WorldWideScience

Sample records for genome spatial organization

  1. Understanding Spatial Genome Organization: Methods and Insights

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    Vijay Ramani

    2016-02-01

    Full Text Available The manner by which eukaryotic genomes are packaged into nuclei while maintaining crucial nuclear functions remains one of the fundamental mysteries in biology. Over the last ten years, we have witnessed rapid advances in both microscopic and nucleic acid-based approaches to map genome architecture, and the application of these approaches to the dissection of higher-order chromosomal structures has yielded much new information. It is becoming increasingly clear, for example, that interphase chromosomes form stable, multilevel hierarchical structures. Among them, self-associating domains like so-called topologically associating domains (TADs appear to be building blocks for large-scale genomic organization. This review describes features of these broadly-defined hierarchical structures, insights into the mechanisms underlying their formation, our current understanding of how interactions in the nuclear space are linked to gene regulation, and important future directions for the field.

  2. Determining spatial chromatin organization of large genomic regions using 5C technology.

    Science.gov (United States)

    van Berkum, Nynke L; Dekker, Job

    2009-01-01

    Spatial organization of chromatin plays an important role at multiple levels of genome regulation. On a global scale, its function is evident in processes like metaphase and chromosome segregation. On a detailed level, long-range interactions between regulatory elements and promoters are essential for proper gene regulation. Microscopic techniques like FISH can detect chromatin contacts, although the resolution is generally low making detection of enhancer-promoter interaction difficult. The 3C methodology allows for high-resolution analysis of chromatin interactions. 3C is now widely used and has revealed that long-range looping interactions between genomic elements are widespread. However, studying chromatin interactions in large genomic regions by 3C is very labor intensive. This limitation is overcome by the 5C technology. 5C is an adaptation of 3C, in which the concurrent use of thousands of primers permits the simultaneous detection of millions of chromatin contacts. The design of the 5C primers is critical because this will determine which and how many chromatin interactions will be examined in the assay. Starting material for 5C is a 3C template. To make a 3C template, chromatin interactions in living cells are cross-linked using formaldehyde. Next, chromatin is digested and subsequently ligated under conditions favoring ligation events between cross-linked fragments. This yields a genome-wide 3C library of ligation products representing all chromatin interactions in vivo. 5C then employs multiplex ligation-mediated amplification to detect, in a single assay, up to millions of unique ligation products present in the 3C library. The resulting 5C library can be analyzed by microarray analysis or deep sequencing. The observed abundance of a 5C product is a measure of the interaction frequency between the two corresponding chromatin fragments. The power of the 5C technique described in this chapter is the high-throughput, high-resolution, and quantitative way

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

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    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.

  4. Creating spatial organizations

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    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

  5. Spatial organization of drumlins

    DEFF Research Database (Denmark)

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

    2017-01-01

    of drumlins in order to provide an improved description of the phenomenon and to guide hypotheses of their formation. We review the literature highlighting contradictory findings regarding drumlin spatial organization and then use this to motivate our study based on a large sample (42 488) of drumlins from...

  6. 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.

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

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    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. Gender Structure and Spatial Organization

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    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.

  9. Genomic Organization of Leishmania Species

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    B Kazemi

    2011-09-01

    Full Text Available Leishmania is a protozoan parasite belonging to the family Trypanosomatidae, which is found among 88 different countries. The parasite lives as an amastigote in vertebrate macro­phages and as a promastigote in the digestive tract of sand fly. It can be cultured in the laboratory us­ing appropriate culture media. Although the sexual cycle of Leishmania has not been observed during the promastigote and amastigote stages, it has been reported by some researchers. Leishma­nia has eukaryotic cell organization. Cell culture is convenient and cost effective, and because posttranslational modifications are common processes in the cultured cells, the cells are used as hosts for preparing eukaryotic recombinant proteins for research. Several transcripts of rDNA in the Leishmania genome are suitable regions for conducting gene transfer. Old World Leishmania spp. has 36 chromosomes, while New World Leishmania spp. has 34 or 35 chromo­somes. The genomic organization and parasitic characteristics have been investigated. Leishmania spp. has a unique genomic organization among eukaryotes; the genes do not have introns, and the chromosomes are smaller with larger numbers of genes confined to a smaller space within the nucleus. Leishmania spp. genes are organized on one or both DNA strands and are transcribed as polycistronic (prokaryotic-like transcripts from undefined promoters. Regulation of gene expres­sion in the members of Trypanosomatidae differs from that in other eukaryotes. The trans-splic­ing phenomenon is a necessary step for mRNA processing in lower eukaryotes and is observed in Leishmania spp. Another particular feature of RNA editing in Leishmania spp. is that mitochon­drial genes encoding respiratory enzymes are edited and transcribed. This review will discuss the chromosomal and mitochondrial (kinetoplast genomes of Leishmania spp. as well as the phenome­non of RNA editing in the kinetoplast genome.

  10. Reconstructing spatial organizations of chromosomes through manifold learning.

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    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. The spatial industrial organization of innovation

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    Bruijn, P.J.M. de

    2010-01-01

    This study offers insight in spatial dimensions of innovation. It combines insights gained from economic geography (territorial innovation models and the geography of innovation), industrial organization (transaction cost economics and the competence-based approach) and international business

  12. Genome Organization Drives Chromosome Fragility.

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    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. Bacterial genomes: habitat specificity and uncharted organisms.

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    Dini-Andreote, Francisco; Andreote, Fernando Dini; Araújo, Welington Luiz; Trevors, Jack T; van Elsas, Jan Dirk

    2012-07-01

    The capability and speed in generating genomic data have increased profoundly since the release of the draft human genome in 2000. Additionally, sequencing costs have continued to plummet as the next generation of highly efficient sequencing technologies (next-generation sequencing) became available and commercial facilities promote market competition. However, new challenges have emerged as researchers attempt to efficiently process the massive amounts of sequence data being generated. First, the described genome sequences are unequally distributed among the branches of bacterial life and, second, bacterial pan-genomes are often not considered when setting aims for sequencing projects. Here, we propose that scientists should be concerned with attaining an improved equal representation of most of the bacterial tree of life organisms, at the genomic level. Moreover, they should take into account the natural variation that is often observed within bacterial species and the role of the often changing surrounding environment and natural selection pressures, which is central to bacterial speciation and genome evolution. Not only will such efforts contribute to our overall understanding of the microbial diversity extant in ecosystems as well as the structuring of the extant genomes, but they will also facilitate the development of better methods for (meta)genome annotation.

  14. Genome sequencing and population genomics in non-model organisms.

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    Ellegren, Hans

    2014-01-01

    High-throughput sequencing technologies are revolutionizing the life sciences. The past 12 months have seen a burst of genome sequences from non-model organisms, in each case representing a fundamental source of data of significant importance to biological research. This has bearing on several aspects of evolutionary biology, and we are now beginning to see patterns emerging from these studies. These include significant heterogeneity in the rate of recombination that affects adaptive evolution and base composition, the role of population size in adaptive evolution, and the importance of expansion of gene families in lineage-specific adaptation. Moreover, resequencing of population samples (population genomics) has enabled the identification of the genetic basis of critical phenotypes and cast light on the landscape of genomic divergence during speciation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. 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.

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

    Indian Academy of Sciences (India)

    48

    specifically appears at the stationary phase when the genome should be organized into a compact structure to ensure that most of the genes are shut down whereas the DNA bending proteins are predominant in the early and late exponential phase to facilitate the recruitment of transcription machineries to complete the life ...

  17. Ancestral genome organization: an alignment approach.

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    Holloway, Patrick; Swenson, Krister; Ardell, David; El-Mabrouk, Nadia

    2013-04-01

    We present a comparative genomics approach for inferring ancestral genome organization and evolutionary scenarios, based on present-day genomes represented as ordered gene sequences with duplicates. We develop our methodology for a model of evolution restricted to duplication and loss, and then show how to extend it to other content-modifying operations, and to inversions. From a combinatorial point of view, the main consequence of ignoring rearrangements is the possibility of formulating the problem as an alignment problem. On the other hand, duplications and losses are asymmetric operations that are applicable to one of the two aligned sequences. Consequently, an ancestral genome can directly be inferred from a duplication-loss scenario attached to a given alignment. Although alignments are a priori simpler to handle than rearrangements, we show that a direct approach based on dynamic programming leads, at best, to an efficient heuristic. We present an exact pseudo-boolean linear programming algorithm to search for the optimal alignment along with an optimal scenario of duplications and losses. Although exponential in the worst case, we show low running times on real datasets as well as synthetic data. We apply our algorithm (*) in a phylogenetic context to the evolution of stable RNA (tRNA and rRNA) gene content and organization in Bacillus genomes. Our results lead to various biological insights, such as rates of ribosomal RNA proliferation among lineages, their role in altering tRNA gene content, and evidence of tRNA class conversion.

  18. Improving Genomic Prediction in Cassava Field Experiments Using Spatial Analysis

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    Ani A. Elias

    2018-01-01

    Full Text Available Cassava (Manihot esculenta Crantz is an important staple food in sub-Saharan Africa. Breeding experiments were conducted at the International Institute of Tropical Agriculture in cassava to select elite parents. Taking into account the heterogeneity in the field while evaluating these trials can increase the accuracy in estimation of breeding values. We used an exploratory approach using the parametric spatial kernels Power, Spherical, and Gaussian to determine the best kernel for a given scenario. The spatial kernel was fit simultaneously with a genomic kernel in a genomic selection model. Predictability of these models was tested through a 10-fold cross-validation method repeated five times. The best model was chosen as the one with the lowest prediction root mean squared error compared to that of the base model having no spatial kernel. Results from our real and simulated data studies indicated that predictability can be increased by accounting for spatial variation irrespective of the heritability of the trait. In real data scenarios we observed that the accuracy can be increased by a median value of 3.4%. Through simulations, we showed that a 21% increase in accuracy can be achieved. We also found that Range (row directional spatial kernels, mostly Gaussian, explained the spatial variance in 71% of the scenarios when spatial correlation was significant.

  19. Improving Genomic Prediction in Cassava Field Experiments Using Spatial Analysis.

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    Elias, Ani A; Rabbi, Ismail; Kulakow, Peter; Jannink, Jean-Luc

    2018-01-04

    Cassava ( Manihot esculenta Crantz) is an important staple food in sub-Saharan Africa. Breeding experiments were conducted at the International Institute of Tropical Agriculture in cassava to select elite parents. Taking into account the heterogeneity in the field while evaluating these trials can increase the accuracy in estimation of breeding values. We used an exploratory approach using the parametric spatial kernels Power, Spherical, and Gaussian to determine the best kernel for a given scenario. The spatial kernel was fit simultaneously with a genomic kernel in a genomic selection model. Predictability of these models was tested through a 10-fold cross-validation method repeated five times. The best model was chosen as the one with the lowest prediction root mean squared error compared to that of the base model having no spatial kernel. Results from our real and simulated data studies indicated that predictability can be increased by accounting for spatial variation irrespective of the heritability of the trait. In real data scenarios we observed that the accuracy can be increased by a median value of 3.4%. Through simulations, we showed that a 21% increase in accuracy can be achieved. We also found that Range (row) directional spatial kernels, mostly Gaussian, explained the spatial variance in 71% of the scenarios when spatial correlation was significant. Copyright © 2018 Elias et al.

  20. Spatial Proximity and Similarity of the Epigenetic State of Genome Domains

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    Khrameeva, Ekaterina E.; Mironov, Andrey A.; Fedonin, Gennady G.; Khaitovich, Philipp; Gelfand, Mikhail S.

