WorldWideScience

Sample records for diverse molecular substituents

  1. 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.

  2. Pentiptycene-derived light-driven molecular brakes: substituent effects of the brake component.

    Science.gov (United States)

    Sun, Wei-Ting; Huang, Yau-Ting; Huang, Guan-Jhih; Lu, Hsiu-Feng; Chao, Ito; Huang, Shou-Ling; Huang, Shing-Jong; Lin, Ying-Chih; Ho, Jinn-Hsuan; Yang, Jye-Shane

    2010-10-11

    Five pentiptycene-derived stilbene systems (1 R; R = H, OM, NO, Pr, and Bu) have been prepared and investigated as light-driven molecular brakes that have different-sized brake components (1 Hbrake component in the trans form ((E)-1 R), which corresponds to the brake-off state. When the brake is turned on by photoisomerization to the cis form ((Z)-1 R), the pentiptycene rotation can be arrested on the NMR spectroscopic timescale at temperatures that depend on the brake component. In the cases of (Z)-1 NO, (Z)-1 Pr, and (Z)-1 Bu, the rotation is nearly blocked (k(rot)=2-6 s(-1)) at 298 K. It is also demonstrated that the rotation is slower in [D(6)]DMSO than in CD(2)Cl(2). A linear relationship between the free energies of the rotational barrier and the steric parameter A values is present only for (Z)-1 H, (Z)-1 OM, and (Z)-1 NO, and it levels off on going from (Z)-1 NO to (Z)-1 Pr and (Z)-1 Bu. DFT calculations provide insights into the substituent effects in the rotational ground and transition states. The molar reversibility of the E-Z photoswitching is up to 46%, and both the E and Z isomers are stable under the irradiation conditions. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Dual fluorescence of excited state intra-molecular proton transfer of HBFO: mechanistic understanding, substituent and solvent effects.

    Science.gov (United States)

    Yang, Wenjing; Chen, Xuebo

    2014-03-07

    A combined approach of the multiconfigurational perturbation theory with the Rice-Ramsperger-Kassel-Marcus methodology has been employed to calculate the minimum potential energy profiles and the rates of excited state intra-molecular proton transfer (ESIPT) for the WOLED material molecule of HBFO and its four meta- or para-substituted compounds in gas phase, acetonitrile and cyclohexane solvents. The kinetic control for these reactions is quantitatively determined and extensively studied on the basis of the accurate potential energy surfaces when the thermodynamic factor associated with the free energy change becomes negligible in the case of the existence of a significant barrier in the ESIPT process. These computational efforts contribute to a deep understanding of the ESIPT mechanism, dual emission characteristics, kinetic controlling factor, substituent and solvent effects for these material molecules. The white light emission is generated by the establishment of dynamic equilibrium between enol and keto forms in the charge transfer excited SCT((1)ππ*) state. The performance of white light emission is quantitatively demonstrated to be mainly sensitive to the molecular tailoring approach of the electronic properties of meta- or para- substituents by the modulation of the forward/backward ESIPT rate ratio. The quality of white light emission is slightly tunable through its surrounding solvent environment. These computational results will provide a useful strategy for the molecular design of OLED and WOLED materials.

  4. 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.

  5. Kinetic and mechanisms of methanimine reactions with singlet and triplet molecular oxygen: Substituent and catalyst effects

    Science.gov (United States)

    Asgharzadeh, Somaie; Vahedpour, Morteza

    2018-06-01

    Methanimine reaction with O2 on singlet and triplet potential energy surfaces are investigated using B3PW91, M06-2X, MP2 and CCSD(T) methods. Thermodynamic and kinetic parameters are calculated at M06-2X method. The most favorable channel involves H-abstraction of CH2NH+O2 to the formation of HCN + H2O2 products via low level energy barrier. The catalytic effect of water molecule on HCN + H2O2 products pathway are investigated. Result shows that contribution of water molecule using complex formation with methanimine can decreases barrier energy of transition state and the reaction rate increases. Also, substituent effect of fluorine atom as deactivating group are investigated on the main reaction pathway.

  6. Heavy Atom Substituents as Molecular Probes for Solvent Effects on the Dynamics of Short-lived Triplet Exciplexes

    OpenAIRE

    Winter, Gerhard; Steiner, Ulrich

    1980-01-01

    The influence of heavy atom substituents (Br, I) in the electron donor aniline on the electron transfer reaction with thiopyronine triplet is investigated by flash spectroscopy in solvents of different viscosity and polarity. Triplet quenching constants and radical yields are determined. The results are analysed in terms of decay constants of an intermediate triplet exciplex where the heavy atom substituents significantly enhance the intersystem crossing process leading to singlet ground stat...

  7. Application of the Fenske-Hall molecular orbital method to the calculation of 11B NMR chemical shifts. Antipodal substituent effects in deltahedral clusters

    International Nuclear Information System (INIS)

    Fehlner, T.P.; Czech, P.T.; Fenske, R.F.

    1990-01-01

    Utilizing Fenske-Hall wave functions and eigenvalues combined with the Ramsey sum over states (SOS) approximation, it is demonstrated that the sign and magnitude of the paramagnetic contribution to the shielding correlates well with the observed 11 B chemical shifts of a substantial variety of boron- and metal-containing compounds. Analysis of the molecular orbital (MO) contributions in the SOS approximation leads to an explanation of the large downfield shifts associated with metal-rich metallaboranes. A similar analysis demonstrates the importance of selected cluster occupied and unoccupied MO's in explaining both exo-cage substituent effects in which the antipodal boron resonance is shifted upfield and endo-cage substituent effects (interchange of isolobal fragments within the cage framework) in which the antipodal boron resonance is shifted downfield. Exo- and endo-cage substitution perturbs these MO's in an understandable fashion, leading to an internally consistent explanation of the observed chemical shift changes. 36 refs., 8 figs., 4 tabs

  8. Pentafluorosulfanyl Substituents in Polymerization Catalysis.

    Science.gov (United States)

    Kenyon, Philip; Mecking, Stefan

    2017-10-04

    Highly electron-withdrawing pentafluorosulfanyl groups were probed as substituents in an organometallic catalyst. In Ni(II) salicylaldiminato complexes as an example case, these highly electron-withdrawing substituents allow for polymerization of ethylene to higher molecular weights with reduced branching due to significant reductions in β-hydrogen elimination. Combined with the excellent functional group tolerance of neutral Ni(II) complexes, this suppression of β-hydrogen elimination allows for the direct polymerization of ethylene in water to nanocrystal dispersions of disentangled, ultrahigh-molecular-weight linear polyethylene.

  9. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

    2001); and molecular methods such as amplified fragment length polymorphism ... to the maintenance and rational use of germplasm resources in the improvement of ... study of diversity of ScMATE1 gene in different species of. Secale genus.

  10. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

    Molecular diversity and genetic relationships in Secale. E. Santos, M. Matos, P. Silva, A. M. Figueiras, C. Benito and O. Pinto-Carnide. J. Genet. 95, 273–281. Table 1. RAPD and ISSR primers used in this study. Primer. 5 –3. Primer. 5 –3. RAPDs (Operon). A1. CAGGCCCTTC. C5. CATGACCGCC. A4. AATCGGGCTG. C6.

  11. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

    The objective of this study was to quantify the molecular diversity and to determine the genetic relationships amongSecalespp. and among cultivars ofSecale ... Faculty of Sciences, Campo Grande, Lisboa, Portugal; Departamento de Genética, Facultad de Biologia, Universidad Complutense, C/ José Antonio Novais, 12, ...

  12. 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.

  13. Molecular and morphological diversity of pezizalean ectomycorrhiza

    DEFF Research Database (Denmark)

    Tedersoo, Leho; Hansen, Karen; Perry, Brian A

    2006-01-01

    A growing body of molecular research is discovering a high diversity of pezizalean ectomycorrhiza (EcM), yet most remain unidentified at the genus or species level. This study describes EcM-forming taxa within the Pezizales. EcM-forming Pezizales were revealed by morphotyping and sequencing of EcM...... root tips from forests in Estonia and Denmark. The taxa on EcM root tips were identified using phylogenetic analyses of large-subunit rDNA sequences derived from sporocarps of 301 pezizalean species, and comparisons with internal transcribed spacer rDNA sequences. Thirty-three species are suggested...... as EcM symbionts, representing all three major clades of Pezizales, the genera Genea, Geopora, Humaria, Tarzetta, Trichophaea, Wilcoxina, Helvella, Hydnotrya, Tuber, Pachyphloeus, Peziza and Sarcosphaera, and two Pezizaceae anamorphs. EcM of Pezizales species are easily distinguished by their anatomy...

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

    African Journals Online (AJOL)

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

  15. Acylated 2-(N-arylaminomethylene)benzo[b]thiophene-3(2H)-Ones: Molecular Switches with Varying Migrants and Substituents

    International Nuclear Information System (INIS)

    Dubonosov, A.D.; Rybalkin, V.P.; Tsukanov, A.V.; Minkin, V.I.; Popova, L.L.; Revinsky, Y.V.; Bren, V.A.; Minkin, V.I.

    2009-01-01

    Synthesis and properties of photo chromic acylated 2-(N-arylaminomethylene)benzo[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.

  16. Stereoelectronic Substituent Effects

    DEFF Research Database (Denmark)

    Bols, Mikael; Jensen, Henrik Helligsø

    2006-01-01

    An investigation was carried Out on the influence of the stereo-chemistry of substituents, particularly hydroxyl groups, on their electronic effects in piperidines, carbohydrates (pyranosides), and related compounds. Polar groups, such as OH, OR, and F, were found in the 3 and 4 position to be much...... more electron-withdrawing when positioned equatorially rather than axially. In contrast, little difference in electronic effects was observed from apolar groups as a result of epimerization. These observations were believed to be caused by differences in charge-dipole interactions and were used...... to explain why stereoisomeric glycosides hydrolyze with different rates. The conformational changes of hydroxylated piperidines and related compounds as a function of pH were likewise explained from the different substituent effects of axial and equatorial OH groups....

  17. N(G)-Acyl-argininamides as NPY Y(1) receptor antagonists: Influence of structurally diverse acyl substituents on stability and affinity.

    Science.gov (United States)

    Weiss, Stefan; Keller, Max; Bernhardt, Günther; Buschauer, Armin; König, Burkhard

    2010-09-01

    N(G)-Acylated argininamides, covering a broad range of lipophilicity (calculated logD values: -1.8-12.5), were synthesized and investigated for NPY Y(1) receptor (Y(1)R) antagonism, Y(1)R affinity and stability in buffer (N(G)-deacylation, yielding BIBP 3226). Broad structural variation of substituents was tolerated. The K(i) (binding) and K(b) values (Y(1)R antagonism) varied from low nM to one-digit muM. Most of the compounds proved to be sufficiently stable at pH 7.4 over 90min to determine reliable pharmacological data in vitro. Exceptionally high instability was detected when a succinyl moiety was attached to the guanidine, probably, due to an intramolecular cleavage mechanism. Copyright 2010 Elsevier Ltd. All rights reserved.

  18. World Wide Web-based system for the calculation of substituent parameters and substituent similarity searches.

    Science.gov (United States)

    Ertl, P

    1998-02-01

    Easy to use, interactive, and platform-independent WWW-based tools are ideal for development of chemical applications. By using the newly emerging Web technologies such as Java applets and sophisticated scripting, it is possible to deliver powerful molecular processing capabilities directly to the desk of synthetic organic chemists. In Novartis Crop Protection in Basel, a Web-based molecular modelling system has been in use since 1995. In this article two new modules of this system are presented: a program for interactive calculation of important hydrophobic, electronic, and steric properties of organic substituents, and a module for substituent similarity searches enabling the identification of bioisosteric functional groups. Various possible applications of calculated substituent parameters are also discussed, including automatic design of molecules with the desired properties and creation of targeted virtual combinatorial libraries.

  19. Molecular diversity among seven Solanum (eggplant and relatives ...

    African Journals Online (AJOL)

    Admin

    2012-11-08

    Nov 8, 2012 ... Seven Solanum species (eggplants) were investigated for molecular diversity. Besides its ... Eggplant comprises three closely related cultivated species .... generated with SSR data was submitted to 2-way Mantel test (Man-.

  20. Molecular characterization and assessment of genetic diversity of ...

    African Journals Online (AJOL)

    R Madhusudhana

    genetic diversity available at molecular level among a set of phenotypically different ... allele matching and cluster analysis based on unweighted neighbor- joining (Gascuel, 1997) ..... on isozyme data-a simulation study. Theor. Appl. Genet.

  1. Molecular characterization of genetic diversity in some durum wheat ...

    African Journals Online (AJOL)

    Molecular characterization of genetic diversity in some durum wheat ... African Journal of Biotechnology ... Thus, RAPD offer a potentially simple, rapid and reliable method to evaluate genetic variation and relatedness among ten wheat ...

  2. Radiation effects on polyacetylenes having substituents

    International Nuclear Information System (INIS)

    Higashimura, Toshinobu; Tang, Ben-Zhong; Masuda, Toshio; Yamaoka, Hitoshi; Matsuyama, Tomochika.

    1985-01-01

    Effects of γ-ray irradiation on high molecular weight polyacetylenes with various substituents were studied in air and in vacuum. The molecular weights of polymers from aliphatic disubstituted acetylenes (2-octyne and 2-decyne) remarkably reduced with irradiation in air. Their G values for chain scission in air were as high as 3 - 12, whereas no degradation occurred in vacuum. The degraded polymers contain carbonyl and hydroxyl groups, and are soluble in polar solvents such as methyl ethyl ketone and acetone. In contrast, polymers of aromatic disubstituted acetylenes (1-phenyl-1-propyne and 1-chloro-2-phenylacetylene) hardly degraded in air even with irradiation up to 40 Mrad. The degradation behavior of poly(t-butylacetylene) was intermediate between those of the above aliphatic and aromatic polymers. Thus the radiolysis of polyacetylenes was found to be greatly dependent on the kind of substituents. (author)

  3. integrating phenotypic evaluations with a molecular diversity ...

    African Journals Online (AJOL)

    JS TENYWA

    2018-05-25

    May 25, 2018 ... 7Department of Plant Sciences / MS1, 1 Shields Avenue, University of California, Davis, USA. Corresponding ... secondary centers of diversity of this species. Hence, this ... Mesoamerican gene pools after introduction of common bean germplasm in Ethiopia. ..... the two gene pools of origin, as evidenced by.

  4. Molecular and pomological diversity among pomegranate (Punica ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-05-02

    May 2, 2008 ... and wine (Poyrazoğlu et al., 2002). Although the ... a* and b* values were used to compute values for hue angle (a = tan-1b*/a*) and ... at –80°C. High molecular weight genomic DNA was extracted from the leaf samples ...

  5. Substituent effect on redox potential of nitrido technetium complexes with Schiff base ligand. Theoretical calculations

    International Nuclear Information System (INIS)

    Takayama, T.; Sekine, T.; Kudo, H.

    2003-01-01

    Theoretical calculations based on the density functional theory (DFT) were performed to understand the effect of substituents on the molecular and electronic structures of technetium nitrido complexes with salen type Schiff base ligands. Optimized structures of these complexes are square pyramidal. The electron density on a Tc atom of the complex with electron withdrawing substituents is lower than that of the complex with electron donating substituents. The HOMO energy is lower in the complex with electron withdrawing substituents than that in the complex with electron donating substituents. The charge on Tc atoms is a good measure that reflects the redox potential of [TcN(L)] complex. (author)

  6. Convergent molecular defects underpin diverse neurodegenerative diseases.

    Science.gov (United States)

    Tofaris, George K; Buckley, Noel J

    2018-02-19

    In our ageing population, neurodegenerative disorders carry an enormous personal, societal and economic burden. Although neurodegenerative diseases are often thought of as clinicopathological entities, increasing evidence suggests a considerable overlap in the molecular underpinnings of their pathogenesis. Such overlapping biological processes include the handling of misfolded proteins, defective organelle trafficking, RNA processing, synaptic health and neuroinflammation. Collectively but in different proportions, these biological processes in neurons or non-neuronal cells lead to regionally distinct patterns of neuronal vulnerability and progression of pathology that could explain the disease symptomology. With the advent of patient-derived cellular models and novel genetic manipulation tools, we are now able to interrogate this commonality despite the cellular complexity of the brain in order to develop novel therapeutic strategies to prevent or arrest neurodegeneration. Here, we describe broadly these concepts and their relevance across neurodegenerative diseases. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  7. 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.

  8. Supplementary data: Molecular assessment of genetic diversity in ...

    Indian Academy of Sciences (India)

    Molecular assessment of genetic diversity in cluster bean. (Cyamopsis tetragonoloba) genotypes. Rakesh Pathak, S. K. Singh, Manjit Singh and A. Henry. J. Genet. 89, 243–246. Figure 1. RAPD profile of 1–16 Cyamopsis tetragonoloba genotypes amplified with arbitrary primer OPA-16. Figure 2. RAPD profile of 17–32 ...

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

    Indian Academy of Sciences (India)

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

  10. Molecular diversity among wild relatives of Cajanus cajan (L.) Millsp ...

    African Journals Online (AJOL)

    In the present study, four wild relatives of pigeonpea were evaluated using 24 simple sequence repeat (SSR) markers to assess their genetic diversity at molecular level. Each marker, on average, amplified 3.3 alleles with polymorphic information content (PIC) value of 0.53. The dendrogram pattern revealed two distinct ...

  11. 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...... for generation of probes and their use in phylogeny of Fusarium spp. are also presented. The concluding part emphasizes the value of molecular markers for assessing genetic variability and reveals that molecular tools are indispensable for providing information not only of one Fusarium species but on whole......-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...

  12. Assessing Date Palm Genetic Diversity Using Different Molecular Markers.

    Science.gov (United States)

    Atia, Mohamed A M; Sakr, Mahmoud M; Adawy, Sami S

    2017-01-01

    Molecular marker technologies which rely on DNA analysis provide powerful tools to assess biodiversity at different levels, i.e., among and within species. A range of different molecular marker techniques have been developed and extensively applied for detecting variability in date palm at the DNA level. Recently, the employment of gene-targeting molecular marker approaches to study biodiversity and genetic variations in many plant species has increased the attention of researchers interested in date palm to carry out phylogenetic studies using these novel marker systems. Molecular markers are good indicators of genetic distances among accessions, because DNA-based markers are neutral in the face of selection. Here we describe the employment of multidisciplinary molecular marker approaches: amplified fragment length polymorphism (AFLP), start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), simple sequence repeats (SSR), and random amplified polymorphic DNA (RAPD) to assess genetic diversity in date palm.

  13. A Brief Review of Molecular Techniques to Assess Plant Diversity

    Directory of Open Access Journals (Sweden)

    Ibrahim A. Arif

    2010-05-01

    Full Text Available Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD, amplified fragment length polymorphism (AFLP, microsatellites and single nucleotide polymorphisms (SNP have recently been used for plant diversity studies. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species.

  14. A Brief Review of Molecular Techniques to Assess Plant Diversity

    Science.gov (United States)

    Arif, Ibrahim A.; Bakir, Mohammad A.; Khan, Haseeb A.; Al Farhan, Ahmad H.; Al Homaidan, Ali A.; Bahkali, Ali H.; Sadoon, Mohammad Al; Shobrak, Mohammad

    2010-01-01

    Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites and single nucleotide polymorphisms (SNP) have recently been used for plant diversity studies. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species. PMID:20559503

  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. 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.

  17. 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.

  18. 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.

  19. How diverse are diversity assessment methods? A comparative analysis and benchmarking of molecular descriptor space.

    Science.gov (United States)

    Koutsoukas, Alexios; Paricharak, Shardul; Galloway, Warren R J D; Spring, David R; Ijzerman, Adriaan P; Glen, Robert C; Marcus, David; Bender, Andreas

    2014-01-27

    Chemical diversity is a widely applied approach to select structurally diverse subsets of molecules, often with the objective of maximizing the number of hits in biological screening. While many methods exist in the area, few systematic comparisons using current descriptors in particular with the objective of assessing diversity in bioactivity space have been published, and this shortage is what the current study is aiming to address. In this work, 13 widely used molecular descriptors were compared, including fingerprint-based descriptors (ECFP4, FCFP4, MACCS keys), pharmacophore-based descriptors (TAT, TAD, TGT, TGD, GpiDAPH3), shape-based descriptors (rapid overlay of chemical structures (ROCS) and principal moments of inertia (PMI)), a connectivity-matrix-based descriptor (BCUT), physicochemical-property-based descriptors (prop2D), and a more recently introduced molecular descriptor type (namely, "Bayes Affinity Fingerprints"). We assessed both the similar behavior of the descriptors in assessing the diversity of chemical libraries, and their ability to select compounds from libraries that are diverse in bioactivity space, which is a property of much practical relevance in screening library design. This is particularly evident, given that many future targets to be screened are not known in advance, but that the library should still maximize the likelihood of containing bioactive matter also for future screening campaigns. Overall, our results showed that descriptors based on atom topology (i.e., fingerprint-based descriptors and pharmacophore-based descriptors) correlate well in rank-ordering compounds, both within and between descriptor types. On the other hand, shape-based descriptors such as ROCS and PMI showed weak correlation with the other descriptors utilized in this study, demonstrating significantly different behavior. We then applied eight of the molecular descriptors compared in this study to sample a diverse subset of sample compounds (4%) from an

  20. Functional Molecular Diversity of Marine Dissolved Organic Matter Is Reduced during Degradation

    Directory of Open Access Journals (Sweden)

    Andrea Mentges

    2017-06-01

    Full Text Available Dissolved organic matter (DOM is a highly diverse mixture of compounds, accounting for one of the world's largest active carbon pools. The surprising recalcitrance of some DOM compounds to bacterial degradation has recently been associated with its diversity. However, little is known about large-scale patterns of marine DOM diversity and its change through degradation, in particular considering the functional diversity of DOM. Here, we analyze the development of marine DOM diversity during degradation in two data sets comprising DOM of very different ages: a three-year mesocosm experiment and highly-resolved field samples from the Atlantic and Southern Ocean. The DOM molecular composition was determined using ultra-high resolution mass spectrometry. We quantify DOM diversity using three conceptually different diversity measures, namely richness of molecular formulas, abundance-based diversity, and functional molecular diversity. Using these measures we find stable molecular richness of DOM with age >1 year, systematic changes in the molecules' abundance distribution with degradation state, and increasing homogeneity with respect to chemical properties for more degraded DOM. Coinciding with differences in sea water density, the spatial field data separated clearly into regions of high and low diversity. The joint application of different diversity measures yields a comprehensive overview on temporal and spatial patterns of molecular diversity, valuable for general conclusions on drivers and consequences of marine DOM diversity.

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

    International Nuclear Information System (INIS)

    Geissler, A.

    2003-04-01

    A culture-independent molecular approach has been applied to investigate the bacterial diversity in three uranium contaminated sites. The three analysed soil samples have been collected from the uranium waste pile Haberland near Johanngeorgenstadt (Germany), from the uranium mill tailings in Gunnison, Colorado (USA) and from the uranium mill tailings in Shiprock, New Mexico (USA). The 16S rDNA fragments which has been isolated through direct lysis of the whole-DNA were amplified by the use of the universal primers 16S 43f and 16S 1404r and cloned. With restriction fragment length polymorphismus (RFLP) were the clones screened and one representative of all RFLP types that occurred more than once in the clone library was sequenced and analysed. In spite of the contamination a considerable diversity and significant differences in the composition of the natural bacterial communities in these three sites have been found. In the sample collected from the waste pile Haberland near Johanngeorgenstadt α-Proteobacteria and representatives of the Holophaga/Acidobacterium were numerically predominant. The distribution of bacteria in the sample collected from uranium mill tailings Gunnison was very similar to those found in the Haberland waste pile, but there were found besides α-Proteobacteria and representatives of Holophaga/Acidobacterium a lot of γ-Proteobacteria. The structure of the bacterial community in the sample collected from the uranium mill tailings Shiprock was significantly different. Only some representatives of the Holophaga/Acidobacterium and α-Proteobacteria were represented. Large populations of Bacilli, γ-Proteobacteria and green non sulfur bacteria were dominant in this sample. (orig.)

  2. Genetic diversity of dog breeds: within-breed diversity comparing genealogical and molecular data.

    Science.gov (United States)

    Leroy, G; Verrier, E; Meriaux, J C; Rognon, X

    2009-06-01

    The genetic diversity of 61 dog breeds raised in France was investigated. Genealogical analyses were performed on the pedigree file of the French kennel club. A total of 1514 dogs were also genotyped using 21 microsatellite markers. For animals born from 2001 to 2005, the average coefficient of inbreeding ranged from 0.2% to 8.8% and the effective number of ancestors ranged from 9 to 209, according to the breed. The mean value of heterozygosity was 0.62 over all breeds (range 0.37-0.77). At the breed level, few correlations were found between genealogical and molecular parameters. Kinship coefficients and individual similarity estimators were, however, significantly correlated, with the best mean correlation being found for the Lynch & Ritland estimator (r = 0.43). According to both approaches, it was concluded that special efforts should be made to maintain diversity for three breeds, namely the Berger des Pyrénées, Braque Saint-Germain and Bull Terrier.

  3. Molecular characterization and diversity analysis in chilli pepper ...

    African Journals Online (AJOL)

    India is considered to be the secondary center of diversity of chilli pepper, especially of Capsicum annuum. Simple sequence repeats (SSRs) are the most widely used marker system for plant variety characterization and diversity analysis especially in cultivated species which have low levels of polymorphism. The diversity ...

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

    International Nuclear Information System (INIS)

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

    2004-01-01

    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 (R 2 ) of 0.863

  5. Towards a physical interpretation of substituent effect: Quantum chemical interpretation of Hammett substituent constants

    Science.gov (United States)

    Varaksin, Konstantin S.; Szatylowicz, Halina; Krygowski, Tadeusz M.

    2017-06-01

    Quantitative description of substituent effects is of a great importance especially in organic chemistry and QSAR-type treatments. The proposed approaches: substituent effect stabilization energy (SESE) and charge of the substituent active region (cSAR) provide substituent effect characteristics, physically independent of the Hammett's substituent constants, σ. To document abilities of these descriptors the B3LYP/6-311++G(d,p) method is employed to examine changes in properties of a reaction center Y (Y = COOH or COO- groups) and a transmitting moiety (benzene ring) due to substituent effects in a series of meta- and para-X-substituted benzoic acid and benzoate anion derivatives (X = NMe2, NH2, OH, OMe, CH3, H, F, Cl, CF3, CN, CHO, COMe, CONH2, COOH, NO2, NO). The transmitting moiety is described by aromaticity indices HOMA and NICS(1). Furthermore, an advantage of the cSAR characteristic is the ability to use it to describe both electron donating/accepting properties of a substituent as well as a reaction center. It allows demonstration of the reverse substituent effects of COOH and COO- groups on substituent X.

  6. Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study

    Directory of Open Access Journals (Sweden)

    Flávio de Oliveira Francisco

    2013-01-01

    Full Text Available Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.

  7. Molecular analysis of genetic diversity in elite II synthetic hexaploid ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-07-20

    Jul 20, 2009 ... The presence of sufficient genetic diversity in the germplam is an important ..... Figure 1. PCR amplification profile of Elite-II SH Wheat using the primer OPG-2. .... genetic relationships among cowpea breeding lines and local.

  8. Diversity in parasitic helminths of Australasian marsupials and monotremes: a molecular perspective.

    Science.gov (United States)

    Beveridge, Ian; Gasser, Robin B

    2014-10-15

    Marsupials and monotremes are a prominent part of the mammalian fauna in Australia, and harbour an extremely diverse and highly distinctive array of helminth parasites. Their study has been relatively neglected, likely because they have no direct, adverse socioeconomic impact. As the body plans of helminths generally are very simple and morphological characterisation likely underestimates true diversity, molecular tools have been employed to assess genetic diversity. Using biochemical and/or molecular methods, recent studies show extensive diversity in helminths of marsupials, with cryptic species being commonly encountered. The purpose of this article is to review current knowledge about the diversity of parasitic helminths of marsupials and monotremes, to raise questions as to whether current molecular data can be used to estimate diversity, what mechanisms lead to such diversity, to critically appraise the molecular tools that have been employed thus far to explore diversity and to discuss the directions which might be taken in the future employing improved techniques. Copyright © 2014 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

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

    African Journals Online (AJOL)

    aykut

    2013-11-06

    Nov 6, 2013 ... using random amplified polymorphic DNA (RAPD) ... 1Department of Molecular Biology and Genetics, Faculty of Science and Arts, Uşak University, 64200 Uşak, Turkey. ..... University Directorate of Scientific Research Projects.

  10. Molecular analysis of genetic diversity in elite II synthetic hexaploid ...

    African Journals Online (AJOL)

    The present study was conducted to assess the genetic diversity of Elite-II synthetic hexaploid (SH) wheat by genome DNA fingerprinting as revealed by random amplified polymorphic DNA (RAPD) analysis. Ten decamer RAPD primers (OPG-1, OPG-2, OPG-3, OPG-4, OPG-5, OPA-3, OPA-4, OPA-5, OPA-8, and OPA-15) ...

  11. Genetic diversity and molecular characterization of physic nut ...

    African Journals Online (AJOL)

    ajl

    2013-02-27

    Feb 27, 2013 ... 2Department of Plant Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil. ... primers were used to characterize toxicity alleles, and none of the accessions presented patterns ... accessions from India (Gupta et al., 2008; Gohil and. Pandya .... ISSR primers, generally low genetic diversity was.

  12. Molecular genetic diversity study of Lepidium sativum population ...

    African Journals Online (AJOL)

    Vostro 2520

    Generally, Tigray and Amhara regions showed moderate to high diversity in ISSR analysis. ... other crops. The main purpose of its cultivation in. Ethiopia is to use it as a medicinal plant. It is used for human abdominal ache and diarrhea. Moreover, L. ... of 10 primers were obtained from the Genetic Research Laboratory.

  13. Molecular and functional diversity in Capsicum landraces of ...

    African Journals Online (AJOL)

    shrawan

    2013-09-25

    Sep 25, 2013 ... of diversity in the local germplasm was much needed to recognize the genetic .... reducing sugar and multiplying with a conversion factor (0.95). The absorbance for ..... Except SPG-3 which was outlier with 54% intra-cluster ...

  14. Molecular and functional diversity in Capsicum landraces of ...

    African Journals Online (AJOL)

    The present study analyzed the diversity in 26 landraces of Capsicum from Andaman Islands using 20 morphological, 16 biochemical and 10 DNA markers. Significant differences were observed in tested landraces and 16 reference genotypes from mainland India. Biochemical markers grouped all the genotypes into eight ...

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

    Indian Academy of Sciences (India)

    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 ...

  16. Morphological and molecular based diversity studies of some ...

    African Journals Online (AJOL)

    Cassava (Manihot esculenta Crantz) is an important food crop in many tropical countries in Africa, South America and Asia. However, yields are below the productivity of the crop. This requires breeding and selection for improved varieties. The current study therefore investigated genetic diversity among some Ghanaian ...

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

    African Journals Online (AJOL)

    Domestic goats in Syria may provide an interesting source of genetic variability due to its proximity to the centers of domestication. This study aimed to assess the morphological variation, genetic diversity and population substructure of the Syrian goat populations. Commonly, three goat genotypes are distinguished in Syria, ...

  18. Preliminary molecular analysis of the genetic diversity of some ...

    African Journals Online (AJOL)

    In the arid and semi arid areas, salt bush (Atriplex) represents an important forage resource. The characterization of the genetic diversity of these species is useful for their classification, their conservation and their improvement. In this context, we used the random amplified polymorphic DNA-polymerase chain reaction ...

  19. Molecular based assessment of genetic diversity of xoconostle ...

    African Journals Online (AJOL)

    aghomotsegin

    2014-01-08

    Jan 8, 2014 ... Xoconostle or acidic prickly pear is an important fruit in Mexico; it is produced by a ... study, we report for the first time the estimation of genetic diversity within a set ... demonstrates the high genetic variation among genotypes of .... O. leucotricha Salm-Dyck × O. joconostle F.A.C Weber Zacatecas Wild Stock.

  20. Molecular characterization and genetic diversity of different genotypes of Oryza sativa and Oryza glaberrima

    Directory of Open Access Journals (Sweden)

    Caijin Chen

    2017-11-01

    Conclusions: Genetic diversity studies revealed that 50 rice types were clustered into different subpopulations whereas three genotypes were admixtures. Molecular fingerprinting and 10 specific markers were obtained to identify the 53 rice genotypes. These results can facilitate the potential utilization of sibling species in rice breeding and molecular classification of O. sativa and O. glaberrima germplasms.

  1. Molecular diversity of neurotoxins from Clostridium botulinum type D strains.

    OpenAIRE

    Moriishi, K; Syuto, B; Kubo, S; Oguma, K

    1989-01-01

    The molecular properties of Clostridium botulinum type D South African (D-SA) were compared with those of neurotoxins from type D strain 1873 (D-1873) and type C strains Stockholm and 6813. D-SA toxin, purified 610-fold from the culture supernatant in an overall yield of 30%, consisted of an intact peptide chain with a molecular weight of 140,000. Limited proteolysis of the toxin by trypsin formed a dichain structure consisting of a light chain (Mr, 50,000) and a heavy chain (Mr, 90,000) link...

  2. 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.; Mukhopadhyay, Sukrit; Risko, Chad; Marder, Seth R.; Bredas, Jean-Luc

    2014-01-01

    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

  3. 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

  4. Phenotypic and molecular evaluation of genetic diversity of rapeseed

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-05

    Oct 5, 2009 ... seed yield per plant, 1000-seed weight, oil content and protein content) were analyzed in a three-year ... regard to many characters of value for breeding process. (Cowling ..... tances determined by molecular markers and heterosis ..... Comparative analysis of cultivated melon groups (Cucumis melo L.).

  5. Molecular markers for genetic diversity and phylogeny research of ...

    African Journals Online (AJOL)

    Brazilian sheep descended from several breeds brought to the New World by Portuguese and Spanish colonists, and they have evolved and adapted to local climatic variations and acquired tolerance or resistance to many diseases. Molecular markers are widely used in analyzing genetic variability, and markers such as ...

  6. 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 ...

  7. Molecular diversity of Rice grassy stunt virus in Vietnam.

    Science.gov (United States)

    Ta, Hoang-Anh; Nguyen, Doan-Phuong; Causse, Sandrine; Nguyen, Thanh-Duc; Ngo, Vinh-Vien; Hébrard, Eugénie

    2013-04-01

    Rice grassy stunt virus (RGSV, Tenuivirus) recently emerged on rice in Vietnam, causing high yield losses during 2006-2009. The genetic diversity of RGSV is poorly documented. In this study, the two genes encoded by each ambisense segment RNA3 and RNA5 of RGSV isolates from six provinces of South Vietnam were sequenced. P3 and Pc3 (RNA3) have unknown function, P5 (RNA5) encodes the putative silencing suppressor, and Pc5 (RNA5) encodes the nucleocapsid protein (N). The sequences of 17 Vietnamese isolates were compared with reference isolates from North and South Philippines. The average nucleotide diversity among the isolates was low. We confirmed a higher variability of RNA3 than RNA5 and Pc3 than P3. No relationships between the genetic diversity and the geographic distribution of RGSV isolates could be ascertained, likely because of the long-distance migration of the insect vector. This data will contribute to a better understanding on the RGSV epidemiology in South Vietnam, a prerequisite for further management of the disease and rice breeding for resistance.

  8. Molecular markers shared by diverse apomictic Pennisetum species.

    Science.gov (United States)

    Lubbers, E L; Arthur, L; Hanna, W W; Ozias-Akins, P

    1994-11-01

    Two molecular markers, a RAPD (randomly amplified polymorphic DNA) and a RFLP/STS (restriction fragment length polymorphism/sequence-tagged site), previously were found associated with apomictic reproductive behavior in a backcross population produced to transfer apomixis from Pennisetum squamulatum to pearl millet. The occurrence of these molecular markers in a range of 29 accessions of Pennisetum comprising 11 apomictic and 8 sexual species was investigated. Both markers were specific for apomictic species in Pennisetum. The RFLP/STS marker, UGT 197, was found to be associated with all taxa that displayed apomictic reproductive behavior except those in section Brevivalvula. Neither UGT197 nor the cloned RAPD fragment OPC-04600 hybridized with any sexually reproducing representatives of the genus. The cloned C04600 was associated with 3 of the 11 apomictic species, P. ciliare, P. massaicum, and P. squamulatum. UGT197 was more consistently associated with apomictic reproductive behavior than OPC04600 or cloned C04600, thus it could be inferred that UGT197 is more closely linked to the gene(s) for apomixis than the cloned C04600. The successful use of these probes to survey other Pennisetum species indicates that apomixis is a trait that can be followed across species by using molecular means. This technique of surveying species within a genus will be useful in determining the relative importance of newly isolated markers and may facilitate the identification of the apomixis gene(s).

  9. 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.

  10. The effects of characteristics of substituents on toxicity of the nitroaromatics: HiT QSAR study

    Science.gov (United States)

    Kuz'min, Victor E.; Muratov, Eugene N.; Artemenko, Anatoly G.; Gorb, Leonid; Qasim, Mohammad; Leszczynski, Jerzy

    2008-10-01

    The present study applies the Hierarchical Technology for Quantitative Structure-Activity Relationships (HiT QSAR) for (i) evaluation of the influence of the characteristics of 28 nitroaromatic compounds (some of which belong to a widely known class of explosives) as to their toxicity; (ii) prediction of toxicity for new nitroaromatic derivatives; (iii) analysis of the effects of substituents in nitroaromatic compounds on their toxicity in vivo. The 50% lethal dose concentration for rats (LD50) was used to develop the QSAR models based on simplex representation of molecular structure. The preliminary 1D QSAR results show that even the information on the composition of molecules reveals the main tendencies of changes in toxicity. The statistic characteristics for partial least squares 2D QSAR models are quite satisfactory ( R 2 = 0.96-0.98; Q 2 = 0.91-0.93; R 2 test = 0.89-0.92), which allows us to carry out the prediction of activity for 41 novel compounds designed by the application of new combinations of substituents represented in the training set. The comprehensive analysis of toxicity changes as a function of substituent position and nature was carried out. Molecular fragments that promote and interfere with toxicity were defined on the basis of the obtained models. It was shown that the mutual influence of substituents in the benzene ring plays a crucial role regarding toxicity. The influence of different substituents on toxicity can be mediated via different C-H fragments of the aromatic ring.

  11. A diversity oriented synthesis of natural product inspired molecular libraries.

    Science.gov (United States)

    Chauhan, Jyoti; Luthra, Tania; Gundla, Rambabu; Ferraro, Antonio; Holzgrabe, Ulrike; Sen, Subhabrata

    2017-11-07

    Natural products are the source of innumerable pharmaceutical drug candidates and also form an important aspect of herbal remedies. They are also a source of various bioactive compounds. Herein we have leveraged the structural attributes of several natural products in building a library of architecturally diverse chiral molecules by harnessing R-tryptophan as the chiral auxiliary. It is converted to its corresponding methyl ester 1 which in turn provided a bevy of 1-aryl-tetrahydro-β-carbolines 2a-d, which were then converted to chiral compounds via a diversity oriented synthetic strategy (DOS). In general, intermolecular and intramolecular ring rearrangements facilitated the formation of the final compounds. Four different classes of molecules with distinct architectures were generated, adding up to nearly twenty-two individual molecules. Phenotypic screening of a representative section of the library revealed two molecules that selectively inhibit MCF7 breast cancer cells with IC 50 of ∼5 μg mL -1 potency.

  12. Molecular analysis of microbial diversity in advanced caries.

    Science.gov (United States)

    Chhour, Kim-Ly; Nadkarni, Mangala A; Byun, Roy; Martin, F Elizabeth; Jacques, Nicholas A; Hunter, Neil

    2005-02-01

    Real-time PCR analysis of the total bacterial load in advanced carious lesions has shown that the total load exceeds the number of cultivable bacteria. This suggests that an unresolved complexity exists in bacteria associated with advanced caries. In this report, the profile of the microflora of carious dentine was explored by using DNA extracted from 10 lesions selected on the basis of comparable total microbial load and on the relative abundance of Prevotella spp. Using universal primers for the 16S rRNA gene, PCR amplicons were cloned, and approximately 100 transformants were processed for each lesion. Phylogenetic analysis of 942 edited sequences demonstrated the presence of 75 species or phylotypes in the 10 carious lesions. Up to 31 taxa were represented in each sample. A diverse array of lactobacilli were found to comprise 50% of the species, with prevotellae also abundant, comprising 15% of the species. Other taxa present in a number of lesions or occurring with high abundance included Selenomonas spp., Dialister spp., Fusobacterium nucleatum, Eubacterium spp., members of the Lachnospiraceae family, Olsenella spp., Bifidobacterium spp., Propionibacterium sp., and Pseudoramibacter alactolyticus. The mechanisms by which such diverse patterns of bacteria extend carious lesions, including the aspect of infection of the vital dental pulp, remain unclear.

  13. Molecular bacterial diversity and bioburden of commercial airliner cabin air

    Energy Technology Data Exchange (ETDEWEB)

    La Duc, M.T.; Stuecker, T.; Venkateswaran, K. [California Inst. of Technology, Pasadena, CA (United States). Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group

    2007-11-15

    Microorganisms that exist in aircraft air systems are considered to be the primary source of microbial contamination that can lead to illness shortly after flying. More than 600 million passengers board commercial airline flights annually in the United States alone. In this study, culture-independent, biomarker-targeted bacterial enumeration and identification strategies were used to estimate total bacterial burden and diversity within the cabin air of commercial airliners. Air-impingement was used to collect samples of microorganisms from 4 flights on 2 commercial carriers. The total viable microbial population ranged from below detection limits to 4.1 x 10{sup 6} cells/m{sup 3} of air. Microbes were found to gradually accumulate from the time of passenger boarding through mid-flight. A sharp decline in bacterial abundance was then observed. Representatives of the {alpha}, {beta} and {gamma} Proteobacteria, as well as Gram-positive bacteria, were isolated in varying abundance. Airline A had large abundances of Neisseria meningitidis rRNA gene sequences and Streptococcus oralis/mitis sequences. Airline B was dominated by pseudomonas synxantha sequences as well as N. meningitidis and S. oralis/mitis. The cabin air samples housed low bacterial diversity and were typically dominated by a particular subset of bacteria, notably opportunistic pathogenic inhabitants of the human respiratory tract and oral cavity. The microbes were found largely around the ventilation ducts and gasper conduits that supply cabin air. 45 refs., 4 tabs., 3 figs.

  14. 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.

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

    Science.gov (United States)

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

    2010-05-01

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

  16. Genetic Diversity Analysis in 27 Tomato Accessions Using Morphological and Molecular Markers

    Directory of Open Access Journals (Sweden)

    Catur Herison

    2018-02-01

    Full Text Available Genetic diversity is the most important aspect in tomato breeding activities. Better assessment on the diversity of the collected accessions will come up with better result of the cultivar development. This study aimed at analyzing the genetic diversity of 27 tomato accessions by morphological and molecular markers. Twenty seven accessions collected from various regions of Indonesia were planted in the field and evaluated for their morphological traits, and RAPD analyzed for their molecular markers. The UPGMA clustering analyzes, elaborating the combination of morphological and molecular data, indicated that the tomato accessions could be grouped into 5 major groups with 70 % genetic similarity levels. Current study indicated that although many accessions came from different locations, they congregated into the same group. Cherry, Kudamati 1 and Lombok 3 were the farthest genetic distant accessions to the others. Those three genotypes will be the most valuable accessions, when they were crossed with other accessions, for designing a prospective breeding program in the future.

  17. Genetic diversity of popcorn genotypes using molecular analysis.

    Science.gov (United States)

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

    2015-08-19

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

  18. Evaluation of achiral templates with fluxional Brønsted basic substituents in enantioselective conjugate additions.

    Science.gov (United States)

    Adachi, Shinya; Takeda, Norihiko; Sibi, Mukund P

    2014-12-19

    Enantioselective conjugate addition of malononitrile to pyrazolidinone-derived enoates proceeds in excellent yields and high enantioselectivities. A comparison of fluxional substituents with and without a Brønsted basic site and their impact on selectivity is detailed. Molecular sieves as an additive were found to be essential to achieve high enantioselectivity.

  19. Chemical Space: Big Data Challenge for Molecular Diversity.

    Science.gov (United States)

    Awale, Mahendra; Visini, Ricardo; Probst, Daniel; Arús-Pous, Josep; Reymond, Jean-Louis

    2017-10-25

    Chemical space describes all possible molecules as well as multi-dimensional conceptual spaces representing the structural diversity of these molecules. Part of this chemical space is available in public databases ranging from thousands to billions of compounds. Exploiting these databases for drug discovery represents a typical big data problem limited by computational power, data storage and data access capacity. Here we review recent developments of our laboratory, including progress in the chemical universe databases (GDB) and the fragment subset FDB-17, tools for ligand-based virtual screening by nearest neighbor searches, such as our multi-fingerprint browser for the ZINC database to select purchasable screening compounds, and their application to discover potent and selective inhibitors for calcium channel TRPV6 and Aurora A kinase, the polypharmacology browser (PPB) for predicting off-target effects, and finally interactive 3D-chemical space visualization using our online tools WebDrugCS and WebMolCS. All resources described in this paper are available for public use at www.gdb.unibe.ch.

  20. Genetic diversity and molecular characterization of Saccharomyces cerevisiae strains from winemaking environments

    OpenAIRE

    Schuller, Dorit Elisabeth

    2004-01-01

    Tese de doutoramento em Ciências The principal aim of the present work is to assess the genetic diversity of fermenting Saccharomyces cerevisiae strains found in vineyards belonging to the Vinho Verde Region in order to create a strain collection representing the region’s biodiversity wealth as a basis for future strain selection and improvement programs. Validation of molecular techniques for accurate genotyping is an indispensable prerequisite for biogeographical surveys. Molecular ty...

  1. Effect of substituents on polarizability and hyperpolarizability values of benzimidazole metal complexes

    Energy Technology Data Exchange (ETDEWEB)

    Praveen, P. A.; Babu, R. Ramesh, E-mail: rampap2k@yahoo.co.in [Crystal Growth and Thin films Laboratory, Department of Physics, Bharathidasan University, Tiruchirappalli - 620 024, Tamilnadu (India)

    2016-05-23

    In this report, the polarizability and first and second order hyperpolarizability values of bis benzimidazole Zn(II)-2R and bis benzimidazole Cd(II)-2R complexes, with different electron donating moieties R (R= Cl, Br, I, Acetate) were calculated using time dependent Hartree-Fock (TDHF) formalism embedded in MOPAC2012 package. Further the role of substituents on polarizability and hyperpolarizability values is investigated for the first time by analyzing the frontier molecular orbitals of the complexes with respect to the electronegativity of the substituents. It is found that the increase in electronegativity of the substituents correspondingly increases the energy gap of the molecules, which in turn reduces the polarizability values of both Zn and Cd benzimidazole complexes. Similarly, increase in electronegativity reduces the electric quadrupole moments of both the metal complexes, which in turn reduces the hyperpolarizability values.

  2. Seroepidemiology and molecular diversity of Leishmania donovani complex in Georgia.

    Science.gov (United States)

    Babuadze, Giorgi; Farlow, Jason; de Koning, Harry P; Carrillo, Eugenia; Chakhunashvili, Giorgi; Murskvaladze, Mari; Kekelidze, Merab; Karseladze, Irakli; Kokaia, Nora; Kalandadze, Irine; Tsereteli, David; Markhvashvili, Ivane; Sidamonidze, Ketevan; Chanturia, Gvantsa; Adeishvili, Ekaterine; Imnadze, Paata

    2016-05-13

    Leishmaniasis includes multiple clinical syndromes, most notably visceral, cutaneous, and mucosal forms. Visceral leishmaniasis (VL), also known as kala-azar, is a potentially fatal disease endemic to large parts of Africa and Asia, and in South-Eastern Europe (Greece, Turkey, Georgia). Visceral leishmaniasis is a parasitic zoonosis caused by species of the L. donovani complex. In the classical epidemiological model the main reservoir for VL are canines. The study included a cohort of 513 individuals of both genders (190 males and 323 females) from the ages of 1 to 70 years that were screened in ten villages across two districts in Kakheti using the Kalazar Detect™ rK39 rapid diagnostic test. The phylogenetic diversity patterns of local strains, based on the rDNA internal transcribed spacer (ITS) sequences, were assessed for samples obtained from patients with suspected L. donovani infection, from canine reservoirs and from Phlebotomus sand flies obtained from different geographical areas of Georgia and from Azerbaijan. Out of a total of 600 domestic dog blood samples 95 (15.8 %) were positive by rK39 rapid diagnostic tests. For symptomatic domestic dogs, the testing of conjunctival swabs or bone marrow aspirates revealed a higher VL incidence in Kvareli District (Kvareli; 19.4 %, n = 329) compared with that observed for Sagarejo District (Sagarejo; 11.4 %, n = 271). A total of 231 sand flies of both genders were collected during the 2-month period; of the 114 females, 1.75 % were PCR positive for the presence of Leishmania spp. VL infection rates remain high in both canines and humans in Georgia, with disease in several known natural foci. The genetic relationships derived from rDNA internal transcribed spacer (ITS) sequence comparisons identified genetic subgroups, revealing preliminary insights into the genetic structure of L. donovani complex members currently circulating in the South Caucasus and demonstrates the utility of ITS-based genotyping

  3. 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. Published by Elsevier B.V.

  4. Diversity

    Science.gov (United States)

    Portraits In Courage Vol. VIII Portraits In Courage Vol. IX Portraits In Courage Vol. X AF Sites Social -Wide Initiative to Promote Diversity and Inclusion in the Federal Workforce Executive Order 13548 : Virtual Diversity Conference Air Force Diversity & Inclusion Air Force Diversity Graphic There is no

  5. Evolution of species diversity in the genus Chamaecostus (Costaceae): molecular phylogenetics and morphometric approaches

    OpenAIRE

    Andre, Thiago; Specht, Chelsea; Salzman, Shayla; Palma-Silva, Clarisse [UNESP; Wendt, Tania

    2015-01-01

    While most species within the genus Chamaecostus (Costaceae) are well defined, the broad geographic range and long list of synonyms associated with Chamaecostus subsessilis led us to believe there may be some cryptic species within the complex. We thus investigate the phylogenetic relationships of species in the Chamaecostus lineage and specifically test the monophyly and diversity of the Chamaecostus subsessilis species complex from a population perspective by analyzing molecular sequence da...

  6. United in Diversity : A Physiological and Molecular Characterization of Subpopulations in the Basal Ganglia Circuitry

    OpenAIRE

    Viereckel, Thomas

    2017-01-01

    The Basal Ganglia consist of a number of different nuclei that form a diverse circuitry of GABAergic, dopaminergic and glutamatergic neurons. This complex network is further organized in subcircuits that govern limbic and motor functions in humans and other vertebrates. Due to the interconnection of the individual structures, dysfunction in one area or cell population can affect the entire network, leading to synaptic and molecular alterations in the circuitry as a whole. The studies in this ...

  7. 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.

    . Sparrow Jr F K (1936) Biological observations of the marine fungi of woods hole waters. Biol Bull 70: 236-263. States JS & Christensen M (2001) Fungi Associated with Biological Soil Crusts in Desert Grasslands of Utah and Wyoming. Mycologia 93: 432... version: Biology of marine fungi. Ed. by: Raghukumar, C. (Prog. Mol. Subcellular Biol). Springer, vol.53 (Chap 10); 2012; 189-208 Chapter # 10 Molecular diversity of fungi from marine oxygen-deficient environments (ODEs) Cathrine S. Jebaraj 1...

  8. Hidden diversity and evolutionary trends in malacosporean parasites (Cnidaria: Myxozoa) identified using molecular phylogenetics

    Czech Academy of Sciences Publication Activity Database

    Bartošová, Pavla; Hrabcová, M.; Pecková, Hana; Patra, Sneha; Kodádková, Alena; Jurajda, Pavel; Tyml, Tomáš; Holzer, Astrid S.

    2014-01-01

    Roč. 44, č. 8 (2014), s. 565-577 ISSN 0020-7519 R&D Projects: GA ČR(CZ) GPP506/11/P724; GA ČR GBP505/12/G112; GA AV ČR(CZ) M200961205 Institutional support: RVO:60077344 ; RVO:68081766 Keywords : Buddenbrockia * Tetracapsuloides * diversity * phylogeny * Bryozoa * fish * cryptic * worm Subject RIV: EB - Genetics ; Molecular Biology; EG - Zoology (UBO-W) Impact factor: 3.872, year: 2014

  9. Morphological and molecular diversity in a collection of the Andean tree tomato (Solanum betaceum Cav.)

    OpenAIRE

    Acosta-Quezada, P.G.; Martinez-Laborde, J.B.; Vilanova Navarro, Santiago; Prohens Tomás, Jaime

    2011-01-01

    Instituto Nacional de Investigaciones Agrarias y Agroalimentarias (RF2008-00008-00-00) Acosta-Quezada, P.; Martinez-Laborde, J.; Vilanova Navarro, S.; Prohens Tomás, J. (2011). Morphological and molecular diversity in a collection of the Andean tree tomato (Solanum betaceum Cav.). Bulletin of University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca : Horticulture. 68(1):500-501. http://hdl.handle.net/10251/63083 Senia 500 501 68 1

  10. Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

    Science.gov (United States)

    Chiu, Isaac M; Barrett, Lee B; Williams, Erika K; Strochlic, David E; Lee, Seungkyu; Weyer, Andy D; Lou, Shan; Bryman, Gregory S; Roberson, David P; Ghasemlou, Nader; Piccoli, Cara; Ahat, Ezgi; Wang, Victor; Cobos, Enrique J; Stucky, Cheryl L; Ma, Qiufu; Liberles, Stephen D; Woolf, Clifford J

    2014-01-01

    The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1) IB4+SNS-Cre/TdTomato+, 2) IB4−SNS-Cre/TdTomato+, and 3) Parv-Cre/TdTomato+ cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation. DOI: http://dx.doi.org/10.7554/eLife.04660.001 PMID:25525749

  11. 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.

  12. 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.

  13. Identification of substituent groups and related genes involved in salecan biosynthesis in Agrobacterium sp. ZX09.

    Science.gov (United States)

    Xu, Linxiang; Cheng, Rui; Li, Jing; Wang, Yang; Zhu, Bin; Ma, Shihong; Zhang, Weiming; Dong, Wei; Wang, Shiming; Zhang, Jianfa

    2017-01-01

    Salecan, a soluble β-1,3-D-glucan produced by a salt-tolerant strain Agrobacterium sp. ZX09, has been the subject of considerable interest in recent years because of its multiple bioactivities and unusual rheological properties in solution. In this study, both succinyl and pyruvyl substituent groups on salecan were identified by an enzymatic hydrolysis following nuclear magnetic resonance (NMR), HPLC, and MS analysis. The putative succinyltransferase gene (sleA) and pyruvyltransferase gene (sleV) were determined and cloned. Disruption of the sleA gene resulted in the absence of succinyl substituent groups on salecan. This defect could be complemented by expressing the sleA cloned in a plasmid. Thus, the sleA and sleV genes located in a 19.6-kb gene cluster may be involved in salecan biosynthesis. Despite the lack of succinyl substituents, the molecular mass of salecan generated by the sleA mutant did not substantially differ from that generated by the wild-type strain. Loss of succinyl substituents on salecan changed its rheological characteristics, especially a decrease in intrinsic viscosity.

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

    KAUST Repository

    Ziegler, Maren; Arif, Chatchanit; Burt, John A.; Dobretsov, Sergey; Roder, Cornelia; Lajeunesse, Todd C.; Voolstra, Christian R.

    2017-01-01

    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.

  15. 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.

  16. 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.

  17. Phylodynamic analysis and molecular diversity of the avian infectious bronchitis virus of chickens in Brazil.

    Science.gov (United States)

    Fraga, Aline Padilha de; Gräf, Tiago; Pereira, Cleiton Schneider; Ikuta, Nilo; Fonseca, André Salvador Kazantzi; Lunge, Vagner Ricardo

    2018-03-21

    Avian infectious bronchitis virus (IBV) is the etiological agent of a highly contagious disease, which results in severe economic losses to the poultry industry. The spike protein (S1 subunit) is responsible for the molecular diversity of the virus and many sero/genotypes are described around the world. Recently a new standardized classification of the IBV molecular diversity was conducted, based on phylogenetic analysis of the S1 gene sequences sampled worldwide. Brazil is one of the biggest poultry producers in the world and the present study aimed to review the molecular diversity and reconstruct the evolutionary history of IBV in the country. All IBV S1 gene sequences, with local and year of collection information available on GenBank, were retrieved. Phylogenetic analyses were carried out based on a maximum likelihood method for the classification of genotypes occurring in Brazil, according to the new classification. Bayesian phylogenetic analyses were performed with the Brazilian clade and related international sequences to determine the evolutionary history of IBV in Brazil. A total of 143 Brazilian sequences were classified as GI-11 and 46 as GI-1 (Mass). Within the GI-11 clade, we have identified a potential recombinant strain circulating in Brazil. Phylodynamic analysis demonstrated that IBV GI-11 lineage was introduced in Brazil in the 1950s (1951, 1917-1975 95% HPD) and population dynamics was mostly constant throughout the time. Despite the national vaccination protocols, our results show the widespread dissemination and maintenance of the IBV GI-11 lineage in Brazil and highlight the importance of continuous surveillance to evaluate the impact of currently used vaccine strains on the observed viral diversity of the country. Copyright © 2018 Elsevier B.V. All rights reserved.

