WorldWideScience

Sample records for genome spatial organization

  1. [Compartmentalization of the cell nucleus and spatial organization of the genome].

    Science.gov (United States)

    Gavrilov, A A; Razin, S V

    2015-01-01

    The eukaryotic cell nucleus is one of the most complex cell organelles. Despite the absence of membranes, the nuclear space is divided into numerous compartments where different processes in- volved in the genome activity take place. The most important nuclear compartments include nucleoli, nuclear speckles, PML bodies, Cajal bodies, histone locus bodies, Polycomb bodies, insulator bodies, transcription and replication factories. The structural basis for the nuclear compartmentalization is provided by genomic DNA that occupies most of the nuclear volume. Nuclear compartments, in turn, guide the chromosome folding by providing a platform for the spatial interaction of individual genomic loci. In this review, we discuss fundamental principles of higher order genome organization with a focus on chromosome territories and chromosome domains, as well as consider the structure and function of the key nuclear compartments. We show that the func- tional compartmentalization of the cell nucleus and genome spatial organization are tightly interconnected, and that this form of organization is highly dynamic and is based on stochastic processes.

  2. Genomic organization and the tissue distribution of alternatively spliced isoforms of the mouse Spatial gene

    Directory of Open Access Journals (Sweden)

    Mattei Marie-Geneviève

    2004-07-01

    Full Text Available Abstract Background The stromal component of the thymic microenvironment is critical for T lymphocyte generation. Thymocyte differentiation involves a cascade of coordinated stromal genes controlling thymocyte survival, lineage commitment and selection. The "Stromal Protein Associated with Thymii And Lymph-node" (Spatial gene encodes a putative transcription factor which may be involved in T-cell development. In the testis, the Spatial gene is also expressed by round spermatids during spermatogenesis. Results The Spatial gene maps to the B3-B4 region of murine chromosome 10 corresponding to the human syntenic region 10q22.1. The mouse Spatial genomic DNA is organised into 10 exons and is alternatively spliced to generate two short isoforms (Spatial-α and -γ and two other long isoforms (Spatial-δ and -ε comprising 5 additional exons on the 3' site. Here, we report the cloning of a new short isoform, Spatial-β, which differs from other isoforms by an additional alternative exon of 69 bases. This new exon encodes an interesting proline-rich signature that could confer to the 34 kDa Spatial-β protein a particular function. By quantitative TaqMan RT-PCR, we have shown that the short isoforms are highly expressed in the thymus while the long isoforms are highly expressed in the testis. We further examined the inter-species conservation of Spatial between several mammals and identified that the protein which is rich in proline and positive amino acids, is highly conserved. Conclusions The Spatial gene generates at least five alternative spliced variants: three short isoforms (Spatial-α, -β and -γ highly expressed in the thymus and two long isoforms (Spatial-δ and -ε highly expressed in the testis. These alternative spliced variants could have a tissue specific function.

  3. Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model.

    Science.gov (United States)

    Gürsoy, Gamze; Xu, Yun; Liang, Jie

    2017-07-01

    Nuclear landmarks and biochemical factors play important roles in the organization of the yeast genome. The interaction pattern of budding yeast as measured from genome-wide 3C studies are largely recapitulated by model polymer genomes subject to landmark constraints. However, the origin of inter-chromosomal interactions, specific roles of individual landmarks, and the roles of biochemical factors in yeast genome organization remain unclear. Here we describe a multi-chromosome constrained self-avoiding chromatin model (mC-SAC) to gain understanding of the budding yeast genome organization. With significantly improved sampling of genome structures, both intra- and inter-chromosomal interaction patterns from genome-wide 3C studies are accurately captured in our model at higher resolution than previous studies. We show that nuclear confinement is a key determinant of the intra-chromosomal interactions, and centromere tethering is responsible for the inter-chromosomal interactions. In addition, important genomic elements such as fragile sites and tRNA genes are found to be clustered spatially, largely due to centromere tethering. We uncovered previously unknown interactions that were not captured by genome-wide 3C studies, which are found to be enriched with tRNA genes, RNAPIII and TFIIS binding. Moreover, we identified specific high-frequency genome-wide 3C interactions that are unaccounted for by polymer effects under landmark constraints. These interactions are enriched with important genes and likely play biological roles.

  4. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  5. Creating spatial organizations

    NARCIS (Netherlands)

    Lekanne Deprez, F.R.E.; Tissen, R.J.

    2009-01-01

    This paper addresses the spatial design of modern organizations in the context of a fundamental change which is currently taking place in the way companies view their organizations and the inherent performance expectations, requirements and results underlying these. This change involves a managerial

  6. Spatial organization of drumlins

    DEFF Research Database (Denmark)

    Clark, Chris D.; Ely, Jeremy; Spagnolo, Matteo

    2017-01-01

    Ice-sheets flowing over soft sediments produce undulations in the bed, typically of metres in relief, of which drumlins are the most abundant and widely investigated. Consensus regarding their mechanism of formation has yet to be achieved. In this paper we examine the spatial organization of drum...

  7. Genome organization, instabilities, stem cells, and cancer

    Directory of Open Access Journals (Sweden)

    Senthil Kumar Pazhanisamy

    2009-01-01

    Full Text Available It is now widely recognized that advances in exploring genome organization provide remarkable insights on the induction and progression of chromosome abnormalities. Much of what we know about how mutations evolve and consequently transform into genome instabilities has been characterized in the spatial organization context of chromatin. Nevertheless, many underlying concepts of impact of the chromatin organization on perpetuation of multiple mutations and on propagation of chromosomal aberrations remain to be investigated in detail. Genesis of genome instabilities from accumulation of multiple mutations that drive tumorigenesis is increasingly becoming a focal theme in cancer studies. This review focuses on structural alterations evolve to raise a variety of genome instabilities that are manifested at the nucleotide, gene or sub-chromosomal, and whole chromosome level of genome. Here we explore an underlying connection between genome instability and cancer in the light of genome architecture. This review is limited to studies directed towards spatial organizational aspects of origin and propagation of aberrations into genetically unstable tumors.

  8. Spatial organization and individual mobility

    Energy Technology Data Exchange (ETDEWEB)

    Maurer, J [Eidgenoessische Technische Hochschule, Zuerich (Switzerland)

    1996-11-01

    The paper deals with the following topics: the notion of spatial organization or spatial development, present options, considerations concerning the main stream of opinions, and the contribution of science. (author) 13 refs.

  9. Gender Structure and Spatial Organization

    Directory of Open Access Journals (Sweden)

    Minoosh Sadoughianzadeh

    2013-11-01

    Full Text Available As a contribution to the widespread debate on the “gender reading” of the “built environment,” this article aims to situate the subject in a new context, the Iranian society. To depict the subject, two distinct traditional architectures of the region, associated with their respective socio-spatial organizations, have been comparatively explored: the “Introvert” and “Extrovert.” These two almost ageless “Introvert” and “Extrovert” architectures, evolved through centuries in different geographical parts of the country, are spatial patterns aptly illustrating how the “gender structure” of each social organization has contributed to the formation of the relevant “physical space” and, further, how the specific “gender relationships” are pertinently structured within each one of the two types of the spaces. Based on a systematic approach and through concentration on the macro-socio-spatial organization, this article is to explore the gender/space associated variations within either of the social systems they belong to. This perspective is particularly instrumental in pinpointing the Introvert and Extrovert architectures in the context of their social organizations and carefully scrutinizing “gender” and “space” categories as systematically integrated variables.

  10. Reconstructing spatial organizations of chromosomes through manifold learning.

    Science.gov (United States)

    Zhu, Guangxiang; Deng, Wenxuan; Hu, Hailin; Ma, Rui; Zhang, Sai; Yang, Jinglin; Peng, Jian; Kaplan, Tommy; Zeng, Jianyang

    2018-02-02

    Decoding the spatial organizations of chromosomes has crucial implications for studying eukaryotic gene regulation. Recently, chromosomal conformation capture based technologies, such as Hi-C, have been widely used to uncover the interaction frequencies of genomic loci in a high-throughput and genome-wide manner and provide new insights into the folding of three-dimensional (3D) genome structure. In this paper, we develop a novel manifold learning based framework, called GEM (Genomic organization reconstructor based on conformational Energy and Manifold learning), to reconstruct the three-dimensional organizations of chromosomes by integrating Hi-C data with biophysical feasibility. Unlike previous methods, which explicitly assume specific relationships between Hi-C interaction frequencies and spatial distances, our model directly embeds the neighboring affinities from Hi-C space into 3D Euclidean space. Extensive validations demonstrated that GEM not only greatly outperformed other state-of-art modeling methods but also provided a physically and physiologically valid 3D representations of the organizations of chromosomes. Furthermore, we for the first time apply the modeled chromatin structures to recover long-range genomic interactions missing from original Hi-C data. © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. CTCF Mediates the Cell-Type Specific Spatial Organization of the Kcnq5 Locus and the Local Gene Regulation

    OpenAIRE

    Ren, Licheng; Wang, Yang; Shi, Minglei; Wang, Xiaoning; Yang, Zhong; Zhao, Zhihu

    2012-01-01

    Chromatin loops play important roles in the dynamic spatial organization of genes in the nucleus. Growing evidence has revealed that the multivalent functional zinc finger protein CCCTC-binding factor (CTCF) is a master regulator of genome spatial organization, and mediates the ubiquitous chromatin loops within the genome. Using circular chromosome conformation capture (4C) methodology, we discovered that CTCF may be a master organizer in mediating the spatial organization of the kcnq5 gene l...

  12. Genome Organization Drives Chromosome Fragility.

    Science.gov (United States)

    Canela, Andres; Maman, Yaakov; Jung, Seolkyoung; Wong, Nancy; Callen, Elsa; Day, Amanda; Kieffer-Kwon, Kyong-Rim; Pekowska, Aleksandra; Zhang, Hongliang; Rao, Suhas S P; Huang, Su-Chen; Mckinnon, Peter J; Aplan, Peter D; Pommier, Yves; Aiden, Erez Lieberman; Casellas, Rafael; Nussenzweig, André

    2017-07-27

    In this study, we show that evolutionarily conserved chromosome loop anchors bound by CCCTC-binding factor (CTCF) and cohesin are vulnerable to DNA double strand breaks (DSBs) mediated by topoisomerase 2B (TOP2B). Polymorphisms in the genome that redistribute CTCF/cohesin occupancy rewire DNA cleavage sites to novel loop anchors. While transcription- and replication-coupled genomic rearrangements have been well documented, we demonstrate that DSBs formed at loop anchors are largely transcription-, replication-, and cell-type-independent. DSBs are continuously formed throughout interphase, are enriched on both sides of strong topological domain borders, and frequently occur at breakpoint clusters commonly translocated in cancer. Thus, loop anchors serve as fragile sites that generate DSBs and chromosomal rearrangements. VIDEO ABSTRACT. Published by Elsevier Inc.

  13. An overview on genome organization of marine organisms.

    Science.gov (United States)

    Costantini, Maria

    2015-12-01

    In this review we will concentrate on some general genome features of marine organisms and their evolution, ranging from vertebrate to invertebrates until unicellular organisms. Before genome sequencing, the ultracentrifugation in CsCl led to high resolution of mammalian DNA (without seeing at the sequence). The analytical profile of human DNA showed that the vertebrate genome is a mosaic of isochores, typically megabase-size DNA segments that belong in a small number of families characterized by different GC levels. The recent availability of a number of fully sequenced genomes allowed mapping very precisely the isochores, based on DNA sequences. Since isochores are tightly linked to biological properties such as gene density, replication timing and recombination, the new level of detail provided by the isochore map helped the understanding of genome structure, function and evolution. This led the current level of knowledge and to further insights. Copyright © 2015. Published by Elsevier B.V.

  14. Genomic Organization of Zebrafish microRNAs

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    Paydar Ima

    2008-05-01

    Full Text Available Abstract Background microRNAs (miRNAs are small (~22 nt non-coding RNAs that regulate cell movement, specification, and development. Expression of miRNAs is highly regulated, both spatially and temporally. Based on direct cloning, sequence conservation, and predicted secondary structures, a large number of miRNAs have been identified in higher eukaryotic genomes but whether these RNAs are simply a subset of a much larger number of noncoding RNA families is unknown. This is especially true in zebrafish where genome sequencing and annotation is not yet complete. Results We analyzed the zebrafish genome to identify the number and location of proven and predicted miRNAs resulting in the identification of 35 new miRNAs. We then grouped all 415 zebrafish miRNAs into families based on seed sequence identity as a means to identify possible functional redundancy. Based on genomic location and expression analysis, we also identified those miRNAs that are likely to be encoded as part of polycistronic transcripts. Lastly, as a resource, we compiled existing zebrafish miRNA expression data and, where possible, listed all experimentally proven mRNA targets. Conclusion Current analysis indicates the zebrafish genome encodes 415 miRNAs which can be grouped into 44 families. The largest of these families (the miR-430 family contains 72 members largely clustered in two main locations along chromosome 4. Thus far, most zebrafish miRNAs exhibit tissue specific patterns of expression.

  15. Genomic analysis of Xenopus organizer function

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    Suhai Sándor

    2006-06-01

    Full Text Available Abstract Background Studies of the Xenopus organizer have laid the foundation for our understanding of the conserved signaling pathways that pattern vertebrate embryos during gastrulation. The two primary activities of the organizer, BMP and Wnt inhibition, can regulate a spectrum of genes that pattern essentially all aspects of the embryo during gastrulation. As our knowledge of organizer signaling grows, it is imperative that we begin knitting together our gene-level knowledge into genome-level signaling models. The goal of this paper was to identify complete lists of genes regulated by different aspects of organizer signaling, thereby providing a deeper understanding of the genomic mechanisms that underlie these complex and fundamental signaling events. Results To this end, we ectopically overexpress Noggin and Dkk-1, inhibitors of the BMP and Wnt pathways, respectively, within ventral tissues. After isolating embryonic ventral halves at early and late gastrulation, we analyze the transcriptional response to these molecules within the generated ectopic organizers using oligonucleotide microarrays. An efficient statistical analysis scheme, combined with a new Gene Ontology biological process annotation of the Xenopus genome, allows reliable and faithful clustering of molecules based upon their roles during gastrulation. From this data, we identify new organizer-related expression patterns for 19 genes. Moreover, our data sub-divides organizer genes into separate head and trunk organizing groups, which each show distinct responses to Noggin and Dkk-1 activity during gastrulation. Conclusion Our data provides a genomic view of the cohorts of genes that respond to Noggin and Dkk-1 activity, allowing us to separate the role of each in organizer function. These patterns demonstrate a model where BMP inhibition plays a largely inductive role during early developmental stages, thereby initiating the suites of genes needed to pattern dorsal tissues

  16. Creating biomaterials with spatially organized functionality.

    Science.gov (United States)

    Chow, Lesley W; Fischer, Jacob F

    2016-05-01

    Biomaterials for tissue engineering provide scaffolds to support cells and guide tissue regeneration. Despite significant advances in biomaterials design and fabrication techniques, engineered tissue constructs remain functionally inferior to native tissues. This is largely due to the inability to recreate the complex and dynamic hierarchical organization of the extracellular matrix components, which is intimately linked to a tissue's biological function. This review discusses current state-of-the-art strategies to control the spatial presentation of physical and biochemical cues within a biomaterial to recapitulate native tissue organization and function. © 2016 by the Society for Experimental Biology and Medicine.

  17. The Spatial Organization of Glucosinolate Biosynthesis

    DEFF Research Database (Denmark)

    Nintemann, Sebastian

    cells is an open question. Likewise, it is not known how glucosinolate biosynthesis is orchestrated at the subcellular level. These open questions were addressed with several approaches in this project, with the aim of shedding light on the spatial organization of glucosinolate biosynthesis from...... between the individual classes of glucosinolates under constitutive and induced conditions and identified the source tissues of these defense compounds. Protein-protein interaction studies were carried out to investigate the subcellular organization of glucosinolate biosynthesis. We identified a family...

  18. Engineering the spatial organization of metabolic pathways

    DEFF Research Database (Denmark)

    Albertsen, Line; Maury, Jerome; Bach, Lars Stougaard

    One of the goals of metabolic engineering is to optimize the production of valuable metabolites in cell factories. In this context, modulating the gene expression and activity of enzymes are tools that have been extensively used. Another approach that is gaining interest is the engineering...... of the spatial organization of biosynthetic pathways. Several natural systems for ensuring optimal spatial arrangement of biosynthetic enzymes exist. Sequentially acting enzymes can for example be positioned in close proximity by attachment to cellular structures, up-concentration in membrane enclosed organelles...... or assembly into large complexes. The vision is that by positioning sequentially acting enzymes in close proximity, the cell can accelerate reaction rates and thereby prevent loss of intermediates through diffusion, degradation or competing pathways. The production of valuable metabolites in cell factories...

  19. Genomic organization of plant aminopropyl transferases.

    Science.gov (United States)

    Rodríguez-Kessler, Margarita; Delgado-Sánchez, Pablo; Rodríguez-Kessler, Gabriela Theresia; Moriguchi, Takaya; Jiménez-Bremont, Juan Francisco

    2010-07-01

    Aminopropyl transferases like spermidine synthase (SPDS; EC 2.5.1.16), spermine synthase and thermospermine synthase (SPMS, tSPMS; EC 2.5.1.22) belong to a class of widely distributed enzymes that use decarboxylated S-adenosylmethionine as an aminopropyl donor and putrescine or spermidine as an amino acceptor to form in that order spermidine, spermine or thermospermine. We describe the analysis of plant genomic sequences encoding SPDS, SPMS, tSPMS and PMT (putrescine N-methyltransferase; EC 2.1.1.53). Genome organization (including exon size, gain and loss, as well as intron number, size, loss, retention, placement and phase, and the presence of transposons) of plant aminopropyl transferase genes were compared between the genomic sequences of SPDS, SPMS and tSPMS from Zea mays, Oryza sativa, Malus x domestica, Populus trichocarpa, Arabidopsis thaliana and Physcomitrella patens. In addition, the genomic organization of plant PMT genes, proposed to be derived from SPDS during the evolution of alkaloid metabolism, is illustrated. Herein, a particular conservation and arrangement of exon and intron sequences between plant SPDS, SPMS and PMT genes that clearly differs with that of ACL5 genes, is shown. The possible acquisition of the plant SPMS exon II and, in particular exon XI in the monocot SPMS genes, is a remarkable feature that allows their differentiation from SPDS genes. In accordance with our in silico analysis, functional complementation experiments of the maize ZmSPMS1 enzyme (previously considered to be SPDS) in yeast demonstrated its spermine synthase activity. Another significant aspect is the conservation of intron sequences among SPDS and PMT paralogs. In addition the existence of microsynteny among some SPDS paralogs, especially in P. trichocarpa and A. thaliana, supports duplication events of plant SPDS genes. Based in our analysis, we hypothesize that SPMS genes appeared with the divergence of vascular plants by a processes of gene duplication and the

  20. Spatial Cytoskeleton Organization Supports Targeted Intracellular Transport

    Science.gov (United States)

    Hafner, Anne E.; Rieger, Heiko

    2018-03-01

    The efficiency of intracellular cargo transport from specific source to target locations is strongly dependent upon molecular motor-assisted motion along the cytoskeleton. Radial transport along microtubules and lateral transport along the filaments of the actin cortex underneath the cell membrane are characteristic for cells with a centrosome. The interplay between the specific cytoskeleton organization and the motor performance realizes a spatially inhomogeneous intermittent search strategy. In order to analyze the efficiency of such intracellular search strategies we formulate a random velocity model with intermittent arrest states. We evaluate efficiency in terms of mean first passage times for three different, frequently encountered intracellular transport tasks: i) the narrow escape problem, which emerges during cargo transport to a synapse or other specific region of the cell membrane, ii) the reaction problem, which considers the binding time of two particles within the cell, and iii) the reaction-escape problem, which arises when cargo must be released at a synapse only after pairing with another particle. Our results indicate that cells are able to realize efficient search strategies for various intracellular transport tasks economically through a spatial cytoskeleton organization that involves only a narrow actin cortex rather than a cell body filled with randomly oriented actin filaments.

  1. Hierarchical spatial organization of geographical networks

    International Nuclear Information System (INIS)

    Travencolo, Bruno A N; Costa, Luciano da F

    2008-01-01

    In this work, we propose a hierarchical extension of the polygonality index as the means to characterize geographical planar networks. By considering successive neighborhoods around each node, it is possible to obtain more complete information about the spatial order of the network at progressive spatial scales. The potential of the methodology is illustrated with respect to synthetic and real geographical networks

  2. Evolution of Genome Organization and Epigenetic Machineries ...

    Indian Academy of Sciences (India)

    48

    The compact folded structure of bacterial genomic material is termed as nucleoid. The ... from pluripotent to the differentiated stage of a cell, there is a dramatic alteration both in the .... Sherratt, D.J. 2003 Bacterial Chromosome Dynamics.

  3. The genomic organization of plant pathogenicity in Fusarium species

    NARCIS (Netherlands)

    Rep, M.; Kistler, H.C.

    2010-01-01

    Comparative genomics is a powerful tool to infer the molecular basis of fungal pathogenicity and its evolution by identifying differences in gene content and genomic organization between fungi with different hosts or modes of infection. Through comparative analysis, pathogenicity-related chromosomes

  4. Approaching the Sequential and Three-Dimensional Organization of Genomes

    NARCIS (Netherlands)

    T.A. Knoch (Tobias)

    2006-01-01

    textabstractGenomes are one of the major foundations of life due to their role in information storage, process regulation and evolution. To achieve a deeper unterstanding of the human genome the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic

  5. Spatial Mapping of Organic Carbon in Returned Samples from Mars

    Science.gov (United States)

    Siljeström, S.; Fornaro, T.; Greenwalt, D.; Steele, A.

    2018-04-01

    To map organic material spatially to minerals present in the sample will be essential for the understanding of the origin of any organics in returned samples from Mars. It will be shown how ToF-SIMS may be used to map organics in samples from Mars.

  6. cDNA structure, genomic organization and expression patterns of ...

    African Journals Online (AJOL)

    Visfatin was a newly identified adipocytokine, which was involved in various physiologic and pathologic processes of organisms. The cDNA structure, genomic organization and expression patterns of silver Prussian carp visfatin were described in this report. The silver Prussian carp visfatin cDNA cloned from the liver was ...

  7. Azolla--a model organism for plant genomic studies.

    Science.gov (United States)

    Qiu, Yin-Long; Yu, Jun

    2003-02-01

    The aquatic ferns of the genus Azolla are nitrogen-fixing plants that have great potentials in agricultural production and environmental conservation. Azolla in many aspects is qualified to serve as a model organism for genomic studies because of its importance in agriculture, its unique position in plant evolution, its symbiotic relationship with the N2-fixing cyanobacterium, Anabaena azollae, and its moderate-sized genome. The goals of this genome project are not only to understand the biology of the Azolla genome to promote its applications in biological research and agriculture practice but also to gain critical insights about evolution of plant genomes. Together with the strategic and technical improvement as well as cost reduction of DNA sequencing, the deciphering of their genetic code is imminent.

  8. Long-Range Order and Fractality in the Structure and Organization of Eukaryotic Genomes

    Science.gov (United States)

    Polychronopoulos, Dimitris; Tsiagkas, Giannis; Athanasopoulou, Labrini; Sellis, Diamantis; Almirantis, Yannis

    2014-12-01

    The late Professor J.S. Nicolis always emphasized, both in his writings and in presentations and discussions with students and friends, the relevance of a dynamical systems approach to biology. In particular, viewing the genome as a "biological text" captures the dynamical character of both the evolution and function of the organisms in the form of correlations indicating the presence of a long-range order. This genomic structure can be expressed in forms reminiscent of natural languages and several temporal and spatial traces l by the functioning of dynamical systems: Zipf laws, self-similarity and fractality. Here we review several works of our group and recent unpublished results, focusing on the chromosomal distribution of biologically active genomic components: Genes and protein-coding segments, CpG islands, transposable elements belonging to all major classes and several types of conserved non-coding genomic elements. We report the systematic appearance of power-laws in the size distribution of the distances between elements belonging to each of these types of functional genomic elements. Moreover, fractality is also found in several cases, using box-counting and entropic scaling.We present here, for the first time in a unified way, an aggregative model of the genomic dynamics which can explain the observed patterns on the grounds of known phenomena accompanying genome evolution. Our results comply with recent findings about a "fractal globule" geometry of chromatin in the eukaryotic nucleus.

  9. Directed spatial organization of zinc oxide nanostructures

    Science.gov (United States)

    Hsu, Julia [Albuquerque, NM; Liu, Jun [Richland, WA

    2009-02-17

    A method for controllably forming zinc oxide nanostructures on a surface via an organic template, which is formed using a stamp prepared from pre-defined relief structures, inking the stamp with a solution comprising self-assembled monolayer (SAM) molecules, contacting the stamp to the surface, such as Ag sputtered on Si, and immersing the surface with the patterned SAM molecules with a zinc-containing solution with pH control to form zinc oxide nanostructures on the bare Ag surface.

  10. Interspecific bacterial interactions are reflected in multispecies biofilm spatial organization

    DEFF Research Database (Denmark)

    Liu, Wenzheng; Røder, Henriette Lyng; Madsen, Jonas Stenløkke

    2016-01-01

    not only the enabling sub-populations. However, the specific molecular mechanisms of cellular processes affecting spatial organization, and vice versa, are poorly understood and very complex to unravel. Therefore, detailed description of the spatial organization of individual bacterial cells...... environments. Species residing in these complex bacterial communities usually interact both intra- and interspecifically. Such interactions are considered to not only be fundamental in shaping overall biomass and the spatial distribution of cells residing in multispecies biofilms, but also to result......, industrial, and clinical implications. This review briefly presents the state of the art of studying interspecies interactions and spatial organization of multispecies communities, aiming to support theoretical and practical arguments for further advancement of this field....

  11. Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

    Directory of Open Access Journals (Sweden)

    Phillips Ruth B

    2010-10-01

    Full Text Available Abstract Background The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent model organisms for studying comparative genomics, evolutionary processes, fates of duplicated genes and the genetic and physiological processes associated with complex behavioral phenotypes. The evolution of the tetrapod hemoglobin genes is well studied; however, little is known about the genomic organization and evolution of teleost hemoglobin genes, particularly those of salmonids. The Atlantic salmon serves as a representative salmonid species for genomics studies. Given the well documented role of hemoglobin in adaptation to varied environmental conditions as well as its use as a model protein for evolutionary analyses, an understanding of the genomic structure and organization of the Atlantic salmon α and β hemoglobin genes is of great interest. Results We identified four bacterial artificial chromosomes (BACs comprising two hemoglobin gene clusters spanning the entire α and β hemoglobin gene repertoire of the Atlantic salmon genome. Their chromosomal locations were established using fluorescence in situ hybridization (FISH analysis and linkage mapping, demonstrating that the two clusters are located on separate chromosomes. The BACs were sequenced and assembled into scaffolds, which were annotated for putatively functional and pseudogenized hemoglobin-like genes. This revealed that the tail-to-tail organization and alternating pattern of the α and β hemoglobin genes are well conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobin genes, including non-Bohr β globin genes, than the genomes of other teleosts that have been sequenced. Conclusions We suggest that the most parsimonious evolutionary path leading to the present organization of the Atlantic salmon

  12. Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

    Science.gov (United States)

    2010-01-01

    Background The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent model organisms for studying comparative genomics, evolutionary processes, fates of duplicated genes and the genetic and physiological processes associated with complex behavioral phenotypes. The evolution of the tetrapod hemoglobin genes is well studied; however, little is known about the genomic organization and evolution of teleost hemoglobin genes, particularly those of salmonids. The Atlantic salmon serves as a representative salmonid species for genomics studies. Given the well documented role of hemoglobin in adaptation to varied environmental conditions as well as its use as a model protein for evolutionary analyses, an understanding of the genomic structure and organization of the Atlantic salmon α and β hemoglobin genes is of great interest. Results We identified four bacterial artificial chromosomes (BACs) comprising two hemoglobin gene clusters spanning the entire α and β hemoglobin gene repertoire of the Atlantic salmon genome. Their chromosomal locations were established using fluorescence in situ hybridization (FISH) analysis and linkage mapping, demonstrating that the two clusters are located on separate chromosomes. The BACs were sequenced and assembled into scaffolds, which were annotated for putatively functional and pseudogenized hemoglobin-like genes. This revealed that the tail-to-tail organization and alternating pattern of the α and β hemoglobin genes are well conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobin genes, including non-Bohr β globin genes, than the genomes of other teleosts that have been sequenced. Conclusions We suggest that the most parsimonious evolutionary path leading to the present organization of the Atlantic salmon hemoglobin genes involves

  13. Heat Energy Markets: Trends of Spatial Organization

    Directory of Open Access Journals (Sweden)

    Olga Valeryevna Dyomina

    2016-12-01

    Full Text Available The author reviews competing forms of heat supply. It is shown that in Finland, Denmark, China and Russia the dominant form of heat supply is district heating system; in the United States and Canada the dominant form of heat supply is individual one. Using the countries’ data the author allocates 4 models of heat energy markets. The analysis is based on combinations of the following characteristics: the type of market, the orientation of market, the stage of market development, forms of state support of district heating systems and the approach to pricing. The results identified the failure of the current model of heat energy market in Russia (noncompetitive, manufacturer-oriented and evolved market with massive state support of its district heating system. The ‘target’ model of heat energy market in Russia is a model of noncompetitive, customer-oriented and evolved market with no state support of its district heating system. However, the ‘target’ model takes into account spatial heterogeneity of local heat energy markets in Russia only technically

  14. HCMI Organization | Office of Cancer Genomics

    Science.gov (United States)

    Consortium The Human Cancer Models Initiative (HCMI) was created and funded by the US National Cancer Institute, Cancer Research UK, the foundation Hubrecht Organoid Technology, and the Wellcome Sanger Institute. Together, these organizations develop policy and make programmatic decisions to contribute to the function of the HCMI. National Cancer Institute

  15. Spatial-functional organization of settlements in Vojvodina

    Directory of Open Access Journals (Sweden)

    Krunić Nikola

    2012-01-01

    Full Text Available This paper summarizes the results of recent exploration of spatial and functional organization of Autonomous Province of Vojvodina in the Republic of Serbia (hereinafter referred to as “Vojvodina” based on identification of the level of development of spatial and functional connections and relationships within its settlement network. The research is theoretically and methodically based on principles of regionalization and recent doctrines of regional development, contemporary spatial planning and social and economics disciplines of social geography. Results to a great extent identify and scientifically explain problems of the development of spatial and functional organization of settlement network in Vojvodina. Based on these results, a recommendation for a possible model of a sustainable settlement network in Vojvodina has been given.

  16. The draft genome of a termite illuminates alternative social organization

    Science.gov (United States)

    Termites have substantial economic and ecological impact worldwide. They are also the oldest organisms living in complex societies, having evolved a caste system independent of that of eusocial Hymenoptera (ants, bees and wasps). Here we provide the first genome sequence for a termite, Zootermopsis ...

  17. Biology, genome organization and evolution of parvoviruses in marine shrimp

    Science.gov (United States)

    A number of parvoviruses are now know to infect marine shrimp, and these viruses alone or in combination with other viruses have the potential to cause major losses in shrimp aquaculture globally. This review provides a comprehensive overview of the biology, genome organization, gene expression, and...

  18. Structural Genomics of Minimal Organisms: Pipeline and Results

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sung-Hou; Shin, Dong-Hae; Kim, Rosalind; Adams, Paul; Chandonia, John-Marc

    2007-09-14

    The initial objective of the Berkeley Structural Genomics Center was to obtain a near complete three-dimensional (3D) structural information of all soluble proteins of two minimal organisms, closely related pathogens Mycoplasma genitalium and M. pneumoniae. The former has fewer than 500 genes and the latter has fewer than 700 genes. A semiautomated structural genomics pipeline was set up from target selection, cloning, expression, purification, and ultimately structural determination. At the time of this writing, structural information of more than 93percent of all soluble proteins of M. genitalium is avail able. This chapter summarizes the approaches taken by the authors' center.

  19. Mycoplasma hyopneumoniae Transcription Unit Organization: Genome Survey and Prediction

    Science.gov (United States)

    Siqueira, Franciele Maboni; Schrank, Augusto; Schrank, Irene Silveira

    2011-01-01

    Mycoplasma hyopneumoniae is associated with swine respiratory diseases. Although gene organization and regulation are well known in many prokaryotic organisms, knowledge on mycoplasma is limited. This study performed a comparative analysis of three strains of M. hyopneumoniae (7448, J and 232), with a focus on genome organization and gene comparison for open read frame (ORF) cluster (OC) identification. An in silico analysis of gene organization demonstrated 117 OCs and 34 single ORFs in M. hyopneumoniae 7448 and J, while 116 OCs and 36 single ORFs were identified in M. hyopneumoniae 232. Genomic comparison revealed high synteny and conservation of gene order between the OCs defined for 7448 and J strains as well as for 7448 and 232 strains. Twenty-one OCs were chosen and experimentally confirmed by reverse transcription–PCR from M. hyopneumoniae 7448 genome, validating our prediction. A subset of the ORFs within an OC could be independently transcribed due to the presence of internal promoters. Our results suggest that transcription occurs in ‘run-on’ from an upstream promoter in M. hyopneumoniae, thus forming large ORF clusters (from 2 to 29 ORFs in the same orientation) and indicating a complex transcriptional organization. PMID:22086999

  20. Interspecific bacterial interactions are reflected in multispecies biofilm spatial organization

    Directory of Open Access Journals (Sweden)

    Wenzheng Liu

    2016-08-01

    Full Text Available Interspecies interactions are essential for the persistence and development of any kind of complex community, and microbial biofilms are no exception. Multispecies biofilms are structured and spatially defined communities that have received much attention due to their omnipresence in natural environments. Species residing in these complex bacterial communities usually interact both intra- and interspecifically. Such interactions are considered to not only be fundamental in shaping overall biomass and the spatial distribution of cells residing in multispecies biofilms, but also to result in coordinated regulation of gene expression in the different species present. These communal interactions often lead to emergent properties in biofilms, such as enhanced tolerance against antibiotics, host immune responses and other stresses, which have been shown to provide benefits to all biofilm members not only the enabling sub-populations. However, the specific molecular mechanisms of cellular processes affecting spatial organization, and vice versa, are poorly understood and very complex to unravel. Therefore, detailed description of the spatial organization of individual bacterial cells in multispecies communities can be an alternative strategy to reveal the nature of interspecies interactions of constituent species. Closing the gap between visual observation and biological processes may become crucial for resolving biofilm related problems, which is of utmost importance to environmental, industrial, and clinical implications. This review briefly presents the state of the art of studying interspecies interactions and spatial organization of multispecies communities, aiming to support theoretical and practical arguments for further advancement of this field.

  1. Ontogenetic shifts and spatial associations in organ positions for snakes.

    Science.gov (United States)

    Anderson, Gretchen E; Secor, Stephen M

    2015-12-01

    Snakes possess an elongated body form and serial placement of organs which provides the opportunity to explore historic and adaptive mechanisms of organ position. We examined the influence of body size and sex on the position of, and spatial associations between, the heart, liver, small intestine, and right kidney for ten phylogenetically diverse species of snakes that vary in body shape and habitat. Snake snout-vent length explained much of the variation in the position of these four organs. For all ten species, the position of the heart and liver relative to snout-vent length decreased as a function of size. As body size increased from neonate to adult, these two organs shifted anteriorly an average of 4.7% and 5.7% of snout-vent length, respectively. Similarly, the small intestine and right kidney shifted anteriorly with an increase in snout-vent length for seven and five of the species, respectively. The absolute and relative positioning of these organs did not differ between male and female Burmese pythons (Python molurus). However, for diamondback water snakes (Nerodia rhombifer), the liver and small intestine were more anteriorly positioned in females as compared to males, whereas the right kidney was positioned more anteriorly for males. Correlations of residuals of organ position (deviation from predicted position) demonstrated significant spatial associations between organs for nine of the ten species. For seven species, individuals with hearts more anterior (or posterior) than predicted also tended to possess livers that were similarly anteriorly (or posteriorly) placed. Positive associations between liver and small intestine positions and between small intestine and right kidney positions were observed for six species, while spatial associations between the heart and small intestine, heart and right kidney, and liver and right kidney were observed in three or four species. This study demonstrates that size, sex, and spatial associations may have

  2. The footprint of metabolism in the organization of mammalian genomes

    Directory of Open Access Journals (Sweden)

    Berná Luisa

    2012-05-01

    Full Text Available Abstract Background At present five evolutionary hypotheses have been proposed to explain the great variability of the genomic GC content among and within genomes: the mutational bias, the biased gene conversion, the DNA breakpoints distribution, the thermal stability and the metabolic rate. Several studies carried out on bacteria and teleostean fish pointed towards the critical role played by the environment on the metabolic rate in shaping the base composition of genomes. In mammals the debate is still open, and evidences have been produced in favor of each evolutionary hypothesis. Human genes were assigned to three large functional categories (as well as to the corresponding functional classes according to the KOG database: (i information storage and processing, (ii cellular processes and signaling, and (iii metabolism. The classification was extended to the organisms so far analyzed performing a reciprocal Blastp and selecting the best reciprocal hit. The base composition was calculated for each sequence of the whole CDS dataset. Results The GC3 level of the above functional categories was increasing from (i to (iii. This specific compositional pattern was found, as footprint, in all mammalian genomes, but not in frog and lizard ones. Comparative analysis of human versus both frog and lizard functional categories showed that genes involved in the metabolic processes underwent the highest GC3 increment. Analyzing the KOG functional classes of genes, again a well defined intra-genomic pattern was found in all mammals. Not only genes of metabolic pathways, but also genes involved in chromatin structure and dynamics, transcription, signal transduction mechanisms and cytoskeleton, showed an average GC3 level higher than that of the whole genome. In the case of the human genome, the genes of the aforementioned functional categories showed a high probability to be associated with the chromosomal bands. Conclusions In the light of different

  3. Early blindness alters the spatial organization of verbal working memory.

    Science.gov (United States)

    Bottini, Roberto; Mattioni, Stefania; Collignon, Olivier

    2016-10-01

    Several studies suggest that serial order in working memory (WM) is grounded on space. For a list of ordered items held in WM, items at the beginning of the list are associated with the left side of space and items at the end of the list with the right side. This suggests that maintaining items in verbal WM is performed in strong analogy to writing these items down on a physical whiteboard for later consultation (The Mental Whiteboard Hypothesis). What drives this spatial mapping of ordered series in WM remains poorly understood. In the present study we tested whether visual experience is instrumental in establishing the link between serial order in WM and spatial processing. We tested early blind (EB), late blind (LB) and sighted individuals in an auditory WM task. Replicating previous studies, left-key responses were faster for early items in the list whereas later items facilitated right-key responses in the sighted group. The same effect was observed in LB individuals. In contrast, EB participants did not show any association between space and serial position in WM. These results suggest that early visual experience plays a critical role in linking ordered items in WM and spatial representations. The analogical spatial structure of WM may depend in part on the actual experience of using spatially organized devices (e.g., notes, whiteboards) to offload WM. These practices are largely precluded to EB individuals, who instead rely to mnemonic devices that are less spatially organized (e.g., recordings, vocal notes). The way we habitually organize information in the external world may bias the way we organize information in our WM. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. The DNA-encoded nucleosome organization of a eukaryotic genome.

    Science.gov (United States)

    Kaplan, Noam; Moore, Irene K; Fondufe-Mittendorf, Yvonne; Gossett, Andrea J; Tillo, Desiree; Field, Yair; LeProust, Emily M; Hughes, Timothy R; Lieb, Jason D; Widom, Jonathan; Segal, Eran

    2009-03-19

    Nucleosome organization is critical for gene regulation. In living cells this organization is determined by multiple factors, including the action of chromatin remodellers, competition with site-specific DNA-binding proteins, and the DNA sequence preferences of the nucleosomes themselves. However, it has been difficult to estimate the relative importance of each of these mechanisms in vivo, because in vivo nucleosome maps reflect the combined action of all influencing factors. Here we determine the importance of nucleosome DNA sequence preferences experimentally by measuring the genome-wide occupancy of nucleosomes assembled on purified yeast genomic DNA. The resulting map, in which nucleosome occupancy is governed only by the intrinsic sequence preferences of nucleosomes, is similar to in vivo nucleosome maps generated in three different growth conditions. In vitro, nucleosome depletion is evident at many transcription factor binding sites and around gene start and end sites, indicating that nucleosome depletion at these sites in vivo is partly encoded in the genome. We confirm these results with a micrococcal nuclease-independent experiment that measures the relative affinity of nucleosomes for approximately 40,000 double-stranded 150-base-pair oligonucleotides. Using our in vitro data, we devise a computational model of nucleosome sequence preferences that is significantly correlated with in vivo nucleosome occupancy in Caenorhabditis elegans. Our results indicate that the intrinsic DNA sequence preferences of nucleosomes have a central role in determining the organization of nucleosomes in vivo.

  5. The role of spatial organization in preference for color pairs.

    Science.gov (United States)

    Schloss, Karen B; Palmer, Stephen E

    2011-01-01

    We investigated how spatial organization influences color-pair preference asymmetries: differential preference for one color pair over another when the pairs contain the same colors in opposite spatial configurations. Schloss and Palmer (2011, Attention, Perception, & Psychophysics 73 55-571) found weak figure ground preference asymmetries for small squares centered on large squares in aesthetic ratings. Here, we found robust preference asymmetries using a more sensitive forced-choice task: participants strongly prefer pairs with yellower, lighter figures on bluer, darker grounds (experiment 1). We also investigated which spatial factors influence these preference asymmetries. Relative area of the two component regions is clearly important, and perceived 3-D area of the 2-D displays (ie after the ground is amodally completed behind the figure) is more influential than 2-D area (experiment 2). Surroundedness is not required, because yellowness blueness effects were comparable for pairs in which the figure was surrounded by the ground, and for mosaic arrangements in which the regions were adjacent and separated by a gap (experiment 3). Lightness darkness effects, however, were opposite for figure ground versus mosaic organizations: people prefer figure-ground organizations in which smaller regions are lighter, but prefer mosaic organizations in which smaller regions are darker. Physiological, phenomenological, and ecological explanations of the reported results are discussed.

  6. novel insights into spatial and functional organization in the cell ...

    Indian Academy of Sciences (India)

    NOVEL INSIGHTS INTO SPATIAL AND FUNCTIONAL ORGANIZATION IN THE CELL NUCLEUS · PowerPoint Presentation · Slide 3 · Slide 4 · Slide 5 · Slide 6 · Slide 7 · Slide 8 · Slide 9 · Slide 10 · Slide 11 · Slide 12 · Slide 13 · Slide 14 · Slide 15 · Slide 16 · Slide 17 · Slide 18 · Slide 19 · Slide 20 · Slide 21 · Slide 22.

  7. Hepatitis A Virus Genome Organization and Replication Strategy.

    Science.gov (United States)

    McKnight, Kevin L; Lemon, Stanley M

    2018-04-02

    Hepatitis A virus (HAV) is a positive-strand RNA virus classified in the genus Hepatovirus of the family Picornaviridae It is an ancient virus with a long evolutionary history and multiple features of its capsid structure, genome organization, and replication cycle that distinguish it from other mammalian picornaviruses. HAV proteins are produced by cap-independent translation of a single, long open reading frame under direction of an inefficient, upstream internal ribosome entry site (IRES). Genome replication occurs slowly and is noncytopathic, with transcription likely primed by a uridylated protein primer as in other picornaviruses. Newly produced quasi-enveloped virions (eHAV) are released from cells in a nonlytic fashion in a unique process mediated by interactions of capsid proteins with components of the host cell endosomal sorting complexes required for transport (ESCRT) system. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

  8. Chromosome organizaton in simple and complex unicellular organisms.

    Science.gov (United States)

    O'Sullivan, Justin M

    2011-01-01

    The genomes of unicellular organisms form complex 3-dimensional structures. This spatial organization is hypothesized to have a significant role in genomic function. Spatial organization is not limited solely to the three-dimensional folding of the chromosome(s) in genomes but also includes genome positioning, and the folding and compartmentalization of any additional genetic material (e.g. episomes) present within complex genomes. In this comment, I will highlight similarities in the spatial organization of eukaryotic and prokaryotic unicellular genomes.

  9. Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms

    Directory of Open Access Journals (Sweden)

    Trent Harold F

    2005-03-01

    Full Text Available Abstract Background The Marine Genomics project is a functional genomics initiative developed to provide a pipeline for the curation of Expressed Sequence Tags (ESTs and gene expression microarray data for marine organisms. It provides a unique clearing-house for marine specific EST and microarray data and is currently available at http://www.marinegenomics.org. Description The Marine Genomics pipeline automates the processing, maintenance, storage and analysis of EST and microarray data for an increasing number of marine species. It currently contains 19 species databases (over 46,000 EST sequences that are maintained by registered users from local and remote locations in Europe and South America in addition to the USA. A collection of analysis tools are implemented. These include a pipeline upload tool for EST FASTA file, sequence trace file and microarray data, an annotative text search, automated sequence trimming, sequence quality control (QA/QC editing, sequence BLAST capabilities and a tool for interactive submission to GenBank. Another feature of this resource is the integration with a scientific computing analysis environment implemented by MATLAB. Conclusion The conglomeration of multiple marine organisms with integrated analysis tools enables users to focus on the comprehensive descriptions of transcriptomic responses to typical marine stresses. This cross species data comparison and integration enables users to contain their research within a marine-oriented data management and analysis environment.

  10. Capturing spatial heterogeneity of soil organic carbon under changing climate

    Science.gov (United States)

    Mishra, U.; Fan, Z.; Jastrow, J. D.; Matamala, R.; Vitharana, U.

    2015-12-01

    The spatial heterogeneity of the land surface affects water, energy, and greenhouse gas exchanges with the atmosphere. Designing observation networks that capture land surface spatial heterogeneity is a critical scientific challenge. Here, we present a geospatial approach to capture the existing spatial heterogeneity of soil organic carbon (SOC) stocks across Alaska, USA. We used the standard deviation of 556 georeferenced SOC profiles previously compiled in Mishra and Riley (2015, Biogeosciences, 12:3993-4004) to calculate the number of observations that would be needed to reliably estimate Alaskan SOC stocks. This analysis indicated that 906 randomly distributed observation sites would be needed to quantify the mean value of SOC stocks across Alaska at a confidence interval of ± 5 kg m-2. We then used soil-forming factors (climate, topography, land cover types, surficial geology) to identify the locations of appropriately distributed observation sites by using the conditioned Latin hypercube sampling approach. Spatial correlation and variogram analyses demonstrated that the spatial structures of soil-forming factors were adequately represented by these 906 sites. Using the spatial correlation length of existing SOC observations, we identified 484 new observation sites would be needed to provide the best estimate of the present status of SOC stocks in Alaska. We then used average decadal projections (2020-2099) of precipitation, temperature, and length of growing season for three representative concentration pathway (RCP 4.5, 6.0, and 8.5) scenarios of the Intergovernmental Panel on Climate Change to investigate whether the location of identified observation sites will shift/change under future climate. Our results showed 12-41 additional observation sites (depending on emission scenarios) will be required to capture the impact of projected climatic conditions by 2100 on the spatial heterogeneity of Alaskan SOC stocks. Our results represent an ideal distribution

  11. Understanding spatial organizations of chromosomes via statistical analysis of Hi-C data

    Science.gov (United States)

    Hu, Ming; Deng, Ke; Qin, Zhaohui; Liu, Jun S.

    2015-01-01

    Understanding how chromosomes fold provides insights into the transcription regulation, hence, the functional state of the cell. Using the next generation sequencing technology, the recently developed Hi-C approach enables a global view of spatial chromatin organization in the nucleus, which substantially expands our knowledge about genome organization and function. However, due to multiple layers of biases, noises and uncertainties buried in the protocol of Hi-C experiments, analyzing and interpreting Hi-C data poses great challenges, and requires novel statistical methods to be developed. This article provides an overview of recent Hi-C studies and their impacts on biomedical research, describes major challenges in statistical analysis of Hi-C data, and discusses some perspectives for future research. PMID:26124977

  12. Spatial conditions - the 3. supervisor in project organized teaching?

    DEFF Research Database (Denmark)

    Bering Keiding, Tina

    through reflection of its own border: is this new issue inside or outside the project. Individual rooms make it easier for the project to stabilize around its eigenvalues, but also enhance the risk of cognitive jog-trot. The challenge in this case becomes to seek out disturbances which can initiate new......The contribution presents a pilot study on project work situated in different spatial contexts. The main question for the study is if and how spatial conditions influence the interaction within and between projects. Possible answers to the question are sought through observations, informal...... interviews and questionnaires. The empirical findings are reflected in a Luhmann-based re-description of project organized group based teaching (Keiding 2008). Preliminary conclusions indicate that one big difference between open-space studio and individual group rooms is related to the immediate public...

  13. Modeling and experimental methods to probe the link between global transcription and spatial organization of chromosomes.

    Directory of Open Access Journals (Sweden)

    K Venkatesan Iyer

    Full Text Available Genomes are spatially assembled into chromosome territories (CT within the nucleus of living cells. Recent evidences have suggested associations between three-dimensional organization of CTs and the active gene clusters within neighboring CTs. These gene clusters are part of signaling networks sharing similar transcription factor or other downstream transcription machineries. Hence, presence of such gene clusters of active signaling networks in a cell type may regulate the spatial organization of chromosomes in the nucleus. However, given the probabilistic nature of chromosome positions and complex transcription factor networks (TFNs, quantitative methods to establish their correlation is lacking. In this paper, we use chromosome positions and gene expression profiles in interphase fibroblasts and describe methods to capture the correspondence between their spatial position and expression. In addition, numerical simulations designed to incorporate the interacting TFNs, reveal that the chromosome positions are also optimized for the activity of these networks. These methods were validated for specific chromosome pairs mapped in two distinct transcriptional states of T-Cells (naïve and activated. Taken together, our methods highlight the functional coupling between topology of chromosomes and their respective gene expression patterns.

  14. Gene organization inside replication domains in mammalian genomes

    Science.gov (United States)

    Zaghloul, Lamia; Baker, Antoine; Audit, Benjamin; Arneodo, Alain

    2012-11-01

    We investigate the large-scale organization of human genes with respect to "master" replication origins that were previously identified as bordering nucleotide compositional skew domains. We separate genes in two categories depending on their CpG enrichment at the promoter which can be considered as a marker of germline DNA methylation. Using expression data in mouse, we confirm that CpG-rich genes are highly expressed in germline whereas CpG-poor genes are in a silent state. We further show that, whether tissue-specific or broadly expressed (housekeeping genes), the CpG-rich genes are over-represented close to the replication skew domain borders suggesting some coordination of replication and transcription. We also reveal that the transcription of the longest CpG-rich genes is co-oriented with replication fork progression so that the promoter of these transcriptionally active genes be located into the accessible open chromatin environment surrounding the master replication origins that border the replication skew domains. The observation of a similar gene organization in the mouse genome confirms the interplay of replication, transcription and chromatin structure as the cornerstone of mammalian genome architecture.

  15. The Role of Librarian in Spatial Organization of Libraries

    Directory of Open Access Journals (Sweden)

    Zeynep Onat Öz

    1996-03-01

    should primarily respond to man and his needs. This is valid for library buildings as well. Especially in a period where the demand for libraries is at very low levels in our country, despite the popularity of the concept of information age, it is important to create library buildings to attract people both with their interior and exterior spaces, that suit to their users and staff, and that offer mediums directed to increase happiness and productivity, is important and inevitable as much as other factors. In this sense, librarians, whose job is basically to organize and present information to society and to individuals to be used in both performing and developing their particular roles in the society, should be equipped with the necessary information for spatial organization of their own habitat and should assume their undeniable role within this process as soon as possible.

  16. Approaching the sequential and three-dimensional organization of Archaea, Bacteria and Eukarya genomes. Dynamic Organization of Nuclear Function

    NARCIS (Netherlands)

    T.A. Knoch (Tobias); M. Göker (Markus); R. Lohner (Rudolf); J. Langowski (Jörg)

    2002-01-01

    textabstractThe largely unresolved sequential organization, i.e. the relations within DNA sequences, and its connection to the three-dimensional organization of genomes was investigated by correlation analyses of completely sequenced chromosomes from Viroids, Archaea, Bacteria, Arabidopsis

  17. Architectural protein subclasses shape 3-D organization of genomes during lineage commitment

    Science.gov (United States)

    Phillips-Cremins, Jennifer E.; Sauria, Michael E. G.; Sanyal, Amartya; Gerasimova, Tatiana I.; Lajoie, Bryan R.; Bell, Joshua S. K.; Ong, Chin-Tong; Hookway, Tracy A.; Guo, Changying; Sun, Yuhua; Bland, Michael J.; Wagstaff, William; Dalton, Stephen; McDevitt, Todd C.; Sen, Ranjan; Dekker, Job; Taylor, James; Corces, Victor G.

    2013-01-01

    Summary Understanding the topological configurations of chromatin may reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development. Here we generate high-resolution architecture maps across seven genomic loci in embryonic stem cells and neural progenitor cells. We observe a hierarchy of 3-D interactions that undergo marked reorganization at the sub-Mb scale during differentiation. Distinct combinations of CTCF, Mediator, and cohesin show widespread enrichment in looping interactions at different length scales. CTCF/cohesin anchor long-range constitutive interactions that form the topological basis for invariant sub-domains. Conversely, Mediator/cohesin together with pioneer factors bridge shortrange enhancer-promoter interactions within and between larger sub-domains. Knockdown of Smc1 or Med12 in ES cells results in disruption of spatial architecture and down-regulation of genes found in cohesin-mediated interactions. We conclude that cell type-specific chromatin organization occurs at the sub-Mb scale and that architectural proteins shape the genome in hierarchical length scales. PMID:23706625

  18. The properties of genome conformation and spatial gene interaction and regulation networks of normal and malignant human cell types.

    Directory of Open Access Journals (Sweden)

    Zheng Wang

    Full Text Available The spatial conformation of a genome plays an important role in the long-range regulation of genome-wide gene expression and methylation, but has not been extensively studied due to lack of genome conformation data. The recently developed chromosome conformation capturing techniques such as the Hi-C method empowered by next generation sequencing can generate unbiased, large-scale, high-resolution chromosomal interaction (contact data, providing an unprecedented opportunity to investigate the spatial structure of a genome and its applications in gene regulation, genomics, epigenetics, and cell biology. In this work, we conducted a comprehensive, large-scale computational analysis of this new stream of genome conformation data generated for three different human leukemia cells or cell lines by the Hi-C technique. We developed and applied a set of bioinformatics methods to reliably generate spatial chromosomal contacts from high-throughput sequencing data and to effectively use them to study the properties of the genome structures in one-dimension (1D and two-dimension (2D. Our analysis demonstrates that Hi-C data can be effectively applied to study tissue-specific genome conformation, chromosome-chromosome interaction, chromosomal translocations, and spatial gene-gene interaction and regulation in a three-dimensional genome of primary tumor cells. Particularly, for the first time, we constructed genome-scale spatial gene-gene interaction network, transcription factor binding site (TFBS - TFBS interaction network, and TFBS-gene interaction network from chromosomal contact information. Remarkably, all these networks possess the properties of scale-free modular networks.

  19. Multiple Whole Genome Alignments Without a Reference Organism

    Energy Technology Data Exchange (ETDEWEB)

    Dubchak, Inna; Poliakov, Alexander; Kislyuk, Andrey; Brudno, Michael

    2009-01-16

    Multiple sequence alignments have become one of the most commonly used resources in genomics research. Most algorithms for multiple alignment of whole genomes rely either on a reference genome, against which all of the other sequences are laid out, or require a one-to-one mapping between the nucleotides of the genomes, preventing the alignment of recently duplicated regions. Both approaches have drawbacks for whole-genome comparisons. In this paper we present a novel symmetric alignment algorithm. The resulting alignments not only represent all of the genomes equally well, but also include all relevant duplications that occurred since the divergence from the last common ancestor. Our algorithm, implemented as a part of the VISTA Genome Pipeline (VGP), was used to align seven vertebrate and sixDrosophila genomes. The resulting whole-genome alignments demonstrate a higher sensitivity and specificity than the pairwise alignments previously available through the VGP and have higher exon alignment accuracy than comparable public whole-genome alignments. Of the multiple alignment methods tested, ours performed the best at aligning genes from multigene families?perhaps the most challenging test for whole-genome alignments. Our whole-genome multiple alignments are available through the VISTA Browser at http://genome.lbl.gov/vista/index.shtml.

  20. Genome-scale modelling of microbial metabolism with temporal and spatial resolution.

    Science.gov (United States)

    Henson, Michael A

    2015-12-01

    Most natural microbial systems have evolved to function in environments with temporal and spatial variations. A major limitation to understanding such complex systems is the lack of mathematical modelling frameworks that connect the genomes of individual species and temporal and spatial variations in the environment to system behaviour. The goal of this review is to introduce the emerging field of spatiotemporal metabolic modelling based on genome-scale reconstructions of microbial metabolism. The extension of flux balance analysis (FBA) to account for both temporal and spatial variations in the environment is termed spatiotemporal FBA (SFBA). Following a brief overview of FBA and its established dynamic extension, the SFBA problem is introduced and recent progress is described. Three case studies are reviewed to illustrate the current state-of-the-art and possible future research directions are outlined. The author posits that SFBA is the next frontier for microbial metabolic modelling and a rapid increase in methods development and system applications is anticipated. © 2015 Authors; published by Portland Press Limited.

  1. Spatial distribution of soil organic carbon stocks in France

    Directory of Open Access Journals (Sweden)

    M. P. Martin

    2011-05-01

    Full Text Available Soil organic carbon plays a major role in the global carbon budget, and can act as a source or a sink of atmospheric carbon, thereby possibly influencing the course of climate change. Changes in soil organic carbon (SOC stocks are now taken into account in international negotiations regarding climate change. Consequently, developing sampling schemes and models for estimating the spatial distribution of SOC stocks is a priority. The French soil monitoring network has been established on a 16 km × 16 km grid and the first sampling campaign has recently been completed, providing around 2200 measurements of stocks of soil organic carbon, obtained through an in situ composite sampling, uniformly distributed over the French territory.

    We calibrated a boosted regression tree model on the observed stocks, modelling SOC stocks as a function of other variables such as climatic parameters, vegetation net primary productivity, soil properties and land use. The calibrated model was evaluated through cross-validation and eventually used for estimating SOC stocks for mainland France. Two other models were calibrated on forest and agricultural soils separately, in order to assess more precisely the influence of pedo-climatic variables on SOC for such soils.

    The boosted regression tree model showed good predictive ability, and enabled quantification of relationships between SOC stocks and pedo-climatic variables (plus their interactions over the French territory. These relationships strongly depended on the land use, and more specifically, differed between forest soils and cultivated soil. The total estimate of SOC stocks in France was 3.260 ± 0.872 PgC for the first 30 cm. It was compared to another estimate, based on the previously published European soil organic carbon and bulk density maps, of 5.303 PgC. We demonstrate that the present estimate might better represent the actual SOC stock distributions of France, and consequently that the

  2. CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.

    Directory of Open Access Journals (Sweden)

    Yi-Feng Chang

    Full Text Available CAGO (Comparative Analysis of Genome Organization is developed to address two critical shortcomings of conventional genome atlas plotters: lack of dynamic exploratory functions and absence of signal analysis for genomic properties. With dynamic exploratory functions, users can directly manipulate chromosome tracks of a genome atlas and intuitively identify distinct genomic signals by visual comparison. Signal analysis of genomic properties can further detect inconspicuous patterns from noisy genomic properties and calculate correlations between genomic properties across various genomes. To implement dynamic exploratory functions, CAGO presents each genome atlas in Scalable Vector Graphics (SVG format and allows users to interact with it using a SVG viewer through JavaScript. Signal analysis functions are implemented using R statistical software and a discrete wavelet transformation package waveslim. CAGO is not only a plotter for generating complex genome atlases, but also a platform for exploring genome atlases with dynamic exploratory functions for visual comparison and with signal analysis for comparing genomic properties across multiple organisms. The web-based application of CAGO, its source code, user guides, video demos, and live examples are publicly available and can be accessed at http://cbs.ym.edu.tw/cago.

  3. Speciation in the Derrida-Higgs model with finite genomes and spatial populations

    Science.gov (United States)

    de Aguiar, Marcus A. M.

    2017-02-01

    The speciation model proposed by Derrida and Higgs demonstrated that a sexually reproducing population can split into different species in the absence of natural selection or any type of geographic isolation, provided that mating is assortative and the number of genes involved in the process is infinite. Here we revisit this model and simulate it for finite genomes, focusing on the question of how many genes it actually takes to trigger neutral sympatric speciation. We find that, for typical parameters used in the original model, it takes the order of 105 genes. We compare the results with a similar spatially explicit model where about 100 genes suffice for speciation. We show that when the number of genes is small the species that emerge are strongly segregated in space. For a larger number of genes, on the other hand, the spatial structure of the population is less important and the species distribution overlap considerably.

  4. Genome organization in the nucleus: From dynamic measurements to a functional model.

    Science.gov (United States)

    Vivante, Anat; Brozgol, Eugene; Bronshtein, Irena; Garini, Yuval

    2017-07-01

    A biological system is by definition a dynamic environment encompassing kinetic processes that occur at different length scales and time ranges. To explore this type of system, spatial information needs to be acquired at different time scales. This means overcoming significant hurdles, including the need for stable and precise labeling of the required probes and the use of state of the art optical methods. However, to interpret the acquired data, biophysical models that can account for these biological mechanisms need to be developed. The structure and function of a biological system are closely related to its dynamic properties, thus further emphasizing the importance of identifying the rules governing the dynamics that cannot be directly deduced from information on the structure itself. In eukaryotic cells, tens of thousands of genes are packed in the small volume of the nucleus. The genome itself is organized in chromosomes that occupy specific volumes referred to as chromosome territories. This organization is preserved throughout the cell cycle, even though there are no sub-compartments in the nucleus itself. This organization, which is still not fully understood, is crucial for a large number of cellular functions such as gene regulation, DNA breakage repair and error-free cell division. Various techniques are in use today, including imaging, live cell imaging and molecular methods such as chromosome conformation capture (3C) methods to better understand these mechanisms. Live cell imaging methods are becoming well established. These include methods such as Single Particle Tracking (SPT), Continuous Photobleaching (CP), Fluorescence Recovery After Photobleaching (FRAP) and Fluorescence Correlation Spectroscopy (FCS) that are currently used for studying proteins, RNA, DNA, gene loci and nuclear bodies. They provide crucial information on its mobility, reorganization, interactions and binding properties. Here we describe how these dynamic methods can be used to

  5. Genome organization of the SARS-CoV

    DEFF Research Database (Denmark)

    Xu, Jing; Hu, Jianfei; Wang, Jing

    2003-01-01

    Annotation of the genome sequence of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) is indispensable to understand its evolution and pathogenesis. We have performed a full annotation of the SARS-CoV genome sequences by using annotation programs publicly available or devel......Annotation of the genome sequence of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) is indispensable to understand its evolution and pathogenesis. We have performed a full annotation of the SARS-CoV genome sequences by using annotation programs publicly available...

  6. Spatial organization of astrocytes in ferret visual cortex

    Science.gov (United States)

    López‐Hidalgo, Mónica; Hoover, Walter B.

    2016-01-01

    ABSTRACT Astrocytes form an intricate partnership with neural circuits to influence numerous cellular and synaptic processes. One prominent organizational feature of astrocytes is the “tiling” of the brain with non‐overlapping territories. There are some documented species and brain region–specific astrocyte specializations, but the extent of astrocyte diversity and circuit specificity are still unknown. We quantitatively defined the rules that govern the spatial arrangement of astrocyte somata and territory overlap in ferret visual cortex using a combination of in vivo two‐photon imaging, morphological reconstruction, immunostaining, and model simulations. We found that ferret astrocytes share, on average, half of their territory with other astrocytes. However, a specific class of astrocytes, abundant in thalamo‐recipient cortical layers (“kissing” astrocytes), overlap markedly less. Together, these results demonstrate novel features of astrocyte organization indicating that different classes of astrocytes are arranged in a circuit‐specific manner and that tiling does not apply universally across brain regions and species. J. Comp. Neurol. 524:3561–3576, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc. PMID:27072916

  7. Distinct mechanisms regulate Lck spatial organization in activated T cells

    Directory of Open Access Journals (Sweden)

    Natasha eKapoor-Kaushik

    2016-03-01

    Full Text Available Phosphorylation of the T cell receptor (TCR by the kinase Lck is the first detectable signaling event upon antigen engagement. The distribution of Lck within the plasma membrane, its conformational state, kinase activity and protein interactions all contribute to determine how efficiently Lck phosphorylates the engaged TCR. Here we used cross-correlation raster image spectroscopy (ccRICS and photoactivated localization microscopy (PALM to identify two mechanisms of Lck clustering: an intrinsic mechanism of Lck clustering induced by locking Lck in its open conformation, and an extrinsic mechanism of clustering controlled by the phosphorylation of tyrosine 192, which regulates the affinity of Lck SH2 domain. Both mechanisms of clustering were differently affected by the absence of the kinase Zap70 or the adaptor Lat. We further observed that the adaptor TSAd bound to and promoted the diffusion of Lck when it is phosphorylated on tyrosine 192. Our data suggest that while Lck open conformation drives aggregation and clustering, the spatial organization of Lck is further controlled by signaling events downstream of TCR phosphorylation.

  8. GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.

    Science.gov (United States)

    Yuan, Lina; Yu, Yang; Zhu, Yanmin; Li, Yulai; Li, Changqing; Li, Rujiao; Ma, Qin; Siu, Gilman Kit-Hang; Yu, Jun; Jiang, Taijiao; Xiao, Jingfa; Kang, Yu

    2017-01-25

    Next-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology. Reference-assisted tools are promising in genome assembly, but tend to result in false assembly when the assigned reference has extensive rearrangements. Herein, we present GAAP, a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Framework (cGOF) described in our previous study. Instead of assigning references, we use the multiple-reference-derived cGOFs as indexes to assist in order and orientation of the scaffolds and build a skeleton structure, and then use read pairs to extend scaffolds, called local scaffolding, and distinguish between true and chimeric adjacencies in the scaffolds. In our performance tests using both empirical and simulated data of 15 genomes in six species with diverse genome size, complexity, and all three categories of cGOFs, GAAP outcompetes or achieves comparable results when compared to three other reference-assisted programs, AlignGraph, Ragout and MeDuSa. GAAP uses both cGOF and pair-end reads to create assemblies in genomic scale, and performs better than the currently available reference-assisted assembly tools as it recovers more assemblies and makes fewer false locations, especially for species with extensive rearranged genomes. Our method is a promising solution for reconstruction of genome sequence from short reads of NGS.

  9. Normalization of Complete Genome Characteristics: Application to Evolution from Primitive Organisms to Homo sapiens.

    Science.gov (United States)

    Sorimachi, Kenji; Okayasu, Teiji; Ohhira, Shuji

    2015-04-01

    Normalized nucleotide and amino acid contents of complete genome sequences can be visualized as radar charts. The shapes of these charts depict the characteristics of an organism's genome. The normalized values calculated from the genome sequence theoretically exclude experimental errors. Further, because normalization is independent of both target size and kind, this procedure is applicable not only to single genes but also to whole genomes, which consist of a huge number of different genes. In this review, we discuss the applications of the normalization of the nucleotide and predicted amino acid contents of complete genomes to the investigation of genome structure and to evolutionary research from primitive organisms to Homo sapiens. Some of the results could never have been obtained from the analysis of individual nucleotide or amino acid sequences but were revealed only after the normalization of nucleotide and amino acid contents was applied to genome research. The discovery that genome structure was homogeneous was obtained only after normalization methods were applied to the nucleotide or predicted amino acid contents of genome sequences. Normalization procedures are also applicable to evolutionary research. Thus, normalization of the contents of whole genomes is a useful procedure that can help to characterize organisms.

  10. Global organization of a positive-strand RNA virus genome.

    Directory of Open Access Journals (Sweden)

    Baodong Wu

    Full Text Available The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements in coding regions and functional long-range intra-genomic base pairing interactions. The ∼4.8 kb long RNA genome of the tombusvirus tomato bushy stunt virus (TBSV contains these types of structural features, including six different functional long-distance interactions. We hypothesized that to achieve these multiple interactions this viral genome must utilize a large-scale organizational strategy and, accordingly, we sought to assess the global conformation of the entire TBSV genome. Atomic force micrographs of the genome indicated a mostly condensed structure composed of interconnected protrusions extending from a central hub. This configuration was consistent with the genomic secondary structure model generated using high-throughput selective 2'-hydroxyl acylation analysed by primer extension (i.e. SHAPE, which predicted different sized RNA domains originating from a central region. Known RNA elements were identified in both domain and inter-domain regions, and novel structural features were predicted and functionally confirmed. Interestingly, only two of the six long-range interactions known to form were present in the structural model. However, for those interactions that did not form, complementary partner sequences were positioned relatively close to each other in the structure, suggesting that the secondary structure level of viral genome structure could provide a basic scaffold for the formation of different long-range interactions. The higher-order structural model for the TBSV RNA genome provides a snapshot of the complex framework that allows multiple functional components to operate in concert within a confined context.

  11. The three-dimensional genome organization of Drosophila melanogaster through data integration.

    Science.gov (United States)

    Li, Qingjiao; Tjong, Harianto; Li, Xiao; Gong, Ke; Zhou, Xianghong Jasmine; Chiolo, Irene; Alber, Frank

    2017-07-31

    Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome's organization. It remains a major challenge to integrate such data from various complementary experimental methods. Here, we present an approach for data integration to determine a population of complete three-dimensional genome structures that are statistically consistent with data from both genome-wide chromosome conformation capture (Hi-C) and lamina-DamID experiments. Our structures resolve the genome at the resolution of topological domains, and reproduce simultaneously both sets of experimental data. Importantly, this data deconvolution framework allows for structural heterogeneity between cells, and hence accounts for the expected plasticity of genome structures. As a case study we choose Drosophila melanogaster embryonic cells, for which both data types are available. Our three-dimensional genome structures have strong predictive power for structural features not directly visible in the initial data sets, and reproduce experimental hallmarks of the D. melanogaster genome organization from independent and our own imaging experiments. Also they reveal a number of new insights about genome organization and its functional relevance, including the preferred locations of heterochromatic satellites of different chromosomes, and observations about homologous pairing that cannot be directly observed in the original Hi-C or lamina-DamID data. Our approach allows systematic integration of Hi-C and lamina-DamID data for complete three-dimensional genome structure calculation, while also explicitly considering genome structural variability.

