships among Cymbidium goeringii cultivars based on inter-simple sequence repeat (ISSR) markers.

    Science.gov (United States)

    Wang, Hui-Zhong; Wu, Zhen-Xing; Lu, Jiang-Jie; Shi, Nong-Nong; Zhao, Yan; Zhang, Zhi-Tao; Liu, Jun-Jun

    2009-07-01

    Spring orchid (Cymbidium goeringii) is a popular flowering plant species. There have been few molecular studies of the genetic diversity and conservation genetics on this species. An assessment of the level of genetic diversity in cultivated spring orchid would facilitate development of the future germplasm conservation for cultivar improvement. In the present study, DNA markers of intersimple sequence repeats (ISSR) were identified and the ISSR fingerprinting technique was used to evaluate genetic diversity in C. goeringii cultivars. Twenty-five ISSR primers were selected to produce a total of 224 ISSR loci for evaluation of the genetic diversity. A wide genetic variation was found in the 50 tested cultivars with Nei's gene diversity (H = 0.2241) and 93.75% of polymorphic loci. Fifty cultivars were unequivocally distinguished based on ISSR fingerprinting. Cultivar-specific ISSR markers were identified in seven of 50 tested cultivars. Unweighted pair-group mean analysis (UPGMA) and principal coordinates analysis (PCA) grouped them into two clusters: one composed the cultivars mainly from Japan, and the other contained three major subclusters mainly from China. Two Chinese subclusters were generally consistent with horticultural classification, and the third Chinese subcluster contained cultivars from various horticultural groups. Our results suggest that the ISSR technique provides a powerful tool for cultivar identification and establishment of genetic relationships of cultivars in C. goeringii.

  14. Contrasting results from molecular and pedigree-based population diversity measures in captive zebra highlight challenges facing genetic management of zoo populations.

    Science.gov (United States)

    Ito, Hideyuki; Ogden, Rob; Langenhorst, Tanya; Inoue-Murayama, Miho

    2017-01-01

    Zoo conservation breeding programs manage the retention of population genetic diversity through analysis of pedigree records. The range of demographic and genetic indices determined through pedigree analysis programs allows the conservation of diversity to be monitored relative to the particular founder population for a species. Such approaches are based on a number of well-documented founder assumptions, however without knowledge of actual molecular genetic diversity there is a risk that pedigree-based measures will be misinterpreted and population genetic diversity misunderstood. We examined the genetic diversity of the captive populations of Grevy's zebra, Hartmann's mountain zebra and plains zebra in Japan and the United Kingdom through analysis of mitochondrial DNA sequences. Very low nucleotide variability was observed in Grevy's zebra. The results were evaluated with respect to current and historic diversity in the wild, and indicate that low genetic diversity in the captive population is likely a result of low founder diversity, which in turn suggests relatively low wild genetic diversity prior to recent population declines. Comparison of molecular genetic diversity measures with analogous diversity indices generated from the studbook data for Grevy's zebra and Hartmann's mountain zebra show contrasting patterns, with Grevy's zebra displaying markedly less molecular diversity than mountain zebra, despite studbook analysis indicating that the Grevy's zebra population has substantially more founders, greater effective population size, lower mean kinship, and has suffered less loss of gene diversity. These findings emphasize the need to validate theoretical estimates of genetic diversity in captive breeding programs with empirical molecular genetic data. Zoo Biol. 36:87-94, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  15. Expanding Diversity in Molecular Structures and Functions of the IL-6/IL-12 Heterodimeric Cytokine Family

    Directory of Open Access Journals (Sweden)

    Hideaki Hasegawa

    2016-11-01

    , promiscuity within the IL-6/IL-12 family cytokines complicates structural and functional clarification and assignment of individual cytokines. A better understanding of the recent advances and expanding diversity in molecular structures and functions of the IL-6/IL-12 family cytokines could allow the creation of novel therapeutic strategies by using them as tools and targeted molecules.

  16. Genetic Diversity Assessment Across Different Genotypes Of Mungbean And Urdbean Using Molecular Markers

    Directory of Open Access Journals (Sweden)

    Ashwini Narasimhan , B.R.Patil and S. Datta, M. Kaashyap

    2010-07-01

    Full Text Available Pulses compliment the daily diet of Indians along with cereals. They are rich in proteins with satisfactory proportion ofcarbohydrates. Mungbean, Vigna radiata and Urd bean, Vigna mungo are the important grain legume crops in agriculture,particularly in India. MYMV (Mungbean Yellow vein Mosaic Virus is a virus transmitted by whitefly, Bemesia tabaci, themost serious disease of Mungbean and Urdbean. In this study, six each of MYMV resistant and susceptible genotypes inMungbean and Urbean respectively were selected for the diversity analysis using molecular markers. Twenty four RGAprimers from cowpea were used to screen the twenty four genotypes. Dendrogram generated clearly indicated two bigclusters at 15% similarity. All mungbean genotypes made one cluster (cluster A except PS16, which was included in othercluster made by Urdbean genotypes (cluster B. Cluster A contained eleven genotypes while cluster B contained thirteengenotypes. Cluster A and B were further classified into two sub clusters namely A1 and A2, B1 and B2 respectively. A1consisted of seven genotypes of which five were resistant (PANT MUNG 1, PANT MUNG 5, HUM 12, PUSA 9531, HUM1 and two were susceptible (TARM 2, KOPERGAON 3, while A2 comprised of remaining four genotypes in which threewere susceptible (TAP 7, SML 134 and SML 668, and one (AKM 8803 was resistant. Further, it was found that fourmungbean resistant genotypes of A1 namely Pant Mung1, Pant Mung5, HUM 12, and PUSA 9531 made one cluster at 55%similarity. Cluster B, again was subdivided into B1 and B2. B1 consisted a single genotype which was a cross between IPU99-25* SPS5 while, B2 consisted of the rest of the twelve genotypes. It was interesting to see that two resistant (IPU 02-33and IPU 6-02 and two susceptible (LBG 20 and T9 genotypes of Urd bean made separate cluster with a similarity of 99 percent and which indicated that though genotypes are differing at resistant locus, they are highly similar at all other loci.

  17. Molecular Mechanism and Energy Basis of Conformational Diversity of Antibody SPE7 Revealed by Molecular Dynamics Simulation and Principal Component Analysis

    Science.gov (United States)

    Chen, Jianzhong; Wang, Jinan; Zhu, Weiliang

    2016-11-01

    More and more researchers are interested in and focused on how a limited repertoire of antibodies can bind and correspondingly protect against an almost limitless diversity of invading antigens. In this work, a series of 200-ns molecular dynamics (MD) simulations followed by principal component (PC) analysis and free energy calculations were performed to probe potential mechanism of conformational diversity of antibody SPE7. The results show that the motion direction of loops H3 and L3 is different relative to each other, implying that a big structural difference exists between these two loops. The calculated energy landscapes suggest that the changes in the backbone angles ψ and φ of H-Y101 and H-Y105 provide significant contributions to the conformational diversity of SPE7. The dihedral angle analyses based on MD trajectories show that the side-chain conformational changes of several key residues H-W33, H-Y105, L-Y34 and L-W93 around binding site of SPE7 play a key role in the conformational diversity of SPE7, which gives a reasonable explanation for potential mechanism of cross-reactivity of single antibody toward multiple antigens.

  18. In vivo recombination as a tool to generate molecular diversity in phage antibody libraries.

    Science.gov (United States)

    Sblattero, D; Lou, J; Marzari, R; Bradbury, A

    2001-06-01

    The creation of diversity in populations of polypeptides has become an important tool in the derivation of polypeptides with useful characteristics. This requires efficient methods to create diversity coupled with methods to select polypeptides with desired properties. In this review we describe the use of in vivo recombination as a powerful way to generate diversity. The novel principles for the recombination process and several applications of this process for the creation of phage antibody libraries are described. The advantage and disadvantages are discussed and possible future exploitation presented.

  19. IcePick: a flexible surface-based system for molecular diversity.

    Science.gov (United States)

    Mount, J; Ruppert, J; Welch, W; Jain, A N

    1999-01-14

    IcePick is a system for computationally selecting diverse sets of molecules. It computes the dissimilarity of the surface-accessible features of two molecules, taking into account conformational flexibility. Then, the intrinsic diversity of an entire set of molecules is calculated from a spanning tree over the pairwise dissimilarities. IcePick's dissimilarity measure is compared against traditional 2D topological approaches, and the spanning tree diversity measure is compared against commonly used variance techniques. The method has proven easy to implement and is fast enough to be used in selection of reactants for numerous production-sized combinatorial libraries.

  20. Processes Underpinning Development and Maintenance of Diversity in Rice in West Africa: Evidence from Combining Morphological and Molecular Markers

    Science.gov (United States)

    Maat, Harro; Richards, Paul; Struik, Paul C.

    2014-01-01

    We assessed the interplay of artificial and natural selection in rice adaptation in low-input farming systems in West Africa. Using 20 morphological traits and 176 molecular markers, 182 farmer varieties of rice (Oryza spp.) from 6 West African countries were characterized. Principal component analysis showed that the four botanical groups (Oryza sativa ssp. indica, O. sativa ssp. japonica, O. glaberrima, and interspecific farmer hybrids) exhibited different patterns of morphological diversity. Regarding O. glaberrima, morphological and molecular data were in greater conformity than for the other botanical groups. A clear difference in morphological features was observed between O. glaberrima rices from the Togo hills and those from the Upper Guinea Coast, and among O. glaberrima rices from the Upper Guinea Coast. For the other three groups such clear patterns were not observed. We argue that this is because genetic diversity is shaped by different environmental and socio-cultural selection pressures. For O. glaberrima, recent socio-cultural selection pressures seemed to restrict genetic diversity while this was not observed for the other botanical groups. We also show that O. glaberrima still plays an important role in the selection practices of farmers and resulting variety development pathways. This is particularly apparent in the case of interspecific farmer hybrids where a relationship was found between pericarp colour, panicle attitude and genetic diversity. Farmer varieties are the product of long and complex trajectories of selection governed by local human agency. In effect, rice varieties have emerged that are adapted to West African farming conditions through genotype × environment × society interactions. The diversity farmers maintain in their rice varieties is understood to be part of a risk-spreading strategy that also facilitates successful and often serendipitous variety innovations. We advocate, therefore, that farmers and farmer varieties should

  1. Processes underpinning development and maintenance of diversity in rice in West Africa: evidence from combining morphological and molecular markers.

    Directory of Open Access Journals (Sweden)

    Alfred Mokuwa

    Full Text Available We assessed the interplay of artificial and natural selection in rice adaptation in low-input farming systems in West Africa. Using 20 morphological traits and 176 molecular markers, 182 farmer varieties of rice (Oryza spp. from 6 West African countries were characterized. Principal component analysis showed that the four botanical groups (Oryza sativa ssp. indica, O. sativa ssp. japonica, O. glaberrima, and interspecific farmer hybrids exhibited different patterns of morphological diversity. Regarding O. glaberrima, morphological and molecular data were in greater conformity than for the other botanical groups. A clear difference in morphological features was observed between O. glaberrima rices from the Togo hills and those from the Upper Guinea Coast, and among O. glaberrima rices from the Upper Guinea Coast. For the other three groups such clear patterns were not observed. We argue that this is because genetic diversity is shaped by different environmental and socio-cultural selection pressures. For O. glaberrima, recent socio-cultural selection pressures seemed to restrict genetic diversity while this was not observed for the other botanical groups. We also show that O. glaberrima still plays an important role in the selection practices of farmers and resulting variety development pathways. This is particularly apparent in the case of interspecific farmer hybrids where a relationship was found between pericarp colour, panicle attitude and genetic diversity. Farmer varieties are the product of long and complex trajectories of selection governed by local human agency. In effect, rice varieties have emerged that are adapted to West African farming conditions through genotype × environment × society interactions. The diversity farmers maintain in their rice varieties is understood to be part of a risk-spreading strategy that also facilitates successful and often serendipitous variety innovations. We advocate, therefore, that farmers and

  2. Organic Semiconductors and Conductors with tert-Butyl Substituents

    Directory of Open Access Journals (Sweden)

    Toshiki Higashino

    2012-08-01

    Full Text Available Tetrathiafulvalene (TTF, pentacene, and quarterthiophene with tert-butyl substituents are synthesized, and the crystal structures and the transistor properties are investigated. The tetracyanoquinodimethane (TCNQ complex of tert-butyl TTF constructs highly one-dimensional segregated columns with tetragonal crystal symmetry.

  3. Electronic structure of α-oligothiophenes with various substituents

    Science.gov (United States)

    Vikramaditya, Talapunur; Saisudhakar, Mukka; Sumithra, Kanakamma

    2015-02-01

    Density functional theory is employed to investigate the effect of various substituents on the electronic structure of α-oligothiophenes. The effect of electron donating and withdrawing groups of oligothiophenes in the regio regular HT-HT form is studied. Depending on the type of substituent and the substitution pattern, large differences in the delocalization pattern are observed between the substituted and unsubstituted oligomers. It is found that the band gaps critically depend on the chemical structure and regioselectivity of the building blocks. For the 3-substitued systems, electron donating and electron withdrawing substituents are shown to decrease and increase band gaps respectively compared to unsubstituted systems. There are charge separation effects introduced as a result of lack of symmetry in some of the substituted oligothiophenes. A new strategy is explained to achieve low band gap materials by making use of the regioselective form with lesser symmetry. Push-pull substitution with an electron donor at one end of the conjugation and an acceptor the other end is also investigated. Comparisons of band gaps of the substituted oligothiophenes with the corresponding polymeric systems are also done.

  4. Substituent influence on the spectra of some benzo[f]quinoline derivatives

    Science.gov (United States)

    Oanca, Gabriel; Stare, Jernej; Todirascu, Antonina Gritco; Creanga, Dorina; Dorohoi, Dana Ortansa

    2016-12-01

    The aim of this study was to investigate the relations between the properties of some organic compounds that are cycloaddition derivatives of benzo[f]quinoline, namely benzo[f]pyrrolo[1,2-a]quinolines (BQCDs) and the structure of variable substituent in the addition cycle. The work was focused on the differences in the molecular parameters like frontier orbitals and dipole moment as well as electronic absorption spectra of substituted BQCDs. The optimized molecular structures of BQCDs were calculated using Gaussian 09, with DFT method, the frontier orbitals and electronic absorption spectra being modeled with restricted Hartree Fock method also implemented in Gaussian 09. Influence of substituted radical on the dipole moments and frontier orbital energies of the BQCDs was evidenced from calculated values. Substituent effect on the BQCDs recorded electronic absorption spectra in diluted solution and protonated diluted solution was also emphasized: different types of the transitions underlying absorption bands in the visible range were presumed based on the quantum chemical and experimental investigation.

  5. Detection of microbial diversity in endocarditis using cultivation-independent molecular techniques

    DEFF Research Database (Denmark)

    Wolff, Tine Y; Moser, Claus Ernst; Bundgaard, Henning

    2011-01-01

    of cultivation and molecular methods, and for these samples the identified bacteria are known to be frequently involved with IE. Many of the additional bacteria only identified by the molecular methods are not reported as common causes of IE. Conclusions: Application of molecular tools in addition to cultivation...... and all were monomicrobial. Molecular methods showed the presence of DNA from multiple bacterial species in 6 of the samples and indicated a larger variety of bacteria in the different samples than identified by cultivation. For 8 of the patients there was a good correlation between the results...

  6. Substituent Effects on the Absorption and Fluorescence Properties of Anthracene.

    Science.gov (United States)

    Abou-Hatab, Salsabil; Spata, Vincent A; Matsika, Spiridoula

    2017-02-16

    Substitution can be used to efficiently tune the photophysical properties of chromophores. In this study, we examine the effect of substituents on the absorption and fluorescence properties of anthracene. The effects of mono-, di-, and tetrasubstitution of electron-donating and -withdrawing functional groups were explored. In addition, the influence of a donor-acceptor substituent pair and the position of substitution were investigated. Eleven functional groups were varied on positions 1, 2, and 9 of anthracene, and on position 6 of 2-methoxyanthracene and 2-carboxyanthracene. Moreover, the donor-acceptor pair NH2/CO2H was added on different positions of anthracene for additional studies of doubly substituted anthracenes. Finally, we looked into quadruple substitutions on positions 1,4,5,8 and 2,3,6,7. Vertical excitation energies and oscillator strengths were computed using density functional theory with the hybrid CAM-B3LYP functional and 6-311G(d) basis set. Correlations between the excitation energies or oscillator strengths of the low-lying bright La state and the Hammett sigma parameter, σp(+), of the substituents were examined. The energy is red-shifted for all cases of substitution. Oscillator strengths increase when substituents are placed along the direction of the transition dipole moment of the bright La excited state. Substitution of long chain conjugated groups significantly increases the oscillator strength in comparison to the cases for other substituents. In addition, the results of quadruply substituted geometries reveal symmetric substitution at the 1,4,5,8 positions significantly increases the oscillator strength and can lower the band gap compared to that of the unsubstituted anthracene molecule by up to 0.5 eV.

  7. Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST

    NARCIS (Netherlands)

    O'Donnell, Kerry; Humber, Richard A; Geiser, David M; Kang, Seogchan; Park, Bongsoo; Robert, Vincent A R G; Crous, Pedro W; Johnston, Peter R; Aoki, Takayuki; Rooney, Alejandro P; Rehner, Stephen A

    2011-01-01

    We constructed several multilocus DNA sequence datasets to assess the phylogenetic diversity of insecticolous fusaria, especially focusing on those housed at the Agricultural Research Service Collection of Entomopathogenic Fungi (ARSEF), and to aid molecular identifications of unknowns via the FUSAR

  8. Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST

    NARCIS (Netherlands)

    O'Donnell, K.; Humber, R.A.; Geiser, D.M.; Kang, S.; Park, B.; Robert, V.; Crous, P.W.; Johnston, P.R.; Aoki, T.; Rooney, A.P.; Rehner, S.A.

    2012-01-01

    We constructed several multilocus DNA sequence datasets to assess the phylogenetic diversity of insecticolous fusaria, especially focusing on those housed in the Agricultural Research Service Collection of Entomopathogenic Fungi (ARSEF), and to facilitate molecular identifications of unknowns via th

  9. Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST

    NARCIS (Netherlands)

    O'Donnell, K.; Humber, R.A.; Geiser, D.M.; Kang, S.; Robert, V.; Park, B.; Crous, P.W.; Johnston, P.; Aoki, T.; Rooney, A.P.; Rehner, S.A.

    2012-01-01

    We constructed several multilocus DNA sequence datasets to assess the phylogenetic diversity of insecticolous fusaria, especially focusing on those housed at the Agricultural Research Service Collection of Entomopathogenic Fungi (ARSEF), and to aid molecular identifications of unknowns via the FUSAR

  10. Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST

    Science.gov (United States)

    We constructed several multilocus Deoxyribonucleic acid (DNA) sequence datasets to assess the phylogenetic diversity of insecticolous fusaria, especially focusing on those housed in the Agricultural Research Service Collection of Entomopathogenic Fungi (ARSEF), and to facilitate molecular identifica...

  11. ISSR markers for analysis of molecular diversity and genetic structure of Indian teak (Tectona grandis L.f. populations

    Directory of Open Access Journals (Sweden)

    Shamin Akhtar Ansari

    2012-06-01

    Full Text Available Inter simple sequence repeats (ISSR constitute a powerful dominant DNA molecular marker system used for diversity analysis, which is indispensable for making estimates of genetic base and demarcation of populations for undertaking conservation and improvement program offorest tree species. Twenty nine populations of teak (Tectona grandis L.f. were collected from central and peninsular India for analysis of genetic diversity and structure. Genomic DNA from ten randomly selected individuals of each population was extracted and amplified using five ISSR primers (UBC-801, 834, 880, 899 and 900. The primers showed 100% polymorphism. UBC-900 recorded the highest Nei's genetic diversity (0.32 to 0.40 and UBC-899 had the highest Shannon's Information Index (0.49 to 0.59. AMOVA revealed a very high intra-population genetic diversity (91%, in comparison to inter-population genetic diversity among states (6.17% and within states (2.77%, were also indirectly confirmed by large standard deviations associated with genetic diversity estimates for individual population, as well as poor bootstrapping values for most of the cluster nodes. However, UPGMA dendrogram revealed several clusters, with populations from central India being present almost in each cluster, making groups with populations of adjoining states and distant states. Nevertheless, the cluster analysis distinguished the drier teak populations of central India from the moist teak populations of south India, which was also confirmed by Principle Coordinate Analysis. The findings advocates the need not only for enhancing selection intensity for large number of plus trees, but also for laying out more number of in situ conservation plots within natural populations of each cluster for germplasm conservation of teak aimed at improving the teak productivity and quality in future. 

  12. ISSR markers for analysis of molecular diversity and genetic structure of Indian teak (Tectona grandis L.f. populations

    Directory of Open Access Journals (Sweden)

    S.A. Ansari

    2012-05-01

    Full Text Available Inter simple sequence repeats (ISSR constitute a powerful dominantDNA molecular marker system used for diversity analysis, which isindispensable for making estimates of genetic base and demarcation of populations for undertaking conservation and improvement program of forest tree species. Twenty nine populations of teak (Tectona grandis L.f. were collected from central and peninsular India for analysis of genetic diversity and structure. Genomic DNA from ten randomly selected individuals of each population was extracted and amplified using five ISSR primers(UBC-801, 834, 880, 899 and 900. The primers showed 100% polymorphism. UBC-900 recorded the highest Nei’s genetic diversity (0.32 to 0.40and UBC-899 had the highest Shannon’s Information Index (0.49 to 0.59. AMOVA revealed a very high intra-population genetic diversity (91%, in comparison to inter-population genetic diversity among states (6.17% and within states (2.77% which were also indirectly confirmed by large standard deviations associated with genetic diversity estimates for individual population, as well as poor bootstrapping values for most of the cluster nodes. However, UPGMA dendrogram revealed several clusters, with populationsfrom central India being present almost in each cluster, makinggroups with populations of adjoining states and distant states. Nevertheless,the cluster analysis distinguished the drier teak populations of central India from the moist teak populations of south India, which was also confirmed by Principle Coordinate Analysis. The findings advocates the need not only for enhancing selection intensity for large number of plus trees, but also for laying out more number of in situ conservation plots within natural populations of each cluster for germplasm conservation of teak aimed at improving the teak productivity and quality in future.

  13. Investigation and Analysis of Genetic Diversity of Diospyros Germplasms Using SCoT Molecular Markers in Guangxi.

    Directory of Open Access Journals (Sweden)

    Libao Deng

    Full Text Available Knowledge about genetic diversity and relationships among germplasms could be an invaluable aid in diospyros improvement strategies.This study was designed to analyze the genetic diversity and relationship of local and natural varieties in Guangxi Zhuang Autonomous Region of China using start codon targeted polymorphism (SCoT markers. The accessions of 95 diospyros germplasms belonging to four species Diospyros kaki Thunb, D. oleifera Cheng, D. kaki var. silverstris Mak, and D. lotus Linn were collected from different eco-climatic zones in Guangxi and were analyzed using SCoT markers.Results indicated that the accessions of 95 diospyros germplasms could be distinguished using SCoT markers, and were divided into three groups at similarity coefficient of 0.608; these germplasms that belong to the same species were clustered together; of these, the degree of genetic diversity of the natural D. kaki var. silverstris Mak population was richest among the four species; the geographical distance showed that the 12 natural populations of D. kaki var. silverstris Mak were divided into two groups at similarity coefficient of 0.19. Meanwhile, in order to further verify the stable and useful of SCoT markers in diospyros germplasms, SSR markers were also used in current research to analyze the genetic diversity and relationship in the same diospyros germplasms. Once again, majority of germplasms that belong to the same species were clustered together. Thus SCoT markers were stable and especially useful for analysis of the genetic diversity and relationship in diospyros germplasms.The molecular characterization and diversity assessment of diospyros were very important for conservation of diospyros germplasm resources, meanwhile for diospyros improvement.

  14. Diversity of Rhodopirellula and related planctomycetes in a North Sea coastal sediment employing carB as molecular marker.

    Science.gov (United States)

    Žure, Marina; Munn, Colin B; Harder, Jens

    2015-09-01

    Rhodopirellula is an abundant marine member of the bacterial phylum Planctomycetes. Cultivation studies revealed the presence of several closely related Rhodopirellula species in European coastal sediments. Because the 16S rRNA gene does not provide the desired taxonomic resolution to differentiate Rhodopirellula species, we performed a comparison of the genomes of nine Rhodopirellula strains and six related planctomycetes and identified carB, coding for the large subunit of carbamoylphosphate synthetase, as a suitable molecular marker. In this study, we investigated the diversity of Rhodopirellula in coastal intertidal surface sediments of Sylt island, North Sea, using the 16S rRNA and carB genes as molecular markers. The carB clone and pyrosequencing libraries revealed the presence of 12 species of Rhodopirellula and of 66 species in closely related undescribed genera, a diversity that was not detected with a 16S rRNA gene library. This study demonstrates that the carB gene is a powerful molecular marker for detecting Rhodopirellula species in the environment and may be used for the taxonomic evaluation of new strains. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. Fish pathogens near the Arctic Circle: molecular, morphological and ecological evidence for unexpected diversity of Diplostomum (Digenea: Diplostomidae) in Iceland.

    Science.gov (United States)

    Blasco-Costa, Isabel; Faltýnková, Anna; Georgieva, Simona; Skírnisson, Karl; Scholz, Tomáš; Kostadinova, Aneta

    2014-09-01

    Host-parasite systems at high latitudes are promising model systems for detecting and predicting the impact of accelerated environmental change. A major challenge is the lack of baselines for the diversity and distribution of parasites in Arctic wildlife, especially in the freshwater environment. Here we present the first known estimates of the species diversity and host associations of Diplostomum spp. in sub-Arctic freshwater ecosystems of the Palaearctic. Our analyses integrating different analytical approaches, phylogenies based on mitochondrial and nuclear DNA, estimates of genetic divergence, character-based barcoding, morphological examination, precise detection of microhabitat specialisation and host use, led to the discovery of one described and five putative new species that complete their life-cycles within a fairly narrow geographic area in Iceland. This increases the species richness of Diplostomum in Iceland by 200% and raises the number of molecularly characterised species from the Palaearctic to 17 species. Our results suggest that the diversity of Diplostomum spp. is underestimated globally in the high latitude ecosystems and call for a cautionary approach to pathogen identification in developing the much needed baselines of pathogen diversity that may help detect effects of climate change in the freshwater environment of the sub-Arctic.

  16. Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria.

    Science.gov (United States)

    Thomas, Pious; Sekhar, Aparna Chandra

    2017-05-01

    The interior of plants constitutes a unique environment for microorganisms with various organisms inhabiting as endophytes. Unlike subterranean plant parts, aboveground parts are relatively less explored for endophytic microbial diversity. We employed a combination of cultivation and molecular approaches to study the endophytic bacterial diversity in banana shoot-tips. Cultivable bacteria from 20 sucker shoot-tips of cv. Grand Naine included 37 strains under 16 genera and three phyla (Proteobacteria, Actinobacteria, Firmicutes). 16S rRNA gene-ribotyping approach on 799f and 1492r PCR-amplicons to avoid plant organelle sequences was ineffective showing limited bacterial diversity. 16S rRNA metagene profiling targeting the V3-V4 hypervariable region after filtering out the chloroplast (74.2 %), mitochondrial (22.9 %), and unknown sequences (1.1 %) revealed enormous bacterial diversity. Proteobacteria formed the predominant phylum (64 %) succeeded by Firmicutes (12.1 %), Actinobacteria (9.5 %), Bacteroidetes (6.4 %), Planctomycetes, Cyanobacteria, and minor shares (bacteria prevailing in banana shoot-tips (20 phyla, 46 classes) with about 2.6 % of the deciphered 269 genera and 1.5 % of the 656 observed species from the same source of shoot-tips attained through cultivation. The predominant genera included several agriculturally important bacteria. The study reveals an immense ecosystem of endophytic bacteria in banana shoot tissues endorsing the earlier documentation of intracellular "Cytobacts" and "Peribacts" with possible roles in plant holobiome and hologenome.

  17. Molecular diversity of eukaryotes in municipal wastewater treatment processes as revealed by 18S rRNA gene analysis.

    Science.gov (United States)

    Matsunaga, Kengo; Kubota, Kengo; Harada, Hideki

    2014-01-01

    Eukaryotic communities involved in sewage treatment processes have been investigated by morphological identification, but have not yet been well-characterized using molecular approaches. In the present study, eukaryotic communities were characterized by constructing 18S rRNA gene clone libraries. The phylogenetic affiliations of a total of 843 clones were Alveolata, Fungi, Rhizaria, Euglenozoa, Stramenopiles, Amoebozoa, and Viridiplantae as protozoans and Rotifera, Gastrotricha, and Nematoda as metazoans. Sixty percent of the clones had <97% sequence identity to described eukaryotes, indicating the greater diversity of eukaryotes than previously recognized. A core OTU closely related to Epistylis chrysemydis was identified, and several OTUs were shared by 4-8 libraries. Members of the uncultured lineage LKM11 in Cryptomycota were predominant fungi in sewage treatment processes. This comparative study represents an initial step in furthering understanding of the diversity and role of eukaryotes in sewage treatment processes.

  18. The characterization of hydroxypropyl methylcellulose through the analysis of its substituents

    Science.gov (United States)

    The methyl and hydroxypropyl substituents in hydroxypropyl methylcellulose (HPMC) affect the resulting gel properties. These substituents in five HPMC gels were characterized using Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy, small-amplitude oscillatory shear measurements, a...

  19. Analysis of genetic diversity of certain species of Piper using RAPD-based molecular markers.

    Science.gov (United States)

    Chowdhury, Utpal; Tanti, Bhaben; Rethy, Parakkal; Gajurel, Padma Raj

    2014-09-01

    The utility of RAPD markers in assessing genetic diversity and phenetic relationships of six different species of Piper from Northeast India was investigated. Polymerase chain reaction (PCR) with four arbitrary 10-mer oligonucleotide primers applied to the six species produced a total of 195 marker bands, of which, 159 were polymorphic. On average, six RAPD fragments were amplified per reaction. In the UPGMA phenetic dendrogram based on Jaccard's coefficient, the different accessions of Piper showed a high level of genetic variation. This study may be useful in identifying diverse genetic stocks of Piper, which may then be conserved on a priority basis.

  20. Molecular analysis reveals hidden diversity in Zungaro (Siluriformes: Pimelodidade): a genus of giant South American catfish.

    Science.gov (United States)

    Pires, Antonio A; Ramirez, Jorge L; Galetti, Pedro M; Troy, Waldo P; Freitas, Patricia D

    2017-06-01

    The genus Zungaro contains some of the largest catfish in South America. Two valid species are currently recognized: Zungaro jahu, inhabiting the Paraná and Paraguay basins, and Zungaro zungaro, occurring in the Amazonas and Orinoco basins. Analysing Zungaro specimens from the Amazonas, Orinoco, Paraguay and Paraná basins, based on the sequencing of COI and D-loop, we found at least three MOTUs, indicating the existence of hidden diversity within this fish group. Considering the ecological and economic values of this fish, our results are surely welcomed for its conservation, disclosing new findings on its diversity and pointing out the necessity for a detailed taxonomic revision.

  1. Rich diversity and potency of skin antioxidant peptides revealed a novel molecular basis for high-altitude adaptation of amphibians.

    Science.gov (United States)

    Yang, Xinwang; Wang, Ying; Zhang, Yue; Lee, Wen-Hui; Zhang, Yun

    2016-01-27

    Elucidating the mechanisms of high-altitude adaptation is an important research area in modern biology. To date, however, knowledge has been limited to the genetic mechanisms of adaptation to the lower oxygen and temperature levels prevalent at high altitudes, with adaptation to UV radiation largely neglected. Furthermore, few proteomic or peptidomic analyses of these factors have been performed. In this study, the molecular adaptation of high-altitude Odorrana andersonii and cavernicolous O. wuchuanensis to elevated UV radiation was investigated. Compared with O. wuchuanensis, O. andersonii exhibited greater diversity and free radical scavenging potentiality of skin antioxidant peptides to cope with UV radiation. This implied that O. andersonii evolved a much more complicated and powerful skin antioxidant peptide system to survive high-altitude UV levels. Our results provided valuable peptidomic clues for understanding the novel molecular basis for adaptation to high elevation habitats.

  2. Hemichannel composition and electrical synaptic transmission: molecular diversity and its implications for electrical rectification.

    Science.gov (United States)

    Palacios-Prado, Nicolás; Huetteroth, Wolf; Pereda, Alberto E

    2014-01-01

    Unapposed hemichannels (HCs) formed by hexamers of gap junction proteins are now known to be involved in various cellular processes under both physiological and pathological conditions. On the other hand, less is known regarding how differences in the molecular composition of HCs impact electrical synaptic transmission between neurons when they form intercellular heterotypic gap junctions (GJs). Here we review data indicating that molecular differences between apposed HCs at electrical synapses are generally associated with rectification of electrical transmission. Furthermore, this association has been observed at both innexin and connexin (Cx) based electrical synapses. We discuss the possible molecular mechanisms underlying electrical rectification, as well as the potential contribution of intracellular soluble factors to this phenomenon. We conclude that asymmetries in molecular composition and sensitivity to cellular factors of each contributing hemichannel can profoundly influence the transmission of electrical signals, endowing electrical synapses with more complex functional properties.

  3. Manipulation of arthropod sex determination by endosymbionts : Diversity and molecular mechanisms

    NARCIS (Netherlands)

    Ma, W. -J.; Vavre, F.; Beukeboom, L. W.

    2014-01-01

    Arthropods exhibit a large variety of sex determination systems both at the chromosomal and molecular level. Male heterogamety, female heterogamety, and haplodiploidy occur frequently, but partially different genes are involved. Endosymbionts, such as Wolbachia, Cardinium, Rickettsia, and

  4. Molecular analyses of microbial diversity associated with the Lonar soda lake in India: an impact crater in a basalt area.

    Science.gov (United States)

    Wani, Aijaz Ahmad; Surakasi, Venkata Prasad; Siddharth, Jay; Raghavan, Raamesh Gowri; Patole, Milind S; Ranade, Dilip; Shouche, Yogesh S

    2006-12-01

    The prokaryotic diversity associated with an Indian soda lake (Lonar Crater Lake) located in a basaltic soil area was investigated using a culture-independent approach. Community DNA was extracted directly from four sediment samples obtained by coring to depths of 10-20 cm. Small subunit rRNA genes (16S rDNA) were amplified by PCR using primers specific to the domains Bacteria and Archaea. The PCR products were cloned and sequenced. For the bacterial rDNA clone library, 500 clones were randomly selected for further analysis. After restriction fragment length polymorphism (RFLP) analysis and subsequent sequencing, a total of 44 unique phylotypes were obtained. These phylotypes spanned a wide range within the domain Bacteria, occupying eight major lineages/phyla. 34% of the clones were classified as firmicutes. The other clones were grouped into proteobacteria (29.5%), actinobacteria (6.8%), deinococcus-thermus (4.5%), cytophages-flavobacterium-bacteroidetes (13.3%), planctomycetes (6.8%), cyanobacteria (4.5%) and spirochetes (2.27%). In the case of the archaeal 16S rDNA library, analysis of 250 randomly selected clones revealed the presence of 13 distinct phylotypes; 5 phylotypes were associated with Crenarchaeota and 8 with Euryarchaeota. Most of the euryarchaeota sequences were related to methanogens. Findings from this molecular study of a site investigated for the first time have revealed the presence of a highly diverse bacterial population and a comparatively less diverse archaeal population. The majority ( approximately 80%) of the cloned sequences show little affiliation with known taxa (<97% sequence similarity) and may represent novel taxa/sequences and organisms specifically adapted to this basaltic soda lake environment. Diversity analyses demonstrate greater diversity and evenness of bacterial species compared to a skewed representation of species for Archaea.

  5. Assessment of genetic diversity in indigenous turmeric (Curcuma longa) germplasm from India using molecular markers.

    Science.gov (United States)

    Verma, Sushma; Singh, Shweta; Sharma, Suresh; Tewari, S K; Roy, R K; Goel, A K; Rana, T S

    2015-04-01

    Curcuma longa L., commonly known as turmeric, is one of the economically and medicinally important plant species. It is predominantly cultivated in the tropical and sub tropical countries. India is the largest producer, and exporter of turmeric in the world, followed by China, Indonesia, Bangladesh and Thailand. In the present study, Directed Amplification of Minisatellite DNA (DAMD) and Inter Simple Sequence Repeats (ISSR), methods were used to estimate the genetic variability in indigenous turmeric germplasm. Cumulative data analysis for DAMD (15) and ISSR (13) markers resulted into 478 fragments, out of which 392 fragments were polymorphic, revealing 82 % polymorphism across the turmeric genotypes. Wide range of pairwise genetic distances (0.03-0.59) across the genotypes revealed that these genotypes are genetically quite diverse. The UPGMA dendrogram generated using cumulative data showed significant relationships amongst the genotypes. All 29 genotypes studied grouped into two clusters irrespective of their geographical affiliations with 100 % bootstrap value except few genotypes, suggesting considerable diversity amongst the genotypes. These results suggested that the current collection of turmeric genotypes preserve the vast majority of natural variations. The results further demonstrate the efficiency and reliability of DAMD and ISSR markers in determining the genetic diversity and relationships among the indigenous turmeric germplasm. DAMD and ISSR profiling have identified diverse turmeric genotypes, which could be further utilized in various genetic improvement programmes including conventional as well as marker assisted breeding towards development of new and desirable turmeric genotypes.

  6. Molecular evolution and nucleotide diversity of nuclear plastid phosphoglycerate kinase (PGK) gene in Triticeae (Poaceae).

    Science.gov (United States)

    Adderley, Shawn; Sun, Genlou

    2014-01-01

    Levels of nucleotide divergence provide key evidence in the evolution of polyploids. The nucleotide diversity of 226 sequences of pgk1 gene in Triticeae species was characterized. Phylogenetic analyses based on the pgk1 gene were carried out to determine the diploid origin of polyploids within the tribe in relation to their A(u), B, D, St, Ns, P, and H haplomes. Sequences from the Ns genome represented the highest nucleotide diversity values for both polyploid and diploid species with π=0.03343 and θ=0.03536 for polyploid Ns genome sequences and π=0.03886 and θ=0.03886 for diploid Psathyrostachys sequences, while Triticum urartu represented the lowest diversity among diploid species at π=0.0011 and θ=0.0011. Nucleotide variation of diploid Aegilops speltoides (π=0.2441, presumed the B genome donor of Triticum species) is five times higher than that (π=0.00483) of B genome in polyploid species. Significant negative Tajima's D values for the St, A(u), and D genomes along with high rates of polymorphisms and low sequence diversity were observed. Origins of the A(u), B, and D genomes were linked to T. urartu, A. speltoides, and A. tauschii, respectively. Putative St genome donor was Pseudoroegneria, while Ns and P donors were Psathyrostachys and Agropyron. H genome diploid donor is Hordeum. © 2013 Elsevier B.V. All rights reserved.

  7. Lipid metabolites in seeds of diverse Gossypium accessions: Molecular identification of a high oleic mutant allele

    Science.gov (United States)

    The domestication and breeding of cotton for elite, high-fiber cultivars has led to reduced genetic variation of seed constituents within currently cultivated upland Cotton genotypes. However, a recent screen of the genetically diverse U.S. National Cotton Germplasm Collection identified Gossypium ...

  8. Geographic diversity assessed by molecular markers in the USDA rice world collection

    Science.gov (United States)

    Knowledge of genetic diversity and relationship in the USDA rice world collection can help utilize, conserve and manage this collection for more efficient service to national and international scientists. The USDA rice core collection, including 1,794 accessions originating from 114 countries in 14 ...

  9. Comparative diversity analysis of southeastern Rubus germplasm through molecular and pedigree techniques

    Science.gov (United States)

    The North Carolina Rubus germplasm collection contains hundreds of diverse blackberry, raspberry, and black raspberry (Rubus L.)selections, among which intra- and interspecific crosses were made to achieve breeding goals for expanding commercial production in the Southeast. For over 50 years, the b...

  10. Molecular characterization of ruminal bacterial diversity in vitro = Caracterização molecular da diversidade bacteriana ruminal in vitro

    Directory of Open Access Journals (Sweden)

    Humberto Maciel França Madeira

    2008-04-01

    Full Text Available PCR analysis is a sensitive and specific tool to detect and monitormicroorganisms in complex environmental samples. The amplification of 16S ribosomal DNA sequences followed by gel electrophoresis under denaturing gradient (DGGE has been a powerful technique to genetically evaluate microbial ecosystems. Changes in rumenmicrobial populations were investigated in vitro using a basal diet with different lipid sources. PCRs were performed with two different sets of primers in order to amplify 16S rRNA sequences, and the amplified fragments were submitted to DGGE analysis. The findings presented in this study show that distinct microbial communities were present in each treatment. The presence of soybean oil seems to maximize growth of bacterial population, whereas fish oil appears to reduce growth. We demonstrated the successful application of molecular ecological techniques to analyze the structure and composition of bacterial communities in rumen ecosystems.A análise por PCR fornece um meio sensível e específico para detectar e monitorar microrganismos em amostras ambientais complexas. Desde sua aplicação inicial, o DNA ribossomal 16S (rRNA em eletroforese com gel com gradiente desnaturante (DGGE, tem sido uma técnica atrativa para a ecologia molecular microbiana. Foram investigadas mudanças na população microbiana no rúmen, a partir de alterações da dieta com tratamentos in vitro de diferentes fontes de lipídeos. ODGGE foi testado com dois pares de primers para o rRNA 16S. O uso do fragmento de 200 pb gerou um perfil de bandas mais discriminatório, mostrando que diferentes comunidades microbianas estavam presentes entre os tratamentos in vitro analisados. A presença de óleo de sojapotencializou o crescimento da população bacteriana, enquanto que óleo de peixe parece ter reduzido esse crescimento. Foi possível demonstrar o sucesso da aplicação de técnicas moleculares para analisar a estrutura e a composição de comunidades

  11. Genetic diversity assessment of sesame core collection in China by phenotype and molecular markers and extraction of a mini-core collection

    Directory of Open Access Journals (Sweden)

    Zhang Yanxin

    2012-11-01

    Full Text Available Abstract Background Sesame (Sesamum indicum L. is one of the four major oil crops in China. A sesame core collection (CC was established in China in 2000, but no complete study on its genetic diversity has been carried out at either the phenotypic or molecular level. To provide technical guidance, a theoretical basis for further collection, effective protection, reasonable application, and a complete analysis of sesame genetic resources, a genetic diversity assessment of the sesame CC in China was conducted using phenotypic and molecular data and by extracting a sesame mini-core collection (MC. Results Results from a genetic diversity assessment of sesame CC in China were significantly inconsistent at the phenotypic and molecular levels. A Mantel test revealed the insignificant correlation between phenotype and molecular marker information (r = 0.0043, t = 0.1320, P = 0.5525. The Shannon-Weaver diversity index (I and Nei genetic diversity index (h were higher (I = 0.9537, h = 0.5490 when calculated using phenotypic data from the CC than when using molecular data (I = 0.3467, h = 0.2218. A mini-core collection (MC containing 184 accessions was extracted based on both phenotypic and molecular data, with a low mean difference percentage (MD, 1.64%, low variance difference percentage (VD, 22.58%, large variable rate of coefficient of variance (VR, 114.86%, and large coincidence rate of range (CR, 95.76%. For molecular data, the diversity indices and the polymorphism information content (PIC for the MC were significantly higher than for the CC. Compared to an alternative random sampling strategy, the advantages of capturing genetic diversity and validation by extracting a MC using an advanced maximization strategy were proven. Conclusions This study provides a comprehensive characterization of the phenotypic and molecular genetic diversities of the sesame CC in China. A MC was extracted using both phenotypic and molecular data. Low MD% and VD%, and

  12. Genetic diversity assessment of sesame core collection in China by phenotype and molecular markers and extraction of a mini-core collection

    Science.gov (United States)

    2012-01-01

    Background Sesame (Sesamum indicum L.) is one of the four major oil crops in China. A sesame core collection (CC) was established in China in 2000, but no complete study on its genetic diversity has been carried out at either the phenotypic or molecular level. To provide technical guidance, a theoretical basis for further collection, effective protection, reasonable application, and a complete analysis of sesame genetic resources, a genetic diversity assessment of the sesame CC in China was conducted using phenotypic and molecular data and by extracting a sesame mini-core collection (MC). Results Results from a genetic diversity assessment of sesame CC in China were significantly inconsistent at the phenotypic and molecular levels. A Mantel test revealed the insignificant correlation between phenotype and molecular marker information (r = 0.0043, t = 0.1320, P = 0.5525). The Shannon-Weaver diversity index (I) and Nei genetic diversity index (h) were higher (I = 0.9537, h = 0.5490) when calculated using phenotypic data from the CC than when using molecular data (I = 0.3467, h = 0.2218). A mini-core collection (MC) containing 184 accessions was extracted based on both phenotypic and molecular data, with a low mean difference percentage (MD, 1.64%), low variance difference percentage (VD, 22.58%), large variable rate of coefficient of variance (VR, 114.86%), and large coincidence rate of range (CR, 95.76%). For molecular data, the diversity indices and the polymorphism information content (PIC) for the MC were significantly higher than for the CC. Compared to an alternative random sampling strategy, the advantages of capturing genetic diversity and validation by extracting a MC using an advanced maximization strategy were proven. Conclusions This study provides a comprehensive characterization of the phenotypic and molecular genetic diversities of the sesame CC in China. A MC was extracted using both phenotypic and molecular data. Low MD% and VD%, and large VR% and CR

  13. Genetic diversity assessment of sesame core collection in China by phenotype and molecular markers and extraction of a mini-core collection.

