WorldWideScience

Sample records for huge structural diversity

  1. On the prediction of hydroelastic behaviors of a huge floating structure in waves. 2nd Report; Choogata futai no harochu dansei kyodo no suiteiho ni tsuite

    Energy Technology Data Exchange (ETDEWEB)

    Murai, M.; Kagemoto, H.; Fujino, M. [The University of Tokyo, Tokyo (Japan)

    1997-08-01

    On the hydroelastic behaviors of a huge floating structure, a mutual interaction theory based on the area division method is used for the analysis of a fluid problem and a mode analysis method is used for the analysis of deformation. On the continuous deformation of a floating structure, the structure is considered as a set of partial structures obtained when the plane shape was divided into squares and discretely handled as a series of rigid motions in the small partial structures obtained by dividing the partial structures more finely. The experimental result in a water tank and the distribution method at a singular point were compared on the deformation of the elastic floating structure estimated by calculation based on this formulation. The result showed that the estimation method on the hydroelastic problem proposed in this paper is valid. On the prediction of hydroelastic behaviors of a huge floating structure, various calculation examples indicate that the hydroelastic behavior is not only the relation between the structure length and wavelength, but also that the bending rigidity of a structure is a very important factor. For a huge floating structure in the 5,000 m class, up to shorter wavelength of about {lambda}/L = 1/100 must be investigated. 6 refs., 14 figs., 5 tabs.

  2. Structural diversity in social contagion.

    Science.gov (United States)

    Ugander, Johan; Backstrom, Lars; Marlow, Cameron; Kleinberg, Jon

    2012-04-17

    The concept of contagion has steadily expanded from its original grounding in epidemic disease to describe a vast array of processes that spread across networks, notably social phenomena such as fads, political opinions, the adoption of new technologies, and financial decisions. Traditional models of social contagion have been based on physical analogies with biological contagion, in which the probability that an individual is affected by the contagion grows monotonically with the size of his or her "contact neighborhood"--the number of affected individuals with whom he or she is in contact. Whereas this contact neighborhood hypothesis has formed the underpinning of essentially all current models, it has been challenging to evaluate it due to the difficulty in obtaining detailed data on individual network neighborhoods during the course of a large-scale contagion process. Here we study this question by analyzing the growth of Facebook, a rare example of a social process with genuinely global adoption. We find that the probability of contagion is tightly controlled by the number of connected components in an individual's contact neighborhood, rather than by the actual size of the neighborhood. Surprisingly, once this "structural diversity" is controlled for, the size of the contact neighborhood is in fact generally a negative predictor of contagion. More broadly, our analysis shows how data at the size and resolution of the Facebook network make possible the identification of subtle structural signals that go undetected at smaller scales yet hold pivotal predictive roles for the outcomes of social processes.

  3. Assessment of structural diversity in combinatorial synthesis.

    Science.gov (United States)

    Fergus, Suzanne; Bender, Andreas; Spring, David R

    2005-06-01

    This article covers the combinatorial synthesis of small molecules with maximal structural diversity to generate a collection of pure compounds that are attractive for lead generation in a phenotypic, high-throughput screening approach. Nature synthesises diverse small molecules, but there are disadvantages with using natural product sources. The efficient chemical synthesis of structural diversity (and complexity) is the aim of diversity-oriented synthesis, and recent progress is reviewed. Specific highlights include a discussion of strategies to obtain structural diversity and an analysis of molecular descriptors used to classify compounds. The assessment of how successful one synthesis is versus another is subjective, therefore we test-drive software to assess structural diversity in combinatorial synthesis, which is freely available via a web interface.

  4. Structural and genetic diversity in antibody repertoires from diverse species.

    Science.gov (United States)

    de los Rios, Miguel; Criscitiello, Michael F; Smider, Vaughn V

    2015-08-01

    The antibody repertoire is the fundamental unit that enables development of antigen specific adaptive immune responses against pathogens. Different species have developed diverse genetic and structural strategies to create their respective antibody repertoires. Here we review the shark, chicken, camel, and cow repertoires as unique examples of structural and genetic diversity. Given the enormous importance of antibodies in medicine and biological research, the novel properties of these antibody repertoires may enable discovery or engineering of antibodies from these non-human species against difficult or important epitopes.

  5. MANAGEMENT OF HUGE ENCEPHALOCELE

    Directory of Open Access Journals (Sweden)

    Rajeev

    2015-11-01

    Full Text Available Among all neural tube defects, encephalocele incidents are 1 in 5000 live births. (1 Newborn with encephalocele may be associated with other congenital malformations. Encephalocele patient’s management pose many challenge to neurosurgeon due to other associated anomalies that may present like ventriculocele, Dandy Walker and Arnold-Chiari malformation, and difficult positioning airway management to anaesthesiologist. We discuss a case of huge encephalocele and its management

  6. Inorganic pyrophosphatases: structural diversity serving the function

    Science.gov (United States)

    Samygina, V. R.

    2016-05-01

    The review is devoted to ubiquitous enzymes, inorganic pyrophosphatases, which are essential in all living organisms. Despite the long history of investigations, these enzymes continue to attract interest. The review focuses on the three-dimensional structures of various representatives of this class of proteins. The structural diversity, the relationship between the structure and some properties of pyrophosphatases and various mechanisms of enzyme action related to the structural diversity of these enzymes are discussed. Interactions of pyrophosphatase with other proteins and possible practical applications are considered. The bibliography includes 56 references.

  7. Topographical effects on wave exciting forces on huge floating structure. 2; Ogata futaishiki kaiyo kozobutsu ni sayosuru haryoku ni kansuru kenkyu. 2

    Energy Technology Data Exchange (ETDEWEB)

    Imai, Y. [Hiroshima University, Hiroshima (Japan); Okusu, M. [Kyushu Univ., Fukuoka (Japan). Research Inst. for Applied Mechanics

    1996-12-31

    A method to predict drift force acting on a floating structure has been developed for a marine structure consisting of a number of floating elements, positioned in a region having a slope at the sea bottom. When a huge marine structure, such as floating air port, is located in a coastal area, scale of the overall structure is very large, of the order of scale of water depth change. The new method assumes that a marine structure consisting of an infinite number of cylindrical floating elements is installed in parallel to the seashore, where symmetrical nature of the configuration allows to predict behavior of the whole system by analyzing one element. Integration of pressures acting on structure surfaces determines the horizontal component of the drift force acting on the structure. Being influenced by topography, drift force predicted peaks at a frequency different from that for the level predicted on the assumption of constant water depth. This indicates the necessity for consideration of seabottom slope and effects of broken waves at the seashore. 6 refs., 12 figs.

  8. Topographical effects on wave exciting forces on huge floating structure. 2; Ogata futaishiki kaiyo kozobutsu ni sayosuru haryoku ni kansuru kenkyu. 2

    Energy Technology Data Exchange (ETDEWEB)

    Imai, Y. [Hiroshima University, Hiroshima (Japan); Okusu, M. [Kyushu Univ., Fukuoka (Japan). Research Inst. for Applied Mechanics

    1996-12-31

    A method to predict drift force acting on a floating structure has been developed for a marine structure consisting of a number of floating elements, positioned in a region having a slope at the sea bottom. When a huge marine structure, such as floating air port, is located in a coastal area, scale of the overall structure is very large, of the order of scale of water depth change. The new method assumes that a marine structure consisting of an infinite number of cylindrical floating elements is installed in parallel to the seashore, where symmetrical nature of the configuration allows to predict behavior of the whole system by analyzing one element. Integration of pressures acting on structure surfaces determines the horizontal component of the drift force acting on the structure. Being influenced by topography, drift force predicted peaks at a frequency different from that for the level predicted on the assumption of constant water depth. This indicates the necessity for consideration of seabottom slope and effects of broken waves at the seashore. 6 refs., 12 figs.

  9. On the estimation method of hydrodynamic forces acting on a huge floating structure; Choogata futai ni hataraku haryoku ryutairyoku no suiteiho ni kansuru kenkyu

    Energy Technology Data Exchange (ETDEWEB)

    Kagemoto, H.; Fujino, M.; Zhu, T. [The University of Tokyo, Tokyo (Japan)

    1996-12-31

    A floating structure such as an international airport is anticipated to have a length of about 5,000 m and a width of about 1,000 m. A singular point method may be used as a method to estimate force that such a floating body is subjected to from waves. In order to derive a solution with practically sufficient accuracy, 1250 elements are required in the length direction and 250 elements in the width direction, or a total of 312,500 elements. Calculating this number of elements should use finally a linear equation system handling complex coefficients comprising 312,500 elements, which would require a huge amount of calculation time. This paper proposes a method to derive solution on wave forces acting on a super-large floating structure or fluid force coefficients such as added mass coefficients and decay coefficients at a practically workable calculation amount and still without degrading the accuracy. The structure was assumed to be a box-shaped structure. Strengths of the singular points to be distributed on each element were assumed to be almost constant except for edges in lateral, oblique and longitudinal waves. Under this assumption, the interior of the floating structure excepting its edges was represented by several large elements to have reduced the number of elements. A calculation method proposed based on this conception was verified of its effectiveness. 2 refs., 25 figs., 3 tabs.

  10. On the sea-covering effect of a huge floating structure on the surrounding water; Choogata futai shuhen no kaisui ni taisuru kaimen shahei no eikyo ni tsuite

    Energy Technology Data Exchange (ETDEWEB)

    Fujino, M.; Kagemoto, H.; Hamada, T. [The University of Tokyo, Tokyo (Japan)

    1996-12-31

    The numerical analysis program based on the difference method for dynamics of sea water with sea-surface displacement, flow rate, salt content and temperature as the parameters is modified to more accurately assess the effects of a huge marine structure on surrounding environment by adding the effects of insolation and boundary conditions of the sea-covering effects of the floating structure. The numerical simulation was done for summer and winter seasons, not in a sea area but using a rectangular bay with the floating structure at the center. A new flow evolves around the floating structure, due to the sea-covering effect. The flow patterns in summer and winter are clearly different, due to difference in insolation. The predicted flow is also sensitive whether stratification is considered or not, by which is meant that it is important what stratification effect is taken into account. Daily insolation changes are accompanied by vertical distribution of water temperature and its temporal change. These effects are also observed under the floating structure which shields insolation. 10 refs., 17 figs., 4 tabs.

  11. On the sea-covering effect of a huge floating structure on the surrounding water; Choogata futai shuhen no kaisui ni taisuru kaimen shahei no eikyo ni tsuite

    Energy Technology Data Exchange (ETDEWEB)

    Fujino, M.; Kagemoto, H.; Hamada, T. [The University of Tokyo, Tokyo (Japan)

    1996-12-31

    The numerical analysis program based on the difference method for dynamics of sea water with sea-surface displacement, flow rate, salt content and temperature as the parameters is modified to more accurately assess the effects of a huge marine structure on surrounding environment by adding the effects of insolation and boundary conditions of the sea-covering effects of the floating structure. The numerical simulation was done for summer and winter seasons, not in a sea area but using a rectangular bay with the floating structure at the center. A new flow evolves around the floating structure, due to the sea-covering effect. The flow patterns in summer and winter are clearly different, due to difference in insolation. The predicted flow is also sensitive whether stratification is considered or not, by which is meant that it is important what stratification effect is taken into account. Daily insolation changes are accompanied by vertical distribution of water temperature and its temporal change. These effects are also observed under the floating structure which shields insolation. 10 refs., 17 figs., 4 tabs.

  12. Structural diversity in social contagion

    Science.gov (United States)

    Ugander, Johan; Backstrom, Lars; Marlow, Cameron; Kleinberg, Jon

    2012-01-01

    The concept of contagion has steadily expanded from its original grounding in epidemic disease to describe a vast array of processes that spread across networks, notably social phenomena such as fads, political opinions, the adoption of new technologies, and financial decisions. Traditional models of social contagion have been based on physical analogies with biological contagion, in which the probability that an individual is affected by the contagion grows monotonically with the size of his or her “contact neighborhood”—the number of affected individuals with whom he or she is in contact. Whereas this contact neighborhood hypothesis has formed the underpinning of essentially all current models, it has been challenging to evaluate it due to the difficulty in obtaining detailed data on individual network neighborhoods during the course of a large-scale contagion process. Here we study this question by analyzing the growth of Facebook, a rare example of a social process with genuinely global adoption. We find that the probability of contagion is tightly controlled by the number of connected components in an individual's contact neighborhood, rather than by the actual size of the neighborhood. Surprisingly, once this “structural diversity” is controlled for, the size of the contact neighborhood is in fact generally a negative predictor of contagion. More broadly, our analysis shows how data at the size and resolution of the Facebook network make possible the identification of subtle structural signals that go undetected at smaller scales yet hold pivotal predictive roles for the outcomes of social processes. PMID:22474360

  13. Generalized Synchronization of Diverse Structure Chaotic Systems

    Institute of Scientific and Technical Information of China (English)

    KADIR Abdurahman; WANG Xing-Yuan; ZHAO Yu-Zhang

    2011-01-01

    @@ Generalized synchronization between two diverse structures of chaotic systems possesses significance in the research of synchronization.We propose an approach based on the Lyapunov stability theory to study it.This method can be used widely.Numerical examples are given to demonstrate the effectiveness of this approach.%Generalized synchronization between two diverse structures of chaotic systems possesses significance in the research of synchronization. We propose an approach based on the Lyapunov stability theory to study it. This method can be used widely. Numerical examples are given to demonstrate the effectiveness of this approach.

  14. Statistical model semiquantitatively approximates arabinoxylooligosaccharides' structural diversity

    DEFF Research Database (Denmark)

    Dotsenko, Gleb; Nielsen, Michael Krogsgaard; Lange, Lene

    2016-01-01

    A statistical model describing the random distribution of substituted xylopyranosyl residues in arabinoxylooligosaccharides is suggested and compared with existing experimental data. Structural diversity of arabinoxylooligosaccharides of various length, originating from different arabinoxylans...... (wheat flour arabinoxylan (arabinose/xylose, A/X = 0.47); grass arabinoxylan (A/X = 0.24); wheat straw arabinoxylan (A/X = 0.15); and hydrothermally pretreated wheat straw arabinoxylan (A/X = 0.05)), is semiquantitatively approximated using the proposed model. The suggested approach can be applied...... not only for prediction and quantification of arabinoxylooligosaccharides' structural diversity, but also for estimate of yield and selection of the optimal source of arabinoxylan for production of arabinoxylooligosaccharides with desired structural features....

  15. A bouquet of DNA structures: Emerging diversity

    Directory of Open Access Journals (Sweden)

    Mahima Kaushik

    2016-03-01

    Full Text Available Structural polymorphism of DNA has constantly been evolving from the time of illustration of the double helical model of DNA by Watson and Crick. A variety of non-canonical DNA structures have constantly been documented across the globe. DNA attracted worldwide attention as a carrier of genetic information. In addition to the classical Watson–Crick duplex, DNA can actually adopt diverse structures during its active participation in cellular processes like replication, transcription, recombination and repair. Structures like hairpin, cruciform, triplex, G-triplex, quadruplex, i-motif and other alternative non-canonical DNA structures have been studied at length and have also shown their in vivo occurrence. This review mainly focuses on non-canonical structures adopted by DNA oligonucleotides which have certain prerequisites for their formation in terms of sequence, its length, number and orientation of strands along with varied solution conditions. This conformational polymorphism of DNA might be the basis of different functional properties of a specific set of DNA sequences, further giving some insights for various extremely complicated biological phenomena. Many of these structures have already shown their linkages with diseases like cancer and genetic disorders, hence making them an extremely striking target for structure-specific drug designing and therapeutic applications.

  16. Presumed fair: ironic effects of organizational diversity structures.

    Science.gov (United States)

    Kaiser, Cheryl R; Major, Brenda; Jurcevic, Ines; Dover, Tessa L; Brady, Laura M; Shapiro, Jenessa R

    2013-03-01

    This research tests the hypothesis that the presence (vs. absence) of organizational diversity structures causes high-status group members (Whites, men) to perceive organizations with diversity structures as procedurally fairer environments for underrepresented groups (racial minorities, women), even when it is clear that underrepresented groups have been unfairly disadvantaged within these organizations. Furthermore, this illusory sense of fairness derived from the mere presence of diversity structures causes high-status group members to legitimize the status quo by becoming less sensitive to discrimination targeted at underrepresented groups and reacting more harshly toward underrepresented group members who claim discrimination. Six experiments support these hypotheses in designs using 4 types of diversity structures (diversity policies, diversity training, diversity awards, idiosyncratically generated diversity structures from participants' own organizations) among 2 high-status groups in tests involving several types of discrimination (discriminatory promotion practices, adverse impact in hiring, wage discrimination). Implications of these experiments for organizational diversity and employment discrimination law are discussed.

  17. Structural diversity and bioactivities of natural benzophenones.

    Science.gov (United States)

    Wu, Shi-Biao; Long, Chunlin; Kennelly, Edward J

    2014-09-01

    Natural benzophenones are a class of compounds consisting of more than 300 members, which exhibit great structural diversity and bioactive properties. Many benzophenones have been reported from higher plants or fungi, most with polyisoprenylated benzophenone skeletons, and are mainly found in the Clusiaceae (formerly Guttiferae) family, a number from edible or medicinal species. Owing to their variable substituents and complex ring systems, many new polyisoprenylated benzophenones (PPBS), including ones with unusual skeletons, were isolated and identified. These natural benzophenones exhibit a range of biological activities including antifungal, anti-HIV, antimicrobial, antioxidant, antiviral and cytotoxic. Because of the increased numbers and biological importance of these unique natural product polyphenols, we will review natural benzophenones and provide an in-depth discussion of their structural diversity and biological activity. By focusing on these key developments in benzophenones, we will contribute a focused review, selecting examples mostly from the last 15 years, but extending our scope to other historically important benzophenones discovered prior to that time.

  18. Information Entropy Measures for Stand Structural Diversity:Joint Entropy

    Institute of Scientific and Technical Information of China (English)

    Lei Xiangdong; Lu Yuanchang

    2004-01-01

    Structural diversity is the key attribute of a stand. A set of biodiversity measures in ecology was introduced in forest management for describing stand structure, of which Shannon information entropy (Shannon index) has been the most widely used measure of species diversity. It is generally thought that tree size diversity could serve as a good proxy for height diversity. However, tree size diversity and height diversity for stand structure is not completely consistent. Stand diameter cannot reflect height information completely. Either tree size diversity or height diversity is one-dimensional information entropy measure. This paper discussed the method of multiple-dimensional information entropy measure with the concept of joint entropy. It is suggested that joint entropy is a good measure for describing overall stand structural diversity.

  19. Structural basis unifying diverse GTP hydrolysis mechanisms.

    Science.gov (United States)

    Anand, Baskaran; Majumdar, Soneya; Prakash, Balaji

    2013-02-12

    Central to biological processes is the regulation rendered by GTPases. Until recently, the GTP hydrolysis mechanism, exemplified by Ras-family (and G-α) GTPases, was thought to be universal. This mechanism utilizes a conserved catalytic Gln supplied "in cis" from the GTPase and an arginine finger "in trans" from a GAP (GTPase activating protein) to stabilize the transition state. However, intriguingly different mechanisms are operative in structurally similar GTPases. MnmE and dynamin like cation-dependent GTPases lack the catalytic Gln and instead employ a Glu/Asp/Ser situated elsewhere and in place of the arginine finger use a K(+) or Na(+) ion. In contrast, Rab33 possesses the Gln but does not utilize it for catalysis; instead, the GAP supplies both a catalytic Gln and an arginine finger in trans. Deciphering the underlying principles that unify seemingly unrelated mechanisms is central to understanding how diverse mechanisms evolve. Here, we recognize that steric hindrance between active site residues is a criterion governing the mechanism employed by a given GTPase. The Arf-ArfGAP structure is testimony to this concept of spatial (in)compatibility of active site residues. This understanding allows us to predict an as yet unreported hydrolysis mechanism and clarifies unexplained observations about catalysis by Rab11 and the need for HAS-GTPases to employ a different mechanism. This understanding would be valuable for experiments in which abolishing GTP hydrolysis or generating constitutively active forms of a GTPase is important.

  20. Genetic diversity and population structure in Meconopsis ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-05-24

    May 24, 2010 ... including the populations distributed in same location together in every group. ... Key words: Meconopsis quintuplinervia Regel, genetic diversity, random amplified ..... in its original center, and Banma population located in ...

  1. Pseudomonas aeruginosa genomic structure and diversity

    Directory of Open Access Journals (Sweden)

    Jens eKlockgether

    2011-07-01

    Full Text Available The Pseudomonas aeruginosa genome (G + C content 65-67%, size 5.5 – 7 Mbp is made up of a single circular chromosome and a variable number of plasmids. Sequencing of complete genomes or blocks of the accessory genome has revealed that the genome encodes a large repertoire of transporters, transcriptional regulators and two-component regulatory systems which reflects its metabolic diversity to utilize a broad range of nutrients. The conserved core component of the genome is largely collinear among P. aeruginosa strains and exhibits an interclonal sequence diversity of 0.5 – 0.7%. Only a few loci of the core genome are subject to diversifying selection. Genome diversity is mainly caused by accessory DNA elements located in 79 regions of genome plasticity that are scattered around the genome and show an anomalous usage of mono- to tetradecanucleotides. Genomic islands of the pKLC102/PAGI-2 family that integrate into tRNALys or tRNAGly genes represent hotspots of inter- and intraclonal genomic diversity. The individual islands differ in their repertoire of metabolic genes that make a large contribution to the pangenome. In order to unravel intraclonal diversity of P. aeruginosa, the genomes of two members of the PA14 clonal complex from diverse habitats and geographic origin were compared. The genome sequences differed by less than 0.01% from each other. 198 of the 231 SNPs were non-randomly distributed in the genome. Non-synonymous SNPs were mainly found in an integrated Pf1-like phage and in genes involved in transcriptional regulation, membrane and extracellular constituents, transport and secretion. In summary, P. aeruginosa is endowed with a highly conserved core genome of low sequence diversity and a highly variable accessory genome that communicates with other pseudomonads and genera via horizontal gene transfer.

  2. Structural Analysis of the Resident Assistant Cultural Diversity Questionnaire

    Science.gov (United States)

    Johnson, Vanessa D.; Kang, Young-Shin; Thompson, George F.

    2011-01-01

    This study investigated the five-factor structure of the Resident Assistant Cultural Diversity (RACD) instrument, which assesses resident assistant (RA) confidence in addressing issues of cultural diversity in college and university residence halls. The instrument has five components that explore RA confidence: (1) belief in the need for cultural…

  3. Structural Analysis of the Resident Assistant Cultural Diversity Questionnaire

    Science.gov (United States)

    Johnson, Vanessa D.; Kang, Young-Shin; Thompson, George F.

    2011-01-01

    This study investigated the five-factor structure of the Resident Assistant Cultural Diversity (RACD) instrument, which assesses resident assistant (RA) confidence in addressing issues of cultural diversity in college and university residence halls. The instrument has five components that explore RA confidence: (1) belief in the need for cultural…

  4. The Underlying Structure of Diverse Work Groups: A Literature Review on Faultlines and Diversity Outcomes

    Directory of Open Access Journals (Sweden)

    Stanciu, A.

    2015-12-01

    Full Text Available Diversity can be seen everywhere, as either a readily observable trait of people, such as gender and ethnicity, or as a hidden set of abilities, such work skills and personality traits. Organizations consider that work-teams with a diverse composition outperform homogeneous work-teams. Although this is often the case, there can be specific types of diversity composition that are detrimental for organizational outcomes. Usually this occurs in situations where members of a team align on more than one diversity attribute, thus creating a diversity faultline. As of yet, however, the literature is lacking a systematic overview as to whether diversity faultlines are always associated with poor organizational outcomes. To address this issue we conducted a literature review in which we sought to unravel the different underlying structures of diversity faultlines and their association with organizational outcomes. We distinguished between affective outcomes and productive outcomes. The findings indicate that faultlines can be categorized as based on social category aspects, information/ decision-making aspects, or a combination of the two attributes. Furthermore, the results suggest that there is no straightforward relationship between the various faultlines and outcomes. We argue that this is potentially due to the fact that these studies have not addressed the normative fit of faultlines. Our review also hints at the necessity of researchers to reach a consensus on how to operationalize some diversity traits.

  5. Structural diversity of forest communities on Baihuashan Mountain,Beijing

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The structural diversity of forests on Baihuashan Mountain,Beijing,was surveyed by a plotless method combined with branch and leaf coverage estimation in the different layers.New structural indices were constructed,calculated and compared among different communities.On the basis of previous work,structural diversity of forest communities at the stand level was described by a vertical complexity index and a horizontal heterogeneity index.From a correlational analysis among the new indices and other commonly used biodiversity indices,we concluded that the new indices are closely related to a tree height inequality index and the Shannon-Wiener index of the tree and shrub layer,which indicated that the new indices were good at indicating structural diversity in the different forests on Baihuashan Mountain.The results show that,in natural forests,structural diversity of pioneer communities is much lower than in late successive communities.In plantations,structural diversity is determined by the stage of development and tree species.Tending would increase horizontal heterogeneity and decrease vertical complexity.

  6. Laparoscopic Management of Huge Cervical Myoma.

    Science.gov (United States)

    Peker, Nuri; Gündoğan, Savaş; Şendağ, Fatih

    . Owing to the anatomic structure of the cervical region, the incision was closed in a monolayer with 0 Vicryl. Total intraoperative blood loss was 300 mL, the total weight of the myoma was 670 g, and the operation lasted approximately 140 minutes. The patient experienced no intraoperative complications. She was discharged on postoperative day 1 and did not exhibit any problems at follow-up. The final histopathological examination confirmed the diagnosis of uterine leiomyoma. Laparoscopic management of huge myomas in difficult locations such as the cervical region seems to be a feasible and safe surgical option, especially in experienced hands. Copyright © 2016 AAGL. Published by Elsevier Inc. All rights reserved.

  7. Genetic diversity and population structure of maize landraces from ...

    African Journals Online (AJOL)

    pc

    2016-11-02

    Nov 2, 2016 ... diversity and genetic structure of 35 maize accessions using 10 microsatellite markers. These accessions ... In addition, they provide new sources of resistance to ..... http://taylor0.biology.ucla.edu/structureHarvester/.The .... environment and in other areas. ..... Molecular population genetics and evolution. In:.

  8. Xyloglucans of Monocotyledons Have Diverse Structures

    Institute of Scientific and Technical Information of China (English)

    Yves S.Y. Hsieh; Philip J. Harris

    2009-01-01

    Except in the Poaceae, little is known about the structures of the xyloglucans in the primary walls of mono-cotyledons. Xyloglucan structures in a range of monocotyledon species were examined. Wall preparations were isolated, extracted with 6 M sodium hydroxide, and the extracts treated with a xyloglucan-specific endo-(1→4)-β-glucanase prep-aration. The oligosaccharides released were analyzed by high-performance anion-exchange chromatography and by ma-trix-assisted laser-desorption ionization time-of-flight mass spectrometry. Oligosaccharide profiles of the non-commelinid monocotyledons were similar to those of most eudicotyledons, indicating the xyloglucans were fucogalactoxyloglucans, with a XXXG ~a core motif and the fucosylated units XXFG and XLFG. An exception was Lemna minor (Araceae), which yielded no fucosylated oligosaccharides and had both XXXG and XXG_n core motifs. Except for the Arecales (palms) and the Dasypogonaceae, which had fucogalactoxyloglucans, the xyloglucans of the commelinid monocotyledons were structurally different. The Zingiberales and Commelinales had xyloglucans with both XXG_n and XXXG core motifs; small proportions of XXFG units, but no XLFG units, were present. In the Poales, the Poaceae had xyloglucans with a XXG_n core motif and no fucosylated units. In the other Poales families, some had both XXXG and XXG_n core motifs, others had only XXXG; XXFG units were present, but XLFG units were not.

  9. Stand structural diversity rather than species diversity enhances aboveground carbon storage in secondary subtropical forests in Eastern China

    Science.gov (United States)

    Ali, Arshad; Yan, En-Rong; Chen, Han Y. H.; Chang, Scott X.; Zhao, Yan-Tao; Yang, Xiao-Dong; Xu, Ming-Shan

    2016-08-01

    Stand structural diversity, typically characterized by variances in tree diameter at breast height (DBH) and total height, plays a critical role in influencing aboveground carbon (C) storage. However, few studies have considered the multivariate relationships of aboveground C storage with stand age, stand structural diversity, and species diversity in natural forests. In this study, aboveground C storage, stand age, tree species, DBH and height diversity indices, were determined across 80 subtropical forest plots in Eastern China. We employed structural equation modelling (SEM) to test for the direct and indirect effects of stand structural diversity, species diversity, and stand age on aboveground C storage. The three final SEMs with different directions for the path between species diversity and stand structural diversity had a similar goodness of fit to the data. They accounted for 82 % of the variation in aboveground C storage, 55-59 % of the variation in stand structural diversity, and 0.1 to 9 % of the variation in species diversity. Stand age demonstrated strong positive total effects, including a positive direct effect (β = 0.41), and a positive indirect effect via stand structural diversity (β = 0.41) on aboveground C storage. Stand structural diversity had a positive direct effect on aboveground C storage (β = 0.56), whereas there was little total effect of species diversity as it had a negative direct association with, but had a positive indirect effect, via stand structural diversity, on aboveground C storage. The negligible total effect of species diversity on aboveground C storage in the forests under study may have been attributable to competitive exclusion with high aboveground biomass, or a historical logging preference for productive species. Our analyses suggested that stand structural diversity was a major determinant for variations in aboveground C storage in the secondary subtropical forests in Eastern China. Hence, maintaining tree DBH and

  10. Structural and functional diversity of desmosomes.

    Science.gov (United States)

    Harmon, Robert M; Green, Kathleen J

    2013-12-01

    Desmosomes anchor intermediate filaments at sites of cell contact established by the interaction of cadherins extending from opposing cells. The incorporation of cadherins, catenin adaptors, and cytoskeletal elements resembles the closely related adherens junction. However, the recruitment of intermediate filaments distinguishes desmosomes and imparts a unique function. By linking the load-bearing intermediate filaments of neighboring cells, desmosomes create mechanically contiguous cell sheets and, in so doing, confer structural integrity to the tissues they populate. This trait and a well-established role in human disease have long captured the attention of cell biologists, as evidenced by a publication record dating back to the mid-1860s. Likewise, emerging data implicating the desmosome in signaling events pertinent to organismal development, carcinogenesis, and genetic disorders will secure a prominent role for desmosomes in future biological and biomedical investigations.

  11. Modeling Forest Structure and Vascular Plant Diversity in Piedmont Forests

    Science.gov (United States)

    Hakkenberg, C.

    2014-12-01

    When the interacting stressors of climate change and land cover/land use change (LCLUC) overwhelm ecosystem resilience to environmental and climatic variability, forest ecosystems are at increased risk of regime shifts and hyperdynamism in process rates. To meet the growing range of novel biotic and environmental stressors on human-impacted ecosystems, the maintenance of taxonomic diversity and functional redundancy in metacommunities has been proposed as a risk spreading measure ensuring that species critical to landscape ecosystem functioning are available for recruitment as local systems respond to novel conditions. This research is the first in a multi-part study to establish a dynamic, predictive model of the spatio-temporal dynamics of vascular plant diversity in North Carolina Piedmont mixed forests using remotely sensed data inputs. While remote sensing technologies are optimally suited to monitor LCLUC over large areas, direct approaches to the remote measurement of plant diversity remain a challenge. This study tests the efficacy of predicting indices of vascular plant diversity using remotely derived measures of forest structural heterogeneity from aerial LiDAR and high spatial resolution broadband optical imagery in addition to derived topo-environmental variables. Diversity distribution modelling of this sort is predicated upon the idea that environmental filtering of dispersing species help define fine-scale (permeable) environmental envelopes within which biotic structural and compositional factors drive competitive interactions that, in addition to background stochasticity, determine fine-scale alpha diversity. Results reveal that over a range of Piedmont forest communities, increasing structural complexity is positively correlated with measures of plant diversity, though the nature of this relationship varies by environmental conditions and community type. The diversity distribution model is parameterized and cross-validated using three high

  12. Opposing Responses of Bird Functional Diversity to Vegetation Structural Diversity in Wet and Dry Forest.

    Science.gov (United States)

    Sitters, Holly; York, Alan; Swan, Matthew; Christie, Fiona; Di Stefano, Julian

    2016-01-01

    Disturbance regimes are changing worldwide, and the consequences for ecosystem function and resilience are largely unknown. Functional diversity (FD) provides a surrogate measure of ecosystem function by capturing the range, abundance and distribution of trait values in a community. Enhanced understanding of the responses of FD to measures of vegetation structure at landscape scales is needed to guide conservation management. To address this knowledge gap, we used a whole-of-landscape sampling approach to examine relationships between bird FD, vegetation diversity and time since fire. We surveyed birds and measured vegetation at 36 landscape sampling units in dry and wet forest in southeast Australia during 2010 and 2011. Four uncorrelated indices of bird FD (richness, evenness, divergence and dispersion) were derived from six bird traits, and we investigated responses of these indices and species richness to both vertical and horizontal vegetation diversity using linear mixed models. We also considered the extent to which the mean and diversity of time since fire were related to vegetation diversity. Results showed opposing responses of FD to vegetation diversity in dry and wet forest. In dry forest, where fire is frequent, species richness and two FD indices (richness and dispersion) were positively related to vertical vegetation diversity, consistent with theory relating to environmental variation and coexistence. However, in wet forest subject to infrequent fire, the same three response variables were negatively associated with vertical diversity. We suggest that competitive dominance by species results in lower FD as vegetation diversity increases in wet forest. The responses of functional evenness were opposite to those of species richness, functional richness and dispersion in both forest types, highlighting the value of examining multiple FD metrics at management-relevant scales. The mean and diversity of time since fire were uncorrelated with vegetation

  13. Conserving Tropical Tree Diversity and Forest Structure: The Value of Small Rainforest Patches in Moderately-Managed Landscapes

    Science.gov (United States)

    Hernández-Ruedas, Manuel A.; Arroyo-Rodríguez, Víctor; Meave, Jorge A.; Martínez-Ramos, Miguel; Ibarra-Manríquez, Guillermo; Martínez, Esteban; Jamangapé, Gilberto; Melo, Felipe P. L.; Santos, Bráulio A.

    2014-01-01

    Rainforests are undergoing severe deforestation and fragmentation worldwide. A huge amount of small forest patches are being created, but their value in conserving biodiversity and forest structure is still controversial. Here, we demonstrate that in a species-rich and moderately-managed Mexican tropical landscape small rainforest patches (<100 ha) can be highly valuable for the conservation of tree diversity and forest structure. These patches showed diverse communities of native plants, including endangered species, and a new record for the country. Although the number of logged trees increased in smaller patches, patch size was a poor indicator of basal area, stem density, number of species, genera and families, and community evenness. Cumulative species-area curves indicated that all patches had a similar contribution to the regional species diversity. This idea also was supported by the fact that patches strongly differed in floristic composition (high β-diversity), independently of patch size. Thus, in agreement with the land-sharing approach, our findings support that small forest patches in moderately-managed landscapes should be included in conservation initiatives to maintain landscape heterogeneity, species diversity, and ecosystem services. PMID:24901954

  14. Conserving tropical tree diversity and forest structure: the value of small rainforest patches in moderately-managed landscapes.

    Science.gov (United States)

    Hernández-Ruedas, Manuel A; Arroyo-Rodríguez, Víctor; Meave, Jorge A; Martínez-Ramos, Miguel; Ibarra-Manríquez, Guillermo; Martínez, Esteban; Jamangapé, Gilberto; Melo, Felipe P L; Santos, Bráulio A

    2014-01-01

    Rainforests are undergoing severe deforestation and fragmentation worldwide. A huge amount of small forest patches are being created, but their value in conserving biodiversity and forest structure is still controversial. Here, we demonstrate that in a species-rich and moderately-managed Mexican tropical landscape small rainforest patches (tree diversity and forest structure. These patches showed diverse communities of native plants, including endangered species, and a new record for the country. Although the number of logged trees increased in smaller patches, patch size was a poor indicator of basal area, stem density, number of species, genera and families, and community evenness. Cumulative species-area curves indicated that all patches had a similar contribution to the regional species diversity. This idea also was supported by the fact that patches strongly differed in floristic composition (high β-diversity), independently of patch size. Thus, in agreement with the land-sharing approach, our findings support that small forest patches in moderately-managed landscapes should be included in conservation initiatives to maintain landscape heterogeneity, species diversity, and ecosystem services.

  15. Conserving tropical tree diversity and forest structure: the value of small rainforest patches in moderately-managed landscapes.

    Directory of Open Access Journals (Sweden)

    Manuel A Hernández-Ruedas

    Full Text Available Rainforests are undergoing severe deforestation and fragmentation worldwide. A huge amount of small forest patches are being created, but their value in conserving biodiversity and forest structure is still controversial. Here, we demonstrate that in a species-rich and moderately-managed Mexican tropical landscape small rainforest patches (<100 ha can be highly valuable for the conservation of tree diversity and forest structure. These patches showed diverse communities of native plants, including endangered species, and a new record for the country. Although the number of logged trees increased in smaller patches, patch size was a poor indicator of basal area, stem density, number of species, genera and families, and community evenness. Cumulative species-area curves indicated that all patches had a similar contribution to the regional species diversity. This idea also was supported by the fact that patches strongly differed in floristic composition (high β-diversity, independently of patch size. Thus, in agreement with the land-sharing approach, our findings support that small forest patches in moderately-managed landscapes should be included in conservation initiatives to maintain landscape heterogeneity, species diversity, and ecosystem services.

  16. Intelligent Classification in Huge Heterogeneous Data Sets

    Science.gov (United States)

    2015-06-01

    INTELLIGENT CLASSIFICATION IN HUGE HETEROGENEOUS DATA SETS JUNE 2015 FINAL TECHNICAL REPORT APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED...To) JUL 2013 – APR 2015 4. TITLE AND SUBTITLE INTELLIGENT CLASSIFICATION IN HUGE HETEROGENEOUS DATA SETS 5a. CONTRACT NUMBER IN-HOUSE 5b. GRANT...signals and through data dimension reduction, and to develop and tailor algorithms for the extraction of intelligence from several huge heterogeneous

  17. Original Paper Patterns of genetic structure and phenotypic diversity ...

    African Journals Online (AJOL)

    Patterns of genetic structure and phenotypic diversity in sorghum landraces in relation to farmers' management in Burkina Faso ... the role of farmer practices in phenotypic and genetic evolution of sorghum. ... varieties to marginal environments such as ...... Supporting the Convention on Biological ... A new method to.

  18. Structural Diversity and Close Interracial Relationships in College

    Science.gov (United States)

    Bowman, Nicholas A.

    2012-01-01

    Recent legal and political actions have challenged the use of race-conscious college admissions policies. Earlier research offers mixed evidence about the link between an institution's racial/ethnic composition (i.e., structural diversity) and the formation of close interracial relationships, so the present study examines this topic directly for…

  19. The influence of compositional and structural diversity on forest productivity

    Science.gov (United States)

    James N. Long; John D. Shaw

    2010-01-01

    Data from ~1500 ponderosa pine (Pinus ponderosa C. Lawson) stands in the western United States were used to examine the potential influence of compositional and structural diversity on forest productivity. Relative density, height and site quality were combined in a conceptually sound expression of the relationship between growth and growing stock for ponderosa pine-...

  20. Interactive diversity promotes the evolution of cooperation in structured populations

    Science.gov (United States)

    Su, Qi; Li, Aming; Zhou, Lei; Wang, Long

    2016-10-01

    Evolutionary games on networks traditionally assume that each individual adopts an identical strategy to interact with all its neighbors in each generation. Considering the prevalent diversity of individual interactions in the real society, here we propose the concept of interactive diversity, which allows individuals to adopt different strategies against different neighbors in each generation. We investigate the evolution of cooperation based on the edge dynamics rather than the traditional nodal dynamics in networked systems. The results show that, without invoking any other mechanisms, interactive diversity drives the frequency of cooperation to a high level for a wide range of parameters in both well-mixed and structured populations. Even in highly connected populations, cooperation still thrives. When interactive diversity and large topological heterogeneity are combined together, however, in the relaxed social dilemma, cooperation level is lower than that with just one of them, implying that the combination of many promotive factors may make a worse outcome. By an analytical approximation, we get the condition under which interactive diversity provides more advantages for cooperation than traditional evolutionary dynamics does. Numerical simulations validating the approximation are also presented. Our work provides a new line to explore the latent relation between the ubiquitous cooperation and individuals’ distinct responses in different interactions. The presented results suggest that interactive diversity should receive more attention in pursuing mechanisms fostering cooperation.

  1. Information diversity in structure and dynamics of simulated neuronal networks.

    Science.gov (United States)

    Mäki-Marttunen, Tuomo; Aćimović, Jugoslava; Nykter, Matti; Kesseli, Juha; Ruohonen, Keijo; Yli-Harja, Olli; Linne, Marja-Leena

    2011-01-01

    Neuronal networks exhibit a wide diversity of structures, which contributes to the diversity of the dynamics therein. The presented work applies an information theoretic framework to simultaneously analyze structure and dynamics in neuronal networks. Information diversity within the structure and dynamics of a neuronal network is studied using the normalized compression distance. To describe the structure, a scheme for generating distance-dependent networks with identical in-degree distribution but variable strength of dependence on distance is presented. The resulting network structure classes possess differing path length and clustering coefficient distributions. In parallel, comparable realistic neuronal networks are generated with NETMORPH simulator and similar analysis is done on them. To describe the dynamics, network spike trains are simulated using different network structures and their bursting behaviors are analyzed. For the simulation of the network activity the Izhikevich model of spiking neurons is used together with the Tsodyks model of dynamical synapses. We show that the structure of the simulated neuronal networks affects the spontaneous bursting activity when measured with bursting frequency and a set of intraburst measures: the more locally connected networks produce more and longer bursts than the more random networks. The information diversity of the structure of a network is greatest in the most locally connected networks, smallest in random networks, and somewhere in between in the networks between order and disorder. As for the dynamics, the most locally connected networks and some of the in-between networks produce the most complex intraburst spike trains. The same result also holds for sparser of the two considered network densities in the case of full spike trains.

  2. A rare clinic entity: Huge trichobezoar.

    Science.gov (United States)

    Hamidi, Hidayatullah; Muhammadi, Marzia; Saberi, Bismillah; Sarwari, Mohammad Arif

    2016-01-01

    Trichobezoar is a rare clinical entity in which a ball of hair amasses within the alimentary tract. It can either be found as isolated mass in the stomach or may extend into the intestine. Trichobezoars mostly occur in young females with psychiatric disorders such as trichophagia and trichotillomania. Authors present a giant trichobezoar in an 18year old female presented with complaints of upper abdominal mass, epigastric area pain, anorexia and weight loss. The patient underwent trans-abdominal ultrasonography (USG), Computed tomography (CT), upper gastrointestinal endoscopy and subsequently laparotomy. USG was inconclusive due to non-specific findings. It revealed a thick echogenic layer with posterior dirty shadowing extending from the left sub-diaphragmatic area to the right sub hepatic region obscuring the adjacent structures. Abdominal CT images revealed a huge, well defined, multi-layered, heterogeneous, solid appearing, non-enhancing mass lesion in the gastric lumen extending from the gastric fundus to the pyloric canal. An endoscopic attempt was performed for removal of this intraluminal mass, but due to its large size, and hard nature, the endoscopic removal was unsuccessful. Finally the large trichobezoar was removed with open laparotomy. Trichobezoars should be suspected in young females with long standing upper abdominal masses; as the possibility of malignancy is not very common in this age group. While USG is inconclusive, trichobezoar can be accurately diagnosed with CT. In patient with huge trichobezoar, laparotomy can be performed firstly because of big size and location of mass, and psychiatric recommendation should be made to prevent relapse of this entity. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  3. Structural Conservation Despite Huge Sequence Diversity Allows EPCR Binding by the PfEMP1 Family Implicated in Severe Childhood Malaria

    DEFF Research Database (Denmark)

    Lau, Clinton K.Y.; Turner, Louise; Jespersen, Jakob S.;

    2015-01-01

    The PfEMP1 family of surface proteins is central for Plasmodium falciparum virulence and must retain the ability to bind to host receptors while also diversifying to aid immune evasion. The interaction between CIDRa1 domains of PfEMP1 and endothelial protein C receptor (EPCR) is associated...

  4. Genetic diversity and population structure of a diverse set of rice germplasm for association mapping.

    Science.gov (United States)

    Jin, Liang; Lu, Yan; Xiao, Peng; Sun, Mei; Corke, Harold; Bao, Jinsong

    2010-08-01

    Germplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations. 63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25-50 cM in different subpopulations. Analysis of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively. More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested that the population may be useful for the genome-wide marker-trait association mapping. This new association population has the potential to identify

  5. The structure of cross-cultural musical diversity.

    Science.gov (United States)

    Rzeszutek, Tom; Savage, Patrick E; Brown, Steven

    2012-04-22

    Human cultural traits, such as languages, musics, rituals and material objects, vary widely across cultures. However, the majority of comparative analyses of human cultural diversity focus on between-culture variation without consideration for within-culture variation. In contrast, biological approaches to genetic diversity, such as the analysis of molecular variance (AMOVA) framework, partition genetic diversity into both within- and between-population components. We attempt here for the first time to quantify both components of cultural diversity by applying the AMOVA model to music. By employing this approach with 421 traditional songs from 16 Austronesian-speaking populations, we show that the vast majority of musical variability is due to differences within populations rather than differences between. This demonstrates a striking parallel to the structure of genetic diversity in humans. A neighbour-net analysis of pairwise population musical divergence shows a large amount of reticulation, indicating the pervasive occurrence of borrowing and/or convergent evolution of musical features across populations.

  6. Hitchhiker's guide to genetic diversity in socially structured populations

    Institute of Scientific and Technical Information of China (English)

    L.S.PREMO

    2012-01-01

    When selection increases the frequency of a beneficial gene substitution it can also increase the frequencies of linked neutral alleles through a process called genetic hitchhiking.A model built to investigate reduced genetic diversity in Pleistocene hominins shows that genetic hitchhiking can have a strong effect on neutral diversity in the presence of culturally mediated migration.Under conditions in which genetic and cultural variants are transmitted symmetrically,neutral genes may also hitchhike to higher frequencies on the coattails of adaptive cultural traits through a process called cultural hitchhiking.Cultural hitchhiking has been proposed to explain why some species of matrilineal whales display relatively low levels of mitochondrial DNA diversity,and it may be applicable to humans as well.This paper provides a critical review of recent models of both types of hitchhiking in socially structured populations.The models' assumptions and predictions are compared and discussed in the hope that studies of reduced genetic diversity in humans might improve our understanding of reduced genetic diversity in other species,and vice versa [Current Zoology 58 (1):287-297,2012].

  7. The big, large and huge case of state-building

    DEFF Research Database (Denmark)

    Harste, Gorm

      Using communication theory as point of departure, it is not evident how to study macro phenomena. Michel Foucault limited his studies to a non-Grand Theory when studying discursive events. At the same time, Charles Tilly wrote about Big Structures, Large Processes, Huge Comparisons when trying...

  8. Genetic diversity and population structure of cucumber (Cucumis sativus L..

    Directory of Open Access Journals (Sweden)

    Jing Lv

    Full Text Available Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.

  9. Soil microbial functional diversity in a montane evergreen broadleaved forest of Chebaling Following the Huge Ice Storm in South China%车八岭山地常绿阔叶林冰灾后土壤微生物群落功能多样性

    Institute of Scientific and Technical Information of China (English)

    区余端; 苏志尧; 彭桂香; 刘刚

    2009-01-01

    研究了我国南方冰灾后常绿阔叶林林冠开度及土壤养分的空间异质性对土壤微生物功能多样性的影响.在受冰灾影响的粤北车八岭山地常绿阔叶林2 hm~2固定样地中按照冠层受损程度选取16个20 m×20 m的样方,用半球面影像技术获取林冠开度,并取0~20 cm的表层土壤混合样品分析土壤的理化性质,同时应用Biolog技术分析微生物功能多样性.按林冠开度梯度对各样方土壤微生物群落利用单一碳源的分析发现,林冠开度大的样方土壤微生物的活性、丰富度、多样性和均匀度都较低,反之则较高.聚类分析的结果与林冠开度的梯度有高度的一致性.主成分分析表明各样方土壤微生物功能多样性具有显著差异(第一轴p<0.005;第二轴p<0.001),其结果与聚类结果基本吻合.冗余分析揭示了土壤全磷、全钾、全氮、速效氮、有机碳、容重、总孔隙度和林冠开度的综合作用对土壤微生物功能多样性有显著影响(p<0.005),其中林冠开度与土壤微生物群落功能多样性的关系最密切.土壤微生物功能多样性受土壤养分的影响,具体表现为:与土壤有机碳呈明显的正相关;与全氮正相关;与速效氮、全磷负相关.研究说明冰灾所造成林冠开度和土壤养分的空间异质性会影响到土壤微生物功能多样性,而土壤微生物功能多样性可用于对生境恢复的指示和评价.%Effect of spatial heterogeneity in canopy openness and soil nutrients on soil microbial functional diversity was investigated following a huge ice storm in south China. Sixteen plots, each 400 m~2, were selected for this study according to the damage degrees of the canopy within a 2 hm~2 permanent plot, which had been set up within the storm-hit montane evergreen broadleaved forest in Chebaling National Nature Reserve. Canopy openness was estimated with hemispherical photography, and a composite sample of surface soil (0-20 cm

  10. Molecular Diversity and Genetic Structure of Durum Wheat Landraces

    Directory of Open Access Journals (Sweden)

    GULNAR SHIKHSEYIDOVA

    2015-06-01

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

  11. Genetic structure and diversity of Shorea obtusa (Dipterocarpaceae) in Thailand

    Institute of Scientific and Technical Information of China (English)

    Chadaporn SENAKUN; Suchitra CHANGTRAGOON; Pairot PRAMUAL; Preecha PRATHEPHA

    2011-01-01

    Shorea obtusa is a keystone species of the dry deciduous dipterocarp forest in Thailand. In this study,the genetic structure and diversity of this species were evaluated by means of five microsatellite markers. A total of 146 trees were collected from five populations encompassing major forest regions of Thailand. High levels of genetic diversity were found among the five populations with the average He of 0.664. Genetic differentiations between populations, although significant, were low with approximately 3% of genetic variation partitioned among populations. This may indicate that the populations sampled were recently part of a continuous population. A tree constructed using the unweighted pair group method with arithmetic average, based on Nei's genetic distance, divided the populations into three groups. This separation was consistent with the altitudinal zonation of the populations,thus indicating that altitude might play a significant role in the genetic structure of S. obtusa. Areas of high genetic diversity were identified which could be considered priorities for conservation.

  12. 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.

  13. Plasmodium vivax Diversity and Population Structure across Four Continents.

    Directory of Open Access Journals (Sweden)

    Cristian Koepfli

    Full Text Available Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999-2008. Diversity was highest in South-East Asia (mean allelic richness 10.0-12.8, intermediate in the South Pacific (8.1-9.9 Madagascar and Sudan (7.9-8.4, and lowest in South America and Central Asia (5.5-7.2. A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60-80% in Latin American populations, suggesting that typing of 2-6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (FST>0.2. Outside Central Asia FST values were highest (0.11-0.16 between South American and all other populations, and lowest (0.04-0.07 between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations.

  14. Outcome of Hepatectomy for Huge Hepatocellular Carcinoma.

    Science.gov (United States)

    Jo, Sungho

    2011-05-01

    In spite of the recent improved results of hepatectomy for huge hepatocellular carcinomas (HCC), the prognosis of patients with huge HCCs is still poor compared to that of patients with small HCCs. This study was performed to compare the results of hepatectomy between patients with huge HCCs and those with small HCCs, to identify the prognostic factors in patients with huge HCCs, and to determine the preoperative selection criteria. We retrospectively analyzed 51 patients who underwent hepatectomy, between July 1994 and February 2009 at Dankook University Hospital. Patients with HCC≥10 cm were classified in large (L) group and others were classified in small (S) group. The clinicopathological features, operative procedures, and postoperative outcome were compared between both groups and various prognostic factors were investigated in group L. Eleven patients were classified in group L. Tumor size, vascular invasion, and tumor stage were higher in group L. Postoperative morbidity was higher in group L, but mortality was not different between the groups. Disease-free survivals were significantly lower in group L than in group S (36.4%, and 24.2% vs. 72.0%, and 44.0% for 1- and 3-year), but overall survival rates were similar in both groups (45.5%, and 15.2% in group L vs. 60.3%, and 41.3% in group S for 3- and 5-year). Presence of satellite nodules was the only prognostic factor in multivariate analysis after surgery for huge HCC. Regardless of tumor size, huge HCCs deserve consideration for surgery in patients with preserved liver function. Furthermore, the effect of surgery could be maximized with appropriate selection criteria, such as huge HCC without satellite nodules.

  15. Situating and Constructing Diversity in Semi-Structured Interviews

    Directory of Open Access Journals (Sweden)

    Michele J. McIntosh

    2015-08-01

    Full Text Available Although semi-structured interviews (SSIs are used extensively in research, scant attention is given to their diversity, underlying assumptions, construction, and broad applications to qualitative and mixed-method research. In this three-part article, we discuss the following: (a how the SSI is situated historically including its evolution and diversification, (b the principles of constructing SSIs, and (c how SSIs are utilized as a stand-alone research method, and as strategy within a mixed-method design.

  16. Structural Diversity of Self-Assembled Iridescent Arthropod Biophotonic Nanostructures

    Science.gov (United States)

    Saranathan, Vinod Kumar; Prum, Richard O.

    2015-03-01

    Many organisms, especially arthropods, produce vivid interference colors using diverse mesoscopic (100-350 nm) integumentary biophotonic nanostructures that are increasingly being investigated for technological applications. Despite a century of interest, we lack precise structural knowledge of many biophotonic nanostructures and mechanisms controlling their development, when such knowledge can open novel biomimetic routes to facilely self-assemble tunable, multi-functional materials. Here, we use synchrotron small angle X-ray scattering and electron microscopy to characterize the photonic nanostructure of 140 iridescent integumentary scales and setae from 127 species of terrestrial arthropods in 85 genera from 5 orders. We report a rich nanostructural diversity, including triply-periodic bicontinuous networks, close-packed spheres, inverse columnar, perforated lamellar, and disordered sponge-like morphologies, commonly observed as stable phases of amphiphilic surfactants, block copolymer, and lyotropic lipid-water systems. Diverse arthropod lineages appear to have independently evolved to utilize the self-assembly of infolding bilayer membranes to develop biophotonic nanostructures that span the phase-space of amphiphilic morphologies, but at optical length scales.

  17. Connecting slow earthquakes to huge earthquakes.

    Science.gov (United States)

    Obara, Kazushige; Kato, Aitaro

    2016-07-15

    Slow earthquakes are characterized by a wide spectrum of fault slip behaviors and seismic radiation patterns that differ from those of traditional earthquakes. However, slow earthquakes and huge megathrust earthquakes can have common slip mechanisms and are located in neighboring regions of the seismogenic zone. The frequent occurrence of slow earthquakes may help to reveal the physics underlying megathrust events as useful analogs. Slow earthquakes may function as stress meters because of their high sensitivity to stress changes in the seismogenic zone. Episodic stress transfer to megathrust source faults leads to an increased probability of triggering huge earthquakes if the adjacent locked region is critically loaded. Careful and precise monitoring of slow earthquakes may provide new information on the likelihood of impending huge earthquakes.

  18. Connecting slow earthquakes to huge earthquakes

    Science.gov (United States)

    Obara, Kazushige; Kato, Aitaro

    2016-07-01

    Slow earthquakes are characterized by a wide spectrum of fault slip behaviors and seismic radiation patterns that differ from those of traditional earthquakes. However, slow earthquakes and huge megathrust earthquakes can have common slip mechanisms and are located in neighboring regions of the seismogenic zone. The frequent occurrence of slow earthquakes may help to reveal the physics underlying megathrust events as useful analogs. Slow earthquakes may function as stress meters because of their high sensitivity to stress changes in the seismogenic zone. Episodic stress transfer to megathrust source faults leads to an increased probability of triggering huge earthquakes if the adjacent locked region is critically loaded. Careful and precise monitoring of slow earthquakes may provide new information on the likelihood of impending huge earthquakes.

  19. Treatment strategies for huge central neurocytomas.

    Science.gov (United States)

    Xiong, Zhong-wei; Zhang, Jian-jian; Zhang, Ting-bao; Sun, Shou-jia; Wu, Xiao-lin; Wang, Hao; You, Chao; Wang, Yu; Zhang, Hua-qiu; Chen, Jin-cao

    2015-02-01

    Central neurocytomas (CNs), initially asymptomatic, sometimes become huge before detection. We described and analyzed the clinical, radiological, operational and outcome data of 13 cases of huge intraventricular CNs, and discussed the treatment strategies in this study. All huge CNs (n=13) in our study were located in bilateral lateral ventricle with diameter ≥5.0 cm and had a broad-based attachment to at least one side of the ventricle wall. All patients received craniotomy to remove the tumor through transcallosal or transcortical approach and CNs were of typical histologic and immunohistochemical features. Adjuvant therapies including conventional radiation therapy (RT) or gamma knife radiosurgery (GKRS) were also performed postoperatively. Transcallosal and transcortical approaches were used in 8 and 5 patients, respectively. Two patients died within one month after operation and 3 patients with gross total resection (GTR) were additionally given a decompressive craniectomy (DC) and/or ventriculoperitoneal shunt (VPS) as the salvage therapy. Six patients received GTR(+RT) and 7 patients received subtotal resection (STR)(+GKRS). Eight patients suffered serious complications such as hydrocephalus, paralysis and seizure after operation, and patients who underwent GTR showed worse functional outcome [less Karnofsky performance scale (KPS) scores] than those having STR(+GKRS) during the follow-up period. The clinical outcome of huge CNs seemed not to be favorable as that described in previous reports. Surgical resection for huge CNs should be meticulously considered to guarantee the maximum safety. Better results were achieved in STR(+GKRS) compared with GTR(+RT) for huge CNs, suggesting that STR(+GKRS) may be a better treatment choice. The recurrent or residual tumor can be treated with GKRS effectively.

  20. The systematic structure and predictability of urban business diversity

    CERN Document Server

    Youn, Hyejin; Lobo, José; Strumsky, Deborah; Samaniego, Horacio; West, Geoffrey B

    2014-01-01

    Understanding cities is central to addressing major global challenges from climate and health to economic resilience. Although increasingly perceived as fundamental socio-economic units, the detailed fabric of urban economic activities is only now accessible to comprehensive analyses with the availability of large datasets. Here, we study abundances of business categories across U.S. metropolitan statistical areas to investigate how diversity of economic activities depends on city size. A universal structure common to all cities is revealed, manifesting self-similarity in internal economic structure as well as aggregated metrics (GDP, patents, crime). A derivation is presented that explains universality and the observed empirical distribution. The model incorporates a generalized preferential attachment process with ceaseless introduction of new business types. Combined with scaling analyses for individual categories, the theory quantitatively predicts how individual business types systematically change rank ...

  1. A Low Cost Structurally Optimized Design for Diverse Filter Types.

    Science.gov (United States)

    Kazmi, Majida; Aziz, Arshad; Akhtar, Pervez; Ikram, Nassar

    2016-01-01

    A wide range of image processing applications deploys two dimensional (2D)-filters for performing diversified tasks such as image enhancement, edge detection, noise suppression, multi scale decomposition and compression etc. All of these tasks require multiple type of 2D-filters simultaneously to acquire the desired results. The resource hungry conventional approach is not a viable option for implementing these computationally intensive 2D-filters especially in a resource constraint environment. Thus it calls for optimized solutions. Mostly the optimization of these filters are based on exploiting structural properties. A common shortcoming of all previously reported optimized approaches is their restricted applicability only for a specific filter type. These narrow scoped solutions completely disregard the versatility attribute of advanced image processing applications and in turn offset their effectiveness while implementing a complete application. This paper presents an efficient framework which exploits the structural properties of 2D-filters for effectually reducing its computational cost along with an added advantage of versatility for supporting diverse filter types. A composite symmetric filter structure is introduced which exploits the identities of quadrant and circular T-symmetries in two distinct filter regions simultaneously. These T-symmetries effectually reduce the number of filter coefficients and consequently its multipliers count. The proposed framework at the same time empowers this composite filter structure with additional capabilities of realizing all of its Ψ-symmetry based subtypes and also its special asymmetric filters case. The two-fold optimized framework thus reduces filter computational cost up to 75% as compared to the conventional approach as well as its versatility attribute not only supports diverse filter types but also offers further cost reduction via resource sharing for sequential implementation of diversified image

  2. Optimization of Dynamically Generated SQL Queries for Tiny-Huge, Huge-Tiny Problem

    Directory of Open Access Journals (Sweden)

    Arjun K Sirohi

    2013-03-01

    Full Text Available In most new commercial business software applications like Customer Relationship Management, the datais stored in the database layer which is usually a Relational Database Management System (RDBMS likeOracle, DB2 UDB or SQL Server. To access data from these databases, Structured Query Language (SQLqueries are used that are generated dynamically at run time based on defined business models and businessrules. One such business rule is visibility- the capability of the application to restrict data access based onthe role and responsibility of the user logged in to the application. This is generally achieved by appendingsecurity predicates in the form of sub-queries to the main query based on the roles and responsibility of theuser. In some cases, the outer query may be more restrictive while in other cases, the security predicatesmay be more restrictive. This often results in a dilemma for the cost-based optimizer (CBO of the backenddatabase whether to drive from the outer query or drive from the security predicate sub-queries. Thisdilemma is sometimes called the “Tiny-Huge, Huge-Tiny” problem and results in serious performancedegradation by way of increased response times on the application User Interface (UI. This paperprovides a case study of a new approach to vastly reduce this CBO dilemma by a combination of denormalizedcolumns and re-writing of the security predicates’ sub-queries at run-time, thereby levelling theouter and security sub-queries. This approach results in more stable execution plans in the database andmuch better performance of such SQLs, effectively leading to higher performance and scalability of theapplication.

  3. A Huge Ancient Schwannoma of the Epiglottis.

    Science.gov (United States)

    Lee, Dong Hoon; Kim, Jo Heon; Yoon, Tae Mi; Lee, Joon Kyoo; Lim, Sang Chul

    2016-03-01

    Ancient schwannoma of the epiglottis is extremely rare. The authors report the first case of a patient with a huge ancient schwannoma of the epiglottis. Clinicians should consider the possibility that ancient schwannoma may originate in the epiglottis mimicking the other more frequently observed lesions.

  4. Population structure and genetic diversity of moose in Alaska.

    Science.gov (United States)

    Schmidt, Jennifer I; Hundertmark, Kris J; Bowyer, R Terry; McCracken, Kevin G

    2009-01-01

    Moose (Alces alces) are highly mobile mammals that occur across arboreal regions of North America, Europe, and Asia. Alaskan moose (Alces alces gigas) range across much of Alaska and are primary herbivore consumers, exerting a prominent influence on ecosystem structure and functioning. Increased knowledge gained from population genetics provides insights into their population dynamics, history, and dispersal of these unique large herbivores and can aid in conservation efforts. We examined the genetic diversity and population structure of moose (n = 141) with 8 polymorphic microsatellites from 6 regions spanning much of Alaska. Expected heterozygosity was moderate (H(E) = 0.483-0.612), and private alleles ranged from 0 to 6. Both F(ST) and R(ST) indicated significant population structure (P moose from the Yakutat and Tetlin regions versus all other moose, with slight substructure observed among the second population. Estimates of dispersal differed between analytical approaches, indicating a high level of historical or current gene flow. Mantel tests indicated that isolation-by-distance partially explained observed structure among moose populations (R(2) = 0.45, P moose in Alaska with population expansion from interior Alaska westward toward the coast.

  5. Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris.

    Science.gov (United States)

    Rodriguez, Monica; Rau, Domenico; Bitocchi, Elena; Bellucci, Elisa; Biagetti, Eleonora; Carboni, Andrea; Gepts, Paul; Nanni, Laura; Papa, Roberto; Attene, Giovanna

    2016-03-01

    Here we studied the organization of genetic variation of the common bean (Phaseolus vulgaris) in its centres of domestication. We used 131 single nucleotide polymorphisms to investigate 417 wild common bean accessions and a representative sample of 160 domesticated genotypes, including Mesoamerican and Andean genotypes, for a total of 577 accessions. By analysing the genetic spatial patterns of the wild common bean, we documented the existence of several genetic groups and the occurrence of variable degrees of diversity in Mesoamerica and the Andes. Moreover, using a landscape genetics approach, we demonstrated that both demographic processes and selection for adaptation were responsible for the observed genetic structure. We showed that the study of correlations between markers and ecological variables at a continental scale can help in identifying local adaptation genes. We also located putative areas of common bean domestication in Mesoamerica, in the Oaxaca Valley, and the Andes, in southern Bolivia-northern Argentina. These observations are of paramount importance for the conservation and exploitation of the genetic diversity preserved within this species and other plant genetic resources.

  6. Genetic Diversity and Population Structure of Theileria annulata in Oman.

    Directory of Open Access Journals (Sweden)

    Salama Al-Hamidhi

    Full Text Available Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle.Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman.We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia. A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075,

  7. Glycosphingolipid Modification: Structural Diversity, Functional and Mechanistic Integration of Diabetes

    Directory of Open Access Journals (Sweden)

    Tadashi Yamashita

    2011-08-01

    Full Text Available Glycosphingolipids (GSLs are present in all mammalian cell plasma membranes and intracellular membrane structures. They are especially concentrated in plasma membrane lipid domains that are specialized for cell signaling. Plasma membranes have typical structures called rafts and caveola domain structures, with large amounts of sphingolipids, cholesterol, and sphingomyelin. GSLs are usually observed in many organs ubiquitously. However, GSLs, including over 400 derivatives, participate in diverse cellular functions. Several studies indicate that GSLs might have an effect on signal transduction related to insulin receptors and epidermal growth factor receptors. GSLs may modulate immune responses by transmitting signals from the exterior to the interior of the cell. Guillain-Barré syndrome is one of the autoimmune disorders characterized by symmetrical weakness in the muscles of the legs. The targets of the immune response are thought to be gangliosides, which are one group of GSLs. Other GSLs may serve as second messengers in several signaling pathways that are important to cell survival or programmed cell death. In the search for clear evidence that GSLs may play critical roles in various biological functions, many researchers have made genetically engineered mice. Before the era of gene manipulation, spontaneous animal models or chemical-induced disease models were used.