  12. Prostate Cancer Diagnostics and Prognostics Based on Interphase Spatial Genome Positioning

    Science.gov (United States)

    2016-03-01

    in lamin A/C and include Emery-Dreifuss muscular dystrophy (EDMD) and the premature aging disease Hutchison-Gilford progeria syndrome (HGPS) (Burke...P a g e Zhang Y, McCord RP, Ho YJ, Lajoie BR, Hildebrand DG, Simon AC, Becker MS, Alt FW, Dekker J (2012) Spatial organization of the mouse...diseases characterized by mutations in lamin A/C, and includes Emery-Dreifuss 483 muscular dystrophy and the premature aging disease Hutchinson-Gilford

  13. High performance computation of landscape genomic models including local indicators of spatial association.

    Science.gov (United States)

    Stucki, S; Orozco-terWengel, P; Forester, B R; Duruz, S; Colli, L; Masembe, C; Negrini, R; Landguth, E; Jones, M R; Bruford, M W; Taberlet, P; Joost, S

    2017-09-01

    With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics - that is the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental data sets. samβada identifies candidate loci using genotype-environment associations while also incorporating multivariate analyses to assess the effect of many environmental predictor variables. This enables the inclusion of explanatory variables representing population structure into the models to lower the occurrences of spurious genotype-environment associations. In addition, samβada calculates local indicators of spatial association for candidate loci to provide information on whether similar genotypes tend to cluster in space, which constitutes a useful indication of the possible kinship between individuals. To test the usefulness of this approach, we carried out a simulation study and analysed a data set from Ugandan cattle to detect signatures of local adaptation with samβada, bayenv, lfmm and an F ST outlier method (FDIST approach in arlequin) and compare their results. samβada - an open source software for Windows, Linux and Mac OS X available at http://lasig.epfl.ch/sambada - outperforms other approaches and better suits whole-genome sequence data processing. © 2016 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

  14. Functional genomics for food microbiology: Molecular mechanisms of weak organic acid preservative adaptation in yeast

    NARCIS (Netherlands)

    Brul, S.; Kallemeijn, W.; Smits, G.

    2008-01-01

    The recent era of genomics has offered tremendous possibilities to biology. This concise review describes the possibilities of applying (functional) genomics studies to the field of microbial food stability. In doing so, the studies on weak-organic-acid stress response in yeast are discussed by way

  15. Spatial self-organization in a multi-strain host–pathogen system

    International Nuclear Information System (INIS)

    Liu, Quan-Xing; Van de Koppel, Johan; Wang, Rong-Hua; Jin, Zhen; Alonso, David

    2010-01-01

    We develop stochastic spatial epidemic models with the competition of two pathogenic strains. The dynamics resulting from different approaches are examined using both non-spatial and spatially explicit models. Our results show that pair approximation, well-mixed ordinary differential equations (ODEs), Gillespie-algorithm-based simulations and spatially explicit models give similar qualitative results. In particular, the temporal evolution of the spatial model can be successfully approximated by pair equations. Simulation results obtained from the spatially explicit model show that, first, mutation plays a major role in multi-strain coexistence, second, mild virulence remarkably decreases the coexistence domain of the parameter space and, third, large-scale self-organized spatial patterns emerge for a wide range of transmission and virulence parameter values, where spatial self-organized clusters reveal a power law behavior within the coexistence domain

  16. Composition and genomic organization of arthropod Hox clusters.

    Science.gov (United States)

    Pace, Ryan M; Grbić, Miodrag; Nagy, Lisa M

    2016-01-01

    The ancestral arthropod is believed to have had a clustered arrangement of ten Hox genes. Within arthropods, Hox gene mutations result in transformation of segment identities. Despite the fact that variation in segment number/character was common in the diversification of arthropods, few examples of Hox gene gains/losses have been correlated with morphological evolution. Furthermore, a full appreciation of the variation in the genomic arrangement of Hox genes in extant arthropods has not been recognized, as genome sequences from each major arthropod clade have not been reported until recently. Initial genomic analysis of the chelicerate Tetranychus urticae suggested that loss of Hox genes and Hox gene clustering might be more common than previously assumed. To further characterize the genomic evolution of arthropod Hox genes, we compared the genomic arrangement and general characteristics of Hox genes from representative taxa from each arthropod subphylum. In agreement with others, we find arthropods generally contain ten Hox genes arranged in a common orientation in the genome, with an increasing number of sampled species missing either Hox3 or abdominal-A orthologs. The genomic clustering of Hox genes in species we surveyed varies significantly, ranging from 0.3 to 13.6 Mb. In all species sampled, arthropod Hox genes are dispersed in the genome relative to the vertebrate Mus musculus. Differences in Hox cluster size arise from variation in the number of intervening genes, intergenic spacing, and the size of introns and UTRs. In the arthropods surveyed, Hox gene duplications are rare and four microRNAs are, in general, conserved in similar genomic positions relative to the Hox genes. The tightly clustered Hox complexes found in the vertebrates are not evident within arthropods, and differential patterns of Hox gene dispersion are found throughout the arthropods. The comparative genomic data continue to support an ancestral arthropod Hox cluster of ten genes with

  17. Modern approaches of control of spatial organization of schoolchildren body in the process of physical education

    Directory of Open Access Journals (Sweden)

    Bondar O.M.

    2012-08-01

    Full Text Available Technology of control of spatial organization of body of schoolboys is developed. Technology includes the diagnostic, informative and practical stages. Research is oriented to the schoolchildren 7-16 years. The diagnostic stage is supposed by a complex inspection and express control of spatial organization of bodies. The informative stage includes computer treatment of research results. The practical stage consists of development of recommendations on the correction of indexes of spatial organization of body of schoolchildren. Logical component allows to expose the level of knowledge of parents and teachers of physical culture about control of spatial organization of body of schoolchildren. The developed technology allows to carry out timely diagnostics of violations of spatial organization of body of schoolchildren and estimate adequacy of pedagogical influences.

  18. Genomic organization of a vancomycin-resistant staphylococcus aureus

    International Nuclear Information System (INIS)

    Mirani, A.Z.; Jamil, N.

    2013-01-01

    Objective: To study the genomic organization of vancomycin resistance in a local isolate of vancomycin resistant Staphylococcus aureus (VRSA). Study Design: Experimental study. Place and Duration of Study: Department of Microbiology, University of Karachi, January 2008 through December 2010. Methodology: A vancomycin-resistant Staphylococcus aureus (VRSA-CP2) isolate (MIC 16 mu g/ml) was isolated from a local hospital of Karachi. Species identification was confirmed by Gram staining, standard biochemical tests and PCR amplification of the nuc gene. The vancomycin MIC was re-confirmed by E-test. For the genetic determination of vancomycin resistance, in-vitro amplification of vanA cassette was performed by using plasmid DNA of CP2, CP2's transformant as template on MWG Thermo-Cycler. Amplified products of vanR, vanS, vanH, vanA, vanY, orf2, orf1D, orf2E, orf-Rev and IS element genes were subjected to Sanger's electrophoresis based sequence determination using specific primers. The Basic Local Alignment Search Tool (BLAST) algorithm was used to identify sequences in GenBank with similarities to the vanA cassette genes. Results: The vancomycin-resistant isolate CP2 was found to be resistant to oxacillin, chloramphenicol, erythromycin, rifampicin, gentamicin, tetracycline and ciprofloxacin, as well. The isolate CP2 revealed four bands: one of large molecular size approx 56.4 kb and three of small size approx 6.5 kb, approx 6.1 kb and approx 1.5 kb by agarose gel electrophoresis indicating the presence of 3 plasmids. The plasmid DNA of isolate CP2 was analyzed by PCR for the presence of the van cassettes with each of the vanA , vanB and vanC specific primers. It carried vanA cassette, which comprises of vanR, vanS, vanH, vanA, vanY, and orf2. The vanA cassette of isolate CP2 also carried an insertion element (IS). However, it did not show the PCR product for orf1. Vancomycin resistance was successfully transferred from the donor CP2 to a vancomycin-sensitive recipient S

  19. Persistent organic pollutants in the atmosphere - spatial and temporal variations

    Energy Technology Data Exchange (ETDEWEB)

    Backe, Cecilia

    2001-05-01

    In this thesis I have studied the spatial and temporal variations of PCBs in the atmosphere and in precipitation in southern Sweden. Further, soil-air exchange processes of PCBs were investigated. Finally, the long-range transport of PCBs and DDT was studied in the Baltic Sea region and in a tropical vs. a temporal region. On the regional scale there were significant differences in PCB concentration in the atmosphere, in precipitation and in soil between nearby sampling-areas. Differences in PCB concentrations between areas probably originated from varying geographical and meteorological conditions that affected exchange processes between air and soil/vegetation surfaces. Temporal variations in PCB concentration in atmosphere and precipitation were also found. For PCBs in the air, a systematic pattern in the deviation from the yearly median value for the region was observed. Wind direction played an important role for PCB concentration in precipitation in coastal areas, while at the inland sites this variable seemed to have a minor influence. To examine the intensity of precipitation scavenging, the total washout ratios were calculated and the highest ratios were observed at the two sites where PCB concentration in the air was high. Further, high concentrations of PCB in precipitation correlated with a composition of highly chlorinated PCB congeners, as shown by principal component analysis. For most of the sites there was a significant negative relationship between PCB concentration and rain volume. Soil type and soil organic matter content was found to be important for the variations in PCB concentration between nearby areas. Highest concentrations were found at two sites with sandy soils, one with an extremely high organic carbon content. Soils with similar soil textures (i.e. sandy silt moraine) did not show any significant differences in PCB concentrations. PCB congener composition was shown to differ between sites, with site-specific congener patterns. No

  20. From hacking the human genome to editing organs.

    Science.gov (United States)

    Tobita, Takamasa; Guzman-Lepe, Jorge; Collin de l'Hortet, Alexandra

    2015-01-01

    In the recent decades, human genome engineering has been one of the major interesting research subjects, essentially because it raises new possibilities for personalized medicine and biotechnologies. With the development of engineered nucleases such as the Zinc Finger Nucleases (ZFNs), the Transcription activator-like effector nucleases (TALENs) and more recently the Clustered Regularly Interspaced short Palindromic Repeats (CRISPR), the field of human genome edition has evolved very rapidly. Every new genetic tool is broadening the scope of applications on human tissues, even before we can completely master each of these tools. In this review, we will present the recent advances regarding human genome edition tools, we will discuss the numerous implications they have in research and medicine, and we will mention the limits and concerns about such technologies.

  1. Lampreys as Diverse Model Organisms in the Genomics Era.

    Science.gov (United States)

    McCauley, David W; Docker, Margaret F; Whyard, Steve; Li, Weiming

    2015-11-01

    Lampreys, one of the two surviving groups of ancient vertebrates, have become important models for study in diverse fields of biology. Lampreys (of which there are approximately 40 species) are being studied, for example, (a) to control pest sea lamprey in the North American Great Lakes and to restore declining populations of native species elsewhere; (b) in biomedical research, focusing particularly on the regenerative capability of lampreys; and (c) by developmental biologists studying the evolution of key vertebrate characters. Although a lack of genetic resources has hindered research on the mechanisms regulating many aspects of lamprey life history and development, formerly intractable questions are now amenable to investigation following the recent publication of the sea lamprey genome. Here, we provide an overview of the ways in which genomic tools are currently being deployed to tackle diverse research questions and suggest several areas that may benefit from the availability of the sea lamprey genome.

  2. 5 Spatial Distribution of Nematodes at Organic.cdr

    African Journals Online (AJOL)

    user

    in organic crop production fields can favour or inhibit nematode build-up. ... that nematode control strategies employed on the organic field might be less effective than expected. ... Method. Study site. Soil samples were collected from an organic vegetable field and a conventional ..... chemical analysis: a practical handbook.

  3. Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis.

    Science.gov (United States)

    Fu, Jianmin; Liu, Huimin; Hu, Jingjing; Liang, Yuqin; Liang, Jinjun; Wuyun, Tana; Tan, Xiaofeng

    2016-01-01

    Diospyros is the largest genus in Ebenaceae, comprising more than 500 species with remarkable economic value, especially Diospyros kaki Thunb., which has traditionally been an important food resource in China, Korea, and Japan. Complete chloroplast (cp) genomes from D. kaki, D. lotus L., D. oleifera Cheng., D. glaucifolia Metc., and Diospyros 'Jinzaoshi' were sequenced using Illumina sequencing technology. This is the first cp genome reported in Ebenaceae. The cp genome sequences of Diospyros ranged from 157,300 to 157,784 bp in length, presenting a typical quadripartite structure with two inverted repeats each separated by one large and one small single-copy region. For each cp genome, 134 genes were annotated, including 80 protein-coding, 31 tRNA, and 4 rRNA unique genes. In all, 179 repeats and 283 single sequence repeats were identified. Four hypervariable regions, namely, intergenic region of trnQ_rps16, trnV_ndhC, and psbD_trnT, and intron of ndhA, were identified in the Diospyros genomes. Phylogenetic analyses based on the whole cp genome, protein-coding, and intergenic and intron sequences indicated that D. oleifera is closely related to D. kaki and could be used as a model plant for future research on D. kaki; to our knowledge, this is proposed for the first time. Further, these analyses together with two large deletions (301 and 140 bp) in the cp genome of D. 'Jinzaoshi', support its placement as a new species in Diospyros. Both maximum parsimony and likelihood analyses for 19 taxa indicated the basal position of Ericales in asterids and suggested that Ebenaceae is monophyletic in Ericales.

  4. Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis.

    Directory of Open Access Journals (Sweden)

    Jianmin Fu

    Full Text Available Diospyros is the largest genus in Ebenaceae, comprising more than 500 species with remarkable economic value, especially Diospyros kaki Thunb., which has traditionally been an important food resource in China, Korea, and Japan. Complete chloroplast (cp genomes from D. kaki, D. lotus L., D. oleifera Cheng., D. glaucifolia Metc., and Diospyros 'Jinzaoshi' were sequenced using Illumina sequencing technology. This is the first cp genome reported in Ebenaceae. The cp genome sequences of Diospyros ranged from 157,300 to 157,784 bp in length, presenting a typical quadripartite structure with two inverted repeats each separated by one large and one small single-copy region. For each cp genome, 134 genes were annotated, including 80 protein-coding, 31 tRNA, and 4 rRNA unique genes. In all, 179 repeats and 283 single sequence repeats were identified. Four hypervariable regions, namely, intergenic region of trnQ_rps16, trnV_ndhC, and psbD_trnT, and intron of ndhA, were identified in the Diospyros genomes. Phylogenetic analyses based on the whole cp genome, protein-coding, and intergenic and intron sequences indicated that D. oleifera is closely related to D. kaki and could be used as a model plant for future research on D. kaki; to our knowledge, this is proposed for the first time. Further, these analyses together with two large deletions (301 and 140 bp in the cp genome of D. 'Jinzaoshi', support its placement as a new species in Diospyros. Both maximum parsimony and likelihood analyses for 19 taxa indicated the basal position of Ericales in asterids and suggested that Ebenaceae is monophyletic in Ericales.

  5. Is Social Categorization Spatially Organized in a "Mental Line"? Empirical Evidences for Spatial Bias in Intergroup Differentiation.

    Science.gov (United States)

    Presaghi, Fabio; Rullo, Marika

    2018-01-01

    Social categorization is the differentiation between the self and others and between one's own group and other groups and it is such a natural and spontaneous process that often we are not aware of it. The way in which the brain organizes social categorization remains an unresolved issue. We present three experiments investigating the hypothesis that social categories are mentally ordered from left to right on an ingroup-outgroup continuum when membership is salient. To substantiate our hypothesis, we consider empirical evidence from two areas of psychology: research on differences in processing of ingroups and outgroups and research on the effects of spatial biases on processing of quantitative information (e.g., time; numbers) which appears to be arranged from left to right on a small-large continuum, an effect known as the spatial-numerical association of response codes (SNARC). In Experiments 1 and 2 we tested the hypothesis that when membership of a social category is activated, people implicitly locate ingroup categories to the left of a mental line whereas outgroup categories are located on the far right of the same mental line. This spatial organization persists even when stimuli are presented on one of the two sides of the screen and their (explicit) position is spatially incompatible with the implicit mental spatial organization of social categories (Experiment 3). Overall the results indicate that ingroups and outgroups are processed differently. The results are discussed with respect to social categorization theory, spatial agency bias, i.e., the effect observed in Western cultures whereby the agent of an action is mentally represented on the left and the recipient on the right, and the SNARC effect.

  6. Is Social Categorization Spatially Organized in a “Mental Line”? Empirical Evidences for Spatial Bias in Intergroup Differentiation

    Directory of Open Access Journals (Sweden)

    Fabio Presaghi

    2018-02-01

    Full Text Available Social categorization is the differentiation between the self and others and between one’s own group and other groups and it is such a natural and spontaneous process that often we are not aware of it. The way in which the brain organizes social categorization remains an unresolved issue. We present three experiments investigating the hypothesis that social categories are mentally ordered from left to right on an ingroup–outgroup continuum when membership is salient. To substantiate our hypothesis, we consider empirical evidence from two areas of psychology: research on differences in processing of ingroups and outgroups and research on the effects of spatial biases on processing of quantitative information (e.g., time; numbers which appears to be arranged from left to right on a small–large continuum, an effect known as the spatial-numerical association of response codes (SNARC. In Experiments 1 and 2 we tested the hypothesis that when membership of a social category is activated, people implicitly locate ingroup categories to the left of a mental line whereas outgroup categories are located on the far right of the same mental line. This spatial organization persists even when stimuli are presented on one of the two sides of the screen and their (explicit position is spatially incompatible with the implicit mental spatial organization of social categories (Experiment 3. Overall the results indicate that ingroups and outgroups are processed differently. The results are discussed with respect to social categorization theory, spatial agency bias, i.e., the effect observed in Western cultures whereby the agent of an action is mentally represented on the left and the recipient on the right, and the SNARC effect.

  7. Spatial organization of adhesion: force-dependent regulation and function in tissue morphogenesis

    OpenAIRE

    Papusheva, Ekaterina; Heisenberg, Carl-Philipp

    2010-01-01

    The Heisenberg laboratory reviews the spatial organization of signalling complexes at cell–matrix and cell–cell contact sites and its impact on cell integrity, cellular polarity and tissue morphogenesis.

  8. A New Approach to Dissect Nuclear Organization: TALE-Mediated Genome Visualization (TGV).

    Science.gov (United States)

    Miyanari, Yusuke

    2016-01-01

    Spatiotemporal organization of chromatin within the nucleus has so far remained elusive. Live visualization of nuclear remodeling could be a promising approach to understand its functional relevance in genome functions and mechanisms regulating genome architecture. Recent technological advances in live imaging of chromosomes begun to explore the biological roles of the movement of the chromatin within the nucleus. Here I describe a new technique, called TALE-mediated genome visualization (TGV), which allows us to visualize endogenous repetitive sequence including centromeric, pericentromeric, and telomeric repeats in living cells.

  9. Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces

    OpenAIRE

    Tecon, Robin; Or, Dani

    2017-01-01

    Mounting evidence suggests that natural microbial communities exhibit a high level of spatial organization at the micrometric scale that facilitate ecological interactions and support biogeochemical cycles. Microbial patterns are difficult to study definitively in natural environments due to complex biodiversity, observability and variable physicochemical factors. Here, we examine how trophic dependencies give rise to self-organized spatial patterns of a well-defined bacterial consortium grow...

  10. Situated Dialogue and Spatial Organization: What, Where and Why?

    Directory of Open Access Journals (Sweden)

    Henrik I. Christensen

    2008-11-01

    Full Text Available The paper presents an HRI architecture for human-augmented mapping, which has been implemented and tested on an autonomous mobile robotic platform. Through interaction with a human, the robot can augment its autonomously acquired metric map with qualitative information about locations and objects in the environ- ment. The system implements various interaction strategies observed in independently performed Wizard-of-Oz studies. The paper discusses an ontology-based approach to multi-layered conceptual spatial mapping that pro- vides a common ground for human-robot dialogue. This is achieved by combining acquired knowledge with innate conceptual commonsense knowledge in order to infer new knowledge. The architecture bridges the gap between the rich semantic representations of the meaning expressed by verbal utterances on the one hand and the robot?s internal sensor-based world representation on the other. It is thus possible to establish references to spatial areas in a situated dialogue between a human and a robot about their environment. The resulting conceptual descrip- tions represent qualitative knowledge about locations in the environment that can serve as a basis for achieving a notion of situational awareness.

  11. Situated Dialogue and Spatial Organization: What, Where… and Why?

    Directory of Open Access Journals (Sweden)

    Geert-Jan M. Kruijff

    2007-03-01

    Full Text Available The paper presents an HRI architecture for human-augmented mapping, which has been implemented and tested on an autonomous mobile robotic platform. Through interaction with a human, the robot can augment its autonomously acquired metric map with qualitative information about locations and objects in the environment. The system implements various interaction strategies observed in independently performed Wizard-of-Oz studies. The paper discusses an ontology-based approach to multi-layered conceptual spatial mapping that provides a common ground for human-robot dialogue. This is achieved by combining acquired knowledge with innate conceptual commonsense knowledge in order to infer new knowledge. The architecture bridges the gap between the rich semantic representations of the meaning expressed by verbal utterances on the one hand and the robot's internal sensor-based world representation on the other. It is thus possible to establish references to spatial areas in a situated dialogue between a human and a robot about their environment. The resulting conceptual descriptions represent qualitative knowledge about locations in the environment that can serve as a basis for achieving a notion of situational awareness.

  12. Bacillus anthracis genome organization in light of whole transcriptome sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Jeffrey; Zhu, Wenhan; Passalacqua, Karla D.; Bergman, Nicholas; Borodovsky, Mark

    2010-03-22

    Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequence determinants such as quantitative scores of promoters and terminators? Are translation efficiency measures, e.g. codon adaptation index and RBS score related to gene expression? We used the whole transcriptome shotgun sequencing of a bacterial pathogen Bacillus anthracis to assess correlation of gene expression level with promoter, terminator and RBS scores, codon adaptation index, as well as with a new measure of gene translational efficiency, average translation speed. We compared computational predictions of operon topologies with the transcript borders inferred from RNA-Seq reads. Transcriptome mapping may also improve existing gene annotation. Upon assessment of accuracy of current annotation of protein-coding genes in the B. anthracis genome we have shown that the transcriptome data indicate existence of more than a hundred genes missing in the annotation though predicted by an ab initio gene finder. Interestingly, we observed that many pseudogenes possess not only a sequence with detectable coding potential but also promoters that maintain transcriptional activity.

  13. Spatial self-organization and the production of the city

    Directory of Open Access Journals (Sweden)

    Romulo Krafta

    1999-03-01

    Full Text Available Production of urban space is assumed to be a rent seeking activity, carried out by many developers who are constantly trying to get the best possible assessment of market and spatial features in order to better produce profit. Developers act locally, that is, they can choose their locations from all over the city, although they do not have a perfect foresight. Different urban locations prompt different types of development, e. g. several housing, commercial, industrial types, although each location can support more than one type development. The more structured the city is, the narrower is the type choice; on the contrary, in areas scarcely occupied the degree of freedom and unpredictability is larger. Developers compete to each other for locations where the land price is lower; in fact land is considered the single most important component of the development, in the sense that it is the only one whose price can vary and hence affect the price of the final good. Developers "invent" new locations constantly, by buying cheap land, investing on it and selling the resulting built space at higher prices. As soon as a developer discover a new location, others follow, making the land price to rise and the advantage to disappear. The resulting urban development is uneven and generally unpredictable; however, urban areas can be assessed from the point of view of its stability, or its resistance to change. A model has been tried out, as follows.Urban space is disaggregated in units of public space, each one presenting a certain level of urbanisation (infrastructure and built form, what affords a measure of spatial differentiation. Built form is also distinguished by their typological affiliation, so that the stocks are classified according to categories, precisely the ones taken on by developers. Moreover, stocks are also characterised by vintages, so that their actual market value can be updated after each iteration. The urban system is constituted by a

  14. Genome complexity, robustness and genetic interactions in digital organisms

    Science.gov (United States)

    Lenski, Richard E.; Ofria, Charles; Collier, Travis C.; Adami, Christoph

    1999-08-01

    Digital organisms are computer programs that self-replicate, mutate and adapt by natural selection. They offer an opportunity to test generalizations about living systems that may extend beyond the organic life that biologists usually study. Here we have generated two classes of digital organism: simple programs selected solely for rapid replication, and complex programs selected to perform mathematical operations that accelerate replication through a set of defined `metabolic' rewards. To examine the differences in their genetic architecture, we introduced millions of single and multiple mutations into each organism and measured the effects on the organism's fitness. The complex organisms are more robust than the simple ones with respect to the average effects of single mutations. Interactions among mutations are common and usually yield higher fitness than predicted from the component mutations assuming multiplicative effects; such interactions are especially important in the complex organisms. Frequent interactions among mutations have also been seen in bacteria, fungi and fruitflies. Our findings support the view that interactions are a general feature of genetic systems.

  15. Spatial organization in cyclic Lotka-Volterra systems

    International Nuclear Information System (INIS)

    Frachebourg, L.; Krapivsky, P.L.; Ben-Naim, E.

    1996-01-01

    We study the evolution of a system of N interacting species which mimics the dynamics of a cyclic food chain. On a one-dimensional lattice with N α , where α=3/4 (1/2) and 1/3 for N=3 with sequential (parallel) dynamics and N=4, respectively. The domain distribution also exhibits a self-similar spatial structure which is characterized by an additional length scale, left-angle L(t)right-angle ∼t β , with β=1 and 2/3 for N=3 and 4, respectively. For N≥5, the system quickly reaches a frozen state with noninteracting neighboring species. We investigate the time distribution of the number of mutations of a site using scaling arguments as well as an exact solution for N=3. Some relevant extensions are also analyzed. copyright 1996 The American Physical Society

  16. Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics

    Directory of Open Access Journals (Sweden)

    Sze Sing-Hoi

    2005-03-01

    Full Text Available Abstract Background Chemokines and their receptors play important roles in host defense, organogenesis, hematopoiesis, and neuronal communication. Forty-two chemokines and 19 cognate receptors have been found in the human genome. Prior to this report, only 11 chicken chemokines and 7 receptors had been reported. The objectives of this study were to systematically identify chicken chemokines and their cognate receptor genes in the chicken genome and to annotate these genes and ligand-receptor binding by a comparative genomics approach. Results Twenty-three chemokine and 14 chemokine receptor genes were identified in the chicken genome. All of the chicken chemokines contained a conserved CC, CXC, CX3C, or XC motif, whereas all the chemokine receptors had seven conserved transmembrane helices, four extracellular domains with a conserved cysteine, and a conserved DRYLAIV sequence in the second intracellular domain. The number of coding exons in these genes and the syntenies are highly conserved between human, mouse, and chicken although the amino acid sequence homologies are generally low between mammalian and chicken chemokines. Chicken genes were named with the systematic nomenclature used in humans and mice based on phylogeny, synteny, and sequence homology. Conclusion The independent nomenclature of chicken chemokines and chemokine receptors suggests that the chicken may have ligand-receptor pairings similar to mammals. All identified chicken chemokines and their cognate receptors were identified in the chicken genome except CCR9, whose ligand was not identified in this study. The organization of these genes suggests that there were a substantial number of these genes present before divergence between aves and mammals and more gene duplications of CC, CXC, CCR, and CXCR subfamilies in mammals than in aves after the divergence.

  17. cDNA structure, genomic organization and expression patterns of ...

    African Journals Online (AJOL)

    use

    2011-11-23

    Nov 23, 2011 ... adenine dinucleotide (NAD) intermediate (Rongvaux et al., 2002). Thereupon ... in house mouse, Norway rat and human. It was not difficult to ... species in freshwater regions, and has been a new model organism in aquatic ...

  18. Spatial variation in the parasite communities and genomic structure of urban rats in New York City.

    Science.gov (United States)

    Angley, L P; Combs, M; Firth, C; Frye, M J; Lipkin, I; Richardson, J L; Munshi-South, J

    2018-02-01

    Brown rats (Rattus norvegicus) are a globally distributed pest. Urban habitats can support large infestations of rats, posing a potential risk to public health from the parasites and pathogens they carry. Despite the potential influence of rodent-borne zoonotic diseases on human health, it is unclear how urban habitats affect the structure and transmission dynamics of ectoparasite and microbial communities (all referred to as "parasites" hereafter) among rat colonies. In this study, we use ecological data on parasites and genomic sequencing of their rat hosts to examine associations between spatial proximity, genetic relatedness and the parasite communities associated with 133 rats at five sites in sections of New York City with persistent rat infestations. We build on previous work showing that rats in New York carry a wide variety of parasites and report that these communities differ significantly among sites, even across small geographical distances. Ectoparasite community similarity was positively associated with geographical proximity; however, there was no general association between distance and microbial communities of rats. Sites with greater overall parasite diversity also had rats with greater infection levels and parasite species richness. Parasite community similarity among sites was not linked to genetic relatedness of rats, suggesting that these communities are not associated with genetic similarity among host individuals or host dispersal among sites. Discriminant analysis identified site-specific associations of several parasite species, suggesting that the presence of some species within parasite communities may allow researchers to determine the sites of origin for newly sampled rats. The results of our study help clarify the roles that colony structure and geographical proximity play in determining the ecology of R. norvegicus as a significant urban reservoir of zoonotic diseases. Our study also highlights the spatial variation present in urban

  19. The complete nucleotide sequence, genome organization, and origin of human adenovirus type 11

    International Nuclear Information System (INIS)

    Stone, Daniel; Furthmann, Anne; Sandig, Volker; Lieber, Andre

    2003-01-01

    The complete DNA sequence and transcription map of human adenovirus type 11 are reported here. This is the first published sequence for a subgenera B human adenovirus and demonstrates a genome organization highly similar to those of other human adenoviruses. All of the genes from the early, intermediate, and late regions are present in the expected locations of the genome for a human adenovirus. The genome size is 34,794 bp in length and has a GC content of 48.9%. Sequence alignment with genomes of groups A (Ad12), C (Ad5), D (Ad17), E (Simian adenovirus 25), and F (Ad40) revealed homologies of 64, 54, 68, 75, and 52%, respectively. Detailed genomic analysis demonstrated that Ads 11 and 35 are highly conserved in all areas except the hexon hypervariable regions and fiber. Similarly, comparison of Ad11 with subgroup E SAV25 revealed poor homology between fibers but high homology in proteins encoded by all other areas of the genome. We propose an evolutionary model in which functional viruses can be reconstituted following fiber substitution from one serotype to another. According to this model either the Ad11 genome is a derivative of Ad35, from which the fiber was substituted with Ad7, or the Ad35 genome is the product of a fiber substitution from Ad21 into the Ad11 genome. This model also provides a possible explanation for the origin of group E Ads, which are evolutionarily derived from a group C fiber substitution into a group B genome

  20. Regulation and spatial organization of PCNA in Trypanosoma brucei

    International Nuclear Information System (INIS)

    Kaufmann, Doris; Gassen, Alwine; Maiser, Andreas; Leonhardt, Heinrich; Janzen, Christian J.

    2012-01-01

    Highlights: ► Characterization of the proliferating cell nuclear antigen in Trypanosoma brucei (TbPCNA). ► TbPCNA is a suitable marker to detect replication in T. brucei. ► TbPCNA distribution and regulation is different compared to closely related parasites T. cruzi and Leishmania donovani. -- Abstract: As in most eukaryotic cells, replication is regulated by a conserved group of proteins in the early-diverged parasite Trypanosoma brucei. Only a few components of the replication machinery have been described in this parasite and regulation, sub-nuclear localization and timing of replication are not well understood. We characterized the proliferating cell nuclear antigen in T. brucei (TbPCNA) to establish a spatial and temporal marker for replication. Interestingly, PCNA distribution and regulation is different compared to the closely related parasites Trypanosoma cruzi and Leishmania donovani. TbPCNA foci are clearly detectable during S phase of the cell cycle but in contrast to T. cruzi they are not preferentially located at the nuclear periphery. Furthermore, PCNA seems to be degraded when cells enter G2 phase in T. brucei suggesting different modes of replication regulation or functions of PCNA in these closely related eukaryotes.

  1. Recombination Proteins Mediate Meiotic Spatial Chromosome Organization and Pairing

    Science.gov (United States)

    Storlazzi, Aurora; Gargano, Silvana; Ruprich-Robert, Gwenael; Falque, Matthieu; David, Michelle; Kleckner, Nancy; Zickler, Denise

    2010-01-01

    SUMMARY Meiotic chromosome pairing involves not only recognition of homology but also juxtaposition of entire chromosomes in a topologically regular way. Analysis of filamentous fungus Sordaria macrospora reveals that recombination proteins Mer3, Msh4 and Mlh1 play direct roles in all of these aspects, in advance of their known roles in recombination. Absence of Mer3 helicase results in interwoven chromosomes, thereby revealing the existence of features that specifically ensure “entanglement avoidance”. Entanglements that remain at zygotene, i.e. “interlockings”, require Mlh1 for resolution, likely to eliminate constraining recombinational connections. Patterns of Mer3 and Msh4 foci along aligned chromosomes show that the double-strand breaks mediating homologous alignment have spatially separated ends, one localized to each partner axis, and that pairing involves interference among developing interhomolog interactions. We propose that Mer3, Msh4 and Mlh1 execute all of these roles during pairing by modulating the state of nascent double-strand break/partner DNA contacts within axis-associated recombination complexes. PMID:20371348

  2. Regulation and spatial organization of PCNA in Trypanosoma brucei

    Energy Technology Data Exchange (ETDEWEB)

    Kaufmann, Doris; Gassen, Alwine [University of Munich (LMU), Department Biology I, Genetics, Grosshaderner Str. 2-4, 82152 Martinsried (Germany); Maiser, Andreas; Leonhardt, Heinrich [University of Munich (LMU), Department Biology II, Grosshaderner Str. 2-4, 82152 Martinsried (Germany); Janzen, Christian J., E-mail: christian.janzen@uni-wuerzburg.de [University of Munich (LMU), Department Biology I, Genetics, Grosshaderner Str. 2-4, 82152 Martinsried (Germany)

    2012-03-23

    Highlights: Black-Right-Pointing-Pointer Characterization of the proliferating cell nuclear antigen in Trypanosoma brucei (TbPCNA). Black-Right-Pointing-Pointer TbPCNA is a suitable marker to detect replication in T. brucei. Black-Right-Pointing-Pointer TbPCNA distribution and regulation is different compared to closely related parasites T. cruzi and Leishmania donovani. -- Abstract: As in most eukaryotic cells, replication is regulated by a conserved group of proteins in the early-diverged parasite Trypanosoma brucei. Only a few components of the replication machinery have been described in this parasite and regulation, sub-nuclear localization and timing of replication are not well understood. We characterized the proliferating cell nuclear antigen in T. brucei (TbPCNA) to establish a spatial and temporal marker for replication. Interestingly, PCNA distribution and regulation is different compared to the closely related parasites Trypanosoma cruzi and Leishmania donovani. TbPCNA foci are clearly detectable during S phase of the cell cycle but in contrast to T. cruzi they are not preferentially located at the nuclear periphery. Furthermore, PCNA seems to be degraded when cells enter G2 phase in T. brucei suggesting different modes of replication regulation or functions of PCNA in these closely related eukaryotes.

  3. Spatial and dynamic organization of molecular structures in the cell nucleus

    NARCIS (Netherlands)

    Brouwer, Anne-Kee

    2010-01-01

    In this thesis we attempt to provide a better understanding of the principles that underlie the spatial dynamic organization of the cell nucleus. Chapter 1 reviews the current status of knowledge about the structural and functional organization of the cell nucleus. In chapter 2, the development of a

  4. Characterizing Spatial Organization of Cell Surface Receptors in Human Breast Cancer with STORM

    Science.gov (United States)

    Lyall, Evan; Chapman, Matthew R.; Sohn, Lydia L.

    2012-02-01

    Regulation and control of complex biological functions are dependent upon spatial organization of biological structures at many different length scales. For instance Eph receptors and their ephrin ligands bind when opposing cells come into contact during development, resulting in spatial organizational changes on the nanometer scale that lead to changes on the macro scale, in a process known as organ morphogenesis. One technique able to probe this important spatial organization at both the nanometer and micrometer length scales, including at cell-cell junctions, is stochastic optical reconstruction microscopy (STORM). STORM is a technique that localizes individual fluorophores based on the centroids of their point spread functions and then reconstructs a composite image to produce super resolved structure. We have applied STORM to study spatial organization of the cell surface of human breast cancer cells, specifically the organization of tyrosine kinase receptors and chemokine receptors. A better characterization of spatial organization of breast cancer cell surface proteins is necessary to fully understand the tumorigenisis pathways in the most common malignancy in United States women.

  5. The integration of signalling and the spatial organization of the T cell synapse

    Directory of Open Access Journals (Sweden)

    Jeremie eRossy

    2012-11-01

    Full Text Available Engagement of the T cell antigen receptor (TCR triggers signalling pathways that lead to T cell selection, differentiation and clonal expansion. Superimposed onto the biochemical network is a spatial organization that describes individual receptor molecules, dimers, oligomers and higher order structures. Here we review recent finding about TCR organization in naïve and memory T cells. A key question that has emerged is how antigen-TCR interactions encode spatial information to direct T cell activation and differentiation. Single molecule super-resolution microscopy may become an important tool in decoding receptor organization at the molecular level.

  6. Genomic organization of the canine herpesvirus US region.

    Science.gov (United States)

    Haanes, E J; Tomlinson, C C

    1998-02-01

    Canine herpesvirus (CHV) is an alpha-herpesvirus of limited pathogenicity in healthy adult dogs and infectivity of the virus appears to be largely limited to cells of canine origin. CHV's low virulence and species specificity make it an attractive candidate for a recombinant vaccine vector to protect dogs against a variety of pathogens. As part of the analysis of the CHV genome, the authors determined the complete nucleotide sequence of the CHV US region as well as portions of the flanking inverted repeats. Seven full open reading frames (ORFs) encoding proteins larger than 100 amino acids were identified within, or partially within the CHV US: cUS2, cUS3, cUS4, cUS6, cUS7, cUS8 and cUS9; which are homologs of the herpes simplex virus type-1 US2; protein kinase; gG, gD, gI, gE; and US9 genes, respectively. An eighth ORF was identified in the inverted repeat region, cIR6, a homolog of the equine herpesvirus type-1 IR6 gene. The authors identified and mapped most of the major transcripts for the predicted CHV US ORFs by Northern analysis.

  7. LEMONS - A Tool for the Identification of Splice Junctions in Transcriptomes of Organisms Lacking Reference Genomes.

    Directory of Open Access Journals (Sweden)

    Liron Levin

    Full Text Available RNA-seq is becoming a preferred tool for genomics studies of model and non-model organisms. However, DNA-based analysis of organisms lacking sequenced genomes cannot rely on RNA-seq data alone to isolate most genes of interest, as DNA codes both exons and introns. With this in mind, we designed a novel tool, LEMONS, that exploits the evolutionary conservation of both exon/intron boundary positions and splice junction recognition signals to produce high throughput splice-junction predictions in the absence of a reference genome. When tested on multiple annotated vertebrate mRNA data, LEMONS accurately identified 87% (average of the splice-junctions. LEMONS was then applied to our updated Mediterranean chameleon transcriptome, which lacks a reference genome, and predicted a total of 90,820 exon-exon junctions. We experimentally verified these splice-junction predictions by amplifying and sequencing twenty randomly selected genes from chameleon DNA templates. Exons and introns were detected in 19 of 20 of the positions predicted by LEMONS. To the best of our knowledge, LEMONS is currently the only experimentally verified tool that can accurately predict splice-junctions in organisms that lack a reference genome.

  8. Organization of plastid genomes in the freshwater red algal order Batrachospermales (Rhodophyta).

    Science.gov (United States)

    Paiano, Monica Orlandi; Del Cortona, Andrea; Costa, Joana F; Liu, Shao-Lun; Verbruggen, Heroen; De Clerck, Olivier; Necchi, Orlando

    2018-02-01

    Little is known about genome organization in members of the order Batrachospermales, and the infra-ordinal relationship remains unresolved. Plastid (cp) genomes of seven members of the freshwater red algal order Batrachospermales were sequenced, with the following aims: (i) to describe the characteristics of cp genomes and compare these with other red algal groups; (ii) to infer the phylogenetic relationships among these members to better understand the infra-ordinal classification. Cp genomes of Batrachospermales are large, with several cases of gene loss, they are gene-dense (high gene content for the genome size and short intergenic regions) and have highly conserved gene order. Phylogenetic analyses based on concatenated nucleotide genome data roughly supports the current taxonomic system for the order. Comparative analyses confirm data for members of the class Florideophyceae that cp genomes in Batrachospermales is highly conserved, with little variation in gene composition. However, relevant new features were revealed in our study: genome sizes in members of Batrachospermales are close to the lowest values reported for Florideophyceae; differences in cp genome size within the order are large in comparison with other orders (Ceramiales, Gelidiales, Gracilariales, Hildenbrandiales, and Nemaliales); and members of Batrachospermales have the lowest number of protein-coding genes among the Florideophyceae. In terms of gene loss, apcF, which encodes the allophycocyanin beta subunit, is absent in all sequenced taxa of Batrachospermales. We reinforce that the interordinal relationships between the freshwater orders Batrachospermales and Thoreales within the Nemaliophycidae is not well resolved due to limited taxon sampling. © 2017 Phycological Society of America.

  9. Genomics dataset on unclassified published organism (patent US 7547531

    Directory of Open Access Journals (Sweden)

    Mohammad Mahfuz Ali Khan Shawan

    2016-12-01

    Full Text Available Nucleotide (DNA sequence analysis provides important clues regarding the characteristics and taxonomic position of an organism. With the intention that, DNA sequence analysis is very crucial to learn about hierarchical classification of that particular organism. This dataset (patent US 7547531 is chosen to simplify all the complex raw data buried in undisclosed DNA sequences which help to open doors for new collaborations. In this data, a total of 48 unidentified DNA sequences from patent US 7547531 were selected and their complete sequences were retrieved from NCBI BioSample database. Quick response (QR code of those DNA sequences was constructed by DNA BarID tool. QR code is useful for the identification and comparison of isolates with other organisms. AT/GC content of the DNA sequences was determined using ENDMEMO GC Content Calculator, which indicates their stability at different temperature. The highest GC content was observed in GP445188 (62.5% which was followed by GP445198 (61.8% and GP445189 (59.44%, while lowest was in GP445178 (24.39%. In addition, New England BioLabs (NEB database was used to identify cleavage code indicating the 5, 3 and blunt end and enzyme code indicating the methylation site of the DNA sequences was also shown. These data will be helpful for the construction of the organisms’ hierarchical classification, determination of their phylogenetic and taxonomic position and revelation of their molecular characteristics.

  10. Draft Genome Sequence of the Model Naphthalene-Utilizing Organism Pseudomonas putida OUS82

    DEFF Research Database (Denmark)

    Tay, Martin; Roizman, Dan; Cohen, Yehuda

    2014-01-01

    Pseudomonas putida OUS82 was isolated from petrol- and oil-contaminated soil in 1992, and ever since, it has been used as a model organism to study the microbial assimilation of naphthalene and phenanthrene. Here, we report the 6.7-Mb draft genome sequence of P. putida OUS82 and analyze its...

  11. Spatial Patterns of Soil Organic Carbon in the United States

    Science.gov (United States)

    Bliss, N. B.

    2005-12-01

    The Department of the Interior (DOI) has jurisdiction influencing approximately 22 percent of the land area of the United States. The poster presents estimates of the current stocks of soil organic carbon (SOC) on all lands and Federal lands. The DOI lands have about 22 percent of the nation's SOC, so the average carbon intensity (8.66 kg C m-2) about matches the average for all lands (8.81 kg C m-2). However the carbon on DOI lands is not evenly distributed. Of the 17.76 Petagrams (1 Pg = 1015 grams) of SOC on DOI lands, 13.07 Pg (74 percent) are in Alaska, and 4.69 Pg (26 percent) are in the Conterminous U.S. The Alaska soils are wetter and colder than the national average, and the DOI lands in the conterminous U.S. are warmer and drier than the average. A set of SOC maps is shown, developed by intersecting the State Soil Geographic (STATSGO) database with data on federal lands from the National Atlas. With 22 percent of the nation's soil carbon, the DOI lands are important in a national accounting of greenhouse gas emission and sequestration. Future behavior of these lands is uncertain, but in scenarios of warming or drying, carbon released by respiration may exceed carbon captured by photosynthesis, resulting in a net release of carbon to the atmosphere. If warming stimulates a net release of greenhouse gases, this represents a positive feedback contributing to future global warming, a very unstable condition for the global climate system.

  12. DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms.

    Science.gov (United States)

    Panova, Marina; Aronsson, Henrik; Cameron, R Andrew; Dahl, Peter; Godhe, Anna; Lind, Ulrika; Ortega-Martinez, Olga; Pereyra, Ricardo; Tesson, Sylvie V M; Wrange, Anna-Lisa; Blomberg, Anders; Johannesson, Kerstin

    2016-01-01

    The marine environment harbors a large proportion of the total biodiversity on this planet, including the majority of the earths' different phyla and classes. Studying the genomes of marine organisms can bring interesting insights into genome evolution. Today, almost all marine organismal groups are understudied with respect to their genomes. One potential reason is that extraction of high-quality DNA in sufficient amounts is challenging for many marine species. This is due to high polysaccharide content, polyphenols and other secondary metabolites that will inhibit downstream DNA library preparations. Consequently, protocols developed for vertebrates and plants do not always perform well for invertebrates and algae. In addition, many marine species have large population sizes and, as a consequence, highly variable genomes. Thus, to facilitate the sequence read assembly process during genome sequencing, it is desirable to obtain enough DNA from a single individual, which is a challenge in many species of invertebrates and algae. Here, we present DNA extraction protocols for seven marine species (four invertebrates, two algae, and a marine yeast), optimized to provide sufficient DNA quality and yield for de novo genome sequencing projects.

  13. Single-cell Hi-C bridges microscopy and genome-wide sequencing approaches to study 3D chromatin organization.

    Science.gov (United States)

    Ulianov, Sergey V; Tachibana-Konwalski, Kikue; Razin, Sergey V

    2017-10-01

    Recent years have witnessed an explosion of the single-cell biochemical toolbox including chromosome conformation capture (3C)-based methods that provide novel insights into chromatin spatial organization in individual cells. The observations made with these techniques revealed that topologically associating domains emerge from cell population averages and do not exist as static structures in individual cells. Stochastic nature of the genome folding is likely to be biologically relevant and may reflect the ability of chromatin fibers to adopt a number of alternative configurations, some of which could be transiently stabilized and serve regulatory purposes. Single-cell Hi-C approaches provide an opportunity to analyze chromatin folding in rare cell types such as stem cells, tumor progenitors, oocytes, and totipotent cells, contributing to a deeper understanding of basic mechanisms in development and disease. Here, we review key findings of single-cell Hi-C and discuss possible biological reasons and consequences of the inferred dynamic chromatin spatial organization. © 2017 WILEY Periodicals, Inc.

  14. Molecular analysis and genomic organization of major DNA satellites in banana (Musa spp.).

    Science.gov (United States)

    Čížková, Jana; Hřibová, Eva; Humplíková, Lenka; Christelová, Pavla; Suchánková, Pavla; Doležel, Jaroslav

    2013-01-01

    Satellite DNA sequences consist of tandemly arranged repetitive units up to thousands nucleotides long in head-to-tail orientation. The evolutionary processes by which satellites arise and evolve include unequal crossing over, gene conversion, transposition and extra chromosomal circular DNA formation. Large blocks of satellite DNA are often observed in heterochromatic regions of chromosomes and are a typical component of centromeric and telomeric regions. Satellite-rich loci may show specific banding patterns and facilitate chromosome identification and analysis of structural chromosome changes. Unlike many other genomes, nuclear genomes of banana (Musa spp.) are poor in satellite DNA and the information on this class of DNA remains limited. The banana cultivars are seed sterile clones originating mostly from natural intra-specific crosses within M. acuminata (A genome) and inter-specific crosses between M. acuminata and M. balbisiana (B genome). Previous studies revealed the closely related nature of the A and B genomes, including similarities in repetitive DNA. In this study we focused on two main banana DNA satellites, which were previously identified in silico. Their genomic organization and molecular diversity was analyzed in a set of nineteen Musa accessions, including representatives of A, B and S (M. schizocarpa) genomes and their inter-specific hybrids. The two DNA satellites showed a high level of sequence conservation within, and a high homology between Musa species. FISH with probes for the satellite DNA sequences, rRNA genes and a single-copy BAC clone 2G17 resulted in characteristic chromosome banding patterns in M. acuminata and M. balbisiana which may aid in determining genomic constitution in interspecific hybrids. In addition to improving the knowledge on Musa satellite DNA, our study increases the number of cytogenetic markers and the number of individual chromosomes, which can be identified in Musa.

  15. Salmonella strains isolated from Galápagos iguanas show spatial structuring of serovar and genomic diversity.

    Directory of Open Access Journals (Sweden)

    Emily W Lankau

    Full Text Available It is thought that dispersal limitation primarily structures host-associated bacterial populations because host distributions inherently limit transmission opportunities. However, enteric bacteria may disperse great distances during food-borne outbreaks. It is unclear if such rapid long-distance dispersal events happen regularly in natural systems or if these events represent an anthropogenic exception. We characterized Salmonella enterica isolates from the feces of free-living Galápagos land and marine iguanas from five sites on four islands using serotyping and genomic fingerprinting. Each site hosted unique and nearly exclusive serovar assemblages. Genomic fingerprint analysis offered a more complex model of S. enterica biogeography, with evidence of both unique strain pools and of spatial population structuring along a geographic gradient. These findings suggest that even relatively generalist enteric bacteria may be strongly dispersal limited in a natural system with strong barriers, such as oceanic divides. Yet, these differing results seen on two typing methods also suggests that genomic variation is less dispersal limited, allowing for different ecological processes to shape biogeographical patterns of the core and flexible portions of this bacterial species' genome.

  16. Salmonella strains isolated from Galápagos iguanas show spatial structuring of serovar and genomic diversity.

    Science.gov (United States)

    Lankau, Emily W; Cruz Bedon, Lenin; Mackie, Roderick I

    2012-01-01

    It is thought that dispersal limitation primarily structures host-associated bacterial populations because host distributions inherently limit transmission opportunities. However, enteric bacteria may disperse great distances during food-borne outbreaks. It is unclear if such rapid long-distance dispersal events happen regularly in natural systems or if these events represent an anthropogenic exception. We characterized Salmonella enterica isolates from the feces of free-living Galápagos land and marine iguanas from five sites on four islands using serotyping and genomic fingerprinting. Each site hosted unique and nearly exclusive serovar assemblages. Genomic fingerprint analysis offered a more complex model of S. enterica biogeography, with evidence of both unique strain pools and of spatial population structuring along a geographic gradient. These findings suggest that even relatively generalist enteric bacteria may be strongly dispersal limited in a natural system with strong barriers, such as oceanic divides. Yet, these differing results seen on two typing methods also suggests that genomic variation is less dispersal limited, allowing for different ecological processes to shape biogeographical patterns of the core and flexible portions of this bacterial species' genome.

  17. Salmonella Strains Isolated from Galápagos Iguanas Show Spatial Structuring of Serovar and Genomic Diversity

    Science.gov (United States)

    Lankau, Emily W.; Cruz Bedon, Lenin; Mackie, Roderick I.

    2012-01-01

    It is thought that dispersal limitation primarily structures host-associated bacterial populations because host distributions inherently limit transmission opportunities. However, enteric bacteria may disperse great distances during food-borne outbreaks. It is unclear if such rapid long-distance dispersal events happen regularly in natural systems or if these events represent an anthropogenic exception. We characterized Salmonella enterica isolates from the feces of free-living Galápagos land and marine iguanas from five sites on four islands using serotyping and genomic fingerprinting. Each site hosted unique and nearly exclusive serovar assemblages. Genomic fingerprint analysis offered a more complex model of S. enterica biogeography, with evidence of both unique strain pools and of spatial population structuring along a geographic gradient. These findings suggest that even relatively generalist enteric bacteria may be strongly dispersal limited in a natural system with strong barriers, such as oceanic divides. Yet, these differing results seen on two typing methods also suggests that genomic variation is less dispersal limited, allowing for different ecological processes to shape biogeographical patterns of the core and flexible portions of this bacterial species' genome. PMID:22615968

  18. Genomic sequence and organization of two members of a human lectin gene family

    International Nuclear Information System (INIS)

    Gitt, M.A.; Barondes, S.H.

    1991-01-01

    The authors have isolated and sequenced the genomic DNA encoding a human dimeric soluble lactose-binding lectin. The gene has four exons, and its upstream region contains sequences that suggest control by glucocorticoids, heat (environmental) shock, metals, and other factors. They have also isolated and sequenced three exons of the gene encoding another human putative lectin, the existence of which was first indicated by isolation of its cDNA. Comparisons suggest a general pattern of genomic organization of members of this lectin gene family

  19. Impact of nuclear organization and chromatin structure on DNA repair and genome stability

    International Nuclear Information System (INIS)

    Batte, Amandine

    2016-01-01

    The non-random organization of the eukaryotic cell nucleus and the folding of genome in chromatin more or less condensed can influence many functions related to DNA metabolism, including genome stability. Double-strand breaks (DSBs) are the most deleterious DNA damages for the cells. To preserve genome integrity, eukaryotic cells thus developed DSB repair mechanisms conserved from yeast to human, among which homologous recombination (HR) that uses an intact homologous sequence to repair a broken chromosome. HR can be separated in two sub-pathways: Gene Conversion (GC) transfers genetic information from one molecule to its homologous and Break Induced Replication (BIR) establishes a replication fork than can proceed until the chromosome end. My doctorate work was focused on the contribution of the chromatin context and 3D genome organization on DSB repair. In S. cerevisiae, nuclear organization and heterochromatin spreading at sub-telomeres can be modified through the overexpression of the Sir3 or sir3A2Q mutant proteins. We demonstrated that reducing the physical distance between homologous sequences increased GC rates, reinforcing the notion that homology search is a limiting step for recombination. We also showed that hetero-chromatinization of DSB site fine-tunes DSB resection, limiting the loss of the DSB ends required to perform homology search and complete HR. Finally, we noticed that the presence of heterochromatin at the donor locus decreased both GC and BIR efficiencies, probably by affecting strand invasion. This work highlights new regulatory pathways of DNA repair. (author) [fr

  20. Novel probabilistic models of spatial genetic ancestry with applications to stratification correction in genome-wide association studies.

    Science.gov (United States)

    Bhaskar, Anand; Javanmard, Adel; Courtade, Thomas A; Tse, David

    2017-03-15

    Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns. Spatial population structure in genetic datasets has been traditionally analyzed using either model-free algorithms, such as principal components analysis (PCA) and multidimensional scaling, or using explicit spatial probabilistic models of allele frequency evolution. We develop a general probabilistic model and an associated inference algorithm that unify the model-based and data-driven approaches to visualizing and inferring population structure. Our spatial inference algorithm can also be effectively applied to the problem of population stratification in genome-wide association studies (GWAS), where hidden population structure can create fictitious associations when population ancestry is correlated with both the genotype and the trait. Our algorithm Geographic Ancestry Positioning (GAP) relates local genetic distances between samples to their spatial distances, and can be used for visually discerning population structure as well as accurately inferring the spatial origin of individuals on a two-dimensional continuum. On both simulated and several real datasets from diverse human populations, GAP exhibits substantially lower error in reconstructing spatial ancestry coordinates compared to PCA. We also develop an association test that uses the ancestry coordinates inferred by GAP to accurately account for ancestry-induced correlations in GWAS. Based on simulations and analysis of a dataset of 10 metabolic traits measured in a Northern Finland cohort, which is known to exhibit significant population structure, we find that our method has superior power to current approaches. Our software is available at https://github.com/anand-bhaskar/gap . abhaskar@stanford.edu or ajavanma@usc.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved

  1. Occupancy of chromatin organizers in the Epstein-Barr virus genome.

    Science.gov (United States)

    Holdorf, Meghan M; Cooper, Samantha B; Yamamoto, Keith R; Miranda, J J L

    2011-06-20

    The human CCCTC-binding factor, CTCF, regulates transcription of the double-stranded DNA genomes of herpesviruses. The architectural complex cohesin and RNA Polymerase II also contribute to this organization. We profiled the occupancy of CTCF, cohesin, and RNA Polymerase II on the episomal genome of the Epstein-Barr virus in a cell culture model of latent infection. CTCF colocalizes with cohesin but not RNA Polymerase II. CTCF and cohesin bind specific sequences throughout the genome that are found not just proximal to the regulatory elements of latent genes, but also near lytic genes. In addition to tracking with known transcripts, RNA Polymerase II appears at two unannotated positions, one of which lies within the latent origin of replication. The widespread occupancy profile of each protein reveals binding near or at a myriad of regulatory elements and suggests context-dependent functions. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. Spatial organization of frequency preference and selectivity in the human inferior colliculus

    OpenAIRE

    De Martino, Federico; Moerel, Michelle; van de Moortele, Pierre-Francois; Ugurbil, Kamil; Goebel, Rainer; Yacoub, Essa; Formisano, Elia

    2013-01-01

    To date, the functional organization of human auditory sub-cortical structures can only be inferred from animal models. Here we use high-resolution functional MRI at ultra-high magnetic fields (7 Tesla) to map the organization of spectral responses in the human inferior colliculus (hIC), a sub-cortical structure fundamental for sound processing. We reveal a tonotopic map with a spatial gradient of preferred frequencies approximately oriented from dorso-lateral (low frequencies) to ventro-medi...

  3. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  4. Integrated genomics and proteomics of the Torpedo californica electric organ: concordance with the mammalian neuromuscular junction

    Directory of Open Access Journals (Sweden)

    Mate Suzanne E

    2011-05-01

    Full Text Available Abstract Background During development, the branchial mesoderm of Torpedo californica transdifferentiates into an electric organ capable of generating high voltage discharges to stun fish. The organ contains a high density of cholinergic synapses and has served as a biochemical model for the membrane specialization of myofibers, the neuromuscular junction (NMJ. We studied the genome and proteome of the electric organ to gain insight into its composition, to determine if there is concordance with skeletal muscle and the NMJ, and to identify novel synaptic proteins. Results Of 435 proteins identified, 300 mapped to Torpedo cDNA sequences with ≥2 peptides. We identified 14 uncharacterized proteins in the electric organ that are known to play a role in acetylcholine receptor clustering or signal transduction. In addition, two human open reading frames, C1orf123 and C6orf130, showed high sequence similarity to electric organ proteins. Our profile lists several proteins that are highly expressed in skeletal muscle or are muscle specific. Synaptic proteins such as acetylcholinesterase, acetylcholine receptor subunits, and rapsyn were present in the electric organ proteome but absent in the skeletal muscle proteome. Conclusions Our integrated genomic and proteomic analysis supports research describing a muscle-like profile of the organ. We show that it is a repository of NMJ proteins but we present limitations on its use as a comprehensive model of the NMJ. Finally, we identified several proteins that may become candidates for signaling proteins not previously characterized as components of the NMJ.

  5. Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data.

    Directory of Open Access Journals (Sweden)

    Can Alkan

    2007-09-01

    Full Text Available The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%-5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution.

  6. Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data.

    Science.gov (United States)

    Alkan, Can; Ventura, Mario; Archidiacono, Nicoletta; Rocchi, Mariano; Sahinalp, S Cenk; Eichler, Evan E

    2007-09-01

    The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%-5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution.

  7. Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.

    Science.gov (United States)

    Pingault, Lise; Choulet, Frédéric; Alberti, Adriana; Glover, Natasha; Wincker, Patrick; Feuillet, Catherine; Paux, Etienne

    2015-02-10

    Because of its size, allohexaploid nature, and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function, and regulation. However, because of the lack of a reference genome sequence, such studies have long been hampered and our knowledge of the wheat gene space is still limited. The access to the reference sequence of the wheat chromosome 3B provided us with an opportunity to study the wheat transcriptome and its relationships to genome and gene structure at a level that has never been reached before. By combining this sequence with RNA-seq data, we construct a fine transcriptome map of the chromosome 3B. More than 8,800 transcription sites are identified, that are distributed throughout the entire chromosome. Expression level, expression breadth, alternative splicing as well as several structural features of genes, including transcript length, number of exons, and cumulative intron length are investigated. Our analysis reveals a non-monotonic relationship between gene expression and structure and leads to the hypothesis that gene structure is determined by its function, whereas gene expression is subject to energetic cost. Moreover, we observe a recombination-based partitioning at the gene structure and function level. Our analysis provides new insights into the relationships between gene and genome structure and function. It reveals mechanisms conserved with other plant species as well as superimposed evolutionary forces that shaped the wheat gene space, likely participating in wheat adaptation.

  8. Networks and spatial patterns of extremist organizations in North and West Africa

    DEFF Research Database (Denmark)

    Walther, Olivier; Leuprecht, Christian; Skillicorn, David

    2018-01-01

    (Cunningham 2006; Findley and Rudloff 2012). Building on network science and spatial analysis, the overall objective of this chapter is to bridge these strands of literature and lay the foundations for a more formal approach to social and spatial networks of belligerents in the region. Examining...... of ensuring border integrity through border patrols and law enforcement. The chapter proceeds as follows. The second section reviews the literature on the social and spatial organization of state and non-state organizations, paying particular attention to the role of networks and national borders. The third...... and stability” (MaliActu 2016). The much-debated letter, which arrived one month before Ansar Dine attacked a UN convoy in the north of the country (RFI 2016), is the latest development in a tortuous military career for ag Ghaly, who, since the 1990s, has been a foreign fighter for the late Colonel Gaddafi...

  9. Scaling impacts on environmental controls and spatial heterogeneity of soil organic carbon stocks

    Science.gov (United States)

    Mishra, U.; Riley, W. J.

    2015-07-01

    The spatial heterogeneity of land surfaces affects energy, moisture, and greenhouse gas exchanges with the atmosphere. However, representing the heterogeneity of terrestrial hydrological and biogeochemical processes in Earth system models (ESMs) remains a critical scientific challenge. We report the impact of spatial scaling on environmental controls, spatial structure, and statistical properties of soil organic carbon (SOC) stocks across the US state of Alaska. We used soil profile observations and environmental factors such as topography, climate, land cover types, and surficial geology to predict the SOC stocks at a 50 m spatial scale. These spatially heterogeneous estimates provide a data set with reasonable fidelity to the observations at a sufficiently high resolution to examine the environmental controls on the spatial structure of SOC stocks. We upscaled both the predicted SOC stocks and environmental variables from finer to coarser spatial scales (s = 100, 200, and 500 m and 1, 2, 5, and 10 km) and generated various statistical properties of SOC stock estimates. We found different environmental factors to be statistically significant predictors at different spatial scales. Only elevation, temperature, potential evapotranspiration, and scrub land cover types were significant predictors at all scales. The strengths of control (the median value of geographically weighted regression coefficients) of these four environmental variables on SOC stocks decreased with increasing scale and were accurately represented using mathematical functions (R2 = 0.83-0.97). The spatial structure of SOC stocks across Alaska changed with spatial scale. Although the variance (sill) and unstructured variability (nugget) of the calculated variograms of SOC stocks decreased exponentially with scale, the correlation length (range) remained relatively constant across scale. The variance of predicted SOC stocks decreased with spatial scale over the range of 50 m to ~ 500 m, and remained

  10. Spatial Organization in Protein Kinase A Signaling Emerged at the Base of Animal Evolution

    NARCIS (Netherlands)

    Peng, Mao; Aye, Thin Thin; Snel, Berend; Van Breukelen, Bas; Scholten, Arjen; Heck, Albert J R

    2015-01-01

    In phosphorylation-directed signaling, spatial and temporal control is organized by complex interaction networks that diligently direct kinases toward distinct substrates to fine-tune specificity. How these protein networks originate and evolve into complex regulatory machineries are among the most

  11. Genomic organization and dynamics of repetitive DNA sequences in representatives of three Fagaceae genera.

    Science.gov (United States)

    Alves, Sofia; Ribeiro, Teresa; Inácio, Vera; Rocheta, Margarida; Morais-Cecílio, Leonor

    2012-05-01

    Oaks, chestnuts, and beeches are economically important species of the Fagaceae. To understand the relationship between these members of this family, a deep knowledge of their genome composition and organization is needed. In this work, we have isolated and characterized several AFLP fragments obtained from Quercus rotundifolia Lam. through homology searches in available databases. Genomic polymorphisms involving some of these sequences were evaluated in two species of Quercus, one of Castanea, and one of Fagus with specific primers. Comparative FISH analysis with generated sequences was performed in interphase nuclei of the four species, and the co-immunolocalization of 5-methylcytosine was also studied. Some of the sequences isolated proved to be genus-specific, while others were present in all the genera. Retroelements, either gypsy-like of the Tat/Athila clade or copia-like, are well represented, and most are dispersed in euchromatic regions of these species with no DNA methylation associated, pointing to an interspersed arrangement of these retroelements with potential gene-rich regions. A particular gypsy-sequence is dispersed in oaks and chestnut nuclei, but its confinement to chromocenters in beech evidences genome restructuring events during evolution of Fagaceae. Several sequences generated in this study proved to be good tools to comparatively study Fagaceae genome organization.

  12. Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

    Directory of Open Access Journals (Sweden)

    Joel Saltz

    2018-04-01

    Full Text Available Summary: Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumor-infiltrating lymphocytes (TILs based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment. : Tumor-infiltrating lymphocytes (TILs were identified from standard pathology cancer images by a deep-learning-derived “computational stain” developed by Saltz et al. They processed 5,202 digital images from 13 cancer types. Resulting TIL maps were correlated with TCGA molecular data, relating TIL content to survival, tumor subtypes, and immune profiles. Keywords: digital pathology, immuno-oncology, machine learning, lymphocytes, tumor microenvironment, deep learning, tumor-infiltrating lymphocytes, artificial intelligence, bioinformatics, computer vision

  13. Spatial arrangement of organic compounds on a model mineral surface: implications for soil organic matter stabilization.

    Science.gov (United States)

    Petridis, Loukas; Ambaye, Haile; Jagadamma, Sindhu; Kilbey, S Michael; Lokitz, Bradley S; Lauter, Valeria; Mayes, Melanie A

    2014-01-01

    The complexity of the mineral-organic carbon interface may influence the extent of stabilization of organic carbon compounds in soils, which is important for global climate futures. The nanoscale structure of a model interface was examined here by depositing films of organic carbon compounds of contrasting chemical character, hydrophilic glucose and amphiphilic stearic acid, onto a soil mineral analogue (Al2O3). Neutron reflectometry, a technique which provides depth-sensitive insight into the organization of the thin films, indicates that glucose molecules reside in a layer between Al2O3 and stearic acid, a result that was verified by water contact angle measurements. Molecular dynamics simulations reveal the thermodynamic driving force behind glucose partitioning on the mineral interface: The entropic penalty of confining the less mobile glucose on the mineral surface is lower than for stearic acid. The fundamental information obtained here helps rationalize how complex arrangements of organic carbon on soil mineral surfaces may arise.

  14. A Strategic Analysis of Investment Opportunities within British Columbia's Private Healthcare Sector for a Non-Profit Genomics Research Organization

    OpenAIRE

    Barclay, John W.

    2010-01-01

    Advances in the genome sciences are leading to the development of new healthcare innovations relevant to the principles of personalized medicine. Genome BC, a non-profit research organization, invests in projects that will help facilitate the integration of these innovations into the delivery of healthcare. This analysis assesses the strategic positioning of private healthcare firms in BC to be early users of such innovations. The analysis assesses the suitability of investment from Genome BC...

  15. [Spatial characteristics of soil organic carbon and nitrogen storages in Songnen Plain maize belt].

    Science.gov (United States)

    Zhang, Chun-Hua; Wang, Zong-Ming; Ren, Chun-Ying; Song, Kai-Shan; Zhang, Bai; Liu, Dian-Wei

    2010-03-01

    By using the data of 382 typical soil profiles from the second soil survey at national and county levels, and in combining with 1:500000 digital soil maps, a spatial database of soil profiles was established. Based on this, the one meter depth soil organic carbon and nitrogen storage in Songnen Plain maize belt of China was estimated, with the spatial characteristics of the soil organic carbon and nitrogen densities as well as the relationships between the soil organic carbon and nitrogen densities and the soil types and land use types analyzed. The soil organic carbon and nitrogen storage in the maize belt was (163.12 +/- 26.48) Tg and (9.53 +/- 1.75) Tg, respectively, mainly concentrated in meadow soil, chernozem, and black soil. The soil organic carbon and nitrogen densities were 5.51-25.25 and 0.37-0.80 kg x m(-2), respectively, and the C/N ratio was about 7.90 -12.67. The eastern and northern parts of the belt had much higher carbon and nitrogen densities than the other parts of the belt, and upland soils had the highest organic carbon density [(19.07 +/- 2.44) kg x m(-2)], forest soils had the highest nitrogen density [(0.82 +/- 0.25) kg x m(-2)], while lowland soils had the lower organic carbon and nitrogen densities.

  16. Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces.

    Science.gov (United States)

    Tecon, Robin; Or, Dani

    2017-03-06

    Mounting evidence suggests that natural microbial communities exhibit a high level of spatial organization at the micrometric scale that facilitate ecological interactions and support biogeochemical cycles. Microbial patterns are difficult to study definitively in natural environments due to complex biodiversity, observability and variable physicochemical factors. Here, we examine how trophic dependencies give rise to self-organized spatial patterns of a well-defined bacterial consortium grown on hydrated surfaces. The model consortium consisted of two Pseudomonas putida mutant strains that can fully degrade the aromatic hydrocarbon toluene. We demonstrated that obligate cooperation in toluene degradation (cooperative mutualism) favored convergence of 1:1 partner ratio and strong intermixing at the microscale (10-100 μm). In contrast, competition for benzoate, a compound degraded independently by both strains, led to distinct segregation patterns. Emergence of a persistent spatial pattern has been predicted for surface attached microbial activity in liquid films that mediate diffusive exchanges while permitting limited cell movement (colony expansion). This study of a simple microbial consortium offers mechanistic glimpses into the rules governing the assembly and functioning of complex sessile communities, and points to general principles of spatial organization with potential applications for natural and engineered microbial systems.