    Science.gov (United States)

    Zhang, Yanxin; Zhang, Xiurong; Che, Zhuo; Wang, Linhai; Wei, Wenliang; Li, Donghua

    2012-11-15

    Sesame (Sesamum indicum L.) is one of the four major oil crops in China. A sesame core collection (CC) was established in China in 2000, but no complete study on its genetic diversity has been carried out at either the phenotypic or molecular level. To provide technical guidance, a theoretical basis for further collection, effective protection, reasonable application, and a complete analysis of sesame genetic resources, a genetic diversity assessment of the sesame CC in China was conducted using phenotypic and molecular data and by extracting a sesame mini-core collection (MC). Results from a genetic diversity assessment of sesame CC in China were significantly inconsistent at the phenotypic and molecular levels. A Mantel test revealed the insignificant correlation between phenotype and molecular marker information (r = 0.0043, t = 0.1320, P = 0.5525). The Shannon-Weaver diversity index (I) and Nei genetic diversity index (h) were higher (I = 0.9537, h = 0.5490) when calculated using phenotypic data from the CC than when using molecular data (I = 0.3467, h = 0.2218). A mini-core collection (MC) containing 184 accessions was extracted based on both phenotypic and molecular data, with a low mean difference percentage (MD, 1.64%), low variance difference percentage (VD, 22.58%), large variable rate of coefficient of variance (VR, 114.86%), and large coincidence rate of range (CR, 95.76%). For molecular data, the diversity indices and the polymorphism information content (PIC) for the MC were significantly higher than for the CC. Compared to an alternative random sampling strategy, the advantages of capturing genetic diversity and validation by extracting a MC using an advanced maximization strategy were proven. This study provides a comprehensive characterization of the phenotypic and molecular genetic diversities of the sesame CC in China. A MC was extracted using both phenotypic and molecular data. Low MD% and VD%, and large VR% and CR% suggested that the MC

  14. The substituent effect from the perspective of local hyper-softness. An example applied on normeloxicam, meloxicam and 4-meloxicam: Non-steroidal anti-inflammatory drugs

    Science.gov (United States)

    Martínez-Araya, Jorge Ignacio; Glossman-Mitnik, Daniel

    2015-01-01

    Normeloxicam, meloxicam and 4-meloxicam were analyzed from the perspective of the conceptual density functional theory perspective to determine the substituent effect exerted by the methyl group that is located at the thiazole ring. This analysis was performed in absence and presence of water. The position of the methyl group suggests that differences that have been experimentally reported in a previous paper can be mainly attributable to electronic effects exerted by the substituent aforementioned group. Finally, the use of total electronic densities is encouraged in future calculations instead of densities of frontier molecular orbitals to obtain more accurate results.

  15. Effects of meso-substituents and core-modification on photophysical and electrochemical properties of porphyrin-ferrocene conjugates

    Science.gov (United States)

    Rai, Smita; Gayatri, G.; Narahari Sastry, G.; Ravikanth, M.

    2008-12-01

    The effects of meso-substituents and porphyrin core-modification on electronic communication between ferrocene and porphyrin in covalently linked porphyrin-ferrocene conjugates are described. The electrochemical and photophysical studies indicated that the electronic communication between porphyrin and ferrocene is strong when meso-substituents are five membered aryl groups than six membered aryl groups. This may be traced to the near orthogonal arrangement of porphyrin ring with six membered meso-aryl groups leading to weaker interaction between the porphyrin and ferrocenyl groups in conjugates, while the five membered furyl and thienyl groups are closer to the porphyrin plane than being orthogonal. Molecular orbital studies are performed at semiempirical PM3 and BLYP levels to rationalize the results.

  16. Molecular and evolutionary bases of within-patient genotypic and phenotypic diversity in Escherichia coli extraintestinal infections.

    Directory of Open Access Journals (Sweden)

    Maxime Levert

    Full Text Available Although polymicrobial infections, caused by combinations of viruses, bacteria, fungi and parasites, are being recognised with increasing frequency, little is known about the occurrence of within-species diversity in bacterial infections and the molecular and evolutionary bases of this diversity. We used multiple approaches to study the genomic and phenotypic diversity among 226 Escherichia coli isolates from deep and closed visceral infections occurring in 19 patients. We observed genomic variability among isolates from the same site within 11 patients. This diversity was of two types, as patients were infected either by several distinct E. coli clones (4 patients or by members of a single clone that exhibit micro-heterogeneity (11 patients; both types of diversity were present in 4 patients. A surprisingly wide continuum of antibiotic resistance, outer membrane permeability, growth rate, stress resistance, red dry and rough morphotype characteristics and virulence properties were present within the isolates of single clones in 8 of the 11 patients showing genomic micro-heterogeneity. Many of the observed phenotypic differences within clones affected the trade-off between self-preservation and nutritional competence (SPANC. We showed in 3 patients that this phenotypic variability was associated with distinct levels of RpoS in co-existing isolates. Genome mutational analysis and global proteomic comparisons in isolates from a patient revealed a star-like relationship of changes amongst clonally diverging isolates. A mathematical model demonstrated that multiple genotypes with distinct RpoS levels can co-exist as a result of the SPANC trade-off. In the cases involving infection by a single clone, we present several lines of evidence to suggest diversification during the infectious process rather than an infection by multiple isolates exhibiting a micro-heterogeneity. Our results suggest that bacteria are subject to trade-offs during an infectious

  17. Molecular and evolutionary bases of within-patient genotypic and phenotypic diversity in Escherichia coli extraintestinal infections.

    Science.gov (United States)

    Levert, Maxime; Zamfir, Oana; Clermont, Olivier; Bouvet, Odile; Lespinats, Sylvain; Hipeaux, Marie Claire; Branger, Catherine; Picard, Bertrand; Saint-Ruf, Claude; Norel, Françoise; Balliau, Thierry; Zivy, Michel; Le Nagard, Hervé; Cruveiller, Stéphane; Cruvellier, Stéphane; Chane-Woon-Ming, Béatrice; Nilsson, Susanna; Gudelj, Ivana; Phan, Katherine; Ferenci, Thomas; Tenaillon, Olivier; Denamur, Erick

    2010-09-30

    Although polymicrobial infections, caused by combinations of viruses, bacteria, fungi and parasites, are being recognised with increasing frequency, little is known about the occurrence of within-species diversity in bacterial infections and the molecular and evolutionary bases of this diversity. We used multiple approaches to study the genomic and phenotypic diversity among 226 Escherichia coli isolates from deep and closed visceral infections occurring in 19 patients. We observed genomic variability among isolates from the same site within 11 patients. This diversity was of two types, as patients were infected either by several distinct E. coli clones (4 patients) or by members of a single clone that exhibit micro-heterogeneity (11 patients); both types of diversity were present in 4 patients. A surprisingly wide continuum of antibiotic resistance, outer membrane permeability, growth rate, stress resistance, red dry and rough morphotype characteristics and virulence properties were present within the isolates of single clones in 8 of the 11 patients showing genomic micro-heterogeneity. Many of the observed phenotypic differences within clones affected the trade-off between self-preservation and nutritional competence (SPANC). We showed in 3 patients that this phenotypic variability was associated with distinct levels of RpoS in co-existing isolates. Genome mutational analysis and global proteomic comparisons in isolates from a patient revealed a star-like relationship of changes amongst clonally diverging isolates. A mathematical model demonstrated that multiple genotypes with distinct RpoS levels can co-exist as a result of the SPANC trade-off. In the cases involving infection by a single clone, we present several lines of evidence to suggest diversification during the infectious process rather than an infection by multiple isolates exhibiting a micro-heterogeneity. Our results suggest that bacteria are subject to trade-offs during an infectious process and that

  18. Effects of Substituents in Polyvinylcarbazole Structures on Their Optical Properties

    CERN Document Server

    Vertsimakha, Ya; Syromyatnikov, V; Savchenko, I

    2016-01-01

    Absorption, photoluminescence, and photoluminescence excitation spectra of solutions and thin films of N-vinylcarbazole polymers and copolymers with various substituents directly on the carbazole moiety and on the polymer chain were studied comprehensively. Polymers that were used previously to develop polymer composites with polymethine dyes having photosensitivity over a broad spectral range including the visible and near-IR regions were selected for the studies.

  19. Tuning the Rainbow: Systematic Modulation of Donor-Acceptor Systems through Donor Substituents and Solvent.

    Science.gov (United States)

    Larsen, Christopher B; van der Salm, Holly; Shillito, Georgina E; Lucas, Nigel T; Gordon, Keith C

    2016-09-06

    A series of donor-acceptor compounds is reported in which the energy of the triarylamine donor is systematically tuned through para substitution with electron-donating methoxy and electron-withdrawing cyano groups. The acceptor units investigated are benzothiadiazole (btd), dipyridophenazine (dppz), and its [ReCl(CO)3(dppz)] complex. The effect of modulating donor energy on the electronic and photophysical properties is investigated using (1)H NMR spectroscopy, DFT calculations, electrochemistry, electronic absorption and emission spectroscopies, ground state and resonance Raman spectroscopy, and transient absorption spectroscopy. Qualitative correlations between the donor energy and the properties of interest are obtained using Hammett σ(+) constants. Methoxy and cyano groups are shown to destabilize and stabilize, respectively, the frontier molecular orbitals, with the HOMO affected more significantly than the LUMO, narrowing the HOMO-LUMO band gap as the substituent becomes more electron-donating-observable as a bathochromic shift in low-energy charge-transfer absorption bands. Charge-transfer emission bands are also dependent on the electron-donating/withdrawing nature of the substituent, and in combination with the highly solvatochromic nature of charge-transfer states, emission can be tuned to span the entire visible region.

  20. Influence of the ortho-methoxyalkyl substituent on the properties of phenylboronic acids

    Science.gov (United States)

    Adamczyk-Woźniak, Agnieszka; Brzózka, Zbigniew; Dąbrowski, Marek; Madura, Izabela D.; Scheidsbach, Roy; Tomecka, Ewelina; Żukowski, Kamil; Sporzyński, Andrzej

    2013-03-01

    Novel phenylboronic acids with methoxyalkyl groups at ortho position were synthesized. Molecular and crystal structures for two compounds were determined by single crystal X-ray diffraction. In both cases the O-H⋯O hydrogen-bonded dimers are the primary supramolecular motives in which the relatively short intramolecular B-O-H⋯O hydrogen bonds are observed between boronic group and oxygen atom of the ortho-substituent. Based on the CSD data for ortho-substitued boronic acids, the relation between the twist of the boronic moiety towards phenyl ring and the intramolecular H-bond angle is discussed. The intermolecular interactions between dimeric motives were investigated with the aid of Hirshfeld surface analysis. The weak C-H⋯O and C-H⋯π interactions were detected together with the agostic B⋯H ones. Sugar-binding ability of the methoxyalkyl compounds was evaluated for D-glucose, D-fructose and D-galactose by the competition assay with Alizarin Red S.

  1. Physical Properties of Phenol Compound: Semi-empirical Calculation of Substituent Effects [Part One

    Directory of Open Access Journals (Sweden)

    Ammar A. Ibrahim

    2009-01-01

    Full Text Available Problem statement: Physical properties of phenol compound such as steric energy, charge of oxygen, ionization potential, dipole moment, LUMO and bond length have been calculated. Approach: All molecular geometries were minimized by quantum mechanic especially at (AM1 method was used to investigate the effect of a variety of substituents on the phenol (H, o-Cl, p-Cl, m-Cl, o-CH3, m-CH3, p-CH3, o-NH2, m-NH2, o-NO2, m-NO2, p-NO2, 2,4-di-NO2. Global descriptor such as electronic chemical potential (µ, hardness (η, the maximum electronic charge and global electrophilicity index (ω were determined and used to predict the (pKa values. Results: The theoretical results (predictive values found were in good agreement with experimental values. The predictive pKa calculated values by AM1 method gave excellent results with experimental values. The correlation between the predicted values especially global electrophilicity index showed excellent qualitative agreement with the experimental pKa (R2 = 0.95. Conclusion: The present research was to calculate the physical properties of phenol derivatives. Then, the calculated values were compared, quite favorably with experimental values of these properties. In future, we can predict any substituent of set of a phenol compound and compare its value with the experimental.

  2. Joint analysis of phenotypic and molecular diversity provides new insights on the genetic variability of the Brazilian physic nut germplasm bank.

    Science.gov (United States)

    Alves, Alexandre Alonso; Bhering, Leonardo Lopes; Rosado, Tatiana Barbosa; Laviola, Bruno Galvêas; Formighieri, Eduardo Fernandes; Cruz, Cosme Damião

    2013-09-01

    The genetic variability of the Brazilian physic nut (Jatropha curcas) germplasm bank (117 accessions) was assessed using a combination of phenotypic and molecular data. The joint dissimilarity matrix showed moderate correlation with the original matrices of phenotypic and molecular data. However, the correlation between the phenotypic dissimilarity matrix and the genotypic dissimilarity matrix was low. This finding indicated that molecular markers (RAPD and SSR) did not adequately sample the genomic regions that were relevant for phenotypic differentiation of the accessions. The dissimilarity values of the joint dissimilarity matrix were used to measure phenotypic + molecular diversity. This diversity varied from 0 to 1.29 among the 117 accessions, with an average dissimilarity among genotypes of 0.51. Joint analysis of phenotypic and molecular diversity indicated that the genetic diversity of the physic nut germplasm was 156% and 64% higher than the diversity estimated from phenotypic and molecular data, respectively. These results show that Jatropha genetic variability in Brazil is not as limited as previously thought.

  3. Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: a molecular and culture-based investigation.

    Directory of Open Access Journals (Sweden)

    Daniel B DiGiulio

    Full Text Available BACKGROUND: Preterm delivery causes substantial neonatal mortality and morbidity. Unrecognized intra-amniotic infections caused by cultivation-resistant microbes may play a role. Molecular methods can detect, characterize and quantify microbes independently of traditional culture techniques. However, molecular studies that define the diversity and abundance of microbes invading the amniotic cavity, and evaluate their clinical significance within a causal framework, are lacking. METHODS AND FINDINGS: In parallel with culture, we used broad-range end-point and real-time PCR assays to amplify, identify and quantify ribosomal DNA (rDNA of bacteria, fungi and archaea from amniotic fluid of 166 women in preterm labor with intact membranes. We sequenced up to 24 rRNA clones per positive specimen and assigned taxonomic designations to approximately the species level. Microbial prevalence, diversity and abundance were correlated with host inflammation and with gestational and neonatal outcomes. Study subjects who delivered at term served as controls. The combined use of molecular and culture methods revealed a greater prevalence (15% of subjects and diversity (18 taxa of microbes in amniotic fluid than did culture alone (9.6% of subjects; 11 taxa. The taxa detected only by PCR included a related group of fastidious bacteria, comprised of Sneathia sanguinegens, Leptotrichia amnionii and an unassigned, uncultivated, and previously-uncharacterized bacterium; one or more members of this group were detected in 25% of positive specimens. A positive PCR was associated with histologic chorioamnionitis (adjusted odds ratio [OR] 20; 95% CI, 2.4 to 172, and funisitis (adjusted OR 18; 95% CI, 3.1 to 99. The positive predictive value of PCR for preterm delivery was 100 percent. A temporal association between a positive PCR and delivery was supported by a shortened amniocentesis-to-delivery interval (adjusted hazard ratio 4.6; 95% CI, 2.2 to 9.5. A dose

  4. Substituent Effect on N-Benzylideneanilines by DFT Energy Partition

    Institute of Scientific and Technical Information of China (English)

    MA Yan-Ping; BAO Peng; YU Zhong-Heng

    2007-01-01

    To investigate the substituent effect on π-electron delocalization of the N-benzylideneaniline (NBA), the vertical resonance energies △EV(θ) of eleven substituted NBAs were separated into π and σ parts at the B3LYP/6-311G(d) level of the Density Functional Theory (DFT). When substituted with an electron-releasing group -OH, the calculated △EV(θ) of NBA was increased, indicative of more resonance destabilization than the mother molecule. However, when substituted with an electron-withdrawing group -NO2, the calculated △EV(θ)values indicated less resonance destabilization. The most destabilizing effect was observed especially when the -OH group located at the ortho-position of the aromatic ring in the fragment -N=CH-Ar. For most of the substituted NBA molecules, it was the destabilized σ framework that determined the destabilizing feature of the vertical resonance energy, instead of the stabilized π system. When the -NO2 substituent at the para-position of the aromatic ring of the -N=CH-Ar group, the π system had the highest stabilizing effect while the σ framework exhibited the highest destabilizing effect. While the -NO2 substituent was at the para-position of the left aromatic ring (Ar-), the NBA had the least vertical resonance energy value.

  5. Cellular and Axonal Diversity in Molecular Layer Heterotopia of the Rat Cerebellar Vermis

    Directory of Open Access Journals (Sweden)

    Sarah E. Van Dine

    2013-01-01

    Full Text Available Molecular layer heterotopia of the cerebellar primary fissure are a characteristic of many rat strains and are hypothesized to result from defect of granule cells exiting the external granule cell layer during cerebellar development. However, the cellular and axonal constituents of these malformations remain poorly understood. In the present report, we use histochemistry and immunocytochemistry to identify neuronal, glial, and axonal classes in molecular layer heterotopia. In particular, we identify parvalbumin-expressing molecular layer interneurons in heterotopia as well as three glial cell types including Bergmann glia, Olig2-expressing oligodendrocytes, and Iba1-expressing microglia. In addition, we document the presence of myelinated, serotonergic, catecholaminergic, and cholinergic axons in heterotopia indicating possible spinal and brainstem afferent projections to heterotopic cells. These findings are relevant toward understanding the mechanisms of normal and abnormal cerebellar development.

  6. Genetic Breeding and Diversity of the Genus Passiflora: Progress and Perspectives in Molecular and Genetic Studies

    Directory of Open Access Journals (Sweden)

    Carlos Bernard M. Cerqueira-Silva

    2014-08-01

    Full Text Available Despite the ecological and economic importance of passion fruit (Passiflora spp., molecular markers have only recently been utilized in genetic studies of this genus. In addition, both basic genetic researches related to population studies and pre-breeding programs of passion fruit remain scarce for most Passiflora species. Considering the number of Passiflora species and the increasing use of these species as a resource for ornamental, medicinal, and food purposes, the aims of this review are the following: (i to present the current condition of the passion fruit crop; (ii to quantify the applications and effects of using molecular markers in studies of Passiflora; (iii to present the contributions of genetic engineering for passion fruit culture; and (iv to discuss the progress and perspectives of this research. Thus, the present review aims to summarize and discuss the relationship between historical and current progress on the culture, breeding, and molecular genetics of passion fruit.

  7. Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

    DEFF Research Database (Denmark)

    Pham, L. D.; Do, Duy Ngoc; Nam, L. Q.

    2014-01-01

    The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers...... eight populations into four groups including Yorkshire, two wild populations, Mong Cai population and a group of four other indigenous populations. The Bayesian clustering with the admixture model implemented in Structure 2.1 indicated seven possible homogenous clusters among eight populations. From 79......% (Ha Lang) to 98% (Mong Cai). individuals in indigenous pigs were assigned to their own populations. The results confirmed high level of genetic diversity and shed a new light on genetic structure of Vietnam indigenous pig populations....

  8. Application of culture culture-independent molecular biology based methods to evaluate acetic acid bacteria diversity during vinegar processing.

    Science.gov (United States)

    Ilabaca, Carolina; Navarrete, Paola; Mardones, Pamela; Romero, Jaime; Mas, Albert

    2008-08-15

    Acetic acid bacteria (AAB) are considered fastidious microorganisms because they are difficult to isolate and cultivate. Different molecular approaches were taken to detect AAB diversity, independently of their capacity to grow in culture media. Those methods were tested in samples that originated during traditional vinegar production. Bacterial diversity was assessed by analysis of 16S rRNA gene, obtained by PCR amplifications of DNA extracted directly from the acetification container. Bacterial composition was analyzed by RFLP-PCR of 16S rRNA gene, Temporal Temperature Gradient Gel Electrophoresis (TTGE) separation of amplicons containing region V3-V5 of 16S rRNA gene and cloning of those amplicons. TTGE bands and clones were grouped based on their electrophoretic pattern similarity and sequenced to be compared with reference strains. The main microorganism identified in vinegar was Acetobacter pasteurianus, which at the end of the acetification process was considered to be the only microorganism present. The diversity was the highest at 2% acetic acid, where indefinite species of Gluconacetobacter xylinus/europaeus/intermedius were also present.

  9. Molecular diversity of fungi from marine oxygen-deficient environments (ODEs)

    Digital Repository Service at National Institute of Oceanography (India)

    Manohar, C.S.; Forster, D.; Kauff, F.; Stoeck, T.

    , 2009), extremely cold habitats in polar regions (Robinson 2001), deep sea sediments (Raghukumar et al. 2004, Edgcomb et al. 2011), hypersaline brine with saturated salt concentrations (Edgcomb et al. 2009), extremely dry soil crusts (States... be sufficient to identify fungal species and strains (Hugenholtz and Pace 1996). A more powerful alternative might be the faster-evolving ITS regions I and II that separate the ribosomal subunit genes from each other (O’Brien et al. 2005). Diversity estimates...

  10. Diverse Molecular Genotypes of Mycobacterium tuberculosis Complex Isolates Circulating in the Free State, South Africa

    Directory of Open Access Journals (Sweden)

    Anneke Van der Spoel van Dijk

    2016-01-01

    Full Text Available Tuberculosis is a serious public health concern especially in Africa and Asia. Studies describing strain diversity are lacking in the Free State region of South Africa. The aim of the study was to describe the diversity of Mycobacterium tuberculosis (M. tuberculosis strain families in the Free State province of South Africa. A total of 86 M. tuberculosis isolates were genotyped using spoligotyping. A 12-locus mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTRs typing was used to further characterize the resulting spoligotyping clusters. SITVITWEB identified 49 different patterns with allocation to six lineages including Latin-American-Mediterranean (LAM (18 isolates, T (14 isolates, Beijing (five isolates, S (six isolates, Haarlem (one isolate, and X (five isolates, while 37 (43.0% orphans were identified. Eight clusters included 37 isolates with identical spoligotypes (2 to 13/cluster. MIRU-VNTR typing further differentiated three spoligotyping clusters: SIT1/Beijing/MIT17, SIT33/LAM3/MIT213, and confirmed one SIT34/S/MIT311. In addition, SpolDB3/RIM assignment of the orphan strains resulted in a further 10 LAM and 13 T families. In total, LAM (28 isolates and T (27 isolates cause 63% of the individual cases of MTB in our study. The Free State has a highly diverse TB population with LAM being predominant. Further studies with inclusion of multidrug-resistant strains with larger sample size are warranted.

  11. Molecular genetic diversity and maternal origin of Chinese black-bone chicken breeds.

    Science.gov (United States)

    Zhu, W Q; Li, H F; Wang, J Y; Shu, J T; Zhu, C H; Song, W T; Song, C; Ji, G G; Liu, H X

    2014-04-29

    Chinese black-bone chickens are valued for the medicinal properties of their meat in traditional Chinese medicine. We investigated the genetic diversity and systematic evolution of Chinese black-bone chicken breeds. We sequenced the DNA of 520 bp of the mitochondrial cyt b gene of nine Chinese black-bone chicken breeds, including Silky chicken, Jinhu black-bone chicken, Jiangshan black-bone chicken, Yugan black-bone chicken, Wumeng black-bone chicken, Muchuan black-bone chicken, Xingwen black-bone chicken, Dehua black-bone chicken, and Yanjin black-bone chicken. We found 13 haplotypes. Haplotype and nucleotide diversity of the nine black-bone chicken breeds ranged from 0 to 0.78571 and 0.00081 to 0.00399, respectively. Genetic diversity was the richest in Jinhu black-bone chickens and the lowest in Yanjin black-bone chickens. Analysis of phylogenetic trees for all birds constructed based on hyplotypes indicated that the maternal origin of black-bone chickens is predominantly from three subspecies of red jungle fowl. These results provide basic data useful for protection of black-bone chickens and help determine the origin of domestic chickens.

  12. Genetic Diversity of Tropical Hybrid Rice Germplasm Measured by Molecular Markers

    Institute of Scientific and Technical Information of China (English)

    HE Zhi-zhou; XIE Fang-ming; CHEN Li-yun; Madonna Angelita DELA PAZ

    2012-01-01

    Investigation of genetic diversity and relationships among breeding lines is of great importance to facilitate parent selection in hybrid rice breeding programs.In this study,we characterized 168 hybrid rice parents from International Rice Research Institute with 207 simple sequence repeat (SSR) and 353 single nucleotide polymorphism (SNP) markers.A total of 1 267 SSR and 706 SNP alleles were detected with the averages of 6.1 (SSR) and 2.0 (SNP) alleles per locus respectively across all lines.Based on the genetic distances estimated from the SSR and SNP markers separately and combined,the unrooted neighbor-joining cluster and STRUCTURE analyses consistently separated the 168 hybrid rice parents into two major groups:B-line and R-line,which is consistent with known parent pedigree information.The genetic distance matrices derived from the SSR and SNP genotyping were highly correlated (r=0.81,P 0.001),indicating that both of the SSR and SNP markers have distinguishable power to detect polymorphism and are appropriate for genetic diversity analysis among tropical hybrid rice parents.A subset of 60 SSR markers were also chosen by the Core Hunter with 368 alleles,and the cluster analysis based on the total and subset of SSR markers highly corresponded at r =0.91 (P < 0.001 ),suggesting that fewer SSR markers can be used to classify and evaluate genetic diversity among parental lines.

  13. Analysis of genetic diversity in pigeon pea germplasm using retrotransposon-based molecular markers

    Indian Academy of Sciences (India)

    MANEESHA; KAILASH C. UPADHYAYA

    2017-09-01

    Pigeon pea (Cajanus cajan), an important legume crop is predominantly cultivated in tropical and subtropical regions of Asia and Africa. It is normally considered to have a low degree of genetic diversity, an impediment in undertaking crop improvement programmes.We have analysed genetic polymorphism of domesticated pigeon pea germplasm (47 accessions) across the world using earlier characterized panzee retrotransposon-based molecularmarkers. Itwas conjectured that since retrotransposons are interspersed throughout the genome, retroelements-based markers would be able to uncover polymorphism possibly inherent in the diversity of retroelement sequences. Two PCR-based techniques, sequence-specific amplified polymorphism (SSAP) and retrotransposon microsatellite amplified polymorphism (REMAP) were utilized for the analyses.We show that a considerable degree of polymorphism could be detected using these techniques. Three primer combinations in SSAP generated 297 amplified products across 47 accessionswith an average of 99 amplicons per assay. Degree of polymorphism varied from 84–95%. In the REMAP assays, the number of amplicons was much less but up to 73% polymorphism could be detected. On the basis of similarity coefficients, dendrograms were constructed. The results demonstrate that the retrotransposon-based markers could serve as a better alternative for the assessment of genetic diversity in crops with apparent low genetic base.

  14. Acrocomia emensis (Arecaceae) genetic structure and diversity using SSR molecular markers.

    Science.gov (United States)

    Neiva, D S; Melo Júnior, A F; Oliveira, D A; Royo, V A; Brandão, M M; Menezes, E V

    2016-03-24

    Acrocomia emensis, popularly known as the creeping tucum, belongs to the family Arecaceae, and is an oilseed specie of the Brazilian Savannah. The expansion of agricultural activity has rapidly destroyed its natural habitat, leading to a decrease in its population size. Genetic studies can be used to investigate the genetic variability, and may assist with the charting future conservation strategies. In this study the genetic diversity and structure of 150 individuals sampled in three locations in Minas Gerais were analysed, based on the transferability of six microsatellite markers, previously developed for A. aculeata. The results indicate that the populations studied have low levels of genetic variability (Ho = 0.148) and high, positive and significant inbreeding coefficient, indicating an excess of homozygotes. The average heterozygosity within the population (Hs = 0.700) accounted for 95.03% of the total genetic diversity, indicating that there is greater variability within population than between them, consistent with low genetic differentiation between population (GST = 0.046). Bayesian analysis identified three distinct groups; however, populations shared large numbers of alleles, which can be explained by the reduced distance between populations. These results reveal the need to implement genetic conservation programs for the maintenance of this species and to prioritize population from Bonito and Brasília, which showed the lowest values of genetic diversity.

  15. Genetic Diversity Analysis of Iranian Jujube Ecotypes (Ziziphus spp. Using RAPD Molecular Marker

    Directory of Open Access Journals (Sweden)

    S Abbasi

    2012-12-01

    Full Text Available Jujube (Ziziphus jujuba Mill. is a valuable medicinal plant which is important in Iranian traditional medicines. Although the regional plants such as jujube play an important role in our economy, but they are forgotten in research and technology. Considering the economic and medicinal importance of jujube, the first step in breeding programs is determination of the genetic diversity among the individuals. 34 ecotypes of jujube, which have been collected from eight provinces of Iran, were used in this study. The genetic relationships of Iranian jujube ecotypes were analyzed using Random Amplified Polymorphic DNA (RAPD marker. Six out of 15 random decamer primers applied for RAPD analysis, showed an informative polymorphism. According to clustering analysis using UPGMA's methods, the ecotypes were classified into two major groups at the 0.81 level of genetic similarity. The highest value of similarity coefficient (0.92 was detected between Mazandaran and Golestan ecotypes and the most genetic diversity was observed in ecotypes of Khorasan-Jonoubi. The affinity of Khorasan-Jonoubi and Esfahan ecotypes indicated a possible common origin for the variation in these areas. Results indicated that RAPD analysis could be successfully used for the estimation of genetic diversity among Ziziphus ecotypes and it can be useful for further investigations.

  16. Molecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers

    Science.gov (United States)

    Pomegranate (Punica granatum L.) is one of the oldest known edible fruits and more and more it arouse interest of scientific community given its numerous biological activities. However, information about its genetic resources and characterization using reliable molecular markers are still scarce. In...

  17. Genetic Diversity of Some Sweet Cherry Cultivars Based on Molecular Markers

    Directory of Open Access Journals (Sweden)

    Ioana Virginia Berindean

    2016-11-01

    Full Text Available Sweet cherry (Prunus avium L., originated around the Caspian and Black Sea, is an important fruit tree species of economic interest, and hence, breeding and conservation are requested (. Genetic analysis at the molecular level can be used effectively to study molecular polymorphism existing between intraspecific and interspecific tree species and phylogenetic relationships between them and their hybrids. The purpose of this study was to characterize and determine genetic relationships among the sweet cherry native genotypes belonging to Fruit Research & Development Station Bistrita, Romania, using RAPD markers. To eliminate the existence of possible synonyms from national romanian collection, we collect four Van cultivars, from four different national collection. For molecular analysis of the 16 varieties of sweet cherry were considered 13 RAPD primers selected from the literature. They were later used to determine the genetic variability at the molecular level using PAST program, and the dendrogram was generated based on Jaccard’s genetic distance. The dendrogram constructed by PAST software. The quantity and quality of the DNA obtained was suitable to achieve PCR amplification step. Only seven out of the 13 RAPD primers have generate polymorphic bands. The rest of seven were monomorphics. The most polymorphic primer was OPB10 which generated 11 bands from which 100% were polymorphic.Seven RAPD primers generated a high level of polymorphism which allowed to divide these cherry varieties into two groups according to their genetic geographical origin and the pedigree.

  18. An exploratory study of microbial diversity in sinus infections of cystic fibrosis patients by molecular methods

    DEFF Research Database (Denmark)

    Rudkjøbing, Vibeke Børsholt; Aanaes, Kasper; Wolff, Tine Yding;

    2014-01-01

    BACKGROUND: For the first time microorganisms in CF sinuses are investigated by molecular methods in response to an absence of anaerobes in CF sinus samples during a two-year period at the Copenhagen CF center. METHODS: Endoscopic sinus surgery was performed in 19 CF patients. DNA from intact...

  19. Genetic Diversity of High and Low Molecular Weight Glutenin Subunits in Algerian Aegilops geniculata

    Directory of Open Access Journals (Sweden)

    Asma MEDOURI

    2014-12-01

    Full Text Available Aegilops geniculata Roth is an annual grass relative to cultivated wheat and is widely distributed in North Algeria. Endosperm storage proteins of wheat and its relatives, namely glutenins and gliadins, play an important role in dough properties and bread making quality. In the present study, the different alleles encoded at the four glutenin loci (Glu-M1, Glu-U1, Glu-M3 and Glu-U3 were identified from thirty five accessions of the tetraploid wild wheat A. geniculata collected in Algeria using Sodium dodecyl Sulfate - Polyacrylamide Gel Electrophoresis (SDS-PAGE. At Glu-M1 and Glu-U1 loci, encoding high molecular weight glutenin subunits (HMW-GS or A-subunits, 15 and 12 alleles were observed respectively, including one new subunit. B-Low molecular weight glutenin subunits zone (B-LMW-GS displayed a far greater variation, as 28 and 25 alleles were identified at loci Glu-M3 and Glu-U3 respectively. Thirty two subunits patterns were revealed at the C subunits- zone and a total of thirty four patterns resulted from the genetic combination of the two zones (B- and C-zone. The wide range of glutenin subunits variation (high molecular weight glutenin subunits and low molecular weight glutenin subunits in this species has the potential to enhance the genetic variability for improving the quality of wheat./span>

  20. Molecular diversity of RelA enzyme in marine bacteria- A bioinformatics analysis

    Digital Repository Service at National Institute of Oceanography (India)

    Nath, A.I.V.; Tresa, R.A.T.; Alornekar, A.; Varghese, N.S.

    cloning, nucleotide sequence, and deletion of the relA gene. Journal of Bacteriology. 176 (19), 5949-5957. 5. Gerhard Klebe (2000). Recent developments in structure-based drug design. Journal of Molecular Medicine. 78, 269-281 . 6. Gropp Michal, Strausz...

  1. Design and synthesis of new biprivileged molecular scaffolds: indolo-fused benzodiazepinyl/quinoxalinyl benzimidazoles.

    Science.gov (United States)

    Barve, Indrajeet J; Chen, Chan-Yu; Salunke, Deepak B; Chung, Wen-Sheng; Sun, Chung-Ming

    2012-06-01

    The present article describes the design and synthesis of new biprivileged molecular scaffolds with diverse structural features. Commercially available, simple heterocyclic building blocks such as 4-fluoro-3-nitrobenzoic acid, 2-chloro-3-nitrobenzoic acid, and indoline were utilized for the synthesis of the novel heterocycles. Pictet-Spengler-type condensation was used as a key step to construct tetracyclic indolo-benzodiazepines and indolo-quinoxalines linked with substituted benzimidazoles. Analysis of single crystals of representative compounds showed that these molecular skeletons have the potential to present various substituents with distinct three-dimensional orientations.

  2. A diverse population of Cryptococcus gattii molecular type VGIII in southern Californian HIV/AIDS patients.

    Directory of Open Access Journals (Sweden)

    Edmond J Byrnes

    2011-09-01

    Full Text Available Cryptococcus gattii infections in southern California have been reported in patients with HIV/AIDS. In this study, we examined the molecular epidemiology, population structure, and virulence attributes of isolates collected from HIV/AIDS patients in Los Angeles County, California. We show that these isolates consist almost exclusively of VGIII molecular type, in contrast to the VGII molecular type isolates causing the North American Pacific Northwest outbreak. The global VGIII population structure can be divided into two molecular groups, VGIIIa and VGIIIb. Isolates from the Californian patients are virulent in murine and macrophage models of infection, with VGIIIa significantly more virulent than VGIIIb. Several VGIII isolates are highly fertile and produce abundant sexual spores that may serve as infectious propagules. The a and α VGIII MAT locus alleles are largely syntenic with limited rearrangements compared to the known VGI (a/α and VGII (α MAT loci, but each has unique characteristics including a distinct deletion flanking the 5' VGIII MATa alleles and the α allele is more heterogeneous than the a allele. Our studies indicate that C. gattii VGIII is endemic in southern California, with other isolates originating from the neighboring regions of Mexico, and in rarer cases from Oregon and Washington state. Given that >1,000,000 cases of cryptococcal infection and >620,000 attributable mortalities occur annually in the context of the global AIDS pandemic, our findings suggest a significant burden of C. gattii may be unrecognized, with potential prognostic and therapeutic implications. These results signify the need to classify pathogenic Cryptococcus cases and highlight possible host differences among the C. gattii molecular types influencing infection of immunocompetent (VGI/VGII vs. immunocompromised (VGIII/VGIV hosts.

  3. Molecular diversity, population structure, and linkage disequilibrium in a worldwide collection of tobacco (Nicotiana tabacum L. germplasm

    Directory of Open Access Journals (Sweden)

    Fricano Agostino

    2012-03-01

    Full Text Available Abstract Background The goals of our study were to assess the phylogeny and the population structure of tobacco accessions representing a wide range of genetic diversity; identify a subset of accessions as a core collection capturing most of the existing genetic diversity; and estimate, in the tobacco core collection, the extent of linkage disequilibrium (LD in seven genomic regions using simple sequence repeat (SSR markers. To this end, a collection of accessions were genotyped with SSR markers. Molecular diversity was evaluated and LD was analyzed across seven regions of the genome. Results A genotyping database for 312 tobacco accessions was profiled with 49 SSR markers. Principal Coordinate Analysis (PCoA and Bayesian cluster analysis revealed structuring of the tobacco population with regard to commercial classes and six main clades were identified, which correspond to "Oriental", Flue-Cured", "Burley", "Dark", "Primitive", and "Other" classes. Pairwise kinship was calculated between accessions, and an overall low level of co-ancestry was observed. A set of 89 genotypes was identified that captured the whole genetic diversity detected at the 49 loci. LD was evaluated on these genotypes, using 422 SSR markers mapping on seven linkage groups. LD was estimated as squared correlation of allele frequencies (r2. The pattern of intrachromosomal LD revealed that in tobacco LD extended up to distances as great as 75 cM with r2 > 0.05 or up to 1 cM with r2 > 0.2. The pattern of LD was clearly dependent on the population structure. Conclusions A global population of tobacco is highly structured. Clustering highlights the accessions with the same market class. LD in tobacco extends up to 75 cM and is strongly dependent on the population structure.

  4. Molecular characterization and genetic diversity analysis of different rice cultivars by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Allhgholipour Mehrzad

    2014-01-01

    Full Text Available A total of 52 rice SSR markers well distributed on 12 chromosomes were used to characterize and assess the genetic diversity among ninety four rice genotypes. The total number of polymorphic alleles was 361 alleles with the average of 5.86 alleles per SSR locus. The study revealed that some markers such as RM276 and RM5642 on chromosome 6 and RM14 and RM1 on chromosome 1 have more than 9 observed alleles compared to other primers like RM16, RM207, RM208 and RM317 with 3-4 alleles. The highest and lowest PIC values were observed for primers RM276 (0.892 and RM208 (0.423 respectively. Using Shannon´s diversity index, a mean genetic diversity of 1.641 was obtained from the analysis, indicating a high level of genetic variation among these cultivars. Cluster analysis using the complete linkage method based on jaccard similarity coefficient revealed that all genotypes were classified to nine clusters at genetic similarity level of 0.010.75, which contained 12, 16, 2, 18, 3, 6, 16, 10 and 11 varieties, respectively. Results of discriminant analysis showed that the nine cluster groups were confirmed at high levels of correct percent (96.8 and revealed true differences among these clusters. As a final result from this study, we selected eight cultivars from different cluster including Daylamani, Tarom mohali (landrace rice cultivars, RI1843046, Back cross line, RI184472, RI184421 (promising cultivars, Line 23 and IR50 (IRRI lines as parents. All of the selected cultivars will be arranged in complete diallel design to obtain combining abilities, gene effects and heterosis for each important morphology and physico-chemical characters.

  5. Molecular diversity, metabolic transformation, and evolution of carotenoid feather pigments in cotingas (Aves: Cotingidae).

    Science.gov (United States)

    Prum, Richard O; LaFountain, Amy M; Berro, Julien; Stoddard, Mary Caswell; Frank, Harry A

    2012-12-01

    Carotenoid pigments were extracted from 29 feather patches from 25 species of cotingas (Cotingidae) representing all lineages of the family with carotenoid plumage coloration. Using high-performance liquid chromatography (HPLC), mass spectrometry, chemical analysis, and ¹H-NMR, 16 different carotenoid molecules were documented in the plumages of the cotinga family. These included common dietary xanthophylls (lutein and zeaxanthin), canary xanthophylls A and B, four well known and broadly distributed avian ketocarotenoids (canthaxanthin, astaxanthin, α-doradexanthin, and adonixanthin), rhodoxanthin, and seven 4-methoxy-ketocarotenoids. Methoxy-ketocarotenoids were found in 12 species within seven cotinga genera, including a new, previously undescribed molecule isolated from the Andean Cock-of-the-Rock Rupicola peruviana, 3'-hydroxy-3-methoxy-β,β-carotene-4-one, which we name rupicolin. The diversity of cotinga plumage carotenoid pigments is hypothesized to be derived via four metabolic pathways from lutein, zeaxanthin, β-cryptoxanthin, and β-carotene. All metabolic transformations within the four pathways can be described by six or seven different enzymatic reactions. Three of these reactions are shared among three precursor pathways and are responsible for eight different metabolically derived carotenoid molecules. The function of cotinga plumage carotenoid diversity was analyzed with reflectance spectrophotometry of plumage patches and a tetrahedral model of avian color visual perception. The evolutionary history of the origin of this diversity is analyzed phylogenetically. The color space analyses document that the evolutionarily derived metabolic modifications of dietary xanthophylls have resulted in the creation of distinctive orange-red and purple visual colors.

  6. Diversity of microorganisms in decaying maize stalks revealed by a molecular method.

    Science.gov (United States)

    Yang, Ming-Xia; Zhang, Han-Bo

    2007-08-01

    Microbial diversity in decaying maize stalk was characterized by constructing and analyzing rRNA gene clone library. Total 47 OTUs were obtained from 82 bacterial clones, including Proteobacteria (64.6%), Actinobacteria (30.5%), Bacteroidetes (2.4%) and Firmicutes (2.4%). Most proteobacterial clones were members of Rhizobium, Pseudomonas and Stenotrophomonas. Eighty-four percent of Actinobacteria was related to Microbacterium. Only 14 OTUs were identified from 124 fungal clones, including Ascomycota (88%) and Basidiomycota (12%). Sixty percent of Ascomycota were members of Eupenicillium and Paecilomyces but all Basidiomycota were close to Kurtzmanomyces nectairei.

  7. Genetic diversity in two introduced biofouling amphipods (Amphipods valida and Jassa marmorata) along the Pacific North American coast: investigation into molecular identification and cryptic diversity

    Science.gov (United States)

    We investigated patterns of genetic diversity among invasive populations of A. valida and J. marmorata from the Pacific North American coast to assess the accuracy of morphological identification and determine whether or not cryptic diversity and multiple introductions contribute...

  8. Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws.

    Science.gov (United States)

    Smajs, David; Norris, Steven J; Weinstock, George M

    2012-03-01

    Pathogenic uncultivable treponemes, similar to syphilis-causing Treponema pallidum subspecies pallidum, include T. pallidum ssp. pertenue, T. pallidum ssp. endemicum and Treponema carateum, which cause yaws, bejel and pinta, respectively. Genetic analyses of these pathogens revealed striking similarity among these bacteria and also a high degree of similarity to the rabbit pathogen, Treponema paraluiscuniculi, a treponeme not infectious to humans. Genome comparisons between pallidum and non-pallidum treponemes revealed genes with potential involvement in human infectivity, whereas comparisons between pallidum and pertenue treponemes identified genes possibly involved in the high invasivity of syphilis treponemes. Genetic variability within syphilis strains is considered as the basis of syphilis molecular epidemiology with potential to detect more virulent strains, whereas genetic variability within a single strain is related to its ability to elude the immune system of the host. Genome analyses also shed light on treponemal evolution and on chromosomal targets for molecular diagnostics of treponemal infections.

  9. Data supporting a molecular phylogeny of the hyper-diverse genus Brueelia

    OpenAIRE

    Bush, Sarah E.; Jason D. Weckstein; Gustafsson, Daniel R.; Julie Allen; Emily DiBlasi; Shreve, Scott M.; Rachel Boldt; Skeen, Heather R.; Johnson, Kevin P.

    2015-01-01

    Data is presented in support of a phylogenetic reconstruction of one of the largest, and most poorly understood, groups of lice: the Brueelia-complex (Bush et al., 2015 [1]). Presented data include the voucher information and molecular data (GenBank accession numbers) of 333 ingroup taxa within the Brueelia-complex and 30 outgroup taxa selected from across the order Phthiraptera. Also included are phylogenetic reconstructions based on Bayesian inference analyses of combined COI and EF-1α sequ...