  8. Structure and diversity in mammalian accessory olfactory bulb.

    Science.gov (United States)

    Meisami, E; Bhatnagar, K P

    1998-12-15

    The accessory olfactory bulb (AOB) is the first neural integrative center for the olfactory-like vomeronasal sensory system. In this article, we first briefly present an overview of vomeronasal system organization and review the history of the discovery of mammalian AOB. Next, we briefly review the evolution of the vomeronasal system in vertebrates, in particular the reptiles. Following these introductory aspects, the structure of the rodent AOB, as typical of the well-developed mammalian AOB, is presented, detailing laminar organization and cell types as well as aspects of the homology with the main olfactory bulb. Then, the evolutionary origin and diversity of the AOB in mammalian orders and species is discussed, describing structural, phylogenetic, and species-specific variation in the AOB location, shape, and size and morphologic differentiation and development. The AOB is believed to be absent in fishes but present in terrestrial tetrapods including amphibians; among the reptiles AOB is absent in crocodiles, present in turtles, snakes, and some lizards where it may be as large or larger than the main bulb. The AOB is absent in bird and in the aquatic mammals (whales, porpoises, manatees). Among other mammals, AOB is present in the monotremes and marsupials, edentates, and in the majority of the placental mammals like carnivores, herbivores, as well as rodents and lagomorphs. Most bat species do not have an AOB and among those where one is found, it shows marked variation in size and morphologic development. Among insectivores and primates, AOB shows marked variation in occurrence, size, and morphologic development. It is small in shrews and moles, large in hedgehogs and prosimians; AOB continues to persist in New World monkeys but is not found in the adults of the higher primates such as the Old World monkeys, apes, and humans. In many species where AOB is absent in the adult, it often develops in the embryo and fetus but regresses in later stages of

  9. A huge presacral Tarlov cyst. Case report.

    Science.gov (United States)

    Ishii, Kazuhiko; Yuzurihara, Masahito; Asamoto, Shunji; Doi, Hiroshi; Kubota, Motoo

    2007-08-01

    Perineural cysts have become a common incidental finding during lumbosacral magnetic resonance (MR) imaging. Only some of the symptomatic cysts warrant treatment. The authors describe the successful operative treatment of a patient with, to the best of their knowledge, the largest perineural cyst reported to date. A 29-year-old woman had been suffering from long-standing constipation and low-back pain. During an obstetric investigation for infertility, the clinician discovered a huge presacral cystic mass. Computed tomography myelography showed the lesion to be a huge Tarlov cyst arising from the left S-3 nerve root and compressing the ipsilateral S-2 nerve. The cyst was successfully treated by ligation of the cyst neck together with sectioning of the S-3 nerve root. Postoperative improvement in her symptoms and MR imaging findings were noted. Identification of the nerve root involved by the cyst wall, operative indication, operative procedure, and treatment of multiple cysts are important preoperative considerations.

  10. Severe microphthalmos with cyst and unusually huge dermolipoma.

    Science.gov (United States)

    Li, Weidong; Zhang, Ping; Chen, Qiwen; Ye, Xuelian; Li, Jianqun; Yan, Jianhua

    2015-03-01

    The purpose of this study was to report an unusual case of severe microphthalmos, together with an orbital cyst and huge ocular surface dermolipoma. This is a clinical report relating clinical features as well as imaging and histopathologic findings, along with surgical management of the patient. A 5-month-old Chinese male infant was referred, with 2 large masses in the left eye that were present since birth. Ocular examination results revealed a complete absence of any eye structures in the left orbit. In its place were 2 large masses between the left upper and lower palpebral fissure. One was a 3 × 3 × 2.5-cm spherical red tumor with a smooth surface. The other was a large solid spherical tumor, 4 × 4 × 5 cm, covered with normal skin located in the temporal region and attached to the red mass by a pedicle. Orbital magnetic resonance imaging examination findings confirmed that no eye structures were present in the left orbit. However, a cystic lesion was found in the left orbit, with a low signal on T1-weighted imaging and high signal on T2-weighted imaging, and another huge spherical heterogeneous mass was located "outside" the left orbit. Anterior orbitotomy by conjunctival incision was performed under general anesthesia. A spherical cystic mass of 1.5 × 1.5 × 1.6 cm, a small eye of 0.7 × 0.7 × 0.6 cm, and a huge dermolipoma were removed completely. Pathologic examination results confirmed the diagnosis of severe microphthalmos, together with orbital dermoid cyst and dermolipoma. This rare case demonstrates that severe microphthalmos with a cyst may be completely covered by conjunctiva and associated with an unusually huge dermolipoma.

  11. The diversity pyramid: an organizational model to structure diversity recruitment and retention in nursing programs.

    Science.gov (United States)

    Rosenberg, Lisa; O'Rourke, Marilyn E

    2011-10-01

    The literature on increasing the diversity of individuals who enter and practice the nursing profession comes with sound argument, yet we have seen only modest gains in diversification over the past 10 years. This article addresses how to develop a sustainable program to increase the recruitment and retention of underrepresented students. The diversity pyramid is suggested as a conceptual planning model for increasing diversity that is matched to an institution and its resources. The foundation of the pyramid is an organizational commitment to attracting and retaining diverse students. The middle level addresses financial support for underrepresented students. From the top of the pyramid, one chooses appropriate media and relational tactics necessary to attract the underrepresented students a program seeks. All three elements of the pyramid-organizational commitment to diversity, significant financial support, and a targeted use of resources-play important and sequential roles in building a sustainable diversity initiative.

  12. From tiny microalgae to huge biorefineries

    OpenAIRE

    Gouveia, L.

    2014-01-01

    Microalgae are an emerging research field due to their high potential as a source of several biofuels in addition to the fact that they have a high-nutritional value and contain compounds that have health benefits. They are also highly used for water stream bioremediation and carbon dioxide mitigation. Therefore, the tiny microalgae could lead to a huge source of compounds and products, giving a good example of a real biorefinery approach. This work shows and presents examples of experimental...

  13. A rare clinic entity: Huge trichobezoar

    Directory of Open Access Journals (Sweden)

    Hidayatullah Hamidi, Dr, MD

    2016-01-01

    Conclusion: Trichobezoars should be suspected in young females with long standing upper abdominal masses; as the possibility of malignancy is not very common in this age group. While USG is inconclusive, trichobezoar can be accurately diagnosed with CT. In patient with huge trichobezoar, laparotomy can be performed firstly because of big size and location of mass, and psychiatric recommendation should be made to prevent relapse of this entity.

  14. Jatropha curcas L. Root Structure and Growth in Diverse Soils

    Directory of Open Access Journals (Sweden)

    Ofelia Andrea Valdés-Rodríguez

    2013-01-01

    Full Text Available Unlike most biofuel species, Jatropha curcas has promise for use in marginal lands, but it may serve an additional role by stabilizing soils. We evaluated the growth and structural responsiveness of young J. curcas plants to diverse soil conditions. Soils included a sand, a sandy-loam, and a clay-loam from eastern Mexico. Growth and structural parameters were analyzed for shoots and roots, although the focus was the plasticity of the primary root system architecture (the taproot and four lateral roots. The sandy soil reduced the growth of both shoot and root systems significantly more than sandy-loam or clay-loam soils; there was particularly high plasticity in root and shoot thickness, as well as shoot length. However, the architecture of the primary root system did not vary with soil type; the departure of the primary root system from an index of perfect symmetry was 14±5% (mean ± standard deviation. Although J. curcas developed more extensively in the sandy-loam and clay-loam soils than in sandy soil, it maintained a consistent root to shoot ratio and root system architecture across all types of soil. This strong genetic determination would make the species useful for soil stabilization purposes, even while being cultivated primarily for seed oil.

  15. Biosynthetic multitasking facilitates thalassospiramide structural diversity in marine bacteria

    KAUST Repository

    Ross, Avena C.

    2013-01-23

    Thalassospiramides A and B are immunosuppressant cyclic lipopeptides first reported from the marine α-proteobacterium Thalassospira sp. CNJ-328. We describe here the discovery and characterization of an extended family of 14 new analogues from four Tistrella and Thalassospira isolates. These potent calpain 1 protease inhibitors belong to six structure classes in which the length and composition of the acylpeptide side chain varies extensively. Genomic sequence analysis of the thalassospiramide-producing microbes revealed related, genus-specific biosynthetic loci encoding hybrid nonribosomal peptide synthetase/polyketide synthases consistent with thalassospiramide assembly. The bioinformatics analysis of the gene clusters suggests that structural diversity, which ranges from the 803.4 Da thalassospiramide C to the 1291.7 Da thalassospiramide F, results from a complex sequence of reactions involving amino acid substrate channeling and enzymatic multimodule skipping and iteration. Preliminary biochemical analysis of the N-terminal nonribosomal peptide synthetase module from the Thalassospira TtcA megasynthase supports a biosynthetic model in which in cis amino acid activation competes with in trans activation to increase the range of amino acid substrates incorporated at the N terminus. © 2012 American Chemical Society.

  16. Metabolic Effects of Berries with Structurally Diverse Anthocyanins

    Directory of Open Access Journals (Sweden)

    John Overall

    2017-02-01

    Full Text Available Overconsumption of energy dense foods and sedentary lifestyle are considered as major causes of obesity-associated insulin resistance and abnormal glucose metabolism. Results from both cohort studies and randomized trials suggested that anthocyanins from berries may lower metabolic risks, however these reports are equivocal. The present study was designed to examine effects of six berries with structurally diverse anthocyanin profiles (normalized to 400 µg/g total anthocyanin content on development of metabolic risk factors in the C57BL/6 mouse model of polygenic obesity. Diets supplemented with blackberry (mono-glycosylated cyanidins, black raspberry (acylated mono-glycosylated cyanidins, blackcurrant (mono- and di-glycosylated cyanidins and delphinidins, maqui berry (di-glycosylated delphinidins, Concord grape (acylated mono-glycosylated delphinidins and petunidins, and blueberry (mono-glycosylated delphinidins, malvidins, and petunidins showed a prominent discrepancy between biological activities of delphinidin/malvidin-versus cyanidin-type anthocyanins that could be explained by differences in their structure and metabolism in the gut. Consumption of berries also resulted in a strong shift in the gastrointestinal bacterial communities towards obligate anaerobes that correlated with decrease in the gastrointestinal luminal oxygen and oxidative stress. Further work is needed to understand mechanisms that lead to nearly anoxic conditions in the gut lumens, including the relative contributions of host, diet and/or microbial oxidative activity, and their implication to human health.

  17. Metabolic Effects of Berries with Structurally Diverse Anthocyanins

    Science.gov (United States)

    Overall, John; Bonney, Sierra A.; Wilson, Mickey; Beermann, Arnold; Grace, Mary H.; Esposito, Debora; Lila, Mary Ann; Komarnytsky, Slavko

    2017-01-01

    Overconsumption of energy dense foods and sedentary lifestyle are considered as major causes of obesity-associated insulin resistance and abnormal glucose metabolism. Results from both cohort studies and randomized trials suggested that anthocyanins from berries may lower metabolic risks, however these reports are equivocal. The present study was designed to examine effects of six berries with structurally diverse anthocyanin profiles (normalized to 400 µg/g total anthocyanin content) on development of metabolic risk factors in the C57BL/6 mouse model of polygenic obesity. Diets supplemented with blackberry (mono-glycosylated cyanidins), black raspberry (acylated mono-glycosylated cyanidins), blackcurrant (mono- and di-glycosylated cyanidins and delphinidins), maqui berry (di-glycosylated delphinidins), Concord grape (acylated mono-glycosylated delphinidins and petunidins), and blueberry (mono-glycosylated delphinidins, malvidins, and petunidins) showed a prominent discrepancy between biological activities of delphinidin/malvidin-versus cyanidin-type anthocyanins that could be explained by differences in their structure and metabolism in the gut. Consumption of berries also resulted in a strong shift in the gastrointestinal bacterial communities towards obligate anaerobes that correlated with decrease in the gastrointestinal luminal oxygen and oxidative stress. Further work is needed to understand mechanisms that lead to nearly anoxic conditions in the gut lumens, including the relative contributions of host, diet and/or microbial oxidative activity, and their implication to human health. PMID:28212306

  18. Genetic diversity of coastal bottlenose dolphins revealed by structurally and functionally diverse hemoglobins.

    Science.gov (United States)

    Remington, Nicole; Stevens, Robert D; Wells, Randall S; Holn, Aleta; Dhungana, Suraj; Taboy, Celine H; Crumbliss, Alvin L; Henkens, Robert; Bonaventura, Celia

    2007-08-15

    Studies of structure-function relationships in the respiratory proteins of marine mammals revealed unexpected variations in the number and types of hemoglobins (Hbs) present in coastal bottlenose dolphins, Tursiops truncatus. We obtained blood samples from free-ranging coastal bottlenose dolphins as a component of capture-release studies. We found that the oxygen-binding functions of bottlenose dolphin blood are poised between effector-saturated and unsaturated levels, enabling exercise-dependent shifts in oxygen transfer functions. Isolated bottlenose dolphin Hbs showed elevated pH sensitivities (Bohr effects) and appreciably lower oxygen affinities than adult human Hb in the absence of allosteric effectors. These properties may be an adaptive modification that enhances oxygen delivery during diving episodes when oxygen tensions and effector levels are low. The Hbs of individual dolphins showed similar oxygen affinities, responses to effectors, and expression of heme-heme interaction in oxygen binding, but differed in their redox potentials and rates of autoxidation. The heterogeneity suggested by these functional variations in Hbs of individual dolphins was born out by variations in the molecular weights and numbers of their alpha and beta globin chains. Although coastal bottlenose dolphins were expected to have a single type of Hb, the mass differences observed revealed considerable genetic diversity. There were multiple Hb forms in some individuals and differences in Hb patterns among individuals within the same community.

  19. Isotopic diversity indices: how sensitive to food web structure?

    Directory of Open Access Journals (Sweden)

    Anik Brind'Amour

    Full Text Available Recently revisited, the concept of niche ecology has lead to the formalisation of functional and trophic niches using stable isotope ratios. Isotopic diversity indices (IDI derived from a set of measures assessing the dispersion/distribution of points in the δ-space were recently suggested and increasingly used in the literature. However, three main critics emerge from the use of these IDI: 1 they fail to account for the isotopic sources overlap, 2 some indices are highly sensitive to the number of species and/or the presence of rare species, and 3 the lack of standardization prevents any spatial and temporal comparisons. Using simulations we investigated the ability of six commonly used IDI to discriminate among different trophic food web structures, with a focus on the first two critics. We tested the sensitivity of the IDI to five food web structures along a gradient of sources overlap, varying from two distinct food chains with differentiated sources to two superimposed food chains sharing two sources. For each of the food web structure we varied the number of species (from 10 to 100 species and the type of species feeding behaviour (i.e. random or selective feeding. Values of IDI were generally larger in food webs with distinct basal sources and tended to decrease as the superimposition of the food chains increased. This was more pronounced when species displayed food preferences in comparison to food webs where species fed randomly on any prey. The number of species composing the food web also had strong effects on the metrics, including those that were supposedly less sensitive to small sample size. In all cases, computing IDI on food webs with low numbers of species always increases the uncertainty of the metrics. A threshold of ~20 species was detected above which several metrics can be safely used.

  20. Huge Left Atrium Accompanied by Normally Functioning Prosthetic Valve.

    Science.gov (United States)

    Sabzi, Feridoun

    2015-01-01

    Giant left atria are defined as those measuring larger than 8 cm and are typically found in patients who have rheumatic mitral valve disease with severe regurgitation. Enlargement of the left atrium may create compression of the surrounding structures such as the esophagus, pulmonary veins, respiratory tract, lung, inferior vena cava, recurrent laryngeal nerve, and thoracic vertebrae and lead to dysphagia, respiratory dysfunction, peripheral edema, hoarse voice, or back pain. However, a huge left atrium is usually associated with rheumatic mitral valve disease but is very rare in a normally functioning prosthetic mitral valve, as was the case in our patient. A 46-year-old woman with a past medical history of mitral valve replacement and chronic atrial fibrillation was admitted to our hospital with a chief complaint of cough and shortness of breath, worsened in the last month. Physical examination showed elevated jugular venous pressure, respiratory distress, cardiac cachexia, heart failure, hepatomegaly, and severe edema in the legs. Chest radiography revealed an inconceivably huge cardiac sell-out. Transthoracic echocardiography demonstrated a huge left atrium, associated with thrombosis, and normal function of the prosthetic mitral valve. Cardiac surgery with left atrial exploration for the extraction of the huge thrombosis and De Vega annuloplasty for tricuspid regurgitation were carried out. The postoperative course was eventful due to right ventricular failure and low cardiac output syndrome; and after two days, the patient expired with multiple organ failure. Thorough literature review showed that our case was the largest left atrium (20 × 22 cm) reported thus far in adults with a normal prosthetic mitral valve function.

  1. Huge Left Atrium Accompanied by Normally Function- ing Prosthetic Valve

    Directory of Open Access Journals (Sweden)

    Feridoun Sabzi

    2015-10-01

    Full Text Available Giant left atria are defined as those measuring larger than 8 cm and are typically found in patients who have rheumatic mitral valve disease with severe regurgitation. Enlargement of the left atrium may create compression of the surrounding structures such as the esophagus, pulmonary veins, respiratory tract, lung, inferior vena cava, recurrent laryngeal nerve, and thoracic vertebrae and lead to dysphagia, respiratory dysfunction, peripheral edema, hoarse voice, or back pain. However, a huge left atrium is usually associated with rheumatic mitral valve disease but is very rare in a normally functioning prosthetic mitral valve, as was the case in our patient. A 46-year-old woman with a past medical history of mitral valve replacement and chronic atrial fibrillation was admitted to our hospital with a chief complaint of cough and shortness of breath, worsened in the last month. Physical examination showed elevated jugular venous pressure, respiratory distress, cardiac cachexia, heart failure, hepatomegaly, and severe edema in the legs. Chest radiography revealed an inconceivably huge cardiac sell-out. Transthoracic echocardiography demonstrated a huge left atrium, associated with thrombosis, and normal function of the prosthetic mitral valve. Cardiac surgery with left atrial exploration for the extraction of the huge thrombosis and De Vega annuloplasty for tricuspid regurgitation were carried out. The postoperative course was eventful due to right ventricular failure and low cardiac output syndrome; and after two days, the patient expired with multiple organ failure. Thorough literature review showed that our case was the largest left atrium (20 × 22 cm reported thus far in adults with a normal prosthetic mitral valve function.

  2. Butterflies show different functional and species diversity in relationship to vegetation structure and land use

    NARCIS (Netherlands)

    Aguirre-Gutiérrez, Jesús; Wallis de Vries, Michiel; Marshall, Leon; Zelfde, van 't Maarten; Villalobos-Arámbula, Alma R.; Boekelo, Bastiaen; Bartholomeus, Harm; Franzén, Markus; Biesmeijer, Jacobus C.

    2017-01-01


    Aim

    Biodiversity is rapidly disappearing at local and global scales also affecting the functional diversity of ecosystems. We aimed to assess whether functional diversity was correlated with species diversity and whether both were affected by similar land use and vegetation structure

  3. Huge music archives on mobile devices

    DEFF Research Database (Denmark)

    Blume, H.; Bischl, B.; Botteck, M.

    2011-01-01

    The availability of huge nonvolatile storage capacities such as flash memory allows large music archives to be maintained even in mobile devices. With the increase in size, manual organization of these archives and manual search for specific music becomes very inconvenient. Automated dynamic...... and difficult to tackle on mobile platforms. Against this background, we provided an overview of algorithms for music classification as well as their computation times and other hardware-related aspects, such as power consumption on various hardware architectures. For mobile platforms such as smartphones...

  4. The genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    SAM

    2014-07-16

    Jul 16, 2014 ... variation and, hence, restricting the amount of adapted genetic diversity ... the phenotypic diversity of common bean in Uganda. The selection ... The place of collection/origin was also consi- dered in ..... Bean Research and Development Programs at NaCRRI and CIAT .... Evolution 92:1101-1104. Kami JA ...

  5. Laparoscopic Management of Huge Myoma Nascendi.

    Science.gov (United States)

    Peker, Nuri; Gündoğan, Savas; Şendağ, Fatih

    To demonstrate the feasibility of laparoscopic management of a huge myoma nascendi. Step-by-step video demonstration of the surgical procedure (Canadian Task Force classification III-C). Uterine myoma is the most common benign neoplasm of the female reproductive tract, with an estimated incidence of 25% to 30% at reproductive age [1,2]. Patients generally have no symptoms; however, those with such symptoms as severe pelvic pain, heavy uterine bleeding, or infertility may be candidates for surgery. The traditional management is surgery; however, uterine artery embolization or hormonal therapy using a gonadotropin-releasing hormone agonist or a selective estrogen receptor modulator should be preferred as the medical approach. Surgical management should be performed via laparoscopy or laparotomy; however, the use of laparoscopic myomectomy is being debated for patients with huge myomas. Difficulties in the excision, removal, and repair of myometrial defects, increased operative time, and blood loss are factors keeping physicians away from laparoscopic myomectomy [1,2]. A 35-year-old woman was admitted to our clinic with complaints of chronic pelvic pain and heavy menstrual bleeding. Her medical history included multiple hospitalizations for blood transfusions, along with a recently measured hemoglobin level of 9.5 g/dL and a hematocrit value of 29%. She had never been married and had no children. Pelvic ultrasonography revealed a 12 × 10-cm uterine myoma located on the posterior side of the corpus uteri and protruding through to the cervical channel. This was a huge intramural submucous myoma in close proximity to the endometrial cavity and spreading through the myometrium. On vaginal examination, the myoma was found to extend into the vagina through the cervical channel. Laparoscopic myomectomy was planned because of the patient's desire for fertility preservation. Abdominopelvic exploration revealed a huge myoma filling the posterior side of the corpus uteri and

  6. Structural and functional diversity of acidic scorpion potassium channel toxins.

    Directory of Open Access Journals (Sweden)

    Zong-Yun Chen

    Full Text Available BACKGROUND: Although the basic scorpion K(+ channel toxins (KTxs are well-known pharmacological tools and potential drug candidates, characterization the acidic KTxs still has the great significance for their potential selectivity towards different K(+ channel subtypes. Unfortunately, research on the acidic KTxs has been ignored for several years and progressed slowly. PRINCIPAL FINDINGS: Here, we describe the identification of nine new acidic KTxs by cDNA cloning and bioinformatic analyses. Seven of these toxins belong to three new α-KTx subfamilies (α-KTx28, α-KTx29, and α-KTx30, and two are new members of the known κ-KTx2 subfamily. ImKTx104 containing three disulfide bridges, the first member of the α-KTx28 subfamily, has a low sequence homology with other known KTxs, and its NMR structure suggests ImKTx104 adopts a modified cystine-stabilized α-helix-loop-β-sheet (CS-α/β fold motif that has no apparent α-helixs and β-sheets, but still stabilized by three disulfide bridges. These newly described acidic KTxs exhibit differential pharmacological effects on potassium channels. Acidic scorpion toxin ImKTx104 was the first peptide inhibitor found to affect KCNQ1 channel, which is insensitive to the basic KTxs and is strongly associated with human cardiac abnormalities. ImKTx104 selectively inhibited KCNQ1 channel with a K(d of 11.69 µM, but was less effective against the basic KTxs-sensitive potassium channels. In addition to the ImKTx104 toxin, HeTx204 peptide, containing a cystine-stabilized α-helix-loop-helix (CS-α/α fold scaffold motif, blocked both Kv1.3 and KCNQ1 channels. StKTx23 toxin, with a cystine-stabilized α-helix-loop-β-sheet (CS-α/β fold motif, could inhibit Kv1.3 channel, but not the KCNQ1 channel. CONCLUSIONS/SIGNIFICANCE: These findings characterize the structural and functional diversity of acidic KTxs, and could accelerate the development and clinical use of acidic KTxs as pharmacological tools and

  7. Heterometallic europium disiloxanediolates: synthesis, structural diversity, and photoluminescence properties.

    Science.gov (United States)

    Rausch, Janek; Lorenz, Volker; Hrib, Cristian G; Frettlöh, Vanessa; Adlung, Matthias; Wickleder, Claudia; Hilfert, Liane; Jones, Peter G; Edelmann, Frank T

    2014-11-03

    This contribution presents a full account of a structurally diverse class of heterometallic europium disiloxanediolates. The synthetic protocol involves in situ metalation of (HO)SiPh2OSiPh2(OH) (1) with either (n)BuLi or KN(SiMe3)2 followed by treatment with EuCl3 in suitable solvents such as 1,2-dimethoxyethane (DME) or tetrahydrofuran (THF). Reaction of EuCl3 with 2 equiv of (LiO)SiPh2OSiPh2(OLi) in DME afforded the Eu(III) bis(disiloxanediolate) "ate" complex [{(Ph2SiO)2O}2{Li(DME)}3]EuCl2 (2), which upon attempted reduction with Zn gave the tris(disiloxanediolate) [{(Ph2SiO)2O}3{Li(DME)}3]Eu (3). Treatment of EuCl3 with (LiO)SiPh2OSiPh2(OLi) in a molar ratio of 1:2 yielded both the ate complex [{(Ph2SiO)2O}3Li{Li(THF)2}{Li(THF)}]EuCl·Li(THF)3 (4) and the LiCl-free europium(III) complex [{(Ph2SiO)2O}2{Li(THF)2}2]EuCl (5). Compound 5 was found to exhibit a brilliant red triboluminescence. When (KO)SiPh2OSiPh2(OK) was used as starting material in a 3:1 reaction with EuCl3, the Eu(III) tris(disiloxanediolate) [{(Ph2SiO)2O}3{K(DME)}3]Eu (6) was isolated. Attempted ligand transfer between 5 and (DAD(Dipp))2Ba(DME) (DAD(Dipp) = N,N'-bis(2,6-diisopropylphenyl)-1,4-diaza-1,3-butadiene) afforded the unique mixed-valent Eu(III)/Eu(II) disiloxanediolate cluster [(Ph2SiO)2O]6Eu(II)4Eu(III)2Li4O2Cl2 (7). All new complexes were structurally characterized by X-ray diffraction. Photoluminescence studies were carried out for complex 5 showing an excellent color quality, due to the strong (5)D0→(7)F2 transition, but a weak antenna effect.

  8. Genetic diversity and structure found in samples of Eritrean bread wheat

    DEFF Research Database (Denmark)

    Desta, Zeratsion Abera; Orabi, Jihad; Jahoor, Ahmed

    2014-01-01

    Genetic diversity and structure plays a key role in the selection of parents for crosses in plant breeding programmes. The aim of the present study was to analyse the genetic diversity and structure of Eritrean bread wheat accessions. We analysed 284 wheat accessions from Eritrea using 30 simple ...

  9. Diversity and structure of woody vegetation across areas with different soils in Gonarezhou National Park, Zimbabwe

    NARCIS (Netherlands)

    Gandiwa, E.; Zisadza-Gandiwa, P.; Goza, D.; Mashapa, C.; Muboko, N.

    2014-01-01

    Despite the importance of edaphic factors in influencing woody vegetation diversity and structure in savannas, there is still limited research on the topic across most savanna ecosystems. Here we investigate the differences and/or similarities of woody vegetation diversity and structure across areas

  10. Diversity and structure of woody vegetation across areas with different soils in Gonarezhou National Park, Zimbabwe

    NARCIS (Netherlands)

    Gandiwa, E.; Zisadza-Gandiwa, P.; Goza, D.; Mashapa, C.; Muboko, N.

    2014-01-01

    Despite the importance of edaphic factors in influencing woody vegetation diversity and structure in savannas, there is still limited research on the topic across most savanna ecosystems. Here we investigate the differences and/or similarities of woody vegetation diversity and structure across areas

  11. Corrigendum: Structural diversity of target-specific homopyrimidine peptide nucleic acid-dsDNA complexes

    DEFF Research Database (Denmark)

    Bentin, T.; Hansen, G.I.; Nielsen, P.E.

    2007-01-01

    This corrects the article "Structural diversity of target-specific homopyrimidine peptide nucleic acid-dsDNA complexes" in volume 34 on page 5790.......This corrects the article "Structural diversity of target-specific homopyrimidine peptide nucleic acid-dsDNA complexes" in volume 34 on page 5790....

  12. Gender Diversity in Top Management and Financial Performance. The Role of Organizational Structure

    DEFF Research Database (Denmark)

    Opstrup, Niels; Villadsen, Anders Ryom

    and financial performance of public organizations. Theory suggests that management diversity can be a positive asset for organizations. It may allow for the use of more diverse knowledge and human skill sets. In this paper it is suggested that organizations, however, may only be able to leverage...... these advantages if they have a supporting management structure. In a longitudinal study of top management teams in Danish municipalities, the study finds top management team gender diversity to be associated with higher financial performance but only in municipalities with a management structure that supports......Recent research has illustrated how demographic diversity influences the outcome of public sector organizations. Most studies focus on workforce diversity and little is known about how managerial diversity affects organizational outcome. This study focuses on top management team gender diversity...

  13. Huge Tongue Lipoma: A Case Report

    Directory of Open Access Journals (Sweden)

    Mohammad Ali Damghani

    2015-03-01

    Full Text Available Introduction: Lipomas are among the most common tumors of the human body. However, they are uncommon in the oral cavity and are observed as slow growing, painless, and asymptomatic yellowish submucosal masses. Surgical excision is the treatment of choice and recurrence is not expected.    Case Report: The case of a 30-year-old woman with a huge lipoma on the tip of her tongue since 3 years, is presented. She had difficulty with speech and mastication because the tongue tumor was filling the oral cavity. Clinical examination revealed a yellowish lesion, measuring 8 cm in maximum diameter, protruding from the lingual surface. The tumor was surgically excised with restoration of normal tongue function and histopathological examination of the tumor confirmed that it was a lipoma.   Conclusion:  Tongue lipoma is rarely seen and can be a cause of macroglossia. Surgical excision for lipoma is indicated for symptomatic relief and exclusion of associated malignancy.

  14. Galaxies Collide to Create Hot, Huge Galaxy

    Science.gov (United States)

    2009-01-01

    This image of a pair of colliding galaxies called NGC 6240 shows them in a rare, short-lived phase of their evolution just before they merge into a single, larger galaxy. The prolonged, violent collision has drastically altered the appearance of both galaxies and created huge amounts of heat turning NGC 6240 into an 'infrared luminous' active galaxy. A rich variety of active galaxies, with different shapes, luminosities and radiation profiles exist. These galaxies may be related astronomers have suspected that they may represent an evolutionary sequence. By catching different galaxies in different stages of merging, a story emerges as one type of active galaxy changes into another. NGC 6240 provides an important 'missing link' in this process. This image was created from combined data from the infrared array camera of NASA's Spitzer Space Telescope at 3.6 and 8.0 microns (red) and visible light from NASA's Hubble Space Telescope (green and blue).

  15. Structural diversity in bacterial ribosomes: mycobacterial 70S ribosome structure reveals novel features.

    Directory of Open Access Journals (Sweden)

    Manidip Shasmal

    Full Text Available Here we present analysis of a 3D cryo-EM map of the 70S ribosome from Mycobacterium smegmatis, a saprophytic cousin of the etiological agent of tuberculosis in humans, Mycobacterium tuberculosis. In comparison with the 3D structures of other prokaryotic ribosomes, the density map of the M. smegmatis 70S ribosome reveals unique structural features and their relative orientations in the ribosome. Dramatic changes in the periphery due to additional rRNA segments and extra domains of some of the peripheral ribosomal proteins like S3, S5, S16, L17, L25, are evident. One of the most notable features appears in the large subunit near L1 stalk as a long helical structure next to helix 54 of the 23S rRNA. The sharp upper end of this structure is located in the vicinity of the mRNA exit channel. Although the M. smegmatis 70S ribosome possesses conserved core structure of bacterial ribosome, the new structural features, unveiled in this study, demonstrates diversity in the 3D architecture of bacterial ribosomes. We postulate that the prominent helical structure related to the 23S rRNA actively participates in the mechanisms of translation in mycobacteria.

  16. Robot-assisted laparoscopic resection of a huge pelvic tumor: A case report.

    Science.gov (United States)

    Jia, Zhuomin; Lyu, Xiangjun; Xu, Yong; Leonardi, Rosario; Zhang, Xu

    2016-07-04

    The traditional open surgery, for the treatment of huge tumor in the narrow space of pelvic cavity and in close proximity to pelvic organs and neurovascular structures, is very difficult and challenging. We report a case of huge neurilemmoma operated using the robot-assisted laparoscopy. We used interventional pre-operation embolization to control blood supply of tumor because MRI showed the tumor had a sufficient blood supply.

  17. Genetic diversity and population structure of cucumber (Cucumis sativus L.)

    Science.gov (United States)

    Understanding genetic variation in germplasm collection is essential for the conservation and their efficient use in plant breeding. Cucumber is an important vegetable crop worldwide. Previous studies revealed a low genetic diversity in cucumber, but detailed insights into the crop’s genetic structu...

  18. Genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    fire7-

    2016-12-28

    Dec 28, 2016 ... markers to assess the genetic diversity within and between common bean landraces, classifying them based on ... since the 1980's from continuous introduction of new ... control genotypes for the Andean and Mesoamerican gene pools, ... http://biology.anu.edu.au/GenAlEx/) was used to calculate genetic.

  19. Genetic structure and diversity within and among six populations of ...

    African Journals Online (AJOL)

    Yomi

    2010-04-24

    Apr 24, 2010 ... positive correlation between molecular genetic variation and actual population size. ... Key words: Capparis decidua, Tandhab, Assos, Population size, RAPD markers, Genetic diversity. .... polymorphism in some population, and were monomorphic ... highly informative and produced 152 bands with an ...

  20. Genetic diversity and population structure of begomoviruses infecting sweet potato

    Science.gov (United States)

    Begomoviruses infecting sweet potatoes (Ipomoea batatas) exhibit high genetic diversity, and approximately eight species including Sweet potato leaf curl virus (SPLCV) have been described from different regions around the world. In this study, the complete genomic sequences of 17 geographically dist...

  1. HUBBLE SPIES HUGE CLUSTERS OF STARS FORMED

    Science.gov (United States)

    2002-01-01

    BY ANCIENT ENCOUNTER This stunningly beautiful image [right] taken with the NASA Hubble Space Telescope shows the heart of the prototypical starburst galaxy M82. The ongoing violent star formation due to an ancient encounter with its large galactic neighbor, M81, gives this galaxy its disturbed appearance. The smaller picture at upper left shows the entire galaxy. The image was taken in December 1994 by the Kitt Peak National Observatory's 0.9-meter telescope. Hubble's view is represented by the white outline in the center. In the Hubble image, taken by the Wide Field and Planetary Camera 2, the huge lanes of dust that crisscross M82's disk are another telltale sign of the flurry of star formation. Below the center and to the right, a strong galactic wind is spewing knotty filaments of hydrogen and nitrogen gas. More than 100 super star clusters -- very bright, compact groupings of about 100,000 stars -- are seen in this detailed Hubble picture as white dots sprinkled throughout M82's central region. The dark region just above the center of the picture is a huge dust cloud. A collaboration of European and American scientists used these clusters to date the ancient interaction between M82 and M81. About 600 million years ago, a region called 'M82 B' (the bright area just below and to the left of the central dust cloud) exploded with new stars. Scientists have discovered that this ancient starburst was triggered by the violent encounter with M81. M82 is a bright (eighth magnitude), nearby (12 million light-years from Earth) galaxy in the constellation Ursa Major (the Great Bear). The Hubble picture was taken Sept. 15, 1997. The natural-color composite was constructed from three Wide Field and Planetary Camera 2 exposures, which were combined in chromatic order: 4,250 seconds through a blue filter (428 nm); 2,800 seconds through a green filter (520 nm); and 2,200 seconds through a red (820 nm) filter. Credits for Hubble image: NASA, ESA, R. de Grijs (Institute of

  2. A huge glandular odontogenic cyst occurring at posterior mandible

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Gi Chung; Han, Won Jeong; Kim, Eun Kyung [Dankook University College of Medicine, Seoul (Korea, Republic of)

    2004-12-15

    The glandular odontogenic cyst is a rare lesion described in 1987. It generally occurs at anterior region of mandible in adults over the age of 40 and has a slight tendency to recur. Histopathologically, a cystic cavity lined by a nonkeratinized, stratified squamous, or cuboidal epithelium varying in thickness is found including a superficial layer with glandular or pseudoglandular structures. A 21-year-old male visited Dankook University Dental Hospital with a chief complaint of swelling of the left posterior mandible. Radiographically, a huge multilocular radiolucent lesion involving impacted 3rd molar at the posterior mandible was observed. Buccolingual cortical expansion with partial perforation of buccal cortical bone was also shown. Histopathologically, this lesion was lined by stratified squamous epithelium with glandular structures in areas of plaque-like thickening. The final diagnosis was made as a glandular odontogenic cyst.

  3. On diversity performance of two-element coupling element based antenna structure for mobile terminal

    DEFF Research Database (Denmark)

    Al-Hadi, Azremi Abdullah; Toivanen, Juha; Laitinen, Tommi

    2010-01-01

    fading. The main challenge of antenna diversity in practical application is the integration of multiple antennas on a small ground plane. Two-element antenna structure based on coupling element antenna concept for diversity application has been studied in previous work and it has shown to be feasible......In wireless communication systems, multipath interference has a significant impact on system design and performance. Fast fading is caused by the coherent summation of one or more echoes from many reflection points reaching the receive antenna. Antenna diversity can be used to mitigate multipath...... for low frequency diversity application with stable and low envelope correlation across wide frequency range. The studied structure has been tuned to be operating at 1600 MHz for measurement evaluation purpose. This paper presents an analysis of diversity performance of the structure in terms...

  4. Network structure and patterns of information diversity on Twitter

    CERN Document Server

    Shore, Jesse; Dellarocas, Chrysanthos

    2016-01-01

    Social media have great potential to support diverse information sharing, but there is widespread concern that platforms like Twitter do not result in communication between those who hold contradictory viewpoints. Because users can choose whom to follow, prior research suggests that social media users exist in 'echo chambers' or become polarized. We seek evidence of this in a complete cross section of hyperlinks posted on Twitter, using previously validated measures of the political slant of news sources to study information diversity. Contrary to prediction, we find that the average account posts links to more politically moderate news sources than the ones they receive in their own feed. However, members of a tiny network core do exhibit cross-sectional evidence of polarization and are responsible for the majority of tweets received overall due to their popularity and activity, which could explain the widespread perception of polarization on social media.

  5. Factor Structure and Short Form of the Miville-Guzman Universality-Diversity Scale.

    Science.gov (United States)

    Fuertes, Jairo N.; Miville, Marie L.; Mohr, Jonathan J.; Sedlacek, William E.; Gretchen, Denise

    2000-01-01

    Examines the factor structure of the Miville-Guzman Universality-Diversity Scale (M-GUDS) and presents a short form of the scale (M-GUDS-S). Findings suggest that the M-GUDS-S measures Universal-Diverse Orientation as a multidimensional construct with three distinct domains: behavioral, emotional, and cognitive. (Contains 21 references and 3…

  6. Forest structure in low diversity tropical forests: a study of Hawaiian wet and dry forests

    Science.gov (United States)

    R. Ostertag; F. Inman-Narahari; S. Cordell; C.P. Giardina; L. Sack

    2014-01-01

    The potential influence of diversity on ecosystem structure and function remains a topic of significant debate, especially for tropical forests where diversity can range widely. We used Center for Tropical Forest Science (CTFS) methodology to establish forest dynamics plots in montane wet forest and lowland dry forest on Hawai‘i Island. We compared the species...

  7. Development of a leafy Brassica rapa fixed line collection for genetic diversity and population structure analysis

    NARCIS (Netherlands)

    Pang, W.; Li, X.; Choi, S.R.; Dhandapani, V.; Im, S.; Park, M.Y.; Jang, C.S.; Yang, M.S.; Ham, I.K.; Lee, E.M.; Kim, W.; Lee, S.S.; Bonnema, A.B.; Park, S.; Piao, Z.; Lim, Y.P.

    2015-01-01

    Brassica rapa is an economically important crop with a wide range of morphologies. Developing a set of fixed lines and understanding their diversity has been challenging, but facilitates resource conservation. We investigated the genetic diversity and population structure of 238 fixed lines of leafy

  8. tree structural and species diversities in okwangwo forest, cross river ...

    African Journals Online (AJOL)

    Tersor

    For sound forest management decisions, appraisal of flora species and forest structure is crucial for any meaningful conservation work. We assessed tree species distribution in Okwangwo Forest, Nigeria. ...... Structures and Yield Models.

  9. Structural Diversity of Eukaryotic Membrane Cytochrome P450s*

    OpenAIRE

    Johnson, Eric F.; Stout, C. David

    2013-01-01

    X-ray crystal structures are available for 29 eukaryotic microsomal, chloroplast, or mitochondrial cytochrome P450s, including two non-monooxygenase P450s. These structures provide a basis for understanding structure-function relations that underlie their distinct catalytic activities. Moreover, structural plasticity has been characterized for individual P450s that aids in understanding substrate binding in P450s that mediate drug clearance.

  10. Umbilicoplasty in children with huge umbilical hernia

    Directory of Open Access Journals (Sweden)

    Akakpo-Numado Gamedzi Komlatsè

    2014-01-01

    Full Text Available Background: Huge umbilical hernias (HUH are voluminous umbilical hernia (UH that are frequent in black African children. Several surgical techniques are used in their treatment for umbilical reconstruction, but techniques using skin flaps provide better aesthetic results. In this study, we presented our technique of umbilicoplasty in HUH, and its results. Patients and Methods: It is a retrospective study on children treated for HUH, from January 2012 to December 2013. The UH was called HUH when its basis diameter (BD exceeds 3 cm. Every HUH was characterised by its height, BD and morphology. Our technique was a two lateral flaps technique; the flaps are symmetrical and drawn so as to reconstitute the different parts of the umbilicus. The results were appreciated with criteria, including the peripheral ring and the central depression of the neo-umbilicus. Results : Twelve children were concerned (7 boys and 5 girls. Their mean age was 5 years and 6 months. The mean BD was 5.6 cm (extremes 3 and 8 cm, and the mean height of the HUH was 7.45 cm (extremes 3 and 9 cm. All underwent umbilicoplasty. In early post-operative period, two children presented a transitory subcutaneous hematoma. Late complications were granulation tissue with two children, and cheloid scar with one. With a mean follow-up of 10 months, we had 10 excellent results and two fair results according to our criteria. Conclusion: Our two lateral flaps umbilicoplasty is well-adapted to HUH in children. It is simple and assures a satisfactory anatomical and cosmetic result.

  11. Hepatectomy for huge hepatocellular carcinoma: single institute's experience.

    Science.gov (United States)

    Yang, Lianyue; Xu, Jiangfeng; Ou, Dipeng; Wu, Wei; Zeng, Zhijun

    2013-09-01

    The surgical resection of huge hepatocellular carcinoma (HCC) is still controversial. This study was designed to introduce our experience of liver resection for huge HCC and evaluate the safety and outcomes of hepatectomy for huge HCC. A total of 258 hepatic resections for the patients with huge HCC were analysed retrospectively from December 2002 to December 2011. The operative outcomes were compared with 293 patients with HCC >5.0 cm but huge HCC group and HCC >5.0 cm but huge HCC group has significantly a more longer overall and disease-free survival time than nodular huge HCC (P = 0.026, P = 0.022). Univariate and multivariate analysis revealed that the types of tumour, vascular invasion, and UICC stage were independent prognostic factors for overall survival (P = 0.047, P = 0.037, P = 0.033). Hepatic resection can be performed safely for huge HCC with a low mortality and favorable survival outcomes. Solitary huge HCC has the better surgical outcomes than nodular huge HCC.

  12. Tree diversity, composition, forest structure and aboveground biomass dynamics after single and repeated fire in a Bornean rain forest.

    Science.gov (United States)

    Slik, J W Ferry; Bernard, Caroline S; Van Beek, Marloes; Breman, Floris C; Eichhorn, Karl A O

    2008-12-01

    Forest fires remain a devastating phenomenon in the tropics that not only affect forest structure and biodiversity, but also contribute significantly to atmospheric CO2. Fire used to be extremely rare in tropical forests, leaving ample time for forests to regenerate to pre-fire conditions. In recent decades, however, tropical forest fires occur more frequently and at larger spatial scales than they used to. We studied forest structure, tree species diversity, tree species composition, and aboveground biomass during the first 7 years since fire in unburned, once burned and twice burned forest of eastern Borneo to determine the rate of recovery of these forests. We paid special attention to changes in the tree species composition during burned forest regeneration because we expect the long-term recovery of aboveground biomass and ecosystem functions in burned forests to largely depend on the successful regeneration of the pre-fire, heavy-wood, species composition. We found that forest structure (canopy openness, leaf area index, herb cover, and stem density) is strongly affected by fire but shows quick recovery. However, species composition shows no or limited recovery and aboveground biomass, which is greatly reduced by fire, continues to be low or decline up to 7 years after fire. Consequently, large amounts of the C released to the atmosphere by fire will not be recaptured by the burned forest ecosystem in the near future. We also observed that repeated fire, with an inter-fire interval of 15 years, does not necessarily lead to a huge deterioration in the regeneration potential of tropical forest. We conclude that burned forests are valuable and should be conserved and that long-term monitoring programs in secondary forests are necessary to determine their recovery rates, especially in relation to aboveground biomass accumulation.

  13. Genetic diversity of microsatellite loci in hierarchically structured populations.

    Science.gov (United States)

    Song, Seongho; Dey, Dipak K; Holsinger, Kent E

    2011-08-01

    Microsatellite loci are widely used for investigating patterns of genetic variation within and among populations. Those patterns are in turn determined by population sizes, migration rates, and mutation rates. We provide exact expressions for the first two moments of the allele frequency distribution in a stochastic model appropriate for studying microsatellite evolution with migration, mutation, and drift under the assumption that the range of allele sizes is bounded. Using these results, we study the behavior of several measures related to Wright's F(ST), including Slatkin's R(ST). Our analytical approximations for F(ST) and R(ST) show that familiar relationships between N(e)m and F(ST) or R(ST) hold when the migration and mutation rates are small. Using the exact expressions for F(ST) and R(ST), our numerical results show that, when the migration and mutation rates are large, these relationships no longer hold. Our numerical results also show that the diversity measures most closely related to F(ST) depend on mutation rates, mutational models (stepwise versus two-phase), migration rates, and population sizes. Surprisingly, R(ST) is relatively insensitive to the mutation rates and mutational models. The differing behaviors of R(ST) and F(ST) suggest that properties of the among-population distribution of allele frequencies may allow the roles of mutation and migration in producing patterns of diversity to be distinguished, a topic of continuing investigation.

  14. Structural and Chemical Diversity of Tl-Based Cuprate Superconductors

    Institute of Scientific and Technical Information of China (English)

    信赢

    2003-01-01

    The Tl-based cuprate superconductor family is the largest family in crystal structure and chemical composition among all high Tc cuprate superconductors. The Tl family can be divided into two sub-families, the Tl single layer family and the Tl double layer family, based on their crystal structural characteristics. The Tl single layer family is an ideal material for investigating the evolution of crystalline formation, charge carrier density, chemical composition, transport properties, superconductivity and their relationships. The Tl family contains almostall possible crystal structures discovered in high-Tc cuprate superconductors. Tl cuprate superconductors are of great importance not only in studying high-temperature superconductivity but also in commercial applications.

  15. plant diversity, vegetation structure and relationship between plant ...

    African Journals Online (AJOL)

    Preferred Customer

    analyses of five Afromontane forests altogether revealed 118 families and 653 vascular plant species; ... structure in the moist evergreen Afromontane forest ..... gradient of complex environmental factors. The .... other tropical montane forests.

  16. Stability of soil microbial structure and activity depends on microbial diversity.

    Science.gov (United States)

    Tardy, Vincent; Mathieu, Olivier; Lévêque, Jean; Terrat, Sébastien; Chabbi, Abad; Lemanceau, Philippe; Ranjard, Lionel; Maron, Pierre-Alain

    2014-04-01

    Despite the central role of microbes in soil processes, empirical evidence concerning the effect of their diversity on soil stability remains controversial. Here, we addressed the ecological insurance hypothesis by examining the stability of microbial communities along a gradient of soil microbial diversity in response to mercury pollution and heat stress. Diversity was manipulated by dilution extinction approach. Structural and functional stabilities of microbial communities were assessed from patterns of genetic structure and soil respiration after the stress. Dilution led to the establishment of a consistent diversity gradient, as revealed by 454 sequencing of ribosomal genes. Diversity stability was enhanced in species-rich communities whatever the stress whereas functional stability was improved with increasing diversity after heat stress, but not after mercury pollution. This discrepancy implies that the relevance of ecological insurance for soil microbial communities might depend on the type of stress. Our results also suggest that the significance of microbial diversity for soil functional stability might increase with available soil resources. This could have strong repercussions in the current 'global changes' context because it suggests that the combined increased frequencies of extreme climatic events, nutrient loading and biotic exploitation may amplify the functional consequences of diversity decrease.

  17. Structural Differences Explain Diverse Functions of Plasmodium Actins

    Science.gov (United States)

    Vahokoski, Juha; Martinez, Silvia Muñico; Ignatev, Alexander; Lepper, Simone; Frischknecht, Friedrich; Sidén-Kiamos, Inga; Sachse, Carsten; Kursula, Inari

    2014-01-01

    Actins are highly conserved proteins and key players in central processes in all eukaryotic cells. The two actins of the malaria parasite are among the most divergent eukaryotic actins and also differ from each other more than isoforms in any other species. Microfilaments have not been directly observed in Plasmodium and are presumed to be short and highly dynamic. We show that actin I cannot complement actin II in male gametogenesis, suggesting critical structural differences. Cryo-EM reveals that Plasmodium actin I has a unique filament structure, whereas actin II filaments resemble canonical F-actin. Both Plasmodium actins hydrolyze ATP more efficiently than α-actin, and unlike any other actin, both parasite actins rapidly form short oligomers induced by ADP. Crystal structures of both isoforms pinpoint several structural changes in the monomers causing the unique polymerization properties. Inserting the canonical D-loop to Plasmodium actin I leads to the formation of long filaments in vitro. In vivo, this chimera restores gametogenesis in parasites lacking actin II, suggesting that stable filaments are required for exflagellation. Together, these data underline the divergence of eukaryotic actins and demonstrate how structural differences in the monomers translate into filaments with different properties, implying that even eukaryotic actins have faced different evolutionary pressures and followed different paths for developing their polymerization properties. PMID:24743229

  18. γ-Protocadherin structural diversity and functional implications

    Science.gov (United States)

    Goodman, Kerry Marie; Rubinstein, Rotem; Thu, Chan Aye; Mannepalli, Seetha; Bahna, Fabiana; Ahlsén, Göran; Rittenhouse, Chelsea; Maniatis, Tom; Honig, Barry; Shapiro, Lawrence

    2016-01-01

    Stochastic cell-surface expression of α-, β-, and γ-clustered protocadherins (Pcdhs) provides vertebrate neurons with single-cell identities that underlie neuronal self-recognition. Here we report crystal structures of ectodomain fragments comprising cell-cell recognition regions of mouse γ-Pcdhs γA1, γA8, γB2, and γB7 revealing trans-homodimers, and of C-terminal ectodomain fragments from γ-Pcdhs γA4 and γB2, which depict cis-interacting regions in monomeric form. Together these structures span the entire γ-Pcdh ectodomain. The trans-dimer structures reveal determinants of γ-Pcdh isoform-specific homophilic recognition. We identified and structurally mapped cis-dimerization mutations to the C-terminal ectodomain structures. Biophysical studies showed that Pcdh ectodomains from γB-subfamily isoforms formed cis dimers, whereas γA isoforms did not, but both γA and γB isoforms could interact in cis with α-Pcdhs. Together, these data show how interaction specificity is distributed over all domains of the γ-Pcdh trans interface, and suggest that subfamily- or isoform-specific cis-interactions may play a role in the Pcdh-mediated neuronal self-recognition code. DOI: http://dx.doi.org/10.7554/eLife.20930.001 PMID:27782885

  19. γ-Protocadherin structural diversity and functional implications

    Energy Technology Data Exchange (ETDEWEB)

    Goodman, Kerry Marie; Rubinstein, Rotem; Thu, Chan Aye; Mannepalli, Seetha; Bahna, Fabiana; Ahlsén, Göran; Rittenhouse, Chelsea; Maniatis, Tom; Honig, Barry; Shapiro, Lawrence

    2016-10-26

    Stochastic cell-surface expression of α-, β-, and γ-clustered protocadherins (Pcdhs) provides vertebrate neurons with single-cell identities that underlie neuronal self-recognition. Here we report crystal structures of ectodomain fragments comprising cell-cell recognition regions of mouse γ-Pcdhs γA1, γA8, γB2, and γB7 revealingtrans-homodimers, and of C-terminal ectodomain fragments from γ-Pcdhs γA4 and γB2, which depictcis-interacting regions in monomeric form. Together these structures span the entire γ-Pcdh ectodomain. Thetrans-dimer structures reveal determinants of γ-Pcdh isoform-specific homophilic recognition. We identified and structurally mappedcis-dimerization mutations to the C-terminal ectodomain structures. Biophysical studies showed that Pcdh ectodomains from γB-subfamily isoforms formedcisdimers, whereas γA isoforms did not, but both γA and γB isoforms could interact inciswith α-Pcdhs. Together, these data show how interaction specificity is distributed over all domains of the γ-Pcdhtransinterface, and suggest that subfamily- or isoform-specificcis-interactions may play a role in the Pcdh-mediated neuronal self-recognition code.

  20. Diverse Family Structures and the Care of Older Persons.

    Science.gov (United States)

    Roberto, Karen A; Blieszner, Rosemary

    2015-09-01

    Demographic and social trends lead to a variety of micro-level and internal structural contexts that influence caregiving in families with older members. The results of macro-level changes have received little focused attention in the aging literature, where much of the caregiving research has addressed issues within the context of traditional family structure. Yet the conventional nuclear family model is increasingly uncommon as new, pluralistic models of family life are emerging in contemporary society. The majority of elder care is provided by relatives, albeit with varying patterns of involvement and responsibility across family structures. Both conventional and pluralistic families face challenges in meeting the care needs of their oldest members, leaving some older adults at risk of having unmet needs. Additional research on family risk and resilience related to the care of older relatives is warranted, particularly with respect to pluralistic models of family life.

  1. Interpenetration in coordination polymers: structural diversities toward porous functional materials

    Directory of Open Access Journals (Sweden)

    Ritesh Haldar

    2015-03-01

    Full Text Available Interpenetration is a natural phenomenon frequently encountered in porous coordination polymers (PCPs or metal-organic frameworks (MOFs. Traditionally interpenetration has been considered as a threat to permanent porosity and several strategies have been adopted to control the framework interpenetration. Recent literature reports have unveiled that interpenetration has paramount importance in several material properties particularly in storage and separation of small gas molecules. Such frameworks also show interesting structural flexibility based on shearing or movement of the nets and also reveals guest induced dynamic structural transformation for modulated specific functions. In this review, we will emphasize several interpenetration phenomena observed in coordination polymers, their intriguing structural aspects and fascinating material properties.

  2. Structural Diversity and Biochemical and Microbiological Characteristics of Aflatoxins

    Directory of Open Access Journals (Sweden)

    Ketney Otto

    2014-12-01

    Full Text Available Among all mycotoxins, Aflatoxin B1 (AFB1 is considered to be the most carcinogenic, and it has been classified by the International Agency for Research on Cancer in Group 1 of human carcinogen. It signifies a high hazard because it contaminates a diversity of agricultural products such as nuts and derivatives, peanuts/hazelnuts, grains, seeds, cottonseed, milk, dairy food. In milk AFB1 is metabolized to aflatoxin M (AFM1 which is 4-hydroxy derivative of AFB1, it is formed in the liver and excreted in the milk into the mammary glands of both human and lactating animals which have been fed with AFB1 contaminated diet. After the food contamination, one part of the aflatoxin B1 which was present in the food is eliminated through the milk. At the molecular level aflatoxin biosynthesis involves several levels of transcriptional and post-transcriptional control, so the main stages subsequent biochemical and genetic constituents of aflatoxin biosynthesis have been demonstrated recently. Recent studies over the last few decades have shown that the metabolism of AFB is an essential component of hepatocarcinogenic, however it was shown that AFB1 is metabolized by cytochrome P450 oxidised to intermediates and other metabolites Therefore, the biotransformation process may also lead to the formation of carcinogenic metabolites.

  3. Quaternary structure of V1 and F1 ATPase: significance of structural homologies and diversities.

    Science.gov (United States)

    Svergun, D I; Konrad, S; Huss, M; Koch, M H; Wieczorek, H; Altendorf, K; Volkov, V V; Grüber, G

    1998-12-22

    The V1 ATPase from the tobacco hornworm Manduca sexta and the Escherichia coli F1 ATPase were characterized by small-angle X-ray scattering (SAXS). The radii of gyration (Rg) of the complexes were 6.2 +/- 0.1 and 4.7 +/- 0.02 nm, respectively. The shape of the M. sexta V1 ATPase was determined ab initio from the scattering data showing six masses, presumed to be the A and B subunits, arranged in an alternating manner about a 3-fold axis. A seventh mass with a length of about 11.0 nm extends perpendicularly to the center of the hexameric unit. This central mass is presumed to be the stalk that connects V1 with the membrane domain (V(O)) in the intact V1V(O)-ATPase. In comparison, the shape of the F1 ATPase from E. coli possesses a quasi-3-fold symmetry over the major part of the enzyme. The overall asymmetry of the structure is given by a stem, assumed to include the central stalk subunits. The features of the V1 and F1 ATPase reveal structural homologies and diversities of the key components of the complexes.

  4. Genetic structure and diversity of Oryza sativa L.in Guizhou, China

    Institute of Scientific and Technical Information of China (English)

    ZHANG DongLing; CAO YongSheng; WANG XiangKun; LI ZiChao; ZHANG HongLiang; WEI XingHua; QI YongWen; WANG MeiXing; SUN JunLi; DING Li; TANG ShengXiang; QIU Zong'En

    2007-01-01

    Preserving many kinds of rice resources and rich variations, Guizhou Province is one of the districts with the highest genetic diversity of cultivated rice (Oryza sativa L.) in China. In the current research, genetic diversity and structure of 537 accessions of cultivated rice from Guizhou were studied using 36 microsatellite markers and 39 phenotypic characters. The results showed that the model-based genetic structure was the same as genetic-distance-based one using SSRs but somewhat different from the documented classification (mainly based on phenotype) of two subspecies. The accessions being classified into indica by phenotype but japonica by genetic structure were much more than that being classified into japonica by phenotype but indica by genetic structure. Like Ding Ying's taxonomic system of cultivated rice, the subspecific differentiation was the most distinct differentiation within cultivated rice. But the differentiation within indica or japonica population was different: japonica presented clearer differentiation between soil-watery ecotypes than indica, and indica presented clearer differentiation between seasonal ecotypes than japonica. Cultivated rices in Guizhou revealed high genetic diversity at both DNA and phenotypic levels. Possessing the highest genetic diversity and all the necessary conditions as a center of genetic diversity, region Southwestern of Guizhou was suggested as the center of genetic diversity of O. sativa L. from Guizhou.

  5. Evolving Structural Diversity and Metallicity in Compressed Lithium Azide

    KAUST Repository

    Prasad, Dasari L. V. K.

    2013-10-10

    In pursuit of new stable nitrogen-rich phases and of a possible insulator-metal transition, the ground-state electronic structure of lithium azide, LiN3, is investigated from 1 atm to 300 GPa (∼2-fold compression) using evolutionary crystal structure exploration methods coupled with density functional theoretical calculations. Two new LiN3 phases, containing slightly reduced and well-separated N2 units, are found to be enthalpically competitive with the known lithium azide crystal structure at 1 atm. At pressures above 36 GPa nitrogen-rich assemblies begin to evolve. These incorporate NN bond formation beyond that in N2 or N3 -. N6 rings and infinite one-dimensional linear nitrogen chains (structural analogues to polyacetylene) appear. Above 200 GPa quasi-one- and two-dimensional extended puckered hexagonal and decagonal nitrogen layers emerge. The high-pressure phase featuring linear chains may be quenchable to P = 1 atm. With increasing pressure the progression in electrical conductivity is from insulator to metal. © 2013 American Chemical Society.

  6. Population structure and genetic diversity of Sudanese native chickens

    African Journals Online (AJOL)

    User

    2013-11-06

    Nov 6, 2013 ... origin of breeding populations, molecular marker informa-. *Corresponding .... on the phenotypic characteristics of each local breed (Desai, 1962). ..... Development of a genetic map of the chicken with markers of ... variation and population structure of Italian native sheep breeds ... evolutionary studies. Mol.

  7. Genetic diversity and population structure of cucumber (Cucumis sativus L.)

    NARCIS (Netherlands)

    Lv, J.; Qi, J.; Shi, Q.; Shen, D.; Zhang, S.; Shao, G.; Li, H.; Sun, Z.; Weng, Y.; Shang, Y.; Gu, X.; Li, X.; Zhu, X.; Zhang, J.; Treuren, van R.; Dooijeweert, van W.; Zhang, Z.; Huang, S.

    2012-01-01

    Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also incl

  8. Sclerotic rings in mosasaurs (Squamata: Mosasauridae: structures and taxonomic diversity.

    Directory of Open Access Journals (Sweden)

    Momo Yamashita

    Full Text Available Mosasaurs (Squamata: Mosasauridae were a highly diverse, globally distributed group of aquatic lizards in the Late Cretaceous (98-66 million years ago that exhibited a high degree of adaptation to life in water. To date, despite their rich fossil record, the anatomy of complete mosasaur sclerotic rings, embedded in the sclera of the eyeball, has not been thoroughly investigated. We here describe and compare sclerotic rings of four mosasaur genera, Tylosaurus, Platecarpus, Clidastes, and Mosasaurus, for the first time. Two specimens of Tylosaurus and Platecarpus share an exact scleral ossicle arrangement, excepting the missing portion in the specimen of Platecarpus. Furthermore, the exact arrangement and the total count of 14 ossicles per ring are shared between Tylosaurus and numerous living terrestrial lizard taxa, pertaining to both Iguania and Scleroglossa. In contrast, two species of Mosasaurus share the identical count of 12 ossicles and the arrangement with each other, while no living lizard taxa share exactly the same arrangement. Such a mosaic distribution of these traits both among squamates globally and among obligatorily aquatic mosasaurs specifically suggests that neither the ossicle count nor their arrangement played major roles in the aquatic adaptation in mosasaur eyes. All the mosasaur sclerotic rings examined consistently exhibit aperture eccentricity and the scleral ossicles with gently convex outer side. Hitherto unknown to any squamate taxa, one specimen of Platecarpus unexpectedly shows a raised, concentric band of roughened surface on the inner surface of the sclerotic ring. It is possible that one or both of these latter features may have related to adaptation towards aquatic vision in mosasaurs, but further quantitative study of extant reptilian clades containing both terrestrial and aquatic taxa is critical and necessary in order to understand possible adaptive significances of such osteological features.

  9. Sclerotic Rings in Mosasaurs (Squamata: Mosasauridae): Structures and Taxonomic Diversity

    Science.gov (United States)

    Yamashita, Momo; Konishi, Takuya; Sato, Tamaki

    2015-01-01

    Mosasaurs (Squamata: Mosasauridae) were a highly diverse, globally distributed group of aquatic lizards in the Late Cretaceous (98–66 million years ago) that exhibited a high degree of adaptation to life in water. To date, despite their rich fossil record, the anatomy of complete mosasaur sclerotic rings, embedded in the sclera of the eyeball, has not been thoroughly investigated. We here describe and compare sclerotic rings of four mosasaur genera, Tylosaurus, Platecarpus, Clidastes, and Mosasaurus, for the first time. Two specimens of Tylosaurus and Platecarpus share an exact scleral ossicle arrangement, excepting the missing portion in the specimen of Platecarpus. Furthermore, the exact arrangement and the total count of 14 ossicles per ring are shared between Tylosaurus and numerous living terrestrial lizard taxa, pertaining to both Iguania and Scleroglossa. In contrast, two species of Mosasaurus share the identical count of 12 ossicles and the arrangement with each other, while no living lizard taxa share exactly the same arrangement. Such a mosaic distribution of these traits both among squamates globally and among obligatorily aquatic mosasaurs specifically suggests that neither the ossicle count nor their arrangement played major roles in the aquatic adaptation in mosasaur eyes. All the mosasaur sclerotic rings examined consistently exhibit aperture eccentricity and the scleral ossicles with gently convex outer side. Hitherto unknown to any squamate taxa, one specimen of Platecarpus unexpectedly shows a raised, concentric band of roughened surface on the inner surface of the sclerotic ring. It is possible that one or both of these latter features may have related to adaptation towards aquatic vision in mosasaurs, but further quantitative study of extant reptilian clades containing both terrestrial and aquatic taxa is critical and necessary in order to understand possible adaptive significances of such osteological features. PMID:25692667

  10. "Presumed fair: Ironic effects of organizational diversity structures": Correction to Kaiser et al. (2013).

    Science.gov (United States)

    2016-06-01

    Reports an error in "Presumed fair: Ironic effects of organizational diversity structures" by Cheryl R. Kaiser, Brenda Major, Ines Jurcevic, Tessa L. Dover, Laura M. Brady and Jenessa R. Shapiro (Journal of Personality and Social Psychology, 2013[Mar], Vol 104[3], 504-519). In the article, a raw data merging error in one racial discrimination claim condition from Experiment 6 inadvertently resulted in data analyses on an inaccurate data set. When the error was discovered by the authors and corrected, all analyses reported in Experiment 6 for claim validity, seriousness of the claim, and support for the claimant were inaccurate and none were statistically significant. The conclusions should be altered to indicate that participants with management experience who reflected on their own workplace diversity policies did not show the predicted effects. The literature review, remaining five studies, and remaining conclusions in the article are unaffected by this error. Experiment 6 should also report that 26.4% (not 26.4.7%) of participants had a graduate degree and eight participants (not 8%) did not provide educational data. Experiment 5 should have referred to the claim validity measure as a six-item measure ( .92) rather than a five-item measure; analyses on claim validity are accurate in text. Table 2's note should have said standard errors, not standard deviations. (The following abstract of the original article appeared in record 2012-31077-001.) This research tests the hypothesis that the presence (vs. absence) of organizational diversity structures causes high-status group members (Whites, men) to perceive organizations with diversity structures as procedurally fairer environments for underrepresented groups (racial minorities, women), even when it is clear that underrepresented groups have been unfairly disadvantaged within these organizations. Furthermore, this illusory sense of fairness derived from the mere presence of diversity structures causes high

  11. Structural diversity and biological importance of ABO, H, Lewis and secretor histo-blood group carbohydrates.

    Science.gov (United States)

    de Mattos, Luiz Carlos

    ABO, H, secretor and Lewis histo-blood system genes control the expression of part of the carbohydrate repertoire present in areas of the body occupied by microorganisms. These carbohydrates, besides having great structural diversity, act as potential receptors for pathogenic and non-pathogenic microorganisms influencing susceptibility and resistance to infection and illness. Despite the knowledge of some structural variability of these carbohydrate antigens and their polymorphic levels of expression in tissue and exocrine secretions, little is known about their biological importance and potential applications in medicine. This review highlights the structural diversity, the biological importance and potential applications of ABO, H, Lewis and secretor histo-blood carbohydrates.

  12. Structural diversity in serine derived homochiral metal organic frameworks

    Indian Academy of Sciences (India)

    Tanay Kundu; Rahul Banerjee

    2014-09-01

    Two new Zn(II) and Cd(II) based homochiral metal-organic frameworks (MOFs) [SerCdOAc and Zn(Ser)2] have been synthesized using pyridyl functionalized amino acid, viz., serine, as an organic linker. The SerCdOAc structure is three dimensional, while that of the Zn(Ser)2 is two dimensional. The polar voids of the corresponding MOFs are filled with solvent molecules (water in the case of SerCdOAc and methanol in the case of Zn(Ser)2). In both cases, metal centres, i.e., Zn(II) and Cd(II), are hexacoordinated. However, with a change in the solvent for synthesis, ligand coordinationmode and incorporation of additional coordinated anion resulted in a great change in the final MOF architecture. Herein, for the first time, we could achieve structural variety and synthesize MOFs composed of only metal ion and pyridyl functionalized amino acid linker.

  13. Multifunctional Benzoxazines Feature Low Polymerization Temperature and Diverse Polymer Structures

    Directory of Open Access Journals (Sweden)

    Marc Soto

    2016-08-01

    Full Text Available 3,4-dihydro-3-phenyl-2H-1,3-benzoxazines derived from phenol-, resorcinol-, and phloroglucinol give monomers with one, two, and three oxazine units at a single benzene ring, respectively. Aside from the synthesis and characterization of such multifunctional benzoxazines, reactivity and polymerization behavior is studied in dependence of the oxazine functionality. Monomer reactivities are directly related to the number of oxazine functionalities present at the benzene ring yielding the lowest polymerization temperature for the trifunctional phloroglucinol-based benzoxazine. Comparing the polymerization processes and resulting structures, the trifunctional benzoxazine derivative enter new polymerization pathways, which include methylene linkages bridging aniline units, as well as the formation of carbonyl-derived structures.