  17. Effects of aneuploidy on genome structure, expression, and interphase organization in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Bruno Huettel

    2008-10-01

    Full Text Available Aneuploidy refers to losses and/or gains of individual chromosomes from the normal chromosome set. The resulting gene dosage imbalance has a noticeable affect on the phenotype, as illustrated by aneuploid syndromes, including Down syndrome in humans, and by human solid tumor cells, which are highly aneuploid. Although the phenotypic manifestations of aneuploidy are usually apparent, information about the underlying alterations in structure, expression, and interphase organization of unbalanced chromosome sets is still sparse. Plants generally tolerate aneuploidy better than animals, and, through colchicine treatment and breeding strategies, it is possible to obtain inbred sibling plants with different numbers of chromosomes. This possibility, combined with the genetic and genomics tools available for Arabidopsis thaliana, provides a powerful means to assess systematically the molecular and cytological consequences of aberrant numbers of specific chromosomes. Here, we report on the generation of Arabidopsis plants in which chromosome 5 is present in triplicate. We compare the global transcript profiles of normal diploids and chromosome 5 trisomics, and assess genome integrity using array comparative genome hybridization. We use live cell imaging to determine the interphase 3D arrangement of transgene-encoded fluorescent tags on chromosome 5 in trisomic and triploid plants. The results indicate that trisomy 5 disrupts gene expression throughout the genome and supports the production and/or retention of truncated copies of chromosome 5. Although trisomy 5 does not grossly distort the interphase arrangement of fluorescent-tagged sites on chromosome 5, it may somewhat enhance associations between transgene alleles. Our analysis reveals the complex genomic changes that can occur in aneuploids and underscores the importance of using multiple experimental approaches to investigate how chromosome numerical changes condition abnormal phenotypes and

  18. Human Ro60 (SSA2) genomic organization and sequence alterations, examined in cutaneous lupus erythematosus.

    Science.gov (United States)

    Millard, T P; Ashton, G H S; Kondeatis, E; Vaughan, R W; Hughes, G R V; Khamashta, M A; Hawk, J L M; McGregor, J M; McGrath, J A

    2002-02-01

    The Ro 60 kDa protein (Ro60 or SSA2) is the major component of the Ro ribonucleoprotein (Ro RNP) complex, to which an immune response is a specific feature of several autoimmune diseases. The genomic organization and any sequence variation within the DNA encoding Ro60 are unknown. To characterize the Ro60 gene structure and to assess whether any sequence alterations might be associated with serum anti-Ro antibody in subacute cutaneous lupus erythematosus (SCLE), thus potentially providing new insight into disease pathogenesis. The cDNA sequence for Ro60 was obtained from the NCBI database and used for a BLAST search for a clone containing the entire genomic sequence. The intron-exon borders were confirmed by designing intronic primer pairs to flank each exon, which were then used to amplify genomic DNA for automated sequencing from 36 caucasian patients with SCLE (anti-Ro positive) and 49 with discoid LE (DLE, anti-Ro negative), in addition to 36 healthy caucasian controls. Heteroduplex analysis of polymerase chain reaction (PCR) products from patients and controls spanning all Ro60 exons (1-8) revealed a common bandshift in the PCR products spanning exon 7. Sequencing of the corresponding PCR products demonstrated an A > G substitution at nucleotide position 1318-7, within the consensus acceptor splice site of exon 7 (GenBank XM001901). The allele frequencies were major allele A (0.71) and minor allele G (0.29) in 72 control chromosomes, with no significant differences found between SCLE patients, DLE patients and controls. The genomic organization of the DNA encoding the Ro60 protein is described, including a common polymorphism within the consensus acceptor splice site of exon 7. Our delineation of a strategy for the genomic amplification of Ro60 forms a basis for further examination of the pathological functions of the Ro RNP in autoimmune disease.

  19. Self-Organization, Urban Transformation, and Spatial Planning in Greater Jakarta, Indonesia

    Directory of Open Access Journals (Sweden)

    Yovi Dzulhijjah Rahmawati

    2015-09-01

    Full Text Available Penelitian ini bertujuan untuk mengidentifikasi peran sistem perencanaan tata ruang dalam menghadapi proses perorganisasian diri, sebagaimana dibuktikan oleh transformasi perkotaan yang kompleks di wilayah Jakarta. Wilayah Jakarta adalah salah satu wilayah megapolitan di Asia Tenggara yang mengalami proses transformasi yang cepat. Sangat disayangkan bahwa sistem perencanaan tata ruang yang ada sekarang di wilayah Jakarta belum mampu merespon transformasi kota secara non-linier. Kekurangan ini terbukti dari ketidaksinkronan antara dokumen-dokumen perencanaan tata ruang dan perubahan tata guna lahan perkotaan yang diperkuat dengan proses pengorganisasian diri. Perbedaan antara situasi empiris dan dokumen-dokumen perencanaan tata ruang yang ada telah menghasilkan ketidakcocokan antara sistem perencanaan tata ruang dengan sistem tata ruang di wilayah Jakarta. Ketidakcocokan ini terjadi karena sistem perencanaan tata ruang saat ini tidak mempertimbangkan ketidakpastian di masa depan. Situasi ini mengindikasikan adanya ‘fuzziness’ dalam implementasi sistem dan proses perencanaan tata ruang, sementara transformasi perkotaan telah berkembang sedemikian kompleksnya dan membutuhkan respon yang cepat dan tepat. Untuk dapat merespon ketidakcocokan ini, sistem perencanaan tata ruang di wilayah Jakarta harus lebih memperhatikan sistem perkotaan yang berkembang dalam proses yang tidak linear.Kata kunci. Pengorganisasian diri, transformasi perkotaan, ketidaklinieran, sistem perencanaan, Megapolitan Jakarta. This study aimed to identify the role of spatial planning in facing self-organizing processes as evidenced by a complex urban transformation in Greater Jakarta. Greater Jakarta is one of the mega urban-regions in Southeast Asia that are undergoing a rapid urban transformation process. This urban transformation has been developing through a non-linear transition. Unfortunately, the current spatial planning system in Greater Jakarta is not yet adequately

  20. Impact of spatial organization on a novel auxotrophic interaction among soil microbes.

    Science.gov (United States)

    Jiang, Xue; Zerfaß, Christian; Feng, Song; Eichmann, Ruth; Asally, Munehiro; Schäfer, Patrick; Soyer, Orkun S

    2018-06-01

    A key prerequisite to achieve a deeper understanding of microbial communities and to engineer synthetic ones is to identify the individual metabolic interactions among key species and how these interactions are affected by different environmental factors. Deciphering the physiological basis of species-species and species-environment interactions in spatially organized environments requires reductionist approaches using ecologically and functionally relevant species. To this end, we focus here on a defined system to study the metabolic interactions in a spatial context among the plant-beneficial endophytic fungus Serendipita indica, and the soil-dwelling model bacterium Bacillus subtilis. Focusing on the growth dynamics of S. indica under defined conditions, we identified an auxotrophy in this organism for thiamine, which is a key co-factor for essential reactions in the central carbon metabolism. We found that S. indica growth is restored in thiamine-free media, when co-cultured with B. subtilis. The success of this auxotrophic interaction, however, was dependent on the spatial and temporal organization of the system; the beneficial impact of B. subtilis was only visible when its inoculation was separated from that of S. indica either in time or space. These findings describe a key auxotrophic interaction in the soil among organisms that are shown to be important for plant ecosystem functioning, and point to the potential importance of spatial and temporal organization for the success of auxotrophic interactions. These points can be particularly important for engineering of minimal functional synthetic communities as plant seed treatments and for vertical farming under defined conditions.

  1. Building a complete image of genome regulation in the model organism Escherichia coli.

    Science.gov (United States)

    Ishihama, Akira

    2018-01-15

    The model organism, Escherichia coli, contains a total of more than 4,500 genes, but the total number of RNA polymerase (RNAP) core enzyme or the transcriptase is only about 2,000 molecules per genome. The regulatory targets of RNAP are, however, modulated by changing its promoter selectivity through two-steps of protein-protein interplay with 7 species of the sigma factor in the first step, and then 300 species of the transcription factor (TF) in the second step. Scientists working in the field of prokaryotic transcription in Japan have made considerable contributions to the elucidation of genetic frameworks and regulatory modes of the genome transcription in E. coli K-12. This review summarizes the findings by this group, first focusing on three sigma factors, the stationary-phase sigma RpoS, the heat-shock sigma RpoH, and the flagellar-chemotaxis sigma RpoF, as examples. It also presents an overview of the current state of the systematic research being carried out to identify the regulatory functions of all TFs from a single and the same bacterium E. coli K-12, using the genomic SELEX and PS-TF screening systems. All these studies have been undertaken with the aim of understanding the genome regulation in E. coli K-12 as a whole.

  2. Genome-Wide Identification, Phylogeny, and Expression Analysis of ARF Genes Involved in Vegetative Organs Development in Switchgrass

    Directory of Open Access Journals (Sweden)

    Jianli Wang

    2018-01-01

    Full Text Available Auxin response factors (ARFs have been reported to play vital roles during plant growth and development. In order to reveal specific functions related to vegetative organs in grasses, an in-depth study of the ARF gene family was carried out in switchgrass (Panicum virgatum L., a warm-season C4 perennial grass that is mostly used as bioenergy and animal feedstock. A total of 47 putative ARF genes (PvARFs were identified in the switchgrass genome (2n = 4x = 36, 42 of which were anchored to the seven pairs of chromosomes and found to be unevenly distributed. Sixteen PvARFs were predicted to be potential targets of small RNAs (microRNA160 and 167. Phylogenetically speaking, PvARFs were divided into seven distinct subgroups based on the phylogeny, exon/intron arrangement, and conserved motif distribution. Moreover, 15 pairs of PvARFs have different temporal-spatial expression profiles in vegetative organs (2nd, 3rd, and 4th internode and leaves, which implies that different PvARFs have specific functions in switchgrass growth and development. In addition, at least 14 pairs of PvARFs respond to naphthylacetic acid (NAA treatment, which might be helpful for us to study on auxin response in switchgrass. The comprehensive analysis, described here, will facilitate the future functional analysis of ARF genes in grasses.

  3. Primary structure of the human follistatin precursor and its genomic organization

    International Nuclear Information System (INIS)

    Shimasaki, Shunichi; Koga, Makoto; Esch, F.

    1988-01-01

    Follistatin is a single-chain gonadal protein that specifically inhibits follicle-stimulating hormone release. By use of the recently characterized porcine follistatin cDNA as a probe to screen a human testis cDNA library and a genomic library, the structure of the complete human follistatin precursor as well as its genomic organization have been determined. Three of eight cDNA clones that were sequenced predicted a precursor with 344 amino acids, whereas the remaining five cDNA clones encoded a 317 amino acid precursor, resulting from alternative splicing of the precursor mRNA. Mature follistatins contain four contiguous domains that are encoded by precisely separated exons; three of the domains are highly similar to each other, as well as to human epidermal growth factor and human pancreatic secretory trypsin inhibitor. The genomic organization of the human follistatin is similar to that of the human epidermal growth factor gene and thus supports the notion of exon shuffling during evolution

  4. Structurally Complex Organization of Repetitive DNAs in the Genome of Cobia (Rachycentron canadum).

    Science.gov (United States)

    Costa, Gideão W W F; Cioffi, Marcelo de B; Bertollo, Luiz A C; Molina, Wagner F

    2015-06-01

    Repetitive DNAs comprise the largest fraction of the eukaryotic genome. They include microsatellites or simple sequence repeats (SSRs), which play an important role in the chromosome differentiation among fishes. Rachycentron canadum is the only representative of the family Rachycentridae. This species has been focused on several multidisciplinary studies in view of its important potential for marine fish farming. In the present study, distinct classes of repetitive DNAs, with emphasis on SSRs, were mapped in the chromosomes of this species to improve the knowledge of its genome organization. Microsatellites exhibited a diversified distribution, both dispersed in euchromatin and clustered in the heterochromatin. The multilocus location of SSRs strengthened the heterochromatin heterogeneity in this species, as suggested by some previous studies. The colocalization of SSRs with retrotransposons and transposons pointed to a close evolutionary relationship between these repetitive sequences. A number of heterochromatic regions highlighted a greater complex organization than previously supposed, harboring a diversity of repetitive elements. In this sense, there was also evidence of colocalization of active genetic regions and different classes of repetitive DNAs in a common heterochromatic region, which offers a potential opportunity for further researches regarding the interaction of these distinct fractions in fish genomes.

  5. An Evaluation of Spatial Organization of the Church Architecture of Kerala during the Sixteenth to Seventeenth Centuries

    Science.gov (United States)

    Panjikaran, S.; Vedamuthu, R.

    2013-05-01

    The churches of Kerala of the sixteenth to seventeenth centuries exhibits an architectural character which is different from that of the indigenous Church Architecture of Kerala. Preliminary studies show that the spatial organization of these churches also varied from that of the indigenous churches of Kerala. Did these variations in spatial organization arise of any change in functional requirements of churches? How did the indigenous Architectural character adapt to these changes or did it give way to a new style? The objective of this study is to understand the spatial organization of the indigenous Church Architecture of Kerala and to evaluate the changes in spatial organization during the sixteenth to seventeenth centuries. This study is primarily based on field survey and documentation, evaluation is done by relying on the Rapoport's theory. It is concluded that the church architecture of this period is a fusion of the Western and Eastern ecclesiastical traditions in terms of spatial organization and planning.

  6. Spatial and seasonal contrasts of sedimentary organic matter in floodplain lakes of the central Amazon basin

    OpenAIRE

    Sobrinho, R. L.; Bernardes, M. C.; Abril, G.; Kim, J. H.; Zell, C. I.; Mortillaro, J. M.; Meziane, T.; Moreira Turcq, Patricia; Damste, J. S. S.

    2016-01-01

    In this study, we investigated the seasonal and spatial pattern of sedimentary organic matter (SOM) in five floodplain lakes of the central Amazon basin (Cabaliana, Janauaca, Canaçari, Miratuba, and Curuai) which have different morphologies, hydrodynamics and vegetation coverages. Surface sediments were collected in four hydrological seasons: low water (LW), rising water (RW), high water (HW) and falling water (FW) in 2009 and 2010. We investigated commonly used bulk geochem...

  7. Temporal, spatial and social patterens of self-organization within street sport

    DEFF Research Database (Denmark)

    Sand, Anne-Lene

    Due to an increased urbanization and digitalization self-organized practices are becoming a central way of doing sports among contemporary young people and adults in urban contexts. The aim of this presentation is to contribute with knowledge about what it means to be self-organized within street...... young people can re-define urban space themselves (Skelton and Valentine 2007). During a multi-sited fieldwork (Marcus 1995) I followed people in Denmark that value to be able to improvise in the way they organize their own street-sport practices through temporal, spatial and social practices. Street...... among young people and adults, in order to redefine and reconstruct future leisure organizations (Rojek 1995) and understand contemporary forms of street sport....

  8. Short-Term Environmental Effects and Their Influence on Spatial Homogeneity of Organic Solar Cell Functionality.

    Science.gov (United States)

    Chien, Huei-Ting; Zach, Peter W; Friedel, Bettina

    2017-08-23

    In this study, we focus on the induced degradation and spatial inhomogeneity of organic photovoltaic devices under different environmental conditions, uncoupled from the influence of any auxiliary hole-transport (HT) layer. During testing of the corresponding devices comprising the standard photoactive layer of poly(3-hexylthiophene) as donor, blended with phenyl-C 61 -butyric acid methyl ester as acceptor, a comparison was made between the nonencapsulated devices upon exposure to argon in the dark, dry air in the dark, dry air with illumination, and humid air in the dark. The impact on the active layer's photophysics is discussed, along with the device physics in terms of integral solar cell performance and spatially resolved photocurrent distribution with point-to-point analysis of the diode characteristics to determine the origin of the observed integrated organic photovoltaic device behavior. The results show that even without the widely used hygroscopic HT layer, poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate), humidity is still a major factor in the short-term environmental degradation of organic solar cells with this architecture, and not only oxygen or light, as is often reported. Different from previous reports where water-induced device degradation was spatially homogeneous and formation of Al 2 O 3 islands was only seen for oxygen permeation through pinholes in aluminum, we observed insulating islands merely after humidity exposure in the present study. Further, we demonstrated with laser beam induced current mapping and point-to-point diode analysis that the water-induced performance losses are a result of the exposed device area comprising regions with entirely unaltered high output and intact diode behavior and those with severe degradation showing detrimentally lowered output and voltage-independent charge blocking, which is essentially insulating behavior. It is suggested that this is caused by transport of water through pinholes to the

  9. Spatially isolated palladium in porous organic polymers by direct knitting for versatile organic transformations

    KAUST Repository

    Wang, Xinbo

    2017-10-03

    We report here a direct knitting Method for preparation of highly robust, effective while air- and moisture-tolerant, and readily recyclable three-dimensional (3D) porous polymer-Pd network (PPPd) from the widely used Pd(PPh3)4. Electro-beam induced Pd atom crystallization was observed for the first time in organic polymer and revealed the ultrafine dispersion of palladium atoms. Challenging types of Suzuki-Miyaura couplings, reductive coupling of aryl halides and oxidative coupling of arylboronic acid were successively catalyzed by PPPd in aqueous media. Also catalytically selective CH functionalization reactions were achieved with orders of magnitude more efficient than conventional Pd homogeneous catalysts. The strategy developed here provides a practical method for easy-to-make yet highly efficient heterogeneous catalysis.

  10. Spatially isolated palladium in porous organic polymers by direct knitting for versatile organic transformations

    KAUST Repository

    Wang, Xinbo; Min, Shixiong; Das, Swapan Kumar; Fan, Wei; Huang, Kuo-Wei; Lai, Zhiping

    2017-01-01

    We report here a direct knitting Method for preparation of highly robust, effective while air- and moisture-tolerant, and readily recyclable three-dimensional (3D) porous polymer-Pd network (PPPd) from the widely used Pd(PPh3)4. Electro-beam induced Pd atom crystallization was observed for the first time in organic polymer and revealed the ultrafine dispersion of palladium atoms. Challenging types of Suzuki-Miyaura couplings, reductive coupling of aryl halides and oxidative coupling of arylboronic acid were successively catalyzed by PPPd in aqueous media. Also catalytically selective CH functionalization reactions were achieved with orders of magnitude more efficient than conventional Pd homogeneous catalysts. The strategy developed here provides a practical method for easy-to-make yet highly efficient heterogeneous catalysis.

  11. No boundaries: genomes, organisms, and ecological interactions responsible for divergence and reproductive isolation.

    Science.gov (United States)

    Etges, William J

    2014-01-01

    Revealing the genetic basis of traits that cause reproductive isolation, particularly premating or sexual isolation, usually involves the same challenges as most attempts at genotype-phenotype mapping and so requires knowledge of how these traits are expressed in different individuals, populations, and environments, particularly under natural conditions. Genetic dissection of speciation phenotypes thus requires understanding of the internal and external contexts in which underlying genetic elements are expressed. Gene expression is a product of complex interacting factors internal and external to the organism including developmental programs, the genetic background including nuclear-cytotype interactions, epistatic relationships, interactions among individuals or social effects, stochasticity, and prevailing variation in ecological conditions. Understanding of genomic divergence associated with reproductive isolation will be facilitated by functional expression analysis of annotated genomes in organisms with well-studied evolutionary histories, phylogenetic affinities, and known patterns of ecological variation throughout their life cycles. I review progress and prospects for understanding the pervasive role of host plant use on genetic and phenotypic expression of reproductive isolating mechanisms in cactophilic Drosophila mojavensis and suggest how this system can be used as a model for revealing the genetic basis for species formation in organisms where speciation phenotypes are under the joint influences of genetic and environmental factors. © The American Genetic Association. 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Genomic organization, transcript variants and comparative analysis of the human nucleoporin 155 (NUP155) gene

    DEFF Research Database (Denmark)

    Zhang, X.; Yang, J.; Yu, J.

    2002-01-01

    Nucleoporin 155 (Nup155) is a major component of the nuclear pore complex (NPC) involved in cellular nucleo-cytoplasmic transport. We have acquired the complete sequence and interpreted the genomic organization of the Nup155 orthologos from human (Homo sapiens) and pufferfish (Fugu rubripes), which...... complementary to RNAs of the Nup155 orthologs from Fugu and mouse. Comparative analysis of the Nup155 orthologs in many species, including H. sapiens, Mus musculus, Rattus norvegicus, F. rubripes, Arabidopsis thaliana, Drosophila melanogaster, and Saccharomyces cerevisiae, has revealed two paralogs in S...

  13. [Influence of information over saturation on quality of creative activity and EEG spatial organization].

    Science.gov (United States)

    Sviderskaia, N E

    2011-01-01

    In work the features of the biopotentials spatial organization are surveyed at successful and unsuccessful (abandoning or bad quality of a product) implementation of creative imagination in conditions of information over saturation. Two groups of the examinees have taken part in experiments: "professionals" (23 able-bodied examinees--students of faculty of an art graphics) and "nonprofessionals" (34 men, which specialty were not linked to systematic visual imagination). During experiment the examinees should mentally frame a visual object on the basis of two simple graphics units--right angle and diagonal, and after EEG registration to draw it on a paper and to give a title. The total number of units exceeded 7 +/- 2, i.e. the possibility of information processing at a realized level was unreal that reduced in necessity of connection of mechanisms of not realized information processes. Estimated quality of a framed product from the point of view successful and unsuccessful of implementation of the job and conforming to each of these variants of a feature of the EEG spatial organization, which shunted with the help of portable telemeter installation "SIT-EEG" from 24 items convexital surface of a head. Is shown, that at successful performance of the job in comparison with unsuccessful for "professionals" biopotentials spatial organization parameters--spatial synchronization (linear processes) and spatial disorder (the nonlinear processes) strengthen (in relation to a background) in frontal-temporal areas of the right hemisphere and parietal-occipital left ones. For "nonprofessionals" the value of these parameters was enlarged in an inverse direction: in frontal-temporal areas of the left hemisphere and in the right parietal-occipital. At unsuccessful performance of the jobs for "professionals" the body height ofbiopotentials spatial disorder almost in all cortical zones was marked, for "nonprofessionals" of change were weak. The between group differences in all

  14. Capturing Three-Dimensional Genome Organization in Individual Cells by Single-Cell Hi-C.

    Science.gov (United States)

    Nagano, Takashi; Wingett, Steven W; Fraser, Peter

    2017-01-01

    Hi-C is a powerful method to investigate genome-wide, higher-order chromatin and chromosome conformations averaged from a population of cells. To expand the potential of Hi-C for single-cell analysis, we developed single-cell Hi-C. Similar to the existing "ensemble" Hi-C method, single-cell Hi-C detects proximity-dependent ligation events between cross-linked and restriction-digested chromatin fragments in cells. A major difference between the single-cell Hi-C and ensemble Hi-C protocol is that the proximity-dependent ligation is carried out in the nucleus. This allows the isolation of individual cells in which nearly the entire Hi-C procedure has been carried out, enabling the production of a Hi-C library and data from individual cells. With this new method, we studied genome conformations and found evidence for conserved topological domain organization from cell to cell, but highly variable interdomain contacts and chromosome folding genome wide. In addition, we found that the single-cell Hi-C protocol provided cleaner results with less technical noise suggesting it could be used to improve the ensemble Hi-C technique.

  15. Polytene Chromosomes - A Portrait of Functional Organization of the Drosophila Genome.

    Science.gov (United States)

    Zykova, Tatyana Yu; Levitsky, Victor G; Belyaeva, Elena S; Zhimulev, Igor F

    2018-04-01

    This mini-review is devoted to the problem genetic meaning of main polytene chromosome structures - bands and interbands. Generally, densely packed chromatin forms black bands, moderately condensed regions form grey loose bands, whereas decondensed regions of the genome appear as interbands. Recent progress in the annotation of the Drosophila genome and epigenome has made it possible to compare the banding pattern and the structural organization of genes, as well as their activity. This was greatly aided by our ability to establish the borders of bands and interbands on the physical map, which allowed to perform comprehensive side-by-side comparisons of cytology, genetic and epigenetic maps and to uncover the association between the morphological structures and the functional domains of the genome. These studies largely conclude that interbands 5'-ends of housekeeping genes that are active across all cell types. Interbands are enriched with proteins involved in transcription and nucleosome remodeling, as well as with active histone modifications. Notably, most of the replication origins map to interband regions. As for grey loose bands adjacent to interbands, they typically host the bodies of house-keeping genes. Thus, the bipartite structure composed of an interband and an adjacent grey band functions as a standalone genetic unit. Finally, black bands harbor tissue-specific genes with narrow temporal and tissue expression profiles. Thus, the uniform and permanent activity of interbands combined with the inactivity of genes in bands forms the basis of the universal banding pattern observed in various Drosophila tissues.

  16. The genome and transcriptome of Phalaenopsis yield insights into floral organ development and flowering regulation

    Directory of Open Access Journals (Sweden)

    Jian-Zhi Huang

    2016-05-01

    Full Text Available The Phalaenopsis orchid is an important potted flower of high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering Phalaenopsis ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads to use these data to identify 41,153 protein-coding genes and 188 miRNA families. We also generated a draft genome for Phalaenopsis pulcherrima ‘B8802,’ a summer flowering species, via resequencing. Comparison of genome data between the two Phalaenopsis cultivars allowed the identification of 691,532 single-nucleotide polymorphisms. In this study, we reveal that the key role of PhAGL6b in the regulation of labellum organ development involves alternative splicing in the big lip mutant. Petal or sepal overexpressing PhAGL6b leads to the conversion into a lip-like structure. We also discovered that the gibberellin pathway that regulates the expression of flowering time genes during the reproductive phase change is induced by cool temperature. Our work thus depicted a valuable resource for the flowering control, flower architecture development, and breeding of the Phalaenopsis orchids.

  17. Genomic organization, sequence divergence, and recombination of feline immunodeficiency virus from lions in the wild

    Science.gov (United States)

    Pecon-Slattery, Jill; McCracken, Carrie L; Troyer, Jennifer L; VandeWoude, Sue; Roelke, Melody; Sondgeroth, Kerry; Winterbach, Christiaan; Winterbach, Hanlie; O'Brien, Stephen J

    2008-01-01

    Background Feline immunodeficiency virus (FIV) naturally infects multiple species of cat and is related to human immunodeficiency virus in humans. FIV infection causes AIDS-like disease and mortality in the domestic cat (Felis catus) and serves as a natural model for HIV infection in humans. In African lions (Panthera leo) and other exotic felid species, disease etiology introduced by FIV infection are less clear, but recent studies indicate that FIV causes moderate to severe CD4 depletion. Results In this study, comparative genomic methods are used to evaluate the full proviral genome of two geographically distinct FIV subtypes isolated from free-ranging lions. Genome organization of FIVPle subtype B (9891 bp) from lions in the Serengeti National Park in Tanzania and FIVPle subtype E (9899 bp) isolated from lions in the Okavango Delta in Botswana, both resemble FIV genome sequence from puma, Pallas cat and domestic cat across 5' LTR, gag, pol, vif, orfA, env, rev and 3'LTR regions. Comparative analyses of available full-length FIV consisting of subtypes A, B and C from FIVFca, Pallas cat FIVOma and two puma FIVPco subtypes A and B recapitulate the species-specific monophyly of FIV marked by high levels of genetic diversity both within and between species. Across all FIVPle gene regions except env, lion subtypes B and E are monophyletic, and marginally more similar to Pallas cat FIVOma than to other FIV. Sequence analyses indicate the SU and TM regions of env vary substantially between subtypes, with FIVPle subtype E more related to domestic cat FIVFca than to FIVPle subtype B and FIVOma likely reflecting recombination between strains in the wild. Conclusion This study demonstrates the necessity of whole-genome analysis to complement population/gene-based studies, which are of limited utility in uncovering complex events such as recombination that may lead to functional differences in virulence and pathogenicity. These full-length lion lentiviruses are integral to

  18. Genomic organization, sequence divergence, and recombination of feline immunodeficiency virus from lions in the wild

    Directory of Open Access Journals (Sweden)

    Sondgeroth Kerry

    2008-02-01

    Full Text Available Abstract Background Feline immunodeficiency virus (FIV naturally infects multiple species of cat and is related to human immunodeficiency virus in humans. FIV infection causes AIDS-like disease and mortality in the domestic cat (Felis catus and serves as a natural model for HIV infection in humans. In African lions (Panthera leo and other exotic felid species, disease etiology introduced by FIV infection are less clear, but recent studies indicate that FIV causes moderate to severe CD4 depletion. Results In this study, comparative genomic methods are used to evaluate the full proviral genome of two geographically distinct FIV subtypes isolated from free-ranging lions. Genome organization of FIVPle subtype B (9891 bp from lions in the Serengeti National Park in Tanzania and FIVPle subtype E (9899 bp isolated from lions in the Okavango Delta in Botswana, both resemble FIV genome sequence from puma, Pallas cat and domestic cat across 5' LTR, gag, pol, vif, orfA, env, rev and 3'LTR regions. Comparative analyses of available full-length FIV consisting of subtypes A, B and C from FIVFca, Pallas cat FIVOma and two puma FIVPco subtypes A and B recapitulate the species-specific monophyly of FIV marked by high levels of genetic diversity both within and between species. Across all FIVPle gene regions except env, lion subtypes B and E are monophyletic, and marginally more similar to Pallas cat FIVOma than to other FIV. Sequence analyses indicate the SU and TM regions of env vary substantially between subtypes, with FIVPle subtype E more related to domestic cat FIVFca than to FIVPle subtype B and FIVOma likely reflecting recombination between strains in the wild. Conclusion This study demonstrates the necessity of whole-genome analysis to complement population/gene-based studies, which are of limited utility in uncovering complex events such as recombination that may lead to functional differences in virulence and pathogenicity. These full-length lion

  19. 3D Spatially Resolved Models of the Intracellular Dynamics of the Hepatitis C Genome Replication Cycle

    KAUST Repository

    Knodel, Markus

    2017-10-02

    Mathematical models of virus dynamics have not previously acknowledged spatial resolution at the intracellular level despite substantial arguments that favor the consideration of intracellular spatial dependence. The replication of the hepatitis C virus (HCV) viral RNA (vRNA) occurs within special replication complexes formed from membranes derived from endoplasmatic reticulum (ER). These regions, termed membranous webs, are generated primarily through specific interactions between nonstructural virus-encoded proteins (NSPs) and host cellular factors. The NSPs are responsible for the replication of the vRNA and their movement is restricted to the ER surface. Therefore, in this study we developed fully spatio-temporal resolved models of the vRNA replication cycle of HCV. Our simulations are performed upon realistic reconstructed cell structures-namely the ER surface and the membranous webs-based on data derived from immunostained cells replicating HCV vRNA. We visualized 3D simulations that reproduced dynamics resulting from interplay of the different components of our models (vRNA, NSPs, and a host factor), and we present an evaluation of the concentrations for the components within different regions of the cell. Thus far, our model is restricted to an internal portion of a hepatocyte and is qualitative more than quantitative. For a quantitative adaption to complete cells, various additional parameters will have to be determined through further in vitro cell biology experiments, which can be stimulated by the results deccribed in the present study.

  20. Novel rod-shaped viruses isolated from garlic, Allium sativum, possessing a unique genome organization.

    Science.gov (United States)

    Sumi, S; Tsuneyoshi, T; Furutani, H

    1993-09-01

    Rod-shaped flexuous viruses were partially purified from garlic plants (Allium sativum) showing typical mosaic symptoms. The genome was shown to be composed of RNA with a poly(A) tail of an estimated size of 10 kb as shown by denaturing agarose gel electrophoresis. We constructed cDNA libraries and screened four independent clones, which were designated GV-A, GV-B, GV-C and GV-D, using Northern and Southern blot hybridization. Nucleotide sequence determination of the cDNAs, two of which correspond to nearly one-third of the virus genomic RNA, shows that all of these viruses possess an identical genomic structure and that also at least four proteins are encoded in the viral cDNA, their M(r)s being estimated to be 15K, 27K, 40K and 11K. The 15K open reading frame (ORF) encodes the core-like sequence of a zinc finger protein preceded by a cluster of basic amino acid residues. The 27K ORF probably encodes the viral coat protein (CP), based on both the existence of some conserved sequences observed in many other rod-shaped or flexuous virus CPs and an overall amino acid sequence similarity to potexvirus and carlavirus CPs. The 11K ORF shows significant amino acid sequence similarities to the corresponding 12K proteins of the potexviruses and carlaviruses. On the other hand, the 40K ORF product does not resemble any other plant virus gene products reported so far. The genomic organization in the 3' region of the garlic viruses resembles, but clearly differs from, that of carlaviruses. Phylogenetic analysis based upon the amino acid sequence of the viral capsid protein also indicates that the garlic viruses have a unique and distinct domain different from those of the potexvirus and carlavirus groups. The results suggest that the garlic viruses described here belong to an unclassified and new virus group closely related to the carlaviruses.

  1. Evaluation of plasmid and genomic DNA calibrants used for the quantification of genetically modified organisms.

    Science.gov (United States)

    Caprioara-Buda, M; Meyer, W; Jeynov, B; Corbisier, P; Trapmann, S; Emons, H

    2012-07-01

    The reliable quantification of genetically modified organisms (GMOs) by real-time PCR requires, besides thoroughly validated quantitative detection methods, sustainable calibration systems. The latter establishes the anchor points for the measured value and the measurement unit, respectively. In this paper, the suitability of two types of DNA calibrants, i.e. plasmid DNA and genomic DNA extracted from plant leaves, for the certification of the GMO content in reference materials as copy number ratio between two targeted DNA sequences was investigated. The PCR efficiencies and coefficients of determination of the calibration curves as well as the measured copy number ratios for three powder certified reference materials (CRMs), namely ERM-BF415e (NK603 maize), ERM-BF425c (356043 soya), and ERM-BF427c (98140 maize), originally certified for their mass fraction of GMO, were compared for both types of calibrants. In all three systems investigated, the PCR efficiencies of plasmid DNA were slightly closer to the PCR efficiencies observed for the genomic DNA extracted from seed powders rather than those of the genomic DNA extracted from leaves. Although the mean DNA copy number ratios for each CRM overlapped within their uncertainties, the DNA copy number ratios were significantly different using the two types of calibrants. Based on these observations, both plasmid and leaf genomic DNA calibrants would be technically suitable as anchor points for the calibration of the real-time PCR methods applied in this study. However, the most suitable approach to establish a sustainable traceability chain is to fix a reference system based on plasmid DNA.

  2. Chloroplast Genome Sequence of pigeonpea (Cajanus cajan (L. Millspaugh and Cajanus scarabaeoides: Genome organization and Comparison with other legumes

    Directory of Open Access Journals (Sweden)

    Tanvi Kaila

    2016-12-01

    Full Text Available Pigeonpea (Cajanus cajan (L. Millspaugh, a diploid (2n = 22 legume crop with a genome size of 852 Mbp, serves as an important source of human dietary protein especially in South East Asian and African regions. In this study, the draft chloroplast genomes of Cajanus cajan and Cajanus scarabaeoides were sequenced. Cajanus scarabaeoides is an important species of the Cajanus gene pool and has also been used for developing promising CMS system by different groups. A male sterile genotype harbouring the Cajanus scarabaeoides cytoplasm was used for sequencing the plastid genome. The cp genome of Cajanus cajan is 152,242bp long, having a quadripartite structure with LSC of 83,455 bp and SSC of 17,871 bp separated by IRs of 25,398 bp. Similarly, the cp genome of Cajanus scarabaeoides is 152,201bp long, having a quadripartite structure in which IRs of 25,402 bp length separates 83,423 bp of LSC and 17,854 bp of SSC. The pigeonpea cp genome contains 116 unique genes, including 30 tRNA, 4 rRNA, 78 predicted protein coding genes and 5 pseudogenes. A 50kb inversion was observed in the LSC region of pigeonpea cp genome, consistent with other legumes. Comparison of cp genome with other legumes revealed the contraction of IR boundaries due to the absence of rps19 gene in the IR region. Chloroplast SSRs were mined and a total of 280 and 292 cpSSRs were identified in Cajanus scarabaeoides and Cajanus cajan respectively. RNA editing was observed at 37 sites in both Cajanus scarabaeoides and Cajanus cajan, with maximum occurrence in the ndh genes. The pigeonpea cp genome sequence would be beneficial in providing informative molecular markers which can be utilized for genetic diversity analysis and aid in understanding the plant systematics studies among major grain legumes.

  3. The elevation of radiation load on ecosystems and genome instability of organisms

    International Nuclear Information System (INIS)

    Gaziyev, A. I.; Bezlepkin, V.Q.

    2002-01-01

    prophylaxis of human disorders. Thus, it was found that the action of low-dose ionizing radiation on living organisms might induce an adaptive repair response in them aimed at decreasing the genetic consequences of the exposure. However, the potentialities of defense and repair systems of an organism are limited, so an increase in genome lesions may cause inheritable mutations, cancer and other pathologies, and death. DNA lesions caused by ionizing radiation in small and sublethal doses can essentially be repaired, whereas unrepaired lesions and errors of repair, replication, and recombination systems lead to formation of mutational changes in DNA sequences. These changes may be transmitted to daughter cells and induce genome instability in the progeny. Induced genome instability in survived somatic cells is characterized by persistence of a high level of acquired variability in many generations of these cells. Genome instability manifests itself as an increased frequency of karyotypic anomalies, chromosome and gene mutations, clonal heterogeneity, and malignant transformation in the progeny of cells exposed to DNA-damaging agents. Besides, cells with genome instability show increased amplification of genes and changes in their expression, as well as disturbances in their differentiation, delays in reproductive death and other phenotypic characters of abnormal development. Whereas some progress has been made towards knowledge of genome instability in the somatic cells of mammals, the radiation-induced genome instability in germ cells transmitted to individuals of the next generation is still not clearly understood. At the same time, evidence has been obtained which suggests that the transmission of genome instability to the somatic cells of the progeny from the germ cells of gamma - radiation-exposed parents is possible. This conclusion is based on the data on mutation frequency in the progeny of parents exposed to DNA-damaging agents. For instance, a significant increase in

  4. Spatial organization of foreshocks as a tool to forecast large earthquakes.

    Science.gov (United States)

    Lippiello, E; Marzocchi, W; de Arcangelis, L; Godano, C

    2012-01-01

    An increase in the number of smaller magnitude events, retrospectively named foreshocks, is often observed before large earthquakes. We show that the linear density probability of earthquakes occurring before and after small or intermediate mainshocks displays a symmetrical behavior, indicating that the size of the area fractured during the mainshock is encoded in the foreshock spatial organization. This observation can be used to discriminate spatial clustering due to foreshocks from the one induced by aftershocks and is implemented in an alarm-based model to forecast m > 6 earthquakes. A retrospective study of the last 19 years Southern California catalog shows that the daily occurrence probability presents isolated peaks closely located in time and space to the epicenters of five of the six m > 6 earthquakes. We find daily probabilities as high as 25% (in cells of size 0.04 × 0.04deg(2)), with significant probability gains with respect to standard models.

  5. From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome.

    Science.gov (United States)

    Lemay, Danielle G; Pollard, Katherine S; Martin, William F; Freeman Zadrowski, Courtneay; Hernandez, Joseph; Korf, Ian; German, J Bruce; Rijnkels, Monique

    2013-01-01

    Even in genomes lacking operons, a gene's position in the genome influences its potential for expression. The mechanisms by which adjacent genes are co-expressed are still not completely understood. Using lactation and the mammary gland as a model system, we explore the hypothesis that chromatin state contributes to the co-regulation of gene neighborhoods. The mammary gland represents a unique evolutionary model, due to its recent appearance, in the context of vertebrate genomes. An understanding of how the mammary gland is regulated to produce milk is also of biomedical and agricultural importance for human lactation and dairying. Here, we integrate epigenomic and transcriptomic data to develop a comprehensive regulatory model. Neighborhoods of mammary-expressed genes were determined using expression data derived from pregnant and lactating mice and a neighborhood scoring tool, G-NEST. Regions of open and closed chromatin were identified by ChIP-Seq of histone modifications H3K36me3, H3K4me2, and H3K27me3 in the mouse mammary gland and liver tissue during lactation. We found that neighborhoods of genes in regions of uniquely active chromatin in the lactating mammary gland, compared with liver tissue, were extremely rare. Rather, genes in most neighborhoods were suppressed during lactation as reflected in their expression levels and their location in regions of silenced chromatin. Chromatin silencing was largely shared between the liver and mammary gland during lactation, and what distinguished the mammary gland was mainly a small tissue-specific repertoire of isolated, expressed genes. These findings suggest that an advantage of the neighborhood organization is in the collective repression of groups of genes via a shared mechanism of chromatin repression. Genes essential to the mammary gland's uniqueness are isolated from neighbors, and likely have less tolerance for variation in expression, properties they share with genes responsible for an organism's survival.

  6. Dynamic spatial organization of the occipito-temporal word form area for second language processing.

    Science.gov (United States)

    Gao, Yue; Sun, Yafeng; Lu, Chunming; Ding, Guosheng; Guo, Taomei; Malins, Jeffrey G; Booth, James R; Peng, Danling; Liu, Li

    2017-08-01

    Despite the left occipito-temporal region having shown consistent activation in visual word form processing across numerous studies in different languages, the mechanisms by which word forms of second languages are processed in this region remain unclear. To examine this more closely, 16 Chinese-English and 14 English-Chinese late bilinguals were recruited to perform lexical decision tasks to visually presented words in both their native and second languages (L1 and L2) during functional magnetic resonance imaging scanning. Here we demonstrate that visual word form processing for L1 versus L2 engaged different spatial areas of the left occipito-temporal region. Namely, the spatial organization of the visual word form processing in the left occipito-temporal region is more medial and posterior for L2 than L1 processing in Chinese-English bilinguals, whereas activation is more lateral and anterior for L2 in English-Chinese bilinguals. In addition, for Chinese-English bilinguals, more lateral recruitment of the occipito-temporal region was correlated with higher L2 proficiency, suggesting higher L2 proficiency is associated with greater involvement of L1-preferred mechanisms. For English-Chinese bilinguals, higher L2 proficiency was correlated with more lateral and anterior activation of the occipito-temporal region, suggesting higher L2 proficiency is associated with greater involvement of L2-preferred mechanisms. Taken together, our results indicate that L1 and L2 recruit spatially different areas of the occipito-temporal region in visual word processing when the two scripts belong to different writing systems, and that the spatial organization of this region for L2 visual word processing is dynamically modulated by L2 proficiency. Specifically, proficiency in L2 in Chinese-English is associated with assimilation to the native language mechanisms, whereas L2 in English-Chinese is associated with accommodation to second language mechanisms. Copyright © 2017

  7. Structural organization of poliovirus RNA replication is mediated by viral proteins of the P2 genomic region

    International Nuclear Information System (INIS)

    Bienz, K.; Egger, D.; Troxler, M.; Pasamontes, L.

    1990-01-01

    Transcriptionally active replication complexes bound to smooth membrane vesicles were isolated from poliovirus-infected cells. In electron microscopic, negatively stained preparations, the replication complex appeared as an irregularly shaped, oblong structure attached to several virus-induced vesicles of a rosettelike arrangement. Electron microscopic immunocytochemistry of such preparations demonstrated that the poliovirus replication complex contains the proteins coded by the P2 genomic region (P2 proteins) in a membrane-associated form. In addition, the P2 proteins are also associated with viral RNA, and they can be cross-linked to viral RNA by UV irradiation. Guanidine hydrochloride prevented the P2 proteins from becoming membrane bound but did not change their association with viral RNA. The findings allow the conclusion that the protein 2C or 2C-containing precursor(s) is responsible for the attachment of the viral RNA to the vesicular membrane and for the spatial organization of the replication complex necessary for its proper functioning in viral transcription. A model for the structure of the viral replication complex and for the function of the 2C-containing P2 protein(s) and the vesicular membranes is proposed

  8. Integrating the genomic architecture of human nucleolar organizer regions with the biophysical properties of nucleoli.

    Science.gov (United States)

    Mangan, Hazel; Gailín, Michael Ó; McStay, Brian

    2017-12-01

    Nucleoli are the sites of ribosome biogenesis and the largest membraneless subnuclear structures. They are intimately linked with growth and proliferation control and function as sensors of cellular stress. Nucleoli form around arrays of ribosomal gene (rDNA) repeats also called nucleolar organizer regions (NORs). In humans, NORs are located on the short arms of all five human acrocentric chromosomes. Multiple NORs contribute to the formation of large heterochromatin-surrounded nucleoli observed in most human cells. Here we will review recent findings about their genomic architecture. The dynamic nature of nucleoli began to be appreciated with the advent of photodynamic experiments using fluorescent protein fusions. We review more recent data on nucleoli in Xenopus germinal vesicles (GVs) which has revealed a liquid droplet-like behavior that facilitates nucleolar fusion. Further analysis in both XenopusGVs and Drosophila embryos indicates that the internal organization of nucleoli is generated by a combination of liquid-liquid phase separation and active processes involving rDNA. We will attempt to integrate these recent findings with the genomic architecture of human NORs to advance our understanding of how nucleoli form and respond to stress in human cells. © 2017 Federation of European Biochemical Societies.

  9. Comparison of spatial association approaches for landscape mapping of soil organic carbon stocks

    Science.gov (United States)

    Miller, B. A.; Koszinski, S.; Wehrhan, M.; Sommer, M.

    2015-03-01

    The distribution of soil organic carbon (SOC) can be variable at small analysis scales, but consideration of its role in regional and global issues demands the mapping of large extents. There are many different strategies for mapping SOC, among which is to model the variables needed to calculate the SOC stock indirectly or to model the SOC stock directly. The purpose of this research is to compare direct and indirect approaches to mapping SOC stocks from rule-based, multiple linear regression models applied at the landscape scale via spatial association. The final products for both strategies are high-resolution maps of SOC stocks (kg m-2), covering an area of 122 km2, with accompanying maps of estimated error. For the direct modelling approach, the estimated error map was based on the internal error estimations from the model rules. For the indirect approach, the estimated error map was produced by spatially combining the error estimates of component models via standard error propagation equations. We compared these two strategies for mapping SOC stocks on the basis of the qualities of the resulting maps as well as the magnitude and distribution of the estimated error. The direct approach produced a map with less spatial variation than the map produced by the indirect approach. The increased spatial variation represented by the indirect approach improved R2 values for the topsoil and subsoil stocks. Although the indirect approach had a lower mean estimated error for the topsoil stock, the mean estimated error for the total SOC stock (topsoil + subsoil) was lower for the direct approach. For these reasons, we recommend the direct approach to modelling SOC stocks be considered a more conservative estimate of the SOC stocks' spatial distribution.

  10. Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.

    Science.gov (United States)

    Hacker, William C; Li, Shuxiang; Elcock, Adrian H

    2017-07-27

    We describe structural models of the Escherichia coli chromosome in which the positions of all 4.6 million nucleotides of each DNA strand are resolved. Models consistent with two basic chromosomal orientations, differing in their positioning of the origin of replication, have been constructed. In both types of model, the chromosome is partitioned into plectoneme-abundant and plectoneme-free regions, with plectoneme lengths and branching patterns matching experimental distributions, and with spatial distributions of highly-transcribed chromosomal regions matching recent experimental measurements of the distribution of RNA polymerases. Physical analysis of the models indicates that the effective persistence length of the DNA and relative contributions of twist and writhe to the chromosome's negative supercoiling are in good correspondence with experimental estimates. The models exhibit characteristics similar to those of 'fractal globules,' and even the most genomically-distant parts of the chromosome can be physically connected, through paths combining linear diffusion and inter-segmental transfer, by an average of only ∼10 000 bp. Finally, macrodomain structures and the spatial distributions of co-expressed genes are analyzed: the latter are shown to depend strongly on the overall orientation of the chromosome. We anticipate that the models will prove useful in exploring other static and dynamic features of the bacterial chromosome. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Seasonal and spatial distribution of particulate organic matter in the Bay of Bengal

    Digital Repository Service at National Institute of Oceanography (India)

    Fernandes, L.; Bhosle, N.B.; Matondkar, S.G.P.; Bhushan, R.

    spatial differences were observed for the offshore stations in SPIM (Table 1). 3.4. POC and % POC In the Bay of Bengal, the surface POC concentrations ranged from 4.3 to 11.1 µMC, 3.1 to 10.9 µMC, and 4.3 to 9.0 µMC in the SWM, FIM, and SPIM.... This is NIO contribution no. 4435. 10 References Bale, A., Morris, A., 1998. Organic carbon in suspended particulate material in the North Sea: effect of mixing resuspended and background particles. Cont. Shelf Res. 18, 1333 –1345. Bates, N. R., Dennis, A...

  12. Visualization of genome signatures of eukaryote genomes by batch-learning self-organizing map with a special emphasis on Drosophila genomes.

    Science.gov (United States)

    Abe, Takashi; Hamano, Yuta; Ikemura, Toshimichi

    2014-01-01

    A strategy of evolutionary studies that can compare vast numbers of genome sequences is becoming increasingly important with the remarkable progress of high-throughput DNA sequencing methods. We previously established a sequence alignment-free clustering method "BLSOM" for di-, tri-, and tetranucleotide compositions in genome sequences, which can characterize sequence characteristics (genome signatures) of a wide range of species. In the present study, we generated BLSOMs for tetra- and pentanucleotide compositions in approximately one million sequence fragments derived from 101 eukaryotes, for which almost complete genome sequences were available. BLSOM recognized phylotype-specific characteristics (e.g., key combinations of oligonucleotide frequencies) in the genome sequences, permitting phylotype-specific clustering of the sequences without any information regarding the species. In our detailed examination of 12 Drosophila species, the correlation between their phylogenetic classification and the classification on the BLSOMs was observed to visualize oligonucleotides diagnostic for species-specific clustering.

  13. Spatial sedimentary distribution, seasonality and the characteristics of organic matter on Fernando de Noronha insular shelf

    Directory of Open Access Journals (Sweden)

    Roberto Lima Barcellos

    Full Text Available Abstract The present study was conducted in the Fernando de Noronha archipelago (4°S/32°W. The objective is the evaluation of the spatial distribution and seasonal variations in the sediments and sedimentary organic matter in the northern insular shelf of Fernando de Noronha ("Mar de Dentro". Nineteen surface sediment samples were collected between December 2013, July 2014 and November 2014. The studied methods included analysis of the grain size, coarse fraction, morphoscopy, total organic matter content, calcium carbonate, organic carbon, total nitrogen, sedimentary phosphorus (organic, inorganic and total, elemental ratios (C/N, C/P and stable isotopic ratios (δ13C-δ15N. The results allowed to infer that there is no seasonal variation in sediment distribution. Whereas, the shelf sediments present a calcareous sandy sedimentary cover (CaCO3≈ 88.3%, predominantly of well-sorted fine sands, with low organic matter content (TOM3.0%; TN>0.4% of mixed origin (δ13C= -24.5 to -23.0%PDB, which were related to anthropogenic impacts and the biotic and abiotic local processes.

  14. 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

    Highlights •Bacterial richness and Shannon diversity showed strong spatial autocorrelations. •Fungal richness and Shannon diversity did not show any clear spatial autocorrelations. •Ratio of clay to organic carbon was found a best predictor of bacterial richness and diversities. •Soil water...

  15. Experience in health care organization for victims of Chernobyl accident under conditions of spatial hospitals

    International Nuclear Information System (INIS)

    Nadezhina, N.M.

    1990-01-01

    Experience in organization of health care for victims of Chernobyl accidents under conditions of spatial hospitals are discussed taking into account patients with residual contamination of skin and clothe. A necessity of well-adjusted organization activites, including an inpatient clinic with well-equipped reception, dosimetric, haryological and bacteriological laboratories, an intensive care department, a surgical (burn) department, a blood transfusion laboratory and equipment for plasmopheresis and hemosorption is marked. Therapy of such patients should be developed along the following lines: 1) prevention and therapy of infectious complications; 2) blood cell substitution therapy; 3) bone marrow transplantation; 4) detoxicating therapy; 5) correction of water-electrolyte metabolism; 6) therapy of local radiation injuries

  16. A Self-Organizing Spatial Clustering Approach to Support Large-Scale Network RTK Systems.

    Science.gov (United States)

    Shen, Lili; Guo, Jiming; Wang, Lei

    2018-06-06

    The network real-time kinematic (RTK) technique can provide centimeter-level real time positioning solutions and play a key role in geo-spatial infrastructure. With ever-increasing popularity, network RTK systems will face issues in the support of large numbers of concurrent users. In the past, high-precision positioning services were oriented towards professionals and only supported a few concurrent users. Currently, precise positioning provides a spatial foundation for artificial intelligence (AI), and countless smart devices (autonomous cars, unmanned aerial-vehicles (UAVs), robotic equipment, etc.) require precise positioning services. Therefore, the development of approaches to support large-scale network RTK systems is urgent. In this study, we proposed a self-organizing spatial clustering (SOSC) approach which automatically clusters online users to reduce the computational load on the network RTK system server side. The experimental results indicate that both the SOSC algorithm and the grid algorithm can reduce the computational load efficiently, while the SOSC algorithm gives a more elastic and adaptive clustering solution with different datasets. The SOSC algorithm determines the cluster number and the mean distance to cluster center (MDTCC) according to the data set, while the grid approaches are all predefined. The side-effects of clustering algorithms on the user side are analyzed with real global navigation satellite system (GNSS) data sets. The experimental results indicate that 10 km can be safely used as the cluster radius threshold for the SOSC algorithm without significantly reducing the positioning precision and reliability on the user side.

  17. Cell shape can mediate the spatial organization of the bacterial cytoskeleton

    Science.gov (United States)

    Wang, Siyuan; Wingreen, Ned

    2013-03-01

    The bacterial cytoskeleton guides the synthesis of cell wall and thus regulates cell shape. Since spatial patterning of the bacterial cytoskeleton is critical to the proper control of cell shape, it is important to ask how the cytoskeleton spatially self-organizes in the first place. In this work, we develop a quantitative model to account for the various spatial patterns adopted by bacterial cytoskeletal proteins, especially the orientation and length of cytoskeletal filaments such as FtsZ and MreB in rod-shaped cells. We show that the combined mechanical energy of membrane bending, membrane pinning, and filament bending of a membrane-attached cytoskeletal filament can be sufficient to prescribe orientation, e.g. circumferential for FtsZ or helical for MreB, with the accuracy of orientation increasing with the length of the cytoskeletal filament. Moreover, the mechanical energy can compete with the chemical energy of cytoskeletal polymerization to regulate filament length. Notably, we predict a conformational transition with increasing polymer length from smoothly curved to end-bent polymers. Finally, the mechanical energy also results in a mutual attraction among polymers on the same membrane, which could facilitate tight polymer spacing or bundling. The predictions of the model can be verified through genetic, microscopic, and microfluidic approaches.

  18. Spatial and temporal dynamics of the genetic organization of small mammal populations

    International Nuclear Information System (INIS)

    Smith, M.H.; Manlove, M.N.; Joule, J.

    1978-01-01

    A functional population is a group of organisms and their offspring that contributes to a common gene pool within a certain area and time period. It is also the unit of evolution and should be viewed both in quantitative and qualitative terms. Selection, drift, dispersal, and mutation can alter the composition of populations. Spatial heterogeneity in allele frequencies argues for a conceptual model that has a series of relatively small populations semi-isolated from one another. Because of the relatively high levels of genetic variability characteristic of most mammalian species, significant amounts of gene flow between these spatially subdivided populations must occur when longer time periods are considered. Fluctuations in the genetic structure of populations seem to be important in altering the fitness of the individuals within the populations. The interaction of populations through gene flow is important in changing the levels of intrapopulational genetic variability. Populations can be characterized as existing on a continuum from relatively stable to unstable numbers and by other associated changes in their characteristics. Temporal changes in allele frequency occur in a variety of mammals. Conceptually, a species can be viewed as a series of dynamic populations that vary in numbers and quality in both a spatial and temporal context even over short distances and time periods. Short term changes in the quality of individuals in a population can be important in altering the short term dynamics of a population

  19. The Spatial Properties of Radical Environmental Organizations in the UK: Do or Die!

    Directory of Open Access Journals (Sweden)

    Zack W Almquist

    Full Text Available Radical environmental groups and their members have a wide and varied agenda which often encompasses both local and global issues. In their efforts to call attention to environmental problems, communicate with like-minded groups, and mobilize support for their activities, radical environmental organizations also produce an enormous amount of text, which can be used to estimate the complex communications and task-based networks that underlie these organizations. Moreover, the tactics employed to garnish attention for these groups' agenda can range from peaceful activities such as information dissemination to violent activities such as fire-bombing buildings. To obtain these varied objectives, radical environmental organizations must harness their networks, which have an important spatial component that structures their ability to communicate, coordinate and act on any given agenda item. Here, we analyze a network built from communications and information provided by the semi-annual "Do or Die" (DoD magazine published in the UK over a 10 year period in the late 1990s and early 2000s. We first employ structural topic model methods to discover violent and nonviolent actors within the larger environmental community. Using this designation, we then compare the spatial structure of these groups, finding that violent groups are especially likely to engage in coordination and/or communication if they are sufficiently close, but exhibit a quickly decreasing probability of interaction over even a few kilometers. Further, violent and nonviolent groups each have a higher probability of coordination with their own group than across groups over even short distances. In these respects, we see that violent groups are especially local in their organization and that their geographic reach is likely very limited. This suggests that nonviolent environmental groups seek each other out over both large and short distances for communication and coordination, but violent

  20. The Spatial Properties of Radical Environmental Organizations in the UK: Do or Die!

    Science.gov (United States)

    Almquist, Zack W; Bagozzi, Benjamin E

    2016-01-01

    Radical environmental groups and their members have a wide and varied agenda which often encompasses both local and global issues. In their efforts to call attention to environmental problems, communicate with like-minded groups, and mobilize support for their activities, radical environmental organizations also produce an enormous amount of text, which can be used to estimate the complex communications and task-based networks that underlie these organizations. Moreover, the tactics employed to garnish attention for these groups' agenda can range from peaceful activities such as information dissemination to violent activities such as fire-bombing buildings. To obtain these varied objectives, radical environmental organizations must harness their networks, which have an important spatial component that structures their ability to communicate, coordinate and act on any given agenda item. Here, we analyze a network built from communications and information provided by the semi-annual "Do or Die" (DoD) magazine published in the UK over a 10 year period in the late 1990s and early 2000s. We first employ structural topic model methods to discover violent and nonviolent actors within the larger environmental community. Using this designation, we then compare the spatial structure of these groups, finding that violent groups are especially likely to engage in coordination and/or communication if they are sufficiently close, but exhibit a quickly decreasing probability of interaction over even a few kilometers. Further, violent and nonviolent groups each have a higher probability of coordination with their own group than across groups over even short distances. In these respects, we see that violent groups are especially local in their organization and that their geographic reach is likely very limited. This suggests that nonviolent environmental groups seek each other out over both large and short distances for communication and coordination, but violent groups tend to be

  1. Near-Infrared Imaging for Spatial Mapping of Organic Content in Petroleum Source Rocks

    Science.gov (United States)

    Mehmani, Y.; Burnham, A. K.; Vanden Berg, M. D.; Tchelepi, H.

    2017-12-01

    Natural gas from unconventional petroleum source rocks (shales) plays a key role in our transition towards sustainable low-carbon energy production. The potential for carbon storage (in adsorbed state) in these formations further aligns with efforts to mitigate climate change. Optimizing production and development from these resources requires knowledge of the hydro-thermo-mechanical properties of the rock, which are often strong functions of organic content. This work demonstrates the potential of near-infrared (NIR) spectral imaging in mapping the spatial distribution of organic content with O(100µm) resolution on cores that can span several hundred feet in depth (Mehmani et al., 2017). We validate our approach for the immature oil shale of the Green River Formation (GRF), USA, and show its applicability potential in other formations. The method is a generalization of a previously developed optical approach specialized to the GRF (Mehmani et al., 2016a). The implications of this work for spatial mapping of hydro-thermo-mechanical properties of excavated cores, in particular thermal conductivity, are discussed (Mehmani et al., 2016b). References:Mehmani, Y., A.K. Burnham, M.D. Vanden Berg, H. Tchelepi, "Quantification of organic content in shales via near-infrared imaging: Green River Formation." Fuel, (2017). Mehmani, Y., A.K. Burnham, M.D. Vanden Berg, F. Gelin, and H. Tchelepi. "Quantification of kerogen content in organic-rich shales from optical photographs." Fuel, (2016a). Mehmani, Y., A.K. Burnham, H. Tchelepi, "From optics to upscaled thermal conductivity: Green River oil shale." Fuel, (2016b).

  2. Investigation of the spatial structure and interactions of the genome at sub-kilobase-pair resolution using T2C.

    Science.gov (United States)

    Kolovos, Petros; Brouwer, Rutger W W; Kockx, Christel E M; Lesnussa, Michael; Kepper, Nick; Zuin, Jessica; Imam, A M Ali; van de Werken, Harmen J G; Wendt, Kerstin S; Knoch, Tobias A; van IJcken, Wilfred F J; Grosveld, Frank

    2018-03-01

    Chromosome conformation capture (3C) and its derivatives (e.g., 4C, 5C and Hi-C) are used to analyze the 3D organization of genomes. We recently developed targeted chromatin capture (T2C), an inexpensive method for studying the 3D organization of genomes, interactomes and structural changes associated with gene regulation, the cell cycle, and cell survival and development. Here, we present the protocol for T2C based on capture, describing all experimental steps and bio-informatic tools in full detail. T2C offers high resolution, a large dynamic interaction frequency range and a high signal-to-noise ratio. Its resolution is determined by the resulting fragment size of the chosen restriction enzyme, which can lead to sub-kilobase-pair resolution. T2C's high coverage allows the identification of the interactome of each individual DNA fragment, which makes binning of reads (often used in other methods) basically unnecessary. Notably, T2C requires low sequencing efforts. T2C also allows multiplexing of samples for the direct comparison of multiple samples. It can be used to study topologically associating domains (TADs), determining their position, shape, boundaries, and intra- and inter-domain interactions, as well as the composition of aggregated loops, interactions between nucleosomes, individual transcription factor binding sites, and promoters and enhancers. T2C can be performed by any investigator with basic skills in molecular biology techniques in ∼7-8 d. Data analysis requires basic expertise in bioinformatics and in Linux and Python environments.

  3. [Spatial organization of bioelectrical brain activity in epilepsy and amenorrhea of central genesis].

    Science.gov (United States)

    Avakian, G N; Oleĭnikova, O M; Nerobkova, L N; Dovletkhanova, E R; Mitrofanov, A A; Gusev, E I

    2002-01-01

    The study aimed at modification of co-herent analysis (CA), as a mathematical method for EEG data processing for objective evaluation of bioelectric brain activity spatial organization in women with epilepsy and secondary amenorrhea of central genesis. One hundred sixty one women (30 with epilepsy, 116 with amenorrhea and 115 controls aged 15 to 41 years) have been examined. Characteristic changes of cortico-cortical inter- and intra-hemisphere relations for patients with catamenial (CTM) and noncatamenial (NCTM) epilepsy in different menstrual cycle terms were found. The most distinct changes were detected in theta-activity analysis. In the beginning of menstrual cycle, the patients with CTM epilepsy exhibited higher CA indices in theta-rhythm range in all right hemisphere pairs studied. On the contrary, patients with NCTM epilepsy exhibited lower CA indices mainly in the right brain hemisphere. alpha-rhythm spatial organization analysis in the same patients showed similar correlations, but they were better expressed in alpha-rhythm generation zone: in the beginning of menstrual cycle CA indices were high in patients with CTM epilepsy and low in those with NCTM epilepsy. Comparing to controls, patients with secondary amenorrhea of central genesis showed most distinct changes in theta-activity towards the CA indices increase in the majority of the leads. In patients with epilepsy and amenorrhea, CA indices of right brain hemisphere and intra-central temporal lead pairs were lower than in patients with amenorrhea without epilepsy by both alpha- and theta-rhythms.

  4. Genomic Organization and Expression of Iron Metabolism Genes in the Emerging Pathogenic Mold Scedosporium apiospermum

    Directory of Open Access Journals (Sweden)

    Yohann Le Govic

    2018-04-01

    Full Text Available The ubiquitous mold Scedosporium apiospermum is increasingly recognized as an emerging pathogen, especially among patients with underlying disorders such as immunodeficiency or cystic fibrosis (CF. Indeed, it ranks the second among the filamentous fungi colonizing the respiratory tract of CF patients. However, our knowledge about virulence factors of this fungus is still limited. The role of iron-uptake systems may be critical for establishment of Scedosporium infections, notably in the iron-rich environment of the CF lung. Two main strategies are employed by fungi to efficiently acquire iron from their host or from their ecological niche: siderophore production and reductive iron assimilation (RIA systems. The aim of this study was to assess the existence of orthologous genes involved in iron metabolism in the recently sequenced genome of S. apiospermum. At first, a tBLASTn analysis using A. fumigatus iron-related proteins as query revealed orthologs of almost all relevant loci in the S. apiospermum genome. Whereas the genes putatively involved in RIA were randomly distributed, siderophore biosynthesis and transport genes were organized in two clusters, each containing a non-ribosomal peptide synthetase (NRPS whose orthologs in A. fumigatus have been described to catalyze hydroxamate siderophore synthesis. Nevertheless, comparative genomic analysis of siderophore-related clusters showed greater similarity between S. apiospermum and phylogenetically close molds than with Aspergillus species. The expression level of these genes was then evaluated by exposing conidia to iron starvation and iron excess. The expression of several orthologs of A. fumigatus genes involved in siderophore-based iron uptake or RIA was significantly induced during iron starvation, and conversely repressed in iron excess conditions. Altogether, these results indicate that S. apiospermum possesses the genetic information required for efficient and competitive iron uptake

  5. Genome-wide comparative analysis of ABC systems in the Bdellovibrio-and-like organisms.

    Science.gov (United States)

    Li, Nan; Chen, Huan; Williams, Henry N

    2015-05-10

    Bdellovibrio-and-like organisms (BALOs) are gram-negative, predatory bacteria with wide variations in genome sizes and GC content and ecological habitats. The ATP-binding cassette (ABC) systems have been identified in several prokaryotes, fungi and plants and have a role in transport of materials in and out of cells and in cellular processes. However, knowledge of the ABC systems of BALOs remains obscure. A total of 269 putative ABC proteins were identified in BALOs. The genes encoding these ABC systems occupy nearly 1.3% of the gene content in freshwater Bdellovibrio strains and about 0.7% in their saltwater counterparts. The proteins found belong to 25 ABC system families based on their structural characteristics and functions. Among these, 16 families function as importers, 6 as exporters and 3 are involved in various cellular processes. Eight of these 25 ABC system families were deduced to be the core set of ABC systems conserved in all BALOs. All Bacteriovorax strains have 28 or less ABC systems. On the contrary, the freshwater Bdellovibrio strains have more ABC systems, typically around 51. In the genome of Bdellovibrio exovorus JSS (CP003537.1), 53 putative ABC systems were detected, representing the highest number among all the BALO genomes examined in this study. Unexpected high numbers of ABC systems involved in cellular processes were found in all BALOs. Phylogenetic analysis suggests that the majority of ABC proteins can be assigned into many separate families with high bootstrap supports (>50%). In this study, a general framework of sequence-structure-function connections for the ABC systems in BALOs was revealed providing novel insights for future investigations. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. The copepod Tigriopus: A promising marine model organism for ecotoxicology and environmental genomics

    Energy Technology Data Exchange (ETDEWEB)

    Raisuddin, Sheikh [Department of Chemistry and the National Research Lab of Marine Molecular and Environmental Bioscience, College of Natural Sciences, Hanyang University, Seoul 133-791 (Korea, Republic of); Kwok, Kevin W.H. [Swire Institute of Marine Science, Department of Ecology and Biodiversity, University of Hong Kong, Pokfulam, Hong Kong (China); Leung, Kenneth M.Y. [Swire Institute of Marine Science, Department of Ecology and Biodiversity, University of Hong Kong, Pokfulam, Hong Kong (China); Schlenk, Daniel [Department of Environmental Sciences, University of California, Riverside, CA 92521 (United States); Lee, Jae-Seong [Department of Chemistry and the National Research Lab of Marine Molecular and Environmental Bioscience, College of Natural Sciences, Hanyang University, Seoul 133-791 (Korea, Republic of)]. E-mail: jslee2@hanyang.ac.kr

    2007-07-20

    There is an increasing body of evidence to support the significant role of invertebrates in assessing impacts of environmental contaminants on marine ecosystems. Therefore, in recent years massive efforts have been directed to identify viable and ecologically relevant invertebrate toxicity testing models. Tigriopus, a harpacticoid copepod has a number of promising characteristics which make it a candidate worth consideration in such efforts. Tigriopus and other copepods are widely distributed and ecologically important organisms. Their position in marine food chains is very prominent, especially with regard to the transfer of energy. Copepods also play an important role in the transportation of aquatic pollutants across the food chains. In recent years there has been a phenomenal increase in the knowledge base of Tigriopus spp., particularly in the areas of their ecology, geophylogeny, genomics and their behavioural, biochemical and molecular responses following exposure to environmental stressors and chemicals. Sequences of a number of important marker genes have been studied in various Tigriopus spp., notably T. californicus and T. japonicus. These genes belong to normal biophysiological functions (e.g. electron transport system enzymes) as well as stress and toxic chemical exposure responses (heat shock protein 20, glutathione reductase, glutathione S-transferase). Recently, 40,740 expressed sequenced tags (ESTs) from T. japonicus, have been sequenced and of them, 5673 ESTs showed significant hits (E-value, >1.0E-05) to the red flour beetle Tribolium genome database. Metals and organic pollutants such as antifouling agents, pesticides, polycyclic aromatic hydrocarbons (PAH) and polychrlorinated biphenyls (PCB) have shown reproducible biological responses when tested in Tigriopus spp. Promising results have been obtained when Tigriopus was used for assessment of risk associated with exposure to endocrine-disrupting chemicals (EDCs). Application of environmental

  7. The copepod Tigriopus: A promising marine model organism for ecotoxicology and environmental genomics

    International Nuclear Information System (INIS)

    Raisuddin, Sheikh; Kwok, Kevin W.H.; Leung, Kenneth M.Y.; Schlenk, Daniel; Lee, Jae-Seong

    2007-01-01

    There is an increasing body of evidence to support the significant role of invertebrates in assessing impacts of environmental contaminants on marine ecosystems. Therefore, in recent years massive efforts have been directed to identify viable and ecologically relevant invertebrate toxicity testing models. Tigriopus, a harpacticoid copepod has a number of promising characteristics which make it a candidate worth consideration in such efforts. Tigriopus and other copepods are widely distributed and ecologically important organisms. Their position in marine food chains is very prominent, especially with regard to the transfer of energy. Copepods also play an important role in the transportation of aquatic pollutants across the food chains. In recent years there has been a phenomenal increase in the knowledge base of Tigriopus spp., particularly in the areas of their ecology, geophylogeny, genomics and their behavioural, biochemical and molecular responses following exposure to environmental stressors and chemicals. Sequences of a number of important marker genes have been studied in various Tigriopus spp., notably T. californicus and T. japonicus. These genes belong to normal biophysiological functions (e.g. electron transport system enzymes) as well as stress and toxic chemical exposure responses (heat shock protein 20, glutathione reductase, glutathione S-transferase). Recently, 40,740 expressed sequenced tags (ESTs) from T. japonicus, have been sequenced and of them, 5673 ESTs showed significant hits (E-value, >1.0E-05) to the red flour beetle Tribolium genome database. Metals and organic pollutants such as antifouling agents, pesticides, polycyclic aromatic hydrocarbons (PAH) and polychrlorinated biphenyls (PCB) have shown reproducible biological responses when tested in Tigriopus spp. Promising results have been obtained when Tigriopus was used for assessment of risk associated with exposure to endocrine-disrupting chemicals (EDCs). Application of environmental

  8. Determining the spatial variability of wetland soil bulk density, organic matter, and the conversion factor between organic matter and organic carbon across coastal Louisiana, U.S.A.

    Science.gov (United States)

    Wang, Hongqing; Piazza, Sarai C.; Sharp, Leigh A.; Stagg, Camille L.; Couvillion, Brady R.; Steyer, Gregory D.; McGinnis, Thomas E.