  10. Molecular Communication Model for Targeted Drug Delivery in Multiple Disease Sites With Diversely Expressed Enzymes.

    Science.gov (United States)

    Chude-Okonkwo, Uche A K; Malekian, Reza; Maharaj, B T Sunil

    2016-04-01

    Targeted drug delivery (TDD) for disease therapy using liposomes as nanocarriers has received extensive attention in the literature. The liposome's ability to incorporate capabilities such as long circulation, stimuli responsiveness, and targeting characteristics, makes it a versatile nanocarrier. Timely drug release at the targeted site requires that trigger stimuli such as pH, light, and enzymes be uniquely overexpressed at the targeted site. However, in some cases, the targeted sites may not express trigger stimuli significantly, hence, achieving effective TDD at those sites is challenging. In this paper, we present a molecular communication-based TDD model for the delivery of therapeutic drugs to multiple sites that may or may not express trigger stimuli. The nanotransmitter and nanoreceiver models for the molecular communication system are presented. Here, the nanotransmitter and nanoreceiver are injected into the targeted body system's blood network. The compartmental pharmacokinetics model is employed to model the transportation of these therapeutic nanocarriers to the targeted sites where they are meant to anchor before the delivery process commences. We also provide analytical expressions for the delivered drug concentration. The effectiveness of the proposed model is investigated for drug delivery on tissue surfaces. Results show that the effectiveness of the proposed molecular communication-based TDD depends on parameters such as the total transmitter volume capacity, the receiver radius, the diffusion characteristic of the microenvironment of the targeted sites, and the concentration of the enzymes associated with the nanotransmitter and the nanoreceiver designs.

  11. Molecular Diversity Assessment Using Sequence Related Amplified Polymorphism (SRAP Markers in Vicia faba L.

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    Salem S. Alghamdi

    2012-12-01

    Full Text Available Sequence-related amplified polymorphism (SRAP markers were used to assess the genetic diversity and relationship among 58 faba bean (Vicia faba L. genotypes. Fourteen SRAP primer combinations amplified a total of 1036 differently sized well-resolved peaks (fragments, of which all were polymorphic with a 0.96 PIC value and discriminated all of the 58 faba bean genotypes. An average pairwise similarity of 21% was revealed among the genotypes ranging from 2% to 65%. At a similarity of 28%, UPGMA clustered the genotypes into three main groups comprising 78% of the genotypes. The local landraces and most of the Egyptian genotypes in addition to the Sudan genotypes were grouped in the first main cluster. The advanced breeding lines were scattered in the second and third main clusters with breeding lines from the ICARDA and genotypes introduced from Egypt. At a similarity of 47%, all the genotypes formed separated clusters with the exceptions of Hassawi 1 and Hassawi 2. Group analysis of the genotypes according to their geographic origin and type showed that the landraces were grouped according to their origin, while others were grouped according to their seed type. To our knowledge, this is the first application of SRAP markers for the assessment of genetic diversity in faba bean. Such information will be useful to determine optimal breeding strategies to allow continued progress in faba bean breeding.

  12. Molecular diversity of human parvovirus B19 during two outbreaks of erythema infectiosum in Brazil

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    Rita de Cássia Nasser Cubel Garcia

    Full Text Available Abstract This study was conducted to provide information on the genetic diversity of human parvovirus B19 (B19V circulating in the municipality of Niterói, Rio de Janeiro, Southeast Brazil during 1996–2006, a period with two distinct outbreaks of B19V infection: 1999–2000 and 2004–2005. A total of 27 sera from patients with erythema infectiosum and five sera from HIV-infected patients that tested positive for B19V DNA during the study period were analyzed. To genotype B19V strains, a semi-nested PCR for partial amplification of the capsid gene was performed and sequence analysis revealed that 31 sequences belonged to subgenotype 1a (G1a of the main genotype 1 and one sequence was characterized as subgenotype 3b (G3b. The phylogenetic tree supported the division of the G1a into two well-defined clades with 1.3% of divergence. The low diversity of the G1a strains may be explained by the fact that all patients had acute B19V infection and 30/32 sera were collected during two distinct outbreaks. The G3b strain was from an HIV-infected patient who seroconverted to anti-B19 IgG antibodies in September/2005. This is the first report of G3b in the state of Rio de Janeiro.

  13. Study Of Genetic Diversity Between Grasspea Landraces Using Morphological And Molecular Marker

    Science.gov (United States)

    Sedehi, Abbasali Vahabi; Lotfi, Asefeh; Solooki, Mahmood

    2008-01-01

    Grass pea is a beneficial crop to Iran since it has some major advantageous such as high grain and forage quality, high drought tolerance and medium level of salinity tolerance and a good native germplasm variation which accessible for breeding programs. This study was carried out to evaluate morphological traits of the grass pea landraces using a randomized complete block design with 3 replications at Research Farm of Isfahan University of Technology. To evaluate genetic diversity of 14 grass pea landraces from various locations in Iran were investigated using 32 RAPD & ISJ primers at Biocenter of University of Zabol. Analysis of variance indicated a highly significant differences among 14 grass pea landrace for the morphological traits. Average of polymorphism percentage of RAPD primer was 73.9%. Among used primer, 12 random primers showed polymorphism and a total of 56 different bands were observed in the genotypes. Jafar-abad and Sar-chahan genotypes with similarity coefficient of 66% and Khoram-abad 2 and Khoram-abad 7 genotypes with similarity coefficient of 3% were the most related and the most distinct genotypes, respectively. Fourteen primers out of 17 semi random primers produced 70 polymorphic bands which included 56% of the total 126 produced bands. Genetic relatedness among population was investigated using Jacard coefficient and unweighted pair group mean analysis (UPGMA) algorithm. The result of this research verified possibility of use of RAPD & ISJ markers for estimation of genetic diversity, management of genetic resources and determination of repetitive accessions in grass pea.

  14. Molecular and functional diversity of yeast and fungal lipases: their role in biotechnology and cellular physiology.

    Science.gov (United States)

    Gupta, Rani; Kumari, Arti; Syal, Poonam; Singh, Yogesh

    2015-01-01

    Lipase catalyzes hydrolysis of fats in lipid water interphase and perform variety of biotransformation reactions under micro aqueous conditions. The major sources include microbial lipases; among these yeast and fungal lipases are of special interest because they can carry out various stereoselective reactions. These lipases are highly diverse and are categorized into three classes on the basis of oxyanion hole: GX, GGGX and Y. The detailed phylogenetic analysis showed that GX family is more diverse than GGGX and Y family. Sequence and structural comparisons revealed that lipases are conserved only in the signature sequence region. Their characteristic structural determinants viz. lid, binding pocket and oxyanion hole are hotspots for mutagenesis. Few examples are cited in this review to highlight the multidisciplinary approaches for designing novel enzyme variants with improved thermo stability and substrate specificity. In addition, we present a brief account on biotechnological applications of lipases. Lipases have also gained attention as virulence factors, therefore, we surveyed the role of lipases in yeast physiology related to colonization, adhesion, biofilm formation and pathogenesis. The new genomic era has opened numerous possibilities to genetically manipulate lipases for food, fuel and pharmaceuticals.

  15. Molecular diversity and phylogeny of rhizobia associated with Lablab purpureus (Linn.) grown in Southern China.

    Science.gov (United States)

    Chang, Yue Li; Wang, En Tao; Sui, Xin Hua; Zhang, Xiao Xia; Chen, Wen Xin

    2011-06-01

    As an introduced plant, Lablab purpureus serves as a vegetable, herbal medicine, forage and green manure in China. In order to investigate the diversity of rhizobia associated with this plant, a total of 49 rhizobial strains isolated from ten provinces of Southern China were analyzed in the present study with restriction fragment length polymorphism and/or sequence analyses of housekeeping genes (16S rRNA, IGS, atpD, glnII and recA) and symbiotic genes (nifH and nodC). The results defined the L. purpureus rhizobia as 24 IGS-types within 15 rrs-IGS clusters or genomic species belonging to Bradyrhizobium, Rhizobium, Ensifer (synonym of Sinorhizobium) and Mesorhizobium. Bradyrhizobium spp. (81.6%) were the most abundant isolates, half of which were B. elkanii. Most of these rhizobia induced nodules on L. purpureus, but symbiotic genes were only amplified from the Bradyrhizobium and Rhizobium leguminosarum strains. The nodC and nifH phylogenetic trees defined five lineages corresponding to B. yuanmingense, B. japonicum, B. elkanii, B. jicamae and R. leguminosarum. The coherence of housekeeping and symbiotic gene phylogenies demonstrated that the symbiotic genes of the Lablab rhizobia were maintained mainly through vertical transfer. However, a putative lateral transfer of symbiotic genes was found in the B. liaoningense strain. The results in the present study clearly revealed that L. purpureus was a promiscuous host that formed nodules with diverse rhizobia, mainly Bradyrhizobium species, harboring different symbiotic genes.

  16. Molecular Diversity and Predictability of Vibrio parahaemolyticus along the Georgian coastal zone of the Black Sea

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    Bradd J. Haley

    2014-02-01

    Full Text Available Vibrio parahaemolyticus is a leading cause of seafood-related gastroenteritis and is also an autochthonous member of marine and estuarine environments worldwide. One hundred seventy strains of V. parahaemolyticus were isolated from water and plankton samples collected along the Georgian coast of the Black Sea during 28 months of sample collection. All isolated strains were tested for presence of tlh, trh, and tdh. A subset of strains were serotyped and tested for additional factors and markers of pandemicity. Twenty-six serotypes, five of which are clinically relevant, were identified. Although all 170 isolates were negative for tdh, trh, and the Kanagawa Phenomenon, 7 possessed the GS-PCR sequence and 27 the 850 bp sequence of V. parahaemolyticus pandemic strains. The V. parahaemolyticus population in the Black Sea was estimated to be genomically heterogeneous by rep-PCR and the serodiversity observed did not correlate with rep-PCR genomic diversity. Statistical modeling was used to predict presence of V. parahaemolyticus as a function of water temperature, with strongest concordance observed for Green Cape site samples (Percent of total variance = 70, P < 0.001. Results demonstrate a diverse population of V. parahaemolyticus in the Black Sea, some of which carry pandemic markers, with increased water temperature correlated to an increase in abundance of V. parahaemolyticus.

  17. Molecular diversity in Coffea canephora germplasm conserved and cultivated in Brazil

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    Flávio de França Souza

    2013-12-01

    Full Text Available This work aimed to characterize accessions that represent the C. canephora germplasm conserved and cultivated in Brazil. A total of 130 accessions from germplasm banks of IAC (São Paulo, UFV (Minas Gerais and also collected in plantations of the State of Espírito Santo and Rondônia were evaluated with a set of 20 new microsatellite primers. Multivariate methods were used to estimate the relationship among the accessions. High level of polymorphism and two major diversity clusters were identified. First cluster was composed by the accessions conserved in the IAC and UFV collections and the second was formed by accessions collected in areas under cultivation. Accessions from Espírito Santo and Rondônia were clear separated, composing two subclusters. Despite the great polymorphism found in Brazilian plantations, the diversity may be increased, because a new threshold in the genetic gains is expected on breeding programs with the intensification of the use of conserved germplasm.

  18. Identifying Genetic Hotspots by Mapping Molecular Diversity of Widespread Trees: When Commonness Matters.

    Science.gov (United States)

    Souto, Cintia P; Mathiasen, Paula; Acosta, María Cristina; Quiroga, María Paula; Vidal-Russell, Romina; Echeverría, Cristian; Premoli, Andrea C

    2015-01-01

    Conservation planning requires setting priorities at the same spatial scale at which decision-making processes are undertaken considering all levels of biodiversity, but current methods for identifying biodiversity hotspots ignore its genetic component. We developed a fine-scale approach based on the definition of genetic hotspots, which have high genetic diversity and unique variants that represent their evolutionary potential and evolutionary novelties. Our hypothesis is that wide-ranging taxa with similar ecological tolerances, yet of phylogenetically independent lineages, have been and currently are shaped by ecological and evolutionary forces that result in geographically concordant genetic patterns. We mapped previously published genetic diversity and unique variants of biparentally inherited markers and chloroplast sequences for 9 species from 188 and 275 populations, respectively, of the 4 woody dominant families of the austral temperate forest, an area considered a biodiversity hotspot. Spatial distribution patterns of genetic polymorphisms differed among taxa according to their ecological tolerances. Eight genetic hotspots were detected and we recommend conservation actions for some in the southern Coastal Range in Chile. Existing spatially explicit genetic data from multiple populations and species can help to identify biodiversity hotspots and guide conservation actions to establish science-based protected areas that will preserve the evolutionary potential of key habitats and species.

  19. Molecular diversity of Mycobacterium tuberculosis isolates from patients with pulmonary tuberculosis in Mozambique

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    Hill Véronique

    2010-07-01

    Full Text Available Abstract Background Mozambique is one of the countries with the highest burden of tuberculosis (TB in Sub-Saharan Africa, and information on the predominant genotypes of Mycobacterium tuberculosis circulating in the country are important to better understand the epidemic. This study determined the predominant strain lineages that cause TB in Mozambique. Results A total of 445 M. tuberculosis isolates from seven different provinces of Mozambique were characterized by spoligotyping and resulting profiles were compared with the international spoligotyping database SITVIT2. The four most predominant lineages observed were: the Latin-American Mediterranean (LAM, n = 165 or 37%; the East African-Indian (EAI, n = 132 or 29.7%; an evolutionary recent but yet ill-defined T clade, (n = 52 or 11.6%; and the globally-emerging Beijing clone, (n = 31 or 7%. A high spoligotype diversity was found for the EAI, LAM and T lineages. Conclusions The TB epidemic in Mozambique is caused by a wide diversity of spoligotypes with predominance of LAM, EAI, T and Beijing lineages.

  20. Lineage diversity and size disparity in Musteloidea: testing patterns of adaptive radiation using molecular and fossil-based methods.

    Science.gov (United States)

    Law, Chris J; Slater, Graham J; Mehta, Rita S

    2017-05-04

    Adaptive radiation is hypothesized to be a primary mechanism that drives the remarkable species diversity and morphological disparity across the Tree of Life. Tests for adaptive radiation in extant taxa are traditionally estimated from calibrated molecular phylogenies with little input from extinct taxa. With 85 putative species in 33 genera and over 400 described extinct species, the carnivoran superfamily Musteloidea is a prime candidate to investigate patterns of adaptive radiation using both extant- and fossil-based macroevolutionary methods. The species diversity and equally impressive ecological and phenotypic diversity found across Musteloidea is often attributed to 2 adaptive radiations coinciding with 2 major climate events, the Eocene-Oligocene transition and the Mid-Miocene Climate Transition. Here, we compiled a novel time-scaled phylogeny for 88% of extant musteloids and used it as a framework for testing the predictions of adaptive radiation hypotheses with respect to rates of lineage diversification and phenotypic evolution. Contrary to expectations, we found no evidence for rapid bursts of lineage diversification at the origin of Musteloidea, and further analyses of lineage diversification rates using molecular and fossil-based methods did not find associations between rates of lineage diversification and the Eocene-Oligocene transition or Mid-Miocene Climate Transition as previously hypothesized. Rather, we found support for decoupled diversification dynamics driven by increased clade carrying capacity in the branches leading to a subclade of elongate mustelids. Supporting decoupled diversification dynamics between the subclade of elongate mustelids and the ancestral musteloid regime is our finding of increased rates of body length evolution, but not body mass evolution, within the decoupled mustelid subclade. The lack of correspondence in rates of body mass and length evolution suggest that phenotypic evolutionary rates under a single

  1. Substituent distribution changes the pasting and emulsion properties of octenylsuccinate starch.

    Science.gov (United States)

    Wang, Chan; He, Xiaowei; Fu, Xiong; Huang, Qiang; Zhang, Bin

    2016-01-01

    An improved preparation method of octenylsuccinate (OS) starch under high shear condition was described in this study. The distribution of OS substituents at the granular and molecular levels was assessed by confocal laser scanning microscopy (CLSM), β-amylase hydrolysis, chromatographic and (1)H NMR techniques. We found that the OS group distribution could change the pasting and emulsion properties of OS starches. Specifically, more uniform OS group distribution was identified in the central region of OS starch granules prepared under high shear condition (H-OS-starch), and OS groups were located both near the branching points and the non-reducing ends. More OS groups exposed outside of non-reducing ends would access the interface between oil and water and give more stabilized emulsion.

  2. Substituent Effects on the Low-Frequency Vibrational Modes of Benzoic Acid and Related Compounds

    Institute of Scientific and Technical Information of China (English)

    GE Min; ZHAO Hong-Wei; WANG Wen-Feng; YU Xiao-Han; LI Wen-Xin

    2007-01-01

    Well-resolved absorption spectra of benzoic acid and its derivatives with one hydrogen atom replaced by a substituent group CH3, OH, NH2 or NO2 were reported in the frequency region between 6 and 67 cm-1 at room temperature with terahertz time-domain spectroscopy (THz-TDS). These substances can be distinguished easily based on the terahertz absorption spectra. The measurements suggested that even minor changes in the molecular configuration and chemical composition lead to distinct differences in THz spectrum. Density functional theory (DFT)method was used to assist the analysis and assignment of the individual THz absorption spectra of benzoic acid and its methyl derivatives. Observed THz responses of samples can be assigned to the collective vibrations associated with intermolecular hydrogen bonds.

  3. Influence of Methyl Substituents on Azo-Dye Photoalignment in Thin Films

    Science.gov (United States)

    Mikulich, V. S.; Murawski, An. A.; Muravsky, Al. A.; Agabekov, V. E.

    2016-03-01

    Photoalignment of azo dyes derived from salicylic acid in thin films (80-200 nm) was studied upon irradiation with polarized light (λmax = 457 nm). It is shown that different trends of molecular reorientation, i.e., in the layer plane or orthogonal to it, are observed depending on the position of the methyl substituent in the dye structure. A new distribution parameter Z that allows the portion of molecules reoriented in the layer plane during exposure to be determined is introduced. The novel azo dye potassium 3,7-bis[1-(4-hydroxy-3-carboxylate)phenylazo]-5,5'-dioxodibenzothiophene was synthesized. Its molecules are photoaligned in the layer plane upon irradiation with polarized light.

  4. Molecular diversity of Pakistani mango (Mangifera indica L.) varieties based on microsatellite markers.

    Science.gov (United States)

    Nazish, T; Shabbir, G; Ali, A; Sami-Ul-Allah, S; Naeem, M; Javed, M; Batool, S; Arshad, H; Hussain, S B; Aslam, K; Seher, R; Tahir, M; Baber, M

    2017-04-05

    Understanding the genetic diversity of different Pakistani mango varieties is important for germplasm management and varietal characterization. Microsatellites are efficient and highly polymorphic markers for comparative genome mapping, and were used in the present study to determine the genetic relatedness and variability among 15 indigenous mango cultivars (Mangifera indica L.). Overall, 181 bands were produced using 12 simple sequence repeat (SSR) primers. Out of the 12 primers used, 10 were polymorphic and two were monomorphic. Genetic relatedness among cultivars was assessed by constructing a dendrogram using the unweighted pair group method of arithmetic means. The accessions exhibited coefficients of similarity ranging from 75 to 100%, indicating the frequent use of only a few parent cultivars and the presence of inbreeding. The primers used in the present study were found to be valuable for identifying genetic relationships among mango cultivars.

  5. Molecular diversity of methanogens in fecal samples from Bactrian camels (Camelus bactrianus) at two zoos.

    Science.gov (United States)

    Turnbull, Kathryn L; Smith, Rachel P; St-Pierre, Benoit; Wright, André-Denis G

    2012-08-01

    Animals are dependent on mutualistic microbial communities that reside in their gastrointestinal track for essential physiological functions such as nutrition and pathogen resistance. The composition of microbial communities in an animal is influenced by various factors, including species, diet and geographical location. In this preliminary study, the population structure of fecal methanogens in Bactrian camels (Camelus bactrianus) from two zoos was studied using separate 16S rRNA gene libraries for each zoo. While methanogen sequences belonging to the genus Methanobrevibacter were dominant in both libraries, they showed significant differences in diversity (p=0.05) and structure (pZoo library and seven OTUs were unique to the Potter Park Zoo library. These preliminary results highlight how methanogen population structures can vary greatly between animals of the same species maintained in captivity at different locations. Copyright © 2011 Elsevier Ltd. All rights reserved.

  6. Diverse formulas for spider dragline fibers demonstrated by molecular and mechanical characterization of spitting spider silk.

    Science.gov (United States)

    Correa-Garhwal, Sandra M; Garb, Jessica E

    2014-12-08

    Spider silks have outstanding mechanical properties. Most research has focused on dragline silk proteins (major ampullate spidroins, MaSps) from orb-weaving spiders. Using silk gland expression libraries from the haplogyne spider Scytodes thoracica, we discovered two novel spidroins (S. thoracica fibroin 1 and 2). The amino acid composition of S. thoracica silk glands and dragline fibers suggest that fibroin 1 is the major component of S. thoracica dragline silk. Fibroin 1 is dominated by glycine-alanine motifs, and lacks sequence motifs associated with orb-weaver MaSps. We hypothesize fibroin 2 is a piriform or aciniform silk protein, based on amino acid composition, spigot morphology, and phylogenetic analyses. S. thoracica's dragline silk is less tough than previously reported, but is still comparable to other dragline silks. Our analyses suggest that dragline silk proteins evolved multiple times. This demonstrates that spider dragline silk is more diverse than previously understood, providing alternative high performance silk designs.

  7. Assessment of genetic diversity in a highly valuable medicinal plant Catharanthus roseus using molecular markers

    Directory of Open Access Journals (Sweden)

    Ranjan Kumar Shaw

    2009-01-01

    Full Text Available Genetic diversity was evaluated among 14 cultivars of Catharanthus roseus using RAPD and ISSR markers.The RAPD primers resulted in the amplification of 56 bands, among which 46 (82% bands were polymorphic Four ISSRprimers amplified 31 loci out of which 17 were polymorphic and 14 are monomorphic. The Jaccard's similarity derived fromthe combined marker system showed that the varieties First Kiss Coral and Cooler Orchid were the most closely relatedcultivars, with 98% similarity. In the dendrogram constructed on the basis of both RAPD and ISSR data two clear clusterswere obtained. The smaller cluster included C. roseus Cv Blue Pearl and C. roseus Cv. Patricia White and the larger clusterwas subdivided into two sub clusters with C. roseus Cv. First Kiss Polka Dot isolated from the rest of the cultivars. This maybe useful for breeding for improved quality.

  8. Genetic molecular diversity, production and resistance to witches’ broom in cacao clones

    Directory of Open Access Journals (Sweden)

    José Luis Pires

    2013-06-01

    Full Text Available The 32 cacao clones selected as being resistant following the witches’ broom epidemic and for having distinct productivitywere characterized according to their genetic diversity and were submitted to a new selection. These plants were assessed for eightyears at the Oceania Farm (FO in Itagibá, Bahia, Brazil. The 13 microsatellite primers generated an average of 11.7 amplicons perlocus, and based on them it was demonstrated that the 32 clones distribute themselves in groups apart from the nine clones used ascontrols. The 32 materials displayed significant differences in relation to the characters assessed in the field. Two criteria were formedfrom the classification of the most productive and resistant plants, and then used to select plants within the clusters. The selected plantsdisplayed potential for the cacao improvement program, that they have a high production and high resistance to witches’ broom.

  9. Genotoxicity of quinolones: substituents contribution and transformation products QSAR evaluation using 2D and 3D models.

    Science.gov (United States)

    Li, Min; Wei, Dongbin; Zhao, Huimin; Du, Yuguo

    2014-01-01

    The genotoxicity of 21 quinolones antibiotics was determined using SOS/umu assay. Some quinolones exhibited high genotoxicity, and the chemical substituent on quinolone ring significantly affected genotoxicity. To establish the relationship between genotoxicity and substituent, a 2D-QSAR model based on quantum chemical parameters was developed. Calculation suggested that both steric and electrostatic properties were correlated well with genotoxicity. Furthermore, the specific effect on three key active sites (1-, 7- and 8-positions) of quinolone ring was investigated using a 3D-QSAR (comparative molecular field analysis, CoMFA) method. From our modeling, the genotoxicity increased when substituents had: (1) big volume and/or positive charge at 1-position; (2) negative charge at 7-position; and (3) small volume and/or negative charge at 8-position. The developed QSAR models were applicable to estimate genotoxicity of quinolones antibiotics and their transformation products. It is noted that some of the transformation products exhibited higher genotoxicity comparing to their precursor (e.g., ciprofloxacin). This study provided an alternative way to understand the molecule genotoxicity of quinolones derivatives, as well as to evaluate their potential environmental risks.

  10. Molecular characterization of insulin from squamate reptiles reveals sequence diversity and possible adaptive evolution.

    Science.gov (United States)

    Yamagishi, Genki; Yoshida, Ayaka; Kobayashi, Aya; Park, Min Kyun

    2016-01-01

    The Squamata are the most adaptive and prosperous group among ectothermic amniotes, reptiles, due to their species-richness and geographically wide habitat. Although the molecular mechanisms underlying their prosperity remain largely unknown, unique features have been reported from hormones that regulate energy metabolism. Insulin, a central anabolic hormone, is one such hormone, as its roles and effectiveness in regulation of blood glucose levels remain to be examined in squamates. In the present study, cDNAs coding for insulin were isolated from multiple species that represent various groups of squamates. The deduced amino acid sequences showed a high degree of divergence, with four lineages showing obviously higher number of amino acid substitutions than most of vertebrates, from teleosts to mammals. Among 18 sites presented to comprise the two receptor binding surfaces (one with 12 sites and the other with 6 sites), substitutions were observed in 13 sites. Among them was the substitution of HisB10, which results in the loss of the ability to hexamerize. Furthermore, three of these substitutions were reported to increase mitogenicity in human analogues. These substitutions were also reported from insulin of hystricomorph rodents and agnathan fishes, whose mitogenic potency have been shown to be increased. The estimated value of the non-synonymous-to-synonymous substitution ratio (ω) for the Squamata clade was larger than those of the other reptiles and aves. Even higher values were estimated for several lineages among squamates. These results, together with the regulatory mechanisms of digestion and nutrient assimilation in squamates, suggested a possible adaptive process through the molecular evolution of squamate INS. Further studies on the roles of insulin, in relation to the physiological and ecological traits of squamate species, will provide an insight into the molecular mechanisms that have led to the adaptivity and prosperity of squamates.

  11. Findings on genetic diversity in cultivated Salvia officinalis using molecular markers

    Directory of Open Access Journals (Sweden)

    ELVIRA BAZINA

    2014-06-01

    Full Text Available Albania continues to be a significant supplier of wild Medicinal and Aromatic Plants to the world markets of which Sage remains the major export item accounting for about 70% of the total sage imports to the US in 2013. Sage plants were randomly picked from different cultivation sites in Albania (North/Koplik; Southeast/Skrapar and South/Libohove in order to screen genetic diversity amongst them employing Randomly Amplified Polymorphic DNA markers using twenty decameric oligonucleotide primers. A total of 2132 DNA bands were generated of which notably clear and scorable were 1555 (from 150 to 1999bp. Primers produced between 63 and 156 bands per Sage plant with an average of 107 bands per primer. Cultivated Sage plant generated between 112 to166 DNA bands with an average of 143 bands per plant. DNA banding patterns, obtained from the Shimadzu Multina PCR-RAPD analysis, were quite polymorphic and were used to carry out hierarchical cluster analysis using the average linkage between groups method of SPSS version 22. The dendrogram showed splitting of the North cultivated Sage from the Southern (southeast and south group due to (dissimilarity in climate and soil structure/texture. Southeast cultivated Sage plants exhibited some genetic diversity within the group (intrinsic factors driven. This study indicates that RAPDs were fast and easy to use and proved to be efficient discriminatory tools detecting a high level of polymorphism within the same species (intraspecific level which is explained with ecological variation and the genetic make-up of each individual.

  12. Molecular Genetic Diversity of Date (Phoenix dactylifera) Germplasm in Qatar based on Microsatellite Markers

    KAUST Repository

    Ahmed, Talaat

    2016-01-25

    Depending on morphological traits alone, studying the genetic diversity of date palm is a very difficult task since morphological characteristics are highly affected by the environment. DNA markers are excellent option that can help and enhance the discriminatory power of morphological characteristics. To study the genetic diversity among date palm cultivars grown in Qatar, fifteen Date palm samples were collected from Qatar University Experimental Farm. DNAs were extracted from fresh leaves by using commercial DNeasy Plant System Kit (Qiagen, Inc., Valencia, CA). Total of 18 (Inter Simple Sequence Repeat) ISSR single primers were used to amplify DNA fragments using genomic DNA of the 15 samples. First screening was done to test the ability of these primers to amplify clear bands using Date palm genomic DNA. All 18 ISSR primers successfully produced clear bands in the first screening. Then, each primer was used separately to genotype the whole set of 15 Date palm samples. Total of 4794 bands were generated using 18 ISSR primers for the 15 Date palm samples. On average, each primer generated 400 bands. The Number of amplified bands varied from cultivar to cultivar. The highest number of bands was obtained using Primers 2, 5 and 12 for the 15 (470 bands), while the lowest number of bands were obtained by Primers 1, 7 and 8 where they produced only 329 bands. Markers were scored for the presence and absence of the corresponding band among the different cultivars. Data were subjected to cluster analysis. A similarity matrix was constructed and the similarity values were used for cluster analysis.

  13. Diversity and molecular phylogeny of mitochondrial DNA of rhesus macaques (Macaca mulatta) in Bangladesh.

    Science.gov (United States)

    Hasan, M Kamrul; Feeroz, M Mostafa; Jones-Engel, Lisa; Engel, Gregory A; Kanthaswamy, Sree; Smith, David Glenn

    2014-11-01

    While studies of rhesus macaques (Macaca mulatta) in the eastern (e.g., China) and western (e.g., India) parts of their geographic range have revealed major genetic differences that warrant the recognition of two different subspecies, little is known about genetic characteristics of rhesus macaques in the transitional zone extending from eastern India and Bangladesh through the northern part of Indo-China, the probable original homeland of the species. We analyzed genetic variation of 762 base pairs of mitochondrial DNA from 86 fecal swab samples and 19 blood samples from 25 local populations of rhesus macaque in Bangladesh collected from January 2010 to August 2012. These sequences were compared with those of rhesus macaques from India, China, and Myanmar. Forty-six haplotypes defined by 200 (26%) polymorphic nucleotide sites were detected. Estimates of gene diversity, expected heterozygosity, and nucleotide diversity for the total population were 0.9599 ± 0.0097, 0.0193 ± 0.0582, and 0.0196 ± 0.0098, respectively. A mismatch distribution of paired nucleotide differences yielded a statistically significantly negative value of Tajima's D, reflecting a population that rapidly expanded after the terminal Pleistocene. Most haplotypes throughout regions of Bangladesh, including an isolated region in the southwestern area (Sundarbans), clustered with haplotypes assigned to the minor haplogroup Ind-2 from India reflecting an east to west dispersal of rhesus macaques to India. Haplotypes from the southeast region of Bangladesh formed a cluster with those from Myanmar, and represent the oldest rhesus macaque haplotypes of Bangladesh. These results are consistent with the hypothesis that rhesus macaques first entered Bangladesh from the southeast, probably from Indo-China, then dispersed westward throughout eastern and central India.

  14. Data supporting a molecular phylogeny of the hyper-diverse genus Brueelia.

    Science.gov (United States)

    Bush, Sarah E; Weckstein, Jason D; Gustafsson, Daniel R; Allen, Julie; DiBlasi, Emily; Shreve, Scott M; Boldt, Rachel; Skeen, Heather R; Johnson, Kevin P

    2015-12-01

    Data is presented in support of a phylogenetic reconstruction of one of the largest, and most poorly understood, groups of lice: the Brueelia-complex (Bush et al., 2015[1]). Presented data include the voucher information and molecular data (GenBank accession numbers) of 333 ingroup taxa within the Brueelia-complex and 30 outgroup taxa selected from across the order Phthiraptera. Also included are phylogenetic reconstructions based on Bayesian inference analyses of combined COI and EF-1α sequences for Brueelia-complex species and outgroup taxa.

  15. Data supporting a molecular phylogeny of the hyper-diverse genus Brueelia

    Directory of Open Access Journals (Sweden)

    Sarah E. Bush

    2015-12-01

    Full Text Available Data is presented in support of a phylogenetic reconstruction of one of the largest, and most poorly understood, groups of lice: the Brueelia-complex (Bush et al., 2015 [1]. Presented data include the voucher information and molecular data (GenBank accession numbers of 333 ingroup taxa within the Brueelia-complex and 30 outgroup taxa selected from across the order Phthiraptera. Also included are phylogenetic reconstructions based on Bayesian inference analyses of combined COI and EF-1α sequences for Brueelia-complex species and outgroup taxa.

  16. Structural diversity of marine cyclic peptides and their molecular mechanisms for anticancer, antibacterial, antifungal, and other clinical applications.

    Science.gov (United States)

    Lee, Yeji; Phat, Chanvorleak; Hong, Soon-Cheol

    2017-09-01

    Many cyclic peptides and analogues derived from marine sources are known to possess biological properties, including anticancer, antitumor, antibacterial, antifungal, antiparasitic, anti-inflammation, anti-proliferative, anti-hypertensive, cytotoxic, and antibiotic properties. These compounds demonstrate different activities and modes of action according to their structure such as cyclic oligopeptide, cyclic lipopeptide, cyclic glycopeptide and cyclic depsipeptide. The recent advances in application of the above-mentioned cyclic peptides were reported in dolastatins, soblidotin, didemnin B, aplidine, salinosporamide A, kahalalide F and bryostatin 1 and they are currently in clinical trials. These cyclic peptides are possible novel drugs discovered and developed from marine origin. Literature data concerning the potential properties of marine cyclic peptides were reviewed here, and the structural diversity and biological activities of marine cyclic peptides are discussed in relation to the molecular mechanisms of these marine cyclic peptides. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells.

    Science.gov (United States)

    La Manno, Gioele; Gyllborg, Daniel; Codeluppi, Simone; Nishimura, Kaneyasu; Salto, Carmen; Zeisel, Amit; Borm, Lars E; Stott, Simon R W; Toledo, Enrique M; Villaescusa, J Carlos; Lönnerberg, Peter; Ryge, Jesper; Barker, Roger A; Arenas, Ernest; Linnarsson, Sten

    2016-10-06

    Understanding human embryonic ventral midbrain is of major interest for Parkinson's disease. However, the cell types, their gene expression dynamics, and their relationship to commonly used rodent models remain to be defined. We performed single-cell RNA sequencing to examine ventral midbrain development in human and mouse. We found 25 molecularly defined human cell types, including five subtypes of radial glia-like cells and four progenitors. In the mouse, two mature fetal dopaminergic neuron subtypes diversified into five adult classes during postnatal development. Cell types and gene expression were generally conserved across species, but with clear differences in cell proliferation, developmental timing, and dopaminergic neuron development. Additionally, we developed a method to quantitatively assess the fidelity of dopaminergic neurons derived from human pluripotent stem cells, at a single-cell level. Thus, our study provides insight into the molecular programs controlling human midbrain development and provides a foundation for the development of cell replacement therapies.

  18. Molecular Evaluation of Genetic Diversity in Wild-Type Mastic Tree (Pistacia lentiscus L.).

    Science.gov (United States)

    Abuduli, Alimu; Aydin, Yıldız; Sakiroglu, Muhammet; Onay, Ahmet; Ercisli, Sezai; Uncuoglu, Ahu Altinkut

    2016-10-01

    In this study, the patterns of genetic variation and phylogenetic relationships of mastic tree (Pistacia lentiscus L.) genotypes including 12 males and 12 females were evaluated using SSR, RAPD, ISSR, and ITS markers yielding 40, 703, 929 alleles, and 260-292 base pairs for ITS1 region, respectively. The average number of alleles produced from SSR, RAPD, and ISSR primers were 5.7, 14, and 18, respectively. The grouping pattern obtained from Bayesian clustering method based on each marker dataset was produced. Principal component analyses (PCA) of molecular data was investigated and neighbor joining dendrograms were subsequently created. Overall, the results indicated that ISSR and RAPD markers were the most powerful to differentiate the genotypes in comparison with other types of molecular markers used in this study. The ISSR results indicated that male and female genotypes were distinctly separated from each other. In this frame, M9 (Alaçatı) and M10 (Mesta Sakız Adası-Chios) were the closest genotypes and while F11 (Seferihisar) and F12 (Bornova/Gökdere) genotypes fall into same cluster and showing closer genetic relation. The RAPD pattern indicated that M8 (Urla) and M10 (Mesta Sakız Adası-Chios), and F10 (Mesta Sakız Adası-Chios) and F11 (Seferihisar) genotypes were the closest male and female genotypes, respectively.

  19. Comparative Studies on the Molecular Genetic Diversities among Haliotis discus hannai,H.discus discus and Their Hybrids

    Institute of Scientific and Technical Information of China (English)

    Wan Junfen(万俊芬); Bao Zhenmin; Zhang Quanqi; Wang Xiaolong

    2004-01-01

    The hybrid (H. discus hannai♀× H. discus discus♂) shows strong heterosis in both growth and survival rates during aquaculture. In order to better understand the genetic basis of heterosis, AFLP markers are adopted to compare the genetic diversities of the two parents and their hybrids. Six primer combinations reveal 552 loci, among which 88 loci show significant difference between the two parent populations (P<0.01). Analysis of molecular variance (AMOVA) indicates the genetic variance between them is significantly different (P<0.001). Thus there should be genetic basis of heterosis for their hybrids. In contrast to parents, more loci with lower frequency are amplified in hybrids than those in parents, whereas the loci with 0% and 100% frequency are less in hybrids than those in parents. Moreover, the genetic diversities of hybrids increase since the similarity indexes are lower and heterozygosities are higher in hybrids than those in parents. In addition, the genetic distances between reciprocal F1s and H. discus discus are both smaller than those between reciprocal F1s H. discus hannai.

  20. Assessment of changes in community level physiological profile and molecular diversity of bacterial communities in different stages of jute retting.

    Science.gov (United States)

    Das, Biswapriya; Chakrabarti, Kalyan; Ghosh, Sagarmoy; Chakraborty, Ashis; Saha, Manabendra Nath

    2013-12-01

    Retting of jute is essentially microbiological and biochemical in nature. Community Level Physiological Profiles (CLPP) as well as genomic diversity of bacterial communities were assessed in water samples collected during pre-retting, after 1st and 2nd charges of retting. The water samples were collected from two widely cultivated jute growing locations, Sonatikari (22 degrees 41'27"N; 88 degrees 35'44"E) and Baduria (22 degrees 44'24"N; 88 degrees 47'24"E), West Bengal, India. The CLPP, expressed as net area under substrate utilization curve, was studied by carbon source utilization patterns in BIOLOG Ecoplates. Molecular diversity was studied by polymerase chain reaction followed by denaturing gradient gel electrophoresis (PCR-DGGE) of total DNA from water samples. Both between locations and stages of retting, substrate utilizations pattern were carbohydrates > carboxylic acids > polymers > amino acids > amines/amides > phenolic compounds. Differential substrate utilization pattern as well as variation in banding pattern in DGGE profiles was observed between the two locations and at different stages of retting. The variations in CLPP in different stages of retting were due to the change in bacterial communities.

  1. Global molecular epidemiology and genetic diversity of Fusarium, a significant emerging group of human opportunists from 1958 to 2015

    Science.gov (United States)

    Al-Hatmi, Abdullah MS; Hagen, Ferry; Menken, Steph BJ; Meis, Jacques F; de Hoog, G Sybren

    2016-01-01

    Fusarium is a rapidly emerging, multidrug-resistant genus of fungal opportunists that was first identified in 1958 and is presently recognized in numerous cases of fusariosis each year. The authors examined trends in global Fusarium distribution, clinical presentation and prevalence since 1958 with the assumption that their distributions in each region had remained unaltered. The phylogeny and epidemiology of 127 geographically diverse isolates, representing 26 Fusarium species, were evaluated using partial sequences of the RPB2 and TEF1 genes, and compared with AFLP fingerprinting data. The molecular data of the Fusarium species were compared with archived data, which enabled the interpretation of hundreds of cases published in the literature. Our findings indicate that fusariosis is globally distributed with a focus in (sub)tropical areas. Considerable species diversity has been observed; genotypic features did not reveal any clustering with either the clinical data or environmental origins. This study suggests that infections with Fusarium species might be truly opportunistic. The three most common species are F. falciforme and F. keratoplasticum (members of F. solani species complex), followed by F. oxysporum (F. oxysporum species complex). PMID:27924809

  2. Global molecular epidemiology and genetic diversity of Fusarium, a significant emerging group of human opportunists from 1958 to 2015.

    Science.gov (United States)

    Al-Hatmi, Abdullah Ms; Hagen, Ferry; Menken, Steph Bj; Meis, Jacques F; de Hoog, G Sybren

    2016-12-07

    Fusarium is a rapidly emerging, multidrug-resistant genus of fungal opportunists that was first identified in 1958 and is presently recognized in numerous cases of fusariosis each year. The authors examined trends in global Fusarium distribution, clinical presentation and prevalence since 1958 with the assumption that their distributions in each region had remained unaltered. The phylogeny and epidemiology of 127 geographically diverse isolates, representing 26 Fusarium species, were evaluated using partial sequences of the RPB2 and TEF1 genes, and compared with AFLP fingerprinting data. The molecular data of the Fusarium species were compared with archived data, which enabled the interpretation of hundreds of cases published in the literature. Our findings indicate that fusariosis is globally distributed with a focus in (sub)tropical areas. Considerable species diversity has been observed; genotypic features did not reveal any clustering with either the clinical data or environmental origins. This study suggests that infections with Fusarium species might be truly opportunistic. The three most common species are F. falciforme and F. keratoplasticum (members of F. solani species complex), followed by F. oxysporum (F. oxysporum species complex).

  3. Anodic oxidation of stilbenes bearing electron-withdrawing ring substituents

    Energy Technology Data Exchange (ETDEWEB)

    Halas, Summer M.; Okyne, Kwame; Fry, Albert J

    2003-06-15

    A number of disubstituted stilbenes bearing either two strong electron-withdrawing groups or one electron-withdrawing and one electron-donating group were synthesized and anodically oxidized in a divided cell in methanol at a carbon anode. A variety of types of products were obtained, most of which have never been observed upon oxidation of alkenes not bearing electron-withdrawing groups. A mechanistic scheme involving 2-methoxy-1,2-diarylethyl cations as key intermediates can account for all of the observed products. The nature of the products from each alkene is strongly correlated with the sum of the Hammett {sigma}{sup +} values of the ring substituents.

  4. Molecular evidence indicates that subarctic willow communities in Scotland support a diversity of host-associated Melampsora rust taxa.

    Science.gov (United States)

    Milne, Jeremy M; Helfer, Stephan; Kirk, Calum; Hollingsworth, Peter M; Ennos, Richard A

    2012-05-01

    Rare and threatened subarctic willow scrub communities in the UK are the subject of ongoing conservation programmes, yet little is known about the diversity of fungal taxa that they support. Isolates of the rust genus Melampsora were sampled from 112 leaves of eight subarctic willow (Salix) taxa and their hybrids from twelve sites in the UK. In order to determine the number of Melampsora taxa present in the samples, isolates were sequenced for the Internal Transcribed Spacer (ITS) region of rDNA and data were subject to phylogenetic analysis. Maximum likelihood and Bayesian analysis indicated that the isolates fell into three strongly supported host-associated clades. Clade I contained only isolates from Salix herbacea and was distinguished morphologically by dense urediniospore echinulation and thin cell walls. Clade II contained isolates from Salix arbuscula and Salix reticulata only. These could not be distinguished morphologically from isolates in Clade III which were found on Salix lapponum, Salix myrsinites, Salix myrsinifolia, Salix aurita, Salix lanata, and their hybrids. Clade II was most distinct in ITS sequence, differing by 50 bases from Clades I and III, while the latter clades differed in sequence by only 24 bases on average. Clades I and III are likely to represent the previously recognised taxa Melampsora alpina Juel 1894 and Melampsora epitea Thüm. 1879 respectively, but Clade II has not apparently been described before. Significant differences in the intensity of infection by isolates of Clade III were found among different Salix species at a single site, suggesting either differences in resistance among Salix taxa, or the presence of further cryptic taxa within Clade III. The study illustrates the power of molecular phylogenetic analysis to reveal cryptic biodiversity within Melampsora, and suggests that conserving Salix host diversity within subarctic willow communities will ensure that a diversity of associated Melampsora taxa is maintained.

  5. Molecular diversity and phylogeny of Triticum-Aegilops species possessing D genome revealed by SSR and ISSR markers

    Directory of Open Access Journals (Sweden)

    Moradkhani Hoda

    2015-12-01

    Full Text Available The aim of this study is investigation the applicability of SSR and ISSR markers in evaluating the genetic relationships in twenty accessions of Aegilops and Triticum species with D genome in different ploidy levels. Totally, 119 bands and 46 alleles were detected using ten primers for ISSR and SSR markers, respectively. Polymorphism Information Content values for all primers ranged from 0.345 to 0.375 with an average of 0.367 for SSR, and varied from 0.29 to 0.44 with the average 0.37 for ISSR marker. Analysis of molecular variance (AMOVA revealed that 81% (ISSR and 84% (SSR of variability was partitioned among individuals within populations. Comparing the genetic diversity of Aegilops and Triticum accessions, based on genetic parameters, shows that genetic variation of Ae. crassa and Ae. tauschii species are higher than other species, especially in terms of Nei’s gene diversity. Cluster analysis, based on both markers, separated total accessions in three groups. However, classification based on SSR marker data was not conformed to classification according to ISSR marker data. Principal co-ordinate analysis (PCoA for SSR and ISSR data showed that, the first two components clarified 53.48% and 49.91% of the total variation, respectively. This analysis (PCoA, also, indicated consistent patterns of genetic relationships for ISSR data sets, however, the grouping of accessions was not completely accorded to their own geographical origins. Consequently, a high level of genetic diversity was revealed from the accessions sampled from different eco-geographical regions of Iran.