  18. Molecular markers to assess genetic diversity and mutant identifications in Jatropha curcas

    International Nuclear Information System (INIS)

    Azhar Mohamad; Yie Min Kwan; Fatin Mastura Derani; Abdul Rahim Harun

    2010-01-01

    Jatropha curcas (Linnaeus) belongs to the Euphorbiaceae family, is a multipurpose use, drought resistant and perennial plant. It is an economic important crop, which generates wide interest in understanding the genetic diversity of the species towards selection and breeding of superior genotypes. Jatropha accessions are closely related family species. Thus, better understanding of the effectiveness of the different DNA-based markers is an important step towards plant germplasm characterization and evaluation. It is becoming a prerequisite for more effective application of marker techniques in breeding programs. Inter-simple sequence repeats (ISSRs) has shown rapid, simple, reproducible and inexpensive means in molecular taxonomy, conservation breeding and genetic diversity analysis. These markers were used to understand diversity and differentiate amongst accessions of Jatropha population and mutant lines generated by acute gamma radiation. The ISSR for marker applications are essential to facilitate management, conservation and genetic improvement programs towards improvement of bio-diesel production and medication substances. A total of 62 ISSR primers were optimized for polymorphism evaluations on five foreign accessions (Africa, India, Myanmar, Indonesia, Thailand), nine local accessions and two mutants of Jatropha. Optimization was resulted 54 ISSR primers affirmative for the polymorphism evaluation study, which encountered 12 ISSR primers, showed significance polymorphism amongst the accessions and mutants. Marker derived from ISSR profiling is a powerful method for identification and molecular classification of Jatropha from accession to generated mutant varieties. (author)

  19. A Computational Study of Structure and Reactivity of N-Substitued-4-Piperidones Curcumin Analogues and Their Radical Anions

    Directory of Open Access Journals (Sweden)

    Maximiliano Martínez-Cifuentes

    2016-12-01

    Full Text Available In this work, a computational study of a series of N-substitued-4-piperidones curcumin analogues is presented. The molecular structure of the neutral molecules and their radical anions, as well as their reactivity, are investigated. N-substituents include methyl and benzyl groups, while substituents on the aromatic rings cover electron-donor and electron-acceptor groups. Substitutions at the nitrogen atom do not significantly affect the geometry and frontier molecular orbitals (FMO energies of these molecules. On the other hand, substituents on the aromatic rings modify the distribution of FMO. In addition, they influence the capability of these molecules to attach an additional electron, which was studied through adiabatic (AEA and vertical electron affinities (VEA, as well as vertical detachment energy (VDE. To study electrophilic properties of these structures, local reactivity indices, such as Fukui (f+ and Parr (P+ functions, were calculated, and show the influence of the aromatic rings substituents on the reactivity of α,β-unsaturated ketones towards nucleophilic attack. This study has potential implications for the design of curcumin analogues based on a 4-piperidone core with desired reactivity.

  20. Substituent effects in heterogeneous catalysis--5. The steric hindrance of bulky alkyl substituents in cyclohexanone hydrogenation

    Energy Technology Data Exchange (ETDEWEB)

    Chihara, T; Tanaka, K

    1979-02-01

    The steric hindrance of bulky alkyl substituents in cyclohexanone hydrogenation was demonstrated by the reactivities of 2-isopropyl and 2-tert.-butyl cyclohexanone relative to cyclohexanone in individual and competitive hydrogenation at 30/sup 0/C over alumina-supported ruthenium, rhodium, and platinum catalysts. The results indicate that the ketone adsorption onto the catalyst is sterically hindered by the alkyl substitution significantly more than the surface reaction which follows the adsorption.

  1. Analysis of genetic diversity among rapeseed cultivars and breeding lines by srap and ssr molecular markers

    International Nuclear Information System (INIS)

    Channa, S.A.; Tian, H.

    2016-01-01

    The knowledge of genetic diversity is very important for developing new rapeseed (Brassica napus L.) cultivars. The genetic diversity among 77 rapeseed accessions, including 22 varieties and 55 advanced breeding lines were analyzed by 47 sequence-related amplified polymorphism (SRAP) and 56 simple sequence repeat (SSR) primers. A total of 270 SRAP and 194 SSR polymorphic fragments were detected with an average of 5.74 and 3.46 for SRAP and SSR primer, respectively. The cluster analysis grouped the 77 accessions into five major clusters. Cluster I contained spring and winter type varieties from Czech Republic and semi-winter varieties and their respective breeding lines from China. The 16 elite breeding lines discovered in Cluster II, III, IV and V indicated higher genetic distance than accessions in Cluster I. The principal component analysis and structure analysis exhibited similar results to the cluster analysis. Analysis of molecular variance revealed that genetic diversity of the selected breeding lines was comparable to the rapeseed varieties, and variation among varieties and lines was significant. The diverse and unique group of 16 elite breeding lines detected in this study can be utilized in the future breeding program as a source for development of commercial varieties with more desirable characters. (author)

  2. Molecular analysis and genetic diversity of Aedes albopictus (Diptera, Culicidae) from China.

    Science.gov (United States)

    Ruiling, Zhang; Peien, Leng; Xuejun, Wang; Zhong, Zhang

    2018-05-01

    Aedes albopictus is one of the most invasive species, which can carry Dengue virus, Yellow fever virus and more than twenty arboviruses. Based on mitochondrial gene cytochrome c oxidase I (COI) and samples collected from 17 populations, we investigated the molecular character and genetic diversity of Ae. albopictus from China. Altogether, 25 haplotypes were detected, including 10 shared haplotypes and 15 private haplotypes. H1 was the dominant haplotype, which is widely distributed in 13 populations. Tajima'D value of most populations was significantly negative, demonstrating that populations experienced rapid range expansion recently. Most haplotypes clustered together both in phylogenetic and median-joining network analysis without clear phylogeographic patterns. However, neutrality tests revealed shallow divergences among Hainan and Guangxi with other populations (0.15599 ≤ F ST ≤ 0.75858), which probably due to interrupted gene flow, caused by geographical isolations. In conclusion, Ae. albopictus populations showed low genetic diversity in China.

  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. Linguistic measures of chemical diversity and the "keywords" of molecular collections.

    Science.gov (United States)

    Woźniak, Michał; Wołos, Agnieszka; Modrzyk, Urszula; Górski, Rafał L; Winkowski, Jan; Bajczyk, Michał; Szymkuć, Sara; Grzybowski, Bartosz A; Eder, Maciej

    2018-05-15

    Computerized linguistic analyses have proven of immense value in comparing and searching through large text collections ("corpora"), including those deposited on the Internet - indeed, it would nowadays be hard to imagine browsing the Web without, for instance, search algorithms extracting most appropriate keywords from documents. This paper describes how such corpus-linguistic concepts can be extended to chemistry based on characteristic "chemical words" that span more than traditional functional groups and, instead, look at common structural fragments molecules share. Using these words, it is possible to quantify the diversity of chemical collections/databases in new ways and to define molecular "keywords" by which such collections are best characterized and annotated.

  5. Incidence, Diversity, and Molecular Epidemiology of Sapoviruses in Swine across Europe

    DEFF Research Database (Denmark)

    Reuter, G.; Zimsek-Mijovski, J.; Poljsak-Prijatelj, M.

    2010-01-01

    report on the incidence, genetic diversity and molecular epidemiology of sapoviruses detected in domestic pigs in a comprehensive study conducted in six European countries (Denmark, Finland, Hungary, Italy, Slovenia and Spain) between 2004 and 2007. A total of 1,050 swine fecal samples from 88 pig farms......) to human sapovirus strains. Sapoviruses are commonly circulating and endemic agents in swine herds throughout Europe. Highly heterogenous and potential new genogroups of sapoviruses were found in pigs; however, no "human-like" sapoviruses were detected....

  6. Molecular Markers for Genetic Diversity Studies of European Hare (Lepus europaeus Pallas, 1778 Populations

    Directory of Open Access Journals (Sweden)

    Noémi Soós

    2015-05-01

    Full Text Available The purpose of this article is to give an overview of different molecular techniques which have been used in studies concerning population genetic issues of Lepus species and specifically of L. europaeus. The importance of these researches is ever-growing as the European populations of the brown hare have suffered several falloffs as a consequent upon both natural and anthropogenic effects. With developing tools and techniques molecular genetics have become the centrepiece of population genetics and conservation biology. Nucleic acid methods based on both bi- and uniparentally inherited DNA (allozymes, microsatellites, Y chromosome, mtDNA are often used to study genetic structure, diversity and phylogeography of different species’ populations due to their effectiveness in identifying genetic variability

  7. Rationalizing substituent effects in 1-azathioxanthone photophysics

    Science.gov (United States)

    Junker, Anne Kathrine R.; Just Sørensen, Thomas

    2018-01-01

    The influence of an electron donating substituent on the photophysical properties of 1-azathioxanthone dyes has been investigated using optical spectroscopy and theoretical models. The motivation behind the study is based on the fact that thioxanthones are efficient triplet sensitizers, and thus promising sensitizers for lanthanide centered emission. By adding an aza group to one of the phenyl ring systems, direct coordination to a lanthanide center becomes possible, which makes azathoixanthones great candidates as antenna chromophores in lanthanide(III) based dyes. Here, three 1-azathioxanthone derivatives have been synthesized targeting efficient triplet formation following absorption in the visible range of the spectrum. This is achieved by adding methoxy groups to the 1-azathioxanthone core. The derivatives were characterized using absorption, emission, and time-gated emission spectroscopy, where fluorescent quantum yields, singlet and triplet excited states lifetimes were determined. The experimentally determined photophysical properties of the three 1-azathioxanthone compounds are contrasted to those of the parent thioxanthone and is rationalized using the Strickler-Berg equation, Hückel MO theory, and Dewar’s rules in combination with computational chemistry. We find that the transition energies follow predictions, but that the overall photophysical properties are determined by the relative energies as well as the nature of the involved states in both the singlet and the triplet excited state manifolds.

  8. Genetic Diversity Analysis of Tagetes Species Using PCR Based Molecular Markers

    International Nuclear Information System (INIS)

    Shahzadi, I.; Ahmad, R.; Waheed, U.; Shah, M. F.

    2016-01-01

    Tagetes is a genus of medicinally important wild and cultivated plants containing several chemical compounds. Lack of information on variation at molecular level present in Tagetes species is paramount to understand the genetic basis of medicinally important compounds. Current study aims at finding genetic variability in Tagetes species using random and specific molecular markers. Two primer systems including 25 RAPD and 3 STS (limonene gene) were used to ascertain genetic diversity of 15 Tagetes genotypes belonging to different species. We found that 20 of the 25 tested RAPD primers generated stable band patterns with 167 loci of amplification products. The proportion of polymorphic bands was 95.21 percent for RAPD primers. Three STS primers generated a total of 29 amplification products, of which 96.55 percent were polymorphic. Homology of genotypes was 53.18 percent and 51.11 percent with RAPD and STS primers respectively. The dendrogram obtained revealed that the range of overall genetic distances estimated was 22 percent to 100 percent through RAPD and 9 percent to 100 percent through STS markers. The findings help to establish that PCR-based assay such as RAPD and STS could be used successfully for estimation of genetic diversity of different genotypes of Tagetes that can be used for selection of parents for improvement of the species. (author)

  9. Theoretical investigation of substituent effects on the dihydroazulene/vinylheptafulvene photoswitch

    DEFF Research Database (Denmark)

    Hansen, Mia Harring; Elm, Jonas; Olsen, Stine Tetzschner

    2016-01-01

    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 dihydroazu......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...... 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...

  10. Morphophysiology, Phenotypic and Molecular Diversity of Auxin-induced Passiflora mucronata Lam. (Passifloraceae).

    Science.gov (United States)

    França, Juliany M; Venial, Lucimara R; Costa, Eloá B; Schmildt, Edilson R; Schmildt, Omar; Bernardes, Paula M; Tatagiba, Sandro D; Lopes, José C; Ferreira, Marcia F S; Alexandre, Rodrigo S

    2018-01-01

    Genetic diversity allows identification of potential intraspecific genotypes in the genus Passiflora. The objective of this study was to examine the morphological and genetic diversity of auxin-induced Passiflora mucronata. The experiments were arranged in a complete randomized block design, with a 9 x 2 factorial arrangement (nine genotypes x presence and absence of auxin, indole-3-butyric acid (IBA)), with four replicates of 16 cuttings. The rooting and vegetative growth responses were variable. Genotype 5 was more responsive in the absence of IBA and genotypes 3, 8 and 9 were more responsive in the presence of IBA. Auxin increased rooting rate and percentage, reducing the average time of root protrusion in eight days. IBA also contributed to increase photosynthesis and dry root and shoot mass in 55.55 and 44.44% of the genotypes, respectively. The highest relative contribution to phenotypic diversity in the absence of auxin was rate (38.75%) and percentage (20.27%) of rooting, whereas in the presence of auxin was stomatal conductance (23.19%) and root dry mass (20.91%). Similarity was found for phenotypic and molecular divergence in the presence of IBA, in which genotypes 1 and 6; genotypes 5, 8 and 9; and genotype 3 were clustered in distinct groups.

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

    Science.gov (United States)

    2011-01-01

    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 ompA as a fine

  12. 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

  13. Molecular diversity patterns among various phytoplankton size-fractions in West Greenland in late summer

    Science.gov (United States)

    Elferink, Stephanie; Neuhaus, Stefan; Wohlrab, Sylke; Toebe, Kerstin; Voß, Daniela; Gottschling, Marc; Lundholm, Nina; Krock, Bernd; Koch, Boris P.; Zielinski, Oliver; Cembella, Allan; John, Uwe

    2017-03-01

    Arctic regions have experienced pronounced biological and biophysical transformations as a result of global change processes over the last several decades. Current hypotheses propose an elevated impact of those environmental changes on the biodiversity, community composition and metabolic processes of species. The effects on ecosystem function and services, particularly when invasive or toxigenic harmful species become dominant, can be expressed over a wide range of temporal and spatial scales in plankton communities. Our study focused on the comparison of molecular biodiversity of three size-fractions (micro-, nano-, picoplankton) in the coastal pelagic zone of West Greenland and their association with environmental parameters. Molecular diversity was assessed via parallel amplicon sequencing the 28S rRNA hypervariable D1/D2 region. We showed that biodiversity distribution within the area of Uummannaq Fjord, Vaigat Strait and Disko Bay differed markedly within and among size-fractions. In general, we observed a higher diversity within the picoplankton size fraction compared to the nano- and microplankton. In multidimensional scaling analysis, community composition of all three size fractions correlated with cell size, silicate and phosphate, chlorophyll a (chl a) and dinophysistoxin (DTX). Individually, each size fraction community composition also correlated with other different environmental parameters, i.e. temperature and nitrate. We observed a more homogeneous community of the picoplankton across all stations compared to the larger size classes, despite different prevailing environmental conditions of the sampling areas. This suggests that habitat niche occupation for larger-celled species may lead to higher functional trait plasticity expressed as an enhanced range of phenotypes, whereas smaller organisms may compensate for lower potential plasticity with higher diversity. The presence of recently identified toxigenic harmful algal bloom (HAB) species (such

  14. Molecular systematics reveals increased diversity within the South African Laurencia complex (Rhodomelaceae, Rhodophyta).

    Science.gov (United States)

    Francis, Caitlynne; Bolton, John J; Mattio, Lydiane; Mandiwana-Neudani, Tshifhiwa G; Anderson, Robert J

    2017-08-01

    Previous publications list ten species in the Laurencia complex from South Africa with all ascribed to the genus Laurencia sensu stricto. However, the diversity of the complex in South Africa has not yet been re-assessed following the numerous recent taxonomic changes. This study investigated the phylogenetic relationships and taxonomy of this group in South Africa using recent collections. Methods included molecular phylogenetic analyses of plastid rbcL gene sequences (a total of 146; including eleven outgroup taxa) using Maximum Likelihood and Bayesian Inference, and the examination of morphological and anatomical characters, including the number of corps en cerise when present. The seven genera of the Laurencia complex formed monophyletic clades with high posterior probabilities. Seventeen morphotypes were identified: 14 in the genus Laurencia sensu stricto, among which eight corresponded to Laurencia species currently recognized from South Africa and one each to species of Palisada, Chondrophycus, and Laurenciella. The six remaining morphotypes in Laurencia sensu stricto did not match any descriptions and are described here as five new species: Laurencia alfredensis sp. nov., Laurencia dichotoma sp. nov., Laurencia digitata sp. nov., Laurencia multiclavata sp. nov. and Laurencia sodwaniensis sp. nov. and a new variety: Laurencia pumila var. dehoopiensis var. nov. Laurencia stegengae nom. nov. is established to replace Laurencia peninsularis Stegenga, Bolton and Anderson nom. illeg. The diversity is likely greater, with six additional unidentified specimens found in this molecular investigation. These findings place South Africa alongside Australia in having one of the most diverse floras of this group in the world. © 2017 Phycological Society of America.

  15. Molecular diversity of the rumen microbiome of Norwegian reindeer on natural summer pasture.

    Science.gov (United States)

    Sundset, Monica A; Edwards, Joan E; Cheng, Yan Fen; Senosiain, Roberto S; Fraile, Maria N; Northwood, Korinne S; Praesteng, Kirsti E; Glad, Trine; Mathiesen, Svein D; Wright, André-Denis G

    2009-02-01

    The molecular diversity of the rumen microbiome was investigated in five semi-domesticated adult female Norwegian reindeer (Rangifer tarandus tarandus) grazing on natural summer pastures on the coast of northern Norway (71.00 degrees N, 25.30 degrees E). Mean population densities (numbers per gram wet weight) of methanogenic archaea, rumen bacteria and ciliate protozoa, estimated using quantitative real-time polymerase chain reaction (PCR), were 3.17x10(9), 5.17x10(11) and 4.02x10(7), respectively. Molecular diversity of rumen methanogens was revealed using a 16S rRNA gene library (54 clones) constructed using pooled PCR products from the whole rumen contents of the five individual reindeer. Based upon a similarity criterion of rumen exhibited a high degree of sequence similarity to methanogens affiliated with the families Methanobacteriaceae (14 OTUs) and Methanosarcinaceae (one OTU). Four of the OTUs detected belonged to a group of uncultivated archaea previously found in domestic ruminants and thought to be dominant in the rumen together with Methanobrevibacter spp. Denaturing gradient gel electrophoresis profiling of the rumen bacterial 16S rRNA gene and the protozoal 18S rRNA gene indicated a high degree of animal variation, although some bands were common to all individuals. Automated ribosomal intergenic spacer analysis (ARISA) profiling of the ruminal Neocallimastigales population indicated that the reindeer are likely to contain more than one type of anaerobic fungus. The ARISA profile from one animal was distinct from the other four. This is the first molecular investigation of the ruminal methanogenic archaea in reindeer, revealing higher numbers than expected based on methane emission data available. Also, many of the reindeer archaeal 16S rRNA gene sequences were similar to those reported in domesticated ruminants in Australia, Canada, China, New Zealand and Venezuela, supporting previous findings that there seems to be no host type or geographical

  16. 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)

  17. Anaerobic C1 metabolism of the O-methyl-14C-labeled substituent of vanillate

    International Nuclear Information System (INIS)

    Frazer, A.C.; Young, L.Y.

    1986-01-01

    The O-methyl substituents of aromatic compounds constitute a C 1 growth substrate for a number of taxonomically diverse anaerobic acetogens. In this study, strain TH-001, an O-demethylating obligate anaerobe, was chosen to represent this physiological group, and the carbon flow when cells were grown on O-methyl substituents as a C 1 substrate was determined by 14 C radiotracer techniques. O-[methyl- 14 C]vanillate (4-hydroxy-3-methoxy-benzoate) was used as the labeled C 1 substrate. The data showed that for every O-methyl carbon converted to [ 14 C]acetate, two were oxidized to 14 CO 2 . Quantitation of the carbon recovered in the two products, acetate and CO 2 , indicated that acetate was formed in part by the fixation of unlabeled CO 2 . The specific activity of 14 C in acetate was 70% of that in the O-methyl substrate, suggesting that only one carbon of acetate was derived from the O-methyl group. Thus, it is postulated that the carboxyl carbon of the product acetate is derived from CO 2 and the methyl carbon is derived from the O-methyl substituent of vanillate

  18. Zoanthid diversity (Anthozoa: Hexacorallia) in the Galapagos Islands: a molecular examination

    Science.gov (United States)

    Reimer, J. D.; Sinniger, F.; Hickman, C. P.

    2008-09-01

    Although the Galapagos are famous for their unique biodiversity, many groups of marine invertebrates from this isolated archipelago remain understudied or not investigated. One such group is the zoanthids (Order Zoantharia, =Zoanthidea, =Zoanthiniaria), anthozoans (Cnidaria) found in marine ecosystems worldwide. Zoanthid taxonomy has been in a state of disorganization and neglect due in large part to the morphological plasticity within species and questions about the accuracy of traditionally used morphological and ecological characteristics. However, recent studies utilizing molecular methodology combined with morphology have proven to be very useful in understanding zoanthid diversity. The results of a survey of zoanthids from the Galapagos and the east Pacific are reported in this study. Shallow water (zoanthid specimens were identified using the molecular markers mitochondrial 16S ribosomal DNA (mt 16S rDNA), cytochrome oxidase subunit I (COI) gene, and the internal transcribed spacer of ribosomal DNA (ITS-rDNA). From the collected specimens seven putative zoanthid species-level clades from three known genera ( Zoanthus, Palythoa, Parazoanthus) were identified at the molecular level. These identifications were further supported by morphological and ecological data. While almost all specimens belonged to known zoanthid genera, based on unique molecular and ecological data one group of specimens (designated unknown zoanthid sp. “03-103”) is potentially a novel undescribed genus. Additionally, the remaining three azooxanthellate Parazoanthus clades may also be undescribed new species, but due to the overall lack of zoanthid research and descriptions from neighboring areas (East Pacific, west coast of South America) further research is needed to clearly ascertain this. Additionally, notes on the four observed nominal azooxanthellate zoanthid species and a key to all eight nominal (seven from known genera, one from a potentially new genus) shallow water zoanthid

  19. Molecular evidence and high genetic diversity of shrew-borne Seewis virus in Slovenia.

    Science.gov (United States)

    Resman, Katarina; Korva, Miša; Fajs, Luka; Zidarič, Tanja; Trilar, Tomi; Zupanc, Tatjana Avšič

    2013-10-01

    Seewis virus, the shrew-borne hantavirus from Sorex araneus, has been molecularly detected in reservoir hosts in many different central European countries and Russia. Slovenia is a known endemic country for rodent-borne hantaviruses, therefore the aim of the study was to investigate the presence of shrew-borne hantaviruses in insectivores. Viral L, S and M segment have been recovered only from tissue samples of 7 S. araneus, despite several shrew species were tested. Phylogenetic analysis showed high genetic diversity of SWSV in Slovenia, ranging from 3 to 19.4% for different viral segments. The most divergent were M segment sequences, with 19.4% nucleotide divergence among Slovenian strains. Above that, different SWSV strains from Slovenia do not group into separate geographic clusters. While three separate genetic clades were determined, two of them were simultaneously present in one location at the same time. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. 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

  1. 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

  2. Molecular phylogeny and larval morphological diversity of the lanternfish genus Hygophum (Teleostei: Myctophidae).

    Science.gov (United States)

    Yamaguchi, M; Miya, M; Okiyama, M; Nishida, M

    2000-04-01

    Larvae of the deep-sea lanternfish genus Hygophum (Myctophidae) exhibit a remarkable morphological diversity that is quite unexpected, considering their homogeneous adult morphology. In an attempt to elucidate the evolutionary patterns of such larval morphological diversity, nucleotide sequences of a portion of the mitochondrially encoded 16S ribosomal RNA gene were determined for seven Hygophum species and three outgroup taxa. Secondary structure-based alignment resulted in a character matrix consisting of 1172 bp of unambiguously aligned sequences, which were subjected to phylogenetic analyses using maximum-parsimony, maximum-likelihood, and neighbor-joining methods. The resultant tree topologies from the three methods were congruent, with most nodes, including that of the genus Hygophum, being strongly supported by various tree statistics. The most parsimonious reconstruction of the three previously recognized, distinct larval morphs onto the molecular phylogeny revealed that one of the morphs had originated as the common ancestor of the genus, the other two having diversified separately in two subsequent major clades. The patterns of such diversification are discussed in terms of the unusual larval eye morphology and geographic distribution. Copyright 2000 Academic Press.

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

    Science.gov (United States)

    Vásquez-Mayorga, Marcela; Fuchs, Eric J.; Hernández, Eduardo J.; Herrera, Franklin; Hernández, Jesús; Moreira, Ileana; Arnáez, Elizabeth

    2017-01-01

    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. PMID:28289556

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

    International Nuclear Information System (INIS)

    Zarei, Mehdi; Hempel, Stefan; Wubet, Tesfaye; Schaefer, Tina; Savaghebi, Gholamreza; Jouzani, Gholamreza Salehi; Nekouei, Mojtaba Khayam; Buscot, Francois

    2010-01-01

    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.

  5. 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.

  6. 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.

  7. 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.

  8. Microbial diversity in an Armenian geothermal spring assessed by molecular and culture-based methods.

    Science.gov (United States)

    Panosyan, Hovik; Birkeland, Nils-Kåre

    2014-11-01

    The phylogenetic diversity of the prokaryotic community thriving in the Arzakan hot spring in Armenia was studied using molecular and culture-based methods. A sequence analysis of 16S rRNA gene clone libraries demonstrated the presence of a diversity of microorganisms belonging to the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Epsilonproteobacteria, Firmicutes, Bacteroidetes phyla, and Cyanobacteria. Proteobacteria was the dominant group, representing 52% of the bacterial clones. Denaturing gradient gel electrophoresis profiles of the bacterial 16S rRNA gene fragments also indicated the abundance of Proteobacteria, Bacteroidetes, and Cyanobacteria populations. Most of the sequences were most closely related to uncultivated microorganisms and shared less than 96% similarity with their closest matches in GenBank, indicating that this spring harbors a unique community of novel microbial species or genera. The majority of the sequences of an archaeal 16S rRNA gene library, generated from a methanogenic enrichment, were close relatives of members of the genus Methanoculleus. Aerobic endospore-forming bacteria mainly belonging to Bacillus and Geobacillus were detected only by culture-dependent methods. Three isolates were successfully obtained having 99, 96, and 96% 16S rRNA gene sequence similarities to Arcobacter sp., Methylocaldum sp., and Methanoculleus sp., respectively. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Genetic diversity analysis of Chrysopidae family (Insecta, Neuroptera) via molecular markers.

    Science.gov (United States)

    Yari, Kheirollah; Mirmoayedi, Alinaghi; Marami, Marzieh; Kazemi, Elham; Kahrizi, Danial

    2014-09-01

    In entomology, improvement of molecular methods would be beneficial tools for accurate identification and detecting the genetic diversity of insect species to discover a corroborative evidence for the traditional classification based on morphology. The aim of this study was focused on RAPD-PCR method for distinguishing the genetic diversity between eight species of Chrysopidae family. In current research, many specimens were collected in different locations of Tehran province (Iran), between them 24 specimens were identified. The wing venation, male genitalia and other morphological characters were used for identification and also the sexing of species was recognized with study of external genitalia. Then, the DNA was extracted with CTAB method. The RAPD-PCR method was carried out with twenty random primers. The agarose gel electrophoresis was used for separation of the PCR products. Based on electrophoresis results, 133 bands were amplified and between them, 126 bands were poly-morph and others were mono-morph. Also, among the applied primers, the primers OPA02 with 19 bands and OPA03 with 8 bands were amplified the maximum and minimum of bands, respectively. The results showed that 80.35 and 73.21 % of genetic similarity existed between Chrysopa pallens-Chrysopa dubitans, and between the Chrysoperla kolthoffi and Chrysoperla carnea, respectively. The minimum (45.53 %) of genetic similarity was observed between C. kolthoffi and C. dubitans, and the maximum (0.80 %) was seen between C. pallens and C. dubitans.

  10. Polyploidy creates higher diversity among Cynodon accessions as assessed by molecular markers.

    Science.gov (United States)

    Gulsen, Osman; Sever-Mutlu, Songul; Mutlu, Nedim; Tuna, Metin; Karaguzel, Osman; Shearman, Robert C; Riordan, Terrance P; Heng-Moss, Tiffany M

    2009-05-01

    Developing a better understanding of associations among ploidy level, geographic distribution, and genetic diversity of Cynodon accessions could be beneficial to bermudagrass breeding programs, and would enhance our understanding of the evolutionary biology of this warm season grass species. This study was initiated to: (1) determine ploidy analysis of Cynodon accessions collected from Turkey, (2) investigate associations between ploidy level and diversity, (3) determine whether geographic and ploidy distribution are related to nuclear genome variation, and (4) correlate among four nuclear molecular marker systems for Cynodon accessions' genetic analyses. One hundred and eighty-two Cynodon accessions collected in Turkey from an area south of the Taurus Mountains along the Mediterranean cost and ten known genotypes were genotyped using sequence related amplified polymorphism (SRAP), peroxidase gene polymorphism (POGP), inter-simple sequence repeat (ISSR), and random amplified polymorphic DNA (RAPD). The diploids, triploids, tetraploids, pentaploids, and hexaploids revealed by flow cytometry had a linear present band frequency of 0.36, 0.47, 0.49, 0.52, and 0.54, respectively. Regression analysis explained that quadratic relationship between ploidy level and band frequency was the most explanatory (r = 0.62, P Cynodon accessions' genetic structure can aid to enhance breeding programs and broaden genetic base of commercial cultivars.

  11. Genetic diversity among Korean bermudagrass (Cynodon spp.) ecotypes characterized by morphological, cytological and molecular approaches.

    Science.gov (United States)

    Kang, Si-Yong; Lee, Geung-Joo; Lim, Ki Byung; Lee, Hye Jung; Park, In Sook; Chung, Sung Jin; Kim, Jin-Baek; Kim, Dong Sub; Rhee, Hye Kyung

    2008-04-30

    The genus Cynodon comprises ten species. The objective of this study was to evaluate the genetic diversity of Korean bermudagrasses at the morphological, cytological and molecular levels. Morphological parameters, the nuclear DNA content and ploidy levels were observed in 43 bermudagrass ecotypes. AFLP markers were evaluated to define the genetic diversity, and chromosome counts were made to confirm the inferred cytotypes. Nuclear DNA contents were in the ranges 1.42-1.56, 1.94-2.19, 2.54, and 2.77-2.85 pg/2C for the triploid, tetraploid, pentaploid, and hexaploid accessions, respectively. The inferred cytotypes were triploid (2n = 3x = 27), tetraploid (2n = 4x = 36), pentaploid (2n = 5x = 45), and hexaploid (2n = 6x = 54), but the majority of the collections were tetraploid (81%). Mitotic chromosome counts verified the corresponding ploidy levels. The fast growing fine-textured ecotypes had lower ploidy levels, while the pentaploids and hexaploids were coarse types. The genetic similarity ranged from 0.42 to 0.94 with an average of 0.64. UPGMA cluster analysis and principle coordinate analysis separated the ecotypes into 6 distinct groups. The genetic similarity suggests natural hybridization between the different cytotypes, which could be useful resources for future breeding and genetic studies.

  12. Molecular Insights into the Genetic Diversity of Hemarthria compressa Germplasm Collections Native to Southwest China

    Directory of Open Access Journals (Sweden)

    Zhi-Hui Guo

    2014-12-01

    Full Text Available Start codon targeted polymorphism (SCoT analysis was employed to distinguish 37 whipgrass (Hemarthria compressa L. clones and assess the genetic diversity and population structure among these genotypes. The informativeness of markers was also estimated using various parameters. Using 25 highly reproducible primer sets, 368 discernible fragments were generated. Of these, 282 (77.21% were polymorphic. The number of alleles per locus ranged from five to 21, and the genetic variation indices varied. The polymorphism information content (PIC was 0.358, the Shannon diversity index (H was 0.534, the marker index (MI was 4.040, the resolving power (RP was 6.108, and the genotype index (GI was 0.782. Genetic similarity coefficients (GS between the accessions ranged from 0.563 to 0.872, with a mean of 0.685. Their patterns observed in a dendrogram constructed using the unweighted pair group method with arithmetic mean analysis (UPGMA based on GS largely confirmed the results of principal coordinate analysis (PCoA. PCoA was further confirmed by Bayesian model-based STRUCTURE analysis, which revealed no direct association between genetic relationship and geographical origins as validated by Mantel’s test (r = 0.2268, p = 0.9999. In addition, high-level genetic variation within geographical groups was significantly greater than that between groups, as determined by Shannon diversity analysis, analysis of molecular variance (AMOVA and Bayesian analysis. Overall, SCoT analysis is a simple, effective and reliable technique for characterizing and maintaining germplasm collections of whipgrass and related species.

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

    Energy Technology Data Exchange (ETDEWEB)

    Augustinos, A.A.; Petropoulos, C.; Karasoulou, V.; Bletsos, F.; Papasotiropoulos, V.

    2016-07-01

    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.

  14. Molecular sequence data of hepatitis B virus and genetic diversity after vaccination.

    Science.gov (United States)

    van Ballegooijen, W Marijn; van Houdt, Robin; Bruisten, Sylvia M; Boot, Hein J; Coutinho, Roel A; Wallinga, Jacco

    2009-12-15

    The effect of vaccination programs on transmission of infectious disease is usually assessed by monitoring programs that rely on notifications of symptomatic illness. For monitoring of infectious diseases with a high proportion of asymptomatic cases or a low reporting rate, molecular sequence data combined with modern coalescent-based techniques offer a complementary tool to assess transmission. Here, the authors investigate the added value of using viral sequence data to monitor a vaccination program that was started in 1998 and was targeted against hepatitis B virus in men who have sex with men in Amsterdam, the Netherlands. The incidence in this target group, as estimated from the notifications of acute infections with hepatitis B virus, was low; therefore, there was insufficient power to show a significant change in incidence. In contrast, the genetic diversity, as estimated from the viral sequence collected from the target group, revealed a marked decrease after vaccination was introduced. Taken together, the findings suggest that introduction of vaccination coincided with a change in the target group toward behavior with a higher risk of infection. The authors argue that molecular sequence data provide a powerful additional monitoring instrument, next to conventional case registration, for assessing the impact of vaccination.

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

    International Nuclear Information System (INIS)

    Augustinos, A.A.; Petropoulos, C.; Karasoulou, V.; Bletsos, F.; Papasotiropoulos, V.

    2016-01-01

    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.

  16. A preliminary molecular phylogeny of shield-bearer moths (Lepidoptera: Adeloidea: Heliozelidae) highlights rich undescribed diversity.

    Science.gov (United States)

    Milla, Liz; van Nieukerken, Erik J; Vijverberg, Ruben; Doorenweerd, Camiel; Wilcox, Stephen A; Halsey, Mike; Young, David A; Jones, Therésa M; Kallies, Axel; Hilton, Douglas J

    2018-03-01

    Heliozelidae are a widespread, evolutionarily early diverging family of small, day-flying monotrysian moths, for which a comprehensive phylogeny is lacking. We generated the first molecular phylogeny of the family using DNA sequences of two mitochondrial genes (COI and COII) and two nuclear genes (H3 and 28S) from 130 Heliozelidae specimens, including eight of the twelve known genera: Antispila, Antispilina, Coptodisca, Heliozela, Holocacista, Hoplophanes, Pseliastis, and Tyriozela. Our results provide strong support for five major Heliozelidae clades: (i) a large widespread clade containing the leaf-mining genera Antispilina, Coptodisca and Holocacista and some species of Antispila, (ii) a clade containing most of the described Antispila, (iii) a clade containing the leaf-mining genus Heliozela and the monotypic genus Tyriozela, (iv) an Australian clade containing Pseliastis and (v) an Australian clade containing Hoplophanes. Each clade includes several new species and potentially new genera. Collectively, our data uncover a rich and undescribed diversity that appears to be especially prevalent in Australia. Our work highlights the need for a major taxonomic revision of the family and for generating a robust molecular phylogeny using multi-gene approaches in order to resolve the relationships among clades. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  17. Molecular markers based identification of diversity for drought tolerance in bread wheat varieties and synthetic hexaploids.

    Science.gov (United States)

    Shah, Zahid Hussain; Munir, Muhammad; Kazi, Abdul Mujeeb; Mujtaba, Tahir; Ahmed, Zaheer

    2009-01-01

    The complexity of the wheat genome has delayed the development and application of molecular markers to this species and wheat now lies behind barley, maize and rice in marker development. However, improvements in marker detection systems and in the techniques used to identify markers linked to useful traits has allowed considerable advances to be made in recent years. To evaluate the genetic diversity 53 genotypes of Richard's selection, were studied at National Agriculture Reseach Center (NARC) Islamabad. The present study found that RAPD analysis is a valuable diagnostic tool. Different sets of RAPD primers were used to study the polymorphism at molecular level. Highest number of amplifications was shown by primer OpG-2 in Richard's material. Coefficient of similarity as well as genetic distances among these three sets of materials was calculated by using Unweighted Pair Group of Arithamatic Means (UPGMA) function (Nei and Li, 1979). The SHs derived genotypes of Richard's selection were highly polymorphic with a polymorphism percentage of 69.70 as compared to NUYT (rainfed) and elite Pakistani bread wheat varieties with a polymorphism of 44.44% and 61.11% respectively. Cluster analysis was done in which grouping of genotypes was done on the basis of genetic distances. Cluster analysis revealed that genotypes of Richard's genotypes are showing high level of among cultivar variation as compared to NUYT (Rainfed) and elite Pakistani drought tolerant bread wheat varieties. These genotypes were also phenotypically evaluated.

  18. 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.

  19. Molecular genetic diversity and population structure of Ethiopian white lupin landraces: Implications for breeding and conservation

    Science.gov (United States)

    Yao, Nasser; Martina, Kyalo; Dagne, Kifle; Wegary, Dagne; Tesfaye, Kassahun

    2017-01-01

    White lupin is one of the four economically important species of the Lupinus genus and is an important grain legume in the Ethiopian farming system. However, there has been limited research effort to characterize the Ethiopian white lupin landraces. Fifteen polymorphic simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 212 Ethiopian white lupin (Lupinus albus) landraces and two genotypes from different species (Lupinus angustifolius and Lupinus mutabilis) were used as out-group. The SSR markers revealed 108 different alleles, 98 of them from 212 landraces and 10 from out-group genotypes, with an average of 6.5 alleles per locus. The average gene diversity was 0.31. Twenty eight landraces harbored one or more private alleles from the total of 28 private alleles identified in the 212 white lupin accessions. Seventy-seven rare alleles with a frequency of less than 5% were identified and accounted for 78.6% of the total alleles detected. Analysis of molecular variance (AMOVA) showed that 92% of allelic diversity was attributed to individual accessions within populations while only 8% was distributed among populations. At 70% similarity level, the UPGMA dendrogram resulted in the formation of 13 clusters comprised of 2 to 136 landraces, with the out-group genotypes and five landraces remaining distinct and ungrouped. Population differentiation and genetic distance were relatively high between Gondar and Ethiopian white lupin populations collected by Australians. A model-based population structure analysis divided the white lupin landraces into two populations. All Ethiopian white lupin landrace populations, except most of the landraces collected by Australians (77%) and about 44% from Awi, were grouped together with significant admixtures. The study also suggested that 34 accessions, as core collections, were sufficient to retain 100% of SSR diversity. These accessions (core G-34) represent 16% of the whole 212

  20. Reconsideration for conservation units of wild Primula sieboldii in Japan based on adaptive diversity and molecular genetic diversity.

    Science.gov (United States)

    Yoshida, Yasuko; Honjo, Masanori; Kitamoto, Naoko; Ohsawa, Ryo

    2009-08-01

    Primula sieboldii E. Morren is a perennial clonal herb that is widely distributed in Japan, but in danger of extinction in the wild. In a previous study, we revealed the genetic diversity of the species using chloroplast and nuclear DNA and used this information to define conservation units. However, we lacked information on adaptive genetic diversity, which is important for long-term survival and, thus, for the definition of conservation units. In order to identify adaptive traits that showed adaptive differentiation among populations, we studied the genetic variation in six quantitative traits within and among populations for 3 years in a common garden using 110 genets from five natural populations from three regions of Japan. The number of days to bud initiation was adaptive quantitative trait for which the degree of genetic differentiation among populations (QST) was considerably larger than that in eight microsatellite markers (FST). The relationship between this trait and environmental factors revealed that the number of days to bud initiation was negatively correlated, with the mean temperature during the growing period at each habitat. This suggests that adaptive differentiation in the delay before bud initiation was caused by selective pressure resulting from temperature differences among habitats. Our results suggest that based on adaptive diversity and neutral genetic diversity, the Saitama population represents a new conservation unit.

  1. Multicomponent domino processes based on the organocatalytic generation of conjugated acetylides: efficient synthetic manifolds for diversity-oriented molecular construction.

    Science.gov (United States)

    Tejedor, David; González-Cruz, David; Santos-Expósito, Alicia; Marrero-Tellado, Jose Juan; de Armas, Pedro; García-Tellado, Fernando

    2005-06-06

    The organocatalytic generation of a strong base by the action of a good nucleophile is the base for the in situ catalytic generation of conjugated acetylides in the presence of aldehydes or activated ketones. The method is affordable in a multicomponent, domino format able to generate a chemically diverse set of multifunctionalized adducts that are very well suited for diversity-oriented molecular construction. The domino process involves a nucleophile as catalyst and a terminal conjugated alkyne (H-C[triple chemical bond]C-Z) and an aldehyde or activated ketone as building blocks. The chemical outcome of this process changes dramatically as a function of the nucleophile (tertiary amine or phosphine), temperature, stoichiometry, and solvent. These multicomponent domino processes achieve molecular construction with good atom economy and, very importantly, with an exquisite chemo-differentiating incorporation of identical starting units into the products (nondegenerated chemical output). These properties convert the H-C[triple chemical bond]C-Z unit into a specific building block for diversity-oriented molecular construction. Applications to the modular and diversity-oriented synthesis of relevant heterocycles are discussed. A protocol involving two coupled domino processes linked in a one-pot manner will be discussed as an efficient synthetic manifold for the modular and diversity-oriented construction of multisubstituted nitrogen-containing heterocycles.

  2. New STS molecular markers for assessment of genetic diversity and DNA fingerprinting in hop (Humulus lupulus L.)

    Czech Academy of Sciences Publication Activity Database

    Patzak, J.; Vrba, Lukáš; Matoušek, Jaroslav

    2007-01-01

    Roč. 50, č. 1 (2007), s. 15-25 ISSN 0831-2796 R&D Projects: GA ČR GA521/03/0072 Institutional research plan: CEZ:AV0Z50510513 Keywords : hop (Humulus lupulus L.) * genetic diversity Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.785, year: 2007

  3. Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity

    Directory of Open Access Journals (Sweden)

    Andrea Hahn

    2018-05-01

    Full Text Available Cystic fibrosis (CF is an autosomal recessive disease associated with recurrent lung infections that can lead to morbidity and mortality. The impact of antibiotics for treatment of acute pulmonary exacerbations on the CF airway microbiome remains unclear with prior studies giving conflicting results and being limited by their use of 16S ribosomal RNA sequencing. Our primary objective was to validate the use of true single molecular sequencing (tSMS and PathoScope in the analysis of the CF airway microbiome. Three control samples were created with differing amounts of Burkholderia cepacia, Pseudomonas aeruginosa, and Prevotella melaninogenica, three common bacteria found in cystic fibrosis lungs. Paired sputa were also obtained from three study participants with CF before and >6 days after initiation of antibiotics. Antibiotic resistant B. cepacia and P. aeruginosa were identified in concurrently obtained respiratory cultures. Direct sequencing was performed using tSMS, and filtered reads were aligned to reference genomes from NCBI using PathoScope and Kraken and unique clade-specific marker genes using MetaPhlAn. A total of 180–518 K of 6–12 million filtered reads were aligned for each sample. Detection of known pathogens in control samples was most successful using PathoScope. In the CF sputa, alpha diversity measures varied based on the alignment method used, but similar trends were found between pre- and post-antibiotic samples. PathoScope outperformed Kraken and MetaPhlAn in our validation study of artificial bacterial community controls and also has advantages over Kraken and MetaPhlAn of being able to determine bacterial strains and the presence of fungal organisms. PathoScope can be confidently used when evaluating metagenomic data to determine CF airway microbiome diversity.

  4. Molecular markers for analyses of intraspecific genetic diversity in the Asian Tiger mosquito, Aedes albopictus.

    Science.gov (United States)

    Manni, Mosè; Gomulski, Ludvik M; Aketarawong, Nidchaya; Tait, Gabriella; Scolari, Francesca; Somboon, Pradya; Guglielmino, Carmela R; Malacrida, Anna R; Gasperi, Giuliano

    2015-03-28

    The dramatic worldwide expansion of Aedes albopictus (the Asian tiger mosquito) and its vector competence for numerous arboviruses represent a growing threat to public health security. Molecular markers are crucially needed for tracking the rapid spread of this mosquito and to obtain a deeper knowledge of population structure. This is a fundamental requirement for the development of strict monitoring protocols and for the improvement of sustainable control measures. Wild population samples from putative source areas and from newly colonised regions were analysed for variability at the ribosomal DNA internal transcribed spacer 2 (ITS2). Moreover, a new set of 23 microsatellite markers (SSR) was developed. Sixteen of these SSRs were tested in an ancestral (Thailand) and two adventive Italian populations. Seventy-six ITS2 sequences representing 52 unique haplotypes were identified, and AMOVA indicated that most of their variation occurred within individuals (74.36%), while only about 8% was detected among populations. Spatial analyses of molecular variance revealed that haplotype genetic similarity was not related to the geographic proximity of populations and the haplotype phylogeny clearly indicated that highly related sequences were distributed across populations from different geographical regions. The SSR markers displayed a high level of polymorphism both in the ancestral and in adventive populations, and F ST estimates suggested the absence of great differentiation. The ancestral nature of the Thai population was corroborated by its higher level of variability. The two types of genetic markers here implemented revealed the distribution of genetic diversity within and between populations and provide clues on the dispersion dynamics of this species. It appears that the diffusion of this mosquito does not conform to a progressive expansion from the native Asian source area, but to a relatively recent and chaotic propagule distribution mediated by human activities

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

    Science.gov (United States)

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

    2014-02-01

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

  6. Molecular diversity of legume root-nodule bacteria in Kakadu National Park, Northern Territory, Australia.

    Directory of Open Access Journals (Sweden)

    Bénédicte Lafay

    2007-03-01

    Full Text Available Symbiotic relationships between leguminous plants (family Fabaceae and nodule-forming bacteria in Australia native ecosystems remain poorly characterized despite their importance. Most studies have focused on temperate parts of the country, where the use of molecular approaches have already revealed the presence of Bradyrhizobium, Ensifer (formerly Sinorhizobium, Mesorhizobium and Rhizobium genera of legume root-nodule bacteria. We here provide the first molecular characterization of nodulating bacteria from tropical Australia.45 nodule-forming bacterial strains, isolated from eight native legume hosts at eight locations in Kakadu National Park, Northern Territory, Australia, were examined for their genetic diversity and phylogenetic position. Using SSU rDNA PCR-RFLPs and phylogenetic analyses, our survey identified nine genospecies, two of which, Bradyrhizobium genospp. B and P, had been previously identified in south-eastern Australia and one, Mesorhizobium genospecies AA, in southern France. Three of the five newly characterized Bradyrhizobium genospecies were more closely related to B. japonicum USDA110, whereas the other two belonged to the B. elkanii group. All five were each more closely related to strains sampled in various tropical areas outside Australia than to strains known to occur in Australia. We also characterized an entirely novel nodule-forming lineage, phylogenetically distant from any previously described rhizobial and non-rhizobial legume-nodulating lineage within the Rhizobiales.Overall, the present results support the hypothesis of tropical areas being centres of biodiversity and diversification for legume root-nodule bacteria and confirm the widespread occurrence of Bradyrhizobium genosp. B in continental Australia.

  7. Genetic Diversity of Some Tunisian Botrytis cinerea Isolates Using Molecular Markers

    Directory of Open Access Journals (Sweden)

    D. ben Ahmed

    2005-12-01

    Full Text Available The genetic diversity of Botrytis cinerea in Tunisia was studied using molecular markers, and the level of resistance to the fungicide fenhexamid was shown. Isolates from different plants (grape, tomato, cucumber, onion, strawberry, gerbera and rose and different parts of the country were analysed in order to determine whether the two groups, transposa and vacuma, that were detected in French vineyards, are also present in Tunisia. A combined PCR and Dot Blot method was developed to identify the transposable elements Boty and Flipper that distinguish between these two B. cinerea groups. Both the transposa and vacuma groups, and isolates containing the transposable element Boty, were found in Tunisia. Moreover, analysis of the Bc-hch locus by PCR and restriction enzyme digestion identified only the B. cinerea group corresponding to one allelic type. Finally, by using the level of resistance shown by B. cinerea to the fungicide fenhexamid as a marker, it was confirmed that this was the only group of B. cinerea in the Tunisian population.

  8. Endohedral Metallofullerene as Molecular High Spin Qubit: Diverse Rabi Cycles in Gd2@C79N.

    Science.gov (United States)

    Hu, Ziqi; Dong, Bo-Wei; Liu, Zheng; Liu, Jun-Jie; Su, Jie; Yu, Changcheng; Xiong, Jin; Shi, Di-Er; Wang, Yuanyuan; Wang, Bing-Wu; Ardavan, Arzhang; Shi, Zujin; Jiang, Shang-Da; Gao, Song

    2018-01-24

    An anisotropic high-spin qubit with long coherence time could scale the quantum system up. It has been proposed that Grover's algorithm can be implemented in such systems. Dimetallic aza[80]fullerenes M 2 @C 79 N (M = Y or Gd) possess an unpaired electron located between two metal ions, offering an opportunity to manipulate spin(s) protected in the cage for quantum information processing. Herein, we report the crystallographic determination of Gd 2 @C 79 N for the first time. This molecular magnet with a collective high-spin ground state (S = 15/2) generated by strong magnetic coupling (J Gd-Rad = 350 ± 20 cm -1 ) has been unambiguously validated by magnetic susceptibility experiments. Gd 2 @C 79 N has quantum coherence and diverse Rabi cycles, allowing arbitrary superposition state manipulation between each adjacent level. The phase memory time reaches 5 μs at 5 K by dynamic decoupling. This molecule fulfills the requirements of Grover's searching algorithm proposed by Leuenberger and Loss.

  9. 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.

  10. 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.

  11. Effects of solar ultraviolet radiation (UVR) on molecular diversity of plankton from the Chubut rivers estuary

    International Nuclear Information System (INIS)

    Manrique, J.M.; Halac, S.; Calvo, A.Y.; Villafane, V.; Jones, L.R.; Helbling, W.E.

    2010-01-01

    Within the framework of a project designed to evaluate the impact of UVR upon estuarine plankton, we present here a molecular analysis of plankton diversity. Water samples were exposed to three radiation treatments (PAR, PAR + UV-A and PAR + UV-A + UV-B) in microcosms for ca 10 days during the Austral summer. At the beginning (t 0 ) and at the end of the experiment samples were filtered 0 through 20, 10, 5 and 0.22 μm pore sizes. The DNA amount retained in each filter indicated that most of the plankton biomass was in the 0.22-5 μm fraction at t0. In contrast, at the end of the experiment this proportion changed according to the radiation treatment and big cells (> 20 μm) dominated. An rDNA library was obtained from the DNA corresponding to the 0.22-5 μm fraction. There was no relationship between treatments and the number and frequency of restriction genotypes. Analyses of 27 clones fraction from t 0 indicated the presence of three genera of Rhodobacteraceae, one genus of Rhodospirillaceae, one SAR11 genus, one genus of Bacillaceae, an unclassified sequences of Alphaproteobacteria, Actinobacteria and Rhodospirillaceae. Also, there were six sequences similar to Ostreococcus tauri (Mamiellales). Even though the sequence analyses are still ongoing, our initial data suggest a big impact of UV-B radiation in the amount and composition of the plankton community towards big cells. (authors)

  12. Transferability of molecular markers from major legumes to Lathyrus spp. for their application in mapping and diversity studies.

    Science.gov (United States)

    Almeida, Nuno Felipe; Trindade Leitão, Susana; Caminero, Constantino; Torres, Ana Maria; Rubiales, Diego; Vaz Patto, Maria Carlota

    2014-01-01

    Lathyrus cicera L. (chickling pea) and L. sativus L. (grass pea) have great potential among grain legumes due to their adaptability to inauspicious environments, high protein content and resistance to serious diseases. Nevertheless, due to its past underused, further activities are required to exploit this potential and to capitalise on the advances in molecular biology that enable improved Lathyrus spp. breeding programmes. In this study we evaluated the transferability of molecular markers developed for closely related legume species to Lathyrus spp. (Medicago truncatula, pea, lentil, faba bean and lupin) and tested the application of those new molecular tools on Lathyrus mapping and diversity studies. Genomic and expressed sequence tag microsatellite, intron-targeted amplified polymorphic, resistance gene analogue and defence-related gene markers were tested. In total 128 (27.7 %) and 132 (28.6 %) molecular markers were successfully cross-amplified, respectively in L. cicera and L. sativus. In total, the efficiency of transferability from genomic microsatellites was 5 %, and from gene-based markers, 55 %. For L. cicera, three cleaved amplified polymorphic sequence markers and one derived cleaved amplified polymorphic sequence marker based on the cross-amplified markers were also developed. Nine of those molecular markers were suitable for mapping in a L. cicera recombinant inbred line population. From the 17 molecular markers tested for diversity analysis, six (35 %) in L. cicera and seven (41 %) in L. sativus were polymorphic and discriminate well all the L. sativus accessions. Additionally, L. cicera accessions were clearly distinguished from L. sativus accessions. This work revealed a high number of transferable molecular markers to be used in current genomic studies in Lathyrus spp. Although their usefulness was higher on diversity studies, they represent the first steps for future comparative mapping involving these species.

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    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

  15. Effect of substituent structure on pyrimidine electrophilic substitution

    CSIR Research Space (South Africa)

    Van der Westhuyzen, CW

    2007-01-01

    Full Text Available In an investigation into the electrophilic nitrosation reactions of a series of 4,6-disubstituted pyrimidine derivatives, a subtle interplay between the electronic nature of the C-4 and C-6 substituents and reactivity was found where these were...

  16. 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.

  17. Effect of substituents on the reactivity of ninhydrin with urea

    NARCIS (Netherlands)

    Jong, Jacobus A.W.; Moret, Marc Etienne; Verhaar, Marianne C.; Hennink, Wim E.; Gerritsen, Karin G.F.; Van Nostrum, Cornelus F.

    2018-01-01

    Ninhydrin, i. e. the stable hydrate of the reactive species indanetrione, is a well-known compound used for the quantification of ammonia and amino acids. However, substituent effects on the reactivity of ninhydrin with nucleophiles are not described. In this work, the kinetics of the reaction of

  18. The impact of phenotypic and molecular data on the inference of Colletotrichum diversity associated with Musa.

    Science.gov (United States)

    Vieira, Willie A S; Lima, Waléria G; Nascimento, Eduardo S; Michereff, Sami J; Câmara, Marcos P S; Doyle, Vinson P

    2017-01-01

    Developing a comprehensive and reliable taxonomy for the Colletotrichum gloeosporioides species complex will require adopting data standards on the basis of an understanding of how methodological choices impact morphological evaluations and phylogenetic inference. We explored the impact of methodological choices in a morphological and molecular evaluation of Colletotrichum species associated with banana in Brazil. The choice of alignment filtering algorithm has a significant impact on topological inference and the retention of phylogenetically informative sites. Similarly, the choice of phylogenetic marker affects the delimitation of species boundaries, particularly if low phylogenetic signal is confounded with strong discordance, and inference of the species tree from multiple-gene trees. According to both phylogenetic informativeness profiling and Bayesian concordance analyses, the most informative loci are DNA lyase (APN2), intergenic spacer (IGS) between DNA lyase and the mating-type locus MAT1-2-1 (APN2/MAT-IGS), calmodulin (CAL), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), glutamine synthetase (GS), β-tubulin (TUB2), and a new marker, the intergenic spacer between GAPDH and an hypothetical protein (GAP2-IGS). Cornmeal agar minimizes the variance in conidial dimensions compared with potato dextrose agar and synthetic nutrient-poor agar, such that species are more readily distinguishable based on phenotypic differences. We apply these insights to investigate the diversity of Colletotrichum species associated with banana anthracnose in Brazil and report C. musae, C. tropicale, C. theobromicola, and C. siamense in association with banana anthracnose. One lineage did not cluster with any previously described species and is described here as C. chrysophilum.

  19. The bladed Bangiales (Rhodophyta) of the South Eastern Pacific: Molecular species delimitation reveals extensive diversity.