    2016-01-01

    Soil bulk density (BD), soil organic matter (SOM) content, and a conversion factor between SOM and soil organic carbon (SOC) are often used in estimating SOC sequestration and storage. Spatial variability in BD, SOM, and the SOM–SOC conversion factor affects the ability to accurately estimate SOC sequestration, storage, and the benefits (e.g., land building area and vertical accretion) associated with wetland restoration efforts, such as marsh creation and sediment diversions. There are, however, only a few studies that have examined large-scale spatial variability in BD, SOM, and SOM–SOC conversion factors in coastal wetlands. In this study, soil cores, distributed across the entire coastal Louisiana (approximately 14,667 km2) were used to examine the regional-scale spatial variability in BD, SOM, and the SOM–SOC conversion factor. Soil cores for BD and SOM analyses were collected during 2006–09 from 331 spatially well-distributed sites in the Coastwide Reference Monitoring System network. Soil cores for the SOM–SOC conversion factor analysis were collected from 15 sites across coastal Louisiana during 2006–07. Results of a split-plot analysis of variance with incomplete block design indicated that BD and SOM varied significantly at a landscape level, defined by both hydrologic basins and vegetation types. Vertically, BD and SOM varied significantly among different vegetation types. The SOM–SOC conversion factor also varied significantly at the landscape level. This study provides critical information for the assessment of the role of coastal wetlands in large regional carbon budgets and the estimation of carbon credits from coastal restoration.

  9. Spatial Associations and Chemical Composition of Organic Carbon Sequestered in Fe, Ca, and Organic Carbon Ternary Systems.

    Science.gov (United States)

    Sowers, Tyler D; Adhikari, Dinesh; Wang, Jian; Yang, Yu; Sparks, Donald L

    2018-05-25

    Organo-mineral associations of organic carbon (OC) with iron (Fe) oxides play a major role in environmental OC sequestration, a process crucial to mitigating climate change. Calcium has been found to have high coassociation with OC in soils containing high Fe content, increase OC sorption extent to poorly crystalline Fe oxides, and has long been suspected to form bridging complexes with Fe and OC. Due to the growing realization that Ca may be an important component of C cycling, we launched a scanning transmission X-ray microscopy (STXM) investigation, paired with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, in order to spatially resolve Fe, Ca, and OC relationships and probe the effect of Ca on sorbed OC speciation. We performed STXM-NEXAFS analysis on 2-line ferrihydrite reacted with leaf litter-extractable dissolved OC and citric acid in the absence and presence of Ca. Organic carbon was found to highly associate with Ca ( R 2 = 0.91). Carboxylic acid moieties were dominantly sequestered; however, Ca facilitated the additional sequestration of aromatic and phenolic moieties. Also, C NEXAFS revealed polyvalent metal ion complexation. Our results provide evidence for the presence of Fe-Ca-OC ternary complexation, which has the potential to significantly impact how organo-mineral associations are modeled.

  10. Genome-wide significant localization for working and spatial memory: Identifying genes for psychosis using models of cognition.

    Science.gov (United States)

    Knowles, Emma E M; Carless, Melanie A; de Almeida, Marcio A A; Curran, Joanne E; McKay, D Reese; Sprooten, Emma; Dyer, Thomas D; Göring, Harald H; Olvera, Rene; Fox, Peter; Almasy, Laura; Duggirala, Ravi; Kent, Jack W; Blangero, John; Glahn, David C

    2014-01-01

    It is well established that risk for developing psychosis is largely mediated by the influence of genes, but identifying precisely which genes underlie that risk has been problematic. Focusing on endophenotypes, rather than illness risk, is one solution to this problem. Impaired cognition is a well-established endophenotype of psychosis. Here we aimed to characterize the genetic architecture of cognition using phenotypically detailed models as opposed to relying on general IQ or individual neuropsychological measures. In so doing we hoped to identify genes that mediate cognitive ability, which might also contribute to psychosis risk. Hierarchical factor models of genetically clustered cognitive traits were subjected to linkage analysis followed by QTL region-specific association analyses in a sample of 1,269 Mexican American individuals from extended pedigrees. We identified four genome wide significant QTLs, two for working and two for spatial memory, and a number of plausible and interesting candidate genes. The creation of detailed models of cognition seemingly enhanced the power to detect genetic effects on cognition and provided a number of possible candidate genes for psychosis. © 2013 Wiley Periodicals, Inc.

  11. Uncovering the functional constraints underlying the genomic organization of the odorant-binding protein genes.

    Science.gov (United States)

    Librado, Pablo; Rozas, Julio

    2013-01-01

    Animal olfactory systems have a critical role for the survival and reproduction of individuals. In insects, the odorant-binding proteins (OBPs) are encoded by a moderately sized gene family, and mediate the first steps of the olfactory processing. Most OBPs are organized in clusters of a few paralogs, which are conserved over time. Currently, the biological mechanism explaining the close physical proximity among OBPs is not yet established. Here, we conducted a comprehensive study aiming to gain insights into the mechanisms underlying the OBP genomic organization. We found that the OBP clusters are embedded within large conserved arrangements. These organizations also include other non-OBP genes, which often encode proteins integral to plasma membrane. Moreover, the conservation degree of such large clusters is related to the following: 1) the promoter architecture of the confined genes, 2) a characteristic transcriptional environment, and 3) the chromatin conformation of the chromosomal region. Our results suggest that chromatin domains may restrict the location of OBP genes to regions having the appropriate transcriptional environment, leading to the OBP cluster structure. However, the appropriate transcriptional environment for OBP and the other neighbor genes is not dominated by reduced levels of expression noise. Indeed, the stochastic fluctuations in the OBP transcript abundance may have a critical role in the combinatorial nature of the olfactory coding process.

  12. Genomic organization of the rat alpha 2u-globulin gene cluster.

    Science.gov (United States)

    McFadyen, D A; Addison, W; Locke, J

    1999-05-01

    The alpha 2u-globulin are a group of similar proteins, belonging to the lipocalin superfamily of proteins, that are synthesized in a subset of secretory tissues in rats. The many alpha 2u-globulin isoforms are encoded by a multigene family that exhibits extensive homology. Despite a high degree of sequence identity, individual family members show diverse expression patterns involving complex hormonal, tissue-specific, and developmental regulation. Analysis suggests that there are approximately 20 alpha 2u-globulin genes in the rat genome. We have used fluorescence in situ hybridization (FISH) to show that the alpha 2u-globulin genes are clustered at a single site on rat Chromosome (Chr) 5 (5q22-24). Southern blots of rat genomic DNA separated by pulsed field gel electrophoresis indicated that the alpha 2u-globulin genes are contained on two NruI fragments with a total size of 880 kbp. Analysis of three P1 clones containing alpha 2u-globulin genes indicated that the alpha 2u-globulin genes are tandemly arranged in a head-to-tail fashion. The organization of the alpha 2u-globulin genes in the rat as a tandem array of single genes differs from the homologous major urinary protein genes in the mouse, which are organized as tandem arrays of divergently oriented gene pairs. The structure of these gene clusters may have consequences for the proposed function, as a pheromone transporter, for the protein products encoded by these genes.

  13. Expression and Organization of Geographic Spatial Relations Based on Topic Maps

    Science.gov (United States)

    Liang, H. J.; Wang, H.; Cui, T. J.; Guo, J. F.

    2017-09-01

    Spatial Relation is one of the important components of Geographical Information Science and Spatial Database. There have been lots of researches on Spatial Relation and many different spatial relations have been proposed. The relationships among these spatial relations such as hierarchy and so on are complex and this brings some difficulties to the applications and teaching of these spatial relations. This paper summaries some common spatial relations, extracts the topic types, association types, resource types of these spatial relations using the technology of Topic Maps, and builds many different relationships among these spatial relations. Finally, this paper utilizes Java and Ontopia to build a topic map among these common spatial relations, forms a complex knowledge network of spatial relations, and realizes the effective management and retrieval of spatial relations.

  14. Spatial interpolation of soil organic carbon using apparent electrical conductivity as secondary information

    Science.gov (United States)

    Martinez, G.; Vanderlinden, K.; Ordóñez, R.; Muriel, J. L.

    2009-04-01

    Soil organic carbon (SOC) spatial characterization is necessary to evaluate under what circumstances soil acts as a source or sink of carbon dioxide. However, at the field or catchment scale it is hard to accurately characterize its spatial distribution since large numbers of soil samples are necessary. As an alternative, near-surface geophysical sensor-based information can improve the spatial estimation of soil properties at these scales. Electromagnetic induction (EMI) sensors provide non-invasive and non-destructive measurements of the soil apparent electrical conductivity (ECa), which depends under non-saline conditions on clay content, water content or SOC, among other properties that determine the electromagnetic behavior of the soil. This study deals with the possible use of ECa-derived maps to improve SOC spatial estimation by Simple Kriging with varying local means (SKlm). Field work was carried out in a vertisol in SW Spain. The field is part of a long-term tillage experiment set up in 1982 with three replicates of conventional tillage (CT) and Direct Drilling (DD) plots with unitary dimensions of 15x65m. Shallow and deep (up to 0.8m depth) apparent electrical conductivity (ECas and ECad, respectively) was measured using the EM38-DD EMI sensor. Soil samples were taken from the upper horizont and analyzed for their SOC content. Correlation coefficients of ECas and ECad with SOC were low (0.331 and 0.175) due to the small range of SOC values and possibly also to the different support of the ECa and SOC data. Especially the ECas values were higher in the DD plots. The normalized ECa difference (ΔECa), calculated as the difference between the normalized ECas and ECad values, distinguished clearly the CT and DD plots, with the DD plots showing positive ΔECa values and CT plots ΔECa negative values. The field was stratified using fuzzy k-means (FKM) classification of ΔECa (FKM1), and ECas and ECad (FKM2). The FKM1 map mainly showed the difference between

  15. Self-Organization of Genome Expression from Embryo to Terminal Cell Fate: Single-Cell Statistical Mechanics of Biological Regulation

    Directory of Open Access Journals (Sweden)

    Alessandro Giuliani

    2017-12-01

    Full Text Available A statistical mechanical mean-field approach to the temporal development of biological regulation provides a phenomenological, but basic description of the dynamical behavior of genome expression in terms of autonomous self-organization with a critical transition (Self-Organized Criticality: SOC. This approach reveals the basis of self-regulation/organization of genome expression, where the extreme complexity of living matter precludes any strict mechanistic approach. The self-organization in SOC involves two critical behaviors: scaling-divergent behavior (genome avalanche and sandpile-type critical behavior. Genome avalanche patterns—competition between order (scaling and disorder (divergence reflect the opposite sequence of events characterizing the self-organization process in embryo development and helper T17 terminal cell differentiation, respectively. On the other hand, the temporal development of sandpile-type criticality (the degree of SOC control in mouse embryo suggests the existence of an SOC control landscape with a critical transition state (i.e., the erasure of zygote-state criticality. This indicates that a phase transition of the mouse genome before and after reprogramming (immediately after the late 2-cell state occurs through a dynamical change in a control parameter. This result provides a quantitative open-thermodynamic appreciation of the still largely qualitative notion of the epigenetic landscape. Our results suggest: (i the existence of coherent waves of condensation/de-condensation in chromatin, which are transmitted across regions of different gene-expression levels along the genome; and (ii essentially the same critical dynamics we observed for cell-differentiation processes exist in overall RNA expression during embryo development, which is particularly relevant because it gives further proof of SOC control of overall expression as a universal feature.

  16. Some Physical Principles Governing Spatial and Temporal Organization in Living Systems

    Science.gov (United States)

    Ali, Md Zulfikar

    Spatial and temporal organization in living organisms are crucial for a variety of biological functions and arise from the interplay of large number of interacting molecules. One of the central questions in systems biology is to understand how such an intricate organization emerges from the molecular biochemistry of the cell. In this dissertation we explore two projects. The first project relates to pattern formation in a cell membrane as an example of spatial organization, and the second project relates to the evolution of oscillatory networks as a simple example of temporal organization. For the first project, we introduce a model for pattern formation in a two-component lipid bilayer and study the interplay between membrane composition and membrane geometry, demonstrating the existence of a rich phase diagram. Pattern formation is governed by the interplay between phase separation driven by lipid-lipid interactions and tendency of lipid domains with high intrinsic curvature to deform the membrane away from its preferred position. Depending on membrane parameters, we find the formation of compact lipid micro-clusters or of striped domains. We calculate the stripe width analytically and find good agreement with stripe widths obtained from the simulations. For the second project, we introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm and apply it to study the following problems. Using the model, we study robustness and designabilty of a 2-component network that generate oscillations. We completely enumerate the sequence space and the phenotypic space, and discuss the relationship between designabilty, robustness and evolvability. We further apply the model to studies of neutral drift in networks that yield oscillatory dynamics, e.g. starting with a relatively simple network and allowing it to evolve by adding nodes and connections while requiring that oscillatory dynamics be preserved

  17. Watershed scale spatial variability in dissolved and total organic and inorganic carbon in contrasting UK catchments

    Science.gov (United States)

    Cumberland, S.; Baker, A.; Hudson, N. J.

    2006-12-01

    Approximately 800 organic and inorganic carbon analyses have been undertaken from watershed scale and regional scale spatial surveys in various British catchments. These include (1) a small (urban catchment (Ouseburn, N England); (2) a headwater, lowland agricultural catchment (River Tern, C England) (3) a large UK catchment (River Tyne, ~3000 sq-km) and (4) a spatial survey of ~300 analyses from rivers from SW England (~1700 sq-km). Results demonstrate that: (1) the majority of organic and inorganic carbon is in the dissolved (DOC and DIC) fractions; (2) that with the exception of peat rich headwaters, DIC concentration is always greater than DOC; (3) In the rural River Tern, riverine DOC and DIC are shown to follow a simple end- member mixing between DIC (DOC) rich (poor) ground waters and DOC (DIC) rich (poor) riparian wetlands for all sample sites. (4) In the urbanized Ouseburn catchment, although many sample sites also show this same mixing trend, some tributaries follow a pollutant trend of simultaneous increases in both DOC and DIC. The Ouseburn is part of the larger Tyne catchment: this larger catchment follows the simple groundwater DIC- soil water DOC end member mixing model, with the exception of the urban catchments which exhibit an elevated DIC compared to rural sites. (5) Urbanization is demonstrated to increase DIC compared to equivalent rural catchments; this DIC has potential sources including diffuse source inputs from the dissolution of concrete, point sources such as trade effluents and landfill leachates, and bedrock derived carbonates relocated to the soil dissolution zone by urban development. (6) DIC in rural SW England demonstrates that spatial variability in DIC can be attributed to variations in geology; but that DIC concentrations in the SW England rivers dataset are typically lower than the urbanized Tyne catchments despite the presence of carbonate bedrock in many of the sample catchments in the SW England dataset. (7) Recent

  18. Global assessment of soil organic carbon stocks and spatial distribution of histosols: the Machine Learning approach

    Science.gov (United States)

    Hengl, Tomislav

    2016-04-01

    Preliminary results of predicting distribution of soil organic soils (Histosols) and soil organic carbon stock (in tonnes per ha) using global compilations of soil profiles (about 150,000 points) and covariates at 250 m spatial resolution (about 150 covariates; mainly MODIS seasonal land products, SRTM DEM derivatives, climatic images, lithological and land cover and landform maps) are presented. We focus on using a data-driven approach i.e. Machine Learning techniques that often require no knowledge about the distribution of the target variable or knowledge about the possible relationships. Other advantages of using machine learning are (DOI: 10.1371/journal.pone.0125814): All rules required to produce outputs are formalized. The whole procedure is documented (the statistical model and associated computer script), enabling reproducible research. Predicted surfaces can make use of various information sources and can be optimized relative to all available quantitative point and covariate data. There is more flexibility in terms of the spatial extent, resolution and support of requested maps. Automated mapping is also more cost-effective: once the system is operational, maintenance and production of updates are an order of magnitude faster and cheaper. Consequently, prediction maps can be updated and improved at shorter and shorter time intervals. Some disadvantages of automated soil mapping based on Machine Learning are: Models are data-driven and any serious blunders or artifacts in the input data can propagate to order-of-magnitude larger errors than in the case of expert-based systems. Fitting machine learning models is at the order of magnitude computationally more demanding. Computing effort can be even tens of thousands higher than if e.g. linear geostatistics is used. Many machine learning models are fairly complex often abstract and any interpretation of such models is not trivial and require special multidimensional / multivariable plotting and data mining

  19. Mapping of soil organic carbon stocks for spatially explicit assessments of climate change mitigation potential

    International Nuclear Information System (INIS)

    Vågen, Tor-Gunnar; Winowiecki, Leigh A

    2013-01-01

    Current methods for assessing soil organic carbon (SOC) stocks are generally not well suited for understanding variations in SOC stocks in landscapes. This is due to the tedious and time-consuming nature of the sampling methods most commonly used to collect bulk density cores, which limits repeatability across large areas, particularly where information is needed on the spatial dynamics of SOC stocks at scales relevant to management and for spatially explicit targeting of climate change mitigation options. In the current study, approaches were explored for (i) field-based estimates of SOC stocks and (ii) mapping of SOC stocks at moderate to high resolution on the basis of data from four widely contrasting ecosystems in East Africa. Estimated SOC stocks for 0–30 cm depth varied both within and between sites, with site averages ranging from 2 to 8 kg m −2 . The differences in SOC stocks were determined in part by rainfall, but more importantly by sand content. Results also indicate that managing soil erosion is a key strategy for reducing SOC loss and hence in mitigation of climate change in these landscapes. Further, maps were developed on the basis of satellite image reflectance data with multiple R-squared values of 0.65 for the independent validation data set, showing variations in SOC stocks across these landscapes. These maps allow for spatially explicit targeting of potential climate change mitigation efforts through soil carbon sequestration, which is one option for climate change mitigation and adaptation. Further, the maps can be used to monitor the impacts of such mitigation efforts over time. (letter)

  20. A Self-Organizing Spatial Clustering Approach to Support Large-Scale Network RTK Systems

    Directory of Open Access Journals (Sweden)

    Lili Shen

    2018-06-01

    Full Text Available The network real-time kinematic (RTK technique can provide centimeter-level real time positioning solutions and play a key role in geo-spatial infrastructure. With ever-increasing popularity, network RTK systems will face issues in the support of large numbers of concurrent users. In the past, high-precision positioning services were oriented towards professionals and only supported a few concurrent users. Currently, precise positioning provides a spatial foundation for artificial intelligence (AI, and countless smart devices (autonomous cars, unmanned aerial-vehicles (UAVs, robotic equipment, etc. require precise positioning services. Therefore, the development of approaches to support large-scale network RTK systems is urgent. In this study, we proposed a self-organizing spatial clustering (SOSC approach which automatically clusters online users to reduce the computational load on the network RTK system server side. The experimental results indicate that both the SOSC algorithm and the grid algorithm can reduce the computational load efficiently, while the SOSC algorithm gives a more elastic and adaptive clustering solution with different datasets. The SOSC algorithm determines the cluster number and the mean distance to cluster center (MDTCC according to the data set, while the grid approaches are all predefined. The side-effects of clustering algorithms on the user side are analyzed with real global navigation satellite system (GNSS data sets. The experimental results indicate that 10 km can be safely used as the cluster radius threshold for the SOSC algorithm without significantly reducing the positioning precision and reliability on the user side.

  1. Genome Compositional Organization in Gars Shows More Similarities to Mammals than to Other Ray-Finned Fish.

    Science.gov (United States)

    Symonová, Radka; Majtánová, Zuzana; Arias-Rodriguez, Lenin; Mořkovský, Libor; Kořínková, Tereza; Cavin, Lionel; Pokorná, Martina Johnson; Doležálková, Marie; Flajšhans, Martin; Normandeau, Eric; Ráb, Petr; Meyer, Axel; Bernatchez, Louis

    2017-11-01

    Genomic GC content can vary locally, and GC-rich regions are usually associated with increased DNA thermostability in thermophilic prokaryotes and warm-blooded eukaryotes. Among vertebrates, fish and amphibians appeared to possess a distinctly less heterogeneous AT/GC organization in their genomes, whereas cytogenetically detectable GC heterogeneity has so far only been documented in mammals and birds. The subject of our study is the gar, an ancient "living fossil" of a basal ray-finned fish lineage, known from the Cretaceous period. We carried out cytogenomic analysis in two gar genera (Atractosteus and Lepisosteus) uncovering a GC chromosomal pattern uncharacteristic for fish. Bioinformatic analysis of the spotted gar (Lepisosteus oculatus) confirmed a GC compartmentalization on GC profiles of linkage groups. This indicates a rather mammalian mode of compositional organization on gar chromosomes. Gars are thus the only analyzed extant ray-finned fishes with a GC compartmentalized genome. Since gars are cold-blooded anamniotes, our results contradict the generally accepted hypothesis that the phylogenomic onset of GC compartmentalization occurred near the origin of amniotes. Ecophysiological findings of other authors indicate a metabolic similarity of gars with mammals. We hypothesize that gars might have undergone convergent evolution with the tetrapod lineages leading to mammals on both metabolic and genomic levels. Their metabolic adaptations might have left footprints in their compositional genome evolution, as proposed by the metabolic rate hypothesis. The genome organization described here in gars sheds new light on the compositional genome evolution in vertebrates generally and contributes to better understanding of the complexities of the mechanisms involved in this process. © 2016 Wiley Periodicals, Inc.

  2. Spatial and environmental correlates of organism colonization and infection in the neonatal intensive care unit.

    Science.gov (United States)

    Goldstein, Neal D; Tuttle, Deborah; Tabb, Loni P; Paul, David A; Eppes, Stephen C

    2018-05-01

    To examine organism colonization and infection in the neonatal intensive care unit as a result of environmental and spatial factors. A retrospective cohort of infants admitted between 2006 and 2015 (n = 11 428), to assess the relationship between location and four outcomes: methicillin-resistant Staphylococcus aureus (MRSA) colonization; culture-confirmed late-onset sepsis; and, if intubated, endotracheal tube colonization with Pseudomonas aeruginosa or Klebsiella pneumonia. Independent risk factors were identified with mixed-effects logistic regression models and Moran's I for spatial autocorrelation. All four outcomes statistically clustered by location; neighboring colonization also influenced risk of MRSA (p < 0.05). For P. aeruginosa, being in a location with space for more medical equipment was associated with 2.61 times the odds of colonization (95% CrI: 1.19, 5.78). Extrinsic factors partially explained risk for neonatal colonization and infection. For P. aeruginosa, infection prevention efforts at locations with space for more equipment may lower future colonization.

  3. Towards a Sustainable Spatial Organization of the Energy System: Backcasting Experiences from Austria

    Directory of Open Access Journals (Sweden)

    Markus Knoflacher

    2012-02-01

    Full Text Available The transition to a sustainable energy system faces more challenges than a simple replacement of fossil energy sources by renewable ones. Since current structures do not favor sustainable energy generation and use, it is indispensable to change the existing infrastructure. A fundamental change of the energy system also requires re-organizing spatial structures and their respective institutions and governance structures. Especially in Austria, urban sprawl and unsustainable settlement structures are regarded as one of the main developments leading to increased energy demand. One of the aims within the project E-Trans 2050 was to identify socio-economic constellations that are central to the further transformation of the energy system and to focus on actors and their socio-technical framework conditions. Based on a sustainable future vision for the year 2050 a backcasting workshop was conducted to identify necessary steps for the envisaged transition to a more sustainable energy system. The results shed light on the necessary changes for a transformation towards sustainability in the specific Austrian situation. Critical issues are region-specific production of energy and its use, settlement and regional structures and values and role models, which all have a determining influence on energy demand. Combining the knowledge of extensive energy use with available energy resources in spatial planning decisions is a main challenge towards a long term sustainable energy system.

  4. Spatial organization and correlation properties quantify structural changes on mesoscale of parenchymatous plant tissue

    Energy Technology Data Exchange (ETDEWEB)

    Valous, N. A.; Delgado, A.; Sun, D.-W., E-mail: dawen.sun@ucd.ie [School of Biosystems Engineering, University College Dublin, National University of Ireland, Belfield, Dublin 4, Dublin (Ireland); Drakakis, K. [Complex and Adaptive Systems Laboratory, University College Dublin, National University of Ireland, Belfield, Dublin 4, Dublin (Ireland)

    2014-02-14

    The study of plant tissue parenchyma's intercellular air spaces contributes to the understanding of anatomy and physiology. This is challenging due to difficulty in making direct measurements of the pore space and the complex mosaic of parenchymatous tissue. The architectural complexity of pore space has shown that single geometrical measurements are not sufficient for characterization. The inhomogeneity of distribution depends not only on the percentage content of phase, but also on how the phase fills the space. The lacunarity morphometric, as multiscale measure, provides information about the distribution of gaps that correspond to degree of spatial organization in parenchyma. Additionally, modern theories have suggested strategies, where the focus has shifted from the study of averages and histograms to the study of patterns in data fluctuations. Detrended fluctuation analysis provides information on the correlation properties of the parenchyma at different spatial scales. The aim is to quantify (with the aid of the aforementioned metrics), the mesostructural changes—that occur from one cycle of freezing and thawing—in the void phase of pome fruit parenchymatous tissue, acquired with X-ray microcomputed tomography. Complex systems methods provide numerical indices and detailed insights regarding the freezing-induced modifications upon the arrangement of cells and voids. These structural changes have the potential to lead to physiological disorders. The work can further stimulate interest for the analysis of internal plant tissue structures coupled with other physico-chemical processes or phenomena.

  5. Spatial organization and correlation properties quantify structural changes on mesoscale of parenchymatous plant tissue

    International Nuclear Information System (INIS)

    Valous, N. A.; Delgado, A.; Sun, D.-W.; Drakakis, K.

    2014-01-01

    The study of plant tissue parenchyma's intercellular air spaces contributes to the understanding of anatomy and physiology. This is challenging due to difficulty in making direct measurements of the pore space and the complex mosaic of parenchymatous tissue. The architectural complexity of pore space has shown that single geometrical measurements are not sufficient for characterization. The inhomogeneity of distribution depends not only on the percentage content of phase, but also on how the phase fills the space. The lacunarity morphometric, as multiscale measure, provides information about the distribution of gaps that correspond to degree of spatial organization in parenchyma. Additionally, modern theories have suggested strategies, where the focus has shifted from the study of averages and histograms to the study of patterns in data fluctuations. Detrended fluctuation analysis provides information on the correlation properties of the parenchyma at different spatial scales. The aim is to quantify (with the aid of the aforementioned metrics), the mesostructural changes—that occur from one cycle of freezing and thawing—in the void phase of pome fruit parenchymatous tissue, acquired with X-ray microcomputed tomography. Complex systems methods provide numerical indices and detailed insights regarding the freezing-induced modifications upon the arrangement of cells and voids. These structural changes have the potential to lead to physiological disorders. The work can further stimulate interest for the analysis of internal plant tissue structures coupled with other physico-chemical processes or phenomena

  6. Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L. Genome

    Directory of Open Access Journals (Sweden)

    Navdeep Gill

    2014-04-01

    Full Text Available Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence.

  7. Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

    Science.gov (United States)

    Gill, Navdeep; Buti, Matteo; Kane, Nolan; Bellec, Arnaud; Helmstetter, Nicolas; Berges, Hélène; Rieseberg, Loren H.

    2014-01-01

    Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence. PMID:24833511

  8. Temporal and spatial distributions of sediment total organic carbon in an estuary river.

    Science.gov (United States)

    Ouyang, Y; Zhang, J E; Ou, L-T

    2006-01-01

    Understanding temporal and spatial distributions of naturally occurring total organic carbon (TOC) in sediments is critical because TOC is an important feature of surface water quality. This study investigated temporal and spatial distributions of sediment TOC and its relationships to sediment contaminants in the Cedar and Ortega Rivers, Florida, USA, using three-dimensional kriging analysis and field measurement. Analysis of field data showed that large temporal changes in sediment TOC concentrations occurred in the rivers, which reflected changes in the characteristics and magnitude of inputs into the rivers during approximately the last 100 yr. The average concentration of TOC in sediments from the Cedar and Ortega Rivers was 12.7% with a maximum of 22.6% and a minimum of 2.3%. In general, more TOC accumulated at the upper 1.0 m of the sediment in the southern part of the Ortega River although the TOC sedimentation varied with locations and depths. In contrast, high concentrations of sediment contaminants, that is, total polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs), were found in sediments from the Cedar River. There was no correlation between TOC and PAHs or PCBs in these river sediments. This finding is in contradiction to some other studies which reported that the sorption of hydrocarbons is highly related to the organic matter content of sediments. This discrepancy occurred because of the differences in TOC and hydrocarbon source input locations. It was found that more TOC loaded into the southern part of the Ortega River, while almost all of the hydrocarbons entered into the Cedar River. This study suggested that the locations of their input sources as well as the land use patterns should also be considered when relating hydrocarbons to sediment TOC.

  9. Spatial and historical distribution of organic phosphorus driven by environment conditions in lake sediments.

    Science.gov (United States)

    Lü, Changwei; He, Jiang; Wang, Bing

    2018-02-01

    The chemistry of sedimentary organic phosphorus (OP) and its fraction distribution in sediments are greatly influenced by environmental conditions such as terrestrial inputs and runoffs. The linkage of OP with environmental conditions was analyzed on the basis of OP spatial and historical distributions in lake sediments. The redundancy analysis and OP spatial distribution results suggested that both NaOH-OP (OP extracted by NaOH) and Re-OP (residual OP) in surface sediments from the selected 13 lakes reflected the gradient effects of environmental conditions and the autochthonous and/or allochthonous inputs driven by latitude zonality in China. The lake level and salinity of Lake Hulun and the runoff and precipitation of its drainage basin were reconstructed on the basis of the geochemistry index. This work showed that a gradient in weather conditions presented by the latitude zonality in China impacts the OP accumulation through multiple drivers and in many ways. The drivers are mainly precipitation and temperature, governing organic matter (OM) production, degradation rate and transportation in the watershed. Over a long temporal dimension (4000years), the vertical distributions of Re-OP and NaOH-OP based on a dated sediment profile from HLH were largely regulated by the autochthonous and/or allochthonous inputs, which depended on the environmental and climate conditions and anthropogenic activities in the drainage basin. This work provides useful environmental geochemistry information to understand the inherent linkage of OP fractionation with environmental conditions and lake evolution. Copyright © 2017. Published by Elsevier B.V.

  10. Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes

    Directory of Open Access Journals (Sweden)

    Schnitzler Christine E

    2012-12-01

    Full Text Available Abstract Background Calcium-activated photoproteins are luciferase variants found in photocyte cells of bioluminescent jellyfish (Phylum Cnidaria and comb jellies (Phylum Ctenophora. The complete genomic sequence from the ctenophore Mnemiopsis leidyi, a representative of the earliest branch of animals that emit light, provided an opportunity to examine the genome of an organism that uses this class of luciferase for bioluminescence and to look for genes involved in light reception. To determine when photoprotein genes first arose, we examined the genomic sequence from other early-branching taxa. We combined our genomic survey with gene trees, developmental expression patterns, and functional protein assays of photoproteins and opsins to provide a comprehensive view of light production and light reception in Mnemiopsis. Results The Mnemiopsis genome has 10 full-length photoprotein genes situated within two genomic clusters with high sequence conservation that are maintained due to strong purifying selection and concerted evolution. Photoprotein-like genes were also identified in the genomes of the non-luminescent sponge Amphimedon queenslandica and the non-luminescent cnidarian Nematostella vectensis, and phylogenomic analysis demonstrated that photoprotein genes arose at the base of all animals. Photoprotein gene expression in Mnemiopsis embryos begins during gastrulation in migrating precursors to photocytes and persists throughout development in the canals where photocytes reside. We identified three putative opsin genes in the Mnemiopsis genome and show that they do not group with well-known bilaterian opsin subfamilies. Interestingly, photoprotein transcripts are co-expressed with two of the putative opsins in developing photocytes. Opsin expression is also seen in the apical sensory organ. We present evidence that one opsin functions as a photopigment in vitro, absorbing light at wavelengths that overlap with peak photoprotein light

  11. Water chemistry in Kuji river. Its spatial and seasonal variations in major ions and organic substances

    Energy Technology Data Exchange (ETDEWEB)

    Niina, Toshiaki; Matsunaga, Takeshi; Amano, Hikaru [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1996-02-01

    As a basic research with a aim to clarify the migration behavior of radionuclides in rivers, the characteristics of dissolved ions and organic substances in river water, which characteristics may affect the behavior, was investigated. The investigation was carried out for the Kuji river in the northern Kanto district (Japan) comprising four sampling campaigns in 1994 for 10 locations from the upstream to the downstream. Concentrations of major ions, iron and manganese species and organic substances were analyzed in laboratory. Values of temperature of the water, pH, conductivity, dissolved oxygen were measured in the field. This investigation was conducted mainly under low water flow conditions of the river, while a limited number of campaigns were under high flow conditions due to precipitation events. The concentrations of major inorganic ions increased steadily toward the down-stream, resulting in approximately two times increase for the traveling distance of 100 km. They showed a seasonal variation that they were highest in the spring and lowest in the autumn when there were most concentrated precipitation events in a year. The constituents were mainly Na{sup +}, Ca{sup 2+}, SO{sub 4}{sup 2-} and HCO{sub 3}{sup -}, and were similar for every sampling locations and seasons. Concentrations of dissolved organic substances (carbon compounds) were lowest in the upstream and increased about twice in the downstream as well as major inorganic ions. Their level was 1-3 mg/l, which can be ranked as relatively lower in general values for fresh water environments. They were highest in the spring (average over the locations: 2.2 mg/l) and lowest in the autumn (1.3 mg/l) and also in the winter (1.3 mg/l). These results will be useful as a basic understanding of spatial and seasonal variations of river water chemistry, especially related to the organic substances which can bind with radionuclides to make a mobile complex. (author).

  12. Water chemistry in Kuji river. Its spatial and seasonal variations in major ions and organic substances

    International Nuclear Information System (INIS)

    Niina, Toshiaki; Matsunaga, Takeshi; Amano, Hikaru

    1996-02-01

    As a basic research with a aim to clarify the migration behavior of radionuclides in rivers, the characteristics of dissolved ions and organic substances in river water, which characteristics may affect the behavior, was investigated. The investigation was carried out for the Kuji river in the northern Kanto district (Japan) comprising four sampling campaigns in 1994 for 10 locations from the upstream to the downstream. Concentrations of major ions, iron and manganese species and organic substances were analyzed in laboratory. Values of temperature of the water, pH, conductivity, dissolved oxygen were measured in the field. This investigation was conducted mainly under low water flow conditions of the river, while a limited number of campaigns were under high flow conditions due to precipitation events. The concentrations of major inorganic ions increased steadily toward the down-stream, resulting in approximately two times increase for the traveling distance of 100 km. They showed a seasonal variation that they were highest in the spring and lowest in the autumn when there were most concentrated precipitation events in a year. The constituents were mainly Na + , Ca 2+ , SO 4 2- and HCO 3 - , and were similar for every sampling locations and seasons. Concentrations of dissolved organic substances (carbon compounds) were lowest in the upstream and increased about twice in the downstream as well as major inorganic ions. Their level was 1-3 mg/l, which can be ranked as relatively lower in general values for fresh water environments. They were highest in the spring (average over the locations: 2.2 mg/l) and lowest in the autumn (1.3 mg/l) and also in the winter (1.3 mg/l). These results will be useful as a basic understanding of spatial and seasonal variations of river water chemistry, especially related to the organic substances which can bind with radionuclides to make a mobile complex. (author)

  13. Spatial variation of dissolved organic matter composition and characteristics in an urbanized watershed

    Science.gov (United States)

    Hsieh, C.; Li, M.

    2013-12-01

    Dissolved organic matter (DOM) is a chemically complex mixture of organic polymers that plays an important role in river ecosystems and originates from various sources. Some DOMs are autochthonous originating through phytoplankton and microbial activity in situ. On the other hand, some DOMs are allochthonous which are transported to river from the surrounding watershed by natural or anthropogenic activities. The studies of DOM in river are usually conducted at the watershed scale; however, factors of local spatial scale affecting DOM composition also need to take into consideration for the study of DOM in an urbanized watershed. Through increasing urbanization, changes in a watershed occur not only in land use patterns but also in river channel characteristics. The objective of this study is to investigate effects of different river channel characteristics and patterns on changes in DOM source and composition. In this study, we chose three tributaries of Tamsui river in Taiwan according to its land use pattern and river channel characteristics. At each sub-basin, river water samples were sampled from three study sites. River water DOM was measured by using optical measurements of UV absorption and fluorescence spectroscopy. Water samples were also collected for laboratory analysis of different water quality parameters. From our study sites, they are from three sub-basins which are in the similar physical environments but with different river channel types: the highly channelized Keelung river, the less channelized Xindian river, and less channelized Dahan river with five human-made wetlands. From the upstream to the urbanized downstream, composition of DOM showed variation among different sampled sites. In all three sub-basins, the trends of 5-day biochemical oxygen demand (BOD5) and suspended solids (SS) are also different. The changes in DOM source and composition as well as different water quality parmaters occur at the local spatial-scale depended on their

  14. Spatial organization of seismicity and fracture pattern at the boundary between Alps and Dinarides

    Science.gov (United States)

    Bressan, Gianni; Ponton, Maurizio; Rossi, Giuliana; Urban, Sandro

    2016-04-01

    The paper affords the study of the spatial organization of seismicity in the easternmost region of the Alps (Friuli, in NE Italy and W Slovenia), dominated by the interference between the Alpine and the Dinaric tectonic systems. Two non-conventional methods of spatial analysis are used: fractal analysis and principal component analysis (PCA). The fractal analysis helps to discriminate the cases in which hypocentres clearly define a plane, from the ones in which hypocenter distribution tends to the planarity, without reaching it. The PCA analysis is used to infer the orientation of planes fitting through earthquake foci, or the direction of propagation of the hypocentres. Furthermore, we study the spatial seismicity pattern at the shallow depths in the context of a general damage model, through the crack density distribution. The results of the three methods concur to a complex and composite model of fracturing in the region. The hypocentre pattern fills only partially a plane, i.e. has a fractal dimension close to 2. The three exceptions regard planes with Dinaric trend, without interference with Alpine lineaments. The shallowest depth range (0-10 km depth) is characterized by the activation of planes with variable orientations, reflecting the interference between the Dinaric and the Alpine tectonic structures, and closely bound to the variation of the mechanical properties of the crust. The seismicity occurs mostly in areas characterized by a variation from low to moderate crack density, indicating the sharp transition from zones of low damage to zones of moderate damage. Low crack density indicates the presence of more competent rocks capable of sustaining high strain energy while high crack density areas pertain to highly fractured rocks that cannot store high strain energy. Brittle failure, i.e. seismic activity, is favoured within the sharp transitions from low to moderate crack density zones. The orientation of the planes depicting the seismic activity

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

    Science.gov (United States)

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

    2016-12-01

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

  16. Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions

    Directory of Open Access Journals (Sweden)

    Balding David J

    2008-12-01

    Full Text Available Abstract Background The power of haplotype-based methods for association studies, identification of regions under selection, and ancestral inference, is well-established for diploid organisms. For polyploids, however, the difficulty of determining phase has limited such approaches. Polyploidy is common in plants and is also observed in animals. Partial polyploidy is sometimes observed in humans (e.g. trisomy 21; Down's syndrome, and it arises more frequently in some human tissues. Local changes in ploidy, known as copy number variations (CNV, arise throughout the genome. Here we present a method, implemented in the software polyHap, for the inference of haplotype phase and missing observations from polyploid genotypes. PolyHap allows each individual to have a different ploidy, but ploidy cannot vary over the genomic region analysed. It employs a hidden Markov model (HMM and a sampling algorithm to infer haplotypes jointly in multiple individuals and to obtain a measure of uncertainty in its inferences. Results In the simulation study, we combine real haplotype data to create artificial diploid, triploid, and tetraploid genotypes, and use these to demonstrate that polyHap performs well, in terms of both switch error rate in recovering phase and imputation error rate for missing genotypes. To our knowledge, there is no comparable software for phasing a large, densely genotyped region of chromosome from triploids and tetraploids, while for diploids we found polyHap to be more accurate than fastPhase. We also compare the results of polyHap to SATlotyper on an experimentally haplotyped tetraploid dataset of 12 SNPs, and show that polyHap is more accurate. Conclusion With the availability of large SNP data in polyploids and CNV regions, we believe that polyHap, our proposed method for inferring haplotypic phase from genotype data, will be useful in enabling researchers analysing such data to exploit the power of haplotype-based analyses.

  17. Linking the spatial patterns of organisms and abiotic factors to ecosystem function and management: insights from semi-arid environments

    Directory of Open Access Journals (Sweden)

    F. T. Maestre

    2006-12-01

    Full Text Available Numerous theoretical and modeling studies have demonstrated the ecological significance of the spatial patterning of organisms on ecosystem functioning and dynamics. However, there is a paucity of empirical evidence that quantitatively shows how changes in the spatial patterns of the organisms forming biotic communities are directly related to ecosystem structure and functioning. In this article, I review a series of experiments and observational studies conducted in semi-arid environments from Spain (degraded calcareous shrubland, steppes dominated by Stipa tenacissima, and gypsum shrublands to: 1 evaluate whether the spatial patterns of the dominant biotic elements in the community are linked to ecosystem structure and functioning, and 2 test if these patterns, and those of abiotic factors, can be used to improve ecosystem restoration. In the semiarid steppes we found a significant positive relationship between the spatial pattern of the perennial plant community and: i the water status of S. tenacissima and ii perennial species richness and diversity. Experimental plantings conducted in these steppes showed that S. tenacissima facilitated the establishment of shrub seedlings, albeit the magnitude and direction of this effect was dependent on rainfall conditions during the first yr after planting. In the gypsum shrubland, a significant, direct relationship between the spatial pattern of the biological soil crusts and surrogates of ecosystem functioning (soil bulk density and respiration was found. In a degraded shrubland with very low vegetation cover, the survival of an introduced population of the shrub Pistacia lentiscus showed marked spatial patterns, which were related to the spatial patterns of soil properties such as soil compaction and sand content. These results provide empirical evidence on the importance of spatial patterns for maintaining ecosystem structure and functioning in semi-arid ecosystems

  18. Looping and clustering model for the organization of protein-DNA complexes on the bacterial genome

    Science.gov (United States)

    Walter, Jean-Charles; Walliser, Nils-Ole; David, Gabriel; Dorignac, Jérôme; Geniet, Frédéric; Palmeri, John; Parmeggiani, Andrea; Wingreen, Ned S.; Broedersz, Chase P.

    2018-03-01

    The bacterial genome is organized by a variety of associated proteins inside a structure called the nucleoid. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the looping and clustering model, which employs a statistical physics approach to describe protein-DNA complexes. The looping and clustering model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins that is organized around a single high-affinity binding site. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and loop closure entropy of this protein-DNA cluster on the one hand, and the positional entropy for placing loops within the cluster on the other. Indeed, we show that the protein interaction strength determines the ‘tightness’ of the loopy protein-DNA complex. Thus, our model provides a theoretical framework for quantitatively computing the binding profiles of ParB-like proteins around a cognate (parS) binding site.

  19. Large differences in the genome organization of different plant Trypanosomatid parasites (Phytomonas spp.) reveal wide evolutionary divergences between taxa.

    Science.gov (United States)

    Marín, C; Dollet, M; Pagès, M; Bastien, P

    2009-03-01

    All currently known plant trypanosomes have been grouped in the genus Phytomonas spp., although they can differ greatly in terms of both their biological properties and effects upon the host. Those parasitizing the phloem sap are specifically associated with lethal syndromes in Latin America, such as, phloem necrosis of coffee, 'Hartrot' of coconut and 'Marchitez sorpresiva' of oil palm, that inflict considerable economic losses in endemic countries. The genomic organization of one group of Phytomonas (D) considered as representative of the genus has been published previously. The present work presents the genomic structure of two representative isolates from the pathogenic phloem-restricted group (H) of Phytomonas, analyzed by pulsed field gel electrophoresis followed by hybridization with chromosome-specific DNA markers. It came as a surprise to observe an extremely different genomic organization in this group as compared with that of group D. Most notably, the chromosome number is 7 in this group (with a genome size of 10 Mb) versus 21 in the group D (totalling 25 Mb). These data unravel an unsuspected genomic diversity within plant trypanosomatids, that may justify a further debate about their division into different genera.

  20. Inter- and intra-organ spatial distributions of sea star saponins by MALDI imaging.

    Science.gov (United States)

    Demeyer, Marie; Wisztorski, Maxence; Decroo, Corentin; De Winter, Julien; Caulier, Guillaume; Hennebert, Elise; Eeckhaut, Igor; Fournier, Isabelle; Flammang, Patrick; Gerbaux, Pascal

    2015-11-01

    Saponins are secondary metabolites that are abundant and diversified in echinoderms. Mass spectrometry is increasingly used not only to identify saponin congeners within animal extracts but also to decipher the structure/biological activity relationships of these molecules by determining their inter-organ and inter-individual variability. The usual method requires extensive purification procedures to prepare saponin extracts compatible with mass spectrometry analysis. Here, we selected the sea star Asterias rubens as a model animal to prove that direct analysis of saponins can be performed on tissue sections. We also demonstrated that carboxymethyl cellulose can be used as an embedding medium to facilitate the cryosectioning procedure. Matrix-assisted laser desorption/ionization (MALDI) imaging was also revealed to afford interesting data on the distribution of saponin molecules within the tissues. We indeed highlight that saponins are located not only inside the body wall of the animals but also within the mucus layer that probably protects the animal against external aggressions. Graphical Abstract Saponins are the most abundant secondary metabolites in sea stars. They should therefore participate in important biological activities. Here, MALDI imaging is presented as a powerful method to determine the spatial distribution of saponins within the animal tissues. The inhomogeneity of the intra-organ saponin distribution is highlighted, paving the way for future elegant structure/activity relationship investigations.

  1. Spatial organization of heterologous metabolic system in vivo based on TALE.

    Science.gov (United States)

    Zhu, Lv-yun; Qiu, Xin-Yuan; Zhu, Ling-Yun; Wu, Xiao-Min; Zhang, Yuan; Zhu, Qian-Hui; Fan, Dong-Yu; Zhu, Chu-Shu; Zhang, Dong-Yi

    2016-05-17

    For years, prokaryotic hosts have been widely applied in bio-engineering. However, the confined in vivo enzyme clustering of heterologous metabolic pathways in these organisms often results in low local concentrations of enzymes and substrates, leading to a low productive efficacy. We developed a new method to accelerate a heterologous metabolic system by integrating a transcription activator-like effector (TALE)-based scaffold system into an Escherichia coli chassis. The binding abilities of the TALEs to the artificial DNA scaffold were measured through ChIP-PCR. The effect of the system was determined through a split GFP study and validated through the heterologous production of indole-3-acetic acid (IAA) by incorporating TALE-fused IAA biosynthetic enzymes in E. coli. To the best of our knowledge, we are the first to use the TALE system as a scaffold for the spatial organization of bacterial metabolism. This technique might be used to establish multi-enzymatic reaction programs in a prokaryotic chassis for various applications.

  2. Function of chemoreceptor organs in spatial orientation of the lobster, Homarus americanus: differences and overlap

    Energy Technology Data Exchange (ETDEWEB)

    Devine, D.V.; Atema, J.

    1982-08-01

    Three of the lobster's main chemoreceptor organs, the lateral and medial antennules (representing smell) and the dactylus-propodus segments of the walking legs (representing taste), are physiologically quite similar. The authors examined their role in spatial orientation in a food-odor stimulus field. Control animals almost always oriented correctly and immediately to an odor plume. Lobsters with unilateral ablations of lateral antennules lost this ability, but did not show preferential turning toward the intact side. Unilateral medial antennule ablation did not affect orientation. Removal of all aesthetasc hairs from one lateral antennule caused loss of orientation ability less severe than unilateral ablation of the entire lateral antennule. Lobsters with unilaterally ablated lateral antennules and blocked walking leg receptors turned preferentially toward the side of the intact antennule. Thus, it appears that intact lobsters orient in odor space by tropotaxis principally using aesthetasc receptor input. Since loss of appendages is relatively common in lobsters, this partial overlap of organ function may serve the animal well in nature.

  3. Spatial Organization and Dynamics of Transcription Elongation and Pre-mRNA Processing in Live Cells

    Directory of Open Access Journals (Sweden)

    Miguel Sánchez-Álvarez

    2011-01-01

    Full Text Available During the last 30 years, systematic biochemical and functional studies have significantly expanded our knowledge of the transcriptional molecular components and the pre-mRNA processing machinery of the cell. However, our current understanding of how these functions take place spatiotemporally within the highly compartmentalized eukaryotic nucleus remains limited. Moreover, it is increasingly clear that “the whole is more than the sum of its parts” and that an understanding of the dynamic coregulation of genes is essential for fully characterizing complex biological phenomena and underlying diseases. Recent technological advances in light microscopy in addition to novel cell and molecular biology approaches have led to the development of new tools, which are being used to address these questions and may contribute to achieving an integrated and global understanding of how the genome works at a cellular level. Here, we review major hallmarks and novel insights in RNA polymerase II activity and pre-mRNA processing in the context of nuclear organization, as well as new concepts and challenges arising from our ability to gather extensive dynamic information at the single-cell resolution.

  4. Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in pineapple (Ananas comosus).

    Science.gov (United States)

    Liu, Chaoyang; Xie, Tao; Chen, Chenjie; Luan, Aiping; Long, Jianmei; Li, Chuhao; Ding, Yaqi; He, Yehua

    2017-07-01

    The MYB proteins comprise one of the largest families of plant transcription factors, which are involved in various plant physiological and biochemical processes. Pineapple (Ananas comosus) is one of three most important tropical fruits worldwide. The completion of pineapple genome sequencing provides a great opportunity to investigate the organization and evolutionary traits of pineapple MYB genes at the genome-wide level. In the present study, a total of 94 pineapple R2R3-MYB genes were identified and further phylogenetically classified into 26 subfamilies, as supported by the conserved gene structures and motif composition. Collinearity analysis indicated that the segmental duplication events played a crucial role in the expansion of pineapple MYB gene family. Further comparative phylogenetic analysis suggested that there have been functional divergences of MYB gene family during plant evolution. RNA-seq data from different tissues and developmental stages revealed distinct temporal and spatial expression profiles of the AcMYB genes. Further quantitative expression analysis showed the specific expression patterns of the selected putative stress-related AcMYB genes in response to distinct abiotic stress and hormonal treatments. The comprehensive expression analysis of the pineapple MYB genes, especially the tissue-preferential and stress-responsive genes, could provide valuable clues for further function characterization. In this work, we systematically identified AcMYB genes by analyzing the pineapple genome sequence using a set of bioinformatics approaches. Our findings provide a global insight into the organization, phylogeny and expression patterns of the pineapple R2R3-MYB genes, and hence contribute to the greater understanding of their biological roles in pineapple.

  5. Spatial and temporal distribution of coloured dissolved organic matter in a hypertrophic freshwater lagoon

    Directory of Open Access Journals (Sweden)

    Diana Vaičiūtė

    2015-05-01

    Full Text Available A dataset of 224 Medium Resolution Imaging Spectrometer (MERIS full resolution satellite images were processed to retrieve the concentration of coloured dissolved organic matter (CDOM in a hypertrophic estuary (Curonian Lagoon, Lithuania and Russia. Images covered a period of 7 months, spanning from the ice melting (March to the late summer (September of 7 consecutive years (2005-2011. The aim of the study was to analyse the spatial and temporal variations of CDOM, by focusing on the main regulating factors (riverine discharge, sea-lagoon water exchange, water temperature, chlorophyll a, wind in a large estuary. The working hypothesis is that CDOM distribution may reveal distinct, site specific seasonal patterns. Our results demonstrated that CDOM concentrations at the whole lagoon level were elevated (1.5-4 m-1 and slightly but significantly higher in spring (1.50 m-1 on average compared to the summer (1.45 m-1 on average. This is due to very different flow of CDOM-rich freshwater from the main lagoon tributary in spring compared to summer. They also highlight macroscopic differences among areas within the lagoon, depending on season, suggesting a complex regulation of CDOM in this system. Significant factors explaining observed differences are the dilution of lagoon water with CDOM-poor brackish water, regeneration of large amounts of dissolved organic matter from sediments and combinations of uptake/release from phytoplankton. CDOM and its variations are understudied due to inherent methodological and analytical difficulties. However, this pool has a demonstrated relevant role in the biogeochemistry of aquatic environments. We speculate that the dissolved organic pool in the Curonian Lagoon has a mainly allochthonous origin in the high discharge period and an autochthonous origin in the summer, algal bloom period. Both positive and negative relationships between CDOM and phytoplankton suggest that pelagic microalgae may act as a source or as

  6. Soil surface organic layers in Arctic Alaska: spatial distribution, rates of formation, and microclimatic effects

    Science.gov (United States)

    Baughman, Carson; Mann, Daniel H.; Verbyla, David L.; Kunz, Michael L.

    2015-01-01

    Organic layers of living and dead vegetation cover the ground surface in many permafrost landscapes and play important roles in ecosystem processes. These soil surface organic layers (SSOLs) store large amounts of carbon and buffer the underlying permafrost and its contained carbon from changes in aboveground climate. Understanding the dynamics of SSOLs is a prerequisite for predicting how permafrost and carbon stocks will respond to warming climate. Here we ask three questions about SSOLs in a representative area of the Arctic Foothills region of northern Alaska: (1) What environmental factors control the thickness of SSOLs and the carbon they store? (2) How long do SSOLs take to develop on newly stabilized point bars? (3) How do SSOLs affect temperature in the underlying ground? Results show that SSOL thickness and distribution correlate with elevation, drainage area, vegetation productivity, and incoming solar radiation. A multiple regression model based on these correlations can simulate spatial distribution of SSOLs and estimate the organic carbon stored there. SSOLs develop within a few decades after a new, sandy, geomorphic surface stabilizes but require 500–700 years to reach steady state thickness. Mature SSOLs lower the growing season temperature and mean annual temperature of the underlying mineral soil by 8 and 3°C, respectively. We suggest that the proximate effects of warming climate on permafrost landscapes now covered by SSOLs will occur indirectly via climate's effects on the frequency, extent, and severity of disturbances like fires and landslides that disrupt the SSOLs and interfere with their protection of the underlying permafrost.

  7. Spatial patterns of soil organic carbon stocks in Estonian arable soils

    Science.gov (United States)

    Suuster, Elsa; Astover, Alar; Kõlli, Raimo; Roostalu, Hugo; Reintam, Endla; Penu, Priit

    2010-05-01

    Soil organic carbon (SOC) determines ecosystem functions, influencing soil fertility, soil physical, chemical and biological properties and crop productivity. Therefore the spatial pattern of SOC stocks and its appropriate management is important at various scales. Due to climate change and the contribution of carbon store in the soils, the national estimates of soil carbon stocks should be determined. Estonian soils have been well studied and mapped at a scale 1:10,000. Previous studies have estimated SOC stocks based on combinations of large groups of Estonian soils and the mean values of the soil profile database, but were not embedded into the geo-referenced databases. These studies have estimated SOC stocks of Estonian arable soils 122.3 Tg. Despite of available soil maps and databases, this information is still very poorly used for spatial soil modelling. The aim of current study is to assess and model spatial pattern of SOC stocks of arable soils on a pilot area Tartu County (area 3089 sq km). Estonian digital soil map and soil monitoring databases are providing a good opportunity to assess SOC stocks at various scales. The qualitative nature of the initial data from a soil map prohibits any straightforward use in modelling. Thus we have used several databases to construct models and linkages between soil properties that can be integrated into soil map. First step was to reorganize the soil map database (44,046 mapping units) so it can be used as an input to modelling. Arable areas were distinguished by a field layer of Agricultural Registers and Information Board, which provides precise information of current land use as it is the basis of paying CAP subsidies. The estimates of SOC content were found by using the arable land evaluation database of Tartu from the Estonian Land Board (comprising 950 sq km and 31,226 fields), where each soil type was assessed separately and average SOC content grouped by texture was derived. SOC content of epipedon varies in

  8. Spatial organization of NG2 glial cells and astrocytes in rat hippocampal CA1 region.

    Science.gov (United States)

    Xu, Guangjin; Wang, Wei; Zhou, Min

    2014-04-01

    Similar to astrocytes, NG2 glial cells are uniformly distributed in the central nervous system (CNS). However, little is known about the interspatial relationship, nor the functional interactions between these two star-shaped glial subtypes. Confocal morphometric analysis showed that NG2 immunostained cells are spatially organized as domains in rat hippocampal CA1 region and that each NG2 glial domain occupies a spatial volume of ∼178, 364 μm(3) . The processes of NG2 glia and astrocytes overlap extensively; each NG2 glial domain interlaces with the processes deriving from 5.8 ± 0.4 neighboring astrocytes, while each astrocytic domain accommodates processes stemming from 4.5 ± 0.3 abutting NG2 glia. In CA1 stratum radiatum, the cell bodies of morphologically identified glial cells often appear to make direct somatic-somata contact, termed as doublets. We used dual patch recording and postrecording NG2/GFAP double staining to determine the glial identities of these doublets. We show that among 44 doublets, 50% were NG2 glia-astrocyte pairs, while another 38.6% and 11.4% were astrocyte-astrocyte and NG2 glia-NG2 glia pairs, respectively. In dual patch recording, neither electrical coupling nor intercellular biocytin transfer was detected in astrocyte-NG2 glia or NG2 glia-NG2 glia doublets. Altogether, although NG2 glia and astrocytes are not gap junction coupled, their cell bodies and processes are interwoven extensively. The anatomical and physiological relationships revealed in this study should facilitate future studies to understand the metabolic coupling and functional communication between NG2 glia and astrocytes. Copyright © 2013 Wiley Periodicals, Inc.

  9. Spatial distribution of heterocyclic organic matter compounds at macropore surfaces in Bt-horizons

    Science.gov (United States)

    Leue, Martin; Eckhardt, Kai-Uwe; Gerke, Horst H.; Ellerbrock, Ruth H.; Leinweber, Peter

    2017-04-01

    The illuvial Bt-horizon of Luvisols is characterized by coatings of clay and organic matter (OM) at the surfaces of cracks, biopores and inter-aggregate spaces. The OM composition of the coatings that originate from preferential transport of suspended matter in macropores determines the physico-chemical properties of the macropore surfaces. The analysis of the spatial distribution of specific OM components such as heterocyclic N-compounds (NCOMP) and benzonitrile and naphthalene (BN+NA) could enlighten the effect of macropore coatings on the transport of colloids and reactive solutes during preferential flow and on OM turnover processes in subsoils. The objective was to characterize the mm-to-cm scale spatial distribution of NCOMP and BN+NA at intact macropore surfaces from the Bt-horizons of two Luvisols developed on loess and glacial till. In material manually separated from macropore surfaces the proportions of NCOMP and BN+NA were determined by pyrolysis-field ionization mass spectrometry (Py-FIMS). These OM compounds, likely originating from combustion residues, were found increased in crack coatings and pinhole fillings but decreased in biopore walls (worm burrows and root channels). The Py-FIMS data were correlated with signals from C=O and C=C groups and with signals from O-H groups of clay minerals as determined by Fourier transform infrared spectroscopy in diffuse reflectance mode (DRIFT). Intensive signals of C15 to C17 alkanes from long-chain alkenes as main components of diesel and diesel exhaust particulates substantiated the assumption that burning residues were prominent in the subsoil OM. The spatial distribution of NCOMP and BN+NA along the macropores was predicted by partial least squares regression (PLSR) using DRIFT mapping spectra from intact surfaces and was found closely related to the distribution of crack coatings and pinholes. The results emphasize the importance of clay coatings in the subsoil to OM sorption and stabilization

  10. Differential solvation of intrinsically disordered linkers drives the formation of spatially organized droplets in ternary systems of linear multivalent proteins

    Science.gov (United States)

    Harmon, Tyler S.; Holehouse, Alex S.; Pappu, Rohit V.

    2018-04-01

    Intracellular biomolecular condensates are membraneless organelles that encompass large numbers of multivalent protein and nucleic acid molecules. The bodies assemble via a combination of liquid–liquid phase separation and gelation. A majority of condensates included multiple components and show multilayered organization as opposed to being well-mixed unitary liquids. Here, we put forward a simple thermodynamic framework to describe the emergence of spatially organized droplets in multicomponent systems comprising of linear multivalent polymers also known as associative polymers. These polymers, which mimic proteins and/or RNA have the architecture of domains or motifs known as stickers that are interspersed by flexible spacers known as linkers. Using a minimalist numerical model for a four-component system, we have identified features of linear multivalent molecules that are necessary and sufficient for generating spatially organized droplets. We show that differences in sequence-specific effective solvation volumes of disordered linkers between interaction domains enable the formation of spatially organized droplets. Molecules with linkers that are preferentially solvated are driven to the interface with the bulk solvent, whereas molecules that have linkers with negligible effective solvation volumes form cores in the core–shell architectures that emerge in the minimalist four-component systems. Our modeling has relevance for understanding the physical determinants of spatially organized membraneless organelles.

  11. Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project

    OpenAIRE

    Dunlap, Jay C.; Borkovich, Katherine A.; Henn, Matthew R.; Turner, Gloria E.; Sachs, Matthew S.; Glass, N. Louise; McCluskey, Kevin; Plamann, Michael; Galagan, James E.; Birren, Bruce W.; Weiss, Richard L.; Townsend, Jeffrey P.; Loros, Jennifer J.; Nelson, Mary Anne; Lambreghts, Randy

    2007-01-01

    A consortium of investigators is engaged in a functional genomics project centered on the filamentous fungus Neurospora, with an eye to opening up the functional genomic analysis of all the filamentous fungi. The overall goal of the four interdependent projects in this effort is to acccomplish functional genomics, annotation, and expression analyses of Neurospora crassa, a filamentous fungus that is an established model for the assemblage of over 250,000 species of nonyeast fungi. Building fr...

  12. Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis

    DEFF Research Database (Denmark)

    Sarusi Portuguez, Avital; Schwartz, Michal; Siersbaek, Rasmus

    2017-01-01

    The three dimensional folding of mammalian genomes is cell type specific and difficult to alter suggesting that it is an important component of gene regulation. However, given the multitude of chromatin-associating factors, the mechanisms driving the colocalization of active chromosomal domains...... by PPARγ and Lpin1, undergoes orchestrated reorganization during adipogenesis. Coupling the dynamics of genome architecture with multiple chromatin datasets indicated that among all the transcription factors (TFs) tested, RXR is central to genome reorganization at the beginning of adipogenesis...

  13. Promoter characterization and genomic organization of the human X11β gene APBA2.

    LENUS (Irish Health Repository)

    Hao, Yan

    2012-02-15

    Overexpression of neuronal adaptor protein X11β has been shown to decrease the production of amyloid-β, a toxic peptide deposited in Alzheimer\\'s disease brains. Therefore, manipulation of the X11β level may represent a potential therapeutic strategy for Alzheimer\\'s disease. As X11β expression can be regulated at the transcription level, we determined the genomic organization and the promoter of the human X11β gene, amyloid β A4 precursor protein-binding family A member 2 (APBA2). By RNA ligase-mediated rapid amplification of cDNA ends, a single APBA2 transcription start site and the complete sequence of exon 1 were identified. The APBA2 promoter was located upstream of exon 1 and was more active in neurons. The core promoter contains several CpG dinucleotides, and was strongly suppressed by DNA methylation. In addition, mutagenesis analysis revealed a putative Pax5-binding site within the promoter. Together, APBA2 contains a potent neuronal promoter whose activity may be regulated by DNA methylation and Pax5.

  14. Genomic organization, expression, and chromosome localization of a third aurora-related kinase gene, Aie1.

    Science.gov (United States)

    Hu, H M; Chuang, C K; Lee, M J; Tseng, T C; Tang, T K

    2000-11-01

    We previously reported two novel testis-specific serine/threonine kinases, Aie1 (mouse) and AIE2 (human), that share high amino acid identities with the kinase domains of fly aurora and yeast Ipl1. Here, we report the entire intron-exon organization of the Aie1 gene and analyze the expression patterns of Aie1 mRNA during testis development. The mouse Aie1 gene spans approximately 14 kb and contains seven exons. The sequences of the exon-intron boundaries of the Aie1 gene conform to the consensus sequences (GT/AG) of the splicing donor and acceptor sites of most eukaryotic genes. Comparative genomic sequencing revealed that the gene structure is highly conserved between mouse Aie1 and human AIE2. However, much less homology was found in the sequence outside the kinase-coding domains. The Aie1 locus was mapped to mouse chromosome 7A2-A3 by fluorescent in situ hybridization. Northern blot analysis indicates that Aie1 mRNA likely is expressed at a low level on day 14 and reaches its plateau on day 21 in the developing postnatal testis. RNA in situ hybridization indicated that the expression of the Aie1 transcript was restricted to meiotically active germ cells, with the highest levels detected in spermatocytes at the late pachytene stage. These findings suggest that Aie1 plays a role in spermatogenesis.

  15. A sequence-based survey of the complex structural organization of tumor genomes

    Energy Technology Data Exchange (ETDEWEB)

    Collins, Colin; Raphael, Benjamin J.; Volik, Stanislav; Yu, Peng; Wu, Chunxiao; Huang, Guiqing; Linardopoulou, Elena V.; Trask, Barbara J.; Waldman, Frederic; Costello, Joseph; Pienta, Kenneth J.; Mills, Gordon B.; Bajsarowicz, Krystyna; Kobayashi, Yasuko; Sridharan, Shivaranjani; Paris, Pamela; Tao, Quanzhou; Aerni, Sarah J.; Brown, Raymond P.; Bashir, Ali; Gray, Joe W.; Cheng, Jan-Fang; de Jong, Pieter; Nefedov, Mikhail; Ried, Thomas; Padilla-Nash, Hesed M.; Collins, Colin C.

    2008-04-03

    The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using End Sequencing Profiling (ESP), which relies on paired-end sequencing of cloned tumor genomes. In this study, brain, breast, ovary and prostate tumors along with three breast cancer cell lines were surveyed with ESP yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent. Sequencing and fluorescence in situ hybridization (FISH) confirmed translocations and complex tumor genome structures that include coamplification and packaging of disparate genomic loci with associated molecular heterogeneity. Comparison of the tumor genomes suggests recurrent rearrangements. Some are likely to be novel structural polymorphisms, whereas others may be bona fide somatic rearrangements. A recurrent fusion transcript in breast tumors and a constitutional fusion transcript resulting from a segmental duplication were identified. Analysis of end sequences for single nucleotide polymorphisms (SNPs) revealed candidate somatic mutations and an elevated rate of novel SNPs in an ovarian tumor. These results suggest that the genomes of many epithelial tumors may be far more dynamic and complex than previously appreciated and that genomic fusions including fusion transcripts and proteins may be common, possibly yielding tumor-specific biomarkers and therapeutic targets.

  16. Are Namibian "fairy circles" the consequence of self-organizing spatial vegetation patterning?

    Directory of Open Access Journals (Sweden)

    Michael D Cramer

    Full Text Available Causes of over-dispersed barren "fairy circles" that are often surrounded by ca. 0.5 m tall peripheral grasses in a matrix of shorter (ca. 0.2 m tall grasses in Namibian grasslands remain mysterious. It was hypothesized that the fairy circles are the consequence of self-organizing spatial vegetation patterning arising from resource competition and facilitation. We examined the edaphic properties of fairy circles and variation in fairy circle size, density and landscape occupancy (% land surface with edaphic properties and water availability at a local scale (<50 km and with climate and vegetation characteristics at a regional scale. Soil moisture in the barren fairy circles declines from the center towards the periphery and is inversely correlated with soil organic carbon, possibly indicating that the peripheral grass roots access soil moisture that persists into the dry season within fairy circles. Fairy circle landscape occupancy is negatively correlated with precipitation and soil [N], consistent with fairy circles being the product of resource-competition. Regional fairy circle presence/absence is highly predictable using an empirical model that includes narrow ranges of vegetation biomass, precipitation and temperature seasonality as predictor variables, indicating that fairy circles are likely a climate-dependent emergent phenomenon. This dependence of fairy circle occurrence on climate explains why fairy circles in some locations may appear and disappear over time. Fairy circles are only over-dispersed at high landscape occupancies, indicating that inter-circle competition may determine their spacing. We conclude that fairy circles are likely to be an emergent arid-grassland phenomenon that forms as a consequence of peripheral grass resource-competition and that the consequent barren circle may provide a resource-reservoir essential for the survival of the larger peripheral grasses and provides a habitat for fossicking fauna.

  17. Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms

    Directory of Open Access Journals (Sweden)

    Meller Jaroslaw

    2007-03-01

    Full Text Available Abstract Background Identifying syntenic regions, i.e., blocks of genes or other markers with evolutionary conserved order, and quantifying evolutionary relatedness between genomes in terms of chromosomal rearrangements is one of the central goals in comparative genomics. However, the analysis of synteny and the resulting assessment of genome rearrangements are sensitive to the choice of a number of arbitrary parameters that affect the detection of synteny blocks. In particular, the choice of a set of markers and the effect of different aggregation strategies, which enable coarse graining of synteny blocks and exclusion of micro-rearrangements, need to be assessed. Therefore, existing tools and resources that facilitate identification, visualization and analysis of synteny need to be further improved to provide a flexible platform for such analysis, especially in the context of multiple genomes. Results We present a new tool, Cinteny, for fast identification and analysis of synteny with different sets of markers and various levels of coarse graining of syntenic blocks. Using Hannenhalli-Pevzner approach and its extensions, Cinteny also enables interactive determination of evolutionary relationships between genomes in terms of the number of rearrangements (the reversal distance. In particular, Cinteny provides: i integration of synteny browsing with assessment of evolutionary distances for multiple genomes; ii flexibility to adjust the parameters and re-compute the results on-the-fly; iii ability to work with user provided data, such as orthologous genes, sequence tags or other conserved markers. In addition, Cinteny provides many annotated mammalian, invertebrate and fungal genomes that are pre-loaded and available for analysis at http://cinteny.cchmc.org. Conclusion Cinteny allows one to automatically compare multiple genomes and perform sensitivity analysis for synteny block detection and for the subsequent computation of reversal distances

  18. Structure and expression strategy of the genome of Culex pipiens densovirus, a mosquito densovirus with an ambisense organization.

    Science.gov (United States)

    Baquerizo-Audiot, Elizabeth; Abd-Alla, Adly; Jousset, Françoise-Xavière; Cousserans, François; Tijssen, Peter; Bergoin, Max

    2009-07-01

    The genome of all densoviruses (DNVs) so far isolated from mosquitoes or mosquito cell lines consists of a 4-kb single-stranded DNA molecule with a monosense organization (genus Brevidensovirus, subfamily Densovirinae). We previously reported the isolation of a Culex pipiens DNV (CpDNV) that differs significantly from brevidensoviruses by (i) having a approximately 6-kb genome, (ii) lacking sequence homology, and (iii) lacking antigenic cross-reactivity with Brevidensovirus capsid polypeptides. We report here the sequence organization and transcription map of this virus. The cloned genome of CpDNV is 5,759 nucleotides (nt) long, and it possesses an inverted terminal repeat (ITR) of 285 nt and an ambisense organization of its genes. The nonstructural (NS) proteins NS-1, NS-2, and NS-3 are located in the 5' half of one strand and are organized into five open reading frames (ORFs) due to the split of both NS-1 and NS-2 into two ORFs. The ORF encoding capsid polypeptides is located in the 5' half of the complementary strand. The expression of NS proteins is controlled by two promoters, P7 and P17, driving the transcription of a 2.4-kb mRNA encoding NS-3 and of a 1.8-kb mRNA encoding NS-1 and NS-2, respectively. The two NS mRNAs species are spliced off a 53-nt sequence. Capsid proteins are translated from an unspliced 2.3-kb mRNA driven by the P88 promoter. CpDNV thus appears as a new type of mosquito DNV, and based on the overall organization and expression modalities of its genome, it may represent the prototype of a new genus of DNV.