  14. Structural diversity of alkaline-earth 2,5-thiophenedicarboxylates

    Science.gov (United States)

    Balendra; Ramanan, Arunachalam

    2017-03-01

    Exploration of the structural landscape of the system containing divalent alkaline-earth metal ion (Mg, Ca and Sr) with the rigid 2,5-thiophenedicarboxylic acid (TDC) under varying solvothermal condition (DMF, DMA and DEF) yielded five new crystals: [Mg(TDC) (DEF)2(H2O)1/2] (1), [Ca(TDC) (DMA)] (2), [Ca(TDC) (DMA) (H2O)] (3), [Sr(TDC) (DMA)] (4) and [Sr(TDC) (DMA) (H2O)] (5) and two known solids. Single crystal structures of all the solids are characteristic of extended coordination interaction between metal and carboxylate ions. While the smaller magnesium ion crystallized into a 2D coordination polymer, the larger calcium and strontium compounds resulted into the growth of 3D metal organic frameworks. All the solids show blue emission arising from intra ligand charge transfer.

  15. Accessing the structural diversity of pyridone alkaloids: concise total synthesis of rac-citridone A.

    Science.gov (United States)

    Fotiadou, Anna D; Zografos, Alexandros L

    2011-09-01

    A unique route to the structural diversity of pyridone alkaloids is described based on the concept of a common synthetic strategy. Three different core structure analogues corresponding to akanthomycin, septoriamycin A, and citridone A have been prepared by using a highly selective and novel carbocyclization reaction.

  16. Petroleum-influenced beach sediments of the campeche bank, Mexico: Diversity and bacterial community structure assessment

    Energy Technology Data Exchange (ETDEWEB)

    Rosano-Hernandez, M. C.; Ramirez-Saad, H.; Fernandez-Linares, L.; Xoconostle, B.

    2009-07-01

    In Mexican, either spilled or seeped out petroleum impacts nearly 300 km of the beach between Dos Bocas (Tabasco State) to Champoton town (Campeche State), where between 9 to exceptionally 9 to exceptionally 300 tonnes of oil as tar balls have been measured. This study was focused to explore, for the first time, the bacterial diversity and community structure ({alpha}-diversity)- in a kilometric scale on petroleum influenced sediments of 100 km of sandy beach. (Author)

  17. Structural diversity of biologically interesting datasets: a scaffold analysis approach

    Directory of Open Access Journals (Sweden)

    Khanna Varun

    2011-08-01

    Full Text Available Abstract Background The recent public availability of the human metabolome and natural product datasets has revitalized "metabolite-likeness" and "natural product-likeness" as a drug design concept to design lead libraries targeting specific pathways. Many reports have analyzed the physicochemical property space of biologically important datasets, with only a few comprehensively characterizing the scaffold diversity in public datasets of biological interest. With large collections of high quality public data currently available, we carried out a comparative analysis of current day leads with other biologically relevant datasets. Results In this study, we note a two-fold enrichment of metabolite scaffolds in drug dataset (42% as compared to currently used lead libraries (23%. We also note that only a small percentage (5% of natural product scaffolds space is shared by the lead dataset. We have identified specific scaffolds that are present in metabolites and natural products, with close counterparts in the drugs, but are missing in the lead dataset. To determine the distribution of compounds in physicochemical property space we analyzed the molecular polar surface area, the molecular solubility, the number of rings and the number of rotatable bonds in addition to four well-known Lipinski properties. Here, we note that, with only few exceptions, most of the drugs follow Lipinski's rule. The average values of the molecular polar surface area and the molecular solubility in metabolites is the highest while the number of rings is the lowest. In addition, we note that natural products contain the maximum number of rings and the rotatable bonds than any other dataset under consideration. Conclusions Currently used lead libraries make little use of the metabolites and natural products scaffold space. We believe that metabolites and natural products are recognized by at least one protein in the biosphere therefore, sampling the fragment and scaffold

  18. Corynebacterium diphtheriae: genome diversity, population structure and genotyping perspectives.

    Science.gov (United States)

    Mokrousov, Igor

    2009-01-01

    The epidemic re-emergence of diphtheria in Russia and the Newly Independent States (NIS) of the former Soviet Union in the 1990s demonstrated the continued threat of this thought to be rare disease. The bacteriophage encoded toxin is a main virulence factor of Corynebacterium diphtheriae, however, an analysis of the first complete genome sequence of C. diphtheriae revealed a recent acquisition of other pathogenicity factors including iron-uptake systems, adhesins and fimbrial proteins as indeed this extracellular pathogen has more possibilities for lateral gene transfer than, e.g., its close relative, mainly intracellular Mycobacterium tuberculosis. C. diphtheriae appears to have a phylogeographical structure mainly represented by area-specific variants whose circulation is under strong influence of human host factors, including health control measures, first of all, vaccination, and social economic conditions. This framework core population structure may be challenged by importation of the endemic and eventually toxigenic strains from new areas thus leading to localized or large epidemics caused directly by imported strains or by bacteriophage-lysogenized indigenous strains converted into toxin production. A feature of C. diphtheriae co-existence with humans is its periodicity: following large epidemic in the 1990s, the present period is marked by increasing heterogeneity of the circulating populations whereas re-emergence of new toxigenic variants along with persistent circulation of invasive non-toxigenic strains appear alarming. To identify and rapidly monitor subtle changes in the genome structure at an infraclonal level during and between epidemics, portable and discriminatory typing methods of C. diphtheriae are still needed. In this view, CRISPRs and minisatellites are promising genomic markers for development of high-resolution typing schemes and databasing of C. diphtheriae.

  19. Diversity and Phylogenetic Structure of Two Complex Marine Microbial Communities

    Science.gov (United States)

    2004-09-01

    Du, Y., et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron...C.A., Newell, S.Y., and Paerl, H.W. (1995) The role References of standing dead Spartina alternfflora and benthic microal- gae in salt marsh food webs ...q Ja 1,4 1 S., fn.i.to) 47. 145-1 156 (19r . lntiutoide Geologia’ Mineria , Universidad Nactonalde Jujuy, Avenida Bolwiva . V~a. C 3. j kLmnnnaommntal

  20. Structural and functional diversity of native brain neuronal nicotinic receptors.

    Science.gov (United States)

    Gotti, Cecilia; Clementi, Francesco; Fornari, Alice; Gaimarri, Annalisa; Guiducci, Stefania; Manfredi, Irene; Moretti, Milena; Pedrazzi, Patrizia; Pucci, Luca; Zoli, Michele

    2009-10-01

    Neuronal nicotinic acetylcholine receptors (nAChRs) are a family of ligand-gated ion channels present in the central and peripheral nervous systems, that are permeable to mono- and divalent cations. They share a common basic structure but their pharmacological and functional properties arise from the wide range of different subunit combinations making up distinctive subtypes. nAChRs are involved in many physiological functions in the central and peripheral nervous systems, and are the targets of the widely used drug of abuse nicotine. In addition to tobacco dependence, changes in their number and/or function are associated with neuropsychiatric disorders, ranging from epilepsy to dementia. Although some of the neural circuits involved in the acute and chronic effects of nicotine have been identified, much less is known about which native nAChR subtypes are involved in specific physiological functions and pathophysiological conditions. We briefly review some recent findings concerning the structure and function of native nAChRs, focusing on the subtypes identified in the mesostriatal and habenulo-interpeduncular pathways, two systems involved in nicotine reinforcement and withdrawal. We also discuss recent findings concerning the effect of chronic nicotine on the expression of native subtypes.

  1. Amidinate Ligands in Zinc coordination sphere: Synthesis and structural diversity

    Indian Academy of Sciences (India)

    SRINIVAS ANGA; INDRANI BANERJEE; TARUN K PANDA

    2016-06-01

    A one-pot reaction involving neosilyllithium and three different carbodiimides (RN=C=NR, R =cyclohexyl, isopropyl and tert-butyl) in diethyl ether, followed by the addition of anhydrous $ZnCl_{2}$, afforded,in high yield, corresponding homoleptic zinc amidinate complexes having the molecular formulae$[Zn{CyN=C(CH_{2}SiMe_{3})NCy}_{2}]$ (1),$[Zn^{{i}PrN=C(CH_{2}SiMe_{3})N^{i}Pr}_{2}]$ (2) and [Zn$^{{t}BuN=C(CH_{2}SiMe_{3})N^{t}Bu}_{2}]$ (3), respectively, and amidinato moieties in the zinc coordination sphere. Solid state structures of complexes1-3 are reported thereafter - all the three complexes are isostructural, and each of them consists of twofour-membered metallacycles.

  2. Structural evolution and diversity of the caterpillar trunk

    DEFF Research Database (Denmark)

    Dupont, Steen Thorleif

    identify possible ground plan characteristics of the Lepidoptera and Amphiesmenoptera (MS1), 2) to describe and understand the evolution of the neolepidopteran caterpillar, and in particularly its crochet-bearing prolegs that are closely linked to walking on silken substrates and an external arboreal......The thesis explores some major transformation series in the structure of the lepidopteran larval trunk, focusing partly on the initial events in the evolution of the order, partly on one of the more spectacular cases of subsequent biological diversification within ‘typical’/’higher’ Lepidoptera...... cuticle thickness, the degree of myrmecopily and the underlying mechanism of lycaenid-ant associations (MS4). In two major manuscripts (MS1-2), comparative descriptions are provided of the larval trunk in, respectively the Micropterigidae and the lowest-grade leaf-mining caterpillars. Available knowledge...

  3. Structural Diversity and Function of Xyloglucan Sidechain Substituents

    Directory of Open Access Journals (Sweden)

    Alex Schultink

    2014-11-01

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

  4. Initial genetic diversity enhances population establishment and alters genetic structuring of a newly established Daphnia metapopulation.

    Science.gov (United States)

    Holmes, Christopher J; Pantel, Jelena H; Schulz, Kimberly L; Cáceres, Carla E

    2016-07-01

    When newly created habitats are initially colonized by genotypes with rapid population growth rates, later arriving colonists may be prevented from establishing. Although these priority effects have been documented in multiple systems, their duration may be influenced by the diversity of the founding population. We conducted a large-scale field manipulation to investigate how initial clonal diversity influences temporal and landscape patterns of genetic structure in a developing metapopulation. Six genotypes of obligately asexual Daphnia pulex were stocked alone (no clonal diversity) or in combination ('high' clonal diversity) into newly created experimental woodland ponds. We also measured the population growth rate of all clones in the laboratory when raised on higher-quality and lower-quality resources. Our predictions were that in the 3 years following stocking, clonally diverse populations would be more likely to persist than nonclonally diverse populations and exhibit evidence for persistent founder effects. We expected that faster growing clones would be found in more pools and comprise a greater proportion of individuals genotyped from the landscape. Genetic composition, both locally and regionally, changed significantly following stocking. Six of 27 populations exhibited evidence for persistent founder effects, and populations stocked with 'high' clonal diversity were more likely to exhibit these effects than nonclonally diverse populations. Performance in the laboratory was not predictive of clonal persistence or overall dominance in the field. Hence, we conclude that although laboratory estimates of fitness did not fully explain metapopulation genetic structure, initial clonal diversity did enhance D. pulex population establishment and persistence in this system.

  5. Experimental warming effects on the bacterial community structure and diversity

    Science.gov (United States)

    Kim, W.; Han, S.; Adams, J.; Son, Y.

    2014-12-01

    The objective of this study is to investigate the responses of soil bacterial community to future temperature increase by conducting open-field warming experiment. We conducted an open-field experimental warming system using infra-red heater in 2011 and regulated the temperature of warmed plots by 3oC higher than that of control plots constantly. The seeds of Pinus densiflora, Abies holophylla, Abies koreana, Betula costata, Quercus variabilis, Fraxinus rhynchophylla, and Zelkova serrata were planted in each 1 m × 1 m plot (n=3) in April, 2012. We collected soil samples from the rhizosphere of 7 tree species. DNA was extracted and PCR-amplified for the bacterial 16S gene targeting V1-V3 region. The paired-end sequencing was performed at Beijing Genome Institute (BGI, Hong Kong, China) using 2× 100 bp Hiseq2000 (Illumina). This study aimed to answer the following prediction/hypothesis: 1) Experimental warming will change the structure of soil bacterial community, 2) There will be distinct 'indicator group' which response to warming treatment relatively more sensitive than other groups. 3) Warming treatment will enhance the microbial activity in terms of soil respiration. 4) The rhizoplane bacterial communities for each of 7 tree species will show different response pattern to warming treatment. Since the sequence data does not arrive before the submission deadline, therefore, we would like to present the results and discussions on December 2014, AGU Fall Meeting.

  6. Genetic diversity and population structure of Clavibacter michiganensis subsp. nebraskensis.

    Science.gov (United States)

    Agarkova, I V; Lambrecht, P A; Vidaver, A K

    2011-05-01

    Clavibacter michiganensis subsp. nebraskensis (CMN) is a gram-positive bacterium and an incitant of Goss's bacterial wilt and leaf blight or "leaf freckles" in corn. A population structure of a wide temporal and geographic collection of CMN strains (n = 131), originating between 1969 and 2009, was determined using amplified fragment length polymorphism (AFLP) analysis and repetitive DNA sequence-based BOX-PCR. Analysis of the composite data set of AFLP and BOX-PCR fingerprints revealed two groups with a 60% cutoff similarity: a major group A (n = 118 strains) and a minor group B (n = 13 strains). The clustering in both groups was not correlated with strain pathogenicity. Group A contained two clusters, A1 (n = 78) and A2 (n = 40), with a linkage of 75%. Group A strains did not show any correlation with historical, geographical, morphological, or physiological properties of the strains. Group B was very heterogeneous and eight out of nine clusters were represented by a single strain. The mean similarity between clusters in group B varied from 13% to 63%. All strains in group B were isolated after 1999. The percentage of group B strains among all strains isolated after 1999 (n = 69) was 18.8%. Implications of the findings are discussed.

  7. Structural and functional diversity of ferredoxin-NADP(+) reductases.

    Science.gov (United States)

    Aliverti, Alessandro; Pandini, Vittorio; Pennati, Andrea; de Rosa, Matteo; Zanetti, Giuliana

    2008-06-15

    Although all ferredoxin-NADP(+) reductases (FNRs) catalyze the same reaction, i.e. the transfer of reducing equivalents between NADP(H) and ferredoxin, they belong to two unrelated families of proteins: the plant-type and the glutathione reductase-type of FNRs. Aim of this review is to provide a general classification scheme for these enzymes, to be used as a framework for the comparison of their properties. Furthermore, we report on some recent findings, which significantly increased the understanding of the structure-function relationships of FNRs, i.e. the ability of adrenodoxin reductase and its homologs to catalyze the oxidation of NADP(+) to its 4-oxo derivative, and the properties of plant-type FNRs from non-photosynthetic organisms. Plant-type FNRs from bacteria and Apicomplexan parasites provide examples of novel ways of FAD- and NADP(H)-binding. The recent characterization of an FNR from Plasmodium falciparum brings these enzymes into the field of drug design.

  8. Diverse Structural Evolution at z > 1 in Cosmologically Simulated Galaxies

    CERN Document Server

    Snyder, Gregory F; Moody, Christopher; Peth, Michael; Freeman, Peter; Ceverino, Daniel; Primack, Joel; Dekel, Avishai

    2014-01-01

    From mock Hubble Space Telescope images, we quantify non-parametric statistics of galaxy morphology, thereby predicting the emergence of relationships among stellar mass, star formation, and observed rest-frame optical structure at 1 10^10 M_sun contain relatively more disc-dominated light profiles than those with lower mass, reflecting significant disc brightening in some haloes at 1 10^10 M_sun. We analyze a cosmological major merger at z~1.5 and find that the newly proposed MID morphology diagnostics trace later stages while G-M20 trace earlier ones. MID is sensitive also to clumpy star-forming discs. The observability time of typical MID-enhanced events in our simulation sample is less than 100 Myr. A larger sample of cosmological assembly histories may be required to calibrate such diagnostics in the face of their sensitivity to viewing angle, segmentation algorithm, and various phenomena such as clumpy star formation and minor mergers.

  9. Analysis of population structure and genetic diversity of Egyptian and exotic rice (Oryza sativa L.) genotypes.

    Science.gov (United States)

    Salem, Khaled F M; Sallam, Ahmed

    2016-01-01

    Understanding the population structure and genetic diversity is a very important goal to improve the economic value of crops. In rice, a loss of genetic diversity in the last few centuries is observed. To address this challenge, a set of 22 lines from three different regions - India (two), and Philippines (six), and Egypt (14) - were used to assess the genetic diversity and the features of population structure. These genotypes were analyzed using 106 SSR alleles that showed a clear polymorphism among the lines. Genetic diversity was estimated based on the number of different alleles, polymorphism information content (PIC), and gene diversity. A total of 106 SSR alleles was identified from the 23 SSR loci and used to study the population structure and carry out a cluster analysis. All SSR loci showed a wide range of the number of different alleles extended from two (one loci) to seven alleles (three loci). Five and eight loci showed high PIC and gene diversity (≥0.70), respectively. The results of population structure are in agreement with cluster analysis results. Both analyses revealed two different subpopulations (G1 and G2) with different genetic properties in number of private alleles, number of different alleles (Na), number of effective alleles (Ne), expected heterozygosity (He), and Shannon's Information Index (SII). Our findings indicate that five SSR loci (RM 111, RM 307, RM 22, RM 19, and RM 271) could be used in breeding programs to enhance the marker-assisted selection through QTL mapping and association studies. A high genetic diversity found between genotypes which can be exploited to improve and produce rice cultivars for important traits (e.g. high agronomic features and tolerance to biotic or/and abiotic stresses).

  10. Scale-dependence of processes structuring dung beetle metacommunities using functional diversity and community deconstruction approaches.

    Science.gov (United States)

    Silva, Pedro Giovâni da; Hernández, Malva Isabel Medina

    2015-01-01

    Community structure is driven by mechanisms linked to environmental, spatial and temporal processes, which have been successfully addressed using metacommunity framework. The relative importance of processes shaping community structure can be identified using several different approaches. Two approaches that are increasingly being used are functional diversity and community deconstruction. Functional diversity is measured using various indices that incorporate distinct community attributes. Community deconstruction is a way to disentangle species responses to ecological processes by grouping species with similar traits. We used these two approaches to determine whether they are improvements over traditional measures (e.g., species composition, abundance, biomass) for identification of the main processes driving dung beetle (Scarabaeinae) community structure in a fragmented mainland-island landscape in southern Brazilian Atlantic Forest. We sampled five sites in each of four large forest areas, two on the mainland and two on the island. Sampling was performed in 2012 and 2013. We collected abundance and biomass data from 100 sampling points distributed over 20 sampling sites. We studied environmental, spatial and temporal effects on dung beetle community across three spatial scales, i.e., between sites, between areas and mainland-island. The γ-diversity based on species abundance was mainly attributed to β-diversity as a consequence of the increase in mean α- and β-diversity between areas. Variation partitioning on abundance, biomass and functional diversity showed scale-dependence of processes structuring dung beetle metacommunities. We identified two major groups of responses among 17 functional groups. In general, environmental filters were important at both local and regional scales. Spatial factors were important at the intermediate scale. Our study supports the notion of scale-dependence of environmental, spatial and temporal processes in the distribution

  11. Radical aryl migration enables diversity-oriented synthesis of structurally diverse medium/macro- or bridged-rings

    Science.gov (United States)

    Li, Lei; Li, Zhong-Liang; Wang, Fu-Li; Guo, Zhen; Cheng, Yong-Feng; Wang, Na; Dong, Xiao-Wu; Fang, Chao; Liu, Jingjiang; Hou, Chunhui; Tan, Bin; Liu, Xin-Yuan

    2016-12-01

    Medium-sized and medium-bridged rings are attractive structural motifs in natural products and therapeutic agents. Due to the unfavourable entropic and/or enthalpic factors with these ring systems, their efficient construction remains a formidable challenge. To address this problem, we herein disclose a radical-based approach for diversity-oriented synthesis of various benzannulated carbon- and heteroatom-containing 8-11(14)-membered ketone libraries. This strategy involves 1,4- or 1,5-aryl migration triggered by radical azidation, trifluoromethylation, phosphonylation, sulfonylation, or perfluoroalkylation of unactivated alkenes followed by intramolecular ring expansion. Demonstration of this method as a highly flexible tool for the construction of 37 synthetically challenging medium-sized and macrocyclic ring scaffolds including bridged rings with diverse functionalities and skeletons is highlighted. Some of these products showed potent inhibitory activity against the cancer cell or derivative of human embryonic kidney line in preliminary biological studies. The mechanism of this novel strategy is investigated by control experiments and DFT calculations.

  12. Newtonian self-gravitating system in a relativistic huge void universe model

    Science.gov (United States)

    Nishikawa, Ryusuke; Nakao, Ken-ichi; Yoo, Chul-Moon

    2016-12-01

    We consider a test of the Copernican Principle through observations of the large-scale structures, and for this purpose we study the self-gravitating system in a relativistic huge void universe model which does not invoke the Copernican Principle. If we focus on the the weakly self-gravitating and slowly evolving system whose spatial extent is much smaller than the scale of the cosmological horizon in the homogeneous and isotropic background universe model, the cosmological Newtonian approximation is available. Also in the huge void universe model, the same kind of approximation as the cosmological Newtonian approximation is available for the analysis of the perturbations contained in a region whose spatial size is much smaller than the scale of the huge void: the effects of the huge void are taken into account in a perturbative manner by using the Fermi-normal coordinates. By using this approximation, we derive the equations of motion for the weakly self-gravitating perturbations whose elements have relative velocities much smaller than the speed of light, and show the derived equations can be significantly different from those in the homogeneous and isotropic universe model, due to the anisotropic volume expansion in the huge void. We linearize the derived equations of motion and solve them. The solutions show that the behaviors of linear density perturbations are very different from those in the homogeneous and isotropic universe model.

  13. Genetic diversity and population structure of endangered Aquilaria malaccensis revealed potential for future conservation.

    Science.gov (United States)

    Singh, Pradeep; Nag, Akshay; Parmar, Rajni; Ghosh, Sneha; Bhau, Brijmohan Singh; Sharma, Ram Kumar

    2015-12-01

    The endangered Aquilaria malaccensis,is an important plant with high economic values. Characterization of genetic diversity and population structure is receiving tremendous attention for effective conservation of genetic resources. Considering important repositories of biological diversity, the genetic relationships of 127 A. malaccensis accessions from 10 home gardens of three states of northeast India were assessed using amplified fragment length polymorphism (AFLP). Of the 1153 fragments amplified with four AFLP primer combinations, 916 (79.4%) were found to be polymorphic. Polymorphic information content (PIC) and marker index (MI) of each primer combination correlate significantly with the number of genotypes resolved. Overall, a high genetic diversity (avg. 71.85%) was recorded. Further, high gene flow (Nm: 3.37), low genetic differentiation (FST: 0.069) and high within population genetic variation (93%) suggests that most of the genetic diversity is restricted within population. Neighbour joining (NJ), principal coordinate analysis (PCoA) and Bayesian-based STRUCTURE grouped all the accessions in two clusters with significant intermixing between populations, therefore, revealed that two genetically distinct gene pools are operating in the A. malaccensis populations cultivated in home gardens. Based on the various diversity inferences, five diverse populations (JOH, FN, HLF, DHM and ITN) were identified, which can be potentially exploited to develop conservation strategies for A. malaccensis.

  14. Genetic diversity and population structure of endangered Aquilaria malaccensis revealed potential for future conservation

    Indian Academy of Sciences (India)

    Pradeep Singh; Akshay Nag; Rajni Parmar; Sneha Ghosh; Brijmohan Singh Bhau; Ram Kumar Sharma

    2015-12-01

    The endangered Aquilaria malaccensis, is an important plant with high economic values. Characterization of genetic diversity and population structure is receiving tremendous attention for effective conservation of genetic resources. Considering important repositories of biological diversity, the genetic relationships of 127 A. malaccensis accessions from 10 home gardens of three states of northeast India were assessed using amplified fragment length polymorphism (AFLP). Of the 1153 fragments amplified with four AFLP primer combinations, 916 (79.4%) were found to be polymorphic. Polymorphic information content (PIC) and marker index (MI) of each primer combination correlate significantly with the number of genotypes resolved. Overall, a high genetic diversity (avg. 71.85%) was recorded. Further, high gene flow (m : 3.37), low genetic differentiation (ST : 0.069) and high within population genetic variation (93%) suggests that most of the genetic diversity is restricted within population. Neighbour joining (NJ), principal coordinate analysis (PCoA) and Bayesian-based STRUCTURE grouped all the accessions in two clusters with significant intermixing between populations, therefore, revealed that two genetically distinct gene pools are operating in the A. malaccensis populations cultivated in home gardens. Based on the various diversity inferences, five diverse populations (JOH, FN, HLF, DHM and ITN) were identified, which can be potentially exploited to develop conservation strategies for A. malaccensis.

  15. The relative importance of host-plant genetic diversity in structuring the associated herbivore community.

    Science.gov (United States)

    Tack, Ayco J M; Roslin, Tomas

    2011-08-01

    Recent studies suggest that intraspecific genetic diversity in one species may leave a substantial imprint on the surrounding community and ecosystem. Here, we test the hypothesis that genetic diversity within host-plant patches translates into consistent and ecologically important changes in the associated herbivore community. More specifically, we use potted, grafted oak saplings to construct 41 patches of four saplings each, with one, two, or four tree genotypes represented among the host plants. These patches were divided among two common gardens. Focusing first at the level of individual trees, we assess how tree-specific genotypic identity, patch-level genetic diversity, garden-level environmental variation, and their interactions affect the structure of the herbivore community. At the level of host-plant patches, we analyze whether the joint responses of herbivore species to environmental variation and genetic diversity result in differences in species diversity among tree quartets. Strikingly, both species-specific abundances and species diversity varied substantially among host-tree genotypes, among common gardens, and among specific locations within individual gardens. In contrast, the genetic diversity of the patch left a detectable imprint on local abundances of only two herbivore taxa. In both cases, the effect of genetic diversity was inconsistent among gardens and among host-plant genotypes. While the insect community differed significantly among individual host-plant genotypes, there were no interactive effects of the number of different genotypes within the patch. Overall, additive effects of intraspecific genetic diversity of the host plant explained a similar or lower proportion (7-10%) of variation in herbivore species diversity than did variation among common gardens. Combined with the few previous studies published to date, our study suggests that the impact of host-plant genetic diversity on the herbivore community can range from none to

  16. Huge Pericardial Cyst Misleading Symptoms of COPD

    Directory of Open Access Journals (Sweden)

    Göktürk Fındık

    2012-04-01

    Full Text Available Pericardial cysts are rare benign congenital mediastinal lesions. It accounts 30% of all mediastinal cysts. They are usually asemptomatic. They can produce the compression of the mediastinal structures typically caused the symptoms of dyspnea, thoracic pain, tachicardia and cough due to the unusual large size of the cyst. It can performed symptoms of lung atelectasia. The case was a sixty-five years old woman followed with a diagnosis of COPD for seven years. The patient was admitted to our center with the diagnosis of elevation of the right hemidiaphragm on chest radiography. The computed tomography revealed a cystic lesion adjacent to the right hemidiaphragm and cyst excision was performed via right thoracotomy. Patient%u2019s postoperative clinical findings indicated that the symptoms of COPD regressed completely and the patient did not require any further bronchodilator therapy. The aim of this case report is to demonstrate that the pericardial cysts can be missed in chest radiographs and impression of cysts may cause COPD like symptoms in these patients.

  17. Huge Coronal Structure and Heating Constraints Determined from Serts Observations

    Science.gov (United States)

    Falconer, D. A.; Davila, J. M.

    2001-01-01

    Intensities of the extreme-ultraviolet (EUV) spectral lines were measured as a function of radius off the solar limb by two flights of the Goddard's Solar Extreme-Ultraviolet Rocket Telescope and Spectrograph (SERTS) for three quiet-Sun regions. Density scale heights were determined for the different spectral lines. Limits on the filling factor were determined. In the one case where an upper limit was determined it was much less than unity. coronal heating above 1.15 solar radii is required for all three regions studied. For reasonable filling factors, local heating is needed.

  18. Forest structure and plant diversity in maritime pine (Pinus pinaster Ait.) stands in central Spain

    Energy Technology Data Exchange (ETDEWEB)

    Osorio, L. F.; Bravo, F.; Zaldivar, P.; Pando, V.

    2009-07-01

    The relationship between forest structure and plant diversity in Mediterranean Maritime pine stands (Pinus pinaster Ait.) in the Iberian Range (Spain) was studied. Forty eight stands were sampled. In each, a circular plot (15 m radius) and a transect (25*1 m{sup 2}) were established to estimate stand variables and record presence and abundance of vascular species respectively. Canonical correlation analysis (CCA), simple correlations and multiple stepwise linear regressions were used to explore the relationship between plant diversity and forest structure. Correlation between diversity measurements and stand variables is very weak, but significant correlations were found when evaluating each set of variables separately. Presence and cover of some species (for instance, Veronica arvensis L. or Micropyrum tenellum (L.) Link) is correlated with stand variables; however, determination coefficients found in step-by-step regression are not significant. (Author) 34 refs.

  19. Does the habitat structure control the distribution and diversity of the Odonatofauna?

    Directory of Open Access Journals (Sweden)

    AM Souza

    Full Text Available AbstractThe statement that the habitat complexity and structure govern the abundance and diversity of biological communities has been widely investigated. In this context, we assumed the hypothesis of habitat heterogeneity, that is, the higher habitat complexity leads to greater diversity of Odonata. In addition, we analyzed the influence of habitat structure on the distribution of this community, and evaluated the effects of abiotic variables. Odonata larvae were collected with sieves and by electrofishing in ten neotropical streams belonging to the Pirapó River basin. Forty species of Odonata were registered, which were distributed in eight families, Libellulidae stood out with the highest richness. The high gamma diversity and distribution of Odonata were associated with habitat heterogeneity in these streams. However, the abiotic variables also seem to affect the distribution of Odonata species, in view of the impact of the land use in the vicinity of streams.

  20. Considering Future Potential Regarding Structural Diversity in Selection of Forest Reserves.

    Science.gov (United States)

    Lundström, Johanna; Öhman, Karin; Rönnqvist, Mikael; Gustafsson, Lena

    2016-01-01

    A rich structural diversity in forests promotes biodiversity. Forests are dynamic and therefore it is crucial to consider future structural potential when selecting reserves, to make robust conservation decisions. We analyzed forests in boreal Sweden based on 17,599 National Forest Inventory (NFI) plots with the main aim to understand how effectiveness of reserves depends on the time dimension in the selection process, specifically by considering future structural diversity. In the study both the economic value and future values of 15 structural variables were simulated during a 100 year period. To get a net present structural value (NPSV), a single value covering both current and future values, we used four discounting alternatives: (1) only considering present values, (2) giving equal importance to values in each of the 100 years within the planning horizon, (3) applying an annual discount rate considering the risk that values could be lost, and (4) only considering the values in year 100. The four alternatives were evaluated in a reserve selection model under budget-constrained and area-constrained selections. When selecting young forests higher structural richness could be reached at a quarter of the cost over almost twice the area in a budget-constrained selection compared to an area-constrained selection. Our results point to the importance of considering future structural diversity in the selection of forest reserves and not as is done currently to base the selection on existing values. Targeting future values increases structural diversity and implies a relatively lower cost. Further, our results show that a re-orientation from old to young forests would imply savings while offering a more extensive reserve network with high structural qualities in the future. However, caution must be raised against a drastic reorientation of the current old-forest strategy since remnants of ancient forests will need to be prioritized due to their role for disturbance

  1. Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm.

    Science.gov (United States)

    Lee, Hea-Young; Ro, Na-Young; Jeong, Hee-Jin; Kwon, Jin-Kyung; Jo, Jinkwan; Ha, Yeaseong; Jung, Ayoung; Han, Ji-Woong; Venkatesh, Jelli; Kang, Byoung-Cheorl

    2016-11-14

    Conservation of genetic diversity is an essential prerequisite for developing new cultivars with desirable agronomic traits. Although a large number of germplasm collections have been established worldwide, many of them face major difficulties due to large size and a lack of adequate information about population structure and genetic diversity. Core collection with a minimum number of accessions and maximum genetic diversity of pepper species and its wild relatives will facilitate easy access to genetic material as well as the use of hidden genetic diversity in Capsicum. To explore genetic diversity and population structure, we investigated patterns of molecular diversity using a transcriptome-based 48 single nucleotide polymorphisms (SNPs) in a large germplasm collection comprising 3,821 accessions. Among the 11 species examined, Capsicum annuum showed the highest genetic diversity (HE = 0.44, I = 0.69), whereas the wild species C. galapagoense showed the lowest genetic diversity (HE = 0.06, I = 0.07). The Capsicum germplasm collection was divided into 10 clusters (cluster 1 to 10) based on population structure analysis, and five groups (group A to E) based on phylogenetic analysis. Capsicum accessions from the five distinct groups in an unrooted phylogenetic tree showed taxonomic distinctness and reflected their geographic origins. Most of the accessions from European countries are distributed in the A and B groups, whereas the accessions from Asian countries are mainly distributed in C and D groups. Five different sampling strategies with diverse genetic clustering methods were used to select the optimal method for constructing the core collection. Using a number of allelic variations based on 48 SNP markers and 32 different phenotypic/morphological traits, a core collection 'CC240' with a total of 240 accessions (5.2 %) was selected from within the entire Capsicum germplasm. Compared to the other core collections, CC240 displayed higher genetic

  2. Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems.

    Directory of Open Access Journals (Sweden)

    Sascha van der Meer

    Full Text Available Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68, which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G"ST = 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands.

  3. Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems.

    Science.gov (United States)

    van der Meer, Sascha; Jacquemyn, Hans

    2015-01-01

    Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68), which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G"ST = 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively) and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands.

  4. Scarless surgery for a huge liver cyst: A case report.

    Science.gov (United States)

    Kashiwagi, Hiroyuki; Kawachi, Jun; Isogai, Naoko; Ishii, Masanori; Miyake, Katsunori; Shimoyama, Rai; Fukai, Ryota; Ogino, Hidemitsu

    2017-09-01

    Symptomatic or complicated liver cysts sometimes require surgical intervention and laparoscopic fenestration is the definitive treatment for these cysts. We performed minimally invasive surgery, hybrid natural orifice transluminal endoscopic surgery (NOTES) without scarring, for a huge liver cyst. An 82-year-old female presented with a month-long history of right upper abdominal pain. We diagnosed her condition as a huge liver cyst by morphological studies. She denied any history of abdominal trauma. Her serum CEA and CA19-9 were normal and a serum echinococcus serologic test was negative. Laparoscopic fenestration, using a hybrid NOTES procedure via a transvaginal approach, was performed for a huge liver cyst because we anticipated difficulty with an umbilical approach, such as single incision laparoscopic surgery (SILS). Her post-operative course was uneventful and she was discharged from our hospital three days after surgery. Pain killers were not required during and after hospitalization. No recurrence of the liver cyst or bulging was detected by clinical examination two years later. A recent trend of laparoscopic procedure has been towards minimizing the number of incisions to achieve less invasiveness. This hybrid NOTES, with a small incision for abdominal access, along with vaginal access, enabled painless operation for a huge liver cyst. We report a huge liver cyst treated by hybrid NOTES. This approach is safe, less invasive, and may be the first choice for a huge liver cyst. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  5. Genetic diversity, population structure, and resistance to Phytophthora capsici of a worldwide collection of eggplant germplasm.

    Directory of Open Access Journals (Sweden)

    Rachel P Naegele

    Full Text Available Eggplant (Solanum melongena L. is an important solanaceous crop with high phenotypic diversity and moderate genotypic diversity. Ninety-nine genotypes of eggplant germplasm (species (S. melongena, S. incanum, S. linnaeanum and S. gilo, landraces and heirloom cultivars from 32 countries and five continents were evaluated for genetic diversity, population structure, fruit shape, and disease resistance to Phytophthora fruit rot. Fruits from each line were measured for fruit shape and evaluated for resistance to two Phytophthora capsici isolates seven days post inoculation. Only one accession (PI 413784 was completely resistant to both isolates evaluated. Partial resistance to Phytophthora fruit rot was found in accessions from all four eggplant species evaluated in this study. Genetic diversity and population structure were assessed using 22 polymorphic simple sequence repeats (SSRs. The polymorphism information content (PIC for the population was moderate (0.49 in the population. Genetic analyses using the program STRUCTURE indicated the existence of four genetic clusters within the eggplant collection. Population structure was detected when eggplant lines were grouped by species, continent of origin, country of origin, fruit shape and disease resistance.

  6. Genetic diversity and population structure of locally adapted South African chicken lines: Implications for conservation.

    NARCIS (Netherlands)

    Marle-Koster, van E.; Hefer, C.A.; Nel, L.H.; Groenen, M.A.M.

    2008-01-01

    In this study microsatellite markers were applied to investigate the genetic diversity and population structure of the six local chicken lines kept in the “Fowls for Africa” program, for better clarification of parameters for breed differentiation and genetic conservation of this valuable resource.

  7. Diversity and biogeochemical structuring of bacterial communities across the Porangahau ridge accretionary prism, New Zealand

    NARCIS (Netherlands)

    Hamdan, L.J.; Gillevet, P.M.; Pohlman, J.W.; Sikaroodi, M.; Greinart, J.; Coffin, R.B.

    2011-01-01

    Sediments from the Porangahau ridge, located off the northeastern coast of New Zealand, were studied to describe bacterial community structure in conjunction with differing biogeochemical regimes across the ridge. Low diversity was observed in sediments from an eroded basin seaward of the ridge and

  8. Interracial Friendship and Structural Diversity: Trends for Greek, Religious, and Ethnic Student Organizations

    Science.gov (United States)

    Park, Julie J.; Kim, Young K.

    2013-01-01

    This article examines how peer interactions in college organizations (Greek, ethnic, and religious) affect interracial friendships, including whether peer interaction in student organizations mediates the relationship between structural diversity and interracial friendship. Involvement in ethnic student organizations was non-significant;…

  9. Zooplankton standing stock, community structure and diversity in the northern Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Goswami, S.C.; Srivastava, Y.

    The effects of large scale oil spill, which occurred during the Gulf War in 1991 on zooplankton standing stock, community structure and diversity in the northern Arabian Sea were studied. Surface (1-0 m) and vertical zooplankton hauls (200-0 m, 250...

  10. Soil Effects on Forest Structure and Diversity in a Moist and a Dry Tropical Forest

    NARCIS (Netherlands)

    Peña-Claros, M.; Poorter, L.; Alarcon, A.; Blate, G.; Choque, U.; Fredericksen, T.S.; Justiniano, J.; Leaño, C.; Licona, J.C.; Pariona, W.; Putz, F.E.; Quevedo, L.; Toledo, M.

    2012-01-01

    Soil characteristics are important drivers of variation in wet tropical forest structure and diversity, but few studies have evaluated these relationships in drier forest types. Using tree and soil data from 48 and 32 1 ha plots, respectively, in a Bolivian moist and dry forest, we asked how soil co

  11. Diversity of condensed tannin structures affects rumen in vitro methane production in sainfoin (Onobrychis viciifolia) accessions

    NARCIS (Netherlands)

    Hatew, B.; Hayot Carbonero, C.; Stringano, E.; Sales, L.F.; Smith, L.M.J.; Mueller-Harvey, I.; Hendriks, W.H.; Pellikaan, W.F.

    2015-01-01

    Sainfoin is a non-bloating temperate forage legume with a moderate-to-high condensed tannin (CT) content. This study investigated whether the diversity of sainfoin accessions in terms of CT structures and contents could be related to rumen in vitro gas and methane (CH4) production and fermentation c

  12. Structure, diversity and evolution of protein toxins from spore-forming entomopathogenic bacteria

    NARCIS (Netherlands)

    Maagd, de R.A.; Bravo, A.; Berry, C.; Crickmore, N.; Schnepf, H.E.

    2003-01-01

    Gram-positive spore-forming entomopathogenic bacteria can utilize a large variety of protein toxins to help them invade, infect, and finally kill their hosts, through their action on the insect midgut. These toxins belong to a number of homology groups containing a diversity of protein structures an

  13. Genetic diversity and structure of a worldwide collection of Phaseolus coccineus L.

    Science.gov (United States)

    Spataro, G; Tiranti, B; Arcaleni, P; Bellucci, E; Attene, G; Papa, R; Spagnoletti Zeuli, P; Negri, V

    2011-05-01

    Phaseolus coccineus L. is closely related to P. vulgaris and is the third most important cultivated Phaseolus species. Little is known about the patterns of its diversity. In this work, a representative collection of its worldwide diversity was initially developed. The collection includes 28 wild forms (WFs) and 52 landraces (LRs) from Mesoamerica (the crop domestication area), and 148 LRs from Europe (where the crop was introduced in the sixteenth century). The collection was studied by using 12 SSR molecular markers that were developed for the P. vulgaris genome. They were proved to be effective and reliable in P. coccineus in this work. Fourteen LRs of P. dumosus (previously identified as a subspecies of P. coccineus) were also studied. The genetic diversity, population structure and phylogenetic relationships were investigated. The results indicate that: (a) the European and Mesoamerican gene pools are clearly differentiated, (b) a certain reduction of diversity occurred with introduction into Europe, and (c) the Mesoamerican LRs (P. dumosus included) and WFs are closely related and are connected by a high gene flow. Inferences on the domestication process of P. coccineus are also presented. This study provides a picture of the genetic diversity distribution and outcomes with introduction into the Old World, which was not available before. It also underlines that the genetic diversity of both WFs and LRs is an important source for Phaseolus spp. breeding programs and deserves to be preserved in situ and ex situ.

  14. Structural diversity and biological importance of ABO, H, Lewis and secretor histo-blood group carbohydrates

    OpenAIRE

    de Mattos, Luiz Carlos

    2016-01-01

    ABO, H, secretor and Lewis histo-blood system genes control the expression of part of the carbohydrate repertoire present in areas of the body occupied by microorganisms. These carbohydrates, besides having great structural diversity, act as potential receptors for pathogenic and non-pathogenic microorganisms influencing susceptibility and resistance to infection and illness. Despite the knowledge of some structural variability of these carbohydrate antigens and their polymorphic levels of ex...

  15. Structurally Diverse Polyamines: Solid-Phase Synthesis and Interaction with DNA.

    Science.gov (United States)

    Umezawa, Naoki; Horai, Yuhei; Imamura, Yuki; Kawakubo, Makoto; Nakahira, Mariko; Kato, Nobuki; Muramatsu, Akira; Yoshikawa, Yuko; Yoshikawa, Kenichi; Higuchi, Tsunehiko

    2015-08-17

    A versatile solid-phase approach based on peptide chemistry was used to construct four classes of structurally diverse polyamines with modified backbones: linear, partially constrained, branched, and cyclic. Their effects on DNA duplex stability and structure were examined. The polyamines showed distinct activities, thus highlighting the importance of polyamine backbone structure. Interestingly, the rank order of polyamine ability for DNA compaction was different to that for their effects on circular dichroism and melting temperature, thus indicating that these polyamines have distinct effects on secondary and higher-order structures of DNA.

  16. Population structure and genetic diversity of native and invasive populations of Solanum rostratum (Solanaceae.

    Directory of Open Access Journals (Sweden)

    Jiali Zhao

    Full Text Available AIMS: We investigate native and introduced populations of Solanum rostratum, an annual, self-compatible plant that has been introduced around the globe. This study is the first to compare the genetic diversity of Solanum rostratum between native and introduced populations. We aim to (1 determine the level of genetic diversity across the studied regions; (2 explore the likely origins of invasive populations in China; and (3 investigate whether there is the evidence of multiple introductions into China. METHODS: We genotyped 329 individuals at 10 microsatellite loci to determine the levels of genetic diversity and to investigate population structure of native and introduced populations of S. rostratum. We studied five populations in each of three regions across two continents: Mexico, the U.S.A. and China. IMPORTANT FINDINGS: We found the highest genetic diversity among Mexican populations of S. rostratum. Genetic diversity was significantly lower in Chinese and U.S.A. populations, but we found no regional difference in inbreeding coefficients (F IS or population differentiation (F ST. Population structure analyses indicate that Chinese and U.S.A. populations are more closely related to each other than to sampled Mexican populations, revealing that introduced populations in China share an origin with the sampled U.S.A. populations. The distinctiveness between some introduced populations indicates multiple introductions of S. rostratum into China.

  17. A Reassessment of the Impact of European Contact on the Structure of Native American Genetic Diversity.

    Science.gov (United States)

    Hunley, Keith; Gwin, Kiela; Liberman, Brendan

    2016-01-01

    Our current understanding of pre-Columbian history in the Americas rests in part on several trends identified in recent genetic studies. The goal of this study is to reexamine these trends in light of the impact of post-Columbian admixture and the methods used to study admixture. The previously-published data consist of 645 autosomal microsatellite genotypes from 1046 individuals in 63 populations. We used STRUCTURE to estimate ancestry proportions and tested the sensitivity of these estimates to the choice of the number of clusters, K. We used partial correlation analyses to examine the relationship between gene diversity and geographic distance from Beringia, controlling for non-Native American ancestry (from Africa, Europe and East Asia), and taking into account alternative paths of migration. Principal component analysis and multidimensional scaling were used to investigate the relationships between Andean and non-Andean populations and to explore gene-language correspondence. We found that 1) European and East Asian ancestry estimates decline as K increases, especially in Native Canadian populations, 2) a north-south decline in gene diversity is driven by low diversity in Amazonian and Paraguayan populations, not serial founder effects from Beringia, 3) controlling for non-Native American ancestry, populations in the Andes and Mesoamerica have higher gene diversity than populations in other regions, and 4) patterns of genetic and linguistic diversity are poorly correlated. We conclude that patterns of diversity previously attributed to pre-Columbian processes may in part reflect post-Columbian admixture and the choice of K in STRUCTURE analyses. Accounting for admixture, the pattern of diversity is inconsistent with a north-south founder effect process, though the genetic similarities between Mesoamerican and Andean populations are consistent with rapid dispersal along the western coast of the Americas. Further, even setting aside the disruptive effects of

  18. Genetic diversity and population structure of Plasmodium vivax isolates from Sudan, Madagascar, French Guiana and Armenia.

    Science.gov (United States)

    Menegon, Michela; Durand, Patrick; Menard, Didier; Legrand, Eric; Picot, Stéphane; Nour, Bakri; Davidyants, Vladimir; Santi, Flavia; Severini, Carlo

    2014-10-01

    Polymorphic genetic markers and especially microsatellite analysis can be used to investigate multiple aspects of the biology of Plasmodium species. In the current study, we characterized 7 polymorphic microsatellites in a total of 281 Plasmodium vivax isolates to determine the genetic diversity and population structure of P. vivax populations from Sudan, Madagascar, French Guiana, and Armenia. All four parasite populations were highly polymorphic with 3-32 alleles per locus. Mean genetic diversity values was 0.83, 0.79, 0.78 and 0.67 for Madagascar, French Guiana, Sudan, and Armenia, respectively. Significant genetic differentiation between all four populations was observed.

  19. Morphological diversity and evolution of egg and clutch structure in amphibians

    Science.gov (United States)

    Altig, Ronald; McDiarmid, Roy W.

    2007-01-01

    The first part of this synthesis summarizes the morphology of the jelly layers surrounding an amphibian ovum. We propose a standard terminology and discuss the evolution of jelly layers. The second part reviews the morphological diversity and arrangement of deposited eggs?the ovipositional mode; we recognize 5 morphological classes including 14 modes. We discuss some of the oviductal, ovipositional, and postovipositional events that contribute to these morphologies. We have incorporated data from taxa from throughout the world but recognize that other types will be discovered that may modify understanding of these modes. Finally, we discuss the evolutionary context of the diversity of clutch structure and present a first estimate of its evolution.

  20. Effects of timber harvest on structural diversity and species composition in hardwood forests

    Directory of Open Access Journals (Sweden)

    FARZAM TAVANKAR

    2015-04-01

    Full Text Available Tavankar F, Bonyad AE. 2015. Effects of timber harvest on structural diversity and species composition in hardwood forests. Biodiversitas 16: 1-9. Forest management leads to changes in structure and species composition of stands. In this research vertical and horizontal structure and species composition were compared in two harvested and protected stands in the Caspian forest of Iran. The results indicated the tree and seedling density, total basal area and stand volume was significantly (P < 0.01 higher in the protected stand. The Fagus orientalis L. had the most density and basal area in the both stands. Species importance value (SIV of Fagus orientalis in the protected stand (92.5 was higher than in the harvested stand (88.5. While, the SIV of shade-intolerant tree species such as Acer insigne, Acer cappadocicum and Alnus subcordata was higher in the harvested stand. The density of trees and seedling of rare tree species, such as Ulmus glabra, Tilia begonifolia, Zelkova caprinifolia and Fraxinus coriarifolia, was also higher in the protected stand. The Shannon-Wiener diversity index in the protected stand (0.84 was significantly higher (P < 0.01 than in the harvested stand (0.72. The highest diversity value in the harvested stand was observed in DBH of 10-40 cm class, while DBH of 40-70 cm had the highest diversity value in the protected stand.

  1. SSR-based genetic diversity and structure of garlic accessions from Brazil.

    Science.gov (United States)

    da Cunha, Camila Pinto; Resende, Francisco Vilela; Zucchi, Maria Imaculada; Pinheiro, José Baldin

    2014-10-01

    Garlic is a spice and a medicinal plant; hence, there is an increasing interest in 'developing' new varieties with different culinary properties or with high content of nutraceutical compounds. Phenotypic traits and dominant molecular markers are predominantly used to evaluate the genetic diversity of garlic clones. However, 24 SSR markers (codominant) specific for garlic are available in the literature, fostering germplasm researches. In this study, we genotyped 130 garlic accessions from Brazil and abroad using 17 polymorphic SSR markers to assess the genetic diversity and structure. This is the first attempt to evaluate a large set of accessions maintained by Brazilian institutions. A high level of redundancy was detected in the collection (50 % of the accessions represented eight haplotypes). However, non-redundant accessions presented high genetic diversity. We detected on average five alleles per locus, Shannon index of 1.2, HO of 0.5, and HE of 0.6. A core collection was set with 17 accessions, covering 100 % of the alleles with minimum redundancy. Overall FST and D values indicate a strong genetic structure within accessions. Two major groups identified by both model-based (Bayesian approach) and hierarchical clustering (UPGMA dendrogram) techniques were coherent with the classification of accessions according to maturity time (growth cycle): early-late and midseason accessions. Assessing genetic diversity and structure of garlic collections is the first step towards an efficient management and conservation of accessions in genebanks, as well as to advance future genetic studies and improvement of garlic worldwide.

  2. Structural diversity and biological importance of ABO, H, Lewis and secretor histo-blood group carbohydrates

    Directory of Open Access Journals (Sweden)

    Luiz Carlos de Mattos

    Full Text Available ABSTRACT ABO, H, secretor and Lewis histo-blood system genes control the expression of part of the carbohydrate repertoire present in areas of the body occupied by microorganisms. These carbohydrates, besides having great structural diversity, act as potential receptors for pathogenic and non-pathogenic microorganisms influencing susceptibility and resistance to infection and illness. Despite the knowledge of some structural variability of these carbohydrate antigens and their polymorphic levels of expression in tissue and exocrine secretions, little is known about their biological importance and potential applications in medicine. This review highlights the structural diversity, the biological importance and potential applications of ABO, H, Lewis and secretor histo-blood carbohydrates.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  4. Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

    Science.gov (United States)

    Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

    2008-01-01

    Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

  5. Overstory structure and soil nutrients effect on plant diversity in unmanaged moist tropical forest

    Science.gov (United States)

    Gautam, Mukesh Kumar; Manhas, Rajesh Kumar; Tripathi, Ashutosh Kumar

    2016-08-01

    Forests with intensive management past are kept unmanaged to restore diversity and ecosystem functioning. Before perpetuating abandonment after protracted restitution, understanding its effect on forest vegetation is desirable. We studied plant diversity and its relation with environmental variables and stand structure in northern Indian unmanaged tropical moist deciduous forest. We hypothesized that post-abandonment species richness would have increased, and the structure of contemporary forest would be heterogeneous. Vegetation structure, composition, and diversity were recorded, in forty 0.1 ha plots selected randomly in four forest ranges. Three soil samples per 0.1 ha were assessed for physicochemistry, fine sand, and clay mineralogy. Contemporary forest had less species richness than pre-abandonment reference period. Fourteen species were recorded as either seedling or sapling, suggesting reappearance or immigration. For most species, regeneration was either absent or impaired. Ordination and multiple regression results showed that exchangeable base cations and phosphorous affected maximum tree diversity and structure variables. Significant correlations between soil moisture and temperature, and shrub layer was observed, besides tree layer correspondence with shrub richness, suggesting that dense overstory resulting from abandonment through its effect on soil conditions, is responsible for dense shrub layer. Herb layer diversity was negatively associated with tree layer and shrub overgrowth (i.e. Mallotus spp.). Protracted abandonment may not reinforce species richness and heterogeneity; perhaps result in high tree and shrub density in moist deciduous forests, which can impede immigrating or reappearing plant species establishment. This can be overcome by density/basal area reduction strategies, albeit for both tree and shrub layer.

  6. Genetic diversity and population structure of leafy kale and Brassica rupestris Raf. in south Italy

    DEFF Research Database (Denmark)

    Maggioni, Lorenzo; von Bothmer, Roland; Poulsen, Gert

    2014-01-01

    Local varieties of leafy kales (Brassica oleracea L.) are grown in home gardens in Calabria and Sicily for self-consumption, in the same area where the wild relative Brassica rupestris Raf. also grows. With the use of AFLP markers, comparisons were made of the genetic diversity and population...... structure of ten wild and 22 cultivated populations, as well as of a hybrid population and of four commercial cultivars of different B. oleracea crops. The level of genetic diversity was higher in leafy kales than in wild populations and this diversity was mainly distributed within populations. Wild...... populations remained distinct from cultivated material. Additionally, most wild populations were distinctively isolated from each other. On the other hand, it was not possible to molecularly distinguish even geographically distant leafy kale populations from each other or from different B. oleracea crops...

  7. High genetic diversity and population structure in the endangered Canarian endemic Ruta oreojasme (Rutaceae).

    Science.gov (United States)

    Meloni, Marilena; Reid, Andrea; Caujapé-Castells, Juli; Soto, Moisés; Fernández-Palacios, José María; Conti, Elena

    2015-10-01

    Insular species are expected to have low genetic diversity, for their populations are often small and isolated, and characterized by restricted gene flow and increased incidence of inbreeding. However, empirical results do not always match this expectation. For example, population genetic analyses of several Canarian endemics, based mainly on allozymes, show levels of genetic diversity exceptionally high for insular species. To investigate whether genetic variation in rare species endemic to Canary Islands is low, as predicted by theoretical expectations, or high, as documented in some previous studies, we analysed genetic diversity of the endangered Ruta oreojasme, a rare endemic of the island of Gran Canaria, using microsatellite markers, which are more variable than allozymes. Our analyses identified very high levels of genetic diversity (A = 7.625, P = 0.984, H o = 0.558, H e = 0.687) for R. oreojasme. Even though the distribution of the species is restricted to the South of Gran Canaria, only one population shows low genetic diversity, isolation and signs of a recent bottleneck/founder event. Some intrinsic characteristics of R. oreojasme (hermaphroditism, proterandry and polyploidy), the relative climatic stability of the Canarian archipelago during Quaternary glacials/interglacials, the size of most populations (thousands of individuals), its age, and the relative proximity of the archipelago to the mainland might have contributed to the high diversity that characterises this endemic. As expected, given the marked topographic complexity of Gran Canaria, we found marked genetic structure in R. oreojasme populations. Our results support the observation that Canarian endemics are characterised by unexpectedly high genetic diversity and provides important insights for potential applications to the conservation of R. oreojasme.

  8. Home Life: Factors Structuring the Bacterial Diversity Found within and between Homes

    Science.gov (United States)

    2013-01-01

    Most of our time is spent indoors where we are exposed to a wide array of different microorganisms living on surfaces and in the air of our homes. Despite their ubiquity and abundance, we have a limited understanding of the microbial diversity found within homes and how the composition and diversity of microbial communities change across different locations within the home. Here we examined the diversity of bacterial communities found in nine distinct locations within each of forty homes in the Raleigh-Durham area of North Carolina, USA, using high-throughput sequencing of the bacterial 16S rRNA gene. We found that each of the sampled locations harbored bacterial communities that were distinct from one another with surfaces that are regularly cleaned typically harboring lower levels of diversity than surfaces that are cleaned infrequently. These location-specific differences in bacterial communities could be directly related to usage patterns and differences in the likely sources of bacteria dispersed onto these locations. Finally, we examined whether the variability across homes in bacterial diversity could be attributed to outdoor environmental factors, indoor habitat structure, or the occupants of the home. We found that the presence of dogs had a significant effect on bacterial community composition in multiple locations within homes as the homes occupied by dogs harbored more diverse communities and higher relative abundances of dog-associated bacterial taxa. Furthermore, we found a significant correlation between the types of bacteria deposited on surfaces outside the home and those found inside the home, highlighting that microbes from outside the home can have a direct effect on the microbial communities living on surfaces within our homes. Together this work provides the first comprehensive analysis of the microbial communities found in the home and the factors that shape the structure of these communities both within and between homes. PMID:23717552

  9. Forest structure in low-diversity tropical forests: a study of Hawaiian wet and dry forests.

    Science.gov (United States)

    Ostertag, Rebecca; Inman-Narahari, Faith; Cordell, Susan; Giardina, Christian P; Sack, Lawren

    2014-01-01

    The potential influence of diversity on ecosystem structure and function remains a topic of significant debate, especially for tropical forests where diversity can range widely. We used Center for Tropical Forest Science (CTFS) methodology to establish forest dynamics plots in montane wet forest and lowland dry forest on Hawai'i Island. We compared the species diversity, tree density, basal area, biomass, and size class distributions between the two forest types. We then examined these variables across tropical forests within the CTFS network. Consistent with other island forests, the Hawai'i forests were characterized by low species richness and very high relative dominance. The two Hawai'i forests were floristically distinct, yet similar in species richness (15 vs. 21 species) and stem density (3078 vs. 3486/ha). While these forests were selected for their low invasive species cover relative to surrounding forests, both forests averaged 5->50% invasive species cover; ongoing removal will be necessary to reduce or prevent competitive impacts, especially from woody species. The montane wet forest had much larger trees, resulting in eightfold higher basal area and above-ground biomass. Across the CTFS network, the Hawaiian montane wet forest was similar to other tropical forests with respect to diameter distributions, density, and aboveground biomass, while the Hawai'i lowland dry forest was similar in density to tropical forests with much higher diversity. These findings suggest that forest structural variables can be similar across tropical forests independently of species richness. The inclusion of low-diversity Pacific Island forests in the CTFS network provides an ∼80-fold range in species richness (15-1182 species), six-fold variation in mean annual rainfall (835-5272 mm yr(-1)) and 1.8-fold variation in mean annual temperature (16.0-28.4°C). Thus, the Hawaiian forest plots expand the global forest plot network to enable testing of ecological theory for

  10. Accounting for a Diverse Forest Ownership Structure in Projections of Forest Sustainability Indicators

    Directory of Open Access Journals (Sweden)

    Jeannette Eggers

    2015-11-01

    Full Text Available In this study, we assessed the effect of a diverse ownership structure with different management strategies within and between owner categories in long-term projections of economic, ecological and social forest sustainability indicators, representing important ecosystem services, for two contrasting Swedish municipalities. This was done by comparing two scenarios: one where the diversity of management strategies was accounted for (Diverse and one where it was not (Simple. The Diverse scenario resulted in a 14% lower total harvested volume for the 100 year period compared to the Simple scenario, which resulted in a higher growing stock and a more favorable development of the ecological indicators. The higher proportion of sparse forests and the lower proportion of clear-felled sites made the Diverse scenario more appropriate for delivering access to common outdoor recreation activities, while the Simple scenario projected more job opportunities. Differences between the scenarios were considerable already in the medium term (after 20 years of simulation. Our results highlight the importance of accounting for the variety of management strategies employed by forest owners in medium- to long-term projections of the development of forest sustainability indicators.

  11. Community structure and diversity of demersal fish assemblages: the role of fishery

    Directory of Open Access Journals (Sweden)

    Mary Labropoulou

    2004-04-01

    Full Text Available Seasonal experimental trawl surveys were carried out in the Northern Aegean and Thracian seas (NE Mediterranean, Greece, from summer 1990 to autumn 1993, during which a total of 172 fish species were caught. In these areas, fishing pressure is very high, since approximately 50% of the Greek otter trawl fleet operates there, producing more than 57% of the total demersal landings. Different statistics were used to assess spatial structure, seasonal changes and diversity of the demersal fish assemblages on the continental shelf and upper slope. The following measures were applied to the species abundance matrix: species diversity, species richness, evenness and dominance. The analysis of 501 bottom trawls revealed that, in general, species diversity, richness and evenness decreased with water depth, with the highest values at depths 200 m. The effect of depth on the diversity patterns observed was always significant, while seasonal trends were similar with those described for the overall diversity characteristics in each area. Classification and ordination methods showed the existence of 4 groups associated with the continental shelf and upper slope in each area. Classification of the top ranking species at each group and area revealed that commercially important species were dominant in the shallowest zone (

  12. Analysis of Structure and Diversity of the Kilengwe Forest in the Morogoro Region, Tanzania

    Directory of Open Access Journals (Sweden)

    David Sylvester Kacholi

    2014-01-01

    Full Text Available This study investigates the structure, species composition, and diversity of a section of the Kilengwe Forest in Tanzania. In order to accomplish the proposed objectives, 18 plots of 20 m × 20 m were randomly established in the forest and the number of tree species in each plot was identified and counted. The most important families and species were determined using importance value indices at the respective taxonomic levels. Diversity was measured using the Shannon-Wiener and Fisher alpha diversity indices. A total of 276 stems/ha representing 93 species/ha within 26 families were documented from 0.72 ha. Fabaceae and Julbernadia globiflora were the dominant family and species, respectively. Seventy-eight percent of the total species were rare. The average basal area of the forest was 7.1 m2/ha. The Shannon-Wiener index (4.02 and Fisher’s alpha diversity (35.5 indicated high species diversity within the forest. The species-area and species-abundance curves revealed an escalating trend implying that more sampling efforts could result in a higher number of species existing in the forest. The size class distribution displayed a reverse J-shaped pattern; however, the larger size classes DBH >50 cm were not represented. The study suggests the necessity for anthropogenic disturbance control as this is the major source of forest degradation in the studied area.

  13. Genetic diversity and population structure of leafy kale and Brassica rupestris Raf. in south Italy.

    Science.gov (United States)

    Maggioni, Lorenzo; von Bothmer, Roland; Poulsen, Gert; Branca, Ferdinando; Bagger Jørgensen, Rikke

    2014-12-01

    Local varieties of leafy kales (Brassica oleracea L.) are grown in home gardens in Calabria and Sicily for self-consumption, in the same area where the wild relative Brassica rupestris Raf. also grows. With the use of AFLP markers, comparisons were made of the genetic diversity and population structure of ten wild and 22 cultivated populations, as well as of a hybrid population and of four commercial cultivars of different B. oleracea crops. The level of genetic diversity was higher in leafy kales than in wild populations and this diversity was mainly distributed within populations. Wild populations remained distinct from cultivated material. Additionally, most wild populations were distinctively isolated from each other. On the other hand, it was not possible to molecularly distinguish even geographically distant leafy kale populations from each other or from different B. oleracea crops. It was possible to detect inter-crossing between leafy kales and B. rupestris. Findings from this study illustrate the existing level of genetic diversity in the B. oleracea gene pool. Individual populations (either wild or leafy kales) with higher levels of genetic diversity have been identified and suggestions are given for an informed conservation strategy. Domestication hypotheses are also discussed.

  14. Architectural design influences the diversity and structure of the built environment microbiome.

    Science.gov (United States)

    Kembel, Steven W; Jones, Evan; Kline, Jeff; Northcutt, Dale; Stenson, Jason; Womack, Ann M; Bohannan, Brendan Jm; Brown, G Z; Green, Jessica L

    2012-08-01

    Buildings are complex ecosystems that house trillions of microorganisms interacting with each other, with humans and with their environment. Understanding the ecological and evolutionary processes that determine the diversity and composition of the built environment microbiome--the community of microorganisms that live indoors--is important for understanding the relationship between building design, biodiversity and human health. In this study, we used high-throughput sequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes and airborne bacterial communities at a health-care facility. We quantified airborne bacterial community structure and environmental conditions in patient rooms exposed to mechanical or window ventilation and in outdoor air. The phylogenetic diversity of airborne bacterial communities was lower indoors than outdoors, and mechanically ventilated rooms contained less diverse microbial communities than did window-ventilated rooms. Bacterial communities in indoor environments contained many taxa that are absent or rare outdoors, including taxa closely related to potential human pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relative humidity and temperature, were correlated with the diversity and composition of indoor bacterial communities. The relative abundance of bacteria closely related to human pathogens was higher indoors than outdoors, and higher in rooms with lower airflow rates and lower relative humidity. The observed relationship between building design and airborne bacterial diversity suggests that we can manage indoor environments, altering through building design and operation the community of microbial species that potentially colonize the human microbiome during our time indoors.

  15. Genetic diversity and population structure in Polygonum cespitosum: insights to an ongoing plant invasion.

    Directory of Open Access Journals (Sweden)

    Silvia Matesanz

    Full Text Available Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America, via the analyses of 516 individuals, and asked the following questions: 1 Do populations have differing levels of within-population genetic diversity? 2 Do populations form distinct genetic clusters? 3 Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering and pairwise FST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further

  16. Spatiotemporal diversity, structure and trophic guilds of insect assemblages in a semi-arid Sabkha ecosystem

    Directory of Open Access Journals (Sweden)

    Haroun Chenchouni

    2015-03-01

    Full Text Available The current study highlights some knowledge on the diversity and structure of insect communities and trophic groups living in Sabkha Djendli (semi-arid area of Northeastern Algeria. The entomofauna was monthly sampled from March to November 2006 using pitfall traps at eight sites located at the vicinity of the Sabkha. Structural and diversity parameters (species richness, Shannon index, evenness were measured for both insect orders and trophic guilds. The canonical correspondence analysis (CCA was applied to determine how vegetation parameters (species richness and cover influence spatial and seasonal fluctuations of insect assemblages. The catches totalled 434 insect individuals classified into 75 species, 62 genera, 31 families and 7 orders, of which Coleoptera and Hymenoptera were the most abundant and constant over seasons and study stations. Spring and autumn presented the highest values of diversity parameters. Individual-based Chao-1 species richness estimator indicated 126 species for the total individuals captured in the Sabkha. Based on catch abundances, the structure of functional trophic groups was predators (37.3%, saprophages (26.7%, phytophages (20.5%, polyphages (10.8%, coprophages (4.6%; whereas in terms of numbers of species, they can be classified as phytophages (40%, predators (25.3%, polyphages (13.3%, saprophages (12%, coprophages (9.3%. The CCA demonstrated that phytophages and saprophages as well as Coleoptera and Orthoptera were positively correlated with the two parameters of vegetation, especially in spring and summer. While the abundance of coprophages was positively correlated with species richness of plants, polyphage density was positively associated with vegetation cover. The insect community showed high taxonomic and functional diversity that is closely related to diversity and vegetation cover in different stations of the wetland and seasons.