    Science.gov (United States)

    Guillemin, Marie-Laure; Contreras-Porcia, Loretto; Ramírez, María Eliana; Macaya, Erasmo C; Contador, Cristian Bulboa; Woods, Helen; Wyatt, Christopher; Brodie, Juliet

    2016-01-01

    A molecular taxonomic study of the bladed Bangiales of the South Eastern Pacific (coast of Chile) was undertaken based on sequence data of the mitochondrial COI and chloroplast rbcL for 193 specimens collected from Arica (18°S) in the north to South Patagonia (53°S) in the south. The results revealed for the first time that four genera, Porphyra, Pyropia, Fuscifolium and Wildemania were present in the region. Species delimitation was determined based on a combination of a General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) coupled with detection of monophyly in tree reconstruction. The overall incongruence between the species delimitation methods within each gene was 29%. The GMYC method led to over-splitting groups, whereas the ABGD method had a tendency to lump groups. Taking a conservative approach to the number of putative species, at least 18 were recognized and, with the exception of the recently described Pyropia orbicularis, all were new to the Chilean flora. Porphyra and Pyropia were the most diverse genera with eight 'species' each, whereas only a 'single' species each was found for Fuscifolium and Wildemania. There was also evidence of recently diverging groups: Wildemania sp. was distinct but very closely related to W. amplissima from the Northern Hemisphere and raises questions in relation to such disjunct distributions. Pyropia orbicularis was very closely related to two other species, making species delimitation very difficult but provides evidence of an incipient speciation. The difference between the 'species' discovered and those previously reported for the region is discussed in relation to the difficulty of distinguishing species based on morphological identification. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Detailed Molecular Epidemiologic Characterization of HIV-1 Infection in Bulgaria Reveals Broad Diversity and Evolving Phylodynamics

    Science.gov (United States)

    Ivanov, Ivailo Alexiev; Beshkov, Danail; Shankar, Anupama; Hanson, Debra L.; Paraskevis, Dimitrios; Georgieva, Viara; Karamacheva, Lyudmila; Taskov, Hristo; Varleva, Tonka; Elenkov, Ivaylo; Stoicheva, Mariana; Nikolova, Daniela; Switzer, William M.

    2013-01-01

    Limited information is available to describe the molecular epidemiology of HIV-1 in Bulgaria. To better understand the genetic diversity and the epidemiologic dynamics of HIV-1 we analyzed 125 new polymerase (pol) sequences from Bulgarians diagnosed through 2009 and 77 pol sequences available from our previous study from persons infected prior to 2007. Epidemiologic and demographic information was obtained from each participant and phylogenetic analysis was used to infer HIV-1 evolutionary histories. 120 (59.5%) persons were infected with one of five different HIV-1 subtypes (A1, B, C, F1 and H) and 63 (31.2%) persons were infected with one of six different circulating recombinant forms (CRFs; 01_AE, 02_AG, 04_cpx, 05_DF, 14_BG, and 36_cpx). We also for the first time identified infection with two different clusters of unique A-like and F-like sub-subtype variants in 12 persons (5.9%) and seven unique recombinant forms (3.5%), including a novel J/C recombinant. While subtype B was the major genotype identified and was more prevalent in MSM and increased between 2000–2005, most non-B subtypes were present in persons ≥45 years old. CRF01_AE was the most common non-B subtype and was higher in women and IDUs relative to other risk groups combined. Our results show that HIV-1 infection in Bulgaria reflects the shifting distribution of genotypes coincident with the changing epidemiology of the HIV-1 epidemic among different risk groups. Our data support increased public health interventions targeting IDUs and MSM. Furthermore, the substantial and increasing HIV-1 genetic heterogeneity, combined with fluctuating infection dynamics, highlights the importance of sustained and expanded surveillance to prevent and control HIV-1 infection in Bulgaria. PMID:23527245

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    2010-01-01

    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. PMID:20678242

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

    Science.gov (United States)

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

    2009-11-01

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

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

    Directory of Open Access Journals (Sweden)

    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.

  5. H2B ubiquitination: Conserved molecular mechanism, diverse physiologic functions of the E3 ligase during meiosis.

    Science.gov (United States)

    Wang, Liying; Cao, Chunwei; Wang, Fang; Zhao, Jianguo; Li, Wei

    2017-09-03

    RNF20/Bre1 mediated H2B ubiquitination (H2Bub) has various physiologic functions. Recently, we found that H2Bub participates in meiotic recombination by promoting chromatin relaxation during meiosis. We then analyzed the phylogenetic relationships among the E3 ligase for H2Bub, its E2 Rad6 and their partner WW domain-containing adaptor with a coiled-coil (WAC) or Lge1, and found that the molecular mechanism underlying H2Bub is evolutionarily conserved from yeast to mammals. However, RNF20 has diverse physiologic functions in different organisms, which might be caused by the evolutionary divergency of their domain/motif architectures. In the current extra view, we not only elucidate the evolutionarily conserved molecular mechanism underlying H2Bub, but also discuss the diverse physiologic functions of RNF20 during meiosis.

  6. Molecular Diversity of Lactic Acid Bacteria on Ileum and Coecum Broiler Chicken Fed by Chrysonilia crassa Fermentation

    Science.gov (United States)

    Nur Jannah, Siti; Khotimah, Husnul; Siti Ferniah, Rejeki; Sugiharto

    2018-05-01

    The Lactid Acid Bakteria (LAB) are microflora in the digestive tract which has positive roles in poultry’s health. One of the factors diversity of LAB in the gatrointestinal tract are influenced by feeding factor. The purpose of this study was to analyze the LAB diversity in ileum and coecum after being fed on fermented Chrysonilia crassa molecularly. LAB species diversity was analysed to provide a baseline profile of the microbial community database on the ileum and coecum digestive tract of broiler chicken of control (commercial feed) and treatment (feed with Chrysonilia crassa fermentation) by the method of Terminal Restriction Fragment Lenght Polymorphism The calculated values werethe number of phylotypes, relative abundace, Shannon-Wiener diversity index (H’), evennes index (E’), and similarity. Group of LAB detected in the control group were Lactobacillus delbrueckii (180 bp), Lactobacillus sp. (187 bp), Lactobacillus plantarum (572 bp), uncultured bacterium (87 bp) and unidentified (50 bp, 582bp). The result of this study showed that by feeding on the fermented Chrysonilia crassa feed had resulted in the decreasing of LAB diversity, i.e. ileum (0.66), coecum (0.48) compared with commercial feed (control) that was ileum (0.84), coecum (1.05).

  7. National survey of molecular bacterial diversity of New Zealand groundwater: relationships between biodiversity, groundwater chemistry and aquifer characteristics.

    Science.gov (United States)

    Sirisena, Kosala A; Daughney, Christopher J; Moreau-Fournier, Magali; Ryan, Ken G; Chambers, Geoffrey K

    2013-12-01

    Groundwater is a vital component of rural and urban water supplies in New Zealand. Although extensive monitoring of chemical and physical properties is conducted due to the high demand for this valuable resource, current information on its bacterial content is limited. However, bacteria provide an immense contribution to drive the biogeochemical processes in the groundwater ecosystem as in any other ecosystem. Therefore, a proper understanding of bacterial diversity is crucial to assess the effectiveness of groundwater management policies. In this study, we investigated the bacterial community structure in NZ groundwater at a national scale using the terminal restriction fragment length polymorphism (T-RFLP) molecular profiling tool and determined the relationships between bacterial diversity and groundwater chemistry, geological parameters and human impact. Considerable bacterial diversity was present and the community structures were strongly related to groundwater chemistry, and in particular to redox potential and human impact, reflecting their potential influence on determination of bacterial diversity. Further, the mean residence time of groundwater also showed relationships with bacterial community structure. These novel findings pertaining to community composition and its relationships with environmental parameters will provide a strong foundation for qualitative exploration of the bacterial diversity in NZ groundwater in relation to sustainable management of this valuable resource. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  8. 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.

  9. Molecular diversity and population structure of the forage grass Hemarthria compressa (Poaceae) in south China based on SRAP markers.

    Science.gov (United States)

    Huang, L-K; Zhang, X-Q; Xie, W-G; Zhang, J; Cheng, L; Yan, H D

    2012-08-16

    Hemarthria compressa is one of the most important and widely utilized forage crops in south China, owing to its high forage yield and capability of adaptation to hot and humid conditions. We examined the population structure and genetic variation within and among 12 populations of H. compressa in south China using sequence-related amplified polymorphism (SRAP) markers. High genetic diversity was found in these samples [percentage polymorphic bands (PPB) = 82.21%, Shannon's diversity index (I) = 0.352]. However, there was relatively low level of genetic diversity at the population level (PPB = 29.17%, I = 0.155). A high degree of genetic differentiation among populations was detected based on other measures and molecular markers (Nei's genetic diversity analysis: G(ST) = 54.19%; AMOVA analysis: F(ST) = 53.35%). The SRAP markers were found to be more efficient than ISSR markers for evaluating population diversity. Based on these findings, we propose changes in sampling strategies for appraising and utilizing the genetic resources of this species.

  10. Prevalence and molecular diversity of invasive Streptococcus dysgalactiae and Streptococcus pyogenes in a German tertiary care medical centre.

    Science.gov (United States)

    Rößler, S; Berner, R; Jacobs, E; Toepfner, N

    2018-05-03

    Prevalence of invasive ß-haemolytic streptococci (BHS) at a tertiary care hospital and molecular diversity of S. pyogenes and S. dysgalactiae was studied. Between 2012 and 2016, all blood culture sets (n = 55,839), CSF (n = 8413) and soft tissue (n = 20,926) samples were analysed for BHS positivity using HYBASE software. Molecular profiles of 99 S. pyogenes and S. dysgalactiae were identified by sequencing of M protein genes (emm types) and multiplex PCR typing of 20 other virulence determinants. Streptococci contributed to 6.2% of blood, 10.7% of CSF and 14.5% of soft tissue isolates, being among the most common invasive isolates. The overall rates of invasive S. pyogenes, S. agalactiae, S. dysgalactiae and S. pneumoniae were 2.4, 4.4, 2.1, and 5.3%. Whereas S. pneumoniae was 1.5% more common in CSF samples, BHS isolates were 2-fold and 11-fold higher in bacteraemia and invasive soft tissue infections. Genetic BHS typing revealed wide molecular diversity of invasive and noninvasive group A and group G BHS, whereas one emm-type (stG62647.0) and no other virulence determinants except scpA were detected in invasive group C BHS. BHS were important invasive pathogens, outpacing S. pneumoniae in bacteraemia and invasive soft tissue infections. The incidence of S. dysgalactiae infections was comparable to that of S. pyogenes even with less diversity of molecular virulence. The results of this study emphasise the need for awareness of BHS invasiveness in humans and the need to develop BHS prevention strategies.

  11. 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

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

    Science.gov (United States)

    Mokuwa, Alfred; Nuijten, Edwin; Okry, Florent; Teeken, Béla; 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

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

    KAUST Repository

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

    2015-01-01

    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

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

    KAUST Repository

    Ahmed, Talaat

    2016-01-01

    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

  15. 'Ogura'-based 'CMS' lines with different nuclear backgrounds of cabbage revealed substantial diversity at morphological and molecular levels.

    Science.gov (United States)

    Parkash, Chander; Kumar, Sandeep; Singh, Rajender; Kumar, Ajay; Kumar, Satish; Dey, Shyam Sundar; Bhatia, Reeta; Kumar, Raj

    2018-01-01

    A comprehensive study on characterization and genetic diversity analysis was carried out in 16 'Ogura'-based 'CMS' lines of cabbage using 14 agro-morphological traits and 29 SSR markers. Agro-morphological characterization depicted considerable variations for different horticultural traits studied. The genotype, ZHA-2, performed better for most of the economically important quantitative traits. Further, gross head weight (0.76), head length (0.60) and head width (0.83) revealed significant positive correlation with net head weight. Dendrogram based on 10 quantitative traits exhibited considerable diversity among different CMS lines and principle component analysis (PCA) indicated that net and gross head weight, and head length and width are the main components of divergence between 16 CMS lines of cabbage. In molecular study, a total of 58 alleles were amplified by 29 SSR primers, averaging to 2.0 alleles in each locus. High mean values of Shannon's Information index (0.62), expected (0.45) and observed (0.32) heterozygosity and polymorphic information content (0.35) depicted substantial polymorphism. Dendrogram based on Jaccard's similarity coefficient constructed two major groups and eight sub-groups, which revealed substantial diversity among different CMS lines. In overall, based on agro-morphological and molecular studies genotype RRMA, ZHA-2 and RCA were found most divergent. Hence, they have immense potential in future breeding programs for the high-yielding hybrid development in cabbage.

  16. Molecular diversity of lactic acid bacteria on ileum broiler chicken fed by bran and bran fermentation

    Science.gov (United States)

    Baniyah, Laelatul; Nur Jannah, Siti; Rukmi, Isworo; Sugiharto

    2018-05-01

    Lactic Acid Bacteria (LAB) is a digestive tract microflora that have a positive role in poultry health. The number and diversity of LAB in the digestive tract affected by several factors, among them was the kind of feed. The purpose of this research was to know diversity of Lactic Acid Bacteria (LAB) ileum broiler’s after feeding with prebiotic bran and Rhizopus oryzae fermented bran which was added to commercial feed. As much as 15 broilers were used to determine the diversity of LAB. All broilers were fed using commercial feed. The control used commercial feed no addition of bran or fermented bran, and commercial feed with fermented bran and nonfermented bran were as a treatment. To determine the diversity of LAB, T-RFLP method was applied. The Hae III and Msp I were used as restriction enzymes. The number of phylotype, relative abundance, Shannon diversity index (H '), evenness (E), and Dominance (D) were examined. The results indicated that the addition of prebiotic bran on commercial feed showed a higher diversity of lactic acid bacteria on broiler’s ileum, compared with control and addition of Rhizopus oryzae fermented bran. LAB group that dominates in the ileum is Lactobacillus sp. and L. delbruecii subs bulgaricus.

  17. 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

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

    Science.gov (United States)

    Deng, Libao; Liang, Qingzhi; He, Xinhua; Luo, Cong; Chen, Hu; Qin, Zhenshi

    2015-01-01

    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.

  19. 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 (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.

  20. 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

  1. 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

  2. Efficiency of Floristic and Molecular Markers to Determine Diversity in Iranian Populations of T. boeoticum

    OpenAIRE

    M. R. Naghavi; M. Maleki; S. F. Tabatabaei

    2009-01-01

    In order to study floristic and molecular classification of common wild wheat (Triticum boeoticum Boiss.), an analysis was conducted on populations of the Triticum boeoticum collected from different regions of Iran. Considering all floristic compositions of habitats, six floristic groups (syntaxa) within the populations were identified. A high level of variation of T. boeoticum also detected using SSR markers. Our results showed that molecular method confirmed the groupin...

  3. Molecular and cytological characterization of the global Musa germplasm collection provides insights into the treasure of banana diversity

    Czech Academy of Sciences Publication Activity Database

    Christelová, Pavla; De Langhe, E.; Hřibová, Eva; Čížková, Jana; Sardos, J.; Hušáková, Markéta; Van den Houwe, I.; Sutanto, A.; Kepler, A.K.; Swennen, R.; Roux, N.; Doležel, Jaroslav

    2017-01-01

    Roč. 26, č. 4 (2017), s. 801-824 ISSN 0960-3115 R&D Projects: GA MŠk(CZ) LO1204; GA MŠk(CZ) LG12021; GA MŠk LG15017 Institutional support: RVO:61389030 Keywords : genetic-linkage map * aab group * balbisiana colla * acuminata colla * black sigatoka * population-structure * marker analysis * flow-cytometry * plantain musa * aflp markers * Classification * Gene bank * Genetic diversity * ITC collection * Microsatellites * Musa Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 2.265, year: 2016

  4. Diversity of radioprobes targeted to tumor angiogenesis on molecular functional imaging

    International Nuclear Information System (INIS)

    Lu Xia; Zhang Huabei

    2013-01-01

    Molecular functional imaging could visualize, characterize, and measure the bio- logical processes including tumor angiogenesis at the molecular and cellular levels in humans and other living systems. The molecular probes labeled by a variety of radionuclide used in the field of the nuclear medicine play pivotal roles in molecular imaging of tumor angiogenesis. However, the regulatory role of different probes in tumor angiogenesis has not been systematically illustrated. The current status of tumor angiogenesis imaging with radiolabeled probes of peptide, monoclonal antibody as well as its fragment, especially nanoparticle-based probes to gain insights into the robust tumor angiogenesis development were summarized. It was recognized that only the probes such as nanoparticle-based probes, which truly target the tumor vasculature rather than tumor cells because of poor extravasation, are really tumor angiogenesis imaging agent. The research of molecular probe targeted to angiogenesis would meet its flourish just after the outstanding improvements in the in vivo stability and biocompatibility, tumor-targeting efficacy, and pharmacokinetics of tumor angiogenesis imaging probes are made. Translation to clinical applications will also be critical for the maximize benefits of these novel agents. The future of tumor angiogenesis imaging lies in liable imaging probes and multiple imaging modalities, imaging of protein-protein interactions, and quantitative molecular imaging. (authors)

  5. Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods.

    Science.gov (United States)

    Pudasaini, Sarita; Wilson, John; Ji, Mukan; van Dorst, Josie; Snape, Ian; Palmer, Anne S; Burns, Brendan P; Ferrari, Belinda C

    2017-01-01

    Browning Peninsula is an ice-free polar desert situated in the Windmill Islands, Eastern Antarctica. The entire site is described as a barren landscape, comprised of frost boils with soils dominated by microbial life. In this study, we explored the microbial diversity and edaphic drivers of community structure across this site using traditional cultivation methods, a novel approach the soil substrate membrane system (SSMS), and culture-independent 454-tag pyrosequencing. The measured soil environmental and microphysical factors of chlorine, phosphate, aspect and elevation were found to be significant drivers of the bacterial community, while none of the soil parameters analyzed were significantly correlated to the fungal community. Overall, Browning Peninsula soil harbored a distinctive microbial community in comparison to other Antarctic soils comprised of a unique bacterial diversity and extremely limited fungal diversity. Tag pyrosequencing data revealed the bacterial community to be dominated by Actinobacteria (36%), followed by Chloroflexi (18%), Cyanobacteria (14%), and Proteobacteria (10%). For fungi, Ascomycota (97%) dominated the soil microbiome, followed by Basidiomycota. As expected the diversity recovered from culture-based techniques was lower than that detected using tag sequencing. However, in the SSMS enrichments, that mimic the natural conditions for cultivating oligophilic "k-selected" bacteria, a larger proportion of rare bacterial taxa (15%), such as Blastococcus, Devosia, Herbaspirillum, Propionibacterium and Methylocella and fungal (11%) taxa, such as Nigrospora, Exophiala, Hortaea , and Penidiella were recovered at the genus level. At phylum level, a comparison of OTU's showed that the SSMS shared 21% of Acidobacteria, 11% of Actinobacteria and 10% of Proteobacteria OTU's with soil. For fungi, the shared OTUs was 4% (Basidiomycota) and <0.5% (Ascomycota). This was the first known attempt to culture microfungi using the SSMS which resulted in

  6. 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.

  7. 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.

  8. Molecular genetic diversity assessment of Citrus species grown in Iran revealed by SSR, ISSR and CAPS molecular markers

    Directory of Open Access Journals (Sweden)

    Ata Allah Sharafi

    2017-12-01

    Full Text Available In this study, genetic diversity in 19 citrus cultivars was analyzed using Simple Sequence Repeat (SSR, Inter-simple Sequence Repeat (ISSR and cleaved amplified polymorphic sequence (CAPS markers. Nine primers for SSR, nine ISSR primers and two primers for CAPS were used for allele scoring. One chloroplast DNA region (rbcL-ORF106 and one mitochondrial DNA region (18S-5S were analyzed using cleaved amplified polymorphic sequence (CAPS marker in 19 citrus accessions grown in Iran. In total, 45 SSR and 131 ISSR polymorphic alleles and tree organelle genome types were detected. Cluster analysis of SSR and ISSR data was performed using UPGMA method and based on Jaccard's coefficient. The result of this investigation showed that the SSR and ISSR primers were highly informative and efficient in detecting genetic variability and relationships of the citrus accessions. And CAPS marker analysis Results showed that Bakraee and one of off type Mexican lime had banding pattern similar to Clementine Mandarin, while Pummelo regarded as maternal parent of other studied genotypes Citron regarded as father parent showed definite banding pattern among 19 studied genotypes which it confirmed Cytoplasmic inheritance from mother cellular organelles.

  9. 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.

  10. Map-based molecular diversity, linkage disequilibrium and association mapping of fruit traits in melon

    Science.gov (United States)

    The wide phenotypic diversity, in melon fruits, is the result of consumer preferences combined with genotype fitness to the different agro-climatic zones. There is no sufficient information with respect to the extent of genetic divergence, population structure and linkage disequilibrium (LD) in mel...

  11. Molecular identification of hybrids from a former hot spot of Potamogeton hybrid diversity

    Czech Academy of Sciences Publication Activity Database

    Kaplan, Zdeněk; Fehrer, Judith

    2013-01-01

    Roč. 105, Feb 2013 (2013), s. 34-40 ISSN 0304-3770 R&D Projects: GA ČR GA206/09/0291 Institutional support: RVO:67985939 Keywords : hybridization * taxonomy * diversity Subject RIV: EF - Botanics Impact factor: 1.471, year: 2013

  12. 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...

  13. Molecular method to assess the diversity of Burkholderia species in environmental samples

    NARCIS (Netherlands)

    Salles, J.; Souza, de F.A.; Elsas, van J.D.

    2002-01-01

    In spite of the importance of many members of the genus Burkholderia in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. The aim of this work was the development of soil DNA-based PCR-denaturing gradient gel electrophoresis (DGGE), a

  14. Molecular method to assess the diversity of Burkholderia species in environmental samples

    NARCIS (Netherlands)

    Salles, Joanna; De Souza, F.A.; Van Elsas, J.D.

    2002-01-01

    In spite of the importance of many members of the genus Burkholderia in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. The aim of this work was the development of soil DNA-based PCR-denaturing gradient get electrophoresis (DGGE), a

  15. Molecular diversity of Theileria parva : a case study of Kilosa district ...

    African Journals Online (AJOL)

    Theileria parva is an apicomplexan protozoan parasite which causes East Coast fever (ECF) in Eastern and Central Africa. A study was conducted between February and May 2012 in Morogoro region to determine the diversity of the T. Parva parasite circulating in cattle in Kilosa district. Also ECF cases reported between ...

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. Molecular Characterization and Genetic Diversity of the Macaw Palm Ex Situ Germplasm Collection Revealed by Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Fekadu G. Mengistu

    2016-10-01

    Full Text Available Macaw palm (Acrocomia aculeata is native to tropical forests in South America and highly abundant in Brazil. It is cited as a highly productive oleaginous palm tree presenting high potential for biodiesel production. The aim of this work was to characterize and study the genetic diversity of A. aculeata ex situ collections from different geographical states in Brazil using microsatellite (Simple Sequence Repeats, SSR markers. A total of 192 accessions from 10 provenances were analyzed with 10 SSR, and variations were detected in allelic diversity, polymorphism, and heterozygosity in the collections. Three major groups of accessions were formed using PCoA—principal coordinate analysis, UPGMA—unweighted pair-group method with arithmetic mean, and Tocher. The Mantel test revealed a weak correlation (r = 0.07 between genetic and geographic distances among the provenances reaffirming the result of the grouping. Reduced average heterozygosity (Ho < 50% per locus (or provenance confirmed the predominance of endogamy (or inbreeding in the germplasm collections as evidenced by positive inbreeding coefficient (F > 0 per locus (or per provenance. AMOVA—Analysis of Molecular Variance revealed higher (48.2% genetic variation within population than among populations (36.5%. SSR are useful molecular markers in characterizing A. aculeata germplasm and could facilitate the process of identifying, grouping, and selecting genotypes. Present results could be used to formulate appropriate conservation strategies in the genebank.

  2. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice.

    Directory of Open Access Journals (Sweden)

    Sharat Kumar Pradhan

    Full Text Available Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright's F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.

  3. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice.

    Science.gov (United States)

    Pradhan, Sharat Kumar; Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai; Pandit, Elssa

    2016-01-01

    Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright's F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.

  4. 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.

  5. Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.

    Directory of Open Access Journals (Sweden)

    Ganal Martin W

    2006-01-01

    Full Text Available Abstract Background The goal of our study was a systematic survey of the molecular diversity in barley genetic resources. To this end 953 cultivated barley accessions originating from all inhabited continents except Australia were genotyped with 48 SSR markers. Molecular diversity was evaluated with routine statistics (allelic richness, gene diversity, allele frequency, heterozygosity and unique alleles, Principal Coordinate Analysis (PCoA, and analysis of genome-wide linkage disequilibrium. Results A genotyping database for 953 cultivated barley accessions profiled with 48 SSR markers was established. The PCoA revealed structuring of the barley population with regard to (i geographical regions and (ii agronomic traits. Geographic origin contributed most to the observed molecular diversity. Genome-wide linkage disequilibrium (LD was estimated as squared correlation of allele frequencies (r2. The values of LD for barley were comparable to other plant species (conifers, poplar, maize. The pattern of intrachromosomal LD with distances between the genomic loci ranging from 1 to 150 cM revealed that in barley LD extended up to distances as long as 50 cM with r2 > 0.05, or up to 10 cM with r2 > 0.2. Few loci mapping to different chromosomes showed significant LD with r2 > 0.05. The number of loci in significant LD as well as the pattern of LD were clearly dependent on the population structure. The LD in the homogenous group of 207 European 2-rowed spring barleys compared to the highly structured worldwide barley population was increased in the number of loci pairs with r2 > 0.05 and had higher values of r2, although the percentage of intrachromosomal loci pairs in significant LD based on P 0.80 provided higher LD values as compared to 19 low polymorphic loci (PIC Conclusion A global population of cultivated barley accessions was highly structured. Clustering highlighted the accessions with the same geographic origin, as well as accessions possessing

  6. Genetic diversity in the oral pathogen Porphyromonas gingivalis: molecular mechanisms and biological consequences

    Science.gov (United States)

    Tribble, Gena D; Kerr, Jennifer E; Wang, Bing-Yan

    2013-01-01

    Porphyromonas gingivalis is a Gram-negative anaerobic bacterium that colonizes the human oral cavity. It is implicated in the development of periodontitis, a chronic periodontal disease affecting half of the adult population in the USA. To survive in the oral cavity, these bacteria must colonize dental plaque biofilms in competition with other bacterial species. Long-term survival requires P. gingivalis to evade host immune responses, while simultaneously adapting to the changing physiology of the host and to alterations in the plaque biofilm. In reflection of this highly variable niche, P. gingivalis is a genetically diverse species and in this review the authors summarize genetic diversity as it relates to pathogenicity in P. gingivalis. Recent studies revealing a variety of mechanisms by which adaptive changes in genetic content can occur are also reviewed. Understanding the genetic plasticity of P. gingivalis will provide a better framework for understanding the host–microbe interactions associated with periodontal disease. PMID:23642116

  7. Molecular sequence data of hepatitis B virus and genetic diversity after vaccination

    NARCIS (Netherlands)

    van Ballegooijen, W. Marijn; van Houdt, Robin; Bruisten, Sylvia M.; Boot, Hein J.; Coutinho, Roel A.; Wallinga, Jacco

    2009-01-01

    The effect of vaccination programs on transmission of infectious disease is usually assessed by monitoring programs that rely on notifications of symptomatic illness. For monitoring of infectious diseases with a high proportion of asymptomatic cases or a low reporting rate, molecular sequence data

  8. 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...

  9. 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

    Background: The aim of this study was to investigate whether the diagnosis of infective endocarditis (IE) could be improved using molecular tools in addition to standard microscopy and cultivation methods. Methods: Cultivation was performed on blood or tissue samples as recommended in the modified...

  10. Assessment of Genetic Diversity in Opuntia spp. Portuguese Populations Using SSR Molecular Markers

    Directory of Open Access Journals (Sweden)

    Carlos M. G. Reis

    2018-04-01

    Full Text Available The Opuntia spp., most likely few individuals, were introduced in the Iberian Peninsula in the beginning of the 16th century, after the discovery of America, spreading afterwards throughout the Mediterranean basin. We analysed, for the first time, the genetic diversity in a set of 19 Portuguese Opuntia spp. populations from the species O. ficus-indica, O. elata, O. dillenii and O. robusta using nuclear microsatellite (nuSSR markers. The Italian cultivars ‘Bianca’, ‘Gialla’ and ‘Rossa’ were included in the study for comparison purposes. The nuSSR amplifications produced from five to 16 alleles, with an average of 9.2 alleles per primer pair, and average polymorphism information content of 0.71. The estimated Dice coefficient among populations varied from 0.26 to 1.0, indicating high interspecific genetic diversity but low genetic diversity at the intraspecific level. The hierarchical clustering analysis revealed four major groups that clearly separated the four Opuntia species. Among the O. ficus-indica populations, two sub-clusters were found, one including the white pulp fruits (with cv. Bianca and the other with the orange pulp ones and including the cv. Gialla, the cv. Rossa, and one pale yellow pulp population. No genetic differences were found between the inermis form, O. ficus-indica f. ficus-indica, and the rewilded spiny one, O. ficus-indica f. amyclaea. The dendrogram indicated that the clustering pattern was unrelated to geographical origin. The results revealed a low level of genetic diversity among the Portuguese populations of O. ficus-indica.

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

    Czech Academy of Sciences Publication Activity Database

    Soldánová, Miroslava; Georgieva, Simona; Roháčová, Jana; Knudsen, R.; Kuhn, J. A.; Henriksen, E. H.; Siwertsson, A.; Shaw, J. C.; Kuris, A. M.; Amundsen, P.-A.; Scholz, Tomáš; Lafferty, K. D.; Kostadinova, Aneta

    2017-01-01

    Roč. 47, č. 6 (2017), s. 327-345 ISSN 0020-7519 R&D Projects: GA ČR GA15-14198S; GA ČR GAP505/10/1562 Institutional support: RVO:60077344 Keywords : Trematode diversity * intermediate hosts * phylogeny * mitochondrial DNA * nuclear DNA * Lake Takvatn * Norway * Sub-Arctic Subject RIV: EG - Zoology OBOR OECD: Zoology Impact factor: 3.730, year: 2016

  12. Molecular phylogeny of mangroves IV. nature and extent of intra-specific genetic variation and species diversity in mangroves

    International Nuclear Information System (INIS)

    Parida, A.; Parani, M.; Lakshmi, M.; Elango, S.; Ram, N.; Anuratha, C.S.

    1998-01-01

    Mangroves occupy estuarine ecosystems in the tropical regions of the world. Despite their highly productive nature and the protective roles they play in the coastal region, the ecosystem as a whole is under severe threat due to various climatic and anthropogenic factors. Therefore, the need for conservation of mangroves is widely emphasised. However, information on existing genetic diversity based on which a strategy for genetic conservation is to be drawn is not available for mangroves. This is primarily because conventional genetic analysis is difficult in these species for various reasons. Therefore, as an aid to our on-going conservation programme, efforts were made to assess the nature and extent of diversity in a number of mangrove species of the Indian coast using molecular markers. The nature and extent of intra-population diversity in sixteen mangrove species and detailed analysis of inter-population genetic polymorphism in four species, Acanthus ilicifolius, Excoecaria agallocha, Avicennia spp and Rhizophora (species and hybrid), is reported in the present communication. (author)

  13. Molecular phylogeny of mangroves IV. nature and extent of intra-specific genetic variation and species diversity in mangroves

    Energy Technology Data Exchange (ETDEWEB)

    Parida, A; Parani, M; Lakshmi, M; Elango, S; Ram, N; Anuratha, C S [M.S. Swaminathan Research Foundation, Taramani, Madras (India)

    1998-10-01

    Mangroves occupy estuarine ecosystems in the tropical regions of the world. Despite their highly productive nature and the protective roles they play in the coastal region, the ecosystem as a whole is under severe threat due to various climatic and anthropogenic factors. Therefore, the need for conservation of mangroves is widely emphasised. However, information on existing genetic diversity based on which a strategy for genetic conservation is to be drawn is not available for mangroves. This is primarily because conventional genetic analysis is difficult in these species for various reasons. Therefore, as an aid to our on-going conservation programme, efforts were made to assess the nature and extent of diversity in a number of mangrove species of the Indian coast using molecular markers. The nature and extent of intra-population diversity in sixteen mangrove species and detailed analysis of inter-population genetic polymorphism in four species, Acanthus ilicifolius, Excoecaria agallocha, Avicennia spp and Rhizophora (species and hybrid), is reported in the present communication. (author) 25 refs, 2 figs, 2 tabs

  14. Genetic diversity and molecular evolution of Naga King Chili inferred from internal transcribed spacer sequence of nuclear ribosomal DNA.

    Science.gov (United States)

    Kehie, Mechuselie; Kumaria, Suman; Devi, Khumuckcham Sangeeta; Tandon, Pramod

    2016-02-01

    Sequences of the Internal Transcribed Spacer (ITS1-5.8S-ITS2) of nuclear ribosomal DNAs were explored to study the genetic diversity and molecular evolution of Naga King Chili. Our study indicated the occurrence of nucleotide polymorphism and haplotypic diversity in the ITS regions. The present study demonstrated that the variability of ITS1 with respect to nucleotide diversity and sequence polymorphism exceeded that of ITS2. Sequence analysis of 5.8S gene revealed a much conserved region in all the accessions of Naga King Chili. However, strong phylogenetic information of this species is the distinct 13 bp deletion in the 5.8S gene which discriminated Naga King Chili from the rest of the Capsicum sp. Neutrality test results implied a neutral variation, and population seems to be evolving at drift-mutation equilibrium and free from directed selection pressure. Furthermore, mismatch analysis showed multimodal curve indicating a demographic equilibrium. Phylogenetic relationships revealed by Median Joining Network (MJN) analysis denoted a clear discrimination of Naga King Chili from its closest sister species (Capsicum chinense and Capsicum frutescens). The absence of star-like network of haplotypes suggested an ancient population expansion of this chili.

  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. Genetic Diversity and Molecular Evolution of a Violaxanthin De-epoxidase Gene in Maize.

    Science.gov (United States)

    Xu, Jing; Li, Zhigang; Yang, Haorui; Yang, Xiaohong; Chen, Cuixia; Li, Hui

    2016-01-01

    Violaxanthin de-epoxidase (VDE) has a critical role in the carotenoid biosynthesis pathway, which is involved in protecting the photosynthesis apparatus from damage caused by excessive light. Here, a VDE gene in maize, ZmVDE1, was cloned and shown to have functional domains in common with the gramineous VDE protein. Candidate gene association analysis indicated that no polymorphic sites in ZmVDE1 were significant association with any of the examined carotenoid-related traits at P = 0.05 in an association panel containing 155 maize inbred lines. Nucleotide diversity analysis of VDE1 in maize and teosinte indicated that its exon had less genetic variation, consistent with the conserved function of VDE1 in plants. In addition, dramatically reduced nucleotide diversity, fewer haplotypes and a significantly negative parameter deviation for Tajima's D test of ZmVDE1 in maize and teosinte suggested that a potential selective force had acted across the ZmVDE1 locus. We further identified a 4.2 Mb selective sweep with low recombination surrounding the ZmVDE1 locus that resulted in severely reduced nucleotide diversity on chromosome 2. Collectively, natural selection and the conserved domains of ZmVDE1 might show an important role in the xanthophyll cycle of the carotenoid biosynthesis pathway.

  17. Genetic Diversity and Molecular Evolution of a Violaxanthin De-Epoxidase Gene in Maize

    Directory of Open Access Journals (Sweden)

    Jing Xu

    2016-07-01

    Full Text Available Violaxanthin de-epoxidase (VDE has a critical role in the carotenoid biosynthesis pathway, which is involved in protecting the photosynthesis apparatus from damage caused by excessive light. Here, a VDE gene in maize, ZmVDE1, was cloned and shown to have functional domains in common with the gramineous VDE protein. Candidate gene association analysis indicated that no polymorphic sites in ZmVDE1 were significant association with any of the examined carotenoid-related traits at P = 0.05 in an association panel containing 155 maize inbred lines. Nucleotide diversity analysis of VDE1 in maize and teosinte indicated that its exon had less genetic variation, consistent with the conserved function of VDE1 in plants. In addition, dramatically reduced nucleotide diversity, fewer haplotypes and a significantly negative parameter deviation for Tajima’s D test of ZmVDE1 in maize and teosinte suggested that a potential selective force had acted across the ZmVDE1 locus. We further identified a 4.2 Mb selective sweep with low recombination surrounding the ZmVDE1 locus that resulted in severely reduced nucleotide diversity on chromosome 2. Collectively, natural selection and the conserved domains of ZmVDE1 might show an important role in the xanthophyll cycle of the carotenoid biosynthesis pathway.

  18. 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.

  19. A molecular epidemiological study of var gene diversity to characterize the reservoir of Plasmodium falciparum in humans in Africa.

    Directory of Open Access Journals (Sweden)

    Donald S Chen

    2011-02-01

    Full Text Available The reservoir of Plasmodium infection in humans has traditionally been defined by blood slide positivity. This study was designed to characterize the local reservoir of infection in relation to the diverse var genes that encode the major surface antigen of Plasmodium falciparum blood stages and underlie the parasite's ability to establish chronic infection and transmit from human to mosquito.We investigated the molecular epidemiology of the var multigene family at local sites in Gabon, Senegal and Kenya which differ in parasite prevalence and transmission intensity. 1839 distinct var gene types were defined by sequencing DBLα domains in the three sites. Only 76 (4.1% var types were found in more than one population indicating spatial heterogeneity in var types across the African continent. The majority of var types appeared only once in the population sample. Non-parametric statistical estimators predict in each population at minimum five to seven thousand distinct var types. Similar diversity of var types was seen in sites with different parasite prevalences.Var population genomics provides new insights into the epidemiology of P. falciparum in Africa where malaria has never been conquered. In particular, we have described the extensive reservoir of infection in local African sites and discovered a unique var population structure that can facilitate superinfection through minimal overlap in var repertoires among parasite genomes. Our findings show that var typing as a molecular surveillance system defines the extent of genetic complexity in the reservoir of infection to complement measures of malaria prevalence. The observed small scale spatial diversity of var genes suggests that var genetics could greatly inform current malaria mapping approaches and predict complex malaria population dynamics due to the import of var types to areas where no widespread pre-existing immunity in the population exists.

  20. A Molecular Epidemiological Study of var Gene Diversity to Characterize the Reservoir of Plasmodium falciparum in Humans in Africa

    Science.gov (United States)

    Leliwa-Sytek, Aleksandra; Smith, Terry-Ann; Peterson, Ingrid; Brown, Stuart M.; Migot-Nabias, Florence; Deloron, Philippe; Kortok, Moses M.; Marsh, Kevin; Daily, Johanna P.; Ndiaye, Daouda; Sarr, Ousmane; Mboup, Souleymane; Day, Karen P.

    2011-01-01

    Background The reservoir of Plasmodium infection in humans has traditionally been defined by blood slide positivity. This study was designed to characterize the local reservoir of infection in relation to the diverse var genes that encode the major surface antigen of Plasmodium falciparum blood stages and underlie the parasite's ability to establish chronic infection and transmit from human to mosquito. Methodology/Principal Findings We investigated the molecular epidemiology of the var multigene family at local sites in Gabon, Senegal and Kenya which differ in parasite prevalence and transmission intensity. 1839 distinct var gene types were defined by sequencing DBLα domains in the three sites. Only 76 (4.1%) var types were found in more than one population indicating spatial heterogeneity in var types across the African continent. The majority of var types appeared only once in the population sample. Non-parametric statistical estimators predict in each population at minimum five to seven thousand distinct var types. Similar diversity of var types was seen in sites with different parasite prevalences. Conclusions/Significance Var population genomics provides new insights into the epidemiology of P. falciparum in Africa where malaria has never been conquered. In particular, we have described the extensive reservoir of infection in local African sites and discovered a unique var population structure that can facilitate superinfection through minimal overlap in var repertoires among parasite genomes. Our findings show that var typing as a molecular surveillance system defines the extent of genetic complexity in the reservoir of infection to complement measures of malaria prevalence. The observed small scale spatial diversity of var genes suggests that var genetics could greatly inform current malaria mapping approaches and predict complex malaria population dynamics due to the import of var types to areas where no widespread pre-existing immunity in the population

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

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    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.

  2. Exploring the diversity and distribution of neotropical avian malaria parasites--a molecular survey from Southeast Brazil.

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    Gustavo A Lacorte

    Full Text Available Southeast Brazil is a neotropical region composed of a mosaic of different tropical habitats and mountain chains, which allowed for the formation of bird-rich communities with distinct ecological niches. Although this region has the potential to harbor a remarkable variety of avian parasites, there is a lack of information about the diversity of malarial parasites. We used molecular approaches to characterize the lineage diversity of Plasmodium and Haemoproteus in bird communities from three different habitats in southeast Brazil based on the prevalence, richness and composition of lineages. We observed an overall prevalence of 35.3%, with a local prevalence ranging from 17.2% to 54.8%. Moreover, no significant association between prevalence and habitat type could be verified (p>0.05. We identified 89 Plasmodium and 22 Haemoproteus lineages, with 86% of them described for the first time here, including an unusual infection of a non-columbiform host by a Haemoproteus (Haemoproteus parasite. The composition analyses of the parasite communities showed that the lineage composition from Brazilian savannah and tropical dry forest was similar, but it was different from the lineage composition of Atlantic rainforest, reflecting the greater likeness of the former habitats with respect to seasonality and forest density. No significant effects of habitat type on lineage richness were observed based on GLM analyses. We also found that sites whose samples had a greater diversity of bird species showed a greater diversity of parasite lineages, providing evidence that areas with high bird richness also have high parasite richness. Our findings point to the importance of the neotropical region (southeast Brazil as a major reservoir of new haemosporidian lineages.

  3. The diverse and expanding role of mass spectrometry in structural and molecular biology.

    Science.gov (United States)

    Lössl, Philip; van de Waterbeemd, Michiel; Heck, Albert Jr

    2016-12-15

    The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes. © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

  4. Study of inter species diversity and population structure by molecular genetic method in Iranian Artemia

    OpenAIRE

    Hajirostamloo, Mahbobeh

    2005-01-01

    Artemia is a small crustacean that adapted to live in brine water and has been seen in different brine water sources in Iran. Considering the importance of genetic studies manifest inter population differences in species, to estimate genetic structure, detect difference at molecular level and separate different Artemia populations of Iran, also study of phylogenic relationships among them, samples of Artemia were collected from nine region: Urmia lake in West Azerbaijan, Sh...

  5. Molecular diversity of thermophilic bacteria isolated from Pasinler hot spring (Erzurum, Turkey)

    OpenAIRE

    ADIGÜZEL, Ahmet; İNAN, Kadriye; ŞAHİN, Fikrettin; ARASOĞLU, Tulin; GÜLLÜCE, Medine

    2011-01-01

    The present study was conducted to determine the phenotypic and genotypic characterization of thermophilic bacteria isolated from Pasinler hot spring, Erzurum, Turkey. Fatty acid profiles, BOX PCR fingerprints, and 16S rDNA sequence data were used for the phenotypic and genotypic characterization of thermophilic bacteria. Totally 9 different bacterial strains were selected based on morphological, physiological, and biochemical tests. These strains were characterized by molecular tests includi...

  6. The centroidal algorithm in molecular similarity and diversity calculations on confidential datasets

    Science.gov (United States)

    Trepalin, Sergey; Osadchiy, Nikolay

    2005-09-01

    Chemical structure provides exhaustive description of a compound, but it is often proprietary and thus an impediment in the exchange of information. For example, structure disclosure is often needed for the selection of most similar or dissimilar compounds. Authors propose a centroidal algorithm based on structural fragments (screens) that can be efficiently used for the similarity and diversity selections without disclosing structures from the reference set. For an increased security purposes, authors recommend that such set contains at least some tens of structures. Analysis of reverse engineering feasibility showed that the problem difficulty grows with decrease of the screen's radius. The algorithm is illustrated with concrete calculations on known steroidal, quinoline, and quinazoline drugs. We also investigate a problem of scaffold identification in combinatorial library dataset. The results show that relatively small screens of radius equal to 2 bond lengths perform well in the similarity sorting, while radius 4 screens yield better results in diversity sorting. The software implementation of the algorithm taking SDF file with a reference set generates screens of various radii which are subsequently used for the similarity and diversity sorting of external SDFs. Since the reverse engineering of the reference set molecules from their screens has the same difficulty as the RSA asymmetric encryption algorithm, generated screens can be stored openly without further encryption. This approach ensures an end user transfers only a set of structural fragments and no other data. Like other algorithms of encryption, the centroid algorithm cannot give 100% guarantee of protecting a chemical structure from dataset, but probability of initial structure identification is very small-order of 10-40 in typical cases.

  7. Molecular detection and sequence characterization of diverse rhabdoviruses in bats, China.

    Science.gov (United States)

    Xu, Lin; Wu, Jianmin; Jiang, Tinglei; Qin, Shaomin; Xia, Lele; Li, Xingyu; He, Biao; Tu, Changchun

    2018-01-15

    The Rhabdoviridae is among the most diverse families of RNA viruses and currently classified into 18 genera with some rhabdoviruses lethal to humans and other animals. Herein, we describe genetic characterization of three novel rhabdoviruses from bats in China. Of these, two viruses (Jinghong bat virus and Benxi bat virus) found in Rhinolophus bats showed a phylogenetic relationship with vesiculoviruses, and sequence analyses indicate that they represent two new species within the genus Vesiculovirus. The remaining Yangjiang bat virus found in Hipposideros larvatus bats were only distantly related to currently known rhabdoviruses. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. 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. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Genetic diversity, identification, and certification of Chilean rice varieties using molecular markers

    Directory of Open Access Journals (Sweden)

    Viviana Becerra

    2015-09-01

    Full Text Available It takes approximately 14 yr to produce a new rice (Oryza sativa L. variety, that is, from initial hybridization to its commercial release. Currently, new varieties are identified based on morphological descriptors, which have been efficient over time. However, due to the main constraints on seed type impose to other breeding objectives and the pressure of continuous release of varieties, high degree of parentage, and genetic and morphological uniformity has been observed in the breeding populations. The objectives of this study were: to determine the genetic variability of Chilean and foreign commercial rice varieties, and determine, identify, and certify the genetic relationships among varieties, using simple sequence repeat (SSR markers. A total of 16 commercial varieties, some of them closely related, were included in the study, which were genétically analyzed using 54 microsatellites. The 54 microsatellite loci allowed the discrimination among the 16 varieties. The number of alleles ranged between 2 and 8 with a mean of 3.54 alleles per locus, while the polymorphism information content (PIC presented a mean of 0.44. The genetic distance and diversity parameters between pairs of varieties indicate a limited diversity among these genotypes. The cluster analysis indicated that varieties were grouped according to their grain type and pedigree. Results demonstrate that the identification and certification of varieties using microsatellite markers could be a good complement to existing agro-morphological data when varieties are closed related.

  10. A molecular study of genetic diversity in shisham (Dalbergia Sissoo) plantation of NWFP, Pakistan

    Energy Technology Data Exchange (ETDEWEB)

    Ashraf, M; Tabassum, S [Nation al Univ. of Science and Technology, Islamabad (Pakistan). Dept. of Plant Sciences; Mumtaz, S; Riasat, R [Quaid-i-Azam Univ., Islamabad (Pakistan)

    2010-02-15

    Genetic diversity of 22 accessions of Dalbergia sissoo that were collected from the canal, road and farmer's field and forest sites of N.W.F.P, Pakistan has been studied, by using a finger printing technique 'RAPD' (Random Amplified Polymorphism DNA). Out of 20 primers OPA-2 was the primer that allows distinguishing the diseased and healthy accessions. The selected primer was used for identification and for establishing a profiling system to estimate genetic relationships and to evaluate the genetic variability among the accessions. A total of 126 DNA bands or fragments were amplified by using the primers. The UPGMA cluster analysis revealed 2 main clusters among 22 accessions of Dalbergia sissoo based on coefficient of similarity and dissimilarity. Overall 72% similarity and 98% dissimilarity were observed. Low level of genetic variation and high level of genetic relatedness occurred among the canal, road, farmer's field and forest sites. The accessions were closely related with each other and showed mix pattern of genetic diversity. Thus RAPD markers have the potential to characterize and establish genetic relationships among the accessions of Dalbergia sissoo. (author)

  11. A molecular study of genetic diversity in shisham (Dalbergia Sissoo) plantation of NWFP, Pakistan

    International Nuclear Information System (INIS)

    Ashraf, M.; Tabassum, S.

    2010-01-01

    Genetic diversity of 22 accessions of Dalbergia sissoo that were collected from the canal, road and farmer's field and forest sites of N.W.F.P, Pakistan has been studied, by using a finger printing technique 'RAPD' (Random Amplified Polymorphism DNA). Out of 20 primers OPA-2 was the primer that allows distinguishing the diseased and healthy accessions. The selected primer was used for identification and for establishing a profiling system to estimate genetic relationships and to evaluate the genetic variability among the accessions. A total of 126 DNA bands or fragments were amplified by using the primers. The UPGMA cluster analysis revealed 2 main clusters among 22 accessions of Dalbergia sissoo based on coefficient of similarity and dissimilarity. Overall 72% similarity and 98% dissimilarity were observed. Low level of genetic variation and high level of genetic relatedness occurred among the canal, road, farmer's field and forest sites. The accessions were closely related with each other and showed mix pattern of genetic diversity. Thus RAPD markers have the potential to characterize and establish genetic relationships among the accessions of Dalbergia sissoo. (author)

  12. 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.

  13. Molecular analysis for genetic diversity and distance of introduced Grus antigone sharpii L. to Thailand.

    Science.gov (United States)

    Tanee, T; Chaveerach, A; Anuniwat, A; Tanomtong, A; Pinthong, K; Sudmoon, R; Mokkamul, P

    2009-01-15

    The genetic relationship was examined in a population of Grus antigone sharpii L. using DNA markers from the ISSR technique for applying towards breeding purposes for conservation of species. Since their extinction from Thailand, sixteen eastern sarus cranes: Grus antigone sharpii L. provided from Cambodia were fed and bred to sixty individuals at Nakhonratchasima Zoo, Northeastern Thailand to re-exist in Thai natural sites. Their genetic diversity and distance were examined to test their possibility to adapt to environmental variation. Blood samples from 27 individuals of Grus antigone sharpii L. were collected and DNA was extracted. These DNA samples were amplified using the successful fifteen from twenty four primers inter simple sequences repeat markers. A dendrogram was constructed and shows distance values of the species between 12.1 and 53.5. The samples produced 63.96% polymorphic banding profiles. The genetic diversity (H') in this population was estimated using Shannon's index. The high H' value of 0.501 reflected the somewhat wide range of distribution sites, which would adapt to environmental variations. Genetic evenness is 0.152. This value supports that all the studied samples have a small equal genetic abundance.

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

    Directory of Open Access Journals (Sweden)

    Rita de Cássia Nasser Cubel Garcia

    2017-01-01

    Full Text Available 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.

  15. Molecular genetic diversity of the Saccharomyces yeasts in Taiwan: Saccharomyces arboricola, Saccharomyces cerevisiae and Saccharomyces kudriavzevii.

    Science.gov (United States)

    Naumov, Gennadi I; Lee, Ching-Fu; Naumova, Elena S

    2013-01-01

    Genetic hybridization, sequence and karyotypic analyses of natural Saccharomyces yeasts isolated in different regions of Taiwan revealed three biological species: Saccharomyces arboricola, Saccharomyces cerevisiae and Saccharomyces kudriavzevii. Intraspecies variability of the D1/D2 and ITS1 rDNA sequences was detected among S. cerevisiae and S. kudriavzevii isolates. According to molecular and genetic analyses, the cosmopolitan species S. cerevisiae and S. kudriavzevii contain local divergent populations in Taiwan, Malaysia and Japan. Six of the seven known Saccharomyces species are documented in East Asia: S. arboricola, S. bayanus, S. cerevisiae, S. kudriavzevii, S. mikatae, and S. paradoxus.

  16. 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.

  17. 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.

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

    Science.gov (United States)

    Zarei, Mehdi; Hempel, Stefan; Wubet, Tesfaye; Schäfer, Tina; Savaghebi, Gholamreza; Jouzani, Gholamreza Salehi; Nekouei, Mojtaba Khayam; Buscot, François

    2010-08-01

    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. Copyright 2010 Elsevier Ltd. All rights reserved.

  19. Genetic diversity and molecular evolution of Ornithogalum mosaic virus based on the coat protein gene sequence

    Directory of Open Access Journals (Sweden)

    Fangluan Gao

    2018-03-01

    Full Text Available Ornithogalum mosaic virus (OrMV has a wide host range and affects the production of a variety of ornamentals. In this study, the coat protein (CP gene of OrMVwas used to investigate the molecular mechanisms underlying the evolution of this virus. The 36 OrMV isolates fell into two groups which have significant subpopulation differentiation with an FST value of 0.470. One isolate was identified as a recombinant and the other 35 recombination-free isolates could be divided into two major clades under different evolutionary constraints with dN/dS values of 0.055 and 0.028, respectively, indicating a role of purifying selection in the differentiation of OrMV. In addition, the results from analysis of molecular variance (AMOVA indicated that the effect of host species on the genetic divergence of OrMV is greater than that of geography. Furthermore, OrMV isolates from the genera Ornithogalum, Lachenalia and Diuri tended to group together, indicating that OrMV diversification was maintained, in part, by host-driven adaptation.

  20. 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. © 2014 Wiley Periodicals, Inc.

  1. 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.

  2. Genetic diversity and structure of tea plant in Qinba area in China by three types of molecular markers.

    Science.gov (United States)

    Zhang, Yu; Zhang, Xiaojuan; Chen, Xi; Sun, Wang; Li, Jiao

    2018-01-01

    Qinba area has a long history of tea planting and is a northernmost region in China where Camellia sinensis L. is grown. In order to provide basic data for selection and optimization of molecular markers of tea plants. 118 markers, including 40 EST-SSR, 40 SRAP and 38 SCoT markers were used to evaluate the genetic diversity of 50 tea plant ( Camellia sinensis. ) samples collected from Qinb. tea germplasm, assess population structure. In this study, a total of 414 alleles were obtained using 38 pairs of SCoT primers, with an average of 10.89 alleles per primer. The percentage of polymorphic bands (PPB), polymorphism information content (PIC), resolving power (Rp), effective multiplex ratio (EMR), average band informativeness (Ib av ), and marker index (MI) were 96.14%, 0.79, 6.71, 10.47, 0.58, and 6.07 respectively. 338 alleles were amplified via 40 pairs of SRAP (8.45 per primer), with PPB, PIC, Rp, EMR, Ib av, and MI values of 89.35%, 0.77, 5.11, 7.55, 0.61, and 4.61, respectively. Furthermore, 320 alleles have been detected using 40 EST-SSR primers (8.00 per primer), with PPB, PIC, Rp, EMR, Ib av , and MI values of 94.06%, 0.85, 4.48, 7.53, 0.56, and 4.22 respectively. These results indicated that SCoT markers had higher efficiency.Mantel test was used to analyze the genetic distance matrix generated by EST-SSRs, SRAPs and SCoTs. The results showed that the correlation between the genetic distance matrix based on EST-SSR and that based on SRAP was very small ( r  = 0.01), followed by SCoT and SRAP ( r  = 0.17), then by SCoT and EST-SSR ( r  = 0.19).The 50 tea samples were divided into two sub-populations using STRUCTURE, Neighbor-joining (NJ) method and principal component analyses (PCA). The results produced by STRUCTURE were completely consistent with the PCA analysis. Furthermore, there is no obvious relationship between the results produced using sub-populational and geographical data. Among the three types of markers, SCoT markers has many

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

    Science.gov (United States)

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

    2018-03-01

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

  4. New STS molecular markers for assessment of genetic diversity and DNA fingerprinting in hop (Humulus lupulus L.).

    Science.gov (United States)

    Patzak, Josef; Vrba, Lukás; Matousek, Jaroslav

    2007-01-01

    Molecular markers have been increasingly used in genetic studies of crop species for their applicability in breeding programs. In this work, we report on the development of new sequence-tagged site (STS) markers based on sequence information from several identified hop (Humulus lupulus L.) genes. 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. We found 3 individual gene variants (A, B, C) of the chs_H1 gene in this collection. The most frequent gene variant, B (AJ304877), was not detected in Mt. Hood, Glacier, and Horizon (US) cultivars. Gene variant A came from an American germplasm through wild hops. We found length polymorphism in intron 1 of the chs2 gene, and 4 different amplified markers were detected in PCRs. The chs3 gene was found in only one third of the cultivars. None of the variants of the studied CHS genes were found in Humulus japonicus. We detected 5 major gene variants of DNA-binding protein in the collection of H. lupulus cultivars and 2 others in H. japonicus. We also found 3 individual gene variants of an endochitinase gene. The distribution of gene variants did not correlate with any resistance. We proved that developed STS markers can be successfully used for the analysis of genetic diversity and can substitute and supplement SSR markers in hop.

  5. Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis.