  19. Modeling of enhanced catalysis in multienzyme nanostructures: effect of molecular scaffolds, spatial organization, and concentration.

    Science.gov (United States)

    Roberts, Christopher C; Chang, Chia-en A

    2015-01-13

    Colocalized multistep enzymatic reaction pathways within biological catabolic and metabolic processes occur with high yield and specificity. Spatial organization on membranes or surfaces may be associated with increased efficiency of intermediate substrate transfer. Using a new Brownian dynamics package, GeomBD, we explored the geometric features of a surface-anchored enzyme system by parallel coarse-grained Brownian dynamics simulations of substrate diffusion over microsecond (μs) to millisecond (ms) time scales. We focused on a recently developed glucose oxidase (GOx), horseradish peroxidase (HRP), and DNA origami-scaffold enzyme system, where the H2O2 substrate of HRP is produced by GOx. The results revealed and explained a significant advantage in catalytic enhancement by optimizing interenzyme distance and orientation in the presence of the scaffold model. The planar scaffold colocalized the enzymes and provided a diffusive barrier that enhanced substrate transfer probability, becoming more relevant with increasing interenzyme distance. The results highlight the importance of protein geometry in the proper assessment of distance and orientation dependence on the probability of substrate transfer. They shed light on strategies for engineering multienzyme complexes and further investigation of enhanced catalytic efficiency for substrate diffusion between membrane-anchoring proteins.

  20. Hierarchical thermoplastic rippled nanostructures regulate Schwann cell adhesion, morphology and spatial organization.

    Science.gov (United States)

    Masciullo, Cecilia; Dell'Anna, Rossana; Tonazzini, Ilaria; Böettger, Roman; Pepponi, Giancarlo; Cecchini, Marco

    2017-10-12

    Periodic ripples are a variety of anisotropic nanostructures that can be realized by ion beam irradiation on a wide range of solid surfaces. Only a few authors have investigated these surfaces for tuning the response of biological systems, probably because it is challenging to directly produce them in materials that well sustain long-term cellular cultures. Here, hierarchical rippled nanotopographies with a lateral periodicity of ∼300 nm are produced from a gold-irradiated germanium mold in polyethylene terephthalate (PET), a biocompatible polymer approved by the US Food and Drug Administration for clinical applications, by a novel three-step embossing process. The effects of nano-ripples on Schwann Cells (SCs) are studied in view of their possible use for nerve-repair applications. The data demonstrate that nano-ripples can enhance short-term SC adhesion and proliferation (3-24 h after seeding), drive their actin cytoskeleton spatial organization and sustain long-term cell growth. Notably, SCs are oriented perpendicularly with respect to the nanopattern lines. These results provide information about the possible use of hierarchical nano-rippled elements for nerve-regeneration protocols.

  1. Changes in Visual/Spatial and Analytic Strategy Use in Organic Chemistry with the Development of Expertise

    Science.gov (United States)

    Vlacholia, Maria; Vosniadou, Stella; Roussos, Petros; Salta, Katerina; Kazi, Smaragda; Sigalas, Michael; Tzougraki, Chryssa

    2017-01-01

    We present two studies that investigated the adoption of visual/spatial and analytic strategies by individuals at different levels of expertise in the area of organic chemistry, using the Visual Analytic Chemistry Task (VACT). The VACT allows the direct detection of analytic strategy use without drawing inferences about underlying mental…

  2. Hydrological Networks and Associated Topographic Variation as Templates for the Spatial Organization of Tropical Forest Vegetation

    OpenAIRE

    Detto, Matteo; Muller-Landau, Helene C.; Mascaro, Joseph; Asner, Gregory P.

    2013-01-01

    An understanding of the spatial variability in tropical forest structure and biomass, and the mechanisms that underpin this variability, is critical for designing, interpreting, and upscaling field studies for regional carbon inventories. We investigated the spatial structure of tropical forest vegetation and its relationship to the hydrological network and associated topographic structure across spatial scales of 10-1000 m using high-resolution maps of LiDAR-derived mean canopy profile heigh...

  3. Global impacts of the meat trade on in-stream organic river pollution: the importance of spatially distributed hydrological conditions

    Science.gov (United States)

    Wen, Yingrong; Schoups, Gerrit; van de Giesen, Nick

    2018-01-01

    In many regions of the world, intensive livestock farming has become a significant source of organic river pollution. As the international meat trade is growing rapidly, the environmental impacts of meat production within one country can occur either domestically or internationally. The goal of this paper is to quantify the impacts of the international meat trade on global organic river pollution at multiple scales (national, regional and gridded). Using the biological oxygen demand (BOD) as an overall indicator of organic river pollution, we compute the spatially distributed organic pollution in global river networks with and without a meat trade, where the without-trade scenario assumes that meat imports are replaced by local production. Our analysis reveals a reduction in the livestock population and production of organic pollutants at the global scale as a result of the international meat trade. However, the actual environmental impact of trade, as quantified by in-stream BOD concentrations, is negative; i.e. we find a slight increase in polluted river segments. More importantly, our results show large spatial variability in local (grid-scale) impacts that do not correlate with local changes in BOD loading, which illustrates: (1) the significance of accounting for the spatial heterogeneity of hydrological processes along river networks, and (2) the limited value of looking at country-level or global averages when estimating the actual impacts of trade on the environment.

  4. The spatial distribution of soil organic carbon in tidal wetland soils of the continental United States.

    Science.gov (United States)

    Hinson, Audra L; Feagin, Rusty A; Eriksson, Marian; Najjar, Raymond G; Herrmann, Maria; Bianchi, Thomas S; Kemp, Michael; Hutchings, Jack A; Crooks, Steve; Boutton, Thomas

    2017-12-01

    Tidal wetlands contain large reservoirs of carbon in their soils and can sequester carbon dioxide (CO 2 ) at a greater rate per unit area than nearly any other ecosystem. The spatial distribution of this carbon influences climate and wetland policy. To assist with international accords such as the Paris Climate Agreement, national-level assessments such as the United States (U.S.) National Greenhouse Gas Inventory, and regional, state, local, and project-level evaluation of CO 2 sequestration credits, we developed a geodatabase (CoBluCarb) and high-resolution maps of soil organic carbon (SOC) distribution by linking National Wetlands Inventory data with the U.S. Soil Survey Geographic Database. For over 600,000 wetlands, the total carbon stock and organic carbon density was calculated at 5-cm vertical resolution from 0 to 300 cm of depth. Across the continental United States, there are 1,153-1,359 Tg of SOC in the upper 0-100 cm of soils across a total of 24 945.9 km 2 of tidal wetland area, twice as much carbon as the most recent national estimate. Approximately 75% of this carbon was found in estuarine emergent wetlands with freshwater tidal wetlands holding about 19%. The greatest pool of SOC was found within the Atchafalaya/Vermilion Bay complex in Louisiana, containing about 10% of the U.S. total. The average density across all tidal wetlands was 0.071 g cm -3 across 0-15 cm, 0.055 g cm -3 across 0-100 cm, and 0.040 g cm -3 at the 100 cm depth. There is inherent variability between and within individual wetlands; however, we conclude that it is possible to use standardized values at a range of 0-100 cm of the soil profile, to provide first-order quantification and to evaluate future changes in carbon stocks in response to environmental perturbations. This Tier 2-oriented carbon stock assessment provides a scientific method that can be copied by other nations in support of international requirements. © 2017 John Wiley & Sons Ltd.

  5. Spatial Reasoning: Improvement of Imagery and Abilities in Sophomore Organic Chemistry. Perspective to Enhance Student Learning

    Science.gov (United States)

    Hornbuckle, Susan F.; Gobin, Latanya; Thurman, Stephanie N.

    2014-01-01

    Spatial reasoning has become a demanded skill for students pursuing a science emphasis to compete with the dynamic growth of our professional society. The ability to reason spatially includes explorations in memory recollection and problem solving capabilities as well as critical thinking and reasoning skills. With these advancements, educational…

  6. Phage-Bacterial Dynamics with Spatial Structure: Self Organization around Phage Sinks Can Promote Increased Cell Densities.

    Science.gov (United States)

    Bull, James J; Christensen, Kelly A; Scott, Carly; Jack, Benjamin R; Crandall, Cameron J; Krone, Stephen M

    2018-01-29

    Bacteria growing on surfaces appear to be profoundly more resistant to control by lytic bacteriophages than do the same cells grown in liquid. Here, we use simulation models to investigate whether spatial structure per se can account for this increased cell density in the presence of phages. A measure is derived for comparing cell densities between growth in spatially structured environments versus well mixed environments (known as mass action). Maintenance of sensitive cells requires some form of phage death; we invoke death mechanisms that are spatially fixed, as if produced by cells. Spatially structured phage death provides cells with a means of protection that can boost cell densities an order of magnitude above that attained under mass action, although the effect is sometimes in the opposite direction. Phage and bacteria self organize into separate refuges, and spatial structure operates so that the phage progeny from a single burst do not have independent fates (as they do with mass action). Phage incur a high loss when invading protected areas that have high cell densities, resulting in greater protection for the cells. By the same metric, mass action dynamics either show no sustained bacterial elevation or oscillate between states of low and high cell densities and an elevated average. The elevated cell densities observed in models with spatial structure do not approach the empirically observed increased density of cells in structured environments with phages (which can be many orders of magnitude), so the empirical phenomenon likely requires additional mechanisms than those analyzed here.

  7. Performance comparison of two efficient genomic selection methods (gsbay & MixP) applied in aquacultural organisms

    Science.gov (United States)

    Su, Hailin; Li, Hengde; Wang, Shi; Wang, Yangfan; Bao, Zhenmin

    2017-02-01

    Genomic selection is more and more popular in animal and plant breeding industries all around the world, as it can be applied early in life without impacting selection candidates. The objective of this study was to bring the advantages of genomic selection to scallop breeding. Two different genomic selection tools MixP and gsbay were applied on genomic evaluation of simulated data and Zhikong scallop ( Chlamys farreri) field data. The data were compared with genomic best linear unbiased prediction (GBLUP) method which has been applied widely. Our results showed that both MixP and gsbay could accurately estimate single-nucleotide polymorphism (SNP) marker effects, and thereby could be applied for the analysis of genomic estimated breeding values (GEBV). In simulated data from different scenarios, the accuracy of GEBV acquired was ranged from 0.20 to 0.78 by MixP; it was ranged from 0.21 to 0.67 by gsbay; and it was ranged from 0.21 to 0.61 by GBLUP. Estimations made by MixP and gsbay were expected to be more reliable than those estimated by GBLUP. Predictions made by gsbay were more robust, while with MixP the computation is much faster, especially in dealing with large-scale data. These results suggested that both algorithms implemented by MixP and gsbay are feasible to carry out genomic selection in scallop breeding, and more genotype data will be necessary to produce genomic estimated breeding values with a higher accuracy for the industry.

  8. Effect of land use on the spatial variability of organic matter and nutrient status in an Oxisol

    Science.gov (United States)

    Paz-Ferreiro, Jorge; Alves, Marlene Cristina; Vidal Vázquez, Eva

    2013-04-01

    Heterogeneity is now considered as an inherent soil property. Spatial variability of soil attributes in natural landscapes results mainly from soil formation factors. In cultivated soils much heterogeneity can additionally occur as a result of land use, agricultural systems and management practices. Organic matter content (OMC) and nutrients associated to soil exchange complex are key attribute in the maintenance of a high quality soil. Neglecting spatial heterogeneity in soil OMC and nutrient status at the field scale might result in reduced yield and in environmental damage. We analyzed the impact of land use on the pattern of spatial variability of OMC and soil macronutrients at the stand scale. The study was conducted in São Paulo state, Brazil. Land uses were pasture, mango orchard and corn field. Soil samples were taken at 0-10 cm and 10-20 cm depth in 84 points, within 100 m x 100 m plots. Texture, pH, OMC, cation exchange capacity (CEC), exchangeable cations (Ca, Mg, K, H, Al) and resin extractable phosphorus were analyzed.. Statistical variability was found to be higher in parameters defining the soil nutrient status (resin extractable P, K, Ca and Mg) than in general soil properties (OMC, CEC, base saturation and pH). Geostatistical analysis showed contrasting patterns of spatial dependence for the different soil uses, sampling depths and studied properties. Most of the studied data sets collected at two different depths exhibited spatial dependence at the sampled scale and their semivariograms were modeled by a nugget effect plus a structure. The pattern of soil spatial variability was found to be different between the three study soil uses and at the two sampling depths, as far as model type, nugget effect or ranges of spatial dependence were concerned. Both statistical and geostatistical results pointed out the importance of OMC as a driver responsible for the spatial variability of soil nutrient status.

  9. Exploring the Role of the Spatial Characteristics of Visible and Near-Infrared Reflectance in Predicting Soil Organic Carbon Density

    Directory of Open Access Journals (Sweden)

    Long Guo

    2017-10-01

    Full Text Available Soil organic carbon stock plays a key role in the global carbon cycle and the precision agriculture. Visible and near-infrared reflectance spectroscopy (VNIRS can directly reflect the internal physical construction and chemical substances of soil. The partial least squares regression (PLSR is a classical and highly commonly used model in constructing soil spectral models and predicting soil properties. Nevertheless, using PLSR alone may not consider soil as characterized by strong spatial heterogeneity and dependence. However, considering the spatial characteristics of soil can offer valuable spatial information to guarantee the prediction accuracy of soil spectral models. Thus, this study aims to construct a rapid and accurate soil spectral model in predicting soil organic carbon density (SOCD with the aid of the spatial autocorrelation of soil spectral reflectance. A total of 231 topsoil samples (0–30 cm were collected from the Jianghan Plain, Wuhan, China. The spectral reflectance (350–2500 nm was used as auxiliary variable. A geographically-weighted regression (GWR model was used to evaluate the potential improvement of SOCD prediction when the spatial information of the spectral features was considered. Results showed that: (1 The principal components extracted from PLSR have a strong relationship with the regression coefficients at the average sampling distance (300 m based on the Moran’s I values. (2 The eigenvectors of the principal components exhibited strong relationships with the absorption spectral features, and the regression coefficients of GWR varied with the geographical locations. (3 GWR displayed a higher accuracy than that of PLSR in predicting the SOCD by VNIRS. This study aimed to help people realize the importance of the spatial characteristics of soil properties and their spectra. This work also introduced guidelines for the application of GWR in predicting soil properties by VNIRS.

  10. Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny.

    Directory of Open Access Journals (Sweden)

    LaDeana W Hillier

    2007-07-01

    Full Text Available To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism-based genetic map to order and orient the whole genome shotgun assembly along the six C. briggsae chromosomes. Although these species are of the same genus, their most recent common ancestor existed 80-110 million years ago, and thus they are more evolutionarily distant than, for example, human and mouse. We found that, like C. elegans chromosomes, C. briggsae chromosomes exhibit high levels of recombination on the arms along with higher repeat density, a higher fraction of intronic sequence, and a lower fraction of exonic sequence compared with chromosome centers. Despite extensive intrachromosomal rearrangements, 1:1 orthologs tend to remain in the same region of the chromosome, and colinear blocks of orthologs tend to be longer in chromosome centers compared with arms. More strikingly, the two species show an almost complete conservation of synteny, with 1:1 orthologs present on a single chromosome in one species also found on a single chromosome in the other. The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that are only poorly understood presently.

  11. Spatially organized «vertical city» as a synthesis of tall buildings and airships

    Science.gov (United States)

    Gagulina, Olga; Matovnikov, Sergei

    2018-03-01

    The paper explores the compact city concept based on the «spatial» urban development principles and describes the prerequisites and possible methods to move from «horizontal» planning to «vertical» urban environments. It highlights the close connection between urban space, high-rise city landscape and conveyance options and sets out the ideas for upgrading the existing architectural and urban planning principles. It also conceptualizes the use of airships to create additional spatial connections between urban structure elements and high-rise buildings. Functional changes are considered in creating both urban environment and internal space of tall buildings, and the environmental aspects of the new spatial model are brought to light. The paper delineates the prospects for making a truly «spatial» multidimensional city space.

  12. Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms.

    Science.gov (United States)

    Gasc, Cyrielle; Peyretaillade, Eric; Peyret, Pierre

    2016-06-02

    The recent expansion of next-generation sequencing has significantly improved biological research. Nevertheless, deep exploration of genomes or metagenomic samples remains difficult because of the sequencing depth and the associated costs required. Therefore, different partitioning strategies have been developed to sequence informative subsets of studied genomes. Among these strategies, hybridization capture has proven to be an innovative and efficient tool for targeting and enriching specific biomarkers in complex DNA mixtures. It has been successfully applied in numerous areas of biology, such as exome resequencing for the identification of mutations underlying Mendelian or complex diseases and cancers, and its usefulness has been demonstrated in the agronomic field through the linking of genetic variants to agricultural phenotypic traits of interest. Moreover, hybridization capture has provided access to underexplored, but relevant fractions of genomes through its ability to enrich defined targets and their flanking regions. Finally, on the basis of restricted genomic information, this method has also allowed the expansion of knowledge of nonreference species and ancient genomes and provided a better understanding of metagenomic samples. In this review, we present the major advances and discoveries permitted by hybridization capture and highlight the potency of this approach in all areas of biology. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet (Acipenser ruthenus).

    Science.gov (United States)

    Biltueva, Larisa S; Prokopov, Dimitry Y; Makunin, Alexey I; Komissarov, Alexey S; Kudryavtseva, Anna V; Lemskaya, Natalya A; Vorobieva, Nadezhda V; Serdyukova, Natalia A; Romanenko, Svetlana A; Gladkikh, Olga L; Graphodatsky, Alexander S; Trifonov, Vladimir A

    2017-01-01

    Acipenseriformes represent a phylogenetically basal clade of ray-finned fish characterized by unusual genomic traits, including paleopolyploid states of extant genomes with high chromosome numbers and slow rates of molecular evolution. Despite a high interest in this fish group, only a limited number of studies have been accomplished on the isolation and characterization of repetitive DNA, karyotype standardization is not yet complete, and sex chromosomes are still to be identified. Here, we applied next-generation sequencing and cluster analysis to characterize major fractions of sterlet (Acipenser ruthenus) repetitive DNA. Using FISH, we mapped 16 tandemly arranged sequences on sterlet chromosomes and found them to be unevenly distributed in the genome with a tendency to cluster in particular regions. Some of the satellite DNAs might be used as specific markers to identify individual chromosomes and their paralogs, resulting in the unequivocal identification of at least 18 chromosome pairs. Our results provide an insight into the characteristic genomic distribution of the most common sterlet repetitive sequences. Biased accumulation of repetitive DNAs in particular chromosomes makes them especially interesting for further search for cryptic sex chromosomes. Future studies of these sequences in other acipenserid species will provide new perspectives regarding the evolution of repetitive DNA within the genomes of this fish order. © 2017 S. Karger AG, Basel.

  14. The Urban Organization of the Socio-Spatial Environment in Towns of the Irkutsk Region

    Directory of Open Access Journals (Sweden)

    Inna Druzhinina

    2015-08-01

    Full Text Available The article observes the problems of formation of socio-spatial environment of new cities of the Irkutsk region in the period of pioneer development of Siberia in the XX century, and the impact of this environment on the modern living conditions. Identification of the key features and main factors affecting the development of new cities and the definition of the specificity of the socio-spatial environment of residential units of Bratsk, Angarsk, Shelekhov and Sayansk cities are presented.

  15. Linkage between the temporal and spatial variability of dissolved organic matter and whole-stream metabolism

    Directory of Open Access Journals (Sweden)

    S. Halbedel

    2013-08-01

    Full Text Available Dissolved organic matter (DOM is an important resource for microbes, thus affecting whole-stream metabolism. However, the factors influencing its chemical composition and thereby also its bio-availability are complex and not thoroughly understood. It was hypothesized that whole-stream metabolism is linked to DOM composition and that the coupling of both is influenced by seasonality and different land-use types. We tested this hypothesis in a comparative study on two pristine forestry streams and two non-forestry streams. The investigated streams were located in the Harz Mountains (central Europe, Germany. The metabolic rate was measured with a classical two-station oxygen change technique and the variability of DOM with fluorescence spectroscopy. All streams were clearly net heterotrophic, whereby non-forestry streams showed a higher primary production, which was correlated to irradiance and phosphorus concentration. We detected three CDOM components (C1, C2, C3 using parallel factor (PARAFAC analysis. We compared the excitation and emission maxima of these components with the literature and correlated the PARAFAC components with each other and with fluorescence indices. The correlations suggest that two PARAFAC components are derived from allochthonous sources (C1, C3 and one is derived autochthonously (C2. The chromophoric DOM matrix was dominated by signals of humic-like substances with a highly complex structure, followed by humic-like, fulfic acids, low-molecular-weight substances, and with minor amounts of amino acids and proteins. The ratios of these PARAFAC components (C1 : C2, C1 : C3, C3 : C2 differed with respect to stream types (forestry versus non-forestry. We demonstrated a significant correlation between gross primary production (GPP and signals of autochthonously derived, low-molecular-weight humic-like substances. A positive correlation between P / R (i.e. GPP/daily community respiration and the fluorescence index FI suggests

  16. Problems of spatial-functional organization of Južno Pomoravlje region’s network of settlements

    Directory of Open Access Journals (Sweden)

    Krunić Nikola

    2009-01-01

    Full Text Available During the elaboration of the Regional spatial plan of the municipalities of Južno Pomoravlje (Region Južno Pomoravlje a special attention was paid to its network of settlements. Demographical and functional determinants of this network were analyzed based on the relevant theoretical-methodological concepts and qualitative-quantitative indicators. Settlement network of Južno Pomoravlje was considered as a subsystem of the Republic of Serbia’s settlements’ system. Correlation and causality between processes of spatial and socio-economic migration of population and functional transformation of settlements have been highlighted, which caused differentiation of the Region’s municipalities to: urban cores - peri-urban rings - suburban more or less urbanized villages and rural surroundings. Models of decentralized concentration and micro-developing nuclei are proposed as instruments for decentralization of the Region or its municipalities. Based on the level of spatial-functional integration of settlements, regional as well as municipal and micro-functional - micro-regional structures have been identified. This paper gives conceptual and strategic proposals of spatial-functional organization of Južno Pomoravlje, which are based on settlements’ determinants. Authors suggest that functional premises define determinants for the Regional spatial plan and steer the sectoral and strategic decisions.

  17. Architecture and spatial organization in a triple-species bacterial biofilm synergistically degrading the phenylurea herbicide linuron

    DEFF Research Database (Denmark)

    Breugelmans, Philip; Barken, Kim Bundvig; Tolker-Nielsen, Tim

    2008-01-01

    influence on the triple-species biofilm architecture. This architecture was dependent on the carbon source supplied, as the biofilm architecture of WDL1 growing on alternative carbon sources was different from that observed under linuron-fed conditions. Linuron-fed triple-species consortium biofilms....... These observations indicate that the spatial organization in the linuron-fed consortium biofilm reflected the metabolic interactions within the consortium....

  18. Complete nucleotide sequence and genome organization of Olive latent virus 3, a new putative member of the family Tymoviridae.

    Science.gov (United States)

    Alabdullah, Abdulkader; Minafra, Angelantonio; Elbeaino, Toufic; Saponari, Maria; Savino, Vito; Martelli, Giovanni P

    2010-09-01

    The complete nucleotide sequence and the genome organization were determined of a putative new member of the family Tymoviridae, tentatively named Olive latent virus 3 (OLV-3), recovered in southern Italy from a symptomless olive tree. The sequenced ssRNA genome comprises 7148 nucleotides excluding the poly(A) tail and contains four open reading frames (ORFs). ORF1 encodes a polyprotein of 221.6kDa in size, containing the conserved signatures of the methyltransferase (MTR), papain-like protease (PRO), helicase (HEL) and RNA-dependent RNA polymerase (RdRp) domains of the replication-associated proteins of positive-strand RNA viruses. ORF2 overlaps completely ORF1 and encodes a putative protein of 43.33kDa showing limited sequence similarity with the putative movement protein of Maize rayado fino virus (MRFV). ORF3 codes for a protein with predicted molecular mass of 28.46kDa, identified as the coat protein (CP), whereas ORF4 overlaps ORF3 and encodes a putative protein of 16kDa with sequence similarity to the p16 and p31 proteins of Citrus sudden death-associated virus (CSDaV) and Grapevine fleck virus (GFkV), respectively. Within the family Tymoviridae, OLV-3 genome has the closest identity level (49-52%) with members of the genus Marafivirus, from which, however, it differs because of the diverse genome organization and the presence of a single type of CP subunits. Copyright (c) 2010 Elsevier B.V. All rights reserved.

  19. A method to employ the spatial organization of catchments into semi-distributed rainfall–runoff models

    Directory of Open Access Journals (Sweden)

    H. Oppel

    2017-08-01

    Full Text Available A distributed or semi-distributed deterministic hydrological model should consider the hydrologically most relevant catchment characteristics. These are heterogeneously distributed within a watershed but often interrelated and subject to a certain spatial organization which results in archetypes of combined characteristics. In order to reproduce the natural rainfall–runoff response the reduction of variance of catchment properties as well as the incorporation of the spatial organization of the catchment are desirable. In this study the width-function approach is utilized as a basic characteristic to analyse the succession of catchment characteristics. By applying this technique we were able to assess the context of catchment properties like soil or topology along the streamflow length and the network geomorphology, giving indications of the spatial organization of a catchment. Moreover, this information and this technique have been implemented in an algorithm for automated sub-basin ascertainment, which included the definition of zones within the newly defined sub-basins. The objective was to provide sub-basins that were less heterogeneous than common separation schemes. The algorithm was applied to two parameters characterizing the topology and soil of four mid-European watersheds. Resulting partitions indicated a wide range of applicability for the method and the algorithm. Additionally, the intersection of derived zones for different catchment characteristics could give insights into sub-basin similarities. Finally, a HBV96 case study demonstrated the potential benefits of modelling with the new subdivision technique.

  20. One-step fabrication of an organ-on-a-chip with spatial heterogeneity using a 3D bioprinting technology.

    Science.gov (United States)

    Lee, Hyungseok; Cho, Dong-Woo

    2016-07-05

    Although various types of organs-on-chips have been introduced recently as tools for drug discovery, the current studies are limited in terms of fabrication methods. The fabrication methods currently available not only need a secondary cell-seeding process and result in severe protein absorption due to the material used, but also have difficulties in providing various cell types and extracellular matrix (ECM) environments for spatial heterogeneity in the organs-on-chips. Therefore, in this research, we introduce a novel 3D bioprinting method for organ-on-a-chip applications. With our novel 3D bioprinting method, it was possible to prepare an organ-on-a-chip in a simple one-step fabrication process. Furthermore, protein absorption on the printed platform was very low, which will lead to accurate measurement of metabolism and drug sensitivity. Moreover, heterotypic cell types and biomaterials were successfully used and positioned at the desired position for various organ-on-a-chip applications, which will promote full mimicry of the natural conditions of the organs. The liver organ was selected for the evaluation of the developed method, and liver function was shown to be significantly enhanced on the liver-on-a-chip, which was prepared by 3D bioprinting. Consequently, the results demonstrate that the suggested 3D bioprinting method is easier and more versatile for production of organs-on-chips.

  1. A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes

    Directory of Open Access Journals (Sweden)

    Baldiri Salvado

    2015-08-01

    Full Text Available Two Component Systems and Phosphorelays (TCS/PR are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping the responses of the circuits. It is thus important to maintain updated censuses of TCS/PR proteins in order to identify the various topologies used by nature and enable a systematic study of the dynamics associated with those topologies. To create such a census, we analyzed the proteomes of 7,609 organisms from all domains of life with fully sequenced and annotated genomes. To begin, we survey each proteome searching for proteins containing domains that are associated with internal signal transmission within TCS/PR: Histidine Kinase (HK, Response Regulator (RR and Histidine Phosphotranfer (HPt domains, and analyze how these domains are arranged in the individual proteins. Then, we find all types of operon organization and calculate how much more likely are proteins that contain TCS/PR domains to be coded by neighboring genes than one would expect from the genome background of each organism. Finally, we analyze if the fusion of domains into single TCS/PR proteins is more frequently observed than one might expect from the background of each proteome. We find 50 alternative ways in which the HK, HPt, and RR domains are observed to organize into single proteins. In prokaryotes, TCS/PR coding genes tend to be clustered in operons. 90% of all proteins identified in this study contain just one of the three domains, while 8% of the remaining proteins combine one copy of an HK, a RR, and/or an HPt domain. In eukaryotes, 25% of all TCS/PR proteins have more than one domain. These results might have implications for how signals are internally transmitted within TCS/PR cascades. These implications could explain the selection of the various designs in alternative circumstances.

  2. Organization and Evolution of Subtelomeric Satellite Repeats in the Potato Genome

    Czech Academy of Sciences Publication Activity Database

    Torres, A.T.; Gong, Z.; Iovene, M.; Hirsch, C.D.; Buell, C.R.; Bryan, G.J.; Novák, Petr; Macas, Jiří; Jiang, J.

    2011-01-01

    Roč. 1, July 2011 (2011), s. 85-92 ISSN 2160-1836 R&D Projects: GA MŠk(CZ) LH11058 Institutional research plan: CEZ:AV0Z50510513 Keywords : Satellite sequences * Potato genome * Repeats Subject RIV: EB - Genetics ; Molecular Biology

  3. Functional organization of the genome may shape the species boundary in the house mouse

    Czech Academy of Sciences Publication Activity Database

    Janoušek, Václav; Munclinger, P.; Wang, L.; Teeter, K. C.; Tucker, P. K.

    2015-01-01

    Roč. 32, č. 5 (2015), s. 1208-1220 ISSN 0737-4038 R&D Projects: GA MŠk EE2.3.20.0303 Institutional support: RVO:68081766 Keywords : hybrid zone * mouse genome * speciation Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 13.649, year: 2015

  4. Molecular cloning and genomic organization of an allatostatin preprohormone from Drosophila melanogaster

    DEFF Research Database (Denmark)

    Lenz, C; Williamson, M; Grimmelikhuijzen, C J

    2000-01-01

    The insect allatostatins are neurohormones, acting on the corpora allata (where they block the release of juvenile hormone) and on the insect gut (where they block smooth muscle contraction). We screened the "Drosophila Genome Project" database with electronic sequences corresponding to various i...

  5. Enabling a community to dissect an organism: overview of the Neurospora functional genomics project.

    Science.gov (United States)

    Dunlap, Jay C; Borkovich, Katherine A; Henn, Matthew R; Turner, Gloria E; Sachs, Matthew S; Glass, N Louise; McCluskey, Kevin; Plamann, Michael; Galagan, James E; Birren, Bruce W; Weiss, Richard L; Townsend, Jeffrey P; Loros, Jennifer J; Nelson, Mary Anne; Lambreghts, Randy; Colot, Hildur V; Park, Gyungsoon; Collopy, Patrick; Ringelberg, Carol; Crew, Christopher; Litvinkova, Liubov; DeCaprio, Dave; Hood, Heather M; Curilla, Susan; Shi, Mi; Crawford, Matthew; Koerhsen, Michael; Montgomery, Phil; Larson, Lisa; Pearson, Matthew; Kasuga, Takao; Tian, Chaoguang; Baştürkmen, Meray; Altamirano, Lorena; Xu, Junhuan

    2007-01-01

    A consortium of investigators is engaged in a functional genomics project centered on the filamentous fungus Neurospora, with an eye to opening up the functional genomic analysis of all the filamentous fungi. The overall goal of the four interdependent projects in this effort is to accomplish functional genomics, annotation, and expression analyses of Neurospora crassa, a filamentous fungus that is an established model for the assemblage of over 250,000 species of non yeast fungi. Building from the completely sequenced 43-Mb Neurospora genome, Project 1 is pursuing the systematic disruption of genes through targeted gene replacements, phenotypic analysis of mutant strains, and their distribution to the scientific community at large. Project 2, through a primary focus in Annotation and Bioinformatics, has developed a platform for electronically capturing community feedback and data about the existing annotation, while building and maintaining a database to capture and display information about phenotypes. Oligonucleotide-based microarrays created in Project 3 are being used to collect baseline expression data for the nearly 11,000 distinguishable transcripts in Neurospora under various conditions of growth and development, and eventually to begin to analyze the global effects of loss of novel genes in strains created by Project 1. cDNA libraries generated in Project 4 document the overall complexity of expressed sequences in Neurospora, including alternative splicing alternative promoters and antisense transcripts. In addition, these studies have driven the assembly of an SNP map presently populated by nearly 300 markers that will greatly accelerate the positional cloning of genes.

  6. Genomic sequence, organization and characteristics of a new nucleopolyhedrovirus isolated from Clanis bilineata larva

    Directory of Open Access Journals (Sweden)

    Wang Yong

    2009-02-01

    Full Text Available Abstract Background Baculoviruses are well known for their potential as biological agents for controlling agricultural and forest pests. They are also widely used as expression vectors in molecular cloning studies. The genome sequences of 48 baculoviruses are currently available in NCBI databases. As the number of sequenced viral genomes increases, it is important for the authors to present sufficiently detailed analyses and annotations to advance understanding of them. In this study, the complete genome of Clanis bilineata nucleopolyhedrovirus (ClbiNPV has been sequenced and analyzed in order to understand this virus better. Results The genome of ClbiNPV contains 135,454 base pairs (bp with a G+C content of 37%, and 139 putative open reading frames (ORFs of at least 150 nucleotides. One hundred and twenty-six of these ORFs have homologues with other baculovirus genes while the other 13 are unique to ClbiNPV. The 30 baculovirus core genes are all present in ClbiNPV. Phylogenetic analysis based on the combined pif-2 and lef-8 sequences places ClbiNPV in the Group II Alphabaculoviruses. This result is consistent with the absence of gp64 from the ClbiNPV genome and the presence instead of a fusion protein gene, characteristic of Group II. Blast searches revealed that ClbiNPV encodes a photolyase-like gene sequence, which has a 1-bp deletion when compared with photolyases of other baculoviruses. This deletion disrupts the sequence into two small photolyase ORFs, designated Clbiphr-1 and Clbiphr-2, which correspond to the CPD-DNA photolyase and FAD-binding domains of photolyases, respectively. Conclusion ClbiNPV belongs to the Group II Alphabaculoviruses and is most closely related to OrleNPV, LdMNPV, TnSNPV, EcobNPV and ChchNPV. It contains a variant DNA photolyase gene, which only exists in ChchNPV, TnSNPV and SpltGV among the baculoviruses.

  7. Understanding the development of human bladder cancer by using a whole-organ genomic mapping strategy.

    Science.gov (United States)

    Majewski, Tadeusz; Lee, Sangkyou; Jeong, Joon; Yoon, Dong-Sup; Kram, Andrzej; Kim, Mi-Sook; Tuziak, Tomasz; Bondaruk, Jolanta; Lee, Sooyong; Park, Weon-Seo; Tang, Kuang S; Chung, Woonbok; Shen, Lanlan; Ahmed, Saira S; Johnston, Dennis A; Grossman, H Barton; Dinney, Colin P; Zhou, Jain-Hua; Harris, R Alan; Snyder, Carrie; Filipek, Slawomir; Narod, Steven A; Watson, Patrice; Lynch, Henry T; Gazdar, Adi; Bar-Eli, Menashe; Wu, Xifeng F; McConkey, David J; Baggerly, Keith; Issa, Jean-Pierre; Benedict, William F; Scherer, Steven E; Czerniak, Bogdan

    2008-07-01

    The search for the genomic sequences involved in human cancers can be greatly facilitated by maps of genomic imbalances identifying the involved chromosomal regions, particularly those that participate in the development of occult preneoplastic conditions that progress to clinically aggressive invasive cancer. The integration of such regions with human genome sequence variation may provide valuable clues about their overall structure and gene content. By extension, such knowledge may help us understand the underlying genetic components involved in the initiation and progression of these cancers. We describe the development of a genome-wide map of human bladder cancer that tracks its progression from in situ precursor conditions to invasive disease. Testing for allelic losses using a genome-wide panel of 787 microsatellite markers was performed on multiple DNA samples, extracted from the entire mucosal surface of the bladder and corresponding to normal urothelium, in situ preneoplastic lesions, and invasive carcinoma. Using this approach, we matched the clonal allelic losses in distinct chromosomal regions to specific phases of bladder neoplasia and produced a detailed genetic map of bladder cancer development. These analyses revealed three major waves of genetic changes associated with growth advantages of successive clones and reflecting a stepwise conversion of normal urothelial cells into cancer cells. The genetic changes map to six regions at 3q22-q24, 5q22-q31, 9q21-q22, 10q26, 13q14, and 17p13, which may represent critical hits driving the development of bladder cancer. Finally, we performed high-resolution mapping using single nucleotide polymorphism markers within one region on chromosome 13q14, containing the model tumor suppressor gene RB1, and defined a minimal deleted region associated with clonal expansion of in situ neoplasia. These analyses provided new insights on the involvement of several non-coding sequences mapping to the region and identified

  8. Spatial and temporal superresolution concepts to study plasma membrane organization by single molecule fluorescence techniques

    International Nuclear Information System (INIS)

    Ruprecht, V.

    2010-01-01

    Fluorescence microscopy techniques are currently among the most important experimental tools to study cellular processes. Ultra-sensitive detection devices nowadays allow for measuring even individual farnesylacetate labeled target molecules with nanometer spatial accuracy and millisecond time resolution. The emergence of single molecule fluorescence techniques especially contributed to the field of membrane biology and provided basic knowledge on structural and dynamic features of the cellular plasma membrane. However, we are still confronted with a rather fragmentary understanding of the complex architecture and functional interrelations of membrane constituents. In this thesis new concepts in one- and dual-color single molecule fluorescence techniques are presented that allow for addressing organization principles and interaction dynamics in the live cell plasma membrane. Two complementary experimental strategies are described which differ in their detection principle: single molecule fluorescence imaging and fluorescence correlation spectroscopy. The presented methods are discussed in terms of their implementation, accuracy, quantitative and statistical data analysis, as well as live cell applications. State-of-the-art dual color single molecule imaging is introduced as the most direct experimental approach to study interaction dynamics between differently labeled target molecules. New analytical estimates for robust data analysis are presented that facilitate quantitative recording and identification of co localizations in dual color single molecule images. A novel dual color illumination scheme is further described that profoundly extends the current range and sensitivity of conventional dual color single molecule experiments. The method enables working at high surface densities of fluorescent molecules - a feature typically incommensurable with single molecule imaging - and is especially suited for the detection of rare interactions by tracking co localized

  9. Spatial representation of organic carbon and active-layer thickness of high latitude soils in CMIP5 earth system models

    Energy Technology Data Exchange (ETDEWEB)

    Mishra, Umakant; Drewniak, Beth; Jastrow, Julie D.; Matamala, Roser M.; Vitharana, U. W. A.

    2017-08-01

    Soil properties such as soil organic carbon (SOC) stocks and active-layer thickness are used in earth system models (F.SMs) to predict anthropogenic and climatic impacts on soil carbon dynamics, future changes in atmospheric greenhouse gas concentrations, and associated climate changes in the permafrost regions. Accurate representation of spatial and vertical distribution of these soil properties in ESMs is a prerequisite for redudng existing uncertainty in predicting carbon-climate feedbacks. We compared the spatial representation of SOC stocks and active-layer thicknesses predicted by the coupled Modellntercomparison Project Phase 5 { CMIP5) ESMs with those predicted from geospatial predictions, based on observation data for the state of Alaska, USA. For the geospatial modeling. we used soil profile observations {585 for SOC stocks and 153 for active-layer thickness) and environmental variables (climate, topography, land cover, and surficial geology types) and generated fine-resolution (50-m spatial resolution) predictions of SOC stocks (to 1-m depth) and active-layer thickness across Alaska. We found large inter-quartile range (2.5-5.5 m) in predicted active-layer thickness of CMIP5 modeled results and small inter-quartile range (11.5-22 kg m-2) in predicted SOC stocks. The spatial coefficient of variability of active-layer thickness and SOC stocks were lower in CMIP5 predictions compared to our geospatial estimates when gridded at similar spatial resolutions (24.7 compared to 30% and 29 compared to 38%, respectively). However, prediction errors. when calculated for independent validation sites, were several times larger in ESM predictions compared to geospatial predictions. Primaly factors leading to observed differences were ( 1) lack of spatial heterogeneity in ESM predictions, (2) differences in assumptions concerning environmental controls, and (3) the absence of pedogenic processes in ESM model structures. Our results suggest that efforts to incorporate

  10. Direct extraction of genomic DNA from maize with aqueous ionic liquid buffer systems for applications in genetically modified organisms analysis.

    Science.gov (United States)

    Gonzalez García, Eric; Ressmann, Anna K; Gaertner, Peter; Zirbs, Ronald; Mach, Robert L; Krska, Rudolf; Bica, Katharina; Brunner, Kurt

    2014-12-01

    To date, the extraction of genomic DNA is considered a bottleneck in the process of genetically modified organisms (GMOs) detection. Conventional DNA isolation methods are associated with long extraction times and multiple pipetting and centrifugation steps, which makes the entire procedure not only tedious and complicated but also prone to sample cross-contamination. In recent times, ionic liquids have emerged as innovative solvents for biomass processing, due to their outstanding properties for dissolution of biomass and biopolymers. In this study, a novel, easily applicable, and time-efficient method for the direct extraction of genomic DNA from biomass based on aqueous-ionic liquid solutions was developed. The straightforward protocol relies on extraction of maize in a 10 % solution of ionic liquids in aqueous phosphate buffer for 5 min at room temperature, followed by a denaturation step at 95 °C for 10 min and a simple filtration to remove residual biopolymers. A set of 22 ionic liquids was tested in a buffer system and 1-ethyl-3-methylimidazolium dimethylphosphate, as well as the environmentally benign choline formate, were identified as ideal candidates. With this strategy, the quality of the genomic DNA extracted was significantly improved and the extraction protocol was notably simplified compared with a well-established method.

  11. Spatial self-organized patterning in seagrasses along a depth gradient of an intertidal ecosystem

    NARCIS (Netherlands)

    van der Heide, Tjisse; Bouma, Tjeerd J.; Nes, Egbert H. van; van de Koppel, Johan; Scheffer, Marten; Roelofs, Jan G.M.; Katwijk, Marieke M. van; Smolders, Alfons J.P.

    2010-01-01

    The spatial structure of seagrass landscapes is typically ascribed to the direct influence of physical factors such as hydrodynamics, light, and sediment transport. We studied regularly interspaced banded patterns, formed by elongated patches of seagrass, in a small-scale intertidal ecosystem. We

  12. The rhythms of steady posture: Motor commands as spatially organized oscillation patterns

    NARCIS (Netherlands)

    Heitmann, S.; Boonstra, T.W.; Gong, P.; Breakspear, M.; Ermentrout, B.

    2015-01-01

    Beta-band (15-30. Hz) oscillations in motor cortex have been implicated in voluntary movement and postural control. Yet the mechanisms linking those oscillations to function remains elusive. Recently, spatial waves of synchronized beta oscillations have been observed in primary and pre-motor cortex

  13. Competence development organizations in project management on the basis of genomic model methodologies

    OpenAIRE

    Бушуев, Сергей Дмитриевич; Рогозина, Виктория Борисовна; Ярошенко, Юрий Федерович

    2013-01-01

    The matrix technology for identification of organisational competencies in project management is presented in the article. Matrix elements are the components of organizational competence in the field of project management and project management methodology represented in the structure of the genome. The matrix model of competence in the framework of the adopted methodologies and scanning method for identifying organizational competences formalised. Proposed methods for building effective proj...

  14. Genome sequence and organization of a nucleopolyhedrovirus isolated from the smaller tea tortrix, Adoxophyes honmai

    International Nuclear Information System (INIS)

    Nakai, Madoka; Goto, Chie; Kang, Won Kyung; Shikata, Masamitsu; Luque, Teresa; Kunimi, Yasuhisa

    2003-01-01

    Adoxophyes honmai nucleopolyhedrovirus (AdhoNPV) has a distinctive pathology in A. honmai larvae, killing the host more slowly than other NPVs. To further understand the pathology of AdhoNPV, its genome was completely sequenced and compared with those of other baculoviruses. The AdhoNPV genome is 113,220 bp, with a G + C content of 35.6%. It contains 125 putative open reading frames (ORFs), of which 8 are unique to AdhoNPV, and 4 homologous regions. The other 117 ORFs display similarity to previously characterized baculovirus genes involved in early and late gene expression, DNA replication, and structural and auxiliary functions. The phylogenetic position of AdhoNPV, in relation to 15 other baculoviruses whose genomes have been completely sequenced, was assessed by three different analyses: gene sequence, gene order, and gene content. Although gene content analysis failed to support the group II NPVs, phylogenetic trees based on gene sequence and gene order showed AdhoNPV to be closely related to the group II NPVs

  15. Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions.

    Science.gov (United States)

    Singh, Anuradha; Mantri, Shrikant; Sharma, Monica; Chaudhury, Ashok; Tuli, Rakesh; Roy, Joy

    2014-01-16

    The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT-PCR. Therefore, this study

  16. Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions

    Science.gov (United States)

    2014-01-01

    Background The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. Results Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT

  17. Quantification of the spatial organization of the nuclear lamina as a tool for cell classification

    NARCIS (Netherlands)

    Righolt, C.H.; Zatreanu, D.A.; Raz, V.

    2013-01-01

    The nuclear lamina is the structural scaffold of the nuclear envelope that plays multiple regulatory roles in chromatin organization and gene expression as well as a structural role in nuclear stability. The lamina proteins, also referred to as lamins, determine nuclear lamina organization and

  18. Self-organization of spatial patterning in human embryonic stem cells

    Science.gov (United States)

    Deglincerti, Alessia; Etoc, Fred; Ozair, M. Zeeshan; Brivanlou, Ali H.

    2017-01-01

    The developing embryo is a remarkable example of self-organization, where functional units are created in a complex spatio-temporal choreography. Recently, human embryonic stem cells (ESCs) have been used to recapitulate in vitro the self-organization programs that are executed in the embryo in vivo. This represents a unique opportunity to address self-organization in humans that is otherwise not addressable with current technologies. In this essay, we review the recent literature on self-organization of human ESCs, with a particular focus on two examples: formation of embryonic germ layers and neural rosettes. Intriguingly, both activation and elimination of TGFβ signaling can initiate self-organization, albeit with different molecular underpinnings. We discuss the mechanisms underlying the formation of these structures in vitro and explore future challenges in the field. PMID:26970615

  19. Self-Organization of Spatial Patterning in Human Embryonic Stem Cells.

    Science.gov (United States)

    Deglincerti, Alessia; Etoc, Fred; Ozair, M Zeeshan; Brivanlou, Ali H

    2016-01-01

    The developing embryo is a remarkable example of self-organization, where functional units are created in a complex spatiotemporal choreography. Recently, human embryonic stem cells (ESCs) have been used to recapitulate in vitro the self-organization programs that are executed in the embryo in vivo. This represents an unique opportunity to address self-organization in humans that is otherwise not addressable with current technologies. In this chapter, we review the recent literature on self-organization of human ESCs, with a particular focus on two examples: formation of embryonic germ layers and neural rosettes. Intriguingly, both activation and elimination of TGFβ signaling can initiate self-organization, albeit with different molecular underpinnings. We discuss the mechanisms underlying the formation of these structures in vitro and explore future challenges in the field. © 2016 Elsevier Inc. All rights reserved.

  20. Spatial analysis of biomineralization associated gene expression from the mantle organ of the pearl oyster Pinctada maxima

    Science.gov (United States)

    2011-01-01

    Background Biomineralization is a process encompassing all mineral containing tissues produced within an organism. One of the most dynamic examples of this process is the formation of the mollusk shell, comprising a variety of crystal phases and microstructures. The organic component incorporated within the shell is said to dictate this architecture. However general understanding of how this process is achieved remains ambiguous. The mantle is a conserved organ involved in shell formation throughout molluscs. Specifically the mantle is thought to be responsible for secreting the protein component of the shell. This study employs molecular approaches to determine the spatial expression of genes within the mantle tissue to further the elucidation of the shell biomineralization. Results A microarray platform was custom generated (PmaxArray 1.0) from the pearl oyster Pinctada maxima. PmaxArray 1.0 consists of 4992 expressed sequence tags (ESTs) originating from mantle tissue. This microarray was used to analyze the spatial expression of ESTs throughout the mantle organ. The mantle was dissected into five discrete regions and analyzed for differential gene expression with PmaxArray 1.0. Over 2000 ESTs were determined to be differentially expressed among the tissue sections, identifying five major expression regions. In situ hybridization validated and further localized the expression for a subset of these ESTs. Comparative sequence similarity analysis of these ESTs revealed a number of the transcripts were novel while others showed significant sequence similarities to previously characterized shell related genes. Conclusions This investigation has mapped the spatial distribution for over 2000 ESTs present on PmaxArray 1.0 with reference to specific locations of the mantle. Expression profile clusters have indicated at least five unique functioning zones in the mantle. Three of these zones are likely involved in shell related activities including formation of nacre

  1. Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha

    Directory of Open Access Journals (Sweden)

    Baumann Paul

    2004-08-01

    Full Text Available Abstract Background With some exceptions, mitochondria within the class Insecta have the same gene content, and generally, a similar gene order allowing the proposal of an ancestral gene order. The principal exceptions are several orders within the Hemipteroid assemblage including the order Thysanoptera, a sister group of the order Hemiptera. Within the Hemiptera, there are available a number of completely sequenced mitochondrial genomes that have a gene order similar to that of the proposed ancestor. None, however, are available from the suborder Sternorryncha that includes whiteflies, psyllids and aphids. Results We have determined the complete nucleotide sequence of the mitochondrial genomes of six species of whiteflies, one psyllid and one aphid. Two species of whiteflies, one psyllid and one aphid have mitochondrial genomes with a gene order very similar to that of the proposed insect ancestor. The remaining four species of whiteflies had variations in the gene order. In all cases, there was the excision of a DNA fragment encoding for cytochrome oxidase subunit III(COIII-tRNAgly-NADH dehydrogenase subunit 3(ND3-tRNAala-tRNAarg-tRNAasn from the ancestral position between genes for ATP synthase subunit 6 and NADH dehydrogenase subunit 5. Based on the position in which all or part of this fragment was inserted, the mitochondria could be subdivided into four different gene arrangement types. PCR amplification spanning from COIII to genes outside the inserted region and sequence determination of the resulting fragments, indicated that different whitefly species could be placed into one of these arrangement types. A phylogenetic analysis of 19 whitefly species based on genes for mitochondrial cytochrome b, NADH dehydrogenase subunit 1, and 16S ribosomal DNA as well as cospeciating endosymbiont 16S and 23S ribosomal DNA indicated a clustering of species that corresponded to the gene arrangement types. Conclusions In whiteflies, the region of the

  2. A Five Species Cyclically Dominant Evolutionary Game with Fixed Direction: A New Way to Produce Self-Organized Spatial Patterns

    Directory of Open Access Journals (Sweden)

    Yibin Kang

    2016-08-01

    Full Text Available Cyclically dominant systems are hot issues in academia, and they play an important role in explaining biodiversity in Nature. In this paper, we construct a five-strategy cyclically dominant system. Each individual in our system changes its strategy along a fixed direction. The dominant strategy can promote a change in the dominated strategy, and the dominated strategy can block a change in the dominant strategy. We use mean-field theory and cellular automaton simulation to discuss the evolving characters of the system. In the cellular automaton simulation, we find the emergence of spiral waves on spatial patterns without a migration rate, which suggests a new way to produce self-organized spatial patterns.

  3. Cytoplasmic Dynein Is Required for the Spatial Organization of Protein Aggregates in Filamentous Fungi

    Directory of Open Access Journals (Sweden)

    Martin J. Egan

    2015-04-01

    Full Text Available Eukaryotes have evolved multiple strategies for maintaining cellular protein homeostasis. One such mechanism involves neutralization of deleterious protein aggregates via their defined spatial segregation. Here, using the molecular disaggregase Hsp104 as a marker for protein aggregation, we describe the spatial and temporal dynamics of protein aggregates in the filamentous fungus Aspergillus nidulans. Filamentous fungi, such as A. nidulans, are a diverse group of species of major health and economic importance and also serve as model systems for studying highly polarized eukaryotic cells. We find that microtubules promote the formation of Hsp104-positive aggregates, which coalesce into discrete subcellular structures in a process dependent on the microtubule-based motor cytoplasmic dynein. Finally, we find that impaired clearance of these inclusions negatively impacts retrograde trafficking of endosomes, a conventional dynein cargo, indicating that microtubule-based transport can be overwhelmed by chronic cellular stress.

  4. Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome

    Directory of Open Access Journals (Sweden)

    Frédéric Pontvianne

    2016-08-01

    Full Text Available The nucleolus is the site of rRNA gene transcription, rRNA processing, and ribosome biogenesis. However, the nucleolus also plays additional roles in the cell. We isolated nucleoli using fluorescence-activated cell sorting (FACS and identified nucleolus-associated chromatin domains (NADs by deep sequencing, comparing wild-type plants and null mutants for the nucleolar protein NUCLEOLIN 1 (NUC1. NADs are primarily genomic regions with heterochromatic signatures and include transposable elements (TEs, sub-telomeric regions, and mostly inactive protein-coding genes. However, NADs also include active rRNA genes and the entire short arm of chromosome 4 adjacent to them. In nuc1 null mutants, which alter rRNA gene expression and overall nucleolar structure, NADs are altered, telomere association with the nucleolus is decreased, and telomeres become shorter. Collectively, our studies reveal roles for NUC1 and the nucleolus in the spatial organization of chromosomes as well as telomere maintenance.

  5. Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome.

    Science.gov (United States)

    Pontvianne, Frédéric; Carpentier, Marie-Christine; Durut, Nathalie; Pavlištová, Veronika; Jaške, Karin; Schořová, Šárka; Parrinello, Hugues; Rohmer, Marine; Pikaard, Craig S; Fojtová, Miloslava; Fajkus, Jiří; Sáez-Vásquez, Julio

    2016-08-09

    The nucleolus is the site of rRNA gene transcription, rRNA processing, and ribosome biogenesis. However, the nucleolus also plays additional roles in the cell. We isolated nucleoli using fluorescence-activated cell sorting (FACS) and identified nucleolus-associated chromatin domains (NADs) by deep sequencing, comparing wild-type plants and null mutants for the nucleolar protein NUCLEOLIN 1 (NUC1). NADs are primarily genomic regions with heterochromatic signatures and include transposable elements (TEs), sub-telomeric regions, and mostly inactive protein-coding genes. However, NADs also include active rRNA genes and the entire short arm of chromosome 4 adjacent to them. In nuc1 null mutants, which alter rRNA gene expression and overall nucleolar structure, NADs are altered, telomere association with the nucleolus is decreased, and telomeres become shorter. Collectively, our studies reveal roles for NUC1 and the nucleolus in the spatial organization of chromosomes as well as telomere maintenance. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  6. Spatial Patterns of Excitation at Tissue and Whole Organ Level Due to Early Afterdepolarizations

    Directory of Open Access Journals (Sweden)

    Nele Vandersickel

    2017-06-01

    Full Text Available Early after depolarizations (EAD occur in many pathological conditions, such as congenital or acquired channelopathies, drug induced arrhythmias, and several other situations that are associated with increased arrhythmogenicity. In this paper we present an overview of the relevant computational studies on spatial EAD dynamics in 1D, 2D, and in 3D anatomical models and discuss the relation of EADs to cardiac arrhythmias. We also discuss unsolved problems and highlight new lines of research in this area.

  7. DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms.

    Science.gov (United States)

    Frías-López, Cristina; Sánchez-Herrero, José F; Guirao-Rico, Sara; Mora, Elisa; Arnedo, Miquel A; Sánchez-Gracia, Alejandro; Rozas, Julio

    2016-12-15

    The development of molecular markers is one of the most important challenges in phylogenetic and genome wide population genetics studies, especially in studies with non-model organisms. A highly promising approach for obtaining suitable markers is the utilization of genomic partitioning strategies for the simultaneous discovery and genotyping of a large number of markers. Unfortunately, not all markers obtained from these strategies provide enough information for solving multiple evolutionary questions at a reasonable taxonomic resolution. We have developed Development Of Molecular markers In Non-model Organisms (DOMINO), a bioinformatics tool for informative marker development from both next generation sequencing (NGS) data and pre-computed sequence alignments. The application implements popular NGS tools with new utilities in a highly versatile pipeline specifically designed to discover or select personalized markers at different levels of taxonomic resolution. These markers can be directly used to study the taxa surveyed for their design, utilized for further downstream PCR amplification in a broader set taxonomic scope, or exploited as suitable templates to bait design for target DNA enrichment techniques. We conducted an exhaustive evaluation of the performance of DOMINO via computer simulations and illustrate its utility to find informative markers in an empirical dataset. DOMINO is freely available from www.ub.edu/softevol/domino CONTACT: elsanchez@ub.edu or jrozas@ub.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  8. Human β satellite DNA: Genomic organization and sequence definition of a class of highly repetitive tandem DNA

    International Nuclear Information System (INIS)

    Waye, J.S.; Willard, H.F.

    1989-01-01

    The authors describe a class of human repetitive DNA, called β satellite, that, at a most fundamental level, exists as tandem arrays of diverged ∼68-base-pair monomer repeat units. The monomer units are organized as distinct subsets, each characterized by a multimeric higher-order repeat unit that is tandemly reiterated and represents a recent unit of amplification. They have cloned, characterized, and determined the sequence of two β satellite higher-order repeat units: one located on chromosome 9, the other on the acrocentric chromosomes (13, 14, 15, 21, and 22) and perhaps other sites in the genome. Analysis by pulsed-field gel electrophoresis reveals that these tandem arrays are localized in large domains that are marked by restriction fragment length polymorphisms. In total, β-satellite sequences comprise several million base pairs of DNA in the human genome. Analysis of this DNA family should permit insights into the nature of chromosome-specific and nonspecific modes of satellite DNA evolution and provide useful tools for probing the molecular organization and concerted evolution of the acrocentric chromosomes

  9. An exploration of collaborative scientific production at MIT through spatial organization and institutional affiliation.

    Science.gov (United States)

    Claudel, Matthew; Massaro, Emanuele; Santi, Paolo; Murray, Fiona; Ratti, Carlo

    2017-01-01

    Academic research is increasingly cross-disciplinary and collaborative, between and within institutions. In this context, what is the role and relevance of an individual's spatial position on a campus? We examine the collaboration patterns of faculty at the Massachusetts Institute of Technology, through their academic output (papers and patents), and their organizational structures (institutional affiliation and spatial configuration) over a 10-year time span. An initial comparison of output types reveals: 1. diverging trends in the composition of collaborative teams over time (size, faculty versus non-faculty, etc.); and 2. substantively different patterns of cross-building and cross-disciplinary collaboration. We then construct a multi-layered network of authors, and find two significant features of collaboration on campus: 1. a network topology and community structure that reveals spatial versus institutional collaboration bias; and 2. a persistent relationship between proximity and collaboration, well fit with an exponential decay model. This relationship is consistent for both papers and patents, and present also in exclusively cross-disciplinary work. These insights contribute an architectural dimension to the field of scientometrics, and take a first step toward empirical space-planning policy that supports collaboration within institutions.

  10. An exploration of collaborative scientific production at MIT through spatial organization and institutional affiliation

    Science.gov (United States)

    Santi, Paolo; Murray, Fiona; Ratti, Carlo

    2017-01-01

    Academic research is increasingly cross-disciplinary and collaborative, between and within institutions. In this context, what is the role and relevance of an individual’s spatial position on a campus? We examine the collaboration patterns of faculty at the Massachusetts Institute of Technology, through their academic output (papers and patents), and their organizational structures (institutional affiliation and spatial configuration) over a 10-year time span. An initial comparison of output types reveals: 1. diverging trends in the composition of collaborative teams over time (size, faculty versus non-faculty, etc.); and 2. substantively different patterns of cross-building and cross-disciplinary collaboration. We then construct a multi-layered network of authors, and find two significant features of collaboration on campus: 1. a network topology and community structure that reveals spatial versus institutional collaboration bias; and 2. a persistent relationship between proximity and collaboration, well fit with an exponential decay model. This relationship is consistent for both papers and patents, and present also in exclusively cross-disciplinary work. These insights contribute an architectural dimension to the field of scientometrics, and take a first step toward empirical space-planning policy that supports collaboration within institutions. PMID:28640829

  11. Spatial organization of the cytoskeleton enhances cargo delivery to specific target areas on the plasma membrane of spherical cells

    Science.gov (United States)

    Hafner, Anne E.; Rieger, Heiko

    2016-12-01

    Intracellular transport is vital for the proper functioning and survival of a cell. Cargo (proteins, vesicles, organelles, etc) is transferred from its place of creation to its target locations via molecular motor assisted transport along cytoskeletal filaments. The transport efficiency is strongly affected by the spatial organization of the cytoskeleton, which constitutes an inhomogeneous, complex network. In cells with a centrosome microtubules grow radially from the central microtubule organizing center towards the cell periphery whereas actin filaments form a dense meshwork, the actin cortex, underneath the cell membrane with a broad range of orientations. The emerging ballistic motion along filaments is frequently interrupted due to constricting intersection nodes or cycles of detachment and reattachment processes in the crowded cytoplasm. In order to investigate the efficiency of search strategies established by the cell’s specific spatial organization of the cytoskeleton we formulate a random velocity model with intermittent arrest states. With extensive computer simulations we analyze the dependence of the mean first passage times for narrow escape problems on the structural characteristics of the cytoskeleton, the motor properties and the fraction of time spent in each state. We find that an inhomogeneous architecture with a small width of the actin cortex constitutes an efficient intracellular search strategy.

  12. Spatial organization of the cytoskeleton enhances cargo delivery to specific target areas on the plasma membrane of spherical cells.

    Science.gov (United States)

    Hafner, Anne E; Rieger, Heiko

    2016-11-15

    Intracellular transport is vital for the proper functioning and survival of a cell. Cargo (proteins, vesicles, organelles, etc) is transferred from its place of creation to its target locations via molecular motor assisted transport along cytoskeletal filaments. The transport efficiency is strongly affected by the spatial organization of the cytoskeleton, which constitutes an inhomogeneous, complex network. In cells with a centrosome microtubules grow radially from the central microtubule organizing center towards the cell periphery whereas actin filaments form a dense meshwork, the actin cortex, underneath the cell membrane with a broad range of orientations. The emerging ballistic motion along filaments is frequently interrupted due to constricting intersection nodes or cycles of detachment and reattachment processes in the crowded cytoplasm. In order to investigate the efficiency of search strategies established by the cell's specific spatial organization of the cytoskeleton we formulate a random velocity model with intermittent arrest states. With extensive computer simulations we analyze the dependence of the mean first passage times for narrow escape problems on the structural characteristics of the cytoskeleton, the motor properties and the fraction of time spent in each state. We find that an inhomogeneous architecture with a small width of the actin cortex constitutes an efficient intracellular search strategy.

  13. Spatial variability of soil carbon, pH, available phosphorous and potassium in organic farm located in Mediterranean Croatia

    Science.gov (United States)

    Bogunović, Igor; Pereira, Paulo; Šeput, Miranda

    2016-04-01

    Soil organic carbon (SOC), pH, available phosphorus (P), and potassium (K) are some of the most important factors to soil fertility. These soil parameters are highly variable in space and time, with implications to crop production. The aim of this work is study the spatial variability of SOC, pH, P and K in an organic farm located in river Rasa valley (Croatia). A regular grid (100 x 100 m) was designed and 182 samples were collected on Silty Clay Loam soil. P, K and SOC showed moderate heterogeneity with coefficient of variation (CV) of 21.6%, 32.8% and 51.9%, respectively. Soil pH record low spatial variability with CV of 1.5%. Soil pH, P and SOC did not follow normal distribution. Only after a Box-Cox transformation, data respected the normality requirements. Directional exponential models were the best fitted and used to describe spatial autocorrelation. Soil pH, P and SOC showed strong spatial dependence with nugget to sill ratio with 13.78%, 0.00% and 20.29%, respectively. Only K recorded moderate spatial dependence. Semivariogram ranges indicate that future sampling interval could be 150 - 200 m in order to reduce sampling costs. Fourteen different interpolation models for mapping soil properties were tested. The method with lowest Root Mean Square Error was the most appropriated to map the variable. The results showed that radial basis function models (Spline with Tension and Completely Regularized Spline) for P and K were the best predictors, while Thin Plate Spline and inverse distance weighting models were the least accurate. The best interpolator for pH and SOC was the local polynomial with the power of 1, while the least accurate were Thin Plate Spline. According to soil nutrient maps investigated area record very rich supply with K while P supply was insufficient on largest part of area. Soil pH maps showed mostly neutral reaction while individual parts of alkaline soil indicate the possibility of penetration of seawater and salt accumulation in the

  14. Spatial and Seasonal Variation of dissolved organic carbon (DOC) concentrations in Irish streams: importance of soil and topography characteristics.

    Science.gov (United States)

    Liu, Wen; Xu, Xianli; McGoff, Nicola M; Eaton, James M; Leahy, Paul; Foley, Nelius; Kiely, Gerard

    2014-05-01

    Dissolved organic carbon (DOC) concentrations have increased in many sites in Europe and North America in recent decades. High DOC concentrations can damage the structure and functions of aquatic ecosystems by influencing water chemistry. This study investigated the spatial and seasonal variation of DOC concentrations in Irish streams across 55 sites at seven time occasions over 1 year (2006/2007). The DOC concentrations ranged from 0.9 to 25.9 mg/L with a mean value of 6.8 and a median value of 5.7 mg/L and varied significantly over the course of the year. The DOC concentrations from late winter (February: 5.2 ± 3.0 mg/L across 55 sites) and early spring (April: 4.5 ± 3.5 mg/L) had significantly lower DOC concentrations than autumn (October: mean 8.3 ± 5.6 mg/L) and early winter (December: 8.3 ± 5.1 mg/L). The DOC production sources (e.g., litterfall) or the accumulation of DOC over dry periods might be the driving factor of seasonal change in Irish stream DOC concentrations. Analysis of data using stepwise multiple linear regression techniques identified the topographic index (TI, an indication of saturation-excess runoff potential) and soil conditions (organic carbon content and soil drainage characteristics) as key factors in controlling DOC spatial variation in different seasons. The TI and soil carbon content (e.g., soil organic carbon; peat occurrence) are positively related to DOC concentrations, while well-drained soils are negatively related to DOC concentrations. The knowledge of spatial and seasonal variation of DOC concentrations in streams and their drivers are essential for optimum riverine water resources management.

  15. The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster

    Science.gov (United States)

    Bushley, Kathryn E.; Raja, Rajani; Jaiswal, Pankaj; Cumbie, Jason S.; Nonogaki, Mariko; Boyd, Alexander E.; Owensby, C. Alisha; Knaus, Brian J.; Elser, Justin; Miller, Daniel; Di, Yanming; McPhail, Kerry L.; Spatafora, Joseph W.

    2013-01-01

    The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of cyclosporin and other secondary metabolites in T. inflatum and related taxa. Phylogenomic analyses reveal previously undetected and complex patterns of homology between the nonribosomal peptide synthetase (NRPS) that encodes for cyclosporin synthetase (simA) and those of other secondary metabolites with activities against insects (e.g., beauvericin, destruxins, etc.), and demonstrate the roles of module duplication and gene fusion in diversification of NRPSs. The secondary metabolite gene cluster responsible for cyclosporin biosynthesis is described. In addition to genes necessary for cyclosporin biosynthesis, it harbors a gene for a cyclophilin, which is a member of a family of immunophilins known to bind cyclosporin. Comparative analyses support a lineage specific origin of the cyclosporin gene cluster rather than horizontal gene transfer from bacteria or other fungi. RNA-Seq transcriptome analyses in a cyclosporin-inducing medium delineate the boundaries of the cyclosporin cluster and reveal high levels of expression of the gene cluster cyclophilin. In medium containing insect hemolymph, weaker but significant upregulation of several genes within the cyclosporin cluster, including the highly expressed cyclophilin gene, was observed. T. inflatum also represents the first reference draft genome of Ophiocordycipitaceae, a third family of insect pathogenic fungi within the fungal order Hypocreales, and supports parallel and qualitatively distinct radiations of insect pathogens. The T. inflatum genome provides additional insight into the evolution and biosynthesis of cyclosporin and lays a foundation for further investigations of the role

  16. Integrated, multi-scale, spatial-temporal cell biology--A next step in the post genomic era.

    Science.gov (United States)

    Horwitz, Rick

    2016-03-01

    New microscopic approaches, high-throughput imaging, and gene editing promise major new insights into cellular behaviors. When coupled with genomic and other 'omic information and "mined" for correlations and associations, a new breed of powerful and useful cellular models should emerge. These top down, coarse-grained, and statistical models, in turn, can be used to form hypotheses merging with fine-grained, bottom up mechanistic studies and models that are the back bone of cell biology. The goal of the Allen Institute for Cell Science is to develop the top down approach by developing a high throughput microscopy pipeline that is integrated with modeling, using gene edited hiPS cell lines in various physiological and pathological contexts. The output of these experiments and models will be an "animated" cell, capable of integrating and analyzing image data generated from experiments and models. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern United States

    Science.gov (United States)

    Lee, Soo-Rang; Jo, Yeong-Seok; Park, Chan-Ho; Friedman, Jonathan M.; Olson, Matthew S.

    2018-01-01

    Understanding the complex influences of landscape and anthropogenic elements that shape the population genetic structure of invasive species provides insight into patterns of colonization and spread. The application of landscape genomics techniques to these questions may offer detailed, previously undocumented insights into factors influencing species invasions. We investigated the spatial pattern of genetic variation and the influences of landscape factors on population similarity in an invasive riparian shrub, saltcedar (Tamarix L.) by analysing 1,997 genomewide SNP markers for 259 individuals from 25 populations collected throughout the southwestern United States. Our results revealed a broad-scale spatial genetic differentiation of saltcedar populations between the Colorado and Rio Grande river basins and identified potential barriers to population similarity along both river systems. River pathways most strongly contributed to population similarity. In contrast, low temperature and dams likely served as barriers to population similarity. We hypothesize that large-scale geographic patterns in genetic diversity resulted from a combination of early introductions from distinct populations, the subsequent influence of natural selection, dispersal barriers and founder effects during range expansion.