  6. Diversity and Inter-Connections in the CXCR4 Chemokine Receptor/Ligand Family: Molecular Perspectives.

    Science.gov (United States)

    Pawig, Lukas; Klasen, Christina; Weber, Christian; Bernhagen, Jürgen; Noels, Heidi

    2015-01-01

    CXCR4 and its ligand CXCL12 mediate the homing of progenitor cells in the bone marrow and their recruitment to sites of injury, as well as affect processes such as cell arrest, survival, and angiogenesis. CXCL12 was long thought to be the sole CXCR4 ligand, but more recently the atypical chemokine macrophage migration inhibitory factor (MIF) was identified as an alternative, non-cognate ligand for CXCR4 and shown to mediate chemotaxis and arrest of CXCR4-expressing T-cells. This has complicated the understanding of CXCR4-mediated signaling and associated biological processes. Compared to CXCL12/CXCR4-induced signaling, only few details are known on MIF/CXCR4-mediated signaling and it remains unclear to which extent MIF and CXCL12 reciprocally influence CXCR4 binding and signaling. Furthermore, the atypical chemokine receptor 3 (ACKR3) (previously CXCR7) has added to the complexity of CXCR4 signaling due to its ability to bind CXCL12 and MIF, and to evoke CXCL12- and MIF-triggered signaling independently of CXCR4. Also, extracellular ubiquitin (eUb) and the viral protein gp120 (HIV) have been reported as CXCR4 ligands, whereas viral chemokine vMIP-II (Herpesvirus) and human β3-defensin (HBD-3) have been identified as CXCR4 antagonists. This review will provide insight into the diversity and inter-connections in the CXCR4 receptor/ligand family. We will discuss signaling pathways initiated by binding of CXCL12 vs. MIF to CXCR4, elaborate on how ACKR3 affects CXCR4 signaling, and summarize biological functions of CXCR4 signaling mediated by CXCL12 or MIF. Also, we will discuss eUb and gp120 as alternative ligands for CXCR4, and describe vMIP-II and HBD-3 as antagonists for CXCR4. Detailed insight into biological effects of CXCR4 signaling und underlying mechanisms, including diversity of CXCR4 ligands and inter-connections with other (chemokine) receptors, is clinically important, as the CXCR4 antagonist AMD3100 has been approved as stem cell mobilizer in specific

  7. Molecular Stirrers in Action

    NARCIS (Netherlands)

    Chen, Jiawen; Kistemaker, Jos C. M.; Robertus, Jort; Feringa, Ben L.

    2014-01-01

    A series of first-generation light-driven molecular motors with rigid substituents of varying length was synthesized to act as "molecular stirrers". Their rotary motion was studied by H-1 NMR and UV-vis absorption spectroscopy in a variety of solvents with different polarity and viscosity. Quantitat

  8. Molecular diversity of volatile compounds in rare willow (Salix spp.) honeydew honey: identification of chemical biomarkers.

    Science.gov (United States)

    Jerković, I; Marijanović, Z; Tuberoso, C I G; Bubalo, D; Kezić, N

    2010-05-01

    Salix spp. honeydew honey volatiles were analyzed for the first time by headspace solid-phase microextraction (HS-SPME) and ultrasonic solvent extraction (USE) followed by gas chromatography and mass spectrometry (GC, GC-MS). The use of HS-SPME and USE had advantageous results over the use of one single technique, as it provided different complementary chromatographic profiles for a comprehensive screening of the honeydew volatile composition. The volatiles with different functionality, molecular weight, and polarity were extracted and identified. High percentages of benzoic acid, phenylacetic acid, 2-hydroxybenzoic acid, 4-hydroxyphenylacetic acid with minor percentages of 4-methoxybenzoic acid, 4-hydroxyphenylethanol, and 4-hydroxybenzoic acid from USE extracts can be emphasized as volatile biomarkers of this honeydew that probably originated from Salix spp., as well as methyl salicylate identified only by HS-SPME. The application of heat treatment at 80 degrees C for 2 h did not change significantly the volatile composition of this honeydew.

  9. Super-resolution microscopy reveals structural diversity in molecular exchange among peptide amphiphile nanofibres

    Science.gov (United States)

    da Silva, Ricardo M. P.; van der Zwaag, Daan; Albertazzi, Lorenzo; Lee, Sungsoo S.; Meijer, E. W.; Stupp, Samuel I.

    2016-05-01

    The dynamic behaviour of supramolecular systems is an important dimension of their potential functions. Here, we report on the use of stochastic optical reconstruction microscopy to study the molecular exchange of peptide amphiphile nanofibres, supramolecular systems known to have important biomedical functions. Solutions of nanofibres labelled with different dyes (Cy3 and Cy5) were mixed, and the distribution of dyes inserting into initially single-colour nanofibres was quantified using correlative image analysis. Our observations are consistent with an exchange mechanism involving monomers or small clusters of molecules inserting randomly into a fibre. Different exchange rates are observed within the same fibre, suggesting that local cohesive structures exist on the basis of β-sheet discontinuous domains. The results reported here show that peptide amphiphile supramolecular systems can be dynamic and that their intermolecular interactions affect exchange patterns. This information can be used to generate useful aggregate morphologies for improved biomedical function.

  10. Invertebrate lysozymes: Diversity and distribution, molecular mechanism and in vivo function

    Indian Academy of Sciences (India)

    Joris M Van Herreweghe; Chris W Michiels

    2012-06-01

    Lysozymes are antibacterial enzymes widely distributed among organisms. Within the animal kingdom, mainly three major lysozyme types occur. Chicken (c)-type lysozyme and goose (g)-type lysozyme are predominantly, but not exclusively, found in vertebrate animals, while the invertebrate (i)-type lysozyme is typical for invertebrate organisms, and hence its name. Since their discovery in 1975, numerous research articles report on the identification of i-type lysozymes in a variety of invertebrate phyla. This review describes the current knowledge on i-type lysozymes, outlining their distribution, molecular mechanism and in vivo function taking the representative from Venerupis philippinarum (formerly Tapes japonica) (Vp-ilys) as a model. In addition, invertebrate g-type and ch-type (chalaropsis) lysozymes, which have been described in molluscs and nematodes, respectively, are also briefly discussed.

  11. Molecular diversity and relationships of North American Elymus trachycaulus and the Eurasian E. caninus species.

    Science.gov (United States)

    Sun, Genlou; Tang, Hemei; Salomon, Björn

    2006-05-01

    The morphological similarity of Elymus trachycaulus to the Eurasian E. caninus has often been noted. This has lead to controversial and contradicting taxonomic treatments. Nevertheless, there has been no systematic investigation on molecular genetic similarity between E. trachycaulus and E. caninus. In this study, random amplified polymorphic DNA (RAPD) analysis was used to study the similarity between the two species. RAPD analysis of 38 samples representing E. caninus and E. trachycaulus complex yielded 111 interpretable RAPD bands. The Jaccard's similarity values for E. caninus ranged from 0.38 between accessions H10345 and H10353 to 0.97 between accessions H8745 and H10096, with an average of 0.67. The Jaccard's similarity values for E. trachycaulus complex ranged from 0.09 between E. trachycaulus ssp. subsecundus (PI 537321) and E. trachycaulus ssp. violaceus (PI 272612) to 0.78 between accessions PI 315368 and PI 372644, with an average of 0.43. The results from different analyses (NJ and PCA) were similar but not identical. The molecular genetic separation between E. caninus and E. trachycaulus was consistent. The PCA analysis clearly separated all E. caninus accessions from E. trachycaulus and its subspecies. The NJ analysis also showed separation between most accessions of E. caninus and E. trachycaulus. Further analysis excluding E. trachycaulus ssp. subsecundus and ssp. violaceus revealed that E. caninus species and E. trachycaulus species were clearly separated into two distinct groups. The RAPD data thus support the treatment of E. caninus and E. trachycaulus as distinct species. The analyses further indicate that E. violaceus is nested within E. trachycaulus, and more related to E. trachycaulus complex rather than to E. caninus.

  12. The molecular basis of beta-thalassemia intermedia in southern China: genotypic heterogeneity and phenotypic diversity

    Directory of Open Access Journals (Sweden)

    Sun Manna

    2010-02-01

    Full Text Available Abstract Background The clinical syndrome of thalassemia intermedia (TI results from the β-globin genotypes in combination with factors to produce fetal haemoglobin (HbF and/or co-inheritance of α-thalassemia. However, very little is currently known of the molecular basis of Chinese TI patients. Methods We systematically analyzed and characterized β-globin genotypes, α-thalassemia determinants, and known primary genetic modifiers linked to the production of HbF and the aggravation of α/β imbalance in 117 Chinese TI patients. Genotype-phenotype correlations were analyzed based on retrospective clinical observations. Results A total of 117 TI patients were divided into two major groups, namely heterozygous β-thalassemia (n = 20 in which 14 were characterized as having a mild TI with the Hb levels of 68-95 g/L except for five co-inherited αααanti-3.7 triplication and one carried a dominant mutation; and β-thalassemia homozygotes or compound heterozygotes for β-thalassemia and other β-globin defects in which the β+-thalassemia mutation was the most common (49/97, hemoglobin E (HbE variants was second (27/97, and deletional hereditary persistence of fetal hemoglobin (HPFH or δβ-thalassemia was third (11/97. Two novel mutations, Term CD+32(A→C and Cap+39(C→T, have been detected. Conclusions Chinese TI patients showed considerable heterogeneity, both phenotypically and genotypically. The clinical outcomes of our TI patients were mostly explained by the genotypes linked to the β- and α-globin gene cluster. However, for a group of 14 patients (13 β0/βN and 1 β+/βN with known heterozygous mutations of β-thalassemia and three with homozygous β-thalassemia (β0/β0, the existence of other causative genetic determinants is remaining to be molecularly defined.

  13. Molecular Diversity and Gene Evolution of the Venom Arsenal of Terebridae Predatory Marine Snails.

    Science.gov (United States)

    Gorson, Juliette; Ramrattan, Girish; Verdes, Aida; Wright, Elizabeth M; Kantor, Yuri; Rajaram Srinivasan, Ramakrishnan; Musunuri, Raj; Packer, Daniel; Albano, Gabriel; Qiu, Wei-Gang; Holford, Mandë

    2015-05-28

    Venom peptides from predatory organisms are a resource for investigating evolutionary processes such as adaptive radiation or diversification, and exemplify promising targets for biomedical drug development. Terebridae are an understudied lineage of conoidean snails, which also includes cone snails and turrids. Characterization of cone snail venom peptides, conotoxins, has revealed a cocktail of bioactive compounds used to investigate physiological cellular function, predator-prey interactions, and to develop novel therapeutics. However, venom diversity of other conoidean snails remains poorly understood. The present research applies a venomics approach to characterize novel terebrid venom peptides, teretoxins, from the venom gland transcriptomes of Triplostephanus anilis and Terebra subulata. Next-generation sequencing and de novo assembly identified 139 putative teretoxins that were analyzed for the presence of canonical peptide features as identified in conotoxins. To meet the challenges of de novo assembly, multiple approaches for cross validation of findings were performed to achieve reliable assemblies of venom duct transcriptomes and to obtain a robust portrait of Terebridae venom. Phylogenetic methodology was used to identify 14 teretoxin gene superfamilies for the first time, 13 of which are unique to the Terebridae. Additionally, basic local algorithm search tool homology-based searches to venom-related genes and posttranslational modification enzymes identified a convergence of certain venom proteins, such as actinoporin, commonly found in venoms. This research provides novel insights into venom evolution and recruitment in Conoidean predatory marine snails and identifies a plethora of terebrid venom peptides that can be used to investigate fundamental questions pertaining to gene evolution.

  14. Identification of EST-SSRs and molecular diversity analysis in Mentha piperita

    Institute of Scientific and Technical Information of China (English)

    Birendra Kumar; Umesh Kumar; Hemant Kumar Yadav

    2015-01-01

    EST sequences of Mentha piperita available in the public domain (NCBI) were exploited to develop SSR markers. A total of 1316 ESTs were assembled into 155 contigs and 653 singletons and of these, 110 sequences were found to contain 130 SSRs, with a frequency of 1 SSR/3.4 kb. Dinucleotide repeat SSRs were most frequent (72.3%) with the AG/CT (43.8%) repeat motif followed by AT/AT (16.2%). Primers were successfully designed for 68 SSR-containing sequences (62.0%). The 68 primers amplified 13 accessions of M. piperita and 54 produced clear amplicons of the expected size. Of these 54, 33 (61%) were found to be polymorphic among M. piperita accessions, showing from 2 to 4 alleles with an average of 2.33 alleles/SSR, and the polymorphic information content (PIC) value varied between 0.13 and 0.51 (average 0.25). All the amplified SSRs showed transferability among four different species of Mentha, with a highest in Mentha arvensis (87.0%) and minimum in Mentha citrata (37.0%). The newly developed SSRs markers were found to be useful for diversity analysis, as they successfully differentiated among species and accessions of Mentha.

  15. Identification of EST–SSRs and molecular diversity analysis in Mentha piperita

    Institute of Scientific and Technical Information of China (English)

    Birendra; Kumar; Umesh; Kumar; Hemant; Kumar; Yadav

    2015-01-01

    EST sequences of Mentha piperita available in the public domain(NCBI) were exploited to develop SSR markers. A total of 1316 ESTs were assembled into 155 contigs and 653 singletons and of these, 110 sequences were found to contain 130 SSRs, with a frequency of1 SSR/3.4 kb. Dinucleotide repeat SSRs were most frequent(72.3%) with the AG/CT(43.8%)repeat motif followed by AT/AT(16.2%). Primers were successfully designed for 68SSR-containing sequences(62.0%). The 68 primers amplified 13 accessions of M. piperita and 54 produced clear amplicons of the expected size. Of these 54, 33(61%) were found to be polymorphic among M. piperita accessions, showing from 2 to 4 alleles with an average of2.33 alleles/SSR, and the polymorphic information content(PIC) value varied between 0.13 and 0.51(average 0.25). All the amplified SSRs showed transferability among four different species of Mentha, with a highest in Mentha arvensis(87.0%) and minimum in Mentha citrata(37.0%). The newly developed SSRs markers were found to be useful for diversity analysis, as they successfully differentiated among species and accessions of Mentha.

  16. Molecular characterization showed limited genetic diversity among Salmonella Enteritidis isolated from humans and animals in Malaysia.

    Science.gov (United States)

    Ngoi, Soo Tein; Thong, Kwai Lin

    2013-12-01

    Salmonella enterica serovar Enteritidis (S. Enteritidis) is the most common causative agent of non-typhoidal salmonellosis in Malaysia. We aimed to characterize S. Enteritidis isolated from humans and animals by analyzing their antimicrobial resistance profiles and genotypes. A total of 111 strains were characterized using multiple-locus variable-number tandem repeat analysis, pulsed-field gel electrophoresis, and antimicrobial susceptibility testing. Both typing methods revealed that genetically similar S. Enteritidis strains had persisted among human and animal populations within the period of study (2003-2008). Only 39% of the strains were multi-drug resistant (i.e., resistant to 3 or more classes of antimicrobial agents), with a majority (73%) of these in low-risk phase (multiple antibiotic resistant index <0.20). Limited genetic diversity among clinical and zoonotic S. Enteritidis suggested that animals are possible sources of human salmonellosis. The degree of multi-drug resistance among the strains was generally low during the study period.

  17. Molecular identification, genetic diversity and distribution of Theileria and Babesia species infecting small ruminants.

    Science.gov (United States)

    Altay, Kursat; Dumanli, Nazir; Aktas, Munir

    2007-06-20

    Detection and identification of Theileria and Babesia species in 920 apparently healthy small ruminants in eastern Turkey, as well as parasite genetic diversity, was investigated using a specifically designed reverse line blot (RLB) assay. The hypervariable V4 region of the 18S ribosomal RNA (rRNA) gene was amplified and hybridized to a membrane onto which catchall and species-specific oligonucleotide probes were covalently linked. Three Theileria and one Babesia genotype were identified. Comparison of the Theileria genotypes revealed 93.6-96.2% similarity among their 18S rRNA genes. Two Theileria shared 100% and 99.7% similarity with the previously described sequences of T. ovis and Theileria sp. OT3, respectively. A third Theileria genotype was found to be clearly different from previously described Theileria species. The genotype was provisionally designated as Theileria sp. MK. The Babesia genotype shared 100% similarity with Babesia ovis. The survey indicated a high prevalence of piroplasm infections in small ruminants (38.36%). Theileria spp. prevalence was 36.08%. Prevalence of B. ovis was 5.43%. The most abundant Theileria species identified was T. ovis (34.56%) followed by Theileia sp. MK (1.30%) and Theileria sp. OT3 (0.43%).

  18. MOLECULAR MARKER STUDIES OF SELECTED MEDICINAL PLANTS FOR ASSESSMENT OF GENETIC DIVERSITY

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    A. RAJALAKSHMI

    2014-07-01

    Full Text Available Objective: The aim of this study is to examine the total antioxidant activity and Genetic relationships between six different medicinal plants were analysed. Method: The total antioxidant were analysed by using DPPH Photometric assay. The genomic DNA and RAPD Work were analyzed in selected medicinal plan using standard method. Mathwork software was used to draw the dendogram. Result: The results observed in the present study are Out of the 5 selected plants showed high antioxidant activity followed by Clitoria ternatea blue leaves, Solanum nigrum blue Berries, Syzygium cumini, Clitoria ternatea white leaves, Solanum nigrum Red berries, Phyllanthus emblica. The Syzygium cumini has the maximum antioxidant property this was confirmed by using DPPH photometric assay Figue 1. Isolation of genomic DNA from six different selected medicinal plants by using Random Amplified Polymorphic DNA (RAPD markers and analyse its genetic diversity. A dendrogram was constructed using Euclidean distance methods. Based on the number of bands the medicinal plants were grouped to form1-4 clusters. Conclusion: To analyse it evolutionary process.

  19. Identification of EST–SSRs and molecular diversity analysis in Mentha piperita

    Directory of Open Access Journals (Sweden)

    Birendra Kumar

    2015-08-01

    Full Text Available EST sequences of Mentha piperita available in the public domain (NCBI were exploited to develop SSR markers. A total of 1316 ESTs were assembled into 155 contigs and 653 singletons and of these, 110 sequences were found to contain 130 SSRs, with a frequency of 1 SSR/3.4 kb. Dinucleotide repeat SSRs were most frequent (72.3% with the AG/CT (43.8% repeat motif followed by AT/AT (16.2%. Primers were successfully designed for 68 SSR-containing sequences (62.0%. The 68 primers amplified 13 accessions of M. piperita and 54 produced clear amplicons of the expected size. Of these 54, 33 (61% were found to be polymorphic among M. piperita accessions, showing from 2 to 4 alleles with an average of 2.33 alleles/SSR, and the polymorphic information content (PIC value varied between 0.13 and 0.51 (average 0.25. All the amplified SSRs showed transferability among four different species of Mentha, with a highest in Mentha arvensis (87.0% and minimum in Mentha citrata (37.0%. The newly developed SSRs markers were found to be useful for diversity analysis, as they successfully differentiated among species and accessions of Mentha.

  20. Molecular epidemiology reveals genetic diversity amongst isolates of the Cryptococcus neoformans/C. gattii species complex in Thailand.

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    Sirada Kaocharoen

    Full Text Available To gain a more detailed picture of cryptococcosis in Thailand, a retrospective study of 498 C. neoformans and C. gattii isolates has been conducted. Among these, 386, 83 and 29 strains were from clinical, environmental and veterinary sources, respectively. A total of 485 C. neoformans and 13 C. gattii strains were studied. The majority of the strains (68.9% were isolated from males (mean age of 37.97 years, 88.5% of C. neoformans and only 37.5% of C. gattii strains were from HIV patients. URA5-RFLP and/or M13 PCR-fingerprinting analysis revealed that the majority of the isolates were C. neoformans molecular type VNI regardless of their sources (94.8%; 94.6% of the clinical, 98.8% of the environmental and 86.2% of the veterinary isolates. In addition, the molecular types VNII (2.4%; 66.7% of the clinical and 33.3% of the veterinary isolates, VNIV (0.2%; 100% environmental isolate, VGI (0.2%; 100% clinical isolate and VGII (2.4%; 100% clinical isolates were found less frequently. Multilocus Sequence Type (MLST analysis using the ISHAM consensus MLST scheme for the C. neoformans/C. gattii species complex identified a total of 20 sequence types (ST in Thailand combining current and previous data. The Thai isolates are an integrated part of the global cryptococcal population genetic structure, with ST30 for C. gattii and ST82, ST83, ST137, ST141, ST172 and ST173 for C. neoformans being unique to Thailand. Most of the C. gattii isolates were ST7 = VGIIb, which is identical to the less virulent minor Vancouver island outbreak genotype, indicating Thailand as a stepping stone in the global spread of this outbreak strain. The current study revealed a greater genetic diversity and a wider range of major molecular types being present amongst Thai cryptococcal isolates than previously reported.

  1. Microsatellite-based molecular diversity of bread wheat germplasm and association mapping of wheat resistance to the Russian wheat aphid.

    Science.gov (United States)

    Peng, J H; Bai, Y; Haley, S D; Lapitan, N L V

    2009-01-01

    Genetic diversity of a set of 71 wheat accessions, including 53 biotype 2 Russian wheat aphid (RWA2)-resistant landraces and 18 RWA2 susceptible accessions, was assessed by examining molecular variation at multiple microsatellite (SSR) loci. Fifty-one wheat SSR primer pairs were used, 81 SSR loci were determined, and 545 SSR alleles were detected. These SSR loci covered all the three genomes, 21 chromosomes, and at least 41 of the 42 chromosome arms. Diversity values averaged over SSR loci were high with mean number of SSR alleles/locus = 6.7, mean Shannon's index (H) = 1.291, and mean Nei's gene diversity (He) = 0.609. The three wheat genomes ranked as A > D > B and the homoeologous groups ranked as 7 > 3 > 1 > 2 > 6 > 5 > 4 based on the number of alleles per locus. Xgwm136 on chromosome arm 1AS is the most polymorphic SSR locus with the largest number of observed and effective alleles and the highest H and He. Among all 2485 pairs of wheat accessions, genetic distance (GD) ranged from 0.054 to 1.933 and averaged 0.9832. A dendrogram based on GD matrix showed that all the wheat accessions could be grouped into distinct clusters. Most of the susceptible cultivars (13/18) were clustered into groups that contains all or mostly susceptible accessions. Most of the U.S. cultivars belong to a group that is distinguishable from all the different RWA2 resistant groups. Diversity analysis was also conducted separately for subgroups containing 53 RWA2-resistant accessions and 18 RWA2-susceptible accessions. Association mapping revealed 28 SSR loci significantly associated with leaf chlorosis, and 8 with leaf rolling. New chromosome regions associated with RWA2 resistance were detected, and indicated existence of new RWA resistance genes located on chromosomes of all other homoeologous groups in addition to the groups 1 and 7 in bread wheat. This information is helpful for development of mapping populations for RWA2 resistance genes from different phylogenetic groups, and for

  2. Enrichment culture and molecular identification of diverse Bartonella species in stray dogs.

    Science.gov (United States)

    Bai, Ying; Kosoy, Michael Y; Boonmar, Sumalee; Sawatwong, Pongpun; Sangmaneedet, Somboon; Peruski, Leonard F

    2010-12-15

    Using pre-enrichment culture in Bartonella alpha-Proteobacteria growth medium (BAPGM) followed by PCR amplification and DNA sequence identification that targeted a fragment of the citrate synthase gene (gltA), we provide evidence of common bartonella infections and diverse Bartonella species in the blood of stray dogs from Bangkok and Khon Kaen, Thailand. The overall prevalence of all Bartonella species was 31.3% (60/192), with 27.9% (31/111) and 35.8% (29/81) in the stray dogs from Bangkok and Khon Kaen, respectively. Phylogenetic analyzes of gltA identified eight species/genotypes of Bartonella in the blood of stray dogs, including B. vinsonii subsp. arupensis, B. elizabethae, B. grahamii, B. quintana, B. taylorii, and three novel genotypes (BK1, KK1 and KK2) possibly representing unique species with ≤ 90.2% similarities to any of the known Bartonella species B. vinsonii subsp. arupensis was the only species detected in dogs from both sites, B. quintana and BK1 were found in the dogs from Bangkok, B. elizabethae, B. taylorii, KK1 and KK2 were found in the dogs from Khon Kaen. We conclude that stray dogs in Thailand are frequently infected with Bartonella species that vary with geographic region. As some Bartonella species detected in the present study are considered pathogenic for humans, stray dogs in Thailand may serve as possible reservoirs for Bartonella causing human illnesses. Further work is needed to determine the role of those newly discovered Bartonella genotypes/species in human and veterinary medicine.

  3. The molecular diversity of freshwater picoeukaryotes reveals high occurrence of putative parasitoids in the plankton.

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    Emilie Lefèvre

    Full Text Available Eukaryotic microorganisms have been undersampled in biodiversity studies in freshwater environments. We present an original 18S rDNA survey of freshwater picoeukaryotes sampled during spring/summer 2005, complementing an earlier study conducted in autumn 2004 in Lake Pavin (France. These studies were designed to detect the small unidentified heterotrophic flagellates (HF, 0.6-5 microm which are considered the main bacterivores in aquatic systems. Alveolates, Fungi and Stramenopiles represented 65% of the total diversity and differed from the dominant groups known from microscopic studies. Fungi and Telonemia taxa were restricted to the oxic zone which displayed two fold more operational taxonomic units (OTUs than the oxycline. Temporal forcing also appeared as a driving force in the diversification within targeted organisms. Several sequences were not similar to those in databases and were considered as new or unsampled taxa, some of which may be typical of freshwater environments. Two taxa known from marine systems, the genera Telonema and Amoebophrya, were retrieved for the first time in our freshwater study. The analysis of potential trophic strategies displayed among the targeted HF highlighted the dominance of parasites and saprotrophs, and provided indications that these organisms have probably been wrongfully regarded as bacterivores in previous studies. A theoretical exercise based on a new 'parasite/saprotroph-dominated HF hypothesis' demonstrates that the inclusion of parasites and saprotrophs may increase the functional role of the microbial loop as a link for carbon flows in pelagic ecosystems. New interesting perspectives in aquatic microbial ecology are thus opened.

  4. Genetic diversity and molecular evolution of Plum bark necrosis stem pitting-associated virus from China.

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    Linning Qu

    Full Text Available Plum bark necrosis stem pitting-associated virus (PBNSPaV, a member of the genus Ampelovirus in the family Closteroviridae, infects different Prunus species and has a worldwide distribution. Yet the population structure and genetic diversity of the virus is still unclear. In this study, sequence analyses of a partial heat shock protein 70 homolog (HSP70h gene and coat protein (CP gene of PBNSPaV isolates from seven Prunus species grown in China revealed a highly divergent Chinese PBNSPaV population, sharing nucleotide similarities of 73.1-100% with HSP70h gene, and 83.9-98.6% with CP gene. Phylogenetic analysis of HSP70h and CP sequences revealed segregation of global PBNSPaV isolates into four phylo-groups (I-IV, of which two newly identified groups, II and IV, solely comprised Chinese isolates. Complete genome sequences of three PBNSPaV isolates, Pch-WH-1 and Pch-GS-3 from peaches, and Plm-WH-3 from a plum tree, were determined. The three isolates showed overall nucleotide identities of 90.0% (Pch-GS-3 and 96.4% (Pch-WH-1 with the type isolate PL186, and the lowest identity of 70.2-71.2% with isolate Nanjing. For the first time, to the best of our knowledge, we report evidence of significant recombination in the HSP70h gene of PBNSPaV variant Pch2 by using five programs implemented in RDP3; in addition, five codon positions in its CP gene (3, 8, 44, 57, and 88 were identified that appeared to be under positive selection. Collectively, these results indicate a divergent Chinese PBNSPaV population. In addition, our findings provide a foundation for elucidating the epidemiological characteristics of virus population.

  5. Molecular diversity of LysM carbohydrate-binding motifs in fungi.

    Science.gov (United States)

    Akcapinar, Gunseli Bayram; Kappel, Lisa; Sezerman, Osman Ugur; Seidl-Seiboth, Verena

    2015-05-01

    LysM motifs are carbohydrate-binding modules found in prokaryotes and eukaryotes. They bind to N-acetylglucosamine-containing carbohydrates, such as chitin, chitio-oligosaccharides and peptidoglycan. In this review, we summarize the features of the protein architecture of LysM-containing proteins in fungi and discuss their so far known biochemical properties, transcriptional profiles and biological functions. Further, based on data from evolutionary analyses and consensus pattern profiling of fungal LysM motifs, we show that they can be classified into a fungal-specific group and a fungal/bacterial group. This facilitates the classification and selection of further LysM proteins for detailed analyses and will contribute to widening our understanding of the functional spectrum of this protein family in fungi. Fungal LysM motifs are predominantly found in subgroup C chitinases and in LysM effector proteins, which are secreted proteins with LysM motifs but no catalytic domains. In enzymes, LysM motifs mediate the attachment to insoluble carbon sources. In plants, receptors containing LysM motifs are responsible for the perception of chitin-oligosaccharides and are involved in beneficial symbiotic interactions between plants and bacteria or fungi, as well as plant defence responses. In plant pathogenic fungi, LysM effector proteins have already been shown to have important functions in the dampening of host defence responses as well as protective functions of fungal hyphae against chitinases. However, the large number and diversity of proteins with LysM motifs that are being unravelled in fungal genome sequencing projects suggest that the functional repertoire of LysM effector proteins in fungi is only partially discovered so far.

  6. Molecular epidemiology and genetic diversity of Entamoeba species in a chelonian collection.

    Science.gov (United States)

    García, Gabriela; Ramos, Fernando; Pérez, Rodrigo Gutiérrez; Yañez, Jorge; Estrada, Mónica Salmerón; Mendoza, Lilian Hernández; Martinez-Hernandez, Fernando; Gaytán, Paul

    2014-02-01

    Veterinary medicine has focused recently on reptiles, due to the existence of captive collections in zoos and an increase in the acquisition of reptiles as pets. The protozoan parasite, Entamoeba can cause amoebiasis in various animal species and humans. Although amoebiasis disease is remarkably rare in most species of chelonians and crocodiles, these species may serve as Entamoeba species carriers that transmit parasites to susceptible reptile species, such as snakes and lizards, which can become sick and die. In this study, we identified the Entamoeba species in a population of healthy (disease-free) chelonians, and evaluated their diversity through the amplification and sequencing of a small subunit rDNA region. Using this procedure, three Entamoeba species were identified: Entamoeba invadens in 4.76 % of chelonians, Entamoeba moshkovskii in 3.96 % and Entamoeba terrapinae in 50 %. We did not detect mixed Entamoeba infections. Comparative analysis of the amplified region allowed us to determine the intra-species variations. The E. invadens and E. moshkovskii strains isolated in this study did not exhibit marked differences with respect to the sequences reported in GenBank. The analysis of the E. terrapinae isolates revealed three different subgroups (A, B and C). Although subgroups A and C were very similar, subgroup B showed a relatively marked difference with respect to subgroups A and C (Fst = 0.984 and Fst = 1.000, respectively; 10-14 % nucleotide variation, as determined by blast) and with respect to the sequences reported in GenBank. These results suggested that E. terrapinae subgroup B may be either in a process of speciation or belong to a different lineage. However, additional research is necessary to support this statement conclusively.

  7. Molecular and Biochemical Diversity Among Isolates of Radopholus spp. from Different Areas of the World.

    Science.gov (United States)

    Fallas, G A; Hahn, M L; Fargette, M; Burrows, P R; Sarah, J L

    1996-12-01

    Eleven isolates of Radopholus similis from various banana-growing areas around the world and one isolate of R. bridgei from turmeric in Indonesia were compared using DNA and isoenzyme analysis. The polymerase chain reaction (PCR) was used to amplify a fragment of ribosomal DNA (rDNA), comprising the two internal transcribed spacers (ITS) and the 5.8S gene. Restriction fragment length polymorphisms (RFLPs) in this rDNA fragment were used to compare the 10 isolates. The analysis of this rDNA region revealed little variation among the isolates tested. However, data also were obtained by random amplified polymorphic DNA (RAPD) analysis of total DNA, and a hierarchical cluster analysis of these data arranged the R. similis isolates into two clusters. The first cluster consisted of isolates from Nigeria, Cameroon, Queensland, and Costa Rica; the second was comprised of isolates from Guinea, Guadeloupe, the Ivory Coast, Uganda, and Sri Lanka. The isolate of R. bridgei from turmeric in Indonesia appeared to be more divergent. This grouping was consistent with that obtained when phosphate glucose isomerase (PGI) isoenzyme patterns were used to compare the R. similis isolates. The results from both RAPD analysis and PGI isoenzyme studies indicate that two gene pools might exist within the R. similis isolates studied. No correlation could be detected between the genomic diversity as determined by RAPD analysis and either geographic distribution of the isolates or differences in their pathogenicity. The results support the hypothesis that R. similis isolates have been spread with banana-planting material.

  8. A Molecular Survey of the Diversity of Microbial Communities in Different Amazonian Agricultural Model Systems

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    Acácio A. Navarrete

    2010-05-01

    Full Text Available The processes of land conversion and agricultural intensification are a significant cause of biodiversity loss, with consequent negative effects both on the environment and the sustainability of food production.The anthrosols associated with pre-Colombian settlements in the Amazonian region are examples of how anthropogenic activities may sustain the native populations against harsh tropical environments for human establishment, even without a previous intentionality of anthropic soil formation. In a case study (Model I—“Slash-and-Burn” the community structures detected by automated ribosomal intergenic spacer analysis (ARISA revealed that soil archaeal, bacterial and fungal communities are heterogeneous and each capable of responding differently to environmental characteristics. ARISA data evidenced considerable difference in structure existing between microbial communities in forest and agricultural soils. In a second study (Model II—“Anthropogenic Soil”, the bacterial community structures revealed by terminal restriction fragment length polymorphism (T-RFLP differed among an Amazonian Dark Earth (ADE, black carbon (BC and its adjacent non-anthropogenic oxisoil. The bacterial 16S rRNA gene (OTU richness estimated by pyrosequencing was higher in ADE than BC. The most abundant bacterial phyla in ADE soils and BC were Proteobacteria—24% ADE, 15% BC; Acidobacteria—10% ADE, 21% BC; Actinobacteria—7% ADE, 12% BC; Verrucomicrobia, 8% ADE; 9% BC; Firmicutes—3% ADE, 8% BC. Overall, unclassified bacteria corresponded to 36% ADE, and 26% BC. Regardless of current land uses, our data suggest that soil microbial community structures may be strongly influenced by the historical soil management and that anthrosols in Amazonia, of anthropogenic origins, in addition to their capacity of enhancing crop yields, may also improve microbial diversity, with the support of the black carbon, which may sustain a particular and unique habitat for the

  9. Molecular Diversity and Plasmid Analysis of KPC-Producing Escherichia coli.

    Science.gov (United States)

    Chavda, Kalyan D; Chen, Liang; Jacobs, Michael R; Bonomo, Robert A; Kreiswirth, Barry N

    2016-07-01

    The emergence and spread of Klebsiella pneumoniae carbapenemase (KPC) among Enterobacteriaceae presents a major public health threat to the world. Although not as common as in K. pneumoniae, KPC is also found in Escherichia coli strains. Here, we genetically characterized 9 carbapenem-resistant E. coli strains isolated from six hospitals in the United States and completely sequenced their blaKPC-harboring plasmids. The nine strains were isolated from different geographical locations and belonged to 8 different E. coli sequence types. Seven blaKPC-harboring plasmids belonged to four different known incompatibility groups (IncN, -FIA, -FIIK2, and -FIIK1) and ranged in size from ∼16 kb to ∼241 kb. In this analysis, we also identified two plasmids that have novel replicons: (i) pBK28610, which is similar to p34978-3 with an insertion of Tn4401b, and (ii) pBK31611, which does not have an apparent homologue in the GenBank database. Moreover, we report the emergence of a pKP048-like plasmid, pBK34397, in E. coli in the United States. Meanwhile, we also found examples of interspecies spread of blaKPC plasmids, as pBK34592 is identical to pBK30683, isolated from K. pneumoniae In addition, we discovered examples of acquisition (pBK32602 acquired an ∼46-kb fragment including a novel replication gene, along with Tn4401b and other resistance genes) and/or loss (pKpQIL-Ec has a 14.5-kb deletion compared to pKpQIL-10 and pBK33689) of DNA, demonstrating the plasticity of these plasmids and their rapid evolution in the clinic. Overall, our study shows that the spread of blaKPC-producing E. coli is largely due to horizontal transfer of blaKPC-harboring plasmids and related mobile elements into diverse genetic backgrounds.

  10. Molecular tools for utilization of mitochondrial diversity in faba bean (Vicia faba

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    Aleksić Jelena M.

    2014-01-01

    Full Text Available We performed in silico PCR analyses utilizing complete mitochondrial (mtDNA genome sequences of faba bean (Vicia faba and two related species, Vigna angularis and Vigna radiata, currently available in GenBank, to infer whether 15 published universal primer pairs for amplification of all 14 cis-spliced introns in genes of NADH subunits (nad genes are suitable for V. faba and related species. Then, we tested via PCR reactions whether seven out of 15 primer pairs would generate PCR products suitable for further manipulation in 16 genotypes of V. faba representing all botanical varieties of this species (major, minor, equina and subsp. paucijuga of various levels of improvement (traditional and improved cultivars originating from Europe, Africa, Asia and south America. We provide new PCR primers for amplification of nad1 intron 2/3 in V. faba, and demonstrate intraspecific variability in primary nucleotide sequences at this locus. Based on outcomes of both in silico predictions and PCR amplification, we report a set of PCR primers for amplification of five introns in nad genes that are promising molecular tools for future phylogeographic and other studies in this species for which unambiguous data on wild ancestors, centre of origin and domestication are lacking. [Projekat Ministarstva nauke Republike Srbije, br. 173005

  11. Amelogenin: A novel protein with diverse applications in genetic and molecular profiling

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    Ajay Kumar Bansal

    2012-01-01

    Full Text Available Tooth enamel is a unique entity among all mineralized tissues because of the presence of high mineral content. It is non collagenous and does not undergo resorption and remodelling. Its formation occurs through a transient collaborating network of enamel matrix proteins which controls hydroxyapatite crystal growth and orientation. Amelogenins constitute about 90% of the total enamel matrix proteins and play a major role in enamel bio mineralization. Amelogenin isoforms coalesce into nanospheres thus dictating the width and thickness of apatite crystals. The X and Y copies of amelogenins do not undergo homologous recombination, thus preferring it for sex determination in modern forensics. Recently, it was discovered that application of amelogenin to diseased periodontal tissue surfaces enhanced the regeneration of all the periodontal tissues. Additionally, low molecular mass amelogenin polypeptides have also been thought to possess osteogenic potential. Recent data regarding usage of immunohistochemical markers for mesenchymal stem cells suggested that amelogenin has the capacity to induce the recruitment of mesenchymal stem cells directly or indirectly during regeneration of the supporting periodontal tissues. Thus, our current concepts of dental enamel formation should be reviewed thoroughly so that this information could be applied to clinical circumstances where this understanding may be particularly relevant.

  12. Molecular detection and genetic diversity of Babesia gibsoni in dogs in Bangladesh.

    Science.gov (United States)

    Terao, Masashi; Akter, Shirin; Yasin, Md Golam; Nakao, Ryo; Kato, Hirotomo; Alam, Mohammad Zahangir; Katakura, Ken

    2015-04-01

    Babesia gibsoni is a tick-borne hemoprotozoan parasite of dogs that often causes fever and hemolytic illness. Detection of B. gibsoni has been predominantly reported in Asian countries, including Japan, Korea, Taiwan, Malaysia, Bangladesh and India. The present study shows the first molecular characterization of B. gibsoni detected from dogs in Bangladesh. Blood samples were collected on FTA® Elute cards from 50 stray dogs in Mymensingh District in Bangladesh. DNA eluted from the cards was subjected to nested PCR for the 18S rRNA gene of Babesia species. Approximately 800bp PCR products were detected in 15 of 50 dogs (30%). Based on restriction fragment length polymorphism (RFLP) and direct sequencing of the PCR products, all parasite isolates were identified as B. gibsoni. Furthermore, the BgTRAP (B. gibsoni thrombospondin-related adhesive protein) gene fragments were detected in 13 of 15 18S rRNA gene PCR positive blood samples. Phylogenetic analysis of the BgTRAP gene revealed that B. gibsoni parasites in Bangladesh formed a cluster, which was genetically different from other Asian B. gibsoni isolates. In addition, tandem repeat analysis of the BgTRAP gene clearly showed considerable genetic variation among Bangladeshi isolates. These results suggested that B. gibsoni parasites in a different genetic clade are endemic in dogs in Bangladesh. Further studies are required to elucidate the origin, distribution, vector and pathogenesis of B. gibsoni parasites circulating in dogs in Bangladesh.

  13. Diverse developmental disorders from The One Ring: distinct molecular pathways underlie the cohesinopathies

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    Julia eHorsfield

    2012-09-01

    Full Text Available The multi-subunit protein complex, cohesin, is responsible for sister chromatid cohesion during cell division. The interaction of cohesin with DNA is controlled by a number of additional regulatory proteins. Mutations in cohesin, or its regulators, cause a spectrum of human developmental syndromes known as the ‘cohesinopathies’. Cohesinopathy disorders include Cornelia de Lange Syndrome and Roberts Syndrome. The discovery of novel roles for chromatid cohesion proteins in regulating gene expression led to the idea that cohesinopathies are caused by dysregulation of multiple genes downstream of mutations in cohesion proteins. Consistent with this idea, Drosophila, mouse and zebrafish cohesinopathy models all show altered expression of developmental genes. However, there appears to be incomplete overlap among dysregulated genes downstream of mutations in different components of the cohesion apparatus. This is surprising because mutations in all cohesion proteins would be predicted to affect cohesin’s roles in cell division and gene expression in similar ways. Here we review the differences and similarities between genetic pathways downstream of components of the cohesion apparatus, and discuss how such differences might arise, and contribute to the spectrum of cohesinopathy disorders. We propose that mutations in different elements of the cohesion apparatus have distinct developmental outcomes that can be explained by sometimes subtly different molecular effects.

  14. Solar energy absorption in norbornadiene-quadricyclane system through electron donating or withdrawing substituents1

    Science.gov (United States)

    Edjlali, L.; Vessally, E.; Abbasian, M.

    2011-05-01

    An attempt is made to maximize the solar energy absorption in norbornadiene ( 1)-quadricyclane ( 2) system, through direct attachment of substituents at C1, C2, or C7 atoms of 1; calculating the corresponding energies at B3LYP/6-311++G** level of theory. The electron donating and electron withdrawing substituents of 1 n-X, attached at C2, were suitable for both solar absorption bands and solar energy storage. DFT calculations indicate that the solar absorption bands of 12-X were shifted to the visible spectrum region through the electron withdrawing substituents more than through electron donating substituents.

  15. Substituent effects on the binding of natural product anthocyanidin inhibitors to influenza neuraminidase with mass spectrometry.

    Science.gov (United States)

    Swaminathan, Kavya; Müller, Patrick; Downard, Kevin M

    2014-05-30

    The binding of three closely related anthocyanins within the 430-cavity of influenza neuraminidase is studied using a combination of mass spectrometry and molecular docking. Despite their similar structures, which differ only in the number and position of the hydroxyl substituents on the phenyl group attached to the chromenylium ring, subtle differences in their binding characteristics are revealed by mass spectrometry and molecular docking that are in accord with their inhibitory properties by neuraminidase inhibition assays. The cyanidin and delphinidin, with the greatest number of hydroxyl groups, bind more strongly and are better inhibitors than pelargonidin that contains a lone hydroxyl group at the 4' position. The study demonstrates, for the first time, the sensitivity of the mass spectrometry based approach for investigating the molecular basis and relative affinity of antiviral inhibitors, with subtly different structures, to their target protein. It has broader application for the screening of other protein interactions more generally with reasonable high-throughput. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Molecular epidemiology and genetic diversity of human rhinovirus affecting hospitalized children in Rome.