    Science.gov (United States)

    Jia, Guanqing; Shi, Shenkui; Wang, Chunfang; Niu, Zhengang; Chai, Yang; Zhi, Hui; Diao, Xianmin

    2013-09-01

    Green foxtail (Setaria viridis) is a new model plant for the genomic investigation of C4 photosynthesis biology. As the ancestor of foxtail millet (Setaria italica), an ancient cereal of great importance in arid regions of the world, green foxtail is crucial for the study of domestication and evolution of this ancient crop. In the present study, 288 green foxtail accessions, which were collected from all geographical regions of China, were analysed using 77 simple sequence repeats (SSRs) that cover the whole genome. A high degree of molecular diversity was detected in these accessions, with an average of 33.5 alleles per locus. Two clusters, which were inconsistent with the distribution of eco-geographical regions in China, were inferred from STRUCTURE, Neighbor-Joining, and principal component analysis, indicating a partially mixed distribution of Chinese green foxtails. The higher subpopulation diversity was from accessions mainly collected from North China. A low level of linkage disequilibrium was observed in the green foxtail genome. Furthermore, a combined analysis of green foxtail and foxtail millet landraces was conducted, and the origin and domestication of foxtail millet was inferred in North China.

  6. 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.

  7. Molecular Characterization of Human Atypical Sorbitol-Fermenting Enteropathogenic Escherichia coli O157 Reveals High Diversity.

    Science.gov (United States)

    Kossow, Annelene; Zhang, Wenlan; Bielaszewska, Martina; Rhode, Sophie; Hansen, Kevin; Fruth, Angelika; Rüter, Christian; Karch, Helge; Mellmann, Alexander

    2016-05-01

    Alongside the well-characterized enterohemorrhagic Escherichia coli (EHEC) O157:H7, serogroup O157 comprises sorbitol-fermenting typical and atypical enteropathogenic E. coli (EPEC/aEPEC) strains that carry the intimin-encoding gene eae but not Shiga toxin-encoding genes (stx). Since little is known about these pathogens, we characterized 30 clinical isolates from patients with hemolytic uremic syndrome (HUS) or uncomplicated diarrhea with respect to their flagellin gene (fliC) type and multilocus sequence type (MLST). Moreover, we applied whole-genome sequencing (WGS) to determine the phylogenetic relationship with other eae-positive EHEC serotypes and the composition of the rfbO157 region. fliC typing resulted in five fliC types (H7, H16, H34, H39, and H45). Isolates of each fliC type shared a unique ST. In comparison to the 42 HUS-associated E. coli (HUSEC) strains, only the stx-negative isolates with fliCH7 shared their ST with EHEC O157:H7/H(-) strains. With the exception of one O157:H(-) fliCH16 isolate, HUS was exclusively associated with fliCH7. WGS corroborated the separation of the fliCH7 isolates, which were closely related to the EHEC O157:H7/H(-) isolates, and the diverse group of isolates exhibiting different fliC types, indicating independent evolution of the different serotypes. This was also supported by the heterogeneity within the rfbO157 region that exhibited extensive recombinations. The genotypic subtypes and distribution of clinical symptoms suggested that the stx-negative O157 strains with fliCH7 were originally EHEC strains that lost stx The remaining isolates form a distinct and diverse group of atypical EPEC isolates that do not possess the full spectrum of virulence genes, underlining the importance of identifying the H antigen for clinical risk assessment. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  8. Retrotransposon-Based Molecular Markers for Analysis of Genetic Diversity within the Genus Linum

    Science.gov (United States)

    Melnikova, Nataliya V.; Kudryavtseva, Anna V.; Zelenin, Alexander V.; Lakunina, Valentina A.; Yurkevich, Olga Yu.; Speranskaya, Anna S.; Dmitriev, Alexey A.; Krinitsina, Anastasia A.; Belenikin, Maxim S.; Uroshlev, Leonid A.; Snezhkina, Anastasiya V.; Sadritdinova, Asiya F.; Koroban, Nadezda V.; Amosova, Alexandra V.; Samatadze, Tatiana E.; Guzenko, Elena V.; Lemesh, Valentina A.; Savilova, Anastasya M.; Rachinskaia, Olga A.; Kishlyan, Natalya V.; Rozhmina, Tatiana A.; Bolsheva, Nadezhda L.; Muravenko, Olga V.

    2014-01-01

    SSAP method was used to study the genetic diversity of 22 Linum species from sections Linum, Adenolinum, Dasylinum, Stellerolinum, and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposons FL9 and FL11. Thus, the validity of SSAP method was demonstrated for flax marking, identification of accessions in genebank collections, and control during propagation of flax varieties. Polymorphism of Fl1a, Fl1b, and Cassandra insertions were very low in flax varieties, but these retrotransposons were successfully used for the investigation of Linum species. Species clusterization based on SSAP markers was in concordance with their taxonomic division into sections Dasylinum, Stellerolinum, Adenolinum, and Linum. All species of sect. Adenolinum clustered apart from species of sect. Linum. The data confirmed the accuracy of the separation in these sections. Members of section Linum are not as closely related as members of other sections, so taxonomic revision of this section is desirable. L. usitatissimum accessions genetically distant from modern flax cultivars were revealed in our work. These accessions are of utmost interest for flax breeding and introduction of new useful traits into flax cultivars. The chromosome localization of Cassandra retrotransposon in Linum species was determined. PMID:25243121

  9. Molecular phylogenetics and character evolution of morphologically diverse groups, Dendrobium section Dendrobium and allies

    Science.gov (United States)

    Takamiya, Tomoko; Wongsawad, Pheravut; Sathapattayanon, Apirada; Tajima, Natsuko; Suzuki, Shunichiro; Kitamura, Saki; Shioda, Nao; Handa, Takashi; Kitanaka, Susumu; Iijima, Hiroshi; Yukawa, Tomohisa

    2014-01-01

    It is always difficult to construct coherent classification systems for plant lineages having diverse morphological characters. The genus Dendrobium, one of the largest genera in the Orchidaceae, includes ∼1100 species, and enormous morphological diversification has hindered the establishment of consistent classification systems covering all major groups of this genus. Given the particular importance of species in Dendrobium section Dendrobium and allied groups as floriculture and crude drug genetic resources, there is an urgent need to establish a stable classification system. To clarify phylogenetic relationships in Dendrobium section Dendrobium and allied groups, we analysed the macromolecular characters of the group. Phylogenetic analyses of 210 taxa of Dendrobium were conducted on DNA sequences of internal transcribed spacer (ITS) regions of 18S–26S nuclear ribosomal DNA and the maturase-coding gene (matK) located in an intron of the plastid gene trnK using maximum parsimony and Bayesian methods. The parsimony and Bayesian analyses revealed 13 distinct clades in the group comprising section Dendrobium and its allied groups. Results also showed paraphyly or polyphyly of sections Amblyanthus, Aporum, Breviflores, Calcarifera, Crumenata, Dendrobium, Densiflora, Distichophyllae, Dolichocentrum, Holochrysa, Oxyglossum and Pedilonum. On the other hand, the monophyly of section Stachyobium was well supported. It was found that many of the morphological characters that have been believed to reflect phylogenetic relationships are, in fact, the result of convergence. As such, many of the sections that have been recognized up to this point were found to not be monophyletic, so recircumscription of sections is required. PMID:25107672

  10. Molecular Epidemiology Reveals Genetic Diversity amongst Isolates of the Cryptococcus neoformans/C. gattii Species Complex in Thailand

    Science.gov (United States)

    Kaocharoen, Sirada; Ngamskulrungroj, Popchai; Firacative, Carolina; Trilles, Luciana; Piyabongkarn, Dumrongdej; Banlunara, Wijit; Poonwan, Natteewan; Chaiprasert, Angkana; Meyer, Wieland; Chindamporn, Ariya

    2013-01-01

    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. PMID:23861989

  11. 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

  12. Photostability enhancement of the pentacene derivative having two nitronyl nitroxide radical substituents.

    Science.gov (United States)

    Shimizu, Akihiro; Ito, Akitaka; Teki, Yoshio

    2016-02-18

    Pentacene derivatives possessing nitronyl nitroxide radical substituents (1a and 1b) were synthesized, and their photochemical properties were evaluated. 1a with two radical substituents showed a remarkable enhancement of photostability compared with pentacene, 6,13-bis(triisopropylsilylethynyl)pentacene and the monoradical, 1b. This is understood due to the presence of the multiple deactivation pathways in the photoexcited states.

  13. Substituent-directed structural and physicochemical controls of diruthenium catecholate complexes with ligand-unsupported Ru-Ru bonds.

    Science.gov (United States)

    Chang, Ho-Chol; Mochizuki, Katsunori; Kitagawa, Susumu

    2005-05-30

    A family of diruthenium complexes with ligand-unsupported Ru-Ru bonds has been systematically synthesized, and their crystal structures and physical properties have been examined. A simple, useful reaction between Ru2(OAc)4Cl (OAc- = acetate) and catechol derivatives in the presence of bases afforded a variety of diruthenium complexes, generally formulated as [Na(n){Ru2(R4Cat)4}] (n = 2 or 3; R4 = -F4, -Cl4, -Br4, -H4, -3,5-di-t-Bu, and -3,6-di-t-Bu; Cat(2-) = catecholate). The most characteristic feature of the complexes is the formation of short ligand-unsupported Ru-Ru bonds (2.140-2.273 A). These comprehensive studies were carried out to evaluate the effects of the oxidation states and the substituents governing the molecular structures and physicochemical properties. The Ru-Ru bond distances, rotational conformations, and bending structures of the complexes were successfully varied. The results presented in this manuscript clearly demonstrate that the complexes with ligand-unsupported Ru-Ru bonds can sensitively respond to redox reactions and ligand substituents on the basis of the greater degree of freedom in their molecular structures.

  14. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Optical properties and molecular diversity of dissolved organic matter in the Bering Strait and Chukchi Sea

    Science.gov (United States)

    Gonsior, Michael; Luek, Jenna; Schmitt-Kopplin, Philippe; Grebmeier, Jacqueline M.; Cooper, Lee W.

    2017-10-01

    Changes in the molecular composition of dissolved organic matter (DOM) and its light absorbing chromophoric component (CDOM) are of particular interest in the Arctic region because of climate change effects that lead to warmer sea surface temperatures and longer exposure to sunlight. We used continuous UV-vis (UV-vis) spectroscopy, excitation emission matrix fluorescence and ultrahigh resolution mass spectrometry during a transect from the Aleutian Islands in the Bering Sea to the Chukchi Sea ice edge through Bering Strait to determine the variability of DOM and CDOM. These data were combined with discrete sampling for stable oxygen isotopes of seawater, in order to evaluate the contributions of melted sea ice versus runoff to the DOM and CDOM components. This study demonstrated that high geographical resolution of optical properties in conjunction with stable oxygen ratios and non-targeted ultrahigh resolution mass spectrometry was able to distinguish between different DOM sources in the Arctic, including identification of labile DOM sources in Bering Strait associated with high algal blooms and sampling locations influenced by terrestrially-derived DOM, such as the terrestrial DOM signal originating from Arctic rivers and dirty/anchor sea ice. Results of this study also revealed the overall variability and chemodiversity of Arctic DOM present in the Bering and Chukchi Seas.

  16. Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade.

    Science.gov (United States)

    Lo, Pei-Chun; Liu, Shu-Hui; Nor, Siti Azizah Mohd; Chen, Wei-Jen

    2017-01-01

    The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species) from one nuclear gene (RAG1) and one mitochondrial gene (COI); the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species); and the dataset with only COI gene sequences (308 samples from 51 currently recognized species). The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC). The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology). Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and suggested a

  17. Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade.

    Directory of Open Access Journals (Sweden)

    Pei-Chun Lo

    Full Text Available The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species from one nuclear gene (RAG1 and one mitochondrial gene (COI; the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species; and the dataset with only COI gene sequences (308 samples from 51 currently recognized species. The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC. The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology. Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and

  18. Molecular characterization of norovirus variants and genetic diversity of noroviruses and sapoviruses in Thailand.

    Science.gov (United States)

    Chaimongkol, Natthawan; Khamrin, Pattara; Malasao, Rungnapa; Thongprachum, Aksara; Kongsricharoern, Tipachan; Ukarapol, Nuthapong; Ushijima, Hiroshi; Maneekarn, Niwat

    2014-07-01

    Norovirus (NoV) and Sapovirus (SaV) have been reported as a common cause of acute gastroenteritis worldwide. For a decade, surveillances of NoV and SaV have been conducted continually in Thailand. To monitor the epidemiological situation and to determine the genetic variation of NoV and SaV in Chiang Mai, Thailand, 567 samples collected from pediatric patients hospitalized with acute gastroenteritis were examined during 2007, and 2010-2011 by semi-nested RT-PCR and nucleotide sequencing methods. NoV was detected at 15.9%. Phylogenetic analysis revealed multiple NoV genotypes, GI/14 (1.1%), GII/1 (1.1%), GII/2 (1.1%), GII/3 (4.4%), GII/4 (65.6%), GII/6 (10.0%), GII/7 (2.2%), GII/12 (4.4%), GII/13 (3.3%), GII/16 (5.7%), and unclassified genotype (1.1%), circulating in this area. Among these, NoV GII/4 was the most prevalent genotype with a predominance of GII/4 2009 over other variants, 1996, 2006a, and 2006b. For SaV, the prevalence was 1.2% which was much lower than those of NoV and only SaV GI/1 was detected. This study highlights the epidemiology of NoV and SaV and genetic diversity of viruses circulating in pediatric patients hospitalized with acute gastroenteritis in Chiang Mai, Thailand. © 2013 Wiley Periodicals, Inc.

  19. Molecular Diversity Analysis and Genetic Mapping of Pod Shatter Resistance Loci in Brassica carinata L.

    Directory of Open Access Journals (Sweden)

    Rosy Raman

    2017-11-01

    Full Text Available Seed lost due to easy pod dehiscence at maturity (pod shatter is a major problem in several members of Brassicaceae family. We investigated the level of pod shatter resistance in Ethiopian mustard (Brassica carinata and identified quantitative trait loci (QTL for targeted introgression of this trait in Ethiopian mustard and its close relatives of the genus Brassica. A set of 83 accessions of B. carinata, collected from the Australian Grains Genebank, was evaluated for pod shatter resistance based on pod rupture energy (RE. In comparison to B. napus (RE = 2.16 mJ, B. carinata accessions had higher RE values (2.53 to 20.82 mJ. A genetic linkage map of an F2 population from two contrasting B. carinata selections, BC73526 (shatter resistant with high RE and BC73524 (shatter prone with low RE comprising 300 individuals, was constructed using a set of 6,464 high quality DArTseq markers and subsequently used for QTL analysis. Genetic analysis of the F2 and F2:3 derived lines revealed five statistically significant QTL (LOD ≥ 3 that are linked with pod shatter resistance on chromosomes B1, B3, B8, and C5. Herein, we report for the first time, identification of genetic loci associated with pod shatter resistance in B. carinata. These characterized accessions would be useful in Brassica breeding programs for introgression of pod shatter resistance alleles in to elite breeding lines. Molecular markers would assist marker-assisted selection for tracing the introgression of resistant alleles. Our results suggest that the value of the germplasm collections can be harnessed through genetic and genomics tools.

  20. Characterization of Unexplored Deadwood Mycobiome in Highly Diverse Subtropical Forests Using Culture-independent Molecular Technique.

    Science.gov (United States)

    Purahong, Witoon; Pietsch, Katherina A; Lentendu, Guillaume; Schöps, Ricardo; Bruelheide, Helge; Wirth, Christian; Buscot, François; Wubet, Tesfaye

    2017-01-01

    The deadwood mycobiome, also known as wood-inhabiting fungi (WIF), are among the key players in wood decomposition, having a large impact on nutrient cycling in forest soils. However, our knowledge of WIF richness and distribution patterns in different forest biomes is limited. Here, we used pyrotag sequencing of the fungal internal transcribed spacer (ITS2) region to characterize the deadwood mycobiome of two tree species with greatly different wood characteristics ( Schima superba and Pinus massoniana ) in a Chinese subtropical forest ecosystem. Specifically, we tested (i) the effects of tree species and wood quality properties on WIF OTU richness and community composition; (ii) the role of biotic and abiotic factors in shaping the WIF communities; and (iii) the relationship between WIF OTU richness, community composition and decomposition rates. Due to different wood chemical properties, we hypothesized that the WIF communities derived from the two tree species would be correlated differently with biotic and abiotic factors. Our results show that deadwood in subtropical forests harbors diverse fungal communities comprising six ecological functional groups. We found interesting colonization patterns for this subtropical biome, where Resinicium spp. were highly detected in both broadleaved and coniferous deadwood. In addition, the members of Xylariales were frequently found in Schima . The two deadwood species differed significantly in WIF OTU richness ( Pinus > Schima ) and community composition ( P < 0.001). Variations in WIF community composition of both tree species were significantly explained by wood pH and ecological factors (biotic: deadwood species, basal area and abiotic: soil pH), but the WIF communities derived from each tree species correlated differently with abiotic factors. Interestingly, we found that deadwood decomposition rate significantly correlated with WIF communities and negatively correlated with WIF OTU richness. We conclude that the

  1. Molecular diversity of Epstein-Barr virus IgG and IgA antibody responses in nasopharyngeal carcinoma: a comparison of Indonesian, Chinese, and European subjects.

    NARCIS (Netherlands)

    Fachiroh, J.; Schouten, T; Hariwiyanto, B; Paramita, D.K.; Harijadi, A; Haryana, SM; Ng, MH; Middeldorp, J.M.

    2004-01-01

    Epstein-Barr virus (EBV)-specific immunoblot analysis was used to reveal the molecular diversity of immunoglobulin (Ig) G and IgA antibody responses against Epstein-Barr nuclear antigen (EBNA), early antigen (EA), and viral capsid antigen (VCA) in serum samples from patients with nasopharyngeal

  2. 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.

  3. 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.

  4. Interchain interactions in charged diacetylenic oligomers carrying bulk substituents revisited

    International Nuclear Information System (INIS)

    Ottonelli, M.; Izzo, G.M.M.; Comoretto, D.; Musso, G.F.; Dellepiane, G.

    2006-01-01

    We are studying how the electronic properties of an aggregate, built with conjugated oligomers carrying bulk substituents, are affected by intermolecular interactions. In this paper we apply the CEO (Collective Electronic Oscillator) method, on the basis of the semiempirical INDO/S Hamiltonian, to compute the electronic density matrix modifications following the photon absorption in a doubly charged cluster of two units of a fully carbazolyl-substituted oligodiacetylene tetramer, taken as a model system. The picture that had emerged from our previous calculations based on the less sophisticated CIS (Configuration Interaction including Singles) approach is seen to be confirmed. Despite the large separation between the backbones, a through-space charge transfer occurs between the two oligomers due to the fact that the excess charge, contrary to what is generally believed, is not localized on the conjugated backbone, but is spread out over the carbazolyl moieties of the charged molecule. Consideration of this kind of interaction improves the theoretical results obtained for the isolated charged oligomer chain, and aids in better explaining some features of the experimental photoinduced spectra of the corresponding polymer

  5. 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.

  6. 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.

  7. 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.

  8. [Evaluation of Molecular Genetic Diversity of Wild Apple Malus sieversii Populations from Zailiysky Alatau by Microsatellite Markers].

    Science.gov (United States)

    Omasheva, M E; Chekalin, S V; Galiakparov, N N

    2015-07-01

    The territory of Kazakhstan is part of the distribution range of Malus sieversii, which is one of the ancestors of cultivated apple tree varieties. The collected samples of Sievers apple leaves from five populations growing in the Zailiysky Alatau region served as a source not only for the creation of a bank of genomic DNA but also for determination ofthe wild apple genetic polymorphism. The seven microsatellite markers used in this study revealed 86 alleles with different frequencies, as well as the characteristic pools of rare alleles for each of the populations. Molecular genetic analysis showed a high level of genetic diversity (H(o) = 0.704; PIC = 0.752; I = 1.617). Moreover, interpopulation variability accounted only for 7.5% of total variability, confirming the genetic closeness of the populations examined. Based on phylogenetic analysis, it was demonstrated that the Bel'bulak and Almaty Reserve populations were closest to each other, while the most distant were the Ketmen and Great Almaty gorge populations, which suggests the dependence of genetic distance on the geographical.

  9. Food-Borne Outbreak Investigation and Molecular Typing: High Diversity of Staphylococcus aureus Strains and Importance of Toxin Detection

    Science.gov (United States)

    Denayer, Sarah; Nia, Yacine; Botteldoorn, Nadine

    2017-01-01

    Staphylococcus aureus is an important aetiological agent of food intoxications in the European Union as it can cause gastro-enteritis through the production of various staphylococcal enterotoxins (SEs) in foods. Reported enterotoxin dose levels causing food-borne illness are scarce and varying. Three food poisoning outbreaks due to enterotoxin-producing S. aureus strains which occurred in 2013 in Belgium are described. The outbreaks occurred in an elderly home, at a barbecue event and in a kindergarten and involved 28, 18, and six cases, respectively. Various food leftovers contained coagulase positive staphylococci (CPS). Low levels of staphylococcal enterotoxins ranging between 0.015 ng/g and 0.019 ng/g for enterotoxin A (SEA), and corresponding to 0.132 ng/g for SEC were quantified in the food leftovers for two of the reported outbreaks. Molecular typing of human and food isolates using pulsed-field gel electrophoresis (PFGE) and enterotoxin gene typing, confirmed the link between patients and the suspected foodstuffs. This also demonstrated the high diversity of CPS isolates both in the cases and in healthy persons carrying enterotoxin genes encoding emetic SEs for which no detection methods currently exist. For one outbreak, the investigation pointed out to the food handler who transmitted the outbreak strain to the food. Tools to improve staphylococcal food poisoning (SFP) investigations are presented. PMID:29261162

  10. 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. Copyright © 2015 Elsevier GmbH. All rights reserved.

  11. Food-Borne Outbreak Investigation and Molecular Typing: High Diversity of Staphylococcus aureus Strains and Importance of Toxin Detection.

    Science.gov (United States)

    Denayer, Sarah; Delbrassinne, Laurence; Nia, Yacine; Botteldoorn, Nadine

    2017-12-20

    Staphylococcus aureus is an important aetiological agent of food intoxications in the European Union as it can cause gastro-enteritis through the production of various staphylococcal enterotoxins (SEs) in foods. Reported enterotoxin dose levels causing food-borne illness are scarce and varying. Three food poisoning outbreaks due to enterotoxin-producing S. aureus strains which occurred in 2013 in Belgium are described. The outbreaks occurred in an elderly home, at a barbecue event and in a kindergarten and involved 28, 18, and six cases, respectively. Various food leftovers contained coagulase positive staphylococci (CPS). Low levels of staphylococcal enterotoxins ranging between 0.015 ng/g and 0.019 ng/g for enterotoxin A (SEA), and corresponding to 0.132 ng/g for SEC were quantified in the food leftovers for two of the reported outbreaks. Molecular typing of human and food isolates using pulsed-field gel electrophoresis (PFGE) and enterotoxin gene typing, confirmed the link between patients and the suspected foodstuffs. This also demonstrated the high diversity of CPS isolates both in the cases and in healthy persons carrying enterotoxin genes encoding emetic SEs for which no detection methods currently exist. For one outbreak, the investigation pointed out to the food handler who transmitted the outbreak strain to the food. Tools to improve staphylococcal food poisoning (SFP) investigations are presented.

  12. A 3D visualization of the substituent effect : A brief analysis of two components of the operational formula of dual descriptor for open-shell systems.

    Science.gov (United States)

    Martínez-Araya, Jorge I; Yepes, Diana; Jaque, Pablo

    2017-12-27

    Six organometallic compounds coming from a basic Mo-based complex were analyzed from the perspective of the dual descriptor in order to detect subtle influences that a substituent group could exert on the reactive core at a long range. Since the aforementioned complexes are open-shell systems, the used operational formula for the dual descriptor is that one defined for those aforementioned systems, which was then compared with spin density. In addition, dual descriptor was decomposed into two terms, each of which was also applied on every molecular system. The obtained results indicated that components of dual descriptor could become more useful than the operational formula of dual descriptor because differences exerted by the substituents at the para position were better detected by components of dual descriptor rather than the dual descriptor by itself.

  13. 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.

  14. 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.

  15. The investigation of substituent effects on the fragmentation pathways of pentacoordinated phenoxyspirophosphoranes by ESI-MSn.

    Science.gov (United States)

    Cui, Xiaoyan; Sun, Can; Zhao, Pei; Wang, Yanyan; Guo, Yanchun; Zhao, Yufen; Cao, Shuxia

    2018-04-01

    The fragmentation pathways of pentacoordinated phenoxyspirophosphoranes were investigated in the positive mode by electrospray ionization multistage mass spectrometry. The results demonstrate that the sodium adducts of the title compounds undergo two competitive fragmentation pathways, and the fragmentation patterns are heavily dependent on the various substituent patterns at the phenolic group. An electron-withdrawing substituent at the ortho-position always results in the removal of a corresponding phenol analogue, while cleavage by spiroring opening becomes the predominant fragmentation pathway if an electron-donating substituent is at the phenolic group. The substituent effects on the competitive fragmentation pathways were further elucidated by theoretical calculations, single crystal structure analysis, and high-resolution mass spectrometry. The results contribute to the understanding of the gas-phase fragmentation reactions and the structure identification of spirophosphorane analogues by electrospray ionization multistage mass spectrometry. Copyright © 2018 John Wiley & Sons, Ltd.

  16. Effects of the Substituents of Boron Atoms on Conjugated Polymers Containing B←N Units.

    Science.gov (United States)

    Liu, Jun; Wang, Tao; Dou, Chuandong; Wang, Lixiang

    2018-06-15

    Organoboron chemistry is a new tool to tune the electronic structures and properties of conjugated polymers, which are important for applications in organic opto-electronic devices. To investigate the effects of substituents of boron atoms on conjugated polymers, we synthesized three conjugated polymers based on double B←N bridged bipyridine (BNBP) with various substituents on the boron atoms. By changing the substituents from four phenyl groups and two phenyl groups/two fluorine atoms to four fluorine atoms, the BNBP-based polymers show the blue-shifted absorption spectra, decreased LUMO/HOMO energy levels and enhanced electron affinities, as well as the increased electron mobilities. Moreover, these BNBP-based polymers can be used as electron acceptors for all-polymer solar cells. These results demonstrate that the substituents of boron atoms can effectively modulate the electronic properties and applications of conjugated polymers. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Towards physical interpretation of substituent effects: the case of N- and C3-substituted pyrrole derivatives

    Czech Academy of Sciences Publication Activity Database

    Zborowski, K. K.; Szatylowicz, H.; Stasyuk, Olga A.; Krygowski, T. M.

    2017-01-01

    Roč. 28, č. 4 (2017), s. 1223-1227 ISSN 1040-0400 Institutional support: RVO:61388963 Keywords : substituent effect * pyrrole derivatives * Hammett equation * charges of the substituent active region Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 1.582, year: 2016 https://link.springer.com/article/10.1007%2Fs11224-017-0938-7

  18. Unravelling the Molecular Epidemiology and Genetic Diversity among Burkholderia pseudomallei Isolates from South India Using Multi-Locus Sequence Typing.

    Science.gov (United States)

    Tellapragada, Chaitanya; Kamthan, Aayushi; Shaw, Tushar; Ke, Vandana; Kumar, Subodh; Bhat, Vinod; Mukhopadhyay, Chiranjay

    2016-01-01

    There is a slow but steady rise in the case detection rates of melioidosis from various parts of the Indian sub-continent in the past two decades. However, the epidemiology of the disease in India and the surrounding South Asian countries remains far from well elucidated. Multi-locus sequence typing (MLST) is a useful epidemiological tool to study the genetic relatedness of bacterial isolates both with-in and across the countries. With this background, we studied the molecular epidemiology of 32 Burkholderia pseudomallei isolates (31 clinical and 1 soil isolate) obtained during 2006-2015 from various parts of south India using multi-locus sequencing typing and analysis. Of the 32 isolates included in the analysis, 30 (93.7%) had novel allelic profiles that were not reported previously. Sequence type (ST) 1368 (n = 15, 46.8%) with allelic profile (1, 4, 6, 4, 1, 1, 3) was the most common genotype observed. We did not observe a genotypic association of STs with geographical location, type of infection and year of isolation in the present study. Measure of genetic differentiation (FST) between Indian and the rest of world isolates was 0.14413. Occurrence of the same ST across three adjacent states of south India suggest the dispersion of B.pseudomallei across the south western coastal part of India with limited geographical clustering. However, majority of the STs reported from the present study remained as "outliers" on the eBURST "Population snapshot", suggesting the genetic diversity of Indian isolates from the Australasian and Southeast Asian isolates.

  19. Unravelling the Molecular Epidemiology and Genetic Diversity among Burkholderia pseudomallei Isolates from South India Using Multi-Locus Sequence Typing.

    Directory of Open Access Journals (Sweden)

    Chaitanya Tellapragada

    Full Text Available There is a slow but steady rise in the case detection rates of melioidosis from various parts of the Indian sub-continent in the past two decades. However, the epidemiology of the disease in India and the surrounding South Asian countries remains far from well elucidated. Multi-locus sequence typing (MLST is a useful epidemiological tool to study the genetic relatedness of bacterial isolates both with-in and across the countries. With this background, we studied the molecular epidemiology of 32 Burkholderia pseudomallei isolates (31 clinical and 1 soil isolate obtained during 2006-2015 from various parts of south India using multi-locus sequencing typing and analysis. Of the 32 isolates included in the analysis, 30 (93.7% had novel allelic profiles that were not reported previously. Sequence type (ST 1368 (n = 15, 46.8% with allelic profile (1, 4, 6, 4, 1, 1, 3 was the most common genotype observed. We did not observe a genotypic association of STs with geographical location, type of infection and year of isolation in the present study. Measure of genetic differentiation (FST between Indian and the rest of world isolates was 0.14413. Occurrence of the same ST across three adjacent states of south India suggest the dispersion of B.pseudomallei across the south western coastal part of India with limited geographical clustering. However, majority of the STs reported from the present study remained as "outliers" on the eBURST "Population snapshot", suggesting the genetic diversity of Indian isolates from the Australasian and Southeast Asian isolates.

  20. Chromosomal diversity and molecular divergence among three undescribed species of Neacomys (Rodentia, Sigmodontinae separated by Amazonian rivers.

    Directory of Open Access Journals (Sweden)

    Willam Oliveira Da Silva

    Full Text Available The Neacomys genus (Rodentia, Sigmodontinae is distributed in the Amazon region, with some species limited to a single endemic area, while others may occur more widely. The number of species within the genus and their geographical boundaries are not known accurately, due to their high genetic diversity and difficulties in taxonomic identification. In this work we collected Neacomys specimens from both banks of the Tapajós River in eastern Amazon, and studied them using chromosome painting with whole chromosome probes of Hylaeamys megacephalus (HME; Rodentia, Sigmodontinae, and molecular analysis using haplotypes of mitochondrial genes COI and Cytb. Chromosome painting shows that Neacomys sp. A (NSP-A, 2n = 58/FN = 68 and Neacomys sp. B (NSP-B, 2n = 54/FN = 66 differ by 11 fusion/fission events, one translocation, four pericentric inversions and four heterochromatin amplification events. Using haplotypes of the concatenated mitochondrial genes COI and Cyt b, Neacomys sp. (2n = 58/FN = 64 and 70 shows a mean divergence of 6.2% for Neacomys sp. A and 9.1% for Neacomys sp. B, while Neacomys sp. A and Neacomys sp. B presents a medium nucleotide divergence of 7.4%. Comparisons were made with other published Neacomys data. The Tapajós and Xingu Rivers act as geographic barriers that define the distribution of these Neacomys species. Furthermore, our HME probes reveal four synapomorphies for the Neacomys genus (associations HME 20/[13,22]/4, 6a/21, [9,10]/7b/[9,10] and 12/[16,17] and demonstrate ancestral traits of the Oryzomyini tribe (HME 8a and 8b, 18 and 25 and Sigmodontinae subfamily (HME 15 and 24, which can be used as taxonomic markers for these groups.

  1. Chromosomal diversity and molecular divergence among three undescribed species of Neacomys (Rodentia, Sigmodontinae) separated by Amazonian rivers.

    Science.gov (United States)

    Oliveira Da Silva, Willam; Pieczarka, Julio Cesar; Ferguson-Smith, Malcolm Andrew; O'Brien, Patricia Caroline Mary; Mendes-Oliveira, Ana Cristina; Sampaio, Iracilda; Carneiro, Jeferson; Nagamachi, Cleusa Yoshiko

    2017-01-01

    The Neacomys genus (Rodentia, Sigmodontinae) is distributed in the Amazon region, with some species limited to a single endemic area, while others may occur more widely. The number of species within the genus and their geographical boundaries are not known accurately, due to their high genetic diversity and difficulties in taxonomic identification. In this work we collected Neacomys specimens from both banks of the Tapajós River in eastern Amazon, and studied them using chromosome painting with whole chromosome probes of Hylaeamys megacephalus (HME; Rodentia, Sigmodontinae), and molecular analysis using haplotypes of mitochondrial genes COI and Cytb. Chromosome painting shows that Neacomys sp. A (NSP-A, 2n = 58/FN = 68) and Neacomys sp. B (NSP-B, 2n = 54/FN = 66) differ by 11 fusion/fission events, one translocation, four pericentric inversions and four heterochromatin amplification events. Using haplotypes of the concatenated mitochondrial genes COI and Cyt b, Neacomys sp. (2n = 58/FN = 64 and 70) shows a mean divergence of 6.2% for Neacomys sp. A and 9.1% for Neacomys sp. B, while Neacomys sp. A and Neacomys sp. B presents a medium nucleotide divergence of 7.4%. Comparisons were made with other published Neacomys data. The Tapajós and Xingu Rivers act as geographic barriers that define the distribution of these Neacomys species. Furthermore, our HME probes reveal four synapomorphies for the Neacomys genus (associations HME 20/[13,22]/4, 6a/21, [9,10]/7b/[9,10] and 12/[16,17]) and demonstrate ancestral traits of the Oryzomyini tribe (HME 8a and 8b, 18 and 25) and Sigmodontinae subfamily (HME 15 and 24), which can be used as taxonomic markers for these groups.

  2. 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

  3. Substituent effects on geometric and electronic properties of iron tetraphenylporphyrin: a DFT investigation.

    Science.gov (United States)

    Wei, Lu; She, Yuanbin; Yu, Yanmin; Yao, Xiaoqian; Zhang, Suojiang

    2012-06-01

    To investigate the effects of the substituents, substituent positions and axial chloride ligand on the geometric and electronic properties of the iron tetraphenylporphyrin (FeTPP), a series of the substituented iron tetraphenylporphyrins and their chlorides, FeT(o/p-R)PP and FeT(o/p-R)PPCl (R = -H, -Cl, -NO(2), -OH, -OCH(3)), were systematically calculated without any symmetry constraint by using DFT method. For geometric structure, the substituent position and axial Cl ligand change the configuration of the iron porphyrin obviously. The ortho-substituents prefer making the phenyls perpendicular to the porphyrin ring; the axial chloride draws the central Fe ion ~0.500 Å out of the porphyrin plane toward the ligand. With regard to electronic properties, it is found that E(LUMO) could be related to the catalytic activity. The electron-withdrawing group always lowers the energies of both frontier orbitals, while the electron-donating one heightens them simultaneously, but they affect the E(HOMO) and E(LUMO) in the same sequence, -NO(2) < -Cl < -H < -OH < -OCH(3). The substituent effects on the central Fe ion were explored by calculating NBO charge distribution, spin density and natural electron configuration.

  4. Indolylarylsulfones as HIV-1 non-nucleoside reverse transcriptase inhibitors: new cyclic substituents at indole-2-carboxamide.

    Science.gov (United States)

    La Regina, Giuseppe; Coluccia, Antonio; Brancale, Andrea; Piscitelli, Francesco; Gatti, Valerio; Maga, Giovanni; Samuele, Alberta; Pannecouque, Christophe; Schols, Dominique; Balzarini, Jan; Novellino, Ettore; Silvestri, Romano

    2011-03-24

    New indolylarylsulfone derivatives bearing cyclic substituents at indole-2-carboxamide linked through a methylene/ethylene spacer were potent inhibitors of the WT HIV-1 replication in CEM and PBMC cells with inhibitory concentrations in the low nanomolar range. Against the mutant L100I and K103N RT HIV-1 strains in MT-4 cells, compounds 20, 24-26, 36, and 40 showed antiviral potency superior to that of NVP and EFV. Against these mutant strains, derivatives 20, 24-26, and 40 were equipotent to ETV. Molecular docking experiments on this novel series of IAS analogues have also suggested that the H-bond interaction between the nitrogen atom in the carboxamide chain of IAS and Glu138:B is important in the binding of these compounds. These results are in accordance with the experimental data obtained on the WT and on the mutant HIV-1 strains tested.

  5. Superoxide radical-mediated photocatalytic oxidation of phenolic compounds over Ag{sup +}/TiO{sub 2}: Influence of electron donating and withdrawing substituents

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Jiadong [National Engineering Laboratory for Hydrometallurgical Cleaner Production Technology, Beijing Engineering Research Center of Process Pollution Control, Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Xie, Yongbing, E-mail: ybxie@ipe.ac.cn [National Engineering Laboratory for Hydrometallurgical Cleaner Production Technology, Beijing Engineering Research Center of Process Pollution Control, Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190 (China); Han, Qingzhen [State Key Laboratory of Multi-phase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190 (China); Cao, Hongbin [National Engineering Laboratory for Hydrometallurgical Cleaner Production Technology, Beijing Engineering Research Center of Process Pollution Control, Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190 (China); Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072 (China); Wang, Yujiao [Department of Chemical and Biomedical Engineering, University of Science and Technology Beijing (China); Nawaz, Faheem; Duan, Feng [National Engineering Laboratory for Hydrometallurgical Cleaner Production Technology, Beijing Engineering Research Center of Process Pollution Control, Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190 (China); University of Chinese Academy of Sciences, Beijing 100049 (China)

    2016-03-05

    Highlights: • A weak EWG benefited photocatalytic oxidation of phenols the most. • Phenolic compounds were dominantly oxidized by ·O{sub 2}{sup −}, rather than ·OH, {sup 1}O{sub 2} or h{sup +}. • ·O{sub 2}{sup −} preferred to nucleophilically attack EDG substituted phenols. • ·O{sub 2}{sup −} more likely electrophilically attacked EWG substituted phenols. • ·O{sub 2}{sup −} simultaneously nucleophilically and electrophilically assaulted p-chlorophenol. - Abstract: 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{sup +}/TiO{sub 2} 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 (·O{sub 2}{sup −}) 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 ·O{sub 2}{sup −} and phenolic compounds, which was further verified by the quantum chemical computation on the frontier molecular orbitals and Mulliken charge distributions of ·O{sub 2}{sup −} and phenolic compounds. It was found that electron donating group (EDG) substituted phenols were more likely nucleophilically attacked by ·O{sub 2}{sup −}, while ·O{sub 2}{sup −} preferred to electrophilically assault electron withdrawing group (EWG) substituted phenols. Exceptionally, electrophilic and nucleophilic attack by ·O{sub 2}{sup −} could simultaneously occur in p-chlorophenol degradation, consequently leading to its highest rate

  6. Superoxide radical-mediated photocatalytic oxidation of phenolic compounds over Ag"+/TiO_2: Influence of electron donating and withdrawing substituents

    International Nuclear Information System (INIS)

    Xiao, Jiadong; Xie, Yongbing; Han, Qingzhen; Cao, Hongbin; Wang, Yujiao; Nawaz, Faheem; Duan, Feng

    2016-01-01

    Highlights: • A weak EWG benefited photocatalytic oxidation of phenols the most. • Phenolic compounds were dominantly oxidized by ·O_2"−, rather than ·OH, "1O_2 or h"+. • ·O_2"− preferred to nucleophilically attack EDG substituted phenols. • ·O_2"− more likely electrophilically attacked EWG substituted phenols. • ·O_2"− simultaneously nucleophilically and electrophilically assaulted p-chlorophenol. - Abstract: 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"+/TiO_2 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 (·O_2"−) 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 ·O_2"− and phenolic compounds, which was further verified by the quantum chemical computation on the frontier molecular orbitals and Mulliken charge distributions of ·O_2"− and phenolic compounds. It was found that electron donating group (EDG) substituted phenols were more likely nucleophilically attacked by ·O_2"−, while ·O_2"− preferred to electrophilically assault electron withdrawing group (EWG) substituted phenols. Exceptionally, electrophilic and nucleophilic attack by ·O_2"− 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.

  7. Quantum chemical molecular dynamical investigation of alkyl nitrite photo-dissociated on copper surfaces

    International Nuclear Information System (INIS)

    Wang Xiaojing; Wang Wei; Han Peilin; Kubo, Momoji; Miyamoto, Akira

    2008-01-01

    An accelerated quantum chemical molecular dynamical code 'Colors-Excite' was used to investigate the photolysis of alkyl nitrites series, RONO (R=CH 3 and C(CH 3 ) 3 ) on copper surfaces. Our calculations showed that the photo-dissociated processes are associated with the alkyl substituents of RONO when adsorbed on copper surfaces. For R=CH 3 , a two-step photolysis reaction occurred, yielding diverse intermediate products including RO radical, NO, and HNO, consistent with those reported in gas phase. While for R=C(CH 3 ) 3 , only one-step photolysis reaction occurred and gave intermediate products of RO radical and NO. Consequently, pure RO species were achieved to adsorb on metal surfaces by removing the NO species in photolysis reaction. The detailed photo-dissociated behaviors of RONO on copper surfaces with different alkyl substituents which are uncovered by the present simulation can be extended to explain the diverse dissociative mechanism experimentally observed. The quantum chemical molecular dynamical code 'Colors-Excite' is proved to be highly applicable to the photo-dissociations on metal surfaces

  8. 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

  9. DFT studies for the substituent effect on the diels-alder reaction of 1,4-diaza-1,3-butadienes

    International Nuclear Information System (INIS)

    Lee, Gab Yong

    2001-01-01

    DFT calculations have been performed on several substituted 1,4-diaza-1,3-butadienes (1,4-DABs) with electron donating and withdrawing groups at the terminal two nitrogens to investigate the reactivity of Diels-Alder reaction with acrolein. The calculated FMO (Frontier Molecular orbital) energies for the optimized 1,4-disubstituted-1,4DABs have been used to explain both normal and inverse electron demand Diels-Alder reactions. It is shown that the electron donating and withdrawing substituents lead to the normal(HOMO diene controlled) and inverse electron demand (LUMO diene controlled) Diels-Alder reactions, respectively

  10. Molecular Identification and Genetic Diversity of Acropora hyacinthus from Boo and Deer Island, Raja Ampat, West Papua

    Science.gov (United States)

    Wijayanti, DP; Indrayanti, E.; Nuryadi, H.; Dewi, RA; Sabdono, A.

    2018-02-01

    Indonesia lies at the centre of biodiversity for corals. However, the reefs suffered from extensive human exploitation. Marine Protected Areas is thought to be best solution to protect coral reefs ecosystem. Understanding genetic diversity is crucial for effective management of the MPAs, however genetic diversity is rarely been corporate in designing an MPA. Moreover, many MPAs are uneffectively manage due to poor designated and demarcated.Raja Ampat which is located in western tip of West Papua, was designated as a park to mitigatethreatsand protect the valuable marine resources.Scleractinian corals in the genus Acropora are among the most dominant distributed in Raja Ampat waters, including the species of Acroporahyacinthus. The research aimed to analyze genetic diversity and to describe the kinship relationship of Acroporahyacinthus between 2 populations: Boo Island and Deer Island, Raja Ampat. Genetic marker Cytochrome Oxidase I (CO I) of the mitochondrial genome DNA (mtDNA) was used to analyze genetic diversity. Reconstruction of phylogenetic tree and genetic diversity were made by usingsoftware MEGA 5.05 (Moleculer Evolutionary Genetics Analysis). The results of this research indicatecorals A. hyacinthus from Boo Island and Deer Island Raja Ampat are in the low category of genetic diversity and overall had a close genetic relationship of kinship. This is likely due to the small size of the population and few numbers of samples that may not represent the population.

  11. Substituent Effects on the Hydrogen Bonding Between Phenolate and HF, H2O and NH3

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    B3LYP/6-31+g(d) calculations were performed on the hydrogen bonded complexes between substituted phenolates and HF, H2O as well as NH3. It was found that some properties of the non-covalent complexes, including the interaction energies, donor-acceptor (host-guest) distances, bond lengths, and vibration frequencies, could show well-defined substituent effects. Thus, from the substituent studies we can not only understand the mechanism of a particular non-covalent interaction better, but also easily predict the interaction energies and structures of a particular non-covalent complex, which might otherwise be very hard or resource-consuming to be known. This means that substituent effect is indeed a useful tool to be used in supramolecular chemistry and therefore, many valuable studies remain to be carried out.

  12. The substituent and solvent effects on the antioxidant activity of the ferulic acid derivations

    International Nuclear Information System (INIS)

    Najafi, M.; Bukhari, S.A.

    2014-01-01

    The antioxidant activity of ortho and meta substituted ferulic acid derivatives have been investigated in the gas phase and water. The reaction enthalpies of antioxidant activity of studied derivatives have been calculated and compared with corresponding values of ferulic acid. Results show that EWG substituents increase the BDE, IP, while EDG ones cause a rise in the PA. The ferulic acid derivatives with lowest BDE, IP and PA values were identified as the compounds with high antioxidant activity. Results show that the substituents at ortho position have high potential for synthesis of novel ferulic acid derivatives. Results show that ferulic acid derivatives can process their protective role via HAT and SPLET mechanism in gas phase and solvent, respectively. The calculated reaction enthalpies of the substituted ferulic acids have linear dependences with Hammett constants and EHOMO that can be utilized in the selection of suitable substituents for the synthesis of novel antioxidants based on ferulic acid. (author)

  13. Effects of p-substituents on electrochemical CO oxidation by Rh porphyrin-based catalysts.

    Science.gov (United States)

    Yamazaki, Shin-ichi; Yamada, Yusuke; Takeda, Sahori; Goto, Midori; Ioroi, Tsutomu; Siroma, Zyun; Yasuda, Kazuaki

    2010-08-21

    Electrochemical CO oxidation by several carbon-supported rhodium tetraphenylporphyrins with systematically varied meso-substituents was investigated. A quantitative analysis revealed that the p-substituents on the meso-phenyl groups significantly affected CO oxidation activity. The electrocatalytic reaction was characterized in detail based on the spectroscopic and X-ray structural results as well as electrochemical analyses. The difference in the activity among Rh porphyrins is discussed in terms of the properties of p-substituents along with a proposed reaction mechanism. Rhodium tetrakis(4-carboxyphenyl)porphyrin (Rh(TCPP)), which exhibited the highest activity among the porphyrins tested, oxidized CO at a high rate at much lower potentials (means that CO is electrochemically oxidized by this catalyst when a slight overpotential is applied during the operation of a proton exchange membrane fuel cell. This catalyst exhibited little H(2) oxidation activity, in contrast to Pt-based catalysts.

  14. pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment

    DEFF Research Database (Denmark)

    El Azhari, Najoi

    2007-01-01

    Microorganisms degrading phenolic compounds play an important role in soil carbon cycling as well as in pesticide degradation. The pcaH gene encoding a key ring-cleaving enzyme of the β-ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were cl......H sequences from Actinobacteria and Proteobacteria phyla. This confirms that the developed primer pair targets a wide diversity of pcaH sequences, thereby constituting a suitable molecular marker to estimate the response of the pca community to agricultural practices....

  15. 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...

  16. Investigating Genetic Diversity Among Cotton Genotypes Available in the Iranian Gene Bank (Gossypium sp. Using ISSR Molecular Marker

    Directory of Open Access Journals (Sweden)

    F Shahriari Ahmadi

    2013-04-01

    Full Text Available Cotton is one of the most important world crops and is considered as a major cash crop in the North East of Iran. All selections in plant breeding are based on diversity and an increase in genetic diversity determines the range of selection. In the present study, 24 cultivars of cotton available at the research station for cotton in the East of Iran -Kashmar- were studied using the ISSR marker. A total number of 13 primers, with repeated simple sequences, were used for the amplification of genomic DNA. Overall, 128 bands were obtained, 109 of which showed polymorphism. To evaluate genetic similarity between cultivars, cluster analysis accompanied by the similarity coefficient developed by Jaccard and Nee (1972, were applied using the UPGMA method. Dendrogram analysis showed a high diversity in the cotton cultivars and two main groups with 70 percent genetic similarity dividing the cotton cultivars into two main groups; namely, tetraploid and diploid. The highest polymorphism percentage was related to 5' (CT8RC3' (100% and the lowest belonged to 5' (AG8YA3' and 5' (TC8G3' (25% primers. Based on the similarity matrix, the highest genetic similarity was found in Varamin and Khordad and the lowest in Avangard and Bakhtegan cultivars. Based on the obtained results, ISSR markers can be efficiently used for the investigation of genetic diversity among cotton cultivars.

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

    KAUST Repository

    Garcí a, Francisca C.; Alonso-Sá ez, Laura; Moran, Xose Anxelu G.; Ló pez-Urrutia, Á ngel

    2015-01-01

    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

  19. Porcine reproductive and respiratory syndrome virus: antigenic and molecular diversity of British isolates and implications for diagnosis.

    Science.gov (United States)

    Frossard, Jean-Pierre; Fearnley, Catherine; Naidu, Brindha; Errington, Jane; Westcott, David G; Drew, Trevor W

    2012-08-17

    Porcine reproductive and respiratory syndrome (PRRS) is an endemic disease of pigs, caused by PRRS virus, a member of the Arteriviridae family. First seen in Britain in 1991, the disease continues to be a significant economic and welfare problem for pig producers. To date, only PRRSV genotype 1 has been found in Britain. At the genetic level, a considerable increase has been reported in the diversity of PRRS viruses isolated in Britain between 2003 and 2007, versus the early 1990 s. In this study, the diversity has been shown to extend to the antigenic level too, with potential consequences for diagnostic methods. Antigenic diversity was assessed using a panel of twelve monoclonal antibodies, only one of which reacted with all isolates tested. Nine diverse viruses were compared as potential antigens in immunoperoxidase monolayer assays, where each one produced quite different results for a common panel of sera. As a single virus is used in each diagnostic assay, results must therefore be interpreted cautiously. For a real-time RT-PCR assay, published oligonucleotide primer and probe sequences were evaluated against available genetic sequences of British and European viruses, and were re-designed where considerable mismatches were found. The multiplex assay incorporating these modified primers to detect genotype 1 and 2 PRRS viruses was then validated for use with diagnostic sera and tissues. As the increasing degree of diversity exhibited by British strains is mirrored in other countries, PRRSV will continue to provide an ongoing challenge to diagnosis at a global, as well as national level. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

  20. Molecular approaches for genetic improvement of seed quality and characterization of genetic diversity in soybean: a critical review.

    Science.gov (United States)

    Tripathi, Niraj; Khare, Dhirendra

    2016-10-01

    Soybean is an economically important leguminous crop. Genetic improvements of soybeans have focused on enhancement of seed and oil yield, development of varieties suited to different cropping systems, and breeding resistant/tolerant varieties for various biotic and abiotic stresses. Plant breeders have used conventional breeding techniques for the improvement of these traits in soybean. The conventional breeding process can be greatly accelerated through the application of molecular and genomic approaches. Molecular markers have proved to be a new tool in soybean breeding by enhancing selection efficiency in a rapid and time-bound manner. An overview of molecular approaches for the genetic improvement of soybean seed quality parameters, considering recent applications of marker-assisted selection and 'omics' research, is provided in this article.

  1. Delocalization does not always stabilize : a quantum chemical analysis of -substituent effects on 54 alkyl and vinyl cations

    NARCIS (Netherlands)

    Alem, van K.; Lodder, G.; Zuilhof, H.

    2002-01-01

    The effects of -substituents on alkyl and vinyl cations are studied using high-level ab initio calculations. The geometries, stabilities, and electronic properties of 27 alkyl cations and 27 vinyl cations with -substituents are computed at the B3LYP/6-311 G(d,p), MP2/6-311 G(d,p), and CBS-Q levels.

  2. Molecules with Linear π-Conjugated Pathways between All Substituents : Omniconjugation

    NARCIS (Netherlands)

    Veen, Marleen H. van der; Rispens, Minze T.; Jonkman, Harry T.; Hummelen, Jan C.

    2004-01-01

    In this paper, omniconjugation is introduced as a topological phenomenon in π-conjugated systems. Omniconjugated molecules are defined by the fact that they provide direct and fully π-conjugated pathways between all substituents attached to them. Surprisingly, until now such topologies have never

  3. Functional dependency of structures of ionic liquids: do substituents govern the selectivity of enzymatic glycerolysis?

    DEFF Research Database (Denmark)

    Guo, Zheng; Chen, Biqiang; Murillo, Rafael López

    2006-01-01

    hydrophobic substituents and hydrophilic ethoxyl or hydroxyl moieties is found, respectively, to be essential for triglycerides (TG) dissolving and equilibrium shifting. The reactions in the ILs with cations consisting of long chain and free hydroxyl groups gave markedly higher conversion of TG and better...

  4. Substituent effif ects on hydrogen bonding in Watson-Crick base pairs. A theoretical study

    NARCIS (Netherlands)

    Fonseca Guerra, C.; van der Wijst, T.; Bickelhaupt, F.M.

    2005-01-01

    We have theoretically analyzed Watson-Crick AT and GC base pairs in which purine C8 and/or pyrimidine C6 positions carry a substituent X = H, F, Cl or Br, using the generalized gradient approximation (GGA) of density functional theory at BP86/TZ2P. The purpose is to study the effects on structure

  5. Role of substituents on the reactivity and electron density profile of ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 125; Issue 5. Role of substituents on the reactivity and electron density profile of diimine ligands: A density functional theory based study. Bhakti S Kulkarni Deepti Mishra Sourav Pal. Volume 125 Issue 5 September 2013 pp 1247-1258 ...

  6. Substituent effects on the excited states of phenyl-capped phenylene vinylene tetramers

    NARCIS (Netherlands)

    Candeias, L.P.; Gelinck, G.H.; Piet, J.J.; Piris, J.; Wegewijs, B.; Peeters, E.; Wildeman, J.; Hadziioannou, G.; Müllen, K.

    2001-01-01

    The singlet and triplet excited states of phenyl-capped tetramers of phenylene vinylene with different alkyl, alkoxy or cyano substituents, were investigated in benzene solution. The lowest singlet states were studied by laser flash-photolysis with time-resolved microwave conductivity and

  7. Substituent effects in the ortho position: Model compounds with a removed reaction centre

    Czech Academy of Sciences Publication Activity Database

    Böhm, S.; Exner, Otto

    2007-01-01

    Roč. 81, 5/6 (2007), s. 993-1006 ISSN 0137- 5083 Institutional research plan: CEZ:AV0Z40550506 Keywords : substituent effect * density functional theory * ortho effect * steric effect Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.483, year: 2007

  8. Extraction of inhibitor-free metagenomic DNA from polluted sediments, compatible with molecular diversity analysis using adsorption and ion-exchange treatments.

    Science.gov (United States)

    Desai, Chirayu; Madamwar, Datta

    2007-03-01

    PCR inhibitor-free metagenomic DNA of high quality and high yield was extracted from highly polluted sediments using a simple remediation strategy of adsorption and ion-exchange chromatography. Extraction procedure was optimized with series of steps, which involved gentle mechanical lysis, treatment with powdered activated charcoal (PAC) and ion-exchange chromatography with amberlite resin. Quality of the extracted DNA for molecular diversity analysis was tested by amplifying bacterial 16S rDNA (16S rRNA gene) with eubacterial specific universal primers (8f and 1492r), cloning of the amplified 16S rDNA and ARDRA (amplified rDNA restriction analysis) of the 16S rDNA clones. The presence of discrete differences in ARDRA banding profiles provided evidence for expediency of the DNA extraction protocol in molecular diversity studies. A comparison of the optimized protocol with commercial Ultraclean Soil DNA isolation kit suggested that method described in this report would be more efficient in removing metallic and organic inhibitors, from polluted sediment samples.

  9. Molecular epidemiology and genetic diversity of Orientia tsutsugamushi from patients with scrub typhus in 3 regions of India.

    Science.gov (United States)

    Varghese, George M; Janardhanan, Jeshina; Mahajan, Sanjay K; Tariang, David; Trowbridge, Paul; Prakash, John A J; David, Thambu; Sathendra, Sowmya; Abraham, O C

    2015-01-01

    Scrub typhus, an acute febrile illness that is widespread in the Asia-Pacific region, is caused by the bacterium Orientia tsutsugamushi, which displays high levels of antigenic variation. We conducted an investigation to identify the circulating genotypes of O. tsutsugamushi in 3 scrub typhus-endemic geographic regions of India: South India, Northern India, and Northeast India. Eschar samples collected during September 2010-August 2012 from patients with scrub typhus were subjected to 56-kDa type-specific PCR and sequencing to identify their genotypes. Kato-like strains predominated (61.5%), especially in the South and Northeast, followed by Karp-like strains (27.7%) and Gilliam and Ikeda strains (2.3% each). Neimeng-65 genotype strains were also observed in the Northeast. Clarifying the genotypic diversity of O. tsutsugamushi in India enhances knowledge of the regional diversity among circulating strains and provides potential resources for future region-specific diagnostic studies and vaccine development.