  18. De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.

    Science.gov (United States)

    Nowrousian, Minou; Stajich, Jason E; Chu, Meiling; Engh, Ines; Espagne, Eric; Halliday, Karen; Kamerewerd, Jens; Kempken, Frank; Knab, Birgit; Kuo, Hsiao-Che; Osiewacz, Heinz D; Pöggeler, Stefanie; Read, Nick D; Seiler, Stephan; Smith, Kristina M; Zickler, Denise; Kück, Ulrich; Freitag, Michael

    2010-04-08

    Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30-90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in approximately 4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data can be used for

  19. De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.

    Directory of Open Access Journals (Sweden)

    Minou Nowrousian

    2010-04-01

    Full Text Available Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30-90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in approximately 4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data

  20. The lemur revolution starts now: the genomic coming of age for a non-model organism.

    Science.gov (United States)

    Yoder, Anne D

    2013-02-01

    Morris Goodman was a revolutionary. Together with a mere handful of like-minded scientists, Morris established himself as a leader in the molecular phylogenetic revolution of the 1960s. The effects of this revolution are most evident in this journal, which he founded in 1992. Happily for lemur biologists, one of Morris Goodman's primary interests was in reconstructing the phylogeny of the primates, including the tooth-combed Lorisifomes of Africa and Asia, and the Lemuriformes of Madagascar (collectively referred to as the suborder Strepsirrhini). This paper traces the development of molecular phylogenetic and evolutionary genetic trends and methods over the 50-year expanse of Morris Goodman's career, particularly as they apply to our understanding of lemuriform phylogeny, biogeography, and biology. Notably, this perspective reveals that the lemuriform genome is sufficiently rich in phylogenetic signal such that the very earliest molecular phylogenetic studies - many of which were conducted by Goodman himself - have been validated by contemporary studies that have exploited advanced computational methods applied to phylogenomic scale data; studies that were beyond imagining in the earliest days of phylogeny reconstruction. Nonetheless, the frontier still beckons. New technologies for gathering and analyzing genomic data will allow investigators to build upon what can now be considered a nearly-known phylogeny of the Lemuriformes in order to ask innovative questions about the evolutionary mechanisms that generate and maintain the extraordinary breadth and depth of biological diversity within this remarkable clade of primates. Copyright © 2012 Elsevier Inc. All rights reserved.

  1. Avian papillomaviruses: the parrot Psittacus erithacus papillomavirus (PePV genome has a unique organization of the early protein region and is phylogenetically related to the chaffinch papillomavirus

    Directory of Open Access Journals (Sweden)

    Jenson A Bennett

    2002-07-01

    Full Text Available Abstract Background An avian papillomavirus genome has been cloned from a cutaneous exophytic papilloma from an African grey parrot (Psittacus erithacus. The nucleotide sequence, genome organization, and phylogenetic position of the Psittacus erithacus papillomavirus (PePV were determined. This PePV sequence represents the first complete avian papillomavirus genome defined. Results The PePV genome (7304 basepairs differs from other papillomaviruses, in that it has a unique organization of the early protein region lacking classical E6 and E7 open reading frames. Phylogenetic comparison of the PePV sequence with partial E1 and L1 sequences of the chaffinch (Fringilla coelebs papillomavirus (FPV reveals that these two avian papillomaviruses form a monophyletic cluster with a common branch that originates near the unresolved center of the papillomavirus evolutionary tree. Conclusions The PePV genome has a unique layout of the early protein region which represents a novel prototypic genomic organization for avian papillomaviruses. The close relationship between PePV and FPV, and between their Psittaciformes and Passeriformes hosts, supports the hypothesis that papillomaviruses have co-evolved and speciated together with their host species throughout evolution.

  2. Driving forces of organic carbon spatial distribution in the tropical seascape

    Science.gov (United States)

    Gillis, L. G.; Belshe, F. E.; Ziegler, A. D.; Bouma, T. J.

    2017-02-01

    An important ecosystem service of tropical coastal vegetation including seagrass beds and mangrove forests is their ability to accumulate carbon. Here we attempt to establish the driving forces for the accumulation of surface organic carbon in southern Thailand coastal systems. Across 12 sites we found that in line with expectations, seagrass beds (0.6 ± 0.09%) and mangrove forests (0.9 ± 0.3%) had higher organic carbon in the surface (top 5 cm) sediment than un-vegetated mudflats (0.4 ± 0.04%). Unexpectedly, however, mangrove forests in this region retained organic carbon, rather than outwell it, under normal tidal conditions. No relationship was found between organic carbon and substrate grain size. The most interesting finding of our study was that climax and pioneer seagrass species retained more carbon than mixed-species meadows, suggesting that plant morphology and meadow characteristics can be important factors in organic carbon accumulation. Insights such as these are important in developing carbon management strategies involving coastal ecosystems such as offsetting of carbon emissions. The ability of tropical coastal vegetation to sequester carbon is an important aspect for valuing the ecosystems. Our results provide some initial insight into the factors affecting carbon sequestration in these ecosystems, but also highlight the need for further research on a global scale.

  3. Quantifying Uncertainty in the Trophic Magnification Factor Related to Spatial Movements of Organisms in a Food Web

    DEFF Research Database (Denmark)

    McLeod, Anne; Arnot, Jon; Borgå, Katrine

    2015-01-01

    included in the model. The model predictions of magnitude of TMFs conformed to empirical studies. There were differences in the relationship between the TMF and the octanol–water partitioning coefficient (KOW) depending on the modeling approach used; a parabolic relationship was predicted under...... deterministic scenarios, whereas a linear TMF–KOW relationship was predicted when the model was run stochastically. Incorporating spatial movements by fish had a major influence on the magnitude and variation of TMFs. Under conditions where organisms are collected exclusively from clean locations in highly...... heterogeneous systems, the results showed bias toward higher TMF estimates, for example the TMF for PCB 153 increased from 2.7 to 5.6 when fish movement was included. Small underestimations of TMFs were found where organisms were exclusively sampled in contaminated regions, although the model was found...

  4. Asymmetric segregation of damaged cellular components in spatially structured multicellular organisms.

    Directory of Open Access Journals (Sweden)

    Charlotte Strandkvist

    Full Text Available The asymmetric distribution of damaged cellular components has been observed in species ranging from fission yeast to humans. To study the potential advantages of damage segregation, we have developed a mathematical model describing ageing mammalian tissue, that is, a multicellular system of somatic cells that do not rejuvenate at cell division. To illustrate the applicability of the model, we specifically consider damage incurred by mutations to mitochondrial DNA, which are thought to be implicated in the mammalian ageing process. We show analytically that the asymmetric distribution of damaged cellular components reduces the overall damage level and increases the longevity of the cell population. Motivated by the experimental reports of damage segregation in human embryonic stem cells, dividing symmetrically with respect to cell-fate, we extend the model to consider spatially structured systems of cells. Imposing spatial structure reduces, but does not eliminate, the advantage of asymmetric division over symmetric division. The results suggest that damage partitioning could be a common strategy for reducing the accumulation of damage in a wider range of cell types than previously thought.

  5. Demography-based adaptive network model reproduces the spatial organization of human linguistic groups

    Science.gov (United States)

    Capitán, José A.; Manrubia, Susanna

    2015-12-01

    The distribution of human linguistic groups presents a number of interesting and nontrivial patterns. The distributions of the number of speakers per language and the area each group covers follow log-normal distributions, while population and area fulfill an allometric relationship. The topology of networks of spatial contacts between different linguistic groups has been recently characterized, showing atypical properties of the degree distribution and clustering, among others. Human demography, spatial conflicts, and the construction of networks of contacts between linguistic groups are mutually dependent processes. Here we introduce an adaptive network model that takes all of them into account and successfully reproduces, using only four model parameters, not only those features of linguistic groups already described in the literature, but also correlations between demographic and topological properties uncovered in this work. Besides their relevance when modeling and understanding processes related to human biogeography, our adaptive network model admits a number of generalizations that broaden its scope and make it suitable to represent interactions between agents based on population dynamics and competition for space.

  6. Climate and landscape influence on indicators of lake carbon cycling through spatial patterns in dissolved organic carbon.

    Science.gov (United States)

    Lapierre, Jean-Francois; Seekell, David A; Del Giorgio, Paul A

    2015-12-01

    Freshwater ecosystems are strongly influenced by both climate and the surrounding landscape, yet the specific pathways connecting climatic and landscape drivers to the functioning of lake ecosystems are poorly understood. Here, we hypothesize that the links that exist between spatial patterns in climate and landscape properties and the spatial variation in lake carbon (C) cycling at regional scales are at least partly mediated by the movement of terrestrial dissolved organic carbon (DOC) in the aquatic component of the landscape. We assembled a set of indicators of lake C cycling (bacterial respiration and production, chlorophyll a, production to respiration ratio, and partial pressure of CO2 ), DOC concentration and composition, and landscape and climate characteristics for 239 temperate and boreal lakes spanning large environmental and geographic gradients across seven regions. There were various degrees of spatial structure in climate and landscape features that were coherent with the regionally structured patterns observed in lake DOC and indicators of C cycling. These different regions aligned well, albeit nonlinearly along a mean annual temperature gradient; whereas there was a considerable statistical effect of climate and landscape properties on lake C cycling, the direct effect was small and the overall effect was almost entirely overlapping with that of DOC concentration and composition. Our results suggest that key climatic and landscape signals are conveyed to lakes in part via the movement of terrestrial DOC to lakes and that DOC acts both as a driver of lake C cycling and as a proxy for other external signals. © 2015 John Wiley & Sons Ltd.

  7. Spatial organization of the settlement network of the municipality of Čačak and tendencies of its development

    Directory of Open Access Journals (Sweden)

    Nikolić Teodora

    2013-01-01

    Full Text Available The balanced and sustainable development of the functional area of Čačak is a precondition for greater integration of geospace. Based on the fact that settlements are the most striking elements of the cultural landscape and they are the holders of the functional organization and spatial transformation of geospace, there will be a special emphasis placed on the networking of these settlements and the analysis of its determinants. Both demographic and socioeconomic indicators were analyzed in order to determine the dominant spatial and functional processes occurring in the area that relate to the development of the municipality. Emphasis is placed on the changes in the type of population movement, functional transformation of the settlements, and changes in the level of social geographic transformation of settlements. Analysis of the demographic and socio-economic indicators showed that the settlement network of Čačak is, to a large extent, incoherent. Socio-geographic and functional transformation of settlements is articulated and directed entirely from the municipal center, and consequently the most affected settlements of periurban zone of Čačak and settlements along major roads. Adjusting to the modern development processes requires new spatial-functional relations at the municipality level in order to strengthen territorial cohesion and equal conditions of life.

  8. Spatial and Temporal Trends in PM2.5 Organic and Elemental Carbon across the United States

    Directory of Open Access Journals (Sweden)

    J. L. Hand

    2013-01-01

    Full Text Available The rural/remote IMPROVE network (Interagency Monitoring of Protected Visual Environments and the Environmental Protection Agency's urban Chemical Speciation Network have measured PM2.5 organic (OC and elemental carbon (EC since 1989 and 2000, respectively. We aggregated OC and EC data from 2007 to 2010 at over 300 sites from both networks in order to characterize the spatial and seasonal patterns in rural and urban carbonaceous aerosols. The spatial extent of OC and EC was more regional in the eastern United States relative to more localized concentrations in the West. The highest urban impacts of OC and EC relative to background concentrations occurred in the West during fall and winter. Urban and rural carbonaceous aerosols experienced a large (although opposite range in seasonality in the West compared to a much lower seasonal variability in the East. Long-term (1990–2010 trend analyses indicated a widespread decrease in rural TC (TC = OC + EC across the country, with positive, though insignificant, trends in the summer and fall in the West. Short-term trends indicated that urban and rural TC concentrations have both decreased since 2000, with the strongest and more spatially homogeneous urban and rural trends in the West relative to the East.

  9. The Contribution of Tissue Level Organization to Genomic Stability Following Low Dose/Low Dose Rate Gamma and Proton Irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Cheryl G. Burrell, Ph.D.

    2012-05-14

    The formation of functional tissue units is necessary in maintaining homeostasis within living systems, with individual cells contributing to these functional units through their three-dimensional organization with integrin and adhesion proteins to form a complex extra-cellular matrix (ECM). This is of particular importance in those tissues susceptible to radiation-induced tumor formation, such as epithelial glands. The assembly of epithelial cells of the thyroid is critical to their normal receipt of, and response to, incoming signals. Traditional tissue culture and live animals present significant challenges to radiation exposure and continuous sampling, however, the production of bioreactor-engineered tissues aims to bridge this gap by improve capabilities in continuous sampling from the same functional tissue, thereby increasing the ability to extrapolate changes induced by radiation to animals and humans in vivo. Our study proposes that the level of tissue organization will affect the induction and persistence of low dose radiation-induced genomic instability. Rat thyroid cells, grown in vitro as 3D tissue analogs in bioreactors and as 2D flask grown cultures were exposed to acute low dose (1, 5, 10 and 200 cGy) gamma rays. To assess immediate (6 hours) and delayed (up to 30 days) responses post-irradiation, various biological endpoints were studied including cytogenetic analyses, apoptosis analysis and cell viability/cytotoxicity analyses. Data assessing caspase 3/7 activity levels show that, this activity varies with time post radiation and that, overall, 3D cultures display more genomic instability (as shown by the lower levels of apoptosis over time) when compared to the 2D cultures. Variation in cell viability levels were only observed at the intermediate and late time points post radiation. Extensive analysis of chromosomal aberrations will give further insight on the whether the level of tissue organization influences genomic instability patterns after

  10. Frugivorous birds influence the spatial organization of tropical forests through the generation of seedling recruitment foci under zoochoric trees

    Science.gov (United States)

    Trolliet, Franck; Forget, Pierre-Michel; Doucet, Jean-Louis; Gillet, Jean-François; Hambuckers, Alain

    2017-11-01

    Animal-mediated seed dispersal is recognized to influence the spatial organization of plant communities but little is known about how frugivores cause such patterns. Here, we explored the role of hornbills and primates in generating recruitment foci under two zoochoric trees, namely Staudtia kamerunensis (Myristicaceae) and Dialium spp. (Fabaceae - Caesalpiniodea) in a forest-savanna mosaic landscape in D.R. Congo. We also examined the influence of the availability of fruits in the neighborhood and the amount of forest cover in the landscape on such clumping patterns. The density and species richness of hornbill-dispersed and the density of primate-dispersed seedlings were significantly higher under Staudtia kamerunensis trees than at control locations. However, we did not find such patterns under Dialium spp. trees compared to control locations except for the density of hornbill-dispersed seedlings which was lower at control locations. Also, we found that an increasing amount of forest cover in the landscape was associated with an increase in the density of hornbill-dispersed seedlings, although the tendency was weak (R2 = 0.065). We concluded that S. kamerunensis acts as a recruitment foci and plays a structuring role in Afrotropical forests. Hornbills were probably the main frugivore taxon responsible for the clumping under that tree and appear as a key ecological component in fragmented and disturbed landscapes where the diversity of large frugivores such as primates is reduced. Our findings improve our understanding of the causal mechanisms responsible for the spatial organization of tropical forests.

  11. Biomonitoring of airborne inorganic and organic pollutants by means of pine tree barks. I. Temporal and spatial variations

    International Nuclear Information System (INIS)

    Schulz, H.; Huhn, G.; Schuermann, G.; Popp, P.; Staerk, H.J.

    2000-01-01

    Scots pine (Pinus sylvestris L.) bark samples were collected at two field sites (Neuglobsow, Roesa) and in different years between 1987 and 1996 in the east of Germany. The barks were analyzed with respect to the following inorganic and organic substances: Al, As, B, Ca, Cd, Ce, Cr, Cu, Fe, Hg, Mo, NH 4 + , Ni, NO 3 - , PO 4 3- , Pb, Sr, SO 4 2- , Ti, V, W, Zr, Zn, benzo(a)pyrene, fluoranthene, pyrene, a-hexachlorocyclohexane (a-HCH) and dichlorodiphenyltrichloroethane (DDT). In addition to bark samples from the site Roesa, 53 test sites were investigated in the Nature Park Duebener Heide. Here, the analysis of the barks aimed at discovering spatial patterns of the above-mentioned substances. Since 1991, most of the determined substances (e.g. sulfate, nitrate, calcium, lead, benzo(a)pyrene, a-HCH) show decreased concentration values in bark samples from both sites. Temporal variations reflect substantial infra-structural changes in eastern Germany, especially at Roesa and in the industrial region around the cities Leipzig, Halle, and Bitterfeld. Moreover, nitrate concentrations in barks are increasing since 1995. The trend can be explained with increased nitrogen emissions from motor traffic and livestock farms. Spatial patterns of sulphate and ammonia reflect inputs from power plants and agriculture in pine stands of the Nature Park Duebener Heide. The results show that barks of pine trees can be used as biomonitoring tools to indicate and characterize depositions of airborne organic and inorganic pollutants. (author)

  12. SPATIAL AND TEMPORAL DISTRIBUTION OF COLORED DISSOLOVED ORGANIC MATTER (CDOM) IN SOUTHERN NEW ENGALND COASTAL WATERS

    Science.gov (United States)

    The concentration of colored dissolved organic matter (CDOM) is a primary factor affecting the absorption of incident sunlight in coastal and estuarine waters. CDOM is extracted from water-soluble humic substances and transported by runoff into lakes and coastal waters. CDOM is a...

  13. Temporal and spatial variations in particulate matter, particulate organic carbon and attenuation coefficient in Cochin Backwaters

    Digital Repository Service at National Institute of Oceanography (India)

    Devi, K.S.

    Nine stations over a stretch of 21 km of Periyar river estuary were sampled during January to December 1981. Particulate matter varied from 3-253 mg.1 super(1) at the surface and 24.8-257mg.1 super(1) at the bottom. Particulate organic carbon ranged...

  14. Towards a spatial theory of organizations : Creating new organizational forms to improve business performance

    NARCIS (Netherlands)

    Tissen, R.J.; Lekanne Deprez, F.R.E.

    2008-01-01

    Research in the field of management and organizational theory generally indicates the absense of space in organizations. Space has largely been a neglected phenomenon, left implicite to practice as something ‘limiting’ without actually ‘existing’. The aim of this research paper is to explore and

  15. Linkage of genomic biomarkers to whole organism endpoints in a Toxicity Identification Evaluation (TIE).

    Science.gov (United States)

    Aquatic organisms are exposed to many toxic chemicals and interpreting the cause and effect relationships between occurrence and impairment is difficult. Toxicity Identification Evaluation (TIE) provides a systematic approach for identifying responsible toxicants. TIE relies on ...

  16. Throughput increase of the covert communication channel organized by the stable steganography algorithm using spatial domain of the image

    Directory of Open Access Journals (Sweden)

    O.V. Kostyrka

    2016-09-01

    Full Text Available At the organization of a covert communication channel a number of requirements are imposed on used steganography algorithms among which one of the main are: resistance to attacks against the built-in message, reliability of perception of formed steganography message, significant throughput of a steganography communication channel. Aim: The aim of this research is to modify the steganography method, developed by the author earlier, which will allow to increase the throughput of the corresponding covert communication channel when saving resistance to attacks against the built-in message and perception reliability of the created steganography message, inherent to developed method. Materials and Methods: Modifications of a steganography method that is steady against attacks against the built-in message which is carrying out the inclusion and decoding of the sent (additional information in spatial domain of the image allowing to increase the throughput of the organized communication channel are offered. Use of spatial domain of the image allows to avoid accumulation of an additional computational error during the inclusion/decoding of additional information due to “transitions” from spatial domain of the image to the area of conversion and back that positively affects the efficiency of decoding. Such methods are considered as attacks against the built-in message: imposing of different noise on a steganography message, filtering, lossy compression of a ste-ganography message where the JPEG and JPEG2000 formats with different quality coefficients for saving of a steganography message are used. Results: It is shown that algorithmic implementations of the offered methods modifications remain steady against the perturbing influences, including considerable, provide reliability of perception of the created steganography message, increase the throughput of the created steganography communication channel in comparison with the algorithm implementing

  17. Performance assessment of the single photon emission microscope: high spatial resolution SPECT imaging of small animal organs

    Directory of Open Access Journals (Sweden)

    J. Mejia

    2013-11-01

    Full Text Available The single photon emission microscope (SPEM is an instrument developed to obtain high spatial resolution single photon emission computed tomography (SPECT images of small structures inside the mouse brain. SPEM consists of two independent imaging devices, which combine a multipinhole collimator, a high-resolution, thallium-doped cesium iodide [CsI(Tl] columnar scintillator, a demagnifying/intensifier tube, and an electron-multiplying charge-coupling device (CCD. Collimators have 300- and 450-µm diameter pinholes on tungsten slabs, in hexagonal arrays of 19 and 7 holes. Projection data are acquired in a photon-counting strategy, where CCD frames are stored at 50 frames per second, with a radius of rotation of 35 mm and magnification factor of one. The image reconstruction software tool is based on the maximum likelihood algorithm. Our aim was to evaluate the spatial resolution and sensitivity attainable with the seven-pinhole imaging device, together with the linearity for quantification on the tomographic images, and to test the instrument in obtaining tomographic images of different mouse organs. A spatial resolution better than 500 µm and a sensitivity of 21.6 counts·s-1·MBq-1 were reached, as well as a correlation coefficient between activity and intensity better than 0.99, when imaging 99mTc sources. Images of the thyroid, heart, lungs, and bones of mice were registered using 99mTc-labeled radiopharmaceuticals in times appropriate for routine preclinical experimentation of <1 h per projection data set. Detailed experimental protocols and images of the aforementioned organs are shown. We plan to extend the instrument's field of view to fix larger animals and to combine data from both detectors to reduce the acquisition time or applied activity.

  18. Performance assessment of the single photon emission microscope: high spatial resolution SPECT imaging of small animal organs

    International Nuclear Information System (INIS)

    Mejia, J.; Reis, M.A.; Miranda, A.C.C.; Batista, I.R.; Barboza, M.R.F.; Shih, M.C.; Fu, G.; Chen, C.T.; Meng, L.J.; Bressan, R.A.; Amaro, E. Jr

    2013-01-01

    The single photon emission microscope (SPEM) is an instrument developed to obtain high spatial resolution single photon emission computed tomography (SPECT) images of small structures inside the mouse brain. SPEM consists of two independent imaging devices, which combine a multipinhole collimator, a high-resolution, thallium-doped cesium iodide [CsI(Tl)] columnar scintillator, a demagnifying/intensifier tube, and an electron-multiplying charge-coupling device (CCD). Collimators have 300- and 450-µm diameter pinholes on tungsten slabs, in hexagonal arrays of 19 and 7 holes. Projection data are acquired in a photon-counting strategy, where CCD frames are stored at 50 frames per second, with a radius of rotation of 35 mm and magnification factor of one. The image reconstruction software tool is based on the maximum likelihood algorithm. Our aim was to evaluate the spatial resolution and sensitivity attainable with the seven-pinhole imaging device, together with the linearity for quantification on the tomographic images, and to test the instrument in obtaining tomographic images of different mouse organs. A spatial resolution better than 500 µm and a sensitivity of 21.6 counts·s -1 ·MBq -1 were reached, as well as a correlation coefficient between activity and intensity better than 0.99, when imaging 99m Tc sources. Images of the thyroid, heart, lungs, and bones of mice were registered using 99m Tc-labeled radiopharmaceuticals in times appropriate for routine preclinical experimentation of <1 h per projection data set. Detailed experimental protocols and images of the aforementioned organs are shown. We plan to extend the instrument's field of view to fix larger animals and to combine data from both detectors to reduce the acquisition time or applied activity

  19. Performance assessment of the single photon emission microscope: high spatial resolution SPECT imaging of small animal organs

    Energy Technology Data Exchange (ETDEWEB)

    Mejia, J. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Reis, M.A. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Laboratório Interdisciplinar de Neurociências Clínicas, Departamento de Psiquiatria, Universidade Federal de São Paulo, São Paulo, SP (Brazil); Miranda, A.C.C. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Batista, I.R. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Laboratório Interdisciplinar de Neurociências Clínicas, Departamento de Psiquiatria, Universidade Federal de São Paulo, São Paulo, SP (Brazil); Barboza, M.R.F.; Shih, M.C. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Fu, G. [GE Global Research, Schenectady, NY (United States); Chen, C.T. [Department of Radiology, University of Chicago, Chicago, IL (United States); Meng, L.J. [Department of Nuclear, Plasma and Radiological Engineering, University of Illinois, Urbana-Champaign, IL (United States); Bressan, R.A. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Laboratório Interdisciplinar de Neurociências Clínicas, Departamento de Psiquiatria, Universidade Federal de São Paulo, São Paulo, SP (Brazil); Amaro, E. Jr [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil)

    2013-11-06

    The single photon emission microscope (SPEM) is an instrument developed to obtain high spatial resolution single photon emission computed tomography (SPECT) images of small structures inside the mouse brain. SPEM consists of two independent imaging devices, which combine a multipinhole collimator, a high-resolution, thallium-doped cesium iodide [CsI(Tl)] columnar scintillator, a demagnifying/intensifier tube, and an electron-multiplying charge-coupling device (CCD). Collimators have 300- and 450-µm diameter pinholes on tungsten slabs, in hexagonal arrays of 19 and 7 holes. Projection data are acquired in a photon-counting strategy, where CCD frames are stored at 50 frames per second, with a radius of rotation of 35 mm and magnification factor of one. The image reconstruction software tool is based on the maximum likelihood algorithm. Our aim was to evaluate the spatial resolution and sensitivity attainable with the seven-pinhole imaging device, together with the linearity for quantification on the tomographic images, and to test the instrument in obtaining tomographic images of different mouse organs. A spatial resolution better than 500 µm and a sensitivity of 21.6 counts·s{sup -1}·MBq{sup -1} were reached, as well as a correlation coefficient between activity and intensity better than 0.99, when imaging {sup 99m}Tc sources. Images of the thyroid, heart, lungs, and bones of mice were registered using {sup 99m}Tc-labeled radiopharmaceuticals in times appropriate for routine preclinical experimentation of <1 h per projection data set. Detailed experimental protocols and images of the aforementioned organs are shown. We plan to extend the instrument's field of view to fix larger animals and to combine data from both detectors to reduce the acquisition time or applied activity.

  20. Imaging buried organic islands by spatially resolved ballistic electron emission spectroscopy

    International Nuclear Information System (INIS)

    Goh, Kuan Eng J; Bannani, A; Troadec, C

    2008-01-01

    The well-known Au/n-Si(111) Schottky interface is modified by a discontinuous pentacene film (∼1.5 nm thick) and studied using spatially resolved ballistic electron emission spectroscopy (BEES). The pentacene film introduced subtle changes to the interface which cannot be definitively detected by current-voltage measurements or a standard BEES analysis of the barrier height. In contrast, analyzing the BEES results in a dual-parameter (transmission attenuation and barrier height) space allows the effect of the pentacene film on the Au/n-Si(111) interface to be clearly demonstrated. We found that the pentacene film behaves like a tunneling barrier and increases the distribution of local barrier heights with a tendency toward lower values. Our results highlight the potential of the dual-parameter BEES analysis for understanding local interface modification by molecules.

  1. Spatial Organization of Environmental Knowledge: Conservation Conflicts in the Inhabited Forest of Northern Thailand

    Directory of Open Access Journals (Sweden)

    Robin Roth

    2004-12-01

    Full Text Available Managing forests for their satisfactory provision of multiple goods and services to both the global and local commons requires effective cross-scale cooperation between local management institutions and state management institutions. Integrating the distinct sets of knowledge produced and used at the two scales of management has proven very challenging. This paper shows how a better understanding of the spatial expression of knowledge operating at distinct scales can help lead to a more fruitful integration of local knowledge and practice with state knowledge and practice. Using a case study from northern Thailand, this paper examines the links between the production of knowledge and the production of space within resource management institutions. It then identifies moments of convergence, compatibility, and conflict between local and state management institutions to inform more effective cross-scale linkages in environmental management.

  2. Spatial statistical analysis of organs for intelligent CAD and its application to disease detection

    International Nuclear Information System (INIS)

    Takizawa, Hotaka

    2009-01-01

    The present article reports our research that was performed in a research project supported by a Grantin-Aid for Scientific Research on Priority Area from the Ministry of Education, Culture Sports, Science and Technology, JAPAN, from 2003 to 2006. Our method developed in the research acquired the trend of variation of spatial relations between true diseases, false positives and image features through statistical analysis of a set of medical images and improved the accuracy of disease detection by predicting their occurrence positions in an image based on the trend. This article describes the formulation of the method in general form and shows the results obtained by applying the method to chest X-ray CT images for detection of pulmonary nodules. (author)

  3. Spatial modelling of marine organisms in Forsmark and Oskarshamn. Including calculation of physical predictor variables

    Energy Technology Data Exchange (ETDEWEB)

    Carlen, Ida; Nikolopoulos, Anna; Isaeus, Martin (AquaBiota Water Research, Stockholm (SE))

    2007-06-15

    GIS grids (maps) of marine parameters were created using point data from previous site investigations in the Forsmark and Oskarshamn areas. The proportion of global radiation reaching the sea bottom in Forsmark and Oskarshamn was calculated in ArcView, using Secchi depth measurements and the digital elevation models for the respective area. The number of days per year when the incoming light exceeds 5 MJ/m2 at the bottom was then calculated using the result of the previous calculations together with measured global radiation. Existing modelled grid-point data on bottom and pelagic temperature for Forsmark were interpolated to create surface covering grids. Bottom and pelagic temperature grids for Oskarshamn were calculated using point measurements to achieve yearly averages for a few points and then using regressions with existing grids to create new maps. Phytoplankton primary production in Forsmark was calculated using point measurements of chlorophyll and irradiance, and a regression with a modelled grid of Secchi depth. Distribution of biomass of macrophyte communities in Forsmark and Oskarshamn was calculated using spatial modelling in GRASP, based on field data from previous surveys. Physical parameters such as those described above were used as predictor variables. Distribution of biomass of different functional groups of fish in Forsmark was calculated using spatial modelling based on previous surveys and with predictor variables such as physical parameters and results from macrophyte modelling. All results are presented as maps in the report. The quality of the modelled predictions varies as a consequence of the quality and amount of the input data, the ecology and knowledge of the predicted phenomena, and by the modelling technique used. A substantial part of the variation is not described by the models, which should be expected for biological modelling. Therefore, the resulting grids should be used with caution and with this uncertainty kept in mind. All

  4. Spatial modelling of marine organisms in Forsmark and Oskarshamn. Including calculation of physical predictor variables

    International Nuclear Information System (INIS)

    Carlen, Ida; Nikolopoulos, Anna; Isaeus, Martin

    2007-06-01

    GIS grids (maps) of marine parameters were created using point data from previous site investigations in the Forsmark and Oskarshamn areas. The proportion of global radiation reaching the sea bottom in Forsmark and Oskarshamn was calculated in ArcView, using Secchi depth measurements and the digital elevation models for the respective area. The number of days per year when the incoming light exceeds 5 MJ/m2 at the bottom was then calculated using the result of the previous calculations together with measured global radiation. Existing modelled grid-point data on bottom and pelagic temperature for Forsmark were interpolated to create surface covering grids. Bottom and pelagic temperature grids for Oskarshamn were calculated using point measurements to achieve yearly averages for a few points and then using regressions with existing grids to create new maps. Phytoplankton primary production in Forsmark was calculated using point measurements of chlorophyll and irradiance, and a regression with a modelled grid of Secchi depth. Distribution of biomass of macrophyte communities in Forsmark and Oskarshamn was calculated using spatial modelling in GRASP, based on field data from previous surveys. Physical parameters such as those described above were used as predictor variables. Distribution of biomass of different functional groups of fish in Forsmark was calculated using spatial modelling based on previous surveys and with predictor variables such as physical parameters and results from macrophyte modelling. All results are presented as maps in the report. The quality of the modelled predictions varies as a consequence of the quality and amount of the input data, the ecology and knowledge of the predicted phenomena, and by the modelling technique used. A substantial part of the variation is not described by the models, which should be expected for biological modelling. Therefore, the resulting grids should be used with caution and with this uncertainty kept in mind. All

  5. Persistent organic pollutants in the Tibetan surface soil: Spatial distribution, air–soil exchange and implications for global cycling

    International Nuclear Information System (INIS)

    Wang Xiaoping; Sheng Jiujiang; Gong Ping; Xue Yonggang; Yao Tandong; Jones, Kevin C.

    2012-01-01

    There are limited data on persistent organic pollutants (POPs) in the soils of the Tibetan Plateau. This paper presents data from a survey of organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) in 40 background surface (0–5 cm) soils of the Tibetan Plateau. Soil concentrations (pg/g, dw) ranged as follows: DDTs, 13-7700; HCHs, 64-847; HCB, 24-564; sum of 15 PCBs, 75-1021; and sum of 9 PBDEs, below detection limit −27. Soil DDT, HCB, PCB and PBDE concentrations were strongly influenced by soil organic carbon content. HCH concentrations were clearly associated with the proximity to source regions in south Asia. The air–soil equilibrium status of POPs suggested the Tibetan soils may be partial “secondary sources” of HCB, low molecular weight PCBs and HCHs and will likely continue to be “sinks” for the less volatile DDE and DDT. - Highlights: ► Soil organic carbon content influence the spatial distribution of persistent organic pollutants. ► The Tibetan soil acts as “secondary sources” for HCB, low molecular weight PCBs and HCHs. ► The Tibetan soil will continue to be “sinks” for DDE and DDT. - Tibetan soils may be potential “secondary sources” of the HCB, low molecular weight PCBs and HCHs that are observed in air.

  6. From the chromatin interaction network to the organization of the human genome into replication N/U-domains

    International Nuclear Information System (INIS)

    Boulos, Rasha E; Julienne, Hanna; Baker, Antoine; Jensen, Pablo; Arneodo, Alain; Audit, Benjamin; Chen, Chun-Long; D'Aubenton-Carafa, Yves; Thermes, Claude; Petryk, Nataliya; Kahli, Malik; Hyrien, Olivier; Goldar, Arach

    2014-01-01

    The three-dimensional (3D) architecture of the mammalian nucleus is now being unraveled thanks to the recent development of chromatin conformation capture (3C) technologies. Here we report the results of a combined multiscale analysis of genome-wide mean replication timing and chromatin conformation data that reveal some intimate relationships between chromatin folding and human DNA replication. We previously described megabase replication N/U-domains as mammalian multiorigin replication units, and showed that their borders are ‘master’ replication initiation zones that likely initiate cascades of origin firing responsible for the stereotypic replication of these domains. Here, we demonstrate that replication N/U-domains correspond to the structural domains of self-interacting chromatin, and that their borders act as insulating regions both in high-throughput 3C (Hi-C) data and high-resolution 3C (4C) experiments. Further analyses of Hi-C data using a graph-theoretical approach reveal that N/U-domain borders are long-distance, interconnected hubs of the chromatin interaction network. Overall, these results and the observation that a well-defined ordering of chromatin states exists from N/U-domain borders to centers suggest that ‘master’ replication initiation zones are at the heart of a high-order, epigenetically controlled 3D organization of the human genome. (paper)

  7. Initial genomics of the human nucleolus.

    Directory of Open Access Journals (Sweden)

    Attila Németh

    2010-03-01

    Full Text Available We report for the first time the genomics of a nuclear compartment of the eukaryotic cell. 454 sequencing and microarray analysis revealed the pattern of nucleolus-associated chromatin domains (NADs in the linear human genome and identified different gene families and certain satellite repeats as the major building blocks of NADs, which constitute about 4% of the genome. Bioinformatic evaluation showed that NAD-localized genes take part in specific biological processes, like the response to other organisms, odor perception, and tissue development. 3D FISH and immunofluorescence experiments illustrated the spatial distribution of NAD-specific chromatin within interphase nuclei and its alteration upon transcriptional changes. Altogether, our findings describe the nature of DNA sequences associated with the human nucleolus and provide insights into the function of the nucleolus in genome organization and establishment of nuclear architecture.

  8. Initial Genomics of the Human Nucleolus

    Science.gov (United States)

    Németh, Attila; Conesa, Ana; Santoyo-Lopez, Javier; Medina, Ignacio; Montaner, David; Péterfia, Bálint; Solovei, Irina; Cremer, Thomas; Dopazo, Joaquin; Längst, Gernot

    2010-01-01

    We report for the first time the genomics of a nuclear compartment of the eukaryotic cell. 454 sequencing and microarray analysis revealed the pattern of nucleolus-associated chromatin domains (NADs) in the linear human genome and identified different gene families and certain satellite repeats as the major building blocks of NADs, which constitute about 4% of the genome. Bioinformatic evaluation showed that NAD–localized genes take part in specific biological processes, like the response to other organisms, odor perception, and tissue development. 3D FISH and immunofluorescence experiments illustrated the spatial distribution of NAD–specific chromatin within interphase nuclei and its alteration upon transcriptional changes. Altogether, our findings describe the nature of DNA sequences associated with the human nucleolus and provide insights into the function of the nucleolus in genome organization and establishment of nuclear architecture. PMID:20361057

  9. Spatial working memory in immersive virtual reality foraging: path organization, traveling distance and search efficiency in humans (Homo sapiens).

    Science.gov (United States)

    De Lillo, Carlo; Kirby, Melissa; James, Frances C

    2014-05-01

    Search and serial recall tasks were used in the present study to characterize the factors affecting the ability of humans to keep track of a set of spatial locations while traveling in an immersive virtual reality foraging environment. The first experiment required the exhaustive exploration of a set of locations following a procedure previously used with other primate and non-primate species to assess their sensitivity to the geometric arrangement of foraging sites. The second experiment assessed the dependency of search performance on search organization by requiring the participants to recall specific trajectories throughout the foraging space. In the third experiment, the distance between the foraging sites was manipulated in order to contrast the effects of organization and traveling distance on recall accuracy. The results show that humans benefit from the use of organized search patterns when attempting to monitor their travel though either a clustered "patchy" space or a matrix of locations. Their ability to recall a series of locations is dependent on whether the order in which they are explored conformed or did not conform to specific organization principles. Moreover, the relationship between search efficiency and search organization is not confounded by effects of traveling distance. These results indicate that in humans, organizational factors may play a large role in their ability to forage efficiently. The extent to which such dependency may pertain to other primates and could be accounted for by visual organization processes is discussed on the basis of previous studies focused on perceptual grouping, search, and serial recall in non-human species. © 2013 Wiley Periodicals, Inc.

  10. Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products.

    Science.gov (United States)

    Holst-Jensen, Arne; Spilsberg, Bjørn; Arulandhu, Alfred J; Kok, Esther; Shi, Jianxin; Zel, Jana

    2016-07-01

    The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.

  11. Biological Parameters and Molecular Markers of Clone CL Brener - The Reference Organism of the Trypanosoma cruzi Genome Project

    Directory of Open Access Journals (Sweden)

    Bianca Zingales

    1997-11-01

    Full Text Available Clone CL Brener is the reference organism used in the Trypanosoma cruzi Genome Project. Some biological parameters of CL Brener were determined: (a the doubling time of epimastigote forms cultured in liver infusion-tryptose (LIT medium at 28oC is 58±13 hr; (b differentiation of epimastigotes to metacyclic trypomastigotes is obtained by incubation in LIT-20% Grace´s medium; (c trypomastigotes infect mammalian cultured cells and perform the complete intracellular cycle at 33 and 37oC; (d blood forms are highly infective to mice; (e blood forms are susceptible to nifurtimox and benznidazole. The molecular typing of CL Brener has been determined: (a isoenzymatic profiles are characteristic of zymodeme ZB; (b PCR amplification of a 24Sa ribosomal RNA sequence indicates it belongs to T. cruzi lineage 1; (c schizodeme, randomly amplified polymorphic DNA (RAPD and DNA fingerprinting analyses were performed

  12. Quantitative Imaging of Cholinergic Interneurons Reveals a Distinctive Spatial Organization and a Functional Gradient across the Mouse Striatum.

    Directory of Open Access Journals (Sweden)

    Miriam Matamales

    Full Text Available Information processing in the striatum requires the postsynaptic integration of glutamatergic and dopaminergic signals, which are then relayed to the output nuclei of the basal ganglia to influence behavior. Although cellularly homogeneous in appearance, the striatum contains several rare interneuron populations which tightly modulate striatal function. Of these, cholinergic interneurons (CINs have been recently shown to play a critical role in the control of reward-related learning; however how the striatal cholinergic network is functionally organized at the mesoscopic level and the way this organization influences striatal function remains poorly understood. Here, we systematically mapped and digitally reconstructed the entire ensemble of CINs in the mouse striatum and quantitatively assessed differences in densities, spatial arrangement and neuropil content across striatal functional territories. This approach demonstrated that the rostral portion of the striatum contained a higher concentration of CINs than the caudal striatum and that the cholinergic content in the core of the ventral striatum was significantly lower than in the rest of the regions. Additionally, statistical comparison of spatial point patterns in the striatal cholinergic ensemble revealed that only a minor portion of CINs (17% aggregated into cluster and that they were predominantly organized in a random fashion. Furthermore, we used a fluorescence reporter to estimate the activity of over two thousand CINs in naïve mice and found that there was a decreasing gradient of CIN overall function along the dorsomedial-to-ventrolateral axis, which appeared to be independent of their propensity to aggregate within the striatum. Altogether this work suggests that the regulation of striatal function by acetylcholine across the striatum is highly heterogeneous, and that signals originating in external afferent systems may be principally determining the function of CINs in the

  13. Discovery of global genomic re-organization based on comparison of two newly sequenced rice mitochondrial genomes with cytoplasmic male sterility-related genes

    Directory of Open Access Journals (Sweden)

    Yamada Mari

    2010-03-01

    Full Text Available Abstract Background Plant mitochondrial genomes are known for their complexity, and there is abundant evidence demonstrating that this organelle is important for plant sexual reproduction. Cytoplasmic male sterility (CMS is a phenomenon caused by incompatibility between the nucleus and mitochondria that has been discovered in various plant species. As the exact sequence of steps leading to CMS has not yet been revealed, efforts should be made to elucidate the factors underlying the mechanism of this important trait for crop breeding. Results Two CMS mitochondrial genomes, LD-CMS, derived from Oryza sativa L. ssp. indica (434,735 bp, and CW-CMS, derived from Oryza rufipogon Griff. (559,045 bp, were newly sequenced in this study. Compared to the previously sequenced Nipponbare (Oryza sativa L. ssp. japonica mitochondrial genome, the presence of 54 out of 56 protein-encoding genes (including pseudo-genes, 22 tRNA genes (including pseudo-tRNAs, and three rRNA genes was conserved. Two other genes were not present in the CW-CMS mitochondrial genome, and one of them was present as part of the newly identified chimeric ORF, CW-orf307. At least 12 genomic recombination events were predicted between the LD-CMS mitochondrial genome and Nipponbare, and 15 between the CW-CMS genome and Nipponbare, and novel genetic structures were formed by these genomic rearrangements in the two CMS lines. At least one of the genomic rearrangements was completely unique to each CMS line and not present in 69 rice cultivars or 9 accessions of O. rufipogon. Conclusion Our results demonstrate novel mitochondrial genomic rearrangements that are unique in CMS cytoplasm, and one of the genes that is unique in the CW mitochondrial genome, CW-orf307, appeared to be the candidate most likely responsible for the CW-CMS event. Genomic rearrangements were dynamic in the CMS lines in comparison with those of rice cultivars, suggesting that 'death' and possible 'birth' processes of the

  14. Complete nucleotide sequence and genome organization of a Chinese isolate of Tobacco vein distorting virus.

    Science.gov (United States)

    Mo, Xiao-han; Chen, Zheng-bin; Chen, Jian-ping

    2010-12-01

    Tobacco bushy top disease is caused by tobacco bushy top virus (TBTV, a member of the genus Umbravirus) which is dependent on tobacco vein-distorting virus (TVDV) to act as a helper virus encapsidating TBTV and enabling its transmission by aphids. Isometric virions from diseased tobacco plants were purified and disease symptoms were reproduced after experimental aphid transmission. The complete genome of TVDV was determined from cloned RT-PCR products derived from viral RNA. It was 5,920 nucleotides (nts) long and had the six major open reading frames (ORFs) typical of a member of the genus Polerovirus. Sequence comparisons showed that it differed significantly from any of the other species in the genus and this was confirmed by phylogenetic analyses of the RdRp and coat protein. SDS-PAGE analysis of purified virions gave two protein bands of about 26 and 59 kDa both of which reacted strongly in Western blots with antiserum produced to prokaryotically expressed TVDV CP showing that the two forms of the TVDV CP were the only protein components of the capsid.

  15. Unsolvable Problems of Biology: It Is Impossible to Create Two Identical Organisms, to Defeat Cancer, or to Map Organisms onto Their Genomes.

    Science.gov (United States)

    Sverdlov, E D

    2018-04-01

    The review is devoted to unsolvable problems of biology. 1) Problems unsolvable due to stochastic mutations occurring during DNA replication that make it impossible to create two identical organisms or even two identical complex cells (Sverdlov, E. D. (2009) Biochemistry (Moscow), 74, 939-944) and to "defeat" cancer. 2) Problems unsolvable due to multiple interactions in complex systems leading to the appearance of unpredictable emergent properties that prevent establishment of unambiguous relationships between the genetic architecture and phenotypic manifestation of the genome and make impossible to predict with certainty responses of the organism, its parts, or pathological processes to external factors. 3) Problems unsolvable because of the uncertainty principle and observer effect in biology, due to which it is impossible to obtain adequate information about cells in their tissue microenvironment by isolating and analyzing individual cells. In particular, we cannot draw conclusions on the properties of stem cells in their niches based on the properties of stem cell cultures. A strategy is proposed for constructing the pattern most closely approximated to the relationship of genotypes with their phenotypes by designing networks of intermediate phenotypes (endophenotypes).

  16. Spatial And Temporal Trends Of Organic Pollutants In Vegetation From Remote And Rural Areas.

    Science.gov (United States)

    Bartrons, Mireia; Catalan, Jordi; Penuelas, Josep

    2016-05-05

    Persistent organic pollutants (POPs) and polycyclic aromatic hydrocarbons (PAHs) used in agricultural, industrial, and domestic applications are widely distributed and bioaccumulate in food webs, causing adverse effects to the biosphere. A review of published data for 1977-2015 for a wide range of vegetation around the globe indicates an extensive load of pollutants in vegetation. On a global perspective, the accumulation of POPs and PAHs in vegetation depends on the industrialization history across continents and distance to emission sources, beyond organism type and climatic variables. International regulations initially reduced the concentrations of POPs in vegetation in rural areas, but concentrations of HCB, HCHs, and DDTs at remote sites did not decrease or even increased over time, pointing to a remobilization of POPs from source areas to remote sites. The concentrations of compounds currently in use, PBDEs and PAHs, are still increasing in vegetation. Differential congener specific accumulation is mostly determined by continent-in accordance to the different regulations of HCHs, PCBs and PBDEs in different countries-and by plant type (PAHs). These results support a concerning general accumulation of toxic pollutants in most ecosystems of the globe that for some compounds is still far from being mitigated in the near future.

  17. Multidecadal persistence of organic matter in soils: insights from spatially resolved investigations at the submicrometer scale

    Science.gov (United States)

    Lutfalla, Suzanne; Barré, Pierre; Bernard, Sylvain; Le Guillou, Corentin; Alléon, Julien; Chenu, Claire

    2016-04-01

    Better understanding the mechanisms responsible for the pluri-decadal persistence of carbon in soils requires well constraining the dynamics, the distribution and the chemical nature of both the soil organic carbon (SOC) and the associated mineral phases. The question we address in this work is whether different mineral species lead to different organo-mineral interactions and stabilize different quantities of SOM and different types of SOC. Here, benefiting from the unique opportunity offered by an INRA long term bare fallow (LTBF) experiment having started in 1928 in Versailles (France), we report the in-situ characterization of SOC dynamics in four clay fractions of this silty loam soil (total clays [TC, clays [CC, 0.2-2μm], intermediate clays [IC, 0.05-0.2μm] and fine clays [FC, 0-0.05μm]). The IC and FC fractions only contain smectite and illite/smectite mixed-layered clay minerals while the CC fraction also contains illite and kaolinite. In the absence of any carbon input, the plant-free LTBF clay fractions from Versailles progressively lost SOC during the first 50 years of the experiment, until they reached a seemingly stable concentration. Of note, the investigated clay fractions did not lose the same amount of SOC and do not exhibit the same final carbon concentrations. The decrease of the organic C:N ratios with LTBF duration corresponds to a progressive enrichment in N-rich SOC for all fractions which can be attributed to microbial material. Even though the speciation of SOC appears to only slightly evolve with LTBF duration, an enrichment in carboxyl and carbonyl groups is revealed by bulk-scale C-NEXAFS data for SOC from all clay fractions. In addition, STXM-based NEXAFS investigations at the submicrometer scale reveal three types of SOC-clay assemblages in addition to clay-free SOC and organic-free clays. While SOC appears mostly adsorbed onto clay surfaces within the IC and FC fractions, other protection mechanisms occur within the CC fraction

  18. How do natural, uncultivated microbes interact with organic matter? Insights from single cell genomics and metagenomics

    DEFF Research Database (Denmark)

    Lloyd, Karen; Bird, Jordan; Schreiber, Lars

    Abstract Since most of the microbes in marine sediments remain uncultured, little is known about the mechanisms by which these natural communities degrade organic matter (OM). Likewise, little is known about the make-up of labile OM in marine sediments beyond general functional classes such as pr......Abstract Since most of the microbes in marine sediments remain uncultured, little is known about the mechanisms by which these natural communities degrade organic matter (OM). Likewise, little is known about the make-up of labile OM in marine sediments beyond general functional classes...... such as proteins, carbohydrates, and lipids, measured as monomers. However, microbes have complex interactions with specific polymers within these functional classes, which can be indicated by a microbe's enzymatic toolkit. We ...

  19. De novo mutations in the genome organizer CTCF cause intellectual disability

    DEFF Research Database (Denmark)

    Gregor, Anne; Oti, Martin; Kouwenhoven, Evelyn N

    2013-01-01

    An increasing number of genes involved in chromatin structure and epigenetic regulation has been implicated in a variety of developmental disorders, often including intellectual disability. By trio exome sequencing and subsequent mutational screening we now identified two de novo frameshift...... mutations and one de novo missense mutation in CTCF in individuals with intellectual disability, microcephaly, and growth retardation. Furthermore, an individual with a larger deletion including CTCF was identified. CTCF (CCCTC-binding factor) is one of the most important chromatin organizers in vertebrates...... and is involved in various chromatin regulation processes such as higher order of chromatin organization, enhancer function, and maintenance of three-dimensional chromatin structure. Transcriptome analyses in all three individuals with point mutations revealed deregulation of genes involved in signal transduction...

  20. Molecular Analysis and Genomic Organization of Major DNA Satellites in Banana (Musa spp.)

    Czech Academy of Sciences Publication Activity Database

    Čížková, Jana; Hřibová, Eva; Humplíková, Lenka; Christelová, Pavla; Suchánková, Pavla; Doležel, Jaroslav

    2013-01-01

    Roč. 8, č. 1 (2013) E-ISSN 1932-6203 R&D Projects: GA AV ČR KJB500380901; GA MŠk(CZ) LG12021 Grant - others:GA MŠk(CZ) ED0007/01/01 Program:ED Institutional research plan: CEZ:AV0Z50380511 Keywords : IN-SITU HYBRIDIZATION * LARGE-SCALE ORGANIZATION * RIBOSOMAL-RNA GENES Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.534, year: 2013

  1. Multiscale analysis of the spatial variability of heavy metals and organic matter in soils and groundwater across Spain

    Science.gov (United States)

    Luque-Espinar, J. A.; Pardo-Igúzquiza, E.; Grima-Olmedo, J.; Grima-Olmedo, C.

    2018-06-01

    During the last years there has been an increasing interest in assessing health risks caused by exposure to contaminants found in soil, air, and water, like heavy metals or emerging contaminants. This work presents a study on the spatial patterns and interaction effects among relevant heavy metals (Sb, As and Pb) that may occur together in different minerals. Total organic carbon (TOC) have been analyzed too because it is an essential component in the regulatory mechanisms that control the amount of metal in soils. Even more, exposure to these elements is associated with a number of diseases and environmental problems. These metals can have both natural and anthropogenic origins. A key component of any exposure study is a reliable model of the spatial distribution the elements studied. A geostatistical analysis have been performed in order to show that selected metals are auto-correlated and cross-correlated and type and magnitude of such cross-correlation varies depending on the spatial scale under consideration. After identifying general trends, we analyzed the residues left after subtracting the trend from the raw variables. Three scales of variability were identified (compounds or factors) with scales of 5, 35 and 135 km. The first factor (F1) basically identifies anomalies of natural origin but, in some places, of anthropogenics origin as well. The other two are related to geology (F2 and F3) although F3 represents more clearly geochemical background related to large lithological groups. Likewise, mapping of two major structures indicates that significant faults have influence on the distribution of the studied elements. Finally, influence of soil and lithology on groundwater by means of contingency analysis was assessed.

  2. U1 snDNA clusters in grasshoppers: chromosomal dynamics and genomic organization

    Science.gov (United States)

    Anjos, A; Ruiz-Ruano, F J; Camacho, J P M; Loreto, V; Cabrero, J; de Souza, M J; Cabral-de-Mello, D C

    2015-01-01

    The spliceosome, constituted by a protein set associated with small nuclear RNA (snRNA), is responsible for mRNA maturation through intron removal. Among snRNA genes, U1 is generally a conserved repetitive sequence. To unveil the chromosomal/genomic dynamics of this multigene family in grasshoppers, we mapped U1 genes by fluorescence in situ hybridization in 70 species belonging to the families Proscopiidae, Pyrgomorphidae, Ommexechidae, Romaleidae and Acrididae. Evident clusters were observed in all species, indicating that, at least, some U1 repeats are tandemly arrayed. High conservation was observed in the first four families, with most species carrying a single U1 cluster, frequently located in the third or fourth longest autosome. By contrast, extensive variation was observed among Acrididae, from a single chromosome pair carrying U1 to all chromosome pairs carrying it, with occasional occurrence of two or more clusters in the same chromosome. DNA sequence analysis in Eyprepocnemis plorans (species carrying U1 clusters on seven different chromosome pairs) and Locusta migratoria (carrying U1 in a single chromosome pair) supported the coexistence of functional and pseudogenic lineages. One of these pseudogenic lineages was truncated in the same nucleotide position in both species, suggesting that it was present in a common ancestor to both species. At least in E. plorans, this U1 snDNA pseudogenic lineage was associated with 5S rDNA and short interspersed elements (SINE)-like mobile elements. Given that we conclude in grasshoppers that the U1 snDNA had evolved under the birth-and-death model and that its intragenomic spread might be related with mobile elements. PMID:25248465

  3. Cloning, functional characterization and genomic organization of 1,8-cineole synthases from Lavandula.

    Science.gov (United States)

    Demissie, Zerihun A; Cella, Monica A; Sarker, Lukman S; Thompson, Travis J; Rheault, Mark R; Mahmoud, Soheil S

    2012-07-01

    Several members of the genus Lavandula produce valuable essential oils (EOs) that are primarily constituted of the low molecular weight isoprenoids, particularly monoterpenes. We isolated over 8,000 ESTs from the glandular trichomes of L. x intermedia flowers (where bulk of the EO is synthesized) to facilitate the discovery of genes that control the biosynthesis of EO constituents. The expression profile of these ESTs in L. x intermedia and its parents L. angustifolia and L. latifolia was established using microarrays. The resulting data highlighted a differentially expressed, previously uncharacterized cDNA with strong homology to known 1,8-cineole synthase (CINS) genes. The ORF, excluding the transit peptide, of this cDNA was expressed in E. coli, purified by Ni-NTA agarose affinity chromatography and functionally characterized in vitro. The ca. 63 kDa bacterially produced recombinant protein, designated L. x intermedia CINS (LiCINS), converted geranyl diphosphate (the linear monoterpene precursor) primarily to 1,8-cineole with K ( m ) and k ( cat ) values of 5.75 μM and 8.8 × 10(-3) s(-1), respectively. The genomic DNA of CINS in the studied Lavandula species had identical exon-intron architecture and coding sequences, except for a single polymorphic nucleotide in the L. angustifolia ortholog which did not alter protein function. Additional nucleotide variations restricted to L. angustifolia introns were also observed, suggesting that LiCINS was most likely inherited from L. latifolia. The LiCINS mRNA levels paralleled the 1,8-cineole content in mature flowers of the three lavender species, and in developmental stages of L. x intermedia inflorescence indicating that the production of 1,8 cineole in Lavandula is most likely controlled through transcriptional regulation of LiCINS.

  4. Quantification of centimeter-scale spatial variation in PAH, glucose and benzoic acid mineralization and soil organic matter in road-side soil

    Energy Technology Data Exchange (ETDEWEB)

    Hybholt, Trine K.; Aamand, Jens [Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Oster Voldgade 10, DK-1350 Copenhagen K (Denmark); Johnsen, Anders R., E-mail: arj@geus.dk [Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Oster Voldgade 10, DK-1350 Copenhagen K (Denmark)

    2011-05-15

    The aim of the study was to determine centimeter-scale spatial variation in mineralization potential in diffusely polluted soil. To this end we employed a 96-well microplate method to measure the mineralization of {sup 14}C-labeled organic compounds in deep-well microplates and thereby compile mineralization curves for 348 soil samples of 0.2-cm{sup 3}. Centimeter-scale spatial variation in organic matter and the mineralization of glucose, benzoic acid, and PAHs (phenanthrene and pyrene) was determined for urban road-side soil sampled as arrays (7 x 11 cm) of 96 subsamples. The spatial variation in mineralization was visualized by means of 2-D contour maps and quantified by means of semivariograms. The geostatistical analysis showed that the easily degradable compounds (glucose and benzoic acid) exhibited little spatial variation in mineralization potential, whereas the mineralization was highly heterogeneous for the PAH compounds that require specialized degraders. The spatial heterogeneity should be taken into account when estimating natural attenuation rates. - Highlights: > Geostatistics were applied at the centimeter scale. > Glucose and benzoic acid mineralization showed little spatial variation. > PAH mineralization was highly variable at the sub-centimeter scale. > High spatial heterogeneity may be caused by low functional redundancy. - This study supports the hypothesis that specialized xenobiotic degraders may show high spatial heterogeneity in soil due to low functional redundancy.

  5. Spatial, Hysteretic, and Adaptive Host-Guest Chemistry in a Metal-Organic Framework with Open Watson-Crick Sites.

    Science.gov (United States)

    Cai, Hong; Li, Mian; Lin, Xiao-Rong; Chen, Wei; Chen, Guang-Hui; Huang, Xiao-Chun; Li, Dan

    2015-09-01

    Biological and artificial molecules and assemblies capable of supramolecular recognition, especially those with nucleobase pairing, usually rely on autonomous or collective binding to function. Advanced site-specific recognition takes advantage of cooperative spatial effects, as in local folding in protein-DNA binding. Herein, we report a new nucleobase-tagged metal-organic framework (MOF), namely ZnBTCA (BTC=benzene-1,3,5-tricarboxyl, A=adenine), in which the exposed Watson-Crick faces of adenine residues are immobilized periodically on the interior crystalline surface. Systematic control experiments demonstrated the cooperation of the open Watson-Crick sites and spatial effects within the nanopores, and thermodynamic and kinetic studies revealed a hysteretic host-guest interaction attributed to mild chemisorption. We further exploited this behavior for adenine-thymine binding within the constrained pores, and a globally adaptive response of the MOF host was observed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. The nanoscale spatial organization of B-cell receptors on immunoglobulin M- and G-expressing human B-cells.

    Science.gov (United States)

    Lee, Jinmin; Sengupta, Prabuddha; Brzostowski, Joseph; Lippincott-Schwartz, Jennifer; Pierce, Susan K

    2017-02-15

    B-cell activation is initiated by the binding of antigen to the B-cell receptor (BCR). Here we used dSTORM superresolution imaging to characterize the nanoscale spatial organization of immunoglobulin M (IgM) and IgG BCRs on the surfaces of resting and antigen--activated human peripheral blood B-cells. We provide insights into both the fundamental process of antigen-driven BCR clustering and differences in the spatial organization of IgM and IgG BCRs that may contribute to the characteristic differences in the responses of naive and memory B-cells to antigen. We provide evidence that although both IgM and IgG BCRs reside in highly heterogeneous protein islands that vary in size and number of BCR single-molecule localizations, both resting and activated B-cells intrinsically maintain a high -frequency of single isolated BCR localizations, which likely represent BCR monomers. IgG BCRs are more clustered than IgM BCRs on resting cells and form larger protein islands after antigen activation. Small, dense BCR clusters likely formed via protein-protein interactions are present on the surface of resting cells, and antigen activation induces these to come together to form less dense, larger islands, a process likely governed, at least in part, by protein-lipid interactions. © 2017 Lee, Sengupta, et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  7. Identification, characterization and metagenome analysis of oocyte-specific genes organized in clusters in the mouse genome

    Directory of Open Access Journals (Sweden)

    Vaiman Daniel

    2005-05-01

    Full Text Available Abstract Background Genes specifically expressed in the oocyte play key roles in oogenesis, ovarian folliculogenesis, fertilization and/or early embryonic development. In an attempt to identify novel oocyte-specific genes in the mouse, we have used an in silico subtraction methodology, and we have focused our attention on genes that are organized in genomic clusters. Results In the present work, five clusters have been studied: a cluster of thirteen genes characterized by an F-box domain localized on chromosome 9, a cluster of six genes related to T-cell leukaemia/lymphoma protein 1 (Tcl1 on chromosome 12, a cluster composed of a SPErm-associated glutamate (E-Rich (Speer protein expressed in the oocyte in the vicinity of four unknown genes specifically expressed in the testis on chromosome 14, a cluster composed of the oocyte secreted protein-1 (Oosp-1 gene and two Oosp-related genes on chromosome 19, all three being characterized by a partial N-terminal zona pellucida-like domain, and another small cluster of two genes on chromosome 19 as well, composed of a TWIK-Related spinal cord K+ channel encoding-gene, and an unknown gene predicted in silico to be testis-specific. The specificity of expression was confirmed by RT-PCR and in situ hybridization for eight and five of them, respectively. Finally, we showed by comparing all of the isolated and clustered oocyte-specific genes identified so far in the mouse genome, that the oocyte-specific clusters are significantly closer to telomeres than isolated oocyte-specific genes are. Conclusion We have studied five clusters of genes specifically expressed in female, some of them being also expressed in male germ-cells. Moreover, contrarily to non-clustered oocyte-specific genes, those that are organized in clusters tend to map near chromosome ends, suggesting that this specific near-telomere position of oocyte-clusters in rodents could constitute an evolutionary advantage. Understanding the biological

  8. Seasonal and spatial variability of the organic matter-to-organic carbon mass ratios in Chinese urban organic aerosols and a first report of high correlations between aerosol oxalic acid and zinc

    Science.gov (United States)

    Xing, L.; Fu, T.-M.; Cao, J. J.; Lee, S. C.; Wang, G. H.; Ho, K. F.; Cheng, M.-C.; You, C.-F.; Wang, T. J.

    2013-01-01

    We calculated the organic matter to organic carbon mass ratios (OM/OC mass ratios) in PM2.5 collected from 14 Chinese cities during summer and winter of 2003 and analyzed the causes for their seasonal and spatial variability. The OM/OC mass ratios were calculated two ways. Using a mass balance method, the calculated OM/OC mass ratios averaged 1.92 ± 0.39 yr-round, with no significant seasonal or spatial variation. The second calculation was based on chemical species analyses of the organic compounds extracted from the PM2.5 samples using dichloromethane/methanol and water. The calculated OM/OC mass ratio in summer was relatively high (1.75 ± 0.13) and spatially-invariant, due to vigorous photochemistry and secondary OA production throughout the country. The calculated OM/OC mass ratio in winter (1.59 ± 0.18) was significantly lower than that in summer, with lower values in northern cities (1.51 ± 0.07) than in southern cities (1.65 ± 0.15). This likely reflects the wider usage of coal for heating purposes in northern China in winter, in contrast to the larger contributions from biofuel and biomass burning in southern China in winter. On average, organic matters constituted 36% and 34% of Chinese urban PM2.5 mass in summer and winter, respectively. We reported, for the first time, high correlations between Zn and oxalic acid in Chinese urban aerosols in summer. This is consistent with the formation of stable Zn oxalate complex in the aerosol phase previously proposed by Furukawa and Takahashi (2011). We found that many other dicarboxylic acids were also highly correlated with Zn in the summer Chinese urban aerosol samples, suggesting that they may also form stable organic complexes with Zn. Such formation may have profound implications for the atmospheric abundance and hygroscopic property of aerosol dicarboxylic acids.

  9. Genome Sequence of Pseudomonas sp. Strain Chol1, a Model Organism for the Degradation of Bile Salts and Other Steroid Compounds

    KAUST Repository

    Holert, Johannes; Alam, Intikhab; Larsen, Michael; Antunes, Andre; Bajic, Vladimir B.; Stingl, Ulrich; Philipp, Bodo

    2013-01-01

    Bacterial degradation of steroid compounds is of high ecological and biotechnological relevance. Pseudomonas sp. strain Chol1 is a model organism for studying the degradation of the steroid compound cholate. Its draft genome sequence is presented and reveals one gene cluster responsible for the metabolism of steroid compounds.

  10. The genomic organization of four b-1,4-endoglucanase genes in plant-parasitic cyst nematodes and its evolutionary implications.

    NARCIS (Netherlands)

    Yan, Y.; Smant, G.; Stokkermans, J.P.W.G.; Qin Ling,; Baum, T.J.; Schots, A.; Davis, E.L.

    1998-01-01

    The genomic organization of genes encoding -1,4-endoglucanases (cellulases) from the plant-parasitic cyst nematodes Heterodera glycines and Globodera rostochiensis (HG-eng1, Hg-eng2, GR-eng1, and GR-eng2) was investigated. HG-eng1 and GR-eng1 both contained eight introns and structural domains of

  11. Genome Sequence of Pseudomonas sp. Strain Chol1, a Model Organism for the Degradation of Bile Salts and Other Steroid Compounds

    KAUST Repository

    Holert, Johannes

    2013-01-15

    Bacterial degradation of steroid compounds is of high ecological and biotechnological relevance. Pseudomonas sp. strain Chol1 is a model organism for studying the degradation of the steroid compound cholate. Its draft genome sequence is presented and reveals one gene cluster responsible for the metabolism of steroid compounds.

  12. Spatial organization of lipids in the human retina and optic nerve by MALDI imaging mass spectrometry.

    Science.gov (United States)

    Zemski Berry, Karin A; Gordon, William C; Murphy, Robert C; Bazan, Nicolas G

    2014-03-01

    MALDI imaging mass spectrometry (IMS) was used to characterize lipid species within sections of human eyes. Common phospholipids that are abundant in most tissues were not highly localized and observed throughout the accessory tissue, optic nerve, and retina. Triacylglycerols were highly localized in accessory tissue, whereas sulfatide and plasmalogen glycerophosphoethanolamine (PE) lipids with a monounsaturated fatty acid were found enriched in the optic nerve. Additionally, several lipids were associated solely with the inner retina, photoreceptors, or retinal pigment epithelium (RPE); a plasmalogen PE lipid containing DHA (22:6), PE(P-18:0/22:6), was present exclusively in the inner retina, and DHA-containing glycerophosphatidylcholine (PC) and PE lipids were found solely in photoreceptors. PC lipids containing very long chain (VLC)-PUFAs were detected in photoreceptors despite their low abundance in the retina. Ceramide lipids and the bis-retinoid, N-retinylidene-N-retinylethanolamine, was tentatively identified and found only in the RPE. This MALDI IMS study readily revealed the location of many lipids that have been associated with degenerative retinal diseases. Complex lipid localization within retinal tissue provides a global view of lipid organization and initial evidence for specific functions in localized regions, offering opportunities to assess their significance in retinal diseases, such as macular degeneration, where lipids have been implicated in the disease process.

  13. Rice sHsp genes: genomic organization and expression profiling under stress and development

    Directory of Open Access Journals (Sweden)

    Grover Anil

    2009-08-01

    Full Text Available Abstract Background Heat shock proteins (Hsps constitute an important component in the heat shock response of all living systems. Among the various plant Hsps (i.e. Hsp100, Hsp90, Hsp70 and Hsp20, Hsp20 or small Hsps (sHsps are expressed in maximal amounts under high temperature stress. The characteristic feature of the sHsps is the presence of α-crystallin domain (ACD at the C-terminus. sHsps cooperate with Hsp100/Hsp70 and co-chaperones in ATP-dependent manner in preventing aggregation of cellular proteins and in their subsequent refolding. Database search was performed to investigate the sHsp gene family across rice genome sequence followed by comprehensive expression analysis of these genes. Results We identified 40 α-crystallin domain containing genes in rice. Phylogenetic analysis showed that 23 out of these 40 genes constitute sHsps. The additional 17 genes containing ACD clustered with Acd proteins of Arabidopsis. Detailed scrutiny of 23 sHsp sequences enabled us to categorize these proteins in a revised scheme of classification constituting of 16 cytoplasmic/nuclear, 2 ER, 3 mitochondrial, 1 plastid and 1 peroxisomal genes. In the new classification proposed herein nucleo-cytoplasmic class of sHsps with 9 subfamilies is more complex in rice than in Arabidopsis. Strikingly, 17 of 23 rice sHsp genes were noted to be intronless. Expression analysis based on microarray and RT-PCR showed that 19 sHsp genes were upregulated by high temperature stress. Besides heat stress, expression of sHsp genes was up or downregulated by other abiotic and biotic stresses. In addition to stress regulation, various sHsp genes were differentially upregulated at different developmental stages of the rice plant. Majority of sHsp genes were expressed in seed. Conclusion We identified twenty three sHsp genes and seventeen Acd genes in rice. Three nucleocytoplasmic sHsp genes were found only in monocots. Analysis of expression profiling of sHsp genes revealed

  14. Spatial distribution of bottlenose dolphins (Tursiops truncatus) inferred from stable isotopes and priority organic pollutants

    International Nuclear Information System (INIS)

    Wilson, Rachel Marie; Kucklick, John R.; Balmer, Brian C.; Wells, Randall S.; Chanton, Jeffrey P.; Nowacek, Douglas P.

    2012-01-01

    Differences in priority organic pollutants (POPs), analyzed by gas chromatography-mass spectrometry, and stable isotope ratios (δ 13 C, δ 34 S, and δ 15 N; analyzed by isotope ratio-mass spectrometry), divide 77 bottlenose dolphins (Tursiops truncatus) from the Florida Gulf Coast into three distinct groups. POP levels reflect human population and historical contamination along the coast. In the least disturbed site, concentrations of ΣPOP in male dolphins were 18,000 ng g −1 ± 6000 (95% confidence interval here and throughout); in the intermediate bay, males had ΣPOP concentrations of 19,000 ng g −1 ± 10,000. St Andrews Bay was home to dolphins with the highest ΣPOP concentrations: 44,000 ng g −1 ± 10,300. δ 34 S and δ 15 N, differed significantly between St. George Sound dolphins and those frequenting each of the other two bays, but not between St. Andrews and St. Joseph Bays. ΣPOP concentrations were statistically higher in dolphins frequenting St. Andrews Bay, but were not significantly different between dolphins occupying St. Joseph Bay and St. George Sound. Thus, using either POP or isotope values alone, we would only be able to identify two dolphin groups, but when POP and isotope data are viewed cumulatively, the results clearly define three distinct communities occupying this region. - Highlights: ► We compare isotopes and POP levels in dolphins occupying three embayments. ► POP levels varied significantly among two embayments separated by < 50 km. ► Differentiation correlated with historical contamination from a SuperFund site. ► Cumulatively, isotopes and POP levels indicate 3 distinct dolphin communities. ► This data provides the first assessment of dolphin POP contamination in the region.