  17. Influence of biotic variables on invertebrate size structure and diversity in coastal wetlands of Southeastern Spain

    Science.gov (United States)

    Antón-Pardo, María; Armengol, Xavier

    2016-10-01

    Biomass and size-based estimations provide relevant information regarding ecosystem functioning and biotic interactions. Our aims were to study the effect of fish and macrophytes on the size structure of invertebrate assemblages (from rotifers to insects) in a set of coastal water bodies, estimating the biomass (total and main invertebrate groups), the biomass-size spectra (model of Pareto) and size diversity. In fishless ponds, cladoceran and ostracod biomass were higher, and they presented greater size diversity. In fish ponds, rotifer biomass presented greater proportion; while in fishless ponds, cladocerans were usually the most abundant taxa and the largest organisms. The biomass size spectra showed more irregularities in fishless ponds, due to the low densities of small taxa (rotifers and copepod juveniles) and big taxa (malacostraceans or insects). Differences is size structure and diversity were also observed between spring and summer, suggesting a higher recruitment of juveniles in spring, and thus, a higher predation pressure upon zooplankton at that moment. Macrophyte cover did not apparently influence those parameters, except for the biomass of ostracods, copepods, and insects. Therefore, predation by fish strongly affected invertebrate biomass, reflecting their selective feeding, and allowing high densities of small taxa. Predation pressure decreased size diversity, by limiting the abundance of vulnerable taxa of specific size. Seasonal changes were likely related to the spring recruitment of fish juveniles. The presence of small fish and invertebrate predator taxa among the macrophytes, restrict their role as refuges for prey invertebrates.

  18. Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure.

    Science.gov (United States)

    Sheik, Cody S; Mitchell, Tyler W; Rizvi, Fariha Z; Rehman, Yasir; Faisal, Muhammad; Hasnain, Shahida; McInerney, Michael J; Krumholz, Lee R

    2012-01-01

    Extensive use of chromium (Cr) and arsenic (As) based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI)) and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils) were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI)-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI). Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways.

  19. SPECIES DIVERSITY AND COMMUNITY STRUCTURE OF SUCKING LICE IN YUNNAN, CHINA

    Institute of Scientific and Technical Information of China (English)

    Xian-guoGuo; Ti-junQian; Li-junGuo; JingWang; Wen-geDong; LiZhang; Zhi-minMa; andWeiLi

    2004-01-01

    On the basis of investigating 9 counties (towns) in Yunnan Province of China, the species diversity and community structure of sucking lice on the body surface of small mammal hosts are studied in the paper. Species richness (S) is used to stand for the species diversity. The calculation of community diversity index and evenness are based on Shannon-Wiener's method. 2745 small mammals captured from the investigated sites belong to 10 families, 25 genera and 41 species in 5 orders (Rodentia, Insectivora, Scandentia, Logomorpha and Carnivora) while 18165 individuals of sucking lice collected from the body surface of the small mammal hosts are identified into 4 families, 6 genera and 22 species. The species of sucking lice are much less than the species of their hosts. Most species of small mammals have their fixed sucking lice on their body surface. One species of small mammals usually have few species of sucking lice (1 to 4 species). The close species of the hosts in the taxonomy are found to have the same or similar dominant species of sucking lice on their body surface. The results reveal that the species diversity of sucking lice on small mammals is very low with a very simple community structure. The results also imply there may be a close co-evolution relationship between the lice and the hosts.

  20. Diversity and coverage of structural sublibraries selected using the SAGE and SCA algorithms.

    Science.gov (United States)

    Reynolds, C H; Tropsha, A; Pfahler, L B; Druker, R; Chakravorty, S; Ethiraj, G; Zheng, W

    2001-01-01

    It is often impractical to synthesize and test all compounds in a large exhaustive chemical library. Herein, we discuss rational approaches to selecting representative subsets of virtual libraries that help direct experimental synthetic efforts for diverse library design. We compare the performance of two stochastic sampling algorithms, Simulating Annealing Guided Evaluation (SAGE; Zheng, W.; Cho, S. J.; Waller, C. L.; Tropsha, A. J. Chem. Inf. Comput. Sci. 1999, 39, 738-746.) and Stochastic Cluster Analysis (SCA; Reynolds, C. H.; Druker, R.; Pfahler, L. B. Lead Discovery Using Stochastic Cluster Analysis (SCA): A New Method for Clustering Structurally Similar Compounds J. Chem. Inf. Comput. Sci. 1998, 38, 305-312.) for their ability to select both diverse and representative subsets of the entire chemical library space. The SAGE and SCA algorithms were compared using u- and s-optimal metrics as an independent assessment of diversity and coverage. This comparison showed that both algorithms were capable of generating sublibraries in descriptor space that are diverse and give reasonable coverage (i.e. are representative) of the original full library. Tests were carried out using simulated two-dimensional data sets and a 27 000 compound proprietary structural library as represented by computed Molconn-Z descriptors. One of the key observations from this work is that the algorithmically simple SCA method is capable of selecting subsets that are comparable to the more computationally intensive SAGE method.

  1. A case of a huge gastroepiploic arterial aneurysm.

    Science.gov (United States)

    Ikeda, Hirokuni; Takeo, Masahiko; Mikami, Ryuuichi; Yamamoto, Mistuo

    2015-08-05

    An 85-year-old man complaining of vague abdominal discomfort was admitted to our hospital. A pulsatile 8 × 7-cm mass in the right upper abdomen was noticed on clinical examination. Computed tomography of the abdomen showed a huge arterial aneurysm in the right gastroepiploic artery, and the left gastroepiploic artery was meandering and expanding. An image diagnosis of gastroepiploic arterial aneurysm (GEAA) was made. Because of the huge size of the aneurysm and the predicted high risk of perforation, surgical intervention was planned. The aneurysm was identified in the greater curve and was found to adhere firmly to the transverse colon. Partial resection of the stomach, aneurysmectomy and partial resection of the transverse colon were performed. Clinically, splanchnic arterial aneurysms are rare. Among them, GEAA is especially rare. We report a rare case of a huge GEAA that was treated successfully by surgery. Published by Oxford University Press and JSCR Publishing Ltd. All rights reserved. © The Author 2015.

  2. Genetic diversity and population structure of indigenous chicken breeds in South China

    Directory of Open Access Journals (Sweden)

    Xunhe HUANG,Jinfeng ZHANG,Danlin HE,Xiquan ZHANG,Fusheng ZHONG,Weina LI,Qingmei ZHENG,Jiebo CHEN,Bingwang DU

    2016-06-01

    Full Text Available A total of 587 individuals from 12 indigenous chicken breeds from South China and two commercial breeds were genotyped for 26 microsatellites to investigate the genetic diversity and population structure. All microsatellites were found to be polymorphic. The number of alleles per locus ranged from 5 to 36, with an average of 12.10 ± 7.00 (SE. All breeds, except White Recessive Rock, had high allelic polymorphism (>0.5. Higher genetic diversity was revealed in the indigenous chicken breeds rather than in the commercial breeds. Potential introgression from the commercial breeds into the indigenous chickens was also detected. The population structure of these indigenous chicken breeds could be explained by their geographical distribution, which suggested the presence of independent history of breed formation. Data generated in this study will provide valuable information to the conservation for indigenous chicken breeds in future.

  3. Discharge capacity of sluiceway channel of water intake structure for diversion power plant in winter

    Directory of Open Access Journals (Sweden)

    N.P. Lavrov

    2013-06-01

    Full Text Available The paper presents results of research hydraulic processes at the intake structures of diversion power plants in winter. On the basis of the physical modeling results the flow characteristics of sluiceway channel of water intake on the river Issyk-Ata, Kyrgyzstan were determined. Statistical models of discharges of elements of sluiceway channel with their mutual influence were obtained, using the methods of experimental design and data analysis. The influence of the concentration of brash ice on the sluiceway channel and its elements is described. The comparison of experimental data with data obtained by other authors before is made by comparing flow coefficients. Recommendations for normal operation of ice pass at sluiceway track channel of water intake structure for diversion power plant are given.

  4. Community diversity, structure and carbon footprint of nematode food web following reforestation on degraded Karst soil

    Science.gov (United States)

    Hu, Ning; Li, Hui; Tang, Zheng; Li, Zhongfang; Tian, Jing; Lou, Yilai; Li, Jianwei; Li, Guichun; Hu, Xiaomin

    2016-06-01

    We examined community diversity, structure and carbon footprint of nematode food web along a chronosequence of T. Sinensis reforestation on degraded Karst. In general, after the reforestation: a serious of diversity parameters and community indices (Shannon-Weinier index (H‧), structure index (SI), etc.) were elevated; biomass ratio of fungivores to bacterivores (FFC/BFC), and fungi to bacteria (F/B) were increased, and nematode channel ratio (NCR) were decreased; carbon footprints of all nematode trophic groups, and biomass of bacteria and fungi were increased. Our results indicate that the Karst aboveground vegetation restoration was accompanied with belowground nematode food web development: increasing community complexity, function and fungal dominance in decomposition pathway, and the driving forces included the bottom-up effect (resource control), connectedness of functional groups, as well as soil environments.

  5. The effects of disturbance on forest structure and diversity at different altitudes in Garhwal Himalaya

    Institute of Scientific and Technical Information of China (English)

    Munesh KUMA; Chandra Mohan SHARMA; Govind Singh RAJWAR

    2009-01-01

    The effects of disturbance on forest structure and diversity along an altitudinal gradient in the temperate, sub-tropical, and tropical regions of Garhwal Himalaya were assessed. Each region was further categorized into undisturbed (UD), mildly disturbed (MD), and highly disturbed (HD) sites on the basis of magnitude of disturbance in these forests. On UD sites of temperate, sub-tropical and tropical regions, Quercus leucotrichophora, Anogeissus latifolia and Holoptelea integrifolia were the dominant tree species respectively. The highest values of tree density (1028 ind*hm-2) and total basal cover at breast height (31.70 m2 *hm-2) were recorded for UD site of temperate region, whereas maximum species diversity (3.128) and equitability (14.09) values were observed for HD site of tropical region. The structure and composition of the forests were greatly affected by the degree of disturbance.

  6. Community diversity, structure and carbon footprint of nematode food web following reforestation on degraded Karst soil

    Science.gov (United States)

    Hu, Ning; Li, Hui; Tang, Zheng; Li, Zhongfang; Tian, Jing; Lou, Yilai; Li, Jianwei; Li, Guichun; Hu, Xiaomin

    2016-01-01

    We examined community diversity, structure and carbon footprint of nematode food web along a chronosequence of T. Sinensis reforestation on degraded Karst. In general, after the reforestation: a serious of diversity parameters and community indices (Shannon-Weinier index (H′), structure index (SI), etc.) were elevated; biomass ratio of fungivores to bacterivores (FFC/BFC), and fungi to bacteria (F/B) were increased, and nematode channel ratio (NCR) were decreased; carbon footprints of all nematode trophic groups, and biomass of bacteria and fungi were increased. Our results indicate that the Karst aboveground vegetation restoration was accompanied with belowground nematode food web development: increasing community complexity, function and fungal dominance in decomposition pathway, and the driving forces included the bottom-up effect (resource control), connectedness of functional groups, as well as soil environments. PMID:27311984

  7. Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide

    Science.gov (United States)

    Wang, Yukun; Chen, Charles H.; Hu, Dan; Ulmschneider, Martin B.; Ulmschneider, Jakob P.

    2016-11-01

    Many antimicrobial peptides (AMPs) selectively target and form pores in microbial membranes. However, the mechanisms of membrane targeting, pore formation and function remain elusive. Here we report an experimentally guided unbiased simulation methodology that yields the mechanism of spontaneous pore assembly for the AMP maculatin at atomic resolution. Rather than a single pore, maculatin forms an ensemble of structurally diverse temporarily functional low-oligomeric pores, which mimic integral membrane protein channels in structure. These pores continuously form and dissociate in the membrane. Membrane permeabilization is dominated by hexa-, hepta- and octamers, which conduct water, ions and small dyes. Pores form by consecutive addition of individual helices to a transmembrane helix or helix bundle, in contrast to current poration models. The diversity of the pore architectures--formed by a single sequence--may be a key feature in preventing bacterial resistance and could explain why sequence-function relationships in AMPs remain elusive.

  8. Disclosing the distinct interfacial behaviors of structurally and configurationally diverse triazologlycolipids.

    Science.gov (United States)

    He, Xiao-Peng; Xu, Xiaolian; Zhang, Hai-Lin; Chen, Guo-Rong; Xu, Shouhong; Liu, Honglai

    2011-08-16

    1- or 6-Triazologluco- and galactolipid derivatives bearing a lipid chain length of 16 carbons were efficiently constructed via click chemistry. The differentiation in their surface pressure-molecular area (π-A) isotherms first implies that these structurally and configurationally diverse amphiphiles adopt different distribution manner at air-water interfaces. The Langmuir-Blodgett (LB) films of the synthesized glycoconjugates on mica surface were subsequently prepared and visualized via atomic force microscopy (AFM), which exhibited diverse topographies and possess different contact angles with water. These data further suggest that the structural variation as well as epimeric identity of triazologlycolipids may result in their distinct interfacial behaviors at the air-solid interface. Furthermore, the addition of increasing amounts of 1-triazologalactolipid 2 to poly-diacetylene (PDA) was determined to impact the π-A isotherm of the latter, prompting us to further fabricate new colorimetrically detectable mixed-type vesicles containing triazologlycolipids for biochemical studies.

  9. A ring-distortion strategy to construct stereochemically complex and structurally diverse compounds from natural products

    Science.gov (United States)

    Huigens, Robert W., III; Morrison, Karen C.; Hicklin, Robert W.; Flood, Timothy A., Jr.; Richter, Michelle F.; Hergenrother, Paul J.

    2013-03-01

    High-throughput screening is the dominant method used to identify lead compounds in drug discovery. As such, the makeup of screening libraries largely dictates the biological targets that can be modulated and the therapeutics that can be developed. Unfortunately, most compound-screening collections consist principally of planar molecules with little structural or stereochemical complexity, compounds that do not offer the arrangement of chemical functionality necessary for the modulation of many drug targets. Here we describe a novel, general and facile strategy for the creation of diverse compounds with high structural and stereochemical complexity using readily available natural products as synthetic starting points. We show through the evaluation of chemical properties (which include fraction of sp3 carbons, ClogP and the number of stereogenic centres) that these compounds are significantly more complex and diverse than those in standard screening collections, and we give guidelines for the application of this strategy to any suitable natural product.

  10. Updated angiosperm family tree for analyzing phylogenetic diversity and community structure

    Directory of Open Access Journals (Sweden)

    Markus Gastauer

    Full Text Available ABSTRACT The computation of phylogenetic diversity and phylogenetic community structure demands an accurately calibrated, high-resolution phylogeny, which reflects current knowledge regarding diversification within the group of interest. Herein we present the angiosperm phylogeny R20160415.new, which is based on the topology proposed by the Angiosperm Phylogeny Group IV, a recently released compilation of angiosperm diversification. R20160415.new is calibratable by different sets of recently published estimates of mean node ages. Its application for the computation of phylogenetic diversity and/or phylogenetic community structure is straightforward and ensures the inclusion of up-to-date information in user specific applications, as long as users are familiar with the pitfalls of such hand-made supertrees.

  11. A Novel Diversity Receiver Structure for Severe Fading and Frequency Offset Conditions

    Directory of Open Access Journals (Sweden)

    B. Dimitrijevic

    2015-12-01

    Full Text Available This paper presents a novel diversity receiver of MPSK signal in fading channel in the presence of the carrier frequency offset. As a part of this receiver, a new algorithm for the estimation of the combining coefficients (ECC algorithm is introduced. Having in mind that the QPSK modulation is one of the most used modulation formats in many wireless communication standards (LTE, WiFi, WiMax, the performance of the proposed receiver is analyzed in more detail for the QPSK modulation. In the presence of Rayleigh fading, representing the most severe fading condition, this algorithm shows significantly better performance comparing to the same receiver structure that uses conventional constant modulus algorithm (CMA1 or CMA2. The proposed diversity receiver structure with ECC algorithm operates within a wide carrier frequency offset range with a very small variation of the performance. For this reason, it can be applied in 4G mobile communication systems.

  12. Anaesthetic management in a case of huge plunging ranula.

    Science.gov (United States)

    Sheet, Jagabandhu; Mandal, Anamitra; Sengupta, Swapnadeep; Jana, Debaleena; Mukherji, Sudakshina; Swaika, Sarbari

    2014-01-01

    Plunging ranula is a rare form of mucous retention cyst arising from submandibular and sublingual salivary glands, which may occasionally become huge occupying the whole of the floor of the mouth and extending into the neck, thus, restricting the neck movement as well as disfiguring the normal airway anatomy. Without fiberoptic assistance, blind or retrograde nasal intubation remains valuable choices in this type of situation. Here, we present a case of successful management of airway by blind nasal intubation in a patient posted for excision of a huge plunging ranula.

  13. Huge Gastric Teratoma in an 8-Year Old Boy.

    Science.gov (United States)

    Sisodiya, Rajpal S; Ratan, Simmi K; Man, Parveen K

    2016-01-01

    Gastric teratoma is very rare tumor and usually presents in early infancy. An 8-year-old boy presented with a huge mass in abdomen extending from epigastrium to the pelvis. Ultrasound and CT scan of abdomen revealed a huge mass with solid and cystic components and internal calcifications. The preoperative diagnosis was a teratoma but not specifically gastric one. At operation, it was found to be gastric teratoma. The mass was excised completely with part of the stomach wall. The histopathology confirmed it to be mature gastric teratoma. The rarity of the teratoma with delayed presentation prompted us to report the case.

  14. Anaesthetic challenges in a patient presenting with huge neck teratoma

    Directory of Open Access Journals (Sweden)

    Gaurav Jain

    2013-01-01

    Full Text Available Paediatric airway management is a great challenge even for an experienced anaesthesiologist. Difficult airway in huge cervical teratoma further exaggerates the complexity. This case report is intended at describing the intubation difficulties that were confronted during the airway management of a three year old girl presenting with huge neck teratoma and respiratory distress. This patient was successfully intubated with uncuffed endotracheal tubes in second attempt under inhalational anaesthesia with halothane and spontaneous ventilation. This case exemplifies the importance of careful preoperative workup of an anticipated difficult airway in paediatric patients with neck swelling to minimize any perioperative complications.

  15. Huge pelvic mass secondary to wear debris causing ureteral obstruction.

    Science.gov (United States)

    Hananouchi, Takehito; Saito, Masanobu; Nakamura, Nobuo; Yamamoto, Tetsuya; Yonenobu, Kazuo

    2005-10-01

    We report an unusual granulomatous reaction of wear debris that produced a huge pelvic mass causing ureteral obstruction. A 72-year-old woman, who received a cemented total hip arthroplasty 30 years ago, was referred to the department of gynecology for examination of a pelvic mass. A computed tomography scan revealed a huge homogenous mass, measuring approximately 20 x 16 x 12 cm, including extensive osteolysis of the left pelvis around the acetabular component. Intravenous pyelogram revealed complete obstruction of the left ureter resulting in hydronephrosis of the left kidney. Histological examination from the biopsy specimen detected polyethylene wear debris in the mass.

  16. Anaesthetic management in a case of huge plunging ranula

    Science.gov (United States)

    Sheet, Jagabandhu; Mandal, Anamitra; Sengupta, Swapnadeep; Jana, Debaleena; Mukherji, Sudakshina; Swaika, Sarbari

    2014-01-01

    Plunging ranula is a rare form of mucous retention cyst arising from submandibular and sublingual salivary glands, which may occasionally become huge occupying the whole of the floor of the mouth and extending into the neck, thus, restricting the neck movement as well as disfiguring the normal airway anatomy. Without fiberoptic assistance, blind or retrograde nasal intubation remains valuable choices in this type of situation. Here, we present a case of successful management of airway by blind nasal intubation in a patient posted for excision of a huge plunging ranula. PMID:25886120

  17. Spatial Diversity in Composition and Structure of Nekton in Ngenep Spring and its Channels, Karangploso - Malang

    Directory of Open Access Journals (Sweden)

    Lia Hapsari

    2014-04-01

    Full Text Available Water springs and its channel degradation due to anthropogenic pollution may alter the community structure of aquatic organisms. Water spring degradation tehrefore affect the quality of water as tourism resources. This study aims to investigate the changes in community structure of nekton  and determine the relationships between water quality characteristics to the diversity of nekton.  The field survey was set up in Ngenep spring and its channels. Results showed that nekton species found in Ngenep spring and its channels consists of 4 classes, 4 orders, 6 families, and 7 species with total 627 nekton samples. It is comprises of fishes, shrimp, frogs and waterstriders. Nekton diversity index (H’ in the spring and irrigation channel were in moderate level (1diversity and community structure. Clustering analyses and PCA result shows correlation pattern between nekton distribution with physico-chemical water quality parameters. However, physico-chemical water quality parameters in Ngenep springs and its channel were still optimum as nekton habitat (PP No. 82/ 2001. Keywords: Community structure, Nekton, Spatial diversity, Spring, Water channel

  18. Syndecans as cell surface receptors: Unique structure equates with functional diversity

    DEFF Research Database (Denmark)

    Choi, Youngsil; Chung, Heesung; Jung, Heyjung

    2011-01-01

    An increasing number of functions for syndecan cell surface heparan sulfate proteoglycans have been proposed over the last decade. Moreover, aberrant syndecan regulation has been found to play a critical role in multiple pathologies, including cancers, as well as wound healing and inflammation. A...... glycosaminoglycan chains, especially heparan sulfate. This heterodisperse polysaccharide has the potential to interact with many ligands from diverse protein families. Here, we relate the structural features of syndecans to some of their known functions....

  19. Land-use systems affect Archaeal community structure and functional diversity in western Amazon soils

    Directory of Open Access Journals (Sweden)

    Acácio Aparecido Navarrete

    2011-10-01

    Full Text Available The study of the ecology of soil microbial communities at relevant spatial scales is primordial in the wide Amazon region due to the current land use changes. In this study, the diversity of the Archaea domain (community structure and ammonia-oxidizing Archaea (richness and community composition were investigated using molecular biology-based techniques in different land-use systems in western Amazonia, Brazil. Soil samples were collected in two periods with high precipitation (March 2008 and January 2009 from Inceptisols under primary tropical rainforest, secondary forest (5-20 year old, agricultural systems of indigenous people and cattle pasture. Denaturing gradient gel electrophoresis of polymerase chain reaction-amplified DNA (PCR-DGGE using the 16S rRNA gene as a biomarker showed that archaeal community structures in crops and pasture soils are different from those in primary forest soil, which is more similar to the community structure in secondary forest soil. Sequence analysis of excised DGGE bands indicated the presence of crenarchaeal and euryarchaeal organisms. Based on clone library analysis of the gene coding the subunit of the enzyme ammonia monooxygenase (amoA of Archaea (306 sequences, the Shannon-Wiener function and Simpson's index showed a greater ammonia-oxidizing archaeal diversity in primary forest soils (H' = 2.1486; D = 0.1366, followed by a lower diversity in soils under pasture (H' = 1.9629; D = 0.1715, crops (H' = 1.4613; D = 0.3309 and secondary forest (H' = 0.8633; D = 0.5405. All cloned inserts were similar to the Crenarchaeota amoA gene clones (identity > 95 % previously found in soils and sediments and distributed primarily in three major phylogenetic clusters. The findings indicate that agricultural systems of indigenous people and cattle pasture affect the archaeal community structure and diversity of ammonia-oxidizing Archaea in western Amazon soils.

  20. Allelic diversity and population structure of Bacillus sphaericus as revealed by multilocus sequence typing.

    Science.gov (United States)

    Ge, Yong; Hu, Xiaomin; Zheng, Dasheng; Wu, Yiming; Yuan, Zhiming

    2011-08-01

    The genetic diversity of 35 Bacillus sphaericus strains was analyzed by a newly developed multilocus sequence typing (MLST) scheme, toxin gene pool survey, and mosquito bioassay. The results demonstrated that strains assigned to the same sequence type (ST) had the same occurrence of toxin genes. Further sequence analysis revealed that toxic strains presented a nearly clonal population structure, whereas nontoxic strains had a high level of heterogeneity and were significantly distinct from toxic strains.

  1. Effect of domestication on the genetic diversity and structure of Saccharina japonica populations in China

    Science.gov (United States)

    Zhang, Jie; Wang, Xiuliang; Yao, Jianting; Li, Qiuying; Liu, Fuli; Yotsukura, Norishige; Krupnova, Tatiana N.; Duan, Delin

    2017-01-01

    Saccharina japonica is a commercially and ecologically important seaweed and is an excellent system for understanding the effects of domestication on marine crops. In this study, we used 19 selected simple sequence repeat (SSR) markers to investigate the influence of domestication on the genetic diversity and structure of S. japonica populations. Wild kelp populations exhibited higher genetic diversity than cultivated populations based on total NA, HE, HO, NP and AR. Discriminant analysis of principal components (DAPC), a neighbour-joining (NJ) tree and STRUCTURE analyses indicated that S. japonica populations could be divided into two groups (a cultivated/introduced group and a wild indigenous group) with significant genetic differentiation (P < 0.0001). Divergent selection, continuous inbreeding and inter-specific hybridization have caused the divergence of these two genetically separate gene pools. The significant genetic differentiation between northern and southern cultivated populations appears to be due to inter-specific hybridization and wild germplasm introduction during the domestication process. In addition, the cultivation of S. japonica has not resulted in any serious genetic disturbance of wild introduced S. japonica populations. An understanding of the genetic diversity and genetic structure of domesticated S. japonica will be necessary for further genetic improvement and effective use of germplasm. PMID:28176848

  2. Population genetic structure of Plasmodium falciparum across a region of diverse endemicity in West Africa

    Directory of Open Access Journals (Sweden)

    Mobegi Victor A

    2012-07-01

    Full Text Available Abstract Background Malaria parasite population genetic structure varies among areas of differing endemicity, but this has not been systematically studied across Plasmodium falciparum populations in Africa where most infections occur. Methods Ten polymorphic P. falciparum microsatellite loci were genotyped in 268 infections from eight locations in four West African countries (Republic of Guinea, Guinea Bissau, The Gambia and Senegal, spanning a highly endemic forested region in the south to a low endemic Sahelian region in the north. Analysis was performed on proportions of mixed genotype infections, genotypic diversity among isolates, multilocus standardized index of association, and inter-population differentiation. Results Each location had similar levels of pairwise genotypic diversity among isolates, although there were many more mixed parasite genotype infections in the south. Apart from a few isolates that were virtually identical, the multilocus index of association was not significant in any population. Genetic differentiation between populations was low (most pairwise FST values  Conclusions Although proportions of mixed genotype infections varied with endemicity as expected, population genetic structure was similar across the diverse sites. Very substantial reduction in transmission would be needed to cause fragmented or epidemic sub-structure in this region.

  3. Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

    KAUST Repository

    Pailles, Yveline

    2017-02-15

    Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance.

  4. Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata L. Walp).

    Science.gov (United States)

    Xiong, Haizheng; Shi, Ainong; Mou, Beiquan; Qin, Jun; Motes, Dennis; Lu, Weiguo; Ma, Jianbing; Weng, Yuejin; Yang, Wei; Wu, Dianxing

    2016-01-01

    The genetic diversity of cowpea was analyzed, and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from the USDA GRIN cowpea collection, originally collected from 56 countries. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the identified SNP alleles were used to estimate the level of genetic diversity, population structure, and phylogenetic relationships. The aim of this study was to detect the gene pool structure of cowpea and to determine its relationship between different regions and countries. Based on the model-based ancestry analysis, the phylogenetic tree, and the principal component analysis, three well-differentiated genetic populations were postulated from 768 worldwide cowpea genotypes. According to the phylogenetic analyses between each individual, region, and country, we may trace the accession from off-original, back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. To our knowledge, this is the first report of the analysis of the genetic variation and relationship between globally cultivated cowpea genotypes. The results will help curators, researchers, and breeders to understand, utilize, conserve, and manage the collection for more efficient contribution to international cowpea research.

  5. Diversity, Antimicrobial Action and Structure-Activity Relationship of Buffalo Cathelicidins.

    Science.gov (United States)

    Brahma, Biswajit; Patra, Mahesh Chandra; Karri, Satyanagalakshmi; Chopra, Meenu; Mishra, Purusottam; De, Bidhan Chandra; Kumar, Sushil; Mahanty, Sourav; Thakur, Kiran; Poluri, Krishna Mohan; Datta, Tirtha Kumar; De, Sachinandan

    2015-01-01

    Cathelicidins are an ancient class of antimicrobial peptides (AMPs) with broad spectrum bactericidal activities. In this study, we investigated the diversity and biological activity of cathelicidins of buffalo, a species known for its disease resistance. A series of new homologs of cathelicidin4 (CATHL4), which were structurally diverse in their antimicrobial domain, was identified in buffalo. AMPs of newly identified buffalo CATHL4s (buCATHL4s) displayed potent antimicrobial activity against selected Gram positive (G+) and Gram negative (G-) bacteria. These peptides were prompt to disrupt the membrane integrity of bacteria and induced specific changes such as blebing, budding, and pore like structure formation on bacterial membrane. The peptides assumed different secondary structure conformations in aqueous and membrane-mimicking environments. Simulation studies suggested that the amphipathic design of buCATHL4 was crucial for water permeation following membrane disruption. A great diversity, broad-spectrum antimicrobial action, and ability to induce an inflammatory response indicated the pleiotropic role of cathelicidins in innate immunity of buffalo. This study suggests short buffalo cathelicidin peptides with potent bactericidal properties and low cytotoxicity have potential translational applications for the development of novel antibiotics and antimicrobial peptidomimetics.

  6. Diversity, Antimicrobial Action and Structure-Activity Relationship of Buffalo Cathelicidins.

    Directory of Open Access Journals (Sweden)

    Biswajit Brahma

    Full Text Available Cathelicidins are an ancient class of antimicrobial peptides (AMPs with broad spectrum bactericidal activities. In this study, we investigated the diversity and biological activity of cathelicidins of buffalo, a species known for its disease resistance. A series of new homologs of cathelicidin4 (CATHL4, which were structurally diverse in their antimicrobial domain, was identified in buffalo. AMPs of newly identified buffalo CATHL4s (buCATHL4s displayed potent antimicrobial activity against selected Gram positive (G+ and Gram negative (G- bacteria. These peptides were prompt to disrupt the membrane integrity of bacteria and induced specific changes such as blebing, budding, and pore like structure formation on bacterial membrane. The peptides assumed different secondary structure conformations in aqueous and membrane-mimicking environments. Simulation studies suggested that the amphipathic design of buCATHL4 was crucial for water permeation following membrane disruption. A great diversity, broad-spectrum antimicrobial action, and ability to induce an inflammatory response indicated the pleiotropic role of cathelicidins in innate immunity of buffalo. This study suggests short buffalo cathelicidin peptides with potent bactericidal properties and low cytotoxicity have potential translational applications for the development of novel antibiotics and antimicrobial peptidomimetics.

  7. Composition, structure and diversity characterization of dry tropical forest of Chhattisgarh using satellite data

    Institute of Scientific and Technical Information of China (English)

    Tarun Thakur; S.L. Swamy; Ajit Singh Nain

    2014-01-01

    The purpose of this study was to characterize the land use, vegetation structure, and diversity in the Barnowpara Sanctuary, Raipur district, Chhattisgarh, India through the use of satellite remote sensing and GIS. Land cover and vegetation were spatially analyzed by digitally classifying IRS 1D LISS III satellite data using a maximum likelihood algorithm. Later, the variations in structure and diversity in different forest types and classes were quantified by adopting quadratic sampling proce-dures. Nine land-cover types were delineated: teak forest, dense mixed forest, degraded mixed forest, Sal mixed forest, open mixed forest, young teak plantation, grasslands, agriculture, habitation, and water bodies. The classification accuracy for different land-use classes ranged from 71.23%to 100%. The highest accuracy was observed in water bodies and grass-land, followed by habitation and agriculture, teak forest, degraded mixed forest, and dense mixed forest. The accuracy was lower in open mixed forest, and sal mixed forest. Results revealed that density of different forest types varied from 324 to 733 trees ha-1, basal area from 8.13 to 28.87 m2·ha-1 and number of species from 20 to 40. Similarly, the diversity ranged from 1.36 to 2.98, concentration of dominance from 0.06 to 0.49, species richness from 3.88 to 6.86, and beta diversity from 1.29 to 2.21. The sal mixed forest type recorded the highest basal area, diversity was highest in the dense mixed forest, and the teak forest recorded maximum density, which was poor in degraded mixed forests. The study also showed that Normalized Difference Vegetation Index (NDVI) was strongly cor-related to with the Shannon Index and species richness.

  8. Diversity and genetic structure analysis of three Amazonian Amerindian populations of Colombia.

    Science.gov (United States)

    Braga, Yamid; Arias B, Leonardo; Barreto, Guillermo

    2012-04-01

    In the departments of the Vaupés and Guaviare, in southeastern Colombia, in a transitional area between Amazonia and the eastern plains, inhabit indigenous groups belonging to the Tukanoan (East) and Guahiban linguistic families. Although some studies have dealt with the culture and the cosmology description of these groups, little research has been done on the biological diversity and genetic relationships of such groups. To estimate the diversity, the structure, and the genetic relationships of one Guahiban and two Tukanoan groups of the Colombian Amazonian region. Samples were collected (n = 106) from unrelated individuals belonging to the Vaupés native indigenous communities. The DNA was extracted and nine autosomal microsatellites were typed. Several measures of diversity, FST, pairwise FST, and population differentiation between groups were calculated. Finally, it was estimated the genetic distances of the groups studied in relation with other Amazonian, Andean and Central American indigenous people. 1. The genetic diversity found stands within the range of other Amazonian populations, whereas compared to the mestizo and afro-descendant Colombian populations, such diversity showed to be lower. 2. The structure and population differentiation tests showed two clusters; one consisting of the Vaupés Tukanoan and Guaviare Tukanoan groups, and a second one formed by the Guayabero. 3. Tukanoan groups are found to be closer related to the Brazilian Amazonian populations than to the Guayabero. The results of this study suggest that the Guayabero group from Guaviare, are genetically differentiated from those Tukanoan groups of the Vaupés and Guaviare.

  9. A New Pixels Flipping Method for Huge Watermarking Capacity of the Invoice Font Image

    Directory of Open Access Journals (Sweden)

    Li Li

    2014-01-01

    Full Text Available Invoice printing just has two-color printing, so invoice font image can be seen as binary image. To embed watermarks into invoice image, the pixels need to be flipped. The more huge the watermark is, the more the pixels need to be flipped. We proposed a new pixels flipping method in invoice image for huge watermarking capacity. The pixels flipping method includes one novel interpolation method for binary image, one flippable pixels evaluation mechanism, and one denoising method based on gravity center and chaos degree. The proposed interpolation method ensures that the invoice image keeps features well after scaling. The flippable pixels evaluation mechanism ensures that the pixels keep better connectivity and smoothness and the pattern has highest structural similarity after flipping. The proposed denoising method makes invoice font image smoother and fiter for human vision. Experiments show that the proposed flipping method not only keeps the invoice font structure well but also improves watermarking capacity.

  10. A new pixels flipping method for huge watermarking capacity of the invoice font image.

    Science.gov (United States)

    Li, Li; Hou, Qingzheng; Lu, Jianfeng; Xu, Qishuai; Dai, Junping; Mao, Xiaoyang; Chang, Chin-Chen

    2014-01-01

    Invoice printing just has two-color printing, so invoice font image can be seen as binary image. To embed watermarks into invoice image, the pixels need to be flipped. The more huge the watermark is, the more the pixels need to be flipped. We proposed a new pixels flipping method in invoice image for huge watermarking capacity. The pixels flipping method includes one novel interpolation method for binary image, one flippable pixels evaluation mechanism, and one denoising method based on gravity center and chaos degree. The proposed interpolation method ensures that the invoice image keeps features well after scaling. The flippable pixels evaluation mechanism ensures that the pixels keep better connectivity and smoothness and the pattern has highest structural similarity after flipping. The proposed denoising method makes invoice font image smoother and fiter for human vision. Experiments show that the proposed flipping method not only keeps the invoice font structure well but also improves watermarking capacity.

  11. Genetic diversity and population structure of Plasmodium falciparum in Thailand, a low transmission country

    Directory of Open Access Journals (Sweden)

    Sitthi-amorn Chitr

    2009-07-01

    Full Text Available Abstract Background The population structure of the causative agents of human malaria, Plasmodium sp., including the most serious agent Plasmodium falciparum, depends on the local epidemiological and demographic situations, such as the incidence of infected people, the vector transmission intensity and migration of inhabitants (i.e. exchange between sites. Analysing the structure of P. falciparum populations at a large scale, such as continents, or with markers that are subject to non-neutral selection, can lead to a masking and misunderstanding of the effective process of transmission. Thus, knowledge of the genetic structure and organization of P. falciparum populations in a particular area with neutral genetic markers is needed to understand which epidemiological factors should be targeted for disease control. Limited reports are available on the population genetic diversity and structure of P. falciparum in Thailand, and this is of particular concern at the Thai-Myanmar and Thai-Cambodian borders, where there is a reported high resistance to anti-malarial drugs, for example mefloquine, with little understanding of its potential gene flow. Methods The diversity and genetic differentiation of P. falciparum populations were analysed using 12 polymorphic apparently neutral microsatellite loci distributed on eight of the 14 different chromosomes. Samples were collected from seven provinces in the western, eastern and southern parts of Thailand. Results A strong difference in the nuclear genetic structure was observed between most of the assayed populations. The genetic diversity was comparable to the intermediate level observed in low P. falciparum transmission areas (average HS = 0.65 ± 0.17, where the lowest is observed in South America and the highest in Africa. However, uniquely the Yala province, had only a single multilocus genotype present in all samples, leading to a strong geographic differentiation when compared to the other Thai

  12. "Common synthetic scaffolds" in the synthesis of structurally diverse natural products.

    Science.gov (United States)

    Anagnostaki, Elissavet E; Zografos, Alexandros L

    2012-09-01

    Selected natural products have long been considered as desirable targets for total synthesis due to their unique biological properties and their challenging structural complexity. Laboratory synthesis of natural compounds usually relies on target-oriented synthesis, involving the production, isolation and purification of successive intermediates, requiring multiple steps to arrive to the final product. A far more economical approach using common synthetic scaffolds that can be readily transformed through biomimetic-like pathways to a range of structurally diverse natural products has been evolved in the last decade, leading synthesis to new directions. This tutorial review critically presents the hallmarks in this field.

  13. Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites

    DEFF Research Database (Denmark)

    Pham, Lan Doan; Do, Duy Ngoc; Binh, Nguyen Trong;

    2013-01-01

    geographic distances. Structure analysis indicated five homogeneous clusters. The Brahman, Lang Son, Ha Giang and U Dau Riu cattle were assigned to independent clusters while Nghe An, Thanh Hoa and Phu Yen cattle were grouped in a single cluster. We conclude that Vietnamese indigenous cattle have high levels...... of genetic diversity and distinct genetic structures. Based on these results, we recommend that for conservation homogenous populations (Nghe An, Thanh Hoa and Phu Yen) can be grouped to reduce costs and U Dau Riu, Lang Son and Ha Giang populations should be conserved separately to avoid loss of genetic...

  14. Modeling and structural analysis of evolutionarily diverse S8 family serine proteases.

    Science.gov (United States)

    Laskar, Aparna; Rodger, Euan James; Chatterjee, Aniruddha; Mandal, Chhabinath

    2011-01-01

    Serine proteases are an abundant class of enzymes that are involved in a wide range of physiological processes and are classified into clans sharing structural homology. The active site of the subtilisin-like clan contains a catalytic triad in the order Asp, His, Ser (S8 family) or a catalytic tetrad in the order Glu, Asp and Ser (S53 family). The core structure and active site geometry of these proteases is of interest for many applications. The aim of this study was to investigate the structural properties of different S8 family serine proteases from a diverse range of taxa using molecular modeling techniques. In conjunction with 12 experimentally determined three-dimensional structures of S8 family members, our predicted structures from an archaeon, protozoan and a plant were used for analysis of the catalytic core. Amino acid sequences were obtained from the MEROPS database and submitted to the LOOPP server for threading based structure prediction. The predicted structures were refined and validated using PROCHECK, SCRWL and MODELYN. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. Encompassing a wide range of taxa, our structural analysis provides an evolutionary perspective on S8 family serine proteases. Focusing on the common core containing the catalytic site of the enzyme, the analysis presented here is beneficial for future molecular modeling strategies and structure-based rational drug design.

  15. Imaging of huge lingual thyroid gland with goitre

    Energy Technology Data Exchange (ETDEWEB)

    Lee, C.C.; Chen, C.Y.; Chen, F.H.; Lee, G.W.; Hsiao, H.S. [Nat. Defense Medical Centre, Taipei (Taiwan, Province of China). Dept. of Diagnostic Radiol.; Zimmermann, R.A. [Department of Radiology, The Children`s Hospital of Philadelphia, 34th St. and Civic Blvd., Philadelphia, PA 19014 (United States)

    1998-05-01

    We present the CT and MRI findings in a 75-year-old woman with a huge pathologically proven lingual thyroid which underwent goitrous degeneration. CT and MRI showed a midline, tongue-based, exophytic mass with areas of necrosis and heterogeneous contrast enhancement, as seen in large goitres in the normal thyroid gland. (orig.) With 1 fig., 7 refs.

  16. Smart Cities as Support and Legacy of Huge Sport Events

    Directory of Open Access Journals (Sweden)

    TAURION, C.

    2012-12-01

    Full Text Available In this paper we discuss the concept of a smart city and the importance of huge Sport events as an incentive to the creation of the infrastructure necessary for the development of cities that provide quality of life for all its citizens using information technology.

  17. [Experience of surgical treatment of huge mediastinal tumors].

    Science.gov (United States)

    Li, Yuanbo; Zhang, Yi; Xu, Qingsheng; Su, Lei; Zhi, Xiuyi; Wang, Ruotian; Qian, Kun; Hu, Mu; Liu, Lei

    2014-09-23

    The diagnosis and surgical treatment of 36 huge mediastinal tumors were summarized in order to evaluate the effect and safety of the operation. Thirty-six huge mediastinal tumor patients treated in our department from June 2006 to June 2013 were retrospective analyzed, of whom clinical manifestations, diagnosis, surgical treatment and prognosis were carefully collected. Twenty-three cases were men and 13 were women. The average age was 39.2 years old. The pathology turned out to be benign in 23 cases and malignant in 13 cases. Complete resection was achieved in 34 cases while palliative resection in 2 cases with no perioperative death. Six cases had developed postoperative complications but all recovered after active treatment. Patients who had been diagnosed with benign tumors were all alive after follow-up periods of 6 months to 7 years. Nine malignat tumor patients developed recurrence or metastasis, including seven deaths. Surgery played a vital role in the diagnosis and treatment of huge mediastinal tumors. Preoperative diagnosis, accurate surgical approach and careful operation were the key to successful treatment. Benign huge mediastinal tumors had excellent prognosis with surgery.

  18. A Huge Ovarian Dermoid Cyst: Successful Laparoscopic Total Excision.

    Science.gov (United States)

    Uyanikoglu, Hacer; Dusak, Abdurrahim

    2017-08-01

    Giant ovarian cysts, ≥15 cm in diameter, are quite rare in women of reproductive age. Here, we present a case of ovarian cyst with unusual presentation treated by laparoscopic surgery. On histology, mass was found to be mature cystic teratoma. The diagnostic and management challenges posed by this huge ovarian cyst were discussed in the light of the literature.

  19. Huge mediastinal liposarcoma resected by clamshell thoracotomy: a case report.

    Science.gov (United States)

    Toda, Michihito; Izumi, Nobuhiro; Tsukioka, Takuma; Komatsu, Hiroaki; Okada, Satoshi; Hara, Kantaro; Ito, Ryuichi; Shibata, Toshihiko; Nishiyama, Noritoshi

    2017-12-01

    Liposarcoma is the single most common soft tissue sarcoma. Because mediastinal liposarcomas often grow rapidly and frequently recur locally despite adjuvant chemotherapy and radiotherapy, they require complete excision. Therefore, the feasibility of achieving complete surgical excision must be carefully considered. We here report a case of a huge mediastinal liposarcoma resected via clamshell thoracotomy. A 64-year-old man presented with dyspnea on effort. Cardiomegaly had been diagnosed 6 years previously, but had been left untreated. A computed tomography scan showed a huge (36 cm diameter) anterior mediastinal tumor expanding into the pleural cavities bilaterally. The tumor comprised mostly fatty tissue but contained two solid areas. Echo-guided needle biopsies were performed and a diagnosis of an atypical lipomatous tumor was established by pathological examination of the biopsy samples. Surgical resection was performed via a clamshell incision, enabling en bloc resection of this huge tumor. Although there was no invasion of surrounding organs, the left brachiocephalic vein was resected because it was circumferentially surrounded by tumor and could not be preserved. The tumor weighed 3500 g. Pathologic examination of the resected tumor resulted in a diagnosis of a biphasic tumor comprising dedifferentiated liposarcoma and non-adipocytic sarcoma with necrotic areas. The patient remains free of recurrent tumor 20 months postoperatively. Clamshell incision provides an excellent surgical field and can be performed safely in patients with huge mediastinal liposarcomas.

  20. Implications for Diverse Functions of the LINC Complexes Based on the Structure

    Directory of Open Access Journals (Sweden)

    Miki Hieda

    2017-01-01

    Full Text Available The linker of nucleoskeleton and cytoskeleton (LINC complex is composed of the outer and inner nuclear membrane protein families Klarsicht, Anc-1, and Syne homology (KASH, and Sad1 and UNC-84 (SUN homology domain proteins. Increasing evidence has pointed to diverse functions of the LINC complex, such as in nuclear migration, nuclear integrity, chromosome movement and pairing during meiosis, and mechanotransduction to the genome. In metazoan cells, the nuclear envelope possesses the nuclear lamina, which is a thin meshwork of intermediate filaments known as A-type and B-type lamins and lamin binding proteins. Both of lamins physically interact with the inner nuclear membrane spanning SUN proteins. The nuclear lamina has also been implicated in various functions, including maintenance of nuclear integrity, mechanotransduction, cellular signalling, and heterochromatin dynamics. Thus, it is clear that the LINC complex and nuclear lamins perform diverse but related functions. However, it is unknown whether the LINC complex–lamins interactions are involved in these diverse functions, and their regulation mechanism has thus far been elusive. Recent structural analysis suggested a dynamic nature of the LINC complex component, thus providing an explanation for LINC complex organization. This review, elaborating on the integration of crystallographic and biochemical data, helps to integrate this research to gain a better understanding of the diverse functions of the LINC complex.

  1. Genetic diversity and structure in the Endangered Allen Cays Rock Iguana, Cyclura cychlura inornata

    Directory of Open Access Journals (Sweden)

    Andrea C. Aplasca

    2016-03-01

    Full Text Available The Endangered Allen Cays Rock Iguana (Cyclura cychlura inornata is endemic to the Allen Cays, a tiny cluster of islands in the Bahamas. Naturally occurring populations exist on only two cays (<4 ha each. However, populations of unknown origin were recently discovered on four additional cays. To investigate patterns of genetic variation among these populations, we analyzed nuclear and mitochondrial markers for 268 individuals. Analysis of three mitochondrial gene regions (2,328 bp and data for eight nuclear microsatellite loci indicated low genetic diversity overall. Estimates of effective population sizes based on multilocus genotypes were also extremely low. Despite low diversity, significant population structuring and variation in genetic diversity measures were detected among cays. Genetic data confirm the source population for an experimentally translocated population while raising concerns regarding other, unauthorized, translocations. Reduced heterozygosity is consistent with a documented historical population decline due to overharvest. This study provides the first range-wide genetic analysis of this subspecies. We suggest strategies to maximize genetic diversity during ongoing recovery including additional translocations to establish assurance populations and additional protective measures for the two remaining natural populations.

  2. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.

    Science.gov (United States)

    Khanshour, Anas; Conant, Eleanore; Juras, Rytis; Cothran, Ernest Gus

    2013-01-01

    The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations.

  3. Diversity and biogeochemical structuring of bacterial communities across the Porangahau ridge accretionary prism, New Zealand

    Science.gov (United States)

    Hamdan, L.J.; Gillevet, P.M.; Pohlman, J.W.; Sikaroodi, M.; Greinert, J.; Coffin, R.B.

    2011-01-01

    Sediments from the Porangahau ridge, located off the northeastern coast of New Zealand, were studied to describe bacterial community structure in conjunction with differing biogeochemical regimes across the ridge. Low diversity was observed in sediments from an eroded basin seaward of the ridge and the community was dominated by uncultured members of the Burkholderiales. Chloroflexi/GNS and Deltaproteobacteria were abundant in sediments from a methane seep located landward of the ridge. Gas-charged and organic-rich sediments further landward had the highest overall diversity. Surface sediments, with the exception of those from the basin, were dominated by Rhodobacterales sequences associated with organic matter deposition. Taxa related to the Desulfosarcina/Desulfococcus and the JS1 candidates were highly abundant at the sulfate-methane transition zone (SMTZ) at three sites. To determine how community structure was influenced by terrestrial, pelagic and in situ substrates, sequence data were statistically analyzed against geochemical data (e.g. sulfate, chloride, nitrogen, phosphorous, methane, bulk inorganic and organic carbon pools) using the Biota-Environmental matching procedure. Landward of the ridge, sulfate was among the most significant structuring factors. Seaward of the ridge, silica and ammonium were important structuring factors. Regardless of the transect location, methane was the principal structuring factor on SMTZ communities. FEMS Microbiology Ecology ?? 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original US government works.

  4. Is the structural diversity of tripeptides sufficient for developing functional food additives with satisfactory multiple bioactivities?

    Science.gov (United States)

    Wang, Jian-Hui; Liu, Yong-Le; Ning, Jing-Heng; Yu, Jian; Li, Xiang-Hong; Wang, Fa-Xiang

    2013-05-01

    Multifunctional peptides have attracted increasing attention in the food science community because of their therapeutic potential, low toxicity and rapid intestinal absorption. However, previous study demonstrated that the limited structural variations make it difficult to optimize dipeptide molecules in a good balance between desirable and undesirable properties (F. Tian, P. Zhou, F. Lv, R. Song, Z. Li, J. Pept. Sci. 13 (2007) 549-566). In the present work, we attempt to answer whether the structural diversity is sufficient for a tripeptide to have satisfactory multiple bioactivities. Statistical test, structural examination and energetic analysis confirm that peptides of three amino acids long can bind tightly to human angiotensin converting enzyme (ACE) and thus exert significant antihypertensive efficacy. Further quantitative structure-activity relationship (QSAR) modeling and prediction of all 8000 possible tripeptides reveal that their ACE-inhibitory potency exhibits a good (positive) relationship to antioxidative activity, but has only a quite modest correlation with bitterness. This means that it is possible to find certain tripeptide entities possessing the optimal combination of strong ACE-inhibitory potency, high antioxidative activity and weak bitter taste, which are the promising candidates for developing multifunctional food additives with satisfactory multiple bioactivities. The marked difference between dipeptide and tripeptide can be attributed to the fact that the structural diversity of peptides increases dramatically with a slight change in sequence length.

  5. Fine-scale habitat structure complexity determines insectivorous bird diversity in a tropical forest

    Science.gov (United States)

    Castaño-Villa, Gabriel J.; Ramos-Valencia, Santiago A.; Fontúrbel, Francisco E.

    2014-11-01

    Habitat complexity in reforested stands has been acknowledged as a key factor that influences habitat use by birds, being especially critical for habitat disturbance-sensitive species such as tropical understory insectivorous birds. Most studies regarding the relationship between forest structure and species diversity were conducted at the landscape scale, but different diversity patterns may emerge at a finer scale (i.e., within a habitat patch). We examined a tropical reforested area (State of Caldas, Colombia), hypothesizing that insectivorous bird richness, abundance, and foraging guild abundance would increase as intra-habitat complexity increases. We established 40 monitoring plots within a reforested area, measured their structural features, and determined their relationships with species richness, total abundance, and foraging guild abundance, using Generalized Additive Models. We found that the increasing variation in basal area, stem diameter, and number of stems was positively correlated with species richness, total abundance, and foraging guild abundance. Relationships between richness or abundance and structural features were not lineal, but showing curvilinear responses and thresholds. Our results show that heterogeneity on basal area, stem diameter, and the number of stems was more correlated to insectivorous bird richness and abundance than the average of those structural features. Promoting structural variation on reforested areas by planting species with different growth rates may contribute to increase the richness and abundance of a tropical vulnerable group of species such as the understory insectivorous birds.

  6. Development of genetic diversity, differentiation and structure over 500 years in four ponderosa pine populations.

    Science.gov (United States)

    Lesser, M R; Parchman, T L; Jackson, S T

    2013-05-01

    Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range-margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range-margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500-year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within-population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (F(ST) and Jost's D(est)) and diversity within populations (F(IS)) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century.

  7. QSAR study on estrogenic activity of structurally diverse compounds using generalized regression neural network

    Institute of Scientific and Technical Information of China (English)

    JI Li; WANG XiaoDong; LUO Si; QIN Liang; YANG XvShu; LIU ShuShen; WANG LianSheng

    2008-01-01

    Computer-based quantitative structure-activity relationship (QSAR) model has been becoming a powerful tool in understanding the structural requirements for chemicals to bind the estrogen receptor (ER), designing drugs for human estrogen replacement therapy, and identifying potential estrogenic endocrine disruptors, in this study, a simple yet powerful neural network technique, generalized regression neural network (GRNN) was used to develop a QSAR model based on 131 structurally diverse estrogens (training set). Only nine descriptors calculated solely from the molecular structures of compounds selected by objective and subjective feature selections were used as inputs of the GRNN model. The predictive power of the built model was found to be comparable to that of the more traditional techniques but requiring significantly easy implementation and a shorter computation-time. The obtained result indicates that the proposed GRNN model is robust and satisfactory, and can provide a feasible and practical tool for the rapid screening of the estrogenic activity of organic compounds.

  8. Discovery of structurally diverse and bioactive compounds from plant resources in China

    Institute of Scientific and Technical Information of China (English)

    Sheng-ping YANG; Jian-min YUE

    2012-01-01

    This review describes the major discoveries of structurally diverse and/or biologically significant compounds from plant resources in China,mainly from the traditional Chinese medicines (TCMs) since the establishment of our research group in 1999.In the past decade,a large array of biologically significant and novel structures has been identified from plant resources (or TCM) in our laboratory.The structural modification of several biologically important compounds led to more than 400 derivatives,some of which exhibited significantly improved activities and provided opportunities to elucidate the structure-activity relationship of the related compound class.These findings are important for drug discovery and help us understand the biological basis for the traditional applications of these plants in TCM.

  9. Structural and functional diversity of nonapeptide hormones from an evolutionary perspective: A review.

    Science.gov (United States)

    Banerjee, P; Joy, K P; Chaube, R

    2017-01-15

    The article presents an overview of the comparative distribution, structure and functions of the nonapeptide hormones in chordates and non chordates. The review begins with a historical preview of the advent of the concept of neurosecretion and birth of neuroendocrine science, pioneered by the works of E. Scharrer and W. Bargmann. The sections which follow discuss different vertebrate nonapeptides, their distribution, comparison, precursor gene structures and processing, highlighting the major differences in these aspects amidst the conserved features across vertebrates. The vast literature on the anatomical characteristics of the nonapeptide secreting nuclei in the brain and their projections was briefly reviewed in a comparative framework. Recent knowledge on the nonapeptide hormone receptors and their intracellular signaling pathways is discussed and few grey areas which require deeper studies are identified. The sections on the functions and regulation of nonapeptides summarize the huge and ever increasing literature that is available in these areas. The nonapeptides emerge as key homeostatic molecules with complex regulation and several synergistic partners. Lastly, an update of the nonapeptides in non chordates with respect to distribution, site of synthesis, functions and receptors, dealt separately for each phylum, is presented. The non chordate nonapeptides share many similarities with their counterparts in vertebrates, pointing the system to have an ancient origin and to be an important substrate for changes during adaptive evolution. The article concludes projecting the nonapeptides as one of the very first common molecules of the primitive nervous and endocrine systems, which have been retained to maintain homeostatic functions in metazoans; some of which are conserved across the animal kingdom and some are specialized in a group/lineage-specific manner.

  10. Stand Structure and Substrate Diversity as Two Major Drivers for Bryophyte Distribution in a Temperate Montane Ecosystem

    Directory of Open Access Journals (Sweden)

    Yun Chen

    2017-05-01

    Full Text Available Elucidating the major drivers of bryophyte distribution is the first step to protecting bryophyte diversity. Topography, forest, substrates (ground, tree trunks, roots, rocks, and rotten wood, and spatial factor, which factors are the major drivers of bryophyte distribution? In this study, 53 plots were set in 400 m2 along the elevation gradient in Xiaoqinling, China. All bryophytes in the plots were collected and identified. Regression analysis was used to examine the relationship between bryophyte and substrate diversity. We compared the patterns of overall bryophyte diversity and diversity of bryophytes found on the ground, tree, and rock along elevational gradients. Canonical correspondence analysis was applied to relate species composition to selected environmental variables. The importance of topography, forest, substrates, and spatial factors was determined by variance partitioning. A total of 1378 bryophyte specimens were collected, and 240 species were identified. Bryophyte diversity was closely related to substrate diversity. The overall bryophyte diversity significantly increased with elevation; however, the response varied among ground, tree, and rock bryophytes. Tree diversity and herb layer were considered important environmental factors in determining bryophyte distribution. Species abundance was best explained by stand structure (17%, and species diversity was best explained by stand structure (35% and substrate (40%. Results directly indicated that substrate diversity can improve bryophyte species diversity. The effects of micro-habitat formed by stand structure and substrate diversity were higher than those of spatial processes and topography factors on bryophyte distribution. This study proved that the determinant factors influencing bryophyte diversity reflect the trends in recent forest management, providing a real opportunity to improve forest biodiversity conservation.

  11. Parasites affect food web structure primarily through increased diversity and complexity.

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    Jennifer A Dunne

    Full Text Available Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity, particularly when including concomitant links (links from predators to parasites of their prey. However, we clarify prior claims that parasites "dominate" food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites' roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites' feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic

  12. Parasites affect food web structure primarily through increased diversity and complexity

    Science.gov (United States)

    Dunne, Jennifer A.; Lafferty, Kevin D.; Dobson, Andrew P.; Hechinger, Ryan F.; Kuris, Armand M.; Martinez, Neo D.; McLaughlin, John P.; Mouritsen, Kim N.; Poulin, Robert; Reise, Karsten; Stouffer, Daniel B.; Thieltges, David W.; Williams, Richard J.; Zander, Claus Dieter

    2013-01-01

    Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity), particularly when including concomitant links (links from predators to parasites of their prey). However, we clarify prior claims that parasites ‘‘dominate’’ food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites’ roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites’ feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic

  13. Status of the genetic diversity and population structure of the Pêga donkey.

    Science.gov (United States)

    Santana, Mário Luiz; Bignardi, Annaiza Braga

    2015-12-01

    Pedigree analysis was extended to the Pêga donkey population in order to evaluate the status of genetic diversity and population structure. All parameters were computed for three reference populations of animals born between 2004 and 2014: all animals, animals with mouse gray coat color, and animals with roan coat color. Although the average inbreeding coefficient observed was low (about 3 %), highly inbred animals are present in the current population. The effective population size based on the individual inbreeding rate was 35, while the effective population size based on the individual coancestry rate was about three times higher. The number of equivalent subpopulations was at around three, indicating that the Pêga donkey population is highly structured. There is no evidence of differentiation between subpopulations based on the coat color of the animals (Nei's minimum distance 0.10 %). The breeding policy of Pêga donkeys is predominantly intra-herd. The loss of genetic diversity since the founder generations can be considered small in Pêga donkeys (1.25 %). The excessive contribution of few ancestors to the gene pool may lead to narrower bottlenecks in the pedigree of this population in the future. The long generation interval in Pêga donkeys (10.7 years) may be considered an advantage to reduce the increase in inbreeding and to maintain the genetic diversity of these animals.

  14. Genetic diversity and population structure of Lactobacillus delbrueckii subspecies bulgaricus isolated from naturally fermented dairy foods.

    Science.gov (United States)

    Song, Yuqin; Sun, Zhihong; Guo, Chenyi; Wu, Yarong; Liu, Wenjun; Yu, Jie; Menghe, Bilige; Yang, Ruifu; Zhang, Heping

    2016-03-04

    Lactobacillus delbrueckii subsp. bulgaricus is one of the most widely used starter culture strains in industrial fermented dairy manufacture. It is also common in naturally fermented dairy foods made using traditional methods. The subsp. bulgaricus strains found in naturally fermented foods may be useful for improving current industrial starter cultures; however, little is known regarding its genetic diversity and population structure. Here, a collection of 298 L. delbrueckii strains from naturally fermented products in Mongolia, Russia, and West China was analyzed by multi-locus sequence typing based on eight conserved genes. The 251 confirmed subsp. bulgaricus strains produced 106 unique sequence types, the majority of which were assigned to five clonal complexes (CCs). The geographical distribution of CCs was uneven, with CC1 dominated by Mongolian and Russian isolates, and CC2-CC5 isolates exclusively from Xinjiang, China. Population structure analysis suggested six lineages, L1-L6, with various homologous recombination rates. Although L2-L5 were mainly restricted within specific regions, strains belonging to L1 and L6 were observed in diverse regions, suggesting historical transmission events. These results greatly enhance our knowledge of the population diversity of subsp. bulgaricus strains, and suggest that strains from CC1 and L4 may be useful as starter strains in industrial fermentation.

  15. Genetic diversity and structure of Brazilian ginger germplasm (Zingiber officinale) revealed by AFLP markers.

    Science.gov (United States)

    Blanco, Eleonora Zambrano; Bajay, Miklos Maximiliano; Siqueira, Marcos Vinícius Bohrer Monteiro; Zucchi, Maria Imaculada; Pinheiro, José Baldin

    2016-12-01

    Ginger is a vegetable with medicinal and culinary properties widely cultivated in the Southern and Southeastern Brazil. The knowledge of ginger species' genetic variability is essential to direct correctly future studies of conservation and genetic improvement, but in Brazil, little is known about this species' genetic variability. In this study, we analyzed the genetic diversity and structure of 55 Brazilian accessions and 6 Colombian accessions of ginger, using AFLP (Amplified Fragment Length Polymorphism) molecular markers. The molecular characterization was based on 13 primers combinations, which generated an average of 113.5 polymorphic loci. The genetic diversity estimates of Nei (Hj), Shannon-Weiner index (I) and an effective number of alleles (n e ) were greater in the Colombian accessions in relation to the Brazilian accessions. The analysis of molecular variance showed that most of the genetic variation occurred between the two countries while in the Brazilian populations there is no genetic structure and probably each region harbors 100 % of genetic variation found in the samples. The bayesian model-based clustering and the dendrogram using the dissimilarity's coefficient of Jaccard were congruent with each other and showed that the Brazilian accessions are highly similar between themselves, regardless of the geographic region of origin. We suggested that the exploration of the interspecific variability and the introduction of new varieties of Z.officinale are viable alternatives for generating diversity in breeding programs in Brazil. The introduction of new genetic materials will certainly contribute to a higher genetic basis of such crop.

  16. Genetic diversity and population structure of genes encoding vaccine candidate antigens of Plasmodium vivax

    Directory of Open Access Journals (Sweden)

    Chenet Stella M

    2012-03-01

    Full Text Available Abstract Background A major concern in malaria vaccine development is genetic polymorphisms typically observed among Plasmodium isolates in different geographical areas across the world. Highly polymorphic regions have been observed in Plasmodium falciparum and Plasmodium vivax antigenic surface proteins such as Circumsporozoite protein (CSP, Duffy-binding protein (DBP, Merozoite surface protein-1 (MSP-1, Apical membrane antigen-1 (AMA-1 and Thrombospondin related anonymous protein (TRAP. Methods Genetic variability was assessed in important polymorphic regions of various vaccine candidate antigens in P. vivax among 106 isolates from the Amazon Region of Loreto, Peru. In addition, genetic diversity determined in Peruvian isolates was compared to population studies from various geographical locations worldwide. Results The structured diversity found in P. vivax populations did not show a geographic pattern and haplotypes from all gene candidates were distributed worldwide. In addition, evidence of balancing selection was found in polymorphic regions of the trap, dbp and ama-1 genes. Conclusions It is important to have a good representation of the haplotypes circulating worldwide when implementing a vaccine, regardless of the geographic region of deployment since selective pressure plays an important role in structuring antigen diversity.

  17. The Sg-1 glycosyltransferase locus regulates structural diversity of triterpenoid saponins of soybean.

    Science.gov (United States)

    Sayama, Takashi; Ono, Eiichiro; Takagi, Kyoko; Takada, Yoshitake; Horikawa, Manabu; Nakamoto, Yumi; Hirose, Aya; Sasama, Hiroko; Ohashi, Mihoko; Hasegawa, Hisakazu; Terakawa, Teruhiko; Kikuchi, Akio; Kato, Shin; Tatsuzaki, Nana; Tsukamoto, Chigen; Ishimoto, Masao

    2012-05-01

    Triterpene saponins are a diverse group of biologically functional products in plants. Saponins usually are glycosylated, which gives rise to a wide diversity of structures and functions. In the group A saponins of soybean (Glycine max), differences in the terminal sugar species located on the C-22 sugar chain of an aglycone core, soyasapogenol A, were observed to be under genetic control. Further genetic analyses and mapping revealed that the structural diversity of glycosylation was determined by multiple alleles of a single locus, Sg-1, and led to identification of a UDP-sugar-dependent glycosyltransferase gene (Glyma07g38460). Although their sequences are highly similar and both glycosylate the nonacetylated saponin A0-αg, the Sg-1(a) allele encodes the xylosyltransferase UGT73F4, whereas Sg-1(b) encodes the glucosyltransferase UGT73F2. Homology models and site-directed mutagenesis analyses showed that Ser-138 in Sg-1(a) and Gly-138 in Sg-1(b) proteins are crucial residues for their respective sugar donor specificities. Transgenic complementation tests followed by recombinant enzyme assays in vitro demonstrated that sg-1(0) is a loss-of-function allele of Sg-1. Considering that the terminal sugar species in the group A saponins are responsible for the strong bitterness and astringent aftertastes of soybean seeds, our findings herein provide useful tools to improve commercial properties of soybean products.

  18. Natural Allelic Diversity, Genetic Structure and Linkage Disequilibrium Pattern in Wild Chickpea

    Science.gov (United States)

    Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Kumar, Vinod; Singh, Mohar; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.

    2014-01-01

    Characterization of natural allelic diversity and understanding the genetic structure and linkage disequilibrium (LD) pattern in wild germplasm accessions by large-scale genotyping of informative microsatellite and single nucleotide polymorphism (SNP) markers is requisite to facilitate chickpea genetic improvement. Large-scale validation and high-throughput genotyping of genome-wide physically mapped 478 genic and genomic microsatellite markers and 380 transcription factor gene-derived SNP markers using gel-based assay, fluorescent dye-labelled automated fragment analyser and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass array have been performed. Outcome revealed their high genotyping success rate (97.5%) and existence of a high level of natural allelic diversity among 94 wild and cultivated Cicer accessions. High intra- and inter-specific polymorphic potential and wider molecular diversity (11–94%) along with a broader genetic base (13–78%) specifically in the functional genic regions of wild accessions was assayed by mapped markers. It suggested their utility in monitoring introgression and transferring target trait-specific genomic (gene) regions from wild to cultivated gene pool for the genetic enhancement. Distinct species/gene pool-wise differentiation, admixed domestication pattern, and differential genome-wide recombination and LD estimates/decay observed in a six structured population of wild and cultivated accessions using mapped markers further signifies their usefulness in chickpea genetics, genomics and breeding. PMID:25222488

  19. Light habitat, structure, diversity and dynamic of the tropical dry forest

    Directory of Open Access Journals (Sweden)

    Omar Melo-Cruz

    2017-01-01

    Full Text Available Tropical dry forests are complex and fragile ecosystems with high anthropic intervention and restricted reproductive cycles. These have unique richness, structural diversity, physiological and phenological . This research was executed  in the Upper Magdalena Valley, in four forest fragments with different successional stages. In each fragment four permanent plots of 0.25 ha were established and lighting habitat associated with richness, relative abundance and rarity of species. The forest dynamics included the mortality, recruitment and diameter growth for a period of 5.25 years. The species rischness found in the mature riparian forestis higher than that reported in other studies of similar areas in Valle del Cauca and the Atlantic coast.  The values of richness, diversity and rarity species are more evidenced  than the magnitudes found in  drier areas of Tolima. The structure, diversity and dynamics of forests were correlated with the lighting habitat, showing differences in canopy architecture and its role in the capture and absorption of radiation. Forests with dense canopy have limited availability of photosynthetically active radiation in understory related low species richness, while illuminated undergrowth are richer and heterogeneous.