    2012-01-01

    Recent studies demonstrate that the organization of the chromatin within the nuclear space might play a crucial role in the regulation of gene expression. The ongoing progress in determination of the 3D structure of the nuclear chromatin allows one to study correlations between spatial proximity of genome domains and their epigenetic state. We combined the data on three-dimensional architecture of the whole human genome with results of high-throughput studies of the chromatin functional state and observed that fragments of different chromosomes that are spatially close tend to have similar patterns of histone modifications, methylation state, DNAse sensitivity, expression level, and chromatin states in general. Moreover, clustering of genome regions by spatial proximity produced compact clusters characterized by the high level of histone modifications and DNAse sensitivity and low methylation level, and loose clusters with the opposite characteristics. We also associated the spatial proximity data with previously detected chimeric transcripts and the results of RNA-seq experiments and observed that the frequency of formation of chimeric transcripts from fragments of two different chromosomes is higher among spatially proximal genome domains. A fair fraction of these chimeric transcripts seems to arise post-transcriptionally via trans-splicing. PMID:22496774

  1. Condensin, master organizer of the genome.

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    Kalitsis, Paul; Zhang, Tao; Marshall, Kathryn M; Nielsen, Christian F; Hudson, Damien F

    2017-03-01

    A fundamental requirement in nature is for a cell to correctly package and divide its replicated genome. Condensin is a mechanical multisubunit complex critical to this process. Condensin uses ATP to power conformational changes in DNA to enable to correct DNA compaction, organization, and segregation of DNA from the simplest bacteria to humans. The highly conserved nature of the condensin complex and the structural similarities it shares with the related cohesin complex have provided important clues as to how it functions in cells. The fundamental requirement for condensin in mitosis and meiosis is well established, yet the precise mechanism of action is still an open question. Mutation or removal of condensin subunits across a range of species disrupts orderly chromosome condensation leading to errors in chromosome segregation and likely death of the cell. There are divergences in function across species for condensin. Once considered to function solely in mitosis and meiosis, an accumulating body of evidence suggests that condensin has key roles in also regulating the interphase genome. This review will examine how condensin organizes our genomes, explain where and how it binds the genome at a mechanical level, and highlight controversies and future directions as the complex continues to fascinate and baffle biologists.

  2. Creating biomaterials with spatially organized functionality.

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    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.

  3. Mitochondrial genome organization and vertebrate phylogenetics

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    Pereira Sérgio Luiz

    2000-01-01

    Full Text Available With the advent of DNA sequencing techniques the organization of the vertebrate mitochondrial genome shows variation between higher taxonomic levels. The most conserved gene order is found in placental mammals, turtles, fishes, some lizards and Xenopus. Birds, other species of lizards, crocodilians, marsupial mammals, snakes, tuatara, lamprey, and some other amphibians and one species of fish have gene orders that are less conserved. The most probable mechanism for new gene rearrangements seems to be tandem duplication and multiple deletion events, always associated with tRNA sequences. Some new rearrangements seem to be typical of monophyletic groups and the use of data from these groups may be useful for answering phylogenetic questions involving vertebrate higher taxonomic levels. Other features such as the secondary structure of tRNA, and the start and stop codons of protein-coding genes may also be useful in comparisons of vertebrate mitochondrial genomes.

  4. The Spatial Organization of Glucosinolate Biosynthesis

    DEFF Research Database (Denmark)

    Nintemann, Sebastian

    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...... resistance and nutritional value and many plant specialized metabolites are of high value due to their health promoting characteristics. Glucosinolates are defense compounds found in many crops from the Brassicaceae family and are of high interest because of their nutritional and antinutritional properties...... 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...

  5. The Role of Spatial Ability and Strategy Preference for Spatial Problem Solving in Organic Chemistry

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    Stieff, Mike; Ryu, Minjung; Dixon, Bonnie; Hegarty, Mary

    2012-01-01

    In organic chemistry, spatial reasoning is critical for reasoning about spatial relationships in three dimensions and representing spatial information in diagrams. Despite its importance, little is known about the underlying cognitive components of spatial reasoning and the strategies that students employ to solve spatial problems in organic…

  6. Spatial organization of proteins in metastasizing cells.

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    Rönnlund, Daniel; Gad, Annica K B; Blom, Hans; Aspenström, Pontus; Widengren, Jerker

    2013-09-01

    The ability of tumor cells to invade into the surrounding tissue is linked to defective adhesive and mechanical properties of the cells, which are regulated by cell surface adhesions and the intracellular filamentous cytoskeleton, respectively. With the aim to further reveal the underlying mechanisms and provide new strategies for early cancer diagnostics, we have used ultrahigh resolution stimulated emission depletion (STED) microscopy as a means to identify metastasizing cells, based on their subcellular protein distribution patterns reflecting their specific adhesive and mechanical properties. We have compared the spatial distribution of cell-matrix adhesion sites and the vimentin filamentous systems in a matched pair of primary, normal, and metastatic human fibroblast cells. We found that the metastatic cells showed significantly increased densities and more homogenous distributions of nanoscale adhesion-related particles. Moreover, they showed an increase in the number but reduced sizes of the areas of cell-matrix adhesion complexes. The organization of the vimentin intermediate filaments was also found to be significantly different in the metastasizing cells, showing an increased entanglement and loss of directionality. Image analysis procedures were established, allowing an objective detection and characterization of these features and distinction of metastatic cells from their normal counterparts. In conclusion, our results suggest that STED microscopy provides a novel tool to identify metastasizing cells from a very sparse number of cells, based on the altered spatial distribution of the cell-matrix adhesions and intermediate filaments. Copyright © 2013 International Society for Advancement of Cytometry.

  7. 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

    and the role of this organization in regulating the transcription program in adipocytes are not clear. Analysis of genome-wide chromosomal associations revealed cell type-specific spatial clustering of adipogenic genes in 3T3-L1 cells. Time course analysis demonstrated that the adipogenic 'hub', sampled...

  8. Genome organization and characteristics of soybean microRNAs

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    Turner Marie

    2012-05-01

    Full Text Available Abstract Background microRNAs (miRNAs are key regulators of gene expression and play important roles in many aspects of plant biology. The role(s of miRNAs in nitrogen-fixing root nodules of leguminous plants such as soybean is not well understood. We examined a library of small RNAs from Bradyrhizobium japonicum-inoculated soybean roots and identified novel miRNAs. In order to enhance our understanding of miRNA evolution, diversification and function, we classified all known soybean miRNAs based on their phylogenetic conservation (conserved, legume- and soybean-specific miRNAs and examined their genome organization, family characteristics and target diversity. We predicted targets of these miRNAs and experimentally validated several of them. We also examined organ-specific expression of selected miRNAs and their targets. Results We identified 120 previously unknown miRNA genes from soybean including 5 novel miRNA families. In the soybean genome, genes encoding miRNAs are primarily intergenic and a small percentage were intragenic or less than 1000 bp from a protein-coding gene, suggesting potential co-regulation between the miRNA and its parent gene. Difference in number and orientation of tandemly duplicated miRNA genes between orthologous genomic loci indicated continuous evolution and diversification. Conserved miRNA families are often larger in size and produce less diverse mature miRNAs than legume- and soybean-specific families. In addition, the majority of conserved and legume-specific miRNA families produce 21 nt long mature miRNAs with distinct nucleotide distribution and regulate a more conserved set of target mRNAs compared to soybean-specific families. A set of nodule-specific target mRNAs and their cognate regulatory miRNAs had inverse expression between root and nodule tissues suggesting that spatial restriction of target gene transcripts by miRNAs might govern nodule-specific gene expression in soybean. Conclusions Genome

  9. Hierarchical spatial organization of geographical networks

    Energy Technology Data Exchange (ETDEWEB)

    Travencolo, Bruno A N; Costa, Luciano da F [Cybernetic Vision Research Group, GII-IFSC, Universidade de Sao Paulo, Caixa Postal 369, Sao Carlos, SP, 13560-970 (Brazil)], E-mail: luciano@if.sc.usp.br

    2008-06-06

    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.

  10. Bacterial genomes : Habitat specificity and uncharted organisms

    NARCIS (Netherlands)

    Dini-Andreote, Francisco; Dini Andreote, Fernando; Araujo, Welington Luiz; Trevors, Jack T.; van Elsas, Jan Dirk

    The capability and speed in generating genomic data have increased profoundly since the release of the draft human genome in 2000. Additionally, sequencing costs have continued to plummet as the next generation of highly efficient sequencing technologies (next-generation sequencing) became available

  11. Representation and processing of complex DNA spatial architecture and its annotated genomic content.

    Science.gov (United States)

    Gherbi, Rachid; Herisson, Joan

    2002-01-01

    This paper presents a new general approach for the spatial representation and visualization of DNA molecule and its annotated information. This approach is based on a biological 3D model that predicts the complex spatial trajectory of huge naked DNA. With such modeling, a global vision of the sequence is possible, which is different and complementary to other representations as textual, linguistics or syntactic ones. The DNA is well known as a three-dimensional structure. Whereas, the spatial information plays a great part during its evolution and its interaction with the other biological elements This work will motivate investigations in order to launch new bioinformatics studies for the analysis of the spatial architecture of the genome. Besides, in order to obtain a friendly interactive visualization, a powerful graphic modeling is proposed including DNA complex trajectory management and its annotated-based content structuring. The paper describes spatial architecture modeling, with consideration of both biological and computational constraints. This work is implemented through a powerful graphic software tool, named ADN-Viewer. Several examples of visualization are shown for various organisms and biological elements.

  12. Automated System Organizations Under Spatial Grasp Technology

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    2014-06-01

    This mode of high-level system vision based on holistic and gestalt principles [6-8] rather than cooperating parts or agents [1] has psychological ...M. Wertheimer, “ Gestalt Theory“, Erlangen. Berlin, 1925. [7] P. Sapaty, “ Gestalt -Based Ideology and Technology for Spatial Control of Distributed...Dynamic Systems”, International Gestalt Theory Congress, 16th Scientific Convention of the GTA, University of Osnabrück, Germany, March 26 - 29

  13. Evolution and genomic organization of muscle microRNAs in fish genomes.

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    Nachtigall, Pedro Gabriel; Dias, Marcos Correa; Pinhal, Danillo

    2014-09-25

    MicroRNAs (miRNAs) are small non-coding RNA molecules with an important role upon post-transcriptional regulation. These molecules have been shown essential for several cellular processes in vertebrates, including muscle biology. Many miRNAs were described as exclusively or highly expressed in skeletal and/or cardiac muscle. However, knowledge on the genomic organization and evolution of muscle miRNAs has been unveiled in a reduced number of vertebrates and mostly only reflects their organization in mammals, whereas fish genomes remain largely uncharted. The main goal of this study was to elucidate particular features in the genomic organization and the putative evolutionary history of muscle miRNAs through a genome-wide comparative analysis of cartilaginous and bony fish genomes. As major outcomes we show that (1) miR-208 was unexpectedly absent in cartilaginous and ray-finned fish genomes whereas it still exist in other vertebrate groups; (2) miR-499 was intergenic in medaka and stickleback conversely to other vertebrates where this miRNA is intronic; (3) the zebrafish genome is the unique harboring two extra paralogous copies of miR-499 and their host gene (Myh7b); (4) a rare deletion event of the intergenic and bicistronic cluster miR-1-1/133a-2 took place only into Tetraodontiformes genomes (pufferfish and spotted green puffer); (5) the zebrafish genome experienced a duplication event of miR-206/-133b; and (6) miR-214 was specifically duplicated in species belonging to superorder Acanthopterygii. Despite of the aforementioned singularities in fish genomes, large syntenic blocks containing muscle-enriched miRNAs were found to persist, denoting colligated functionality between miRNAs and neighboring genes. Based on the genomic data here obtained, we envisioned a feasible scenario for explaining muscle miRNAs evolution in vertebrates.