  10. What are the cyanobacterial genera Cyanothece and Cyanobacterium? Contribution to the combined molecular and phenotype taxonomic evaluation of cyanobacterial diversity

    Czech Academy of Sciences Publication Activity Database

    Komárek, Jiří; Cepák, Vladislav; Kaštovský, J.; Sulek, J.

    2004-01-01

    Roč. 153, č. 113 (2004), s. 1-36 ISSN 0342-1120 R&D Projects: GA AV ČR KSK6005114; GA AV ČR IAA6005308 Institutional research plan: CEZ:AV0Z6005908 Keywords : taxonomy * cyanobacteria * molecular evaluation Subject RIV: EF - Botanics

  11. Network diversity through two-step crystal engineering of a decorated 6-connected primary molecular building block

    KAUST Repository

    Yang, Qing-Yuan; Chen, Kai-Jie; Schoedel, Alexander; Wojtas, Lukasz; Perry IV, John J.; Zaworotko, Michael J.

    2016-01-01

    [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.

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

    NARCIS (Netherlands)

    Mokuwa, G.A.; Nuijten, H.A.C.P.; Okry, F.; Teeken, B.W.E.; Maat, H.; Richards, P.; Struik, P.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

  14. Molecular Phylogenetic Exploration of Bacterial Diversity in a Bakreshwar (India) Hot Spring and Culture of Shewanella-Related Thermophiles

    Science.gov (United States)

    Ghosh, Dhritiman; Bal, Bijay; Kashyap, V. K.; Pal, Subrata

    2003-01-01

    The bacterial diversity of a hot spring in Bakreshwar, India, was investigated by a culture-independent approach. 16S ribosomal DNA clones derived from the sediment samples were found to be associated with gamma-Proteobacteria, cyanobacteria, and green nonsulfur and low-GC gram-positive bacteria. The first of the above phylotypes cobranches with Shewanella, a well-known iron reducer. This phylogenetic correlation has been exploited to develop culture conditions for thermophilic iron-reducing microorganisms. PMID:12839826

  15. Genetic diversity of Plasmodium falciparum isolates from naturally infected children in north-central Nigeria using the merozoite surface protein-2 as molecular marker.

    Science.gov (United States)

    Oyedeji, Segun Isaac; Awobode, Henrietta Oluwatoyin; Anumudu, Chiaka; Kun, Jürgen

    2013-08-01

    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. 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. 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. 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. Copyright © 2013 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

  16. 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.

  17. 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.

  18. Assessment of sorghum genetic resources for genetic diversity and drought tolerance using molecular markers and agro-morphological traits

    Energy Technology Data Exchange (ETDEWEB)

    Abu Assar, A H; Salih, M; Ali, A M [Agricultural Research Corporation (ARC), P.O. Box 126 Wad Medani (Sudan); Uptmoor, R [Institute of Vegetable and Fruit Science, University of Hannover, Herrengauser Strabe 2.30419 Hanover (Greece); Abdelmula, A A [Department of Agronomy, Faculty of Agriculture, University of Khartoum, postal code: 13314 Shambat (Sudan); Ordon, F [Institute of Eqidemiology and Resistance, Federal Centre for Breeding Research on Cultivated Plants, Theodor-Roemer-Weg 4, D-06449 Aschersleben (Greece); Wagner, C; Friedt, W [Institute of Crop Science and Plant Breedin 1, Heinrich-Buff-Ring 26-32, D-35392 Giessen (Greece)

    2009-07-01

    Forty sorghum genotype were investigated for genetic diversity and drought tolerance. Diversity parameters were estimated using 16 simple sequence repeats markers. For assessment of drought tolerance, the genotype were field evaluated under normal and drought stress condition for two seasons in three environments, in Sudan. In total, 98 SSRs alleles were detected with an average of 6.1 alleles per locus. The estimated polymorphic information contents ranged from 0.33 to 0.86. The genetic similarity ranged from 0.00 to 0.88 with a low mean of 0.32. The dendrogram, generated from the UPGMA cluster analysis, showed two main clusters differentiated into nine sub-clusters with close relationship to morphological characters and pedigree information. Mantel statistics revealed a good fit of the cophenetic values to the original data set (r= 0.88). The overall mean genetic diversity was 0.67. Significant differences were detected among genotypes under both normal and drought stressed conditions for all measured traits. Based on the relative yield, the most drought-tolerant genotypes were Arfa Gadamak, Wad Ahmed, El-Najada, Korcola, ICSR 92003 And Sham Sham. Drought five days delay in flowering, and the earliest genotypes were PI 569695, PI 570446, PI 569953, Dwarf White Milo and PI 56995. (Author)

  19. Assessment of sorghum genetic resources for genetic diversity and drought tolerance using molecular markers and agro-morphological traits

    International Nuclear Information System (INIS)

    Abu Assar, A. H.; Salih, M.; Ali, A. M.; Uptmoor, R.; Abdelmula, A. A.; Ordon, F.; Wagner, C.; Friedt, W.

    2009-01-01

    Forty sorghum genotype were investigated for genetic diversity and drought tolerance. Diversity parameters were estimated using 16 simple sequence repeats markers. For assessment of drought tolerance, the genotype were field evaluated under normal and drought stress condition for two seasons in three environments, in Sudan. In total, 98 SSRs alleles were detected with an average of 6.1 alleles per locus. The estimated polymorphic information contents ranged from 0.33 to 0.86. The genetic similarity ranged from 0.00 to 0.88 with a low mean of 0.32. The dendrogram, generated from the UPGMA cluster analysis, showed two main clusters differentiated into nine sub-clusters with close relationship to morphological characters and pedigree information. Mantel statistics revealed a good fit of the cophenetic values to the original data set (r= 0.88). The overall mean genetic diversity was 0.67. Significant differences were detected among genotypes under both normal and drought stressed conditions for all measured traits. Based on the relative yield, the most drought-tolerant genotypes were Arfa Gadamak, Wad Ahmed, El-Najada, Korcola, ICSR 92003 And Sham Sham. Drought five days delay in flowering, and the earliest genotypes were PI 569695, PI 570446, PI 569953, Dwarf White Milo and PI 56995. (Author)

  20. 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.

  1. Molecular Analysis of the Diversity of Sulfate-Reducing and Sulfur-Oxidizing Prokaryotes in the Environment, Using aprA as Functional Marker Gene▿ †

    Science.gov (United States)

    Meyer, Birte; Kuever, Jan

    2007-01-01

    The dissimilatory adenosine-5′-phosposulfate reductase is a key enzyme of the microbial sulfate reduction and sulfur oxidation processes. Because the alpha- and beta-subunit-encoding genes, aprBA, are highly conserved among sulfate-reducing and sulfur-oxidizing prokaryotes, they are most suitable for molecular profiling of the microbial community structure of the sulfur cycle in environment. In this study, a new aprA gene-targeting assay using a combination of PCR and denaturing gradient gel electrophoresis is presented. The screening of sulfate-reducing and sulfur-oxidizing reference strains as well as the analyses of environmental DNA from diverse habitats (e.g., microbial mats, invertebrate tissue, marine and estuarine sediments, and filtered hydrothermal water) by the new primer pair revealed an improved microbial diversity coverage and less-pronounced template-to-PCR product bias in direct comparison to those of the previously published primer set (B. Deplancke, K. R. Hristova, H. A. Oakley, V. J. McCracken, R. Aminov, R. I. Mackie, and H. R. Gaskins, Appl. Environ. Microbiol. 66:2166-2174, 2000). The concomitant molecular detection of sulfate-reducing and sulfur-oxidizing prokaryotes was confirmed. The new assay was applied in comparison with the 16S rRNA gene-based analysis to investigate the microbial diversity of the sulfur cycle in sediment, seawater, and manganese crust samples from four study sites in the area of the Lesser Antilles volcanic arc, Caribbean Sea (Caribflux project). The aprA gene-based approach revealed putative sulfur-oxidizing Alphaproteobacteria of chemolithoheterotrophic lifestyle to have been abundant in the nonhydrothermal sediment and water column. In contrast, the sulfur-based microbial community that inhabited the surface of the volcanic manganese crust was more complex, consisting predominantly of putative chemolithoautotrophic sulfur oxidizers of the Betaproteobacteria and Gammaproteobacteria. PMID:17921272

  2. Molecular analysis of the diversity of sulfate-reducing and sulfur-oxidizing prokaryotes in the environment, using aprA as functional marker gene.

    Science.gov (United States)

    Meyer, Birte; Kuever, Jan

    2007-12-01

    The dissimilatory adenosine-5'-phosphosulfate reductase is a key enzyme of the microbial sulfate reduction and sulfur oxidation processes. Because the alpha- and beta-subunit-encoding genes, aprBA, are highly conserved among sulfate-reducing and sulfur-oxidizing prokaryotes, they are most suitable for molecular profiling of the microbial community structure of the sulfur cycle in environment. In this study, a new aprA gene-targeting assay using a combination of PCR and denaturing gradient gel electrophoresis is presented. The screening of sulfate-reducing and sulfur-oxidizing reference strains as well as the analyses of environmental DNA from diverse habitats (e.g., microbial mats, invertebrate tissue, marine and estuarine sediments, and filtered hydrothermal water) by the new primer pair revealed an improved microbial diversity coverage and less-pronounced template-to-PCR product bias in direct comparison to those of the previously published primer set (B. Deplancke, K. R. Hristova, H. A. Oakley, V. J. McCracken, R. Aminov, R. I. Mackie, and H. R. Gaskins, Appl. Environ. Microbiol. 66:2166-2174, 2000). The concomitant molecular detection of sulfate-reducing and sulfur-oxidizing prokaryotes was confirmed. The new assay was applied in comparison with the 16S rRNA gene-based analysis to investigate the microbial diversity of the sulfur cycle in sediment, seawater, and manganese crust samples from four study sites in the area of the Lesser Antilles volcanic arc, Caribbean Sea (Caribflux project). The aprA gene-based approach revealed putative sulfur-oxidizing Alphaproteobacteria of chemolithoheterotrophic lifestyle to have been abundant in the nonhydrothermal sediment and water column. In contrast, the sulfur-based microbial community that inhabited the surface of the volcanic manganese crust was more complex, consisting predominantly of putative chemolithoautotrophic sulfur oxidizers of the Betaproteobacteria and Gammaproteobacteria.

  3. Identification of three new isolates of Tomato spotted wilt virus from different hosts in China: molecular diversity, phylogenetic and recombination analyses.

    Science.gov (United States)

    Zhang, Zhenjia; Wang, Deya; Yu, Chengming; Wang, Zenghui; Dong, Jiahong; Shi, Kerong; Yuan, Xuefeng

    2016-01-14

    Destructive diseases caused by Tomato spotted wilt virus (TSWV) have been reported associated with many important plants worldwide. Recently, TSWV was reported to infect different hosts in China. It is of value to clone TSWV isolates from different hosts and examine diversity and evolution among different TSWV isolates in China as well as worldwide. RT-PCR was used to clone the full-length genome (L, M and S segments) of three new isolates of TSWV that infected different hosts (tobacco, red pepper and green pepper) in China. Identity of nucleotide and amino acid sequences among TSWV isolates were analyzed by DNAMAN. MEGA 5.0 was used to construct phylogenetic trees. RDP4 was used to detect recombination events during evolution of these isolates. Whole-genome sequences of three new TSWV isolates in China were determined. Together with other available isolates, 29 RNA L, 62 RNA M and 66 RNA S of TSWV isolates were analyzed for molecular diversity, phylogenetic and recombination events. This analysis revealed that the entire TSWV genome, especially the M and S RNAs, had major variations in genomic size that mainly involve the A-U rich intergenic region (IGR). Phylogenetic analyses on TSWV isolates worldwide revealed evidence for frequent reassortments in the evolution of tripartite negative-sense RNA genome. Significant numbers of recombination events with apparent 5' regional preference were detected among TSWV isolates worldwide. Moreover, TSWV isolates with similar recombination events usually had closer relationships in phylogenetic trees. All five Chinese TSWV isolates including three TSWV isolates of this study and previously reported two isolates can be divided into two groups with different origins based on molecular diversity and phylogenetic analysis. During their evolution, both reassortment and recombination played roles. These results suggest that recombination could be an important mechanism in the evolution of multipartite RNA viruses, even negative

  4. Evaluation of Genetic Diversity in Collection from Iranian Jujube Ecotypes (Ziziphus spp. using ISSR-molecular Marker

    Directory of Open Access Journals (Sweden)

    hajar shayesteh

    2018-02-01

    Full Text Available Introduction Jujube (Zizyphus jujuba Mill. as a valuable medicinal plant and adapted to different climatic conditions is widespread in many parts of Iran. Nowadays, beside the export of its fruit, jujube is also used as an herbal medicine to treat the diseases, so it has a high economic value. Study on genetic diversity is the first step to identify and preservation of germplasm. It is also considered as the basic principles of plant breeding. DNA markers seem to be the best way in determination of the genetic diversity. Inter simple sequence repeats (ISSR markers are highly polymorphic and combine most benefits of Simple Sequence Repeats (SSRs and amplified fragment length polymorphism (AFLP to the generality of random amplified polymorphic DNA (RAPD. Materials and Methods In order to study of the genetic diversity among 31 ecotypes collected from eight Jujube-rich provinces, including South Khorasan, Razavi Khorasan, Mazandaran, Golestan, Qom, Isfahan, Lorestan and Fars. Genomic DNA was extracted by CTAB method and polymerase chain reaction (PCR was performed with 13 ISSR primers in which six most efficient primers were selected. Cluster analysis based on Dice similarity coefficient and Unweighed Pair Group Method with Arithmetic Mean (UPGMA was carried out and POPGENe.3.2 software was used to determine the similarity of populations with each other. Results and Discussion 84 loci were amplified and 70 of them (83% revealed a proper polymorphism with the size between 200 and 2000 base pair. The average number of amplified and polymorphic bands per primer was 14 and 11.6 respectively. Primers with di-nucleotide repeats produced more polymorphic bands than ones with tri-nucleotide repeats. It seems that this is due to a higher frequency of sequences containing di-nucleotide repeats in intergenic regions and higher possibility of mutation revealed in more diversity in comparison to gene coding regions. Anchored primers with 1 or 2 nucleotides at

  5. High gene flow and genetic diversity in three economically important Zanthoxylum Spp. of Upper Brahmaputra Valley Zone of NE India using molecular markers.

    Science.gov (United States)

    Medhi, K; Sarmah, D K; Deka, M; Bhau, B S

    2014-12-01

    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).

  6. Molecular cytogenetics of the Androctonus scorpions: an oasis of calm in turbulent karyotype evolution of the diverse family Buthidae

    Czech Academy of Sciences Publication Activity Database

    Sadílek, D.; Nguyen, Petr; Koç, H.; Kovařík, F.; Yağmur, E. A.; Šťáhlavský, F.

    2015-01-01

    Roč. 115, č. 1 (2015), s. 69-76 ISSN 0024-4066 R&D Projects: GA ČR(CZ) GP14-35819P Grant - others:Mšk ČR(CZ) SVV 260 087/2014 Institutional support: RVO:60077344 Keywords : 18S rDNA * FISH * holocentric chromosomes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.984, year: 2015 http://onlinelibrary.wiley.com/doi/10.1111/bij.12488/epdf

  7. 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

  8. Genetic diversity in intraspecific hybrid populations of Eucommia ulmoides Oliver evaluated from ISSR and SRAP molecular marker analysis.

    Science.gov (United States)

    Yu, J; Wang, Y; Ru, M; Peng, L; Liang, Z S

    2015-07-03

    Eucommia ulmoides Oliver, the only extant species of Eucommiaceae, is a second-category state-protected endangered plant in China. Evaluation of genetic diversity among some intraspecific hybrid populations of E. ulmoides Oliver is vital for breeding programs and further conservation of this rare species. We studied the genetic diversity of 130 accessions from 13 E. ulmoides intraspecific hybrid populations using inter-simple sequence related (ISSR) and sequence-related amplified polymorphism (SRAP) markers. Of the 100 ISSR primers and 100 SRAP primer combinations screened, eight ISSRs and eight SRAPs were used to evaluate the level of polymorphism and discriminating capacity. A total number of 65 bands were amplified using eight ISSR primers, in which 50 bands (76.9%) were polymorphic, with an average of 8.1 polymorphic fragments per primer. Alternatively, another 244 bands were observed using eight SRAP primer combinations, and 163 (66.8%) of them were polymorphic, with an average of 30.5 polymorphic fragments per primer. The unweighted pair-group method (UPGMA) analysis showed that these 13 populations could be classified into three groups by the ISSR marker and two groups by the SRAP marker. Principal coordinate analysis using SRAP was completely identical to the UPGMA-based clustering, although this was partly confirmed by the results of UPGMA cluster analysis using the ISSR marker. This study provides insights into the genetic background of E. ulmoides intraspecific hybrids. The progenies of the variations "Huazhong-3", "big fruit", "Yanci", and "smooth bark" present high genetic diversity and offer great potential for E. ulmoides breeding and conservation.

  9. Bacterial diversity in Adélie penguin, Pygoscelis adeliae, guano: molecular and morpho-physiological approaches.

    Science.gov (United States)

    Zdanowski, Marek K; Weglenski, Piotr; Golik, Pawel; Sasin, Joanna M; Borsuk, Piotr; Zmuda, Magdalena J; Stankovic, Anna

    2004-11-01

    The total number of bacteria and culturable bacteria in Adélie penguin (Pygoscelis adeliae) guano was determined during 42 days of decomposition in a location adjacent to the rookery in Admiralty Bay, King George Island, Antarctica. Of the culturable bacteria, 72 randomly selected colonies were described using 49 morpho-physiological tests, 27 of which were subsequently considered significant in characterizing and differentiating the isolates. On the basis of the nucleotide sequence of a fragment of the 16S rRNA gene in each of 72 pure isolates, three major phylogenetic groups were identified, namely the Moraxellaceae/Pseudomonadaceae (29 isolates), the Flavobacteriaceae (14), and the Micrococcaceae (29). Grouping of the isolates on the basis of morpho-physiological tests (whether 49 or 27 parameters) showed similar results to those based on 16S rRNA gene sequences. Clusters were characterized by considerable intra-cluster variation in both 16S rRNA gene sequences and morpho-physiological responses. High diversity in abundance and morphometry of total bacterial communities during penguin guano decomposition was supported by image analysis of epifluorescence micrographs. The results indicate that the bacterial community in penguin guano is not only one of the richest in Antarctica, but is extremely diverse, both phylogenetically and morpho-physiologically.

  10. De novo assembly of mitochondrial genomes provides insights into genetic diversity and molecular evolution in wild boars and domestic pigs.

    Science.gov (United States)

    Ni, Pan; Bhuiyan, Ali Akbar; Chen, Jian-Hai; Li, Jingjin; Zhang, Cheng; Zhao, Shuhong; Du, Xiaoyong; Li, Hua; Yu, Hui; Liu, Xiangdong; Li, Kui

    2018-05-10

    Up to date, the scarcity of publicly available complete mitochondrial sequences for European wild pigs hampers deeper understanding about the genetic changes following domestication. Here, we have assembled 26 de novo mtDNA sequences of European wild boars from next generation sequencing (NGS) data and downloaded 174 complete mtDNA sequences to assess the genetic relationship, nucleotide diversity, and selection. The Bayesian consensus tree reveals the clear divergence between the European and Asian clade and a very small portion (10 out of 200 samples) of maternal introgression. The overall nucleotides diversities of the mtDNA sequences have been reduced following domestication. Interestingly, the selection efficiencies in both European and Asian domestic pigs are reduced, probably caused by changes in both selection constraints and maternal population size following domestication. This study suggests that de novo assembled mitogenomes can be a great boon to uncover the genetic turnover following domestication. Further investigation is warranted to include more samples from the ever-increasing amounts of NGS data to help us to better understand the process of domestication.

  11. Molecular and morphological analysis of the critically endangered Fijian iguanas reveals cryptic diversity and a complex biogeographic history.

    Science.gov (United States)

    Keogh, J Scott; Edwards, Danielle L; Fisher, Robert N; Harlow, Peter S

    2008-10-27

    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

  12. 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

  13. Molecular analysis reveals the diversity of Hepatozoon species naturally infecting domestic dogs in a northern region of Brazil.

    Science.gov (United States)

    Gomes, Laise de Azevedo; Moraes, Pablo Henrique Gonçalves; do Nascimento, Luciana de Cássia Silva; O'Dwyer, Lucia Helena; Nunes, Márcio Roberto Teixeira; Rossi, Adriana Dos Reis Ponce; Aguiar, Délia Cristina Figueira; Gonçalves, Evonnildo Costa

    2016-10-01

    This study aimed to optimize molecular methods for detecting DNA of Hepatozoon spp. as well as identify the phylogenetic relationships of Hepatozoon strains naturally infecting domestic dogs in Belém, Pará, northern Brazil. Blood samples were collected from 138 dogs, and screened for Hepatozoon spp. using a new nested PCR assay. Positive samples were subjected to genetic characterization based on amplification and sequencing of approximately 670bp of the Hepatozoon spp. 18S rRNA. Of the positive dogs, four shared the haplotype Belém 01, one dog presented the haplotype Belém 02 and two dogs shared the haplotype Belém 03. A Bayesian inference indicates that haplotypes Belém 01 and Belém 02 are phylogenetically related to H. canis, while Belém 03 is related to H. americanum. Overall, based on the first molecular evidence of H. americanum in Brazilian domestic dogs, the proposed protocol may improve the epidemiological investigation of canine hepatozoonosis. Copyright © 2016 Elsevier GmbH. All rights reserved.

  14. Molecular diversity analysis and bacterial population dynamics of an adapted seawater microbiota during the degradation of Tunisian zarzatine oil.

    Science.gov (United States)

    Zrafi-Nouira, Ines; Guermazi, Sonda; Chouari, Rakia; Safi, Nimer M D; Pelletier, Eric; Bakhrouf, Amina; Saidane-Mosbahi, Dalila; Sghir, Abdelghani

    2009-07-01

    The indigenous microbiota of polluted coastal seawater in Tunisia was enriched by increasing the concentration of zarzatine crude oil. The resulting adapted microbiota was incubated with zarzatine crude oil as the only carbon and energy source. Crude oil biodegradation capacity and bacterial population dynamics of the microbiota were evaluated every week for 28 days (day 7, day 14, day 21, and day 28). Results show that the percentage of petroleum degradation was 23.9, 32.1, 65.3, and 77.8%, respectively. At day 28, non-aromatic and aromatic hydrocarbon degradation rates reached 92.6 and 68.7%, respectively. Bacterial composition of the adapted microflora was analysed by 16S rRNA gene cloning and sequencing, using total genomic DNA extracted from the adapted microflora at days 0, 7, 14, 21, and 28. Five clone libraries were constructed and a total of 430 sequences were generated and grouped into OTUs using the ARB software package. Phylogenetic analysis of the adapted microbiota shows the presence of four phylogenetic groups: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Diversity indices show a clear decrease in bacterial diversity of the adapted microflora according to the incubation time. The Proteobacteria are the most predominant (>80%) at day 7, day 14 and day 21 but not at day 28 for which the microbiota was reduced to only one OTU affiliated with the genus Kocuria of the Actinobacteria. This study shows that the degradation of zarzatine crude oil components depends on the activity of a specialized and dynamic seawater consortium composed of different phylogenetic taxa depending on the substrate complexity.

  15. [Analysis of diversity of Russian and Ukrainian bread wheat (Triticum aestivum L.) cultivars for high-molecular-weight glutenin subunits].

    Science.gov (United States)

    Dobrotvorskaia, T V; Martynov, S P

    2011-07-01

    The allelic diversity of high-moleculat-weght glutenin subunits (H WIGS) in Russian and Ukrainian bread wheat cultivars was analyzed. The diversity of spring wheat cultivars for alleles of the Glu-1 loci is characterized by medium values of the polymorphism index (polymorphism information content, PlC), and in winter wheats it varies from high at the Glu-A1 locus to low at the Glu-D1 locus. The spring and winter cultivars differ significantly in the frequencies of alleles of the glutenin loci. The combination of the Glu-A1b, Glu-B1c, and Glu-D1a alleles prevails among the spring cultivars, and the combination of the Glu-A1a, Glu-B1c, and Glu-D1d alleles prevails among the winter cultivars. The distribution of the Glu-1 alleles significantly depends on the moisture and heat supply in the region of origin of the cultivars. Drought resistance is associated with the Glu-D1a allele in the spring wheat and with the Glu-B1b allele in the winter wheat. The sources of the Glu-1 alleles were identified in the spring and wheat cultivars. The analysis of independence of the distribution of the spring and winter cultivars by the market classes and by the alleles of the HMWGS loci showed a highly significant association of the alleles of three Glu-1 loci with the market classes in foreign cultivars and independence or a weak association in the Russian and Ukrainian cultivars. This seems to be due to the absence of a statistically substantiated system of classification of the domestic cultivars on the basis of their quality.

  16. 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. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  17. High molecular diversity in the true service tree (Sorbus domestica) despite rareness: data from Europe with special reference to the Austrian occurrence.

    Science.gov (United States)

    George, Jan-Peter; Konrad, Heino; Collin, Eric; Thevenet, Jean; Ballian, Dalibor; Idzojtic, Marilena; Kamm, Urs; Zhelev, Peter; Geburek, Thomas

    2015-06-01

    Sorbus domestica (Rosaceae) is one of the rarest deciduous tree species in Europe and is characterized by a scattered distribution. To date, no large-scale geographic studies on population genetics have been carried out. Therefore, the aims of this study were to infer levels of molecular diversity across the major part of the European distribution of S. domestica and to determine its population differentiation and structure. In addition, spatial genetic structure was examined together with the patterns of historic and recent gene flow between two adjacent populations. Leaf or cambium samples were collected from 17 populations covering major parts of the European native range from north-west France to south-east Bulgaria. Seven nuclear microsatellites and one chloroplast minisatellite were examined and analysed using a variety of methods. Allelic richness was unexpectedly high for both markers within populations (mean per locus: 3·868 for nSSR and 1·647 for chloroplast minisatellite). Moreover, there was no evidence of inbreeding (mean Fis = -0·047). The Italian Peninsula was characterized as a geographic region with comparatively high genetic diversity for both genomes. Overall population differentiation was moderate (FST = 0·138) and it was clear that populations formed three groups in Europe, namely France, Mediterranean/Balkan and Austria. Historic gene flow between two local Austrian populations was high and asymmetric, while recent gene flow seemed to be disrupted. It is concluded that molecular mechanisms such as self-incompatibility and high gene flow distances are responsible for the observed level of allelic richness as well as for population differentiation. However, human influence could have contributed to the present genetic pattern, especially in the Mediterranean region. Comparison of historic and recent gene flow may mirror the progress of habitat fragmentation in eastern Austria. © The Author 2015. Published by Oxford University Press

  18. Fine-Tuning of Saponification-Triggered Gelation by Strategic Modification of Peripheral Substituents: Gelation Regulators.

    Science.gov (United States)

    Kumar, Ashish; Singh, Roop Shikha; Kumar, Amit; Ali, Afsar; Biswas, Arnab; Pandey, Daya Shankar

    2016-09-19

    A pioneering approach towards controlling the efficiency of saponification assisted gelation in ethyl ester based Zn II -complexes have been described. Using four new ester containing bis-salen Zn II complexes (C1-C4) involving different para-azo phenyl substituted ligands it has been clearly shown that gelation efficiency is greatly influenced by the electronic effects of the substituents (-H (C1), -CH 3 (C2), -NO 2 (C3), and -OCH 3 (C4)). Morphological, photophysical, and rheological investigations corroborated the experimental observations well and established that gelation efficiency was enhanced with electron-withdrawing characteristics of substituents (C4

  19. Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments

    Science.gov (United States)

    Hurt, Richard A.; Robeson, Michael S.; Shakya, Migun; Moberly, James G.; Vishnivetskaya, Tatiana A.; Gu, Baohua; Elias, Dwayne A.

    2014-01-01

    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. PMID:25033199

  20. Molecular Epidemiology of P. vivax in Iran: High Diversity and Complex Sub-Structure Using Neutral Markers, but No Evidence of Y976F Mutation at pvmdr1.

    Science.gov (United States)

    Hamedi, Yaghoob; Sharifi-Sarasiabi, Khojasteh; Dehghan, Farzaneh; Safari, Reza; To, Sheren; Handayuni, Irene; Trimarsanto, Hidayat; Price, Ric N; Auburn, Sarah

    2016-01-01

    Malaria remains endemic at low levels in the south-eastern provinces of Iran bordering Afghanistan and Pakistan, with the majority of cases attributable to P. vivax. The national guidelines recommend chloroquine (CQ) as blood-stage treatment for uncomplicated P. vivax, but the large influx of imported cases enhances the risk of introducing CQ resistance (CQR). The genetic diversity at pvmdr1, a putative modulator of CQR, and across nine putatively neutral short tandem repeat (STR) markers were assessed in P. vivax clinical isolates collected between April 2007 and January 2013 in Hormozgan Province, south-eastern Iran. One hundred blood samples were collected from patients with microscopy-confirmed P. vivax enrolled at one of five district clinics. In total 73 (73%) were autochthonous cases, 23 (23%) imported cases from Afghanistan or Pakistan, and 4 (4%) with unknown origin. 97% (97/100) isolates carried the F1076L mutation, but none carried the Y976F mutation. STR genotyping was successful in 71 (71%) isolates, including 57(57%) autochthonous and 11 (11%) imported cases. Analysis of population structure revealed 2 major sub-populations, K1 and K2, with further sub-structure within K2. The K1 sub-population had markedly lower diversity than K2 (HE = 0.06 vs HE = 0.82) suggesting that the sub-populations were sustained by distinct reservoirs with differing transmission dynamics, possibly reflecting local versus imported/introduced populations. No notable separation was observed between the local and imported cases although the sample size was limited. The contrasting low versus high diversity in the two sub-populations (K1 and K2) infers that a combination of local transmission and cross-border malaria from higher transmission regions shape the genetic make-up of the P. vivax population in south-eastern Iran. There was no molecular evidence of CQR amongst the local or imported cases, but ongoing clinical surveillance is warranted.

  1. Molecular detection and genetic diversity of bovine Babesia spp., Theileria orientalis, and Anaplasma marginale in beef cattle in Thailand.

    Science.gov (United States)

    Jirapattharasate, Charoonluk; Adjou Moumouni, Paul Franck; Cao, Shinuo; Iguchi, Aiko; Liu, Mingming; Wang, Guanbo; Zhou, Mo; Vudriko, Patrick; Efstratiou, Artemis; Changbunjong, Tanasak; Sungpradit, Sivapong; Ratanakorn, Parntep; Moonarmart, Walasinee; Sedwisai, Poonyapat; Weluwanarak, Thekhawet; Wongsawang, Witsanu; Suzuki, Hiroshi; Xuan, Xuenan

    2017-02-01

    Babesia spp., Theileria orientalis, and Anaplasma marginale are significant tick-borne pathogens that affect the health and productivity of cattle in tropical and subtropical areas. In this study, we used PCR to detect the presence of Babesia bovis, Babesia bigemina, and T. orientalis in 279 beef cattle from Western Thailand and A. marginale in 608 beef cattle from the north, northeastern, and western regions. The PCRs were performed using species-specific primers based on the B. bovis spherical body protein 2 (BboSBP2), B. bigemina rhoptry-associated protein 1a (BbiRAP-1a), T. orientalis major piroplasm surface protein (ToMPSP), and A. marginale major surface protein 4 (AmMSP4) genes. To determine the genetic diversity of the above parasites, amplicons of B. bovis and B. bigemina ITS1-5.8s rRNA gene-ITS2 regions (B. bovis ITS, B. bigemina ITS), ToMPSP, and AmMSP4 genes were sequenced for phylogenetic analysis. PCR results revealed that the prevalence of B. bovis, B. bigemina, T. orientalis, and A. marginale in the Western region was 11.1, 12.5, 7.8, and 39.1 %, respectively. Coinfections of two or three parasites were observed in 17.9 % of the animals sampled. The study revealed that the prevalence of A. marginale in the western region was higher than in the north and northeastern regions (7 %). Sequence analysis showed the BboSBP2 gene to be more conserved than B. bovis ITS in the different isolates and, similarly, the BbiRAP-1a was more conserved than B. bigemina ITS. In the phylogenetic analysis, T. orientalis MPSP sequences were classified into types 3, 5, and 7 as previously reported. A. marginale MSP4 gene sequences shared high identity and similarity with each other and clustered with isolates from other countries. This study provides information on the prevalence and genetic diversity of tick-borne pathogens in beef cattle and highlights the need for effective strategies to control these pathogens in Thailand.

  2. 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.

  3. Molecular diversity of bacterial communities from subseafloor rock samples in a deep-water production basin in Brazil.

    Science.gov (United States)

    von der Weid, Irene; Korenblum, Elisa; Jurelevicius, Diogo; Rosado, Alexandre Soares; Dino, Rodolfo; Sebastian, Gina Vasquez; Seldin, Lucy

    2008-01-01

    The deep subseafloor rock in oil reservoirs represents a unique environment in which a high oilcontamination and very low biomass can be observed. Sampling this environment has been a challenge owing to the techniques used for drilling and coring. In this study, the facilities developed by the Brazilian oil company PETROBRAS for accessing deep subsurface oil reservoirs were used to obtain rock samples at 2,822-2,828 m below the ocean floor surface from a virgin field located in the Atlantic Ocean, Rio de Janeiro. To address the bacterial diversity of these rock samples, PCR amplicons were obtained using the DNA from four core sections and universal primers for 16S rRNA and for APS reductase (aps) genes. Clone libraries were generated from these PCR fragments and 87 clones were sequenced. The phylogenetic analyses of the 16S rDNA clone libraries showed a wide distribution of types in the domain bacteria in the four core samples, and the majority of the clones were identified as belonging to Betaproteobacteria. The sulfate-reducing bacteria community could only be amplified by PCR in one sample, and all clones were identified as belonging to Gammaproteobacteria. For the first time, the bacterial community was assessed in such deep subsurface environment.

  4. 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.

  5. 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

  6. 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.

  7. Novel cancer gene variants and gene fusions of triple-negative breast cancers (TNBCs) reveal their molecular diversity conserved in the patient-derived xenograft (PDX) model.

    Science.gov (United States)

    Jung, Jaeyun; Jang, Kiwon; Ju, Jung Min; Lee, Eunji; Lee, Jong Won; Kim, Hee Jung; Kim, Jisun; Lee, Sae Byul; Ko, Beom Seok; Son, Byung Ho; Lee, Hee Jin; Gong, Gyungyup; Ahn, Sei Yeon; Choi, Jung Kyoon; Singh, Shree Ram; Chang, Suhwan

    2018-04-20

    Despite the improved 5-year survival rate of breast cancer, triple-negative breast cancer (TNBC) remains a challenge due to lack of effective targeted therapy and higher recurrence and metastasis than other subtypes. To identify novel druggable targets and to understand its unique biology, we tried to implement 24 patient-derived xenografts (PDXs) of TNBC. The overall success rate of PDX implantation was 45%, much higher than estrogen receptor (ER)-positive cases. Immunohistochemical analysis revealed conserved ER/PR/Her2 negativity (with two exceptions) between the original and PDX tumors. Genomic analysis of 10 primary tumor-PDX pairs with Ion AmpliSeq CCP revealed high degree of variant conservation (85.0% to 96.9%) between primary and PDXs. Further analysis showed 44 rare variants with a predicted high impact in 36 genes including Trp53, Pten, Notch1, and Col1a1. Among them, we confirmed frequent Notch1 variant. Furthermore, RNA-seq analysis of 24 PDXs revealed 594 gene fusions, of which 163 were in-frame, including AZGP1-GJC3 and NF1-AARSD1. Finally, western blot analysis of oncogenic signaling proteins supporting molecular diversity of TNBC PDXs. Overall, our report provides a molecular basis for the usefulness of the TNBC PDX model in preclinical study. Copyright © 2018. Published by Elsevier B.V.

  8. Morphological and molecular genetic diversity of Strongyluris calotis (Nematoda: Ascaridida: Heterakidae) in South East and East Asian lizards.

    Science.gov (United States)

    Tran, Binh Thi; Ong, An Vinh; Luc, Pham Van; Sato, Hiroshi

    2016-07-01

    Strongyluris calotis is a heterakid nematode in the large intestine of agamid lizards (Reptilia: Sauria: Agamidae) from the Oriental Region. The standard light microscopic definition of the species counts the "caudal papillae" as 10 pairs on male worms. However, previous work from our group using scanning electron microscopy (SEM) on the heterakid from agamid lizards in Japan, Taiwan, and Singapore revealed that this counting contained a pair of phasmids and that two pairs of postcloacal papillae were completely fused to form a pair of united papillae, thus resulting in "10 pairs." In the present study, we examined S. calotis specimens from the Emma Gray's forest lizard, Calotes emma (Agamidae), living in the plain forest at low altitude, and the Vietnam false bloodsucker, Pseudocalotes brevipes (Agamidae), living in the mountainous forest at high altitude in the northern part of Vietnam. Using SEM, the arrangement of caudal papillae in male worms from an Emma Gray's forest lizard was found to be comparable to classical S. calotis specimens from agamid lizards collected in Japan, Taiwan, and Singapore. However, male worms from Vietnam false bloodsuckers did not have a pair of united papillae but had 10 pairs of independent caudal papillae with a pair of phasmids. Molecular genetic analyses of the ribosomal RNA gene (rDNA) of worms of the classical S. calotis morphotype from Japan and Singapore and two S. calotis morphotypes from Vietnam demonstrated absolutely identical nucleotide sequences of partial 18S rDNA (at least 1764 base pairs (bp)) and 5.8S rDNA (158 bp). However, intraspecific differences were detected in other regions of the rDNA, related to the geographical distribution of hosts regardless of morphotype: 97.8-98.5 % identity (443-446 bp/453 bp) in the internal transcribed spacer (ITS)-1 region, 96.6-98.0 % identity (425-431 bp/440 bp) in the ITS-2 region, and 99.6-99.7 % identity (1149-1151 bp/1154 bp) in the 28S rDNA. Thus, in the future, taxonomic

  9. 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.

  10. Genetic diversity of K-antigen gene clusters of Escherichia coli and their molecular typing using a suspension array.

    Science.gov (United States)

    Yang, Shuang; Xi, Daoyi; Jing, Fuyi; Kong, Deju; Wu, Junli; Feng, Lu; Cao, Boyang; Wang, Lei

    2018-04-01

    Capsular polysaccharides (CPSs), or K-antigens, are the major surface antigens of Escherichia coli. More than 80 serologically unique K-antigens are classified into 4 groups (Groups 1-4) of capsules. Groups 1 and 4 contain the Wzy-dependent polymerization pathway and the gene clusters are in the order galF to gnd; Groups 2 and 3 contain the ABC-transporter-dependent pathway and the gene clusters consist of 3 regions, regions 1, 2 and 3. Little is known about the variations among the gene clusters. In this study, 9 serotypes of K-antigen gene clusters (K2ab, K11, K20, K24, K38, K84, K92, K96, and K102) were sequenced and correlated with their CPS chemical structures. On the basis of sequence data, a K-antigen-specific suspension array that detects 10 distinct CPSs, including the above 9 CPSs plus K30, was developed. This is the first report to catalog the genetic features of E. coli K-antigen variations and to develop a suspension array for their molecular typing. The method has a number of advantages over traditional bacteriophage and serum agglutination methods and lays the foundation for straightforward identification and detection of additional K-antigens in the future.

  11. Molecular characterization and diversity of a novel non-autonomous mutator-like transposon family in brassica

    International Nuclear Information System (INIS)

    Nouroz, F.

    2015-01-01

    Transposable elements (TEs) are capable of mobilizing from one genomic location to other, with changes in their copy numbers. Mutator-like elements (MULEs) are DNA transposons characterized by 9 bp target site duplications (TSDs), with high variability in sequence and length, and include non-conserved terminal inverted repeats (TIRs). We identified and characterized a family of Mutator-like elements designated as Shahroz. The structural and molecular analyses revealed that family had a small number of mostly defective non-autonomous MULEs and has shown limited activity in the evolutionary history of the Brassica A-genome. The Shahroz elements range in size from 2734 to 3160 bp including 76 bp imperfect TIRs and 9 bp variable TSDs. The individual copies have shown high homology (52-99%) in their entire lengths. The study revealed that the elements are less in numbers but active in Brassica rapa genomes and PCR amplification revealed their specificity and amplification in A-genome containing diploid and polyploids Brassica. The phylogenetic analysis of Brassica MULEs with other plant Mutator elements revealed that no correlation exists between Brassica MULEs and other elements suggesting a separate line of evolution. Analyzing the regions flanking the insertions revealed that the insertions have showed a preference for AT rich regions. The detailed study of these insertions revealed that although less in number and small sizes, they have played a role in Brassica genome evolution by their mobilization. (author)

  12. New Eocene Coleoid (Cephalopoda Diversity from Statolith Remains: Taxonomic Assignation, Fossil Record Analysis, and New Data for Calibrating Molecular Phylogenies.

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    Pascal Neige

    Full Text Available New coleoid cephalopods are described from statolith remains from the Middle Eocene (Middle Lutetian of the Paris Basin. Fifteen fossil statoliths are identified and assigned to the Sepiidae (Sepia boletzkyi sp. nov.,? Sepia pira sp. nov., Loliginidae (Loligo clarkei sp. nov., and Ommastrephidae (genus indet. families. The sediments containing these fossils indicate permanent aquatic settings in the infralittoral domain. These sediments range in age from 46 Mya to 43 Mya. Analysis of the fossil record of statoliths (from findings described here, together with a review of previously published data indicates marked biases in our knowledge. Fossil statoliths are known from as far back as the Early Jurassic (199.3 to 190.8 Mya but surprisingly, to the best of our knowledge, no record occurs in the Cretaceous. This is a "knowledge bias" and clearly calls for further studies. Finally, we attempt to compare findings described here with fossils previously used to constrain divergence and/or diversification ages of some coleoid subclades in molecular phylogenies. This comparison clearly indicates that the new records detailed here will challenge some estimated divergence times of coleoid cephalopod subclades.

  13. New Eocene Coleoid (Cephalopoda) Diversity from Statolith Remains: Taxonomic Assignation, Fossil Record Analysis, and New Data for Calibrating Molecular Phylogenies.

    Science.gov (United States)

    Neige, Pascal; Lapierre, Hervé; Merle, Didier

    2016-01-01

    New coleoid cephalopods are described from statolith remains from the Middle Eocene (Middle Lutetian) of the Paris Basin. Fifteen fossil statoliths are identified and assigned to the Sepiidae (Sepia boletzkyi sp. nov.,? Sepia pira sp. nov.), Loliginidae (Loligo clarkei sp. nov.), and Ommastrephidae (genus indet.) families. The sediments containing these fossils indicate permanent aquatic settings in the infralittoral domain. These sediments range in age from 46 Mya to 43 Mya. Analysis of the fossil record of statoliths (from findings described here, together with a review of previously published data) indicates marked biases in our knowledge. Fossil statoliths are known from as far back as the Early Jurassic (199.3 to 190.8 Mya) but surprisingly, to the best of our knowledge, no record occurs in the Cretaceous. This is a "knowledge bias" and clearly calls for further studies. Finally, we attempt to compare findings described here with fossils previously used to constrain divergence and/or diversification ages of some coleoid subclades in molecular phylogenies. This comparison clearly indicates that the new records detailed here will challenge some estimated divergence times of coleoid cephalopod subclades.

  14. Molecular diversity and hypoglycemic polypeptide-P content of Momordica charantia in different accessions and different seasons.

    Science.gov (United States)

    Tian, Miao; Zeng, Xiang-Qing; Song, Huan-Lei; Hu, Shan-Xin; Wang, Fu-Jun; Zhao, Jian; Hu, Zhi-Bi

    2015-04-01

    Momordica charantia (MC) has been used for treating diabetes mellitus from ancient times in Asia, Africa and South America. There are many MC accessions in local markets. Polypeptide-P as a main hypoglycemic component in MC was first studied in this experiment to illustrate the different contents in MC of different accessions and different harvesting times. Nineteen MC accessions collected from different regions were clustered into three groups using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) molecular markers. Content of polypeptide-P in the tested MC accessions was detected by western blot (WB) method. The WB results revealed that polypeptide-P was detected in MC accessions harvested in June and July but not in September and October. Furthermore, Polypeptide-P content corresponded well with the MC accessions. Our results suggest that the MC accessions and the harvesting times or the weather during harvest play significant roles in high content of polypeptide-P. © 2014 Society of Chemical Industry.

  15. 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.

  16. 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.

  17. Molecular diversity assessed by VNTR and IS1296 typing of historical Mycoplasma mycoides subsp. mycoides SC strains.

    Science.gov (United States)

    Varela, Filipa; Inácio, João; Botelho, Ana

    2010-12-15

    The last case of Contagious Bovine Pleuropneumonia (CBPP), caused by Mycoplasma mycoides subsp. mycoides SC (MmmSC), in Europe was reported in Portugal in 1999. However, in view of its insidious nature, it is still possible that CBPP could re-emerge. Despite differences in animal host and geographical origin, most of the European MmmSC field isolates were traditionally considered to be very homogeneous. In the present study we performed a retrospective variable-number tandem repeat (VNTR) and IS1296 genotyping analysis of 65 MmmSC field isolates associated to the last CBPP outbreaks that occurred in Portugal in order to elucidate their intra-specific genetic variability. A 8.8 kb region and two VNTR loci (VNTR4 and VNTR5) were analyzed for polymorphisms by PCR amplification. All but one strain presented the same IS1296 profile, in contrast with the VNTR genotyping that confirmed some diversity of Portuguese strains showing VNTR4, the most discriminatory one, four different patterns. VNTR4 type "9" (numbering according to the estimated number of repeats) was the most predominant one mainly in the Entre Douro-Minho region. All isolates from one geographic region (Beira Litoral) presented VNTR4 type "8" suggesting the existence of a region-specific VNTR. These facts raise the hypothesis that at least two CBPP re-emergence events could have occurred in Portugal since 1983 after 30 years of silence. This aspect represents a major concern and is a major reason for the maintenance of intensive research on this disease. Copyright © 2010 Elsevier B.V. All rights reserved.

  18. Discovery and Molecular Basis of a Diverse Set of Polycomb Repressive Complex 2 Inhibitors Recognition by EED.

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    Ling Li

    Full Text Available Polycomb repressive complex 2 (PRC2, a histone H3 lysine 27 methyltransferase, plays a key role in gene regulation and is a known epigenetics drug target for cancer therapy. The WD40 domain-containing protein EED is the regulatory subunit of PRC2. It binds to the tri-methylated lysine 27 of the histone H3 (H3K27me3, and through which stimulates the activity of PRC2 allosterically. Recently, we disclosed a novel PRC2 inhibitor EED226 which binds to the K27me3-pocket on EED and showed strong antitumor activity in xenograft mice model. Here, we further report the identification and validation of four other EED binders along with EED162, the parental compound of EED226. The crystal structures for all these five compounds in complex with EED revealed a common deep pocket induced by the binding of this diverse set of compounds. This pocket was created after significant conformational rearrangement of the aromatic cage residues (Y365, Y148 and F97 in the H3K27me3 binding pocket of EED, the width of which was delineated by the side chains of these rearranged residues. In addition, all five compounds interact with the Arg367 at the bottom of the pocket. Each compound also displays unique features in its interaction with EED, suggesting the dynamics of the H3K27me3 pocket in accommodating the binding of different compounds. Our results provide structural insights for rational design of novel EED binder for the inhibition of PRC2 complex activity.

  19. Molecular diversity of the ammonia-oxidizing bacteria community in disused tin-mining ponds located within 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

    2014-02-01

    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.

  20. Molecular Detection of Tick-Borne Pathogen Diversities in Ticks from Livestock and Reptiles along the Shores and Adjacent Islands of Lake Victoria and Lake Baringo, Kenya

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    David Omondi

    2017-06-01

    Full Text Available Although diverse tick-borne pathogens (TBPs are endemic to East Africa, with recognized impact on human and livestock health, their diversity and specific interactions with tick and vertebrate host species remain poorly understood in the region. In particular, the role of reptiles in TBP epidemiology remains unknown, despite having been implicated with TBPs of livestock among exported tortoises and lizards. Understanding TBP ecologies, and the potential role of common reptiles, is critical for the development of targeted transmission control strategies for these neglected tropical disease agents. During the wet months (April–May; October–December of 2012–2013, we surveyed TBP diversity among 4,126 ticks parasitizing livestock and reptiles at homesteads along the shores and islands of Lake Baringo and Lake Victoria in Kenya, regions endemic to diverse neglected tick-borne diseases. After morphological identification of 13 distinct Rhipicephalus, Amblyomma, and Hyalomma tick species, ticks were pooled (≤8 individuals by species, host, sampling site, and collection date into 585 tick pools. By supplementing previously established molecular assays for TBP detection with high-resolution melting analysis of PCR products before sequencing, we identified high frequencies of potential disease agents of ehrlichiosis (12.48% Ehrlichia ruminantium, 9.06% Ehrlichia canis, anaplasmosis (6.32% Anaplasma ovis, 14.36% Anaplasma platys, and 3.08% Anaplasma bovis,, and rickettsiosis (6.15% Rickettsia africae, 2.22% Rickettsia aeschlimannii, 4.27% Rickettsia rhipicephali, and 4.95% Rickettsia spp., as well as Paracoccus sp. and apicomplexan hemoparasites (0.51% Theileria sp., 2.56% Hepatozoon fitzsimonsi, and 1.37% Babesia caballi among tick pools. Notably, we identified E. ruminantium in both Amblyomma and Rhipicephalus pools of ticks sampled from livestock in both study areas as well as in Amblyomma falsomarmoreum (66.7% and Amblyomma nuttalli (100

  1. Molecular Detection of Tick-Borne Pathogen Diversities in Ticks from Livestock and Reptiles along the Shores and Adjacent Islands of Lake Victoria and Lake Baringo, Kenya.

    Science.gov (United States)

    Omondi, David; Masiga, Daniel K; Fielding, Burtram C; Kariuki, Edward; Ajamma, Yvonne Ukamaka; Mwamuye, Micky M; Ouso, Daniel O; Villinger, Jandouwe

    2017-01-01

    Although diverse tick-borne pathogens (TBPs) are endemic to East Africa, with recognized impact on human and livestock health, their diversity and specific interactions with tick and vertebrate host species remain poorly understood in the region. In particular, the role of reptiles in TBP epidemiology remains unknown, despite having been implicated with TBPs of livestock among exported tortoises and lizards. Understanding TBP ecologies, and the potential role of common reptiles, is critical for the development of targeted transmission control strategies for these neglected tropical disease agents. During the wet months (April-May; October-December) of 2012-2013, we surveyed TBP diversity among 4,126 ticks parasitizing livestock and reptiles at homesteads along the shores and islands of Lake Baringo and Lake Victoria in Kenya, regions endemic to diverse neglected tick-borne diseases. After morphological identification of 13 distinct Rhipicephalus, Amblyomma , and Hyalomma tick species, ticks were pooled (≤8 individuals) by species, host, sampling site, and collection date into 585 tick pools. By supplementing previously established molecular assays for TBP detection with high-resolution melting analysis of PCR products before sequencing, we identified high frequencies of potential disease agents of ehrlichiosis (12.48% Ehrlichia ruminantium , 9.06% Ehrlichia canis ), anaplasmosis (6.32% Anaplasma ovis , 14.36% Anaplasma platys , and 3.08% Anaplasma bovis ,), and rickettsiosis (6.15% Rickettsia africae , 2.22% Rickettsia aeschlimannii , 4.27% Rickettsia rhipicephali , and 4.95% Rickettsia spp.), as well as Paracoccus sp. and apicomplexan hemoparasites (0.51% Theileria sp., 2.56% Hepatozoon fitzsimonsi , and 1.37% Babesia caballi ) among tick pools. Notably, we identified E. ruminantium in both Amblyomma and Rhipicephalus pools of ticks sampled from livestock in both study areas as well as in Amblyomma falsomarmoreum (66.7%) and Amblyomma nuttalli (100%) sampled

  2. Dissemination and genetic diversity of chlamydial agents in Polish wildfowl: Isolation and molecular characterisation of avian Chlamydia abortus strains.

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    Monika Szymańska-Czerwińska

    Full Text Available Wild birds are considered as a reservoir for avian chlamydiosis posing a potential infectious threat to domestic poultry and humans. Analysis of 894 cloacal or fecal swabs from free-living birds in Poland revealed an overall Chlamydiaceae prevalence of 14.8% (n = 132 with the highest prevalence noted in Anatidae (19.7% and Corvidae (13.4%. Further testing conducted with species-specific real-time PCR showed that 65 samples (49.2% were positive for C. psittaci whereas only one was positive for C. avium. To classify the non-identified chlamydial agents and to genotype the C. psittaci and C. avium-positive samples, specimens were subjected to ompA-PCR and sequencing (n = 83. The ompA-based NJ dendrogram revealed that only 23 out of 83 sequences were assigned to C. psittaci, in particular to four clades representing the previously described C. psittaci genotypes B, C, Mat116 and 1V. Whereas the 59 remaining sequences were assigned to two new clades named G1 and G2, each one including sequences recently obtained from chlamydiae detected in Swedish wetland birds. G1 (18 samples from Anatidae and Rallidae grouped closely together with genotype 1V and in relative proximity to several C. abortus isolates, and G2 (41 samples from Anatidae and Corvidae grouped closely to C. psittaci strains of the classical ABE cluster, Matt116 and M56. Finally, deep molecular analysis of four representative isolates of genotypes 1V, G1 and G2 based on 16S rRNA, IGS and partial 23S rRNA sequences as well as MLST clearly classify these isolates within the C. abortus species. Consequently, we propose an expansion of the C. abortus species to include not only the classical isolates of mammalian origin, but also avian isolates so far referred to as atypical C. psittaci or C. psittaci/C. abortus intermediates.

  3. Dissemination and genetic diversity of chlamydial agents in Polish wildfowl: Isolation and molecular characterisation of avian Chlamydia abortus strains

    Science.gov (United States)

    Szymańska-Czerwińska, Monika; Mitura, Agata; Niemczuk, Krzysztof; Zaręba, Kinga; Jodełko, Agnieszka; Pluta, Aneta; Scharf, Sabine; Vitek, Bailey; Aaziz, Rachid; Vorimore, Fabien; Laroucau, Karine; Schnee, Christiane

    2017-01-01

    Wild birds are considered as a reservoir for avian chlamydiosis posing a potential infectious threat to domestic poultry and humans. Analysis of 894 cloacal or fecal swabs from free-living birds in Poland revealed an overall Chlamydiaceae prevalence of 14.8% (n = 132) with the highest prevalence noted in Anatidae (19.7%) and Corvidae (13.4%). Further testing conducted with species-specific real-time PCR showed that 65 samples (49.2%) were positive for C. psittaci whereas only one was positive for C. avium. To classify the non-identified chlamydial agents and to genotype the C. psittaci and C. avium-positive samples, specimens were subjected to ompA-PCR and sequencing (n = 83). The ompA-based NJ dendrogram revealed that only 23 out of 83 sequences were assigned to C. psittaci, in particular to four clades representing the previously described C. psittaci genotypes B, C, Mat116 and 1V. Whereas the 59 remaining sequences were assigned to two new clades named G1 and G2, each one including sequences recently obtained from chlamydiae detected in Swedish wetland birds. G1 (18 samples from Anatidae and Rallidae) grouped closely together with genotype 1V and in relative proximity to several C. abortus isolates, and G2 (41 samples from Anatidae and Corvidae) grouped closely to C. psittaci strains of the classical ABE cluster, Matt116 and M56. Finally, deep molecular analysis of four representative isolates of genotypes 1V, G1 and G2 based on 16S rRNA, IGS and partial 23S rRNA sequences as well as MLST clearly classify these isolates within the C. abortus species. Consequently, we propose an expansion of the C. abortus species to include not only the classical isolates of mammalian origin, but also avian isolates so far referred to as atypical C. psittaci or C. psittaci/C. abortus intermediates. PMID:28350846

  4. Dissemination and genetic diversity of chlamydial agents in Polish wildfowl: Isolation and molecular characterisation of avian Chlamydia abortus strains.