  20. Facile synthesis of diverse graphene nanomeshes based on simultaneous regulation of pore size and surface structure

    Science.gov (United States)

    Zhang, Jia; Song, Huaibing; Zeng, Dawen; Wang, Hao; Qin, Ziyu; Xu, Keng; Pang, Aimin; Xie, Changsheng

    2016-08-01

    Recently, graphene nanomesh (GNM) has attracted great attentions due to its unique porous structure, abundant active sites, finite band gap and possesses potential applications in the fields of electronics, gas sensor/storage, catalysis, etc. Therefore, diverse GNMs with different physical and chemical properties are required urgently to meet different applications. Herein we demonstrate a facile synthetic method based on the famous Fenton reaction to prepare GNM, by using economically fabricated graphene oxide (GO) as a starting material. By precisely controlling the reaction time, simultaneous regulation of pore size from 2.9 to 11.1 nm and surface structure can be realized. Ultimately, diverse GNMs with tunable band gap and work function can be obtained. Specially, the band gap decreases from 4.5-2.3 eV for GO, which is an insulator, to 3.9-1.24 eV for GNM-5 h, which approaches to a semiconductor. The dual nature of electrophilic addition and oxidizability of HO• is responsible for this controllable synthesis. This efficient, low-cost, inherently scalable synthetic method is suitable for provide diverse and optional GNMs, and may be generalized to a universal technique.

  1. Mechanisms shaping size structure and functional diversity of phytoplankton communities in the ocean

    Science.gov (United States)

    Acevedo-Trejos, Esteban; Brandt, Gunnar; Bruggeman, Jorn; Merico, Agostino

    2015-03-01

    The factors regulating phytoplankton community composition play a crucial role in structuring aquatic food webs. However, consensus is still lacking about the mechanisms underlying the observed biogeographical differences in cell size composition of phytoplankton communities. Here we use a trait-based model to disentangle these mechanisms in two contrasting regions of the Atlantic Ocean. In our model, the phytoplankton community can self-assemble based on a trade-off emerging from relationships between cell size and (1) nutrient uptake, (2) zooplankton grazing, and (3) phytoplankton sinking. Grazing `pushes' the community towards larger cell sizes, whereas nutrient uptake and sinking `pull' the community towards smaller cell sizes. We find that the stable environmental conditions of the tropics strongly balance these forces leading to persistently small cell sizes and reduced size diversity. In contrast, the seasonality of the temperate region causes the community to regularly reorganize via shifts in species composition and to exhibit, on average, bigger cell sizes and higher size diversity than in the tropics. Our results raise the importance of environmental variability as a key structuring mechanism of plankton communities in the ocean and call for a reassessment of the current understanding of phytoplankton diversity patterns across latitudinal gradients.

  2. Fungal endophytes of aquatic macrophytes: diverse host-generalists characterized by tissue preferences and geographic structure.

    Science.gov (United States)

    Sandberg, Dustin C; Battista, Lorna J; Arnold, A Elizabeth

    2014-05-01

    Most studies of endophytic symbionts have focused on terrestrial plants, neglecting the ecologically and economically important plants present in aquatic ecosystems. We evaluated the diversity, composition, host and tissue affiliations, and geographic structure of fungal endophytes associated with common aquatic plants in lentic waters in northern Arizona, USA. Endophytes were isolated in culture from roots and photosynthetic tissues during two growing seasons. A total of 226 isolates representing 60 putative species was recovered from 9,600 plant tissue segments. Although isolation frequency was low, endophytes were phylogenetically diverse and species-rich. Comparisons among the most thoroughly sampled species and reservoirs revealed that isolation frequency and diversity did not differ significantly between collection periods, among species, among reservoirs, or as a function of depth. However, community structure differed significantly among reservoirs and tissue types. Phylogenetic analyses of a focal genus (Penicillium) corroborated estimates of species boundaries and informed community analyses, highlighting clade- and genotype-level affiliations of aquatic endophytes with both sediment- and waterborne fungi, and endophytes of proximate terrestrial plants. Together these analyses provide a first quantitative examination of endophytic associations in roots and foliage of aquatic plants and can be used to optimize survey strategies for efficiently capturing fungal biodiversity at local and regional scales.

  3. Earthworm-Mycorrhiza Interactions Can Affect the Diversity, Structure and Functioning of Establishing Model Grassland Communities

    Science.gov (United States)

    Zaller, Johann G.; Heigl, Florian; Grabmaier, Andrea; Lichtenegger, Claudia; Piller, Katja; Allabashi, Roza; Frank, Thomas; Drapela, Thomas

    2011-01-01

    belowground-aboveground linkages involving earthworms and AMF are important mediators of the diversity, structure and functioning of plant communities. PMID:22216236

  4. Earthworm-mycorrhiza interactions can affect the diversity, structure and functioning of establishing model grassland communities.

    Directory of Open Access Journals (Sweden)

    Johann G Zaller

    demonstrates that belowground-aboveground linkages involving earthworms and AMF are important mediators of the diversity, structure and functioning of plant communities.

  5. Forest structure, diversity and regeneration potential along altitudinal gradient in Dhanaulti of Garhwal Himalaya

    Directory of Open Access Journals (Sweden)

    Sushil Saha

    2016-07-01

    Full Text Available Aim of the study: The aim of the present study was to understatnd the forest composition, structure, diversity and regeneration potential along altitudinal gradient. Area of study: The study was carried out in Dhanaulti forest which falls under temperate region of Garhwal Himalaya in Uttarakhand state, India. Material and Methods: Vegetation analysis was carried out using 10 quadrats at each altitude using a quadrate size of 10×10 m2. In each quadrate, categories of trees >30 cm cbh were considered as trees, 10-30cm cbh as saplings and <10 cm cbh as seedlings. The data were quantitatively analyzed. Main results: In upper and middle altitudes, Cedrus deodara was reported dominant tree whereas, in lower altitude Quercus leucotrichophora was reported dominant. Tree density was highest in lower altitude which reduced middle and upper altitudes whereas, total basal cover increased with increasing altitude. The increasing total basal cover with altitude could be because of the presence of Cedrus deodara trees having higher girth classes. In tree, sapling and seedling layers, diversity (H and equitabiltiy (EC decreased with increasing altitude. However, concentrations of dominace (CD and beta diversity (BD have shown reverse trend with H and EC which increased with increasing altitudes, in each layer of tree, sapling and seedling. The distribution pattern of most species in all layers of trees, saplings and seedlings was contagious. The regeneration potential of the species has shown that some of the species in the absence of tree layer are still regenerating particularly, Rhododendron arboreum, Benthamidia capitata, Neolitsea pallens etc. It indicates that most of the species are shifting upward as they are getting suitable conditions. Research highlights: Altitude influence species composition, diversity and regeneration potential of species. Key words: Distribution pattern; tree diversity; regeneration; mountains; temperate; Himalaya.

  6. Octopus vulgaris (Cuvier, 1797) in the Mediterranean Sea: Genetic Diversity and Population Structure.

    Science.gov (United States)

    De Luca, Daniele; Catanese, Gaetano; Procaccini, Gabriele; Fiorito, Graziano

    2016-01-01

    The common octopus, Octopus vulgaris Cuvier 1797, is a largely exploited cephalopod species in the Mediterranean Sea and the Atlantic Ocean, as well as along the coasts of Africa, Brazil and Japan, where its taxonomic identity is still debated. The assessment of its genetic structure is a pressing need to correctly manage the resource and to avoid overfishing and collapsing of local stocks. Here we analysed genetic variation and population structure of O. vulgaris using thirteen microsatellite loci in seven sampling localities from the Mediterranean Sea and one from the Atlantic Ocean. We also used a DNA barcoding approach by COI gene fragment to understand the phylogenetic relationships among the specimens here investigated and the ones whose sequences are available in literature. Our results reveal high levels of allelic richness and moderate heterozygosity in all samples investigated, and a pronounced differentiation of the Atlantic and Sicilian specimens. This latter aspect seems to support the isolation of the biota within the Strait of Messina. A certain degree of differentiation was detected among the other geographic samples within the Mediterranean Sea, which is more compatible with an island model than isolation by distance. The occurrence of null alleles affected more genetic diversity indices than population structure estimations. This study provides new insights about the genetic diversity and structure of O. vulgaris in the area of interest, which can be used as guidelines for a fisheries management perspective.

  7. Octopus vulgaris (Cuvier, 1797 in the Mediterranean Sea: Genetic Diversity and Population Structure.

    Directory of Open Access Journals (Sweden)

    Daniele De Luca

    Full Text Available The common octopus, Octopus vulgaris Cuvier 1797, is a largely exploited cephalopod species in the Mediterranean Sea and the Atlantic Ocean, as well as along the coasts of Africa, Brazil and Japan, where its taxonomic identity is still debated. The assessment of its genetic structure is a pressing need to correctly manage the resource and to avoid overfishing and collapsing of local stocks. Here we analysed genetic variation and population structure of O. vulgaris using thirteen microsatellite loci in seven sampling localities from the Mediterranean Sea and one from the Atlantic Ocean. We also used a DNA barcoding approach by COI gene fragment to understand the phylogenetic relationships among the specimens here investigated and the ones whose sequences are available in literature. Our results reveal high levels of allelic richness and moderate heterozygosity in all samples investigated, and a pronounced differentiation of the Atlantic and Sicilian specimens. This latter aspect seems to support the isolation of the biota within the Strait of Messina. A certain degree of differentiation was detected among the other geographic samples within the Mediterranean Sea, which is more compatible with an island model than isolation by distance. The occurrence of null alleles affected more genetic diversity indices than population structure estimations. This study provides new insights about the genetic diversity and structure of O. vulgaris in the area of interest, which can be used as guidelines for a fisheries management perspective.

  8. Bacterial community structure and diversity in a black soil as affected by long-term fertilization

    Institute of Scientific and Technical Information of China (English)

    WEI Dan; YANG Qian; ZHANG Jun-Zheng; WANG Shuang; CHEN Xue-Li; ZHANG Xi-Lin; LI Wei-Qun

    2008-01-01

    Black soil (Mollisol) is one of the main soil types in northeastern China.Biolog and polymerase chain reactiondenaturing gradient gel electrophoresis (PCR-DGGE) methods were used to examine the influence of various fertilizer combinations on the structure and function of the bacterial community in a black soil collected from Harbin,Heilongjiang Province.Biolog results showed that substrate richness and catabolic diversity of the soil bacterial community were the greatest in the chemical fertilizer and chemical fertilizer+manure treatments.The metabolic ability of the bacterial community in the manure treatment was similar to the control.DGGE fingerprinting indicated similarity in the distribution of most 16S rDNA bands among all treatments,suggesting that microorganisms with those bands were stable and not influenced by fertilization.However,chemical fertilizer increased the diversity of soil bacterial community.Principal component analysis of Biolog and DGGE data revealed that the structure and function of the bacterial community were similar in the control and manure treatments,suggesting that the application of manure increased the soil microbial population,but had no effect on the bacterial community structure.Catabolic function was similar in the chemical fertilizer and chemical fertilizer+manure treatments,but the composition structure of the soil microbes differed between them.The use of chemical fertilizers could result in a decline in the catabolic activity of fast-growing or eutrophic bacteria.

  9. Diversity and Structure of the Gama Gallery Forest in Central Brazil in 2009

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    Roberto Tramontina Araujo

    2016-06-01

    Full Text Available The objective of this study was to evaluate the diversity and structure of the tree community of the Gama gallery forest, in the Federal District, in 2009. A total of 151 permanent plots of 10×20 m were allocated continually along ten lines perpendicular to the watercourse. All individuals with diameter at breast height (DBH equal or greater than 10 cm were tagged and measured. In total, 114 species in 52 families and 96 genera were identified. The density was 643 ind.ha-1, the basal area was 31.52 m2.ha-1 and 13 species were frequently at least in 25% of the plots. The Shannon index was 3.91 nats.ind-1 and the Pielou index was 82%, expressing the good conservation condition and the high diversity of the vegetation. The diameter distribution curve showed an "inverted J" pattern.

  10. Fish diversity and assemblage structure in Ken River of Panna landscape, central India

    Directory of Open Access Journals (Sweden)

    J.A. Johnson

    2012-10-01

    Full Text Available Fish diversity and assemblage structure in relation to habitat variables were studied in 15 sites in Panna landscape, central India. The sampling was performed between February-April 2009. Fifty species of fishes belonging to 32 genera, 15 families and four orders were recorded from the study area. Cyprinids were the dominant assemblage members in all study streams (abundance ranges from 56.6-94.5 %. The cyprinid Devario aequipinnatus and the snakehead Channa gachua had highest local dominance (80% each in Panna landscape. High Shannon and Margalef’s diversity was recorded in Madla region of Ken River. Similarity cluster analysis explained the study sites along Ken River (Gahrighat, Magradabri and Madla had similar faunal assemblage. Canonical Correspondence Analysis (CCA was performed to study the species association with a set of environmental variables. The CCA revealed that cyprinid abundance was associated with stream order, deeper habitat, flow and water temperature.

  11. Genetic diversity and population structure of 20 North European cattle breeds

    DEFF Research Database (Denmark)

    kantanen, J; Olsaker, Ingrid; Holm, Lars-Erik

    2000-01-01

    , allelic diversity has been reduced in several breeds, which was explained by limited effective population sizes over the course of man-directed breed development and demographic bottlenecks of indigenous breeds. A tree showing genetic relationships between breeds was constructed from a matrix of random......Blood samples were collected from 743 animals from 15 indigenous, 2 old imported, and 3 commercial North European cattle breeds. The samples were analyzed for 11 erythrocyte antigen systems, 8 proteins, and 10 microsatellites, and used to assess inter- and intrabreed genetic variation and genetic...... population structures. The microsatellites BoLA-DRBP1 and CSSM66 were nonneutral markers according to the Ewens-Watterson test, suggesting some kind of selection imposed on these loci. North European cattle breeds displayed generally similar levels of multilocus heterozygosity and allelic diversity. However...

  12. Modeling the binding affinity of structurally diverse industrial chemicals to carbon using the artificial intelligence approaches.

    Science.gov (United States)

    Gupta, Shikha; Basant, Nikita; Rai, Premanjali; Singh, Kunwar P

    2015-11-01

    Binding affinity of chemical to carbon is an important characteristic as it finds vast industrial applications. Experimental determination of the adsorption capacity of diverse chemicals onto carbon is both time and resource intensive, and development of computational approaches has widely been advocated. In this study, artificial intelligence (AI)-based ten different qualitative and quantitative structure-property relationship (QSPR) models (MLPN, RBFN, PNN/GRNN, CCN, SVM, GEP, GMDH, SDT, DTF, DTB) were established for the prediction of the adsorption capacity of structurally diverse chemicals to activated carbon following the OECD guidelines. Structural diversity of the chemicals and nonlinear dependence in the data were evaluated using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. The generalization and prediction abilities of the constructed models were established through rigorous internal and external validation procedures performed employing a wide series of statistical checks. In complete dataset, the qualitative models rendered classification accuracies between 97.04 and 99.93%, while the quantitative models yielded correlation (R(2)) values of 0.877-0.977 between the measured and the predicted endpoint values. The quantitative prediction accuracies for the higher molecular weight (MW) compounds (class 4) were relatively better than those for the low MW compounds. Both in the qualitative and quantitative models, the Polarizability was the most influential descriptor. Structural alerts responsible for the extreme adsorption behavior of the compounds were identified. Higher number of carbon and presence of higher halogens in a molecule rendered higher binding affinity. Proposed QSPR models performed well and outperformed the previous reports. A relatively better performance of the ensemble learning models (DTF, DTB) may be attributed to the strengths of the bagging and boosting algorithms which enhance the predictive accuracies. The

  13. Forest structure in low-diversity tropical forests: a study of Hawaiian wet and dry forests.

    Directory of Open Access Journals (Sweden)

    Rebecca Ostertag

    Full Text Available The potential influence of diversity on ecosystem structure and function remains a topic of significant debate, especially for tropical forests where diversity can range widely. We used Center for Tropical Forest Science (CTFS methodology to establish forest dynamics plots in montane wet forest and lowland dry forest on Hawai'i Island. We compared the species diversity, tree density, basal area, biomass, and size class distributions between the two forest types. We then examined these variables across tropical forests within the CTFS network. Consistent with other island forests, the Hawai'i forests were characterized by low species richness and very high relative dominance. The two Hawai'i forests were floristically distinct, yet similar in species richness (15 vs. 21 species and stem density (3078 vs. 3486/ha. While these forests were selected for their low invasive species cover relative to surrounding forests, both forests averaged 5->50% invasive species cover; ongoing removal will be necessary to reduce or prevent competitive impacts, especially from woody species. The montane wet forest had much larger trees, resulting in eightfold higher basal area and above-ground biomass. Across the CTFS network, the Hawaiian montane wet forest was similar to other tropical forests with respect to diameter distributions, density, and aboveground biomass, while the Hawai'i lowland dry forest was similar in density to tropical forests with much higher diversity. These findings suggest that forest structural variables can be similar across tropical forests independently of species richness. The inclusion of low-diversity Pacific Island forests in the CTFS network provides an ∼80-fold range in species richness (15-1182 species, six-fold variation in mean annual rainfall (835-5272 mm yr(-1 and 1.8-fold variation in mean annual temperature (16.0-28.4°C. Thus, the Hawaiian forest plots expand the global forest plot network to enable testing of ecological

  14. The impact of structural diversity and parameterization on maps of the protein universe.

    Science.gov (United States)

    Asarnow, Daniel; Singh, Rahul

    2013-12-20

    Low dimensional maps of protein structure space (MPSS) provide a powerful global representation of all proteins. In such mappings structural relationships are depicted through spatial adjacency of points, each of which represents a molecule. MPSS can help in understanding the local and global topological characteristics of the structure space, as well as elucidate structure-function relationships within and between sets of proteins. A number of meta- and method-dependent parameters are involved in creating MPSS. However, at the state-of-the-art, a systematic investigation of the influence of these parameters on MPSS construction has yet to be carried out. Further, while specific cases in which MPSS out-perform pairwise distances for prediction of functional annotations have been noted, no general explanation for this phenomenon has yet been advanced. We address the above questions within the technical context of creating MPSS by utilizing multidimensional scaling (MDS) for obtaining low-dimensional projections of structure alignment distances. MDS is demonstrated as an effective method for construction of MPSS where related structures are co-located, even when their functional and evolutionary proximity cannot be deduced from distributions of pairwise comparisons alone. In particular, we show that MPSS exceed pairwise distance distributions in predictive capability for those annotations of shared function or origin which are characterized by a high level of structural diversity. We also determine the impact of the choice of structure alignment and MDS algorithms on the accuracy of such predictions.

  15. Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure.

    Directory of Open Access Journals (Sweden)

    Cody S Sheik

    Full Text Available Extensive use of chromium (Cr and arsenic (As based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI. Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways.

  16. Forest structure, diversity and soil properties in a dry tropical forest in Rajasthan, Western India

    Directory of Open Access Journals (Sweden)

    J. I. Nirmal Kumar

    2011-06-01

    Full Text Available Structure, species composition, and soil properties of a dry tropical forest in Rajasthan Western India, were examined by establishment of 25 plots. The forest was characterized by a relatively low canopy and a large number of small-diameter trees. Mean canopy height for this forest was 10 m and stands contained an average of 995 stems ha-1 (= 3.0 cm DBH; 52% of those stems were smaller than 10 cm DBH. The total basal area was 46.35 m2ha-1, of which Tectona grandis L. contributed 48%. The forest showed high species diversity of trees. 50 tree species (= 3.0 cm DBH from 29 families were identified in the 25 sampling plots. T. grandis (20.81% and Butea monosperma (9% were the dominant and subdominant species in terms of importance value. The mean tree species diversity indices for the plots were 1.08 for Shannon diversity index (H´, 0.71 for equitability index (J´ and 5.57 for species richness index (S´, all of which strongly declined with the increase of importance value of the dominant, T. grandis. Measures of soil nutrients indicated low fertility, extreme heterogeneity. Regression analysis showed that stem density and the dominant tree height were significantly correlated with soil pH. There was a significant positive relationship between species diversity index and soil available P, exchangeable K+, Ca2+ (all p values < 0.001 and a negative relationship with N, C, C:N and C:P ratio. The results suggest that soil properties are major factors influencing forest composition and structure within the dry tropical forest in Rajasthan.

  17. Orientation of aromatic residues in amyloid cores: Structural insights into prion fiber diversity

    KAUST Repository

    Reymer, Anna

    2014-11-17

    Structural conversion of one given protein sequence into different amyloid states, resulting in distinct phenotypes, is one of the most intriguing phenomena of protein biology. Despite great efforts the structural origin of prion diversity remains elusive, mainly because amyloids are insoluble yet noncrystalline and therefore not easily amenable to traditional structural-biology methods. We investigate two different phenotypic prion strains, weak and strong, of yeast translation termination factor Sup35 with respect to angular orientation of tyrosines using polarized light spectroscopy. By applying a combination of alignment methods the degree of fiber orientation can be assessed, which allows a relatively accurate determination of the aromatic ring angles. Surprisingly, the strains show identical average orientations of the tyrosines, which are evenly spread through the amyloid core. Small variations between the two strains are related to the local environment of a fraction of tyrosines outside the core, potentially reflecting differences in fibril packing.

  18. Fine structure of Tibetan kefir grains and their yeast distribution, diversity, and shift.

    Directory of Open Access Journals (Sweden)

    Man Lu

    Full Text Available Tibetan kefir grains (TKGs, a kind of natural starter for fermented milk in Tibet, China, host various microorganisms of lactic acid bacteria, yeasts, and occasionally acetic acid bacteria in a polysaccharide/protein matrix. In the present study, the fine structure of TKGs was studied to shed light on this unusual symbiosis with stereomicroscopy and thin sections. The results reveal that TKGs consist of numerous small grain units, which are characterized by a hollow globular structure with a diameter between 2.0 and 9.0 mm and a wall thickness of approximately 200 µm. A polyhedron-like net structure, formed mainly by the bacteria, was observed in the wall of the grain units, which has not been reported previously to our knowledge. Towards the inside of the grain unit, the polyhedron-like net structures became gradually larger in diameter and fewer in number. Such fine structures may play a crucial role in the stability of the grains. Subsequently, the distribution, diversity, and shift of yeasts in TKGs were investigated based on thin section, scanning electron microscopy, cloning and sequencing of D1/D2 of the 26S rRNA gene, real-time quantitative PCR, and in situ hybridization with specific fluorescence-labeled oligonucleotide probes. These show that (i yeasts appear to localize on the outer surface of the grains and grow normally together to form colonies embedded in the bacterial community; (ii the diversity of yeasts is relatively low on genus level with three dominant species--Saccharomyces cerevisiae, Kluyveromyces marxianus, and Yarrowia lipolytica; (iii S. cerevisiae is the stable predominant yeast species, while the composition of Kluyveromyces and Yarrowia are subject to change over time. Our results indicate that TKGs are relatively stable in structure, and culture conditions to some extent shape the microbial community and interaction in kefir grains. These findings pave the way for further study of the specific symbiotic

  19. Fine Structure of Tibetan Kefir Grains and Their Yeast Distribution, Diversity, and Shift

    Science.gov (United States)

    Lu, Man; Wang, Xingxing; Sun, Guowei; Qin, Bing; Xiao, Jinzhou; Yan, Shuling; Pan, Yingjie; Wang, Yongjie

    2014-01-01

    Tibetan kefir grains (TKGs), a kind of natural starter for fermented milk in Tibet, China, host various microorganisms of lactic acid bacteria, yeasts, and occasionally acetic acid bacteria in a polysaccharide/protein matrix. In the present study, the fine structure of TKGs was studied to shed light on this unusual symbiosis with stereomicroscopy and thin sections. The results reveal that TKGs consist of numerous small grain units, which are characterized by a hollow globular structure with a diameter between 2.0 and 9.0 mm and a wall thickness of approximately 200 µm. A polyhedron-like net structure, formed mainly by the bacteria, was observed in the wall of the grain units, which has not been reported previously to our knowledge. Towards the inside of the grain unit, the polyhedron-like net structures became gradually larger in diameter and fewer in number. Such fine structures may play a crucial role in the stability of the grains. Subsequently, the distribution, diversity, and shift of yeasts in TKGs were investigated based on thin section, scanning electron microscopy, cloning and sequencing of D1/D2 of the 26S rRNA gene, real-time quantitative PCR, and in situ hybridization with specific fluorescence-labeled oligonucleotide probes. These show that (i) yeasts appear to localize on the outer surface of the grains and grow normally together to form colonies embedded in the bacterial community; (ii) the diversity of yeasts is relatively low on genus level with three dominant species – Saccharomyces cerevisiae, Kluyveromyces marxianus, and Yarrowia lipolytica; (iii) S. cerevisiae is the stable predominant yeast species, while the composition of Kluyveromyces and Yarrowia are subject to change over time. Our results indicate that TKGs are relatively stable in structure, and culture conditions to some extent shape the microbial community and interaction in kefir grains. These findings pave the way for further study of the specific symbiotic associations between S

  20. Large-scale impacts of herbivores on the structural diversity of African savannas.

    Science.gov (United States)

    Asner, Gregory P; Levick, Shaun R; Kennedy-Bowdoin, Ty; Knapp, David E; Emerson, Ruth; Jacobson, James; Colgan, Matthew S; Martin, Roberta E

    2009-03-24

    African savannas are undergoing management intensification, and decision makers are increasingly challenged to balance the needs of large herbivore populations with the maintenance of vegetation and ecosystem diversity. Ensuring the sustainability of Africa's natural protected areas requires information on the efficacy of management decisions at large spatial scales, but often neither experimental treatments nor large-scale responses are available for analysis. Using a new airborne remote sensing system, we mapped the three-dimensional (3-D) structure of vegetation at a spatial resolution of 56 cm throughout 1640 ha of savanna after 6-, 22-, 35-, and 41-year exclusions of herbivores, as well as in unprotected areas, across Kruger National Park in South Africa. Areas in which herbivores were excluded over the short term (6 years) contained 38%-80% less bare ground compared with those that were exposed to mammalian herbivory. In the longer-term (> 22 years), the 3-D structure of woody vegetation differed significantly between protected and accessible landscapes, with up to 11-fold greater woody canopy cover in the areas without herbivores. Our maps revealed 2 scales of ecosystem response to herbivore consumption, one broadly mediated by geologic substrate and the other mediated by hillslope-scale variation in soil nutrient availability and moisture conditions. Our results are the first to quantitatively illustrate the extent to which herbivores can affect the 3-D structural diversity of vegetation across large savanna landscapes.

  1. Genetic diversity and population structure of long-tailed macaque (Macaca fascicularis) populations in Peninsular Malaysia.

    Science.gov (United States)

    Nikzad, Sonia; Tan, Soon Guan; Yong Seok Yien, Christina; Ng, Jillian; Alitheen, Noorjahan Banu; Khan, Razib; Rovie-Ryan, Jeffrine J; Valdiani, Alireza; Khajeaian, Parastoo; Kanthaswamy, Sree

    2014-12-01

    The genetic diversity and structure of long-tailed macaques (Macaca fascicularis) in Peninsular Malaysia, a widely used non-human primate species in biomedical research, have not been thoroughly characterized. Thirteen sites of wild populations of long-tailed macaques representing six states were sampled and analyzed with 18 STR markers. The Sunggala and Penang Island populations showed the highest genetic diversity estimates, while the Jerejak Island population was the most genetically discrete due to isolation from the mainland shelf. Concordant with pairwise F(st) estimates, STRUCTURE analyses of the seven PCA-correlated clusters revealed low to moderate differentiation among the sampling sites. No association between geographic and genetic distances exists, suggesting that the study sites, including island study sites, are genetically if not geographically contiguous. The status of the genetic structure and composition of long-tailed macaque populations require further scrutiny to develop this species as an important animal model in biomedical research. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  2. Structure, diversity, and biophysical properties of old-growth forestsin the Klamath region, USA

    Science.gov (United States)

    van Mantgem, Phillip J.; Starr, Daniel A

    2015-01-01

    The diverse old-growth forests in Klamath region of northern California and southern Oregon provide valuable ecosystem services (e.g., maintaining watersheds, wildlife habitat, recreation), but may be vulnerable to a wide range of stressors, including invasive species, disrupted disturbance regimes, and climatic change. Yet our understanding of how forest structure in the Klamath region relates to the current physical environment is limited. Here we provide present-day benchmarks for old-growth forest structure across a climatic gradient ranging from coastal to dry interior sites. We established 16 large (1 ha) forest plots where all stems > 5 cm in diameter were identified to species and mapped. Climate across these sites was highly variable, with estimated actual evapotranspiration correlated to several basic measures of forest structure, including plot basal area, stem size-class inequality, tree species diversity and, to a lesser extent, tree species richness. Analyses of the spatial arrangement of stems indicated a high degree of non-uniformity, with 75% of plots showing significant stem clumping at small spatial scales (0 to 10 m). Downscaled predictions of future site water balance suggest changes will be dominated by rapidly increasing climatic water deficit (D, a biologically meaningful index of drought). While these plots give a picture of current conditions, continued monitoring of these stands is needed to describe forest dynamics and to detect forest responses to ongoing and future stressors.

  3. Landscape structure and bird's diversity in the rural areas of Taiwan

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    This study tries to discuss the relationship between landscape structure and organisms in the perspective of landscape architecture.The research hypotheses were then proposed as (1) there are relationships between landscape structure indexes and birds' diversity in the ruralareas of Taiwan; (2) the relationships between landscape structure and birds' diversity will be different in different hierarchical levels.In order to increase the bird species, landscape planners could tries to increase the density of water bodies, but decrease the farms andhuman planted woods.Decrease the density of constructed and human planted grasslands.Increase the area of un-worked acres, naturalgrasslands, and the area of water bodies and circular the water bodies and natural forest.In order to increase birds' diversity, landscapeplanners could decrease the concentration of paved areas.Concentrate the human planted trees to increase the core areas of woodlands.Increasethe area of natural grassland circular.In order to increase the total number of birds in the planning areas, landscape planners could scatteredthe paved areas and lengthen the constructed areas.Decreases the core region of the constructed areas.Increase the area of un-worked acresand water bodies.Decrease the disturbance of both the interior area of natural and human planted woodlands and try to increase the density ofwater bodies.The analysis results showed that the small grain size indexes are more suitable for the rural areas of Taiwan to capture the influential factorsof bird communities.The high fragmentation of land usages in Taiwan lessens the influences of the regional landscape pattern.

  4. Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

    Science.gov (United States)

    Pailles, Yveline; Ho, Shwen; Pires, Inês S.; Tester, Mark; Negrão, Sónia; Schmöckel, Sandra M.

    2017-01-01

    Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance. PMID:28261227

  5. Huge uterine-cervical diverticulum mimicking as a cyst

    Directory of Open Access Journals (Sweden)

    S Chufal

    2012-01-01

    Full Text Available Here we report an incidental huge uterine-cervical diverticulum from a total abdominal hysterectomy specimen in a perimenopausal woman who presented with acute abdominal pain. The diverticulum was mimicking with various cysts present in the lateral side of the female genital tract. Histopathological examination confirmed this to be a cervical diverticulum with communication to uterine cavity through two different openings. They can attain huge size if left ignored for long duration and present a diagnostic challenge to clinicians, radiologists, as well as pathologists because of its extreme rarity. Therefore, diverticula should also be included as a differential diagnosis. Its histopathological confirmation also highlights that diverticula can present as an acute abdomen, requiring early diagnosis with appropriate timely intervention. Immunohistochemistry CD 10 has also been used to differentiate it from a mesonephric cyst.

  6. Huge uterine-cervical diverticulum mimicking as a cyst.

    Science.gov (United States)

    Chufal, S; Thapliyal, Naveen; Gupta, Manoj; Pangtey, Nirmal

    2012-01-01

    Here we report an incidental huge uterine-cervical diverticulum from a total abdominal hysterectomy specimen in a perimenopausal woman who presented with acute abdominal pain. The diverticulum was mimicking with various cysts present in the lateral side of the female genital tract. Histopathological examination confirmed this to be a cervical diverticulum with communication to uterine cavity through two different openings. They can attain huge size if left ignored for long duration and present a diagnostic challenge to clinicians, radiologists, as well as pathologists because of its extreme rarity. Therefore, diverticula should also be included as a differential diagnosis. Its histopathological confirmation also highlights that diverticula can present as an acute abdomen, requiring early diagnosis with appropriate timely intervention. Immunohistochemistry CD 10 has also been used to differentiate it from a mesonephric cyst.

  7. A case of huge primary liposarcoma in the liver

    Institute of Scientific and Technical Information of China (English)

    Liang-Mou Kuo; Hong-Shiue Chou; Kun-Ming Chan; Ming-Chin Yu; Wei-Chen Lee

    2006-01-01

    Primary liver liposarcoma is a rare disease. Because of its rarity, the knowledge of the clinical course, management, and prognosis of primary liver liposarcoma are all limited for clinicians. A 61-year-old female patient who suffered from a huge primary liposarcoma in the central portion of the liver had the clinical presentations of fever, nausea, vomiting, jaundice, and body weight loss.The huge tumor was resected successfully. However,the tumor recurred repeatedly and she had repeated hepatectomies to remove the tumor. Thetumor became aggravating after repeated surgeries. Eventually, the patient had cervical spinal metastasis of liposarcoma and she survived for 26 months after liver liposarcoma was diagnosed. Although the tumor may become aggravating after repeated surgeries, repeated hepatectomies are still the best policy to achieve a long-term survival for the patients.

  8. Black Hole Firewalls Require Huge Energy of Measurement

    CERN Document Server

    Hotta, Masahiro; Funo, Ken

    2013-01-01

    The unitary moving mirror model is one of the best quantum systems for checking the reasoning of the firewall paradox in quantum black holes. The reasoning of Almheiri et al. inevitably raises a firewall paradox in the model. We resolve this paradox from the viewpoint of the energy cost of quantum measurements. No firewall with a deadly, huge energy flux appears, as long as the energy for the measurement is much smaller than the ultraviolet cutoff scale.

  9. Huge plastic bezoar: a rare cause of gastrointestinal obstruction.

    Science.gov (United States)

    Yaka, Mbarek; Ehirchiou, Abdelkader; Alkandry, Tariq Tajdin Sifeddine; Sair, Khalid

    2015-01-01

    Bezoars are rare causes of gastrointestinal obstruction. Basically, they are of four types: trichobezoars, phytobezoars, pharmacobezoars, and lactobezoars. Some rare types of bezoars are also known. In this article a unique case of plastic bezoars is presented. We describe a girl aged 14 years who ingested large amounts of plastic material used for knitting chairs and charpoys. The conglomerate of plastic threads, entrapped food material and other debris, formed a huge mass occupying the whole stomach and extended into small bowel.

  10. A Huge Cystic Retroperitoneal Lymphangioma Presenting with Back Pain

    Science.gov (United States)

    Kubachev, Kubach; Abdullaev, Elbrus; Babyshin, Valentin; Neronov, Dmitriy; Abdullaev, Abakar

    2016-01-01

    Retroperitoneal lymphangioma is a rare location and type of benign abdominal tumors. The clinical presentation of this rare disease is nonspecific, ranging from abdominal distention to sepsis. Here we present a 73-year-old female patient with 3-month history of back pain. USG and CT revealed a huge cystic mass which was surgically excised and appeared to be lymphangioma on histopathology. PMID:27843456

  11. Huge Nevus Lipomatosus Cutaneous Superficialis on Back: An Unusual Presentation.

    Science.gov (United States)

    Das, Dipti; Das, Anupam; Bandyopadhyay, Debabrata; Kumar, Dhiraj

    2015-01-01

    Nevus lipomatosus cutaneous superficialis (NLCS) is a benign dermatosis, histologically characterized by the presence of mature ectopic adipocytes in the dermis. We hereby report a case of a 10-year-old boy who presented with multiple huge swellings on the scapular regions and lower back. The lesions were surmounted by small papules, along with peau-d orange appearance at places. Histology showed features consistent with NLCS. The case is being reported for the unusual clinical presentation.

  12. Huge nevus lipomatosus cutaneous superficialis on back: An unusual presentation

    Directory of Open Access Journals (Sweden)

    Dipti Das

    2015-01-01

    Full Text Available Nevus lipomatosus cutaneous superficialis (NLCS is a benign dermatosis, histologically characterized by the presence of mature ectopic adipocytes in the dermis. We hereby report a case of a 10-year-old boy who presented with multiple huge swellings on the scapular regions and lower back. The lesions were surmounted by small papules, along with peau-d orange appearance at places. Histology showed features consistent with NLCS. The case is being reported for the unusual clinical presentation.

  13. Diversity of Pyrrolizidine Alkaloids in the Boraginaceae Structures, Distribution, and Biological Properties

    Directory of Open Access Journals (Sweden)

    Assem El-Shazly

    2014-04-01

    Full Text Available Among the diversity of secondary metabolites which are produced by plants as means of defence against herbivores and microbes, pyrrolizidine alkaloids (PAs are common in Boraginaceae, Asteraceae and some other plant families. Pyrrolizidine alkaloids are infamous as toxic compounds which can alkylate DNA und thus cause mutations and even cancer in herbivores and humans. Almost all genera of the family Boraginaceae synthesize and store this type of alkaloids. This review reports the available information on the present status (literature up to early 2014 of the pyrrolizidine alkaloids in the Boraginaceae and summarizes the topics structure, distribution, chemistry, chemotaxonomic significance, and biological properties.

  14. Design of synchronization technique for uncertain discrete network group with diverse structures

    Science.gov (United States)

    Lü, Ling; Li, Chengren; Li, Gang; Sun, Ao; Yan, Zhe; Rong, Tingting; Gao, Yan

    2017-01-01

    In this work, we design a novel synchronization technique to realize the synchronization of the network group which is constituted by some uncertain discrete networks with diverse structures. Based on Lyapunov theorem, the selection principle of the control inputs and identification law of uncertain parameters in networks are determined, and the synchronization conditions of network group are obtained. Finally, numerical simulations using one-dimensional convective equations with spatiotemporal chaos behaviors illustrate the performance of the synchronization scheme. The research results show that our synchronization technique can be suitable for the network connecting arbitrarily, and not only the network number but also node number in each network can also be chosen freely.

  15. Genetic structure and diversity in Juniperus communis populations in Saxony, Germany

    Directory of Open Access Journals (Sweden)

    Reim Stefanie

    2016-06-01

    Full Text Available In recent years, land use changes led to a rapid decline and fragmentation of J. communis populations in Germany. Population isolation may lead to a restricted gene flow and, further, to negative effects on genetic variation. In this study, genetic diversity and population structure in seven fragmented J. communis populations in Saxony, Germany, were investigated using nuclear microsatellites (nSSR and chloroplast single nucleotide polymorphism (cpSNP. In all Saxony J. communis populations, a high genetic diversity was determined but no population differentiation could be detected whatever method was applied (Bayesian cluster analysis, F-statistics, AMOVA. The same was true for three J. communis out-group samples originating from Italy, Slovakia and Norway, which also showed high genetic diversity and low genetic differences regarding other J. communis populations. Low genetic differentiation among the J. communis populations ascertained with nuclear and chloroplast markers indicated high levels of gene flow by pollen and also by seeds between the sampled locations. Low genetic differentiation may also provide an indicator of Juniper survival during the last glacial maximum (LGM in Europe. The results of this study serve as a basis for the implementation of appropriate conservation measures in Saxony.

  16. Genetic diversity and structure in semiwild and domesticated chiles (Capsicum annuum; Solanaceae) from Mexico.

    Science.gov (United States)

    Aguilar-Meléndez, Araceli; Morrell, Peter L; Roose, Mikeal L; Kim, Seung-Chul

    2009-06-01

    The chile of Mesoamerica, Capsicum annuum, is one of five domesticated chiles in the Americas. Among the chiles, it varies the most in size, form, and color of its fruits. Together with maize, C. annuum is one of the principal elements of the neotropical diets of Mesoamerican civilizations. Despite the great economic and cultural importance of C. annuum both worldwide and in Mexico, however, very little is known about its geographic origin and number of domestications. Here we sampled a total of 80 accessions from Mexico (58 semiwild and 22 domesticated) and examined nucleotide sequence diversity at three single- or low-copy nuclear loci, Dhn, G3pdh, and Waxy. Across the three loci, we found an average reduction of ca. 10% in the diversity of domesticates relative to semiwild chiles and geographic structure within Mexican populations. The Yucatan Peninsula contained a large number of haplotypes, many of which were unique, suggesting an important region of chile domestication and center of diversity. The present sampling of loci did not conclusively resolve the number and location of domestications, but several lines of evidence suggest multiple independent domestications from widely distributed progenitor populations.

  17. Microbial Diversity and Population Structure of Extremely Acidic Sulfur-Oxidizing Biofilms From Sulfidic Caves

    Science.gov (United States)

    Jones, D.; Stoffer, T.; Lyon, E. H.; Macalady, J. L.

    2005-12-01

    Extremely acidic (pH 0-1) microbial biofilms called snottites form on the walls of sulfidic caves where gypsum replacement crusts isolate sulfur-oxidizing microorganisms from the buffering action of limestone host rock. We investigated the phylogeny and population structure of snottites from sulfidic caves in central Italy using full cycle rRNA methods. A small subunit rRNA bacterial clone library from a Frasassi cave complex snottite sample contained a single sequence group (>60 clones) similar to Acidithiobacillus thiooxidans. Bacterial and universal rRNA clone libraries from other Frasassi snottites were only slightly more diverse, containing a maximum of 4 bacterial species and probably 2 archaeal species. Fluorescence in situ hybridization (FISH) of snottites from Frasassi and from the much warmer Rio Garrafo cave complex revealed that all of the communities are simple (low-diversity) and dominated by Acidithiobacillus and/or Ferroplasma species, with smaller populations of an Acidimicrobium species, filamentous fungi, and protists. Our results suggest that sulfidic cave snottites will be excellent model microbial ecosystems suited for ecological and metagenomic studies aimed at elucidating geochemical and ecological controls on microbial diversity, and at mapping the spatial history of microbial evolutionary events such as adaptations, recombinations and gene transfers.

  18. Structural Diversity of Arthropod Biophotonic Nanostructures Spans Amphiphilic Phase-Space

    Energy Technology Data Exchange (ETDEWEB)

    Saranathan, Vinod Kumar; Seago, Ainsley E.; Sandy, Alec; Narayanan, Suresh; Mochrie, Simon G.J.; Dufresne, Eric R.; Cao, Hui; Osuji, Chinedum O.; Prum, Richard Owen

    2015-05-04

    Many organisms, especially arthropods, produce vivid interference colors using diverse mesoscopic (100-350 nm) integumentary biophotonic nanostructures that are increasingly being investigated for technological applications. Despite a century of interest, precise structural knowledge of many biophotonic nanostructures and the mechanisms controlling their development remain tentative, when such knowledge can open novel biomimetic routes to facilely self-assemble tunable, multifunctional materials. Here, we use synchrotron small-angle X-ray scattering and electron microscopy to characterize the photonic nanostructure of 140 integumentary scales and setae from ~127 species of terrestrial arthropods in 85 genera from 5 orders. We report a rich nanostructural diversity, including triply periodic bicontinuous networks, close-packed spheres, inverse columnar, perforated lamellar, and disordered spongelike morphologies, commonly observed as stable phases of amphiphilic surfactants, block copolymer, and lyotropic lipid-water systems. Diverse arthropod lineages appear to have independently evolved to utilize the self-assembly of infolding lipid-bilayer membranes to develop biophotonic nanostructures that span the phase-space of amphiphilic morphologies, but at optical length scales.

  19. Petroleum-influenced beach sediments of the Campeche Bank, Mexico: diversity and bacterial community structure assessment.

    Science.gov (United States)

    Rosano-Hernández, María C; Ramírez-Saad, Hugo; Fernández-Linares, Luis

    2012-03-01

    The bacterial diversity and community structure were surveyed in intertidal petroleum-influenced sediments of ≈ 100 km of a beach, in the southern Gulf of Mexico. The beach was divided in twenty sampling sites according to high, moderate and low petroleum influence. Densities of cultured heterotrophic (HAB) and hydrocarbon degrading bacteria (HDB) were highly variable in sediments, with little morphological assortment in colonies. PCR-RISA banding patterns differentiated distinct communities along the beach, and the bacterial diversity changed inversely to the degree of petroleum hydrocarbon influence: the higher TPH concentration, the lower genotype diversity. Seven DNA sequences (Genbank EF191394 -EF191396 and EF191398 -EF191401) were affiliated to uncultured members of Gemmatimonas, Acidobacterium, Desulfobacteraceae, Rubrobacterales, Actinobacterium and the Fibrobacteres/Acidobacteria group; all the above taxa are known for having members with active roles in biogeochemical transformations. The remaining sequences (EF191388 - EF191393 and EF191397) affiliated to Pseudoalteromonas, and to oil-degrading genera such as Pseudomonas, Vibrio and Marinobacter, being the last one an obligate oil-degrading bacterium. An exchange of bacteria between the beach and the oil seep environment, and the potential cleaning-up role of bacteria at the southern Gulf of Mexico are discussed.

  20. IMPACT OF STAND STRUCTURE TO THE DIVERSITY OF TREE SAPLING IN RUBBER AGROFOREST SYSTEM

    Directory of Open Access Journals (Sweden)

    Saida Rasnovi

    2013-10-01

    Full Text Available The study of stand structure of rubber agroforest system and its effect on tree sapling diversity was carried out in Bungo District, Jambi Province from August 2004 to August 2005. Basal area (BA and tree density were surveyed using variable-area transect method. Tree sapling species was surveyed using standard plots combined with circular elementary subplots laid along 60 m transect line. The result shown that BA and tree density of rubber agroforest system were lower significantly with forest at the diameter class > 30 cm, but at the diameter class < 30 cm there were not differ significantly. PCA analysis shown there was a positive correlation between BA non rubber tree with the species diversity and richness indices of tree sapling in rubber agroforest system and there was no correlation between density of non rubber tree and the indices. However, in the forest, BA and tree density were have a negative correlation with the species diversity and richness indices of tree sapling.

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

    Science.gov (United States)

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

    2016-03-24

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

  2. Diversity, Host Specialization, and Geographic Structure of Filarial Nematodes Infecting Malagasy Bats.

    Science.gov (United States)

    Ramasindrazana, Beza; Dellagi, Koussay; Lagadec, Erwan; Randrianarivelojosia, Milijaona; Goodman, Steven M; Tortosa, Pablo

    2016-01-01

    We investigated filarial infection in Malagasy bats to gain insights into the diversity of these parasites and explore the factors shaping their distribution. Samples were obtained from 947 individual bats collected from 52 sites on Madagascar and representing 31 of the 44 species currently recognized on the island. Samples were screened for the presence of micro- and macro-parasites through both molecular and morphological approaches. Phylogenetic analyses showed that filarial diversity in Malagasy bats formed three main groups, the most common represented by Litomosa spp. infecting Miniopterus spp. (Miniopteridae); a second group infecting Pipistrellus cf. hesperidus (Vespertilionidae) embedded within the Litomosoides cluster, which is recognized herein for the first time from Madagascar; and a third group composed of lineages with no clear genetic relationship to both previously described filarial nematodes and found in M. griveaudi, Myotis goudoti, Neoromicia matroka (Vespertilionidae), Otomops madagascariensis (Molossidae), and Paratriaenops furculus (Hipposideridae). We further analyzed the infection rates and distribution pattern of Litomosa spp., which was the most diverse and prevalent filarial taxon in our sample. Filarial infection was disproportionally more common in males than females in Miniopterus spp., which might be explained by some aspect of roosting behavior of these cave-dwelling bats. We also found marked geographic structure in the three Litomosa clades, mainly linked to bioclimatic conditions rather than host-parasite associations. While this study demonstrates distinct patterns of filarial nematode infection in Malagasy bats and highlights potential drivers of associated geographic distributions, future work should focus on their alpha taxonomy and characterize arthropod vectors.

  3. Diversity, abundance, and structure of tree communities in the Uluguru forests in the Morogoro region, Tanzania

    Institute of Scientific and Technical Information of China (English)

    David Sylvester Kacholi; Anthony Michael Whitbread; Martin Worbes

    2015-01-01

    Uluguru forests are globally recognized as important biodiversity hotspots, but anthropogenic pressure threatens their value. This study examined species diver-sity, abundance, and structure of trees in the Uluguru for-ests. All trees of diameter at breast height (DBH) C 10 cm were inventoried in seven forests ranging from 3 to 995 ha in area. A total of 900 stems, 101 species and 34 families were inventoried. Fabaceae was the most speciose family. Ehretia amoena Klotzsch was the most abundant species with relative abundance of 9.22%. The forests differed significantly in species richness (26–93 species ha-1), tree density (85–390 stems ha-1), basal area (3–24 m2 ha-1) and Shannon-Wiener diversity (2.50–4.02). Forest area was significantly and positively correlated with species richness (r=0.92) and species diversity (r=0.95). Tree density showed significant positive correlation with species richness (r=0.80) and basal area (r=0.85). Milawilila and Nemele forests had highest floristic similarity (0.55) followed by Kimboza and Kilengwe (0.54) while the rest had similarity coefficients of less than 0.50. Despite leg-islative protection, many forests remain at risk and there-fore the possibility to conserve highly valuable tree species via enhanced protection or cultivation must be considered.

  4. Huge Intravascular Tumor Extending to the Heart: Leiomyomatosis

    Directory of Open Access Journals (Sweden)

    Suat Doganci

    2015-01-01

    Full Text Available Intravenous leiomyomatosis (IVL is a rare neoplasm characterized by histologically benign-looking smooth muscle cell tumor mass, which is growing within the intrauterine and extrauterine venous system. In this report we aimed to present an unusual case of IVL, which is originating from iliac vein and extended throughout to right cardiac chambers. A 49-year-old female patient, who was treated with warfarin sodium due to right iliac vein thrombosis, was admitted to our department with intermittent dyspnea, palpitation, and dizziness. Physical examination was almost normal except bilateral pretibial edema. On magnetic resonance venography, there was an intravenous mass, which is originated from right internal iliac vein and extended into the inferior vena cava. Transthoracic echocardiography and transesophageal echocardiography revealed a huge mass extending from the inferior vena cava through the right atrium, with obvious venous occlusion. Thoracic, abdominal, and pelvic MR showed an intravascular mass, which is concordant with leiomyomatosis. Surgery was performed through median sternotomy. A huge mass with 25-cm length and 186-gr weight was excised through right atrial oblique incision, on beating heart with cardiopulmonary bypass. Histopathologic assessment was compatible with IVL. Exact strategy for the surgical treatment of IVL is still controversial. We used one-stage approach, with complete resection of a huge IVL extending from right atrium to right iliac vein. In such cases, high recurrence rate is a significant problem; therefore it should be kept in mind.

  5. Multimodality treatment with radiotherapy for huge hepatocellular carcinoma.

    Science.gov (United States)

    Han, Hee Ji; Kim, Mi Sun; Cha, Jihye; Choi, Jin Sub; Han, Kwang Hyub; Seong, Jinsil

    2014-01-01

    For huge hepatocellular carcinoma (HCC), therapeutic decisions have varied from local therapy to systemic therapy, with radiotherapy (RT) playing only a palliative role. In this study, we investigated whether multimodality treatment involving RT could be effective in huge HCC. This study was performed in 116 patients with HCC >10 cm. The number of patients in stage II, III and IV was 12, 54 and 50, respectively. RT was given as a combined modality in most patients. The median dose was 45 Gy, with 1.8 Gy per fraction. The median overall survival (OS) and progression-free survival (PFS) were 14.8 and 6.5 months, respectively. The median infield PFS was not reached. Infield failure, outfield intrahepatic and extrahepatic failure were observed in 8.6, 18.1, and 12.1% of patients, respectively. For OS and PFS, number of tumors, initial alpha-fetoprotein (AFP) level, treatment response, percent AFP decrement, and hepatic resection were significant prognostic factors. Tumor characteristics and treatment response were significantly different between long-term survivors and the other patients. Although huge HCC presents an aggressive clinical course, multimodality approaches involving RT can offer an opportunity for prolonged survival. © 2014 S. Karger AG, Basel.

  6. Huge Intravascular Tumor Extending to the Heart: Leiomyomatosis.

    Science.gov (United States)

    Doganci, Suat; Kaya, Erkan; Kadan, Murat; Karabacak, Kubilay; Erol, Gökhan; Demirkilic, Ufuk

    2015-01-01

    Intravenous leiomyomatosis (IVL) is a rare neoplasm characterized by histologically benign-looking smooth muscle cell tumor mass, which is growing within the intrauterine and extrauterine venous system. In this report we aimed to present an unusual case of IVL, which is originating from iliac vein and extended throughout to right cardiac chambers. A 49-year-old female patient, who was treated with warfarin sodium due to right iliac vein thrombosis, was admitted to our department with intermittent dyspnea, palpitation, and dizziness. Physical examination was almost normal except bilateral pretibial edema. On magnetic resonance venography, there was an intravenous mass, which is originated from right internal iliac vein and extended into the inferior vena cava. Transthoracic echocardiography and transesophageal echocardiography revealed a huge mass extending from the inferior vena cava through the right atrium, with obvious venous occlusion. Thoracic, abdominal, and pelvic MR showed an intravascular mass, which is concordant with leiomyomatosis. Surgery was performed through median sternotomy. A huge mass with 25-cm length and 186-gr weight was excised through right atrial oblique incision, on beating heart with cardiopulmonary bypass. Histopathologic assessment was compatible with IVL. Exact strategy for the surgical treatment of IVL is still controversial. We used one-stage approach, with complete resection of a huge IVL extending from right atrium to right iliac vein. In such cases, high recurrence rate is a significant problem; therefore it should be kept in mind.

  7. Diversity, population structure, and evolution of local peach cultivars in China identified by simple sequence repeats.

    Science.gov (United States)

    Shen, Z J; Ma, R J; Cai, Z X; Yu, M L; Zhang, Z

    2015-01-15

    The fruit peach originated in China and has a history of domestication of more than 4000 years. Numerous local cultivars were selected during the long course of cultivation, and a great morphological diversity exists. To study the diversity and genetic background of local peach cultivars in China, a set of 158 accessions from different ecological regions, together with 27 modern varieties and 10 wild accessions, were evaluated using 49 simple sequence repeats (SSRs) covering the peach genome. Broad diversity was also observed in local cultivars at the SSR level. A total of 648 alleles were amplified with an average of 13.22 observed alleles per locus. The number of genotypes detected ranged from 9 (UDP96015) to 58 (BPPCT008) with an average of 27.00 genotypes per marker. Eight subpopulations divided by STRUCTURE basically coincided with the dendrogram of genetic relationships and could be explained by the traditional groups. The 8 subpopulations were juicy honey peach, southwestern peach I, wild peach, Buddha peach + southwestern peach II, northern peach, southern crisp peach, ornamental peach, and Prunus davidiana + P. kansuensis. Most modern varieties carried the genetic backgrounds of juicy honey peach and southwestern peach I, while others carried diverse genetic backgrounds, indicating that local cultivars were partly used in modern breeding programs. Based on the traditional evolution pathway, a modified pathway for the development of local peach cultivars in China was proposed using the genetic background of subpopulations that were identified by SSRs. Current status and prospects of utilization of Chinese local peach cultivars were also discussed according to the SSR information.

  8. Forest structure, diversity and regeneration potential along altitudinal gradient in Dhanaulti of Garhwal Himalaya

    Energy Technology Data Exchange (ETDEWEB)

    Saha, S.; Rajwar, G.S.; Kumar, M.

    2016-07-01

    Aim of the study: The aim of the present study was to understatnd the forest composition, structure, diversity and regeneration potential along altitudinal gradient. Area of study: The study was carried out in Dhanaulti forest which falls under temperate region of Garhwal Himalaya in Uttarakhand state, India. Material and Methods: Vegetation analysis was carried out using 10 quadrats at each altitude using a quadrate size of 10×10 m2. In each quadrate, categories of trees >30 cm cbh were considered as trees, 10-30cm cbh as saplings and <10 cm cbh as seedlings. The data were quantitatively analyzed. Main results: In upper and middle altitudes, Cedrus deodara was reported dominant tree whereas, in lower altitude Quercus leucotrichophora was reported dominant. Tree density was highest in lower altitude which reduced middle and upper altitudes whereas, total basal cover increased with increasing altitude. The increasing total basal cover with altitude could be because of the presence of Cedrus deodara trees having higher girth classes. In tree, sapling and seedling layers, diversity (H) and equitabiltiy (EC) decreased with increasing altitude. However, concentrations of dominace (CD) and beta diversity (BD have shown reverse trend with H and EC which increased with increasing altitudes, in each layer of tree, sapling and seedling. The distribution pattern of most species in all layers of trees, saplings and seedlings was contagious. The regeneration potential of the species has shown that some of the species in the absence of tree layer are still regenerating particularly, Rhododendron arboreum, Benthamidia capitata, Neolitsea pallens etc. It indicates that most of the species are shifting upward as they are getting suitable conditions. Research highlights: Altitude influence species composition, diversity and regeneration potential of species. (Author)

  9. Genetic Diversity and Population Structure of Mesoamerican Jaguars (Panthera onca): Implications for Conservation and Management

    Science.gov (United States)

    Wultsch, Claudia; Caragiulo, Anthony; Dias-Freedman, Isabela; Quigley, Howard; Rabinowitz, Salisa; Amato, George

    2016-01-01

    Mesoamerican jaguars (Panthera onca) have been extirpated from over 77% of their historic range, inhabiting fragmented landscapes at potentially reduced population sizes. Maintaining and restoring genetic diversity and connectivity across human-altered landscapes has become a major conservation priority; nonetheless large-scale genetic monitoring of natural populations is rare. This is the first regional conservation genetic study of jaguars to primarily use fecal samples collected in the wild across five Mesoamerican countries: Belize, Costa Rica, Guatemala, Honduras, and Mexico. We genotyped 445 jaguar fecal samples and examined patterns of genetic diversity and connectivity among 115 individual jaguars using data from 12 microsatellite loci. Overall, moderate levels of genetic variation were detected (NA = 4.50 ± 1.05, AR = 3.43 ± 0.22, HE = 0.59 ± 0.04), with Mexico having the lowest genetic diversity, followed by Honduras, Guatemala, Belize, and Costa Rica. Population-based gene flow measures (FST = 0.09 to 0.15, Dest = 0.09 to 0.21), principal component analysis, and Bayesian clustering applied in a hierarchical framework revealed significant genetic structure in Mesoamerican jaguars, roughly grouping individuals into four genetic clusters with varying levels of admixture. Gene flow was highest among Selva Maya jaguars (northern Guatemala and central Belize), whereas genetic differentiation among all other sampling sites was moderate. Genetic subdivision was most pronounced between Selva Maya and Honduran jaguars, suggesting limited jaguar movement between these close geographic regions and ultimately refuting the hypothesis of contemporary panmixia. To maintain a critical linkage for jaguars dispersing through the Mesoamerican landscape and ensure long-term viability of this near threatened species, we recommend continued management and maintenance of jaguar corridors. The baseline genetic data provided by this study underscores the importance of

  10. Huge thick conglomerate movement induced by full thick longwall mining huge thick coal seam

    Institute of Scientific and Technical Information of China (English)

    Ma Liqiang; Qiu Xiaoxiang; Dong Tao; Zhang Jixiong; Huang Yanli

    2012-01-01

    A discrete elemental method was used to study the thickness of conglomerate layer in a full thick seam mining activities under the influence of the law,pointing out the thickness of the conglomerate at different seam mining,and during the destruction and instability of existing state of laws.At 21141 thick seam mining,the face toward the direction of separation between the thick layer of conglomerate rock and the next bit after reaching its maximum capacity due to pull from the bottom of the plastic zone,formed a stratified and hierarchical down collapse.The shape of caving area is a "triangular block",the length of the plastic zone and face advancement from the linear fit between the height of the plastic zone and the advancing face is a quadratic function of distance,while the top layer of thick gravel layer is the overall bending subsidence trend.Tilting the direction of the face,a thick gob of collapsed conglomerate layer is formed in the coal gob entity on both sides of the thick conglomerate at the top of the overall fracture morphology performance,thus forming a mutual extrusion of articulated block structure.The instability,separation and balance of the thick conglomerate layer in the hinged block stope stress leads to abnormal occurrence of rock burst induced by face as the major factor in the accident.This research reveals the form of stress distribution in the destroyed layer of the thick conglomerate rock,analyzes the stope law of coupling for the pressure burst behavior law for the mining work face,and the choice of preventive measures to provide a theoretical basis and implementation.

  11. Investigations of fungal diversity in wooden structures and soils at historic sites on the Antarctic Peninsula.

    Science.gov (United States)

    Arenz, Brett E; Blanchette, Robert A

    2009-01-01

    Investigations of microbial diversity in Antarctic are important to begin to understand ecosystem functioning and decomposition processes. This study documents fungi at 9 historic sites on the Antarctic Peninsula collected from wooden structures, other organic materials, and soils during a joint National Science Foundation and British Antarctic Survey expedition in 2007. Many of these sites had wooden structures built by the British during the World War II Operation Tabarin, but others visited included the American "East Base" on Stonington Island and the Swedish hut on Snow Hill Island. Fungi were cultured on several different media and pure cultures were obtained and identified by DNA sequencing of the internal transcribed spacer region. Cadophora species previously found to attack historic wooden structures on Ross Island, Antarctica, were found at all but 1 location sampled in the Peninsula region. Fungi causing decay in the historic wooden structures and artifacts and those causing mold problems inside the structures are of great concern, and conservation efforts are urgently needed to help preserve these important polar heritage structures. The results presented also expand our knowledge on the identity of fungi present throughout the Antarctic Peninsula region and provide insights into the organisms responsible for decomposition and nutrient recycling.

  12. Structural model for gamma-aminobutyric acid receptor noncompetitive antagonist binding: widely diverse structures fit the same site.

    Science.gov (United States)

    Chen, Ligong; Durkin, Kathleen A; Casida, John E

    2006-03-28

    Several major insecticides, including alpha-endosulfan, lindane, and fipronil, and the botanical picrotoxinin are noncompetitive antagonists (NCAs) for the GABA receptor. We showed earlier that human beta(3) homopentameric GABA(A) receptor recognizes all of the important GABAergic insecticides and reproduces the high insecticide sensitivity and structure-activity relationships of the native insect receptor. Despite large structural diversity, the NCAs are proposed to fit a single binding site in the chloride channel lumen lined by five transmembrane 2 segments. This hypothesis is examined with the beta(3) homopentamer by mutagenesis, pore structure studies, NCA binding, and molecular modeling. The 15 amino acids in the cytoplasmic half of the pore were mutated to cysteine, serine, or other residue for 22 mutants overall. Localization of A-1'C, A2'C, T6'C, and L9'C (index numbers for the transmembrane 2 region) in the channel lumen was established by disulfide cross-linking. Binding of two NCA radioligands [(3)H]1-(4-ethynylphenyl)-4-n-propyl-2,6,7-trioxabicyclo[2.2.2]octane and [(3)H] 3,3-bis-trifluoromethyl-bicyclo[2,2,1]heptane-2,2-dicarbonitrile was dramatically reduced with 8 of the 15 mutated positions, focusing attention on A2', T6', and L9' as proposed binding sites, consistent with earlier mutagenesis studies. The cytoplasmic half of the beta3 homopentamer pore was modeled as an alpha-helix. The six NCAs listed above plus t-butylbicyclophosphorothionate fit the 2' to 9' pore region forming hydrogen bonds with the T6' hydroxyl and hydrophobic interactions with A2', T6', and L9' alkyl substituents, thereby blocking the channel. Thus, widely diverse NCA structures fit the same GABA receptor beta subunit site with important implications for insecticide cross-resistance and selective toxicity between insects and mammals.

  13. Predicting acute aquatic toxicity of structurally diverse chemicals in fish using artificial intelligence approaches.

    Science.gov (United States)

    Singh, Kunwar P; Gupta, Shikha; Rai, Premanjali

    2013-09-01

    The research aims to develop global modeling tools capable of categorizing structurally diverse chemicals in various toxicity classes according to the EEC and European Community directives, and to predict their acute toxicity in fathead minnow using set of selected molecular descriptors. Accordingly, artificial intelligence approach based classification and regression models, such as probabilistic neural networks (PNN), generalized regression neural networks (GRNN), multilayer perceptron neural network (MLPN), radial basis function neural network (RBFN), support vector machines (SVM), gene expression programming (GEP), and decision tree (DT) were constructed using the experimental toxicity data. Diversity and non-linearity in the chemicals' data were tested using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. Predictive and generalization abilities of various models constructed here were compared using several statistical parameters. PNN and GRNN models performed relatively better than MLPN, RBFN, SVM, GEP, and DT. Both in two and four category classifications, PNN yielded a considerably high accuracy of classification in training (95.85 percent and 90.07 percent) and validation data (91.30 percent and 86.96 percent), respectively. GRNN rendered a high correlation between the measured and model predicted -log LC50 values both for the training (0.929) and validation (0.910) data and low prediction errors (RMSE) of 0.52 and 0.49 for two sets. Efficiency of the selected PNN and GRNN models in predicting acute toxicity of new chemicals was adequately validated using external datasets of different fish species (fathead minnow, bluegill, trout, and guppy). The PNN and GRNN models showed good predictive and generalization abilities and can be used as tools for predicting toxicities of structurally diverse chemical compounds. Copyright © 2013 Elsevier Inc. All rights reserved.

  14. The relationship between species diversity and genetic structure in the rare Picea chihuahuana tree species community, Mexico.

    Science.gov (United States)

    Simental-Rodríguez, Sergio Leonel; Quiñones-Pérez, Carmen Zulema; Moya, Daniel; Hernández-Tecles, Enrique; López-Sánchez, Carlos Antonio; Wehenkel, Christian

    2014-01-01

    Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as "Endangered" on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between

  15. Impacts of feeding strategy on microbial community structure diversity in vertical flow constructed wetlands

    Science.gov (United States)

    Jia, W. L.; Zhang, J.; Wang, Q.

    2016-08-01

    The impacts of feeding strategy (intermittently or continuously) on contaminant removal performance and microbial community structure in vertical flow constructed wetlands (VFCWs) were evaluated. The results showed that intermittent feeding strategy improved the removal of COD, TP and ammonium in VFCWs, although TN removal was weakened correspondingly The bacterial diversity decreased with the increase of substratum depth in all CWs. The intermittent feeding favored the growth of microorganisms due to the enhancement of oxygen content in the substratum. The feeding strategy had little impact on the microbial community in the surface substratum. However, in the bottom substratum, the impacts were of great significance. The microbial community structure similarity between the CWs with different feeding strategies was low.