    Science.gov (United States)

    Pierangeli, Alessandra; Ciccozzi, Massimo; Chiavelli, Stefano; Concato, Carlo; Giovanetti, Marta; Cella, Eleonora; Spano, Lucia; Scagnolari, Carolina; Moretti, Corrado; Papoff, Paola; Muraca, Maurizio; Midulla, Fabio; Antonelli, Guido

    2013-08-01

    Human rhinoviruses (HRV) have been re-classified into three species (A-C), but the recently discovered HRV-C strains are not fully characterized yet. This study aimed to undertake a molecular and epidemiological characterization of HRV strains infecting children hospitalized over one year in two large research hospitals in Rome. Nasal washings from single HRV infections were retrospectively subjected to phylogenetic analysis on two genomic regions: the central part of the 5'Untranslated Region (5'UTR) and the Viral Protein (VP) 4 gene with the 5' portion of the VP2 gene (VP4/2). Forty-five different strains were identified in 73 HRV-positive children: 55 % of the cases were HRV-A, 38 % HRV-C and only 7 % HRV-B. HRV-C cases were less frequent than HRV-A during summer months and more frequent in cases presenting wheezing with respect to HRV-A. Species distribution was similar with respect to patient age, and seasonality differed during summer months with fewer HRV-C than HRV-A cases. On admission, a significantly higher number of HRV-C cases presented with wheezing with respect to HRV-A. The inter- and intra-genotype variability in VP4/2 was higher than in 5'UTR; in particular, HRV-A patient VP4/2 sequences were highly divergent (8-14 %) at the nucleotide level from those of their reference strains, but VP4 amino acid sequence was highly conserved. In HRV-C isolates, the region preceding the initiator AUG, the amino acids involved in VP4 myristoylation, the VP4-VP2 cleavage site and the cis-acting replication element were highly conserved. Differently, VP4 amino acid conservation was significantly lower in HRV-C than in HRV-A strains, especially in the transiently exposed VP4 N-terminus. This study confirmed the high number of different HRV genotypes infecting hospitalized children over one year and reveals a greater than expected variability in HRV-C VP4 protein, potentially suggestive of differences in replication.

  17. Molecular profiling reveals diversity of stress signal transduction cascades in highly penetrant Alzheimer's disease human skin fibroblasts.

    Directory of Open Access Journals (Sweden)

    Graziella Mendonsa

    Full Text Available The serious and growing impact of the neurodegenerative disorder Alzheimer's disease (AD as an individual and societal burden raises a number of key questions: Can a blanket test for Alzheimer's disease be devised forecasting long-term risk for acquiring this disorder? Can a unified therapy be devised to forestall the development of AD as well as improve the lot of present sufferers? Inflammatory and oxidative stresses are associated with enhanced risk for AD. Can an AD molecular signature be identified in signaling pathways for communication within and among cells during inflammatory and oxidative stress, suggesting possible biomarkers and therapeutic avenues? We postulated a unique molecular signature of dysfunctional activity profiles in AD-relevant signaling pathways in peripheral tissues, based on a gain of function in G-protein-coupled bradykinin B2 receptor (BKB2R inflammatory stress signaling in skin fibroblasts from AD patients that results in tau protein Ser hyperphosphorylation. Such a signaling profile, routed through both phosphorylation and proteolytic cascades activated by inflammatory and oxidative stresses in highly penetrant familial monogenic forms of AD, could be informative for pathogenesis of the complex multigenic sporadic form of AD. Comparing stimulus-specific cascades of signal transduction revealed a striking diversity of molecular signaling profiles in AD human skin fibroblasts that express endogenous levels of mutant presenilins PS-1 or PS-2 or the Trisomy 21 proteome. AD fibroblasts bearing the PS-1 M146L mutation associated with highly aggressive AD displayed persistent BKB2R signaling plus decreased ERK activation by BK, correctible by gamma-secretase inhibitor Compound E. Lack of these effects in the homologous PS-2 mutant cells indicates specificity of presenilin gamma-secretase catalytic components in BK signaling biology directed toward MAPK activation. Oxidative stress revealed a JNK-dependent survival

  18. Assessment of the prevalence and diversity of emergent campylobacteria in human stool samples using a combination of traditional and molecular methods.

    Science.gov (United States)

    Collado, Luis; Gutiérrez, Magali; González, Mario; Fernández, Heriberto

    2013-04-01

    This study aims to assess the diversity of campylobacteria (Campylobacter and Arcobacter) in human fecal samples from patients with diarrhea (n = 140) and asymptomatic controls (n = 116) in Chile, using a combination of traditional culture and molecular methods. The culture methods detected campylobacteria in 10.7% of the patients with diarrhea and in 1.7% of the controls. In contrast, the molecular methods detected campylobacteria more often than the traditional culture, with a prevalence of 25.7% and 5.2%, respectively. The traditional methods only recovered the species Campylobacter jejuni, Campylobacter coli, and Arcobacter butzleri, whereas the molecular methods additionally detected the emergent species Campylobacter concisus and Campylobacter ureolyticus.

  19. High diversity of hepatitis B virus genotypes in Panamanian blood donors: a molecular analysis of new variants.

    Directory of Open Access Journals (Sweden)

    Alexander A Martínez

    Full Text Available Hepatitis B Virus (HBV is an infectious agent that causes more than half of the cases of liver disease and cancer in the world. Globally there are around 250 million people chronically infected with this virus. Despite 16% of the cases of liver disease in Central America are caused by HBV, the information regarding its genetic diversity, genotypes and circulation is scarce. The purpose of this study was to evaluate the genetic variability of the HBV genotypes from HBV-DNA positive samples obtained from screening blood donors at the Social Security System of Panama and to estimate its possible origin. From 59,696 blood donors tested for HBV infection during 2010-2012, there were 74 HBV-DNA positive subjects. Analysis of the partial PreS2-S region of 27 sequences shows that 21% of the infections were caused by genotype A, 3% by genotype D and 76% by genotype F. In addition, we were able to confirm circulation of six sub-genotypes A1, A2, A3, D4, F3, F1 and a proposed new sub-genotype denominated F5pan. We found a confinement of sub-genotypes F1 and F5pan to the western area of Panama. The tMRCA analysis suggests a simultaneous circulation of previously described sub-genotypes rather than recent introductions of the Panamanian sub-genotypes in the country. Moreover, these results highlight the need of more intensive research of the HBV strains circulating in the region at the molecular level. In conclusion, Panama has a high HBV genotype diversity that includes a new proposed sub-genotype, an elevated number of PreCore-Core mutations, and confinement of these variants in a specific geographical location.

  20. Seasonal occurrence and molecular diversity of clostridia species spores along cheesemaking streams of 5 commercial dairy plants.

    Science.gov (United States)

    Bermúdez, Jorge; González, Marcela J; Olivera, Jorge A; Burgueño, Juan A; Juliano, Pablo; Fox, Edward M; Reginensi, Stella M

    2016-05-01

    Five commercial dairy plants were monitored over a 17-mo period to determine the seasonal occurrence of Clostridium spores in streams from the cheesemaking process. Every 2 mo, samples of raw milk (RM), separated cream (SC), pasteurized and standardized vat milk (PSVM), PSVM + lysozyme (PSVM+L), and manufactured cheese aged for 60 to 90 d were processed for analysis. Molecular diversity of the main species identified was determined using repetitive element palindromic PCR. The mean anaerobic spore counts (μ ± SE) were 3.16±0.054, 3.00±0.054, 2.89±0.059, and 2.03±0.054 log10 most probable number/L for RM, PSVM, PSVM+L, and SC, respectively. Although spore counts did not differ between dairy plants, seasonal variation was observed; spore counts of RM, PSVM, and PSVM+L were higher during winter (June to August) and summer (December to February) months, but no seasonal variation was seen in SC counts. The most frequently isolated species was Clostridium tyrobutyricum, ranging from 50 to 58.3% of isolates from milk and cream samples. Clostridium sporogenes was the second most common species identified (16.7-21.1%); Clostridium beijerinckii and Clostridium butyricum were also found, although at lower prevalence (7.9-13.2%). Analysis of the C. tyrobutyricum and C. sporogenes population structure through repetitive element palindromic PCR indicated a high diversity, with unique isolates found in each positive sample. The occurrence of Clostridia spores in incoming streams to cheesemaking was most prominent in the winter and summer seasons, with higher prevalence of C. tyrobutyricum in the months of June and August.

  1. Sex-dependent diversity in ventral tegmental dopaminergic neurons and developmental programing: A molecular, cellular and behavioral analysis.

    Science.gov (United States)

    Gillies, G E; Virdee, K; McArthur, S; Dalley, J W

    2014-12-12

    The knowledge that diverse populations of dopaminergic neurons within the ventral tegmental area (VTA) can be distinguished in terms of their molecular, electrophysiological and functional properties, as well as their differential projections to cortical and subcortical regions has significance for key brain functions, such as the regulation of motivation, working memory and sensorimotor control. Almost without exception, this understanding has evolved from landmark studies performed in the male sex. However, converging evidence from both clinical and pre-clinical studies illustrates that the structure and functioning of the VTA dopaminergic systems are intrinsically different in males and females. This may be driven by sex differences in the hormonal environment during adulthood ('activational' effects) and development (perinatal and/or pubertal 'organizational' effects), as well as genetic factors, especially the SRY gene on the Y chromosome in males, which is expressed in a sub-population of adult midbrain dopaminergic neurons. Stress and stress hormones, especially glucocorticoids, are important factors which interact with the VTA dopaminergic systems in order to achieve behavioral adaptation and enable the individual to cope with environmental change. Here, also, there is male/female diversity not only during adulthood, but also in early life when neurobiological programing by stress or glucocorticoid exposure differentially impacts dopaminergic developmental trajectories in male and female brains. This may have enduring consequences for individual resilience or susceptibility to pathophysiological change induced by stressors in later life, with potential translational significance for sex bias commonly found in disorders involving dysfunction of the mesocorticolimbic dopaminergic systems. These findings highlight the urgent need for a better understanding of the sexual dimorphism in the VTA if we are to improve strategies for the prevention and treatment of

  2. Molecular genetics and diversity of primary biogenic aerosol particles in urban, rural, and high-alpine air

    Directory of Open Access Journals (Sweden)

    V. Després

    2007-02-01

    Full Text Available This study explores the applicability of molecular methods for the characterization of primary biogenic aerosol (PBA particles in the atmosphere. Samples of fine particulate matter (PM2.5 and total suspended particulates (TSP have been collected on different types of filter materials at urban, rural, and high-alpine locations along an altitude transect in the south of Germany (Munich, Hohenpeissenberg, Mt. Zugspitze.

    From filter aliquots loaded with about one milligram of air particulate matter, DNA could be extracted and DNA sequences could be determined for bacteria, fungi, plants and animals. Sequence analyses were used to determine the identity of biological organisms, and terminal restriction length polymorphism analyses (T-RFLP were applied to estimate diversities and relative abundances of bacteria. Investigations of blank and background samples showed that filter materials have to be decontaminated prior to use, and that the sampling and handling procedures have to be carefully controlled to avoid artifacts in the analyses.

    Mass fractions of DNA in PM2.5 were found to be around 0.05% in urban, rural, and high alpine aerosols. The average concentration of DNA determined for urban air was on the order of ~7 ng m−3, indicating that human adults may inhale about one microgram of DNA per day (corresponding to ~105 haploid human genomes.

    Most of the bacterial sequences found in PM2.5 were from Proteobacteria (42 and some from Actinobacteria (10 and Firmicutes (1. The fungal sequences were characteristic for Ascomycota (3 and Basidiomycetes (1, which are known to actively discharge spores into the atmosphere. The plant sequences could be attributed to green plants (2 and moss spores (2, while animal DNA was found only for one unicellular eukaryote (protist.

    Over 80% of the 53 bacterial sequences could be matched with about 40% of the 19 T-RF peaks (58

  3. Congruence between morphological and molecular markers inferred from the analysis of the intra-morphotype genetic diversity and the spatial structure of Oxalis tuberosa Mol.

    Science.gov (United States)

    Pissard, Audrey; Arbizu, Carlos; Ghislain, Marc; Faux, Anne-Michèle; Paulet, Sébastien; Bertin, Pierre

    2008-01-01

    Oxalis tuberosa is an important crop cultivated in the highest Andean zones. A germplasm collection is maintained ex situ by CIP, which has developed a morphological markers system to classify the accessions into morphotypes, i.e. groups of morphologically identical accessions. However, their genetic uniformity is currently unknown. The ISSR technique was used in two experiments to determine the relationships between both morphological and molecular markers systems. The intra-morphotype genetic diversity, the spatial structures of the diversity and the congruence between both markers systems were determined. In the first experience, 44 accessions representing five morphotypes, clearly distinct from each other, were analyzed. At the molecular level, the accessions exactly clustered according to their morphotypes. However, a genetic variability was observed inside each morphotype. In the second experiment, 34 accessions gradually differing from each other on morphological base were analyzed. The morphological clustering showed no geographical structure. On the opposite, the molecular analysis showed that the genetic structure was slightly related to the collection site. The correlation between both markers systems was weak but significant. The lack of perfect congruence between morphological and molecular data suggests that the morphological system may be useful for the morphotypes management but is not appropriate to study the genetic structure of the oca. The spatial structure of the genetic diversity can be related to the evolution of the species and the discordance between the morphological and molecular structures may result from similar selection pressures at different places leading to similar forms with a different genetic background.

  4. Phylogeography and molecular diversity analysis of Jatropha curcas L. and the dispersal route revealed by RAPD, AFLP and nrDNA-ITS analysis.

    Science.gov (United States)

    Sudheer Pamidimarri, D V N; Reddy, Muppala P

    2014-05-01

    Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits. Very few attempts were made to understand the extent of genetic diversity and its distribution. This study was aimed to study the diversity and deduce the phylogeography of Jatropha curcas L. which is said to be the most primitive species of the genus Jatropha. Here we studied the intraspecific genetic diversity of the species distributed in different parts of the globe. The study also focused to understand the molecular diversity at reported probable center of origin (Mexico), and to reveal the dispersal route to other regions based on random amplified polymorphic DNA, amplified fragment length polymorphism and nrDNA-ITS sequences data. The overall genetic diversity of J. curcas found in the present study was narrow. The highest genetic diversity was observed in the germplasm collected from Mexico and supports the earlier hypothesis based on morphological data and natural distribution, it is the center for origin of the species. Least genetic diversity found in the Indian germplasm and clustering results revealed that the species was introduced simultaneously by two distinct germplasm and subsequently distributed in different parts of India. The present molecular data further revealed that J. curcas might have spread from the center of the origin to Cape Verde, than to Spain, Portuguese to other neighboring countries and simultaneously to Africa. The molecular evidence supports the Burkill et al. (A dictionary of the economic products of the Malay Peninsula, Governments of Malaysia and Singapore by the Ministry of Agriculture and Co-operatives. Kuala Lumpur, Malaysia, 1966) view of Portuguese might have introduced the species to India. The clustering pattern suggests that the distribution was interfered by human activity.

  5. Phylogeography and molecular diversity analysis of Jatropha curcas L. and the dispersal route revealed by RAPD, AFLP and nrDNA-ITS analysis

    KAUST Repository

    Sudheer Pamidimarri, D. V N

    2014-01-29

    Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits. Very few attempts were made to understand the extent of genetic diversity and its distribution. This study was aimed to study the diversity and deduce the phylogeography of Jatropha curcas L. which is said to be the most primitive species of the genus Jatropha. Here we studied the intraspecific genetic diversity of the species distributed in different parts of the globe. The study also focused to understand the molecular diversity at reported probable center of origin (Mexico), and to reveal the dispersal route to other regions based on random amplified polymorphic DNA, amplified fragment length polymorphism and nrDNA-ITS sequences data. The overall genetic diversity of J. curcas found in the present study was narrow. The highest genetic diversity was observed in the germplasm collected from Mexico and supports the earlier hypothesis based on morphological data and natural distribution, it is the center for origin of the species. Least genetic diversity found in the Indian germplasm and clustering results revealed that the species was introduced simultaneously by two distinct germplasm and subsequently distributed in different parts of India. The present molecular data further revealed that J. curcas might have spread from the center of the origin to Cape Verde, than to Spain, Portuguese to other neighboring countries and simultaneously to Africa. The molecular evidence supports the Burkill et al. (A dictionary of the economic products of the Malay Peninsula, Governments of Malaysia and Singapore by the Ministry of Agriculture and Co-operatives. Kuala Lumpur, Malaysia, 1966) view of Portuguese might have introduced the species to India. The clustering pattern suggests that the distribution was interfered by human activity. © Springer Science+Business Media 2014.

  6. Influences of Alkyl and Aryl Substituents on Iminopyridine Fe(II- and Co(II-Catalyzed Isoprene Polymerization

    Directory of Open Access Journals (Sweden)

    Lihua Guo

    2016-11-01

    Full Text Available A series of alkyl- and aryl-substituted iminopyridine Fe(II complexes 1a–7a and Co(II complexes 2b, 3b, 5b, and 6b were synthesized. The activator effect, influence of temperature, and, particularly, the alkyl and aryl substituents’ effect on catalytic activity, polymer molecular weight, and regio-/stereoselectivity were investigated when these complexes were applied in isoprene polymerization. All of the Fe(II complexes afforded polyisoprene with high molecular weight and moderate cis-1,4 selectivity. In contrast, the Co(II complexes produced polymers with low molecular weight and relatively high cis-1,4 selectivity. In the iminopyridine Fe(II system, the alkyl and aryl substituents’ effect exhibits significant variation on the isoprene polymerization. In the iminopyridine Co(II system, there is little influence observed on isoprene polymerization by alkyl and aryl substituents.

  7. Effect of substituent structure on pyrimidine electrophilic substitution

    CSIR Research Space (South Africa)

    Van der Westhuyzen, CW

    2007-01-01

    Full Text Available 1R2 Cl NO NR1R2 N N NR3R4 NO NR1R2 1 2 34 HNR1R2iPrOH, ∆ Base NaNO2 H+ HNR3R4 toluene, ∆ conditions Scheme 1. General preparation of bisaminated 5-nitrosopyrimidines 4. Effect of substituent structur substitutio Christiaan W. van...). The exceptions were products 4b and 4g, which were prepared by heating 3a and 3c in neat pyrrolidine at 150 �C for 1 h. Table 1. Amination of 1 and nitrosation reactions of amines 2a–j N N Cl NR1R2 2 X=H 3 X=NO X a R1 = Me, R2 = H b R1= Bn, R2 = H c R...

  8. Anionic substituent control of the electronic structure of aromatic nitrenes.

    Science.gov (United States)

    Rau, Nathan J; Welles, Emily A; Wenthold, Paul G

    2013-01-16

    The electronic structures of phenylnitrenes with anionic π-donating substituents are investigated by using mass spectrometry and electronic structure calculations. Reactions of para-CH(2)(-)-substituted phenylnitrene, formed by dissociative deprotonation of p-azidotoluene, with CS(2) and NO indicate that it has a closed-shell singlet ground state, whereas reactions of p-oxidophenylnitrene formed by dissociative deprotonation of p-azidophenol indicate either a triplet ground state or a singlet with a small singlet-triplet splitting. The ground electronic state assignments based on ion reactivity are consistent with electronic structure calculations. The stability of the closed-shell singlet states in nitrenes is shown by Natural Resonance Theory to be very sensitive to the amount of deprotonated-imine character in the wave function, such that large changes in state energies can be achieved by small modifications of the electronic structure.

  9. Superoxide radical-mediated photocatalytic oxidation of phenolic compounds over Ag⁺/TiO₂: Influence of electron donating and withdrawing substituents.

    Science.gov (United States)

    Xiao, Jiadong; Xie, Yongbing; Han, Qingzhen; Cao, Hongbin; Wang, Yujiao; Nawaz, Faheem; Duan, Feng

    2016-03-05

    A comparative study was constructed to correlate the electronic property of the substituents with the degradation rates of phenolic compounds and their oxidation pathways under UV with Ag(+)/TiO2 suspensions. It was verified that a weak electron withdrawing substituent benefited photocatalytic oxidation the most, while an adverse impact appeared when a substituent was present with stronger electron donating or withdrawing ability. The addition of p-benzoquinone dramatically blocked the degradation, confirming superoxide radicals (O2(-)) as the dominant photooxidant, rather than hydroxyl radicals, singlet oxygen or positive holes, which was also independent of the substituent. Hammett relationship was established based on pseudo-first-order reaction kinetics, and it revealed two disparate reaction patterns between O2(-) and phenolic compounds, which was further verified by the quantum chemical computation on the frontier molecular orbitals and Mulliken charge distributions of O2(-) and phenolic compounds. It was found that electron donating group (EDG) substituted phenols were more likely nucleophilically attacked by O2(-), while O2(-) preferred to electrophilically assault electron withdrawing group (EWG) substituted phenols. Exceptionally, electrophilic and nucleophilic attack by O2(-) could simultaneously occur in p-chlorophenol degradation, consequently leading to its highest rate constant. Possible reactive positions on the phenolic compounds were also detailedly uncovered.

  10. Genetic diversity of Cercospora kikuchii isolates from soybean cultured in Argentina as revealed by molecular markers and cercosporin production.

    Science.gov (United States)

    Lurá, María Cristina; Latorre Rapela, María Gabriela; Vaccari, María Celia; Maumary, Roxana; Soldano, Anabel; Mattio, Mónica; González, Ana María

    2011-05-01

    Leaf blight and purple seed, caused by the fungal pathogen Cercospora kikuchii (Matsumoto & Tomoyasu) M. W. Gardner are very important diseases of soybean (Glycine max L. Merr.) in Argentina. The aims of this work were: (a) to confirm and to assess the genetic variability among C. kikuchii isolates collected from different soybean growing areas in Santa Fe province using inter simple sequence repeats (ISSR) markers and sequence information from the internal transcribed spacer (ITS) region of rDNA and (b) to analyze the cercosporin production of the regional C. kikuchi isolates in order to assess whether there was any relationship between the molecular profiles and the toxin production. Isolates from different regions in Santa Fe province were studied. The sequence of the ITS regions showed high similarity (99-100%) to the GenBank sequences of C. kikuchii BRCK179 (accession number AY633838). The ISSR markers clustered all the isolates into many groups and cercosporin content was highly variable among isolates. No relationship was observed between ITS region, ISSR groups and origin or cercosporin content. The high degree of genetic variability and cercosporin production among isolates compared in this study characterizes a diverse population of C. kikuchii in the region.

  11. Sodium channel genes and the evolution of diversity in communication signals of electric fishes: convergent molecular evolution.

    Science.gov (United States)

    Zakon, Harold H; Lu, Ying; Zwickl, Derrick J; Hillis, David M

    2006-03-07

    We investigated whether the evolution of electric organs and electric signal diversity in two independently evolved lineages of electric fishes was accompanied by convergent changes on the molecular level. We found that a sodium channel gene (Na(v)1.4a) that is expressed in muscle in nonelectric fishes has lost its expression in muscle and is expressed instead in the evolutionarily novel electric organ in both lineages of electric fishes. This gene appears to be evolving under positive selection in both lineages, facilitated by its restricted expression in the electric organ. This view is reinforced by the lack of evidence for selection on this gene in one electric species in which expression of this gene is retained in muscle. Amino acid replacements occur convergently in domains that influence channel inactivation, a key trait for shaping electric communication signals. Some amino acid replacements occur at or adjacent to sites at which disease-causing mutations have been mapped in human sodium channel genes, emphasizing that these replacements occur in functionally important domains. Selection appears to have acted on the final step in channel inactivation, but complementarily on the inactivation "ball" in one lineage, and its receptor site in the other lineage. Thus, changes in the expression and sequence of the same gene are associated with the independent evolution of signal complexity.

  12. Molecular Techniques Revealed Highly Diverse Microbial Communities in Natural Marine Biofilms on Polystyrene Dishes for Invertebrate Larval Settlement

    KAUST Repository

    Lee, On On

    2014-01-09

    Biofilm microbial communities play an important role in the larval settlement response of marine invertebrates. However, the underlying mechanism has yet to be resolved, mainly because of the uncertainties in characterizing members in the communities using traditional 16S rRNA gene-based molecular methods and in identifying the chemical signals involved. In this study, pyrosequencing was used to characterize the bacterial communities in intertidal and subtidal marine biofilms developed during two seasons. We revealed highly diverse biofilm bacterial communities that varied with season and tidal level. Over 3,000 operational taxonomic units with estimates of up to 8,000 species were recovered in a biofilm sample, which is by far the highest number recorded in subtropical marine biofilms. Nineteen phyla were found, of which Cyanobacteria and Proteobacteria were the most dominant one in the intertidal and subtidal biofilms, respectively. Apart from these, Actinobacteria, Bacteroidetes, and Planctomycetes were the major groups recovered in both intertidal and subtidal biofilms, although their relative abundance varied among samples. Full-length 16S rRNA gene clone libraries were constructed for the four biofilm samples and showed similar bacterial compositions at the phylum level to those revealed by pyrosequencing. Laboratory assays confirmed that cyrids of the barnacle Balanus amphitrite preferred to settle on the intertidal rather than subtidal biofilms. This preference was independent of the biofilm bacterial density or biomass but was probably related to the biofilm community structure, particularly, the Proteobacterial and Cyanobacterial groups. © 2014 Springer Science+Business Media New York.

  13. Molecular phylogeny and phylogeography of the Cuban cave-fishes of the genus Lucifuga: evidence for cryptic allopatric diversity.

    Science.gov (United States)

    García-Machado, Erik; Hernández, Damir; García-Debrás, Alfredo; Chevalier-Monteagudo, Pedro; Metcalfe, Cushla; Bernatchez, Louis; Casane, Didier

    2011-11-01

    Underground environments are increasingly recognized as reservoirs of faunal diversity. Extreme environmental conditions and limited dispersal ability of underground organisms have been acknowledged as important factors promoting divergence between species and conspecific populations. However, in many instances, there is no correlation between genetic divergence and morphological differentiation. Lucifuga Poey is a stygobiotic fish genus that lives in Cuban and Bahamian caves. In Cuba, it offers a unique opportunity to study the influence of habitat fragmentation on the genetic divergence of stygobiotic species and populations. The genus includes four species and one morphological variant that have contrasting geographical distributions. In this study, we first performed a molecular phylogenetic analysis of the Lucifuga Cuban species using mitochondrial and nuclear markers. The mitochondrial phylogeny revealed three deeply divergent clades that were supported by nuclear and morphological characters. Within two of these main clades, we identified five lineages that are candidate cryptic species and a taxonomical synonymy between Lucifuga subterranea and Lucifuga teresinarum. Secondly, phylogeographic analysis using a fragment of the cytochrome b gene was performed for Lucifuga dentata, the most widely distributed species. We found strong geographical organization of the haplotype clades at different geographic scales that can be explained by episodes of dispersal and population expansion followed by population fragmentation and restricted gene flow. At a larger temporal scale, these processes could also explain the diversification and the distribution of the different species.

  14. [Molecular diversity of arbuscular mycorrhizal fungi in wild and cultured Gynostemma pentaphyllum roots in Xishuangbanna, Southwest China].

    Science.gov (United States)

    Zhou, Li-Si; Guo, Shun-Xing

    2013-09-01

    By using nested-PCR, DNA cloning, and sequencing techniques, this paper studied the diversity of the community structure of arbuscular mycorrhizal fungi (AMF) in wild and cultured Gynostemma pentaphyllum roots. A total of 551 clones containing 18S rDNA genes of AMF were obtained from the roots. After the analysis of the restriction fragment length polymorphism, 100 different RFLP types were obtained, which were further divided into 20 AMF phylotypes belonging to seven families. The comparison of the sequences of 20 AMF phylotypes with the GenBank database showed that there were 5 AMF phylotypes having high similarity to the sequences of reported AMF species Glomus viscosum, Claroideoglomus etunicatum, Racocetra tropicana, Acaulospora spinosa, and Acaulospora mellea, respectively. These sequences were then assessed for the similarities against the MaarjAM database, and 12 phylotypes showed high similarity to the corresponding molecular virtual taxa, of which, 7 phylotypes were not obtained by the morphological identification of soil asexual spores. Statistical analysis indicated that there were significant differences in the AMF community between wild and cultured G. pentaphyllum roots. The analysis of relative abundance data indicated that Glo-2, Amb-1, and Para-1 were the dominant phylotypes in wild G. pentaphyllum roots, while Glo-3, Glo-8, Glo-10, and Div-1 were the prevalent phylotypes in cultured ones. Claroideoglomeraceae and Ambisporaceae were only detected in wild G. pentaphyllum roots, and Diversisporaceae was only identified in cultured ones.

  15. Diversity and Phylogeny of Gymnodiniales (Dinophyceae) from the NW Mediterranean Sea Revealed by a Morphological and Molecular Approach.

    Science.gov (United States)

    Reñé, Albert; Camp, Jordi; Garcés, Esther

    2015-05-01

    The diversity and phylogeny of dinoflagellates belonging to the Gymnodiniales were studied during a 3-year period at several coastal stations along the Catalan coast (NW Mediterranean) by combining analyses of their morphological features with rDNA sequencing. This approach resulted in the detection of 59 different morphospecies, 13 of which were observed for the first time in the Mediterranean Sea. Fifteen of the detected species were HAB producers; four represented novel detections on the Catalan coast and two in the Mediterranean Sea. Partial rDNA sequences were obtained for 50 different morphospecies, including novel LSU rDNA sequences for 27 species, highlighting the current scarcity of molecular information for this group of dinoflagellates. The combination of morphology and genetics allowed the first determinations of the phylogenetic position of several genera, i.e., Torodinium and many Gyrodinium and Warnowiacean species. The results also suggested that among the specimens belonging to the genera Gymnodinium, Apicoporus, and Cochlodinium were those representing as yet undescribed species. Furthermore, the phylogenetic data suggested taxonomic incongruences for some species, i.e., Gyrodinium undulans and Gymnodinium agaricoides. Although a species complex related to G. spirale was detected, the partial LSU rDNA sequences lacked sufficient resolution to discriminate between various other Gyrodinium morphospecies.

  16. Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity.

    Science.gov (United States)

    Loisel, Patrice; Harmand, Jérôme; Zemb, Olivier; Latrille, Eric; Lobry, Claude; Delgenès, Jean-Philippe; Godon, Jean-Jacques

    2006-04-01

    The exact extent of microbial diversity remains unknowable. Nevertheless, fingerprinting patterns [denaturing gradient electrophoresis (DGE), single-strand conformation polymorphism (SSCP)] provide an image of a microbial ecosystem and contain diversity data. We generated numerical simulation fingerprinting patterns based on three types of distribution (uniform, geometric and lognormal) with a range of units from 10 to 500,000. First, simulated patterns containing a diversity of around 1000 units or more gave patterns similar to those obtained in experiments. Second, the number of bands or peaks saturated quickly to about 35 and were unrelated to the degree of diversity. Finally, assuming lognormal distribution, we used an estimator of diversity on in silico and experimental fingerprinting patterns. Results on in silico patterns corresponded to the simulation inputs. Diversity results in experimental patterns were in the same range as those obtained from the same DNA sample in molecular inventories. Thus, fingerprinting patterns contain extractable data about diversity although not on the basis of a number of bands or peaks, as is generally assumed to be the case.

  17. Substituent distribution within cross-linked and hydroxypropylated sweet potato starch and potato starch

    NARCIS (Netherlands)

    Zhao, J.; Schols, H.A.; Chen Zenghong,; Jin Zhengyu,; Buwalda, P.L.; Gruppen, H.

    2012-01-01

    Revealing the substituents distribution within starch can help to understand the changes of starch properties after modification. The distribution of substituents over cross-linked and hydroxypropylated sweet potato starch was investigated and compared with modified potato starch. The starches were

  18. Theoretical Investigation of Substituent Effects on the Dihydroazulene/Vinylheptafulvene Photoswitch: Increasing the Energy Storage Capacity.

    Science.gov (United States)

    Hansen, Mia Harring; Elm, Jonas; Olsen, Stine T; Gejl, Aske Nørskov; Storm, Freja E; Frandsen, Benjamin N; Skov, Anders B; Nielsen, Mogens Brøndsted; Kjaergaard, Henrik G; Mikkelsen, Kurt V

    2016-12-15

    We have investigated the effects of substituents on the properties of the dihydroazulene/vinylheptafulvene photoswitch. The focus is on the changes of the thermochemical properties by placing electron withdrawing and donating groups on the monocyano and dicyano structures of the parent dihydroazulene and vinylheptafulvene compounds. We wish to increase the energy storage capacity, that is, the energy difference between the dihydroazulene and vinylheptafulvene isomers, of the photoswitch by computational molecular design and have performed over 9000 electronic structure calculations using density functional theory. Based on these calculations, we obtain design rules for how to increase the energy storage capacity of the photoswitch. Furthermore, we have investigated how the activation energy for the thermally induced vinylheptafulvene to dihydroazulene conversion depends on the substitution pattern, and based on these results, we have outlined molecular design considerations for obtaining new desired target structures exhibiting long energy storage times. Selected candidate systems have also been investigated in terms of optical properties to elucidate how sensitive the absorption maxima are to the functionalizations.

  19. Thermodynamic origin of selective binding of β-cyclodextrin derivatives with chiral chromophoric substituents toward steroids.

    Science.gov (United States)

    Chen, Yong; Li, Fang; Liu, Bo-Wen; Jiang, Bang-Ping; Zhang, Heng-Yi; Wang, Li-Hua; Liu, Yu

    2010-12-16

    Two β-cyclodextrin derivatives with chiral chromophoric substituents, that is, L- (1) and D-tyrosine-modified β-cyclodextrin (2), were synthesized and fully characterized. Their inclusion modes, binding abilities, and molecular selectivities with four steroid guests, that is, cholic acid sodium salt (CA), deoxycholic acid sodium salt (DCA), glycochoic acid sodium salt (GCA), and taurocholic acid sodium salt (TCA), were investigated by the circular dichroism, 2D NMR, and isothermal titration microcalorimetry (ITC). The results obtained from the circular dichroism and 2D NMR showed that two hosts adopted the different binding geometry, and these differences subsequently resulted in the significant differences of molecular binding abilities and selectivities. As compared with native β-cyclodextrin and tryptophan-modified β-cyclodextrin, host 2 showed the enhanced binding abilities for CA and DCA but the decreased binding abilities for GCA and TCA; however, host 1 showed the decreased binding abilities for all four bile salts. The best guest selectivity and the best host selectivity were K(S)(2-DCA)/K(S)(2-TCA) = 12.6 and K(S)(2-CA)/K(S)(1-CA) = 10, respectively, both exhibiting great enhancement as compared with the corresponding values of the previously reported L- and D-tryptophan-modified β-cyclodextrins. Thermodynamically, it was the favorable enthalpic gain that led to the high guest selectivity and host selectivity.

  20. Identification of single-copy orthologous genes between Physalis and Solanum lycopersicum and analysis of genetic diversity in Physalis using molecular markers.

    Directory of Open Access Journals (Sweden)

    Jingli Wei

    Full Text Available The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG Release2.3 Predicted CDS (SL2.40 discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2% of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei's genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis.

  1. Identification of single-copy orthologous genes between Physalis and Solanum lycopersicum and analysis of genetic diversity in Physalis using molecular markers.

    Science.gov (United States)

    Wei, Jingli; Hu, Xiaorong; Yang, Jingjing; Yang, Wencai

    2012-01-01

    The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG) Release2.3 Predicted CDS (SL2.40) discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2%) of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei's genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis.

  2. Viral sequence analysis from HIV-infected mothers and infants: molecular evolution, diversity, and risk factors for mother-to-child transmission.

    Science.gov (United States)

    Bulterys, Philip L; Dalai, Sudeb C; Katzenstein, David A

    2010-12-01

    Great progress has been made in understanding the pathogenesis, treatment, and transmission of HIV and the factors influencing the risk of mother-to-child transmission (MTCT). Many questions regarding the molecular evolution and genetic diversity of HIV in the context of MTCT remain unanswered. Further research to identify the selective factors governing which variants are transmitted, how the compartmentalization of HIV in different cells and tissues contributes to transmission, and the influence of host immunity, viral diversity, and recombination on MTCT may provide insight into new prevention strategies and the development of an effective HIV vaccine. Copyright © 2010 Elsevier Inc. All rights reserved.

  3. Bacterial diversity of a consortium degrading high-molecular-weight polycyclic aromatic hydrocarbons in a two-liquid phase biosystem.

    Science.gov (United States)

    Lafortune, Isabelle; Juteau, Pierre; Déziel, Eric; Lépine, François; Beaudet, Réjean; Villemur, Richard

    2009-04-01

    High-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs) are pollutants that persist in the environment due to their low solubility in water and their sequestration by soil and sediments. Although several PAH-degrading bacterial species have been isolated, it is not expected that a single isolate would exhibit the ability to degrade completely all PAHs. A consortium composed of different microorganisms can better achieve this. Two-liquid phase (TLP) culture systems have been developed to increase the bioavailability of poorly soluble substrates for uptake and biodegradation by microorganisms. By combining a silicone oil-water TLP system with a microbial consortium capable of degrading HMW PAHs, we previously developed a highly efficient PAH-degrading system. In this report, we characterized the bacterial diversity of the consortium with a combination of culture-dependent and culture-independent methods. Polymerase chain reaction (PCR) of part of the 16S ribosomal RNA gene (rDNA) sequences combined with denaturing gradient gel electrophoresis was used to monitor the bacterial population changes during PAH degradation of the consortium when pyrene, chrysene, and benzo[a]pyrene were provided together or separately in the TLP cultures. No substantial changes in bacterial profiles occurred during biodegradation of pyrene and chrysene in these cultures. However, the addition of the low-molecular-weight PAHs phenanthrene or naphthalene in the system favored one bacterial species related to Sphingobium yanoikuyae. Eleven bacterial strains were isolated from the consortium but, interestingly, only one-IAFILS9 affiliated to Novosphingobium pentaromativorans-was capable of growing on pyrene and chrysene as sole source of carbon. A 16S rDNA library was derived from the consortium to identify noncultured bacteria. Among 86 clones screened, 20 were affiliated to different bacterial species-genera. Only three strains were represented in the screened clones. Eighty

  4. Genetic diversity and molecular characterization of enteroviruses from sewage-polluted urban and rural rivers in the Philippines.

    Science.gov (United States)

    Apostol, Lea Necitas G; Imagawa, Tomifumi; Suzuki, Akira; Masago, Yoshifumi; Lupisan, Socorro; Olveda, Remigio; Saito, Mariko; Omura, Tatsuo; Oshitani, Hitoshi

    2012-10-01

    Despite the vast distribution and expansive diversity of enteroviruses reported globally, indicators defining a complete view of the epidemiology of enteroviruses in tropical countries such as the Philippines are yet to be established. Detection of enteroviruses in the environment has been one of the markers of circulating viruses in a community. This study aimed to bridge the gap in the epidemiology of enteroviruses in the Philippines by providing an overview of the occurrence of enteroviruses in both urban and rural rivers. Molecular detection directed at the VP1 region of the enterovirus genome was performed on 44 grab river water samples collected from April to December 2009. The majority of the enterovirus serotypes detected were clustered with human enterovirus C species (HEV-C; 21/42), followed by HEV-B (12/42) and HEV-A (9/42). Porcine enterovirus 9 was also found in 12 out of 44 water samples. Phylogenetic analysis indicated that the viruses detected were closely related, if not all forming a monophyletic clade, with those enteroviruses detected previously from acute flaccid paralysis cases in the country. The clustering of environmental and human enterovirus strains implies that the circulation of these strains were associated with river contamination. This study gives further evidence of the environmental persistence of enteroviruses once they are shed in feces and likewise, provides additional data which may help in understanding the epidemiology of enteroviruses in humans, highlighting the need for more studies on the potential public health risks linked with enteroviruses found in the environment and their eventual clinical consequences in the country.

  5. Yeast diversity associated with invasive Dendroctonus valens killing Pinus tabuliformis in China using culturing and molecular methods.

    Science.gov (United States)

    Lou, Qiao-Zhe; Lu, Min; Sun, Jiang-Hua

    2014-08-01

    Bark beetle-associated yeasts are much less studied than filamentous fungi, yet they are also considered to play important roles in beetle nutrition, detoxification, and chemical communication. The red turpentine beetle, Dendroctonus valens, an invasive bark beetle introduced from North America, became one of the most destructive pests in China, having killed more than 10 million Pinus tabuliformis as well as other pine species. No investigation of yeasts associated with this bark beetle in its invaded ranges has been conducted so far. The aim of this study was to assess the diversity of yeast communities in different microhabitats and during different developmental stages of Den. valens in China using culturing and denaturing gradient gel electrophoresis (DGGE) approaches and to compare the yeast flora between China and the USA. The yeast identity was confirmed by sequencing the D1/D2 domain of LSU ribosomal DNA (rDNA). In total, 21 species (13 ascomycetes and eight basidiomycetes) were detected by culturing method, and 12 species (11 ascomycetes and one basidiomycetes) were detected by molecular methods from China. The most frequent five species in China were Candida piceae (Ogataea clade), Cyberlindnera americana, Candida oregonensis (Metschnikowia clade), Candida nitratophila (Ogataea clade) and an undescribed Saccharomycopsis sp., detected by both methods. Seven species were exclusively detected by DGGE. Ca. oregonensis (Metschnikowia clade) was the most frequently detected species by DGGE method. Eight species (all were ascomycetes) from the USA were isolated; seven of those were also found in China. We found significant differences in yeast total abundance as well as community composition between different developmental stages and significant differences between the surface and the gut. The frass yeast community was more similar to that of Den. valens surface or larvae than to the community of the gut or adults. Possible functions of the yeast associates are

  6. Diversity in the major polysaccharide antigen of Acinetobacter baumannii assessed by DNA sequencing, and development of a molecular serotyping scheme.

    Directory of Open Access Journals (Sweden)

    Dalong Hu

    Full Text Available We have sequenced the gene clusters for type strains of the Acinetobacter baumannii serotyping scheme developed in the 1990s, and used the sequences to better understand diversity in surface polysaccharides of the genus. We obtained genome sequences for 27 available serovar type strains, and identified 25 polysaccharide gene cluster sequences. There are structures for 12 of these polysaccharides, and in general the genes present are appropriate to the structure where known. This greatly facilitates interpretation. We also find 53 different glycosyltransferase genes, and for 7 strains can provisionally allocate specific genes to all linkages. We identified primers that will distinguish the 25 sequence forms by PCR or microarray, or alternatively the genes can be used to determine serotype by "molecular serology". We applied the latter to 190 Acinetobacter genome-derived gene-clusters, and found 76 that have one of the 25 gene-cluster forms. We also found novel gene clusters and added 52 new gene-cluster sequence forms with different wzy genes and different gene contents. Altogether, the strains that have one of the original 25 sequence forms include 98 A. baumannii (24 from our strains and 5 A. nosocomialis (3 from our strains, whereas 32 genomes from 12 species other than A. baumannii or A. nosocomialis, all have new sequence forms. One of the 25 serovar type sequences is found to be in European clone I (EC I, 2 are in EC II but none in EC III. The public genome strains add an additional 52 new sequence forms, and also bring the number found in EC I to 5, in EC II to 9 and in EC III to 2.

  7. Molecular and serological diversity of Neisseria meningitidis carrier strains isolated from Italian students aged 14 to 22 years.

    Science.gov (United States)

    Gasparini, Roberto; Comanducci, Maurizio; Amicizia, Daniela; Ansaldi, Filippo; Canepa, Paola; Orsi, Andrea; Icardi, Giancarlo; Rizzitelli, Emanuela; De Angelis, Gabriella; Bambini, Stefania; Moschioni, Monica; Comandi, Sara; Simmini, Isabella; Boccadifuoco, Giueseppe; Brunelli, Brunella; Giuliani, Marzia Monica; Pizza, Mariagrazia; Panatto, Donatella

    2014-06-01

    Neisseria meningitidis is an obligate human commensal that commonly colonizes the oropharyngeal mucosa. Carriage is age dependent and very common in young adults. The relationships between carriage and invasive disease are not completely understood. In this work, we performed a longitudinal carrier study in adolescents and young adults (173 subjects). Overall, 32 subjects (18.5%) had results that were positive for meningococcal carriage in at least one visit (average monthly carriage rate, 12.1%). Only five subjects tested positive at all four visits. All meningococcal isolates were characterized by molecular and serological techniques. Multilocus sequence typing, PorA typing, and sequencing of the 4CMenB vaccine antigens were used to assess strain diversity. The majority of positive subjects were colonized by capsule null (34.4%) and capsular group B strains (28.1%), accounting for 23.5% and 29.4% of the total number of isolates, respectively. The fHbp and nhba genes were present in all isolates, while the nadA gene was present in 5% of the isolates. The genetic variability of the 4CMenB vaccine antigens in this collection was relatively high compared with that of other disease-causing strain panels. Indications about the persistence of the carriage state were limited to the time span of the study. All strains isolated from the same subject were identical or cumulated minor changes over time. The expression levels and antigenicities of the 4CMenB vaccine antigens in each strain were analyzed by the meningococcal antigen typing system (MATS), which revealed that expression can change over time in the same individual. Future analysis of antigen variability and expression in carrier strains after the introduction of the MenB vaccine will allow for a definition of its impact on nasopharyngeal/oropharyngeal carriage.