    Science.gov (United States)

    Szymańska-Czerwińska, Monika; Mitura, Agata; Niemczuk, Krzysztof; Zaręba, Kinga; Jodełko, Agnieszka; Pluta, Aneta; Scharf, Sabine; Vitek, Bailey; Aaziz, Rachid; Vorimore, Fabien; Laroucau, Karine; Schnee, Christiane

    2017-01-01

    Wild birds are considered as a reservoir for avian chlamydiosis posing a potential infectious threat to domestic poultry and humans. Analysis of 894 cloacal or fecal swabs from free-living birds in Poland revealed an overall Chlamydiaceae prevalence of 14.8% (n = 132) with the highest prevalence noted in Anatidae (19.7%) and Corvidae (13.4%). Further testing conducted with species-specific real-time PCR showed that 65 samples (49.2%) were positive for C. psittaci whereas only one was positive for C. avium. To classify the non-identified chlamydial agents and to genotype the C. psittaci and C. avium-positive samples, specimens were subjected to ompA-PCR and sequencing (n = 83). The ompA-based NJ dendrogram revealed that only 23 out of 83 sequences were assigned to C. psittaci, in particular to four clades representing the previously described C. psittaci genotypes B, C, Mat116 and 1V. Whereas the 59 remaining sequences were assigned to two new clades named G1 and G2, each one including sequences recently obtained from chlamydiae detected in Swedish wetland birds. G1 (18 samples from Anatidae and Rallidae) grouped closely together with genotype 1V and in relative proximity to several C. abortus isolates, and G2 (41 samples from Anatidae and Corvidae) grouped closely to C. psittaci strains of the classical ABE cluster, Matt116 and M56. Finally, deep molecular analysis of four representative isolates of genotypes 1V, G1 and G2 based on 16S rRNA, IGS and partial 23S rRNA sequences as well as MLST clearly classify these isolates within the C. abortus species. Consequently, we propose an expansion of the C. abortus species to include not only the classical isolates of mammalian origin, but also avian isolates so far referred to as atypical C. psittaci or C. psittaci/C. abortus intermediates.

  5. Shared molecular pathways and gene networks for cardiovascular disease and type 2 diabetes mellitus in women across diverse ethnicities.

    Science.gov (United States)

    Chan, Kei Hang K; Huang, Yen-Tsung; Meng, Qingying; Wu, Chunyuan; Reiner, Alexander; Sobel, Eric M; Tinker, Lesley; Lusis, Aldons J; Yang, Xia; Liu, Simin

    2014-12-01

    Although cardiovascular disease (CVD) and type 2 diabetes mellitus (T2D) share many common risk factors, potential molecular mechanisms that may also be shared for these 2 disorders remain unknown. Using an integrative pathway and network analysis, we performed genome-wide association studies in 8155 blacks, 3494 Hispanic American, and 3697 Caucasian American women who participated in the national Women's Health Initiative single-nucleotide polymorphism (SNP) Health Association Resource and the Genomics and Randomized Trials Network. Eight top pathways and gene networks related to cardiomyopathy, calcium signaling, axon guidance, cell adhesion, and extracellular matrix seemed to be commonly shared between CVD and T2D across all 3 ethnic groups. We also identified ethnicity-specific pathways, such as cell cycle (specific for Hispanic American and Caucasian American) and tight junction (CVD and combined CVD and T2D in Hispanic American). In network analysis of gene-gene or protein-protein interactions, we identified key drivers that included COL1A1, COL3A1, and ELN in the shared pathways for both CVD and T2D. These key driver genes were cross-validated in multiple mouse models of diabetes mellitus and atherosclerosis. Our integrative analysis of American women of 3 ethnicities identified multiple shared biological pathways and key regulatory genes for the development of CVD and T2D. These prospective findings also support the notion that ethnicity-specific susceptibility genes and process are involved in the pathogenesis of CVD and T2D. © 2014 American Heart Association, Inc.

  6. Inhibition coefficient and molecular diversity of multi stress tolerant Trichoderma as potential biocontrol agent against Sclerotium rolfsii Sacc.

    Science.gov (United States)

    Hirpara, Darshna G; Gajera, H P; Hirapara, Jaydeep G; Golakiya, B A

    2017-11-01

    Trichoderma is one of the most exploited biocontrol agent for the management of plant diseases. Twenty strains of Trichoderma (six of T. harzianum, four of T. viride, three of T. virens, three of T. koningii, each one of T. hamatum, T. reesei, T. parceramosum and Trichoderma spp.) subjected to in vitro antagonism up to 12days after inoculation against Sclerotium rolfsii Sacc. causing stem rot in groundnut. A new concept was developed to determine inhibition coefficient representing pathogen biology and biocontrol related biophysical variables. Results explained differential inhibition coefficient of test pathogen by Trichoderma antagonists. The inhibition coefficient of test pathogen was examined highest (91.13%) by T. virens NBAII Tvs12 followed by T. virens MTCC 794 (89.33%) and T. koningii MTCC 796 (62.39%). Microscopic study confirmed biocontrol mechanism as mycoparasitism for Tvs12 and antibiosis for T. koningii MTCC 796. The sclerotial biogenesis of test pathogen was elevated during weak antagonism and diminished in interactions with strong antagonists. The inhibition coefficient of S. rolfsii was significantly negatively correlated with sclerotia formation and lipid peroxidation during the antagonism. Trichoderma strains were screened for fungicides (carbendazim and tebuconazole, thiram and mancozeb) and abiotic stress (drought and salt) tolerance. Results indicated that T. koningii MTCC 796 efficiently grew better than the other strains with maximum radial growth under adverse conditions. The genetic variability among the Trichoderma was determined using 34 gene specific markers which amplified 146 alleles. The SSR similarities explained substantial diversity (15 to 87%) across Trichoderma strains and pathogen S. rolfsii. Principal coordinates analysis (PCA) were comparable to the cluster analysis and first three most informative PC components explained 64.45% of the total variation. In PCA, potent antagonists appear to be distinct from other strains. Five

  7. MLVA Based Classification of Mycobacterium tuberculosis Complex Lineages for a Robust Phylogeographic Snapshot of Its Worldwide Molecular Diversity

    Science.gov (United States)

    Hill, Véronique; Zozio, Thierry; Sadikalay, Syndia; Viegas, Sofia; Streit, Elisabeth; Kallenius, Gunilla; Rastogi, Nalin

    2012-01-01

    Multiple-locus variable-number tandem repeat analysis (MLVA) is useful to establish transmission routes and sources of infections for various microorganisms including Mycobacterium tuberculosis complex (MTC). The recently released SITVITWEB database contains 12-loci Mycobacterial Interspersed Repetitive Units – Variable Number of Tandem DNA Repeats (MIRU-VNTR) profiles and spoligotype patterns for thousands of MTC strains; it uses MIRU International Types (MIT) and Spoligotype International Types (SIT) to designate clustered patterns worldwide. Considering existing doubts on the ability of spoligotyping alone to reveal exact phylogenetic relationships between MTC strains, we developed a MLVA based classification for MTC genotypic lineages. We studied 6 different subsets of MTC isolates encompassing 7793 strains worldwide. Minimum spanning trees (MST) were constructed to identify major lineages, and the most common representative located as a central node was taken as the prototype defining different phylogenetic groups. A total of 7 major lineages with their respective prototypes were identified: Indo-Oceanic/MIT57, East Asian and African Indian/MIT17, Euro American/MIT116, West African-I/MIT934, West African-II/MIT664, M. bovis/MIT49, M.canettii/MIT60. Further MST subdivision identified an additional 34 sublineage MIT prototypes. The phylogenetic relationships among the 37 newly defined MIRU-VNTR lineages were inferred using a classification algorithm based on a bayesian approach. This information was used to construct an updated phylogenetic and phylogeographic snapshot of worldwide MTC diversity studied both at the regional, sub-regional, and country level according to the United Nations specifications. We also looked for IS6110 insertional events that are known to modify the results of the spoligotyping in specific circumstances, and showed that a fair portion of convergence leading to the currently observed bias in phylogenetic classification of strains may

  8. Cultivation-Based and Molecular Assessment of Bacterial Diversity in the Rhizosheath of Wheat under Different Crop Rotations.

    Directory of Open Access Journals (Sweden)

    Muhammad Tahir

    Full Text Available A field study was conducted to compare the formationand bacterial communities of rhizosheaths of wheat grown under wheat-cotton and wheat-rice rotation and to study the effects of bacterial inoculation on plant growth. Inoculation of Azospirillum sp. WS-1 and Bacillus sp. T-34 to wheat plants increased root length, root and shoot dry weight and dry weight of rhizosheathsoil when compared to non-inoculated control plants, and under both crop rotations. Comparing both crop rotations, root length, root and shoot dry weight and dry weight of soil attached with roots were higher under wheat-cotton rotation. Organic acids (citric acid, malic acid, acetic acid and oxalic acid were detected in rhizosheaths from both rotations, with malic acid being most abundant with 24.8±2 and 21.3±1.5 μg g(-1 dry soil in wheat-cotton and wheat-rice rotation, respectively. Two sugars (sucrose, glucose were detected in wheat rhizosheath under both rotations, with highest concentrations of sucrose (4.08±0.5 μg g(-1 and 7.36±1.0 μg g(-1 and glucose (3.12±0.5 μg g(-1 and 3.01± μg g(-1 being detected in rhizosheaths of non-inoculated control plants under both rotations. Diversity of rhizosheath-associated bacteria was evaluated by cultivation, as well as by 454-pyrosequencing of PCR-tagged 16S rRNA gene amplicons. A total of 14 and 12 bacterial isolates predominantly belonging to the genera Arthrobacter, Azospirillum, Bacillus, Enterobacter and Pseudomonaswere obtained from the rhizosheath of wheat grown under wheat-cotton and wheat-rice rotation, respectively. Analysis of pyrosequencing data revealed Proteobacteria, Bacteriodetes and Verrucomicrobia as the most abundant phyla in wheat-rice rotation, whereas Actinobacteria, Firmicutes, Chloroflexi, Acidobacteria, Planctomycetes and Cyanobacteria were predominant in wheat-cotton rotation. From a total of 46,971 sequences, 10.9% showed ≥97% similarity with 16S rRNA genes of 32 genera previously shown to include

  9. Genetic diversity and molecular characterization of Babesia motasi-like in small ruminants and ixodid ticks from China.

    Science.gov (United States)

    Niu, Qingli; Liu, Zhijie; Yang, Jifei; Yu, Peifa; Pan, Yuping; Zhai, Bintao; Luo, Jianxun; Yin, Hong

    2016-07-01

    Ovine babesioses, an important tick-borne disease of sheep and goats in China, is caused by the reproduction of intraerythrocytic protozoa of the Babesia genus. Babesia motasi-like is a Babesia parasite that infects small ruminant in China, and two sub-groups of B. motasi-like can be subdivided based on differences in the rhoptry-associated-protein-1 gene. This study aimed to characterize the distribution, epidemiology and genetics of B. motasi-like in animals and ticks. A molecular investigation was carried out from 2009 to 2015 in 16 provinces in China. In total, 1081 blood samples were collected from sheep and goats originating from 27 different regions, and 778 ixodid tick samples were collected from 8 regions; the samples were tested for the presence of B. motasi-like using a specific nested PCR assay based on the rap-1b gene. The results indicated that 139 (12.9%), 91 (8.4%), 48 (4.4%) and 6 (0.7%) of the blood samples were positive for general B. motasi-like, Babesia sp. BQ1 (Lintan and Ningxian), Babesia sp. Tianzhu and Babesia sp. Hebei sub-groups, mixed infections, respectively. Among the collected 778 ixodid ticks (including Haemaphysalis longicornis, Haemaphysalis qinghaiensis, Dermacentor silvarum, Ixodes persulcatus, Rhipicephalus sanguineus and Rhipicephalus (Boophilus) microplus), the most frequently infected with Babesia were D. silvarum and I. persulcatus (35.7%), followed by H. longicornis (26.8%), H. qinghaiensis (24.8%) and R. sanguineus (9.3%). The PCR results were confirmed by DNA sequencing. The positive rates of B. motasi-like infection in ticks were found to be higher in China, compared with previous studies in other countries. B. motasi-like infections have not previously been reported in D. silvarum, I. persulcatus or R. sanguineus. The findings obtained in this study could be used for planning effective control strategies against babesiosis in China. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Molecular evolution of avian reovirus: evidence for genetic diversity and reassortment of the S-class genome segments and multiple cocirculating lineages

    International Nuclear Information System (INIS)

    Liu, Hung J.; Lee, Long H.; Hsu, Hsiao W.; Kuo, Liam C.; Liao, Ming H.

    2003-01-01

    Nucleotide sequences of the S-class genome segments of 17 field-isolates and vaccine strains of avian reovirus (ARV) isolated over a 23-year period from different hosts, pathotypes, and geographic locations were examined and analyzed to define phylogenetic profiles and evolutionary mechanism. The S1 genome segment showed noticeably higher divergence than the other S-class genes. The σC-encoding gene has evolved into six distinct lineages. In contrast, the other S-class genes showed less divergence than that of the σC-encoding gene and have evolved into two to three major distinct lineages, respectively. Comparative sequence analysis provided evidence indicating extensive sequence divergence between ARV and other orthoreoviruses. The evolutionary trees of each gene were distinct, suggesting that these genes evolve in an independent manner. Furthermore, variable topologies were the result of frequent genetic reassortment among multiple cocirculating lineages. Results showed genetic diversity correlated more closely with date of isolation and geographic sites than with host species and pathotypes. This is the first evidence demonstrating genetic variability among circulating ARVs through a combination of evolutionary mechanisms involving multiple cocirculating lineages and genetic reassortment. The evolutionary rates and patterns of base substitutions were examined. The evolutionary rate for the σC-encoding gene and σC protein was higher than for the other S-class genes and other family of viruses. With the exception of the σC-encoding gene, which nonsynonymous substitutions predominate over synonymous, the evolutionary process of the other S-class genes can be explained by the neutral theory of molecular evolution. Results revealed that synonymous substitutions predominate over nonsynonymous in the S-class genes, even though genetic diversity and substitution rates vary among the viruses

  11. Genetic Diversity Studies Based on Morphological Variability, Pathogenicity and Molecular Phylogeny of the Sclerotinia sclerotiorum Population From Indian Mustard (Brassica juncea

    Directory of Open Access Journals (Sweden)

    Pankaj Sharma

    2018-06-01

    Full Text Available White mold or stem rot disease are ubiquitously distributed throughout the world and the causal organism of this disease Sclerotinia sclerotiorum (Lib. de Bary, is known to infect over 400 plant species. Sclerotinia stem rot is one of the most devastating fungal diseases and poses a serious threat to the worldwide cultivation of oilseed Brassica including India. S. sclerotiorum pathogen usually infects the stem but in severe cases leaves and pods also affected at different developmental stages that deteriorate not only the oil quality but also causing the seed and oil yield losses up to 90% depending on the severity of the disease infestation. This study investigated the morphological and molecular characterization of pathogenic S. sclerotiorum (Lib de Bary geographical isolates from oilseed Brassica including Brassica juncea (Indian mustard. The aim of this study was to compare isolates of S. sclerotiorum originated from different agro-climatic conditions and to analyse similarity or differences between them as well as to examine the virulence of this pathogen specifically in Brassica for the first time. The collection of S. sclerotiorum isolates from symptomatic Brassica plants was done and analyzed for morphological features, and molecular characterization. The virulence evaluation test of 65 isolates on four Brassica cultivars has shown 5 of them were highly virulent, 46 were virulent and 14 were moderately virulent. Phylogenetic analysis encompassing all the morphological features, SSR polymorphism, and ITS sequencing has shown the existence of high genetic diversity among the isolates that categorized all the isolates in three evolutionary lineages in the derived dendrogram. Further, genetic variability analysis based on sequences variation in ITS region of all the isolates has shown the existence of either insertions or deletions of the nucleotides in the ITS region has led to the interspecies variability and observed the variation were

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

    Science.gov (United States)

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

    2017-01-01

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

  13. Changes in Soil Organic Matter Abundance, Molecular Composition, and Diversity in an Arid Ecosystem in Response to Long-term Elevated CO2 Manipulation.

    Science.gov (United States)

    Hess, N. J.; Tfaily, M.; Evans, R. D.; Koyama, A.

    2017-12-01

    Little is known about how soils in arid ecosystems will respond to rising atmospheric CO2 concentration yet arid and semi-arid ecosystems cover more than 40% of Earth's land surface. Previous work in the Mojave Desert (Evans et al., 2014 Nature Climate Change) reported higher soil organic carbon (SOC) and total nitrogen (N) concentrations following 10 years exposure to elevated atmospheric CO2 at the Nevada Desert Free-Air-Carbon dioxide-Enrichment (FACE) Facility (NDFF). In this study, we investigated potential mechanisms that resulted in increased SOC and total N accumulation and stabilization using high resolution mass spectrometry at the NDFF site. Samples were collected from soil profiles to 1 m in depth with a 0.2 m a increment under the dominant evergreen shrub Larrea tridentata. The differences in the molecular composition and diversity of soil organic matter (SOM) were more evident in surface soils and declined with depth, and were consistent with higher SOC and total N concentrations under elevated than ambient CO2. Our molecular analysis also suggested increased root exudation and/or microbial necromass from stabilization of labile C and N contributed to SOM and N stocks. Increased microbial activity and metabolism under elevated CO2 compared to ambient plots suggested that elevated CO2 altered microbial carbon (C) use patterns, reflecting changes in the quality and quantity of SOC inputs. We found that plant-derived compounds were primary substrates for microbial activity under elevated CO2 and microbial products were the main constituents of stabilized SOM. Our results suggest that arid ecosystems are a potential large C sink under elevated CO2, give the extensive coverage of the land surface, and that labile compounds are transformed to stable SOM via microbial processes. Arid systems are limited by water, and thus may have a different C storage potential under changing climates than other ecosystems that are limited by nitrogen or phosphorus.

  14. Molecular evidence of cryptic diversity in Paracaryophyllaeus (Cestoda: Caryophyllidea), parasites of loaches (Cobitidae) in Eurasia, including description of P. vladkae n. sp.

    Science.gov (United States)

    Scholz, Tomáš; Oros, Mikuláš; Bazsalovicsová, Eva; Brabec, Jan; Waeschenbach, Andrea; Xi, Bing-Wen; Aydoğdu, Ali; Besprozvannykh, Vladimir; Shimazu, Takeshi; Králová-Hromadová, Ivica; Littlewood, D Timothy J

    2014-12-01

    Molecular phylogenetic analysis of an extensive collection of monozoic tapeworms of the genus Paracaryophyllaeus Kulakovskaya, 1961 (Cestoda: Caryophyllidea), parasites of loaches (Cypriniformes: Cobitidae) in Eurasia, has revealed cryptic species diversity within this long-time monotypic genus, especially in the Paracaryophyllaeus gotoi (Motomura, 1927) species complex [syn. Paracaryophyllaeus dubininorum (Kulakovskaya, 1961); type species]. Three independent, well-supported clades were discovered on the basis of molecular data: (i) specimens from Misgurnus anguillicaudatus and Cobitis lutheri from China, Russian Far East and Japan - called herein P. cf. gotoi 1, which may be conspecific with P. gotoi (Motomura, 1927), although in the absence of sequence data for P. gotoi from its type locality (basin of the River Kumkan in Korea), no certain inferences about their identity can currently be made; (ii) specimens from M. anguillicaudatus from China and Japan - P. cf. gotoi 2, which are morphologically indistinguishable from those of P. cf. gotoi 1; and (iii) morphologically distinct tapeworms from the endemic loach Cobitis bilseli from southwestern Turkey (Beyşehir Lake), which are described herein as a new species. Paracaryophyllaeus vladkae Scholz, Oros and Aydoğdu n. sp. differs from the remaining species of the genus in the following characteristics: the testes begin anterior to the first vitelline follicles (versus posterior), the body is short and robust (versus more elongate and slender), and the scolex is wide, rounded or apically tapered (versus claviform to truncate). Species composition of the genus, host specificity of species and geographical distribution are briefly discussed. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  15. Molecular Epidemiology of P. vivax in Iran: High Diversity and Complex Sub-Structure Using Neutral Markers, but No Evidence of Y976F Mutation at pvmdr1.

    Directory of Open Access Journals (Sweden)

    Yaghoob Hamedi

    Full Text Available Malaria remains endemic at low levels in the south-eastern provinces of Iran bordering Afghanistan and Pakistan, with the majority of cases attributable to P. vivax. The national guidelines recommend chloroquine (CQ as blood-stage treatment for uncomplicated P. vivax, but the large influx of imported cases enhances the risk of introducing CQ resistance (CQR.The genetic diversity at pvmdr1, a putative modulator of CQR, and across nine putatively neutral short tandem repeat (STR markers were assessed in P. vivax clinical isolates collected between April 2007 and January 2013 in Hormozgan Province, south-eastern Iran. One hundred blood samples were collected from patients with microscopy-confirmed P. vivax enrolled at one of five district clinics. In total 73 (73% were autochthonous cases, 23 (23% imported cases from Afghanistan or Pakistan, and 4 (4% with unknown origin. 97% (97/100 isolates carried the F1076L mutation, but none carried the Y976F mutation. STR genotyping was successful in 71 (71% isolates, including 57(57% autochthonous and 11 (11% imported cases. Analysis of population structure revealed 2 major sub-populations, K1 and K2, with further sub-structure within K2. The K1 sub-population had markedly lower diversity than K2 (HE = 0.06 vs HE = 0.82 suggesting that the sub-populations were sustained by distinct reservoirs with differing transmission dynamics, possibly reflecting local versus imported/introduced populations. No notable separation was observed between the local and imported cases although the sample size was limited.The contrasting low versus high diversity in the two sub-populations (K1 and K2 infers that a combination of local transmission and cross-border malaria from higher transmission regions shape the genetic make-up of the P. vivax population in south-eastern Iran. There was no molecular evidence of CQR amongst the local or imported cases, but ongoing clinical surveillance is warranted.

  16. Molecular analyses reveal an abundant diversity of ticks and rickettsial agents associated with wild birds in two regions of primary Brazilian Atlantic Rainforest.

    Science.gov (United States)

    Luz, Hermes Ribeiro; Faccini, João Luiz Horacio; McIntosh, Douglas

    2017-06-01

    Brazilian wild birds are recognized as frequent and important hosts for immature stages of more than half of the 32 recognized species of Amblyomma ticks recorded in that country. Several species of Amblyomma harbor rickettsial agents, including members of the spotted fever group (SFG). Most studies on this topic relied primarily on morphological characterization and reported large portions of the collected ticks at the genus rather than species level. Clearly, this factor may have contributed to an underestimation of tick diversity and distribution and makes comparisons between studies difficult. The current investigation combined morphological and molecular analyses to assess the diversity of ticks and rickettsial agents associated with wild birds, captured in two regions of native Atlantic rainforest, in the state of Rio de Janeiro, Brazil. A total of 910 birds were captured, representing two orders, 34 families and 106 species, among which 93 specimens (10.2%), were parasitized by 138 immature ticks (60 larvae and 78 nymphs), representing 10 recognized species of the genus Amblyomma; together with two reasonably well classified haplotypes (Amblyomma sp. haplotype Nazaré and Amblyomma sp. strain USNTC 6792). Amplification by PCR and sequencing of rickettsial genes (htrA, gltA, ompA and ompB), demonstrated the presence of Rickettsia DNA in 48 (34%) of the ticks. Specifically, Rickettsia bellii was detected in a single larva and a single nymph of A. aureolatum; R. amblyomatis was found in 16 of 37 A. longirostre and was recorded for the first time in three nymphs of A. calcaratum; R. rhipicephali was detected in 9 (47%) of 19 Amblyomma sp. haplotype Nazaré ticks. The remaining ticks were infected with genetic variants of R. parkeri, namely strain ApPR in 12 A. parkeri and seven Amblyomma sp. haplotype Nazaré ticks, with the strain NOD found in two specimens of A. nodosum. Interestingly, a single larvae of A. ovale was shown to be infected with the emerging

  17. Substituent Effects on the Stability of Thallium and Phosphorus Triple Bonds: A Density Functional Study.

    Science.gov (United States)

    Lu, Jia-Syun; Yang, Ming-Chung; Su, Ming-Der

    2017-07-05

    Three computational methods (M06-2X/Def2-TZVP, B3PW91/Def2-TZVP and B3LYP/LANL2DZ+dp) were used to study the effect of substitution on the potential energy surfaces of RTl≡PR (R = F, OH, H, CH₃, SiH₃, SiMe(Si t Bu₃)₂, Si i PrDis₂, Tbt (=C₆H₂-2,4,6-(CH(SiMe₃)₂)₃), and Ar* (=C₆H₃-2,6-(C₆H₂-2, 4,6- i -Pr₃)₂)). The theoretical results show that these triply bonded RTl≡PR compounds have a preference for a bent geometry (i.e., ∠R⎼Tl⎼P ≈ 180° and ∠Tl⎼P⎼R ≈ 120°). Two valence bond models are used to interpret the bonding character of the Tl≡P triple bond. One is model [I], which is best described as TlP. This interprets the bonding conditions for RTl≡PR molecules that feature small ligands. The other is model [II], which is best represented as TlP. This explains the bonding character of RTl≡PR molecules that feature large substituents. Irrespective of the types of substituents used for the RTl≡PR species, the theoretical investigations (based on the natural bond orbital, the natural resonance theory, and the charge decomposition analysis) demonstrate that their Tl≡P triple bonds are very weak. However, the theoretical results predict that only bulkier substituents greatly stabilize the triply bonded RTl≡PR species, from the kinetic viewpoint.

  18. Substituent effects on the optical properties of naphthalenediimides: A frontier orbital analysis across the periodic table.

    Science.gov (United States)

    Mulder, Joshua R; Guerra, Célia Fonseca; Slootweg, J Chris; Lammertsma, Koop; Bickelhaupt, F Matthias

    2016-01-15

    A comprehensive theoretical treatment is presented for the electronic excitation spectra of ca. 50 different mono-, di-, and tetrasubstituted naphthalenediimides (NDI) using time-dependent density functional theory (TDDFT) at ZORA-CAM-B3LYP/TZ2P//ZORA-BP86/TZ2P with COSMO for simulating the effect of dichloromethane (DCM) solution. The substituents -XHn are from groups 14-17 and rows 2-5 of the periodic table. The lowest dipole-allowed singlet excitation (S0 -S1 ) of the monosubstituted NDIs can be tuned from 3.39 eV for -F to 2.42 eV for -TeH, while the S0 -S2 transition is less sensitive to substitution with energies ranging between 3.67 eV for -CH3 and 3.44 eV for -SbH2 . In the case of NDIs with group-15 and -16 substituents, the optical transitions strongly depend on the extent to which -XHn is planar or pyramidal as well as on the possible formation of intramolecular hydrogen bonds. The accumulative effect of double and quadruple substitution leads in general to increasing bathochromic shifts, but the increased steric hindrance in tetrasubstituted NDIs can lead to deformations that diminish the effectiveness of the substituents. Detailed analyses of the Kohn-Sham orbital electronic structure in monosubstituted NDIs reveal the mesomeric destabilization of the HOMO as the primary cause of the bathochromic shift of the S0-S1 transition. © 2015 Wiley Periodicals, Inc.

  19. Cu(II) bis(thiosemicarbazone) radiopharmaceutical binding to serum albumin: further definition of species dependence and associated substituent effects

    International Nuclear Information System (INIS)

    Basken, Nathan E.; Green, Mark A.

    2009-01-01

    Introduction: The pyruvaldehyde bis(N 4 -methylthiosemicarbazonato)copper(II) (Cu-PTSM) and diacetyl bis(N 4 -methylthiosemicarbazonato)copper(II) (Cu-ATSM) radiopharmaceuticals exhibit strong, species-dependent binding to the IIA site of human serum albumin (HSA), while the related ethylglyoxal bis(thiosemicarbazonato)copper(II) (Cu-ETS) radiopharmaceutical appears to exhibit only nonspecific binding to HSA and animal serum albumins. Methods: To further probe the structural basis for the species dependence of this albumin binding interaction, we examined protein binding of these three radiopharmaceuticals in solutions of albumin and/or serum from a broader array of mammalian species (rat, sheep, donkey, rabbit, cow, pig, dog, baboon, mouse, cat and elephant). We also evaluated the albumin binding of several copper(II) bis(thiosemicarbazone) chelates offering more diverse substitution of the ligand backbone. Results: Cu-PTSM and Cu-ATSM exhibit a strong interaction with HSA that is not apparent with the albumins of other species, while the binding of Cu-ETS to albumin is much less species dependent. The strong interaction of Cu-PTSM with HSA does not appear to simply correlate with variation, relative to the animal albumins, of a single amino acid lining HSA's IIA site. Those agents that selectively interact with HSA share the common feature of only methyl or hydrogen substitution at the carbon atoms of the diimine fragment of the ligand backbone. Conclusions: The interspecies variations in albumin binding of Cu-PTSM and Cu-ATSM are not simply explained by unique amino acid substitutions in the IIA binding pocket of the serum albumins. However, the specific affinity for this region of HSA is disrupted when substituents bulkier than a methyl group appear on the imine carbons of the copper bis(thiosemicarbazone) chelate.

  20. Cu(II) bis(thiosemicarbazone) radiopharmaceutical binding to serum albumin: further definition of species dependence and associated substituent effects

    Energy Technology Data Exchange (ETDEWEB)

    Basken, Nathan E. [Division of Nuclear Pharmacy, Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN 47907 (United States); Green, Mark A. [Division of Nuclear Pharmacy, Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN 47907 (United States)], E-mail: magreen@purdue.edu

    2009-07-15

    Introduction: The pyruvaldehyde bis(N{sup 4}-methylthiosemicarbazonato)copper(II) (Cu-PTSM) and diacetyl bis(N{sup 4}-methylthiosemicarbazonato)copper(II) (Cu-ATSM) radiopharmaceuticals exhibit strong, species-dependent binding to the IIA site of human serum albumin (HSA), while the related ethylglyoxal bis(thiosemicarbazonato)copper(II) (Cu-ETS) radiopharmaceutical appears to exhibit only nonspecific binding to HSA and animal serum albumins. Methods: To further probe the structural basis for the species dependence of this albumin binding interaction, we examined protein binding of these three radiopharmaceuticals in solutions of albumin and/or serum from a broader array of mammalian species (rat, sheep, donkey, rabbit, cow, pig, dog, baboon, mouse, cat and elephant). We also evaluated the albumin binding of several copper(II) bis(thiosemicarbazone) chelates offering more diverse substitution of the ligand backbone. Results: Cu-PTSM and Cu-ATSM exhibit a strong interaction with HSA that is not apparent with the albumins of other species, while the binding of Cu-ETS to albumin is much less species dependent. The strong interaction of Cu-PTSM with HSA does not appear to simply correlate with variation, relative to the animal albumins, of a single amino acid lining HSA's IIA site. Those agents that selectively interact with HSA share the common feature of only methyl or hydrogen substitution at the carbon atoms of the diimine fragment of the ligand backbone. Conclusions: The interspecies variations in albumin binding of Cu-PTSM and Cu-ATSM are not simply explained by unique amino acid substitutions in the IIA binding pocket of the serum albumins. However, the specific affinity for this region of HSA is disrupted when substituents bulkier than a methyl group appear on the imine carbons of the copper bis(thiosemicarbazone) chelate.

  1. Carborane-stilbene dyads: the influence of substituents and cluster isomers on photoluminescence properties.

    Science.gov (United States)

    Ferrer-Ugalde, A; Cabrera-González, J; Juárez-Pérez, E J; Teixidor, F; Pérez-Inestrosa, E; Montenegro, J M; Sillanpää, R; Haukka, M; Núñez, R

    2017-02-14

    Two novel styrene-containing meta-carborane derivatives substituted at the second carbon cluster atom (C c ) with either a methyl (Me) or a phenyl (Ph) group are introduced herein along with a new set of stilbene-containing ortho- (o-) and meta- (m-) carborane dyads. The latter set of compounds have been prepared from styrene-containing carborane derivatives via a Heck coupling reaction. High regioselectivity has been achieved for these compounds by using a combination of palladium complexes [Pd 2 (dba) 3 ]/[Pd(t-Bu 3 P) 2 ] as a catalytic system, yielding exclusively E isomers. All compounds have been fully characterised and the crystal structures of seven of them were analysed by X-ray diffraction. The absorption spectra of these compounds are similar to those of their respective fluorophore groups (styrene or stilbene), showing a very small influence of the substituent (Me or Ph) linked to the second C c atom or the cluster isomer (o- or m-). On the other hand, fluorescence spectroscopy revealed high emission intensities for Me-o-carborane derivatives, whereas their Ph-o-carborane analogues evidenced an almost total lack of fluorescence, confirming the significant role of the substituent bound to the adjacent C c in o-carboranes. In contrast, all the m-carborane derivatives display similar photoluminescence (PL) behavior regardless of the substituent attached to the second C c , demonstrating its small influence on emission properties. Additionally, m-carborane derivatives are significantly more fluorescent than their o-counterparts, reaching quantum yield values as high as 30.2%. Regarding solid state emission, only stilbene-containing Ph-o-carborane derivatives, which showed very low fluorescence in solution, exhibited notable PL emission in films attributed to aggregation-induced emission. DFT calculations were performed to successfully complement the photoluminescence studies, supporting the experimentally observed photophysical behavior of the styrene and

  2. The Influence of Substituents on the Tautomerism of Symmetrically Substituted 2,2'-Bis-benzimidazoles

    Directory of Open Access Journals (Sweden)

    Dall'Oglio Evandro

    2002-01-01

    Full Text Available The tautomerism of five symmetrically substituted 2,2'-bis-benzimidazoles [5(6,5'(6'-tetramethyl- (1; 5(6,5'(6'-dimethyl-(2; 5(6,5'(6'-dichloro- (3; 5(6,5'(6'-dimethoxy- (4 and 4(7,4'(7'-dimethyl-2,2'-bis-benzimidazole (5], was studied by means of ¹H NMR spectroscopy at variable temperatures, and the influence of the substituents on the energy barriers for tautomeric interconversion was interpreted with the aid of theoretical calculations.

  3. Excited-state dynamics of pentacene derivatives with stable radical substituents.

    Science.gov (United States)

    Ito, Akitaka; Shimizu, Akihiro; Kishida, Noriaki; Kawanaka, Yusuke; Kosumi, Daisuke; Hashimoto, Hideki; Teki, Yoshio

    2014-06-23

    The excited-state dynamics of pentacene derivatives with stable radical substituents were evaluated in detail through transient absorption measurements. The derivatives showed ultrafast formation of triplet excited state(s) in the pentacene moiety from a photoexcited singlet state through the contributions of enhanced intersystem crossing and singlet fission. Detailed kinetic analyses for the transient absorption data were conducted to quantify the excited-state characteristics of the derivatives. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Electronic effects of substituents in o-hydroxyazo compounds and azoquinone-hydrazone tautomerism

    International Nuclear Information System (INIS)

    Raikhshtat, M.M.; Zhogina, V.V.; Savvin, S.B.

    1987-01-01

    The authors have investigated the electronic structure of p-substituted phenylazonaphthol and some o-hydroxyazo compounds of the general structure X-N=N-Y. The influence of structural changes of the X and Y radicals on the electronic structure of the o-hydroxyazo group was studied. The results are compared with experimental data, obtained by NMR 13 C, by tautomerism of these compounds in solution in CDCl 3 . The electronic structure of o-hydroxyazo compounds was calculated by the PPDP/2 method. This method satisfactorily describes the electronic structure of organic compounds and correctly reproduces electronic effects of the substituents

  5. Pinworm diversity in free-ranging howler monkeys (Alouatta spp.) in Mexico: Morphological and molecular evidence for two new Trypanoxyuris species (Nematoda: Oxyuridae).

    Science.gov (United States)

    Solórzano-García, Brenda; Nadler, Steven A; Pérez-Ponce de León, Gerardo

    2016-10-01

    Two new species of Trypanoxyuris are described from the intestine of free-ranging howler monkeys in Mexico, Trypanoxyuris multilabiatus n. sp. from the mantled howler Alouatta palliata, and Trypanoxyuris pigrae n. sp. from the black howler Alouatta pigra. An integrative taxonomic approach is followed, where conspicuous morphological traits and phylogenetic trees based on DNA sequences are used to test the validity of the two new species. The mitochondrial cytochrome oxidase subunit 1 gene, and the nuclear ribosomal 18S and 28S rRNA genes were used for evolutionary analyses, with the concatenated dataset of all three genes used for maximum likelihood and Bayesian phylogenetic analyses. The two new species of pinworms from howler monkeys were morphologically distinct and formed reciprocally monophyletic lineages in molecular phylogenetic trees. The three species from howler monkeys, T. multilabiatus n. sp., T. pigrae n. sp., and Trypanoxyuris minutus, formed a monophyletic group with high bootstrap and posterior probability support values. Phylogenetic patterns inferred from sequence data support the hypothesis of a close evolutionary association between these primate hosts and their pinworm parasites. The results suggest that the diversity of pinworm parasites from Neotropical primates might be underestimated. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  6. Molecular Genetic Diversity and Quantitation of Methanogen in Ruminal Fluid of Buffalo (Bubalus bubalis Fed Ration (Wheat Straw and Concentrate Mixture Diet

    Directory of Open Access Journals (Sweden)

    K. M. Singh

    2013-01-01

    Full Text Available High roughage diet causes more methane emissions; however, the total methanogen abundance is not influenced by roughage proportion. Technologies to reduce methane emissions are lacking, and development of inhibitors and vaccines that mitigate rumen-derived methane by targeting methanogens relies on present knowledge of the methanogens. In this work, we have investigated molecular diversity of rumen methanogens of Surti buffalo. DNA from rumen fluid was extracted, and 16S rRNA encoding genes were amplified using methanogen specific primer to generate 16S rDNA clone libraries. Seventy-six clones were randomly selected and analysed by RFLP resulting in 21 operational taxonomic units (OTUs. BLAST analysis with available sequences in database revealed sequences of 13 OTUs (55 clones showing similarity with Methanomicrobium sp, 3 OTUs (15 clones with Methanobrevibacter sp. The remaining 5 OTUs (6 clones belonged to uncultured archaea. The phylogenetic analysis indicated that methanogenic communities found in the library were clustered in the order of Methanomicrobiales (18 OTUs and Methanobacteriales (3 OTUs. The population of Methanomicrobiales, Methanobacteriales, and Methanococcales were also observed, accounting for 1.94%, 0.72%, and 0.47% of total archaea, respectively.

  7. Photoelectron spectra and electronic structure of nitrogen analogues of boron β-diketonates with aromatic substituents

    Energy Technology Data Exchange (ETDEWEB)

    Tikhonov, Sergey A., E-mail: allser@bk.ru [Far Eastern Federal University, 8 Sukhanova St., Vladivostok, 690950 (Russian Federation); Vovna, Vitaliy I. [Far Eastern Federal University, 8 Sukhanova St., Vladivostok, 690950 (Russian Federation); Borisenko, Aleksandr V. [Vladivostok Branch of Russian Customs Academy, 16v Strelkovaya St., Vladivostok, 690034 (Russian Federation)

    2016-11-15

    Highlights: • The electronic structures of three nitrogen analogues of boron β-diketonates have been investigated. • UV photoelectron spectra have been interpreted. • The structure of the UV photoelectron spectra is in good agreement with the energies and compositions of Kohn-Sham orbitals. - Abstract: The electronic structure of three nitrogen analogoues of boron β-diketonates containing aromatic substituents was studied by the ultraviolet photoelectron spectroscopy and within the density functional theory. In order to determine effects of heteroatom substitution in the chelate ligand, a comparative analysis was carried out for the electronic structure of three model compounds. In a range of model compounds, the HOMO's nature was revealed to be the same. The HOMO-1 orbital of nitrogen containing compounds is determined by the presence of lone electron pairs of nitrogen. In a range of the complexes under study, the influence of aromatic substituents on the electronic structure was defined. In the imidoylamidinate complex, in contrast to formazanates and β-diketonates, it was found the absence of any noticeable mixing of π-orbitals of the chelate and benzene rings. It was shown that within energy range to 11 eV, the calculated results reproduce well the energy differences between the ionized states of complexes.

  8. The Influence of Substituent Orientation on the Photovoltaic Performance of Phthalocyanine-Sensitized Solar Cells.

    Science.gov (United States)

    Tejerina, Lara; Martínez-Díaz, M Victoria; Nazeeruddin, Mohammad Khaja; Torres, Tomas

    2016-03-18

    Phthalocyanines (Pcs) are used as sensitizers in dye-sensitized solar cells (DSSCs) because of their stability and intense absorption in the red and near-IR regions. Impressive progress has been made in photovoltaic efficiencies by introduction of bulky peripheral substituents to help suppress macrocycle aggregation. To reach benchmark efficiencies reported for other related dyes, new designs need to be explored. Single carboxy-ZnPc regioisomers substituted at the non-peripheral positions by rigid aryl groups have now been studied, which has shed light on the influence of steric hindrance and/or orientation of the substituent around the anchoring group on the photovoltaic response. The regioisomer bearing the aryl group far away from the anchoring group produces a more effective sensitization of the TiO2 films and higher short-circuit photocurrent density (Jsc). Taking advantage of the good photovoltaic performance in the near-IR region of this ZnPc, it was combined with another appropriate dye for panchromatic sensitization of the mesoporous photoelectrode and an increase of the overall device efficiency. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. DFT study on the effect of exocyclic substituents on the proton affinity of 1-methylimidazole

    International Nuclear Information System (INIS)

    Liu, Haining; Bara, Jason E.; Turner, C. Heath

    2013-01-01

    Highlights: • DFT calculations are used to predict the proton affinity of 1-methylimidazoles. • The electron-withdrawing groups dominate the predicted proton affinity. • The effects of multiple substituents on the proton affinity can be accurately predicted. • Large compound libraries can be screened for imidazoles with tailored reactivity. - Abstract: A deeper understanding of the acid/base properties of imidazole derivatives will aid the development of solvents, polymer membranes and other materials that can be used for CO 2 capture and acid gas removal. In this study, we employ density functional theory calculations to investigate the effect of various electron-donating and electron-withdrawing groups on the proton affinity of 1-methylimidazole. We find that electron-donating groups are able to increase the proton affinity relative to 1-methylimidazole, i.e., making the molecule more basic. In contrast, electron-withdrawing groups cause a decrease of the proton affinity. When multiple substituents are present, their effects on the proton affinity were found to be additive. This finding offers a quick approach for predicting and targeting the proton affinities of this series of molecules, and we show the strong correlation between the calculated proton affinities and experimental pK a values

  10. Design, synthesis, characterization, and OFET properties of amphiphilic heteroleptic tris(phthalocyaninato) europium(III) complexes. The effect of crown ether hydrophilic substituents.

    Science.gov (United States)

    Gao, Yingning; Ma, Pan; Chen, Yanli; Zhang, Ying; Bian, Yongzhong; Li, Xiyou; Jiang, Jianzhuang; Ma, Changqin

    2009-01-05

    Two amphiphilic heteroleptic tris(phthalocyaninato) europium complexes with hydrophilic crown ether heads and hydrophobic octyloxy tails [Pc(mCn)(4)]Eu[Pc(mCn)(4)]Eu[Pc(OC(8)H(17))(8)] [m = 12, n = 4, H(2)Pc(12C4)(4) = 2,3,9,10,16,17,23,24-tetrakis(12-crown-4)phthalocyanine; m = 18, n = 6, H(2)Pc(18C6)(4) = 2,3,9,10,16,17,23,24-tetrakis(18-crown-6)phthalocyanine; H(2)Pc(OC(8)H(17))(8) = 2,3,9,10,16,17,23,24-octakis(octyloxy)phthalocyanine] (1, 2) were designed and prepared from the reaction between homoleptic bis(phthalocyaninato) europium compound [Pc(mCn)(4)]Eu[Pc(mCn)(4)] (m = 12, n = 4; m = 18, n = 6) and metal-free H(2)Pc(OC(8)H(17))(8) in the presence of Eu(acac)(3).H(2)O (Hacac = acetylacetone) in boiling 1,2,4-trichlorobenzene. These novel sandwich triple-decker complexes were characterized by a wide range of spectroscopic methods and electrochemically studied. With the help of the Langmuir-Blodgett technique, these typical amphiphilic triple-decker complexes were fabricated into organic field effect transistors (OFET) with top contact configuration on bare SiO(2)/Si substrate, hexamethyldisilazane-treated SiO(2)/Si substrate, and octadecyltrichlorosilane (OTS)-treated SiO(2)/Si substrate, respectively. The device performance is revealed to be dependent on the species of crown ether substituents and substrate surface treatment. OFETs fabricated from the triple decker with 12-crown-4 hydrophilic substituents, 1, allow the hole transfer in the direction parallel to the aromatic phthalocyanine rings. In contrast, the devices of a triple-decker compound containing 18-crown-6 as hydrophilic heads, 2, transfer holes in a direction along the long axis of the assembly composed of face-to-face aggregated triple-decker molecules, revealing the effect of molecular structure, specifically the crown ether substituents on the film structure and OFET functional properties. The carrier mobility for hole as high as 0.33 cm(2) V(-1) s(-1) and current modulation of 7.91 x 10

  11. Molecular genetic diversity of Vibrio harveyi%哈维氏弧菌的分子遗传多样性研究

    Institute of Scientific and Technical Information of China (English)

    徐芝亮; 吴灶和; 简纪常; 黄郁葱

    2012-01-01

    Vibrio harveyi is known to be a major pathogen in mariculture animal systems. Disease outbreaks attributed to V. harveyi have been reported in main mariculture animal farm production. In recent years,mass mortalities of many cultured kinds of maricultured fishes, such as Litopenaeus vannamei, Pseudosciaena crocea, and Lutjanus sanguineus have occurred frequently infected by V. harveyi. In this article the 101 isolates of V. harveyi were subjected to random amplified polymorphic DNA (RAPD)-PCR and BOX-PCR analysis to investigate the genetic variability among V. harveyi strains. A total of 10 RAPD primers were designed for their specificity in detecting V. harveyi, and only the primer PM2 was highly reproducible and found suitable to use in RAPD-PCR. The genetic diversity among V. harveyi isolates assessed by RAPD-PCR by PM2 primer yielded 15 different RAPD patterns which clustered the isolates into 18 groups at 65% similarity level. Similarly, BOX-PCR clustered the 20 patterns into 15 groups at 40% similarity. However, with RAPD-PCR and BOX-PCR, 101 V. harveyi could be divided into 18 groups at 50% similarity. We could obtain the accurate results of molecular genetic diversity by both RAPD-PCR and BOX-PCR.%运用RAPD分型和BOX分型分子方法研究患病的海水鱼类体内和海水环境的101株哈维氏弧菌的分子遗传多样性.结果显示,从10个RAPD引物中发现只有PM2引物的分辨率和重复性较好,出现15条不同RAPD条带,在相似度65%下,101株哈维氏弧菌可以分为18种不同型;BOX分型出现20条不同的条带,在相似度为40%的情况下,可以把101株哈维式弧菌分15种不同的型;综合RAPD PM2和BOX分型,发现在相似度50%下,101株哈维氏弧菌可分18种型.综合RAPD和BOX分型数据可以很好地克服各自的缺点,得到更加准确的分型结果.

  12. Characterization of molecular diversity and genome-wide mapping of loci associated with resistance to stripe rust and stem rust in Ethiopian bread wheat accessions.

    Science.gov (United States)

    Muleta, Kebede T; Rouse, Matthew N; Rynearson, Sheri; Chen, Xianming; Buta, Bedada G; Pumphrey, Michael O

    2017-08-04

    The narrow genetic basis of resistance in modern wheat cultivars and the strong selection response of pathogen populations have been responsible for periodic and devastating epidemics of the wheat rust diseases. Characterizing new sources of resistance and incorporating multiple genes into elite cultivars is the most widely accepted current mechanism to achieve durable varietal performance against changes in pathogen virulence. Here, we report a high-density molecular characterization and genome-wide association study (GWAS) of stripe rust and stem rust resistance in 190 Ethiopian bread wheat lines based on phenotypic data from multi-environment field trials and seedling resistance screening experiments. A total of 24,281 single nucleotide polymorphism (SNP) markers filtered from the wheat 90 K iSelect genotyping assay was used to survey Ethiopian germplasm for population structure, genetic diversity and marker-trait associations. Upon screening for field resistance to stripe rust in the Pacific Northwest of the United States and Ethiopia over multiple growing seasons, and against multiple races of stripe rust and stem rust at seedling stage, eight accessions displayed resistance to all tested races of stem rust and field resistance to stripe rust in all environments. Our GWAS results show 15 loci were significantly associated with seedling and adult plant resistance to stripe rust at false discovery rate (FDR)-adjusted probability (P) rust in the Ethiopian wheat accessions. Many of the identified resistance loci were mapped close to previously identified rust resistance genes; however, three loci on the short arms of chromosomes 5A and 7B for stripe rust resistance and two on chromosomes 3B and 7B for stem rust resistance may be novel. Our results demonstrate that considerable genetic variation resides within the landrace accessions that can be utilized to broaden the genetic base of rust resistance in wheat breeding germplasm. The molecular markers identified in

  13. Effect of substituents on electronic properties, thin film structure and device performance of dithienothiophene-phenylene cooligomers

    International Nuclear Information System (INIS)

    Zhang Shiming; Guo Yunlong; Xi Hongxia; Di Chongan; Yu Jian; Zheng Kai; Liu Ruigang; Zhan Xiaowei; Liu Yunqi

    2009-01-01

    Dithienothiophene-phenylene cooligomers with n-hexyloxy or n-dodecyloxy substituents have been synthesized and compared to the previously reported unsubstituted parent compound. The effect of substituents on the thermal, electronic, optical, thin film structure and field-effect transistor (OFET) properties was investigated. Structural phase transitions from highly-ordered nanocrystalline to liquid crystalline were observed at 241 and 213 deg. C for n-hexyloxy- and n-dodecyloxy-substituted compounds respectively, different from the parent compound. For the alkoxy-substituted compounds, the absorption spectra in thin film blue shift 50 nm, while the fluorescence spectra in thin film red shift 88-100 nm compared to those in solution. The OFET devices based on the alkoxy-substituted compounds exhibit mobilities as high as ca 0.02 cm 2 V -1 s -1 and their performance is sensitive to the alkoxy substituents and substrate temperatures

  14. A molecular phylogeny of Afromontane dwarf geckos (Lygodactylus) reveals a single radiation and increased species diversity in a South African montane center of endemism.

    Science.gov (United States)

    Travers, Scott L; Jackman, Todd R; Bauer, Aaron M

    2014-11-01

    Afromontane habitats throughout eastern sub-Saharan Africa support remarkable levels of microendemism. However, despite being the subject of decades of research interest, biogeographical patterns of diversification throughout this disjunct montane system still remain largely unknown. We examined the evolutionary relationships of diurnal dwarf geckos (Lygodactylus) from several Afromontane regions throughout southeastern Africa, focusing primarily on two species groups (rex and bonsi groups). Using both mitochondrial and nuclear markers, we generate a molecular phylogeny containing all members of the rex and bonsi groups, to evaluate the monophyly of these groups along with previous biogeographic hypotheses suggesting independent southward invasions into the greater Drakensberg Afromontane center of endemism in northeastern South Africa by each group. Our results provide no support for these taxonomic and biogeographic hypotheses, and instead reveal geographically circumscribed patterns of diversification. One clade is restricted to the highlands of southern Malawi and northern Mozambique and the other to the greater Drakensberg region of northeastern South Africa and Swaziland. Interestingly, L. bernardi from the Nyanga Highlands of eastern Zimbabwe is nested within the primarily savanna-dwelling capensis group. We use Bayesian species delimitation methods to evaluate species limits within the greater Drakensberg clade, which support the elevation of the subspecies of L. ocellatus and L. nigropunctatus, thus bringing the total to eight species within a relatively confined geographic area. These results further highlight the greater Drakensberg Afromontane region as both an important center of endemism, as well as a center of diversification contributing to the accumulation of southern Africa's rich species diversity. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Substituent effects on the electron affinities and ionization energies of tria-, penta-, and heptafulvenes: a computational investigation

    DEFF Research Database (Denmark)

    Dahlstrand, Christian; Yamazaki, Kaoru; Kilså, Kristine

    2010-01-01

    (TCNQ) and tetrathiafulvalene (TTF) as representing strong electron-acceptor and -donor compounds, respectively. The substituents X at the exocyclic positions of the fulvenes were either NH(2), H, or CN, while the substituents Y at the ring positions were H, Cl, F, CN, or NH(2). The variations...... of bis(fulvene)s, i.e., compounds composed of a donor-type heptafulvene fused with an acceptor-type pentafulvene, and it was revealed that these bis(fulvene)s can be designed so that the IE and EA of the two separate fulvene segments are retained, potentially allowing for the design of compact donor...

  16. Theoretical research on effects of substituents and the solvent on quadruple hydrogen bonded complexes

    Directory of Open Access Journals (Sweden)

    Lingjia Xu

    2007-04-01

    Full Text Available Semiempirical AM1 and INDO/CIS methods were used to study the structures and spectroscopy of hydrogen bonded complexes formed by the oligophenyleneethynylene (monomer A with isophthalic acid (monomer B. The binding energies of the complexes are lowered by increasing electron-donating abilities of the substituents near the hydrogen bonds on monomer A. The first absorptions in the electronic spectra and the vibration frequencies of the N-H bonds in the IR spectra for the complexes are both red-shifted compared with those of the monomers. The presence of dimethylsulfoxide (DMSO can reduce the binding energy of the complex through hydrogen bonding. This results in a blue-shift for the first absorption in the electronic spectrum and red-shift for the vibration frequencies of the N-H bonds in the IR spectrum of the complex.

  17. Effects of para-substituents of styrene derivatives on their chemical reactivity on platinum nanoparticle surfaces

    Science.gov (United States)

    Hu, Peiguang; Chen, Limei; Deming, Christopher P.; Lu, Jia-En; Bonny, Lewis W.; Chen, Shaowei

    2016-06-01

    Stable platinum nanoparticles were successfully prepared by the self-assembly of para-substituted styrene derivatives onto the platinum surfaces as a result of platinum-catalyzed dehydrogenation and transformation of the vinyl groups to the acetylene ones, forming platinum-vinylidene/-acetylide interfacial bonds. Transmission electron microscopic measurements showed that the nanoparticles were well dispersed without apparent aggregation, suggesting sufficient protection of the nanoparticles by the organic capping ligands, and the average core diameter was estimated to be 2.0 +/- 0.3 nm, 1.3 +/- 0.2 nm, and 1.1 +/- 0.2 nm for the nanoparticles capped with 4-tert-butylstyrene, 4-methoxystyrene, and 4-(trifluoromethyl)styrene, respectively, as a result of the decreasing rate of dehydrogenation with the increasing Taft (polar) constant of the para-substituents. Importantly, the resulting nanoparticles exhibited unique photoluminescence, where an increase of the Hammett constant of the para-substituents corresponded to a blue-shift of the photoluminescence emission, suggesting an enlargement of the HOMO-LUMO band gap of the nanoparticle-bound acetylene moieties. Furthermore, the resulting nanoparticles exhibited apparent electrocatalytic activity towards oxygen reduction in acidic media, with the best performance among the series of samples observed with the 4-tert-butylstyrene-capped nanoparticles due to an optimal combination of the nanoparticle core size and ligand effects on the bonding interactions between platinum and oxygen species.Stable platinum nanoparticles were successfully prepared by the self-assembly of para-substituted styrene derivatives onto the platinum surfaces as a result of platinum-catalyzed dehydrogenation and transformation of the vinyl groups to the acetylene ones, forming platinum-vinylidene/-acetylide interfacial bonds. Transmission electron microscopic measurements showed that the nanoparticles were well dispersed without apparent

  18. Exothermic or Endothermic Decomposition of Disubstituted Tetrazoles Tuned by Substitution Fashion and Substituents.

    Science.gov (United States)

    Jia, Yu-Hui; Yang, Kai-Xiang; Chen, Shi-Lu; Huang, Mu-Hua

    2018-01-11

    Nitrogen-rich compounds such as tetrazoles are widely used as candidates in gas-generating agents. However, the details of the differentiation of the two isomers of disubstituted tetrazoles are rarely studied, which is very important information for designing advanced materials based on tetrazoles. In this article, pairs of 2,5- and 1,5-disubstituted tetrazoles were carefully designed and prepared for study on their thermal decomposition behavior. Also, the substitution fashion of 2,5- and 1,5- and the substituents at C-5 position were found to affect the endothermic or exothermic properties. This is for the first time to the best of our knowledge that the thermal decomposition properties of different tetrazoles could be tuned by substitution ways and substitute groups, which could be used as a useful platform to design advanced materials for temperature-dependent rockets. The aza-Claisen rearrangement was proposed to understand the endothermic decomposition behavior.

  19. Molecular analysis of the bacterial diversity in a specialized consortium for diesel oil degradation Análise molecular da diversidade bacteriana de um consórcio degradador de óleo diesel

    Directory of Open Access Journals (Sweden)

    Douglas Antonio Alvaredo Paixão

    2010-06-01

    Full Text Available 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 metagenomic 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.O óleo diesel é um composto derivado do petróleo, constituído basicamente por hidrocarbonetos. Condições precárias no processo de transporte e armazenagem

  20. Tunable photoluminescent materials based on two phenylcarbazole-based dimers through the substituent groups

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Gui-Mei, E-mail: meiguit@163.com; Chi, Rui-Hai; Wan, Wen-Zhu; Chen, Zhi-Qiang; Yan, Ting-Xiang; Dong, Yan-Ping; Wang, Yong-Tao, E-mail: ceswyt@qlu.edu.cn; Cui, Yue-Zhi

    2017-05-15

    Two phenylcarbazole-based dimers, namely, 9,9'-diphenyl-9H,9'H−3,3'-bicarbazole (1) and 9,9'-bis(4-bromophenyl)−9H,9'H−3,3'-bicarbazole (2), have been obtained through the oxidation of 9-phenylcarbazole and 9-(4’-bromophenyl) in the presence of FeCl{sub 3}, respectively, which show strong photoluminescent properties with the fluorescence quantum yields of 0.2 and 0.21 based on the reference of Quinin sulfate, respectively. The maximal emission peak of compounds 1 and 2 were observed at 465 and 413 nm in the solid state, respectively, revealing that the luminescent properties were tuned by the substituent group. The title compounds were characterized by FI-IR, UV–vis, {sup 1}H-NMR, {sup 13}C-NMR, {sup 1}H−{sup 13}C NMR, mass spectra, elemental analysis (EA) and single-crystal X-ray diffraction. Both compounds 1 and 2 crystallize in space group P-1, and supramolecular hydrogen bondings and stacking interactions between aromatic rings are observed. Compounds 1 and 2 display trans- and cis-formation structures, respectively. Two compounds show high thermal stabilities, in which the decomposition temperature is 414 and 363 °C for 1 and 2, respectively. - Graphical abstract: Two phenylcarbazole-based dimers have been obtained through the oxidation of 9-phenylcarbazole and 9-(4’-bromophenyl) in the presence of FeCl{sub 3}, respectively. The maximal emission peaks of compounds 1 and 2 were observed at 465 and 413 nm, respectively, revealing that the luminescent properties were tuned by the substituent group. Compounds 1 and 2 display trans- and cis-formation structures, respectively, and they show high thermal stabilities.