  16. Exploring advantages of diverse carbon nanotube forests with tailored structures synthesized by supergrowth from engineered catalysts.

    Science.gov (United States)

    Zhao, Bin; Futaba, Don N; Yasuda, Satoshi; Akoshima, Megumi; Yamada, Takeo; Hata, Kenji

    2009-01-27

    We explored advantages of diverse carbon nanotube forests with tailored structures synthesized by water-assisted chemical vapor deposition (CVD) growth (supergrowth) from engineered catalysts. By controlling the catalyst film thickness, we synthesized carbon nanotube (CNT) forests composed from nanotubes with different size and wall number. With extensive characterizations, many interesting dependencies among CNT forest structures and their properties, which were unknown previously, were found. For example, multiwalled carbon nanotubes (MWNTs) showed superior electronic conductivity while single-walled carbon nanotubes (SWNTs) showed superior thermal diffusivity, and sparse MWNTs achieved lower threshold voltage for field emission than dense SWNTs. These interesting trends highlight the complexity in designing and choosing the optimum CNT forest for use in applications.

  17. Structural Basis for Inhibition of Histamine N-Methyltransferase by Diverse Drugs

    Energy Technology Data Exchange (ETDEWEB)

    Horton,J.; Sawada, K.; Nishibori, M.; Cheng, X.

    2005-01-01

    In mammals, histamine action is terminated through metabolic inactivation by histamine N-methyltransferase (HNMT) and diamine oxidase. In addition to three well-studied pharmacological functions, smooth muscle contraction, increased vascular permeability, and stimulation of gastric acid secretion, histamine plays important roles in neurotransmission, immunomodulation, and regulation of cell proliferation. The histamine receptor H1 antagonist diphenhydramine, the antimalarial drug amodiaquine, the antifolate drug metoprine, and the anticholinesterase drug tacrine (an early drug for Alzheimer's disease) are surprisingly all potent HNMT inhibitors, having inhibition constants in the range of 10-100 nM. We have determined the structural mode of interaction of these four inhibitors with HNMT. Despite their structural diversity, they all occupy the histamine-binding site, thus blocking access to the enzyme's active site. Near the N terminus of HNMT, several aromatic residues (Phe9, Tyr15, and Phe19) adopt different rotamer conformations or become disordered in the enzyme-inhibitor complexes, accommodating the diverse, rigid hydrophobic groups of the inhibitors. The maximized shape complementarity between the protein aromatic side-chains and aromatic ring(s) of the inhibitors are responsible for the tight binding of these varied inhibitors.

  18. Population structure and genetic diversity in natural populations of Theobroma speciosum Willd. Ex Spreng (Malvaceae).

    Science.gov (United States)

    Giustina, L D; Luz, L N; Vieira, F S; Rossi, F S; Soares-Lopes, C R A; Pereira, T N S; Rossi, A A B

    2014-02-14

    The genus Theobroma found in the Amazon region is composed of 22 species, including Theobroma speciosum, better known as cacauí. These species are constantly threatened by forest fragmentation caused by human activities and require conservation strategies and management aimed at preserving them in their natural environments. The main objective of this study was to analyze the population structure and genetic diversity within and between natural populations of T. speciosum by using ISSR molecular markers to understand the population structure of the species. Four natural populations belonging to the Amazon rainforest (BAC, CRO, FLA, and PNA), located in the State of Mato Grosso, were selected. Amplification reactions were performed using 15 ISSR primers. A total of 101 loci were found, of which 54.46% were polymorphic at the species level. The BAC population showed higher genetic diversity (H=0.095 and I=0.144) and higher percentage of polymorphism (28.71%). The populations showed an FST value of 0.604, indicating marked genetic differentiation. The highest genetic variation was found between populations. Gene flow was low between populations, indicating genetic isolation between populations.

  19. Genetic diversity, population structure and marker trait associations for seed quality traits in cotton (Gossypium hirsutum)

    Indian Academy of Sciences (India)

    Ashok Badigannavar; Gerald O. Myers

    2015-03-01

    Cottonseed contains 16% seed oil and 23% seed protein by weight. High levels of palmitic acid provides a degree of stability to the oil, while the presence of bound gossypol in proteins considerably changes their properties, including their biological value. This study uses genetic principles to identify genomic regions associated with seed oil, protein and fibre content in upland cotton cultivars. Cotton association mapping panel representing the US germplasm were genotyped using amplified fragment length polymorphism markers, yielding 234 polymorphic DNA fragments. Phenotypic analysis showed high genetic variability for the seed traits, seed oil range from 6.47–25.16%, protein from 1.85–28.45% and fibre content from 15.88–37.12%. There were negative correlations between seed oil and protein content. With reference to genetic diversity, the average estimate of ST was 8.852 indicating a low level of genetic differentiation among subpopulations. The AMOVA test revealed that variation was 94% within and 6% among subpopulations. Bayesian population structure identified five subpopulations and was in agreement with their geographical distribution. Among the mixed models analysed, mixed linear model (MLM) identified 21 quantitative trait loci for lint percentage and seed quality traits, such as seed protein and oil. Establishing genetic diversity, population structure and marker trait associations for the seed quality traits could be valuable in understanding the genetic relationships and their utilization in breeding programmes.

  20. Imidacloprid induces changes in the structure, genetic diversity and catabolic activity of soil microbial communities.

    Science.gov (United States)

    Cycoń, Mariusz; Markowicz, Anna; Borymski, Sławomir; Wójcik, Marcin; Piotrowska-Seget, Zofia

    2013-12-15

    This is the first report describing the effect of imidacloprid applied at field rate (FR, 1 mg/kg of soil) and 10 times the FR (10*FR, 10 mg/kg of soil) on the structural, genetic and physiological diversity of soil bacterial community as determined by the phospholipid fatty acid (PLFA), the denaturing gradient gel electrophoresis (DGGE), and the community level physiological profile (CLPP) approaches. PLFA profiles showed that imidacloprid significantly shifted the microbial community structure and decreased the biomass of the total, bacterial and fungal PLFAs, however, this effect was transient at the FR dosage. The alterations in DGGE patterns caused by imidacloprid application, confirmed considerable changes in the overall richness and diversity of dominant bacteria. Although, as a result of imidacloprid application, the metabolic activity of microbial communities was generally lower, the richness and functional biodiversity of the soil microbial community were not negatively affected. In general, the analysis of the variance indicated that the measured parameters were significantly affected by treatment and the incubation time, however, the incubation time effect explained most of the observed variance. Imidacloprid degradation and the appearance of some new bands in DGGE profiles suggest the evolution of bacteria capable of degrading imidacloprid among indigenous microflora.

  1. Enzymatic hydrolysis of structurally diverse phthalic acid esters by porcine and bovine pancreatic cholesterol esterases.

    Science.gov (United States)

    Saito, Takao; Hong, Peng; Tanabe, Rima; Nagai, Kazuo; Kato, Katsuya

    2010-12-01

    A weak hydrolyzing activity against bis (2-ethylhexyl) phthalate (DEHP) was discovered in a commercial crude lipase (EC 3.1.1.3) preparation from porcine pancreas. DEHP was hydrolyzed to mono (2-ethylhexyl) phthalate (MEHP) not by a pancreatic lipase but by a cholesterol esterase (CEase, EC 3.1.1.13), a trace contaminant in the crude lipase preparation. Enzymatic hydrolysis of phthalic acid esters (PAEs), suspected to be endocrine-disrupting chemicals, was investigated using CEases from two species of mammals and a microorganism. Eight structurally diverse PAEs, namely diethyl phthalate (DEP), di-n-propyl phthalate (DPrP), di-n-butyl phthalate (DBP), di-n-pentyl phthalate (DPeP), di-n-hexyl phthalate (DHP), DEHP, n-butyl benzyl phthalate (BBP), and dicyclohexyl phthalate (DCHP), were hydrolyzed to their corresponding monoesters by both porcine and bovine pancreatic CEases, while a microbial CEase from Pseudomonas sp. had no hydrolyzing activity against these PAEs. The hydrolysis experiments with bovine pancreatic CEase (50 U) indicated complete hydrolysis of every PAE (5 μmole) except for BBP and DCHP within 15 min; BBP and DCHP were hydrolyzed within 30 min and 6h, respectively. The rates of PAE hydrolysis could be affected by the bulkiness of alkyl side chains in the PAEs. This study provides important evidence that mammalian pancreatic CEases, such as those from porcine and bovine sources, are potential enzymes for nonspecific degradation of structurally diverse PAEs.

  2. Structure-function characterization reveals new catalytic diversity in the galactose oxidase and glyoxal oxidase family.

    Science.gov (United States)

    Yin, DeLu Tyler; Urresti, Saioa; Lafond, Mickael; Johnston, Esther M; Derikvand, Fatemeh; Ciano, Luisa; Berrin, Jean-Guy; Henrissat, Bernard; Walton, Paul H; Davies, Gideon J; Brumer, Harry

    2015-12-18

    Alcohol oxidases, including carbohydrate oxidases, have a long history of research that has generated fundamental biological understanding and biotechnological applications. Despite a long history of study, the galactose 6-oxidase/glyoxal oxidase family of mononuclear copper-radical oxidases, Auxiliary Activity Family 5 (AA5), is currently represented by only very few characterized members. Here we report the recombinant production and detailed structure-function analyses of two homologues from the phytopathogenic fungi Colletotrichum graminicola and C. gloeosporioides, CgrAlcOx and CglAlcOx, respectively, to explore the wider biocatalytic potential in AA5. EPR spectroscopy and crystallographic analysis confirm a common active-site structure vis-à-vis the archetypal galactose 6-oxidase from Fusarium graminearum. Strikingly, however, CgrAlcOx and CglAlcOx are essentially incapable of oxidizing galactose and galactosides, but instead efficiently catalyse the oxidation of diverse aliphatic alcohols. The results highlight the significant potential of prospecting the evolutionary diversity of AA5 to reveal novel enzyme specificities, thereby informing both biology and applications.

  3. Genetic diversity and structure of natural fragmented Chamaecyparis obtusa populations as revealed by microsatellite markers.

    Science.gov (United States)

    Matsumoto, Asako; Uchida, Kohji; Taguchi, Yuriko; Tani, Naoki; Tsumura, Yoshihiko

    2010-09-01

    The genetic diversity and population structure of hinoki (Chamaecyparis obtusa) in Japan were investigated by examining the distribution of alleles at 13 microsatellite loci in 25 natural populations from Iwaki in northern Japan to Yakushima Island in southern Japan. On average, 26.9 alleles per locus were identified across all populations and 4.0% of the genetic variation was retained among populations (G(ST) = 0.040). According to linkage disequilibrium analysis, estimates of effective population size and detected evidence of bottleneck events, the genetic diversity of some populations may have declined as a result of fragmentation and/or over-exploitation. The central populations located in the Chubu district appear to have relatively large effective population sizes, while marginal populations, such as the Yakushima, Kobayashi and Iwaki populations, have smaller effective population sizes and are isolated from the other populations. Microsatellite analysis revealed the genetic uniqueness of the Yakushima population. Although genetic differentiation between populations was low, we detected a gradual cline in the genetic structure and found that locus Cos2619 may be non-neutral with respect to natural selection.

  4. Responses of Soil Microbial Community Structure and Diversity to Agricultural Deintensification

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wei-Jian; S.HU; RUI Wen-Yi; C.TU; H.G.DIAB; F.J.LOUWS; J.P.MUELLER; N.CREAMER; M.BELL; M.G.WAGGER

    2005-01-01

    Using a scheme of agricultural fields with progressively less intensive management (deintensification), different management practices in six agroecosystems located near Goldsboro, NC, USA were tested in a large-scale experiment, including two cash-grain cropping systems employing either tillage (CT) or no-tillage (NT), an organic farming system (OR), an integrated cropping system with animals (IN), a successional field (SU), and a plantation woodlot (WO). Microbial phospholipid fatty acid (PLFA) profiles and substrate utilization patterns (BIOLOG ECO plates) were measured to examine the effects of deintensification on the structure and diversity of soil microbial communities. Principle component analyses of PLFA and BIOLOG data showed that the microbial community structure diverged among the soils of the six systems.Lower microbial diversity was found in lowly managed ecosystem than that in intensive and moderately managed agroecosystems, and both fungal contribution to the total identified PLFAs and the ratio of microbial biomass C/N increased along with agricultural deintensification. Significantly higher ratios of C/N (P < 0.05) were found in the WO and SU systems, and for fungal/bacterial PLFAs in the WO system (P < 0.05). There were also significant decreases (P < 0.05)along with agricultural deintensification for contributions of total bacterial and gram positive (G+) bacterial PLFAs.Agricultural deintensification could facilitate the development of microbial communities that favor soil fungi over bacteria.

  5. Exploring the role of asexual multiplication in poplar rust epidemics: impact on diversity and genetic structure.

    Science.gov (United States)

    Barrès, Benoît; Dutech, Cyril; Andrieux, Axelle; Halkett, Fabien; Frey, Pascal

    2012-10-01

    Fungal plant pathogens, especially rust fungi (Pucciniales), are well known for their complex life cycles, which include phases of sexual and asexual reproduction. The effect of asexual multiplication on population genetic diversity has been investigated in the poplar rust fungus Melampsora larici-populina using a nested hierarchical sampling scheme. Four hierarchical levels were considered: leaf, twig, tree and site. Both cultivated and wild poplar stands were sampled at two time points at the start and end of rust epidemics. A total of 641 fungal isolates was analysed using nine microsatellite markers. This study revealed that the genetic signature of asexual multiplication in the wild poplar stand was seen only at lower hierarchical levels (leaf and twig). Moreover, we observed an erosion of clonal structure through time, with an increase in both gene and genotypic diversity. New genotypes contributed to host infection over time, which demonstrates the importance of allo-infection in the epidemic process in this host-pathogen system. Compared with the wild stands, the nearly lack of detection of clonal structure in the cultivated stands reflects the higher infection level on cultivated poplars. More generally, this genetic analysis illustrates the utility of population genetics approach for elucidating the proportion of asexual reproduction in the multiplication of isolates during an epidemic, and for proper quantification of asexual dispersal in plant pathogens.

  6. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    Directory of Open Access Journals (Sweden)

    Jian-Wei Zong

    Full Text Available Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777. According to the coefficient of genetic differentiation (Fst = 0.1215, genetic variation within the populations (87.85% were remarkably higher than among populations (12.15%. The average gene flow (Nm = 1.8080 significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080 among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km among populations (r = 0.419, P = 0.005, suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic

  7. Levels and Patterns of Genetic Diversity and Population Structure in Domestic Rabbits.

    Directory of Open Access Journals (Sweden)

    Joel M Alves

    Full Text Available Over thousands of years humans changed the genetic and phenotypic composition of several organisms and in the process transformed wild species into domesticated forms. From this close association, domestic animals emerged as important models in biomedical and fundamental research, in addition to their intrinsic economical and cultural value. The domestic rabbit is no exception but few studies have investigated the impact of domestication on its genetic variability. In order to study patterns of genetic structure in domestic rabbits and to quantify the genetic diversity lost with the domestication process, we genotyped 45 microsatellites for 471 individuals belonging to 16 breeds and 13 wild localities. We found that both the initial domestication and the subsequent process of breed formation, when averaged across breeds, culminated in losses of ~20% of genetic diversity present in the ancestral wild population and domestic rabbits as a whole, respectively. Despite the short time elapsed since breed diversification we uncovered a well-defined structure in domestic rabbits where the FST between breeds was 22%. However, we failed to detect deeper levels of structure, probably consequence of a recent and single geographic origin of domestication together with a non-bifurcating process of breed formation, which were often derived from crosses between two or more breeds. Finally, we found evidence for intrabreed stratification that is associated with demographic and selective causes such as formation of strains, colour morphs within the same breed, or country/breeder of origin. These additional layers of population structure within breeds should be taken into account in future mapping studies.

  8. Genetic diversity and population structure of different varieties of Morada Nova hair sheep from Brazil.

    Science.gov (United States)

    Ferreira, J S B; Paiva, S R; Silva, E C; McManus, C M; Caetano, A R; Façanha, D A E; de Sousa, M A N

    2014-01-01

    The aim of this study was to analyze genetic diversity and population structure among varieties of White (N = 40), Red (N = 32), and Black (N = 31) Morada Nova hair sheep from flocks in the northeastern Brazilian semiarid region. Fifteen nuclear microsatellite markers and two regions of mitochondrial DNA were used. The intra-population analysis demonstrated that the White variety had higher diversity, while the Red variety had the lowest values. The Bayesian analysis to assess the genetic population structure allowed differentiation between White, Red, and Black varieties, and revealed a tendency towards sub-structuring in the White variety flocks from the States of Ceará and Paraíba. The results of analyses of molecular variance showed that the greatest genetic structure was found when comparing flocks rather than varieties (8.59 vs 6.64% of the total variation, P Dtl, both the dendrogram analysis and the principal coordinate analysis showed the formation of two main groups: one composed of White and another of Black and Red individuals. Five and two haplotypes were found for the D-loop region and the ND5 gene, respectively. A haplotype unique to the Red variety was found in the D-loop region and a variety haplotype unique to the Black variety was found in the ND5 gene; however, these frequencies were low and therefore require further validation. These results support the existence of substantial differences between the Red and White varieties and should be used as separate genetic resources and to improve conservation programs.

  9. Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase

    Energy Technology Data Exchange (ETDEWEB)

    Agarwal R.; Swaminathan S.; Burley, S. K.

    2012-01-01

    The araBAD operon encodes three different enzymes required for catabolism of L-arabinose, which is one of the most abundant monosaccharides in nature. L-ribulokinase, encoded by the araB gene, catalyzes conversion of L-ribulose to L-ribulose-5-phosphate, the second step in the catabolic pathway. Unlike other kinases, ribulokinase exhibits diversity in substrate selectivity and catalyzes phosphorylation of all four 2-ketopentose sugars with comparable k{sub cat} values. To understand ribulokinase recognition and phosphorylation of a diverse set of substrates, we have determined the X-ray structure of ribulokinase from Bacillus halodurans bound to L-ribulose and investigated its substrate and ATP co-factor binding properties. The polypeptide chain is folded into two domains, one small and the other large, with a deep cleft in between. By analogy with related sugar kinases, we identified {sup 447}{und GG}LPQ{und K}{sup 452} as the ATP-binding motif within the smaller domain. L-ribulose binds in the cleft between the two domains via hydrogen bonds with the side chains of highly conserved Trp126, Lys208, Asp274, and Glu329 and the main chain nitrogen of Ala96. The interaction of L-ribulokinase with L-ribulose reveals versatile structural features that help explain recognition of various 2-ketopentose substrates and competitive inhibition by L-erythrulose. Comparison of our structure to that of the structures of other sugar kinases revealed conformational variations that suggest domain-domain closure movements are responsible for establishing the observed active site environment.

  10. Population structure and genetic diversity of the parasite Trichomonas vaginalis in Bristol, UK.

    Science.gov (United States)

    Hawksworth, Joseph; Levy, Max; Smale, Chloe; Cheung, Dean; Whittle, Alice; Longhurst, Denise; Muir, Peter; Gibson, Wendy

    2015-08-01

    The protozoan parasite Trichomonas vaginalis is the causative agent of trichomoniasis, an extremely common, but non-life-threatening, sexually-transmitted disease throughout the world. Recent population genetics studies of T. vaginalis have detected high genetic diversity and revealed a two-type population structure, associated with phenotypic differences in sensitivity to metronidazole, the drug commonly used for treatment, and presence of T. vaginalis virus. There is currently a lack of data on UK isolates; most isolates examined to date are from the US. Here we used a recently described system for multilocus sequence typing (MLST) of T. vaginalis to study diversity of clinical isolates from Bristol, UK. We used MLST to characterise 23 clinical isolates of T. vaginalis collected from female patients during 2013. Seven housekeeping genes were PCR-amplified for each isolate and sequenced. The concatenated sequences were then compared with data from other MLST-characterised isolates available from http://tvaginalis.mlst.net/ to analyse the population structure and construct phylogenetic trees. Among the 23 isolates from the Bristol population of T. vaginalis, we found 23 polymorphic nucleotide sites, 25 different alleles and 19 sequence types (genotypes). Most isolates had a unique genotype, in agreement with the high levels of heterogeneity observed elsewhere in the world. A two-type population structure was evident from population genetic analysis and phylogenetic reconstruction split the isolates into two major clades. Tests for recombination in the Bristol population of T. vaginalis gave conflicting results, suggesting overall a clonal pattern of reproduction. We conclude that the Bristol population of T. vaginalis parasites conforms to the two-type population structure found in most other regions of the world. We found the MLST scheme to be an efficient genotyping method. The online MLST database provides a useful repository and resource that will prove

  11. Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics

    DEFF Research Database (Denmark)

    Sicheritz-Pontén, Thomas; Noel, CJ; Diaz, N

    2010-01-01

    were characterized by a considerable structural diversity between their TpLRR and other types of repetitive sequences and two subfamilies possessed distinct classic sorting signal motifs for endocytosis. One TvBspA subfamily also shared a glycine-rich protein domain with proteins from Clostridium...... difficile pathogenic strains and C. difficile phages. Consistent with the hypothesis that TvBspA protein structural diversity implies diverse roles, we demonstrated for several TvBspA genes differential expression at the transcript level in different growth conditions. Identified variants of repetitive...... were also demonstrated. CONCLUSIONS: The biased mucosal habitat for microbial species encoding BspA-like proteins, the characterization of a vast structural diversity for the TvBspA proteins, differential expression of a subset of TvBspA genes and the cellular localisation and immunological data...

  12. Species Diversity Based on Vertical Structure as Indicators of Artificial Restoration for Coniferous Forests in Southwest China

    Institute of Scientific and Technical Information of China (English)

    ZHANG Qiaoying; ZHANG Yunchun; Eshetu Yirdaw; LUO Peng; YI Shaoliang; Wu Ning

    2006-01-01

    Five indices of species richness, species diversity and species evenness were used to assess α diversity of four types of coniferous forests undergone different artificial regeneration time. The study was based on the vertical structure of forests, involving growth-forms of total plants as well as vertical layers of woody plants. The results showed that, except for the fourth layer of woody plants, the vertical structure of the four forests exhibited significant difference in terms of their species richness, species diversity and species evenness, suggesting that α species diversity index provided more detailed information and was a better index reflecting the regeneration processes in this region. It was recommended that silvicultural management of artificially regenerated forests should be strengthened to conserve the biodiversity of the forests, optimize forest structure and, in the long run, promote sustainable development of forest ecosystems.

  13. Competition for shelter in a high-diversity system: structure use by large reef fishes

    Science.gov (United States)

    Kerry, J. T.; Bellwood, D. R.

    2016-03-01

    Competition among large reef fishes for shelter beneath tabular structures provides a rare opportunity to study competition in a species-rich environment. The system permits a detailed study of localised competition with major implications for coral reefs with respect to human impacts including climate change. Using underwater video cameras, this study examined competition among 30 species of large reef fishes (from nine families) for access to shelter provided by 26 tabular structures, which may be the highest reported diversity of vertebrates competing for a single resource. Mean concentrations of fishes under tabular structures were also among the highest biomass recorded on reefs (4.71 kg m-2). A generated dominance hierarchy for the occupation of shelter appeared to be primarily driven by the size of fishes. In contrast to previous studies, fishes higher in the hierarchy tended to exhibit the lowest levels of aggression. However, size difference between fishes was found to be strongly negatively correlated with the proportion of aggressive interactions ( R 2 = 0.971, P concerns about future shifts in the structure of large reef fish communities as corals are lost. This is particularly concerning given the critical functional roles played by certain species of large reef fishes that utilise tabular structure for shelter and which occupy the lower ranks of the dominance hierarchy.

  14. Efficient visualization of unsteady and huge scalar and vector fields

    Science.gov (United States)

    Vetter, Michael; Olbrich, Stephan

    2016-04-01

    The simulation of climate data tends to produce very large data sets, which hardly can be processed in classical post-processing visualization applications. Within the most traditional post-processing scenarios the visualization pipeline consisting of the processes data generation, visualization mapping and rendering is distributed into two parts over the network or separated via file transfer: the data generation on a supercomputer on the one hand and the other tasks on a special visualization system on the other hand. That way either temporary data sets with huge volume have to be transferred over the network, which leads to bandwidth bottlenecks and volume limitations. As an alternative all simulation and visualization processes are integrated in a monolithic application, where just 2D pixel data is stored, which reduces the user's possibilities for 3D interaction with visualization to frame skipping. Within the Climate Visualization Lab - as part of the Cluster of Excellence "Integrated Climate System Analysis and Prediction" (CliSAP at the University of Hamburg, in cooperation with the German Climate Computing Center (DKRZ) - we plan to integrate a different approach, which has been proven to be successful in former meteorology applications, e.g. PALM (Parallel Large Eddy Simulation Model). Our software framework DSVR is based on the separation of the process chain between the mapping and the rendering processes. We have developed a parallelized visualization library based on MPI and evaluated on various supercomputers. DSVR can be used to integrate the visualization into a parallel simulation model to support in-situ processing, resulting in a sequence of time-based geometric 3D objects which can be interactively rendered in a separate 3D viewer application. To meet the actual requirements (a) to visualize existing data sets, (b) to support more than rectilinear grids, and (c) to integrate in-situ processing in the ICON model, all based on our DSVR framework

  15. Analyzing huge pathology images with open source software.

    Science.gov (United States)

    Deroulers, Christophe; Ameisen, David; Badoual, Mathilde; Gerin, Chloé; Granier, Alexandre; Lartaud, Marc

    2013-06-06

    Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer's memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. The virtual slide(s) for this article can be found here

  16. Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, But Not Diversity.

    Science.gov (United States)

    Wang, Jichen; Xue, Chao; Song, Yang; Wang, Lei; Huang, Qiwei; Shen, Qirong

    2016-01-01

    Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer (OF) regimes represents an important practice in attempts to preserve soil quality. However, little is known about the dynamic response of bacterial communities to fertilization regimes across crop growth stages. In this study, we examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic-inorganic mixed fertilizer (OIMF), and OF. Quantitative PCR (QPCR) and high-throughput sequencing of bacterial 16S rRNA gene fragments revealed that growth stage as the best predictor of bacterial community abundance and structure. Additionally, bacterial community compositions differed between wheat and rice rotations. Relative to soils under wheat rotation, soils under rice rotation contained higher relative abundances (RA) of anaerobic and mesophilic microbes and lower RA of aerophilic microbes. With respect to fertilization regime, NNF plots had a higher abundance of nitrogen-fixing Cyanobacteria. OIMF had a lower abundance of ammonia-oxidizing Thaumarchaeota compared with CF. Application of chemical fertilizers (CF and OIMF treatments) significantly increased the abundance of some generally oligotrophic bacteria such those belonging to the Acidobacteria, while more copiotrophic of the phylum Proteobacteria increased with OF application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR vs. sequence analysis, yet poor correlations were found for the α- and β- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil microbial community structure, but not total levels of alpha

  17. Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, but Not Diversity

    Directory of Open Access Journals (Sweden)

    Jichen Wang

    2016-08-01

    Full Text Available Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer regimes represents an important practice in attempts to preserve soil quality. However, little is known about the dynamic response of bacterial communities to fertilization regimes across crop growth stages. In this study, we examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF, chemical fertilizer (CF, organic-inorganic mixed fertilizer (OIMF and organic fertilizer (OF. Quantitative PCR (QPCR and high-throughput sequencing of bacterial 16S rRNA gene fragments revealed that growth stage as the best predictor of bacterial community abundance and structure. Additionally, bacterial community compositions differed between wheat and rice rotations. Relative to soils under wheat rotation, soils under rice rotation contained higher relative abundances (RA of anaerobic and mesophilic microbes and lower RA of aerophilic microbes. With respect to fertilization regime, NNF plots had a higher abundance of nitrogen–fixing Cyanobacteria. OIMF had a lower abundance of ammonia-oxidizing Thaumarchaeota compared with CF. Application of chemical fertilizers (CF and OIMF treatments significantly increased the abundance of some generally oligotrophic bacteria such those belonging to the Acidobacteria, while more copiotrophic of the phylum Proteobacteria increased with organic fertilizer application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR versus sequence analysis, yet poor correlations were found for the Alpha- and Beta- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil

  18. Identification and Analysis of Genetic Diversity Structure Within Pisum Genus Based on Microsatellite Markers

    Institute of Scientific and Technical Information of China (English)

    ZONG Xu-xiao; Rebecca Ford; Robert R Redden; GUAN Jian-ping; WANG Shu-min

    2009-01-01

    To assesse the genetic diversity among wild and cultivated accessions of 8 taxonomic groups in 2 species, and 5 subspecies under Pisum genus, and to analyze population structure and their genetic relationships among various groups of taxonomy,the study tried to verify the fitness of traditionally botanical taxonomic system under Pisum genus and to provide essential information for the exploration and utilization of wild relatives of pea genetic resources. 197 Pisum accessions from 62 counties of 5 continents were employed for SSR analysis using 21 polymorphic primer pairs in this study. Except for cultivated field pea Pisum sativum ssp. sativum vat. sativum (94 genotypes), also included were wild relative genotypes that were classified as belonging to P. fulvum, P. sativum ssp.abyssinicum, P. sativum ssp. asiaticum, P. sativum ssp. transcaucasicum, P. sativum ssp. elatius vat. elatius, P. sativum ssp. elatius vat. pumilio and P. sativum ssp.sativum vat. arvense (103 genotypes). The PCA analyses and 3-dimension PCA graphs were conducted and drawn by NTSYSpe 2.2d statistical package. Nei78 genetic distances among groups of genetic resources were calculated, and cluster analysis using UPGMA method was carried out by using Popgene V1.32 statistical package, the dendrogram was drawn by MEGA3.1 statistical package. Allelie statistics were carried out by Popgene V1.32. The significance test between groups of genotypes was carried out by Fstat V2.9.3.2 statistical package. 104 polymorphic bands were amplified using 21 SSR primer pairs with unambiguous unique polymorphic bands. 4.95 alleles were detected by each SSR primer pair in average, of which 65.56% were effective alleles for diversity. PSAD270, PSAC58, PSAA18, PSAC75, PSAA175 and PSAB72 were the most effective SSR pairs. SSR alleles were uniformly distributed among botanical taxon units under Pisum genus, but significant difference appeared in most pairwise comparisons for genetic diversity between taxon unit based

  19. A NOVEL APPROACH FOR PATTERN ANALYSIS FROM HUGE DATAWAREHOUSE

    Directory of Open Access Journals (Sweden)

    BABITA

    2014-05-01

    Full Text Available Due to the tremendous growth of data and large databases, efficient extraction of required data has become a challenging task. This paper propose a novel approach for knowledge discovery from huge unlabeled temporal databases by employing a combination of HMM and K-means technique. We propose to recursively divide the entire database into clusters having similar characteristics, this process is repeated until we get the cluster’s where no further diversification is possible. Thereafter, the clusters are labeled for knowledge extraction for various purposes.

  20. A young woman with a huge paratubal cyst

    Directory of Open Access Journals (Sweden)

    Ceren Golbasi

    2016-09-01

    Full Text Available Paratubal cysts are asymptomatic embryological remnants. These cysts are usually diagnosed during adolescence and reproductive age. In general, their sizes are small but can be complicated by rupture, torsion, or hemorrhage. Paratubal cysts are often discovered fortuitously on routine ultrasound examination. We report a 19-year-old female patient who presented with irregular menses and abdominal pain. Ultrasound examination revealed a huge cystic mass at the right adnexial area. The diagnosis was confirmed as paratubal cyst during laporotomy and, hence, cystectomy and right salpingectomy were performed. [Cukurova Med J 2016; 41(3.000: 573-576

  1. Modeling huge sound sources in a room acoustical calculation program

    DEFF Research Database (Denmark)

    Christensen, Claus Lynge

    1999-01-01

    A room acoustical model capable of modeling point sources, line sources, and surface sources is presented. Line and surface sources are modeled using a special ray-tracing algorithm detecting the radiation pattern of the surfaces of the room. Point sources are modeled using a hybrid calculation...... method combining this ray-tracing method with image source modeling. With these three source types it is possible to model huge and complex sound sources in industrial environments. Compared to a calculation with only point sources, the use of extended sound sources is shown to improve the agreement...

  2. A huge renal capsular leiomyoma mimicking retroperitoneal sarcoma

    Directory of Open Access Journals (Sweden)

    Lal Anupam

    2009-01-01

    Full Text Available A huge left renal capsular leiomyoma mimicking retroperitoneal sarcoma presented in a patient as an abdominal mass. Computed tomography displayed a large heterogeneous retro-peritoneal mass in the left side of the abdomen with inferior and medial displacement as well as loss of fat plane with the left kidney. Surgical exploration revealed a capsulated mass that was tightly adherent to the left kidney; therefore, total tumor resection with radical left nephrectomy was performed. Histopathology ultimately confirmed the benign nature of the mass. This is the largest leiomyoma reported in literature to the best of our knowledge.

  3. Huge pyometra in a postmenopausal age: a diagnostic dilemma

    Directory of Open Access Journals (Sweden)

    Pramila Yadav

    2015-10-01

    Full Text Available Pyometra in postmenopausal women is an extremely rare disease that hardly responds to the usual treatment of antibiotics therapy. Our case presented as a postmenopausal woman with a huge pyometra. Pyometra drainage was done with great difficulty after a blind biopsy. Endometrial and cervical biopsy followed by endometrial curettage was done. An intrauterine foley's catheter was kept for seven days and Histopathological report was suggestive of squamous cell carcinoma of cervix. [Int J Reprod Contracept Obstet Gynecol 2015; 4(5.000: 1549-1551

  4. Leaf structural diversity is related to hydraulic capacity in tropical rain forest trees.

    Science.gov (United States)

    Sack, Lawren; Frole, Kristen

    2006-02-01

    The hydraulic resistance of the leaf (R1) is a major bottleneck in the whole plant water transport pathway and may thus be linked with the enormous variation in leaf structure and function among tropical rain forest trees. A previous study found that R1 varied by an order of magnitude across 10 tree species of Panamanian tropical lowland rain forest. Here, correlations were tested between R1 and 24 traits relating to leaf venation and mesophyll structure, and to gross leaf form. Across species, R1 was related to both venation architecture and mesophyll structure. R1 was positively related to the theoretical axial resistivity of the midrib, determined from xylem conduit numbers and dimensions, and R1 was negatively related to venation density in nine of 10 species. R1 was also negatively related to both palisade mesophyll thickness and to the ratio of palisade to spongy mesophyll. By contrast, numerous leaf traits were independent of R1, including area, shape, thickness, and density, demonstrating that leaves can be diverse in gross structure without intrinsic trade-offs in hydraulic capacity. Variation in both R1-linked and R1-independent traits related strongly to regeneration irradiance, indicating the potential importance of both types of traits in establishment ecology.

  5. QSAR study on estrogenic activity of structurally diverse compounds using generalized regression neural network

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Computer-based quantitative structure-activity relationship (QSAR) model has been becoming a pow- erful tool in understanding the structural requirements for chemicals to bind the estrogen receptor (ER), designing drugs for human estrogen replacement therapy, and identifying potential estrogenic endo- crine disruptors. In this study, a simple yet powerful neural network technique, generalized regression neural network (GRNN) was used to develop a QSAR model based on 131 structurally diverse estro- gens (training set). Only nine descriptors calculated solely from the molecular structures of com- pounds selected by objective and subjective feature selections were used as inputs of the GRNN model. The predictive power of the built model was found to be comparable to that of the more traditional techniques but requiring significantly easy implementation and a shorter computation-time. The ob- tained result indicates that the proposed GRNN model is robust and satisfactory, and can provide a feasible and practical tool for the rapid screening of the estrogenic activity of organic compounds.

  6. Accessing Structurally Diverse Near-Infrared Cyanine Dyes for Folate Receptor-Targeted Cancer Cell Staining.

    Science.gov (United States)

    König, Sandra G; Krämer, Roland

    2017-03-24

    Folate receptor (FR) targeting is one of the most promising strategies for the development of small-molecule based cancer imaging agents since the FR is highly overexpressed on the surface of many cancer cell types. FR-targeted conjugates of NIR emissive cyanine dyes are in advanced clinical trials for fluorescence-guided surgery and are valuable research tools for optical molecular imaging in animal models. Only a small number of promising conjugates has been evaluated so far. Analysis of structure-performance relations to identify critical factors modulating the performance of targeted conjugates is essential for successful further optimization. This contribution addresses the need for convenient synthetic access to structurally diverse NIR-emissive cyanine dyes for conjugation with folic acid. Structural variations were introduced to readily available cyanine precursors in particular via C-C-coupling reactions including Suzuki- and (for the first time with these types of dyes) Sonogashira cross couplings. Photophysical properties such as absorbance maxima, brightness, and photostability are highly dependent on the molecular structure. Selected modified cyanines were conjugated to folic acid for cancer cell targeting. Several conjugates display a favorable combination of high fluorescence brightness and photostability with high affinity to FR positive cancer cells, and enable the selective imaging of these cells with low background.

  7. Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function

    Directory of Open Access Journals (Sweden)

    Ville Y. P. Väre

    2017-03-01

    Full Text Available RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability of RNAs to play multiple roles in cellular metabolism is made possible by extensive variation in length, conformational dynamics, and the over 100 post-transcriptional modifications. There are several reviews of the biochemical pathways leading to RNA modification, but the physicochemical nature of modified nucleosides and how they facilitate RNA function is of keen interest, particularly with regard to the contributions of modified nucleosides. Transfer RNAs (tRNAs are the most extensively modified RNAs. The diversity of modifications provide versatility to the chemical and structural environments. The added chemistry, conformation and dynamics of modified nucleosides occurring at the termini of stems in tRNA’s cloverleaf secondary structure affect the global three-dimensional conformation, produce unique recognition determinants for macromolecules to recognize tRNAs, and affect the accurate and efficient decoding ability of tRNAs. This review will discuss the impact of specific chemical moieties on the structure, stability, electrochemical properties, and function of tRNAs.

  8. Species diversity of remnant calcareous grasslands in south eastern Germany depends on litter cover and landscape structure

    Science.gov (United States)

    Huber, Stephanie; Huber, Birgit; Stahl, Silvia; Schmid, Christoph; Reisch, Christoph

    2017-08-01

    Species diversity depends on, often interfering, multiple ecological drivers. Comprehensive approaches are hence needed to understand the mechanisms determining species diversity. In this study, we analysed the impact of vegetation structure, soil properties and fragmentation on the plant species diversity of remnant calcareous grasslands, therefore, in a comparative approach. We determined plant species diversity of 18 calcareous grasslands in south eastern Germany including all species and grassland specialists separately. Furthermore, we analysed the spatial structure of the grasslands as a result of fragmentation during the last 150 years (habitat area, distance to the nearest calcareous grassland and connectivity in 1830 and 2013). We also collected data concerning the vegetation structure (height of the vegetation, cover of bare soil, grass and litter) and the soil properties (content of phosphorous and potassium, ratio of carbon and nitrogen) of the grassland patches. Data were analysed using Bayesian multiple regressions. We observed a habitat loss of nearly 80% and increasing isolation between grasslands since 1830. In the Bayesian multiple regressions the species diversity of the studied grasslands depended negatively on cover of litter and to a lower degree on the distance to the nearest calcareous grassland in 2013, whereas soil properties had no significant impact. Our study supports the observation that vegetation structure, which strongly depends on land use, is often more important for the species richness of calcareous grasslands than fragmentation or soil properties. Even small and isolated grasslands may, therefore, contribute significantly to the conservation of species diversity, when they are still grazed.

  9. Genetic diversity and structure of elite cotton germplasm (Gossypium hirsutum L.) using genome-wide SNP data.

    Science.gov (United States)

    Ai, XianTao; Liang, YaJun; Wang, JunDuo; Zheng, JuYun; Gong, ZhaoLong; Guo, JiangPing; Li, XueYuan; Qu, YanYing

    2017-07-28

    Cotton (Gossypium spp.) is the most important natural textile fiber crop, and Gossypium hirsutum L. is responsible for 90% of the annual cotton crop in the world. Information on cotton genetic diversity and population structure is essential for new breeding lines. In this study, we analyzed population structure and genetic diversity of 288 elite Gossypium hirsutum cultivar accessions collected from around the world, and especially from China, using genome-wide single nucleotide polymorphisms (SNP) markers. The average polymorphsim information content (PIC) was 0.25, indicating a relatively low degree of genetic diversity. Population structure analysis revealed extensive admixture and identified three subgroups. Phylogenetic analysis supported the subgroups identified by STRUCTURE. The results from both population structure and phylogenetic analysis were, for the most part, in agreement with pedigree information. Analysis of molecular variance revealed a larger amount of variation was due to diversity within the groups. Establishment of genetic diversity and population structure from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in upland cotton.

  10. Diversity, Host Specialization, and Geographic Structure of Filarial Nematodes Infecting Malagasy Bats.

    Directory of Open Access Journals (Sweden)

    Beza Ramasindrazana

    Full Text Available We investigated filarial infection in Malagasy bats to gain insights into the diversity of these parasites and explore the factors shaping their distribution. Samples were obtained from 947 individual bats collected from 52 sites on Madagascar and representing 31 of the 44 species currently recognized on the island. Samples were screened for the presence of micro- and macro-parasites through both molecular and morphological approaches. Phylogenetic analyses showed that filarial diversity in Malagasy bats formed three main groups, the most common represented by Litomosa spp. infecting Miniopterus spp. (Miniopteridae; a second group infecting Pipistrellus cf. hesperidus (Vespertilionidae embedded within the Litomosoides cluster, which is recognized herein for the first time from Madagascar; and a third group composed of lineages with no clear genetic relationship to both previously described filarial nematodes and found in M. griveaudi, Myotis goudoti, Neoromicia matroka (Vespertilionidae, Otomops madagascariensis (Molossidae, and Paratriaenops furculus (Hipposideridae. We further analyzed the infection rates and distribution pattern of Litomosa spp., which was the most diverse and prevalent filarial taxon in our sample. Filarial infection was disproportionally more common in males than females in Miniopterus spp., which might be explained by some aspect of roosting behavior of these cave-dwelling bats. We also found marked geographic structure in the three Litomosa clades, mainly linked to bioclimatic conditions rather than host-parasite associations. While this study demonstrates distinct patterns of filarial nematode infection in Malagasy bats and highlights potential drivers of associated geographic distributions, future work should focus on their alpha taxonomy and characterize arthropod vectors.

  11. Genetic Diversity, Population Structure, and Heritability of Fruit Traits in Capsicum annuum.

    Directory of Open Access Journals (Sweden)

    Rachel P Naegele

    Full Text Available Cultivated pepper (Capsicum annuum is a phenotypically diverse species grown throughout the world. Wild and landrace peppers are typically small-fruited and pungent, but contain many important traits such as insect and disease resistance. Cultivated peppers vary dramatically in size, shape, pungency, and color, and often lack resistance traits. Fruit characteristics (e.g. shape and pericarp thickness are major determinants for cultivar selection, and their association with disease susceptibility can reduce breeding efficacy. This study evaluated a diverse collection of peppers for mature fruit phenotypic traits, correlation among fruit traits and Phytophthora fruit rot resistance, genetic diversity, population structure, and trait broad sense heritability. Significant differences within all fruit phenotype categories were detected among pepper lines. Fruit from Europe had the thickest pericarp, and fruit from Ecuador had the thinnest. For fruit shape index, fruit from Africa had the highest index, while fruit from Europe had the lowest. Five genetic clusters were detected in the pepper population and were significantly associated with fruit thickness, end shape, and fruit shape index. The genetic differentiation between clusters ranged from little to very great differentiation when grouped by the predefined categories. Broad sense heritability for fruit traits ranged from 0.56 (shoulder height to 0.98 (pericarp thickness. When correlations among fruit phenotypes and fruit disease were evaluated, fruit shape index was negatively correlated with pericarp thickness, and positively correlated with fruit perimeter. Pepper fruit pericarp, perimeter, and width had a slight positive correlation with Phytophthora fruit rot, whereas fruit shape index had a slight negative correlation.

  12. Genetic Diversity, Population Structure, and Heritability of Fruit Traits in Capsicum annuum

    Science.gov (United States)

    Naegele, Rachel P.; Mitchell, Jenna; Hausbeck, Mary K.

    2016-01-01

    Cultivated pepper (Capsicum annuum) is a phenotypically diverse species grown throughout the world. Wild and landrace peppers are typically small-fruited and pungent, but contain many important traits such as insect and disease resistance. Cultivated peppers vary dramatically in size, shape, pungency, and color, and often lack resistance traits. Fruit characteristics (e.g. shape and pericarp thickness) are major determinants for cultivar selection, and their association with disease susceptibility can reduce breeding efficacy. This study evaluated a diverse collection of peppers for mature fruit phenotypic traits, correlation among fruit traits and Phytophthora fruit rot resistance, genetic diversity, population structure, and trait broad sense heritability. Significant differences within all fruit phenotype categories were detected among pepper lines. Fruit from Europe had the thickest pericarp, and fruit from Ecuador had the thinnest. For fruit shape index, fruit from Africa had the highest index, while fruit from Europe had the lowest. Five genetic clusters were detected in the pepper population and were significantly associated with fruit thickness, end shape, and fruit shape index. The genetic differentiation between clusters ranged from little to very great differentiation when grouped by the predefined categories. Broad sense heritability for fruit traits ranged from 0.56 (shoulder height) to 0.98 (pericarp thickness). When correlations among fruit phenotypes and fruit disease were evaluated, fruit shape index was negatively correlated with pericarp thickness, and positively correlated with fruit perimeter. Pepper fruit pericarp, perimeter, and width had a slight positive correlation with Phytophthora fruit rot, whereas fruit shape index had a slight negative correlation. PMID:27415818

  13. A tri-oceanic perspective: DNA barcoding reveals geographic structure and cryptic diversity in Canadian polychaetes.

    Directory of Open Access Journals (Sweden)

    Christina M Carr

    Full Text Available BACKGROUND: Although polychaetes are one of the dominant taxa in marine communities, their distributions and taxonomic diversity are poorly understood. Recent studies have shown that many species thought to have broad distributions are actually a complex of allied species. In Canada, 12% of polychaete species are thought to occur in Atlantic, Arctic, and Pacific Oceans, but the extent of gene flow among their populations has not been tested. METHODOLOGY/PRINCIPAL FINDINGS: Sequence variation in a segment of the mitochondrial cytochrome c oxidase I (COI gene was employed to compare morphological versus molecular diversity estimates, to examine gene flow among populations of widespread species, and to explore connectivity patterns among Canada's three oceans. Analysis of 1876 specimens, representing 333 provisional species, revealed 40 times more sequence divergence between than within species (16.5% versus 0.38%. Genetic data suggest that one quarter of previously recognized species actually include two or more divergent lineages, indicating that richness in this region is currently underestimated. Few species with a tri-oceanic distribution showed genetic cohesion. Instead, large genetic breaks occur between Pacific and Atlantic-Arctic lineages, suggesting their long-term separation. High connectivity among Arctic and Atlantic regions and low connectivity with the Pacific further supports the conclusion that Canadian polychaetes are partitioned into two distinct faunas. CONCLUSIONS/SIGNIFICANCE: Results of this study confirm that COI sequences are an effective tool for species identification in polychaetes, and suggest that DNA barcoding will aid the recognition of species overlooked by the current taxonomic system. The consistent geographic structuring within presumed widespread species suggests that historical range fragmentation during the Pleistocene ultimately increased Canadian polychaete diversity and that the coastal British Columbia

  14. Woody species composition, diversity and structure of riparian forests of four watercourses types in Burkina Faso

    Institute of Scientific and Technical Information of China (English)

    Oumarou Sambaré; Fidèle Bognounou; Rüdiger Wittig; Adjima Thiombiano

    2011-01-01

    Riparian forests are classified as endangered ecosystems in general, particularly in sahelian countries like Burkina Faso because of human-induced alterations and civil engineering works. The modification of this important habitat is continuing, with little attention being paid to the ecological or human consequences of these changes. The objective of this study is to describe the variation of woody species diversity and dynamic in riparian forests on different type of watercourse banks along phytogeographical gradient in Burkina Faso. All woody species were systematically measured in 90 sample plots with sides of 50 m × 20 m.Density, dominance, frequency and species and family importance values were computed to characterize the species composition. Different diversity indices were calculated to examine the heterogeneity of riparian forests. A total of 196 species representing 139 genera and 51 families were recorded in the overall riparian forests. The species richness of individuals with dbh ≥ 5cm increased significantly from the North to the South along the phytogeographical gradient and varied significantly between the different types of riparian forests. Similarity in tree species composition between riparian forests was low, which indicates high beta diversity and reflects differences in habitat conditions and topography.The structural characteristics varied significantly along the phytogeographical gradient and between the different types of riparian forests.The diameter class distribution of trees in all riparian forests showed a reverse “J” shaped curve except riparian forest of stream indicating vegetation dominated by juvenile individuals. Considering the ecological importance of riparian forest, there is a need to delineate and classify them along watercourses throughout the country.

  15. Spatial variability of microbial richness and diversity and relationships with soil organic carbon, texture and structure across an agricultural field

    DEFF Research Database (Denmark)

    Naveed, Muhammad; Herath, Lasantha; Møldrup, Per;

    2016-01-01

    no spatial autocorrelation was observed for them. Fungal Shannon diversity slightly increased from south to north, with spatial autocorrelation for distances larger than 100 m. The ratio of clay to organic carbon (n) was found to be the best predictor of bacterial richness and diversity indices. Neither...... organic carbon nor clay content was significantly correlated with fungal richness and diversity indices. For soil structural parameters, soil water retention in the pF range 5–6.8 (parameter B) was significantly correlated with both bacterial and fungal Shannon diversities. Amount of macropores (> 30 μm......) and total porosity (ϕ) were only significantly correlated with fungal Shannon diversity. These results suggest that variation in microbial communities is not random but strongly related with variations in organic carbon, clay content, and soil water characteristics at the field scale....

  16. Structural and Functional Diversity of Weed Species in Organic and Conventional Rice Agro-Ecosystems

    Directory of Open Access Journals (Sweden)

    S. Y. Mousawi Toghani

    2016-02-01

    Full Text Available Introduction Diversity reflects the complexity of a system and can maintain its sustainability. Higherdiversity, results in higher inherent complexity of agro-ecosystems and strengthen their processes. It is necessary to realize the spatial distribution and temporal properties of the biodiversity components in agro-ecosystems, for the conservation and optimal utilization. Since weeds as a complementary component of agro-ecosystems and are inseparable, so the study of species, their functional and structural diversity of them can play an important role in weed management and balance in ecological systems. Materials and Methods This study was performed to determine the effects of different management systems on structural, and functional diversity of paddy weeds in Mazandaran province. Three rice fields, ranged from 0.3 to 0.5 ha, were chosen for each management system. Samples were collected from three fields running under each selected management system (organic and conventional. Data (number of weed species and their density were randomly gathered from 9 quadrates (1m×1m per each field in four stages (tillering, stem elongation, grain filling and after harvest. The diversity, evenness, frequency and similarity indices for weeds were determined at genera and species level. Data analysis carried out through T-test and grouping performed via cluster analysis as hierarchy. Results and Discussion All monitored weeds can be classified into four plant family including cereals (Poaceae, sedges (Cyperaceae, plantain (Plantaginaceae and chicory (Asteraceae.Under conventional systems the values of weed diversity indices were higher during tillering and stem elongation compared with organic ones, and were lower during grain filling and after harvest stages. However indices of weed evenness showed contrary tendency. Both Sympson and Shanon-Wiener diversity indices, consist of two clusters in 76% similarity. Evenness indices of Kamargo and Smith

  17. Exposing the subunit diversity and modularity of protein complexes by structural mass spectrometry approaches.

    Science.gov (United States)

    Chorev, Dror S; Ben-Nissan, Gili; Sharon, Michal

    2015-08-01

    Although the number of protein-encoding genes in the human genome is only about 20 000 not far from the amount found in the nematode worm genome, the number of proteins that are translated from these sequences is larger by several orders of magnitude. A number of mechanisms have evolved to enable this diversity. For example, genes can be alternatively spliced to create multiple transcripts; they may also be translated from different alternative initiation sites. After translation, hundreds of chemical modifications can be introduced in proteins, altering their chemical properties, folding, stability, and activity. The complexity is then further enhanced by the various combinations that are generated from the assembly of different subunit variants into protein complexes. This, in turn, confers structural and functional flexibility, and endows the cell with the ability to adapt to various environmental conditions. Therefore, exposing the variability of protein complexes is an important step toward understanding their biological functions. Revealing this enormous diversity, however, is not a simple task. In this review, we will focus on the array of MS-based strategies that are capable of performing this mission. We will also discuss the challenges that lie ahead, and the future directions toward which the field might be heading.

  18. Genetic diversity and population structure of the Guinea pig (Cavia porcellus, Rodentia, caviidae in Colombia

    Directory of Open Access Journals (Sweden)

    William Burgos-Paz

    2011-01-01

    Full Text Available The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven production zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allelic richness ranging from 3.0 to 6.56, and observed heterozygosity (Ho from 0.33 to 0.60, with a deficit in heterozygous individuals. Although statistically significant (p < 0.05, genetic differentiation between population pairs was found to be low. Genetic distance, as well as clustering of guinea-pig lines and populations, coincided with the historical and geographical distribution of the populations. Likewise, high genetic identity between improved and native lines was established. An analysis of group probabilistic assignment revealed that each line should not be considered as a genetically homogeneous group. The findings corroborate the absorption of native genetic material into the improved line introduced into Colombia from Peru. It is necessary to establish conservation programs for native-line individuals in Nariño, and control genealogical and production records in order to reduce the inbreeding values in the populations.

  19. pH dominates variation in tropical soil archaeal diversity and community structure.

    Science.gov (United States)

    Tripathi, Binu M; Kim, Mincheol; Lai-Hoe, Ang; Shukor, Nor A A; Rahim, Raha A; Go, Rusea; Adams, Jonathan M

    2013-11-01

    Little is known of the factors influencing soil archaeal community diversity and composition in the tropics. We sampled soils across a range of forest and nonforest environments in the equatorial tropics of Malaysia, covering a wide range of pH values. DNA was PCR-amplified for the V1-V3 region of the 16S rRNA gene, and 454-pyrosequenced. Soil pH was the best predictor of diversity and community composition of Archaea, being a stronger predictor than land use. Archaeal OTU richness was highest in the most acidic soils. Overall archaeal abundance in tropical soils (determined by qPCR) also decreased at higher pH. This contrasts with the opposite trend previously found in temperate soils. Thaumarcheota group 1.1b was more abundant in alkaline soils, whereas group 1.1c was only detected in acidic soils. These results parallel those found in previous studies in cooler climates, emphasizing niche conservatism among broad archaeal groups. Among the most abundant operational taxonomic units (OTUs), there was clear evidence of niche partitioning by pH. No individual OTU occurred across the entire range of pH values. Overall, the results of this study show that pH plays a major role in structuring tropical soil archaeal communities.

  20. Embryo impacts and gas giant mergers - II. Diversity of hot Jupiters' internal structure

    Science.gov (United States)

    Liu, Shang-Fei; Agnor, Craig B.; Lin, D. N. C.; Li, Shu-Lin

    2015-01-01

    We consider the origin of compact, short-period, Jupiter-mass planets. We propose that their diverse structure is caused by giant impacts of embryos and super-Earths or mergers with other gas giants during the formation and evolution of these hot Jupiters. Through a series of numerical simulations, we show that typical head-on collisions generally lead to total coalescence of impinging gas giants. Although extremely energetic collisions can disintegrate the envelope of gas giants, these events seldom occur. During oblique and moderately energetic collisions, the merger products retain higher fraction of the colliders' cores than their envelopes. They can also deposit considerable amount of spin angular momentum to the gas giants and desynchronize their spins from their orbital mean motion. We find that the oblateness of gas giants can be used to infer the impact history. Subsequent dissipation of stellar tide inside the planets' envelope can lead to runaway inflation and potentially a substantial loss of gas through Roche lobe overflow. The impact of super-Earths on parabolic orbits can also enlarge gas giant planets' envelope and elevates their tidal dissipation rate over ˜100 Myr time scale. Since giant impacts occur stochastically with a range of impactor sizes and energies, their diverse outcomes may account for the dispersion in the mass-radius relationship of hot Jupiters.

  1. Genetic diversity and matrilineal structure in Chinese tree shrews inhabiting Kunming, China.

    Science.gov (United States)

    Chen, Shi-Yi; Xu, Ling; Lü, Long-Bao; Yao, Yong-Gang

    2011-02-01

    Due to their special phylogenetic position in the Euarchontoglires and close affinity to primates, tree shrews have been proposed as an alternative experimental animal to primates in biomedical research. However, the population genetic structure of tree shrews has largely remained unknown and this has hindered the development of tree shrew breeding and selection. Here we sampled 80 Chinese tree shrews (Tupaia belangeri chinensis) in Kunming, China, and analyzed partial mtDNA control region sequence variation. Based on our samples and two published sequences from northern tree shrews (T. belangeri), we identified 29 substitutions in the mtDNA control region fragment (~604 bp) across 82 individuals and defined 13 haplotypes. Seventeen samples were selected for sequencing of the cytochrome b (Cyt b; 1134 bp) gene based on control region sequence variation and were analyzed in combination with 34 published sequences to solidify the phylogenetic pattern obtained from control region data. Overall, tree shrews from Kunming have high genetic diversity and present a remarkable long genetic distance to the two reported northern tree shrews outside China. Our results provide some caution when using tree shrews to establish animal models because of this apparent genetic difference. In addition, the high genetic diversity of Chinese tree shrews inhabiting Kunming suggests that systematic genetic investigations should be conducted before establishing an inbred strain for medical and biological research.

  2. Microbial functional diversity alters the structure and sensitivity of oxygen deficient zones

    Science.gov (United States)

    Penn, Justin; Weber, Thomas; Deutsch, Curtis

    2016-09-01

    Oxygen deficient zones (ODZs) below the ocean surface regulate marine productivity by removing bioavailable nitrogen (N). A complex microbial community mediates N loss, but the interplay of its diverse metabolisms is poorly understood. We present an ecosystem model of the North Pacific ODZ that reproduces observed chemical distributions yet predicts different ODZ structure, rates, and climatic sensitivity compared to traditional geochemical models. An emergent lower O2 limit for aerobic nitrification lies below the upper O2 threshold for anaerobic denitrification, creating a zone of microbial coexistence that causes a larger ODZ but slower total rates of N loss. The O2-dependent competition for the intermediate nitrite produces gradients in its oxidation versus reduction, anammox versus heterotrophic denitrification, and the net ecological stoichiometry of N loss. The latter effect implies that an externally driven ODZ expansion should favor communities that more efficiently remove N, increasing the sensitivity of the N cycle to climate change.

  3. Structurally Diverse π-Extended Conjugated Polycarbo- and Heterocycles through Pd-Catalyzed Autotandem Cascades.

    Science.gov (United States)

    Barroso, Raquel; Cabal, María-Paz; Badía-Laiño, Rosana; Valdés, Carlos

    2015-11-09

    The Pd-catalyzed reaction between 2,2'-dibromobiphenyls and related systems with tosylhydrazones gives rise to new π-extended conjugated polycarbo- and heterocycles through an autotandem process involving a cross-coupling reaction followed by an intramolecular Heck cyclization. The reaction shows wide scope regarding both coupling partners. Cyclic and acyclic tosylhydrazones can participate in the process. Additionally, a variety of aromatic and heteroaromatic dibromoderivatives have been employed, leading to an array of diverse scaffolds featuring a fluorene or acridine central nucleus, and containing binaphthyl, thiophene, benzothiophene and indole moieties. The application to appropriate tetrabrominated systems led to greater structural complexity through two consecutive autotandem cascades. The photophysical properties of selected compounds were studied through their absorption and emission spectra. Fluorescence molecules featuring very high quantum yields were identified, showing the potential of this methodology in the development of molecules with interesting optoelectronic properties.

  4. Embryo impacts and gas giant mergers II: Diversity of Hot Jupiters' internal structure

    CERN Document Server

    Liu, Shang-Fei; Lin, D N C; Li, Shu-Lin

    2014-01-01

    We consider the origin of compact, short-period, Jupiter-mass planets. We propose that their diverse structure is caused by giant impacts of embryos and super-Earths or mergers with other gas giants during the formation and evolution of these hot Jupiters. Through a series of numerical simulations, we show that typical head-on collisions generally lead to total coalescence of impinging gas giants. Although extremely energetic collisions can disintegrate the envelope of gas giants, these events seldom occur. During oblique and moderately energetic collisions, the merger products retain higher fraction of the colliders' cores than their envelopes. They can also deposit considerable amount of spin angular momentum to the gas giants and desynchronize their spins from their orbital mean motion. We find that the oblateness of gas giants can be used to infer the impact history. Subsequent dissipation of stellar tide inside the planets' envelope can lead to runaway inflation and potentially a substantial loss of gas ...

  5. Diversity and genetic structure of Ornithogalum L. (Hyacinthaceae populations as revealed by RAPD-PCR markers

    Directory of Open Access Journals (Sweden)

    Andrić Andrijana

    2015-01-01

    Full Text Available Random amplified polymorphic DNA (RAPD PCR method was used to assess the level of diversity and genetic structure in Ornithogalum L. populations from Serbia and Hungary with the main goal of improving the knowledge of this genus in the given region. The material was collected from 19 populations and identified as two morphologically similar and phylogenetically close taxa: O. umbellatum L. 1753 and O. divergens Boreau 1887. All ten RAPD primers used for the analysis gave PCR products, with length between 3000bp and 300bp. There were 101 amplified fragments in total; number of polymorphic bands per primer varied between seven and 13. Percentage of polymorphic loci was 96% in total and 12% in average in each population. Genetic variation statistics for all loci also showed that genetic diversity for all populations was 0.29 and Shannon index 0.45, while mean values for these parameters calculated for each population were 0.04 and 0.06, respectively. Analysis of molecular variance demonstrated high population genetic differentiation; however Mantel test showed no significant correlation between geographic distances of populations and genetic distances expressed through population pairwise FST. UPGMA dendrogram based on Jaccard genetic similarity coefficients showed subclustering and principal coordinate analysis based on Nei and Li coefficients of genetic distances indicated grouping. Analysis of populations genetic structure was in accordance with these results and clearly separated populations of O. umbellatum from O. divergens. RAPDs proved to be a reliable and rapid method suitable for distinguishing genetic differentiation in Ornithogalum, thus could be applied as a useful additional tool in resolving taxonomic problems. [Projekat Ministarstva nauke Republike Srbije, br. 173002

  6. The big, large and huge case of state-building

    DEFF Research Database (Denmark)

    Harste, Gorm

      Using communication theory as point of departure, it is not evident how to study macro phenomena. Michel Foucault limited his studies to a non-Grand Theory when studying discursive events. At the same time, Charles Tilly wrote about Big Structures, Large Processes, Huge Comparisons when trying...... to establish a perspective on a macro phenomena as European state formation. With Luhmann's system theory, the claim is that there is no such contradiction between Grand evolution and particular semantic history. Passing through some classic studies of the historical establishment of interaction systems...

  7. The  Big, Large and Huge Case of State-Building

    DEFF Research Database (Denmark)

    Harste, Gorm

    2009-01-01

      Using communication theory as point of departure it is not evident how to study macro phenomena. Michel Foucault delimited his studies to a non-Grand Theory when he studied discursive events. At the same time Charles Tilly wrote about Big Structures, Large Processes, Huge Comparisons when he...... tried to establish a perspective on a macro phenomena as European state formation. With Luhmann's system theory, the claim is that there is no such contradiction between Grand evolution and particular semantic history. Passing through some classic studies of the historical establishment of interaction...

  8. Anthraquinones and Derivatives from Marine-Derived Fungi: Structural Diversity and Selected Biological Activities

    Directory of Open Access Journals (Sweden)

    Mireille Fouillaud

    2016-03-01

    Full Text Available Anthraquinones and their derivatives constitute a large group of quinoid compounds with about 700 molecules described. They are widespread in fungi and their chemical diversity and biological activities recently attracted attention of industries in such fields as pharmaceuticals, clothes dyeing, and food colorants. Their positive and/or negative effect(s due to the 9,10-anthracenedione structure and its substituents are still not clearly understood and their potential roles or effects on human health are today strongly discussed among scientists. As marine microorganisms recently appeared as producers of an astonishing variety of structurally unique secondary metabolites, they may represent a promising resource for identifying new candidates for therapeutic drugs or daily additives. Within this review, we investigate the present knowledge about the anthraquinones and derivatives listed to date from marine-derived filamentous fungi′s productions. This overview highlights the molecules which have been identified in microorganisms for the first time. The structures and colors of the anthraquinoid compounds come along with the known roles of some molecules in the life of the organisms. Some specific biological activities are also described. This may help to open doors towards innovative natural substances.

  9. Structural determinants of phenotypic diversity and replication rate of human prions.

    Directory of Open Access Journals (Sweden)

    Jiri G Safar

    2015-04-01

    Full Text Available The infectious pathogen responsible for prion diseases is the misfolded, aggregated form of the prion protein, PrPSc. In contrast to recent progress in studies of laboratory rodent-adapted prions, current understanding of the molecular basis of human prion diseases and, especially, their vast phenotypic diversity is very limited. Here, we have purified proteinase resistant PrPSc aggregates from two major phenotypes of sporadic Creutzfeldt-Jakob disease (sCJD, determined their conformational stability and replication tempo in vitro, as well as characterized structural organization using recently emerged approaches based on hydrogen/deuterium (H/D exchange coupled with mass spectrometry. Our data clearly demonstrate that these phenotypically distant prions differ in a major way with regard to their structural organization, both at the level of the polypeptide backbone (as indicated by backbone amide H/D exchange data as well as the quaternary packing arrangements (as indicated by H/D exchange kinetics for histidine side chains. Furthermore, these data indicate that, in contrast to previous observations on yeast and some murine prion strains, the replication rate of sCJD prions is primarily determined not by conformational stability but by specific structural features that control the growth rate of prion protein aggregates.

  10. Microsatellite analysis of genetic diversity and population structure of Chinese mitten crab (Eriocheir sinensis)

    Institute of Scientific and Technical Information of China (English)

    Yumei Chang; Liqun Liang; Haitao Ma; Jianguo He; Xiaowen Sun

    2008-01-01

    Chinese mitten crab (Eriocheir sinensis) has higher commercial value as food source than any other species of Eriocheir in China.To evaluate the germplasm resources and characterize the genetic diversity and population structure of the crabs in different water systems,two stocks and two farming populations were assessed with 25 polymorphic microsallite loci available in public GenBank.Basic statistics showed that the average observed heterozygosity (Ho) amongst populations ranged from 0.5789 to 0.6824.However,a remarkable presence of inbreeding and heterozygote deficiencies were observed.To analyze population structure,pairwise FST coefficients explained only ~10.3% variability from the subdivision of mitten crab populations,the remaining variability stems from the subdivision within subpopulations.Although the four populations had slight differentiation,different allelic frequencies resulted in distinct population structures.Two stocks and one farming population were clustered together to the phylogenetic branch of Yangtze crab,with an approximate membership of 95%.Whereas,another fanning population was clustered singly to the phylogenetic branch of the Liaohe crab,with a membership of 97.1%.The tests for individual admixture showed that Yangtze crab had probably been contaminated with individuals from other water systems.Genetic relationships between populations also supported the conclusion that Yangtze crab and Liaohe crab had different gene pools in spite of the origins of the same species.