  8. Molecular diversity and distribution pattern of ciliates in sediments from deep-sea hydrothermal vents in the Okinawa Trough and adjacent sea areas

    Science.gov (United States)

    Zhao, Feng; Xu, Kuidong

    2016-10-01

    In comparison with the macrobenthos and prokaryotes, patterns of diversity and distribution of microbial eukaryotes in deep-sea hydrothermal vents are poorly known. The widely used high-throughput sequencing of 18S rDNA has revealed a high diversity of microeukaryotes yielded from both living organisms and buried DNA in marine sediments. More recently, cDNA surveys have been utilized to uncover the diversity of active organisms. However, both methods have never been used to evaluate the diversity of ciliates in hydrothermal vents. By using high-throughput DNA and cDNA sequencing of 18S rDNA, we evaluated the molecular diversity of ciliates, a representative group of microbial eukaryotes, from the sediments of deep-sea hydrothermal vents in the Okinawa Trough and compared it with that of an adjacent deep-sea area about 15 km away and that of an offshore area of the Yellow Sea about 500 km away. The results of DNA sequencing showed that Spirotrichea and Oligohymenophorea were the most diverse and abundant groups in all the three habitats. The proportion of sequences of Oligohymenophorea was the highest in the hydrothermal vents whereas Spirotrichea was the most diverse group at all three habitats. Plagiopyleans were found only in the hydrothermal vents but with low diversity and abundance. By contrast, the cDNA sequencing showed that Plagiopylea was the most diverse and most abundant group in the hydrothermal vents, followed by Spirotrichea in terms of diversity and Oligohymenophorea in terms of relative abundance. A novel group of ciliates, distinctly separate from the 12 known classes, was detected in the hydrothermal vents, indicating undescribed, possibly highly divergent ciliates may inhabit this environment. Statistical analyses showed that: (i) the three habitats differed significantly from one another in terms of diversity of both the rare and the total ciliate taxa, and; (ii) the adjacent deep sea was more similar to the offshore area than to the

  9. Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.

    Science.gov (United States)

    Wang, Bo; Li, Liwei; Hurley, Thomas D; Meroueh, Samy O

    2013-10-28

    End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal·mol(-1) highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10), but larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the nonpolar and entropy components, rather than a better representation of the electrostatics. The SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal-mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo, and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by prescoring

  10. Effects of alkyl substituents of xanthine on phosphodiesterase isoenzymes.

    Science.gov (United States)

    Miyamoto, K; Sakai, R; Kurita, M; Ohmae, S; Sanae, F; Sawanishi, H; Hasegawa, T; Takagi, K

    1995-03-01

    The structure-activity relationships of a series of alkylxanthine derivatives were investigated. The partition coefficient of alkylxanthines enlarged with an elongation of the alkyl chain at the 1-, 3-, or 7-position of xanthine. There was a mild correlation between the apparent partition coefficient and the tracheal relaxant activity or the inhibitory activity on phosphodiesterase (PDE) IV isoenzyme, while the tracheal relaxant activity closely correlated with the PDE IV inhibitory activity. Regarding substituents at different positions, the alkylation at the 3-position increased the inhibitory activity on every PDE isoenzyme. The alkylation at the 1-position potentiated the inhibitory activity on PDE IV with the alkyl chain length, but decreased the activities on other PDE isoenzymes. The alkylation at the 7-position was characteristic in its decrease in inhibitory activity on PDE III. These results suggested that the potency of the inhibitory activity of xanthine derivatives on PDE isoenzymes is not dependent simply upon their hydrophobicity but upon change in the affinity for the active sites on PDE isoenzymes by the introduction of the alkyl group at particular positions of the xanthine skeleton.

  11. Interaction of albumin with perylene-diimides with aromatic substituents

    Science.gov (United States)

    Farooqi, Mohammed; Penick, Mark; Burch, Jessica; Negrete, George; Brancaleon, Lorenzo

    2015-03-01

    Polyaromatic hydrocarbons (PAH) binding to proteins remains one of the fundamental aspects of research in biophysics. Ligand binding can regulate the function of proteins. Binding to small ligands remains a very important aspect in the study of the function of many proteins. Perylene diimide or PDI derivatives have attracted initial interest as industrial dyes and pigments. Recently, much attention has been focused on their strong π - π stacks resulting from the large PDI aromatic core. These PDI stacks have distinct optical properties, and provide informative models that mimic the light-harvesting system and initial charge separation and charge transfer in the photosynthetic system. The absorption property of PDI derivatives may be largely tuned from visible to near-infrared region by chemical modifications at the bay-positions. We are currently studying a new class of PDI derivatives with substituents made of the side chains of aromatic amino acids (Tyrosine, Tryptophan and Phenylalanine). We have looked at the fluorescence absorption and emission of these PDIs in water and other organic solvents. PDIs show evidence of dimerization and possible aggregation. We also present binding studies of these PDIs with Human Serum Albumin (HSA). The binding was studied using fluorescence emission quenching of the HSA Tryptophan residue. Stern-Volmer equation is used to derive the quenching constants. PDI binding to HSA also has an effect on the fluorescence emission of the PDIs themselves by red shifting the spectra. Funded by RCMI grant.

  12. Quantum Chemical Studies of the Substituent Effect on the Reaction of Carbonyl Oxime with Amine.

    Science.gov (United States)

    Kaya, Yunus

    2016-07-21

    The reaction of the two different substitue carbonyl oximes (isonitrosoacetylnaphthaline, inanH and nitro-isonitrosoacetophenone, ninapH) with two different amines (1-phenylethanol amine, pea, and ethanol amine, ea) was carried out and characterized by elemental analyses, IR, and (1)H and (13)C NMR spectroscopic methods. As a result of these experimental studies, two different levels for all reactions were determined: (I) formation of imine oxime and (II) rearrangement of imine oxime or formation of amido alcohol. After a mechanism was suggested for all of these reactions, the reaction mechanism of carbonyl oxime with amine was first studied by means of the B3LYP/6-311G(d,p) method. Because of the deficiency of density functional theory (DFT) on dispersion effects, the wB97X-D/6-311G(d,p) method, which includes dispersion correction, was used to obtain the reaction heat and free energy barriers to explain why the formation (imine oxime) and unexpected rearrangement products (amido alcohol) occurred or did not occur. The statistical thermodynamic method was used to obtain the changes in thermodynamic properties of the studied molecules between 100 and 500 K. From a kinetic viewpoint, the slowest step of the reactions is the IN1-TS2-IN2 step, which determines the steps of the reaction kinetics. In addition, spectroscopic properties such as vibrational and NMR chemical shifts were studied for all of the molecules. The frontier molecular orbitals (FMOs), highest occupied molecular orbitals (HOMOs), and lowest unoccupied molecular orbitals (LUMOs) were monitored for all of the molecules.

  13. Substituent effects on non-covalent interactions with aromatic rings: insights from computational chemistry.

    Science.gov (United States)

    Raju, Rajesh K; Bloom, Jacob W G; An, Yi; Wheeler, Steven E

    2011-12-09

    Non-covalent interactions with aromatic rings pervade modern chemical research. The strength and orientation of these interactions can be tuned and controlled through substituent effects. Computational studies of model complexes have provided a detailed understanding of the origin and nature of these substituent effects, and pinpointed flaws in entrenched models of these interactions in the literature. Here, we provide a brief review of efforts over the last decade to unravel the origin of substituent effects in π-stacking, XH/π, and ion/π interactions through detailed computational studies. We highlight recent progress that has been made, while also uncovering areas where future studies are warranted.

  14. Surface relief measurements in side-chain azobenzene polyesters with different substituents

    DEFF Research Database (Denmark)

    Helgert, M.; Wenke, L.; Hvilsted, Søren

    2001-01-01

    that the formation of the surface relief is dependent on the substituents. In both experiments irradiation with p-polarized light generates peaks for the CN, CF3, CH3 and F substituents, while fur a Cl substituent valleys art: observed. Also s-polarized light is found to produce surface deformations. An amorphous...... azobenzene polyester was included in the study for comparison. The results point to a mechanism of the surface relief phenomenon, in which the architecture of the polyesters plays a crucial role....

  15. Synthesis and properties of ApU analogues containing 2'-halo-2'-deoxyadenosines. Effects of 2' substituents on oligonucleotide conformation.

    Science.gov (United States)

    Uesugi, S; Kaneyasu, T; Ikehara, M

    1982-11-01

    Five A-U analogues containing deoxyadenosine or 2'-halo-2'-deoxyadenosines, which are known to have widely different C3'-endo conformer populations according to their electronegativities of the halogen substituents, dAfl-U, dAcl-U, dAbr-U, dAio-U, and dA-U, were synthesized chemically. Characterization of these dimers has been performed by UV absorption, circular dichroism, and proton nuclear magnetic resonance spectroscopy. The results show that the dimers containing 2'-halo-2'-deoxyadenosines have stacked conformations with a geometry similar to that of A-U and the degree of stacking decreases in the order dAfl-U greater than dAcl-U greater than dAbr-U greater than dAio-U. dAcl-U is assumed to have the same degree of stacking as A-U. dA-U takes a more stacked conformation than does dAio-U, but the mode of stacking is different from those of the other dimers. The effects of the 2' substituents on dimer conformation are discussed in terms of electronegativity, molecular size, and hydrophobicity.

  16. Contraceptive progestins. Various 11-substituents combined with four 17-substituents: 17alpha-ethynyl, five- and six-membered spiromethylene ethers or six-membered spiromethylene lactones.

    Science.gov (United States)

    Schoonen, W G; Deckers, G; de Gooijer, M E; de Ries, R; Mathijssen-Mommers, G; Hamersma, H; Kloosterboer, H J

    2000-10-01

    Norethisterone (NET) is a 19-nortestosterone derivative with progestagenic and some androgenic activity, which was used in the first generation of contraceptives. NET was succeeded by levonorgestrel (LNG) and later on by desogestrel (DSG) and gestodene (GSD). Although these latter two progestins had increased potency, there was still androgenicity with gestodene and to a lesser extent with desogestrel. New progestins were synthesized in order to further enhance progestagenic and to reduce androgenic activity. Four different chemical moieties were introduced in position 17 of 19-nortestosterone, viz. 17alpha-ethynyl, five- and six-membered spiromethylene ethers, and a six-membered-spiromethylene lactone. In combination with these structures seven different substituents were added at position 11, i.e. methylene, methyl, ethyl, ethenyl, ethynyl, 2-propenyl and 1-propynyl. All substituents except for methylene occupied the 11beta-position. All these 32 compounds were synthesized and analysed in vitro and in vivo against etonogestrel (ETG, 3-keto-desogestrel), the biologically active metabolite of desogestrel. Their relative binding potency to progesterone (PR), androgen (AR) and estrogen (ER) receptors were determined in cell lysates of human breast tumor MCF-7 cells and to glucocorticoid (GR) receptors in that of human leukemic IM-9 cells. Moreover, their relative agonistic activities were assessed in Chinese hamster ovary cell-based transactivation assays. All in vivo activities were determined in McPhail (progestagenic), ovulation inhibition (progestagenic and estrogenic), Hershberger (androgenic), hormone screening (glucocorticoid and estrogen) and Allen-Doisy (estrogenic) tests after oral and for the McPhail test also after subcutaneous administration. The progestagenic binding and transactivation potencies of all compounds in the three 17-spiro series were higher than those of the corresponding analogues in the 17alpha-ethynyl series. None of the compounds showed

  17. Detection and molecular diversity of Giardia duodenalis and Cryptosporidium spp. in sheltered dogs and cats in Northern Spain.

    Science.gov (United States)

    Gil, Horacio; Cano, Lourdes; de Lucio, Aida; Bailo, Begoña; de Mingo, Marta Hernández; Cardona, Guillermo A; Fernández-Basterra, José A; Aramburu-Aguirre, Juan; López-Molina, Nuria; Carmena, David

    2017-06-01

    Domestic dogs and cats may act as natural reservoirs of a large number of zoonotic pathogens, including the enteric parasites Giardia duodenalis and Cryptosporidium spp., the most relevant protozoan species causing gastrointestinal disease worldwide. A cross-sectional epidemiological study aiming to assess the prevalence and molecular diversity of G. duodenalis and Cryptosporidium spp. was conducted in an animal rescue centre in the province of Álava (Northern Spain). A total of 194 and 65 faecal dropping samples from individual dogs and cats, respectively, were collected between November 2013 and June 2016. G. duodenalis cysts and Cryptosporidium spp. oocysts were detected by direct fluorescence microscopy and PCR-based methods targeting the small subunit ribosomal RNA gene of these parasites. Overall, G. duodenalis and Cryptosporidium spp. were detected in 33% (63/194) and 4.1% (8/194) of dogs, and 9.2% (6/65) and 4.6% (3/65) of cats, respectively. G. duodenalis and Cryptosporidium co-infections were observed in 1.5% (3/194) of dogs, but not in cats. No significant differences in infection rates could be demonstrated among dogs or cats according to their sex, age group, status, or geographical origin. Multi-locus sequence-based genotyping of the glutamate dehydrogenase and β-giardin genes of G. duodenalis allowed the characterization of 19 canine isolates that were unambiguously assigned to sub-assemblages AII (n=7), BIII (n=1), and BIV (n=7), and assemblages C (n=3) and D (n=1). Two feline isolates were genotyped as assemblages A and F, respectively. No mixed assemblage or sub-assemblage infections were identified. C. canis (n=5) and C. hominis (n=1) were the Cryptosporidium species found in dogs, whereas C. felis (n=1) was identified in cats. The finding of G. duodenalis sub-assemblages AII, BIII, and BIV circulating in dogs (but not cats) may have zoonotic potential, although most of the AII and BIV isolates sub-genotyped corresponded to genetic variants not

  18. Electronic substituent effects in bicyclo[1.1.1]pentane and [n]staffane derivatives: a quantum chemical study based on structural variation.

    Science.gov (United States)

    Campanelli, Anna Rita; Domenicano, Aldo; Piacente, Giovanni; Ramondo, Fabio

    2010-04-22

    The transmission of electronic substituent effects through one or more bicyclo[1.1.1]pentane units has been investigated by ascertaining how a variable substituent at a bridgehead position perturbs the geometry of a phenyl group at the opposite end of the molecule. We have analyzed the molecular structures of many bicyclo[1.1.1]pentane and [n]staffane derivatives of general formula Ph-[C(CH(2))(3)C](n)-X (n = 1-5), as obtained from molecular orbital calculations at the HF/6-31G* and B3LYP/6-311++G** levels of theory. When n = 1, the structural variation of the benzene ring is controlled primarily by the long-range polar effect of X, with significant contributions from electronegativity and pi-transfer effects. The capability of the bicyclo[1.1.1]pentane framework to transmit these short-range effects originates from the rather high electron density inside the cage and the hyperconjugative interactions occurring between substituent and framework. A set of at least two bicyclo[1.1.1]pentane units appears to be necessary to remove most of the electronegativity and pi-transfer effects. In higher [n]staffanes (n >or= 3), the very small variation of the benzene ring geometry is controlled entirely by the long-range polar effect of X. With charged groups and for n >or= 2, the potential energy of the ring deformation decreases linearly with n(-3). In Ph-C(CH(2))(3)C-X molecules, the relatively large deformation of the bicyclo[1.1.1]pentane cage is determined primarily by the electronegativity of X, similar to the electronegativity distortion of the benzene ring in Ph-X molecules. Transfer of pi electrons from substituent to cage or vice versa also plays a role in determining the cage deformation.

  19. A molecular study of the tardigrade Echiniscus testudo (Echiniscidae reveals low DNA sequence diversity over a large geographical area

    Directory of Open Access Journals (Sweden)

    Aslak JØRGENSEN

    2007-09-01

    Full Text Available In the present study we investigate the genetic diversity within the asexually reproducing tardigrade Echiniscus testudo. The present study is the first to sample a tardigrade species for comparison of DNA sequence diversity between widely separated samples. Echiniscus testudo was sampled at 13 localities spanning three continents. DNA sequences of the mitochondrial COI gene and the nuclear ITS2 sequence were used to investigate the genetic diversity and phylogeographic structure of the various asexual lineages. Terrestrial tardigrades with the capability of entering a cryptobiotic state are assumed to have a high passive dispersal potential through airborne transport. Our results show moderate (ITS2 to high (COI haplotype diversity and low sequence diversity that indicate evolution of haplotypes within distinct asexual lineages and a high dispersal potential. No isolation by distance was detected by Mantel tests. Different phylogeny inference methods (neighbor-joining, maximum parsimony, maximum likelihood and Bayesian inference revealed little topological resolution, but minimum spanning networks showed some phylogeographic patterns. The COI and ITS2 minimum spanning networks show patterns that indicate dispersal of several haplotypes from founding populations. In conclusion our data show a low genetic diversity and a relatively high haplotype diversity indicating that E. testudo is a young species with a high dispersal potential.

  20. Substituent effects on the second ionization energies of hydroxy- and methoxy benzenes

    Science.gov (United States)

    Roithová, Jana; Schröder, Detlef

    2007-11-01

    The second ionization energies of phenol and the isomeric dihydroxybenzenes as well as their methyl ethers are determined by means of charge-stripping mass spectrometry. Compared to the parent molecule benzene, introduction of a hydroxy substituent lowers the second ionization energy by ca. 0.6 eV, whereas a methoxy substituent exerts a much more pronounced effect of about 1.6 eV. With regard to disubstitution, the effects behave almost completely additive for the para-derivatives, whereas the ortho-compounds are stabilized only about half that much by the second substituent, and for the meta-derivatives the influence of a second donor substituent is even smaller. The trends observed highlight the role of quinoid resonance structures for the stabilization of the dicationic compounds.

  1. New STS molecular markers for assessment of genetic diversity and DNA fingerprinting in hop (Humulus lupulus L.)

    National Research Council Canada - National Science Library

    Vrba, Lukas; Matousek, Jaroslav; Patzak, Josef

    2007-01-01

    .... We demonstrate the usefulness of these STS markers and compare them to SSRs for identifying hop genotypes and estimating genetic diversity in a collection of 68 hop cultivars from around the world...

  2. Rich diversity and potency of skin antioxidant peptides revealed a novel molecular basis for high-altitude adaptation of amphibians

    National Research Council Canada - National Science Library

    Yang, Xinwang; Wang, Ying; Zhang, Yue; Lee, Wen-Hui; Zhang, Yun

    2016-01-01

    .... wuchuanensis to elevated UV radiation was investigated. Compared with O. wuchuanensis, O. andersonii exhibited greater diversity and free radical scavenging potentiality of skin antioxidant peptides to cope with UV radiation...

  3. Molecular biodiversity of cassava begomoviruses in Tanzania: evolution of cassava geminiviruses in Africa and evidence for East Africa being a center of diversity of cassava geminiviruses

    Directory of Open Access Journals (Sweden)

    Aveling TAS

    2005-03-01

    Full Text Available Abstract Cassava is infected by numerous geminiviruses in Africa and India that cause devastating losses to poor farmers. We here describe the molecular diversity of seven representative cassava mosaic geminiviruses (CMGs infecting cassava from multiple locations in Tanzania. We report for the first time the presence of two isolates in East Africa: (EACMCV-[TZ1] and EACMCV-[TZ7] of the species East African cassava mosaic Cameroon virus, originally described in West Africa. The complete nucleotide sequence of EACMCV-[TZ1] DNA-A and DNA-B components shared a high overall sequence identity to EACMCV-[CM] components (92% and 84%. The EACMCV-[TZ1] and -[TZ7] genomic components have recombinations in the same genome regions reported in EACMCV-[CM], but they also have additional recombinations in both components. Evidence from sequence analysis suggests that the two strains have the same ancient origin and are not recent introductions. EACMCV-[TZ1] occurred widely in the southern part of the country. Four other CMG isolates were identified: two were close to the EACMV-Kenya strain (named EACMV-[KE/TZT] and EACMV-[KE/TZM] with 96% sequence identity; one isolate, TZ10, had 98% homology to EACMV-UG2Svr and was named EACMV-UG2 [TZ10]; and finally one isolate was 95% identical to EACMV-[TZ] and named EACMV-[TZ/YV]. One isolate of African cassava mosaic virus with 97% sequence identity with other isolates of ACMV was named ACMV-[TZ]. It represents the first ACMV isolate from Tanzania to be sequenced. The molecular variability of CMGs was also evaluated using partial B component nucleotide sequences of 13 EACMV isolates from Tanzania. Using the sequences of all CMGs currently available, we have shown the presence of a number of putative recombination fragments that are more prominent in all components of EACMV than in ACMV. This new knowledge about the molecular CMG diversity in East Africa, and in Tanzania in particular, has led us to hypothesize about the

  4. Utilization of molecular, phenotypic and geographical diversity to develop compact composite core collection in the oilseed crop, Safflower (Carthamus tinctorius L. through maximization strategy

    Directory of Open Access Journals (Sweden)

    Shivendra Kumar

    2016-10-01

    Full Text Available Carthamus tinctorius L. is a dryland oilseed crop yielding high quality edible oil. Previous studies have described significant phenotypic variability in the crop and used geographical distribution and phenotypic trait values to develop core collections. However, the molecular diversity component was lacking in the earlier collections thereby limiting their utility in breeding programs. The present study evaluated the phenotypic variability for twelve agronomically important traits during two growing seasons (2011-12 and 2012-13 in a global reference collection of 531 safflower accessions, assessed earlier by our group for genetic diversity and population structure using AFLP markers. Significant phenotypic variation was observed for all the agronomic traits in the representative collection. Cluster analysis of phenotypic data grouped the accessions into five major clusters. Accessions from the Indian Subcontinent and America harboured maximal phenotypic variability with unique characters for a few traits. MANOVA analysis indicated significant interaction between genotypes and environment for both the seasons. Initially, six independent core collections (CC1 – CC6 were developed using molecular marker and phenotypic data for two seasons through POWERCORE and MSTRAT. These collections captured the entire range of trait variability but failed to include complete genetic diversity represented in 19 clusters reported earlier through Bayesian Analysis of Population Structure (BAPS. Therefore, we merged the three POWERCORE core collections (CC1 – CC3 to generate a composite core collection, CartC1 and three MSTRAT core collections (CC4 – CC6to generate another composite core collection, CartC2.The mean difference percentage, variance difference percentage, variable rate of coefficient of variance percentage, coincidence rate of range percentage, Shannon’s diversity index and Nei’s gene diversity for CartC1 were 11.2, 43.7, 132.4, 93.4, 0

  5. The Origin, Development and Molecular Diversity of Rodent Olfactory Bulb Glutamatergic Neurons Distinguished by Expression of Transcription Factor NeuroD1.

    Directory of Open Access Journals (Sweden)

    Laurent Roybon

    Full Text Available Production of olfactory bulb neurons occurs continuously in the rodent brain. Little is known, however, about cellular diversity in the glutamatergic neuron subpopulation. In the central nervous system, the basic helix-loop-helix transcription factor NeuroD1 (ND1 is commonly associated with glutamatergic neuron development. In this study, we utilized ND1 to identify the different subpopulations of olfactory bulb glutamategic neurons and their progenitors, both in the embryo and postnatally. Using knock-in mice, transgenic mice and retroviral transgene delivery, we demonstrate the existence of several different populations of glutamatergic olfactory bulb neurons, the progenitors of which are ND1+ and ND1- lineage-restricted, and are temporally and regionally separated. We show that the first olfactory bulb glutamatergic neurons produced - the mitral cells - can be divided into molecularly diverse subpopulations. Our findings illustrate the complexity of neuronal diversity in the olfactory bulb and that seemingly homogenous neuronal populations can consist of multiple subpopulations with unique molecular signatures of transcription factors and expressing neuronal subtype-specific markers.

  6. Development of genome-wide informative simple sequence repeat markers for molecular diversity analysis in chickpea and development of web resource

    Directory of Open Access Journals (Sweden)

    SWARUP KUMAR PARIDA

    2015-08-01

    Full Text Available Development of informative polymorphic simple sequence repeat (SSR markers at a genome-wide scale is essential for efficient large-scale genotyping applications. We identified genome-wide 1835 SSRs showing polymorphism between desi and kabuli chickpea. A total of 1470 polymorphic SSR markers from diverse coding and non-coding regions of the chickpea genome were developed. These physically-mapped SSR markers exhibited robust amplification efficiency (73.9% and high intra- and inter-specific polymorphic potential (63.5%, thereby suggesting their immense use in various genomics-assisted breeding applications. The SSR markers particularly derived from intergenic and intronic sequences revealed high polymorphic potential. Using the mapped SSR markers, a wider functional molecular diversity (16-94%, mean: 68%, and parentage- and cultivar-specific admixed domestication pattern and phylogenetic relationships in a structured population of desi and kabuli chickpea genotypes was evident. The intra-specific polymorphism (47.6% and functional molecular diversity (65% potential of polymorphic SSR markers developed in our study is much higher than that of previous documentations. Finally, we have developed a user-friendly web resource, Chickpea Microsatellite Database (CMsDB; http://www.nipgr.res.in/CMsDB.html, which provides public access to the data and results reported in this study. The developed informative SSR markers can serve as a resource for various genotyping applications, including genetic enhancement studies in chickpea.

  7. Molecular diversity of Bacteroides spp. in human fecal microbiota as determined by group-specific 16S rRNA gene clone library analysis.

    Science.gov (United States)

    Li, Min; Zhou, Haokui; Hua, Weiying; Wang, Baohong; Wang, Shengyue; Zhao, Guoping; Li, Lanjuan; Zhao, Liping; Pang, Xiaoyan

    2009-05-01

    Bacteroides spp. represent a prominent bacterial group in human intestinal microbiota with roles in symbiosis and pathogenicity; however, the detailed composition of this group in human feces has yet to be comprehensively characterized. In this study, the molecular diversity of Bacteroides spp. in human fecal microbiota was analyzed from a seven-member, four-generation Chinese family using Bacteroides spp. group-specific 16S rRNA gene clone library analysis. A total of 549 partial 16S rRNA sequences amplified by Bacteroides spp.-specific primers were classified into 52 operational taxonomic units (OTUs) with a 99% sequence identity cut-off. Twenty-three OTUs, representing 83% of all clones, were related to 11 validly described Bacteroides species, dominated by Bacteroides coprocola, B. uniformis, and B. vulgatus. Most of the OTUs did not correspond to known species and represented hitherto uncharacterized bacteria. Relative to 16S rRNA gene universal libraries, the diversity of Bacteroides spp. detected by the group-specific libraries was much higher than previously described. Remarkable inter-individual differences were also observed in the composition of Bacteroides spp. in this family cohort. The comprehensive observation of molecular diversity of Bacteroides spp. provides new insights into potential contributions of various species in this group to human health and disease.

  8. Influence of substituent type on properties of starch derivates

    Directory of Open Access Journals (Sweden)

    Stojanović Željko P.

    2010-01-01

    Full Text Available The subject of the study was investigation of influence of substituent type on the properties of starch derivates in diluted solutions. Three samples were prepared: two anionic (carboxymethyl starch, CMS and one cationic starch (KS. Starch derivates were synthesized in two steps. The first step was preparation of alkali starch by the addition of sodium-hydroxide to the starch dispersed in ethanol or water. In the second step, the required amount of sodium monocloracetate or 3-chloro-2-hydroxypropyl-threemethylamonium chloride was added to the obtained alkali starch in order to prepare CMS or KS, respectively. The degree of substitution of carboxymethyl starch was determined by back titration method, and the degree of substitution of cationic starch was determined by potentiometric titration. The degrees of substitution of prepared samples were: 0.50 (assigned as CMS-0.50 and 0.70 (assigned as CMS-0.70 for carboxymethyl starch and 0.30 (assigned as KS-0.30 for cationic starch. The properties of starch derivatives in dilute solutions were investigated by the methods of static and dynamic light scattering. Aqueous solutions of sodium chloride of different concentrations were used as solvent. The values of the mass average molar mass, MW, radius of gyration, Rg, and second virial coefficient, A2, were determined for all samples together with hydrodynamic radius, Rh. Molar masses of the samples were: 5.06×106, 15.4×106 and 19.2×106 g/mol for CMS-0.50, CMS-0.70 and KS-0.30, respectively. The samples, CMS-0.70 and KS-0.30 had similar molar mass and hydrodynamic radius, but radius of gyration of KS-0.30 was smaller then radius of gyration of CMS-0.70 at all sodium chloride concentrations. Consequently, ρ value for KS-0.30 was smaller then for CMS-0.70, as a result of more compact architecture of KS-0.30 then of CMS-0.70. Kratky graph confirmed this result. For all samples, radius of gyration and hydrodynamic radius decreased with increasing of

  9. Resonance Raman Intensities Demonstrate that C5 Substituents Affect the Initial Excited-State Structural Dynamics of Uracil More than C6 Substituents.

    Science.gov (United States)

    Teimoory, Faranak; Loppnow, Glen R

    2016-05-04

    Resonance Raman derived initial excited-state structural dynamics provide insight into the photochemical mechanisms of pyrimidine nucleobases, in which the photochemistry appears to be dictated by the C5 and C6 substituents. The absorption and resonance Raman spectra and excitation profiles of 5,6-dideuterouracil were measured to further test this photochemical dependence on the C5 and C6 substituents. The resulting set of excited-state reorganization energies of the observed internal coordinates were calculated and compared to those of other 5- and 6-substituted uracils. The results show that the initial excited-state dynamics along the C5C6 stretch responds to changes in mass at C5 and C6 in the same manner but that the in-plane bends at C5 and C6 are more sensitive to substituents at the C5 position than at the C6 position. In addition, the presence of two deuterium substituents at C5 and C6 decreases the initial excited-state structural dynamics along these in-plane bends, in contrast to what is observed in the presence of two CH3 groups on C5 and C6. The results are discussed in the context of DNA nucleobase photochemistry.

  10. Effects of low dose GM-CSF on microglial inflammatory profiles to diverse pathogen-associated molecular patterns (PAMPs

    Directory of Open Access Journals (Sweden)

    Kielian Tammy

    2007-03-01

    Full Text Available Abstract Background It is well appreciated that obtaining sufficient numbers of primary microglia for in vitro experiments has always been a challenge for scientists studying the biological properties of these cells. Supplementing culture medium with granulocyte-macrophage colony-stimulating factor (GM-CSF partially alleviates this problem by increasing microglial yield. However, GM-CSF has also been reported to transition microglia into a dendritic cell (DC-like phenotype and consequently, affect their immune properties. Methods Although the concentration of GM-CSF used in our protocol for mouse microglial expansion (0.5 ng/ml is at least 10-fold less compared to doses reported to affect microglial maturation and function (≥ 5 ng/ml, in this study we compared the responses of microglia derived from mixed glial cultures propagated in the presence/absence of low dose GM-CSF to establish whether this growth factor significantly altered the immune properties of microglia to diverse bacterial stimuli. These stimuli included the gram-positive pathogen Staphylococcus aureus (S. aureus and its cell wall product peptidoglycan (PGN, a Toll-like receptor 2 (TLR2 agonist; the TLR3 ligand polyinosine-polycytidylic acid (polyI:C, a synthetic mimic of viral double-stranded RNA; lipopolysaccharide (LPS a TLR4 agonist; and the TLR9 ligand CpG oligonucleotide (CpG-ODN, a synthetic form of bacteria/viral DNA. Results Interestingly, the relative numbers of microglia recovered from mixed glial cultures following the initial harvest were not influenced by GM-CSF. However, following the second and third collections of the same mixed cultures, the yield of microglia from GM-CSF-supplemented flasks was increased two-fold. Despite the ability of GM-CSF to expand microglial numbers, cells propagated in the presence/absence of GM-CSF demonstrated roughly equivalent responses following S. aureus and PGN stimulation. Specifically, the induction of tumor necrosis factor

  11. Role of substituents on the reactivity and electron density profile of diimine ligands: A density functional theory based study

    Indian Academy of Sciences (India)

    Bhakti S Kulkarni; Deepti Mishra; Sourav Pal

    2013-09-01

    In this paper, we study the reactivity of diimines like 2, 2'-bipyridine, 1, l0-phenanthroline and 1, 2, 4-triazines using density-based reactivity descriptors. We discuss the enhancement or diminution in the reactivity of these ligands as a function of two substituent groups, namely methyl (-CH3) group and phenyl (-C6H5) group. The global reactivity descriptors explain the global affinity and philicity of these ligands, whereas the local softness depicts the particular site selectivity. The inter-molecular reactivity trends for the same systems are analysed through the philicity and group philicity indices. The -donor character of these ligands is quantified with the help of electron density profile. In addition, the possible strength of interaction of these ligands with metal ions is supported with actual reaction energies of Ru-L complexes.

  12. Molecular species delimitation methods and population genetics data reveal extensive lineage diversity and cryptic species in Aglaopheniidae (Hydrozoa).

    Science.gov (United States)

    Postaire, Bautisse; Magalon, Hélène; Bourmaud, Chloé A-F; Bruggemann, J Henrich

    2016-12-01

    A comprehensive inventory of global biodiversity would be greatly improved by automating methods for species delimitation. The Automatic Barcode Gap Discovery method, the Poisson tree processes algorithm and the Generalized mixed Yule-coalescent model have been proposed as means of increasing the rate of biodiversity description using single locus data. We applied these methods to explore the diversity within the Aglaopheniidae, a hydrozoan family with many species widely distributed across tropical and temperate oceans. Our analyses revealed widespread cryptic diversity in this family, almost half of the morpho-species presenting several independent evolutionary lineages, as well as support for cases of synonymy. For two common species of this family, Lytocarpia brevirostris and Macrorhynchia phoenicea, we compared the outputs to clustering analyses based on microsatellite data and to nuclear gene phylogenies. For L. brevirostris, microsatellite data were congruent with results of the species delimitation methods, revealing the existence of two cryptic species with Indo-Pacific distribution. For M. phoenicea, all analyses confirmed the presence of two cryptic species within the South-Western Indian Ocean. Our study suggests that the diversity of Aglaopheniidae might be much higher than assumed, likely related to low dispersal capacities. Sequence-based species delimitation methods seem highly valuable to reveal cryptic diversity in hydrozoans; their application in an integrative framework will be very useful in describing the phyletic diversity of these organisms. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Relative substituent orientation in the structure of cis-3-chloro-1,3-dimethyl-N-(4-nitro-phen-yl)-2-oxo-cyclo-pentane-1-carboxamide.

    Science.gov (United States)

    Zeller, Matthias; Warneke, Jonas; Azov, Vladimir

    2014-09-01

    The structure of the title compound, C14H15ClN2O4, prepared by reaction of a methacryloyl dimer with nitro-aniline, was determined to establish the relative substituent orientation on the cyclo-penta-none ring. In agreement with an earlier proposed reaction mechanism, the amide group and the methyl group adjacent to the chloro substituent adopt equatorial positions and relative cis orientation, whereas the Cl substituent itself and the methyl group adjacent to the amide have axial orientations relative to the mean plane of the five-membered ring. The conformation of the mol-ecule is stabilized by one classical N-H⋯O (2.18 Å) and one non-classical C-H⋯O (2.23 Å) hydrogen bond, each possessing an S(6) graph-set motif. The crystal packing is defined by several non-classical intra-molecular hydrogen bonds, as well as by partial stacking of the aromatic rings.

  14. The SRAP based molecular diversity related to antifungal and antioxidant bioactive constituents for biocontrol potentials of Trichoderma against Sclerotium rolfsii Scc.

    Science.gov (United States)

    Hirpara, Darshna G; Gajera, H P; Bhimani, R D; Golakiya, B A

    2016-08-01

    The study was performed to examine 11 isolates of Trichoderma for their bio-control potentials against Sclerotium rolfsii Sacc. causing stem rot in groundnut. The antagonists Trichoderma were subjected to sequence related amplified polymorphism (SRAP) based molecular diversity analysis and compared with their hardness to S. rolfsii with respect to secretary antifungal and antioxidant profile. T. virens NBAII Tvs 12 evident highest (87.91 %) growth inhibition of test pathogen followed by T. koningii MTCC 796 (67.03 %) at 7 days after inoculation (DAI). Microscopic study confirmed biocontrol mechanism as mycoparasitism for Tvs 12 and antibiosis for MTCC 796. The growth inhibition of test pathogen was significantly negatively correlated with sclerotia formation and lipid peroxidation during antagonism due to release of secretary bioactive antioxidants by antagonists to terminate oxidative burst generated by S. rolfsii and causing inhibition of sclerotium formation. The GC-MS profile identified antifungal and antioxidant constituents hexadecane, 1,2-benzenedicarboxylic acid, mono (2-ethylhexyl) ester, 1-hexadecanesulfonyl chloride, and octadecane in potent antagonists Tvs 12; and nonacosane and octadecane in MTCC 796 along with two novel compounds 1-pentadecene and 1-heneicosyl formate for biocontrol activity. Molecular diversity of Trichoderma isolates associated with antagonistic activity was assessed by SRAP markers. The 115 primer combinations generate total 1328 amplified products of which, 1095 are shared polymorphic and 199 are unique polymorphic. The 15 SRAP combinations produced 18 bands to diagnose best antagonist Tvs 12 and 13 SRAP combinations generated 19 unique bands for identification of MTCC 796. The mycoparasitic antagonist Tvs 12 would be the best antagonist and released unique antifungal and antioxidant constituents to combat pathogen infection. The SRAP based genetic diversity indicates Tvs12 strain clustered with T. viride NBAII Tv23 and shared

  15. Molecular diversity of arbuscular mycorrhizal fungi in onion roots from organic and conventional farming systems in the Netherlands

    NARCIS (Netherlands)

    Galvan Vivero, G.A.; Paradi, I.; Burger, K.; Baar, J.; Kuyper, T.W.; Scholten, O.E.; Kik, C.

    2009-01-01

    Diversity and colonization levels of naturally occurring arbuscular mycorrhizal fungi (AMF) in onion roots were studied to compare organic and conventional farming systems in the Netherlands. In 2004, 20 onion fields were sampled in a balanced survey between farming systems and between two regions,

  16. Use of molecular markers aids in the development of diverse inbred backcross lines in Beit Alpha cucumber (Cucumis sativus L.)

    Science.gov (United States)

    Beit Alpha cucumber (Cucumis sativus L.) is a Mediterranean fresh-market type with a relatively narrow genetic base. To broaden its base for plant improvement, 42 diverse accessions were compared employing a previously defined standard marker array to choose wide-based parental lines for use in bac...

  17. Genetic diversity in a Poincianella pyramidalis (Tul.) L.P. Queiroz population assessed by RAPD molecular markers.

    Science.gov (United States)

    Belarmino, K S; Rêgo, M M; Bruno, R L A; Medeiros, G D A; Andrade, A P; Rêgo, E R

    2017-08-31

    Poincianella pyramidalis (Tul.) L.P. Queiroz is an endemic Caatinga (Brazilian savannah biome) species that has been exploited for different purposes, although information is necessary about still existing natural populations. The objective of this study was to evaluate the genetic diversity among 20 P. pyramidalis individuals occurring in a population localized in the Caatinga biome of Paraíba State, aiming at seed collection, using RAPD markers. For the DNA extraction, young shoots of the individuals were used, and amplification was carried out using 20 primers. The obtained markers were converted to a binary matrix, from which a genetic dissimilarity matrix was built using the arithmetic complement of Jaccard's coefficient, and the dendrogram was built by the UPGMA analysis. No amplified fragment was monomorphic, resulting in 100% polymorphism of the analyzed population. The mean genetic diversity among the matrices was 63.28%, ranging from 30.9 to 97.7%. Individuals 09 and 17 showed relevant genetic proximity, and thus planting their seedlings at close sites would not be indicated. The population evaluated in this study showed high genetic diversity, originating twelve groups from the UPGMA hierarchical cluster analysis. Based on the results, individuals 09 and 17 can provide plant material for the evaluation of the physiological performance of P. pyramidalis seeds, and the set of individuals of this population has a high genetic diversity that characterizes them as adequate matrices for projects of restoration and conservation of the seed species.

  18. Avian picornaviruses: molecular evolution, genome diversity and unusual genome features of a rapidly expanding group of viruses in birds.

    Science.gov (United States)

    Boros, Ákos; Pankovics, Péter; Reuter, Gábor

    2014-12-01

    Picornaviridae is one of the most diverse families of viruses infecting vertebrate species. In contrast to the relative small number of mammal species compared to other vertebrates, the abundance of mammal-infecting picornaviruses was significantly overrepresented among the presently known picornaviruses. Therefore most of the current knowledge about the genome diversity/organization patterns and common genome features were based on the analysis of mammal-infecting picornaviruses. Beside the well known reservoir role of birds in case of several emerging viral pathogens, little is known about the diversity of picornaviruses circulating among birds, although in the last decade the number of known avian picornavirus species with complete genome was increased from one to at least 15. However, little is known about the geographic distribution, host spectrum or pathogenic potential of the recently described picornaviruses of birds. Despite the low number of known avian picornaviruses, the phylogenetic and genome organization diversity of these viruses were remarkable. Beside the common L-4-3-4 and 4-3-4 genome layouts unusual genome patterns (3-4-4; 3-5-4, 3-6-4; 3-8-4) with variable, multicistronic 2A genome regions were found among avian picornaviruses. The phylogenetic and genomic analysis revealed the presence of several conserved structures at the untranslated regions among phylogenetically distant avian and non-avian picornaviruses as well as at least five different avian picornavirus phylogenetic clusters located in every main picornavirus lineage with characteristic genome layouts which suggests the complex evolution history of these viruses. Based on the remarkable genetic diversity of the few known avian picornaviruses, the emergence of further divergent picornaviruses causing challenges in the current taxonomy and also in the understanding of the evolution and genome organization of picornaviruses will be strongly expected. In this review we would like to

  19. Liquid Crystalline Epoxies with Lateral Substituents Showing a Low Dielectric Constant and High Thermal Conductivity

    Science.gov (United States)

    Guo, Huilong; Lu, Mangeng; Liang, Liyan; Wu, Kun; Ma, Dong; Xue, Wei

    2017-02-01

    In this work, liquid crystalline epoxies with lateral substituents were synthesized and cured with aromatic amines or anhydride. The liquid crystalline phase structure of liquid crystalline epoxies with lateral substituents was determined by polarized optical microscopy. The relationship between thermal conductivity and dielectric properties and liquid crystalline domain structure was discussed in the paper. The samples show high thermal conductivity up to 0.29 W/(m × K), due to the orientation of mesogenic units in epoxies. The sample's low dielectric constant of 2.29 is associated with the oriented mesogenic units and long nonpolar lateral substituents. This indicates a new way to obtain materials with high thermal conductivity and a low dielectric constant by introducing oriented mesogenic units into cross-linked epoxy systems. The water repellency is reflected in the contact angles of 92-98°, which are apparently higher than that of conventional epoxy systems. It was also found that the better toughness of liquid crystalline epoxies with lateral substituents was attributed to the existence of long flexible alkyl lateral substituents.

  20. Phylogenetic analysis, genetic diversity and relationships between the recently segregated species of Corynandra and Cleoserrata from the genus Cleome using DNA barcoding and molecular markers.

    Science.gov (United States)

    Tamboli, Asif Shabodin; Patil, Swapnil Mahadeo; Gholave, Avinash Ramchandra; Kadam, Suhas Kishor; Kotibhaskar, Shreya Vijaykumar; Yadav, Shrirang Ramchandra; Govindwar, Sanjay Prabhu

    2016-01-01

    Cleome is the largest genus in the family Cleomaceae and it is known for its various medicinal properties. Recently, some species from the Cleome genus (Cleome viscosa, Cleome chelidonii, Cleome felina and Cleome speciosa) are split into genera Corynandra (Corynandra viscosa, Corynandra chelidonii, Corynandra felina), and Cleoserrata (Cleoserrata speciosa). The objective of this study was to obtain DNA barcodes for these species for their accurate identification and determining phylogenetic relationships. Out of 10 screened barcoding regions, rbcL, matK and ITS1 regions showed higher PCR efficiency and sequencing success. This study added matK, rbcL and ITS1 barcodes for the identification of Corynandra chelidonii, Corynandra felina, Cleome simplicifolia and Cleome aspera species in existing barcode data. Corynandra chelidonii and Corynandra felina species belong to the Corynandra genus, but they are not grouped with the Corynandra viscosa species, however clustered with the Cleome species. Molecular marker analysis showed 100% polymorphism among the studied plant samples. Diversity indices for molecular markers were ranged from He=0.1115-0.1714 and I=0.2268-0.2700, which indicates a significant amount of genetic diversity among studied species. Discrimination of the Cleome and Corynandra species from Cleoserrata speciosa was obtained by two RAPD primers (OPA-4 and RAPD-17) and two ISSR primers (ISSR-1 and ISSR-2). RAPD and ISSR markers are useful for the genetic characterization of these studied species. The present investigation will be helpful to understand the relationships of Cleome lineages with Corynandra and Cleoserrata species.

  1. Is the mega-diverse genus Ocyptamus (Diptera, Syrphidae) monophyletic? Evidence from molecular characters including the secondary structure of 28S rRNA.

    Science.gov (United States)

    Mengual, Ximo; Ståhls, Gunilla; Rojo, Santos

    2012-01-01

    Phylogenetic relationships between two New World Syrphinae taxa (Diptera, Syrphidae), i.e. the highly diverse genus Ocyptamus and the large genus Toxomerus, were analysed based on molecular characters. The monophyly of both taxa was tested and the taxonomic status of included subgenera and species groups was examined. Toxomerus constitutes the monogeneric tribe Toxomerini with more than 140 described species, while Ocyptamus (tribe Syrphini) is a very diverse genus (over 300 spp.) with multiple recognised subgenera and species groups. Sequence data from three gene regions were used: the mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) and the nuclear 28S and 18S ribosomal RNA genes. The secondary structure of two expansion segments (D2, D3) of the ribosomal 28S RNA gene is presented for the family Syrphidae and used for the first time in a multiple sequence alignment. Molecular data were analysed using parsimony, maximum likelihood and Bayesian inference. Toxomerus was always recovered as monophyletic within Ocyptamus, and relationships to other New World taxa such as Salpingogaster (Eosalpingogaster) were well-supported. Only the subgenera and species groups of Ocyptamus were consistently recovered as monophyletic lineages, thus the apparent non-monophyly of Ocyptamus demands reclassification of this clade. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. Assessment of genetic diversity and variation of Robinia pseudoacacia seeds induced by short-term spaceflight based on two molecular marker systems and morphological traits.