  15. THE SPATIAL DISTRIBUTION OF COMPLEX ORGANIC MOLECULES IN THE L1544 PRE-STELLAR CORE

    Energy Technology Data Exchange (ETDEWEB)

    Jiménez-Serra, Izaskun [Astronomy Unit, School of Physics and Astronomy, Queen Mary University of London, Mile End Road, London E1 4NS (United Kingdom); Vasyunin, Anton I.; Caselli, Paola [Max-Planck-Institut für extraterrestrische Physik (MPE), Gießenbachstr., D-85741 Garching (Germany); Marcelino, Nuria [INAF, Osservatorio di Radioastronomia, Via P. Gobetti 101, I-40129 Bologna (Italy); Billot, Nicolas [Instituto de Radioastronomía Milimétrica, Avenida Divina Pastora 7, E-18012 Granada (Spain); Viti, Serena [Department of Physics and Astronomy, University College London, 132 Hampstead Road, London NW1 2PS (United Kingdom); Testi, Leonardo [European Southern Observatory (ESO), Karl-Schwarzschild-Str. 2, D-85748 Garching (Germany); Vastel, Charlotte [Université de Toulouse, UPS-OMP, IRAP, F-31400 Toulouse (France); Lefloch, Bertrand [Univ. Grenoble Alpes, IPAG, F-38000 Grenoble (France); Bachiller, Rafael, E-mail: i.jimenez-serra@qmul.ac.uk [Observatorio Astronómico Nacional (OAN, IGN), Calle Alfonso XII 3, E-28014 Madrid (Spain)

    2016-10-10

    The detection of complex organic molecules (COMs) toward cold sources such as pre-stellar cores (with T < 10 K) has challenged our understanding of the formation processes of COMs in the interstellar medium. Recent modeling on COM chemistry at low temperatures has provided new insight into these processes predicting that COM formation depends strongly on parameters such as visual extinction and the level of CO freeze out. We report deep observations of COMs toward two positions in the L1544 pre-stellar core: the dense, highly extinguished continuum peak with A{sub V}≥ 30 mag within the inner 2700 au; and a low-density shell with average A{sub V}∼ 7.5–8 mag located at 4000 au from the core’s center and bright in CH{sub 3}OH. Our observations show that CH{sub 3}O, CH{sub 3}OCH{sub 3}, and CH{sub 3}CHO are more abundant (by factors of ∼2–10) toward the low-density shell than toward the continuum peak. Other COMs such as CH{sub 3}OCHO, c-C{sub 3}H{sub 2}O, HCCCHO, CH{sub 2}CHCN, and HCCNC show slight enhancements (by factors ≤3), but the associated uncertainties are large. This suggests that COMs are actively formed and already present in the low-density shells of pre-stellar cores. The modeling of the chemistry of O-bearing COMs in L1544 indicates that these species are enhanced in this shell because (i) CO starts freezing out onto dust grains driving an active surface chemistry; (ii) the visual extinction is sufficiently high to prevent the UV photo-dissociation of COMs by the external interstellar radiation field; and (iii) the density is still moderate to prevent severe depletion of COMs onto grains.

  16. THE SPATIAL DISTRIBUTION OF COMPLEX ORGANIC MOLECULES IN THE L1544 PRE-STELLAR CORE

    International Nuclear Information System (INIS)

    Jiménez-Serra, Izaskun; Vasyunin, Anton I.; Caselli, Paola; Marcelino, Nuria; Billot, Nicolas; Viti, Serena; Testi, Leonardo; Vastel, Charlotte; Lefloch, Bertrand; Bachiller, Rafael

    2016-01-01

    The detection of complex organic molecules (COMs) toward cold sources such as pre-stellar cores (with T < 10 K) has challenged our understanding of the formation processes of COMs in the interstellar medium. Recent modeling on COM chemistry at low temperatures has provided new insight into these processes predicting that COM formation depends strongly on parameters such as visual extinction and the level of CO freeze out. We report deep observations of COMs toward two positions in the L1544 pre-stellar core: the dense, highly extinguished continuum peak with A_V≥ 30 mag within the inner 2700 au; and a low-density shell with average A_V∼ 7.5–8 mag located at 4000 au from the core’s center and bright in CH_3OH. Our observations show that CH_3O, CH_3OCH_3, and CH_3CHO are more abundant (by factors of ∼2–10) toward the low-density shell than toward the continuum peak. Other COMs such as CH_3OCHO, c-C_3H_2O, HCCCHO, CH_2CHCN, and HCCNC show slight enhancements (by factors ≤3), but the associated uncertainties are large. This suggests that COMs are actively formed and already present in the low-density shells of pre-stellar cores. The modeling of the chemistry of O-bearing COMs in L1544 indicates that these species are enhanced in this shell because (i) CO starts freezing out onto dust grains driving an active surface chemistry; (ii) the visual extinction is sufficiently high to prevent the UV photo-dissociation of COMs by the external interstellar radiation field; and (iii) the density is still moderate to prevent severe depletion of COMs onto grains.

  17. Spatial distribution of bottlenose dolphins (Tursiops truncatus) inferred from stable isotopes and priority organic pollutants

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, Rachel Marie, E-mail: ryounge@ocean.fsu.edu [Department of EOAS-Oceanography, Florida State University, 117 North Woodward Avenue, Tallahassee, Florida, 32306 (United States); Kucklick, John R. [National Institute of Standards and Technology, Hollings Marine Laboratory, Charleston, 331 Fort Johnson Road, Charleston, South Carolina 29412 (United States); Balmer, Brian C.; Wells, Randall S. [Chicago Zoological Society c/o Mote Marine Laboratory, 1600 Ken Thompson Parkway Sarasota, FL, 34236 (United States); Chanton, Jeffrey P. [Department of EOAS-Oceanography, Florida State University, 117 North Woodward Avenue, Tallahassee, Florida, 32306 (United States); Nowacek, Douglas P. [Nicholas School of the Environment and Pratt School of Engineering, Duke University - Marine Laboratory, 135 Duke Marine Lab Rd., Beaufort, NC 28516 (United States)

    2012-05-15

    Differences in priority organic pollutants (POPs), analyzed by gas chromatography-mass spectrometry, and stable isotope ratios ({delta}{sup 13}C, {delta}{sup 34}S, and {delta}{sup 15}N; analyzed by isotope ratio-mass spectrometry), divide 77 bottlenose dolphins (Tursiops truncatus) from the Florida Gulf Coast into three distinct groups. POP levels reflect human population and historical contamination along the coast. In the least disturbed site, concentrations of {Sigma}POP in male dolphins were 18,000 ng g{sup -1} {+-} 6000 (95% confidence interval here and throughout); in the intermediate bay, males had {Sigma}POP concentrations of 19,000 ng g{sup -1} {+-} 10,000. St Andrews Bay was home to dolphins with the highest {Sigma}POP concentrations: 44,000 ng g{sup -1} {+-} 10,300. {delta}{sup 34}S and {delta}{sup 15}N, differed significantly between St. George Sound dolphins and those frequenting each of the other two bays, but not between St. Andrews and St. Joseph Bays. {Sigma}POP concentrations were statistically higher in dolphins frequenting St. Andrews Bay, but were not significantly different between dolphins occupying St. Joseph Bay and St. George Sound. Thus, using either POP or isotope values alone, we would only be able to identify two dolphin groups, but when POP and isotope data are viewed cumulatively, the results clearly define three distinct communities occupying this region. - Highlights: Black-Right-Pointing-Pointer We compare isotopes and POP levels in dolphins occupying three embayments. Black-Right-Pointing-Pointer POP levels varied significantly among two embayments separated by < 50 km. Black-Right-Pointing-Pointer Differentiation correlated with historical contamination from a SuperFund site. Black-Right-Pointing-Pointer Cumulatively, isotopes and POP levels indicate 3 distinct dolphin communities. Black-Right-Pointing-Pointer This data provides the first assessment of dolphin POP contamination in the region.

  18. Hot regions of labile and stable soil organic carbon in Germany - Spatial variability and driving factors

    Science.gov (United States)

    Vos, Cora; Jaconi, Angélica; Jacobs, Anna; Don, Axel

    2018-06-01

    Atmospheric carbon dioxide levels can be mitigated by sequestering carbon in the soil. Sequestration can be facilitated by agricultural management, but its influence is not the same on all soil carbon pools, as labile pools with a high turnover may be accumulated much faster but are also more vulnerable to losses. The aims of this study were to (1) assess how soil organic carbon (SOC) is distributed among SOC fractions on a national scale in Germany, (2) identify factors influencing this distribution and (3) identify regions with high vulnerability to SOC losses. The SOC content and proportion of two different SOC fractions were estimated for more than 2500 mineral topsoils (soil texture, bulk soil C / N ratio, total SOC content and pH. For some regions, the drivers were linked to the land-use history of the sites. Arable topsoils in central and southern Germany were found to contain the highest proportions and contents of stable SOC fractions, and therefore have the lowest vulnerability to SOC losses. North-western Germany contains an area of sandy soils with unusually high SOC contents and high proportions of light SOC fractions, which are commonly regarded as representing a labile carbon pool. This is true for the former peat soils in this area, which have already lost and are at high risk of losing high proportions of their SOC stocks. Those black sands can, however, also contain high amounts of stable SOC due to former heathland vegetation and need to be treated and discussed separately from non-black sand agricultural soils. Overall, it was estimated that, in large areas all over Germany, over 30 % of SOC is stored in easily mineralisable forms. Thus, SOC-conserving management of arable soils in these regions is of great importance.

  19. A comparative study: The spatial organization of pre and post disaster house in traditional cultured area; study case: Core house project in Kasongan, Yogyakarta, Indonesia

    Science.gov (United States)

    Agustina, Vicky

    2017-11-01

    This study involves revealing the spatial organization typology differences between pre and post disaster houses through core house project in Kasongan, Yogyakarta, Indonesia. The goal is to gain understanding of the way of traditional cultured people re-shaping their space and environment after disaster reconstruction through the core house and find the factors that determine the form. The study has been done by comparing and analyzing the spatial properties and functions between both objects using justified graph technique which is one of the basic methodology that able to identify how people are organized in space. Upon the comparison and analysis of these aspects, it appears that the old house size has impact toward significant changes of the spatial properties also the dwellers put physical factor over culture when evaluating the present house. Through these findings, this study highlights that spatial organization of traditional house has temporal spatial value and the core house concept had influenced the changes of the local spatial behaviour and their perception of their house standard.

  20. The problem of induced genomic instability in the child organism under conditions of long-term effect of small radiation doses

    International Nuclear Information System (INIS)

    Suskov, I.I.; Kuz'mina, N.S.

    2001-01-01

    The phenomenological aspects of the genomic instability induced in the descendants of the multi-divided cells having been exposed to the radiation are examined. It is demonstrated that the regularity of the genomic instability induction do not correspond to the classical conception of the radiation genetics (hit principle and target theory). The mechanisms and the biological significance of this new genetic phenomenon in the child organism under conditions of low-intensive effect of small-dose radiation and its connection with the state of health are discussed [ru

  1. Tempo-spatial variation of emission inventories of speciated volatile organic compounds from on-road vehicles in China

    Directory of Open Access Journals (Sweden)

    H. Cai

    2009-09-01

    Full Text Available Emission inventories of sixty-seven speciated non-methane volatile organic compounds (NMVOC from on-road vehicles in China were estimated for the period of 1980–2005, using seven NMVOC emission profiles, which were summarized based on local and international measurements from published literatures dealing with specific vehicle categories running under particular modes.

    Results show an exponential growth trend of China's historical emissions of alkanes, alkenes, alkines, aromatics and carbonyls during the period of 1980–2005, increasing from 63.9, 39.3, 6.9, 36.8 and 24.1 thousand tons, respectively, in 1980 to 2778.2, 1244.5, 178.7, 1351.7 and 406.0 thousand tons, respectively, in 2005, which coincided well with China's economic growth. Emission inventories of alkenes, aromatics and carbonyls were gridded at a high resolution of 40 km×40 km for air quality simulation and health risk evaluation, using the geographic information system (GIS methodology. Spatial distribution of speciated NMVOC emissions shows a clear difference in emission densities between developed eastern and relatively underdeveloped western and inland China. Besides, the appearance and expansion of high-emission areas was another notable characteristic of spatial distribution of speciated NMVOC emissions during the period.

    Emission contributions of vehicle categories to speciated NMVOC groups showed annual variation, due to the variance in the provincial emissions and in the relative fractions of the seven emission profiles adopted at the provincial level. Highly reactive and toxic compounds accounted for high proportions of emissions of speciated NMVOC groups. The most abundant compounds were isopentane, pentane and butane from alkanes; ethene, propene, 2-methyl-2-butene and ethyne from alkenes and alkines; benzene, toluene, ethylbenzene, o-xylene, and m,p-xylene (BTEX and 1,2,4-trimethylbenzene from aromatics and formaldehyde, acetaldehyde

  2. Genomic Organization, Phylogenetic Comparison and Differential Expression of the SBP-Box Family Genes in Grape

    Science.gov (United States)

    Hou, Hongmin; Li, Jun; Gao, Min; Singer, Stacy D.; Wang, Hao; Mao, Linyong; Fei, Zhangjun; Wang, Xiping

    2013-01-01

    Background The SBP-box gene family is specific to plants and encodes a class of zinc finger-containing transcription factors with a broad range of functions. Although SBP-box genes have been identified in numerous plants including green algae, moss, silver birch, snapdragon, Arabidopsis, rice and maize, there is little information concerning SBP-box genes, or the corresponding miR156/157, function in grapevine. Methodology/Principal Findings Eighteen SBP-box gene family members were identified in Vitis vinifera, twelve of which bore sequences that were complementary to miRNA156/157. Phylogenetic reconstruction demonstrated that plant SBP-domain proteins could be classified into seven subgroups, with the V. vinifera SBP-domain proteins being more closely related to SBP-domain proteins from dicotyledonous angiosperms than those from monocotyledonous angiosperms. In addition, synteny analysis between grape and Arabidopsis demonstrated that homologs of several grape SBP genes were found in corresponding syntenic blocks of Arabidopsis. Expression analysis of the grape SBP-box genes in various organs and at different stages of fruit development in V. quinquangularis ‘Shang-24’ revealed distinct spatiotemporal patterns. While the majority of the grape SBP-box genes lacking a miR156/157 target site were expressed ubiquitously and constitutively, most genes bearing a miR156/157 target site exhibited distinct expression patterns, possibly due to the inhibitory role of the microRNA. Furthermore, microarray data mining and quantitative real-time RT-PCR analysis identified several grape SBP-box genes that are potentially involved in the defense against biotic and abiotic stresses. Conclusion The results presented here provide a further understanding of SBP-box gene function in plants, and yields additional insights into the mechanism of stress management in grape, which may have important implications for the future success of this crop. PMID:23527172

  3. The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation

    Directory of Open Access Journals (Sweden)

    Zhou Bai-Cheng

    2010-04-01

    Full Text Available Abstract Background Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gram-negative bacterium that represents a new genus of Flavobacteriaceae. This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes. Results The Z. profunda SM-A87 genome has a single 5 128 187-bp circular chromosome with no extrachromosomal elements and harbors 4 653 predicted protein-coding genes. SM-A87 produces a large amount of capsular polysaccharides and possesses two polysaccharide biosynthesis gene clusters. It has a total of 130 peptidases, 61 of which have signal peptides. In addition to extracellular peptidases, SM-A87 also has various extracellular enzymes for carbohydrate, lipid and DNA degradation. These extracellular enzymes suggest that the bacterium is able to hydrolyze organic materials in the sediment, especially carbohydrates and proteinaceous organic nitrogen. There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases. SM-A87 is a moderate halophile. Our protein isoelectric point analysis indicates that extracellular proteins have lower predicted isoelectric points than intracellular proteins. SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins. Conclusion Here, we present the first complete genome of a deep-sea sedimentary bacterium from the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some common features of deep-sea bacteria, as well as an important capacity to hydrolyze sedimentary organic nitrogen.

  4. Fine organization of genomic regions tagged to the 5S rDNA locus of the bread wheat 5B chromosome.

    Science.gov (United States)

    Sergeeva, Ekaterina M; Shcherban, Andrey B; Adonina, Irina G; Nesterov, Michail A; Beletsky, Alexey V; Rakitin, Andrey L; Mardanov, Andrey V; Ravin, Nikolai V; Salina, Elena A

    2017-11-14

    The multigene family encoding the 5S rRNA, one of the most important structurally-functional part of the large ribosomal subunit, is an obligate component of all eukaryotic genomes. 5S rDNA has long been a favored target for cytological and phylogenetic studies due to the inherent peculiarities of its structural organization, such as the tandem arrays of repetitive units and their high interspecific divergence. The complex polyploid nature of the genome of bread wheat, Triticum aestivum, and the technically difficult task of sequencing clusters of tandem repeats mean that the detailed organization of extended genomic regions containing 5S rRNA genes remains unclear. This is despite the recent progress made in wheat genomic sequencing. Using pyrosequencing of BAC clones, in this work we studied the organization of two distinct 5S rDNA-tagged regions of the 5BS chromosome of bread wheat. Three BAC-clones containing 5S rDNA were identified in the 5BS chromosome-specific BAC-library of Triticum aestivum. Using the results of pyrosequencing and assembling, we obtained six 5S rDNA- containing contigs with a total length of 140,417 bp, and two sets (pools) of individual 5S rDNA sequences belonging to separate, but closely located genomic regions on the 5BS chromosome. Both regions are characterized by the presence of approximately 70-80 copies of 5S rDNA, however, they are completely different in their structural organization. The first region contained highly diverged short-type 5S rDNA units that were disrupted by multiple insertions of transposable elements. The second region contained the more conserved long-type 5S rDNA, organized as a single tandem array. FISH using probes specific to both 5S rDNA unit types showed differences in the distribution and intensity of signals on the chromosomes of polyploid wheat species and their diploid progenitors. A detailed structural organization of two closely located 5S rDNA-tagged genomic regions on the 5BS chromosome of bread

  5. Ecological and spatial factors drive intra- and interspecific variation in exposure of subarctic predatory bird nestlings to persistent organic pollutants.

    Science.gov (United States)

    Eulaers, Igor; Jaspers, Veerle L B; Bustnes, Jan O; Covaci, Adrian; Johnsen, Trond V; Halley, Duncan J; Moum, Truls; Ims, Rolf A; Hanssen, Sveinn A; Erikstad, Kjell E; Herzke, Dorte; Sonne, Christian; Ballesteros, Manuel; Pinxten, Rianne; Eens, Marcel

    2013-07-01

    Top predators in northern ecosystems may suffer from exposure to persistent organic pollutants (POPs) as this exposure may synergistically interact with already elevated natural stress in these ecosystems. In the present study, we aimed at identifying biological (sex, body condition), ecological (dietary carbon source, trophic level) and spatial factors (local habitat, regional nest location) that may influence intra- and interspecific variation in exposure of subarctic predatory bird nestlings to polychlorinated biphenyl 153 (CB 153), polybrominated diphenyl ether 47 (BDE 47), dichlorodiphenyldichloroethylene (p,p'-DDE) and hexachlorobenzene (HCB). During three breeding seasons (2008-2010), we sampled body feathers from fully-grown nestlings of three ecologically distinct predatory bird species in subarctic Norway: Northern Goshawk (Accipiter gentilis), White-tailed Eagle (Haliaeetus albicilla) and Golden Eagle (Aquila chrysaetos). The present study analysed, for the first time, body feathers for both POPs and carbon (δ(13)C) and nitrogen (δ(15)N) stable isotopes, thus integrating the dietary carbon source, trophic level and POP exposure for the larger part of the nestling stage. Intraspecific variation in exposure was driven by a combination of ecological and spatial factors, often different for individual compounds. In addition, combinations for individual compounds differed among species. Trophic level and local habitat were the predominant predictors for CB 153, p,p'-DDE and BDE 47, indicating their biomagnification and decreasing levels according to coast>fjord>inland. Variation in exposure may also have been driven by inter-annual variation arisen from primary sources (e.g. p,p'-DDE) and/or possible revolatilisation from secondary sources (e.g. HCB). Interspecific differences in POP exposure were best explained by a combination of trophic level (biomagnification), dietary carbon source (food chain discrimination) and regional nest location (historical POP

  6. dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms.

    Science.gov (United States)

    Puritz, Jonathan B; Hollenbeck, Christopher M; Gold, John R

    2014-01-01

    Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is due to the fact that dDocent quality trims instead of filtering, incorporates both forward and reverse reads (including reads with INDEL polymorphisms) in assembly, mapping, and SNP calling. The pipeline and a comprehensive user guide can be found at http://dDocent.wordpress.com.

  7. The family Rhabdoviridae: Mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins

    Science.gov (United States)

    Dietzgen, Ralf G.; Kondo, Hideki; Goodin, Michael M.; Kurath, Gael; Vasilakis, Nikos

    2017-01-01

    The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- and bipartite genomes.

  8. Spatial changes in soil organic carbon density and storage of cultivated soils in China from 1980 to 2000

    Science.gov (United States)

    Yu, Yanyan; Guo, Zhengtang; Wu, Haibin; Kahmann, Julia A.; Oldfield, Frank

    2009-06-01

    We address the spatial changes in organic carbon density and storage in cultivated soils in China from 1980 to 2000 on the basis of measured data from individual studies and those acquired during the second national soil survey in China. The results show a carbon gain in ˜66% of the cultivated area of China as a whole with the increase in soil organic carbon (SOC) density mostly ranging from 10% to 30%. Soil organic carbon density increased in fluvi-aquic soils (fluvisols, Food and Agriculture Organization (FAO) of the United Nations) in north China, irrigated silting soils (calcaric fluvisols) in northwest China, latosolic red earths (haplic acrisols/alisols), and paddy soils (fluvisols/cambisols) in south China. In contrast, significant decreases are observed in black soils (phaeozems) in northeast China and latosols (haplic acrisols) in southwest China. No significant changes are detected in loessial soils (calcaric regosols) and dark loessial soils (calcisols) in the loess plateau region. The total SOC storage and average density in the upper 20 cm in the late 1990s are estimated to be ˜5.37 Pg C and 2.77 kg/m2, respectively, compared with the values of ˜5.11 Pg C and 2.63 kg/m2 in the early 1980s. This reveals an increase of SOC storage of 0.26 Pg C and suggests an overall carbon sink for cultivated soils in China, which has contributed 2-3% to the global terrestrial ecosystem carbon absorption from 1980 to 2000. Statistical analyses suggest an insignificant contribution to the observed SOC increase from climate change, and we infer that it is mostly attributable to improved agricultural practices. Despite the SOC density increases over 20 years, the SOC density of the cultivated soils in China in the late 1990s is still ˜30% lower compared to their uncultivated counterparts in comparable soil types, suggesting a considerable potential for SOC restoration through improving management practices. Assuming a restoration of ˜50% of the lost SOC in the next 30

  9. Sequence analysis of the PIP5K locus in Eimeria maxima provides further evidence for eimerian genome plasticity and segmental organization.

    Science.gov (United States)

    Song, B K; Pan, M Z; Lau, Y L; Wan, K L

    2014-07-29

    Commercial flocks infected by Eimeria species parasites, including Eimeria maxima, have an increased risk of developing clinical or subclinical coccidiosis; an intestinal enteritis associated with increased mortality rates in poultry. Currently, infection control is largely based on chemotherapy or live vaccines; however, drug resistance is common and vaccines are relatively expensive. The development of new cost-effective intervention measures will benefit from unraveling the complex genetic mechanisms that underlie host-parasite interactions, including the identification and characterization of genes encoding proteins such as phosphatidylinositol 4-phosphate 5-kinase (PIP5K). We previously identified a PIP5K coding sequence within the E. maxima genome. In this study, we analyzed two bacterial artificial chromosome clones presenting a ~145-kb E. maxima (Weybridge strain) genomic region spanning the PIP5K gene locus. Sequence analysis revealed that ~95% of the simple sequence repeats detected were located within regions comparable to the previously described feature-rich segments of the Eimeria tenella genome. Comparative sequence analysis with the orthologous E. maxima (Houghton strain) region revealed a moderate level of conserved synteny. Unique segmental organizations and telomere-like repeats were also observed in both genomes. A number of incomplete transposable elements were detected and further scrutiny of these elements in both orthologous segments revealed interesting nesting events, which may play a role in facilitating genome plasticity in E. maxima. The current analysis provides more detailed information about the genome organization of E. maxima and may help to reveal genotypic differences that are important for expression of traits related to pathogenicity and virulence.

  10. Spatial variability and response of soil organic carbon stocks to land abandonment and erosion in mountainous drylands (Invited)

    Science.gov (United States)

    De Baets, S. L.; Meersmans, J.; Vanacker, V.; Quine, T. A.; van oost, K.

    2013-12-01

    This research focuses on understanding the impact of human activities on C dynamics in a mountainous and semi-arid environment. Despite the low C status of drylands, soil organic carbon (SOC) is the largest C pool in these systems and hence possess a large restoration capacity. Still, regional estimates of SOC stocks and insights in their determining factors are lacking. This study therefore aims 1) to interpret the variability of soil organic carbon in relation to key soil, topographical and land use variables and 2) to quantify the effects of land regeneration following abandonment on SOC stocks. Soil profiles were taken in the Sierra de los Filabres (SE Spain) in different land units along geomorphic and degradation gradients. SOC contents were modelled using recovery period, soil and topographical variables. Sample depth, topographical position, altitude, recovery period and stone content are identified as the main factors for predicting SOC concentrations. SOC stocks in 1 m depth of soil vary between 3.16 and 76.44 t ha-1. Recovery period (years since abandonment), topographical position and altitude were used to predict and map SOC stocks in the top 0.2 m. The results show that C accumulates fast during the first 10-50 years following abandonment, whereafter the stocks evolve towards a steady state level. The erosion zones in the study area demonstrate a higher potential to increase their SOC stocks when abandoned. Deposition zones have higher SOC stocks, although their C accumulation rate is lower compared to erosion dominated landscapes in the first 10-50 years following abandonment. Therefore, full understanding of the C sequestration potential of land use change in areas of complex topography requires knowledge of spatial variability in soil properties and in particular SOC.

  11. Spatial variability in the abundance, composition, and age of organic matter in surficial sediments of the East China Sea

    Science.gov (United States)

    Wu, Ying; Eglinton, Timothy; Yang, Liyang; Deng, Bing; Montluçon, Daniel; Zhang, Jing

    2013-12-01

    the sources and fate of organic matter (OM) sequestered in continental margin sediments is of importance because the mode and efficiency of OM burial impact the carbon cycle and the regulation of atmospheric CO2 over long time scales. We carried out molecular (lignin-derived phenols from CuO oxidation), elemental, isotopic (δ13C, Δ14C), and sedimentological (grain size and mineral surface area) analyses in order to examine spatial variability in the abundance, source, age of surface sediments of the East China Sea. Higher terrigenous organic matter values were found in the main accumulating areas of fluvial sediments, including the Changjiang (Yangtze) Estuary and Zhejiang-Fujian coastal zone. Isotopic and biomarker data suggest that the sedimentary OM in the inner shelf region was dominated by aged (Δ14C = -423 ± 42‰) but relatively lignin-rich OM (Λ = 0.94 ± 0.57 mg/100 mg OC) associated with fine-grained sediments, suggesting important contributions from soils. In contrast, samples from the outer shelf, while of similar age (Δ14 C = -450 ± 99‰), are lignin poor (Λ = 0.25 ± 0.14 mg/100 mg OC) and associated with coarse-grained material. Regional variation of lignin phenols and OM ages indicates that OM content is fundamentally controlled by hydrodynamic sorting (especially, sediment redistribution and winnowing) and in situ primary production. Selective sorption of acid to aldehyde in clay fraction also modified the ratios of lignin phenols. The burial of lignin in East China Sea is estimated to be relatively efficient, possibly as a consequence of terrigenous OM recalcitrance and/or relatively high sedimentation rates in the Changjiang Estuary and the adjacent Zhejing-Fujian mud belt.

  12. Short interspersed nuclear elements (SINEs) are abundant in Solanaceae and have a family-specific impact on gene structure and genome organization.

    Science.gov (United States)

    Seibt, Kathrin M; Wenke, Torsten; Muders, Katja; Truberg, Bernd; Schmidt, Thomas

    2016-05-01

    Short interspersed nuclear elements (SINEs) are highly abundant non-autonomous retrotransposons that are widespread in plants. They are short in size, non-coding, show high sequence diversity, and are therefore mostly not or not correctly annotated in plant genome sequences. Hence, comparative studies on genomic SINE populations are rare. To explore the structural organization and impact of SINEs, we comparatively investigated the genome sequences of the Solanaceae species potato (Solanum tuberosum), tomato (Solanum lycopersicum), wild tomato (Solanum pennellii), and two pepper cultivars (Capsicum annuum). Based on 8.5 Gbp sequence data, we annotated 82 983 SINE copies belonging to 10 families and subfamilies on a base pair level. Solanaceae SINEs are dispersed over all chromosomes with enrichments in distal regions. Depending on the genome assemblies and gene predictions, 30% of all SINE copies are associated with genes, particularly frequent in introns and untranslated regions (UTRs). The close association with genes is family specific. More than 10% of all genes annotated in the Solanaceae species investigated contain at least one SINE insertion, and we found genes harbouring up to 16 SINE copies. We demonstrate the involvement of SINEs in gene and genome evolution including the donation of splice sites, start and stop codons and exons to genes, enlargement of introns and UTRs, generation of tandem-like duplications and transduction of adjacent sequence regions. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  13. Mass distribution and spatial organization of the linear bacterial motor of Spiroplasma citri R8A2.

    Science.gov (United States)

    Trachtenberg, Shlomo; Andrews, S Brian; Leapman, Richard D

    2003-03-01

    In the simple, helical, wall-less bacterial genus Spiroplasma, chemotaxis and motility are effected by a linear, contractile motor arranged as a flat cytoskeletal ribbon attached to the inner side of the membrane along the shortest helical line. With scanning transmission electron microscopy and diffraction analysis, we determined the hierarchical and spatial organization of the cytoskeleton of Spiroplasma citri R8A2. The structural unit appears to be a fibril, approximately 5 nm wide, composed of dimers of a 59-kDa protein; each ribbon is assembled from seven fibril pairs. The functional unit of the intact ribbon is a pair of aligned fibrils, along which pairs of dimers form tetrameric ring-like repeats. On average, isolated and purified ribbons contain 14 fibrils or seven well-aligned fibril pairs, which are the same structures observed in the intact cell. Scanning transmission electron microscopy mass analysis and sodium dodecyl sulfate-polyacrylamide gel electrophoresis of purified cytoskeletons indicate that the 59-kDa protein is the only constituent of the ribbons.

  14. Spatial organization of mesenchymal stem cells in vitro--results from a new individual cell-based model with podia.

    Directory of Open Access Journals (Sweden)

    Martin Hoffmann

    Full Text Available Therapeutic application of mesenchymal stem cells (MSC requires their extensive in vitro expansion. MSC in culture typically grow to confluence within a few weeks. They show spindle-shaped fibroblastoid morphology and align to each other in characteristic spatial patterns at high cell density. We present an individual cell-based model (IBM that is able to quantitatively describe the spatio-temporal organization of MSC in culture. Our model substantially improves on previous models by explicitly representing cell podia and their dynamics. It employs podia-generated forces for cell movement and adjusts cell behavior in response to cell density. At the same time, it is simple enough to simulate thousands of cells with reasonable computational effort. Experimental sheep MSC cultures were monitored under standard conditions. Automated image analysis was used to determine the location and orientation of individual cells. Our simulations quantitatively reproduced the observed growth dynamics and cell-cell alignment assuming cell density-dependent proliferation, migration, and morphology. In addition to cell growth on plain substrates our model captured cell alignment on micro-structured surfaces. We propose a specific surface micro-structure that according to our simulations can substantially enlarge cell culture harvest. The 'tool box' of cell migratory behavior newly introduced in this study significantly enhances the bandwidth of IBM. Our approach is capable of accommodating individual cell behavior and collective cell dynamics of a variety of cell types and tissues in computational systems biology.

  15. Spatial variation in sediment-water exchange of phosphorus in Florida Bay: AMP as a model organic compound.

    Science.gov (United States)

    Huang, Xiao-Lan; Zhang, Jia-Zhong

    2010-10-15

    Dissolved organic phosphorus (DOP) has been recognized as dominant components in total dissolved phosphorus (TDP) pools in many coastal waters, and its exchange between sediment and water is an important process in biogeochemical cycle of phosphorus. Adenosine monophosphate (AMP) was employed as a model DOP compound to simulate phosphorus exchange across sediment-water interface in Florida Bay. The sorption data from 40 stations were fitted to a modified Freundlich equation and provided a detailed spatial distribution both of the sediment's zero equilibrium phosphorus concentration (EPC(0-T)) and of the distribution coefficient (K(d-T)) with respect to TDP. The K(d-T) was found to be a function of the index of phosphorus saturation (IPS), a molar ratio of the surface reactive phosphorus to the surface reactive iron oxide content in the sediment, across the entire bay. However, the EPC(0-T) was found to correlate to the contents of phosphorus in the eastern bay only. Sediment in the western bay might act as a source of the phosphorus in the exchange process due to their high EPC(0-T) and low K(d-T), whereas sediments in the eastern bay might act as a sink because of their low EPC(0-T) and high K(d-T). These results strongly support the hypothesis that both phosphorus and iron species in calcareous marine sediments play a critical role in governing the sediment-water exchange of both phosphate and DOP in the coastal and estuarine ecosystems.

  16. Levels and spatial distributions of levoglucosan and dissolved organic carbon in snowpits over the Tibetan Plateau glaciers.

    Science.gov (United States)

    Li, Quanlian; Wang, Ninglian; Barbante, Carlo; Kang, Shichang; Yao, Ping; Wan, Xin; Barbaro, Elena; Del Carmen Villoslada Hidalgo, Maria; Gambaro, Andrea; Li, Chaoliu; Niu, Hewen; Dong, Zhiwen; Wu, Xiaobo

    2018-01-15

    In this study, we collected 60 snowpit samples in nine glaciers from the northern to the southern Tibetan Plateau (TP), to study the levels and spatial distributions of levoglucosan and dissolved organic carbon (DOC). The lowest concentration of levoglucosan was found in the Yuzhufeng (YZF) glacier with a mean value of 0.24±0.08ngmL -1 , while the highest concentration of levoglucosan was detected in the Gurenhekou (GRHK) glacier with a mean value of 11.72±15.61ngmL -1 . However, the average DOC concentration in TP glaciers were comparable, without significant regional differences. The levoglucosan/DOC ratio ranged from 0.02 to 6.03% in the Tibetan Plateau glaciers. This ratios and the correlations between levoglucosan and DOC suggested that biomass burning products contributed only marginally to DOC levels in the TP glaciers. Moreover, the analysis of air mass backward trajectories suggested that levoglucosan and DOC in TP glaciers should be transported from the northwestern TP, internal TP, Central Asia, South and East Asia regions. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Spatial and seasonal changes in optical properties of autochthonous and allochthonous chromophoric dissolved organic matter in a stratified mountain lake.

    Science.gov (United States)

    Bracchini, Luca; Dattilo, Arduino Massimo; Hull, Vincent; Loiselle, Steven Arthur; Nannicini, Luciano; Picchi, Maria Pia; Ricci, Maso; Santinelli, Chiara; Seritti, Alfredo; Tognazzi, Antonio; Rossi, Claudio

    2010-03-01

    In this study, we present results on seasonal and spatial changes in CDOM absorption and fluorescence (fCDOM) in a deep mountain lake (Salto Lake, Italy). A novel approach was used to describe the shape of CDOM absorption between 250-700 nm (distribution of the spectral slope, S(lambda)) and a new fluorescence ratio is used to distinguish between humic and amino acid-like components. Solar ultraviolet irradiance, dissolved organic carbon (DOC), DOM fluorescence and absorption measurements were analysed and compared to other physicochemical parameters. We show that in the UV-exposed mixed layer: (i) fluorescence by autochthonous amino acid-like CDOM, (ii) values of S(lambda) across UV-C and UV-B wavebands increased during the summer months, whereas (i) average molar absorption coefficient and (ii) fluorescence by allochthonous humic CDOM decreased. In the unexposed deep layer of the water column (and in the entire water column in winter), humic-like CDOM presented high values of molar absorption coefficients and low values of S(lambda). UV attenuation coefficients correlated with both chlorophyll a concentrations and CDOM absorption. In agreement with changes in CDOM, minimal values in UV attenuation were found in summer. The S(lambda) curve was used as a signature of the mixture between photobleached and algal-derived CDOM with respect to the unexposed chromophoric dissolved compounds in this thermal stratified lake. Furthermore, S(lambda) curves were useful to distinguish between low and high molecular weight CDOM.

  18. Mapping and spatial analysis of the distribution of indicator organisms for water quality in the stream of Ayura (Envigado, Antioquia)

    International Nuclear Information System (INIS)

    Guerra Rojas, Adriana; Aguirre Ramirez, Nestor Jaime; Caicedo Quintero, Orlando

    2011-01-01

    This research evaluates and analyzes the spatial distribution communities of periphyton and aquatic macroinvertebrates used in determining water quality, considering the work done previously by de GAIA group at the University of Antioquia on water stream Ayura. We used the functions of hydrological models preset into GIS tool, which was conducted the layout of the stream netting with. Through the overlay of thematic layers, was obtained a mapping tool that allowed us to determine the relationship between land uses given to near areas where the sampling stations were located and the population of collected organisms, they were identified at each point. The results allow us to say that, both communities of protists and aquatic macroinvertebrates as indexes established, BMWP Colombia, Dinius and INSG, show a good quality of water resources for the station 1, which are coniferous forest, high and low stubbles; in station 2, it has an acceptable quality, and it has been noticed some buildings there, pastures and monocultures; finally at station 3, located in urban areas, the water quality is lower than previous stations

  19. Genome Analyses of Icelandic Strains of Sulfolobus islandicus, Model Organisms for Genetic and Virus-Host Interaction Studies

    DEFF Research Database (Denmark)

    Guo, Li; Brügger, Kim; Liu, Chao

    2011-01-01

    The genomes of two Sulfolobus islandicus strains obtained from Icelandic solfataras were sequenced and analyzed. Strain REY15A is a host for a versatile genetic toolbox. It exhibits a genome of minimal size, is stable genetically, and is easy to grow and manipulate. Strain HVE10/4 shows a broad h...

  20. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  1. Spatial Variation of Soil Organic Carbon and Total Nitrogen in the Coastal Area of Mid-Eastern China.

    Science.gov (United States)

    Xu, Yan; Pu, Lijie; Liao, Qilin; Zhu, Ming; Yu, Xue; Mao, Tianying; Xu, Chenxing

    2017-07-14

    Soils play an important role in sequestrating atmospheric CO₂. Coastal tidal flats have been intensively reclaimed for food security and living spaces worldwide. We aimed to identify the changes of soil organic carbon (SOC) and total nitrogen (TN) following coastal reclamation and their spatial variation in the coastal area of mid-Eastern China to provide information for coastal cropland management. We measured SOC and TN of 463 soil samples in the coastal plain of mid-Eastern China. The results showed that SOC and TN increased highly from the uncultivated coastal tidal flat (2.49 g·kg -1 and 0.21 g·kg -1 , respectively) to the cropland (10.73 g·kg -1 and 1.3 g·kg -1 , respectively). After long-term cultivation, SOC and TN in the old farmland (12.98 g·kg -1 and 1.49 g·kg -1 , respectively) were greater than those in the young farmland (5.76 g·kg -1 and 0.86 g·kg -1 , respectively). The density of SOC in the uncultivated coastal tidal flat, young farmland, and old farmland were 0.68 kg·C·m -2 , 1.52 kg·C·m -2 , and 3.31 kg·C·m -2 , respectively. The density of TN in the uncultivated coastal tidal flat, young farmland and old farmland were 0.05 kg·N·m -2 , 0.23 kg·N·m -2 , and 0.38 kg·N·m -2 , respectively. The C/N (11.17) in the uncultivated coastal tidal flat was highest comparing to that in the young and old farmland due to lower nitrogen. The C/N increased from 6.78 to 8.71 following cultivation. Reclaimed coastal tidal flats had high carbon and nitrogen sequestration potential that not only mitigated the threat of global warming, but also improved soil fertility for crop production. Coastal management of cropland should consider the spatial distribution of SOC and TN to improve ecosystem services of coastal soils.

  2. MIPS plant genome information resources.

    Science.gov (United States)

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  3. Persistent organic pollutants and mercury in marine biota of the Canadian Arctic: an overview of spatial and temporal trends.

    Science.gov (United States)

    Braune, B M; Outridge, P M; Fisk, A T; Muir, D C G; Helm, P A; Hobbs, K; Hoekstra, P F; Kuzyk, Z A; Kwan, M; Letcher, R J; Lockhart, W L; Norstrom, R J; Stern, G A; Stirling, I

    2005-12-01

    This review summarizes and synthesizes the significant amount of data which was generated on mercury (Hg) and persistent organic pollutants (POPs) in Canadian Arctic marine biota since the first Canadian Arctic Contaminants Assessment Report (CACAR) was published in 1997. This recent body of work has led to a better understanding of the current levels and spatial and temporal trends of contaminants in biota, including the marine food species that northern peoples traditionally consume. Compared to other circumpolar countries, concentrations of many organochlorines (OCs) in Canadian Arctic marine biota are generally lower than in the European Arctic and eastern Greenland but are higher than in Alaska, whereas Hg concentrations are substantially higher in Canada than elsewhere. Spatial coverage of OCs in ringed seals, beluga and seabirds remains a strength of the Arctic contaminant data set for Canada. Concentrations of OCs in marine mammals and seabirds remain fairly consistent across the Canadian Arctic although subtle differences from west to east and south to north are found in the proportions of various chemicals. The most significant development since 1997 is improvement in the temporal trend data sets, thanks to the use of archived tissue samples from the 1970s and 1980s, long-term studies using archeological material, as well as the continuation of sampling. These data cover a range of species and chemicals and also include retrospective studies on new chemicals such as polybrominated diphenyl ethers. There is solid evidence in a few species (beluga, polar bear, blue mussels) that Hg at some locations has significantly increased from pre-industrial times to the present; however, the temporal trends of Hg over the past 20-30 years are inconsistent. Some animal populations exhibited significant increases in Hg whereas others did not. Therefore, it is currently not possible to determine if anthropogenic Hg is generally increasing in Canadian Arctic biota. It is

  4. Feasibility analysis and performance characteristics investigation of spatial recuperative expander based on organic Rankine cycle for waste heat recovery

    International Nuclear Information System (INIS)

    Han, Yongqiang; Li, Runzhao; Liu, Zhongchang; Tian, Jing; Wang, Xianfeng; Kang, Jianjian

    2016-01-01

    Highlights: • A new concept of spatial recuperative expander for waste heat recovery is proposed. • Simulation model of spatial recuperative expander is established and verified. • The performance characteristics of spatial recuperative expander are investigated. • Comparison between spatial recuperative expander and traditional one is performed. • Spatial recuperative expander achieves better performance than traditional one. - Abstract: This paper proposes a new concept of spatial recuperative expander which injects cold refrigerant during exhaust stroke as a measure of direct contact heat transfer. The commercial simulation tool GT-SUIT 7.4 is employed to model and verify the feasibility of spatial recuperative expander. The research contents are comprised of the following aspects: Firstly, the principles and performance characteristics between traditional reciprocating piston expander and spatial recuperative expander have been investigated. Secondly, the potential of spatial recuperation by adjusting cold refrigerant injection timing has been studied. Thirdly, the relation between expander performance and variable expansion ratio under constant operating condition has been discussed. Fourthly, the thermodynamic performance of spatial recuperative expander under various operating conditions has been examined. The simulation results indicate that: Firstly, the torque per unit mass, thermal efficiency, exergetic efficiency, isentropic efficiency and recuperative efficiency of optimum spatial recuperative expander are 51.00%, 6.74%, 20.79%, 5.68% and 11.36% higher than traditional reciprocating piston expander respectively. Secondly, the cold refrigerant injection timing has little influence on recuperative efficiency because the recuperation process can complete within 16.67 ms. Thirdly, different operating conditions correspond to particular optimal expansion ratio. Fourthly, increasing the pump pressure and maintaining appropriate superheated degree

  5. Inorganic nanoparticles for the spatial and temporal control of organic reactions: Applications to radical degradation of biopolymer networks

    Science.gov (United States)

    Walker, Joan Marie

    Nanoparticles of gold and iron oxide not only possess remarkable optical and magnetic properties, respectively, but are also capable of influencing their local environment with an astounding degree of precision. Using nanoparticles to direct the reactivity of organic molecules near their surface provides a unique method of spatial and temporal control. Enediynes represent an exceptional class of compounds that are thermally reactive to produce a diradical intermediate via Bergman cycloaromatization. While natural product enediynes are famously cytotoxic, a rich chemistry of synthetic enediynes has developed utilizing creative means to control this reactivity through structure, electronics, metal chelation, and external triggering mechanisms. In a heretofore unexplored arena for Bergman cyclization, we have investigated the reactivity of enediynes in connection with inorganic nanoparticles in which the physical properties of the nanomaterial are directly excited to thermally promote aromatization. As the first example of this methodology, gold nanoparticles conjugated with (Z)-octa-4-en-2,6-diyne-1,8-dithiol were excited with 514 nm laser irradiation. The formation of aromatic and polymeric products was confirmed through Raman spectroscopy and electron microscopy. Water soluble analogues Au-PEG-EDDA and Fe3O4-PEG-EDDA (EDDA = (Z)-octa-4-en-2,6-diyne-1,8-diamine) show similar reactivity under laser irradiation or alternating magnetic field excitation, respectively. Furthermore, we have used these functionalized nanoparticles to attack proteinaceous substrates including fibrin and extracellular matrix proteins, capitalizing on the ability of diradicals to disrupt peptidic bonds. By delivering a locally high payload of reactive molecules and thermal energy to the large biopolymer, network restructuring and collapse is achieved. As a synthetic extension towards multifunctional nanoparticles, noble metal seed-decorated iron oxides have also been prepared and assessed for

  6. Spatial and temporal patterns of dissolved organic matter quantity and quality in the Mississippi River Basin, 1997–2013

    Science.gov (United States)

    Stackpoole, Sarah M.; Stets, Edward G.; Clow, David W.; Burns, Douglas A.; Aiken, George R.; Aulenbach, Brent T.; Creed, Irena F.; Hirsch, Robert M.; Laudon, Hjalmar; Pellerin, Brian; Striegl, Robert G.

    2017-01-01

    Recent studies have found insignificant or decreasing trends in time-series dissolved organic carbon (DOC) datasets, questioning the assumption that long-term DOC concentrations in surface waters are increasing in response to anthropogenic forcing, including climate change, land use, and atmospheric acid deposition. We used the weighted regressions on time, discharge, and season (WRTDS) model to estimate annual flow-normalized concentrations and fluxes to determine if changes in DOC quantity and quality signal anthropogenic forcing at 10 locations in the Mississippi River Basin. Despite increases in agriculture and urban development throughout the basin, net increases in DOC concentration and flux were significant at only 3 of 10 sites from 1997 to 2013 and ranged between −3.5% to +18% and −0.1 to 19%, respectively. Positive shifts in DOC quality, characterized by increasing specific ultraviolet absorbance at 254 nm, ranged between +8% and +45%, but only occurred at one of the sites with significant DOC quantity increases. Basinwide reductions in atmospheric sulfate deposition did not result in large increases in DOC either, likely because of the high buffering capacity of the soil. Hydroclimatic factors including annual discharge, precipitation, and temperature did not significantly change during the 17-year timespan of this study, which contrasts with results from previous studies showing significant increases in precipitation and discharge over a century time scale. Our study also contrasts with those from smaller catchments, which have shown stronger DOC responses to climate, land use, and acidic deposition. This temporal and spatial analysis indicated that there was a potential change in DOC sources in the Mississippi River Basin between 1997 and 2013. However, the overall magnitude of DOC trends was not large, and the pattern in quantity and quality increases for the 10 study sites was not consistent throughout the basin.

  7. The family Rhabdoviridae: mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins.

    Science.gov (United States)

    Dietzgen, Ralf G; Kondo, Hideki; Goodin, Michael M; Kurath, Gael; Vasilakis, Nikos

    2017-01-02

    The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- and bipartite genomes. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. The family Rhabdoviridae: mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins

    OpenAIRE

    Dietzgen, Ralf G.; Kondo, Hideki; Goodin, Michael M.; Kurath, Gael; Vasilakis, Nikos

    2016-01-01

    The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the char...

  9. Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium.

    Directory of Open Access Journals (Sweden)

    Humira Sonah

    Full Text Available Plant genomes are complex and contain large amounts of repetitive DNA including microsatellites that are distributed across entire genomes. Whole genome sequences of several monocot and dicot plants that are available in the public domain provide an opportunity to study the origin, distribution and evolution of microsatellites, and also facilitate the development of new molecular markers. In the present investigation, a genome-wide analysis of microsatellite distribution in monocots (Brachypodium, sorghum and rice and dicots (Arabidopsis, Medicago and Populus was performed. A total of 797,863 simple sequence repeats (SSRs were identified in the whole genome sequences of six plant species. Characterization of these SSRs revealed that mono-nucleotide repeats were the most abundant repeats, and that the frequency of repeats decreased with increase in motif length both in monocots and dicots. However, the frequency of SSRs was higher in dicots than in monocots both for nuclear and chloroplast genomes. Interestingly, GC-rich repeats were the dominant repeats only in monocots, with the majority of them being present in the coding region. These coding GC-rich repeats were found to be involved in different biological processes, predominantly binding activities. In addition, a set of 22,879 SSR markers that were validated by e-PCR were developed and mapped on different chromosomes in Brachypodium for the first time, with a frequency of 101 SSR markers per Mb. Experimental validation of 55 markers showed successful amplification of 80% SSR markers in 16 Brachypodium accessions. An online database 'BraMi' (Brachypodium microsatellite markers of these genome-wide SSR markers was developed and made available in the public domain. The observed differential patterns of SSR marker distribution would be useful for studying microsatellite evolution in a monocot-dicot system. SSR markers developed in this study would be helpful for genomic studies in Brachypodium

  10. The draft genome of Mycobacterium aurum , a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae

    Directory of Open Access Journals (Sweden)

    Jody Phelan

    2015-01-01

    Full Text Available Mycobacterium aurum (M. aurum is an environmental mycobacteria that has previously been used in studies of anti-mycobacterial drugs due to its fast growth rate and low pathogenicity. The M. aurum genome has been sequenced and assembled into 46 contigs, with a total length of 6.02 Mb containing 5684 annotated protein-coding genes. A phylogenetic analysis using whole genome alignments positioned M. aurum close to Mycobacterium vaccae and Mycobacterium vanbaalenii, within a clade related to fast-growing mycobacteria. Large-scale genomic rearrangements were identified by comparing the M. aurum genome to those of Mycobacterium tuberculosis and Mycobacterium leprae. M. aurum orthologous genes implicated in resistance to anti-tuberculosis drugs in M. tuberculosis were observed. The sequence identity at the DNA level varied from 68.6% for pncA (pyrazinamide drug-related to 96.2% for rrs (streptomycin, capreomycin. We observed two homologous genes encoding the catalase-peroxidase enzyme (katG that is associated with resistance to isoniazid. Similarly, two emb B homologues were identified in the M. aurum genome. In addition to describing for the first time the genome of M. aurum , this work provides a resource to aid the use of M. aurum in studies to develop improved drugs for the pathogenic mycobacteria M. tuberculosis and M. leprae.

  11. The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae

    KAUST Repository

    Phelan, Jody

    2015-06-04

    Mycobacterium aurum (M. aurum) is an environmental mycobacteria that has previously been used in studies of anti-mycobacterial drugs due to its fast growth rate and low pathogenicity. The M. aurum genome has been sequenced and assembled into 46 contigs, with a total length of 6.02 Mb containing 5684 annotated protein-coding genes. A phylogenetic analysis using whole genome alignments positioned M. aurum close to Mycobacterium vaccae and Mycobacterium vanbaalenii, within a clade related to fast-growing mycobacteria. Large-scale genomic rearrangements were identified by comparing the M. aurum genome to those of Mycobacterium tuberculosis and Mycobacterium leprae. M. aurum orthologous genes implicated in resistance to anti-tuberculosis drugs in M. tuberculosis were observed. The sequence identity at the DNA level varied from 68.6% for pncA (pyrazinamide drug-related) to 96.2% for rrs (streptomycin, capreomycin). We observed two homologous genes encoding the catalase-peroxidase enzyme (katG) that is associated with resistance to isoniazid. Similarly, two embB homologues were identified in the M. aurum genome. In addition to describing for the first time the genome of M. aurum, this work provides a resource to aid the use of M. aurum in studies to develop improved drugs for the pathogenic mycobacteria M. tuberculosis and M. leprae.

  12. The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae

    KAUST Repository

    Phelan, Jody; Maitra, Arundhati; McNerney, Ruth; Nair, Mridul; Gupta, Antima; Coll, Francesc; Pain, Arnab; Bhakta, Sanjib; Clark, Taane G.

    2015-01-01

    Mycobacterium aurum (M. aurum) is an environmental mycobacteria that has previously been used in studies of anti-mycobacterial drugs due to its fast growth rate and low pathogenicity. The M. aurum genome has been sequenced and assembled into 46 contigs, with a total length of 6.02 Mb containing 5684 annotated protein-coding genes. A phylogenetic analysis using whole genome alignments positioned M. aurum close to Mycobacterium vaccae and Mycobacterium vanbaalenii, within a clade related to fast-growing mycobacteria. Large-scale genomic rearrangements were identified by comparing the M. aurum genome to those of Mycobacterium tuberculosis and Mycobacterium leprae. M. aurum orthologous genes implicated in resistance to anti-tuberculosis drugs in M. tuberculosis were observed. The sequence identity at the DNA level varied from 68.6% for pncA (pyrazinamide drug-related) to 96.2% for rrs (streptomycin, capreomycin). We observed two homologous genes encoding the catalase-peroxidase enzyme (katG) that is associated with resistance to isoniazid. Similarly, two embB homologues were identified in the M. aurum genome. In addition to describing for the first time the genome of M. aurum, this work provides a resource to aid the use of M. aurum in studies to develop improved drugs for the pathogenic mycobacteria M. tuberculosis and M. leprae.

  13. The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae.

    Science.gov (United States)

    Phelan, Jody; Maitra, Arundhati; McNerney, Ruth; Nair, Mridul; Gupta, Antima; Coll, Francesc; Pain, Arnab; Bhakta, Sanjib; Clark, Taane G

    2015-09-01

    Mycobacterium aurum (M. aurum) is an environmental mycobacteria that has previously been used in studies of anti-mycobacterial drugs due to its fast growth rate and low pathogenicity. The M. aurum genome has been sequenced and assembled into 46 contigs, with a total length of 6.02Mb containing 5684 annotated protein-coding genes. A phylogenetic analysis using whole genome alignments positioned M. aurum close to Mycobacterium vaccae and Mycobacterium vanbaalenii, within a clade related to fast-growing mycobacteria. Large-scale genomic rearrangements were identified by comparing the M. aurum genome to those of Mycobacterium tuberculosis and Mycobacterium leprae. M. aurum orthologous genes implicated in resistance to anti-tuberculosis drugs in M. tuberculosis were observed. The sequence identity at the DNA level varied from 68.6% for pncA (pyrazinamide drug-related) to 96.2% for rrs (streptomycin, capreomycin). We observed two homologous genes encoding the catalase-peroxidase enzyme (katG) that is associated with resistance to isoniazid. Similarly, two embB homologues were identified in the M. aurum genome. In addition to describing for the first time the genome of M. aurum, this work provides a resource to aid the use of M. aurum in studies to develop improved drugs for the pathogenic mycobacteria M. tuberculosis and M. leprae. Copyright © 2015 Asian-African Society for Mycobacteriology. Published by Elsevier Ltd. All rights reserved.

  14. Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius

    Directory of Open Access Journals (Sweden)

    Shimada Yukinori

    2010-05-01

    Full Text Available Abstract Background Identification of genes involved in adaptation and speciation by targeting specific genes of interest has become a plausible strategy also for non-model organisms. We investigated the potential utility of available sequenced fish genomes to develop microsatellite (cf. simple sequence repeat, SSR markers for functionally important genes in nine-spined sticklebacks (Pungitius pungitius, as well as cross-species transferability of SSR primers from three-spined (Gasterosteus aculeatus to nine-spined sticklebacks. In addition, we examined the patterns and degree of SSR conservation between these species using their aligned sequences. Results Cross-species amplification success was lower for SSR markers located in or around functionally important genes (27 out of 158 than for those randomly derived from genomic (35 out of 101 and cDNA (35 out of 87 libraries. Polymorphism was observed at a large proportion (65% of the cross-amplified loci independently of SSR type. To develop SSR markers for functionally important genes in nine-spined sticklebacks, SSR locations were surveyed in or around 67 target genes based on the three-spined stickleback genome and these regions were sequenced with primers designed from conserved sequences in sequenced fish genomes. Out of the 81 SSRs identified in the sequenced regions (44,084 bp, 57 exhibited the same motifs at the same locations as in the three-spined stickleback. Di- and trinucleotide SSRs appeared to be highly conserved whereas mononucleotide SSRs were less so. Species-specific primers were designed to amplify 58 SSRs using the sequences of nine-spined sticklebacks. Conclusions Our results demonstrated that a large proportion of SSRs are conserved in the species that have diverged more than 10 million years ago. Therefore, the three-spined stickleback genome can be used to predict SSR locations in the nine-spined stickleback genome. While cross-species utility of SSR primers is limited due

  15. The eukaryotic genome is structurally and functionally more like a social insect colony than a book.

    Science.gov (United States)

    Qiu, Guo-Hua; Yang, Xiaoyan; Zheng, Xintian; Huang, Cuiqin

    2017-11-01

    Traditionally, the genome has been described as the 'book of life'. However, the metaphor of a book may not reflect the dynamic nature of the structure and function of the genome. In the eukaryotic genome, the number of centrally located protein-coding sequences is relatively constant across species, but the amount of noncoding DNA increases considerably with the increase of organismal evolutional complexity. Therefore, it has been hypothesized that the abundant peripheral noncoding DNA protects the genome and the central protein-coding sequences in the eukaryotic genome. Upon comparison with the habitation, sociality and defense mechanisms of a social insect colony, it is found that the genome is similar to a social insect colony in various aspects. A social insect colony may thus be a better metaphor than a book to describe the spatial organization and physical functions of the genome. The potential implications of the metaphor are also discussed.

  16. Functional Annotation, Genome Organization and Phylogeny of the Grapevine (Vitis vinifera Terpene Synthase Gene Family Based on Genome Assembly, FLcDNA Cloning, and Enzyme Assays

    Directory of Open Access Journals (Sweden)

    Toub Omid

    2010-10-01

    Full Text Available Abstract Background Terpenoids are among the most important constituents of grape flavour and wine bouquet, and serve as useful metabolite markers in viticulture and enology. Based on the initial 8-fold sequencing of a nearly homozygous Pinot noir inbred line, 89 putative terpenoid synthase genes (VvTPS were predicted by in silico analysis of the grapevine (Vitis vinifera genome assembly 1. The finding of this very large VvTPS family, combined with the importance of terpenoid metabolism for the organoleptic properties of grapevine berries and finished wines, prompted a detailed examination of this gene family at the genomic level as well as an investigation into VvTPS biochemical functions. Results We present findings from the analysis of the up-dated 12-fold sequencing and assembly of the grapevine genome that place the number of predicted VvTPS genes at 69 putatively functional VvTPS, 20 partial VvTPS, and 63 VvTPS probable pseudogenes. Gene discovery and annotation included information about gene architecture and chromosomal location. A dense cluster of 45 VvTPS is localized on chromosome 18. Extensive FLcDNA cloning, gene synthesis, and protein expression enabled functional characterization of 39 VvTPS; this is the largest number of functionally characterized TPS for any species reported to date. Of these enzymes, 23 have unique functions and/or phylogenetic locations within the plant TPS gene family. Phylogenetic analyses of the TPS gene family showed that while most VvTPS form species-specific gene clusters, there are several examples of gene orthology with TPS of other plant species, representing perhaps more ancient VvTPS, which have maintained functions independent of speciation. Conclusions The highly expanded VvTPS gene family underpins the prominence of terpenoid metabolism in grapevine. We provide a detailed experimental functional annotation of 39 members of this important gene family in grapevine and comprehensive information

  17. Plant STAND P-loop NTPases: a current perspective of genome distribution, evolution, and function : Plant STAND P-loop NTPases: genomic organization, evolution, and molecular mechanism models contribute broadly to plant pathogen defense.

    Science.gov (United States)

    Arya, Preeti; Acharya, Vishal

    2018-02-01

    STAND P-loop NTPase is the common weapon used by plant and other organisms from all three kingdoms of life to defend themselves against pathogen invasion. The purpose of this study is to review comprehensively the latest finding of plant STAND P-loop NTPase related to their genomic distribution, evolution, and their mechanism of action. Earlier, the plant STAND P-loop NTPase known to be comprised of only NBS-LRRs/AP-ATPase/NB-ARC ATPase. However, recent finding suggests that genome of early green plants comprised of two types of STAND P-loop NTPases: (1) mammalian NACHT NTPases and (2) NBS-LRRs. Moreover, YchF (unconventional G protein and members of P-loop NTPase) subfamily has been reported to be exceptionally involved in biotic stress (in case of Oryza sativa), thereby a novel member of STAND P-loop NTPase in green plants. The lineage-specific expansion and genome duplication events are responsible for abundance of plant STAND P-loop NTPases; where "moderate tandem and low segmental duplication" trajectory followed in majority of plant species with few exception (equal contribution of tandem and segmental duplication). Since the past decades, systematic research is being investigated into NBS-LRR function supported the direct recognition of pathogen or pathogen effectors by the latest models proposed via 'integrated decoy' or 'sensor domains' model. Here, we integrate the recently published findings together with the previous literature on the genomic distribution, evolution, and distinct models proposed for functional molecular mechanism of plant STAND P-loop NTPases.

  18. High resolution linkage maps of the model organism Petunia reveal substantial synteny decay with the related genome of tomato.

    Science.gov (United States)

    Bossolini, Eligio; Klahre, Ulrich; Brandenburg, Anna; Reinhardt, Didier; Kuhlemeier, Cris

    2011-04-01

    Two linkage maps were constructed for the model plant Petunia. Mapping populations were obtained by crossing the wild species Petunia axillaris subsp. axillaris with Petunia inflata, and Petunia axillaris subsp. parodii with Petunia exserta. Both maps cover the seven chromosomes of Petunia, and span 970 centimorgans (cM) and 700 cM of the genomes, respectively. In total, 207 markers were mapped. Of these, 28 are multilocus amplified fragment length polymorphism (AFLP) markers and 179 are gene-derived markers. For the first time we report on the development and mapping of 83 Petunia microsatellites. The two maps retain the same marker order, but display significant differences of recombination frequencies at orthologous mapping intervals. A complex pattern of genomic rearrangements was detected with the related genome of tomato (Solanum lycopersicum), indicating that synteny between Petunia and other Solanaceae crops has been considerably disrupted. The newly developed markers will facilitate the genetic characterization of mutants and ecological studies on genetic diversity and speciation within the genus Petunia. The maps will provide a powerful tool to link genetic and genomic information and will be useful to support sequence assembly of the Petunia genome.

  19. Spiking neurons in a hierarchical self-organizing map model can learn to develop spatial and temporal properties of entorhinal grid cells and hippocampal place cells.

    Directory of Open Access Journals (Sweden)

    Praveen K Pilly

    Full Text Available Medial entorhinal grid cells and hippocampal place cells provide neural correlates of spatial representation in the brain. A place cell typically fires whenever an animal is present in one or more spatial regions, or places, of an environment. A grid cell typically fires in multiple spatial regions that form a regular hexagonal grid structure extending throughout the environment. Different grid and place cells prefer spatially offset regions, with their firing fields increasing in size along the dorsoventral axes of the medial entorhinal cortex and hippocampus. The spacing between neighboring fields for a grid cell also increases along the dorsoventral axis. This article presents a neural model whose spiking neurons operate in a hierarchy of self-organizing maps, each obeying the same laws. This spiking GridPlaceMap model simulates how grid cells and place cells may develop. It responds to realistic rat navigational trajectories by learning grid cells with hexagonal grid firing fields of multiple spatial scales and place cells with one or more firing fields that match neurophysiological data about these cells and their development in juvenile rats. The place cells represent much larger spaces than the grid cells, which enable them to support navigational behaviors. Both self-organizing maps amplify and learn to categorize the most frequent and energetic co-occurrences of their inputs. The current results build upon a previous rate-based model of grid and place cell learning, and thus illustrate a general method for converting rate-based adaptive neural models, without the loss of any of their analog properties, into models whose cells obey spiking dynamics. New properties of the spiking GridPlaceMap model include the appearance of theta band modulation. The spiking model also opens a path for implementation in brain-emulating nanochips comprised of networks of noisy spiking neurons with multiple-level adaptive weights for controlling autonomous

  20. Comparison of different interpolation methods for spatial distribution of soil organic carbon and some soil properties in the Black Sea backward region of Turkey

    Science.gov (United States)

    Göl, Ceyhun; Bulut, Sinan; Bolat, Ferhat

    2017-10-01

    The purpose of this research is to compare the spatial variability of soil organic carbon (SOC) in four adjacent land uses including the cultivated area, the grassland area, the plantation area and the natural forest area in the semi - arid region of Black Sea backward region of Turkey. Some of the soil properties, including total nitrogen, SOC, soil organic matter, and bulk density were measured on a grid with a 50 m sampling distance on the top soil (0-15 cm depth). Accordingly, a total of 120 samples were taken from the four adjacent land uses. Data was analyzed using geostatistical methods. The methods used were: Block kriging (BK), co - kriging (CK) with organic matter, total nitrogen and bulk density as auxiliary variables and inverse distance weighting (IDW) methods with the power of 1, 2 and 4. The methods were compared using a performance criteria that included root mean square error (RMSE), mean absolute error (MAE) and the coefficient of correlation (r). The one - way ANOVA test showed that differences between the natural (0.6653 ± 0.2901) - plantation forest (0.7109 ± 0.2729) areas and the grassland (1.3964 ± 0.6828) - cultivated areas (1.5851 ± 0.5541) were statistically significant at 0.05 level (F = 28.462). The best model for describing spatially variation of SOC was CK with the lowest error criteria (RMSE = 0.3342, MAE = 0.2292) and the highest coefficient of correlation (r = 0.84). The spatial structure of SOC could be well described by the spherical model. The nugget effect indicated that SOC was moderately dependent on the study area. The error distributions of the model showed that the improved model was unbiased in predicting the spatial distribution of SOC. This study's results revealed that an explanatory variable linked SOC increased success of spatial interpolation methods. In subsequent studies, this case should be taken into account for reaching more accurate outputs.

  1. The mitochondrial genome of the stingless bee Melipona bicolor (Hymenoptera, Apidae, Meliponini: sequence, gene organization and a unique tRNA translocation event conserved across the tribe Meliponini

    Directory of Open Access Journals (Sweden)

    Daniela Silvestre

    2008-01-01

    Full Text Available At present a complete mtDNA sequence has been reported for only two hymenopterans, the Old World honey bee, Apis mellifera and the sawfly Perga condei. Among the bee group, the tribe Meliponini (stingless bees has some distinction due to its Pantropical distribution, great number of species and large importance as main pollinators in several ecosystems, including the Brazilian rain forest. However few molecular studies have been conducted on this group of bees and few sequence data from mitochondrial genomes have been described. In this project, we PCR amplified and sequenced 78% of the mitochondrial genome of the stingless bee Melipona bicolor (Apidae, Meliponini. The sequenced region contains all of the 13 mitochondrial protein-coding genes, 18 of 22 tRNA genes, and both rRNA genes (one of them was partially sequenced. We also report the genome organization (gene content and order, gene translation, genetic code, and other molecular features, such as base frequencies, codon usage, gene initiation and termination. We compare these characteristics of M. bicolor to those of the mitochondrial genome of A. mellifera and other insects. A highly biased A+T content is a typical characteristic of the A. mellifera mitochondrial genome and it was even more extreme in that of M. bicolor. Length and compositional differences between M. bicolor and A. mellifera genes were detected and the gene order was compared. Eleven tRNA gene translocations were observed between these two species. This latter finding was surprising, considering the taxonomic proximity of these two bee tribes. The tRNA Lys gene translocation was investigated within Meliponini and showed high conservation across the Pantropical range of the tribe.

  2. Spatial variability of primary organic sources regulates ichthyofauna distribution despite seasonal influence in Terminos lagoon and continental shelf of Campeche, Mexico

    Science.gov (United States)

    Romo Rios, J. A.; Aguíñiga-García, S.; Sanchez, A.; Zetina-Rejón, M.; Arreguín-Sánchez, F.; Tripp-Valdéz, A.; Galeana-Cortazár, A.

    2013-05-01

    Human activities have strong impacts on coastal ecosystems functioning through their effect on primary organic sources distributions and resulting biodiversity. Hence, it appears to be of utmost importance to quantify contribution of primary producers to sediment organic matter (SOM) spatial variability and its associated ichthyofauna. The Terminos lagoon (Gulf of Mexico) is a tropical estuary severely impacted by human activities even though of primary concern for its biodiversity, its habitats, and its resource supply. Stable isotope data (d13C, d15N) from mangrove, seaweed, seagrass, phytoplankton, ichthyofauna and SOM were sampled in four zones of the lagoon and the continental shelf through windy (November to February), dry (March to June) and rainy (July to October) seasons. Stable Isotope Analysis in R (SIAR) mixing model were used to determine relative contributions of the autotrophic sources to the ichthyofauna and SOM. Analysis of variance of ichthyofauna isotopic values showed significant differences (P < 0.001) in the four zones of lagoon despite the variability introduced by the windy, dry and rainy seasons. In lagoons rivers discharge zone, the mangrove contribution to ichthyofauna was 40% and 84% to SOM. Alternative use of habitat by ichthyofauna was evidenced since in the deep area of the lagoon (4 m), the contribution of mangrove to fish is 50%, and meanwhile contribution to SOM is only 77%. Although phytoplankton (43%) and seaweed (41%) contributions to the adjacent continental shelf ichthyofauna were the main organic sources, there was 37% mangrove contribution to SOM, demonstrating conspicuous terrigenous influence from lagoon ecosystem. Our results point toward organic sources spatial variations that regulate fish distribution. In Terminos lagoon, significant correlation (p-value = 0.2141 and r=0.79) of Ariopsis felis and Sphoeroides testudineus abundances and seaweed and seagrasses contributions (30-35%) during both dry and rainy seasons

  3. Chloroplast Genome of the Folk Medicine and Vegetable Plant Talinum paniculatum (Jacq.) Gaertn.: Gene Organization, Comparative and Phylogenetic Analysis.