  1. Ring substituents mediate the morphology of PBDTTPD-PCBM bulk-heterojunction solar cells

    KAUST Repository

    Warnan, Julien

    2014-04-08

    Among π-conjugated polymer donors for efficient bulk-heterojunction (BHJ) solar cell applications, poly(benzo[1,2-b:4,5-b′]dithiophene- thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers yield some of the highest open-circuit voltages (VOC, ca. 0.9 V) and fill-factors (FF, ca. 70%) in conventional (single-cell) BHJ devices with PCBM acceptors. In PBDTTPD, side chains of varying size and branching affect polymer self-assembly, nanostructural order, and impact material performance. However, the role of the polymer side-chain pattern in the intimate mixing between polymer donors and PCBM acceptors, and on the development of the BHJ morphology is in general less understood. In this contribution, we show that ring substituents such as furan (F), thiophene (T) and selenophene (S)-incorporated into the side chains of PBDTTPD polymers-can induce significant and, of importance, very different morphological effects in BHJs with PCBM. A combination of experimental and theoretical (via density functional theory) characterizations sheds light on how varying the heteroatom of the ring substituents impacts (i) the preferred side-chain configurations and (ii) the ionization, electronic, and optical properties of the PBDTTPD polymers. In parallel, we find that the PBDT(X)TPD analogs (with X = F, T, or S) span a broad range of power conversion efficiencies (PCEs, 3-6.5%) in optimized devices with improved thin-film morphologies via the use of 1,8-diiodooctane (DIO), and discuss that persistent morphological impediments at the nanoscale can be at the origin of the spread in PCE across optimized PBDT(X)TPD-based devices. With their high VOC ∼1 V, PBDT(X)TPD polymers are promising candidates for use in the high-band gap cell of tandem solar cells. © 2014 American Chemical Society.

  2. Ring substituents mediate the morphology of PBDTTPD-PCBM bulk-heterojunction solar cells

    KAUST Repository

    Warnan, Julien; El Labban, Abdulrahman; Cabanetos, Clement; Hoke, Eric T.; Shukla, Pradeep Kumar; Risko, Chad; Bré das, Jean Luc; McGehee, Michael D.; Beaujuge, Pierre

    2014-01-01

    Among π-conjugated polymer donors for efficient bulk-heterojunction (BHJ) solar cell applications, poly(benzo[1,2-b:4,5-b′]dithiophene- thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers yield some of the highest open-circuit voltages (VOC, ca. 0.9 V) and fill-factors (FF, ca. 70%) in conventional (single-cell) BHJ devices with PCBM acceptors. In PBDTTPD, side chains of varying size and branching affect polymer self-assembly, nanostructural order, and impact material performance. However, the role of the polymer side-chain pattern in the intimate mixing between polymer donors and PCBM acceptors, and on the development of the BHJ morphology is in general less understood. In this contribution, we show that ring substituents such as furan (F), thiophene (T) and selenophene (S)-incorporated into the side chains of PBDTTPD polymers-can induce significant and, of importance, very different morphological effects in BHJs with PCBM. A combination of experimental and theoretical (via density functional theory) characterizations sheds light on how varying the heteroatom of the ring substituents impacts (i) the preferred side-chain configurations and (ii) the ionization, electronic, and optical properties of the PBDTTPD polymers. In parallel, we find that the PBDT(X)TPD analogs (with X = F, T, or S) span a broad range of power conversion efficiencies (PCEs, 3-6.5%) in optimized devices with improved thin-film morphologies via the use of 1,8-diiodooctane (DIO), and discuss that persistent morphological impediments at the nanoscale can be at the origin of the spread in PCE across optimized PBDT(X)TPD-based devices. With their high VOC ∼1 V, PBDT(X)TPD polymers are promising candidates for use in the high-band gap cell of tandem solar cells. © 2014 American Chemical Society.

  3. Amides with nitrogenous heterocyclic substituent, their manufacturing process and their use to draw out selectively Actinium series (III) and to separate them in particular from Lanthanides (III)

    International Nuclear Information System (INIS)

    Cuillerdier, C.; Musikas, C.

    1993-01-01

    Present invention is concerned with new amides with nitrogenous heterocyclic substituent utilizable to separate trivalent actinium series from trivalent lanthanides. In these molecules, it is possible to obtain particularly covalent liaison which has more affinity with 5f series, that is to say actinium series; included a manufacturing process for these amides with nitrogenous heterocyclic substituent

  4. New photoresponsive (meth)acrylate (co)polymers containing azobenzene pendant sidegroups with carboxylic and dimethylamino substituents .1. Synthesis and characterization of the monomers

    NARCIS (Netherlands)

    Haitjema, HJ; Buruma, R; VanEkenstein, GORA; Tan, YY; Challa, G

    1996-01-01

    New azobenzene-based (az.b.) monomers with CO2H (acid) or N(CH3)(2) (basic) substituents were synthesized. For some of these compounds new synthetic routes had to be developed, especially for the az.b. monomers with a CO2H substituent (azoacids) where their synthesis, purification and (thermal)

  5. Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers.

    Science.gov (United States)

    Qiang, Haiping; Chen, Zhihong; Zhang, Zhengli; Wang, Xuemin; Gao, Hongwen; Wang, Zan

    2015-01-01

    Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding.

  6. Bipolar Alq3-based complexes: Effect of hole-transporting substituent on the properties of Alq3-center

    International Nuclear Information System (INIS)

    Luo Jianxin; Lu Mangeng; Yang Chaolong; Tong Bihai; Liang Liyan

    2012-01-01

    Two bipolar Alq 3 -based complexes, tris{5-[(carbazole-9'-yl)methyl]-8-hydroxyquinoline} aluminum (Al(CzHQ) 3 ) and tris{5-[(phenothiazine-9'-yl)methyl]-8-hydroxyquinoline} aluminum (Al(PHQ) 3 ), involving an Alq 3 -center and three hole-transporting substituents (carbazole or phenothiazine), were prepared and characterized. Effects of hole-transporting substituent on the properties of Alq 3 -center were investigated in detail. It is found that the two complexes have improved hole-transporting performance and appropriate thermal stability (the 5%-weight-loss temperatures T 5% >260 °C). Photoluminescence (PL) spectra indicate that both energy transfer and electron transfer can take place simultaneously in the PL process of these complexes. Both thermodynamics and dynamics of the electron transfer were studied and corresponding parameters were calculated. Energy transfer is favorable for the PL of Alq 3 -center, while electron transfer is unfavorable for the PL of Alq 3 -center. These results will be useful to explore novel OLEDs material with increased efficiency. - Highlights: ► Effects of substituent on the properties of Alq 3 -center were investigated. ► Energy transfer and electron transfer can transfer from substituent to Alq 3 -center. ► The thermodynamics and dynamics of electron transfer were studied. ► The mechanisms of PL and EL of Al(CzHQ) 3 were studied and compared with each other.

  7. Supramolecular Switches Based on the Guanine–Cytosine (GC) Watson–Crick Pair: Effect of Neutral and Ionic Substituents

    NARCIS (Netherlands)

    Guerra, C.F.; van der Wijst, T.; Bickelhaupt, F.M.

    2006-01-01

    We have theoretically analyzed Watson–Crick guanine–cytosine (GC) base pairs in which purine-C8 and/or pyrimidine-C6 positions carry a substituent X = NH−, NH2, NH3+ (N series), O−, OH, or OH2+ (O series), using the generalized gradient approximation (GGA) of density functional theory at the

  8. Substituent Effects Dehalogenation of Aryl Bromides with NaAlH2(OCH2CH2OCH3)2

    Czech Academy of Sciences Publication Activity Database

    Czakoová, Marie; Hetflejš, Jiří; Včelák, Jaroslav

    2001-01-01

    Roč. 72, č. 2 (2001), s. 277-287 ISSN 0133-1736 R&D Projects: GA ČR GA203/97/1173 Institutional research plan: CEZ:AV0Z4072921 Keywords : substituent effects * aryl bromides * Co-assisted debromination Subject RIV: CC - Organic Chemistry Impact factor: 0.475, year: 2001

  9. Synthesis and Crystal Structures of Dimethylsilylene-Bridged (Amidocyclopentadienyl)Dichlorotitanium(IV) Complexes with Various Substituents on the Cyclopentadienyl Ligand

    Czech Academy of Sciences Publication Activity Database

    Zemánek, Jaroslav; Štěpnička, P.; Fejfarová, K.; Gyepes, R.; Císařová, I.; Horáček, Michal; Kubišta, Jiří; Varga, V.; Mach, Karel

    2001-01-01

    Roč. 66, č. 4 (2001), s. 605-620 ISSN 0010-0765 R&D Projects: GA AV ČR IBS4040017 Institutional research plan: CEZ:AV0Z4040901 Keywords : titanium * (amidocyclopentadienyl)dichlorotitanium(IV) complexes * substituent effects Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.778, year: 2001

  10. The proton transfer reaction in malonaldehyde derivatives: Substituent effects and quasi-aromaticity of the proton bridge

    International Nuclear Information System (INIS)

    Palusiak, Marcin; Simon, Silvia; Sola, Miquel

    2007-01-01

    The proton transfer in malonaldehyde and in some of its derivatives have been considered in order to study the interrelation between the reaction barrier and the π-delocalization in the quasi-ring. A set of simple and mostly common substituents having different properties in resonance effect according to values of substituents constants were chosen in order to simulate the influence of substitution in position 2 or in position 1 (or 3) of malonaldehyde on the quasi-aromaticity and H-bonding. The following substituents have been taken into consideration: NO, NO 2 , CN, CHO, F, H, CH 3 , OCH 3 , OH, and NH 2 . Our results show that when the substituent is attached at position 2 of the quasi-ring, the resonance effect predominates over the field/inductive effect which leads to changes in H-bonding and quasi-aromaticity of the ring motif, while in the case of 1(3) substitution the field/inductive effect is significantly more effective influencing the HB strength, and thus, the proton transfer barrier. Somehow counterintuitively, for the 1(3) substituted systems, the most stable isomer is the one having the weakest HB and lower aromaticity. The reason for this surprising behaviour is discussed

  11. Effect of Polyhedral Oligomeric Silsesquioxane (POSS) Substituents on the Rheological Behavior in Butyl Methacrylate/POSS Copolymers

    Science.gov (United States)

    2008-10-27

    was repeated twice, dissolving the product in chloroform and diethyl ether, respectively. The polymer was dried at 60 °C under vacuum overnight...the Tg of the i Bu remains the same. Table 1. Tg for Butyl Methacrylate-co- Propyl Methacryl POSS Polymers with Various POSS Substituents

  12. Calculation of spectral shifts in UV–visible region and photoresponsive behaviour of fluorinated liquid crystals: Effect of solvent and substituent

    International Nuclear Information System (INIS)

    Lakshmi Praveen, P.; Ojha, Durga P.

    2012-01-01

    The photoresponsive behaviour of fluorinated liquid crystals p-phenylene-4-methoxy benzoate-4-trifluoromethylbenzoate (FLUORO1), and 4-propyloxyphenyl-4-(4-trifluoromethylbenzoyloxy) benzoate (FLUORO2) has been systematically investigated using the CNDO/S + CI and INDO/S + CI methods. These methods have been employed to calculate/analyze the spectral shifts, and absorbance measurements in UV–visible region of the systems. The electronic transitions, absorption wavelength, HOMO (highest occupied molecular orbital), and LUMO (lowest unoccupied molecular orbital) energies have been calculated. Further, ultraviolet (UV) stability of the molecules has been discussed in the light of absorption wavelength and electronic transition oscillator strength (f). The effect of different solvent media and substituents on transition energies, oscillator strength, and other absorption parameters have also been reported. The present article provides valuable information regarding enhancing the UV stability of molecules by marinating their conductivity. Highlights: ► The strongest bands of FLUORO molecules can be assigned as π → π ∗ transitions. ► A small red-shift indicates a weak exciton coupling of chromophores. ► No n → π ∗ transition occurs due to the rigidity of the ring system of the molecules. ► The HOMO, LUMO, and E g values have been found to be independent of solvent effect.

  13. Calculation of spectral shifts in UV-visible region and photoresponsive behaviour of fluorinated liquid crystals: Effect of solvent and substituent

    Energy Technology Data Exchange (ETDEWEB)

    Lakshmi Praveen, P. [Liquid Crystal Research Laboratory, Post-Graduate Department of Physics, Andhra Loyola College, Vijayawada 520 008, A.P. (India); Ojha, Durga P., E-mail: durga_ojha@hotmail.com [Liquid Crystal Research Laboratory, Post-Graduate Department of Physics, Andhra Loyola College, Vijayawada 520 008, A.P. (India)

    2012-08-15

    The photoresponsive behaviour of fluorinated liquid crystals p-phenylene-4-methoxy benzoate-4-trifluoromethylbenzoate (FLUORO1), and 4-propyloxyphenyl-4-(4-trifluoromethylbenzoyloxy) benzoate (FLUORO2) has been systematically investigated using the CNDO/S + CI and INDO/S + CI methods. These methods have been employed to calculate/analyze the spectral shifts, and absorbance measurements in UV-visible region of the systems. The electronic transitions, absorption wavelength, HOMO (highest occupied molecular orbital), and LUMO (lowest unoccupied molecular orbital) energies have been calculated. Further, ultraviolet (UV) stability of the molecules has been discussed in the light of absorption wavelength and electronic transition oscillator strength (f). The effect of different solvent media and substituents on transition energies, oscillator strength, and other absorption parameters have also been reported. The present article provides valuable information regarding enhancing the UV stability of molecules by marinating their conductivity. Highlights: Black-Right-Pointing-Pointer The strongest bands of FLUORO molecules can be assigned as {pi} {yields} {pi}{sup Asterisk-Operator} transitions. Black-Right-Pointing-Pointer A small red-shift indicates a weak exciton coupling of chromophores. Black-Right-Pointing-Pointer No n {yields} {pi}{sup Asterisk-Operator} transition occurs due to the rigidity of the ring system of the molecules. Black-Right-Pointing-Pointer The HOMO, LUMO, and E{sub g} values have been found to be independent of solvent effect.

  14. Exploring coherent transport through π-stacked systems for molecular electronic devices

    DEFF Research Database (Denmark)

    Li, Qian; Solomon, Gemma

    2014-01-01

    Understanding electron transport across π-stacked systems can help to elucidate the role of intermolecular tunneling in molecular junctions and potentially with the design of high-efficiency molecular devices. Here we show how conjugation length and substituent groups influence the electron trans...

  15. Substituent effects on the photolysis of methyl 2-carboxylate substituted aliphatic 2 H-azirines

    Science.gov (United States)

    Gómez-Zavaglia, Andrea; Kaczor, Agnieszka; Cardoso, Ana L.; Pinho e Melo, Teresa M. V. D.; Fausto, Rui

    2007-05-01

    In this study, the UV induced photochemical reactions of two 2 H-azirines - methyl 2-chloro-3-methyl-2 H-azirine-2-carboxylate (MCMAC) and methyl 3-methyl-2 H-azirine-2-carboxylate (MMAC) - isolated in argon matrices are compared. For both compounds, irradiation with λ > 235 nm led to observation of two primary photoprocesses: (a) C sbnd C bond cleavage, with production of nitrile ylides (P1-type products), and (b) C sbnd N bond cleavage, with production of methylated ketene imines (P2-type products). However, subsequent photoprocesses were found to be different in the two cases. In MCMAC, both primary photoproducts were shown to undergo further reactions: P1-type products decarboxylate, giving [(1-chloroethylidene)imino]ethanide, which bears a C dbnd N +dbnd C - group (P3-type product); P2-type products decarbonylate, yielding a substituted ylidene methanamine (P4-type product). In MMAC, only P2-type primary photoproducts appeared to react, undergoing decarbonylation or decarboxylation (both reactions leading to P4-type products), whereas P1-type products were found to be non-reactive. The non-observation of any secondary photoproduct resulting from photolysis of P1-MMAC revealed the higher photostability of this species when compared with the corresponding photoproduct obtained from MCMAC. The C sbnd N photochemical cleavage is an unusual process in aliphatic 2 H-azirines. In the studied compounds, its preference over the commonly observed C sbnd C azirine-ring bond photocleavage is attributed to the presence of electron withdrawing substituents (methylcarboxy group in both azirines and also the chlorine atom in MCMAC), which accelerates intersystem crossing towards the triplet state from where the cleavage of the C sbnd N bond takes place. The lack of the chlorine atom in MMAC may be partially compensated by the significantly higher stabilization of the P2-type photoproduct derived from this molecule ( ca. -52 kJ mol -1) relatively to the reactant, when

  16. Genetic Structure and Molecular Diversity of Cacao Plants Established as Local Varieties for More than Two Centuries: The Genetic History of Cacao Plantations in Bahia, Brazil.

    Science.gov (United States)

    Santos, Elisa S L; Cerqueira-Silva, Carlos Bernard M; Mori, Gustavo M; Ahnert, Dário; Mello, Durval L N; Pires, José Luis; Corrêa, Ronan X; de Souza, Anete P

    2015-01-01

    Bahia is the most important cacao-producing state in Brazil, which is currently the sixth-largest country worldwide to produce cacao seeds. In the eighteenth century, the Comum, Pará and Maranhão varieties of cacao were introduced into southern Bahia, and their descendants, which are called 'Bahian cacao' or local Bahian varieties, have been cultivated for over 200 years. Comum plants have been used to start plantations in African countries and extended as far as countries in South Asia and Oceania. In Brazil, two sets of clones selected from Bahian varieties and their mutants, the Agronomic Institute of East (SIAL) and Bahian Cacao Institute (SIC) series, represent the diversity of Bahian cacao in germplasm banks. Because the genetic diversity of Bahian varieties, which is essential for breeding programs, remains unknown, the objective of this work was to assess the genetic structure and diversity of local Bahian varieties collected from farms and germplasm banks. To this end, 30 simple sequence repeat (SSR) markers were used to genotype 279 cacao plants from germplasm and local farms. The results facilitated the identification of 219 cacao plants of Bahian origin, and 51 of these were SIAL or SIC clones. Bahian cacao showed low genetic diversity. It could be verified that SIC and SIAL clones do not represent the true diversity of Bahian cacao, with the greatest amount of diversity found in cacao trees on the farms. Thus, a core collection to aid in prioritizing the plants to be sampled for Bahian cacao diversity is suggested. These results provide information that can be used to conserve Bahian cacao plants and applied in breeding programs to obtain more productive Bahian cacao with superior quality and tolerance to major diseases in tropical cacao plantations worldwide.

  17. Influence of substituents in vinyl groups on reactivity of parylene during polymerization process

    International Nuclear Information System (INIS)

    Freza, Sylwia; Skurski, Piotr; Bobrowski, Maciej

    2010-01-01

    The MCSCF calculations indicate that both triplet and singlet state of biradical di-para-xylylene can exist during polymerization of parylene in gas phase and both can potentially react with vinyl molecules. The singlet-state open-shell dimer turned out to exhibit multiconfigurational character. In the case of triplet state of the dimer two mechanisms of the reactions with various species containing vinyl groups have been examined at the B3LYP/6-31G level. The kinetic and thermodynamical barriers have been estimated for the reaction path involving the π-bond cleavage as well as for the route describing the hydrogen atom transfer. It was found that the overall reactions are thermodynamically favorable, whereas appropriate kinetic barriers for certain derivatives are very small (close to 0 kcal/mol) which in turn makes allowances for easy reactivity under accessible conditions. The calculated mechanisms indicate the influence of substituents in vinyl groups for reactivity of parylene during LPCVD process.

  18. Infrared matrix isolation study of hydrogen bonds involving C-H bonds: Substituent effects

    International Nuclear Information System (INIS)

    Jeng, M.L.H.; Ault, B.S.

    1989-01-01

    The matrix isolation technique combined with infrared spectroscopy has been employed to isolate and characterize hydrogen-bonded complexes between a series of substituted alkynes and several oxygen and nitrogen bases. Distinct evidence for hydrogen bond formation was observed in each case, with a characteristic red shift of the hydrogen stretching motion ν r . Shifts between 100 and 300 cm -1 were observed, the largest being for the complex of CF 3 CCH with (CH 3 ) 3 N. The perturbed carbon-carbon triple bond stretching vibration was observed for most complexes, as was the alkynic hydrogen bending motion. Attempts were made to correlate the magnitude of the red shift of ν s with substituent constants for the different substituted alkynes; a roughly linear correlation was found with the Hammett σ parameter. Lack of correlation Δν s with either σ 1 or σ R alone suggests that both inductive and resonance contributions to the strength of the hydrogen-bonding interaction are important

  19. Substituent effects on furan-phenylene copolymer for photovoltaic improvement: A density functional study

    Science.gov (United States)

    Janprapa, Nuttaporn; Vchirawongkwin, Viwat; Kritayakornupong, Chinapong

    2018-06-01

    The structural, electronic and photovoltaic properties of furan-phenylene copolymer ((Fu-co-Ph)4) and its derivatives were evaluated using density functional theory (DFT) and time-dependent density functional theory (TD-DFT). The calculated band gaps of pristine furan and phenylene are in good agreement with the available experimental data. The lower band gap value of 2.72 eV was obtained from -NO2 and -NHCH3 substituents, leading to broader solar absorption range. With respected to the reorganization energy, -OCH3, -NHCH3, -OH, -SCH3, -CH3, -CF3, -NO2, and -F substituted (Fu-co-Ph)4 structures were classified as better electron donor materials. For combination with PC61BM, -NO2, -CN, -CF3 and -F functionalized copolymers demonstrated significantly higher open circuit voltage (Voc) values ranging from 1.07 to 2.10 eV. Our results revealed that electron withdrawing group substitution on furan-phenylene copolymers was an effective way for improving electronic and optical properties of donor materials used in photovoltaic applications.

  20. Competitive/co-operative interactions in acid base sandwich: role of cation vs. substituents.

    Science.gov (United States)

    Kalpana, Ayyavoo; Akilandeswari, Lakshminarayanan

    2017-11-15

    The cation-π interaction can be envisaged as a lewis acid base interaction, and it is in line with Pearson's acid base concept. The critical examination of interactions between the π-acids (alkali metal cations - Li + , Na + and alkaline earth metal cations Mg 2+ , Ca 2+ ) on one face and tripodal Cr(CO) 3 moiety on the other π face of substituted arenes demonstrates the role of cation and substitutents in manipulating the interactions between them. The interaction of the two π acids on both faces of arene is not expectedly additive, rather it shows either depreciation of interaction energy revealing the competition of acids toward the base or enhancement of interaction energy denoting a cooperative effect. Among the metal cations under study, Mg 2+ shows a cooperative gesture. Although the substituents play a meek role, they unfailingly exert their electronic effects and are amply documented by excellent correlation of various parameters with the Hammett constant σ m . The elusive switching of λ max from the UV to IR region on binding Mg 2+ with substituted arene-Cr(CO) 3 complex is a characteristic clue that TDDFT can help design the ionic sensors for Mg 2+ cations.

  1. Influence of Introduced Substituents on the Anion-selectivity of [14]Tetraazaannulene Complexes.

    Science.gov (United States)

    Moriuchi-Kawakami, Takayo; Obita, Minako; Tsujinaka, Toshiki; Shibutani, Yasuhiko

    2015-01-01

    Nickel(II) complexes of [14]tetraazaannulene derivatives incorporating aromatic rings into their azaannulene framework were synthesized, and the anion-selectivity of the [14]tetraazaannulene nickel complexes 1 - 4 was evaluated by potentiometric measurements with solvent polymeric membrane electrodes. All of the [14]Tetraazaannulene nickel complexes, except 3, were found to exhibit high selectivity for the I(-) ion over the SCN(-) ion, although considerable interference of the ClO4(-) ion was observed in all 1 - 4 complexes. Concerning the anion-selectivities of 1 and 4, the incorporation of naphthalene rings into the azaannulene framework decreased not only the interference of the ClO4(-) ion but also the I(-) ion-selectivity over the SCN(-) ion. Comparison studies between the dibenzotetraaza[14]annulene nickel complexes 1 - 3 indicated that differences in the attached substituents of the [14]tetraazaannulene nickel complexes greatly influenced the ion-selectivity as ionophores. According to our computational results, the ionophoric properties of [14]tetraazaannulene nickel complexes 1 - 4 were influenced by their electrostatic properties rather than their topological properties.

  2. Abundance and diversity of n-alkane-degrading bacteria in a forest soil co-contaminated with hydrocarbons and metals: a molecular study on alkB homologous genes.

    Science.gov (United States)

    Pérez-de-Mora, Alfredo; Engel, Marion; Schloter, Michael

    2011-11-01

    Unraveling functional genes related to biodegradation of organic compounds has profoundly improved our understanding of biological remediation processes, yet the ecology of such genes is only poorly understood. We used a culture-independent approach to assess the abundance and diversity of bacteria catalyzing the degradation of n-alkanes with a chain length between C(5) and C(16) at a forest site co-contaminated with mineral oil hydrocarbons and metals for nearly 60 years. The alkB gene coding for a rubredoxin-dependent alkane monooxygenase enzyme involved in the initial activation step of aerobic aliphatic hydrocarbon metabolism was used as biomarker. Within the area of study, four different zones were evaluated: one highly contaminated, two intermediately contaminated, and a noncontaminated zone. Contaminant concentrations, hydrocarbon profiles, and soil microbial respiration and biomass were studied. Abundance of n-alkane-degrading bacteria was quantified via real-time PCR of alkB, whereas genetic diversity was examined using molecular fingerprints (T-RFLP) and clone libraries. Along the contamination plume, hydrocarbon profiles and increased respiration rates suggested on-going natural attenuation at the site. Gene copy numbers of alkB were similar in contaminated and control areas. However, T-RFLP-based fingerprints suggested lower diversity and evenness of the n-alkane-degrading bacterial community in the highly contaminated zone compared to the other areas; both diversity and evenness were negatively correlated with metal and hydrocarbon concentrations. Phylogenetic analysis of alkB denoted a shift of the hydrocarbon-degrading bacterial community from Gram-positive bacteria in the control zone (most similar to Mycobacterium and Nocardia types) to Gram-negative genotypes in the contaminated zones (Acinetobacter and alkB sequences with little similarity to those of known bacteria). Our results underscore a qualitative rather than a quantitative response of

  3. Molecular phylogeny of Indo-Pacific carpenter ants (Hymenoptera: Formicidae, Camponotus) reveals waves of dispersal and colonization from diverse source areas

    Czech Academy of Sciences Publication Activity Database

    Clouse, R. M.; Janda, Milan; Blanchard, B.; Sharma, P.; Hoffmann, B. D.; Andersen, A. N.; Czekanski-Moir, J. E.; Krushelnycky, P.; Rabeling, C.; Wilson, E. O.; Economo, E. P.; Sarnat, E. M.; General, D. M.; Alpert, G. D.; Wheeler, W. C.

    2015-01-01

    Roč. 31, č. 4 (2015), s. 424-437 ISSN 0748-3007 R&D Projects: GA ČR GAP505/12/2467 Grant - others:Marie Curie Felloswhip(CZ) PIOFGA2009-25448 Institutional support: RVO:60077344 Keywords : Hymenoptera * Camponotus * molecular phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.952, year: 2015 http://onlinelibrary.wiley.com/doi/10.1111/cla.12099/epdf

  4. Influence of substituents of nickel(II) complexes of Schiff bases of substituted (S)-2-N-(benzylpropyl)aminobenzophenones and amino-acids on their asymmetric induction

    International Nuclear Information System (INIS)

    Nadvornik, M.; Lycka, A.; Gee, A.; Popkov, A.

    1999-01-01

    The aim of this work was to study of influence of substituents on benzophenone substituent on thermodynamic controlled induction of complexes as well as influence of substituents on benzyl group and on benzophenone on kinetically controlled asymmetric induction of complexes. [ 13 C]methyl iodide was used in the synthesis. Replace of benzyl group by 2,4,6-trimethylbenzyl group increase kinetically controlled asymmetric induction of synthesis of (S)-α-[ 13 C]methylalanine from 43% d.e. to 66% d.e

  5. Diversity management

    OpenAIRE

    Knákalová, Lucie

    2009-01-01

    The key topic of the work is diversity management, i.e. management of em-ployees" diversity within organization. Opening part of the work identifies the position of diversity within society and related phenomena such as stereotypes, biases and various forms of discrimination. Then the work discusses the role of diversity management in organizations, its principles and basic areas of focus. Attention is paid to certain social groups that the diversity management concept should especially deal ...

  6. Substituent Effects on the Hydrogen Bonding between 4-Substituted Phenols and HF, H2O, NH3

    Institute of Scientific and Technical Information of China (English)

    程宇辉; 傅尧; 刘磊; 郭庆祥

    2003-01-01

    Density function theory UB3LYP/6-31+g(d) calculations were performed to study the hydrogen bonds between para-substituted phenols and HF, H2O, or NH3. It revealed that many properties of the non-covalent complexes, such as the interaction energies, donor-acceptor distances, bond lengths and vibration frequencies, showed well-defined substituent effects. Therefore, from the substituent effects not only the mechanism of a certain non-covalent interaction can be better understood, but also the interaction energies and structures of a certain non-covalent complex, which otherwise might be very hard or resource-consuming to estimate, can be easily predicted.

  7. Substituent effects on the redox states of locally functionalized single-walled carbon nanotubes revealed by in situ photoluminescence spectroelectrochemistry.

    Science.gov (United States)

    Shiraishi, Tomonari; Shiraki, Tomohiro; Nakashima, Naotoshi

    2017-11-09

    Single-walled carbon nanotubes (SWNTs) with local chemical modification have been recognized as a novel near infrared (NIR) photoluminescent nanomaterial due to the emergence of a new red-shifted photoluminescence (PL) with enhanced quantum yields. As a characteristic feature of the locally functionalized SWNTs (lf-SWNTs), PL wavelength changes occur with the structural dependence of the substituent structures in the modified aryl groups, showing up to a 60 nm peak shift according to an electronic property difference of the aryl groups. Up to now, however, the structural effect on the electronic states of the lf-SWNTs has been discussed only on the basis of theoretical calculations due to the very limited amount of modifications. Herein, we describe the successfully-determined electronic states of the aryl-modified lf-SWNTs with different substituents (Ar-X SWNTs) using an in situ PL spectroelectrochemical method based on electrochemical quenching of the PL intensities analyzed by the Nernst equation. In particular, we reveal that the local functionalization of (6,5)SWNTs induced potential changes in the energy levels of the HOMO and the LUMO by -23 to -38 meV and +20 to +22 meV, respectively, compared to those of the pristine SWNTs, which generates exciton trapping sites with narrower band gaps. Moreover, the HOMO levels of the Ar-X SWNTs specifically shift in a negative potential direction by 15 meV according to an enhancement of the electron-accepting property of the substituents in the aryl groups that corresponds to an increase in the Hammet substituent constants, suggesting the importance of the dipole effect from the aryl groups on the lf-SWNTs to the level shift of the frontier orbitals. Our method is a promising way to characterize the electronic features of the lf-SWNTs.

  8. Fluoroalkyl Amino Reagents (FARs: A General Approach towards the Synthesis of Heterocyclic Compounds Bearing Emergent Fluorinated Substituents

    Directory of Open Access Journals (Sweden)

    Bruno Commare

    2017-06-01

    Full Text Available Fluorinated heterocycles are important building blocks in pharmaceutical, agrochemical and material sciences. Therefore, organofluorine chemistry has witnessed high interest in the development of efficient methods for the introduction of emergent fluorinated substituents (EFS onto heterocycles. In this context, fluoroalkyl amino reagents (FARs—a class of chemicals that was slightly forgotten over the last decades—has emerged again recently and proved to be a powerful tool for the introduction of various fluorinated groups onto (heteroaromatic derivatives.

  9. Fluoroalkyl Amino Reagents (FARs): A General Approach towards the Synthesis of Heterocyclic Compounds Bearing Emergent Fluorinated Substituents.

    Science.gov (United States)

    Commare, Bruno; Schmitt, Etienne; Aribi, Fallia; Panossian, Armen; Vors, Jean-Pierre; Pazenok, Sergiy; Leroux, Frédéric R

    2017-06-12

    Fluorinated heterocycles are important building blocks in pharmaceutical, agrochemical and material sciences. Therefore, organofluorine chemistry has witnessed high interest in the development of efficient methods for the introduction of emergent fluorinated substituents (EFS) onto heterocycles. In this context, fluoroalkyl amino reagents (FARs)-a class of chemicals that was slightly forgotten over the last decades-has emerged again recently and proved to be a powerful tool for the introduction of various fluorinated groups onto (hetero)aromatic derivatives.

  10. Eukaryotic plankton diversity in the sunlit ocean

    Czech Academy of Sciences Publication Activity Database

    de Vargas, C.; Audic, S.; Henry, N.; Decelle, J.; Mahé, F.; Logares, R.; Lara, E.; Berney, C.; Le Bescot, N.; Probert, I.; Carmichael, M.; Poulain, J.; Romac, S.; Colin, S.; Aury, J.-M.; Bittner, L.; Chaffron, S.; Dunthorn, M.; Engelen, S.; Flegontova, Olga; Guidi, L.; Horák, Aleš; Jaillon, O.; Lima-Mendez, G.; Lukeš, Julius

    2015-01-01

    Roč. 348, č. 6237 (2015), UNSP 1261605 ISSN 0036-8075 Institutional support: RVO:60077344 Keywords : ribosomal RNA gene * protistan diversity * extreme diversity Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 34.661, year: 2015

  11. Substituent Inductive Effects on the Electrochemical Oxidation of Flavonoids Studied by Square Wave Voltammetry and Ab Initio Calculations.

    Science.gov (United States)

    Arroyo-Currás, Netzahualcóyotl; Rosas-García, Víctor M; Videa, Marcelo

    2016-10-27

    Flavonoids are natural products commonly found in the human diet that show antioxidant, anti-inflammatory and anti-hepatotoxic activities. These nutraceutical properties may relate to the electrochemical activity of flavonoids. To increase the understanding of structure-electrochemical activity relations and the inductive effects that OH substituents have on the redox potential of flavonoids, we carried out square-wave voltammetry experiments and ab initio calculations of eight flavonoids selected following a systematic variation in the number of hydroxyl substituents and their location on the flavan backbone: three flavonols, three anthocyanidins, one anthocyanin and the flavonoid backbone flavone. We compared the effect that the number of -OH groups in the ring B of flavan has on the oxidation potential of the flavonoids considered, finding linear correlations for both flavonols and anthocyanidins ( R 2 = 0.98 ). We analyzed the effects that position and number of -OH substituents have on electron density distributions via ab initio quantum chemical calculations. We present direct correlations between structural features and oxidation potentials that provide a deeper insight into the redox chemistry of these molecules.

  12. Interaction between D-fructose dehydrogenase and methoxy-substituent-functionalized carbon surface to increase productive orientations

    International Nuclear Information System (INIS)

    Xia, Hong-qi; Hibino, Yuya; Kitazumi, Yuki; Shirai, Osamu; Kano, Kenji

    2016-01-01

    Highlights: • Methoxy-functionalized surface improves the DET-type bioelectrocatalysis of FDH. • Methoxy-functionalized surface increases productive orientations. • The total catalytic activity of FDH is almost independent of the modification. • High current density as well as good stability is useful for biofuel cells. - Abstract: D-Fructose dehydrogenase (FDH) from Gluconobacter japonicus NBRC3260 catalyzes the two-electron oxidation of D-fructose to 5-keto-D-fructose, and it is widely used in biofuel cells and biosensors. In this study, methoxy-substituent-functionalized carbon electrodes are constructed by electrochemical oxidation of methoxy-aniline derivatives on Ketjen Black (KB)-modified electrodes to improve the immobilization and bioelectrocatalysis of FDH. It is proposed that the specific interaction between FDH, especially the heme c moiety, and methoxy substituent(s) of amines on carbon electrode increases the proportion of the productively oriented FDH molecules to the total FDHs. Consequently, the limiting catalytic current density of the D-fructose oxidation increases to as much as 23 ± 2 mA cm −2 in FDH/2,4-dimethoxyaniline/KB/glassy carbon electrode, for example.

  13. The unique role of halogen substituents in the design of modern agrochemicals.

    Science.gov (United States)

    Jeschke, Peter

    2010-01-01

    The past 30 years have witnessed a period of significant expansion in the use of halogenated compounds in the field of agrochemical research and development. The introduction of halogens into active ingredients has become an important concept in the quest for a modern agrochemical with optimal efficacy, environmental safety, user friendliness and economic viability. Outstanding progress has been made, especially in synthetic methods for particular halogen-substituted key intermediates that were previously prohibitively expensive. Interestingly, there has been a rise in the number of commercial products containing 'mixed' halogens, e.g. one or more fluorine, chlorine, bromine or iodine atoms in addition to one or more further halogen atoms. Extrapolation of the current trend indicates that a definite growth is to be expected in fluorine-substituted agrochemicals throughout the twenty-first century. A number of these recently developed agrochemical candidates containing halogen substituents represent novel classes of chemical compounds with new modes of action. However, the complex structure-activity relationships associated with biologically active molecules mean that the introduction of halogens can lead to either an increase or a decrease in the efficacy of a compound, depending on its changed mode of action, physicochemical properties, target interaction or metabolic susceptibility and transformation. In spite of modern design concepts, it is still difficult to predict the sites in a molecule at which halogen substitution will result in optimal desired effects. This review describes comprehensively the successful utilisation of halogens and their unique role in the design of modern agrochemicals, exemplified by various commercial products from Bayer CropScience coming from different agrochemical areas.

  14. New aminoporphyrins bearing urea derivative substituents: synthesis, characterization, antibacterial and antifungal activity

    Directory of Open Access Journals (Sweden)

    Gholamreza Karimipour

    2015-06-01

    Full Text Available This work studied the synthesis of 5,10,15-tris(4-aminophenyl-20-(N,N-dialkyl/diaryl-N-phenylurea porphyrins (P1-P4 with alkyl or aryl groups of Ph, iPr, Et and Me, respectively and also the preparation of their manganese (III and cobalt (II complexes (MnP and CoP. The P1-P4 ligands were characterized by different spectroscopic techniques (1H NMR, FTIR, UV-Vis and elemental analysis, and metalated with Mn and Co acetate salts. The antibacterial and antifungal activities of these compounds in vitro were investigated by agar-disc diffusion method against Escherichia coli (-, Pseudomonas aeruginosa (-, Staphylococcus aureus(+, Bacillus subtilis (+ and Aspergillus oryzae and Candida albicans. Results showed that antibacterial and antifungal activity of the test samples increased with increase of their concentrations and the highest activity was obtained when the concentration of porphyrin compounds was 100 µg/mL. The activity for the porphyrin ligands depended on the nature of the urea derivative substituents and increased in the order P1 > P2 > P3 >P4, which was consistent with the order of their liposolubility. MnP and CoP complexes exhibited much higher antibacterial and antifungal activity than P1-P4ligands. Further, the growth inhibitory effects of these compounds was generally in the order CoP complexes > MnP complexes > P1-P4 ligands. Among these porphyrin compounds, CoP1displayed the highest antibacterial and antifungal activity, especially with a concentration of 100 µg/mL, against all the four tested bacteria and two fungi, and therefore it could be potential to be used as drug.

  15. The unexpected influence of aryl substituents in N-aryl-3-oxobutanamides on the behavior of their multicomponent reactions with 5-amino-3-methylisoxazole and salicylaldehyde

    Directory of Open Access Journals (Sweden)

    Volodymyr V. Tkachenko

    2014-12-01

    Full Text Available The switchable three-component reactions of 5-amino-3-methylisoxazole, salicylaldehyde and N-aryl-3-oxobutanamides under different conditions were studied and discussed. The unexpected influence of the aryl substituent in N-aryl-3-oxobutanamides on the behavior of the reaction was discovered. The key influence of ultrasonication and Lewis acid catalysts led to an established protocol to selectively obtain two or three types of heterocyclic scaffolds depending on the substituent in the N-aryl moiety.

  16. 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; Reddy, Muppala P.

    2014-01-01

    . 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

  17. Molecular evidence of cryptic diversity in Paracaryophyllaeus (Cestoda: Caryophyllidea), parasites of loaches (Cobitidae) in Eurasia, including description of P. vladkae n. sp

    Czech Academy of Sciences Publication Activity Database

    Scholz, Tomáš; Oros, M.; Bazsalovicsová, E.; Brabec, Jan; Waeschenbach, A.; Xi, B. W.; Aydoğdu, A.; Besprozvannykh, V. V.; Shimazu, T.; Kraľová-Hromadová, I.; Littlewood, D. T. J.

    2014-01-01

    Roč. 63, č. 6 (2014), s. 841-850 ISSN 1383-5769 R&D Projects: GA ČR GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Taxonomy * Molecular phylogeny * Caryophyllidea * Species complex * Freshwater fishes * Eurasia Subject RIV: EG - Zoology Impact factor: 1.859, year: 2014

  18. Diversity Index

    Data.gov (United States)

    Town of Chapel Hill, North Carolina — This map service summarizes racial and ethnic diversity in the United States in 2012.The Diversity Index shows the likelihood that two persons chosen at random from...

  19. Managing Diversity.

    Science.gov (United States)

    Geber, Beverly

    1990-01-01

    Demographic trends imply that organizations must learn to manage a diverse work force. Ways to change organizational systems, structures, and practices to eliminate subtle barriers are awareness training, attitude change, and valuing diversity. (SK)

  20. Molecular evidence for a diverse green algal community growing in the hair of sloths and a specific association with Trichophilus welckeri (Chlorophyta, Ulvophyceae

    Directory of Open Access Journals (Sweden)

    Chiarello Adriano G

    2010-03-01

    Full Text Available Abstract Background Sloths are slow-moving arboreal mammals inhabiting tropical rainforests in Central and South America. The six living species of sloths are occasionally reported to display a greenish discoloration of their pelage. Trichophilus welckeri, a green algal species first described more than a century ago, is widely believed to discolor the animals fur and provide the sloth with effective camouflage. However, this phenomenon has not been explored in any detail and there is little evidence to substantiate this widely held opinion. Results Here we investigate the genetic diversity of the eukaryotic community present in fur of all six extant species of sloth. Analysis of 71 sloth hair samples yielding 426 partial 18S rRNA gene sequences demonstrates a diverse eukaryotic microbial assemblage. Phylogenetic analysis reveals that sloth fur hosts a number of green algal species and suggests that acquisition of these organisms from the surrounding rainforest plays an important role in the discoloration of sloth fur. However, an alga corresponding to the morphological description of Trichophilus welckeri was found to be frequent and abundant on sloth fur. Phylogenetic analysis demonstrated the retention of this alga on the fur of sloths independent of geographic location. Conclusions These results demonstrate a unique diverse microbial eukaryotic community in the fur of sloths from Central and South America. Our analysis streghtens the case for symbiosis between sloths and Trichophilus welckeri.

  1. Theoretical Investigation on Charge Transfer Properties of 1,3,5-Tripyrrolebenzene (TPB and its Derivatives with Electron-withdrawing Substituents

    Directory of Open Access Journals (Sweden)

    Yong Hu

    2016-06-01

    Full Text Available The electronic structures and charge transport properties of 1,3,5-tripyrrolebenzene (TPB and its substituted derivatives with –F and –CN groups have been investigated by DFT calculations in combination with the Marcus hopping model. The dimer geometry was optimized by density functional theory method with dispersion force correction being included (DFT-D. Consequently, the charge transfer integral was evaluated. The calculation results show that the introduction of electron-withdrawing substituents does not significantly change the bond lengths and molecular symmetry of TPB, but lower the coplanarity between the pyrrole and benzene rings, especially in the case of CN substitution. Meanwhile, the introduction of electron-withdrawing groups can decrease the energy of the frontier molecular orbital and enhance the air stability. Fluorination makes the λe increase obviously while cyanation dose not. Generally speaking, the λe values of the title compounds are larger than their λh. Except for compounds 6 and 9, all others keep the face to face packing or have a slight slip in dimers, but the center of mass distances increase after fluorination or cyanation due to the distortion of the monomer’s coplanarity. The predicted quasi-one-dimensional electron mobility of the dimers is up to 0.433 cm2 V-1 s-1 at 298.15 K. The electron injection barriers of 2 and 7 are lower than that of TPB. The TPB derivatives of 1, 2, and 7 are potential n-channel materials with the high electron mobility. This work is licensed under a Creative Commons Attribution 4.0 International License.

  2. Rethinking Diversity.

    Science.gov (United States)

    1996

    These three papers were presented at a symposium on rethinking diversity in human resource development (HRD) moderated by Neal Chalofsky at the 1996 conference of the Academy of Human Resource Development. "Diversity: A Double-Edged Sword" (Sally F. Angus) presents the notion of work force diversity through two differing perspectives in order to…

  3. Molecular diversity of leuconostoc mesenteroides and leuconostoc citreum isolated from traditional french cheeses as revealed by RAPD fingerprinting, 16S rDNA sequencing and 16S rDNA fragment amplification.

    Science.gov (United States)

    Cibik, R; Lepage, E; Talliez, P

    2000-06-01

    For a long time, the identification of the Leuconostoc species has been limited by a lack of accurate biochemical and physiological tests. Here, we use a combination of RAPD, 16S rDNA sequencing, and 16S rDNA fragment amplification with specific primers to classify different leuconostocs at the species and strain level. We analysed the molecular diversity of a collection of 221 strains mainly isolated from traditional French cheeses. The majority of the strains were classified as Leuconostoc mesenteroides (83.7%) or Leuconostoc citreum (14%) using molecular techniques. Despite their presence in French cheeses, the role of L. citreum in traditional technologies has not been determined, probably because of the lack of strain identification criteria. Only one strain of Leuconostoc lactis and Leuconostoc fallax were identified in this collection, and no Weissella paramesenteroides strain was found. However, dextran negative variants of L. mesenteroides, phenotypically misclassified as W. paramesenteroides, were present. The molecular techniques used did not allow us to separate strains of the three L. mesenteroides subspecies (mesenteroides, dextranicum and cremoris). In accordance with previously published results, our findings suggest that these subspecies may be classified as biovars. Correlation found between phenotypes dextranicum and mesenteroides of L. mesenteroides and cheese technology characteristics suggests that certain strains may be better adapted to particular technological environments.

  4. The ITS1-5.8S-ITS2 Sequence Region in the Musaceae: Structure, Diversity and Use in Molecular Phylogeny

    Czech Academy of Sciences Publication Activity Database

    Hřibová, Eva; Čížková, Jana; Christelová, Pavla; Taudien, S.; De Langhe, E.; Doležel, Jaroslav

    2011-01-01

    Roč. 6, č. 3 (2011), e17863-e17863 E-ISSN 1932-6203 R&D Projects: GA AV ČR IAA600380703; GA AV ČR KJB500380901 Institutional research plan: CEZ:AV0Z50380511 Keywords : INTERNAL TRANSCRIBED SPACER * NUCLEAR RIBOSOMAL DNA * RNA SECONDARY STRUCTURE Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.092, year: 2011

  5. The ITS1-5.8S-ITS2 sequence region in the Musaceae: structure, diversity and use in molecular phylogeny.

    Directory of Open Access Journals (Sweden)

    Eva Hřibová

    2011-03-01

    Full Text Available Genes coding for 45S ribosomal RNA are organized in tandem arrays of up to several thousand copies and contain 18S, 5.8S and 26S rRNA units separated by internal transcribed spacers ITS1 and ITS2. While the rRNA units are evolutionary conserved, ITS show high level of interspecific divergence and have been used frequently in genetic diversity and phylogenetic studies. In this work we report on the structure and diversity of the ITS region in 87 representatives of the family Musaceae. We provide the first detailed information on ITS sequence diversity in the genus Musa and describe the presence of more than one type of ITS sequence within individual species. Both Sanger sequencing of amplified ITS regions and whole genome 454 sequencing lead to similar phylogenetic inferences. We show that it is necessary to identify putative pseudogenic ITS sequences, which may have negative effect on phylogenetic reconstruction at lower taxonomic levels. Phylogenetic reconstruction based on ITS sequence showed that the genus Musa is divided into two distinct clades--Callimusa and Australimusa and Eumusa and Rhodochlamys. Most of the intraspecific banana hybrids analyzed contain conserved parental ITS sequences, indicating incomplete concerted evolution of rDNA loci. Independent evolution of parental rDNA in hybrids enables determination of genomic constitution of hybrids using ITS. The observation of only one type of ITS sequence in some of the presumed interspecific hybrid clones warrants further study to confirm their hybrid origin and to unravel processes leading to evolution of their genomes.

  6. Investigating the Genetic Diversity, Population Differentiation and Population Dynamics of Cycas segmentifida (Cycadaceae Endemic to Southwest China by Multiple Molecular Markers

    Directory of Open Access Journals (Sweden)

    Xiuyan Feng

    2017-05-01

    Full Text Available Climate change, species dispersal ability and habitat fragmentation are major factors influencing species distribution and genetic diversity, especially for the range-restricted and threatened taxa. Here, using four sequences of chloroplast DNAs (cpDNAs, three nuclear genes (nDNAs and 12 nuclear microsatellites (SSRs, we investigated the genetic diversity, genetic structure, divergence time and population dynamics of Cycas segmentifida D. Y. Wang and C. Y. Deng, a threatened cycad species endemic to Southwest China. High levels of genetic diversity and genetic differentiation were revealed in C. segmentifida. Haplotypes of networks showed two evolutionary units in C. segmentifida, with the exception of the nuclear gene GTP network. Meanwhile, the UPGMA tree, structure and PCoA analyses suggested that 14 populations of C. segmentifida were divided into two clades. There was significant effect of isolation by distance (IBD in this species. However, this species did not display a significant phylogeographic structure. The divergence time estimation suggested that its haplotypes diverged during the Middle Pleistocene. Additionally, the population dynamics inferred from different DNA sequences analyses were discordant. Bottleneck analysis showed that populations of C. segmentifida did not experience any recent bottleneck effect, but rather pointed to a contraction of its effective population size over time. Furthermore, our results suggested that the population BM which held an intact population structure and occupied undisturbed habitat was at the Hardy–Weinberg equilibrium, implying that this population is a free-mating system. These genetic features provide important information for the sustainable management of C. segmentifida.

  7. Influence of the substituents on the electronic and electrochemical properties of a new square-planar nickel-bis(quinoxaline-6,7-dithiolate) system: synthesis, spectroscopy, electrochemistry, crystallography, and theoretical investigation.

    Science.gov (United States)

    Bolligarla, Ramababu; Reddy, Samala Nagaprasad; Durgaprasad, Gummadi; Sreenivasulu, Vudagandla; Das, Samar K

    2013-01-07

    We describe the synthesis, crystal structures, electronic absorption spectra, and electrochemistry of a series of square-planar nickel-bis(quinoxaline-6,7-dithiolate) complexes with the general formula [Bu(4)N](2)[Ni(X(2)6,7-qdt)(2)], where X = H (1a), Ph (2a), Cl (3), and Me (4). The solution and solid-state electronic absorption spectral behavior and electrochemical properties of these compounds are strongly dependent on the electron donating/accepting nature of the substituent X, attached to the quinoxaline-6,7-dithiolate ring in the system [Bu(4)N](2)[Ni(X(2)6,7-qdt)(2)]. Particularly, the charge transfer (CT) transition bands observed in the visible region are greatly affected by the electronic nature of the substituent. A possible explanation for this influence of the substituents on electronic absorption and electrochemistry is described based on highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) gaps, which is further supported by ground-state electronic structure calculations. In addition to this, the observed CT bands in all the complexes are sensitive to the solvent polarity. Interestingly, compounds 1a, 2a, 3, and 4 undergo reversible oxidation at very low oxidation potentials appearing at E(1/2) = +0.12 V, 0.033 V, 0.18 V, and 0.044 V vs Ag/AgCl, respectively, in MeOH solutions, corresponding to the respective couples [Ni(X(2)6,7-qdt)(2)](-)/[Ni(X(2)6,7-qdt)(2)](2-). Compounds 1a, 3, and 4 have been characterized unambiguously by single crystal X-ray structural analysis; compound 2a could not be characterized by single crystal X-ray structure determination because of the poor quality of the concerned crystals. Thus, we have synthesized the tetraphenyl phosphonium salt of the complex anion of 2a, [PPh(4)](2)[Ni(Ph(2)6,7-qdt)(2)]·3DMF (2b) for its structural characterization.

  8. Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale.

    Science.gov (United States)

    Aminov, Rustam I; Walker, Alan W; Duncan, Sylvia H; Harmsen, Hermie J M; Welling, Gjalt W; Flint, Harry J

    2006-09-01

    Phylogenetic analysis was used to compare 16S rRNA sequences from 19 cultured human gut strains of Roseburia and Eubacterium rectale with 356 related sequences derived from clone libraries. The cultured strains were found to represent five of the six phylotypes identified. A new oligonucleotide probe, Rrec584, and the previous group probe Rint623, when used in conjunction with a new helper oligonucleotide, each recognized an average of 7% of bacteria detected by the eubacterial probe Eub338 in feces from 10 healthy volunteers. Most of the diversity within this important group of butyrate-producing gut bacteria can apparently be retrieved through cultivation.

  9. Molecular Comparison and Evolutionary Analyses of VP1 Nucleotide Sequences of New African Human Enterovirus 71 Isolates Reveal a Wide Genetic Diversity

    Science.gov (United States)

    Nougairède, Antoine; Joffret, Marie-Line; Deshpande, Jagadish M.; Dubot-Pérès, Audrey; Héraud, Jean-Michel

    2014-01-01

    Most circulating strains of Human enterovirus 71 (EV-A71) have been classified primarily into three genogroups (A to C) on the basis of genetic divergence between the 1D gene, which encodes the VP1 capsid protein. The aim of the present study was to provide further insights into the diversity of the EV-A71 genogroups following the recent description of highly divergent isolates, in particular those from African countries, including Madagascar. We classified recent EV-A71 isolates by a large comparison of 3,346 VP1 nucleotidic sequences collected from GenBank. Analysis of genetic distances and phylogenetic investigations indicated that some recently-reported isolates did not fall into the genogroups A-C and clustered into three additional genogroups, including one Indian genogroup (genogroup D) and 2 African ones (E and F). Our Bayesian phylogenetic analysis provided consistent data showing that the genogroup D isolates share a recent common ancestor with the members of genogroup E, while the isolates of genogroup F evolved from a recent common ancestor shared with the members of the genogroup B. Our results reveal the wide diversity that exists among EV-A71 isolates and suggest that the number of circulating genogroups is probably underestimated, particularly in developing countries where EV-A71 epidemiology has been poorly studied. PMID:24598878

  10. Piperazines as nootropic agents: New derivatives of the potent cognition-enhancer DM235 carrying hydrophilic substituents.

    Science.gov (United States)

    Martino, Maria Vittoria; Guandalini, Luca; Di Cesare Mannelli, Lorenzo; Menicatti, Marta; Bartolucci, Gianluca; Dei, Silvia; Manetti, Dina; Teodori, Elisabetta; Ghelardini, Carla; Romanelli, Maria Novella

    2017-03-15

    The piperazine ring of the potent nootropic drug DM235 has been decorated with H-bond donor and acceptor groups (CH 2 OH, CH 2 OMe, CH 2 OCOMe, COOEt); the aim was to insert new functional groups, suitable for further chemical manipulation. The influence of these modifications on nootropic activity was assessed by means of the mouse passive avoidance test; some of the newly synthesized molecules (alcohol 7b, acetate 8b and ester 10d) showed interesting in vivo potency. This makes it possible to use these functional groups for adding other residues, in order to increase molecular diversity, or for anchoring a biotin group, to obtain compounds useful to capture the biological target. Moreover, the new compounds will improve our knowledge of structure activity relationships of this family of drugs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Identity, Diversity and Diversity Management

    DEFF Research Database (Denmark)

    Holck, Lotte; Muhr, Sara Louise; Villeseche, Florence

    2016-01-01

    – The work can encourage policy makers, diversity and HR managers to question their own practices and assumptions leading to more theoretical informed diversity management practices. Originality/value – The theoretical connections between identity and diversity literature have so far not been reviewed......The purpose of this paper is to examine the relationship between the identity and diversity literatures and discuss how a better understanding of the theoretical connections between the two informs both diversity research and diversity management practices. Design/methodology/approach – Literature...... and limitations – is crucial for successful diversity management research and practice. Research limitations/implications – The authors argue for a better understanding of differences, overlaps and limits of different identity perspectives, and for a stronger engagement with practice. Practical implications...