  14. 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 ...

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

    African Journals Online (AJOL)

    use

    2011-11-23

    Nov 23, 2011 ... 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 ...

  16. 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

    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...... 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......, 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....

  17. 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

  18. Genomic organization of the REF gene in Hevea brasiliensis

    International Nuclear Information System (INIS)

    Attanayaka, D.P.S.T.G.; Karunanayake, E.H.; Lawrence, M.J.; Franklin, F.C.H.; Kekwick, R.G.O.

    1995-01-01

    The genomic organization of the rubber elongation factor (REF) gene in the Hevea genome was investigated by nucelotide sequence analysis and genomic Southern blots. The nucleotide sequence of a genomic clone of the REF gene was obtained. A genomic library of Hevea brasiliensis was constructed and screened with a REF cDNA clone. Ten putative positive clones were detected, five of which were purified by secondary screening. A total of 1099 nucleotides was determined from the insert contained in pGREF1 and found to encode 127 amino acids, including the carboxyl terminus of the REF protein. Nucleotide sequences that encode the rest of the amino terminal amino acids were then obtained using a polymerase chain reaction (PCR) product derived from the same genomic fragment. The nucleotide sequence of the genomic clone revealed the presence of two introns within the coding of the gene. The location of the putative intron/exon splicing sites of both the introns falls between the two codons. The coding region of the REF genomic clone showed 85% nucleotide homology with the REF cDNA sequence, and the deduced amino acid sequence showed 91% homology. The difference in nucleotide sequence between the cDNA and the genomic clones showed the occurrence of polymorphic forms of the REF gene in the Hevea genome. Genomic Southern blot analysis of different Hevea genotypes with the REF cDNA probe revealed the presence of restriction fragment length polymorphism (RFLP). Preliminary studies indicated that this polymorphism could be due to the presence of a multi-allelic REF gene locus. The RFLP pattern obtained using this DNA probe also showed that fingerprinting of the commercial rubber clones is possible. 1 ref., 2 figs

  19. The cooperative genome: organisms as social contracts.

    Science.gov (United States)

    Weiss, Kenneth M; Buchanan, Anne V

    2009-01-01

    A predominant theme in much of evolutionary biology is that organisms are the product of relentless and precise natural selection among them, and that life is about the competition of all-against-all for success. However, developmental genetics has rapidly been revealing a very different picture of the nature of life. The organizing principles by which organisms are made are thoroughly based on complex hierarchies of molecular interactions that require multiple factors to be relentlessly cooperating with each other. Reconciling these two points of view involves changing the scale of observation, and a different understanding of evolution, in which cooperation and tolerance are more important than competition and intolerance.

  20. Genome organization during the cell cycle: unity in division.

    Science.gov (United States)

    Golloshi, Rosela; Sanders, Jacob T; McCord, Rachel Patton

    2017-09-01

    During the cell cycle, the genome must undergo dramatic changes in structure, from a decondensed, yet highly organized interphase structure to a condensed, generic mitotic chromosome and then back again. For faithful cell division, the genome must be replicated and chromosomes and sister chromatids physically segregated from one another. Throughout these processes, there is feedback and tension between the information-storing role and the physical properties of chromosomes. With a combination of recent techniques in fluorescence microscopy, chromosome conformation capture (Hi-C), biophysical experiments, and computational modeling, we can now attribute mechanisms to many long-observed features of chromosome structure changes during cell division. Apparent conflicts that arise when integrating the concepts from these different proposed mechanisms emphasize that orchestrating chromosome organization during cell division requires a complex system of factors rather than a simple pathway. Cell division is both essential for and threatening to proper genome organization. As interphase three-dimensional (3D) genome structure is quite static at a global level, cell division provides an important window of opportunity to make substantial changes in 3D genome organization in daughter cells, allowing for proper differentiation and development. Mistakes in the process of chromosome condensation or rebuilding the structure after mitosis can lead to diseases such as cancer, premature aging, and neurodegeneration. WIREs Syst Biol Med 2017, 9:e1389. doi: 10.1002/wsbm.1389 For further resources related to this article, please visit the WIREs website. © 2017 Wiley Periodicals, Inc.

  1. Genome-wide analysis of spatial gene expression in Arabidopsis flowers.

    Science.gov (United States)

    Wellmer, Frank; Riechmann, José Luis; Alves-Ferreira, Márcio; Meyerowitz, Elliot M

    2004-05-01

    We have compared the gene expression profiles of inflorescences of the floral homeotic mutants apetala1, apetala2, apetala3, pistillata, and agamous with that of wild-type plants using a flower-specific cDNA microarray and a whole genome oligonucleotide array. By combining the data sets from the individual mutant/wild type comparisons, we were able to identify a large number of genes that are, within flowers, predicted to be specifically or at least predominantly expressed in one type of floral organ. We have analyzed the expression patterns of several of these genes by in situ hybridization and found that they match the predictions that were made based on the microarray experiments. Moreover, genes with known floral organ-specific expression patterns were correctly assigned by our analysis. The vast majority of the identified transcripts are found in stamens or carpels, whereas few genes are predicted to be expressed specifically or predominantly in sepals or petals. These findings indicate that spatially limited expression of a large number of genes is part of flower development and that its extent differs significantly between the reproductive organs and the organs of the perianth.

  2. 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

  3. 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

  4. [The influence of visual imagery experience on EEG spatial organization].

    Science.gov (United States)

    Sviderskaia, N E; Taratynova, G V; Kozhedub, R G

    2005-01-01

    The comparison of EEG spatial organization between groups of 23 students of graphic arts department ("professional" subjects) and 39 subjects of another specialization ("non-professional" subjects) was made in order to find EEG correlates of visual imagery experience. Changes in the spatial organization of biopotentials (spatial synchronization and spatial disorder, spectral power and coherence) were analyzed while subjects mentally composed visual images from two simple elements, right angle and oblique line. The total number of elements presented for the image composition increased with each subsequent task (in total, four tasks were presented) from the number adequate to simultaneous perception and conscious processing (less than 7 +/- 2) to a much higher number. Intergroup differences, especially, in the degree of the spatial disorder (non-linear processes), were most evident under conditions when the subjects operated with a greater number of elements (tasks 3 and 4). This parameter increased more rapidly in "professionals" than in "non-professionals". These changes were most pronounced in the right anterior cortex. In "non-professional" subjects, spatial synchronization (linear processes) increased in the right posterior area. In "professional" subjects, coherence and spectral power increased in a greater number of narrow EEG frequency subbands than in "non-professional" subjects. The findings suggest that the imagery performance in subjects with visual imagery experience involves complicated neurodynamic processes such as non-linear dynamics and numerous EEG spatial resonance systems.

  5. Genomic organization of the adrenoleukodystrophy gene

    Energy Technology Data Exchange (ETDEWEB)

    Sarde, C.O.; Mosser, J.; Kretz, C. [Institut de Chimie Biologique, Strasbourg (France)] [and others

    1994-07-01

    Adrenoleukodystrophy (ALD), the most frequent peroxisomal disorder, is a severe neurodegenerative disease associated with an impairment of very long chain fatty acids {beta}-oxidation. The authors have recently identified by positional cloning the gene responsible for ALD, located in Xq28. It encodes a new member of the {open_quotes}ABC{close_quotes} superfamily of membrane-associated transporters that shows, in particular, significant homology to the 70-kDa peroxisomal membrane protein (PMP70). They report here a detailed characterization of the ALD gene structure. It extends over 21 kb and consists of 10 exons. To facilitate the detection of mutations in ALD patients, they have determined the intronic sequences flanking the exons as well as the sequence of the 3{prime} untranslated region and of the immediate 5{prime} promoter region. Sequences present in distal exons cross-hybridize strongly to additional sequences in the human genome. The ALD gene has been positioned on a pulsed-field map between DXS15 and the L1CAM gene, about 650 kb upstream from the color pigment genes. The frequent occurrence of color vision anomalies observed in patients with adrenomyeloneuropathy (the adult onset form of ALD) thus does not represent a contiguous gene syndrome but a secondary manifestation of ALD. 37 refs., 6 figs.

  6. Genome-Wide Analysis of Spatial Gene Expression in Arabidopsis FlowersW⃞

    Science.gov (United States)

    Wellmer, Frank; Riechmann, José Luis; Alves-Ferreira, Márcio; Meyerowitz, Elliot M.

    2004-01-01

    We have compared the gene expression profiles of inflorescences of the floral homeotic mutants apetala1, apetala2, apetala3, pistillata, and agamous with that of wild-type plants using a flower-specific cDNA microarray and a whole genome oligonucleotide array. By combining the data sets from the individual mutant/wild type comparisons, we were able to identify a large number of genes that are, within flowers, predicted to be specifically or at least predominantly expressed in one type of floral organ. We have analyzed the expression patterns of several of these genes by in situ hybridization and found that they match the predictions that were made based on the microarray experiments. Moreover, genes with known floral organ–specific expression patterns were correctly assigned by our analysis. The vast majority of the identified transcripts are found in stamens or carpels, whereas few genes are predicted to be expressed specifically or predominantly in sepals or petals. These findings indicate that spatially limited expression of a large number of genes is part of flower development and that its extent differs significantly between the reproductive organs and the organs of the perianth. PMID:15100403

  7. 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 ...

  8. 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...

  9. Chromosomal localization of rDNA genes and genomic organization ...

    Indian Academy of Sciences (India)

    Genomic organization analysis of 5S rDNA revealed two different types of 5S rDNA sequences, 5S type I and 5S type II. Moreover, fluorescence in situ hybridization (FISH) with 5S rDNA probes showed six positive fluorescence signals on six chromosomes of all the analysed metaphases from the three tilapia samples.

  10. 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

  11. 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.

  12. 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

  13. 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

  14. Spatial organization and correlations of cell nuclei in brain tumors.

    Directory of Open Access Journals (Sweden)

    Yang Jiao

    Full Text Available Accepting the hypothesis that cancers are self-organizing, opportunistic systems, it is crucial to understand the collective behavior of cancer cells in their tumorous heterogeneous environment. In the present paper, we ask the following basic question: Is this self-organization of tumor evolution reflected in the manner in which malignant cells are spatially distributed in their heterogeneous environment? We employ a variety of nontrivial statistical microstructural descriptors that arise in the theory of heterogeneous media to characterize the spatial distributions of the nuclei of both benign brain white matter cells and brain glioma cells as obtained from histological images. These descriptors, which include the pair correlation function, structure factor and various nearest neighbor functions, quantify how pairs of cell nuclei are correlated in space in various ways. We map the centroids of the cell nuclei into point distributions to show that while commonly used local spatial statistics (e.g., cell areas and number of neighboring cells cannot clearly distinguish spatial correlations in distributions of normal and abnormal cell nuclei, their salient structural features are captured very well by the aforementioned microstructural descriptors. We show that the tumorous cells pack more densely than normal cells and exhibit stronger effective repulsions between any pair of cells. Moreover, we demonstrate that brain gliomas are organized in a collective way rather than randomly on intermediate and large length scales. The existence of nontrivial spatial correlations between the abnormal cells strongly supports the view that cancer is not an unorganized collection of malignant cells but rather a complex emergent integrated system.