    Science.gov (United States)

    Liu, Xia; Li, Yuan; Yang, Hongyuan; Zhou, Boyang

    2018-04-09

    The complete chloroplast (cp) genome of Talinum paniculatum (Caryophyllale), a source of pharmaceutical efficacy similar to ginseng, and a widely distributed and planted edible vegetable, were sequenced and analyzed. The cp genome size of T. paniculatum is 156,929 bp, with a pair of inverted repeats (IRs) of 25,751 bp separated by a large single copy (LSC) region of 86,898 bp and a small single copy (SSC) region of 18,529 bp. The genome contains 83 protein-coding genes, 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes and four pseudogenes. Fifty one (51) repeat units and ninety two (92) simple sequence repeats (SSRs) were found in the genome. The pseudogene rpl23 (Ribosomal protein L23) was insert AATT than other Caryophyllale species by sequence alignment, which located in IRs region. The gene of trnK-UUU (tRNA-Lys) and rpl16 (Ribosomal protein L16) have larger introns in T. paniculatum , and the existence of matK (maturase K) genes, which usually located in the introns of trnK-UUU , rich sequence divergence in Caryophyllale. Complete cp genome comparison with other eight Caryophyllales species indicated that the differences between T. paniculatum and P. oleracea were very slight, and the most highly divergent regions occurred in intergenic spacers. Comparisons of IR boundaries among nine Caryophyllales species showed that T. paniculatum have larger IRs region and the contraction is relatively slight. The phylogenetic analysis among 35 Caryophyllales species and two outgroup species revealed that T. paniculatum and P. oleracea do not belong to the same family. All these results give good opportunities for future identification, barcoding of Talinum species, understanding the evolutionary mode of Caryophyllale cp genome and molecular breeding of T. paniculatum with high pharmaceutical efficacy.

  4. How entorhinal grid cells may learn multiple spatial scales from a dorsoventral gradient of cell response rates in a self-organizing map.

    Directory of Open Access Journals (Sweden)

    Stephen Grossberg

    Full Text Available Place cells in the hippocampus of higher mammals are critical for spatial navigation. Recent modeling clarifies how this may be achieved by how grid cells in the medial entorhinal cortex (MEC input to place cells. Grid cells exhibit hexagonal grid firing patterns across space in multiple spatial scales along the MEC dorsoventral axis. Signals from grid cells of multiple scales combine adaptively to activate place cells that represent much larger spaces than grid cells. But how do grid cells learn to fire at multiple positions that form a hexagonal grid, and with spatial scales that increase along the dorsoventral axis? In vitro recordings of medial entorhinal layer II stellate cells have revealed subthreshold membrane potential oscillations (MPOs whose temporal periods, and time constants of excitatory postsynaptic potentials (EPSPs, both increase along this axis. Slower (faster subthreshold MPOs and slower (faster EPSPs correlate with larger (smaller grid spacings and field widths. A self-organizing map neural model explains how the anatomical gradient of grid spatial scales can be learned by cells that respond more slowly along the gradient to their inputs from stripe cells of multiple scales, which perform linear velocity path integration. The model cells also exhibit MPO frequencies that covary with their response rates. The gradient in intrinsic rhythmicity is thus not compelling evidence for oscillatory interference as a mechanism of grid cell firing. A response rate gradient combined with input stripe cells that have normalized receptive fields can reproduce all known spatial and temporal properties of grid cells along the MEC dorsoventral axis. This spatial gradient mechanism is homologous to a gradient mechanism for temporal learning in the lateral entorhinal cortex and its hippocampal projections. Spatial and temporal representations may hereby arise from homologous mechanisms, thereby embodying a mechanistic "neural relativity" that

  5. The complete chloroplast genome sequence of the chlorophycean green alga Scenedesmus obliquus reveals a compact gene organization and a biased distribution of genes on the two DNA strands

    Science.gov (United States)

    de Cambiaire, Jean-Charles; Otis, Christian; Lemieux, Claude; Turmel, Monique

    2006-01-01

    Background The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. While the basal position of the Prasinophyceae is well established, the divergence order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae (UTC) remains uncertain. The five complete chloroplast DNA (cpDNA) sequences currently available for representatives of these classes display considerable variability in overall structure, gene content, gene density, intron content and gene order. Among these genomes, that of the chlorophycean green alga Chlamydomonas reinhardtii has retained the least ancestral features. The two single-copy regions, which are separated from one another by the large inverted repeat (IR), have similar sizes, rather than unequal sizes, and differ radically in both gene contents and gene organizations relative to the single-copy regions of prasinophyte and ulvophyte cpDNAs. To gain insights into the various changes that underwent the chloroplast genome during the evolution of chlorophycean green algae, we have sequenced the cpDNA of Scenedesmus obliquus, a member of a distinct chlorophycean lineage. Results The 161,452 bp IR-containing genome of Scenedesmus features single-copy regions of similar sizes, encodes 96 genes, i.e. only two additional genes (infA and rpl12) relative to its Chlamydomonas homologue and contains seven group I and two group II introns. It is clearly more compact than the four UTC algal cpDNAs that have been examined so far, displays the lowest proportion of short repeats among these algae and shows a stronger bias in clustering of genes on the same DNA strand compared to Chlamydomonas cpDNA. Like the latter genome, Scenedesmus cpDNA displays only a few ancestral gene clusters. The two chlorophycean genomes share 11 gene clusters that are not found in previously sequenced trebouxiophyte and ulvophyte cpDNAs as well as a few genes that have an unusual structure; however, their single-copy regions differ

  6. The Hidden Structure of Organic Informal-like Settlements in Jogjakarta City: An Investigation of Socio-Spatial Relationship in an Urban Kampung

    Science.gov (United States)

    Hutama, I. A. W.

    2018-05-01

    Some urban kampungs are registered as informal settlements in Indonesian cities. The existence of a kampung amidst the cities is crucial in providing an affordable access to housing for most of the city’s residents. As an integral part of the city, urban kampungs face many problems such as social segregation, low and deteriorated physical quality, and exclusion from spatial plans which may worsen the residents’ quality of life. Apart from this condition, an urban kampung is believed to have a strong social cohesion and resilient community which are able to persist and survive socially and economically. Towards the sustainability of the city, kampungs as part of the city structure need to be addressed spatially through proper plan and design strategy. In doing so, planners and architects must understand the unique characteristics of urban kampungs to appreciate their positive contribution to the cities. This paper is presented to understand the underlying information on the organic spatial layout of the informal kampung and its impact on social composition within the framework of lively, vibrant, and safe neighborhoods. We utilized Space Syntax (SSX) combined with activity snapshot to understand the socio-spatial relationship and then triangulated the results with a questionnaire on the residents’ perception. Kampung Code, located in the inner city of Yogyakarta, was selected as the case study area as it represents the informal-like settlements. This study revealed that the complex interplays of the organic spatial layout does not significantly affect the frequency of outdoor activities. However, the presence of eight popular spaces (streets, house’s terraces, local shops/taverns, small open spaces, riverbanks, guard posts, community buildings, and small mosques) distributed within Kampung Code does influence it, and it is the driving factor for the residents to engage with others in the form of social interactions. Popular places are able to accommodate

  7. Structure and genome organization of AFV2, a novel archaeal lipothrixvirus with unusual terminal and core structures

    DEFF Research Database (Denmark)

    Häring, Monika; Vestergaard, Gisle Alberg; Brügger, Kim

    2005-01-01

    A novel filamentous virus, AFV2, from the hyperthermophilic archaeal genus Acidianus shows structural similarity to lipothrixviruses but differs from them in its unusual terminal and core structures. The double-stranded DNA genome contains 31,787 bp and carries eight open reading frames homologous...

  8. The complete chloroplast genome sequence of Ampelopsis: gene organization, comparative analysis and phylogenetic relationships to other angiosperms

    Directory of Open Access Journals (Sweden)

    Gurusamy eRaman

    2016-03-01

    Full Text Available Ampelopsis brevipedunculata is an economically important plant that belongs to the Vitaceae family of angiosperms. The phylogenetic placement of Vitaceae is still unresolved. Recent phylogenetic studies suggested that it should be placed in various alternative families including Caryophyllaceae, asteraceae, Saxifragaceae, Dilleniaceae, or with the rest of the rosid families. However, these analyses provided weak supportive results because they were based on only one of several genes. Accordingly, complete chloroplast genome sequences are required to resolve the phylogenetic relationships among angiosperms. Recent phylogenetic analyses based on the complete chloroplast genome sequence suggested strong support for the position of Vitaceae as the earliest diverging lineage of rosids and placed it as a sister to the remaining rosids. These studies also revealed relationships among several major lineages of angiosperms; however, they highlighted the significance of taxon sampling for obtaining accurate phylogenies. In the present study, we sequenced the complete chloroplast genome of A. brevipedunculata and used these data to assess the relationships among 32 angiosperms, including 18 taxa of rosids. The Ampelopsis chloroplast genome is 161,090 bp in length, and includes a pair of inverted repeats of 26,394 bp that are separated by small and large single copy regions of 19,036 bp and 89,266 bp, respectively. The gene content and order of Ampelopsis is identical to many other unrearranged angiosperm chloroplast genomes, including Vitis and tobacco. A phylogenetic tree constructed based on 70 protein-coding genes of 33 angiosperms showed that both Saxifragales and Vitaceae diverged from the rosid clade and formed two clades with 100% bootstrap value. The position of the Vitaceae is sister to Saxifragales, and both are the basal and earliest diverging lineages. Moreover, Saxifragales forms a sister clade to Vitaceae of rosids. Overall, the results of

  9. Genomic organization and molecular phylogenies of the beta (β keratin multigene family in the chicken (Gallus gallus and zebra finch (Taeniopygia guttata: implications for feather evolution

    Directory of Open Access Journals (Sweden)

    Sawyer Roger H

    2010-05-01

    Full Text Available Abstract Background The epidermal appendages of reptiles and birds are constructed of beta (β keratins. The molecular phylogeny of these keratins is important to understanding the evolutionary origin of these appendages, especially feathers. Knowing that the crocodilian β-keratin genes are closely related to those of birds, the published genomes of the chicken and zebra finch provide an opportunity not only to compare the genomic organization of their β-keratins, but to study their molecular evolution in archosaurians. Results The subfamilies (claw, feather, feather-like, and scale of β-keratin genes are clustered in the same 5' to 3' order on microchromosome 25 in chicken and zebra finch, although the number of claw and feather genes differs between the species. Molecular phylogenies show that the monophyletic scale genes are the basal group within birds and that the monophyletic avian claw genes form the basal group to all feather and feather-like genes. Both species have a number of feather clades on microchromosome 27 that form monophyletic groups. An additional monophyletic cluster of feather genes exist on macrochromosome 2 for each species. Expression sequence tag analysis for the chicken demonstrates that all feather β-keratin clades are expressed. Conclusions Similarity in the overall genomic organization of β-keratins in Galliformes and Passeriformes suggests similar organization in all Neognathae birds, and perhaps in the ancestral lineages leading to modern birds, such as the paravian Anchiornis huxleyi. Phylogenetic analyses demonstrate that evolution of archosaurian epidermal appendages in the lineage leading to birds was accompanied by duplication and divergence of an ancestral β-keratin gene cluster. As morphological diversification of epidermal appendages occurred and the β-keratin multigene family expanded, novel β-keratin genes were selected for novel functions within appendages such as feathers.

  10. Genome-wide analysis of the grapevine stilbene synthase multigenic family: genomic organization and expression profiles upon biotic and abiotic stresses

    Directory of Open Access Journals (Sweden)

    Vannozzi Alessandro

    2012-08-01

    Full Text Available Abstract Background Plant stilbenes are a small group of phenylpropanoids, which have been detected in at least 72 unrelated plant species and accumulate in response to biotic and abiotic stresses such as infection, wounding, UV-C exposure and treatment with chemicals. Stilbenes are formed via the phenylalanine/polymalonate-route, the last step of which is catalyzed by the enzyme stilbene synthase (STS, a type III polyketide synthase (PKS. Stilbene synthases are closely related to chalcone synthases (CHS, the key enzymes of the flavonoid pathway, as illustrated by the fact that both enzymes share the same substrates. To date, STSs have been cloned from peanut, pine, sorghum and grapevine, the only stilbene-producing fruiting-plant for which the entire genome has been sequenced. Apart from sorghum, STS genes appear to exist as a family of closely related genes in these other plant species. Results In this study a complete characterization of the STS multigenic family in grapevine has been performed, commencing with the identification, annotation and phylogenetic analysis of all members and integration of this information with a comprehensive set of gene expression analyses including healthy tissues at differential developmental stages and in leaves exposed to both biotic (downy mildew infection and abiotic (wounding and UV-C exposure stresses. At least thirty-three full length sequences encoding VvSTS genes were identified, which, based on predicted amino acid sequences, cluster in 3 principal groups designated A, B and C. The majority of VvSTS genes cluster in groups B and C and are located on chr16 whereas the few gene family members in group A are found on chr10. Microarray and mRNA-seq expression analyses revealed different patterns of transcript accumulation between the different groups of VvSTS family members and between VvSTSs and VvCHSs. Indeed, under certain conditions the transcriptional response of VvSTS and VvCHS genes appears to be

  11. Insights into the Evolution of a Snake Venom Multi-Gene Family from the Genomic Organization of Echis ocellatus SVMP Genes

    Directory of Open Access Journals (Sweden)

    Libia Sanz

    2016-07-01

    Full Text Available The molecular events underlying the evolution of the Snake Venom Metalloproteinase (SVMP family from an A Disintegrin And Metalloproteinase (ADAM ancestor remain poorly understood. Comparative genomics may provide decisive information to reconstruct the evolutionary history of this multi-locus toxin family. Here, we report the genomic organization of Echis ocellatus genes encoding SVMPs from the PII and PI classes. Comparisons between them and between these genes and the genomic structures of Anolis carolinensis ADAM28 and E. ocellatus PIII-SVMP EOC00089 suggest that insertions and deletions of intronic regions played key roles along the evolutionary pathway that shaped the current diversity within the multi-locus SVMP gene family. In particular, our data suggest that emergence of EOC00028-like PI-SVMP from an ancestral PII(e/d-type SVMP involved splicing site mutations that abolished both the 3′ splice AG acceptor site of intron 12* and the 5′ splice GT donor site of intron 13*, and resulted in the intronization of exon 13* and the consequent destruction of the structural integrity of the PII-SVMP characteristic disintegrin domain.

  12. Does age matter? Controls on the spatial organization of age and life expectancy in hillslopes, and implications for transport parameterization using rSAS

    Science.gov (United States)

    Kim, M.; Harman, C. J.; Troch, P. A. A.

    2017-12-01

    Hillslopes have been extensively explored as a natural fundamental unit for spatially-integrated hydrologic models. Much of this attention has focused on their use in predicting the quantity of discharge, but hillslope-based models can potentially be used to predict the composition of discharge (in terms of age and chemistry) if they can be parameterized terms of measurable physical properties. Here we present advances in the use of rank StorAge Selection (rSAS) functions to parameterize transport through hillslopes. These functions provide a mapping between the distribution of water ages in storage and in outfluxes in terms of a probability distribution over storage. It has previously been shown that rSAS functions are related to the relative partitioning and arrangement of flow pathways (and variabilities in that arrangement), while separating out the effect of changes in the overall rate of fluxes in and out. This suggests that rSAS functions should have a connection to the internal organization of flow paths in a hillslope.Using a combination of numerical modeling and theoretical analysis we examined: first, the controls of physical properties on internal spatial organization of age (time since entry), life expectancy (time to exit), and the emergent transit time distribution and rSAS functions; second, the possible parameterization of the rSAS function using the physical properties. The numerical modeling results showed the clear dependence of the rSAS function forms on the physical properties and relations between the internal organization and the rSAS functions. For the different rates of the exponential saturated hydraulic conductivity decline with depth the spatial organization of life expectancy varied dramatically and determined the rSAS function forms, while the organizaiton of the age showed less qualitative differences. Analytical solutions predicting this spatial organization and the resulting rSAS function were derived for simplified systems. These

  13. Planning Strategies in an Age of Active Citizenship : A Post-structuralist Agenda for Self-organization in Spatial Planning

    NARCIS (Netherlands)

    Boonstra, B.

    2015-01-01

    Civic initiatives in spatial development are on the rise. Whereas for a long time they were just a fringe movement, sometimes even a stand in the way of planned urban development, civic initiatives today are increasingly seen as valuable strategies for urban development. So far, however, when

  14. Land use and soil organic matter in South Africa 1: A review on spatial variability and the influence of rangeland stock production

    Directory of Open Access Journals (Sweden)

    Pearson N.S. Mnkeni

    2011-05-01

    Full Text Available Degradation of soil as a consequence of land use poses a threat to sustainable agriculture in South Africa, resulting in the need for a soil protection strategy and policy. Development of such a strategy and policy require cognisance of the extent and impact of soil degradation processes. One of the identified processes is the decline of soil organic matter, which also plays a central role in soil health or quality. The spatial variability of organic matter and the impact of grazing and burning under rangeland stock production are addressed in this first part of the review. Data from uncoordinated studies showed that South African soils have low organic matter levels. About 58% of soils contain less than 0.5% organic carbon and only 4% contain more than 2% organic carbon. Furthermore, there are large differences in organic matter content within and between soil forms, depending on climatic conditions, vegetative cover, topographical position and soil texture. A countrywide baseline study to quantify organic matter contents within and between soil forms is suggested for future reference. Degradation of rangeland because of overgrazing has resulted in significant losses of soil organic matter, mainly as a result of lower biomass production. The use of fire in rangeland management decreases soil organic matter because litter is destroyed by burning. Maintaining or increasing organic matter levels in degraded rangeland soils by preventing overgrazing and restricting burning could contribute to the restoration of degraded rangelands. This restoration is of the utmost importance because stock farming uses the majority of land in South Africa.

  15. Simulating land-use changes by incorporating spatial autocorrelation and self-organization in CLUE-S modeling: a case study in Zengcheng District, Guangzhou, China

    Science.gov (United States)

    Mei, Zhixiong; Wu, Hao; Li, Shiyun

    2018-06-01

    The Conversion of Land Use and its Effects at Small regional extent (CLUE-S), which is a widely used model for land-use simulation, utilizes logistic regression to estimate the relationships between land use and its drivers, and thus, predict land-use change probabilities. However, logistic regression disregards possible spatial autocorrelation and self-organization in land-use data. Autologistic regression can depict spatial autocorrelation but cannot address self-organization, while logistic regression by considering only self-organization (NElogistic regression) fails to capture spatial autocorrelation. Therefore, this study developed a regression (NE-autologistic regression) method, which incorporated both spatial autocorrelation and self-organization, to improve CLUE-S. The Zengcheng District of Guangzhou, China was selected as the study area. The land-use data of 2001, 2005, and 2009, as well as 10 typical driving factors, were used to validate the proposed regression method and the improved CLUE-S model. Then, three future land-use scenarios in 2020: the natural growth scenario, ecological protection scenario, and economic development scenario, were simulated using the improved model. Validation results showed that NE-autologistic regression performed better than logistic regression, autologistic regression, and NE-logistic regression in predicting land-use change probabilities. The spatial allocation accuracy and kappa values of NE-autologistic-CLUE-S were higher than those of logistic-CLUE-S, autologistic-CLUE-S, and NE-logistic-CLUE-S for the simulations of two periods, 2001-2009 and 2005-2009, which proved that the improved CLUE-S model achieved the best simulation and was thereby effective to a certain extent. The scenario simulation results indicated that under all three scenarios, traffic land and residential/industrial land would increase, whereas arable land and unused land would decrease during 2009-2020. Apparent differences also existed in the

  16. High resolution linkage maps of the model organism Petunia reveal substantial synteny decay with the related genome of tomato

    OpenAIRE

    Bossolini, Eligio; Klahre, Ulrich; Brandenburg, Anna; Reinhardt, Didier; Kuhlemeier, Cris

    2011-01-01

    Two linkage maps were constructed for the model plant Petunia. Mapping populations were obtained by crossing the wild species Petunia axillaris subsp. axillaris with Petunia inflata, and Petunia axillaris subsp. parodii with Petunia exserta. Both maps cover the seven chromosomes of Petunia, and span 970 centimorgans (cM) and 700 cM of the genomes, respectively. In total, 207 markers were mapped. Of these, 28 are multilocus amplified fragment length polymorphism (AFLP) markers and 179 are gene...

  17. Characterization of the genomic organization of the region bordering the centromere of chromosome V of Podospora anserina by direct sequencing.

    Science.gov (United States)

    Silar, Philippe; Barreau, Christian; Debuchy, Robert; Kicka, Sébastien; Turcq, Béatrice; Sainsard-Chanet, Annie; Sellem, Carole H; Billault, Alain; Cattolico, Laurence; Duprat, Simone; Weissenbach, Jean

    2003-08-01

    A Podospora anserina BAC library of 4800 clones has been constructed in the vector pBHYG allowing direct selection in fungi. Screening of the BAC collection for centromeric sequences of chromosome V allowed the recovery of clones localized on either sides of the centromere, but no BAC clone was found to contain the centromere. Seven BAC clones containing 322,195 and 156,244bp from either sides of the centromeric region were sequenced and annotated. One 5S rRNA gene, 5 tRNA genes, and 163 putative coding sequences (CDS) were identified. Among these, only six CDS seem specific to P. anserina. The gene density in the centromeric region is approximately one gene every 2.8kb. Extrapolation of this gene density to the whole genome of P. anserina suggests that the genome contains about 11,000 genes. Synteny analyses between P. anserina and Neurospora crassa show that co-linearity extends at the most to a few genes, suggesting rapid genome rearrangements between these two species.

  18. Unravelling ground stone life histories: the spatial organization of stone tools and human activities at LN Makriyalos, Greece:

    OpenAIRE

    Tsoraki, Christina

    2007-01-01

    Unlike previous studies of ground stone technology in the Greek Neolithic, this paper follows a more contextualised approach by looking at contexts of deposition of ground stone from Late Neolithic Makriyalos, Northern Greece. The patterns attested in the distribution of ground stone objects between domestic and communal areas will be discussed in terms of the spatial and social contexts of tool use, curation and deposition, contributing to wider discussions about the way acts of production, ...

  19. Improving the Spatial Prediction of Soil Organic Carbon Stocks in a Complex Tropical Mountain Landscape by Methodological Specifications in Machine Learning Approaches.

    Directory of Open Access Journals (Sweden)

    Mareike Ließ

    Full Text Available Tropical forests are significant carbon sinks and their soils' carbon storage potential is immense. However, little is known about the soil organic carbon (SOC stocks of tropical mountain areas whose complex soil-landscape and difficult accessibility pose a challenge to spatial analysis. The choice of methodology for spatial prediction is of high importance to improve the expected poor model results in case of low predictor-response correlations. Four aspects were considered to improve model performance in predicting SOC stocks of the organic layer of a tropical mountain forest landscape: Different spatial predictor settings, predictor selection strategies, various machine learning algorithms and model tuning. Five machine learning algorithms: random forests, artificial neural networks, multivariate adaptive regression splines, boosted regression trees and support vector machines were trained and tuned to predict SOC stocks from predictors derived from a digital elevation model and satellite image. Topographical predictors were calculated with a GIS search radius of 45 to 615 m. Finally, three predictor selection strategies were applied to the total set of 236 predictors. All machine learning algorithms-including the model tuning and predictor selection-were compared via five repetitions of a tenfold cross-validation. The boosted regression tree algorithm resulted in the overall best model. SOC stocks ranged between 0.2 to 17.7 kg m-2, displaying a huge variability with diffuse insolation and curvatures of different scale guiding the spatial pattern. Predictor selection and model tuning improved the models' predictive performance in all five machine learning algorithms. The rather low number of selected predictors favours forward compared to backward selection procedures. Choosing predictors due to their indiviual performance was vanquished by the two procedures which accounted for predictor interaction.

  20. Improving the Spatial Prediction of Soil Organic Carbon Stocks in a Complex Tropical Mountain Landscape by Methodological Specifications in Machine Learning Approaches.

    Science.gov (United States)

    Ließ, Mareike; Schmidt, Johannes; Glaser, Bruno

    2016-01-01

    Tropical forests are significant carbon sinks and their soils' carbon storage potential is immense. However, little is known about the soil organic carbon (SOC) stocks of tropical mountain areas whose complex soil-landscape and difficult accessibility pose a challenge to spatial analysis. The choice of methodology for spatial prediction is of high importance to improve the expected poor model results in case of low predictor-response correlations. Four aspects were considered to improve model performance in predicting SOC stocks of the organic layer of a tropical mountain forest landscape: Different spatial predictor settings, predictor selection strategies, various machine learning algorithms and model tuning. Five machine learning algorithms: random forests, artificial neural networks, multivariate adaptive regression splines, boosted regression trees and support vector machines were trained and tuned to predict SOC stocks from predictors derived from a digital elevation model and satellite image. Topographical predictors were calculated with a GIS search radius of 45 to 615 m. Finally, three predictor selection strategies were applied to the total set of 236 predictors. All machine learning algorithms-including the model tuning and predictor selection-were compared via five repetitions of a tenfold cross-validation. The boosted regression tree algorithm resulted in the overall best model. SOC stocks ranged between 0.2 to 17.7 kg m-2, displaying a huge variability with diffuse insolation and curvatures of different scale guiding the spatial pattern. Predictor selection and model tuning improved the models' predictive performance in all five machine learning algorithms. The rather low number of selected predictors favours forward compared to backward selection procedures. Choosing predictors due to their indiviual performance was vanquished by the two procedures which accounted for predictor interaction.

  1. Disruption of spatial organization and interjoint coordination in Parkinson's disease, progressive supranuclear palsy, and multiple system atrophy.

    Science.gov (United States)

    Leiguarda, R; Merello, M; Balej, J; Starkstein, S; Nogues, M; Marsden, C D

    2000-07-01

    Patients with basal ganglia diseases may exhibit ideomotor apraxia. To define the nature of the impairment of the action production system, we studied a repetitive gesture of slicing bread by three-dimensional computergraphic analysis in eight nondemented patients with Parkinson's disease in the "on" state, five with progressive supranuclear palsy and four with multiple system atrophy. Two patients with Parkinson's disease and two with progressive supranuclear palsy showed ideomotor apraxia for transitive movements on standard testing. A Selspott II system was used for kinematic analysis of wrist trajectories and angular motions of the shoulder and elbow joints. Patients with Parkinson's disease, progressive supranuclear palsy, and even some with multiple system atrophy exhibited kinematic deficits in the spatial precision of movement and velocity-curvature relationships; in addition, they failed to maintain proper angle/angle relationships and to apportion their relative joint amplitudes normally. Spatial disruption of wrist trajectories was more severe in patients with ideomotor apraxia. We posit that the basal ganglia are part of the parallel parieto-frontal circuits devoted to sensorimotor integration for object-oriented behavior. The severity and characteristics of spatial abnormalities of a transitive movement would therefore depend on the location and distribution of the pathologic process within these circuits.

  2. Spatial distribution and mobility of organic carbon (POC and DOC) in a coastal Mediterranean environment (Saronikos Gulf, Greece) during 2007-2009 period.

    Science.gov (United States)

    Evangeliou, Nikolaos; Florou, Heleny

    2013-08-01

    Particulate (POC) and dissolved organic carbon (DOC) is an important parameter for the pollution assessment of coastal marine systems, especially those affected by anthropogenic, domestic, and industrial activities. In the present paper, a similar marine system (Saronikos Gulf) located in the west-central Aegean Sea (eastern Mediterranean Sea) was examined, in terms of the temporal and spatial distribution of organic carbon (POC and DOC), with respect to marine sources and pathways. POC was maximum in winter in the Saronikos Gulf, due to the bloom of phytoplankton, whereas in the Elefsis Bay (located in the north side of the Saronikos Gulf) in summer, since phytoplankton grazes in the Bay in the end of summer (except for winter). Approximately 60 % of the bulk DOC of the water column was estimated as non-refractory (labile and semi-labile), due to the major anthropogenic, domestic, and industrial effects of the region and the shallow depths. The spatial distribution of POC and DOC mainly affects the northeastern section of the Gulf, since that region has been accepted major organic discharges for a long time period, in connection to the relatively long renewal times of its waters.

  3. Genome-wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages of Populus alba (Salicaceae), a widespread forest tree.

    Science.gov (United States)

    Stölting, Kai N; Paris, Margot; Meier, Cécile; Heinze, Berthold; Castiglione, Stefano; Bartha, Denes; Lexer, Christian

    2015-08-01

    Studying the divergence continuum in plants is relevant to fundamental and applied biology because of the potential to reveal functionally important genetic variation. In this context, whole-genome sequencing (WGS) provides the necessary rigour for uncovering footprints of selection. We resequenced populations of two divergent phylogeographic lineages of Populus alba (n = 48), thoroughly characterized by microsatellites (n = 317), and scanned their genomes for regions of unusually high allelic differentiation and reduced diversity using > 1.7 million single nucleotide polymorphisms (SNPs) from WGS. Results were confirmed by Sanger sequencing. On average, 9134 high-differentiation (≥ 4 standard deviations) outlier SNPs were uncovered between populations, 848 of which were shared by ≥ three replicate comparisons. Annotation revealed that 545 of these were located in 437 predicted genes. Twelve percent of differentiation outlier genome regions exhibited significantly reduced genetic diversity. Gene ontology (GO) searches were successful for 327 high-differentiation genes, and these were enriched for 63 GO terms. Our results provide a snapshot of the roles of 'hard selective sweeps' vs divergent selection of standing genetic variation in distinct postglacial recolonization lineages of P. alba. Thus, this study adds to our understanding of the mechanisms responsible for the origin of functionally relevant variation in temperate trees. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  4. A bio-inspired, microchanneled hydrogel with controlled spacing of cell adhesion ligands regulates 3D spatial organization of cells and tissue.

    Science.gov (United States)

    Lee, Min Kyung; Rich, Max H; Lee, Jonghwi; Kong, Hyunjoon

    2015-07-01

    Bioactive hydrogels have been extensively studied as a platform for 3D cell culture and tissue regeneration. One of the key desired design parameters is the ability to control spatial organization of biomolecules and cells and subsequent tissue in a 3D matrix. To this end, this study presents a simple but advanced method to spatially organize microchanneled, cell adherent gel blocks and non-adherent ones in a single construct. This hydrogel system was prepared by first fabricating a bimodal hydrogel in which the microscale, alginate gel blocks modified with cell adhesion peptides containing Arg-Gly-Asp sequence (RGD peptides), and those free of RGD peptides, were alternatingly presented. Then, anisotropically aligned microchannels were introduced by uniaxial freeze-drying of the bimodal hydrogel. The resulting gel system could drive bone marrow stromal cells to adhere to and differentiate into neuron and glial cells exclusively in microchannels of the alginate gel blocks modified with RGD peptides. Separately, the bimodal gel loaded with microparticles releasing vascular endothelial growth factor stimulated vascular growth solely into microchannels of the RGD-alginate gel blocks in vivo. These results were not attained by the bimodal hydrogel fabricated to present randomly oriented micropores. Overall, the bimodal gel system could regulate spatial organization of nerve-like tissue or blood vessels at sub-micrometer length scale. We believe that the hydrogel assembly demonstrated in this study will be highly useful in developing a better understanding of diverse cellular behaviors in 3D tissue and further improve quality of a wide array of engineered tissues. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. SPATIAL AND TEMPORAL DISTRIBUTION OF COLOURED DISSOLVED ORGANIC MATTER (CDOM) IN NARRAGANSETT BAY, RI: IMPLICATIONS FOR PHYTOPLANKTON IN COASTAL WATERS

    Science.gov (United States)

    One indicator of health in estuarine and coastal ecosystems is the ability of local waters to transmit sunlight to planktonic, macrophytic, and other submerged vegetation for photosynthesis. The concentration of coloured dissolved organic matter (CDOM) is a primary factor affecti...

  6. Genomic signatures of local directional selection in a high gene flow marine organism, the Atlantic cod (Gadus morhua)

    DEFF Research Database (Denmark)

    Eg Nielsen, Einar; Hansen, Jakob Hemmer; Poulsen, Nina Aagaard

    2009-01-01

    -associated single nucleotide polymorphisms (SNPs) for evidence of selection in local populations of Atlantic cod (Gadus morhua L.) across the species distribution. Results: Our global genome scan analysis identified eight outlier gene loci with very high statistical support, likely to be subject to directional...... selection in local demes, or closely linked to loci under selection. Likewise, on a regional south/north transect of central and eastern Atlantic populations, seven loci displayed strongly elevated levels of genetic differentiation. Selection patterns among populations appeared to be relatively widespread...

  7. Structural-Functional Organization of the Eukaryotic Cell Nucleus and Transcription Regulation: Introduction to This Special Issue of Biochemistry (Moscow).

    Science.gov (United States)

    Razin, S V

    2018-04-01

    This issue of Biochemistry (Moscow) is devoted to the cell nucleus and mechanisms of transcription regulation. Over the years, biochemical processes in the cell nucleus have been studied in isolation, outside the context of their spatial organization. Now it is clear that segregation of functional processes within a compartmentalized cell nucleus is very important for the implementation of basic genetic processes. The functional compartmentalization of the cell nucleus is closely related to the spatial organization of the genome, which in turn plays a key role in the operation of epigenetic mechanisms. In this issue of Biochemistry (Moscow), we present a selection of review articles covering the functional architecture of the eukaryotic cell nucleus, the mechanisms of genome folding, the role of stochastic processes in establishing 3D architecture of the genome, and the impact of genome spatial organization on transcription regulation.

  8. Seasonal and spatial variability of the OM/OC mass ratios and high regional correlation between oxalic acid and zinc in Chinese urban organic aerosols

    Directory of Open Access Journals (Sweden)

    L. Xing

    2013-04-01

    Full Text Available We calculated the organic matter to organic carbon mass ratios (OM/OC mass ratios in PM2.5 collected from 14 Chinese cities during summer and winter of 2003 and analyzed the causes for their seasonal and spatial variability. The OM/OC mass ratios were calculated two ways. Using a mass balance method, the calculated OM/OC mass ratios averaged 1.92 ± 0.39 year-round, with no significant seasonal or spatial variation. The second calculation was based on chemical species analyses of the organic compounds extracted from the PM2.5 samples using dichloromethane/methanol and water. The calculated OM/OC mass ratio in summer was relatively high (1.75 ± 0.13 and spatially-invariant due to vigorous photochemistry and secondary organic aerosol (OA production throughout the country. The calculated OM/OC mass ratio in winter (1.59 ± 0.18 was significantly lower than that in summer, with lower values in northern cities (1.51 ± 0.07 than in southern cities (1.65 ± 0.15. This likely reflects the wider usage of coal for heating purposes in northern China in winter, in contrast to the larger contributions from biofuel and biomass burning in southern China in winter. On average, organic matter constituted 36% and 34% of Chinese urban PM2.5 mass in summer and winter, respectively. We report, for the first time, a high regional correlation between Zn and oxalic acid in Chinese urban aerosols in summer. This is consistent with the formation of stable Zn oxalate complex in the aerosol phase previously proposed by Furukawa and Takahashi (2011. We found that many other dicarboxylic acids were also highly correlated with Zn in the summer Chinese urban aerosol samples, suggesting that they may also form stable organic complexes with Zn. Such formation may have profound implications for the atmospheric abundance and hygroscopic properties of aerosol dicarboxylic acids.

  9. Seasonal and spatial variability of the OM/OC mass ratios and high regional correlation between oxalic acid and zinc in Chinese urban organic aerosols

    Science.gov (United States)

    Xing, L.; Fu, T.-M.; Cao, J. J.; Lee, S. C.; Wang, G. H.; Ho, K. F.; Cheng, M.-C.; You, C.-F.; Wang, T. J.

    2013-04-01

    We calculated the organic matter to organic carbon mass ratios (OM/OC mass ratios) in PM2.5 collected from 14 Chinese cities during summer and winter of 2003 and analyzed the causes for their seasonal and spatial variability. The OM/OC mass ratios were calculated two ways. Using a mass balance method, the calculated OM/OC mass ratios averaged 1.92 ± 0.39 year-round, with no significant seasonal or spatial variation. The second calculation was based on chemical species analyses of the organic compounds extracted from the PM2.5 samples using dichloromethane/methanol and water. The calculated OM/OC mass ratio in summer was relatively high (1.75 ± 0.13) and spatially-invariant due to vigorous photochemistry and secondary organic aerosol (OA) production throughout the country. The calculated OM/OC mass ratio in winter (1.59 ± 0.18) was significantly lower than that in summer, with lower values in northern cities (1.51 ± 0.07) than in southern cities (1.65 ± 0.15). This likely reflects the wider usage of coal for heating purposes in northern China in winter, in contrast to the larger contributions from biofuel and biomass burning in southern China in winter. On average, organic matter constituted 36% and 34% of Chinese urban PM2.5 mass in summer and winter, respectively. We report, for the first time, a high regional correlation between Zn and oxalic acid in Chinese urban aerosols in summer. This is consistent with the formation of stable Zn oxalate complex in the aerosol phase previously proposed by Furukawa and Takahashi (2011). We found that many other dicarboxylic acids were also highly correlated with Zn in the summer Chinese urban aerosol samples, suggesting that they may also form stable organic complexes with Zn. Such formation may have profound implications for the atmospheric abundance and hygroscopic properties of aerosol dicarboxylic acids.

  10. Genome-wide analysis of the potato Hsp20 gene family: identification, genomic organization and expression profiles in response to heat stress.

    Science.gov (United States)

    Zhao, Peng; Wang, Dongdong; Wang, Ruoqiu; Kong, Nana; Zhang, Chao; Yang, Chenghui; Wu, Wentao; Ma, Haoli; Chen, Qin

    2018-01-18

    Heat shock proteins (Hsps) are essential components in plant tolerance mechanism under various abiotic stresses. Hsp20 is the major family of heat shock proteins, but little of Hsp20 family is known in potato (Solanum tuberosum), which is an important vegetable crop that is thermosensitive. To reveal the mechanisms of potato Hsp20s coping with abiotic stresses, analyses of the potato Hsp20 gene family were conducted using bioinformatics-based methods. In total, 48 putative potato Hsp20 genes (StHsp20s) were identified and named according to their chromosomal locations. A sequence analysis revealed that most StHsp20 genes (89.6%) possessed no, or only one, intron. A phylogenetic analysis indicated that all of the StHsp20 genes, except 10, were grouped into 12 subfamilies. The 48 StHsp20 genes were randomly distributed on 12 chromosomes. Nineteen tandem duplicated StHsp20s and one pair of segmental duplicated genes (StHsp20-15 and StHsp20-48) were identified. A cis-element analysis inferred that StHsp20s, except for StHsp20-41, possessed at least one stress response cis-element. A heatmap of the StHsp20 gene family showed that the genes, except for StHsp20-2 and StHsp20-45, were expressed in various tissues and organs. Real-time quantitative PCR was used to detect the expression level of StHsp20 genes and demonstrated that the genes responded to multiple abiotic stresses, such as heat, salt or drought stress. The relative expression levels of 14 StHsp20 genes (StHsp20-4, 6, 7, 9, 20, 21, 33, 34, 35, 37, 41, 43, 44 and 46) were significantly up-regulated (more than 100-fold) under heat stress. These results provide valuable information for clarifying the evolutionary relationship of the StHsp20 family and in aiding functional characterization of StHsp20 genes in further research.

  11. Detecting small-scale spatial differences and temporal dynamics of soil organic carbon (SOC) stocks: a comparison between automatic chamber-derived C budgets and repeated soil inventories

    Science.gov (United States)

    Hoffmann, Mathias; Jurisch, Nicole; Garcia Alba, Juana; Albiac Borraz, Elisa; Schmidt, Marten; Huth, Vytas; Rogasik, Helmut; Rieckh, Helene; Verch, Gernot; Sommer, Michael; Augustin, Jürgen

    2017-04-01

    Carbon (C) sequestration in soils plays a key role in the global C cycle. It is therefore crucial to adequately monitor dynamics in soil organic carbon (ΔSOC) stocks when aiming to reveal underlying processes and potential drivers. However, small-scale spatial and temporal changes in SOC stocks, particularly pronounced on arable lands, are hard to assess. The main reasons for this are limitations of the well-established methods. On the one hand, repeated soil inventories, often used in long-term field trials, reveal spatial patterns and trends in ΔSOC but require a longer observation period and a sufficient number of repetitions. On the other hand, eddy covariance measurements of C fluxes towards a complete C budget of the soil-plant-atmosphere system may help to obtain temporal ΔSOC patterns but lack small-scale spatial resolution. To overcome these limitations, this study presents a reliable method to detect both short-term temporal as well as small-scale spatial dynamics of ΔSOC. Therefore, a combination of automatic chamber (AC) measurements of CO2 exchange and empirically modeled aboveground biomass development (NPPshoot) was used. To verify our method, results were compared with ΔSOC observed by soil resampling. AC measurements were performed from 2010 to 2014 under a silage maize/winter fodder rye/sorghum-Sudan grass hybrid/alfalfa crop rotation at a colluvial depression located in the hummocky ground moraine landscape of NE Germany. Widespread in large areas of the formerly glaciated Northern Hemisphere, this depression type is characterized by a variable groundwater level (GWL) and pronounced small-scale spatial heterogeneity in soil properties, such as SOC and nitrogen (Nt). After monitoring the initial stage during 2010, soil erosion was experimentally simulated by incorporating topsoil material from an eroded midslope soil into the plough layer of the colluvial depression. SOC stocks were quantified before and after soil manipulation and at the end

  12. Detecting small-scale spatial heterogeneity and temporal dynamics of soil organic carbon (SOC) stocks: a comparison between automatic chamber-derived C budgets and repeated soil inventories

    Science.gov (United States)

    Hoffmann, Mathias; Jurisch, Nicole; Garcia Alba, Juana; Albiac Borraz, Elisa; Schmidt, Marten; Huth, Vytas; Rogasik, Helmut; Rieckh, Helene; Verch, Gernot; Sommer, Michael; Augustin, Jürgen

    2017-03-01

    Carbon (C) sequestration in soils plays a key role in the global C cycle. It is therefore crucial to adequately monitor dynamics in soil organic carbon (ΔSOC) stocks when aiming to reveal underlying processes and potential drivers. However, small-scale spatial (10-30 m) and temporal changes in SOC stocks, particularly pronounced in arable lands, are hard to assess. The main reasons for this are limitations of the well-established methods. On the one hand, repeated soil inventories, often used in long-term field trials, reveal spatial patterns and trends in ΔSOC but require a longer observation period and a sufficient number of repetitions. On the other hand, eddy covariance measurements of C fluxes towards a complete C budget of the soil-plant-atmosphere system may help to obtain temporal ΔSOC patterns but lack small-scale spatial resolution. To overcome these limitations, this study presents a reliable method to detect both short-term temporal dynamics as well as small-scale spatial differences of ΔSOC using measurements of the net ecosystem carbon balance (NECB) as a proxy. To estimate the NECB, a combination of automatic chamber (AC) measurements of CO2 exchange and empirically modeled aboveground biomass development (NPPshoot) were used. To verify our method, results were compared with ΔSOC observed by soil resampling. Soil resampling and AC measurements were performed from 2010 to 2014 at a colluvial depression located in the hummocky ground moraine landscape of northeastern Germany. The measurement site is characterized by a variable groundwater level (GWL) and pronounced small-scale spatial heterogeneity regarding SOC and nitrogen (Nt) stocks. Tendencies and magnitude of ΔSOC values derived by AC measurements and repeated soil inventories corresponded well. The period of maximum plant growth was identified as being most important for the development of spatial differences in annual ΔSOC. Hence, we were able to confirm that AC-based C budgets are able

  13. Organization dependent collective magnetic properties of secondary nanostructures with differential spatial ordering and magnetic easy axis orientation

    Energy Technology Data Exchange (ETDEWEB)

    Saikia, K. [Department of Physics, Tezpur University (Central University), Tezpur 784028 (India); Sarma, D.D. [Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012 (India); Deb, P., E-mail: pdeb@tezu.ernet.in [Department of Physics, Tezpur University (Central University), Tezpur 784028 (India)

    2016-06-15

    Achieving control on the formation of different organization states of magnetic nanoparticles is crucial to harness their organization dependent physical properties in desired ways. In this study, three organization states of iron oxide nanoparticles (γ-Fe{sub 2}O{sub 3}), defining as (i) assembly (ii) network aggregate and (iii) cluster, have been developed by simply changing the solvent evaporation conditions. All three systems have retained the same phase and polydispersity of primary particles. Magnetic measurements show that the partial alignment of the easy axes of the particles in the network system due to the stacking aggregation morphology can result in significant enhancement of the coercivity and remanence values, while the opposite is obtained for the cluster system due to the random orientation of easy axes. Partial alignment in the aggregate system also results in noticeable non-monotonic field dependence of ZFC peak temperature (T{sub peak}). The lowest value of the blocking temperature (T{sub B}) for the cluster system is related to the lowering of the effective anisotropy due to the strongest demagnetizing effect. FC (Field cooled) memory effect was observed to be decreasing with the increasing strength of dipolar interaction of organization states. Therefore, the stacking aggregation and the cluster formation are two interesting ways of magnetic nanoparticles organization for modulating collective magnetic properties significantly, which can have renewed application potentials from recording devices to biomedicine. - Highlights: • Three organization states of magnetic nanoparticles were developed. • Aggregation enhances the H{sub c} and M{sub r}/M{sub s,} while spherical clustering shows opposite. • Organization morphology hardly effects on FC memory effect. • Developed secondary systems can have renewed application potentials in wide spectrum.

  14. An original SERPINA3 gene cluster: Elucidation of genomic organization and gene expression in the Bos taurus 21q24 region

    Directory of Open Access Journals (Sweden)

    Ouali Ahmed

    2008-04-01

    Full Text Available Abstract Background The superfamily of serine proteinase inhibitors (serpins is involved in numerous fundamental biological processes as inflammation, blood coagulation and apoptosis. Our interest is focused on the SERPINA3 sub-family. The major human plasma protease inhibitor, α1-antichymotrypsin, encoded by the SERPINA3 gene, is homologous to genes organized in clusters in several mammalian species. However, although there is a similar genic organization with a high degree of sequence conservation, the reactive-centre-loop domains, which are responsible for the protease specificity, show significant divergences. Results We provide additional information by analyzing the situation of SERPINA3 in the bovine genome. A cluster of eight genes and one pseudogene sharing a high degree of identity and the same structural organization was characterized. Bovine SERPINA3 genes were localized by radiation hybrid mapping on 21q24 and only spanned over 235 Kilobases. For all these genes, we propose a new nomenclature from SERPINA3-1 to SERPINA3-8. They share approximately 70% of identity with the human SERPINA3 homologue. In the cluster, we described an original sub-group of six members with an unexpected high degree of conservation for the reactive-centre-loop domain, suggesting a similar peptidase inhibitory pattern. Preliminary expression analyses of these bovSERPINA3s showed different tissue-specific patterns and diverse states of glycosylation and phosphorylation. Finally, in the context of phylogenetic analyses, we improved our knowledge on mammalian SERPINAs evolution. Conclusion Our experimental results update data of the bovine genome sequencing, substantially increase the bovSERPINA3 sub-family and enrich the phylogenetic tree of serpins. We provide new opportunities for future investigations to approach the biological functions of this unusual subset of serine proteinase inhibitors.

  15. Human genome I

    International Nuclear Information System (INIS)

    Anon.

    1989-01-01

    An international conference, Human Genome I, was held Oct. 2-4, 1989 in San Diego, Calif. Selected speakers discussed: Current Status of the Genome Project; Technique Innovations; Interesting regions; Applications; and Organization - Different Views of Current and Future Science and Procedures. Posters, consisting of 119 presentations, were displayed during the sessions. 119 were indexed for inclusion to the Energy Data Base

  16. Black Carbon, Dust and Organic Matter at South Cascade Glacier in Washington State, USA: A Comprehensive Characterization of Temporal (1865-2014) and Spatial Variability

    Science.gov (United States)

    Kaspari, S.; Pittenger, D.; Swick, M.; Skiles, M.; Perez, A.; Sethi, H.; Sevier, E.

    2017-12-01

    Rising temperatures are a widely recognized cause of glacial retreat in Washington, however light absorbing aerosols (LAA, including black carbon (BC), dust and organic matter) can also contribute to increased melt by reducing snow albedo. We present updated results of BC and dust variability at South Cascade (SOCAS) glacier spanning 1865-1994 using a 158 m ice core. Peak BC deposition occurred between 1940-1958, when median BC concentrations were 25 times higher than background levels. Post 1958 BC concentrations decrease, followed by an increase post 1980 associated with melt consolidation and/or trans-Pacific aerosol transport. Dust deposition at SOCAS is dominated by local sources. Albedo reductions from LAA are dominated by dust deposition, except during high BC deposition events from wildfires, and during the 1940-1958 period when BC contributes equally to albedo reductions. Results from a 2014 field campaign that included collection of 3 shallow ice cores, surface snow, and snow albedo measurements allow the 1865-1994 ice core record to be extended toward present, and spatial variability in LAA to be characterized. Snow albedo transects were measured using a spectrometer. BC concentrations were measured using a Single Particle Soot Photometer (SP2). Gravimetric filtration was used to determine the total LAA, and a thermal gravimetric technique was used to partition the LAA between dust and organic matter. The organic matter was partitioned into organic and elemental carbon using a thermal optical method. These methods allow LAA abundances be measured, but to partition the contribution of the LAA to albedo reductions requires characterization of LAA optical properties. This was accomplished using a Hyperspectral Imaging Microscope Spectrometer method that allows particle reflectance to be measured at 138 nm2 pixel resolution. By combining these methods, we provide a comprehensive characterization of spatial and temporal LAA variability at SOCAS.

  17. Spatial distribution of soils determines export of nitrogen and dissolved organic carbon from an intensively managed agricultural landscape

    DEFF Research Database (Denmark)

    Wohlfart, T; Exbrayat, J-F; Schelde, Kirsten

    2012-01-01

    nitrogen (TDN), nitrate (NO3−), ammonium nitrogen and dissolved organic carbon (DOC) concentrations were measured, and dissolved organic nitrogen (DON) was calculated for each grabbed sample. Electrical conductivity, pH and flow velocity were measured during sampling. Statistical analyses showed...... significant differences between the northern, southern and converged stream parts, especially for NO3− concentrations with average values between 1.4 mg N l−1 and 9.6 mg N l−1. Furthermore, throughout the sampling period DON concentrations increased to 2.8 mg N l−1 in the northern stream contributing up to 81...

  18. A Comprehensive Analysis of the Phylogeny, Genomic Organization and Expression of Immunoglobulin Light Chain Genes in Alligator sinensis, an Endangered Reptile Species

    Science.gov (United States)

    Lu, Yan; Zhang, Chenglin; Wu, Xiaobing; Han, Haitang; Zhao, Yaofeng; Ren, Liming

    2016-01-01

    Crocodilians are evolutionarily distinct reptiles that are distantly related to lizards and are thought to be the closest relatives of birds. Compared with birds and mammals, few studies have investigated the Ig light chain of crocodilians. Here, employing an Alligator sinensis genomic bacterial artificial chromosome (BAC) library and available genome data, we characterized the genomic organization of the Alligator sinensis IgL gene loci. The Alligator sinensis has two IgL isotypes, λ and κ, the same as Anolis carolinensis. The Igλ locus contains 6 Cλ genes, each preceded by a Jλ gene, and 86 potentially functional Vλ genes upstream of (Jλ-Cλ)n. The Igκ locus contains a single Cκ gene, 6 Jκs and 62 functional Vκs. All VL genes are classified into a total of 31 families: 19 Vλ families and 12 Vκ families. Based on an analysis of the chromosomal location of the light chain genes among mammals, birds, lizards and frogs, the data further confirm that there are two IgL isotypes in the Alligator sinensis: Igλ and Igκ. By analyzing the cloned Igλ/κ cDNA, we identified a biased usage pattern of V families in the expressed Vλ and Vκ. An analysis of the junctions of the recombined VJ revealed the presence of N and P nucleotides in both expressed λ and κ sequences. Phylogenetic analysis of the V genes revealed V families shared by mammals, birds, reptiles and Xenopus, suggesting that these conserved V families are orthologous and have been retained during the evolution of IgL. Our data suggest that the Alligator sinensis IgL gene repertoire is highly diverse and complex and provide insight into immunoglobulin gene evolution in vertebrates. PMID:26901135

  19. A Comprehensive Analysis of the Phylogeny, Genomic Organization and Expression of Immunoglobulin Light Chain Genes in Alligator sinensis, an Endangered Reptile Species.

    Directory of Open Access Journals (Sweden)

    Xifeng Wang

    Full Text Available Crocodilians are evolutionarily distinct reptiles that are distantly related to lizards and are thought to be the closest relatives of birds. Compared with birds and mammals, few studies have investigated the Ig light chain of crocodilians. Here, employing an Alligator sinensis genomic bacterial artificial chromosome (BAC library and available genome data, we characterized the genomic organization of the Alligator sinensis IgL gene loci. The Alligator sinensis has two IgL isotypes, λ and κ, the same as Anolis carolinensis. The Igλ locus contains 6 Cλ genes, each preceded by a Jλ gene, and 86 potentially functional Vλ genes upstream of (Jλ-Cλn. The Igκ locus contains a single Cκ gene, 6 Jκs and 62 functional Vκs. All VL genes are classified into a total of 31 families: 19 Vλ families and 12 Vκ families. Based on an analysis of the chromosomal location of the light chain genes among mammals, birds, lizards and frogs, the data further confirm that there are two IgL isotypes in the Alligator sinensis: Igλ and Igκ. By analyzing the cloned Igλ/κ cDNA, we identified a biased usage pattern of V families in the expressed Vλ and Vκ. An analysis of the junctions of the recombined VJ revealed the presence of N and P nucleotides in both expressed λ and κ sequences. Phylogenetic analysis of the V genes revealed V families shared by mammals, birds, reptiles and Xenopus, suggesting that these conserved V families are orthologous and have been retained during the evolution of IgL. Our data suggest that the Alligator sinensis IgL gene repertoire is highly diverse and complex and provide insight into immunoglobulin gene evolution in vertebrates.

  20. Spatial variation in diesel-related elemental and organic PM2.5 components during workweek hours across a downtown core.

    Science.gov (United States)

    Tunno, Brett J; Shmool, Jessie L C; Michanowicz, Drew R; Tripathy, Sheila; Chubb, Lauren G; Kinnee, Ellen; Cambal, Leah; Roper, Courtney; Clougherty, Jane E

    2016-12-15

    Capturing intra-urban variation in diesel-related pollution exposures remains a challenge, given its complex chemical mix, and relatively few well-characterized ambient-air tracers for the multiple diesel sources in densely-populated urban areas. To capture fine-scale spatial resolution (50×50m grid cells) in diesel-related pollution, we used geographic information systems (GIS) to systematically allocate 36 sampling sites across downtown Pittsburgh, PA, USA (2.8km 2 ), cross-stratifying to disentangle source impacts (i.e., truck density, bus route frequency, total traffic density). For buses, outbound and inbound trips per week were summed by route and a kernel density was calculated across sites. Programmable monitors collected fine particulate matter (PM 2.5 ) samples specific to workweek hours (Monday-Friday, 7 am-7 pm), summer and winter 2013. Integrated filters were analyzed for black carbon (BC), elemental carbon (EC), organic carbon (OC), elemental constituents, and diesel-related organic compounds [i.e., polycyclic aromatic hydrocarbons (PAHs), hopanes, steranes]. To our knowledge, no studies have collected this suite of pollutants with such high sampling density, with the ability to capture spatial patterns during specific hours of interest. We hypothesized that we would find substantial spatial variation for each pollutant and significant associations with key sources (e.g. diesel and gasoline vehicles), with higher concentrations near the center of this small downtown core. Using a forward stepwise approach, we developed seasonal land use regression (LUR) models for PM 2.5 , BC, total EC, OC, PAHs, hopanes, steranes, aluminum (Al), calcium (Ca), and iron (Fe). Within this small domain, greater concentration differences were observed in most pollutants across sites, on average, than between seasons. Higher PM 2.5 and BC concentrations were found in the downtown core compared to the boundaries. PAHs, hopanes, and steranes displayed different spatial

  1. Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date

    DEFF Research Database (Denmark)

    Leong, Su-lin L.; Lantz, Henrik; Pettersson, Olga V.

    2015-01-01

    -related genes; among these, certain (not all) steps for glycerol synthesis were upregulated. Xeromyces bisporus increased glycerol production during hypo- and hyper-osmotic stress, and much of its wet weight comprised water and rinsable solutes; leaked solutes may form a protective slime. Xeromyces bisporus......Xeromyces bisporus can grow on sugary substrates down to 0.61, an extremely low water activity. Its genome size is approximately 22 Mb. Gene clusters encoding for secondary metabolites were conspicuously absent; secondary metabolites were not detected experimentally. Thus, in its 'dry' but nutrient...... and other food-borne moulds increased membrane fatty acid saturation as water activity decreased. Such modifications did not appear to be transcriptionally regulated in X. bisporus; however, genes modulating sterols, phospholipids and the cell wall were differentially expressed. Xeromyces bisporus...

  2. Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua

    Directory of Open Access Journals (Sweden)

    Mittelholzer Christian

    2009-12-01

    Full Text Available Abstract Background Marine fishes have been shown to display low levels of genetic structuring and associated high levels of gene flow, suggesting shallow evolutionary trajectories and, possibly, limited or lacking adaptive divergence among local populations. We investigated variation in 98 gene-associated single nucleotide polymorphisms (SNPs for evidence of selection in local populations of Atlantic cod (Gadus morhua L. across the species distribution. Results Our global genome scan analysis identified eight outlier gene loci with very high statistical support, likely to be subject to directional selection in local demes, or closely linked to loci under selection. Likewise, on a regional south/north transect of central and eastern Atlantic populations, seven loci displayed strongly elevated levels of genetic differentiation. Selection patterns among populations appeared to be relatively widespread and complex, i.e. outlier loci were generally not only associated with one of a few divergent local populations. Even on a limited geographical scale between the proximate North Sea and Baltic Sea populations four loci displayed evidence of adaptive evolution. Temporal genome scan analysis applied to DNA from archived otoliths from a Faeroese population demonstrated stability of the intra-population variation over 24 years. An exploratory landscape genetic analysis was used to elucidate potential effects of the most likely environmental factors responsible for the signatures of local adaptation. We found that genetic variation at several of the outlier loci was better correlated with temperature and/or salinity conditions at spawning grounds at spawning time than with geographic distance per se. Conclusion These findings illustrate that adaptive population divergence may indeed be prevalent despite seemingly high levels of gene flow, as found in most marine fishes. Thus, results have important implications for our understanding of the interplay of

  3. Nano-Sized Secondary Organic Aerosol of Diesel Engine Exhaust Origin Impairs Olfactory-Based Spatial Learning Performance in Preweaning Mice

    Directory of Open Access Journals (Sweden)

    Tin-Tin Win-Shwe

    2015-06-01

    Full Text Available The aims of our present study were to establish a novel olfactory-based spatial learning test and to examine the effects of exposure to nano-sized diesel exhaust-origin secondary organic aerosol (SOA, a model environmental pollutant, on the learning performance in preweaning mice. Pregnant BALB/c mice were exposed to clean air, diesel exhaust (DE, or DE-origin SOA (DE-SOA from gestational day 14 to postnatal day (PND 10 in exposure chambers. On PND 11, the preweaning mice were examined by the olfactory-based spatial learning test. After completion of the spatial learning test, the hippocampus from each mouse was removed and examined for the expressions of neurological and immunological markers using real-time RT-PCR. In the test phase of the study, the mice exposed to DE or DE-SOA took a longer time to reach the target as compared to the control mice. The expression levels of neurological markers such as the N-methyl-d-aspartate (NMDA receptor subunits NR1 and NR2B, and of immunological markers such as TNF-α, COX2, and Iba1 were significantly increased in the hippocampi of the DE-SOA-exposed preweaning mice as compared to the control mice. Our results indicate that DE-SOA exposure in utero and in the neonatal period may affect the olfactory-based spatial learning behavior in preweaning mice by modulating the expressions of memory function–related pathway genes and inflammatory markers in the hippocampus.

  4. Analysis of the Spatial Organization of Pastures as a Contact Network, Implications for Potential Disease Spread and Biosecurity in Livestock, France, 2010.

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    Aurore Palisson

    Full Text Available The use of pastures is part of common herd management practices for livestock animals, but contagion between animals located on neighbouring pastures is one of the major modes of infectious disease transmission between herds. At the population level, this transmission is strongly constrained by the spatial organization of pastures. The aim of this study was to answer two questions: (i is the spatial configuration of pastures favourable to the spread of infectious diseases in France? (ii would biosecurity measures allow decreasing this vulnerability? Based on GIS data, the spatial organization of pastures was represented using networks. Nodes were the 3,159,787 pastures reported in 2010 by the French breeders to claim the Common Agricultural Policy subsidies. Links connected pastures when the distance between them was below a predefined threshold. Premises networks were obtained by aggregating into a single node all the pastures under the same ownership. Although the pastures network was very fragmented when the distance threshold was short (1.5 meters, relevant for a directly-transmitted disease, it was not the case when the distance threshold was larger (500 m, relevant for a vector-borne disease: 97% of the nodes in the largest connected component. The premises network was highly connected as the largest connected component always included more than 83% of the nodes, whatever the distance threshold. Percolation analyses were performed to model the population-level efficacy of biosecurity measures. Percolation thresholds varied according to the modelled biosecurity measures and to the distance threshold. They were globally high (e.g. >17% of nodes had to be removed, mimicking the confinement of animals inside farm buildings, to obtain the disappearance of the large connected component. The network of pastures thus appeared vulnerable to the spread of diseases in France. Only a large acceptance of biosecurity measures by breeders would allow

  5. Protein Interaction Analysis Provides a Map of the Spatial and Temporal Organization of the Ciliary Gating Zone.

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    Takao, Daisuke; Wang, Liang; Boss, Allison; Verhey, Kristen J

    2017-08-07

    The motility and signaling functions of the primary cilium require a unique protein and lipid composition that is determined by gating mechanisms localized at the base of the cilium. Several protein complexes localize to the gating zone and may regulate ciliary protein composition; however, the mechanisms of ciliary gating and the dynamics of the gating components are largely unknown. Here, we used the BiFC (bimolecular fluorescence complementation) assay and report for the first time on the protein-protein interactions that occur between ciliary gating components and transiting cargoes during ciliary entry. We find that the nucleoporin Nup62 and the C termini of the nephronophthisis (NPHP) proteins NPHP4 and NPHP5 interact with the axoneme-associated kinesin-2 motor KIF17 and thus spatially map to the inner region of the ciliary gating zone. Nup62 and NPHP4 exhibit rapid turnover at the transition zone and thus define dynamic components of the gate. We find that B9D1, AHI1, and the N termini of NPHP4 and NPHP5 interact with the transmembrane protein SSTR3 and thus spatially map to the outer region of the ciliary gating zone. B9D1, AHI1, and NPHP5 exhibit little to no turnover at the transition zone and thus define components of a stable gating structure. These data provide the first comprehensive map of the molecular orientations of gating zone components along the inner-to-outer axis of the ciliary gating zone. These results advance our understanding of the functional roles of gating zone components in regulating ciliary protein composition. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Process Inference from High Frequency Temporal Variations in Dissolved Organic Carbon (DOC) Dynamics Across Nested Spatial Scales

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    Tunaley, C.; Tetzlaff, D.; Lessels, J. S.; Soulsby, C.

    2014-12-01

    In order to understand aquatic ecosystem functioning it is critical to understand the processes that control the spatial and temporal variations in DOC. DOC concentrations are highly dynamic, however, our understanding at short, high frequency timescales is still limited. Optical sensors which act as a proxy for DOC provide the opportunity to investigate near-continuous DOC variations in order to understand the hydrological and biogeochemical processes that control concentrations at short temporal scales. Here we present inferred 15 minute stream water DOC data for a 12 month period at three nested scales (1km2, 3km2 and 31km2) for the Bruntland Burn, a headwater catchment in NE Scotland. High frequency data were measured using FDOM and CDOM probes which work by measuring the fluorescent component and coloured component, respectively, of DOC when exposed to ultraviolet light. Both FDOM and CDOM were strongly correlated (r2 >0.8) with DOC allowing high frequency estimations. Results show the close coupling of DOC with discharge throughout the sampling period at all three spatial scales. However, analysis at the event scale highlights anticlockwise hysteresis relationships between DOC and discharge due to the delay in DOC being flushed from the increasingly large areas of peaty soils as saturation zones expand and increase hydrological connectivity. Lag times vary between events dependent on antecedent conditions. During a 10 year drought period in late summer 2013 it was apparent that very small changes in discharge on a 15 minute timescale result in high increases in DOC. This suggests transport limitation during this period where DOC builds up in the soil and is not flushed regularly, therefore any subsequent increase in discharge results in large DOC peaks. The high frequency sensors also reveal diurnal variability during summer months related to the photo-oxidation, evaporative and biological influences of DOC during the day. This relationship is less

  7. Producing genome structure populations with the dynamic and automated PGS software.

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    Hua, Nan; Tjong, Harianto; Shin, Hanjun; Gong, Ke; Zhou, Xianghong Jasmine; Alber, Frank

    2018-05-01

    Chromosome conformation capture technologies such as Hi-C are widely used to investigate the spatial organization of genomes. Because genome structures can vary considerably between individual cells of a population, interpreting ensemble-averaged Hi-C data can be challenging, in particular for long-range and interchromosomal interactions. We pioneered a probabilistic approach for the generation of a population of distinct diploid 3D genome structures consistent with all the chromatin-chromatin interaction probabilities from Hi-C experiments. Each structure in the population is a physical model of the genome in 3D. Analysis of these models yields new insights into the causes and the functional properties of the genome's organization in space and time. We provide a user-friendly software package, called PGS, which runs on local machines (for practice runs) and high-performance computing platforms. PGS takes a genome-wide Hi-C contact frequency matrix, along with information about genome segmentation, and produces an ensemble of 3D genome structures entirely consistent with the input. The software automatically generates an analysis report, and provides tools to extract and analyze the 3D coordinates of specific domains. Basic Linux command-line knowledge is sufficient for using this software. A typical running time of the pipeline is ∼3 d with 300 cores on a computer cluster to generate a population of 1,000 diploid genome structures at topological-associated domain (TAD)-level resolution.

  8. Genome Writing: Current Progress and Related Applications

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    Yueqiang Wang

    2018-02-01

    Full Text Available The ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic writing technologies are required to build such an artificial genome. Recently, the partially-completed synthetic yeast genome project represents a milestone in this field. In this mini review, we briefly introduce the techniques for de novo genome synthesis and genome editing. Furthermore, we summarize recent research progresses and highlight several applications in the synthetic genome field. Finally, we discuss current challenges and future prospects. Keywords: Synthetic biology, Genome writing, Genome editing, Bioethics, Biosafety

  9. Evaluation of pond lands utilization and study of organic matter spatial distribution of Vanname shrimp (Litopenaeus vannamei aquaculture in the coastal area of Lamongan Regency

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    Insani L.

    2018-04-01

    Full Text Available Coastal areas have a wide range of resources that can be utilized in multiple ways. Land utilization of coastal areas has been done for various interests, one of which is for shrimp aquaculture (farming. Continuous shrimp farming activities will lead to environmental degradation, characterized by decreased water quality. Besides, the area or spatial arrangement of shrimp aquaculture development that does not pay attention to the environmental carrying capacity due to improper management can cause environmental problems with all aspects of its complications in a long period of time, one of which is the problem emerging from shrimp farming with the use of intensive technology. Intensive shrimp farming can produce organic wastes, primarily from the residual feed, feces, and dissolved matters discharged into waters that significantly affect the quality of the coastal environment. This study aimed to determine the distribution pattern of organic matters resulted from Vanname shrimp (Litopenaeus vannamei aquaculture in the coastal area of Lamongan Regency. This study was conducted from January to March 2018. The study used a descriptive method with Geographical Information System (GIS approach. The spatial distribution analysis of organic materials was carried out using geostatistical analysis, by interpolating point data into areas (polygons using IDW method. The interpolation results of each water quality of the ponds, river, and coastal waters were arranged in the form of thematic maps. The value pollution load index (PLI value of the shrimp farming activities was determined based on six main indicators, namely dissolved oxygen, BOD5, TOM, Ammonia, Nitrate, and Phosphate. Based on the results obtained, the highest spatial distribution value of organic matters was showed by the BOD parameter of 3.12 mg/l – 3.25 mg/l, included in the medium-polluted category. Meanwhile, the measurement result of the phosphate content as an indicator of water

  10. Spatial networks

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    Barthélemy, Marc

    2011-02-01

    Complex systems are very often organized under the form of networks where nodes and edges are embedded in space. Transportation and mobility networks, Internet, mobile phone networks, power grids, social and contact networks, and neural networks, are all examples where space is relevant and where topology alone does not contain all the information. Characterizing and understanding the structure and the evolution of spatial networks is thus crucial for many different fields, ranging from urbanism to epidemiology. An important consequence of space on networks is that there is a cost associated with the length of edges which in turn has dramatic effects on the topological structure of these networks. We will thoroughly explain the current state of our understanding of how the spatial constraints affect the structure and properties of these networks. We will review the most recent empirical observations and the most important models of spatial networks. We will also discuss various processes which take place on these spatial networks, such as phase transitions, random walks, synchronization, navigation, resilience, and disease spread.

  11. Genomic and in Situ Analyses Reveal the Micropruina spp. as Abundant Fermentative Glycogen Accumulating Organisms in Enhanced Biological Phosphorus Removal Systems

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    Simon J. McIlroy

    2018-05-01

    Full Text Available Enhanced biological phosphorus removal (EBPR involves the cycling of biomass through carbon-rich (feast and carbon-deficient (famine conditions, promoting the activity of polyphosphate accumulating organisms (PAOs. However, several alternate metabolic strategies, without polyphosphate storage, are possessed by other organisms, which can compete with the PAO for carbon at the potential expense of EBPR efficiency. The most studied are the glycogen accumulating organisms (GAOs, which utilize aerobically stored glycogen to energize anaerobic substrate uptake and storage. In full-scale systems the Micropruina spp. are among the most abundant of the proposed GAO, yet little is known about their ecophysiology. In the current study, genomic and metabolomic studies were performed on Micropruina glycogenica str. Lg2T and compared to the in situ physiology of members of the genus in EBPR plants using state-of-the-art single cell techniques. The Micropruina spp. were observed to take up carbon, including sugars and amino acids, under anaerobic conditions, which were partly fermented to lactic acid, acetate, propionate, and ethanol, and partly stored as glycogen for potential aerobic use. Fermentation was not directly demonstrated for the abundant members of the genus in situ, but was strongly supported by the confirmation of anaerobic uptake of carbon and glycogen storage in the absence of