  11. Catalytic and structural diversity of the fluazifop-inducible glutathione transferases from Phaseolus vulgaris.

    Science.gov (United States)

    Chronopoulou, Evangelia; Madesis, Panagiotis; Asimakopoulou, Basiliki; Platis, Dimitrios; Tsaftaris, Athanasios; Labrou, Nikolaos E

    2012-06-01

    Plant glutathione transferases (GSTs) comprise a large family of inducible enzymes that play important roles in stress tolerance and herbicide detoxification. Treatment of Phaseolus vulgaris leaves with the aryloxyphenoxypropionic herbicide fluazifop-p-butyl resulted in induction of GST activities. Three inducible GST isoenzymes were identified and separated by affinity chromatography. Their full-length cDNAs with complete open reading frame were isolated using RACE-RT and information from N-terminal amino acid sequences. Analysis of the cDNA clones showed that the deduced amino acid sequences share high homology with GSTs that belong to phi and tau classes. The three isoenzymes were expressed in E. coli and their substrate specificity was determined towards 20 different substrates. The results showed that the fluazifop-inducible glutathione transferases from P. vulgaris (PvGSTs) catalyze a broad range of reactions and exhibit quite varied substrate specificity. Molecular modeling and structural analysis was used to identify key structural characteristics and to provide insights into the substrate specificity and the catalytic mechanism of these enzymes. These results provide new insights into catalytic and structural diversity of GSTs and the detoxifying mechanism used by P. vulgaris.

  12. Structural diversity and biological significance of lipoteichoic acid in Gram-positive bacteria: focusing on beneficial probiotic lactic acid bacteria.

    Science.gov (United States)

    Shiraishi, Tsukasa; Yokota, Shinichi; Fukiya, Satoru; Yokota, Atsushi

    2016-01-01

    Bacterial cell surface molecules are at the forefront of host-bacterium interactions. Teichoic acids are observed only in Gram-positive bacteria, and they are one of the main cell surface components. Teichoic acids play important physiological roles and contribute to the bacterial interaction with their host. In particular, lipoteichoic acid (LTA) anchored to the cell membrane has attracted attention as a host immunomodulator. Chemical and biological characteristics of LTA from various bacteria have been described. However, most of the information concerns pathogenic bacteria, and information on beneficial bacteria, including probiotic lactic acid bacteria, is insufficient. LTA is structurally diverse. Strain-level structural diversity of LTA is suggested to underpin its immunomodulatory activities. Thus, the structural information on LTA in probiotics, in particular strain-associated diversity, is important for understanding its beneficial roles associated with the modulation of immune response. Continued accumulation of structural information is necessary to elucidate the detailed physiological roles and significance of LTA. In this review article, we summarize the current state of knowledge on LTA structure, in particular the structure of LTA from lactic acid bacteria. We also describe the significance of structural diversity and biological roles of LTA.

  13. The technical research on the huge glazed brick from the relic of Nanyue Kingdom Palace

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    'Qin brick and Han tile' has a great worldwide reputation in the architectural history of China. According to the former archaeological materials, the big hollow brick is usually one meter long and thirty to forty centimeters wide, while the solid brick is generally much smaller. But in 1995, large scale vestiges and structures were unearthed at the center of Guangzhou's old district, from the relic of Nanyue Kingdom Palace, which was built some 2000 years ago during the Western-Han Dynasty, A great number of earthen structural members were discovered, especially the solid glazed bricks in various beautiful patterns with an astonishing thickness and size. Some of them are one meter square, more than 20 centimeters thick, and weight half a ton, which are named ‘Brick No.1 in the world' by excavators. People have shown great interest in how to make these huge glazed bricks at the ancient technical conditions, because it is very difficult to manufacture such huge bricks even with the modern technology. At the request of Guangdong Nanyue Kingdom Palace Museum, Shanghai Institute of Ceramics carried out systematical measurements and analysis on these bricks and studied the physical and chemical forming mechanisms from their chemical compositions, structure, and physical characteristics. Here the technical characteristics of the bricks are also discussed.

  14. The technical research on the huge glazed brick from the relic of Nanyue Kingdom Palace

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    ‘Qin brick and Han tile’ has a great worldwide reputation in the architectural history of China. According to the former archaeological materials, the big hollow brick is usually one meter long and thirty to forty centimeters wide, while the solid brick is generally much smaller. But in 1995, large scale vestiges and structures were un- earthed at the center of Guangzhou’s old district, from the relic of Nanyue Kingdom Palace, which was built some 2000 years ago during the Western-Han Dynasty. A great number of earthen structural members were discovered, especially the solid glazed bricks in various beautiful patterns with an astonishing thickness and size. Some of them are one meter square, more than 20 centimeters thick, and weight half a ton, which are named ‘Brick No.1 in the world’ by excavators. People have shown great interest in how to make these huge glazed bricks at the ancient tech- nical conditions, because it is very difficult to manufacture such huge bricks even with the modern technology. At the request of Guangdong Nanyue Kingdom Palace Museum, Shanghai Institute of Ceramics carried out systematical measurements and analysis on these bricks and studied the physical and chemical forming mechanisms from their chemical compositions, structure, and physical character- istics. Here the technical characteristics of the bricks are also discussed.

  15. Errors in Seismic Hazard Assessment are Creating Huge Human Losses

    Science.gov (United States)

    Bela, J.

    2015-12-01

    The current practice of representing earthquake hazards to the public based upon their perceived likelihood or probability of occurrence is proven now by the global record of actual earthquakes to be not only erroneous and unreliable, but also too deadly! Earthquake occurrence is sporadic and therefore assumptions of earthquake frequency and return-period are both not only misleading, but also categorically false. More than 700,000 people have now lost their lives (2000-2011), wherein 11 of the World's Deadliest Earthquakes have occurred in locations where probability-based seismic hazard assessments had predicted only low seismic low hazard. Unless seismic hazard assessment and the setting of minimum earthquake design safety standards for buildings and bridges are based on a more realistic deterministic recognition of "what can happen" rather than on what mathematical models suggest is "most likely to happen" such future huge human losses can only be expected to continue! The actual earthquake events that did occur were at or near the maximum potential-size event that either already had occurred in the past; or were geologically known to be possible. Haiti's M7 earthquake, 2010 (with > 222,000 fatalities) meant the dead could not even be buried with dignity. Japan's catastrophic Tohoku earthquake, 2011; a M9 Megathrust earthquake, unleashed a tsunami that not only obliterated coastal communities along the northern Japanese coast, but also claimed > 20,000 lives. This tsunami flooded nuclear reactors at Fukushima, causing 4 explosions and 3 reactors to melt down. But while this history of huge human losses due to erroneous and misleading seismic hazard estimates, despite its wrenching pain, cannot be unlived; if faced with courage and a more realistic deterministic estimate of "what is possible", it need not be lived again. An objective testing of the results of global probability based seismic hazard maps against real occurrences has never been done by the

  16. A Common Precursor Approach to Structurally Diverse Natural Products: The Synthesis of the Core Structure of (±)-Clausenamide and the Total Synthesis of (±)-Hyalodendrin

    OpenAIRE

    Szulc, B. R.; Sil, B. C.; Ruiz, A; Hilton, S. T.

    2015-01-01

    Structurally diverse natural products from unrelated sources typically require the development of individual synthetic routes. In a novel approach, we have shown that the epidithiodiketopiperazine-derived natural product (±)-hyalodendrin and the core structure of the unrelated pyrrolidine-derived natural product clausenamide can be synthesised from a common synthetic precursor in good yield by simple variation of the reaction conditions.

  17. Genetic diversity and population structure of Pisum sativum accessions for marker-trait association of lipid content

    Institute of Scientific and Technical Information of China (English)

    Sajjad Ahmad; Simerjeet Kaur; Neil Dylan Lamb-Palmer; Mark Lefsrud; Jaswinder Singh

    2015-01-01

    Field pea (Pisum sativum L.) is an important protein-rich pulse crop produced globally. Increasing the lipid content of Pisum seeds through conventional and contemporary molecular breeding tools may bring added value to the crop. However, knowledge about genetic diversity and lipid content in field pea is limited. An understanding of genetic diversity and population structure in diverse germplasm is important and a prerequisite for genetic dissection of complex characteristics and marker-trait associations. Fifty polymorphic microsatellite markers detecting a total of 207 alleles were used to obtain information on genetic diversity, population structure and marker-trait associations. Cluster analysis was performed using UPGMA to construct a dendrogram from a pairwise similarity matrix. Pea genotypes were divided into five major clusters. A model-based population structure analysis divided the pea accessions into four groups. Percentage lipid content in 35 diverse pea accessions was used to find potential associations with the SSR markers. Markers AD73, D21, and AA5 were significantly associated with lipid content using a mixed linear model (MLM) taking population structure (Q) and relative kinship (K) into account. The results of this preliminary study suggested that the population could be used for marker-trait association mapping studies.

  18. Genetic diversity and population structure of Pisum sativum accessions for marker-trait association of lipid content

    Directory of Open Access Journals (Sweden)

    Sajjad Ahmad

    2015-06-01

    Full Text Available Field pea (Pisum sativum L. is an important protein-rich pulse crop produced globally. Increasing the lipid content of Pisum seeds through conventional and contemporary molecular breeding tools may bring added value to the crop. However, knowledge about genetic diversity and lipid content in field pea is limited. An understanding of genetic diversity and population structure in diverse germplasm is important and a prerequisite for genetic dissection of complex characteristics and marker-trait associations. Fifty polymorphic microsatellite markers detecting a total of 207 alleles were used to obtain information on genetic diversity, population structure and marker-trait associations. Cluster analysis was performed using UPGMA to construct a dendrogram from a pairwise similarity matrix. Pea genotypes were divided into five major clusters. A model-based population structure analysis divided the pea accessions into four groups. Percentage lipid content in 35 diverse pea accessions was used to find potential associations with the SSR markers. Markers AD73, D21, and AA5 were significantly associated with lipid content using a mixed linear model (MLM taking population structure (Q and relative kinship (K into account. The results of this preliminary study suggested that the population could be used for marker-trait association mapping studies.

  19. Genetic diversity and population structure of Pisum sativum accessions for marker-trait association of lipid content

    Institute of Scientific and Technical Information of China (English)

    Sajjad; Ahmad; Simerjeet; Kaur; Neil; Dylan; Lamb-Palmer; Mark; Lefsrud; Jaswinder; Singh

    2015-01-01

    Field pea(Pisum sativum L.) is an important protein-rich pulse crop produced globally. Increasing the lipid content of Pisum seeds through conventional and contemporary molecular breeding tools may bring added value to the crop. However, knowledge about genetic diversity and lipid content in field pea is limited. An understanding of genetic diversity and population structure in diverse germplasm is important and a prerequisite for genetic dissection of complex characteristics and marker-trait associations. Fifty polymorphic microsatellite markers detecting a total of 207 alleles were used to obtain information on genetic diversity, population structure and marker-trait associations. Cluster analysis was performed using UPGMA to construct a dendrogram from a pairwise similarity matrix. Pea genotypes were divided into five major clusters. A model-based population structure analysis divided the pea accessions into four groups. Percentage lipid content in 35 diverse pea accessions was used to find potential associations with the SSR markers. Markers AD73, D21, and AA5 were significantly associated with lipid content using a mixed linear model(MLM) taking population structure(Q) and relative kinship(K) into account. The results of this preliminary study suggested that the population could be used for marker-trait association mapping studies.

  20. Inferring the population structure of Myzus persicae in diverse agroecosystems using microsatellite markers.

    Science.gov (United States)

    Sanchez, Juan Antonio; La-Spina, Michelangelo; Guirao, Pedro; Cánovas, Fernando

    2013-08-01

    Diverse agroecosystems offer phytophagous insects a wide choice of host plants. Myzus persicae is a polyphagous aphid common in moderate climates. During its life cycle it alternates between primary and secondary hosts. A spatial genetic population structure may arise due to environmental factors and reproduction modes. The aim of this work was to determine the spatial and temporal genetic population structure of M. persicae in relation to host plants and climatic conditions. For this, 923 individuals of M. persicae collected from six plant families between 2005 and 2008 in south-eastern Spain were genotyped for eight microsatellite loci. The population structure was inferred by neighbour-joining, analysis of molecular variance (AMOVA) and Bayesian analyses. Moderate polymorphism was observed for the eight loci in almost all the samples. No differences in the number of alleles were observed between primary and secondary hosts or between geographical areas. The proportion of unique genotypes found in the primary host was similar in the north (0.961 ± 0.036) and the south (0.987 ± 0.013), while in the secondary host it was higher in the north (0.801 ± 0.159) than in the south (0.318 ± 0.063). Heterozygosity excess and linkage disequilibrium suggest a high representation of obligate parthenogens in areas with warmer climate and in the secondary hosts. The F ST-values pointed to no genetic differentiation of M. persicae on the different plant families. F ST-values, AMOVA and Bayesian model-based cluster analyses pointed to a significant population structure that was related to primary and secondary hosts. Differences between primary and secondary hosts could be due to the overrepresentation of parthenogens on herbaceous plants.

  1. Distributed and parallel approach for handle and perform huge datasets

    Science.gov (United States)

    Konopko, Joanna

    2015-12-01

    Big Data refers to the dynamic, large and disparate volumes of data comes from many different sources (tools, machines, sensors, mobile devices) uncorrelated with each others. It requires new, innovative and scalable technology to collect, host and analytically process the vast amount of data. Proper architecture of the system that perform huge data sets is needed. In this paper, the comparison of distributed and parallel system architecture is presented on the example of MapReduce (MR) Hadoop platform and parallel database platform (DBMS). This paper also analyzes the problem of performing and handling valuable information from petabytes of data. The both paradigms: MapReduce and parallel DBMS are described and compared. The hybrid architecture approach is also proposed and could be used to solve the analyzed problem of storing and processing Big Data.

  2. Anaethetic management of a neonate with huge cystic hygroma.

    Directory of Open Access Journals (Sweden)

    Bindi Palkhiwala

    2013-01-01

    Full Text Available We discuss here the case of a 7 day old neonate with huge cystic hygroma on the left side of the neck invading the major vessels of neck, facial nerve, strap muscles and sternocleidomastoid. Anasethtic implications in this case were maintaining airway patency after induction, difficult intubation, risk perioperative dislodgement of tube and judgement of proper time for extubation. Following gaseous induction and adequate mask ventilation, patient was intubated with muscle relaxant. peroperatively to avoid accidental extubation, we choose to manually hold the ET tube after fixing it. At the end of relatively uneventful surgery, we could extubate the patient in OT. patient was shifted to NICU for observation. Post operatively on 3rd day, facial palsy was observed. Ptient was discharged on 21st day.

  3. Huge Intracanal lumbar Disc Herniation: a Review of Four Cases

    Directory of Open Access Journals (Sweden)

    Farzad Omidi-Kashani

    2016-01-01

    Full Text Available Lumbar disc herniation (LDH is the most common cause of sciatica and only in about 10% of the affected patients, surgical intervention is necessary. The side of the patient (the side of most prominent clinical complaints is usually consistent with the side of imaging (the side with most prominent disc herniation on imaging scans. In this case series, we presented our experience in four cases with huge intracanal LDH that a mismatch between the patient’s side and the imaging’s side was present. In these cases, for deciding to do the operation, the physicians need to rely more on clinical findings, but for deciding the side of discectomy, imaging characteristic (imaging side may be a more important criterion.

  4. A parallel solver for huge dense linear systems

    Science.gov (United States)

    Badia, J. M.; Movilla, J. L.; Climente, J. I.; Castillo, M.; Marqués, M.; Mayo, R.; Quintana-Ortí, E. S.; Planelles, J.

    2011-11-01

    HDSS (Huge Dense Linear System Solver) is a Fortran Application Programming Interface (API) to facilitate the parallel solution of very large dense systems to scientists and engineers. The API makes use of parallelism to yield an efficient solution of the systems on a wide range of parallel platforms, from clusters of processors to massively parallel multiprocessors. It exploits out-of-core strategies to leverage the secondary memory in order to solve huge linear systems O(100.000). The API is based on the parallel linear algebra library PLAPACK, and on its Out-Of-Core (OOC) extension POOCLAPACK. Both PLAPACK and POOCLAPACK use the Message Passing Interface (MPI) as the communication layer and BLAS to perform the local matrix operations. The API provides a friendly interface to the users, hiding almost all the technical aspects related to the parallel execution of the code and the use of the secondary memory to solve the systems. In particular, the API can automatically select the best way to store and solve the systems, depending of the dimension of the system, the number of processes and the main memory of the platform. Experimental results on several parallel platforms report high performance, reaching more than 1 TFLOP with 64 cores to solve a system with more than 200 000 equations and more than 10 000 right-hand side vectors. New version program summaryProgram title: Huge Dense System Solver (HDSS) Catalogue identifier: AEHU_v1_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHU_v1_1.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 87 062 No. of bytes in distributed program, including test data, etc.: 1 069 110 Distribution format: tar.gz Programming language: Fortran90, C Computer: Parallel architectures: multiprocessors, computer clusters Operating system

  5. Does China's Huge External Surplus Imply an Undervalued Renminbi?

    Institute of Scientific and Technical Information of China (English)

    Anthony J. Makin

    2007-01-01

    A pegged exchange rate regime has been pivotal to China's export-led development strategy. However, its huge trade surpluses and massive build up of international reserves have been matched by large deficits for major trading partners, creating acute policy concerns abroad, especially in the USA. This paper provides a straightforward conceptual framework for interpreting the effect of China's exchange rate policy on its own trade balance and that of trading partners in the context of discrepant economic growth rates. It shows how pegging the exchange rate when output is outstripping expenditure induces China's trade surpluses and counterpart deficits for its trading partners. An important corollary is that given its strictly regulated capital account, China's persistently large surpluses imply a significantly undervalued renminbi, which should gradually become more flexible.

  6. Wide diversity in structure and expression profiles among members of the Caenorhabditis elegans globin protein family

    Directory of Open Access Journals (Sweden)

    Vinogradov Serge

    2007-10-01

    Full Text Available Abstract Background The emergence of high throughput genome sequencing facilities and powerful high performance bioinformatic tools has highlighted hitherto unexpected wide occurrence of globins in the three kingdoms of life. In silico analysis of the genome of C. elegans identified 33 putative globin genes. It remains a mystery why this tiny animal might need so many globins. As an inroad to understanding this complexity we initiated a structural and functional analysis of the globin family in C. elegans. Results All 33 C. elegans putative globin genes are transcribed. The translated sequences have the essential signatures of single domain bona fide globins, or they contain a distinct globin domain that is part of a larger protein. All globin domains can be aligned so as to fit the globin fold, but internal interhelical and N- and C-terminal extensions and a variety of amino acid substitutions generate much structural diversity among the globins of C. elegans. Likewise, the encoding genes lack a conserved pattern of intron insertion positioning. We analyze the expression profiles of the globins during the progression of the life cycle, and we find that distinct subsets of globins are induced, or repressed, in wild-type dauers and in daf-2(e1370/insulin-receptor mutant adults, although these animals share several physiological features including resistance to elevated temperature, oxidative stress and hypoxic death. Several globin genes are upregulated following oxygen deprivation and we find that HIF-1 and DAF-2 each are required for this response. Our data indicate that the DAF-2 regulated transcription factor DAF-16/FOXO positively modulates hif-1 transcription under anoxia but opposes expression of the HIF-1 responsive globin genes itself. In contrast, the canonical globin of C. elegans, ZK637.13, is not responsive to anoxia. Reduced DAF-2 signaling leads to enhanced transcription of this globin and DAF-16 is required for this effect

  7. From structure to redox: the diverse functional roles of disulfides and implications in disease

    Science.gov (United States)

    Bechtel, Tyler J.; Weerapana, Eranthie

    2017-01-01

    This review provides a comprehensive overview of the functional roles of disulfide bonds and their relevance to human disease. The critical roles of disulfide bonds in protein structure stabilization and redox regulation of protein activity are addressed. Disulfide bonds are essential to the structural stability of many proteins within the secretory pathway and can exist as intramolecular or inter-domain disulfides. The proper formation of these bonds often relies on folding chaperones and oxidases such as members of the protein disulfide isomerase (PDI) family. Many of the PDI family members catalyze disulfide-bond formation, reduction and isomerization through redox-active disulfides and perturbed PDI activity is characteristic of carcinomas and neurodegenerative diseases. In addition to catalytic function in oxidoreductases, redox-active disulfides are also found on a diverse array of cellular proteins and act to regulate protein activity and localization in response to oxidative changes in the local environment. These redox-active disulfides are either dynamic intramolecular protein disulfides or mixed disulfides with small-molecule thiols generating glutathionylation and cysteinylation adducts. The oxidation and reduction of redox-active disulfides are mediated by cellular reactive oxygen species and activity of reductases, such as glutaredoxin and thioredoxin. Dysregulation of cellular redox conditions and resulting changes in mixed disulfide formation are directly linked to diseases such as cardiovascular disease and Parkinson’s disease. PMID:28044432

  8. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-01-01

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management. PMID:27650273

  9. A ligand-directed divergent catalytic approach to establish structural and functional scaffold diversity

    Science.gov (United States)

    Lee, Yen-Chun; Patil, Sumersing; Golz, Christopher; Strohmann, Carsten; Ziegler, Slava; Kumar, Kamal; Waldmann, Herbert

    2017-02-01

    The selective transformation of different starting materials by different metal catalysts under individually optimized reaction conditions to structurally different intermediates and products is a powerful approach to generate diverse molecular scaffolds. In a more unified albeit synthetically challenging strategy, common starting materials would be exposed to a common metal catalysis, leading to a common intermediate and giving rise to different scaffolds by tuning the reactivity of the metal catalyst through different ligands. Herein we present a ligand-directed synthesis approach for the gold(I)-catalysed cycloisomerization of oxindole-derived 1,6-enynes that affords distinct molecular scaffolds following different catalytic reaction pathways. Varying electronic properties and the steric demand of the gold(I) ligands steers the fate of a common intermediary gold carbene to selectively form spirooxindoles, quinolones or df-oxindoles. Investigation of a synthesized compound collection in cell-based assays delivers structurally novel, selective modulators of the Hedgehog and Wnt signalling pathways, autophagy and of cellular proliferation.

  10. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-09-01

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management.

  11. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests.

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-09-21

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management.

  12. Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis.

    Directory of Open Access Journals (Sweden)

    Antoine Claessens

    2014-12-01

    Full Text Available The most polymorphic gene family in P. falciparum is the ∼60 var genes distributed across parasite chromosomes, both in the subtelomeres and in internal regions. They encode hypervariable surface proteins known as P. falciparum erythrocyte membrane protein 1 (PfEMP1 that are critical for pathogenesis and immune evasion in Plasmodium falciparum. How var gene sequence diversity is generated is not currently completely understood. To address this, we constructed large clone trees and performed whole genome sequence analysis to study the generation of novel var gene sequences in asexually replicating parasites. While single nucleotide polymorphisms (SNPs were scattered across the genome, structural variants (deletions, duplications, translocations were focused in and around var genes, with considerable variation in frequency between strains. Analysis of more than 100 recombination events involving var exon 1 revealed that the average nucleotide sequence identity of two recombining exons was only 63% (range: 52.7-72.4% yet the crossovers were error-free and occurred in such a way that the resulting sequence was in frame and domain architecture was preserved. Var exon 1, which encodes the immunologically exposed part of the protein, recombined in up to 0.2% of infected erythrocytes in vitro per life cycle. The high rate of var exon 1 recombination indicates that millions of new antigenic structures could potentially be generated each day in a single infected individual. We propose a model whereby var gene sequence polymorphism is mainly generated during the asexual part of the life cycle.

  13. Structural basis for perception of diverse chemical substances by T1r taste receptors.

    Science.gov (United States)

    Nuemket, Nipawan; Yasui, Norihisa; Kusakabe, Yuko; Nomura, Yukiyo; Atsumi, Nanako; Akiyama, Shuji; Nango, Eriko; Kato, Yukinari; Kaneko, Mika K; Takagi, Junichi; Hosotani, Maiko; Yamashita, Atsuko

    2017-05-23

    The taste receptor type 1 (T1r) family perceives 'palatable' tastes. These receptors function as T1r2-T1r3 and T1r1-T1r3 heterodimers to recognize a wide array of sweet and umami (savory) tastes in sugars and amino acids. Nonetheless, it is unclear how diverse tastes are recognized by so few receptors. Here we present crystal structures of the extracellular ligand-binding domains (LBDs), the taste recognition regions of the fish T1r2-T1r3 heterodimer, bound to different amino acids. The ligand-binding pocket in T1r2LBD is rich in aromatic residues, spacious and accommodates hydrated percepts. Biophysical studies show that this binding site is characterized by a broad yet discriminating chemical recognition, contributing for the particular trait of taste perception. In contrast, the analogous pocket in T1r3LBD is occupied by a rather loosely bound amino acid, suggesting that the T1r3 has an auxiliary role. Overall, we provide a structural basis for understanding the chemical perception of taste receptors.

  14. Structural characterization of alkaline hydrogen peroxide pretreated grasses exhibiting diverse lignin phenotypes

    Science.gov (United States)

    2012-01-01

    Background For cellulosic biofuels processes, suitable characterization of the lignin remaining within the cell wall and correlation of quantified properties of lignin to cell wall polysaccharide enzymatic deconstruction is underrepresented in the literature. This is particularly true for grasses which represent a number of promising bioenergy feedstocks where quantification of grass lignins is particularly problematic due to the high fraction of p-hydroxycinnamates. The main focus of this work is to use grasses with a diverse range of lignin properties, and applying multiple lignin characterization platforms, attempt to correlate the differences in these lignin properties to the susceptibility to alkaline hydrogen peroxide (AHP) pretreatment and subsequent enzymatic deconstruction. Results We were able to determine that the enzymatic hydrolysis of cellulose to to glucose (i.e. digestibility) of four grasses with relatively diverse lignin phenotypes could be correlated to total lignin content and the content of p-hydroxycinnamates, while S/G ratios did not appear to contribute to the enzymatic digestibility or delignification. The lignins of the brown midrib corn stovers tested were significantly more condensed than a typical commercial corn stover and a significant finding was that pretreatment with alkaline hydrogen peroxide increases the fraction of lignins involved in condensed linkages from 88–95% to ~99% for all the corn stovers tested, which is much more than has been reported in the literature for other pretreatments. This indicates significant scission of β-O-4 bonds by pretreatment and/or induction of lignin condensation reactions. The S/G ratios in grasses determined by analytical pyrolysis are significantly lower than values obtained using either thioacidolysis or 2DHSQC NMR due to presumed interference by ferulates. Conclusions It was found that grass cell wall polysaccharide hydrolysis by cellulolytic enzymes for grasses exhibiting a diversity of

  15. Structural characterization of alkaline hydrogen peroxide pretreated grasses exhibiting diverse lignin phenotypes

    Directory of Open Access Journals (Sweden)

    Li Muyang

    2012-06-01

    exhibiting a diversity of lignin structures and compositions could be linked to quantifiable changes in the composition of the cell wall and properties of the lignin including apparent content of the p-hydroxycinnamates while the limitations of S/G estimation in grasses is highlighted.

  16. Allelic Diversity and Population Structure in Oenococcus oeni as Determined from Sequence Analysis of Housekeeping Genes

    Science.gov (United States)

    de las Rivas, Blanca; Marcobal, Ángela; Muñoz, Rosario

    2004-01-01

    Oenococcus oeni is the organism of choice for promoting malolactic fermentation in wine. The population biology of O. oeni is poorly understood and remains unclear. For a better understanding of the mode of genetic variation within this species, we investigated by using multilocus sequence typing (MLST) with the gyrB, pgm, ddl, recP, and mleA genes the genetic diversity and genetic relationships among 18 O. oeni strains isolated in various years from wines of the United States, France, Germany, Spain, and Italy. These strains have also been characterized by ribotyping and restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S-23S rRNA gene intergenic spacer region (ISR). Ribotyping grouped the strains into two groups; however, the RFLP analysis of the ISRs showed no differences in the strains analyzed. In contrast, MLST in oenococci had a good discriminatory ability, and we have found a higher genetic diversity than indicated by ribotyping analysis. All sequence types were represented by a single strain, and all the strains could be distinguished from each other because they had unique combinations of alleles. Strains assumed to be identical showed the same sequence type. Phylogenetic analyses indicated a panmictic population structure in O. oeni. Sequences were analyzed for evidence of recombination by split decomposition analysis and analysis of clustered polymorphisms. All results indicated that recombination plays a major role in creating the genetic heterogeneity of O. oeni. A low standardized index of association value indicated that the O. oeni genes analyzed are close to linkage equilibrium. This study constitutes the first step in the development of an MLST method for O. oeni and the first example of the application of MLST to a nonpathogenic food production bacteria. PMID:15574919

  17. Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere.

    Science.gov (United States)

    Trivedi, Pankaj; He, Zhili; Van Nostrand, Joy D; Albrigo, Gene; Zhou, Jizhong; Wang, Nian

    2012-02-01

    The diversity and stability of bacterial communities present in the rhizosphere heavily influence soil and plant quality and ecosystem sustainability. The goal of this study is to understand how 'Candidatus Liberibacter asiaticus' (known to cause Huanglongbing, HLB) influences the structure and functional potential of microbial communities associated with the citrus rhizosphere. Clone library sequencing and taxon/group-specific quantitative real-time PCR results showed that 'Ca. L. asiaticus' infection restructured the native microbial community associated with citrus rhizosphere. Within the bacterial community, phylum Proteobacteria with various genera typically known as successful rhizosphere colonizers were significantly greater in clone libraries from healthy samples, whereas phylum Acidobacteria, Actinobacteria and Firmicutes, typically more dominant in the bulk soil were higher in 'Ca. L. asiaticus'-infected samples. A comprehensive functional microarray GeoChip 3.0 was used to determine the effects of 'Ca. L. asiaticus' infection on the functional diversity of rhizosphere microbial communities. GeoChip analysis showed that HLB disease has significant effects on various functional guilds of bacteria. Many genes involved in key ecological processes such as nitrogen cycling, carbon fixation, phosphorus utilization, metal homeostasis and resistance were significantly greater in healthy than in the 'Ca. L. asiaticus'-infected citrus rhizosphere. Our results showed that the microbial community of the 'Ca. L. asiaticus'-infected citrus rhizosphere has shifted away from using more easily degraded sources of carbon to the more recalcitrant forms. Overall, our study provides evidence that the change in plant physiology mediated by 'Ca. L. asiaticus' infection could elicit shifts in the composition and functional potential of rhizosphere microbial communities. In the long term, these fluctuations might have important implications for the productivity and sustainability

  18. Genetic diversity and community structure of rhizobia nodulating Sesbania cannabina in saline-alkaline soils.

    Science.gov (United States)

    Li, Yan; Li, Xiangyue; Liu, Yajing; Wang, En Tao; Ren, Chenggang; Liu, Wei; Xu, Hualing; Wu, Hailong; Jiang, Nan; Li, Yunzhao; Zhang, Xiaoli; Xie, Zhihong

    2016-05-01

    Sesbania cannabina is a plant that grows naturally along the seashores in Rudong County, China (RDC) and it has been introduced into the Yellow River Delta (YRD) as a pioneer plant to improve the saline-alkaline soils. In order to investigate the diversity of S. cannabina rhizobia in these soils, a total of 198 rhizobial isolates were characterized and phylogenetic trees were constructed based on data from multilocus sequence analysis (MLSA) of the housekeeping genes recA, atpD and glnII, as well as 16S rRNA. Symbiotic features were also studied by establishing the phylogeny of the symbiotic genes nodA and nifH, and by performing nodulation assays. The isolates had highly conserved symbiotic genes and were classified into nine genospecies belonging to the genera Ensifer, Agrobacterium, Neorhizobium and Rhizobium. A unique community structure was detected in the rhizobia associated with S. cannabina in the saline-alkaline soils that was characterized by five novel genospecies and four defined species. In addition, Ensifer sp. I was the predominant rhizobia in YRD, whereas Ensifer meliloti and Neorhizobium huautlense were the dominant species in RDC. Therefore, the study demonstrated for the first time that this plant strongly selected the symbiotic gene background but not the genomic background of its microsymbionts. In addition, biogeographic patterns existed in the rhizobial populations associated with S. cannabina, which were mainly correlated with pH and salinity, as well as the mineral nutrient contents. This study provided novel information concerning the interaction between soil conditions, host plant and rhizobia, in addition to revealing the diversity of S. cannabina rhizobia in saline-alkaline soils.

  19. A structural equation model analysis of postfire plant diversity in California shrublands

    Science.gov (United States)

    Grace, J.B.; Keeley, J.E.

    2006-01-01

    This study investigates patterns of plant diversity following wildfires in fire-prone shrublands of California, seeks to understand those patterns in terms of both local and landscape factors, and considers the implications for fire management. Ninety study sites were established following extensive wildfires in 1993, and 1000-m2 plots were used to sample a variety of parameters. Data on community responses were collected for five years following fire. Structural equation modeling (SEM) was used to relate plant species richness to plant abundance, fire severity, abiotic conditions, within-plot heterogeneity, stand age, and position in the landscape. Temporal dynamics of average richness response was also modeled. Richness was highest in the first year following fire, indicating postfire enhancement of diversity. A general decline in richness over time was detected, with year-to-year variation attributable to annual variations in precipitation. Peak richness in the landscape was found where (1) plant abundance was moderately high, (2) within-plot heterogeneity was high, (3) soils were moderately low in nitrogen, high in sand content, and with high rock cover, (4) fire severity was low, and (5) stands were young prior to fire. Many of these characteristics were correlated with position in the landscape and associated conditions. We infer from the SEM results that postfire richness in this system is strongly influenced by local conditions and that these conditions are, in turn, predictably related to landscape-level conditions. For example, we observed that older stands of shrubs were characterized by more severe fires, which were associated with a low recovery of plant cover and low richness. These results may have implications for the use of prescribed fire in this system if these findings extrapolate to prescribed burns as we would expect. ?? 2006 by the Ecological Society of America.

  20. Ethnolinguistic structuring of sorghum genetic diversity in Africa and the role of local seed systems.

    Science.gov (United States)

    Westengen, Ola T; Okongo, Mark Atam; Onek, Leo; Berg, Trygve; Upadhyaya, Hari; Birkeland, Siri; Kaur Khalsa, Siri Dharma; Ring, Kristoffer H; Stenseth, Nils C; Brysting, Anne K

    2014-09-30

    Sorghum is a drought-tolerant crop with a vital role in the livelihoods of millions of people in marginal areas. We examined genetic structure in this diverse crop in Africa. On the continent-wide scale, we identified three major sorghum populations (Central, Southern, and Northern) that are associated with the distribution of ethnolinguistic groups on the continent. The codistribution of the Central sorghum population and the Nilo-Saharan language family supports a proposed hypothesis about a close and causal relationship between the distribution of sorghum and languages in the region between the Chari and the Nile rivers. The Southern sorghum population is associated with the Bantu languages of the Niger-Congo language family, in agreement with the farming-language codispersal hypothesis as it has been related to the Bantu expansion. The Northern sorghum population is distributed across early Niger-Congo and Afro-Asiatic language family areas with dry agroclimatic conditions. At a finer geographic scale, the genetic substructure within the Central sorghum population is associated with language-group expansions within the Nilo-Saharan language family. A case study of the seed system of the Pari people, a Western-Nilotic ethnolinguistic group, provides a window into the social and cultural factors involved in generating and maintaining the continent-wide diversity patterns. The age-grade system, a cultural institution important for the expansive success of this ethnolinguistic group in the past, plays a central role in the management of sorghum landraces and continues to underpin the resilience of their traditional seed system.

  1. Plasmids of Carotenoid-Producing Paracoccus spp. (Alphaproteobacteria) - Structure, Diversity and Evolution

    Science.gov (United States)

    Maj, Anna; Dziewit, Lukasz; Czarnecki, Jakub; Wlodarczyk, Miroslawa; Baj, Jadwiga; Skrzypczyk, Grazyna; Giersz, Dorota; Bartosik, Dariusz

    2013-01-01

    Plasmids are components of many bacterial genomes. They enable the spread of a large pool of genetic information via lateral gene transfer. Many bacterial strains contain mega-sized replicons and these are particularly common in Alphaproteobacteria. Considerably less is known about smaller alphaproteobacterial plasmids. We analyzed the genomes of 14 such plasmids residing in 4 multireplicon carotenoid-producing strains of the genus Paracoccus (Alphaproteobacteria): P. aestuarii DSM 19484, P. haeundaensis LG P-21903, P. marcusii DSM 11574 and P. marcusii OS22. Comparative analyses revealed mosaic structures of the plasmids and recombinational shuffling of diverse genetic modules involved in (i) plasmid replication, (ii) stabilization (including toxin-antitoxin systems of the relBE/parDE, tad-ata, higBA, mazEF and toxBA families) and (iii) mobilization for conjugal transfer (encoding relaxases of the MobQ, MobP or MobV families). A common feature of the majority of the plasmids is the presence of AT-rich sequence islets (located downstream of exc1-like genes) containing genes, whose homologs are conserved in the chromosomes of many bacteria (encoding e.g. RelA/SpoT, SMC-like proteins and a retron-type reverse transcriptase). The results of this study have provided insight into the diversity and plasticity of plasmids of Paracoccus spp., and of the entire Alphaproteobacteria. Some of the identified plasmids contain replication systems not described previously in this class of bacteria. The composition of the plasmid genomes revealed frequent transfer of chromosomal genes into plasmids, which significantly enriches the pool of mobile DNA that can participate in lateral transfer. Many strains of Paracoccus spp. have great biotechnological potential, and the plasmid vectors constructed in this study will facilitate genetic studies of these bacteria. PMID:24260361

  2. Evaluation of a Diverse, Worldwide Collection of Wild, Cultivated, and Landrace Pepper (Capsicum annuum) for Resistance to Phytophthora Fruit Rot, Genetic Diversity, and Population Structure.

    Science.gov (United States)

    Naegele, R P; Tomlinson, A J; Hausbeck, M K

    2015-01-01

    Pepper is the third most important solanaceous crop in the United States and fourth most important worldwide. To identify sources of resistance for commercial breeding, 170 pepper genotypes from five continents and 45 countries were evaluated for Phytophthora fruit rot resistance using two isolates of Phytophthora capsici. Genetic diversity and population structure were assessed on a subset of 157 genotypes using 23 polymorphic simple sequence repeats. Partial resistance and isolate-specific interactions were identified in the population at both 3 and 5 days postinoculation (dpi). Plant introductions (PIs) 640833 and 566811 were the most resistant lines evaluated at 5 dpi to isolates 12889 and OP97, with mean lesion areas less than Criollo de Morelos. Genetic diversity was moderate (0.44) in the population. The program STRUCTURE inferred four genetic clusters with moderate to very great differentiation among clusters. Most lines evaluated were susceptible or moderately susceptible at 5 dpi, and no lines evaluated were completely resistant to Phytophthora fruit rot. Significant population structure was detected when pepper varieties were grouped by predefined categories of disease resistance, continent, and country of origin. Moderately resistant or resistant PIs to both isolates of P. capsici at 5 dpi were in genetic clusters one and two.

  3. Nanoscale superstructures assembled by polymerase chain reaction (PCR): programmable construction, structural diversity, and emerging applications.

    Science.gov (United States)

    Kuang, Hua; Ma, Wei; Xu, Liguang; Wang, Libing; Xu, Chuanlai

    2013-11-19

    networks, (5) protein-DNA co-assembly structures, and (6) DNA block copolymers including trimers and pentamers. These results affirm that this method can produce a variety of chemical structures and in yields that are tunable. Using PCR-based preparation of DNA-bridged nanostructures, we can program the assembly of the nanoscale blocks through the adjustment of the primer intensity on the assembled units, the number of PCR cycles, or both. The resulting structures are highly complex and diverse and have interesting dynamics and collective properties. Potential applications of these materials include chirooptical materials, probe fabrication, and environmental and biomedical sensors.

  4. Biogeographical boundaries, functional group structure and diversity of Rocky Shore communities along the Argentinean coast.

    Directory of Open Access Journals (Sweden)

    Evie A Wieters

    Full Text Available We investigate the extent to which functional structure and spatial variability of intertidal communities coincide with major biogeographical boundaries, areas where extensive compositional changes in the biota are observed over a limited geographic extension. We then investigate whether spatial variation in the biomass of functional groups, over geographic (10's km and local (10's m scales, could be associated to species diversity within and among these groups. Functional community structure expressed as abundance (density, cover and biomass and composition of major functional groups was quantified through field surveys at 20 rocky intertidal shores spanning six degrees of latitude along the southwest Atlantic coast of Argentina and extending across the boundaries between the Argentinean and Magellanic Provinces. Patterns of abundance of individual functional groups were not uniformly matched with biogeographical regions. Only ephemeral algae showed an abrupt geographical discontinuity coincident with changes in biogeographic boundaries, and this was limited to the mid intertidal zone. We identified 3-4 main 'groups' of sites in terms of the total and relative abundance of the major functional groups, but these did not coincide with biogeographical boundaries, nor did they follow latitudinal arrangement. Thus, processes that determine the functional structure of these intertidal communities are insensitive to biogeographical boundaries. Over both geographical and local spatial scales, and for most functional groups and tidal levels, increases in species richness within the functional group was significantly associated to increased total biomass and reduced spatial variability of the group. These results suggest that species belonging to the same functional group are sufficiently uncorrelated over space (i.e. metres and site-to-site to stabilize patterns of biomass variability and, in this manner, provide a buffer, or "insurance", against

  5. Biogeographical boundaries, functional group structure and diversity of Rocky Shore communities along the Argentinean coast.

    Science.gov (United States)

    Wieters, Evie A; McQuaid, Christopher; Palomo, Gabriela; Pappalardo, Paula; Navarrete, Sergio A

    2012-01-01

    We investigate the extent to which functional structure and spatial variability of intertidal communities coincide with major biogeographical boundaries, areas where extensive compositional changes in the biota are observed over a limited geographic extension. We then investigate whether spatial variation in the biomass of functional groups, over geographic (10's km) and local (10's m) scales, could be associated to species diversity within and among these groups. Functional community structure expressed as abundance (density, cover and biomass) and composition of major functional groups was quantified through field surveys at 20 rocky intertidal shores spanning six degrees of latitude along the southwest Atlantic coast of Argentina and extending across the boundaries between the Argentinean and Magellanic Provinces. Patterns of abundance of individual functional groups were not uniformly matched with biogeographical regions. Only ephemeral algae showed an abrupt geographical discontinuity coincident with changes in biogeographic boundaries, and this was limited to the mid intertidal zone. We identified 3-4 main 'groups' of sites in terms of the total and relative abundance of the major functional groups, but these did not coincide with biogeographical boundaries, nor did they follow latitudinal arrangement. Thus, processes that determine the functional structure of these intertidal communities are insensitive to biogeographical boundaries. Over both geographical and local spatial scales, and for most functional groups and tidal levels, increases in species richness within the functional group was significantly associated to increased total biomass and reduced spatial variability of the group. These results suggest that species belonging to the same functional group are sufficiently uncorrelated over space (i.e. metres and site-to-site ) to stabilize patterns of biomass variability and, in this manner, provide a buffer, or "insurance", against spatial variability

  6. Phylogeography and population structure of the grape powdery mildew fungus, Erysiphe necator, from diverse Vitis species

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    Brewer Marin

    2010-09-01

    Full Text Available Abstract Background The grape powdery mildew fungus, Erysiphe necator, was introduced into Europe more than 160 years ago and is now distributed everywhere that grapes are grown. To understand the invasion history of this pathogen we investigated the evolutionary relationships between introduced populations of Europe, Australia and the western United States (US and populations in the eastern US, where E. necator is thought to be native. Additionally, we tested the hypothesis that populations of E. necator in the eastern US are structured based on geography and Vitis host species. Results We sequenced three nuclear gene regions covering 1803 nucleotides from 146 isolates of E. necator collected from the eastern US, Europe, Australia, and the western US. Phylogeographic analyses show that the two genetic groups in Europe represent two separate introductions and that the genetic groups may be derived from eastern US ancestors. Populations from the western US and Europe share haplotypes, suggesting that the western US population was introduced from Europe. Populations in Australia are derived from European populations. Haplotype richness and nucleotide diversity were significantly greater in the eastern US populations than in the introduced populations. Populations within the eastern US are geographically differentiated; however, no structure was detected with respect to host habitat (i.e., wild or cultivated. Populations from muscadine grapes, V. rotundifolia, are genetically distinct from populations from other Vitis host species, yet no differentiation was detected among populations from other Vitis species. Conclusions Multilocus sequencing analysis of the grape powdery mildew fungus is consistent with the hypothesis that populations in Europe, Australia and the western US are derived from two separate introductions and their ancestors were likely from native populations in the eastern US. The invasion history of E. necator follows a pattern

  7. Flying Under the LiDAR: Relating Forest Structure to Bat Community Diversity

    Science.gov (United States)

    Swanson, A. C.; Weishampel, J. F.

    2015-12-01

    Bats are important to many ecological processes such as pollination, insect (and by proxy, disease) control, and seed dispersal and can be used to monitor ecosystem health. However, they are facing unprecedented extinction risks from habitat degradation as well as pressures from pathogens (e.g., white-nose syndrome) and wind turbines. LiDAR allows ecologists to measure structural variables of forested landscapes with increased precision and accuracy at broader spatial scales than previously possible. This study used airborne LiDAR to classify forest habitat/canopy structure at the Ordway-Swisher Biological Station (OSBS) in north central Florida. LiDAR data were acquired by the NEON airborne observation platform in summer 2014. OSBS consists of open-canopy pine savannas, closed-canopy hardwood hammocks, and seasonally wet prairies. Multiple forest structural parameters (e.g., mean, maximum, and standard deviation of height returns) were derived from LiDAR point clouds using the USDA software program FUSION. K-means clustering was used to segregate each 5x5 m raster across the ~3765 ha OSBS area into six different clusters based on the derived canopy metrics. Cluster averages for maximum, mean, and standard deviation of return heights ranged from 0 to 19.4 m, 0 to 15.3 m, and 0 to 3.0 m, respectively. To determine the relationships among these landscape-canopy features and bat species diversity and abundances, AnaBat II bat detectors were deployed from May to September in 2015 stratified by these distinct clusters. Bat calls were recorded from sunset to sunrise during each sampling period. Species were identified using AnalookW. A statistical regression model selection approach was performed in order to evaluate how forest attributes such as understory clutter, open regions, open and closed canopy, etc. influence bat communities. This knowledge provides a deeper understanding of habitat-species interactions to better manage survival of these species.

  8. The Structural Diversity of Carbohydrate Antigens of Selected Gram-Negative Marine Bacteria

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    Elena P. Ivanova

    2011-10-01

    Full Text Available Marine microorganisms have evolved for millions of years to survive in the environments characterized by one or more extreme physical or chemical parameters, e.g., high pressure, low temperature or high salinity. Marine bacteria have the ability to produce a range of biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents, and as a result, they have been a topic of research interest for many years. Among these biologically active molecules, the carbohydrate antigens, lipopolysaccharides (LPSs, O-antigens found in cell walls of Gram-negative marine bacteria, show great potential as candidates in the development of drugs to prevent septic shock due to their low virulence. The structural diversity of LPSs is thought to be a reflection of the ability for these bacteria to adapt to an array of habitats, protecting the cell from being compromised by exposure to harsh environmental stress factors. Over the last few years, the variety of structures of core oligosaccharides and O-specific polysaccharides from LPSs of marine microrganisms has been discovered. In this review, we discuss the most recently encountered structures that have been identified from bacteria belonging to the genera Aeromonas, Alteromonas, Idiomarina, Microbulbifer, Pseudoalteromonas, Plesiomonas and Shewanella of the Gammaproteobacteria phylum; Sulfitobacter and Loktanella of the Alphaproteobactera phylum and to the genera Arenibacter, Cellulophaga, Chryseobacterium, Flavobacterium, Flexibacter of the Cytophaga-Flavobacterium-Bacteroides phylum. Particular attention is paid to the particular chemical features of the LPSs, such as the monosaccharide type, non-sugar substituents and phosphate groups, together with some of the typifying traits of LPSs obtained from marine bacteria. A possible correlation is then made between such features and the environmental adaptations undertaken by marine bacteria.

  9. Habitat fragmentation, tree diversity, and plant invasion interact to structure forest caterpillar communities.

    Science.gov (United States)

    Stireman, John O; Devlin, Hilary; Doyle, Annie L

    2014-09-01

    Habitat fragmentation and invasive species are two of the most prominent threats to terrestrial ecosystems. Few studies have examined how these factors interact to influence the diversity of natural communities, particularly primary consumers. Here, we examined the effects of forest fragmentation and invasion of exotic honeysuckle (Lonicera maackii, Caprifoliaceae) on the abundance and diversity of the dominant forest herbivores: woody plant-feeding Lepidoptera. We systematically surveyed understory caterpillars along transects in 19 forest fragments over multiple years in southwestern Ohio and evaluated how fragment area, isolation, tree diversity, invasion by honeysuckle and interactions among these factors influence species richness, diversity and abundance. We found strong seasonal variation in caterpillar communities, which responded differently to fragmentation and invasion. Abundance and richness increased with fragment area, but these effects were mitigated by high levels of honeysuckle, tree diversity, landscape forest cover, and large recent changes in area. Honeysuckle infestation was generally associated with decreased caterpillar abundance and diversity, but these effects were strongly dependent on other fragment traits. Effects of honeysuckle on abundance were moderated when fragment area, landscape forest cover and tree diversity were high. In contrast, negative effects of honeysuckle invasion on caterpillar diversity were most pronounced in fragments with high tree diversity and large recent increases in area. Our results illustrate the complex interdependencies of habitat fragmentation, plant diversity and plant invasion in their effects on primary consumers and emphasize the need to consider these processes in concert to understand the consequences of anthropogenic habitat change for biodiversity.

  10. Microbiomes structure and diversity in different horizons of full soil profiles

    Science.gov (United States)

    Chernov, Timofey; Tkhakakhova, Azida; Zhelezova, Alena; Semenov, Mikhail; Kutovaya, Olga

    2017-04-01

    Topsoil is a most common object for soil metagenomic studies; sometimes soil profile is being formally split in layers by depth. However, Russian Soil Science School formulated the idea of soil profile as a complex of soil horizons, which can differ in their properties and genesis. In this research we analyzed 57 genetic soil horizons of 8 different soils from European part of Russia: Albeluvisol, Greyzemic Phaeozem, three Chermozems (different land use - till, fallow, wind-protecting tree line), Rhodic Cambisol, Haplic Kastanozem and Salic Solonetz (WRB classification). Sampling was performed from all genetic horizons in each soil profile starting from topsoil until subsoil. Total DNA was extracted and 16S rRNA sequencing was provided together with chemical analysis of soil (pH measurement, C and N contents, etc.). Structure and diversity of prokaryotic community are significantly different in those soil horizons, which chemical properties and processes of origin are contrasting with nearest horizons: Na-enriched horizon of Solonetz, eluvial horizon of Albeluvisol, plough pan of Agrochernozem. Actinobacteria were abundant in top horizons of soils in warm and dry climate, while Acidobacteria had the highest frequency in soils of moist and cold regions. Concerning Archaea, Thaumarchaeota prevailed in all studied soils. Their rate was higher in microbiomes of upper horizons of steppe soils and it was reducing with depth down the profile. Prokaryotic communities in Chernozems were clustered by soil horizons types: microbiomes of A (organic topsoil) and B (mineral) horizons formed non-overlapping clusters by principal component analysis, cluster formed by prokaryotic communities of transitional soil horizons (AB) take place between clusters of A and B horizons. Moreover, prokaryotic communities of A horizons differ from each other strongly, while microbiomes of B horizons formed a narrow small cluster. It must be explaned by more diverse conditions in upper A horizons

  11. Genetic diversity and genetic structure of different types of natural populations in Osmanthus fragrans Lour. and the relationships with sex ratio, population structure, and geographic isolation.

    Science.gov (United States)

    Hu, Shaoqing; Wu, Shuai; Wang, Yiguang; Zhao, Hongbo; Zhang, Yuanyan

    2014-01-01

    Osmanthus fragrans Lour., an evergreen small tree, has the rare sexual system of androdioecy (coexistence of males and hermaphrodites), once with wide-spread natural distribution in the areas of the South Yangzi river basin. However, due to excessive human utilization, natural distribution became fragmented and the number and size of natural populations reduced sharply. With four different types of natural populations from the same region as research object, we aim to provide a comparative analysis on the relationships among genetic diversity, sexual system, population structure and size, and geographic isolation by ISSR. In genetic parameters of N e , H e , and I, the LQGC population had the highest value and the LQZGQ population had the lowest value. These indicated that LQGC population showed the highest genetic diversity, followed by QDH and JN population, and LQZGQ population exhibited the lowest genetic diversity. Genetic diversity in populations is closely related to population structure, reproduction mode, and sex ratio. However, there seems to be no obvious correlation between genetic diversity and population size. The results of AMOVA showed that genetic variations mostly occurred within populations. It indicates that no significant genetic differentiation among populations occurs, and geographic isolation has no significant effect on genetic diversity.

  12. Genetic Diversity and Genetic Structure of Different Types of Natural Populations in Osmanthus fragrans Lour. and the Relationships with Sex Ratio, Population Structure, and Geographic Isolation

    Directory of Open Access Journals (Sweden)

    Shaoqing Hu

    2014-01-01

    Full Text Available Osmanthus fragrans Lour., an evergreen small tree, has the rare sexual system of androdioecy (coexistence of males and hermaphrodites, once with wide-spread natural distribution in the areas of the South Yangzi river basin. However, due to excessive human utilization, natural distribution became fragmented and the number and size of natural populations reduced sharply. With four different types of natural populations from the same region as research object, we aim to provide a comparative analysis on the relationships among genetic diversity, sexual system, population structure and size, and geographic isolation by ISSR. In genetic parameters of Ne, He, and I, the LQGC population had the highest value and the LQZGQ population had the lowest value. These indicated that LQGC population showed the highest genetic diversity, followed by QDH and JN population, and LQZGQ population exhibited the lowest genetic diversity. Genetic diversity in populations is closely related to population structure, reproduction mode, and sex ratio. However, there seems to be no obvious correlation between genetic diversity and population size. The results of AMOVA showed that genetic variations mostly occurred within populations. It indicates that no significant genetic differentiation among populations occurs, and geographic isolation has no significant effect on genetic diversity.

  13. Woody plant diversity and structure of shade-grown-coffee plantations in Northern Chiapas, Mexico

    Directory of Open Access Journals (Sweden)

    Lorena Soto-Pinto

    2001-12-01

    Full Text Available Shade-grown coffee is an agricultural system that contains some forest-like characteristics. However, structure and diversity are poorly known in shade coffee systems. In 61 coffee-growers’ plots of Chiapas, Mexico, structural variables of shade vegetation and coffee yields were measured, recording species and their use. Coffee stands had five vegetation strata. Seventy seven woody species mostly used as wood were found (mean density 371.4 trees per hectare. Ninety percent were native species (40% of the local flora, the remaining were introduced species, mainly fruit trees/shrubs. Diametric distribution resembles that of a secondary forest. Principal Coordinates Analysis grouped plots in four classes by the presence of Inga, however the majority of plots are diverse. There was no difference in equitability among groups or coffee yields. Coffee yield was 835 g clean coffee per shrub, or ca. 1668 kg ha-1. There is a significant role of shade-grown coffee as diversity refuge for woody plants and presumably associated fauna, as well as an opportunity for shade-coffee growers to participate in the new biodiversity-friendly-coffee marketEl café bajo sombra es un sistema agrícola que contiene algunas características de los bosques. Sin embargo, las características estructurales y de diversidad de la sombra del café son poco conocidas. En 61 parcelas de productores del norte de Chiapas, Mexico, se midieron variables estructurales de la vegetación de sombra y los rendimientos de café, registrando las especies y sus usos. Los cafetales presentaron cinco estratos de vegetación. Se encontraron 77 especies leñosas, la mayoría de uso maderable (densidad promedio de 371.4 árboles por hectárea. Noventa por ciento fueron especies nativas (40% de la flora local, el porcentaje restante fueron especies introducidas, principalmente árboles o arbustos frutales. La distribución diamétrica se asemeja a la distribución típica de bosques secundarios

  14. Assessment of Genetic Diversity and Structure of Large Garlic (Allium sativum) Germplasm Bank, by Diversity Arrays Technology "Genotyping-by-Sequencing" Platform (DArTseq).

    Science.gov (United States)

    Egea, Leticia A; Mérida-García, Rosa; Kilian, Andrzej; Hernandez, Pilar; Dorado, Gabriel

    2017-01-01

    Garlic (Allium sativum) is used worldwide in cooking and industry, including pharmacology/medicine and cosmetics, for its interesting properties. Identifying redundancies in germplasm blanks to generate core collections is a major concern, mostly in large stocks, in order to reduce space and maintenance costs. Yet, similar appearance and phenotypic plasticity of garlic varieties hinder their morphological classification. Molecular studies are challenging, due to the large and expected complex genome of this species, with asexual reproduction. Classical molecular markers, like isozymes, RAPD, SSR, or AFLP, are not convenient to generate germplasm core-collections for this species. The recent emergence of high-throughput genotyping-by-sequencing (GBS) approaches, like DArTseq, allow to overcome such limitations to characterize and protect genetic diversity. Therefore, such technology was used in this work to: (i) assess genetic diversity and structure of a large garlic-germplasm bank (417 accessions); (ii) create a core collection; (iii) relate genotype to agronomical features; and (iv) describe a cost-effective method to manage genetic diversity in garlic-germplasm banks. Hierarchical-cluster analysis, principal-coordinates analysis and STRUCTURE showed general consistency, generating three main garlic-groups, mostly determined by variety and geographical origin. In addition, high-resolution genotyping identified 286 unique and 131 redundant accessions, used to select a reduced size germplasm-bank core collection. This demonstrates that DArTseq is a cost-effective method to analyze species with large and expected complex genomes, like garlic. To the best of our knowledge, this is the first report of high-throughput genotyping of a large garlic germplasm. This is particularly interesting for garlic adaptation and improvement, to fight biotic and abiotic stresses, in the current context of climate change and global warming.

  15. Assessment of Genetic Diversity and Structure of Large Garlic (Allium sativum) Germplasm Bank, by Diversity Arrays Technology “Genotyping-by-Sequencing” Platform (DArTseq)

    Science.gov (United States)

    Egea, Leticia A.; Mérida-García, Rosa; Kilian, Andrzej; Hernandez, Pilar; Dorado, Gabriel

    2017-01-01

    Garlic (Allium sativum) is used worldwide in cooking and industry, including pharmacology/medicine and cosmetics, for its interesting properties. Identifying redundancies in germplasm blanks to generate core collections is a major concern, mostly in large stocks, in order to reduce space and maintenance costs. Yet, similar appearance and phenotypic plasticity of garlic varieties hinder their morphological classification. Molecular studies are challenging, due to the large and expected complex genome of this species, with asexual reproduction. Classical molecular markers, like isozymes, RAPD, SSR, or AFLP, are not convenient to generate germplasm core-collections for this species. The recent emergence of high-throughput genotyping-by-sequencing (GBS) approaches, like DArTseq, allow to overcome such limitations to characterize and protect genetic diversity. Therefore, such technology was used in this work to: (i) assess genetic diversity and structure of a large garlic-germplasm bank (417 accessions); (ii) create a core collection; (iii) relate genotype to agronomical features; and (iv) describe a cost-effective method to manage genetic diversity in garlic-germplasm banks. Hierarchical-cluster analysis, principal-coordinates analysis and STRUCTURE showed general consistency, generating three main garlic-groups, mostly determined by variety and geographical origin. In addition, high-resolution genotyping identified 286 unique and 131 redundant accessions, used to select a reduced size germplasm-bank core collection. This demonstrates that DArTseq is a cost-effective method to analyze species with large and expected complex genomes, like garlic. To the best of our knowledge, this is the first report of high-throughput genotyping of a large garlic germplasm. This is particularly interesting for garlic adaptation and improvement, to fight biotic and abiotic stresses, in the current context of climate change and global warming. PMID:28775737

  16. Assessment of Genetic Diversity and Structure of Large Garlic (Allium sativum Germplasm Bank, by Diversity Arrays Technology “Genotyping-by-Sequencing” Platform (DArTseq

    Directory of Open Access Journals (Sweden)

    Leticia A. Egea

    2017-07-01

    Full Text Available Garlic (Allium sativum is used worldwide in cooking and industry, including pharmacology/medicine and cosmetics, for its interesting properties. Identifying redundancies in germplasm blanks to generate core collections is a major concern, mostly in large stocks, in order to reduce space and maintenance costs. Yet, similar appearance and phenotypic plasticity of garlic varieties hinder their morphological classification. Molecular studies are challenging, due to the large and expected complex genome of this species, with asexual reproduction. Classical molecular markers, like isozymes, RAPD, SSR, or AFLP, are not convenient to generate germplasm core-collections for this species. The recent emergence of high-throughput genotyping-by-sequencing (GBS approaches, like DArTseq, allow to overcome such limitations to characterize and protect genetic diversity. Therefore, such technology was used in this work to: (i assess genetic diversity and structure of a large garlic-germplasm bank (417 accessions; (ii create a core collection; (iii relate genotype to agronomical features; and (iv describe a cost-effective method to manage genetic diversity in garlic-germplasm banks. Hierarchical-cluster analysis, principal-coordinates analysis and STRUCTURE showed general consistency, generating three main garlic-groups, mostly determined by variety and geographical origin. In addition, high-resolution genotyping identified 286 unique and 131 redundant accessions, used to select a reduced size germplasm-bank core collection. This demonstrates that DArTseq is a cost-effective method to analyze species with large and expected complex genomes, like garlic. To the best of our knowledge, this is the first report of high-throughput genotyping of a large garlic germplasm. This is particularly interesting for garlic adaptation and improvement, to fight biotic and abiotic stresses, in the current context of climate change and global warming.

  17. Early impact of alternative thinning approaches on structure diversity and complexity at stand level in two beech forests in Italy

    Directory of Open Access Journals (Sweden)

    Claudia Becagli

    2013-12-01

    Full Text Available Stand structure, tree density as well as tree spatial pattern define natural dynamics and competition process. They are therefore parameters used to define any silvicultural management type. This work aims to report first data resulting from a silvicultural experiment in beech forests. The objective of the trial is testing the structure manipulation in terms of diversity and the reduction of inter-tree competition of different thinning approaches. Alternative thinning methods have been applied in two independent experimental sites located in the pre-Alps and Southern Apennines, in Italy. Specific goals were to: (i verify the impact early after thinning implementation on forest structure through a set of diversity and competition metrics resulting from a literature review; (ii the sensitivity of tested indexes to effectively detect thinning manipulation. Main result show the low sensitivity of stand structure indexes and the ability of competition metrics to detect thinning outcome.

  18. Genetic Diversity and Spatial Genetic Structure of an Epiphytic Bromeliad in Costa Rican Montane Secondary Forest Patches

    NARCIS (Netherlands)

    Cascante-Marín, A.; Oostermeijer, G.; Wolf, J.; Fuchs, E.J.

    2014-01-01

    Information on genetic variation and its distribution in tropical plant populations relies mainly on studies of ground-rooted species, while genetic information of epiphytic plants is still limited. Particularly, the effect of forest successional condition on genetic diversity and structure of

  19. The Influence of Ethnic Diversity on Social Network Structure in a Common-Pool Resource System: Implications for Collaborative Management

    Directory of Open Access Journals (Sweden)

    Michele Barnes-Mauthe

    2013-03-01

    Full Text Available Social networks have recently been identified as key features in facilitating or constraining collaborative arrangements that can enhance resource governance and adaptability in complex social-ecological systems. Nonetheless, the effect of ethnicity on social network structure in an ethnically diverse common-pool resource system is virtually unknown. We characterize the entire social network of Hawaii's longline fishery, an ethnically diverse competitive pelagic fishery, and investigate network homophily, network structure, and cross-scale linkages. Results show that ethnicity significantly influences social network structure and is responsible for a homophily effect, which can create challenges for stakeholder collaboration across groups. Our analysis also suggests that ethnicity influences the formation of diverse network structures, and can affect the level of linkages to outside industry leaders, government or management officials, and members of the scientific community. This study provides the first empirical examination of the impact of ethnic diversity on resource user's social networks in the common-pool resource literature, having important implications for collaborative resource management.

  20. Early modern human diversity suggests subdivided population structure and a complex out-of-Africa scenario.

    Science.gov (United States)

    Gunz, Philipp; Bookstein, Fred L; Mitteroecker, Philipp; Stadlmayr, Andrea; Seidler, Horst; Weber, Gerhard W

    2009-04-14

    The interpretation of genetic evidence regarding modern human origins depends, among other things, on assessments of the structure and the variation of ancient populations. Because we lack genetic data from the time when the first anatomically modern humans appeared, between 200,000 and 60,000 years ago, instead we exploit the phenotype of neurocranial geometry to compare the variation in early modern human fossils with that in other groups of fossil Homo and recent modern humans. Variation is assessed as the mean-squared Procrustes distance from the group average shape in a representation based on several hundred neurocranial landmarks and semilandmarks. We find that the early modern group has more shape variation than any other group in our sample, which covers 1.8 million years, and that they are morphologically similar to recent modern humans of diverse geographically dispersed populations but not to archaic groups. Of the currently competing models of modern human origins, some are inconsistent with these findings. Rather than a single out-of-Africa dispersal scenario, we suggest that early modern humans were already divided into different populations in Pleistocene Africa, after which there followed a complex migration pattern. Our conclusions bear implications for the inference of ancient human demography from genetic models and emphasize the importance of focusing research on those early modern humans, in particular, in Africa.

  1. Different patterns of developmental toxicity in the rat following prenatal administration of structurally diverse chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Simmons, D.L.; Valentine, D.M.; Bradshaw, W.S.

    1984-01-01

    Differences in the profiles of developmental toxicity for four structurally diverse chemical compounds have been defined following prenatal exposure in the rat. Diethylstilbestrol (DES), 3,4,3',4'-tetrachlorobiphenyl (4CB), zeranol, and cadmium were administered by gavage to Sprague-Dawley rats daily from d 6 through d 18 of gestation. Dams were sacrificed at four prenatal endpoints and the numbers of live and dead fetuses and resorbed embryos were counted. Additional dams were allowed to bring their litters to term, and their offspring were monitored until they reached adulthood. DES induced prenatal death primarily in early embryonic life, and also during parturition. 4CB increased mortality from late in gestation up to 24 h after birth, and altered the sex ratio of survivors by selectively acting against males in utero. Exposure to zeranol resulted in embryolethality only. Cadmium was not lethal to the conceptus at any dose below the dose that caused maternal mortality. Only 4CB had an obvious teratogenic effect, causing intestinal hemorrhage. All compounds produced transient perinatal decreases in the weight of the offspring. 30 references, 6 tables.

  2. The Diversity and Geographical Structure of Orientia tsutsugamushi Strains from Scrub Typhus Patients in Laos.

    Science.gov (United States)

    Phetsouvanh, Rattanaphone; Sonthayanon, Piengchan; Pukrittayakamee, Sasithon; Paris, Daniel H; Newton, Paul N; Feil, Edward J; Day, Nicholas P J

    2015-01-01

    Orientia tsutsugamushi is the causative agent of scrub typhus, a disease transmitted by Leptotrombidium mites which is responsible for a severe and under-reported public health burden throughout Southeast Asia. Here we use multilocus sequence typing (MLST) to characterize 74 clinical isolates from three geographic locations in the Lao PDR (Laos), and compare them with isolates described from Udon Thani, northeast Thailand. The data confirm high levels of diversity and recombination within the natural O. tsutsugamushi population, and a rate of mixed infection of ~8%. We compared the relationships and geographical structuring of the strains and populations using allele based approaches (eBURST), phylogenetic approaches, and by calculating F-statistics (FST). These analyses all point towards low levels of population differentiation between isolates from Vientiane and Udon Thani, cities which straddle the Mekong River which defines the Lao/Thai border, but with a very distinct population in Salavan, southern Laos. These data highlight how land use, as well as the movement of hosts and vectors, may impact on the epidemiology of zoonotic infections.