  15. Spatial organization and correlations of cell nuclei in brain tumors.

    Science.gov (United States)

    Jiao, Yang; Berman, Hal; Kiehl, Tim-Rasmus; Torquato, Salvatore

    2011-01-01

    Accepting the hypothesis that cancers are self-organizing, opportunistic systems, it is crucial to understand the collective behavior of cancer cells in their tumorous heterogeneous environment. In the present paper, we ask the following basic question: Is this self-organization of tumor evolution reflected in the manner in which malignant cells are spatially distributed in their heterogeneous environment? We employ a variety of nontrivial statistical microstructural descriptors that arise in the theory of heterogeneous media to characterize the spatial distributions of the nuclei of both benign brain white matter cells and brain glioma cells as obtained from histological images. These descriptors, which include the pair correlation function, structure factor and various nearest neighbor functions, quantify how pairs of cell nuclei are correlated in space in various ways. We map the centroids of the cell nuclei into point distributions to show that while commonly used local spatial statistics (e.g., cell areas and number of neighboring cells) cannot clearly distinguish spatial correlations in distributions of normal and abnormal cell nuclei, their salient structural features are captured very well by the aforementioned microstructural descriptors. We show that the tumorous cells pack more densely than normal cells and exhibit stronger effective repulsions between any pair of cells. Moreover, we demonstrate that brain gliomas are organized in a collective way rather than randomly on intermediate and large length scales. The existence of nontrivial spatial correlations between the abnormal cells strongly supports the view that cancer is not an unorganized collection of malignant cells but rather a complex emergent integrated system.

  16. 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.

  17. Integrating landscape genomics and spatially explicit approaches to detect loci under selection in clinal populations.

    Science.gov (United States)

    Jones, Matthew R; Forester, Brenna R; Teufel, Ashley I; Adams, Rachael V; Anstett, Daniel N; Goodrich, Betsy A; Landguth, Erin L; Joost, Stéphane; Manel, Stéphanie

    2013-12-01

    Uncovering the genetic basis of adaptation hinges on the ability to detect loci under selection. However, population genomics outlier approaches to detect selected loci may be inappropriate for clinal populations or those with unclear population structure because they require that individuals be clustered into populations. An alternate approach, landscape genomics, uses individual-based approaches to detect loci under selection and reveal potential environmental drivers of selection. We tested four landscape genomics methods on a simulated clinal population to determine their effectiveness at identifying a locus under varying selection strengths along an environmental gradient. We found all methods produced very low type I error rates across all selection strengths, but elevated type II error rates under "weak" selection. We then applied these methods to an AFLP genome scan of an alpine plant, Campanula barbata, and identified five highly supported candidate loci associated with precipitation variables. These loci also showed spatial autocorrelation and cline patterns indicative of selection along a precipitation gradient. Our results suggest that landscape genomics in combination with other spatial analyses provides a powerful approach for identifying loci potentially under selection and explaining spatially complex interactions between species and their environment. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  18. Breast Cancer Diagnostics Based on Spatial Genome Organization

    Science.gov (United States)

    2012-07-01

    breast tissues made up of invasive breast carcinomas, benign diseased tissues ( fibroadenoma and hyperplasia) and normal breast tissues [11]. To enable an...positioning patterns were also compared between benign disease ( fibroadenoma and hyperplasia; not including atypical hyperplasia, which is linked to breast ...AD_________________ Award Number: W81XWH-08-2-0098 TITLE: Breast Cancer Diagnostics Based on

  19. DNA Methylation Landscape Reflects the Spatial Organization of Chromatin in Different Cells.

    Science.gov (United States)

    Zhang, Ling; Xie, Wen Jun; Liu, Sirui; Meng, Luming; Gu, Chan; Gao, Yi Qin

    2017-10-03

    The relationship between DNA methylation and chromatin structure is still largely unknown. By analyzing a large set of published sequencing data, we observed a long-range power law correlation of DNA methylation with cell class-specific scaling exponents in the range of tens of kilobases. We showed that such cell class-specific scaling exponents are caused by different patchiness of DNA methylation in different cells. By modeling the chromatin structure using high-resolution chromosome conformation capture data and mapping the methylation level onto the modeled structure, we demonstrated that the patchiness of DNA methylation is related to chromatin structure. The scaling exponents of the power law correlation are thus a display of the spatial organization of chromatin. Besides the long-range correlation, we also showed that the local correlation of DNA methylation is associated with nucleosome positioning. The local correlation of partially methylated domains is different from that of nonpartially methylated domains, suggesting that their chromatin structures differ at the scale of several hundred base pairs (covering a few nucleosomes). Our study provides a novel, to our knowledge, view of the spatial organization of chromatin structure from a perspective of DNA methylation, in which both long-range and local correlations of DNA methylation along the genome reflect the spatial organization of chromatin. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  20. From cells to chromatin: capturing snapshots of genome organization with 5C technology.

    Science.gov (United States)

    Ferraiuolo, Maria A; Sanyal, Amartya; Naumova, Natalia; Dekker, Job; Dostie, Josée

    2012-11-01

    In eukaryotes, genome organization can be observed on many levels and at different scales. This organization is important not only to reduce chromosome length but also for the proper execution of various biological processes. High-resolution mapping of spatial chromatin structure was made possible by the development of the chromosome conformation capture (3C) technique. 3C uses chemical cross-linking followed by proximity-based ligation of fragmented DNA to capture frequently interacting chromatin segments in cell populations. Several 3C-related methods capable of higher chromosome conformation mapping throughput were reported afterwards. These techniques include the 3C-carbon copy (5C) approach, which offers the advantage of being highly quantitative and reproducible. We provide here an updated reference protocol for the production of 5C libraries analyzed by next-generation sequencing or onto microarrays. A procedure used to verify that 3C library templates bear the high quality required to produce superior 5C libraries is also described. We believe that this detailed protocol will help guide researchers in probing spatial genome organization and its role in various biological processes. Copyright © 2012 Elsevier Inc. All rights reserved.

  1. Spatial expression of transcription factors in Drosophila embryonic organ development.

    Science.gov (United States)

    Hammonds, Ann S; Bristow, Christopher A; Fisher, William W; Weiszmann, Richard; Wu, Siqi; Hartenstein, Volker; Kellis, Manolis; Yu, Bin; Frise, Erwin; Celniker, Susan E

    2013-12-20

    Site-specific transcription factors (TFs) bind DNA regulatory elements to control expression of target genes, forming the core of gene regulatory networks. Despite decades of research, most studies focus on only a small number of TFs and the roles of many remain unknown. We present a systematic characterization of spatiotemporal gene expression patterns for all known or predicted Drosophila TFs throughout embryogenesis, the first such comprehensive study for any metazoan animal. We generated RNA expression patterns for all 708 TFs by in situ hybridization, annotated the patterns using an anatomical controlled vocabulary, and analyzed TF expression in the context of organ system development. Nearly all TFs are expressed during embryogenesis and more than half are specifically expressed in the central nervous system. Compared to other genes, TFs are enriched early in the development of most organ systems, and throughout the development of the nervous system. Of the 535 TFs with spatially restricted expression, 79% are dynamically expressed in multiple organ systems while 21% show single-organ specificity. Of those expressed in multiple organ systems, 77 TFs are restricted to a single organ system either early or late in development. Expression patterns for 354 TFs are characterized for the first time in this study. We produced a reference TF dataset for the investigation of gene regulatory networks in embryogenesis, and gained insight into the expression dynamics of the full complement of TFs controlling the development of each organ system.

  2. Genome supranucleosomal organization and genetic susceptibility to diseases

    Science.gov (United States)

    Jablonski, K. P.; Fretter, C.; Carron, L.; Forné, T.; Hütt, M.-T.; Lesne, A.

    2017-09-01

    The notion of disease-associated single-nucleotide polymorphisms (da-SNP), as determined in genome-wide association studies (GWAS), is relevant for many complex pathologies, including cancers. It appeared that da-SNPs are not only markers of causal genetic variation but may contribute to the disease development through an influence on gene expression levels. We argue that understanding this possible functional role of da-SNPs requires to consider their embedding in the tridimensional (3D) multi-scale organization of the human genome. We then focus on the potential impact of da-SNPs on chromatin loops and recently observed topologically associating domains (TADs). We show that for some diseases and cancer types, da-SNPs are over-represented in the borders of these topological domains, in a way that cannot be explained by an increased exon density. This analysis of the distribution of da-SNPs within the 3D genome organization suggests candidate loci for further experimental investigation of the mechanisms underlying genetic susceptibility to diseases, in particular cancer.

  3. Genome Editing and Its Applications in Model Organisms

    Directory of Open Access Journals (Sweden)

    Dongyuan Ma

    2015-12-01

    Full Text Available Technological advances are important for innovative biological research. Development of molecular tools for DNA manipulation, such as zinc finger nucleases (ZFNs, transcription activator-like effector nucleases (TALENs, and the clustered regularly-interspaced short palindromic repeat (CRISPR/CRISPR-associated (Cas, has revolutionized genome editing. These approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. In the last few years, substantial progress has been made in CRISPR/Cas technology, including technical improvements and wide application in many model systems. This review describes recent advancements in genome editing with a particular focus on CRISPR/Cas, covering the underlying principles, technological optimization, and its application in zebrafish and other model organisms, disease modeling, and gene therapy used for personalized medicine.

  4. Genome Editing and Its Applications in Model Organisms.

    Science.gov (United States)

    Ma, Dongyuan; Liu, Feng

    2015-12-01

    Technological advances are important for innovative biological research. Development of molecular tools for DNA manipulation, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly-interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas), has revolutionized genome editing. These approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. In the last few years, substantial progress has been made in CRISPR/Cas technology, including technical improvements and wide application in many model systems. This review describes recent advancements in genome editing with a particular focus on CRISPR/Cas, covering the underlying principles, technological optimization, and its application in zebrafish and other model organisms, disease modeling, and gene therapy used for personalized medicine. Copyright © 2016 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

  5. 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

  6. 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.

  7. Genomic organization of Bruton`s tyrosine kinase

    Energy Technology Data Exchange (ETDEWEB)

    Rohrer, J.; Conley, M.E. [Univ. of Tennessee, Memphis, TN (United States)

    1994-09-01

    Bruton`s tyrosine kinase (Btk), is a nonreceptor tyrosine kinase that has been identified as the defective gene in X-linked agammaglobulinemia (XLA). XLA patients have profound hypogammaglobulinemia and markedly reduced numbers of B cells while their T cell and phagocyte numbers remain normal. To determine the genomic organization of Btk, intron/exon borders were identified by sequencing cosmid DNA using cDNA primers. Nineteen exons spanning 37 kb of genomic DNA were identified. All the intron/exon splice junctions followed the GT/AG rule. The translational ATG start codon was in exon 2 which was 6 kb downstream of exon 1. Exon 19, 519 bp in length and 3.8 kb distal to exon 18, was the largest exon and included the 450 bp of the 3{prime} untranslated region. Exons 6 through 18 formed the largest cluster of exons with no intron being longer than 1550 bp. There was no apparent correlation between the exon boundaries of Btk and the functional domains of the protein or the exon boundaries of src, the nonreceptor protein tyrosine kinase prototype. The region 500 bp upstream of the presumed transcriptional start site was sequenced and found to have a G+C content of 52%. No TATA-type promoter elements in the -20 bp to -30 bp region were identified. However, at position -48 bp, a TGTGAA motif was found that bears some similarity to the TATA box. This sequence was preceded by a perfect inverted CCAAT box at position -90 bp. Three retinoic acid binding sites were also identified at positions -50 bp, -83 bp and -197 bp. Defining the genomic structure of Btk will permit us to identify regulatory elements in this gene and to identify mutations in genomic DNA of patients with XLA.