    Science.gov (United States)

    Yuan, C Q; Li, Y F; Sun, P; Sun, Y H; Zhang, G J; Yang, M S; Zhang, Y Y; Li, Y; Wang, L

    2012-12-17

    The black locust (Robinia pseudoacacia) is a forest legume that is highly valued as a honey plant and for its wood. We explored the effect of short-term spaceflight on development of R. pseudoacacia seedlings derived from seeds that endured a 15-day flight; the genetic diversity and variation of plants sampled from space-mutagenized seeds were compared to plants from parallel ground-based control seeds using molecular markers and morphological traits. In the morphology analysis, the space-mutagenized group had apparent variation compared with the control group in morphological traits, including plant height, basal diameter, number of branches, branch stipular thorn length, branch stipular thorn middle width, leaflet vertex angle, and tippy leaf vertex angle. Simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) molecular marker analyses showed a slightly higher levels of genetic diversity in the space-mutagenized group compared to the control group. In the SRAP analysis, the space-mutagenized group had 115 polymorphic bands vs 98 in the controls; 91.27% polymorphic loci vs 77.78% in the controls; 1.9127 ± 0.2834 alleles vs 1.7778 ± 0.4174 in the controls; Nei's genetic diversity (h) was 0.2930 ± 0.1631 vs 0.2688 ± 0.1862 in the controls, and the Shannon's information index (I) was 0.4452 ± 0.2177 vs 0.4031 ± 0.2596 in the controls. The number of alleles was significantly higher in the space-mutagenized group. In the SSR analysis, the space-mutagenized group also had more polymorphic bands (51 vs 46), a greater percentage of polymorphic loci (89.47% vs 80.70%); h was also higher (0.2534 ± 0.1533 vs 0.2240 ± 0.1743), as was I (0.3980 ± 0.2069 vs 0.3501 ± 0.2412). These results demonstrated that the range of genetic variation in the populations of R. pseudoacacia increased after spaceflight. It also suggested that the SSR and SRAP markers are effective markers for studying mutations and genetic diversity in R. pseudoacacia. The data

  3. Molecular diversity and distribution of indigenous arbuscular mycorrhizal communities colonizing roots of two different winter cover crops in response to their root proliferation.

    Science.gov (United States)

    Higo, Masao; Isobe, Katsunori; Miyazawa, Yusuke; Matsuda, Yukiya; Drijber, Rhae A; Torigoe, Yoichi

    2016-02-01

    A clear understanding of how crop root proliferation affects the distribution of the spore abundance of arbuscular mycorrhizal fungi (AMF) and the composition of AMF communities in agricultural fields is imperative to identify the potential roles of AMF in winter cover crop rotational systems. Toward this goal, we conducted a field trial using wheat (Triticum aestivum L.) or red clover (Trifolium pratense L.) grown during the winter season. We conducted a molecular analysis to compare the diversity and distribution of AMF communities in roots and spore abundance in soil cropped with wheat and red clover. The AMF spore abundance, AMF root colonization, and abundance of root length were investigated at three different distances from winter crops (0 cm, 7.5 cm, and 15 cm), and differences in these variables were found between the two crops. The distribution of specific AMF communities and variables responded to the two winter cover crops. The majority of Glomerales phylotypes were common to the roots of both winter cover crops, but Gigaspora phylotypes in Gigasporales were found only in red clover roots. These results also demonstrated that the diversity of the AMF colonizing the roots did not significantly change with the three distances from the crop within each rotation but was strongly influenced by the host crop identity. The distribution of specific AMF phylotypes responded to the presence of wheat and red clover roots, indicating that the host crop identity was much more important than the proliferation of crop roots in determining the diversity of the AMF communities.

  4. First insight into dead wood protistan diversity: a molecular sampling of bright-spored Myxomycetes (Amoebozoa, slime-moulds) in decaying beech logs.

    Science.gov (United States)

    Clissmann, Fionn; Fiore-Donno, Anna Maria; Hoppe, Björn; Krüger, Dirk; Kahl, Tiemo; Unterseher, Martin; Schnittler, Martin

    2015-06-01

    Decaying wood hosts a large diversity of seldom investigated protists. Environmental sequencing offers novel insights into communities, but has rarely been applied to saproxylic protists. We investigated the diversity of bright-spored wood-inhabiting Myxomycetes by environmental sequencing. Myxomycetes have a complex life cycle culminating in the formation of mainly macroscopic fruiting bodies, highly variable in shape and colour that are often found on decaying logs. Our hypothesis was that diversity of bright-spored Myxomycetes would increase with decay. DNA was extracted from wood chips collected from 17 beech logs of varying decay stages from the Hainich-Dün region in Central Germany. We obtained 260 partial small subunit ribosomal RNA gene sequences of bright-spored Myxomycetes that were assembled into 29 OTUs, of which 65% were less than 98% similar to those in the existing database. The OTU richness revealed by molecular analysis surpassed that of a parallel inventory of fruiting bodies. We tested several environmental variables and identified pH, rather than decay stage, as the main structuring factor of myxomycete distribution. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. Genetic diversity of Plasmodium falciparum isolates from naturally infected children in north-central Nigeria using the merozoite surface protein-2 as molecular marker

    Institute of Scientific and Technical Information of China (English)

    Segun Isaac Oyedeji; Henrietta Oluwatoyin Awobode; Chiaka Anumudu; Jrgen Kun

    2013-01-01

    Objective:To characterize the genetic diversity of Plasmodium falciparum (P. falciparum) field isolates in children from Lafia, North-central Nigeria, using the highly polymorphic P. falciparum merozoite surface protein 2 (MSP-2) gene as molecular marker. Methods: Three hundred and twenty children were enrolled into the study between 2005 and 2006. These included 140 children who presented with uncomplicated malaria at the Dalhatu Araf Specialist Hospital, Lafia and another 180 children from the study area with asymptomatic infection. DNA was extracted from blood spot on filter paper and MSP-2 genes were genotyped using allele-specific nested PCR in order to analyze the genetic diversity of parasite isolates. Results:A total of 31 and 34 distinct MSP-2 alleles were identified in the asymptomatic and uncomplicated malaria groups respectively. No difference was found between the multiplicity of infection in the asymptomatic group and that of the uncomplicated malaria group (P>0.05). However, isolates of the FC27 allele type were dominant in the asymptomatic group whereas isolates of the 3D7 allele type were dominant in the uncomplicated malaria group. Conclusions: This study showed a high genetic diversity of P. falciparum isolates in North-central Nigeria and is comparable to reports from similar areas with high malaria transmission intensity.

  6. Molecular-based rapid inventories of sympatric diversity: a comparison of DNA barcode clustering methods applied to geography-based vs clade-based sampling of amphibians.

    Science.gov (United States)

    Paz, Andrea; Crawford, Andrew J

    2012-11-01

    Molecular markers offer a universal source of data for quantifying biodiversity. DNA barcoding uses a standardized genetic marker and a curated reference database to identify known species and to reveal cryptic diversity within wellsampled clades. Rapid biological inventories, e.g. rapid assessment programs (RAPs), unlike most barcoding campaigns, are focused on particular geographic localities rather than on clades. Because of the potentially sparse phylogenetic sampling, the addition of DNA barcoding to RAPs may present a greater challenge for the identification of named species or for revealing cryptic diversity. In this article we evaluate the use of DNA barcoding for quantifying lineage diversity within a single sampling site as compared to clade-based sampling, and present examples from amphibians. We compared algorithms for identifying DNA barcode clusters (e.g. species, cryptic species or Evolutionary Significant Units) using previously published DNA barcode data obtained from geography-based sampling at a site in Central Panama, and from clade-based sampling in Madagascar. We found that clustering algorithms based on genetic distance performed similarly on sympatric as well as clade-based barcode data, while a promising coalescent-based method performed poorly on sympatric data. The various clustering algorithms were also compared in terms of speed and software implementation. Although each method has its shortcomings in certain contexts, we recommend the use of the ABGD method, which not only performs fairly well under either sampling method, but does so in a few seconds and with a user-friendly Web interface.

  7. Molecular-based rapid inventories of sympatric diversity: A comparison of DNA barcode clustering methods applied to geography-based vs clade-based sampling of amphibians

    Indian Academy of Sciences (India)

    Andrea Paz; Andrew J Crawford

    2012-11-01

    Molecular markers offer a universal source of data for quantifying biodiversity. DNA barcoding uses a standardized genetic marker and a curated reference database to identify known species and to reveal cryptic diversity within well-sampled clades. Rapid biological inventories, e.g. rapid assessment programs (RAPs), unlike most barcoding campaigns, are focused on particular geographic localities rather than on clades. Because of the potentially sparse phylogenetic sampling, the addition of DNA barcoding to RAPs may present a greater challenge for the identification of named species or for revealing cryptic diversity. In this article we evaluate the use of DNA barcoding for quantifying lineage diversity within a single sampling site as compared to clade-based sampling, and present examples from amphibians. We compared algorithms for identifying DNA barcode clusters (e.g. species, cryptic species or Evolutionary Significant Units) using previously published DNA barcode data obtained from geography-based sampling at a site in Central Panama, and from clade-based sampling in Madagascar. We found that clustering algorithms based on genetic distance performed similarly on sympatric as well as clade-based barcode data, while a promising coalescent-based method performed poorly on sympatric data. The various clustering algorithms were also compared in terms of speed and software implementation. Although each method has its shortcomings in certain contexts, we recommend the use of the ABGD method, which not only performs fairly well under either sampling method, but does so in a few seconds and with a user-friendly Web interface.

  8. Molecular phylogeny reveals high diversity, geographic structure and limited ranges in neotenic net-winged beetles platerodrilus (coleoptera: lycidae).

    Science.gov (United States)

    Masek, Michal; Palata, Vaclav; Bray, Timothy C; Bocak, Ladislav

    2014-01-01

    The neotenic Platerodrilus net-winged beetles have strongly modified development where females do not pupate and retain larval morphology when sexually mature. As a result, dispersal propensity of females is extremely low and the lineage can be used for reconstruction of ancient dispersal and vicariance patterns and identification of centres of diversity. We identified three deep lineages in Platerodrilus occurring predominantly in (1) Borneo and the Philippines, (2) continental Asia, and (3) Sumatra, the Malay Peninsula and Java. We document limited ranges of all species of Platerodrilus and complete species level turnover between the Sunda Islands and even between individual mountain regions in Sumatra. Few dispersal events were recovered among the major geographical regions despite long evolutionary history of occurrence; all of them were dated at the early phase of Platerodrilus diversification up to the end of Miocene and no exchange of island faunas was identified during the Pliocene and Pleistocene despite the frequently exposed Sunda Shelf as sea levels fluctuated with each glacial cycle. We observed high diversity in the regions with persisting humid tropical forests during cool periods. The origins of multiple species were inferred in Sumatra soon after the island emerged and the mountain range uplifted 15 million years ago with the speciation rate lower since then. We suppose that the extremely low dispersal propensity makes Platerodrilus a valuable indicator of uninterrupted persistence of rainforests over a long time span. Additionally, if the diversity of these neotenic lineages is to be protected, a high dense system of protected areas would be necessary.

  9. Genetic diversity and relationship in American and African oil palm as revealed by RFLP and AFLP molecular markers

    Directory of Open Access Journals (Sweden)

    Barcelos Edson

    2002-01-01

    Full Text Available The objective of this work was to evaluate the genetic diversity, its organization and the genetic relationships within oil palm (Elaeis oleifera (Kunth Cortés, from America, and E. guineensis (Jacq., from Africa germplasm using Restriction Fragment Length Polymorphism (RFLP and Amplified Fragment Length Polymorphism (AFLP. In complement to a previous RFLP study on 241 E. oleifera accessions, 38 E. guineensis accessions were analyzed using the same 37 cDNA probes. These accessions covered a large part of the geographical distribution areas of these species in America and Africa. In addition, AFLP analysis was performed on a sub-set of 40 accessions of E. oleifera and 22 of E. guineensis using three pairs of enzyme/primer combinations. Data were subjected to Factorial Analysis of Correspondence (FAC and cluster analysis, with parameters of genetic diversity being also studied. Results appeared congruent between RFLP and AFLP. In the E. oleifera, AFLP confirmed the strong structure of genetic diversity revealed by RFLP, according to geographical origin of the studied material, with the identification of the same four distinct genetic groups: Brazil, French Guyana/Surinam, Peru, north of Colombia/Central America. Both markers revealed that genetic divergence between the two species is of the same magnitude as that among provenances of E. oleifera. This finding is in discrepancy with the supposed early tertiary separation of the two species.

  10. Molecular diversity of arbuscular mycorrhizal fungi in onion roots from organic and conventional farming systems in the Netherlands.

    Science.gov (United States)

    Galván, Guillermo A; Parádi, István; Burger, Karin; Baar, Jacqueline; Kuyper, Thomas W; Scholten, Olga E; Kik, Chris

    2009-06-01

    Diversity and colonization levels of naturally occurring arbuscular mycorrhizal fungi (AMF) in onion roots were studied to compare organic and conventional farming systems in the Netherlands. In 2004, 20 onion fields were sampled in a balanced survey between farming systems and between two regions, namely, Zeeland and Flevoland. In 2005, nine conventional and ten organic fields were additionally surveyed in Flevoland. AMF phylotypes were identified by rDNA sequencing. All plants were colonized, with 60% for arbuscular colonization and 84% for hyphal colonization as grand means. In Zeeland, onion roots from organic fields had higher fractional colonization levels than those from conventional fields. Onion yields in conventional farming were positively correlated with colonization level. Overall, 14 AMF phylotypes were identified. The number of phylotypes per field ranged from one to six. Two phylotypes associated with the Glomus mosseae-coronatum and the G. caledonium-geosporum species complexes were the most abundant, whereas other phylotypes were infrequently found. Organic and conventional farming systems had similar number of phylotypes per field and Shannon diversity indices. A few organic and conventional fields had larger number of phylotypes, including phylotypes associated with the genera Glomus-B, Archaeospora, and Paraglomus. This suggests that farming systems as such did not influence AMF diversity, but rather specific environmental conditions or agricultural practices.

  11. From Amazonia to the Atlantic forest: molecular phylogeny of Phyzelaphryninae frogs reveals unexpected diversity and a striking biogeographic pattern emphasizing conservation challenges.

    Science.gov (United States)

    Fouquet, Antoine; Loebmann, Daniel; Castroviejo-Fisher, Santiago; Padial, José M; Orrico, Victor G D; Lyra, Mariana L; Roberto, Igor Joventino; Kok, Philippe J R; Haddad, Célio F B; Rodrigues, Miguel T

    2012-11-01

    Documenting the Neotropical amphibian diversity has become a major challenge facing the threat of global climate change and the pace of environmental alteration. Recent molecular phylogenetic studies have revealed that the actual number of species in South American tropical forests is largely underestimated, but also that many lineages are millions of years old. The genera Phyzelaphryne (1 sp.) and Adelophryne (6 spp.), which compose the subfamily Phyzelaphryninae, include poorly documented, secretive, and minute frogs with an unusual distribution pattern that encompasses the biotic disjunction between Amazonia and the Atlantic forest. We generated >5.8 kb sequence data from six markers for all seven nominal species of the subfamily as well as for newly discovered populations in order to (1) test the monophyly of Phyzelaphryninae, Adelophryne and Phyzelaphryne, (2) estimate species diversity within the subfamily, and (3) investigate their historical biogeography and diversification. Phylogenetic reconstruction confirmed the monophyly of each group and revealed deep subdivisions within Adelophryne and Phyzelaphryne, with three major clades in Adelophryne located in northern Amazonia, northern Atlantic forest and southern Atlantic forest. Our results suggest that the actual number of species in Phyzelaphryninae is, at least, twice the currently recognized species diversity, with almost every geographically isolated population representing an anciently divergent candidate species. Such results highlight the challenges for conservation, especially in the northern Atlantic forest where it is still degraded at a fast pace. Molecular dating revealed that Phyzelaphryninae originated in Amazonia and dispersed during early Miocene to the Atlantic forest. The two Atlantic forest clades of Adelophryne started to diversify some 7 Ma minimum, while the northern Amazonian Adelophryne diversified much earlier, some 13 Ma minimum. This striking biogeographic pattern coincides with

  12. Network diversity through two-step crystal engineering of a decorated 6-connected primary molecular building block

    KAUST Repository

    Yang, Qing-Yuan

    2016-10-04

    [Cr3O(nicotinate)6]+ was isolated and then utilised as a new primary molecular building block, PMBB, linked by 2-, 3- and 4-connected metal centres. Five novel metal–organic materials (MOMs) with acs, stp, rtl, fsc and pcu topologies were thereby isolated and characterised.

  13. Unexpected diversity of Anopheles species in Eastern Zambia: implications for evaluating vector behavior and interventions using molecular tools.

    Science.gov (United States)

    Lobo, Neil F; St Laurent, Brandyce; Sikaala, Chadwick H; Hamainza, Busiku; Chanda, Javan; Chinula, Dingani; Krishnankutty, Sindhu M; Mueller, Jonathan D; Deason, Nicholas A; Hoang, Quynh T; Boldt, Heather L; Thumloup, Julie; Stevenson, Jennifer; Seyoum, Aklilu; Collins, Frank H

    2015-12-09

    The understanding of malaria vector species in association with their bionomic traits is vital for targeting malaria interventions and measuring effectiveness. Many entomological studies rely on morphological identification of mosquitoes, limiting recognition to visually distinct species/species groups. Anopheles species assignments based on ribosomal DNA ITS2 and mitochondrial DNA COI were compared to morphological identifications from Luangwa and Nyimba districts in Zambia. The comparison of morphological and molecular identifications determined that interpretations of species compositions, insecticide resistance assays, host preference studies, trap efficacy, and Plasmodium infections were incorrect when using morphological identification alone. Morphological identifications recognized eight Anopheles species while 18 distinct sequence groups or species were identified from molecular analyses. Of these 18, seven could not be identified through comparison to published sequences. Twelve of 18 molecularly identified species (including unidentifiable species and species not thought to be vectors) were found by PCR to carry Plasmodium sporozoites - compared to four of eight morphological species. Up to 15% of morphologically identified Anopheles funestus mosquitoes in insecticide resistance tests were found to be other species molecularly. The comprehension of primary and secondary malaria vectors and bionomic characteristics that impact malaria transmission and intervention effectiveness are fundamental in achieving malaria elimination.

  14. Comparative Evaluation of Substituent Effect on the Photochromic Properties of Spiropyrans and Spirooxazines.

    Science.gov (United States)

    Balmond, Edward I; Tautges, Brandon K; Faulkner, Andrea L; Or, Victor W; Hodur, Blanka M; Shaw, Jared T; Louie, Angelique Y

    2016-10-07

    Spiropyrans and spirooxazines represent an important class of photochromic compounds with a wide variety of applications. In order to effectively utilize and design these photoswitches it is desirable to understand how the substituents affect photochromic properties, and how the different structural motifs compare under identical conditions. In this work a small library of photoswitches was synthesized in order to comparatively evaluate the effect of substituent modifications and structure on photochromism. The library was designed to modify positions that were believed to have the greatest effect on C-O bond lability and therefore the photochromic properties. Herein we report a comparative analysis of the UV and visible light responses of 30 spiropyrans, spiroindolinonaphthopyrans, and spirooxazines. The influence of gadolinium(III) binding was also investigated on the library of compounds to determine its effect on photoswitching. Both assays demonstrated different trends in substituent and structural requirements for optimal photochromism.

  15. Interaction energies of CO2·amine complexes: effects of amine substituents.

    Science.gov (United States)

    Jorgensen, Kameron R; Cundari, Thomas R; Wilson, Angela K

    2012-10-25

    To focus on the identification of potential alternative amine carbon capture compounds, CO(2) with methyl, silyl, and trifluoromethyl monosubstituted and disubstituted amine compounds were studied. Interaction energies of these CO(2)·amine complexes were determined via two methods: (a) an ab initio composite method, the correlation consistent composite approach (ccCA), to determine interaction energies and (b) density functional theories, B3LYP/aug-cc-pVTZ and B97D/aug-cc-pVTZ. Substituent effects on the interaction energies were examined by interchanging electron donating and electron withdrawing substituents on the amine compounds. The calculations suggested two different binding modes, hydrogen bonding and acid-base interactions, which arise from the modification of the amine substituents, echoing previous work by our group on modeling protein·CO(2) interactions. Recommendations have been noted for the development of improved amine scrubber complexes.

  16. An analysis of substituent effects in ethane derivatives: the quantum theory of atoms in molecules approach.

    Science.gov (United States)

    Grabowski, Slawomir J; Krygowski, Tadeusz M; Leszczynski, Jerzy

    2009-02-12

    MP2/6-311++G(d,p) calculations were performed on ethane and its simple derivatives. Different substituents such as: Li, Na, BeH, BH(2), OH, NH(2), F and NO(2) were considered. The mono- and disubstituted derivatives of ethane were analyzed. The quantum theory of "atoms in molecules" was applied to localize bond critical points and to analyze relationships between their locations and characteristics of the species. The numerous correlations were found showing the crucial influence of substituent effects. It was also revealed that such parameters as the carbon-carbon distance, or the electron density at C-C bond critical point do not show the systematic changes caused by substituent effects. This means that some of QTAIM parameters, especially the positions of BCPs may be useful to detect numerous sensitive effects if the latter ones do not affect the traditionally analyzed geometrical parameters of a molecule, such as bond lengths.

  17. High gene flow and genetic diversity in three economically important Zanthoxylum Spp. of Upper Brahmaputra Valley Zone of NE India using molecular markers

    Directory of Open Access Journals (Sweden)

    K. Medhi

    2014-12-01

    Full Text Available The genetic diversity in Zanthoxylum species viz. Zanthoxylum nitidum, Zanthoxylum oxyphyllum and Zanthoxylum rhesta collected from the Upper Brahmaputra Valley Zone of Assam (NE India was amplified using 13 random amplified polymorphic DNA (RAPD markers and 9 inter-simple sequence repeat (ISSR markers. RAPD markers were able to detect 81.82% polymorphism whereas ISSR detected 98.02% polymorphism. The genetic similarities were analyzed from the dendrogram constructed by RAPD and ISSR fingerprinting methods which divided the 3 species of Zanthoxylum into 3 clear different clusters. The principle component analysis (PCA was carried out to confirm the clustering pattern of RAPD and ISSR analysis. Analysis of molecular variance (AMOVA revealed the presence of significant variability between different Zanthoxylum species and within the species by both RAPD and ISSR markers. Z. nitidum was found to be sharing a high degree of variation with the other two Zanthoxylum species under study. The Nei's gene diversity (h, Shannon's information index (I, observed number of alleles (na and effective number of alleles (ne were also found to be higher in ISSR markers (0.3526, 0.5230, 1.9802 and 1.6145 than in RAPD markers (0.3144, 0.4610, 1.8182 and 1.5571. The values for total genotype diversity for among population (HT, within population diversity (Hs and gene flow (Nm were more in ISSR (0.3491, 0.2644 and 1.5610 than RAPD (0.3128, 0.2264 and 1.3087 but the mean coefficient of gene differentiation (GST was more in RAPD (0.2764 than ISSR (0.2426. A comparison of this two finger printing methods was done by calculating MR, EMI and MI. The correlation coefficient between data matrices of RAPD and ISSR based on Mantel test was found to be significant (r = 0.65612.

  18. Porphodilactones as synthetic chlorophylls: relative orientation of β-substituents on a pyrrolic ring tunes NIR absorption.

    Science.gov (United States)

    Ke, Xian-Sheng; Chang, Yi; Chen, Jia-Zhen; Tian, Jiangwei; Mack, John; Cheng, Xin; Shen, Zhen; Zhang, Jun-Long

    2014-07-09

    Porphodilactones represent the porphyrin analogues, in which the peripheral bonds of two pyrrole rings are replaced by lactone moieties. They provide an opportunity to investigate how β-substituent orientation of porphyrinoids modulates the electronic structures and optical properties, in a manner similar to what is observed with naturally occurring chlorophylls. In this work, a comprehensive description of the synthesis, characterization, and optical properties of meso-tetrakispentafluorophenylporphodilactone isomers is first reported. The β-dilactone moieties are found to lie at opposite pyrrole positions (trans- and cis-configurations are defined by the relative orientations of the carbonyl group when one lactone moiety is fixed), in accordance with earlier computational predictions (Gouterman, M. J. Am. Chem. Soc. 1989, 111, 3702). The relative orientation of the β-dilactone moieties has a significant influence on the electronic structures and photophysical properties. For example, the Qy band of trans-porphodilactone is red-shifted by 19 nm relative to that of the cis-isomer, and there is a 2-fold increase in the absorption intensity, which resembles the similar trends that have been reported for natural chlorophyll f and d. An in depth analysis of magnetic circular dichroism spectral data and TD-DFT calculations at the B3LYP/6-31G(d) level of theory demonstrates that the trans- and cis-orientations of the dilactone moieties have a significant effect on the relative energies of the frontier π-molecular orbitals. Importantly, the biological behaviors of the isomers reveal their different photocytotoxicity in NIR region (>650 nm). The influence of the relative orientation of the β-substituents on the optical properties in this context provides new insights into the electronic structures of porphyrinoids which could prove useful during the development of near-infrared absorbing photosensitizers.

  19. Quinazoline antifolate thymidylate synthase inhibitors: nitrogen, oxygen, sulfur, and chlorine substituents in the C2 position.

    Science.gov (United States)

    Marsham, P R; Chambers, P; Hayter, A J; Hughes, L R; Jackman, A L; O'Connor, B M; Bishop, J A; Calvert, A H

    1989-03-01

    The synthesis of 16 new N10-propargylquinazoline antifolates with methylamino, ethylamino, (2-aminoethyl)amino, [2-(dimethylamino)ethyl]amino, (2-hydroxyethyl)amino, (carboxymethyl)amino, dimethylamino, imidazol-1-yl, methoxy, ethoxy, phenoxy, 2-methoxyethoxy, 2-hydroxyethoxy, mercapto, methylthio, and chloro substituents at C2 is described. In general, the synthetic route involved the coupling of diethyl N-[4-(prop-2-ynylamino)benzoyl]-L-glutamate (5a) with 6-(bromomethyl)-2-chloro-3,4-dihydro-4-oxoquinazoline in N,N-dimethylformamide with calcium carbonate as the base, displacement of the C2-chloro substituent with nitrogen and sulfur nucleophiles, and deprotection using mild alkali. The C2-ether analogues were most conveniently prepared by coupling 5a with 6-(bromomethyl)-2,4-diakoxy(or diphenoxy)quinazolines. In this series the final deprotection step with aqueous alkali gave simultaneous selective hydrolysis of the C4-alkoxy or C4-phenoxy substituent. The compounds were tested as inhibitors of partially purified L1210 thymidylate synthase (TS). As a measure of cytotoxicity, they were examined for their inhibition of the growth of L1210 cells in culture. The C2-methoxy analogue 11a was equivalent to the previously described tight binding TS inhibitor N10-propargyl-5,8-dideazafolic acid (CB3717, ICI 155387, 1a) against the TS enzyme and exhibited enhanced potency in culture. The C2-methoxy substituent also gave a 110-fold enhancement in aqueous solubility relative to the C2-amine. These results suggest that 11a will be an interesting compound for further study as a potential antitumor agent in vivo. A further series of 2-methoxyquinazoline antifolates with modified alkyl substituents at N10 is also described. None of these analogues equalled the activity of 11a. Thus the propargyl group appears to be the optimum N10 substituent in both 2-amino- and 2-methoxyquinazoline antifolates.

  20. Predicting Where a Radiation Will Occur: Acoustic and Molecular Surveys Reveal Overlooked Diversity in Indian Ocean Island Crickets (Mogoplistinae: Ornebius).

    Science.gov (United States)

    Warren, Ben H; Baudin, Rémy; Franck, Antoine; Hugel, Sylvain; Strasberg, Dominique

    2016-01-01

    Recent theory suggests that the geographic location of island radiations (local accumulation of species diversity due to cladogenesis) can be predicted based on island area and isolation. Crickets are a suitable group for testing these predictions, as they show both the ability to reach some of the most isolated islands in the world, and to speciate at small spatial scales. Despite substantial song variation between closely related species in many island cricket lineages worldwide, to date this characteristic has not received attention in the western Indian Ocean islands; existing species descriptions are based on morphology alone. Here we use a combination of acoustics and DNA sequencing to survey these islands for Ornebius crickets. We uncover a small but previously unknown radiation in the Mascarenes, constituting a three-fold increase in the Ornebius species diversity of this archipelago (from two to six species). A further new species is detected in the Comoros. Although double archipelago colonisation is the best explanation for species diversity in the Seychelles, in situ cladogenesis is the best explanation for the six species in the Mascarenes and two species of the Comoros. Whether the radiation of Mascarene Ornebius results from intra- or purely inter- island speciation cannot be determined on the basis of the phylogenetic data alone. However, the existence of genetic, song and ecological divergence at the intra-island scale is suggestive of an intra-island speciation scenario in which ecological and mating traits diverge hand-in-hand. Our results suggest that the geographic location of Ornebius radiations is partially but not fully explained by island area and isolation. A notable anomaly is Madagascar, where our surveys are consistent with existing accounts in finding no Ornebius species present. Possible explanations are discussed, invoking ecological differences between species and differences in environmental history between islands.

  1. Predicting Where a Radiation Will Occur: Acoustic and Molecular Surveys Reveal Overlooked Diversity in Indian Ocean Island Crickets (Mogoplistinae: Ornebius.

    Directory of Open Access Journals (Sweden)

    Ben H Warren

    Full Text Available Recent theory suggests that the geographic location of island radiations (local accumulation of species diversity due to cladogenesis can be predicted based on island area and isolation. Crickets are a suitable group for testing these predictions, as they show both the ability to reach some of the most isolated islands in the world, and to speciate at small spatial scales. Despite substantial song variation between closely related species in many island cricket lineages worldwide, to date this characteristic has not received attention in the western Indian Ocean islands; existing species descriptions are based on morphology alone. Here we use a combination of acoustics and DNA sequencing to survey these islands for Ornebius crickets. We uncover a small but previously unknown radiation in the Mascarenes, constituting a three-fold increase in the Ornebius species diversity of this archipelago (from two to six species. A further new species is detected in the Comoros. Although double archipelago colonisation is the best explanation for species diversity in the Seychelles, in situ cladogenesis is the best explanation for the six species in the Mascarenes and two species of the Comoros. Whether the radiation of Mascarene Ornebius results from intra- or purely inter- island speciation cannot be determined on the basis of the phylogenetic data alone. However, the existence of genetic, song and ecological divergence at the intra-island scale is suggestive of an intra-island speciation scenario in which ecological and mating traits diverge hand-in-hand. Our results suggest that the geographic location of Ornebius radiations is partially but not fully explained by island area and isolation. A notable anomaly is Madagascar, where our surveys are consistent with existing accounts in finding no Ornebius species present. Possible explanations are discussed, invoking ecological differences between species and differences in environmental history between

  2. Theoretical and Experimental Study of New Photochromic Bis-Spiropyrans with Hydroxyethyl and Carboxyethyl Substituents

    Directory of Open Access Journals (Sweden)

    E. L. Mukhanov

    2013-01-01

    Full Text Available Two new asymmetrical bis-spiropyrans with nonequivalent spiropyran units have been investigated. Hydroxyethyl and carboxyethyl substituents have been used to improve thermal stability of the photoinduced merocyanine forms of the bis-spiropyrans. 2-Hydroxyethyl substituted compound is characterized by 4 times more stable merocyanine isomer. 2-Carboxyethyl substituent in the hetarene part enables chelation by metal ions and controllably stabilizes the merocyanine from thermal decay. As a result of theoretical modeling and photochemical experiments, it was shown that obtained compounds are perspective prototypes for multistate light-driven switches with improved stability of photoinduced forms.

  3. Using remote substituents to control solution structure and anion binding in lanthanide complexes

    DEFF Research Database (Denmark)

    Tropiano, Manuel; Blackburn, Octavia A.; Tilney, James A.

    2013-01-01

    of the molecule, at a substantial distance from the binding pocket. Herein, we explore these remote substituent effects and explain the observed behaviour through discussion of the way in which remote substituents can influence and control the global structure of a molecule through their demands upon...... to isophthalate through a well-defined conformer. Addition of steric bulk remote from the binding site restricts conformational mobility, giving rise to an increase in binding constant on entropic grounds as long as the ideal binding conformation is not excluded from the available range of conformers....

  4. IR and NMR spectral studies of 4-bromo-1-naphthyl chalcones-assessment of substituent effects

    Science.gov (United States)

    Thirunarayanan, G.; Gopalakrishnan, M.; Vanangamudi, G.

    2007-07-01

    Infrared νCO (cm -1) of s-cis and s-trans frequencies and nuclear magnetic resonance chemical shifts δ1H (ppm) of H-α and H-β, δ13C (ppm) of C-α and C-β data were assigned from their respective spectra of a series of various substituted styryl 4-bromo-1-naphthyl chalcones. These values are correlated with various Hammett substituent constants. From the results of statistical analysis, the effect of substituents can be explained.

  5. Design of molecular scaffolds based on unusual geometries for magnetic modulation of spin-diverse complexes with selective redox response.

    Science.gov (United States)

    Lanznaster, Maurício; Heeg, Mary Jane; Yee, Gordon T; McGarvey, Bruce R; Verani, Claudio N

    2007-01-08

    A weakly coupled heterometallic [CuFe] complex has been prepared in which the metal centers are coordinated to a new electroactive ligand. The spin-diverse system delivers distinct ground states upon application of selective redox potentials. Ligand oxidation fosters radical generation, and the initial ground state associated with a weakly coupled [CuFe] core switches to a ground state associated with the [Fe-radical] coupling; the Cu(II) ion remains uncoupled. A third state is obtained upon reduction of the cupric center and in absence of the radical. The possibilities and limitations of these systems are discussed.

  6. Molecular Analysis of Bacterial Community DNA in Sludge Undergoing Autothermal Thermophilic Aerobic Digestion (ATAD: Pitfalls and Improved Methodology to Enhance Diversity Recovery

    Directory of Open Access Journals (Sweden)

    Anna V. Piterina

    2010-03-01

    Full Text Available Molecular analysis of the bacterial community structure associated with sludge processed by autothermal thermophilic aerobic digestion (ATAD, was performed using a number of extraction and amplification procedures which differed in yield, integrity, ability to amplify extracted templates and specificity in recovering species present. Interference to PCR and qPCR amplification was observed due to chelation, nuclease activity and the presence of thermolabile components derived from the ATAD sludge. Addition of selected adjuvant restored the ability to amplify community DNA, derived from the thermophilic sludge, via a number of primer sets of ecological importance and various DNA polymerases. Resolution of community profiles by molecular techniques was also influenced by the ATAD sludge extraction procedure as demonstrated by PCR-DGGE profiling and comparison of taxonomic affiliations of the most predominant members within 16S rRNA gene libraries constructed from ATAD DNA extracted by different methods. Several modifications have been shown to be necessary to optimize the molecular analysis of the ATAD thermal niche which may have general applicability to diversity recovery from similar environments.

  7. Anopheline Diversity: Morphological and Molecular Variation of An. subpictus in Rural and Urban Areas of West Bengal

    Directory of Open Access Journals (Sweden)

    Satarupa Paul

    2013-04-01

    Full Text Available A systematic survey (March 2012- Feb 2013of Anopheline population in rural(Mogra and urban(Dumdum areas of West Bengal has been conducted to know the present population load of Anopheles subpictus. A reliminary attempt has been made to assess the potential morphological (wing as well as molecular variation of Anopheles subpictus by using ITS-2 sequence primer. A considerable sequence variation is observed between the rural and urban population of West Bengal.

  8. Fossils and a large molecular phylogeny show that the evolution of species richness, generic diversity, and turnover rates are disconnected.

    Science.gov (United States)

    Xing, Yaowu; Onstein, Renske E; Carter, Richard J; Stadler, Tanja; Peter Linder, H

    2014-10-01

    The magnitude and extent of global change during the Cenozoic is remarkable, yet the impacts of these global changes on the biodiversity and evolutionary dynamics of species diversification remain poorly understood. To investigate this question, we combine paleontological and neontological data for the angiosperm order Fagales, an ecologically important clade of about 1370 species of trees with an exceptional fossil record. We show differences in patterns of accumulation of generic diversity, species richness, and turnover rates for Fagales. Generic diversity evolved rapidly since the Late Cretaceous and peaked during the Eocene or Oligocene. Turnover rates were high during periods of extreme global climate change, but relatively low when the climate remained stable. Species richness accumulated gradually throughout the Cenozoic, possibly at an accelerated pace after the Middle Miocene. Species diversification occurred in new environments: Quercoids radiating in Oligocene subtropical seasonally arid habitats, Casuarinaceae in Australian pyrophytic biomes, and Betula in Late Neogene holarctic habitats. These radiations were counterbalanced by regional extinctions in Late Neogene mesic warm-temperate forests. Thus, the overall diversification at species level is linked to regional radiations of clades with appropriate ecologies exploiting newly available habitats.

  9. Molecular analyses of the diversity in marine bacterioplankton assemblages along the coastline of the northeastern Gulf of Mexico.

    Science.gov (United States)

    Olapade, Ola A

    2010-10-01

    Bacterial community diversity in marine bacterioplankton assemblages were examined in 3 coastal locations along the northeastern Gulf of Mexico (GOM) using 16S rRNA gene libraries and fluorescence in situ hybridization approaches. The majority of the sequences (30%-60%) were similar to the 16S rRNA gene sequences of unknown bacteria; however, the operational taxonomic units from members of the Cyanobacteria, Proteobacteria, and Bacteroidetes were also present at the 3 GOM sites. Overall, sequence diversity was more similar between the Gulf sites of Carrabelle and Ochlockonee than between either of the Gulf sites and Apalachicola Bay. Fluorescence in situ hybridization analyses revealed the quantitative predominance of members of the Alphaproteobacteria subclass and the Cytophaga-Flavobacterium cluster within the bacterioplankton assemblages. In general, the study further reveals the presence of many bacterial taxa that have been previously found to be dominant in coastal marine environments. Differences observed in the representation of the various bacterial phylogenetic groups among the GOM coastal sites could be partly attributed to dynamic variations in several site-specific conditions, including intermittent tidal events, nutrient availability, and anthropogenic influences.

  10. Molecular and functional diversity of PGPR fluorescent Pseudomonads based on 16S rDNA-RFLP and RAPD markers.

    Science.gov (United States)

    Singh, Bhim Pratap

    2015-09-01

    The genetic and functional diversity of plant growth promoting rhizobacterial (PGPR) fluorescent pseudomonads associated with chickpea (Cicer arietinum L.) rhizosphere was analyzed. In total, 34 isolates along with two reference isolates were screened for various plant growth promoting traits (phosphorous solubilization, ACC deaminase, HCN, IAA and siderophore productions) and antagonist activity against four fungal phytopathogens and three bacterial pathogens. Most of the isolates, that showed PGPR activity, also showed antagonistic activity against all the three fungal pathogens. The genetic relationship was assessed by using random amplification of polymorphic DNA (RAPD) and PCR-restriction fragment length polymorphism (16S rDNA-RFLP). Relationship between both the markers was analyzed based on mantel test and a negative correlation was observed. The study concluded that PGPR traits appeared to be strain specific rather than specific to any phylogenetic group. The study also reported that 16S rDNA based profiling differentiated PGPR fluorescent Pseudomonas on the basis of location rather than biological trait. RAPD profiling could be useful to differentiate among the closely related isolates. The genetic and functional diversity of fluorescent pseudomonads, associated with the chickpea rhizosphere, has useful ecological role and potential utilization in sustainable agriculture.

  11. Increased sampling reveals novel lineages of Entamoeba: consequences of genetic diversity and host specificity for taxonomy and molecular detection.

    Science.gov (United States)

    Stensvold, C Rune; Lebbad, Marianne; Victory, Emma L; Verweij, Jaco J; Tannich, Egbert; Alfellani, Mohammed; Legarraga, Paulette; Clark, C Graham

    2011-07-01

    To expand the representation for phylogenetic analysis, ten additional complete Entamoeba small-subunit rRNA gene sequences were obtained from humans, non-human primates, cattle and a tortoise. For some novel sequences no corresponding morphological data were available, and we suggest that these organisms should be referred to as ribosomal lineages (RL) rather than being assigned species names at present. To investigate genetic diversity and host specificity of selected Entamoeba species, a total of 91 new partial small subunit rRNA gene sequences were obtained, including 49 from Entamoeba coli, 18 from Entamoeba polecki, and 17 from Entamoeba hartmanni. We propose a new nomenclature for significant variants within established Entamoeba species. Based on current data we propose that the uninucleated-cyst-producing Entamoeba infecting humans is called Entamoeba polecki and divided into four subtypes (ST1-ST4) and that Entamoeba coli is divided into two subtypes (ST1-ST2). New hosts for several species were detected and, while host specificity and genetic diversity of several species remain to be clarified, it is clear that previous reliance on cultivated material has given us a misleading and incomplete picture of variation within the genus Entamoeba.

  12. Molecular detection and environment-specific diversity of glycosyl hydrolase family 1 β-glucosidase in different habitats

    Directory of Open Access Journals (Sweden)

    Rameshwar Tiwari

    2016-10-01

    Full Text Available β-glucosidase is a crucial element of the microbial cellulose multienzyme complex since it is responsible for the regulation of the entire cellulose hydrolysis process. Therefore, the aim of the present work was to explore the diversity and distribution of glycosyl hydrolase family 1 β-glucosidase genes in three different environmental niches including, Himalayan soil, cow dung and compost by metagenomic approach. Preliminary evaluation through metabolic profiling using BIOLOG based utilization patterns of carbon, nitrogen, phosphorus and sulphur revealed the environment and substrate specific nature of the indigenous microbial population. Furthermore, clonal library selection, screening and sequence analysis revealed that most of the GH1 β-glucosidase proteins had low identities with the available database. Analysis of the distribution of GH1 β-glucosidase gene fragments and β-glucosidase producing microbial community revealed the environment specific nature. The OTUs obtained from Himalayan soil and compost metagenomic libraries were grouped into 19 different genera comprising 6 groups. The cow dung sample displayed the least diversity of GH1 β-glucosidase sequences, with only 14 genera, distributed among three groups- Bacteroidetes, Firmicutes and Actinobacteria. The metagenomic study coupled with metabolic profiling of GH1 β-glucosidase illustrated the existence of intricate relationship between the geochemical environmental factors and inherent microbial community.

  13. Molecular diversity of serial Cryptococcus neoformans isolates from AIDS patients in the city of São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    Marilena A Martins

    2007-11-01

    Full Text Available Despite highly active anti-retroviral therapy, cryptococcal meningoencephalitis is the second most prevalent neurological disease in Brazilian AIDS patients, being frequently a defining condition with several episodes. As knowledge of Cryptococcus neoformans isolates in the same episode is critical for understanding why some patients develop several episodes, we investigated the genotype characteristics of C. neoformans isolates in two different situations. By pulsed field gel electrophoresis and random amplifield polymorphic DNA analysis, 54 isolates from 12 patients with AIDS and cryptococcosis were analyzed. Group 1 comprised 39 isolates from nine patients with a single episode and hospitalization. Group 2 comprised 15 isolates from three patients with two episodes and hospitalizations. Except for three patients from group 1 probably infected with a single C. neoformans isolate, the other nine patients probably were infected with multiple isolates selected in different collection periods, or the infecting isolate might have underwent mutation to adapt and survive the host immune system and/or the antifungal therapy. However, the three patients from group 2 presented genetic diversity among isolates collected in both hospitalizations, possibly having hosted the initial isolate in both periods. These data, emphasize that Cryptococcus diversity in infection can contribute to strategies of treatment and prevention of cryptococcosis.

  14. Molecular Detection and Environment-Specific Diversity of Glycosyl Hydrolase Family 1 β-Glucosidase in Different Habitats

    Science.gov (United States)

    Tiwari, Rameshwar; Kumar, Kanika; Singh, Surender; Nain, Lata; Shukla, Pratyoosh

    2016-01-01

    β-glucosidase is a crucial element of the microbial cellulose multienzyme complex since it is responsible for the regulation of the entire cellulose hydrolysis process. Therefore, the aim of the present work was to explore the diversity and distribution of glycosyl hydrolase family 1 β-glucosidase genes in three different environmental niches including, Himalayan soil, cow dung and compost by metagenomic approach. Preliminary evaluation through metabolic profiling using BIOLOG based utilization patterns of carbon, nitrogen, phosphorus and sulfur revealed the environment and substrate specific nature of the indigenous microbial population. Furthermore, clonal library selection, screening and sequence analysis revealed that most of the GH1 β-glucosidase proteins had low identities with the available database. Analysis of the distribution of GH1 β-glucosidase gene fragments and β-glucosidase producing microbial community revealed the environment specific nature. The OTUs obtained from Himalayan soil and compost metagenomic libraries were grouped into 19 different genera comprising 6 groups. The cow dung sample displayed the least diversity of GH1 β-glucosidase sequences, with only 14 genera, distributed among three groups- Bacteroidetes, Firmicutes, and Actinobacteria. The metagenomic study coupled with metabolic profiling of GH1 β-glucosidase illustrated the existence of intricate relationship between the geochemical environmental factors and inherent microbial community.