  3. The Diversity and Geographical Structure of Orientia tsutsugamushi Strains from Scrub Typhus Patients in Laos.

    Directory of Open Access Journals (Sweden)

    Rattanaphone Phetsouvanh

    Full Text Available Orientia tsutsugamushi is the causative agent of scrub typhus, a disease transmitted by Leptotrombidium mites which is responsible for a severe and under-reported public health burden throughout Southeast Asia. Here we use multilocus sequence typing (MLST to characterize 74 clinical isolates from three geographic locations in the Lao PDR (Laos, and compare them with isolates described from Udon Thani, northeast Thailand. The data confirm high levels of diversity and recombination within the natural O. tsutsugamushi population, and a rate of mixed infection of ~8%. We compared the relationships and geographical structuring of the strains and populations using allele based approaches (eBURST, phylogenetic approaches, and by calculating F-statistics (FST. These analyses all point towards low levels of population differentiation between isolates from Vientiane and Udon Thani, cities which straddle the Mekong River which defines the Lao/Thai border, but with a very distinct population in Salavan, southern Laos. These data highlight how land use, as well as the movement of hosts and vectors, may impact on the epidemiology of zoonotic infections.

  4. Genetic diversity and population structure of native maize populations in Latin America and the Caribbean

    Science.gov (United States)

    Bedoya, Claudia A.; Dreisigacker, Susanne; Hearne, Sarah; Franco, Jorge; Mir, Celine; Prasanna, Boddupalli M.; Taba, Suketoshi; Charcosset, Alain; Warburton, Marilyn L.

    2017-01-01

    This study describes the genetic diversity and population structure of 194 native maize populations from 23 countries of Latin America and the Caribbean. The germplasm, representing 131 distinct landraces, was genetically characterized as population bulks using 28 SSR markers. Three main groups of maize germplasm were identified. The first, the Mexico and Southern Andes group, highlights the Pre-Columbian and modern exchange of germplasm between North and South America. The second group, Mesoamerica lowland, supports the hypothesis that two separate human migration events could have contributed to Caribbean maize germplasm. The third, the Andean group, displayed early introduction of maize into the Andes, with little mixing since then, other than a regional interchange zone active in the past. Events and activities in the pre- and post-Columbian Americas including the development and expansion of pre-Columbian cultures and the arrival of Europeans to the Americas are discussed in relation to the history of maize migration from its point of domestication in Mesoamerica to South America and the Caribbean through sea and land routes. PMID:28403177

  5. Genetic Diversity and Structure of Lolium Species Surveyed on Nuclear Simple Sequence Repeat and Cytoplasmic Markers

    Directory of Open Access Journals (Sweden)

    Hongwei Cai

    2017-04-01

    Full Text Available To assess the genetic diversity and population structure of Lolium species, we used 32 nuclear simple sequence repeat (SSR markers and 7 cytoplasmic gene markers to analyze a total of 357 individuals from 162 accessions of 9 Lolium species. This survey revealed a high level of polymorphism, with an average number of alleles per locus of 23.59 and 5.29 and an average PIC-value of 0.83 and 0.54 for nuclear SSR markers and cytoplasmic gene markers, respectively. Analysis of molecular variance (AMOVA revealed that 16.27 and 16.53% of the total variation was due to differences among species, with the remaining 56.35 and 83.47% due to differences within species and 27.39 and 0% due to differences within individuals in 32 nuclear SSR markers set and 6 chloroplast gene markers set, respectively. The 32 nuclear SSR markers detected three subpopulations among 357 individuals, whereas the 6 chloroplast gene markers revealed three subpopulations among 160 accessions in the STRUCTURE analysis. In the clustering analysis, the three inbred species clustered into a single group, whereas the outbreeding species were clearly divided, especially according to nuclear SSR markers. In addition, almost all Lolium multiflorum populations were clustered into group C4, which could be further divided into three subgroups, whereas Lolium perenne populations primarily clustered into two groups (C2 and C3, with a few lines that instead grouped with L. multiflorum (C4 or Lolium rigidum (C6. Together, these results will useful for the use of Lolium germplasm for improvement and increase the effectiveness of ryegrass breeding.

  6. Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent.

    Science.gov (United States)

    McLellan, S L; Huse, S M; Mueller-Spitz, S R; Andreishcheva, E N; Sogin, M L

    2010-02-01

    The release of untreated sewage introduces non-indigenous microbial populations of uncertain composition into surface waters. We used massively parallel 454 pyrosequencing of hypervariable regions in rRNA genes to profile microbial communities from eight untreated sewage influent samples of two wastewater treatment plants (WWTPs) in metropolitan Milwaukee. The sewage profiles included a discernible human faecal signature made up of several taxonomic groups including multiple Bifidobacteriaceae, Coriobacteriaceae, Bacteroidaceae, Lachnospiraceae and Ruminococcaceae genera. The faecal signature made up a small fraction of the taxa present in sewage but the relative abundance of these sequence tags mirrored the population structures of human faecal samples. These genera were much more prevalent in the sewage influent than standard indicators species. High-abundance sequences from taxonomic groups within the Beta- and Gammaproteobacteria dominated the sewage samples but occurred at very low levels in faecal and surface water samples, suggesting that these organisms proliferate within the sewer system. Samples from Jones Island (JI--servicing residential plus a combined sewer system) and South Shore (SS--servicing a residential area) WWTPs had very consistent community profiles, with greater similarity between WWTPs on a given collection day than the same plant collected on different days. Rainfall increased influent flows at SS and JI WWTPs, and this corresponded to greater diversity in the community at both plants. Overall, the sewer system appears to be a defined environment with both infiltration of rainwater and stormwater inputs modulating community composition. Microbial sewage communities represent a combination of inputs from human faecal microbes and enrichment of specific microbes from the environment to form a unique population structure.

  7. Diversity of eukaryotic DNA replication origins revealed by genome-wide analysis of chromatin structure.

    Directory of Open Access Journals (Sweden)

    Nicolas M Berbenetz

    2010-09-01

    Full Text Available Eukaryotic DNA replication origins differ both in their efficiency and in the characteristic time during S phase when they become active. The biological basis for these differences remains unknown, but they could be a consequence of chromatin structure. The availability of genome-wide maps of nucleosome positions has led to an explosion of information about how nucleosomes are assembled at transcription start sites, but no similar maps exist for DNA replication origins. Here we combine high-resolution genome-wide nucleosome maps with comprehensive annotations of DNA replication origins to identify patterns of nucleosome occupancy at eukaryotic replication origins. On average, replication origins contain a nucleosome depleted region centered next to the ACS element, flanked on both sides by arrays of well-positioned nucleosomes. Our analysis identified DNA sequence properties that correlate with nucleosome occupancy at replication origins genome-wide and that are correlated with the nucleosome-depleted region. Clustering analysis of all annotated replication origins revealed a surprising diversity of nucleosome occupancy patterns. We provide evidence that the origin recognition complex, which binds to the origin, acts as a barrier element to position and phase nucleosomes on both sides of the origin. Finally, analysis of chromatin reconstituted in vitro reveals that origins are inherently nucleosome depleted. Together our data provide a comprehensive, genome-wide view of chromatin structure at replication origins and suggest a model of nucleosome positioning at replication origins in which the underlying sequence occludes nucleosomes to permit binding of the origin recognition complex, which then (likely in concert with nucleosome modifiers and remodelers positions nucleosomes adjacent to the origin to promote replication origin function.

  8. Structural basis for action by diverse antidepressants on biogenic amine transporters.

    Science.gov (United States)

    Wang, Hui; Goehring, April; Wang, Kevin H; Penmatsa, Aravind; Ressler, Ryan; Gouaux, Eric

    2013-11-07

    The biogenic amine transporters (BATs) regulate endogenous neurotransmitter concentrations and are targets for a broad range of therapeutic agents including selective serotonin reuptake inhibitors (SSRIs), serotonin-noradrenaline reuptake inhibitors (SNRIs) and tricyclic antidepressants (TCAs). Because eukaryotic BATs are recalcitrant to crystallographic analysis, our understanding of the mechanism of these inhibitors and antidepressants is limited. LeuT is a bacterial homologue of BATs and has proven to be a valuable paradigm for understanding relationships between their structure and function. However, because only approximately 25% of the amino acid sequence of LeuT is in common with that of BATs, and as LeuT is a promiscuous amino acid transporter, it does not recapitulate the pharmacological properties of BATs. Indeed, SSRIs and TCAs bind in the extracellular vestibule of LeuT and act as non-competitive inhibitors of transport. By contrast, multiple studies demonstrate that both TCAs and SSRIs are competitive inhibitors for eukaryotic BATs and bind to the primary binding pocket. Here we engineered LeuT to harbour human BAT-like pharmacology by mutating key residues around the primary binding pocket. The final LeuBAT mutant binds the SSRI sertraline with a binding constant of 18 nM and displays high-affinity binding to a range of SSRIs, SNRIs and a TCA. We determined 12 crystal structures of LeuBAT in complex with four classes of antidepressants. The chemically diverse inhibitors have a remarkably similar mode of binding in which they straddle transmembrane helix (TM) 3, wedge between TM3/TM8 and TM1/TM6, and lock the transporter in a sodium- and chloride-bound outward-facing open conformation. Together, these studies define common and simple principles for the action of SSRIs, SNRIs and TCAs on BATs.

  9. 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.

  10. Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape

    Science.gov (United States)

    2013-01-01

    Background The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples. Results We investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions of V. vinifera and non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability. Conclusions The comprehensive molecular characterization of our grape

  11. Low genetic diversity and strong population structure shaped by anthropogenic habitat fragmentation in a critically endangered primate, Trachypithecus leucocephalus.

    Science.gov (United States)

    Wang, W; Qiao, Y; Li, S; Pan, W; Yao, M

    2017-06-01

    Habitat fragmentation may strongly impact population genetic structure and reduce the genetic diversity and viability of small and isolated populations. The white-headed langur (Trachypithecus leucocephalus) is a critically endangered primate species living in a highly fragmented and human-modified habitat in southern China. We examined the population genetic structure and genetic diversity of the species and investigated the environmental and anthropogenic factors that may have shaped its population structure. We used 214 unique multi-locus genotypes from 41 social groups across the main distribution area of T. leucocephalus, and found strong genetic structure and significant genetic differentiation among local populations. Our landscape genetic analyses using a causal modelling framework suggest that a large habitat gap and geographical distance represent the primary landscape elements shaping genetic structure, yet high levels of genetic differentiation also exist between patches separated by a small habitat gap or road. This is the first comprehensive study that has evaluated the population genetic structure and diversity of T. leucocephalus using nuclear markers. Our results indicate strong negative impacts of anthropogenic land modifications and habitat fragmentation on primate genetic connectivity between forest patches. Our analyses suggest that two management units of the species could be defined, and indicate that habitat continuity should be enforced and restored to reduce genetic isolation and enhance population viability.

  12. Treating Huge Tear-Drop Fracture of Axis With Trapezoidal Bone: A Case Report and Literature Review.

    Science.gov (United States)

    Yang, Xiaobin; Zheng, Bolong; Hao, Dingjun; Liu, Benyin; Yan, Liang; He, Baorong

    2015-11-01

    Case report and review of relevant literature. To discuss the surgical strategies and clinical outcome of managing huge tear drop fracture of axis. Teardrop fracture of axis is rarely seen, especially the huge type. The surgical technique is demanding because of the special anatomical structure and difficulty with bone grafting. Moreover, the surgical approach is controversial in the literature. A 51-year-old male patient suffered from neck pain after falling from the bicycle, neck movement was limited with no neurological compromise. X-ray suggested huge tear-drop fracture of anterior-inferior corner of axis, narrowing of C2/3 intervertebral disc. Fusion with self-designed tricortical trapezoidal iliac bone was performed. Treating huge teardrop fracture of axis by anterior bone grafting with self-designed tricortical trapezoidal iliac bone is effective and stable. A 3-month follow-up showed fusion was achieved, upper cervical curvature was restored, and neck pain disappeared. Self-designed tricortical trapezoidal iliac bone provided adequate fusion area of bone grafting, restoring the normal intervertebral height and cervical alignment, and the midterm outcome is satisfactory. 5.

  13. Late Intervention-Related Complication - A Huge Subepicardial Hematoma.

    Science.gov (United States)

    Ko, Po-Yen; Chang, Chih-Ping; Yang, Chen-Chia; Lin, Jen-Jyh

    2013-05-01

    A 75-year-old man had a history of triple vessel coronary artery disease. In August 2009, he had undergone successful percutaneous coronary intervention to the left circumflex coronary artery (LCX) for management of an in-stent restenosis (ISR) lesion. However, in September 2010, he began experiencing recurrent episodes of exertional chest pain. Chest radiography showed the left cardiac border bulging upwards. Transthoracic echocardiography and chest computed tomography revealed a huge oval mass of about 10.4 cm × 7.9 cm × 8.6 cm, which showed calcification and was obliterating the LCX. Subsequent coronary angiography revealed significant instent restenosis, with extravasation of a small amount of contrast material at the stent location, suggesting that the coronary artery had ruptured. We implanted a polytetrafluoroethylene-covered stent to seal the coronary perforation and to release the occlusion. The patient was symptom-free and had an uneventful outcome until the 1-year follow up. Coronary artery perforation; Covered stent; Hematoma.

  14. A huge posteromedial mediastinal cyst complicated with vertebral dislodgment

    Directory of Open Access Journals (Sweden)

    Manoussaridis Jordan T

    2006-08-01

    Full Text Available Abstract Background Mediastinal cysts compromise almost 20% of all mediastinal masses with bronchogenic subtype accounting for 60% of all cystic lesions. Although compression of adjoining soft tissues is usual, spinal complications and neurological symptoms are outmost rare and tend to characterize almost exclusively the neuroenteric cysts. Case presentation A young patient with intermittent, dull pain in his back and free medical history presented in the orthopaedic department of our hospital. There, the initial clinical and radiologic evaluation revealed a mediastinal mass and the patient was referred to the thoracic surgery department for further exploration. The following computed tomography (CT and magnetic resonance imaging (MRI shown a huge mediastinal cyst compressing the T4-T6 vertebral bodies. The neurological symptoms of the patient were attributed to this specific pathology due to the complete agreement between the location of the cyst and the nervous rule area of the compressed thoracic vertebrae. Despite our strongly suggestions for surgery the patient denied any treatment. Conclusion In controversy with the common faith that the spine plays the role of the natural barrier to the further expansion of cystic lesions, our case clearly indicates that, exceptionally, mediastinal cysts may cause severe vertebral complications. Therefore, early excision should be considered especially in young patients or where close follow up is uncertain.

  15. A probabilistic algorithm for interactive huge genome comparison.

    Science.gov (United States)

    Courtois, P R; Moncany, M L

    1995-12-01

    We designed a new probabilistic algorithm, named PAGEC (probabilistic algorithm for genome comparison), which allowed a highly interactive study of long genomic strings. The comparison between two nucleic acid sequences is based on the creation of multiple index tables, which drastically reduces processing time for huge genomes, e.g. 13 min for a 4 Mb/4 Mb comparison. PAGEC lowered the need for memory when compared with other types of algorithm and took into account the low resolution of the final representation (paper or computer screen). Considering that standard printers permit a 300 d.p.i. resolution, the loss of computed information due to the probabilistic conception of the algorithm was not usually noticeable in the present study, mainly due to increased genomic sizes. Refinement was possible through an interactive zooming system, which enabled the visualization of the lexical base sequences of a considered part of both of the studied genomes. Biological examples of computation based on yeast and animal nucleic acid sequences presented in this paper reveal the flexibility of the PAGEC program, which is a valuable tool for genetic studies as it offers a solution to an important problem that will become even more important as time passes.

  16. Relationships among Structural Diversity, Informal Peer Interactions and Perceptions of the Campus Environment

    Science.gov (United States)

    Pike, Gary R.; Kuh, George D.

    2006-01-01

    Recent research and critiques of affirmative action in college admissions raise questions about popular approaches for enhancing learning outcomes, suggesting that a diverse student body is neither a necessary nor a sufficient condition for experiencing diversity, creating supportive learning environments, or fostering desired outcomes of college.…

  17. Challenging the time complexity of exact subgraph isomorphism for huge and dense graphs with VF3.

    Science.gov (United States)

    Carletti, Vincenzo; Foggia, Pasquale; Saggese, Alessia; Vento, Mario

    2017-04-24

    Graph matching is essential in several fields that use structured information, such as biology, chemistry, social networks, knowledge management, document analysis and others. Except for special classes of graphs, graph matching has in the worst-case an exponential complexity; however, there are algorithms that show an acceptable execution time, as long as the graphs are not too large and not too dense. In this paper we introduce a novel subgraph isomorphism algorithm, VF3, particularly efficient in the challenging case of graphs with thousands of nodes and a high edge density. Its performance, both in terms of time and memory, has been assessed on a large dataset of 12700 random graphs with a size up to 10000 nodes, made publicly available. VF3 has been compared with four other state-of-the-art algorithms, and the huge experimentation required more than two years of processing time. The results confirm that VF3 definitely outperforms the other algorithms when the graphs become huge and dense, but also has a very good performance on smaller or sparser graphs.

  18. Genetic diversity and structure of the zombi pea (Vigna vexillata (L.) A. Rich) gene pool based on SSR marker analysis.

    Science.gov (United States)

    Dachapak, Sujinna; Somta, Prakit; Poonchaivilaisak, Supalak; Yimram, Tarika; Srinives, Peerasak

    2017-04-01

    Zombi pea (Vigna vexillata (L.) A. Rich) is an underutilized legume species and a useful gene source for resistance to biotic and abiotic stresses, although there is little understanding on its genetic diversity and structure. In this study, 422 (408 wild and 14 cultivated) accessions of zombi pea from diverse origins (201 from Africa, 126 from America, 85 from Australia, 5 from Asia and 5 from unknown origin) were analyzed with 20 simple sequence repeat (SSR) markers to determine its genetic diversity and genetic structure. The SSR markers detected 273 alleles in total with a mean of 13.6 alleles per locus. Polymorphism information content values of the markers varied from 0.58 to 0.90 with an average of 0.76. Overall gene diversity was 0.715. Gene diversity and average allelic richness was highest in Africa (0.749 and 8.08, respectively) and lowest in America (0.435 and 4.10, respectively). Nei's genetic distance analysis revealed that the highest distance was between wild Australia and cultivated Africa (0.559), followed by wild West Africa and wild Australia (0.415). STRUCTURE, neighbor-joining (NJ), and principal coordinate analyses consistently showed that these zombi pea accessions were clustered into three major groups, viz. America, Africa and Asia, and Australia. NJ tree also suggested that American and Australian accessions are originated from East African zombi peas, and that the cultivated accessions from Africa and Asia were genetically distinct, while those from America were clustered with some cultivated accessions from Africa. These results suggest that Africa is the center of origin and diversity of zombi pea, and that domestication of this pea took place more than once in different regions.

  19. The role of historical and contemporary processes on phylogeographic structure and genetic diversity in the Northern Cardinal, Cardinalis cardinalis

    Directory of Open Access Journals (Sweden)

    Navarro-Sigüenza Adolfo G

    2011-05-01

    Full Text Available Abstract Background Earth history events such as climate change are believed to have played a major role in shaping patterns of genetic structure and diversity in species. However, there is a lag between the time of historical events and the collection of present-day samples that are used to infer contemporary population structure. During this lag phase contemporary processes such as dispersal or non-random mating can erase or reinforce population differences generated by historical events. In this study we evaluate the role of both historical and contemporary processes on the phylogeography of a widespread North American songbird, the Northern Cardinal, Cardinalis cardinalis. Results Phylogenetic analysis revealed deep mtDNA structure with six lineages across the species' range. Ecological niche models supported the same geographic breaks revealed by the mtDNA. A paleoecological niche model for the Last Glacial Maximum indicated that cardinals underwent a dramatic range reduction in eastern North America, whereas their ranges were more stable in México. In eastern North America cardinals expanded out of glacial refugia, but we found no signature of decreased genetic diversity in areas colonized after the Last Glacial Maximum. Present-day demographic data suggested that population growth across the expansion cline is positively correlated with latitude. We propose that there was no loss of genetic diversity in areas colonized after the Last Glacial Maximum because recent high-levels of gene flow across the region have homogenized genetic diversity in eastern North America. Conclusion We show that both deep historical events as well as demographic processes that occurred following these events are critical in shaping genetic pattern and diversity in C. cardinalis. The general implication of our results is that patterns of genetic diversity are best understood when information on species history, ecology, and demography are considered

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

    Science.gov (United States)

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

    2012-09-01

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

  1. Role of vermicompost chemical composition, microbial functional diversity, and fungal community structure in their microbial respiratory response to three pesticides.

    Science.gov (United States)

    Fernández-Gómez, Manuel J; Nogales, Rogelio; Insam, Heribert; Romero, Esperanza; Goberna, Marta

    2011-10-01

    The relationships between vermicompost chemical features, enzyme activities, community-level physiological profiles (CLPPs), fungal community structures, and its microbial respiratory response to pesticides were investigated. Fungal community structure of vermicomposts produced from damaged tomato fruits (DT), winery wastes (WW), olive-mill waste and biosolids (OB), and cattle manure (CM) were determined by denaturing gradient gel electrophoresis of 18S rDNA. MicroResp™ was used for assessing vermicompost CLPPs and testing the microbial response to metalaxyl, imidacloprid, and diuron. Vermicompost enzyme activities and CLPPs indicated that WW, OB, and DT had higher microbial functional diversity than CM. The microbiota of the former tolerated all three pesticides whereas microbial respiration in CM was negatively affected by metalaxyl and imidacloprid. The response of vermicompost microbiota to the fungicide metalaxyl was correlated to its fungal community structure. The results suggest that vermicomposts with higher microbial functional diversity can be useful for the management of pesticide pollution in agriculture.

  2. PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information

    Directory of Open Access Journals (Sweden)

    Salamon Peter

    2005-03-01

    Full Text Available Abstract Background Phages, viruses that infect prokaryotes, are the most abundant microbes in the world. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. One way around this limitation is to directly clone and sequence shotgun libraries of uncultured viral communities (i.e., metagenomic analyses. PHACCS http://phage.sdsu.edu/phaccs, Phage Communities from Contig Spectrum, is an online bioinformatic tool to assess the biodiversity of uncultured viral communities. PHACCS uses the contig spectrum from shotgun DNA sequence assemblies to mathematically model the structure of viral communities and make predictions about diversity. Results PHACCS builds models of possible community structure using a modified Lander-Waterman algorithm to predict the underlying contig spectrum. PHACCS finds the most appropriate structure model by optimizing the model parameters until the predicted contig spectrum is as close as possible to the experimental one. This model is the basis for making estimates of uncultured viral community richness, evenness, diversity index and abundance of the most abundant genotype. Conclusion PHACCS analysis of four different environmental phage communities suggests that the power law is an important rank-abundance form to describe uncultured viral community structure. The estimates support the fact that the four phage communities were extremely diverse and that phage community biodiversity and structure may be correlated with that of their hosts.

  3. Early Changes in Soil Metabolic Diversity and Bacterial Community Structure in Sugarcane under Two Harvest Management Systems

    Directory of Open Access Journals (Sweden)

    Lucas Carvalho Basilio Azevedo

    2015-06-01

    Full Text Available Preharvest burning is widely used in Brazil for sugarcane cropping. However, due to environmental restrictions, harvest without burning is becoming the predominant option. Consequently, changes in the microbial community are expected from crop residue accumulation on the soil surface, as well as alterations in soil metabolic diversity as of the first harvest. Because biological properties respond quickly and can be used to monitor environmental changes, we evaluated soil metabolic diversity and bacterial community structure after the first harvest under sugarcane management without burning compared to management with preharvest burning. Soil samples were collected under three sugarcane varieties (SP813250, SP801842 and RB72454 and two harvest management systems (without and with preharvest burning. Microbial biomass C (MBC, carbon (C substrate utilization profiles, bacterial community structure (based on profiles of 16S rRNA gene amplicons, and soil chemical properties were determined. MBC was not different among the treatments. C-substrate utilization and metabolic diversity were lower in soil without burning, except for the evenness index of C-substrate utilization. Soil samples under the variety SP801842 showed the greatest changes in substrate utilization and metabolic diversity, but showed no differences in bacterial community structure, regardless of the harvest management system. In conclusion, combined analysis of soil chemical and microbiological data can detect early changes in microbial metabolic capacity and diversity, with lower values in management without burning. However, after the first harvest, there were no changes in the soil bacterial community structure detected by PCR-DGGE under the sugarcane variety SP801842. Therefore, the metabolic profile is a more sensitive indicator of early changes in the soil microbial community caused by the harvest management system.

  4. Network Structure, Diversity, and Proactive Resilience Building: a Response to Tompkins and Adger

    Directory of Open Access Journals (Sweden)

    Ann Dale

    2005-06-01

    Full Text Available Although community social networks can build resilience, and thus, aid adaptation to unexpected environmental change (Tomkins and Adger 2004, not all social networks are created equal. Networks composed of a diversity of “bridging” links to a diverse web of resources and “bonding” links that build trust strengthen a community's ability to adapt to change, but networks composed only of “bonding” links can impose constraining social norms and foster group homophily, reducing resilience. Diversity fosters the resilience needed to adapt to unexpected change, and can also enlarge the ability to proactively make collective decisions that optimize future options.

  5. A population on the edge: genetic diversity and population structure of the world's northernmost harbour seals (Phoca vitulina)

    DEFF Research Database (Denmark)

    Andersen, Liselotte Wesley; Lydersen, Christian; Frie, Anne Kirstine

    2011-01-01

      It is crucial to examine the genetic diversity and structure of small, isolated populations, especially those at the edge of their distribution range, because they are vulnerable to stochastic processes if genetic diversity is low and isolation level high, and because such populations provide...... microsatellites and variation in the D-loop. Each of the four locations was a genetically distinct population. The Svalbard population was highly genetically distinct, had reduced genetic diversity, received limited gene flow, had a rather low effective population size and showed an indication of having...... experienced a bottleneck resulting from a recent population decline. The significant heterozygote excess observed in the Svalbard sample might be attributed to the low effective population size, which could initiate future population inbreeding effects. This phenomenon has not been reported earlier from other...

  6. Effect of the invader Boccardia proboscidea (Polychaeta: Spionidae) on richness, diversity and structure of SW Atlantic epilithic intertidal community.

    Science.gov (United States)

    Elías, Rodolfo; Jaubet, María L; Llanos, Elizabeth N; Sanchez, María A; Rivero, María S; Garaffo, Griselda V; Sandrini-Neto, Leonardo

    2015-02-28

    In Mar del Plata (Argentine, SW Atlantic), a large seaside resort, the sewage discharges impact the littoral ecosystem. The invader polychaete Boccardia proboscidea has developed reefs since spring of 2008. The effect of this species on the richness, diversity and structure of epilithic intertidal community was assessed through an MBACI design in both sewage-impacted and reference sites, and Before/After the invasion. The presence of reefs of B. proboscidea since spring 2008 has caused a significant reduction of total individuals, total taxa and diversity in sewage-impacted sites regarding the reference ones. The species analyzed showed a high variable response because patterns were dominated by small-scale variability. Occasional peaks in abundance were observed on a single sampling site and time and a large variation among replicates. The associated fauna, formerly rich and diverse in impacted sites, shows a tendency to disappear as the ecosystem engineer Brachidontes rodriguezii is replaced by monocultures of B. proboscidea.

  7. MRI Verification of a Case of Huge Infantile Rhabdomyoma

    Science.gov (United States)

    Ramadani, Naser; Kreshnike, Kreshnike Dedushi; Muçaj, Sefedin; Kabashi, Serbeze; Hoxhaj, Astrit; Jerliu, Naim; Bejiçi, Ramush

    2016-01-01

    Introduction: Cardiac rhabdomyoma is type of benign myocardial tumor that is the most common fetal cardiac tumor. Cardiac rhabdomyomas are usually detected before birth or during the first year of life. They account for over 60% of all primary cardiac tumors. Case report: A 6 month old child with coughing and obstruction in breathing, was hospitalized in the Pediatric Clinic in UCCK, Pristine. The difficulty of breathing was heard and the pathological noise of the heart was noticed from the pediatrician. In the echo of the heart at the posterior and apico-lateral part of the left ventricle a tumoral mass was presented with the dimensions of 56 × 54 mm that forwarded the contractions of the left ventricle, the mass involved also the left ventricle wall and was not vascularized. The right ventricle was deformed and with the shifting of the SIV on the right the contractility was preserved. Aorta, the left arch and AP were normal with laminar circulation. The pericard was presented free. Radiography of thoracic organs was made; it resulted on cardiomegaly and significant bronchovascular drawing. It was completed with an MRI and it resulted on: Cardiomegaly due to large tumoral mass lesion (60×34 mm) involving lateral wall of left ventricle. It was isointense to the muscle on T1W images, markedly hyperintense on T2W images. There were a few septa or bant like hypointensities within lesion. On postcontrast study it showed avid enhancement. The left ventricle volume was decreased. Mild pericardial effusion was also noted. Surgical intervention was performed and it resulted on the histopathological aspect as a huge infantile rhadbomyoma. Conclusion: In most cases no treatment is required and these lesions regress spontaneously. Patients with left ventricular outflow tract obstruction or refractory arrhythmias respond well to surgical excision. Rhabdomyomas are frequently diagnosed by means of fetal echocardiography during the prenatal period. PMID:27147810

  8. Single-Path Sigma from a Huge Dataset in Taiwan

    Science.gov (United States)

    Sung, Chih-Hsuan; Lee, Chyi-Tyi

    2014-05-01

    Ground-motion variability, which was used in the probabilistic seismic hazard analysis (PSHA) in computing annual exceedence probability, is composed of random variability (aleatory uncertainty) and model uncertainty (epistemic uncertainty). Finding random variability of ground motions has become an important issue in PSHA, and only the random variability can be used in deriving the annual exceedence probability of ground-motion. Epistemic uncertainty will be put in the logic tree to estimate the total uncertainty of ground-motion. In the present study, we used about 18,859 records from 158 shallow earthquakes (Mw > 3.0, focal depth ≤ 35 km, each station has at least 20 records) form the Taiwan Strong-Motion Instrumentation Program (TSMIP) network to analyse the random variability of ground-motion. First, a new ground-motion attenuation model was established by using this huge data set. Second, the residuals from the median attenuation were analysed by direct observation on inter-event variability and site-specific variability. Finally, the single-path variability was found by a moving-window method on either single-earthquake residuals or single-station residuals. A variogram method was also used to find minimum variability for intra-event residuals and inter-event residuals, respectively. Results reveal that 90% of the single-path sigma σSP are ranging from 0.219 to 0.254 (ln unit) and are 58% to 64% smaller than the total sigma (σT =0.601). The single-site sigma (σSS) are also 39%-43% smaller. If we use only random variability (single-path sigma) in PSHA, then the resultant hazard level would be 28% and 25% lower than the traditional one (using total sigma) in 475-year and in 2475-year return period, respectively, in Taipei.

  9. Genetic structure and diversity of indigenous rice (Oryza sativa) varieties in the Eastern Himalayan region of Northeast India.

    Science.gov (United States)

    Choudhury, Baharul; Khan, Mohamed Latif; Dayanandan, Selvadurai

    2013-12-01

    The Eastern Himalayan region of Northeast (NE) India is home to a large number of indigenous rice varieties, which may serve as a valuable genetic resource for future crop improvement to meet the ever-increasing demand for food production. However, these varieties are rapidly being lost due to changes in land-use and agricultural practices, which favor agronomically improved varieties. A detailed understanding of the genetic structure and diversity of indigenous rice varieties is crucial for efficient utilization of rice genetic resources and for developing suitable conservation strategies. To explore the genetic structure and diversity of rice varieties in NE India, we genotyped 300 individuals of 24 indigenous rice varieties representing sali, boro, jum and glutinous types, 5 agronomically improved varieties, and one wild rice species (O. rufipogon) using seven SSR markers. A total of 85 alleles and a very high level of gene diversity (0.776) were detected among the indigenous rice varieties of the region. Considerable level of genetic variation was found within indigenous varieties whereas improved varieties were monoporphic across all loci. The comparison of genetic diversity among different types of rice revealed that sali type possessed the highest gene diversity (0.747) followed by jum (0.627), glutinous (0.602) and boro (0.596) types of indigenous rice varieties, while the lowest diversity was detected in agronomically improved varieties (0.459). The AMOVA results showed that 66% of the variation was distributed among varieties indicating a very high level of genetic differentiation in rice varieties in the region. Two major genetically defined clusters corresponding to indica and japonica groups were detected in rice varieties of the region. Overall, traditionally cultivated indigenous rice varieties in NE India showed high levels of genetic diversity comparable to levels of genetic diversity reported from wild rice populations in various parts of the

  10. Microsatellite based genetic diversity and population structure of the endangered Spanish Guadarrama goat breed

    Directory of Open Access Journals (Sweden)

    Jurado Juan J

    2009-09-01

    Full Text Available Abstract Background Assessing genetic biodiversity and population structure of minor breeds through the information provided by neutral molecular markers, allows determination of their extinction risk and to design strategies for their management and conservation. Analysis of microsatellite loci is known to be highly informative in the reconstruction of the historical processes underlying the evolution and differentiation of animal populations. Guadarrama goat is a threatened Spanish breed which actual census (2008 consists of 3057 females and 203 males distributed in 22 populations more or less isolated. The aim of this work is to study the genetic status of this breed through the analysis of molecular data from 10 microsatellites typed in historic and actual live animals. Results The mean expected heterozygosity across loci within populations ranged from 0.62 to 0.77. Genetic differentiation measures were moderate, with a mean FST of 0.074, GST of 0.081 and RST of 0.085. Percentages of variation among and within populations were 7.5 and 92.5, respectively. Bayesian clustering analyses pointed out a population subdivision in 16 clusters, however, no correlation between geographical distances and genetic differences was found. Management factors such as the limited exchange of animals between farmers (estimated gene flow Nm = 3.08 mostly due to sanitary and social constraints could be the major causes affecting Guadarrama goat population subdivision. Conclusion Genetic diversity measures revealed a good status of biodiversity in the Guadarrama goat breed. Since diseases are the first cause affecting the census in this breed, population subdivision would be an advantage for its conservation. However, to maintain private alleles present at low frequencies in such small populations minimizing the inbreeding rate, it would necessitate some mating designs of animals carrying such alleles among populations. The systematic use of molecular markers will

  11. Microsatellite based genetic diversity and population structure of the endangered Spanish Guadarrama goat breed

    Science.gov (United States)

    Serrano, Magdalena; Calvo, Jorge H; Martínez, Marta; Marcos-Carcavilla, Ane; Cuevas, Javier; González, Carmen; Jurado, Juan J; de Tejada, Paloma Díez

    2009-01-01

    Background Assessing genetic biodiversity and population structure of minor breeds through the information provided by neutral molecular markers, allows determination of their extinction risk and to design strategies for their management and conservation. Analysis of microsatellite loci is known to be highly informative in the reconstruction of the historical processes underlying the evolution and differentiation of animal populations. Guadarrama goat is a threatened Spanish breed which actual census (2008) consists of 3057 females and 203 males distributed in 22 populations more or less isolated. The aim of this work is to study the genetic status of this breed through the analysis of molecular data from 10 microsatellites typed in historic and actual live animals. Results The mean expected heterozygosity across loci within populations ranged from 0.62 to 0.77. Genetic differentiation measures were moderate, with a mean FST of 0.074, GST of 0.081 and RST of 0.085. Percentages of variation among and within populations were 7.5 and 92.5, respectively. Bayesian clustering analyses pointed out a population subdivision in 16 clusters, however, no correlation between geographical distances and genetic differences was found. Management factors such as the limited exchange of animals between farmers (estimated gene flow Nm = 3.08) mostly due to sanitary and social constraints could be the major causes affecting Guadarrama goat population subdivision. Conclusion Genetic diversity measures revealed a good status of biodiversity in the Guadarrama goat breed. Since diseases are the first cause affecting the census in this breed, population subdivision would be an advantage for its conservation. However, to maintain private alleles present at low frequencies in such small populations minimizing the inbreeding rate, it would necessitate some mating designs of animals carrying such alleles among populations. The systematic use of molecular markers will facilitate the

  12. Diversity and community structure of cyanobacteria and other microbes in recycling irrigation reservoirs.

    Science.gov (United States)

    Kong, Ping; Richardson, Patricia; Hong, Chuanxue

    2017-01-01

    Recycling irrigation reservoirs (RIRs) are emerging aquatic environments of global significance to crop production, water conservation and environmental sustainability. This study characterized the diversity and population structure of cyanobacteria and other detected microbes in water samples from eight RIRs and one adjacent runoff-free stream at three ornamental crop nurseries in eastern (VA1 and VA3) and central (VA2) Virginia after cloning and sequencing the 16S rRNA gene targeting cyanobacteria and chloroplast of eukaryotic phytoplankton. VA1 and VA2 utilize a multi-reservoir recycling irrigation system with runoff channeled to a sedimentation reservoir which then overflows into transition and retention reservoirs where water was pumped for irrigation. VA3 has a single sedimentation reservoir which was also used for irrigation. A total of 208 operational taxonomic units (OTU) were identified from clone libraries of the water samples. Among them, 53 OTUs (358 clones) were cyanobacteria comprising at least 12 genera dominated by Synechococcus species; 59 OTUs (387 clones) were eukaryotic phytoplankton including green algae and diatoms; and 96 were other bacteria (111 clones). Overall, cyanobacteria were dominant in sedimentation reservoirs, while eukaryotic phytoplankton and other bacteria were dominant in transition/retention reservoirs and the stream, respectively. These results are direct evidence demonstrating the negative impact of nutrient-rich horticultural runoff, if not contained, on natural water resources. They also help in understanding the dynamics of water quality in RIRs and have practical implications. Although both single- and multi-reservoir recycling irrigation systems reduce the environmental footprint of horticultural production, the former is expected to have more cyanobacterial blooming, and consequently water quality issues, than the latter. Thus, a multi-reservoir recycling irrigation system should be preferred where feasible.

  13. Design and construction of diverse structures of coordination polymers: Photocatalytic properties

    Science.gov (United States)

    Wu, Yu; Lu, Lu; Feng, Jianshen; Li, Yulong; Sun, Yanchun; Ma, Aiqing

    2017-01-01

    The reaction of Cu(NO3)2·3H2O/Ni(NO3)2·6H2O with 4‧-(4-(3,5-dicarboxylphenoxy)phenyl)-4,2‧:6‧,4‧‧-terpyridine (H2dbp) gave [Cu0.5(Hdbp)]n (1) and [Ni(dbp)(H2O)]n (2), while the reactions of Co(NO3)2·6H2O with H2dbp in the presence of 4,4‧-bipy and 2,2‧-bpy generated [Co(dbp)(4,4‧-bipy)]n (3) and {[Co(dbp)(2,2‧-bipy)]n·H2O} (4), respectively (4,4‧-bipy=4.4‧-pyridine and 2,2‧-bipy=2,2‧-bipyridine). X-Ray single-crystal analyses reveal that 1 contains a 1D double chain. 2 possesses a 3D architecture with (4.620.83)2 topology that is interpenetrated with each other to form a 2-fold network. In 3, the 2D [Co(dbp)]n sheets are pillared by 4,4‧-bpy to form a 3D framework with 1D open channel. Compound 4 consists of a 1D ladder-like chain. The results showed that the structural diversity of the coordination polymers resulted from the different geometries of metal ions and effect of assistant ligands. Furthermore, the photocatalytic properties of 1-4 for degradation of the methyl violet (MV) have been examined.

  14. Population Structure, Diversity and Reproductive Mode of the Grape Phylloxera (Daktulosphaira vitifoliae) across Its Native Range

    Science.gov (United States)

    Walker, M. Andrew

    2017-01-01

    Grape Phylloxera, Daktulosphaira vitifoliae, is a gall-forming insect that feeds on the leaves and roots of many Vitis species. The roots of the cultivated V. vinifera cultivars and hybrids are highly susceptible to grape phylloxera feeding damage. The native range of this insect covers most of North America, and it is particularly abundant in the eastern and central United States. Phylloxera was introduced from North America to almost all grape-growing regions across five of the temperate zone continents. It devastated vineyards in each of these regions causing large-scale disruptions to grape growers, wine makers and national economies. In order to understand the population diversity of grape phylloxera in its native range, more than 500 samples from 19 States and 34 samples from the introduced range (northern California, Europe and South America) were genotyped with 32 simple sequence repeat markers. STRUCTURE, a model based clustering method identified five populations within these samples. The five populations were confirmed by a neighbor-joining tree and principal coordinate analysis (PCoA). These populations were distinguished by their Vitis species hosts and their geographic locations. Samples collected from California, Europe and South America traced back to phylloxera sampled in the northeastern United States on V. riparia, with some influence from phylloxera collected along the Atlantic Coast and Central Plains on V. vulpina. Reproductive statistics conclusively confirmed that sexual reproduction is common in the native range and is combined with cyclical parthenogenesis. Native grape phylloxera populations were identified to be under Hardy-Weinberg equilibrium. The identification of admixed samples between many of these populations indicates that shared environments facilitate sexual reproduction between different host associated populations to create new genotypes of phylloxera. This study also found that assortative mating might occur across the

  15. Clinicopathological profile, airway management, and outcome in huge multinodular goiters: an institutional experience from an endemic goiter region.

    Science.gov (United States)

    Agarwal, Amit; Agarwal, Sudhi; Tewari, Prabhat; Gupta, Sushil; Chand, Gyan; Mishra, Anjali; Agarwal, Gaurav; Verma, A K; Mishra, S K

    2012-04-01

    Huge goiters are common in iodine-deficient endemic regions. They are of concern to the surgeons because of the anticipated risk of difficult dissection and increased chances of surgical complications. Similarly, they are of concern to the anesthesiologists because of anticipated intubation-related difficulties and post-thyroidectomy tracheomalacia. In the present study we aimed to present our experience of managing goiters based on their gross weight, highlighting their clinicopathological profile, perioperative airway-related difficulties, and management of surgical morbidity. Retrospective analysis of patients who underwent total thyroidectomy in the primary setting at our institute from 1995 to 2009 was carried out based on the gross gland weight. The patients were thus grouped into group A: ≤200 g; group B: 201 to ≤400 g; group C: 401 to ≤600 g; group D: >600 g. Group A (660 cases); group B (108 cases); group C (36 cases); and group D (9 cases) were included. As the goiter size increased, the mean duration of goiter, compressive symptoms, retrosternal extension (RSE), airway deformity, intubation difficulty, and tracheomalacia increased. The rate of tracheostomy, sternotomy, hemorrhage, visceral injury, and hospital stay was high with huge goiters. These features were more marked in malignant goiters compared to benign goiters. However, the postoperative complications were comparable in both of those groups. Long-standing huge goiters are common in iodine-deficient endemic areas. The majority of patients have symptomatic or clinicoradiological evidence of airway involvement. The incidence of RSE, airway deformity, intubation difficulty, and tracheomalacia is high with huge goiters. The surgery is technically demanding with greater associated chances of injury to native structures. Malignancy influences the presentation and outcome in smaller goiters. In centers with experienced endocrine surgeons and dedicated anesthetists, huge goiters can be

  16. Analysis of Genetic Diversity and Population Structure of Maize Landraces from the South Maize Region of China

    Institute of Scientific and Technical Information of China (English)

    LIU Zhi-zhai; WANG Tian-yu; LI Yu; GUO Rong-hua; ZHAO Jiu-ran; CAI Yi-lin; WANG Feng-ge; CAO Mo-ju; WANG Rong-huan; SHI Yun-su; SONG Yan-chun

    2010-01-01

    Understanding genetic diversity and population structure of landraces is important in utilization of these germplasm in breeding programs.In the present study,a total of 143 core maize landraces from the South Maize Region(SR)of China,which can represent the general profile of the genetic diversity in the landraces germplasm of SR,were genotyped by 54DNA microsatellite markers.Totally,517 alleles(ranging from 4 to 22)were detected among these iandraces,with an average of 9.57 alleles per locus.The total gene diversity of these core landraces was 0.61,suggesting a rather higher level of genetic diversity.Analysis of population structure based on Bayesian method obtained the samilar result as the phylogeny neighbor-joining(NJ)method.The results indicated that the whole set of 143 core landraces could be clustered into two distinct groups.All landraces from Guangdong,Hainan,and 15 landraces from Jiangxi were clustered into group 1,while those from the other regions of SR formed the group 2.The results from the analysis of genetic diversity showed that both of groups possessed a similar gene diversity,but group 1 possessed relatively lower mean alleles per locus(6.63)and distinet alleles(91)than group 2(7.94 and 110,respectively).The relatively high richness of total alleles and distinet alleles preserved in the core landraces from SR suggested that all these germplasm could be useful resources in germplasm enhancement and maize breeding in China.

  17. Bacterial diversity and community structure of supragingival plaques in adults with dental health or caries revealed by 16S pyrosequencing

    Directory of Open Access Journals (Sweden)

    Cuicui Xiao

    2016-07-01

    Full Text Available Dental caries has a polymicrobial etiology within the complex oral microbial ecosystem. However, the overall diversity and structure of supragingival plaque microbiota in adult dental health and caries are not well understood. Here, 160 supragingival plaque samples from patients with dental health and different severities of dental caries were collected for bacterial genomic DNA extraction, pyrosequencing by amplification of the 16S rDNA V1–V3 hypervariable regions, and bioinformatic analysis. High-quality sequences (2,261,700 clustered into 10,365 operational taxonomic units (OTUs; 97% identity, representing 453 independent species belonging to 122 genera, 66 families, 34 orders, 21 classes, and 12 phyla. All groups shared 7522 OTUs, indicating the presence of a core plaque microbiome. Smooth rarefaction curves were suggestive of plaque microbial diversity. α diversity analysis showed that healthy plaque microbial diversity exceeded that of dental caries, with the diversity decreasing gradually with the severity of caries. The dominant phyla of plaque microbiota included Bacteroidetes, Actinobacteria, Proteobacteria, Firmicutes, Fusobacteria, and TM7. The dominant genera included Capnocytophaga, Prevotella, Actinomyces, Corynebacterium, Neisseria, Streptococcus, Rothia, and Leptotrichia. β diversity analysis showed that the plaque microbial community structure was similar in all groups and that group members were relatively constant, only showing differences in abundance. Analysis of composition differences identified 10 health-related and 21 caries-related genera. Key genera (27 that potentially contributed to plaque microbiota distributions between groups were identified. Finally, co-occurrence network analysis and function prediction were performed. Treatment strategies directed toward modulating microbial interactions and their functional output should be further developed.

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

    Directory of Open Access Journals (Sweden)

    Hideaki Hasegawa

    2016-11-01

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

  19. Three-component assembly of structurally diverse 2-aminopyrimidine-5-carbonitriles.

    Science.gov (United States)

    Val, Cristina; Crespo, Abel; Yaziji, Vicente; Coelho, Alberto; Azuaje, Jhonny; El Maatougui, Abdelaziz; Carbajales, Carlos; Sotelo, Eddy

    2013-07-08

    An expedient route for the synthesis of libraries of diversely decorated 2-aminopyrimidine-5-carbonitriles is reported. This approach is based on a three-component reaction followed by spontaneous aromatization.

  20. Is spatial structure the key to promote plant diversity in Mediterranean forets plantations?

    NARCIS (Netherlands)

    González-Moreno, P.; Quero, J.L.; Poorter, L.; Bonet, F.J.; Zamora, R.

    2011-01-01

    Mediterranean forest plantations are currently under an intense debate related to their ecological function, sustainability and future performance. In several Mediterranean countries, efforts are directed to convert pine plantations into mixed and more diverse forests. This research aims to evaluate

  1. The Liana assemblage of a Congolian rainforest : diversity, structure and dynamics

    NARCIS (Netherlands)

    Ewango Ekokinya, Corneille

    2010-01-01

    Key words: Liana assemblage, species composition, community, dynamics, canopy openness, Manniophyton fulvum, functional traits, population density, pervasive change. This study analyzes the diversity, composition, and dynamics of the liana assemblage of the Ituri rain forest in northeastern DR Con

  2. Microbial diversity and structure are drivers of the biological barrier effect against Listeria monocytogenes in soil.

    Science.gov (United States)

    Vivant, Anne-Laure; Garmyn, Dominique; Maron, Pierre-Alain; Nowak, Virginie; Piveteau, Pascal

    2013-01-01

    Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment.

  3. Is spatial structure the key to promote plant diversity in Mediterranean forets plantations?

    NARCIS (Netherlands)

    González-Moreno, P.; Quero, J.L.; Poorter, L.; Bonet, F.J.; Zamora, R.

    2011-01-01

    Mediterranean forest plantations are currently under an intense debate related to their ecological function, sustainability and future performance. In several Mediterranean countries, efforts are directed to convert pine plantations into mixed and more diverse forests. This research aims to evaluate

  4. [Investigation of the microbial diversity and structure of biological activated carbon from different sources in drinking water treatment process].

    Science.gov (United States)

    Du, Er-Deng; Zheng, Lu; Feng, Xin-Xin; Gao, Nai-Yun

    2014-11-01

    Restriction fragment length polymorphism (RFLP) technology was used to investigate the microbial diversity and structure of biological activated carbon (BAC) from different sources in drinking water advanced treatment process. Diversity indices of samples A, B and C, with relatively high tannic acid and humic acid adsorption capacity, were close to each other, which meant higher microbial diversity. However, samples D and E had relatively lower diversity indices with the low tannic acid and humic acid adsorption capacity. There were five species including β-Proteobacteria, α-Proteobacteria, Planctomycetes, γ-Proteobacteria, Bacteroidetes in the phylogenetic tree of BAC samples. Among them, β-Proteobacteria and α-Proteobacteria were the dominant microbial species in these BAC samples, which played an important role in organic matter removal. Planctomycetes, γ-Proteobacteria, and Bacteroidetes were the non-dominant microbial species. Bacteroidetes only existed in samples A, B, C and D, while did not occur in sample E. The BAC samples with the higher tannic acid and humic acid adsorption capacity had higher microbial diversity. This research should deepen the understanding of microbial community in BAC, and provide a theoretical basis for the safety of drinking water.

  5. Sampling strategy for wild soybean (Glycine soja) populations based on their genetic diversity and fine-scale spatial genetic structure

    Institute of Scientific and Technical Information of China (English)

    ZHU Weiyue; ZHOU Taoying; ZHONG Ming; LU Baorong

    2007-01-01

    A total of 892 individuals sampled from a wild soybean population in a natural reserve near the Yellow River estuary located in Kenli of Shandong Province (China) were investigated.Seventeen SSR (simple sequence repeat) primer pairs from cultivated soybeans were used to estimate the genetic diversity of the population and its variation pattern versus changes of the sample size (sub-samples),in addition to investigating the fine-scale spatial genetic structure within the population.The results showed relatively high genetic diversity of the population with the mean value of allele number (A) being 2.88,expected heterozygosity (He) 0.431,Shannon diversity index (/) 0.699,and percentage of polymorphic loci (P) 100%.Sub-samples of different sizes (ten groups) were randomly drawn from the population and their genetic diversity was calculated by computer simulation.The regression model of the four diversity indexes with the change of sample sizes was computed.As a result,27-52 individuals can reach 95% of total genetic variability of the population.Spatial autocorrelation analysis revealed that the genetic patch size of this wild soybean population is about 18 m.The study provided a scientific basis for the sampling strategy of wild soybean populations.

  6. Plant diversity reduces the effect of multiple heavy metal pollution on soil enzyme activities and microbial community structure

    Institute of Scientific and Technical Information of China (English)

    Yang GAO; Chiyuan MIAO; Jun XIA; Liang MAO; Yafeng WANG; Pei ZHOU

    2012-01-01

    It is unclear whether certain plant species and plant diversity could reduce the impacts of multiple heavy metal pollution on soil microbial structure and soil enzyme activities. Random amplified polymorphic DNA (RAPD) was used to analyze the genetic diversity and microbial similarity in planted and unplanted soil under combined cadmium (Cd) and lead (Pb) pollution. A metal hyper- accumulator, Brassica juncea, and a common plant, Festuca arundinacea Schreb, were used in this research. The results showed that microorganism quantity in planted soil significantly increased, compared with that in unplanted soil with Cd and Pb pollution. The order of microbial community sensitivity in response to Cd and Pb stress was as follows: actinomycetes 〉 bacteria 〉 fungi. Respiration, phosphatase, urease and dehydrogenase activity were significantly inhibited due to Cd and Pb stress. Compared with unplanted soil, planted soils have frequently been reported to have higher rates of microbial activity due to the presence of additional surfaces for microbial colonization and organic compounds released by the plant roots. Two coexisting plants could increase microbe population and the activity of phosphatases, dehydrogenases and, in particular, ureases. Soil enzyme activity was higher in B. juncea phytoremediated soil than in F. arundinacea planted soil in this study. Heavy metal pollution decreased the richness of the soil microbial community, but plant diversity increased DNA sequence diversity and maintained DNA sequence diversity at highlevels. The genetic polymorphism under heavy metal stress was higher in B. juncea phytoremediated soil than in F. arundinacea planted soil.

  7. Analysis of Genetic Diversity and Population Structure of Sesame Accessions from Africa and Asia as Major Centers of Its Cultivation

    Directory of Open Access Journals (Sweden)

    Komivi Dossa

    2016-04-01

    Full Text Available Sesame is an important oil crop widely cultivated in Africa and Asia. Understanding the genetic diversity of accessions from these continents is critical to designing breeding methods and for additional collection of sesame germplasm. To determine the genetic diversity in relation to geographical regions, 96 sesame accessions collected from 22 countries distributed over six geographic regions in Africa and Asia were genotyped using 33 polymorphic SSR markers. Large genetic variability was found within the germplasm collection. The total number of alleles was 137, averaging 4.15 alleles per locus. The accessions from Asia displayed more diversity than those from Africa. Accessions from Southern Asia (SAs, Eastern Asia (EAs, and Western Africa (WAf were highly diversified, while those from Western Asia (WAs, Northern Africa (NAf, and Southeastern Africa (SAf had the lowest diversity. The analysis of molecular variance revealed that more than 44% of the genetic variance was due to diversity among geographic regions. Five subpopulations, including three in Asia and two in Africa, were cross-identified through phylogenetic, PCA, and STRUCTURE analyses. Most accessions clustered in the same population based on their geographical origins. Our results provide technical guidance for efficient management of sesame genetic resources in breeding programs and further collection of sesame germplasm from these different regions.

  8. [Effects of nitrogen and water addition on soil bacterial diversity and community structure in temperate grasslands in northern China].

    Science.gov (United States)

    Yang, Shan; Li, Xiao-bing; Wang, Ru-zhen; Cai, Jiang-ping; Xu, Zhu-wen; Zhang, Yu-ge; Li, Hui; Jiang, Yong

    2015-03-01

    In this study, we measured the responses of soil bacterial diversity and community structure to nitrogen (N) and water addition in the typical temperate grassland in northern China. Results showed that N addition significantly reduced microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) under regular precipitation treatment. Similar declined trends of MBC and MBN caused by N addition were also found under increased precipitation condition. Nevertheless, water addition alleviated the inhibition by N addition. N addition exerted no significant effects. on bacterial α-diversity indices, including richness, Shannon diversity and evenness index under regular precipitation condition. Precipitation increment tended to increase bacterial α-diversity, and the diversity indices of each N gradient under regular precipitation were much lower than that of the corresponding N addition rate under increased precipitation. Correlation analysis showed that soil moisture, nitrate (NO3(-)-N) and ammonium (NH4+-N) were significantly negatively correlated with bacterial evenness index, and MBC and MBN had a significant positive correlation with bacterial richness and evenness. Non-metric multidimensional scaling (NMDS) ordination illustrated that the bacterial communities were significantly separated by N addition rates, under both water ambient and water addition treatments. Redundancy analysis (RDA) revealed that soil MBC, MBN, pH and NH4+-N were the key environmental factors for shaping bacterial communities.

  9. Diversity, abundance and community structure of benthic macro- and megafauna on the Beaufort shelf and slope.

    Science.gov (United States)

    Nephin, Jessica; Juniper, S Kim; Archambault, Philippe

    2014-01-01

    Diversity and community patterns of macro- and megafauna were compared on the Canadian Beaufort shelf and slope. Faunal sampling collected 247 taxa from 48 stations with box core and trawl gear over the summers of 2009-2011 between 50 and 1,000 m in depth. Of the 80 macrofaunal and 167 megafaunal taxa, 23% were uniques, present at only one station. Rare taxa were found to increase proportional to total taxa richness and differ between the shelf (shelf and maldanid polychaetes (up to 92% in relative abundance/station) dominant on the slope. The megafauna principally comprised echinoderms with Ophiocten sp. (up to 90% in relative abundance/station) dominant on the shelf and Ophiopleura sp. dominant on the slope. Macro- and megafauna had divergent patterns of abundance, taxa richness (α diversity) and β diversity. A greater degree of macrofaunal than megafaunal variation in abundance, richness and β diversity was explained by confounding factors: location (east-west), sampling year and the timing of sampling with respect to sea-ice conditions. Change in megafaunal abundance, richness and β diversity was greatest across the depth gradient, with total abundance and richness elevated on the shelf compared to the slope. We conclude that megafaunal slope taxa were differentiated from shelf taxa, as faunal replacement not nestedness appears to be the main driver of megafaunal β diversity across the depth gradient.

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

    Directory of Open Access Journals (Sweden)

    Fricano Agostino

    2012-03-01

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

  11. Floristic diversity, regeneration status, and vegetation structure of woodlands in Metema Area, Amhara National Regional State, Northwestern Ethiopia

    Institute of Scientific and Technical Information of China (English)

    Haile Adamu Wale; Tamrat Bekele; Gemedo Dalle

    2012-01-01

    We studied woodland vegetation in broad-leaved deciduous woodlands of Metema in northwestern Amhara regional state,Ethiopia Our objective was to describe plant species composition,diversity,regeneration status,and population structure by a selective approach with a systematic sampling design.A total of 74 quadrats (each for 25 m × 25 m,spaced at intervals of 150-200 m) were sampled along established transect lines following the homogeneity of the vegetation.Vegetation data including cover-abundance,height,diameter at breast height (DBH),and numbers of seedlings and saplings of woody species were analyzed using Excel spreadsheet,Shannon Weiner diversity index,and PAST version 1.62.A total of 87 vascular plant species of 74 genera and 36 families were recorded.The dominant family was Fabaceae represented by 16 (18.39 %) species of 13 genera.Shannon Weiner diversity and evenness were 3.67 and 0.82,respectively,which showed that the area was endowed with rich floral diversity evenly distributed.The vegetation structure,as quantified by cumulative diameter class frequency distribution,plotted as an interrupted inverted-J- shape pattern with a sharp decrease in the 2nd diameter class.This indicated poor vegetation structure.The diameter classes frequency distributions of selected species plotted in four general patterns i.e.,interrupted Inverted-J-shape,J-shape,Bell-shape and Irregular-shape.In conclusion,although the area showel high floral diversity and evenness,woody species including Sterculea setigera,Boswellia papyrifera,and Pterocarpus lucens showed lowest recruitment of seedlings and saplings.

  12. Linking Remotely Sensed Functional Diversity of Structural Traits to the Radiative Regime of a Temperate Mixed Forest

    Science.gov (United States)

    Schneider, F. D.; Morsdorf, F.; Furrer, R.; Schmid, B.; Schaepman, M. E.

    2015-12-01

    Patterns of functional diversity reflect the inter- and intraspecific variability of plant traits and are linked to other aspects of biodiversity, environmental factors and ecosystem function. To study the patterns at plot and stand level, spatially continuous trait measurements are required. Remote sensing methods based on airborne observations can offer such continuous high-resolution measurements, resolving individual trees of a forest at a regional extent. The study was performed at the Laegern forest, a temperate mixed forest dominated by deciduous and coniferous trees (Fagus sylvatica, Picea abies; 47°28'42.0" N, 8°21'51.8" E, 682 m asl; Switzerland). Canopy height, plant area index and foliage height diversity were derived from full-waveform airborne laser scanning data. These structural traits were used to calculate functional richness, functional evenness and functional divergence at a range of scales. A Bayesian multiresolution scale analysis was used to infer the scales at which functional diversity patterns occur. The radiative regime of the forest was simulated using the 3D radiative transfer model DART. Using a voxel-based forest reconstruction allowed us to derive top of canopy, bottom of canopy and absorbed photosynthetically active radiation. The results of this study will provide new insights on linking forest canopy structure to the radiative regime of the forest. Light availability is a critical factor determining plant growth and competition. Within canopy light scattering is mainly driven by the arrangement of leaves and their leaf optical properties. Therefore, we expect a link between the structural complexity of the forest as encompassed by functional diversity and the light availability within and below the canopy. Ultimately, this information can be used in dynamic ecosystem models such as ED2, allowing us to predict the influence of functional diversity and radiative properties on ecosystem functioning under current conditions and

  13. Changes in diversity, abundance, and structure of soil bacterial communities in Brazilian Savanna under different land use systems.

    Science.gov (United States)

    Rampelotto, Pabulo Henrique; de Siqueira Ferreira, Adão; Barboza, Anthony Diego Muller; Roesch, Luiz Fernando Wurdig

    2013-10-01

    The Brazilian Savanna, also known as "Cerrado", is the richest and most diverse savanna in the world and has been ranked as one of the main hotspots of biodiversity. The Cerrado is a representative biome in Central Brazil and the second largest biome in species diversity of South America. Nevertheless, large areas of native vegetation have been converted to agricultural land including grain production, livestock, and forestry. In this view, understanding how land use affects microbial communities is fundamental for the sustainable management of agricultural ecosystems. The aim of this work was to analyze and compare the soil bacterial communities from the Brazilian Cerrado associated with different land use systems using high throughput pyrosequencing of 16S rRNA genes. Relevant differences were observed in the abundance and structure of bacterial communities in soils under different land use systems. On the other hand, the diversity of bacterial communities was not relevantly changed among the sites studied. Land use systems had also an important impact on specific bacterial groups in soil, which might change the soil function and the ecological processes. Acidobacteria, Proteobacteria, and Actinobacteria were the most abundant groups in the Brazilian Cerrado. These findings suggest that more important than analyzing the general diversity is to analyze the composition of the communities. Since soil type was the same among the sites, we might assume that land use was the main factor defining the abundance and structure of bacterial communities.

  14. Analysis of genetic diversity and population structure of Bellamya quadrata from lakes of middle and lower Yangtze River.

    Science.gov (United States)

    Gu, Qianhong; Zhang, Man; Zhou, Chuanjiang; Zhu, Guorong; Dong, Jing; Gao, Yunni; Chen, Jie; Chen, Peng

    2015-10-01

    As an endemic species of freshwater gastropods in China, Bellamya quadrata plays an important role in ecosystem service provision and commercial importance. However, the species is overharvested and its natural habitats are under severe threat due to fragmentation and loss. To estimate the genetic diversity and population structure of B. quadrata, 285 individuals from eight lake populations across middle and lower Yangtze River were sampled. Seven microsatellite loci were genotyped. Our results showed that (i) the genetic diversity of B. quadrata was high in most of the studied populations, yet effective population sizes appear to be rather small in some populations; (ii) low levels of genetic differentiation exists among populations but gene flow was generally high; (iii) no clear geographic or genetic structure was observed in the studied region, implying mechanisms (zoochoric dispersal and anthropogenic translocations) that enhance dispersal and gene flow have promoted population connectivity. However, the comparatively high genetic diversity of B. quadrata could be attributed to a lag phase, suggesting that the genetic diversity of this species may be lost in the future and the priorities for conservation of B. quadrata are necessary.

  15. In silico analysis of sequential, structural and functional diversity of wheat cystatins and its implication in plant defense.

    Science.gov (United States)

    Dutt, Shriparna; Singh, V K; Marla, Soma S; Kumar, Anil

    2010-03-01

    Phytocystatins constitute a multigene family that regulates the activity of endogenous and/or exogenous cysteine proteinases. Cereal crops like wheat are continuously threatened by a multitude of pathogens, therefore cystatins offer to play a pivotal role in deciding the plant response. In order to study the need of having diverse specificities and activities of various cystatins, we conducted comparative analysis of six wheat cystatins (WCs) with twelve rice, seven barley, one sorghum and ten corn cystatin sequences employing different bioinformatics tools. The obtained results identified highly conserved signature sequences in all the cystatins considered. Several other motifs were also identified, based on which the sequences could be categorized into groups in congruence with the phylogenetic clustering. Homology modeling of WCs revealed 3D structural topology so well shared by other cystatins. Protein-protein interaction of WCs with papain supported the notion that functional diversity is a con-sequence of existing differences in amino acid residues in highly conserved as well as relatively less conserved motifs. Thus there is a significant conservation at the sequential and structural levels; however, concomitant variations maintain the functional diversity in this protein family, which constantly modulates itself to reciprocate the diversity while counteracting the cysteine proteinases.

  16. Observation and analysis of electrical structure change and diversity in thunderstorms on the Qinghai-Tibet Plateau

    Science.gov (United States)

    Li, Yajun; Zhang, Guangshu; Wang, Yanhui; Wu, Bin; Li, Jing

    2017-09-01

    A comprehensive observation on thunderstorms was conducted in the Qinghai area by using a very high frequency three-dimensional lightning mapping system and Doppler radar. The spatio-temporal evolution of the charge structure of the isolated thunderstorm was analyzed according to the developing process of thunderstorm, and the reasons for the change in charge structure diversity were studied. During the initial developing and mature stages of the thunderstorm, the charge structure was a steady negative dipole polarity, i.e., the negative charge region was above the positive charge region. Furthermore, the total number of flashes was lower during these two stages. During the thunderstorm's dissipation stage, the charge structure was varied and complicated, with a positive dipole, negative dipole, and a tripole charge structure changing and coexisting during this stage. This charge structure diversity was primarily caused by the collision and merging of two local thunderstorm cells, leading to a charge rearrangement and distribution and the formation of a new charge structure. The frequency of the negative cloud-to-ground and intracloud flashes increased sharply in the dissipation stage, reaching a maximum value. The increase in frequency of negative cloud-to-ground was mainly caused by the lower positive charge weakening during the dissipation stage. In addition, the relationship between charging regions and temperature layers was analyzed by combining sounding temperature data with the theory of a non-inductive charging mechanism.

  17. Pulmonary hypertension with a huge thrombosis in main stem of pulmonary artery

    Institute of Scientific and Technical Information of China (English)

    杨萍; 曾红; 孟繁波; 赵林阳

    2001-01-01

    @@A huge thrombosis in the main stem of the pulmonary artery (PA) with pulmonary hypertension has rarely been reported. We present two cases diagnosed and treated in our hospital. One suffered from polyarteritis with a huge thrombus in PA revealed at autopsy. The second case had congenital heart disease of the patent artery duct; and the huge thrombus was found on echocardiogram and extirpated in surgery.

  18. Huge ascending aortic aneurysm with an intraluminal thrombus in an embolic event-free patient.

    Science.gov (United States)

    Parato, Vito Maurizio; Prifti, Edvin; Pezzuoli, Franco; Labanti, Benedetto; Baboci, Arben

    2015-03-01

    We present a case of an 87-year-old male patient with a huge ascending aortic aneurysm, filled by a huge thrombus most probably due to previous dissection. This finding was detected by two-dimensional transthoracic echocardiography and contrast-enhanced computed tomography (CT) angiography scan. The patient refused surgical treatment and was medically treated. Despite the huge and mobile intraluminal thrombus, the patient remained embolic event-free up to 6 years later, and this makes the case unique.

  19. Bioinspired oil strider floating at the oil/water interface supported by huge superoleophobic force.

    Science.gov (United States)

    Liu, Xueli; Gao, Jun; Xue, Zhongxin; Chen, Li; Lin, Ling; Jiang, Lei; Wang, Shutao

    2012-06-2