  8. 3D genome organization in health and disease: emerging opportunities in cancer translational medicine.

    Science.gov (United States)

    Babu, Deepak; Fullwood, Melissa J

    2015-01-01

    Organizing the DNA to fit inside a spatially constrained nucleus is a challenging problem that has attracted the attention of scientists across all disciplines of science. Increasing evidence has demonstrated the importance of genome geometry in several cellular contexts that affect human health. Among several approaches, the application of sequencing technologies has substantially increased our understanding of this intricate organization, also known as chromatin interactions. These structures are involved in transcriptional control of gene expression by connecting distal regulatory elements with their target genes and regulating co-transcriptional splicing. In addition, chromatin interactions play pivotal roles in the organization of the genome, the formation of structural variants, recombination, DNA replication and cell division. Mutations in factors that regulate chromatin interactions lead to the development of pathological conditions, for example, cancer. In this review, we discuss key findings that have shed light on the importance of these structures in the context of cancers, and highlight the applicability of chromatin interactions as potential biomarkers in molecular medicine as well as therapeutic implications of chromatin interactions.

  9. 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

  10. 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

  11. 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

  12. Tools for Optimizing Management of a Spatially Variable Organic Field

    Directory of Open Access Journals (Sweden)

    Thomas Panagopoulos

    2015-03-01

    Full Text Available Geostatistical tools were used to estimate spatial relations between wheat yield and soil parameters under organic farming field conditions. Thematic maps of each factor were created as raster images in R software using kriging. The Geographic Resources Analysis Support System (GRASS calculated the principal component analysis raster images for soil parameters and yield. The correlation between the raster arising from the PC1 of soil and yield parameters showed high linear correlation (r = 0.75 and explained 48.50% of the data variance. The data show that durum wheat yield is strongly affected by soil parameter variability, and thus, the average production can be substantially lower than its potential. Soil water content was the limiting factor to grain yield and not nitrate as in other similar studies. The use of precision agriculture tools helped reduce the level of complexity between the measured parameters by the grouping of several parameters and demonstrating that precision agriculture tools can be applied in small organic fields, reducing costs and increasing wheat yield. Consequently, site-specific applications could be expected to improve the yield without increasing excessively the cost for farmers and enhance environmental and economic benefits.

  13. 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.

  14. 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.

  15. 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.

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

    Science.gov (United States)

    Chang, Yi-Feng; Chang, Chuan-Hsiung

    2011-01-01

    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.

  17. Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription.

    Science.gov (United States)

    Cagliero, Cedric; Grand, Ralph S; Jones, M Beatrix; Jin, Ding J; O'Sullivan, Justin M

    2013-07-01

    To fit within the confines of the cell, bacterial chromosomes are highly condensed into a structure called the nucleoid. Despite the high degree of compaction in the nucleoid, the genome remains accessible to essential biological processes, such as replication and transcription. Here, we present the first high-resolution chromosome conformation capture-based molecular analysis of the spatial organization of the Escherichia coli nucleoid during rapid growth in rich medium and following an induced amino acid starvation that promotes the stringent response. Our analyses identify the presence of origin and terminus domains in exponentially growing cells. Moreover, we observe an increased number of interactions within the origin domain and significant clustering of SeqA-binding sequences, suggesting a role for SeqA in clustering of newly replicated chromosomes. By contrast, 'histone-like' protein (i.e. Fis, IHF and H-NS) -binding sites did not cluster, and their role in global nucleoid organization does not manifest through the mediation of chromosomal contacts. Finally, genes that were downregulated after induction of the stringent response were spatially clustered, indicating that transcription in E. coli occurs at transcription foci.

  18. CDK activity provides temporal and quantitative cues for organizing genome duplication.

    Directory of Open Access Journals (Sweden)

    Anthony Perrot

    2018-02-01

    Full Text Available In eukaryotes, the spatial and temporal organization of genome duplication gives rise to distinctive profiles of replication origin usage along the chromosomes. While it has become increasingly clear that these programs are important for cellular physiology, the mechanisms by which they are determined and modulated remain elusive. Replication initiation requires the function of cyclin-dependent kinases (CDKs, which associate with various cyclin partners to drive cell proliferation. Surprisingly, although we possess detailed knowledge of the CDK regulators and targets that are crucial for origin activation, little is known about whether CDKs play a critical role in establishing the genome-wide pattern of origin selection. We have addressed this question in the fission yeast, taking advantage of a simplified cell cycle network in which cell proliferation is driven by a single cyclin-CDK module. This system allows us to precisely control CDK activity in vivo using chemical genetics. First, in contrast to previous reports, our results clearly show that distinct cyclin-CDK pairs are not essential for regulating specific subsets of origins and for establishing a normal replication program. Importantly, we then demonstrate that the timing at which CDK activity reaches the S phase threshold is critical for the organization of replication in distinct efficiency domains, while the level of CDK activity at the onset of S phase is a dose-dependent modulator of overall origin efficiencies. Our study therefore implicates these different aspects of CDK regulation as versatile mechanisms for shaping the architecture of DNA replication across the genome.

  19. 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.

  20. 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

  1. 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...

  2. Complex spatial organization and flagellin composition of flagellar propeller from marine magnetotactic ovoid strain MO-1.

    Science.gov (United States)

    Zhang, Wei-Jia; Santini, Claire-Lise; Bernadac, Alain; Ruan, Juanfang; Zhang, Sheng-Da; Kato, Takayuki; Li, Ying; Namba, Keiichi; Wu, Long-Fei

    2012-03-02

    Marine magnetotactic ovoid bacterium MO-1 is capable of swimming along the geomagnetic field lines by means of its two sheathed flagellar bundles at a speed up to 300 μm/s. In this study, by using electron microscopy, we showed that, in each bundle, six individual flagella were organized in hexagon with a seventh in the middle. We identified 12 flagellin paralogs and 2 putative flagellins in the genome of MO-1. Among them, 13 were tandemly located on an ~ 17-kb segment while the 14th was on a separated locus. Using reverse transcription PCR and quantitative PCR, we found that all the 14 flagellin or putative flagellin genes were transcribed and that 2 of them were more abundantly expressed than others. A nLC (nanoliquid chromatography)-ESI (electrospray ionization)-MS/MS (mass spectrometry/mass spectrometry) mass spectrometry analysis identified all the 12 flagellin proteins in three glycosylated polypeptide bands resolved by one-dimensional denaturing polyacrylamide gel electrophoresis and 10 of them in 21 spots obtained by means of two-dimensional electrophoresis of flagellar extracts. Most spots contained more than one flagellin, and eight of the ten identified flagellins existed in multiple isoforms. Taken together, these results show unprecedented complexity in the spatial organization and flagellin composition of the flagellar propeller. Such architecture is observed only for ovoid-coccoid, bilophotrichously flagellated magnetotactic bacteria living in marine sediments, suggesting a species and environmental specificity. Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. 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.

  4. Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics.

    Science.gov (United States)

    Nevado, B; Ramos-Onsins, S E; Perez-Enciso, M

    2014-04-01

    Decreasing costs of next-generation sequencing (NGS) experiments have made a wide range of genomic questions open for study with nonmodel organisms. However, experimental designs and analysis of NGS data from less well-known species are challenging because of the lack of genomic resources. In this work, we investigate the performance of alternative experimental designs and bioinformatics approaches in estimating variability and neutrality tests based on the site-frequency-spectrum (SFS) from individual resequencing data. We pay particular attention to challenges faced in the study of nonmodel organisms, in particular the absence of a species-specific reference genome, although phylogenetically close genomes are assumed to be available. We compare the performance of three alternative bioinformatics approaches – genotype calling, genotype–haplotype calling and direct estimation without calling genotypes. We find that relying on genotype calls provides biased estimates of population genetic statistics at low to moderate read depth (2–8X). Genotype–haplotype calling returns more accurate estimates irrespective of the divergence to the reference genome, but requires moderate depth (8–20X). Direct estimation without calling genotypes returns the most accurate estimates of variability and of most SFS tests investigated, including at low read depth (2–4X). Studies without species-specific reference genome should thus aim for low read depth and avoid genotype calling whenever individual genotypes are not essential. Otherwise, aiming for moderate to high depth at the expense of number of individuals, and using genotype–haplotype calling, is recommended.

  5. What transposable elements tell us about genome organization and evolution: the case of Drosophila.

    Science.gov (United States)

    Biémont, C; Vieira, C

    2005-01-01

    Transposable elements (TEs) have been identified in every organism in which they have been looked for. The sequencing of large genomes, such as the human genome and those of Drosophila, Arabidopsis, Caenorhabditis, has also shown that they are a major constituent of these genomes, accounting for 15% of the genome of Drosophila, 45% of the human genome, and more than 70% in some plants and amphibians. Compared with the 1% of genomic DNA dedicated to protein-coding sequences in the human genome, this has prompted various researchers to suggest that the TEs and the other repetitive sequences that constitute the so-called "noncoding DNA", are where the most stimulating discoveries will be made in the future (Bromham, 2002). We are therefore getting further and further from the original idea that this DNA was simply "junk DNA", that owed its presence in the genome entirely to its capacity for selfish transposition. Our understanding of the structures of TEs, their distribution along the genomes, their sequence and insertion polymorphisms within genomes, and within and between populations and species, their impact on genes and on the regulatory mechanisms of genetic expression, their effects on exon shuffling and other phenomena that reshape the genome, and their impact on genome size has increased dramatically in recent years. This leads to a more general picture of the impact of TEs on genomes, though many copies are still mainly selfish or junk DNA. In this review we focus mainly on discoveries made in Drosophila, but we also use information about other genomes when this helps to elucidate the general processes involved in the organization, plasticity, and evolution of genomes.

  6. Bonus Organisms in High-Throughput Eukaryotic Whole-Genome Shorgun Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Pangilinan, Jasmyn; Shapiro, Harris; Tu, Hank; Platt, Darren

    2006-02-06

    The DOE Joint Genome Institute has sequenced over 50 eukaryotic genomes, ranging in size from 15 MB to 1.6 GB, over a wide range of organism types. In the course of doing so, it has become clear that a substantial fraction of these data sets contains bonus organisms, usually prokaryotes, in addition to the desired genome. While some of these additional organisms are extraneous contamination, they are sometimes symbionts, and so can be of biological interest. Therefore, it is desirable to assemble the bonus organisms along with the main genome. This transforms the problem into one of metagenomic assembly, which is considerably more challenging than traditional whole-genome shotgun (WGS) assembly. The different organisms will usually be present at different sequence depths, which is difficult to handle in most WGS assemblers. In addition, with multiple distinct genomes present, chimerism can produce cross-organism combinations. Finally, there is no guarantee that only a single bonus organism will be present. For example, one JGI project contained at least two different prokaryotic contaminants, plus a 145 KB plasmid of unknown origin. We have developed techniques to routinely identify and handle such bonus organisms in a high-throughput sequencing environment. Approaches include screening and partitioning the unassembled data, and iterative subassemblies. These methods are applicable not only to bonus organisms, but also to desired components such as organelles. These procedures have the additional benefit of identifying, and allowing for the removal of, cloning artifacts such as E.coli and spurious vector inclusions.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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...... regions. The analysis of TRS supports the minus strand extending transcription mechanism of coronavirus. The SNP analysis of different isolates reveals that mutations of the sequences do not affect the prediction results of ORFs. Udgivelsesdato: 2003-Aug...