  12. Detecting in situ copepod diet diversity using molecular technique: development of a copepod/symbiotic ciliate-excluding eukaryote-inclusive PCR protocol.

    Science.gov (United States)

    Hu, Simin; Guo, Zhiling; Li, Tao; Carpenter, Edward J; Liu, Sheng; Lin, Senjie

    2014-01-01

    Knowledge of in situ copepod diet diversity is crucial for accurately describing pelagic food web structure but is challenging to achieve due to lack of an easily applicable methodology. To enable analysis with whole copepod-derived DNAs, we developed a copepod-excluding 18S rDNA-based PCR protocol. Although it is effective in depressing amplification of copepod 18S rDNA, its applicability to detect diverse eukaryotes in both mono- and mixed-species has not been demonstrated. Besides, the protocol suffers from the problem that sequences from symbiotic ciliates are overrepresented in the retrieved 18S rDNA libraries. In this study, we designed a blocking primer to make a combined primer set (copepod/symbiotic ciliate-excluding eukaryote-common: CEEC) to depress PCR amplification of symbiotic ciliate sequences while maximizing the range of eukaryotes amplified. We firstly examined the specificity and efficacy of CEEC by PCR-amplifying DNAs from 16 copepod species, 37 representative organisms that are potential prey of copepods and a natural microplankton sample, and then evaluated the efficiency in reconstructing diet composition by detecting the food of both lab-reared and field-collected copepods. Our results showed that the CEEC primer set can successfully amplify 18S rDNA from a wide range of isolated species and mixed-species samples while depressing amplification of that from copepod and targeted symbiotic ciliate, indicating the universality of CEEC in specifically detecting prey of copepods. All the predetermined food offered to copepods in the laboratory were successfully retrieved, suggesting that the CEEC-based protocol can accurately reconstruct the diets of copepods without interference of copepods and their associated ciliates present in the DNA samples. Our initial application to analyzing the food composition of field-collected copepods uncovered diverse prey species, including those currently known, and those that are unsuspected, as copepod prey

  13. Study on effect of substituents in α positron of N,N-diethylamides by nuclear magnetic resonance

    International Nuclear Information System (INIS)

    Martins, M.A.P.

    1982-01-01

    The effect of a substituent in the α position of some N,N-diethylamides, through the 1 H and 13 C n.m.r. spectroscopy is studied. Eight N,N-diethylamides having the structure: Y-CH 2 -C(O) - NEt 2 , where Y=H, Me, Cl, Br, I, OMe, SMe, and NMe 2 were prepared by usual procedures; all these compounds were characterized by their 1 H and 13 C n.m.r. and infrared spectra, as well as by their elementary analysis. (M.J.C.) [pt

  14. Halogen–Metal Exchange on Bromoheterocyclics with Substituents Containing an Acidic Proton via Formation of a Magnesium Intermediate

    Directory of Open Access Journals (Sweden)

    Qingqiang Tian

    2017-11-01

    Full Text Available A selective and practical bromine–metal exchange on bromoheterocyclics bearing substituents with an acidic proton under non-cryogenic conditions was developed by a simple modification of an existing protocol. Our protocol of using a combination of i-PrMgCl and n-BuLi has not only solved the problem of intermolecular quenching that often occurred when using alkyl lithium alone as the reagent for halogen–lithium exchange, but also offered a highly selective method for performing bromo–metal exchange on dibrominated arene compounds through chelation effect.

  15. Influence of Halogen Substituents on the Catalytic Oxidation of 2,4,6-Halogenated Phenols by Fe(III-Tetrakis(p-hydroxyphenyl porphyrins and Potassium Monopersulfate

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    Seiya Nagao

    2011-12-01

    Full Text Available The influence of halogen substituents on the catalytic oxidation of 2,4,6-trihalogenated phenols (TrXPs by iron(III-porphyrin/KHSO5 catalytic systems was investigated. Iron(III-5,10,15,20-tetrakis(p-hydroxyphenylporphyrin (FeTHP and its supported variants were employed, where the supported catalysts were synthesized by introducing FeTHP into hydroquinone-derived humic acids via formaldehyde poly-condensation. F (TrFP, Cl (TrCP, Br (TrBP and I (TrIP were examined as halogen substituents for TrXPs. Although the supported catalysts significantly enhanced the degradation and dehalogenation of TrFP and TrCP, the oxidation of TrBP and TrIP was not enhanced, compared to the FeTHP catalytic system. These results indicate that the degree of oxidation of TrXPs is strongly dependent on the types of halogen substituent. The order of dehalogenation levels for halogen substituents in TrXPs was F > Cl > Br > I, consistent with their order of electronegativity. The electronegativity of a halogen substituent affects the nucleophilicity of the carbon to which it is attached. The levels of oxidation products in the reaction mixtures were analyzed by GC/MS after extraction with n-hexane. The most abundant dimer product from TrFP via 2,6-difluoroquinone is consistent with a scenario where TrXP, with a more electronegative halogen substituent, is readily oxidized, while less electronegative halogen substituents are oxidized less readily by iron(III-porphyrin/KHSO5 catalytic systems.

  16. Spectroscopic study of 2-, 4- and 5-substituents on p Ka values of imidazole heterocycles prone to intramolecular proton-electrons transfer

    Science.gov (United States)

    Eseola, Abiodun O.; Obi-Egbedi, Nelson O.

    2010-02-01

    New 2-(1H-imidazol-2-yl)phenols ( L1Et- L8tBuPt) bearing a phenolic proton in the vicinity of the imidazole base were prepared and characterized. Experimental studies of the dependence of their protonation/deprotonation equilibrium on substituent identities and intramolecular hydrogen bonding tendencies were carried out using electronic absorption spectroscopy at varying pH values. In order to make comparison, 2-(anthracen-10-yl)-4,5-diphenyl-1H-imidazole ( L9Anthr) bearing no phenolic proton and 4,5-diphenyl-2-(4,5-diphenyl-1H-imidazol-2-yl)-1H-imidazole ( L10BisIm) bearing two symmetrical imidazole base fragments were also prepared and experimentally investigated. DFT calculations were carried out to study frontier orbitals of the investigated molecules. While electron-releasing substituents produced increase in protonation-deprotonation p Kas for the hydroxyl group, values for the imidazole base were mainly affected by polarization of the imidazole ring aromaticity across the 2-imidazole carbon and the 4,5-imidazole carbons axis of the imidazole ring. It was concluded that electron-releasing substituents on the phenol ring and/or electron-withdrawing substituents on 4,5-imidazole carbons negatively affects donor strengths/coordination chemistries of 2-(1H-imidazol-2-yl)phenols, and vice versa. Change of substituents on the phenol ring significantly altered the donor strength of the imidazole base. The understanding of p Ka variation on account of electronic effects of substituents in this work should aid the understanding of biochemical properties and substituent environments of imidazole-containing biomacromolecules.

  17. Transcriptomic profiling of diverse Aedes aegypti strains reveals increased basal-level immune activation in dengue virus-refractory populations and identifies novel virus-vector molecular interactions.

    Directory of Open Access Journals (Sweden)

    Shuzhen Sim

    Full Text Available Genetic variation among Aedes aegypti populations can greatly influence their vector competence for human pathogens such as the dengue virus (DENV. While intra-species transcriptome differences remain relatively unstudied when compared to coding sequence polymorphisms, they also affect numerous aspects of mosquito biology. Comparative molecular profiling of mosquito strain transcriptomes can therefore provide valuable insight into the regulation of vector competence. We established a panel of A. aegypti strains with varying levels of susceptibility to DENV, comprising both laboratory-maintained strains and field-derived colonies collected from geographically distinct dengue-endemic regions spanning South America, the Caribbean, and Southeast Asia. A comparative genome-wide gene expression microarray-based analysis revealed higher basal levels of numerous immunity-related gene transcripts in DENV-refractory mosquito strains than in susceptible strains, and RNA interference assays further showed different degrees of immune pathway contribution to refractoriness in different strains. By correlating transcript abundance patterns with DENV susceptibility across our panel, we also identified new candidate modulators of DENV infection in the mosquito, and we provide functional evidence for two potential DENV host factors and one potential restriction factor. Our comparative transcriptome dataset thus not only provides valuable information about immune gene regulation and usage in natural refractoriness of mosquito populations to dengue virus but also allows us to identify new molecular interactions between the virus and its mosquito vector.

  18. Bacterial Diversity Studies Using the 16S rRNA Gene Provide a Powerful Research-Based Curriculum for Molecular Biology Laboratory

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    Bryan E. Dutton

    2002-12-01

    Full Text Available We have developed a ten-week curriculum for molecular biology that uses 16S ribosomal RNA genes to characterize and compare novel bacteria from hot spring communities in Yellowstone National Park. The 16S rRNA approach bypasses selective culture-based methods. Our molecular biology course offered the opportunity for students to learn broadly applicable methods while contributing to a long-term research project. Specifically, students isolated and characterized clones that contained novel 16S rRNA inserts using restriction enzyme, DNA sequencing, and computer-based phylogenetic methods. In both classes, students retrieved novel bacterial 16S rRNA genes, several of which were most similar to Green Nonsulfur bacterial isolates. During class, we evaluated student performance and mastery of skills and concepts using quizzes, formal lab notebooks, and a broad project assignment. For this report, we also assessed student performance alongside data quality and discussed the significance, our goal being to improve both research and teaching methods.

  19. Molecular characterization and genetic diversity of ESBL-producing Escherichia coli colonizing the migratory Franklin's gulls (Leucophaeus pipixcan) in Antofagasta, North of Chile.

    Science.gov (United States)

    Báez, John; Hernández-García, Marta; Guamparito, Constanza; Díaz, Sofía; Olave, Abdon; Guerrero, Katherine; Cantón, Rafael; Baquero, Fernando; Gahona, Joselyne; Valenzuela, Nicomedes; Del Campo, Rosa; Silva, Juan

    2015-02-01

    The role of wild animals, particularly migratory birds, in the dissemination of antibiotic-resistant bacteria between geographically distant ecosystems is usually underestimated. The aim of this work was to characterize the Escherichia coli population from Franklin's gull feces, focusing on the extended-spectrum β-lactamase (ESBL)-producing strains. In the summer of 2011, 124 fecal swabs from seagulls (1 of each) migrating from the United States and Canada to the coast of Antofagasta, north of Chile, were collected. Samples were seeded on MacConkey agar supplemented with 2 μg/ml of cefotaxime and a single colony from each plate was tested for ESBL production by the double-disk ESBL synergy test. Antibiotic susceptibility was determined by the disk diffusion method and blaESBL genes were amplified and sequenced. The genetic diversity of isolates was explored by pulsed-field gel electrophoresis (PFGE)-XbaI and multilocus sequence typing. A total of 91 E. coli isolates with high rates of antibiotic resistance were identified. Carbapenemase production was not detected, whereas 67 of the 91 (54%) isolates exhibited an ESBL phenotype due to the presence of CTX-M-15 (61.3%), CTX-M-2 (19.3%), CTX-M-22 (16.1%), and CTX-M-3 (1.6%) coding genes. High genetic diversity was observed, with 30 PFGE patterns and 23 sequence types (STs), including ST131 (18%), ST44 (15%), ST617 (9%), and ST10 (9%). Results presented here are complementary to those previously reported by Hernández et al. in the same gull species, but located in the Central Region of Chile. Differences observed between gulls from both areas lead us to hypothesize that gulls from the northern location retain, as gut carriers, those resistant bacteria acquired in the United States and/or Canada.

  20. Molecular characterisation and interpretation of genetic diversity within globally distributed germplasm collections of tall fescue (Festuca arundinacea Schreb.) and meadow fescue (F. pratensis Huds.).

    Science.gov (United States)

    Hand, Melanie L; Cogan, Noel O I; Forster, John W

    2012-04-01

    Allohexaploid tall fescue (Festuca arundinacea Schreb. syn. Lolium arundinaceum [Schreb.] Darbysh.) is an agriculturally important grass cultivated for pasture and turf world-wide. Genetic improvement of tall fescue could benefit from the use of non-domesticated germplasm to diversify breeding populations through the incorporation of novel and superior allele content. However, such potential germplasm must first be characterised, as three major morphotypes (Continental, Mediterranean and rhizomatous) with varying degrees of hybrid interfertility are commonly described within this species. As hexaploid tall fescue is also a member of a polyploid species complex that contains tetraploid, octoploid and decaploid taxa, it is also possible that germplasm collections may have inadvertently sampled some of these sub-species. In this study, 1,040 accessions from the publicly available United States Department of Agriculture tall fescue and meadow fescue germplasm collections were investigated. Sequence of the chloroplast genome-located matK gene and the nuclear ribosomal DNA internal transcribed spacer (rDNA ITS) permitted attribution of accessions to the three previously known morphotypes and also revealed the presence of tall fescue sub-species of varying ploidy levels, as well as other closely related species. The majority of accessions were, however, identified as Continental hexaploid tall fescue. Analysis using 34 simple sequence repeat markers was able to further investigate the level of genetic diversity within each hexaploid tall fescue morphotype group. At least two genetically distinct sub-groups of Continental hexaploid tall fescue were identified which are probably associated with palaeogeographic range expansion of this morphotype. This work has comprehensively characterised a large and complex germplasm collection and has identified genetically diverse accessions which may potentially contribute valuable alleles at agronomic loci for tall fescue cultivar

  1. Efficient Syntheses of Novel Fluoro-Substituted Pentacenes and Azapentacenes: Molecular and Solid-State Properties.

    Science.gov (United States)

    Schwaben, Jonas; Münster, Niels; Klues, Michael; Breuer, Tobias; Hofmann, Philipp; Harms, Klaus; Witte, Gregor; Koert, Ulrich

    2015-09-21

    Non-symmetrical 6,13-disubstituted pentacenes bearing trifluoromethyl and aryl substituents have been synthesized starting from pentacenequinone. Diazapentacenes with a variety of fluorine substituents were prepared either via a Hartwig-Buchwald aryl amination route or by a SNAr strategy. As a result of a non-symmetric substitution pattern containing electron-donating substituents in combination with electron-accepting fluorine substituents, the synthesized compounds feature distinct molecular dipoles. All compounds are analyzed regarding their optoelectronic properties in solution with special focus on the frontier orbital energies as well as their molecular packing in the crystal structures. The analyses of isolated molecules are complemented by thin-film studies to examine their solid-state properties. A precise comparison between these and the molecular properties gave detailed insights into the exciton binding energies of these compounds, which are explained by means of a simple model considering the molecular packing and polarizabilities. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Molecular diversity analysis of Tetradium ruticarpum (WuZhuYu) in China based on inter-primer binding site (iPBS) markers and inter-simple sequence repeat (ISSR) markers.

    Science.gov (United States)

    Xu, Jing-Yuan; Zhu, Yan; Yi, Ze; Wu, Gang; Xie, Guo-Yong; Qin, Min-Jian

    2018-01-01

    "Wu zhu yu", which is obtained from the dried unripe fruits of Tetradium ruticarpum (A. Jussieu) T. G. Hartley, has been used as a traditional Chinese medicine for treatment of headaches, abdominal colic, and hypertension for thousands of years. The present study was designed to assess the molecular genetic diversity among 25 collected accessions of T. ruticarpum (Wu zhu yu in Chinese) from different areas of China, based on inter-primer binding site (iPBS) markers and inter-simple sequence repeat (ISSR) markers. Thirteen ISSR primers generated 151 amplification bands, of which 130 were polymorphic. Out of 165 bands that were amplified using 10 iPBS primers, 152 were polymorphic. The iPBS markers displayed a higher proportion of polymorphic loci (PPL = 92.5%) than the ISSR markers (PPL = 84.9%). The results showed that T. ruticarpum possessed high loci polymorphism and genetic differentiation occurred in this plant. The combined data of iPBS and ISSR markers scored on 25 accessions produced five clusters that approximately matched the geographic distribution of the species. The results indicated that both iPBS and ISSR markers were reliable and effective tools for analyzing the genetic diversity in T. ruticarpum. Copyright © 2018 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.

  3. Approaches for introducing high molecular diversity in scaffolds: fast parallel synthesis of highly substituted 1H-quinolin-4-one libraries.

    Science.gov (United States)

    Kuznetsov, Vladimir; Gorohovsky, Sofia; Levy, Amalia; Meir, Simcha; Shkoulev, Vladimir; Menashe, Naim; Greenwald, Moshe; Aizikovich, Alexander; Ofer, Dror; Byk, Gerardo; Gellerman, Garry

    2004-01-01

    We have developed a two steps strategy for the parallel synthesis of highly diversified quinolin-ones. In the first step we have combined and improved different synthetic methods for generating quinolin-4-ones bearing four different substitutions at specific positions using round bottomed flasks. The synthesis was assessed for a large number of substituted quinolin-4-ones. In the second step, the improved method was adapted to a parallel array synthesis using a 12 positions carrousel as demonstrated for the synthesis of 42-variable quinolin-4-ones. The first combinatorial library set 14(a-x) was obtained with a chemical purity of more than 95% without purification, the second library set 15(a-r), which included two synthetic steps, needed combinatorial purification using an innovative parallel purifier. The proposed approach contributes to a more extensive diversification of molecular scaffolds in general and provides access to highly substituted quinolinones in particular.

  4. Plant molecular phylogeography in China and adjacent regions: Tracing the genetic imprints of Quaternary climate and environmental change in the world's most diverse temperate flora.

    Science.gov (United States)

    Qiu, Ying-Xiong; Fu, Cheng-Xing; Comes, Hans Peter

    2011-04-01

    The Sino-Japanese Floristic Region (SJFR) of East Asia harbors the most diverse of the world's temperate flora, and was the most important glacial refuge for its Tertiary representatives ('relics') throughout Quaternary ice-age cycles. A steadily increasing number of phylogeographic studies in the SJFR of mainland China and adjacent areas, including the Qinghai-Tibetan-Plateau (QTP) and Sino-Himalayan region, have documented the population histories of temperate plant species in these regions. Here we review this current literature that challenges the oft-stated view of the SJFR as a glacial sanctuary for temperate plants, instead revealing profound effects of Quaternary changes in climate, topography, and/or sea level on the current genetic structure of such organisms. There are three recurrent phylogeographic scenarios identified by different case studies that broadly agree with longstanding biogeographic or palaeo-ecological hypotheses: (i) postglacial re-colonization of the QTP from (south-)eastern glacial refugia; (ii) population isolation and endemic species formation in Southwest China due to tectonic shifts and river course dynamics; and (iii) long-term isolation and species survival in multiple localized refugia of (warm-)temperate deciduous forest habitats in subtropical (Central/East/South) China. However, in four additional instances, phylogeographic findings seem to conflict with a priori predictions raised by palaeo-data, suggesting instead: (iv) glacial in situ survival of some hardy alpine herbs and forest trees on the QTP platform itself; (v) long-term refugial isolation of (warm-)temperate evergreen taxa in subtropical China; (vi) 'cryptic' glacial survival of (cool-)temperate deciduous forest trees in North China; and (vii) unexpectedly deep (Late Tertiary/early-to-mid Pleistocene) allopatric-vicariant differentiation of disjunct lineages in the East China-Japan-Korea region due to past sea transgressions. We discuss these and other consequences

  5. Diversity Management

    DEFF Research Database (Denmark)

    Ravazzani, Silvia

    2018-01-01

    This entry provides an overview of diversity management which, in the context of organizations, consists in the strategic process of harnessing the potential of all employees to create an inclusive environment and, at the same time, contribute to meeting organizational goals. The entry first...... describes the complex construct of diversity that has been variously conceptualized in the literature, embracing multiple social and informational diversity dimensions such as gender, age, culture, values, and workstyle. This is followed by illustration of the historical development of diversity-management...... discourse and practice, and possible overarching approaches guiding organizations. It goes on to elucidate elements linked to the implementation of diversity management: positive and negative outcomes, most spread practices including communication, and contingency factors shaping the understanding...

  6. Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems.

    Science.gov (United States)

    Yamada, Mari; Watanabe, Yuto; Gootenberg, Jonathan S; Hirano, Hisato; Ran, F Ann; Nakane, Takanori; Ishitani, Ryuichiro; Zhang, Feng; Nishimasu, Hiroshi; Nureki, Osamu

    2017-03-16

    The RNA-guided endonuclease Cas9 generates a double-strand break at DNA target sites complementary to the guide RNA and has been harnessed for the development of a variety of new technologies, such as genome editing. Here, we report the crystal structures of Campylobacter jejuni Cas9 (CjCas9), one of the smallest Cas9 orthologs, in complex with an sgRNA and its target DNA. The structures provided insights into a minimal Cas9 scaffold and revealed the remarkable mechanistic diversity of the CRISPR-Cas9 systems. The CjCas9 guide RNA contains a triple-helix structure, which is distinct from known RNA triple helices, thereby expanding the natural repertoire of RNA triple helices. Furthermore, unlike the other Cas9 orthologs, CjCas9 contacts the nucleotide sequences in both the target and non-target DNA strands and recognizes the 5'-NNNVRYM-3' as the protospacer-adjacent motif. Collectively, these findings improve our mechanistic understanding of the CRISPR-Cas9 systems and may facilitate Cas9 engineering. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Molecular Interaction Study of some ortho and para Substituted Anilines with 1-Octanol

    Directory of Open Access Journals (Sweden)

    M. S. Manjunatha

    2010-01-01

    Full Text Available Interactions between ortho and para substituents of anilines such as chloroaniline, methylaniline and methoxyaniline with 1-octanol have been studied in carbon tetrachloride. The most likely association of complex between 1-octanol and substituents of anilines is 1:1 stoichiometric complex, through hydroxyl group of 1-octanol and amine group of ortho and para substituents of anilines. Interactions are studied on the bases of formation constant and free energy changes. Formation constant of the complex has been calculated using Nash method. The result shows that molecular interaction of 1-octanol as proton donor with methyl and chloride substitution of anilines in ortho position is smaller than the para position substitution of anilines. The results shows, the ability of acceptors is in the order p-methoxyaniline < o-chloroaniline

  8. [The molecular genetic typification of planarians in the genus Bdellocephala (Dendrocoelidae, Tricladida, Turbellaria) from Lake Baikal with an assessment of their species diversity].

    Science.gov (United States)

    Kuznedelov, K D; Novikova, O A; Naumova, T V

    2000-01-01

    Baikal planaria from genus Bdellocephala were typified using rDNA locus coding 5'--end domain of 18S ribosome RNA. Five colour forms of 24 possible variants that differ in diapason 0-1.3% of genotype were determined by comparative analysis of nucleotide sequences. The authors use back colour--one of the most variable and typical character in the given group--to collect material for investigation. It allows to minimize the size of investigation sample and at the same time to cover maximum variability of Bdellocephala. One of the positive result of molecular typification of colour forms was a discovery of unique individuals that belong to new species. Karyological analysis of colour forms shows variations in chromosome numbers that divide planaria into 3 groups (2n = 20, 24, 26). Comparative analysis of morphological and ecological characters and karyotypes of some forms united by the same genotype allows to distinguish them as separate species. Criteria of modern phenetic system of Baikal planaria are discussed.

  9. Antipathy of Trichoderma against Sclerotium rolfsii Sacc.: Evaluation of Cell Wall-Degrading Enzymatic Activities and Molecular Diversity Analysis of Antagonists.

    Science.gov (United States)

    Hirpara, Darshna G; Gajera, Harsukh P; Hirpara, Hitesh Z; Golakiya, Balubhai A

    2017-01-01

    The fungus Trichoderma is a teleomorph of the Hypocrea genus and associated with biological control of plant diseases. The microscopic, biochemical, and molecular characterization of Trichoderma was carried out and evaluated for in vitro antagonistic activity against the fungal pathogen Sclerotium rolfsii causing stem rot disease in groundnut. In total, 11 isolates of Trichoderma were examined for antagonism at 6 and 12 days after inoculation (DAI). Out of 11, T. virens NBAII Tvs12 evidenced the highest (87.91%) growth inhibition of the test pathogen followed by T. koningii MTCC 796 (67.03%), T. viride NBAII Tv23 (63.74%), and T. harzianum NBAII Th1 (60.44%). Strong mycoparasitism was observed in the best antagonist Tvs12 strain during 6-12 DAI. The specific activity of cell wall-degrading enzymes - chitinase and β-1,3-glucanase - was positively correlated with growth inhibition of the test pathogen. In total, 18 simple sequence repeat (SSR) polymorphisms were reported to amplify 202 alleles across 11 Trichoderma isolates. The average polymorphism information content for SSR markers was found to be 0.80. The best antagonist Tvs 12 was identified with 7 unique SSR alleles amplified by 5 SSR markers. Clustering patterns of 11 Trichoderma strains showed the best antagonist T. virens NBAII Tvs 12 outgrouped with a minimum 3% similarity from the rest of Trichoderma. © 2017 S. Karger AG, Basel.

  10. Molecular diversity in irregular or refugee immigrant patients with HBV-genotype-E infection living in the metropolitan area of Naples.

    Science.gov (United States)

    Sagnelli, Caterina; Ciccozzi, Massimo; Coppola, Nicola; Minichini, Carmine; Lo Presti, Alessandra; Starace, Mario; Alessio, Loredana; Macera, Margherita; Cella, Eleonora; Gualdieri, Luciano; Caprio, Nunzio; Pasquale, Giuseppe; Sagnelli, Evangelista

    2017-06-01

    In a recent testing in the metropolitan area of Naples, Italy, on 945 irregular immigrants or refugees, 87 HBsAg chronic carriers were identified, 53 of whom were infected by HBV-genotype E. The aim of the present study was to identify the genetic diversity of HBV-genotype E in these 53 immigrants. The 53 immigrant patients with HBV-genotype-E infection were born in Africa, central or eastern Asia, eastern Europe or Latin America. These patients had been seen for a clinical consultation at one of the four first-level units from January 2012 to 2013. The first dataset contained 53 HBV-S gene isolates plus 128 genotype/subgenotype specific reference sequences downloaded from the National Center for Biotechnology Information. The second dataset, comprising the 53 HBV-S gene isolates, previously classified as HBV-genotype E, was used to perform the time-scaled phylogeny reconstruction using a Bayesian approach. Phylogenetic analysis showed that all 53 HBV-S isolates belonged to HBV-genotype E. Bayes factor analysis showed that the relaxed clock exponential growth model fitted the data significantly better than the other models. The time-scaled Bayesian phylogenetic tree of the second dataset showed that the root of the tree dated back to the year 1990 (95% HPD:1984-2000). Four statistically supported clusters were identified. Cluster A dated back to 2012 (95% HPD:1997-2012); cluster B dated back to 2008 (95% HPD:2001-2015); cluster C to 2006 (95% HPD:1999-2013); cluster D to 2004 (95% HPD:1998-2011). This study disclosed the genetic evolution and phylogenesis in a group of HBV-genotype-E-infected immigrants. J. Med. Virol. 89:1015-1024, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  11. Identity, diversity, and molecular phylogeny of the endophytic mycobiota in the roots of rare wild rice (Oryza granulate) from a nature reserve in Yunnan, China.

    Science.gov (United States)

    Yuan, Zhi-Lin; Zhang, Chu-Long; Lin, Fu-Cheng; Kubicek, Christian P

    2010-03-01

    Rice (Oryza sativa L.) is, on a global scale, one of the most important food crops. Although endophytic fungi and bacteria associated with rice have been investigated, little is known about the endophytic fungi of wild rice (Oryza granulate) in China. Here we studied the root endophytic mycobiota residing in roots of O. granulate by the use of an integrated approach consisting of microscopy, cultivation, ecological indices, and direct PCR. Microscopy confirmed the ubiquitousness of dark septate endophytes (DSEs) and sclerotium-like structures in root tissues. Isolations from 204 root segments from 15 wild rice plants yielded 58 isolates, for which 31 internal transcribed spacer (ITS)-based genotypes were recorded. The best BLAST match indicated that 34.5% of all taxa encountered may represent hitherto undescribed species. Most of the fungi were isolated with a very low frequency. Calculation of ecological indices and estimation of taxon accumulation curves indicated a high diversity of fungal species. A culture-independent approach was also performed to analyze the endophytic fungal community. Three individual clone libraries were constructed. Using a threshold of 90% similarity, 35 potentially different sequences (phylotypes) were found among 186 positive clones. Phylogenetic analysis showed that frequently detected clones were classified as Basidiomycota, and 60.2% of total analyzed clones were affiliated with unknown taxa. Exophiala, Cladophialophora, Harpophora, Periconia macrospinosa, and the Ceratobasidium/Rhizoctonia complex may act as potential DSE groups. A comparison of the fungal communities characterized by the two approaches demonstrated distinctive fungal groups, and only a few taxa overlapped. Our findings indicate a complex and rich endophytic fungal consortium in wild rice roots, thus offering a potential bioresource for establishing a novel model of plant-fungal mutualistic interactions.

  12. Hidden Diversity in the Populations of the Armored Catfish Ancistrus Kner, 1854 (Loricariidae, Hypostominae from the Paraná River Basin Revealed by Molecular and Cytogenetic Data

    Directory of Open Access Journals (Sweden)

    Ana C. Prizon

    2017-11-01

    Full Text Available Only one species of armored catfish, Ancistrus cirrhosus Valenciennes 1836, has been historically described in the basin of the Paraná River, from Misiones (Argentina. However, the ample variation found in the morphology and coloration of the populations sampled in the tributaries of the Brazilian state of Paraná makes it difficult to establish the real taxonomic status and evolutionary history of the Ancistrus specimens, suggesting that A. cirrhosus is not the only species found in this basin. By combining data on mitochondrial DNA (COI gene and chromosomal markers from different Ancistrus populations, totaling 144 specimens, in the tributaries of the Paraná, and specimens from Misiones (type-locality of A. cirrhosus, we detected five distinct evolutionary lineages. All the specimens were 2n = 50, but had four distinct karyotype formulae. The results of the Generalized Mixed Yule Coalescent (GYMC and the genetic distances (uncorrected P-values between lineages ranged from 3 to 5%. Clusters of 18S rDNA were observed in a single chromosome pair in seven populations of Ancistrus, but at different positions, in some cases, in synteny with the 5S rDNA sites. Multiple 5S sites were observed in all populations. Overall, the cytogenetic data reinforce the genetic evidence of the diversification of lineages, and indicate the existence of candidate species in the study region. The evidence indicates that at least four candidate species of the Ancistrus may coexist in the Paraná basin besides A. cirrhosus. Overall, our results provide a comprehensive scenario for the genetic variation among Ancistrus populations and reinforce the conclusion that the true diversity of the freshwater fish of the Neotropical regions has been underestimated.

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

    Directory of Open Access Journals (Sweden)

    M. Jorjandi

    2014-08-01

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

  14. The Diels-Alder Cycloaddition Reaction of Substituted Hemifullerenes with 1,3-Butadiene: Effect of Electron-Donating and Electron-Withdrawing Substituents.

    Science.gov (United States)

    Mojica, Martha; Méndez, Francisco; Alonso, Julio A

    2016-02-12

    The Diels-Alder (DA) reaction provides an attractive route to increase the number of six member rings in substituted Polycyclic Aromatic Hydrocarbons (PAHs). The density functional theory (DFT) B3LYP method has been used in this work to inquire if the substitution of H over the edge of triindenetriphenylene (pristine hemifullerene 1) and pentacyclopentacorannulene (pristine hemifullerene 2), could improve the DA cycloaddition reaction with 1,3-butadiene. The substituents tested include electron-donating (NH₂, OMe, OH, Me, i-Pr) and electron-withdrawing groups (F, COOH, CF₃, CHO, CN, NO₂). The electronic, kinetic and thermodynamic parameters of the DA reactions of the substituted hemifullerenes with 1,3-butadiene have been analyzed. The most promising results were obtained for the NO₂ substituent; the activation energy barriers for reactions using this substituent were lower than the barriers for the pristine hemifullerenes. This leads us to expect that the cycloadditions to a starting fullerene fragment will be possible.

  15. Relative substituent orientation in the structure of cis-3-chloro-1,3-dimethyl-N-(4-nitrophenyl-2-oxocyclopentane-1-carboxamide

    Directory of Open Access Journals (Sweden)

    Matthias Zeller

    2014-09-01

    Full Text Available The structure of the title compound, C14H15ClN2O4, prepared by reaction of a methacryloyl dimer with nitroaniline, was determined to establish the relative substituent orientation on the cyclopentanone 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 molecule 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 intramolecular hydrogen bonds, as well as by partial stacking of the aromatic rings.

  16. Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state.

    Directory of Open Access Journals (Sweden)

    Becka M Warfield

    Full Text Available RNA aptamers are oligonucleotides that bind with high specificity and affinity to target ligands. In the absence of bound ligand, secondary structures of RNA aptamers are generally stable, but single-stranded and loop regions, including ligand binding sites, lack defined structures and exist as ensembles of conformations. For example, the well-characterized theophylline-binding aptamer forms a highly stable binding site when bound to theophylline, but the binding site is unstable and disordered when theophylline is absent. Experimental methods have not revealed at atomic resolution the conformations that the theophylline aptamer explores in its unbound state. Consequently, in the present study we applied 21 microseconds of molecular dynamics simulations to structurally characterize the ensemble of conformations that the aptamer adopts in the absence of theophylline. Moreover, we apply Markov state modeling to predict the kinetics of transitions between unbound conformational states. Our simulation results agree with experimental observations that the theophylline binding site is found in many distinct binding-incompetent states and show that these states lack a binding pocket that can accommodate theophylline. The binding-incompetent states interconvert with binding-competent states through structural rearrangement of the binding site on the nanosecond to microsecond timescale. Moreover, we have simulated the complete theophylline binding pathway. Our binding simulations supplement prior experimental observations of slow theophylline binding kinetics by showing that the binding site must undergo a large conformational rearrangement after the aptamer and theophylline form an initial complex, most notably, a major rearrangement of the C27 base from a buried to solvent-exposed orientation. Theophylline appears to bind by a combination of conformational selection and induced fit mechanisms. Finally, our modeling indicates that when Mg2+ ions are

  17. Molecular and phenotypic diversity in Chionactis occipitalis (Western Shovel-nosed Snake), with emphasis on the status of C. o. klauberi (Tucson Shovel-nosed Snake).

    Science.gov (United States)

    Wood, D.A.; Meik, J.M.; Holycross, A.T.; Fisher, R.N.; Vandergast, A.G.

    2008-01-01

    Chionactis occipitalis (Western Shovel-nosed Snake) is a small colubrid snake inhabiting the arid regions of the Mojave, Sonoran, and Colorado deserts. Morphological assessments of taxonomy currently recognize four subspecies. However, these taxonomic proposals were largely based on weak morphological differentiation and inadequate geographic sampling. Our goal was to explore evolutionary relationships and boundaries among subspecies of C. occipitalis, with particular focus on individuals within the known range of C. o. klauberi (Tucson Shovel-nosed snake). Population sizes and range for C. o. klauberi have declined over the last 25 years due to habitat alteration and loss prompting a petition to list this subspecies as endangered. We examined the phylogeography, population structure, and subspecific taxonomy of C. occipitalis across its geographic range with genetic analysis of 1100 bases of mitochondrial DNA sequence and reanalysis of 14 morphological characters from 1543 museum specimens. We estimated the species gene phylogeny from 81 snakes using Bayesian inference and explored possible factors influencing genetic variation using landscape genetic analyses. Phylogenetic and population genetic analyses reveal genetic isolation and independent evolutionary trajectories for two primary clades. Our data indicate that diversification between these clades has developed as a result of both historical vicariance and environmental isolating mechanisms. Thus these two clades likely comprise 'evolutionary significant units' (ESUs). Neither molecular nor morphological data are concordant with the traditional C. occipitalis subspecies taxonomy. Mitochondrial sequences suggest specimens recognized as C. o. klauberi are embedded in a larger geographic clade whose range has expanded from western Arizona populations, and these data are concordant with clinal longitudinal variation in morphology. ?? 2007 Springer Science+Business Media B.V.

  18. Molecular diversity of bacterial endosymbionts associated with dagger nematodes of the genus Xiphinema (Nematoda: Longidoridae) reveals a high degree of phylogenetic congruence with their host.

    Science.gov (United States)

    Palomares-Rius, Juan E; Archidona-Yuste, Antonio; Cantalapiedra-Navarrete, Carolina; Prieto, Pilar; Castillo, Pablo

    2016-12-01

    Bacterial endosymbionts have been detected in some groups of plant-parasitic nematodes, but few cases have been reported compared to other groups in the phylum Nematoda, such as animal-parasitic or free-living nematodes. This study was performed on a wide variety of plant-parasitic nematode families and species from different host plants and nematode populations. A total of 124 nematode populations (previously identified morphologically and molecularly) were screened for the presence of potential bacterial endosymbionts using the partial 16S rRNA gene and fluorescence in situ hybridization (FISH) and confocal microscopy. Potential bacterial endosymbionts were only detected in nematode species belonging to the genus Xiphinema and specifically in the X. americanum group. Fifty-seven partial 16S rRNA sequences were obtained from bacterial endosymbionts in this study. One group of sequences was closely related to the genus 'Candidatus Xiphinematobacter' (19 bacterial endosymbiont sequences were associated with seven nematode host species, including two that have already been described and three unknown bacterial endosymbionts). The second bacterial endosymbiont group (38 bacterial endosymbiont sequences associated with six nematode species) was related to the family Burkholderiaceae, which includes fungal and soil-plant bacterial endosymbionts. These endosymbionts were reported for the first time in the phylum Nematoda. Our findings suggest that there is a highly specific symbiotic relationship between nematode host and bacterial endosymbionts. Overall, these results were corroborated by a phylogeny of nematode host and bacterial endosymbionts that suggested that there was a high degree of phylogenetic congruence and long-term evolutionary persistence between hosts and endosymbionts. © 2016 John Wiley & Sons Ltd.

  19. Evaluation of Diversity Based on Morphological Variabilities and ISSR Molecular Markers in Iranian Cynodon dactylon (L.) Pers. Accessions to Select and Introduce Cold-Tolerant Genotypes.

    Science.gov (United States)

    Akbari, M; Salehi, H; Niazi, A

    2018-04-01

    The main goals of the present study were to screen Iranian common bermudagrasses to find cold-tolerant accessions and evaluate their genetic and morphological variabilities. In this study, 49 accessions were collected from 18 provinces of Iran. One foreign cultivar of common bermudagrass was used as control. Morphological variation was evaluated based on 14 morphological traits to give information about taxonomic position of Iranian common bermudagrass. Data from morphological traits were evaluated to categorize all accessions as either cold sensitive or tolerant using hierarchical clustering with Ward's method in SPSS software. Inter-Simple Sequence Repeat (ISSR) primers were employed to evaluate genetic variability of accessions. The results of our taxonomic investigation support the existence of two varieties of Cynodon dactylon in Iran: var. dactylon (hairless plant) and var. villosous (plant with hairs at leaf underside and/or upper side surfaces or exterior surfaces of sheath). All 15 primers amplified and gave clear and highly reproducible DNA fragments. In total, 152 fragments were produced, of which 144 (94.73%) being polymorphic. The polymorphic information content (PIC) values ranged from 0.700 to 0.928. The average PIC value obtained with 15 ISSR primers was 0.800, which shows that all primers were informative. Probability identity (PI) and discriminating power between all primers ranged from 0.029 to 0.185 and 0.815 to 0.971, respectively. Genetic data were converted into a binary data matrix. NTSYS software was used for data analysis. Clustering was done by the unweighted pair-group method with arithmetic averages and principle coordinate analysis, separated the accessions into six main clusters. According to both morphological and genetic diversity investigations of accessions, they can be clustered into three groups: cold sensitive, cold semi-tolerant, and cold tolerant. The most cold-tolerant accessions were: Taft, Malayear, Gorgan, Safashahr

  20. Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China.

    Science.gov (United States)

    Li, Zhi Peng; Liu, Han Lu; Li, Guang Yu; Bao, Kun; Wang, Kai Ying; Xu, Chao; Yang, Yi Feng; Yang, Fu He; Wright, André-Denis G

    2013-07-08

    Sika deer (Cervus nippon) have different dietary preferences to other ruminants and are tolerant to tannin-rich plants. Because the rumen bacteria in domestic Sika deer have not been comprehensively studied, it is important to investigate its rumen bacterial population in order to understand its gut health and to improve the productivity of domestic Sika deer. The rumen bacterial diversity in domestic Sika deer (Cervus nippon) fed oak leaves- (OL group) and corn stalks-based diets (CS group) were elucidated using 16S rRNA gene libraries and denaturing gradient gel electrophoresis (DGGE). Overall, 239 sequences were examined from the two groups, 139 clones from the OL group were assigned to 57 operational taxonomic units (OTUs) and 100 sequences from the CS group were divided into 50 OTUs. Prevotella-like sequences belonging to the phylum Bacteroidetes were the dominant bacteria in both groups (97.2% OL and 77% CS), and sequences related to Prevotella brevis were present in both groups. However, Prevotella shahii-like, Prevotella veroralis-like, Prevotella albensis-like, and Prevotella salivae-like sequences were abundant in the OL group compared to those in the CS group, while Succinivibrio dextrinosolvens-like and Prevotella ruminicola-like sequences were prevalent in the CS group. PCR-DGGE showed that bacterial communities clustered with respect to diets and the genus Prevotella was the dominant bacteria in the rumen of domestic Sika deer. However, the distribution of genus Prevotella from two groups was apparent. In addition, other fibrolytic bacteria, such as Clostridium populeti and Eubacterium cellulosolvens were found in the rumen of domestic Sika deer. The rumen of domestic Sika deer harbored unique bacteria which may represent novel species. The bacterial composition appeared to be affected by diet, and sequences related to Prevotella spp. may represent new species that may be related to the degradation of fiber biomass or tannins. Moreover, the mechanism

  1. Edge-on gating effect in molecular wires.

    Science.gov (United States)

    Lo, Wai-Yip; Bi, Wuguo; Li, Lianwei; Jung, In Hwan; Yu, Luping

    2015-02-11

    This work demonstrates edge-on chemical gating effect in molecular wires utilizing the pyridinoparacyclophane (PC) moiety as the gate. Different substituents with varied electronic demands are attached to the gate to simulate the effect of varying gating voltages similar to that in field-effect transistor (FET). It was observed that the orbital energy level and charge carrier's tunneling barriers can be tuned by changing the gating group from strong electron acceptors to strong electron donors. The single molecule conductance and current-voltage characteristics of this molecular system are truly similar to those expected for an actual single molecular transistor.

  2. Influence of the substituent on azobenzene side-chain polyester optical storage materials

    DEFF Research Database (Denmark)

    Pedersen, M; Hvilsted, Søren; Holme, NCR

    1999-01-01

    , chloro, and bromo. C-13 NMR spectroscopic and molecular mass investigations substantiate good film forming characteristics. The optical storage performance of thin polyester films are investigated through polarization holography. The resulting diffraction efficiency is mapped and discussed as a function...... of irradiation power and exposure time. Polytetradecanedioates with cyano-, nitro-, methyl-, fluoro-, or trinuoromethyl-azobenzene reach more than 50% diffraction efficiency. Investigations of anisotropy induced at different temperatures reveal that the polyesters are only photosensitive in a narrow temperature...

  3. Understanding Diversity

    NARCIS (Netherlands)

    D.L. van Knippenberg (Daan)

    2007-01-01

    textabstractDaan van Knippenberg is Professor of Organizational Behavior at RSM Erasmus University, Erasmus University Rotterdam, The Netherlands. His research interests include work group performance, especially work group diversity and group decision making, leadership, in particular the roles of

  4. Substituent and structural effects on the kinetics of the reaction of N-(substituted phenylmethylene-m- and -p-aminobenzoic acids with diazodiphenylmethane

    Directory of Open Access Journals (Sweden)

    BRATISLAV Z. JOVANOVIC

    2007-12-01

    Full Text Available The rate constants for the reaction of twenty-two N-(substituted phenyl methylene-m- and -p-aminobenzoic acids with diazodiphenylmethane were determined in absolute ethanol at 30 °C. The effects of substituents on the reactivity of the investigated compounds were interpreted by correlation of the rate constants with LFER equations. The results of quantum mechanical calculations of the mole cular structure together with experimental results gave a better insight into the effects of structure on the transmission of electronic effects of the substituents. New σ constants for substituted benzylideneamino group were calculated.

  5. Catharanthine C16 substituent effects on the biomimetic coupling with vindoline: preparation and evaluation of a key series of vinblastine analogues

    Science.gov (United States)

    Tam, Annie; Gotoh, Hiroaki; Robertson, William M.; Boger, Dale L.

    2010-01-01

    The examination of the catharanthine C16 substituent effects on the Fe(III)-promoted biomimetic coupling reaction with vindoline is detailed, confirming the importance of the presence of a C16 electron-withdrawing substituent, and establishing an unanticipated unique role (>10-fold) that the C16 methyl ester plays in the expression of the natural product properties. Thus, replacement of the vinblastine C16′ methyl ester with an ethyl ester (10-fold), a cyano group (100-fold), an aldehyde (100-fold), a hydroxymethyl group (1000-fold), or a primary carboxamide (>1000-fold) led to surprisingly large reductions in cytotoxic activity. PMID:20932748

  6. Molecular Beacons in Diagnostics

    OpenAIRE

    Tyagi, Sanjay; Kramer, Fred Russell

    2012-01-01

    Recent technical advances have begun to realize the potential of molecular beacons to test for diverse infections in clinical diagnostic laboratories. These include the ability to test for, and quantify, multiple pathogens in the same clinical sample, and to detect antibiotic resistant strains within hours. The design principles of molecular beacons have also spawned a variety of allied technologies.

  7. Molecular microbial ecology manual

    NARCIS (Netherlands)

    Kowalchuk, G.A.; Bruijn, de F.J.; Head, I.M.; Akkermans, A.D.L.

    2004-01-01

    The field of microbial ecology has been revolutionized in the past two decades by the introduction of molecular methods into the toolbox of the microbial ecologist. This molecular arsenal has helped to unveil the enormity of microbial diversity across the breadth of the earth's ecosystems, and has

  8. Structural dependence of the multi-functionalized carbon nanotubes to the substituents on the grafted diazo compounds

    Science.gov (United States)

    Amiri, Rahebeh; Rasouli, Sousan; Ghasemi, Alireza; Eghbali, Babak; Mohammadi, Soutodeh

    2014-05-01

    Systematic studies on the covalent functionalization of multi-walled carbon nanotubes were performed by a series of azo molecules with different substituents. For this investigation, 4-substituted diazonium reagents have been used in the reaction with the functionalized multi-walled carbon nanotubes. We analyzed the effect of the substituted groups on the diazo component affinity in the grafting. Also, the structural differences of the final products were evaluated by visual dispersion test, UV-Vis absorption. Fourier transforms infrared, Raman, and several complementary techniques (scanning electron microscopy, thermal gravimetric analysis, and colorimetry test). Nuclear magnetic resonance spectroscopy has been used to confirm the allylic protons attached to the surface of carbon nanotubes after functionalization.

  9. Substituent effects in heterogeneous catalysis--4. Adsorption estimations during competitive hydrogenation of cyclohexanone and its 2-alkyl derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Chihara, T; Tanaka, K

    1979-02-01

    Adsorption estimations during competitive hydrogenation of cyclohexanone and its 2-alkyl derivatives alumina-supported ruthenium, rhodium, and platinum catalysts were obtained in a study to determine the relative contributions of the rate constants and the adsorption equilibrium constants to the substituent-dependent constant. The reaction rates obtained during competitive hydrogenation were in the order cyclohexanone (A) Vertical Bar3:Vertical Bar3: 2-methyl cyclohexanone (B) Vertical Bar3: 2-ethyl cyclohexanone (C) Vertical Bar3: 2-propyl cyclohexanone (D) for all catalysts, whereas the rates obtained during individual hydrogenation were in the order A Vertical Bar3: B approx. C approx. D. The adsorption equilibrium constants which were estimated by analyzing the kinetic data agreed well with the theoretical values derived from statistical mechanics by using a model in which the substrate ketones were immobilely adsorbed.

  10. Photomechanical Deformation of Azobenzene-Functionalized Polyimides Synthesized with Bulky Substituents (Postprint)

    Science.gov (United States)

    2017-12-06

    comparative UV − vis result (Figure S6, Supporting Information) that azoCBODA-BPADA has the lowest absorbance change for its azobenzene trans−cis...or trans−cis−trans reorientation processes upon irradiation of 365 nm UV or blue-green light (440−530 nm), respectively. Exposure of these materials...to UV light induces a trans−cis isomerization, resulting in a length reduction of the molecular axis of azobenzene from 9 Å (trans) to 5.5 Å (cis).10

  11. 13C nuclear magnetic resonance data of lanosterol derivatives—Profiling the steric topology of the steroid skeleton via substituent effects on its 13C NMR

    Science.gov (United States)

    Dias, Jerry Ray; Gao, Hongwu

    2009-12-01

    The 13C NMR spectra of over 24 tetracyclic triterpenoid derivatives have been structurally analyzed. The 13C NMR chemical shifts allow one to probe the steric topology of the rigid steroid skeleton and inductive effects of its substituents. Use of deuterium labeling in chemical shift assignment and B-ring aromatic terpenoids are also featured.

  12. Photochemical generation of highly destabilized vinyl cations: the effects of alpha- and beta-trifluoromethyl versus alpha- and beta-methyl substituents

    NARCIS (Netherlands)

    Alem, van K.; Belder, G.; Lodder, G.; Zuilhof, H.

    2005-01-01

    The photochemical reactions in methanol of the vinylic halides 1-4, halostyrenes with a methyl or a trifluoromethyl substituent at the - or -position, have been investigated quantitatively. Next to E/Z isomerization, the reactions are formation of vinyl radicals, leading to reductive dehalogenation

  13. Directing the breathing behavior of pillared-layered metal-organic frameworks via a systematic library of functionalized linkers bearing flexible substituents.

    Science.gov (United States)

    Henke, Sebastian; Schneemann, Andreas; Wütscher, Annika; Fischer, Roland A

    2012-06-06

    Flexible metal-organic frameworks (MOFs), also referred to as soft porous crystals (SPCs), show reversible structural transitions dependent on the nature and quantity of adsorbed guest molecules. In recent studies it has been reported that covalent functionalization of the organic linker can influence or even integrate framework flexibility ("breathing") in MOFs. However, rational fine-tuning of such responsive properties is very desirable but challenging as well. Here we present a powerful approach for the targeted manipulation of responsiveness and framework flexibility of an important family of pillared-layered MOFs based on the parent structure [Zn(2)(bdc)(2)(dabco)](n) (bdc = 1,4-benzenedicarboxylate; dabco = 1,4-diazabicyclo[2.2.2]octane). A library of functionalized bdc-type linkers (fu-bdc), which bear additional dangling side groups at different positions of the benzene core (alkoxy groups of varying chain length with diverse functionalities and polarity), was generated. Synthesis of the materials [Zn(2)(fu-bdc)(2)(dabco)](n) yields the respective collection of highly responsive MOFs. The parent MOF is only weakly flexible; however, the substituted frameworks of [Zn(2)(fu-bdc)(2)(dabco)](n) contract drastically upon guest removal and expand again upon adsorption of DMF (N,N-dimethylformamide), EtOH, or CO(2), etc., while N(2) is hardly adsorbed and does not open the narrow-pored form. These "breathing" dynamics are attributed to the dangling side chains that act as immobilized "guests", which interact with mobile guest molecules as well as with themselves and with the framework backbone. The structural details of the guest-free, contracted form and the gas sorption behavior (phase transition pressure, hysteresis loop) are highly dependent on the nature of the substituent at the linker and can therefore be adjusted using our approach. Combining our library of functionalized linkers with the concept of mixed-component MOFs (solid solutions) offers very rich

  14. Gender Diversities

    DEFF Research Database (Denmark)

    Agustin, Lise Rolandsen; Siim, Birte

    2014-01-01

    by non-citizen/citizen and redistribution/recognition divisions. Employing intersectionality as the methodological approach to gender diversities, the article shows how gender and ethnicity are articulated in the policy-making process which led to the adoption of EY 201, the activities undertaken during...

  15. Generational diversity.

    Science.gov (United States)

    Kramer, Linda W

    2010-01-01

    Generational diversity has proven challenges for nurse leaders, and generational values may influence ideas about work and career planning. This article discusses generational gaps, influencing factors and support, and the various generational groups present in today's workplace as well as the consequences of need addressing these issues. The article ends with a discussion of possible solutions.

  16. PLANT DIVERSITY

    Science.gov (United States)

    Habitat change statistics and species-area curves were used to estimate the effects of alternative future scenarios for agriculture on plant diversity in Iowa farmlands. Study areas were two watersheds in central Iowa of about 50 and 90 square kilometers, respectively. Future s...

  17. The influence of different cyclometalated ligand substituents and ancillary ligand on the phosphorescent properties of iridium(III) complexes

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qing; Li, Yuanyuan; Wang, Xin; Wang, Li, E-mail: chemwangl@henu.edu.cn; Zhang, Jinglai, E-mail: zhangjinglai@henu.edu.cn

    2016-07-01

    Four iridium(III) complexes, (dfpmpy){sub 2}Ir(pic), (1), (dfpmpy){sub 2}Ir(EO{sub 2}-pic) (2), (dfpmpy){sub 2}Ir(pic-N-O) (3), and (dfpmpy){sub 2}Ir(EO{sub 2}-pic-N-O) (4) (dfpmpy = 2-(2,4-difluorophenyl)-4-methylpyridine, pic = picolinic acid, EO{sub 2}-pic = 4-(2-ethoxyethoxy) picolinic acid, pic-N-O = picolinic acid N-oxide, and EO{sub 2}-pic-N-O = 4-(2-ethoxyethoxy) picolinic acid N-oxide) are investigated by means of the density functional theory/time-dependent density functional theory (DFT/TD-DFT) to explore the influence of the ancillary ligand on the electronic structures, phosphorescent properties, and organic light-emitting diode (OLED) performance. Employing pic-N-O and EO{sub 2}-pic-N-O as the ancillary ligands would decrease the vertical energy and result in the red-shifted wavelength. Then, other four iridium(III) complexes (2a-2d) (See Scheme 1) are designed by introduction of the phenyl and −CHO substituents on the pyridine ring and phenyl ring of complex 2, respectively. As compared with complex 2, theoretical results show that newly designed complexes 2a-2c might be potential candidates for blue-emitting phosphors with better/comparable quantum yield and Δλ. Moreover, the performance of complexes 2a and 2c, i.e., introducing phenyl on the para-position of pyridine ring and phenyl ring in dfpmpy ligand, are better than that of 2b. - Highlights: • The structure-property relationship of Ir(III) complexes are investigated. • The effect of different substituents/positions on properties is explored. • Do the emissions follow the Kasha or non-Kasha scenario? • Newly possible blue-emitting Ir(III) complexes are theoretically designed.

  18. Effects of Bulky Substituents of Push-Pull Porphyrins on Photovoltaic Properties of Dye-Sensitized Solar Cells.

    Science.gov (United States)

    Higashino, Tomohiro; Kawamoto, Kyosuke; Sugiura, Kenichi; Fujimori, Yamato; Tsuji, Yukihiro; Kurotobi, Kei; Ito, Seigo; Imahori, Hiroshi

    2016-06-22

    To evaluate the effects of substituent bulkiness around a porphyrin core on the photovoltaic properties of porphyrin-sensitized solar cells, long alkoxy groups were introduced at the meso-phenyl group (ZnPBAT-o-C8) and the anchoring group (ZnPBAT-o-C8Cn, n = 4, 8) of an asymmetrically substituted push-pull porphyrin with double electron-donating diarylamino groups and a single electron-withdrawing carboxyphenylethynyl anchoring group. The spectroscopic and electrochemical properties of ZnPBAT-o-C8 and ZnPBAT-o-C8Cn were found to be superior to those of a push-pull porphyrin reference (YD2-o-C8), demonstrating their excellent light-harvesting and redox properties for dye-sensitized solar cells. A power conversion efficiency (η) of the ZnPBAT-o-C8-sensitized solar cell (η = 9.1%) is higher than that of the YD2-o-C8-sensitized solar cell (η = 8.6%) using iodine-based electrolyte due to the enhanced light-harvesting ability of ZnPBAT-o-C8. In contrast, the solar cells based on ZnPBAT-o-C8Cn, possessing the additional alkoxy chains in the anchoring group, revealed the lower η values of 7.3% (n = 4) and 7.0% (n = 8). Although ZnPBAT-o-C8Cn exhibited higher resistance at the TiO2-dye-electrolyte interface by virtue of the extra alkoxy chains, the reduced amount of the porphyrins on TiO2 by excessive addition of coadsorbent chenodeoxycholic acid (CDCA) for mitigating the aggregation on TiO2 resulted in the low η values. Meanwhile, the ZnPBAT-o-C8-sensitized solar cell showed the lower η value of 8.1% than the YD2-o-C8-sensitized solar cell (η = 9.8%) using cobalt-based electrolyte. The smaller η value of the ZnPBAT-o-C8-sensitized solar cell may be attribute