  15. The molecular prevalence and MSA-2b gene-based genetic diversity of Babesia bovis in dairy cattle in Thailand.

    Science.gov (United States)

    Simking, Pacharathon; Saengow, Sinsamuth; Bangphoomi, Kunan; Sarataphan, Nachai; Wongnarkpet, Sirichai; Inpankaew, Tawin; Jittapalapong, Sathaporn; Munkhjargal, Tserendorj; Sivakumar, Thillaiampalam; Yokoyama, Naoaki; Igarashi, Ikuo

    2013-11-08

    Bovine babesiosis is an economically significant disease that affects dairy farming operations in Thailand. In the present study, 1824 blood-DNA samples prepared from cattle bred in 4 different regions of the country (North, Northeast, Central, and South) were screened using a nested PCR for the specific detection of Babesia bovis. While the overall prevalence of B. bovis was 8.8%, the Central region of Thailand was found to be a high-risk area of the country, as the prevalence of the parasite was 15.0%. The positive rate was relatively higher among the animals of 1-5 years of age. The genetic diversity among the B. bovis parasites was also studied based on their MSA-2b gene, and the findings showed that the Thai sequences were dispersed across 8 of 13 total clades observed in the phylogram. Three of these clades were formed only of Thai sequences. Similarity among the deduced MSA-2b amino acid sequences determined in the present study was 68.3-100%. In conclusion, the present study found that all the locations surveyed were infected with B. bovis and that the parasite populations in Thailand were genetically diverse. Our findings highlight the need for further studies in Thailand to generate more information before a sound control strategy could be implemented against B. bovis.

  16. Molecular genetic diversity of bacteria in the bottom section of arctic sea ice from the Canada Basin

    Institute of Scientific and Technical Information of China (English)

    LI Huirong; YU Yong; CHEN Bo; ZENG Yinxin; REN Daming

    2005-01-01

    PCR-DGGE approach was used to analyze bacterial diversity in the bottom section of seven arctic sea ice samples colleted from the Canada Basin. Thirty-two 16S rDNA sequences were obtained from prominent DGGE bands. The closest relatives of these sequences are found to be those of cultivated or uncultured bacteria from antarctic or arctic sea ice. Phylogenetic analysis clustered these sequences or phylotypes within α- proteobacteria, γ-proteobacteria and CFB (cytophaga-flexibacter-bacteroides) group. Sequences belonging to γ-proteobacteria were dominant and members of the CFB group were highly abundant. It was suggested that the CFB group was the representative of the bottom section of sea ice samples.

  17. Molecular and morphological analysis of the critically endangered Fijian iguanas reveals cryptic diversity and a complex biogeographic history

    Science.gov (United States)

    Keogh, J.S.; Edwards, D.L.; Fisher, R.N.; Harlow, P.S.

    2008-01-01

    The Pacific iguanas of the Fijian and Tongan archipelagos are a biogeographic enigma in that their closest relatives are found only in the New World. They currently comprise two genera and four species of extinct and extant taxa. The two extant species, Brachylophus fasciatus from Fiji, Tonga, and Vanuatu and Brachylophus vitiensis from western Fiji, are of considerable conservation concern with B. vitiensis listed as critically endangered. A recent molecular study has shown that Brachylophus comprised three evolutionarily significant units. To test these conclusions and to reevaluate the phylogenetic and biogeographic relationships within Brachylophus, we generated an mtDNA dataset consisting of 1462 base pairs for 61 individuals from 13 islands, representing both Brachylophus species. Unweighted parsimony analyses and Bayesian analyses produced a well-resolved phylogenetic hypothesis supported by high bootstrap values and posterior probabilities within Brachylophus. Our data reject the monophyly of specimens previously believed to comprise B. fasciatus. Instead, our data demonstrate that living Brachylophus comprise three robust and well-supported clades that do not correspond to current taxonomy. One of these clades comprises B. fasciatus from the Lau group of Fiji and Tonga (type locality for B. fasciatus), while a second comprises putative B. fasciatus from the central regions of Fiji, which we refer to here as B. n. sp. Animals in this clade form the sister group to B. vitiensis rather than other B. fasciatus. We herein describe this clade as a new species of Brachylophus based on molecular and morphological data. With only one exception, every island is home to one or more unique haplotypes. We discuss alternative biogeographic hypotheses to explain their distribution in the Pacific and the difficulties of distinguishing these. Together, our molecular and taxonomic results have important implications for future conservation initiatives for the Pacific

  18. Diversity, molecular phylogeny, and bioactive potential of fungal endophytes associated with the Himalayan blue pine (Pinus wallichiana).

    Science.gov (United States)

    Qadri, Masroor; Rajput, Roopali; Abdin, Malik Z; Vishwakarma, Ram A; Riyaz-Ul-Hassan, Syed

    2014-05-01

    In this study, we investigated the diversity of fungal endophytes associated with Pinus wallichiana from the Western Himalayas, with emphasis on comparison of endophytic communities harbored by the stem and needle tissues of the host and their antimicrobial potential. A total number of 130 isolates, comprising of 38 different genera, were recovered from 210 fragments of the plant. Among the isolated fungi, only a single isolate, Tritirachium oryzae, belonged to the Phylum Basidiomycota whereas the rest belonged to Ascomycota. Dothideomycetes was the dominant class with the highest isolation frequency of 49.2 %. The most frequent colonizers of the host were Alternaria spp., Pestalotiopsis spp., Preussia spp., and Sclerostagonospora spp. The diversity and species richness were higher in needle tissues than in the stems. Antimicrobial activities were displayed by extracts from a total number of 22 endophytes against one or more pathogens. Endophytes designated as P1N13 (Coniothyrium carteri), P2N8 (Thielavia subthermophila), P4S6b (Truncatella betulae), P7N10 (Cochliobolus australiensis), and P8S4 (Tritirachium oryzae) were highly active against Candida albicans. Broad spectrum antimicrobial activities were obtained with the extracts of P8-S4 (Tritirachium oryzae) and P5-N26 (Coniochaeta gigantospora) that were potentially active against the Gram-positive and Gram-negative bacteria as well as the fungal pathogen, Candida albicans. The most prominent antagonistic activity against fungal pathogens was shown by P8-S4 (Tritirachium oryzae), P5-N31a (Truncatella spadicea), and P5-N20 (Fusarium larvarum). Our findings indicate that Pinus wallichiana harbors a rich endophytic fungal community with potential antimicrobial activities. Further studies are needed to understand the ecology and evolutionary context of the associations between the Himalayan pine and its endophytes.

  19. Spiropyrans Containing the Reactive Substituents in the 2H-Chromene Moiety

    Directory of Open Access Journals (Sweden)

    B. S. Lukyanov

    2007-01-01

    Full Text Available Some spiropyrans containing functional substituents in the [2H]-chromene part of the molecule were synthesized and their photochromic properties in solution and solid state were investigated. The presence of the formyl group in the [2H]-chromene fragment enhances the possibility to show photochromic properties in solution.

  20. The sEDA(=) and pEDA(=) descriptors of the double bonded substituent effect.

    Science.gov (United States)

    Mazurek, Andrzej; Dobrowolski, Jan Cz

    2013-05-14

    New descriptors of the double bonded substituent effect, sEDA(=) and pEDA(=), were constructed based on quantum chemical calculations and NBO methodology. They show to what extent the σ and π electrons are donated to or withdrawn from the substituted system by a double bonded substituent. The new descriptors differ from descriptors of the classical substituent effect for which the pz orbital of the ipso carbon atom is engaged in the π-electron system of the two neighboring atoms in the ring. For double bonded substituents, the pz orbital participates in double bond formation with only one external atom. Moreover, the external double bond forces localization of the double bond system of the ring, significantly changing the core molecule. We demonstrated good agreement between our descriptors and the Weinhold and Landis' "natural σ and π-electronegativities": so far only descriptors allowing for evaluation of the substitution effect by a double bonded atom. The equivalency between descriptors constructed for 5- and 6-membered model structures as well as linear dependence/independence of the constructed parameters was discussed. Some interrelations between sEDA(=) and pEDA(=) and the other descriptors of (hetero)cyclic systems such as aromaticity and electron density in the ring and bond critical points were also examined.

  1. Substituent effect on the thermodynamic solubility of structural analogs: relative contribution of crystal packing and hydration.

    Science.gov (United States)

    Ozaki, Shunsuke; Nakagawa, Yoshiaki; Shirai, Osamu; Kano, Kenji

    2014-11-01

    Thermodynamic analysis of the solubility of benzoylphenylurea (BPU) derivatives was conducted to investigate the relative importance of crystal packing and hydration for improving solubility with minor structural modification. The contribution of crystal packing to solubility was evaluated from the change in Gibbs energy on the transition from the crystalline to liquid state. Hydration Gibbs energy was estimated using a linear free-energy relationship between octanol-water partition coefficients and gas-water partition coefficients. The established solubility model satisfactorily explained the relative thermodynamic solubility of the model compounds and revealed that crystal packing and hydration equally controlled solubility of the structural analogs. All hydrophobic substituents were undesirable for solubility in terms of hydration, as expected. On the other hand, some of these hydrophobic substituents destabilized crystal packing and improved the solubility of the BPU derivatives when their impact on crystal packing exceeded their negative influence on hydration. The replacement of a single substituent could cause more than a 10-fold enhancement in thermodynamic solubility; this degree of improvement was comparable to that generally achieved by amorphous formulations. Detailed analysis of thermodynamic solubility will allow us to better understand the true substituent effect and design drug-like candidates efficiently.

  2. Electrochemical studies and self diffusion coefficients in cyclic ammonium based ionic liquids with allyl substituents

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Tzi-Yi [Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan (China); Department of Polymer Materials, Kun Shan University, Tainan 71003, Taiwan (China); Su, Shyh-Gang [Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan (China); Wang, H. Paul [Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan (China); Lin, Yuan-Chung [Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung 804, Taiwan (China); Gung, Shr-Tusen; Lin, Ming-Wei [Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan (China); Sun, I.-Wen, E-mail: iwsun@mail.ncku.edu.t [Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan (China)

    2011-03-30

    Research highlights: Cyclic ammonium-based ionic liquids with allyl substituent have high conductivity. Ionic liquids with allyl substituent have wide electrochemical window. Electrochemical and self diffusion coefficients are available for comparison. The Stokes-Einstein plots of DT{sup -1} vs. {eta}{sup -1} for redox couples in ILs are evaluated. Stokes-Einstein product of ferrocene is larger than that of cobaltocenium in ILs. - Abstract: Several cyclic ammonium-based ionic liquids (ILs) with allyl substituent are synthesized, these allyl substituent ILs have high ionic conductivity (up to 4.72 mS cm{sup -1} at 30 {sup o}C) and wide electrochemical window of 5 V. The electrochemical behaviors of two organometallic redox couples Fc/Fc{sup +} (ferrocene/ferrocenium) and Cc/Cc{sup +} (cobaltocene/cobaltocenium) have been studied in these ILs, the calculated Stokes-Einstein product (D{eta} T{sup -1}) of ferrocene in ILs is larger than that of cobaltocenium in ILs. The self-diffusion coefficients of cation and anion in these ILs are studied using pulsed gradient spin-echo NMR technique. There are very few reports where electrochemically derived diffusion coefficients and self diffusion coefficients are available for comparison, so a new key concept in electrochemistry could be developed in this paper.

  3. A new flavonoid with a benzoic acid substituent from Selaginella uncinata

    Institute of Scientific and Technical Information of China (English)

    Jun Xia Zheng; Nai Li Wang; Hao Gao; Hong Wei Liu; Hai Feng Chen; Ming Fan; Xin Sheng Yao

    2008-01-01

    6-(5-Carboxyl-2-methoxyphenyl)-apigenin (1), a new flavonoid, was isolated from the 60% ethanol extract of Selaginella uncinata (Desv.) Spring. Its structure was established by spectroscopic methods. Compound 1 represents the first example of the flavonoids possessing a benzoic acid substituent at C-6.

  4. PLE CATALYZED HYDROLYZES OF ALPHA-SUBSTITUTED ALPHA-HYDROXY ESTERS - THE INFLUENCE OF THE SUBSTITUENTS

    NARCIS (Netherlands)

    MOORLAG, H; KELLOGG, RM

    1991-01-01

    The enzymatic hydrolyses of a variety of alpha-substituted mandelic and lactic esters using pig liver esterase (PLE) have been investigated. High to moderate enantioselectivity was found for various alpha-substituted mandelic esters, whereas PLE showed low to no enantioselectivity for alpha-substitu

  5. First molecular identification and report of genetic diversity of Strongyloides stercoralis, a current major soil-transmitted helminth in humans from Lao People's Democratic Republic.

    Science.gov (United States)

    Laymanivong, Sakhone; Hangvanthong, Bouasy; Insisiengmay, Bounnaloth; Vanisaveth, Viengxay; Laxachack, Pinnakhone; Jongthawin, Jurairat; Sanpool, Oranuch; Thanchomnang, Tongjit; Sadaow, Lakkhana; Phosuk, Issarapong; Rodpai, Rutchanee; Maleewong, Wanchai; Intapan, Pewpan M

    2016-08-01

    Strongyloidiasis is a major soil-transmitted helminth (STH) disease that affects people worldwide. We present updated data on prevalence in the Lao People's Democratic Republic (Lao PDR) in 2015, arising from a community cross-sectional helminthiasis survey. Fecal samples were collected from 327 individuals across three provinces in Lao PDR (Luang Prabang in the north, Khammouane in the center, and Champasack in the south). Agar plate culture and Kato-Katz methods were used to examine duplicate stool samples from each participant to detect Strongyloides stercoralis and co-infecting helminths. Overall prevalences of S. strercoralis human hookworm, Taenia spp., Trichuris trichiura, Ascaris lumbricoides, and Enterobius vermicularis were 41.0, 28.1, 4.9, 4.0, 1.5, and 0.9 %, respectively. The prevalence of miscellaneous trematodiases (including opisthorchiasis) was 37.9 % and of Schistosoma mekongi infection was 0.3 %. Strongyloidiasis is a current major STH disease in Lao PDR. We also report the molecular-phylogenetic identification of S. stercoralis adult males collected from 40 representative human strongyliodiasis fecal samples. DNA was extracted, amplified, and sequenced from a portion of the mitochondrial cox1 gene and the nuclear 18S ribosomal DNA. Phylogenetic analyses indicated that all specimens sequenced belonged to S. stercoralis (Bavay, 1876) Stiles and Hassall, 1902. The cox1 sequences exhibited great diversity (24 haplotypes) in Lao PDR. This is the first molecular identification and report of genetic diversity of S. stercoralis in humans from Lao PDR. An effective parasite control program is needed to reduce the serious health impacts.

  6. A novel approach to inherently chiral calix[4]arenes by direct introduction of a substituent at the meta position

    NARCIS (Netherlands)

    Verboom, Willem; Bodewes, P.; Bodewes, Paul J.; van Essen, Georget; Timmerman, P.; van Hummel, G.J.; Harkema, Sybolt; Reinhoudt, David

    1995-01-01

    A novel method for the preparation of inherently chiral calix[4]arenes is described by direct introduction of a substituent in para-acetamido substituted calix[4]arenes. Bromination and nitration of mono(acetamido)calix[4]arenes 5, 6 afforded calix[4]arenes 7¿10, in which the substituent was

  7. Improved yield of high molecular weight DNA coincides with increased microbial diversity access from iron oxide cemented sub-surface clay environments.

    Directory of Open Access Journals (Sweden)

    Richard A Hurt

    Full Text Available Despite over three decades of progress, extraction of high molecular weight (HMW DNA from high clay soils or iron oxide cemented clay has remained challenging. HMW DNA is desirable for next generation sequencing as it yields the most comprehensive coverage. Several DNA extraction procedures were compared from samples that exhibit strong nucleic acid adsorption. pH manipulation or use of alternative ion solutions offered no improvement in nucleic acid recovery. Lysis by liquid N2 grinding in concentrated guanidine followed by concentrated sodium phosphate extraction supported HMW DNA recovery from clays high in iron oxides. DNA recovered using 1 M sodium phosphate buffer (PB as a competitive desorptive wash was 15.22±2.33 µg DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46±0.25 µg DNA/g clay with the Powerlyzer system (MoBio. Increasing PB concentration in the lysis reagent coincided with increasing DNA fragment length during initial extraction. Rarefaction plots of 16S rRNA (V1-V3 region pyrosequencing from A-horizon and clay soils showed an ∼80% and ∼400% larger accessed diversity compared to the Powerlyzer soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more operational taxonomic units (OTU recovered.

  8. Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST.

    Science.gov (United States)

    O'Donnell, Kerry; Humber, Richard A; Geiser, David M; Kang, Seogchan; Park, Bongsoo; Robert, Vincent A R G; Crous, Pedro W; Johnston, Peter R; Aoki, Takayuki; Rooney, Alejandro P; Rehner, Stephen A

    2012-01-01

    We constructed several multilocus DNA sequence datasets to assess the phylogenetic diversity of insecticolous fusaria, especially focusing on those housed at the Agricultural Research Service Collection of Entomopathogenic Fungi (ARSEF), and to aid molecular identifications of unknowns via the FUSARIUM-ID and Fusarium MLST online databases and analysis packages. Analyses of a 190-taxon, two-locus dataset, which included 159 isolates from insects, indicated that: (i) insect-associated fusaria were nested within 10 species complexes spanning the phylogenetic breadth of Fusarium, (ii) novel, putatively unnamed insecticolous species were nested within 8/10 species complexes and (iii) Latin binomials could be applied with confidence to only 18/58 phylogenetically distinct fusaria associated with pest insects. Phylogenetic analyses of an 82-taxon, three-locus dataset nearly fully resolved evolutionary relationships among the 10 clades containing insecticolous fusaria. Multilocus typing of isolates within four species complexes identified surprisingly high genetic diversity in that 63/65 of the fusaria typed represented newly discovered haplotypes. The DNA sequence data, together with corrected ABI sequence chromatograms and alignments, have been uploaded to the following websites dedicated to identifying fusaria: FUSARIUM-ID (http://isolate.fusariumdb.org) at Pennsylvania State University's Department of Plant Pathology and Fusarium MLST (http://www.cbs.knaw.nl/fusarium) at the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center.

  9. Comparative analysis of genetic diversity of sesame (Sesamum indicum L.) from Vietnam and Cambodia using agro-morphological and molecular markers.

    Science.gov (United States)

    Pham, Toan Duc; Geleta, Mulatu; Bui, Tri Minh; Bui, Tuyen Cach; Merker, Arnulf; Carlsson, Anders S

    2011-02-01

    The purpose of this study was to comparatively analyze the genetic diversity of sesame (Sesamum indicum L.) using agro-morphological and molecular markers. Twelve sesame populations collected from three regions in Cambodia and Vietnam were used in this study. A high genetic variation was revealed both by agro-morphological and RAPD markers within and among the 12 sesame populations. The range of agro-morphological trait based average taxonomic distance among populations (0.02 to 0.47) was wider than that of RAPD based genetic distance (0.06 to 0.27). The mean distance revealed by agro-morphological markers (0.23) and RAPD markers (0.22) was similar. RAPD based analysis revealed a relatively higher genetic diversity in populations from South Vietnam as compared to the other two regions. Interestingly, populations from this region also had higher values for yield related traits such as number of capsules per plant, number of seeds per capsule, and seed yield per plant suggesting positive correlation between the extent of genetic variation within population and yield related traits in sesame. A highly significant positive correlation (r = 0.88, P sesame, their combined use would give superior results. © 2011 The Authors.

  10. Multilocus molecular phylogeny of the ornamental wood-eating catfishes (Siluriformes, Loricariidae, Panaqolus and Panaque) reveals undescribed diversity and parapatric clades.

    Science.gov (United States)

    Lujan, Nathan K; Cramer, Christian A; Covain, Raphael; Fisch-Muller, Sonia; López-Fernández, Hernán

    2017-04-01

    Approximately two-dozen species in three genera of the Neotropical suckermouth armored catfish family Loricariidae are the only described fishes known to specialize on diets consisting largely of wood. We conducted a molecular phylogenetic analysis of 10 described species and 14 undescribed species or morphotypes assigned to the wood-eating catfish genus Panaqolus, and four described species and three undescribed species or morphotypes assigned to the distantly related wood-eating catfish genus Panaque. Our analyses included individuals and species from both genera that are broadly distributed throughout tropical South America east of the Andes Mountains and 13 additional genera hypothesized to have also descended from the most recent common ancestor of Panaqolus and Panaque. Bayesian and maximum likelihood analyses of two mitochondrial and three nuclear loci totaling 4293bp confirmed respective monophyly of Panaqolus, exclusive of the putative congener 'Panaqolus' koko, and Panaque. Members of Panaqolus sensu stricto were distributed across three strongly monophyletic clades: a clade of 10 generally darkly colored, lyretail species distributed across western headwaters of the Amazon Basin, a clade of three irregularly and narrowly banded species from the western Orinoco Basin, and a clade of 11 generally brown, broadly banded species that are widely distributed throughout the Amazon Basin. We erect new subgenera for each of these clades and a new genus for the morphologically, biogeographically and ecologically distinct species 'Panaqolus' koko. Our finding that perhaps half of the species-level diversity in the widespread genus Panaqolus remains undescribed illustrates the extent to which total taxonomic diversity of small and philopatric, yet apparently widely distributed, Amazonian fishes may remain underestimated. Ranges for two Panaqolus subgenera and the genus Panaque overlap with the wood-eating genus Cochliodon in central Andean tributaries of the upper

  11. Molecular characterization of ruminal bacterial diversity in vitro - DOI: 10.4025/actascianimsci.v30i2.4699

    Directory of Open Access Journals (Sweden)

    Dante Pazzanese Duarte Lanna

    2008-08-01

    Full Text Available PCR analysis is a sensitive and specific tool to detect and monitor microorganisms in complex environmental samples. The amplification of 16S ribosomal DNA sequences followed by gel electrophoresis under denaturing gradient (DGGE has been a powerful technique to genetically evaluate microbial ecosystems. Changes in rumen microbial populations were investigated in vitro using a basal diet with different lipid sources. PCRs were performed with two different sets of primers in order to amplify 16S rRNA sequences, and the amplified fragments were submitted to DGGE analysis. The findings presented in this study show that distinct microbial communities were present in each treatment. The presence of soybean oil seems to maximize growth of bacterial population, whereas fish oil appears to reduce growth. We demonstrated the successful application of molecular ecological techniques to analyze the structure and composition of bacterial communities in rumen ecosystems.

  12. Molecular analysis of red wine yeast diversity in the Ribera del Duero D.O. (Spain) area.

    Science.gov (United States)

    Muñoz-Bernal, Eugenia; Rodríguez, María Esther; Benítez, Patricia; Fernández-Acero, Francisco Javier; Rebordinos, Laureana; Cantoral, Jesús Manuel

    2013-05-01

    Molecular characterization of wine yeast population during spontaneous fermentation in biodynamic wines from Ribera del Duero D.O. located at northern plateau of Spain has been carried out during two consecutive years. A total of 829 yeast strains were isolated from the samples and characterized by electrophoretic karyotype. The results show the presence of three population of yeast differentiated by their electrophoretic karyotypes, (1) non-Saccharomyces yeast dominant in the initial phase of the fermentations (NS); (2) Saccharomyces bayanus var uvarum detected mainly mid-way through the fermentation process at 20-25 °C; and (3) Saccharomyces cerevisiae which remained dominant until the end of the fermentation. This is the first study showing the population dynamic of S. bayanus var. uvarum in red wines produced in Ribera del Duero that could represent an important source of autochthonous wine yeasts with novel oenological properties.

  13. Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species.

    Science.gov (United States)

    Baroncelli, Riccardo; Zapparata, Antonio; Sarrocco, Sabrina; Sukno, Serenella A; Lane, Charles R; Thon, Michael R; Vannacci, Giovanni; Holub, Eric; Sreenivasaprasad, Surapareddy

    2015-01-01

    Fragaria × ananassa (common name: strawberry) is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l.) is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production.

  14. Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species.

    Directory of Open Access Journals (Sweden)

    Riccardo Baroncelli

    Full Text Available Fragaria × ananassa (common name: strawberry is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l. is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production.

  15. Molecular Phylogenies of Blastocystis Isolates from Different Hosts: Implications for Genetic Diversity, Identification of Species, and Zoonosis

    Science.gov (United States)

    Noël, Christophe; Dufernez, Fabienne; Gerbod, Delphine; Edgcomb, Virginia P.; Delgado-Viscogliosi, Pilar; Ho, Lip-Chuen; Singh, Mulkit; Wintjens, René; Sogin, Mitchell L.; Capron, Monique; Pierce, Raymond; Zenner, Lionel; Viscogliosi, Eric

    2005-01-01

    Small-subunit (SSU) rRNA gene sequences were obtained by PCR from 12 Blastocystis isolates from humans, rats, and reptiles for which elongation factor 1α (EF-1α) gene sequences are already available. These new sequences were analyzed by the Bayesian method in a broad phylogeny including, for the first time, all Blastocystis sequences available in the databases. Phylogenetic trees identified seven well-resolved groups plus several discrete lineages that could represent newly defined clades. Comparative analysis of SSU rRNA- and EF-1α-based trees obtained by maximum-likelihood methods from a restricted sampling (13 isolates) revealed overall agreement between the two phylogenies. In spite of their morphological similarity, sequence divergence among Blastocystis isolates reflected considerable genetic diversity that could be correlated with the existence of potentially ≥12 different species within the genus. Based on this analysis and previous PCR-based genotype classification data, six of these major groups might consist of Blastocystis isolates from both humans and other animal hosts, confirming the low host specificity of Blastocystis. Our results also strongly suggest the existence of numerous zoonotic isolates with frequent animal-to-human and human-to-animal transmissions and of a large potential reservoir in animals for infections in humans. PMID:15634993

  16. Molecular diversity of the methanotrophic bacteria communities associated with disused tin-mining ponds in Kampar, Perak, Malaysia.

    Science.gov (United States)

    Sow, S L S; Khoo, G; Chong, L K; Smith, T J; Harrison, P L; Ong, H K A

    2014-10-01

    In a previous study, notable differences of several physicochemical properties, as well as the community structure of ammonia oxidizing bacteria as judged by 16S rRNA gene analysis, were observed among several disused tin-mining ponds located in the town of Kampar, Malaysia. These variations were associated with the presence of aquatic vegetation as well as past secondary activities that occurred at the ponds. Here, methane oxidizing bacteria (MOB), which are direct participants in the nutrient cycles of aquatic environments and biological indicators of environmental variations, have been characterised via analysis of pmoA functional genes in the same environments. The MOB communities associated with disused tin-mining ponds that were exposed to varying secondary activities were examined in comparison to those in ponds that were left to nature. Comparing the sequence and phylogenetic analysis of the pmoA clone libraries at the different ponds (idle, lotus-cultivated and post-aquaculture), we found pmoA genes indicating the presence of type I and type II MOB at all study sites, but type Ib sequences affiliated with the Methylococcus/Methylocaldum lineage were most ubiquitous (46.7 % of clones). Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture was observed to harbor the highest richness of MOB. However, varying secondary activity or sample type did not show a strong variation in community patterns as compared to the ammonia oxidizers in our previous study.

  17. Toward a Molecular Lego Approach for the Diversity-Oriented Synthesis of Cyclodextrin Analogues Designed as Scaffolds for Multivalent Systems.

    Science.gov (United States)

    Lepage, Mathieu L; Schneider, Jérémy P; Bodlenner, Anne; Compain, Philippe

    2015-11-06

    A modular strategy has been developed to access a diversity of cyclic and acyclic oligosaccharide analogues designed as prefunctionalized scaffolds for the synthesis of multivalent ligands. This convergent approach is based on bifunctional sugar building blocks with two temporarily masked functionalities that can be orthogonally activated to perform Cu(I)-catalyzed azide-alkyne cycloaddition reactions (CuAAC). The reducing end is activated as a glycosyl azide and masked as a 1,6-anhydro sugar, while the nonreducing end is activated as a free alkyne and masked as a triethylsilyl-alkyne. Following a cyclooligomerization approach, the first examples of close analogues of cyclodextrins composed of d-glucose residues and triazole units bound together through α-(1,4) linkages were obtained. The cycloglucopyranoside analogue containing four sugar units was used as a template to prepare multivalent systems displaying a protected d-mannose derivative or an iminosugar by way of CuAAC. On the other hand, the modular approach led to acyclic alkyne-functionalized scaffolds of a controlled size that were used to synthesize multivalent iminosugars.

  18. Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species

    Science.gov (United States)

    Baroncelli, Riccardo; Zapparata, Antonio; Sarrocco, Sabrina; Sukno, Serenella A.; Lane, Charles R.; Thon, Michael R.; Vannacci, Giovanni; Holub, Eric; Sreenivasaprasad, Surapareddy

    2015-01-01

    Fragaria × ananassa (common name: strawberry) is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l.) is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production. PMID:26086351

  19. Brownian molecular rotors: Theoretical design principles and predicted realizations

    Science.gov (United States)

    Schönborn, Jan Boyke; Herges, Rainer; Hartke, Bernd

    2009-06-01

    We propose simple design concepts for molecular rotors driven by Brownian motion and external photochemical switching. Unidirectionality and efficiency of the motion is measured by explicit simulations. Two different molecular scaffolds are shown to yield viable molecular rotors when decorated with suitable substituents.

  20. Practical benefits of knowing the enemy: modern molecular tools for diagnosing the etiology of bacterial diseases and understanding the taxonomy and diversity of plant-pathogenic bacteria.

    Science.gov (United States)

    Bull, Carolee T; Koike, Steven T

    2015-01-01

    Knowing the identity of bacterial plant pathogens is essential to strategic and sustainable disease management in agricultural systems. This knowledge is critical for growers, diagnosticians, extension agents, and others dealing with crops. However, such identifications are linked to bacterial taxonomy, a complicated and changing discipline that depends on methods and information that are often not used by those who are diagnosing field problems. Modern molecular tools for fingerprinting and sequencing allow for pathogen identification in the absence of distinguishing or conveniently tested phenotypic characteristics. These methods are also useful in studying the etiology and epidemiology of phytopathogenic bacteria from epidemics, as was done in numerous studies conducted in California's Salinas Valley. Multilocus and whole-genome sequence analyses are becoming the cornerstones of studies of microbial diversity and bacterial taxonomy. Whole-genome sequence analysis needs to become adequately accessible, automated, and affordable in order to be used routinely for identification and epidemiology. The power of molecular tools in accurately identifying bacterial pathogenesis is therefore of value to the farmer, diagnostician, phytobacteriologist, and taxonomist.

  1. Combined morphological and molecular data unveils relationships of Pseudobranchiomma (Sabellidae, Annelida and reveals higher diversity of this intriguing group of fan worms in Australia, including potentially introduced species

    Directory of Open Access Journals (Sweden)

    Maria Capa

    2016-10-01

    Full Text Available Pseudobranchiomma (Sabellidae, Annelida is a small and heterogeneous group of fan worms found in shallow marine environments and is generally associated with hard substrates. The delineation and composition of this genus is problematic since it has been defined only by plesiomorphic characters that are widely distributed among other sabellids. In this study we have combined morphological and molecular (mitochondrial and nuclear DNA sequences data to evaluate species diversity in Australia and assess the phylogenetic relationships of these and other related sabellids. Unlike morphological data alone, molecular data and combined datasets suggest monophyly of Pseudobranchiomma. In this study, a new species of Pseudobranchiomma is described and three others are considered as potential unintentional introductions to Australian waters, one of them reported for the first time for the continent. Pseudobranchiomma pallida sp. n. bears 4–6 serrations along the radiolar flanges, lacks radiolar eyes and has uncini with three transverse rows of teeth over the main fang. In the new species the colour pattern as well is characteristic and species specific.

  2. Substituent effects on the gas-phase fragmentation reactions of sulfonium ion containing peptides.

    Science.gov (United States)

    Sierakowski, James; Amunugama, Mahasilu; Roberts, Kade D; Reid, Gavin E

    2007-01-01

    The multistage mass spectrometric (MS/MS and MS3) gas-phase fragmentation reactions of methionine side-chain sulfonium ion containing peptides formed by reaction with a series of para-substituted phenacyl bromide (XBr where X=CH2COC6H4R, and R=--COOH, --COOCH3, --H, --CH3 and --CH2CH3) alkylating reagents have been examined in a linear quadrupole ion trap mass spectrometer. MS/MS of the singly (M+) and multiply ([M++nH](n+1)+) charged precursor ions results in exclusive dissociation at the fixed charge containing side chain, independently of the amino acid composition and precursor ion charge state (i.e., proton mobility). However, loss of the methylphenacyl sulfide side-chain fragment as a neutral versus charged (protonated) species was observed to be highly dependent on the proton mobility of the precursor ion, and the identity of the phenacyl group para-substituent. Molecular orbital calculations were performed at the B3LYP/6-31+G** level of theory to calculate the theoretical proton affinities of the neutral side-chain fragments. The log of the ratio of neutral versus protonated side-chain fragment losses from the derivatized side chain were found to exhibit a linear dependence on the proton affinity of the side-chain fragmentation product, as well as the proton affinities of the peptide product ions. Finally, MS3 dissociation of the nominally identical neutral and protonated loss product ions formed by MS/MS of the [M++H]2+ and [M++2H]3+ precursor ions, respectively, from the peptide GAILM(X)GAILK revealed significant differences in the abundances of the resultant product ions. These results suggest that the protonated peptide product ions formed by gas-phase fragmentation of sulfonium ion containing precursors in an ion trap mass spectrometer do not necessarily undergo intramolecular proton 'scrambling' prior to their further dissociation, in contrast to that previously demonstrated for peptide ions introduced by external ionization sources.

  3. Functionalizable oligoprolines as molecular scaffolds.

    Science.gov (United States)

    Nagel, Yvonne A; Kuemin, Michael; Wennemers, Helma

    2011-01-01

    Azidoproline (Azp) containing oligoprolines are conformationally well-defined, helical molecular scaffolds that allow for facile functionalization. Within this article we describe the synthesis of Azp-containing oligoprolines and different strategies to introduce functional moieties. In addition, the influence of factors such as substituents at the y-position of proline as well as functional groups at the termini on the conformational stability of the molecular scaffolds are briefly presented.

  4. Molecular Differentiation of Fasciola Species and Characterization of Genetic Diversity of F. gigantica Using NADH Dehydrogenase I (ND1 Gene in the Endemic Areas of Iran.

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    Shabnam Tadayon

    2015-03-01

    Full Text Available Fasciola hepatica and F. gigantica are the causative agents of fasciolosis in domestic animals and humans. Based on the morphometric criteria, differential diagnosis between them is problematic. In addition, intermediate forms of Fasciola have been found in Iran, which makes the differentiation more difficult. The aim of the present study was to provide molecular evidence for the existence of F. gigantica in Iran using sequencing analysis of ND1 and PCR-RFLP analysis of ITS2 regions and to study the intraspecies variations of F. gigantica based on mitochondrial ND1 gene polymorphism.Forty Fasciola spp. samples collected from four distinct provinces (Fars, Khuzestan, Gilan, Khorasan Razavi in Iran were collected for morphological and molecular characterization. In molecular method, PCR-RFLP analysis of ITS2 using pagI restriction enzyme was used as a screening approach for F. gigantica differentiation. Then mitochondrial DNA sequence variations in the ND1 gene were used for phylogenetic analysis.Based on the morphometric criteria and RFLP analysis, 14 parasitic samples were initially identified to be F. gigantica. Phylogenetic results showed that there are at least 10 different genotypes of F. gigantica in Iran, which are different from those existing in the GenBank. Twenty-six points out of 410 base pairs of sequenced ND1 gene in 10 varieties of F. gigantica were diagnosed to be polymorphic. From 26 points of polymorphism, only eight resulted in the post-translational amino acid changes in ND1 gene product structure.Data revealed noticeable genetic diversity (up to 4.63% between different varieties of F. gigantica in Iran.

  5. In Silico study for diversing the molecular pathway of pigment formation: An alternative to manual coloring in cotton fibers.

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    Ammara eAhad

    2015-09-01

    Full Text Available Diversity of colors in flowers and fruits is largely due to anthocyanin pigments. The flavonoid/anthocyanin pathway has been most extensively studied. Dihydroflavonol 4-reductase (DFR is a vibrant enzyme of the flavonoid pathway which displays major impact on the formation of anthocyanins, flavan 3-ols and flavonols. The substrate specificity of the DFR was found to play a crucial role in determination of type of anthocyanidins. Altering the flavonoid/ anthocyanin pathway through genetic engineering to develop color of our own choice is an exciting subject of future research. In the present study, comparison among four DFR genes (Gossypium hirsutum, Iris × hollandica, Ang. DFRI and DFRII, sequence alignment for homology as well as protein modeling and docking is demonstrated. Estimation of catalytic sites, prediction of substrate preference and protein docking were the key features of this article. For specific substrate uptake, a proline rich region and positions 12 plus 26 along with other positions emphasizing the 26-amino acid residue region (132-157 was tested. Results showed that proline rich region position 12, 26 and 132-157 plays an important role in selective attachment of DFRs with respective substrates. Further, ‘Expasy ProtParam tool’ results showed that Iris × hollandica DFR amino acids (Asn 9: Asp 23 favorable for reducing DHQ and DHM thus accumulating delphinidin, while Gossypium hirsutum DFR has (Asn 13: Asp 21 hypothesized to consume DHK. Protein docking data showed that amino acid residues in above mentioned positions were just involved in attachment of DFR with substrate and had no role in specific substrate uptake.Advanced bioinformatics analysis has revealed that all above mentioned positions have role in substrate attachment. For substrate specificity, other residues region is involved. It will help in color manipulations in different plant species.

  6. Diversity, molecular characterization and expression of T cell receptor γ in a teleost fish, the sea bass (Dicentrarchus labrax, L.

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    Francesco Buonocore

    Full Text Available Two lineages of T cells, expressing either the αβ T cell receptor (TR or the γδ TR, exist in Gnathostomes. The latter type of T cells account for 1-10 % of T cells in blood and up to 30 % in the small intestine. They may recognize unconventional antigens (phosphorylated microbial metabolites, lipid antigens without the need of major histocompatibility class I (MH1 or class II (MH2 presentation. In this work we have described cloning and structural characterization of TR -chain (TRG from the teleost Dicentrarchus labrax. Further, by means of quantitative PCR analysis, we analyzed TRG expression levels both in poly I:C stimulated leukocytes in vitro, and following infection with betanodavirus in vivo. Two full length cDNAs relative to TRG, with the highest peptide and nucleotide identity with Japanese flounder, were identified. A multiple alignment analysis showed the conservation of peptides fundamental for TRG biological functions, and of the FGXG motif in the FR4 region, typical of most TR and immunoglobulin light chains. A 3D structure consisting of two domains mainly folded as beta strands with a sandwich architecture for each domain was also reported. TRG CDR3 of 8-18 AA in length and diversity in the TRG rearrangements expressed in thymus and intestine for a given V/C combination were evidenced by junction length spectratyping. TRG mRNA expression levels were high in basal conditions both in thymus and intestine, while in kidney and gut leukocytes they were up-regulated after in vitro stimulation by poly I:C. Finally, in juveniles the TRG expression levels were up-regulated in the head kidney and down-regulated in intestine after in vivo infection with betanodavirus. Overall, in this study the involvement of TRG-bearing T cells during viral stimulation was described for the first time, leading to new insights for the identification of T cell subsets in fish.

  7. Molecular diversity of the ammonia-oxidizing bacteria community in disused tin-mining ponds located within Kampar, Perak, Malaysia.

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    Sow, S L S; Khoo, G; Chong, L K; Smith, T J; Harrison, P L; Ong, H K A

    2014-02-01

    Disused tin-mining ponds make up a significant amount of water bodies in Malaysia particularly at the Kinta Valley in the state of Perak where tin-mining activities were the most extensive, and these abundantly available water sources are widely used in the field of aquaculture and agriculture. However, the natural ecology and physicochemical conditions of these ponds, many of which have been altered due to secondary post-mining activities, remains to be explored. As ammonia-oxidizing bacteria (AOB) are directly related to the nutrient cycles of aquatic environments and are useful bioindicators of environmental variations, the focus of this study was to identify AOBs associated with disused tin-mining ponds that have a history of different secondary activities in comparison to ponds which were left untouched and remained as part of the landscape. The 16S rDNA gene was used to detect AOBs in the sediment and water sampled from the three types of disused mining ponds, namely ponds without secondary activity, ponds that were used for lotus cultivation and post-aquaculture ponds. When the varying pond types were compared with the sequence and phylogenetic analysis of the AOB clone libraries, both Nitrosomonas and Nitrosospira-like AOB were detected though Nitrosospira spp. was seen to be the most ubiquitous AOB as it was present in all ponds types. However, AOBs were not detected in the sediments of idle ponds. Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture indicated the highest richness of AOBs. Canonical correspondence analysis indicated that among the physicochemical properties of the pond sites, TAN and nitrite were shown to be the main factors that influenced the community structure of AOBs in these disused tin-mining ponds.

  8. Genetic diversity of common bean accessions from former Yugoslav Republic of Macedonia as revealed by molecular and morphological markers

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    Maras Marko

    2016-01-01

    Full Text Available Cultivation of common bean has a long tradition in the Former Yugoslav Republic of Macedonia (FYROM and is still nowadays important part of the human diet. In a study reported here 71 accessions from the FYROM were assessed for genetic diversity with the aim to provide information on genetic structure of Macedonian common bean germplasm and to depict its peculiarities. A total of 71 accessions were assessed using 13 microsatellite and 16 morphological markers. The average number of alleles per microsatellite was 5.8, and ranged from three to 16 alleles. High capacity of selected markers for distinguishing genotypes was identified by the calculation of a very low value of probability of identity. The relationship among 71 studied accessions was assessed by hierarchical cluster analysis. A very clear separation of accessions into two groups was observed in the UPGMA dendrogram. The larger represented Andean gene pool and contained 40 accessions (56% of total, while the other 31 accessions (44% of total composed Mesoamerican gene pool. The two groups were successfully discriminated by eight morphological traits. Within the larger Andean cluster in the UPGMA dendrogram a sub-group of 16 climbing accessions was separated from 24 bush accessions. The absence of the string in the pods of the climbers suggests that this sub-group comprises snap beans grown primarily for their fresh pods. There were eight morphological traits in total that distinguished the two Andean sub-groups. Assessment of genetic relationship among accessions, their classification into respective gene pool and identification of morphological peculiarities provided valuable information for the management of plant gene bank and Macedonian bean breeding program.

  9. Diverse Melting Modes and Structural Collapse of Hollow Bimetallic Core-Shell Nanoparticles: A Perspective from Molecular Dynamics Simulations

    Science.gov (United States)

    Huang, Rao; Shao, Gui-Fang; Zeng, Xiang-Ming; Wen, Yu-Hua

    2014-11-01

    Introducing hollow structures into metallic nanoparticles has become a promising route to improve their catalytic performances. A fundamental understanding of thermal stability of these novel nanostructures is of significance for their syntheses and applications. In this article, molecular dynamics simulations have been employed to offer insights into the thermodynamic evolution of hollow bimetallic core-shell nanoparticles. Our investigation reveals that for hollow Pt-core/Au-shell nanoparticle, premelting originates at the exterior surface, and a typical two-stage melting behavior is exhibited, similar to the solid ones. However, since the interior surface provides facilitation for the premelting initiating at the core, the two-stage melting is also observed in hollow Au-core/Pt-shell nanoparticle, remarkably different from the solid one. Furthermore, the collapse of hollow structure is accompanied with the overall melting of the hollow Pt-core/Au-shell nanoparticle while it occurs prior to that of the hollow Au-core/Pt-shell nanoparticle and leads to the formation of a liquid-core/solid-shell structure, although both of them finally transform into a mixing alloy with Au-dominated surface. Additionally, the existence of stacking faults in the hollow Pt-core/Au-shell nanoparticle distinctly lowers its melting point. This study could be of great importance to the design and development of novel nanocatalysts with both high activity and excellent stability.

  10. Diverse Melting Modes and Structural Collapse of Hollow Bimetallic Core-Shell Nanoparticles: A Perspective from Molecular Dynamics Simulations

    Science.gov (United States)

    Huang, Rao; Shao, Gui-Fang; Zeng, Xiang-Ming; Wen, Yu-Hua

    2014-01-01

    Introducing hollow structures into metallic nanoparticles has become a promising route to improve their catalytic performances. A fundamental understanding of thermal stability of these novel nanostructures is of significance for their syntheses and applications. In this article, molecular dynamics simulations have been employed to offer insights into the thermodynamic evolution of hollow bimetallic core-shell nanoparticles. Our investigation reveals that for hollow Pt-core/Au-shell nanoparticle, premelting originates at the exterior surface, and a typical two-stage melting behavior is exhibited, similar to the solid ones. However, since the interior surface p