  12. 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

  13. Genomic organization of selected genes in the small monogonont rotifer, Brachionus koreanus.

    Science.gov (United States)

    Rhee, Jae-Sung; Kim, Ryeo-Ok; Kim, Bo-Mi; Dahms, Hans-Uwe; Lee, Jae-Seong

    2012-08-15

    Information of genome structure with its size variation may provide important clues for evolutionary processes at lower taxon level in eukaryotes. Here, we analyzed the compact genome structure of the monogonont rotifer, Brachionus koreanus in the light of transphyletic genome comparison and economic genome usage. To confirm the genome compactness of B. koreanus, we compared the genomic structure of several selected genes with those of human and pufferfish. For example, one of the large genes, DNA-dependent protein kinase (DNA-PK) with dimeric protein Ku70 and Ku80, showed high similarity, even though genomic DNA lengths were quite different. The replication protein As (RPAs) as a heterotrimeric protein also showed a compact genomic structure including all the essential domains and motifs in B. koreanus. Regarding transmembrane protein-containing genes, the B. koreanus P-glycoprotein (P-gp) showed exactly the same topology of the TM domain compared to those of human and pufferfish, even though it had a compact genome structure. In addition, the gene structure of an inducible repair enzyme O(6)-methylguanine DNA methyltransferase (O(6)-MGMT) of B. koreanus showed the highest compactness among the genes tested. The objective of this report is to evaluate the potential for whole genome sequencing and functional genomic research using the monogonont rotifer B. koreanus as a non-model organism that plays important roles in aquatic food-webs. Subsequently, we discussed possible reasons for compact genome structures as well as small and fewer introns from several perspectives. We conclude that the small size genome of B. koreanus would make this species potentially useful for comparative genome structure analysis of non-model species through whole genome sequencing and genetic mapping. Copyright © 2012 Elsevier B.V. All rights reserved.

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

    DEFF Research Database (Denmark)

    Bering Keiding, Tina

    surroundings. Unforeseen disturbances from observations of physical and social environment contribute to enhanced complexity in the projects placed in open-space studio. On one hand this is described as an advantage for the projects. On the other hand projects are forced to an ongoing reduction of complexity......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...

  15. 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

  16. Food in space: The spatial organization of food systems

    NARCIS (Netherlands)

    Carsjens, G.J.

    2015-01-01

    Contemporary food production is facing many challenges. One of these challenges is to re-connect the food system with various public domains, such as spatial planning. Sustainable food planning is a growing domain in planning research. One of the important topics of research concerns the

  17. 5 Spatial Distribution of Nematodes at Organic.cdr

    African Journals Online (AJOL)

    user

    live in the thin films of water surrounding soil particles because water aids their mobility (Freckman ... Geostatistics can be used to analyse and quantify spatial autocorrelation by distance and direction (Evans et al., 1999). Geostatistical analysis in previous studies has shown that field-scale autocorrelation in nematode ...

  18. 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.

  19. Spatial organization of astrocytes in ferret visual cortex

    OpenAIRE

    L?pez?Hidalgo, M?nica; Hoover, Walter B.; Schummers, James

    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 soma...

  20. Genomic organization of a cellulase gene family in Phanerochaete chrysosporium

    Science.gov (United States)

    Sarah F. Covert; Jennifer Bolduc; Daniel Cullen

    1992-01-01

    Southern blot and nucleotide sequence analysis of Phanerochaete chrysosporium BKM-F-1767 genomic clones indicate that this wood-degrading fungus contains at least six genes with significant homology to the Trichoderma reesei cellobiohydrolase I gene (cbh1). Using pulsed-field gel electrophoresis to separate P. chrysosporium chromosomes, the six cellulase genes were...

  1. Epigenetics, chromatin and genome organization: recent advances from the ENCODE project.

    Science.gov (United States)

    Siggens, L; Ekwall, K

    2014-09-01

    The organization of the genome into functional units, such as enhancers and active or repressed promoters, is associated with distinct patterns of DNA and histone modifications. The Encyclopedia of DNA Elements (ENCODE) project has advanced our understanding of the principles of genome, epigenome and chromatin organization, identifying hundreds of thousands of potential regulatory regions and transcription factor binding sites. Part of the ENCODE consortium, GENCODE, has annotated the human genome with novel transcripts including new noncoding RNAs and pseudogenes, highlighting transcriptional complexity. Many disease variants identified in genome-wide association studies are located within putative enhancer regions defined by the ENCODE project. Understanding the principles of chromatin and epigenome organization will help to identify new disease mechanisms, biomarkers and drug targets, particularly as ongoing epigenome mapping projects generate data for primary human cell types that play important roles in disease. © 2014 The Association for the Publication of the Journal of Internal Medicine.

  2. 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.

    The temporal, spatial and depth related variation of suspended particulate organic matter (POM) in the Bay of Bengal are assessed in this paper. For this purpose, suspended particulate matter (SPM) samples were collected from eight depths (2 to 1000...

  3. Biogenic gradients in algal density affect the emergent properties of spatially self-organized mussel beds

    NARCIS (Netherlands)

    Liu, Q.X.; Weerman, E.J.; Gupta, R.; Herman, P.M.J.; Olff, H.; van de Koppel, J.

    2014-01-01

    Theoretical models highlight that spatially self-organized patterns can have important emergent effects on the functioning of ecosystems, for instance by increasing productivity and affecting the vulnerability to catastrophic shifts. However, most theoretical studies presume idealized homogeneous

  4. 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...

  5. Genomic organization and evolution of ruminant lysozyme c genes

    OpenAIRE

    IRWIN, David M

    2015-01-01

    Ruminant stomach lysozyme is a long established model of adaptive gene evolution. Evolution of stomach lysozyme function required changes in the site of expression of the lysozyme c gene and changes in the enzymatic properties of the enzyme. In ruminant mammals, these changes were associated with a change in the size of the lysozyme c gene family. The recent release of near complete genome sequences from several ruminant species allows a more complete examination of the evolution and diversif...

  6. 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.

  7. 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.

  8. 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

  9. Spatial variation of volatile organic compounds and carbon ...

    African Journals Online (AJOL)

    GREG

    2013-05-12

    May 12, 2013 ... carbon monoxide in Blantyre City, Malawi. Mapoma, H. W. T.1*, Zimba J. J. 2, Utembe ... This study assessed variations of ambient volatile organic compounds and carbon monoxide (CO) levels in Blantyre City, Malawi. .... the ground to capture maximum emissions from both vehicles and industrial sources.

  10. Spatial variation of volatile organic compounds and carbon ...

    African Journals Online (AJOL)

    The study focused on methane volatile organic compounds and non-methane volatile compounds besides carbon monoxide. Results of the analysis showed that non-methane volatile compound levels were highest at public bus terminuses with 12.40 ± 0.83 ppm, and lowest for industrial locations (2.16 ± 0.09 ppm).

  11. Predicting Spatial Variability of Soil Organic Carbon in Delmarva Bays

    OpenAIRE

    Blumenthal, Kinsey Megan

    2016-01-01

    Agricultural productivity, ecosystem health, and wetland restoration rely on soil organic carbon (SOC) as vital for microbial activity and plant health. This study assessed: (1) accuracy of topographic-based non-linear models for predicting SOC; and (2) the effect of analytic strategies and soil condition on performance of spectral-based models for predicting SOC. SOC data came from 28 agriculturally converted Delmarva Bays sampled down to 1 meter. R2 was used as an indicator of model perform...

  12. Does a Spatial Perspective Offer New Insights into Inclusive Organizing?

    DEFF Research Database (Denmark)

    Holck, Lotte

    : In fact it can be enacted as an obstacle to inclusion, in that it induces an opaque power structure difficult to navigate for non-traditional members. My research demonstrates how analyzing the organizational space an external ‘effect’, as embodiment and as the product of membership actions, can render...... and that space can be utilized as a lever when working to change the organization in favor of a more inclusive climate....

  13. Spatial genomic heterogeneity in diffuse intrinsic pontine and midline high-grade glioma: implications for diagnostic biopsy and targeted therapeutics.

    Science.gov (United States)

    Hoffman, Lindsey M; DeWire, Mariko; Ryall, Scott; Buczkowicz, Pawel; Leach, James; Miles, Lili; Ramani, Arun; Brudno, Michael; Kumar, Shiva Senthil; Drissi, Rachid; Dexheimer, Phillip; Salloum, Ralph; Chow, Lionel; Hummel, Trent; Stevenson, Charles; Lu, Q Richard; Jones, Blaise; Witte, David; Aronow, Bruce; Hawkins, Cynthia E; Fouladi, Maryam

    2016-01-04

    Diffuse intrinsic pontine glioma (DIPG) and midline high-grade glioma (mHGG) are lethal childhood brain tumors. Spatial genomic heterogeneity has been well-described in adult HGG but has not been comprehensively characterized in pediatric HGG. We performed whole exome sequencing on 38-matched primary, contiguous, and metastatic tumor sites from eight children with DIPG (n = 7) or mHGG (n = 1) collected using a unique MRI-guided autopsy protocol. Validation was performed using Sanger sequencing, Droplet Digital polymerase-chain reaction, immunohistochemistry, and fluorescent in-situ hybridization. Median age at diagnosis was 6.1 years (range: 2.9-23.3 years). Median overall survival was 13.2 months (range: 11.2-32.2 months). Contiguous tumor infiltration and distant metastases were observed in seven and six patients, respectively, including leptomeningeal dissemination in three DIPGs. Histopathological heterogeneity was evident in seven patients, including intra-pontine heterogeneity in two DIPGs, ranging from World Health Organization grade II to IV astrocytoma. We found conservation of heterozygous K27M mutations in H3F3A (n = 4) or HIST1H3B (n = 3) across all primary, contiguous, and metastatic tumor sites in all DIPGs. ACVR1 (n = 2), PIK3CA (n = 2), FGFR1 (n = 2), and MET (n = 1) were also intra-tumorally conserved. ACVR1 was co-mutated with HIST1H3B (n = 2). In contrast, PDGFRA amplification and mutation were spatially heterogeneous, as were mutations in BCOR (n = 1), ATRX (n = 2), and MYC (n = 1). TP53 aberrations (n = 3 patients) varied by type and location between primary and metastatic tumors sites but were intra-tumorally conserved. Spatial conservation of prognostically-relevant and therapeutically-targetable somatic mutations in DIPG and mHGG contrasts the significant heterogeneity of driver mutations seen in adult HGG and supports uniform implementation of diagnostic biopsy in DIPG and mHGG to

  14. 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.

  15. Does a Spatial Perspective Offer New Insights into Inclusive Organizing?

    DEFF Research Database (Denmark)

    Holck, Lotte

    Inclusion has long been associated with concerns of tearing down the ranked and filed “gendered and racialized” hierarchical spaces of traditional organizations, most infamously imbued in Taylorism and Scientific management with its Panopticon apparatus designed to sustain and stabilize the power......-scape (Taylor & Spicer 2007, Clegg & Kornberger 2006, Foucault 1984, Soja 1996, Lefebvre 1991, Butler 1990, Acker 2006, 2009, 1990, Ashcraft 2013, 2001). Counter intuitively my research shows how the allegedly borderless, flat, free seating open office space does not a priory convey membership inclusion...

  16. 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

  17. 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.

  18. A Comprehensive Description and Evolutionary Analysis of 22 Grouper (Perciformes, Epinephelidae) Mitochondrial Genomes with Emphasis on Two Novel Genome Organizations

    Science.gov (United States)

    Zhang, Xiang; Ding, Shaoxiong

    2013-01-01

    Groupers of the family Epinephelidae are a diverse and economically valuable group of reef fishes. To investigate the evolution of their mitochondrial genomes we characterized and compared these genomes among 22 species, 17 newly sequenced. Among these fishes we identified three distinct genome organizations, two of them never previously reported in vertebrates. In 19 of these species, mitochondrial genomes followed the typical vertebrate canonical organization with 13 protein-coding genes, 22 tRNAs, two rRNAs, and a non-coding control region. Differing from this, members of genus Variola have an extra tRNA-Ile between tRNA-Val and 16S rRNA. Evidence suggests that this evolved from tRNA-Val via a duplication event due to slipped strand mispairing during replication. Additionally, Cephalopholis argus has an extra tRNA-Asp in the midst of the control region, likely resulting from long-range duplication of the canonical tRNA-Asp through illicit priming of mitochondrial replication by tRNAs. Along with their gene contents, we characterized the regulatory elements of these mitochondrial genomes’ control regions, including putative termination-associated sequences and conserved sequence blocks. Looking at the mitochondrial genomic constituents, rRNA and tRNA are the most conserved, followed by protein-coding genes, and non-coding regions are the most divergent. Divergence rates vary among the protein-coding genes, and the three cytochrome oxidase subunits (COI, II, III) are the most conserved, while NADH dehydrogenase subunit 6 (ND6) and the ATP synthase subunit 8 (ATP8) are the most divergent. We then tested the phylogenetic utility of this new mt genome data using 12 protein-coding genes of 48 species from the suborder Percoidei. From this, we provide further support for the elevation of the subfamily Epinephelinae to family Epinephelidae, the resurrection of the genus Hyporthodus, and the combination of the monotypic genera Anyperodon and Cromileptes to genus

  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. 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.

  1. Landscape genomics of Sphaeralcea ambigua in the Mojave Desert: a multivariate, spatially-explicit approach to guide ecological restoration

    Science.gov (United States)

    Shryock, Daniel F.; Havrilla, Caroline A.; DeFalco, Lesley; Esque, Todd C.; Custer, Nathan; Wood, Troy E.

    2015-01-01

    Local adaptation influences plant species’ responses to climate change and their performance in ecological restoration. Fine-scale physiological or phenological adaptations that direct demographic processes may drive intraspecific variability when baseline environmental conditions change. Landscape genomics characterize adaptive differentiation by identifying environmental drivers of adaptive genetic variability and mapping the associated landscape patterns. We applied such an approach to Sphaeralcea ambigua, an important restoration plant in the arid southwestern United States, by analyzing variation at 153 amplified fragment length polymorphism loci in the context of environmental gradients separating 47 Mojave Desert populations. We identified 37 potentially adaptive loci through a combination of genome scan approaches. We then used a generalized dissimilarity model (GDM) to relate variability in potentially adaptive loci with spatial gradients in temperature, precipitation, and topography. We identified non-linear thresholds in loci frequencies driven by summer maximum temperature and water stress, along with continuous variation corresponding to temperature seasonality. Two GDM-based approaches for mapping predicted patterns of local adaptation are compared. Additionally, we assess uncertainty in spatial interpolations through a novel spatial bootstrapping approach. Our study presents robust, accessible methods for deriving spatially-explicit models of adaptive genetic variability in non-model species that will inform climate change modelling and ecological restoration.

  2. 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.

  3. 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.

  4. Genomic organization and expression of the 3' end of the canine and feline enteric coronaviruses

    NARCIS (Netherlands)

    Vennema, H; Rossen, J W; Wesseling, J; Horzinek, M C; Rottier, P J

    1992-01-01

    The genomic organization at the 3' end of canine coronavirus (CCV) and feline enteric coronavirus (FECV) was determined by sequence analysis and compared to that of feline infectious peritonitis virus (FIPV) and transmissible gastroenteritis virus (TGEV) of swine. Comparison of the latter two has

  5. Genomic organization and expression of the 3' end of the canine and feline enteric coronaviruses

    NARCIS (Netherlands)

    Vennema, H; Rossen, J W; Wesseling, J; Horzinek, M C; Rottier, P J

    1993-01-01

    The genomic organization at the 3' end of canine coronavirus (CCV) and feline enteric coronavirus (FECV) was determined by sequence analysis and compared to that of feline infectious peritonitis virus (FIPV) and transmissible gastroenteritis virus (TGEV) of swine. Comparison of the latter two has

  6. The organization of the histone genes in the genome of Xenopus laevis

    NARCIS (Netherlands)

    van Dongen, W.; de Laaf, L.; Zaal, R.; Moorman, A.; Destrée, O.

    1981-01-01

    We have studied the organization of the histone genes in the DNA from several individuals of Xenopus laevis. For that purpose, Southern blots of genomic DNA, that was digested with several restriction enzymes, were hybridized with radioactively labeled DNA fragments from clone X1-hi-1 (14),

  7. 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...

  8. 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.

  9. Molecular cloning and organization of two leghaemoglobin genomic sequences of soybean

    Science.gov (United States)

    Sullivan, D.; Brisson, N.; Goodchild, B.; Verma, D. P. S.

    1981-02-01

    The leghaemoglobins (Lb) are myoglobin-like proteins found in all nitrogen-fixing root nodules of legumes1-3. They are encoded by plant nuclear genes4 which are specifically induced and form the predominant protein in nodules developed in symbiosis with the appropriate species of Rhizobium. The Lb is located in the host-cell cytoplasm of the infected cell5 and is thought to facilitate oxygen diffusion6,7. Amino acid sequencing of the soybean Lbs has revealed at least four primary structures differing only in a few amino acids8-10. We have previously estimated about 40 copies of Lb sequences in the soybean (Glycine max L.) genome by cDNA hybridization4. To investigate Lb gene organization and function, we prepared and characterized a Lb cDNA recombinant molecule, pLb1, and used it to isolate two genomic Lb sequences from a library constructed in Charon 4. We report here that the organization of the two genomic Lb sequences is quite distinct and one of them seems to have an intervening sequence(s). Hybridization of pLb1 with genomic DNA from various tissues showed that Lb sequences are dispersed through more than 30 kilobases of genomic DNA and that there is no apparent sequence rearrangement or methylation changes following induction of Lb genes.

  10. 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.

  11. The Spatial Distribution of Organic Matter and Mineralogical Relationships in Carbonaceous Chondrites

    Science.gov (United States)

    Clemett, S. J.; Messenger, S.; Thomas-Keprta, K. L.; Nakamura-Messenger, K.

    2012-01-01

    Organic matter present within primitive carbonaceous meteorites represents the complex conglomeration of species formed in a variety of physically and temporally distinct environments including circumstellar space, the interstellar medium, the Solar Nebula & Jovian sub-nebulae and asteroids. In each case, multiple chemical pathways would have been available for the synthesis of organic molecules. Consequently these meteorites constitute a unique record of organic chemical evolution in the Universe and one of the biggest challenges in organic cosmochemistry has been in deciphering this record. While bulk chemical analysis has provided a detailed description of the range and diversity of organic species present in carbonaceous chondrites, there is virtually no hard experimental data as to how these species are spatially distributed and their relationship to the host mineral matrix, (with one exception). The distribution of organic phases is nevertheless critical to understanding parent body processes. The CM and CI chondrites all display evidence of low temperature (bodies. This pervasive aqueous alteration may have led to aqueous geochromatographic separation of organics and synthesis of new organics coupled to aqueous mineral alteration. To address such issues we have applied the technique of microprobe two-step laser desorption / photoionization mass spectrometry (L2MS) to map in situ the spatial distribution of a broad range of organic species at the micron scale in the freshly exposed matrices of the Bells, Tagish Lake and Murchison (CM2) carbonaceous chondrites.

  12. Genomic expansion of Domain Archaea highlights roles for organisms from new phyla in anaerobic carbon cycling

    Energy Technology Data Exchange (ETDEWEB)

    Castelle, Cindy; Wrighton, Kelly C.; Thomas, Brian C.; Hug, Laura A.; Brown, Christopher T.; Wilkins, Michael J.; Frischkorn, Kyle R.; Tringe, Susannah G.; Singh, Andrea; Markillie, Lye Meng; Taylor, Ronald C.; Williams, Kenneth H.; Banfield, Jillian F.

    2015-03-01

    Domain Archaea is currently represented by one phylum (Euryarchaeota) and two superphyla (TACK and DPANN). However, gene surveys indicate the existence of a vast diversity of uncultivated archaea for which metabolic information is lacking. We sequenced DNA from complex sediment- and groundwater-associated microbial communities sampled prior to and during an acetate biostimulation field experiment to investigate the diversity and physiology of uncultivated subsurface archaea. We sampled 15 genomes that improve resolution of a new phylum within the TACK superphylum and 119 DPANN genomes that highlight a major subdivision within the archaeal domain that separates DPANN from TACK/Euryarchaeota lineages. Within the DPANN superphylum, which lacks any isolated representatives, we defined two new phyla using sequences from 100 newly sampled genomes. The first new phylum, for which we propose the name Woesearchaeota, was defined using 54 new sequences. We reconstructed a complete (finished) genome for an archaeon from this phylum that is only 0.8 Mb in length and lacks almost all core biosynthetic pathways, but has genes encoding enzymes predicted to interact with bacterial cell walls, consistent with a symbiotic lifestyle. The second new phylum, for which we propose the name Pacearchaeota, was defined based on 46 newly sampled archaeal genomes. This phylum includes the first non-methanogen with an intermediate Type II/III RuBisCO. We also reconstructed a complete (1.24 Mb) genome for another DPANN archaeon, a member of the Diapherotrites phylum. Metabolic prediction and transcriptomic data indicate that this organism has a fermentation-based lifestyle. In fact, genomic analyses consistently indicate lack of recognizable pathways for sulfur, nitrogen, methane, oxygen, and metal cycling, and suggest that symbiotic and fermentation-based lifestyles are widespread across the DPANN superphylum. Thus, as for a recently identified superphylum of bacteria with small genomes and no

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    Jana Čížková

    Full Text Available 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. 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

  16. 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.

  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.

  18. 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

  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. 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

  1. 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.

  2. Insights From Genomics Into Spatial and Temporal Variation in Batrachochytrium dendrobatidis.

    Science.gov (United States)

    Byrne, A Q; Voyles, J; Rios-Sotelo, G; Rosenblum, E B

    2016-01-01

    Advances in genetics and genomics have provided new tools for the study of emerging infectious diseases. Researchers can now move quickly from simple hypotheses to complex explanations for pathogen origin, spread, and mechanisms of virulence. Here we focus on the application of genomics to understanding the biology of the fungal pathogen Batrachochytrium dendrobatidis (Bd), a novel and deadly pathogen of amphibians. We provide a brief history of the system, then focus on key insights into Bd variation garnered from genomics approaches, and finally, highlight new frontiers for future discoveries. Genomic tools have revealed unexpected complexity and variation in the Bd system suggesting that the history and biology of emerging pathogens may not be as simple as they initially seem. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. 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

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

    Science.gov (United States)

    Saltz, Joel; Gupta, Rajarsi; Hou, Le; Kurc, Tahsin; Singh, Pankaj; Nguyen, Vu; Samaras, Dimitris; Shroyer, Kenneth R; Zhao, Tianhao; Batiste, Rebecca; Van Arnam, John; Shmulevich, Ilya; Rao, Arvind U K; Lazar, Alexander J; Sharma, Ashish; Thorsson, Vésteinn

    2018-04-03

    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. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  5. Tempo-Spatial Compressed Sensing of Organ-on-a-Chip for Pervasive Health.

    Science.gov (United States)

    Song, Chen; Wang, Aosen; Lin, Feng; Asmani, Mohammadnabi; Zhao, Ruogang; Jin, Zhanpeng; Xiao, Jian; Xu, Wenyao

    2018-03-01

    As a micro-engineered biomimetic system to replicate key functions of living organs, organ-on-a-chip (OC) technology provides a high-throughput model for investigating complex cell interactions with both high temporal and spatial resolutions in biological studies. Typically, microscopy and high-speed video cameras are used for data acquisition, which are expensive and bulky. Recently, compressed sensing (CS) has increasingly attracted attentions due to its extremely low-complexity structure and low sampling rate. However, there is no CS solution tailored for tempo-spatial information acquisition. In this paper, we propose tempo-spatial CS (TS-CS), a unified CS architecture for OC stream, which achieves significant cost reduction and truly combines sensing with compression along the temporal and spatial domains. We point out that TS-CS can consistently achieve better performance by exploiting tempo-spatial compressibility in OC data. To this end, we comprehensively evaluate the system performance by employing four different bases for CS. With comparison to the traditional way, we show that TS-CS always obtains better recovery result with a throughput bound and can achieve around throughput improvement under a reconstruction demand by applying discrete cosine transform matrix as the basis.

  6. 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.

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

    Science.gov (United States)

    2011-01-01

    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. PMID:21798097

  8. [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.

  9. 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.

  10. Chromatin organization and cytological features of carnivorous Genlisea species with large genome size differences

    Directory of Open Access Journals (Sweden)

    Trung D. Tran

    2015-08-01

    Full Text Available The monophyletic carnivorous genus Genlisea (Lentibulariaceae is characterized by a bi-directional genome size evolution resulting in a 25-fold difference in nuclear DNA content. This is one of the largest ranges found within a genus so far and makes Genlisea an interesting subject to study mechanisms of genome and karyotype evolution.G. nigrocaulis, with 86 Mbp one of the smallest plant genomes, and the 18-fold larger genome of G. hispidula (1550 Mbp possess identical chromosome numbers (2n=40 but differ considerably in chromatin organization, nuclear and cell size. Interphase nuclei of G. nigrocaulis and of related species with small genomes, G. aurea (133 Mbp, 2n=104 and G. pygmaea (179 Mbp, 2n=80, are hallmarked by intensely DAPI-stained chromocenters, carrying typical heterochromatin-associated methylation marks (5-methylcytosine, H3K9me2, while in G. hispidula and surprisingly also in the small genome of G. margaretae (184 Mbp, 2=38 the heterochromatin marks are more evenly distributed. Probes of tandem repetitive sequences together with rDNA allow the unequivocal discrimination of 13 out of 20 chromosome pairs of G. hispidula. One of the repetitive sequences labeled half of the chromosome set almost homogenously supporting an allopolyploid status of G. hispidula and its close relative G. subglabra (1622 Mbp, 2n=40. In G. nigrocaulis eleven chromosome pairs could be individualized using a combination of rDNA and unique genomic probes. The presented data provide a basis for future studies of karyotype evolution within the genus Genlisea.

  11. 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.

  12. 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.

  13. 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.

  14. Spatial analysis of soil organic carbon in Zhifanggou catchment of the Loess Plateau.

    Directory of Open Access Journals (Sweden)

    Mingming Li

    Full Text Available Soil organic carbon (SOC reflects soil quality and plays a critical role in soil protection, food safety, and global climate changes. This study involved grid sampling at different depths (6 layers between 0 and 100 cm in a catchment. A total of 1282 soil samples were collected from 215 plots over 8.27 km(2. A combination of conventional analytical methods and geostatistical methods were used to analyze the data for spatial variability and soil carbon content patterns. The mean SOC content in the 1282 samples from the study field was 3.08 g · kg(-1. The SOC content of each layer decreased with increasing soil depth by a power function relationship. The SOC content of each layer was moderately variable and followed a lognormal distribution. The semi-variograms of the SOC contents of the six different layers were fit with the following models: exponential, spherical, exponential, Gaussian, exponential, and exponential, respectively. A moderate spatial dependence was observed in the 0-10 and 10-20 cm layers, which resulted from stochastic and structural factors. The spatial distribution of SOC content in the four layers between 20 and 100 cm exhibit were mainly restricted by structural factors. Correlations within each layer were observed between 234 and 562 m. A classical Kriging interpolation was used to directly visualize the spatial distribution of SOC in the catchment. The variability in spatial distribution was related to topography, land use type, and human activity. Finally, the vertical distribution of SOC decreased. Our results suggest that the ordinary Kriging interpolation can directly reveal the spatial distribution of SOC and the sample distance about this study is sufficient for interpolation or plotting. More research is needed, however, to clarify the spatial variability on the bigger scale and better understand the factors controlling spatial variability of soil carbon in the Loess Plateau region.

  15. [Spatial interpolation of soil organic matter using regression Kriging and geographically weighted regression Kriging].

    Science.gov (United States)

    Yang, Shun-hua; Zhang, Hai-tao; Guo, Long; Ren, Yan

    2015-06-01

    Relative elevation and stream power index were selected as auxiliary variables based on correlation analysis for mapping soil organic matter. Geographically weighted regression Kriging (GWRK) and regression Kriging (RK) were used for spatial interpolation of soil organic matter and compared with ordinary Kriging (OK), which acts as a control. The results indicated that soil or- ganic matter was significantly positively correlated with relative elevation whilst it had a significantly negative correlation with stream power index. Semivariance analysis showed that both soil organic matter content and its residuals (including ordinary least square regression residual and GWR resi- dual) had strong spatial autocorrelation. Interpolation accuracies by different methods were esti- mated based on a data set of 98 validation samples. Results showed that the mean error (ME), mean absolute error (MAE) and root mean square error (RMSE) of RK were respectively 39.2%, 17.7% and 20.6% lower than the corresponding values of OK, with a relative-improvement (RI) of 20.63. GWRK showed a similar tendency, having its ME, MAE and RMSE to be respectively 60.6%, 23.7% and 27.6% lower than those of OK, with a RI of 59.79. Therefore, both RK and GWRK significantly improved the accuracy of OK interpolation of soil organic matter due to their in- corporation of auxiliary variables. In addition, GWRK performed obviously better than RK did in this study, and its improved performance should be attributed to the consideration of sample spatial locations.

  16. Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea

    Science.gov (United States)

    Li, Meng; Baker, Brett J.; Anantharaman, Karthik; Jain, Sunit; Breier, John A.; Dick, Gregory J.

    2015-01-01

    Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans. Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Genome-enabled metabolic reconstructions and gene expression patterns show that these marine archaea are motile heterotrophs with extensive mechanisms for scavenging organic matter. Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling. PMID:26573375

  17. Human papillomavirus 1a complete DNA sequence: a novel type of genome organization among papovaviridae.

    OpenAIRE

    Danos, O; Katinka, M; Yaniv, M

    1982-01-01

    The complete nucleotide sequence of human papillomavirus type 1a (7811 nucleotides) has been established. The overall organization of the viral genome is different from that of other related papovaviruses (SV40, BKV, polyoma). Firstly, genetic information seems to be coded by one strand. Secondly, no significant homology is found with SV40 or polyoma coding sequence for either DNA or deducted protein sequences. The relatedness of human and bovine papillomaviruses is revealed by a conserved co...

  18. 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...

  19. 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...

  20. 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

  1. Soil organic carbon stocks in Alaska estimated with spatial and pedon data

    Science.gov (United States)

    Bliss, Norman B.; Maursetter, J.

    2010-01-01

    Temperatures in high-latitude ecosystems are increasing faster than the average rate of global warming, which may lead to a positive feedback for climate change by increasing the respiration rates of soil organic C. If a positive feedback is confirmed, soil C will represent a source of greenhouse gases that is not currently considered in international protocols to regulate C emissions. We present new estimates of the stocks of soil organic C in Alaska, calculated by linking spatial and field data developed by the USDA NRCS. The spatial data are from the State Soil Geographic database (STATSGO), and the field and laboratory data are from the National Soil Characterization Database, also known as the pedon database. The new estimates range from 32 to 53 Pg of soil organic C for Alaska, formed by linking the spatial and field data using the attributes of Soil Taxonomy. For modelers, we recommend an estimation method based on taxonomic subgroups with interpolation for missing areas, which yields an estimate of 48 Pg. This is a substantial increase over a magnitude of 13 Pg estimated from only the STATSGO data as originally distributed in 1994, but the increase reflects different estimation methods and is not a measure of the change in C on the landscape. Pedon samples were collected between 1952 and 2002, so the results do not represent a single point in time. The linked databases provide an improved basis for modeling the impacts of climate change on net ecosystem exchange.

  2. Nanoscale Spatial Organization of Prokaryotic Cells Studied by Super-Resolution Optical Microscopy

    Science.gov (United States)

    McEvoy, Andrea Lynn

    All cells spatially organize their interiors, and this arrangement is necessary for cell viability. Until recently, it was believed that only eukaryotic cells spatially segregate their components. However, it is becoming increasingly clear that bacteria also assemble their proteins into complex patterns. In eukaryotic cells, spatial organization arises from membrane bound organelles as well as motor transport proteins which can move cargos within the cell. To date, there are no known motor transport proteins in bacteria and most microbes lack membrane bound organelles, so it remains a mystery how bacterial spatial organization emerges. In hind-sight it is not surprising that bacteria also exhibit complex spatial organization considering much of what we have learned about the basic processes that take place in all cells, such as transcription and translation was first discovered in prokaryotic cells. Perhaps the fundamental principles that govern spatial organization in prokaryotic cells may be applicable in eukaryotic cells as well. In addition, bacteria are attractive model organism for spatial organization studies because they are genetically tractable, grow quickly and much biochemical and structural data is known about them. A powerful tool for observing spatial organization in cells is the fluorescence microscope. By specifically tagging a protein of interest with a fluorescent probe, it is possible to examine how proteins organize and dynamically assemble inside cells. A significant disadvantage of this technology is its spatial resolution (approximately 250 nm laterally and 500 nm axially). This limitation on resolution causes closely spaced proteins to look blurred making it difficult to observe the fine structure within the complexes. This resolution limit is especially problematic within small cells such as bacteria. With the recent invention of new optical microscopies, we now can surpass the existing limits of fluorescence imaging. In some cases, we can

  3. 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

  4. 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.

  5. 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

  6. Discrete spatial organization of TGFβ receptors couples receptor multimerization and signaling to cellular tension.

    Science.gov (United States)

    Rys, Joanna P; DuFort, Christopher C; Monteiro, David A; Baird, Michelle A; Oses-Prieto, Juan A; Chand, Shreya; Burlingame, Alma L; Davidson, Michael W; Alliston, Tamara N

    2015-12-10

    Cell surface receptors are central to the cell's ability to generate coordinated responses to the multitude of biochemical and physical cues in the microenvironment. However, the mechanisms by which receptors enable this concerted cellular response remain unclear. To investigate the effect of cellular tension on cell surface receptors, we combined novel high-resolution imaging and single particle tracking with established biochemical assays to examine TGFβ signaling. We find that TGFβ receptors are discretely organized to segregated spatial domains at the cell surface. Integrin-rich focal adhesions organize TβRII around TβRI, limiting the integration of TβRII while sequestering TβRI at these sites. Disruption of cellular tension leads to a collapse of this spatial organization and drives formation of heteromeric TβRI/TβRII complexes and Smad activation. This work details a novel mechanism by which cellular tension regulates TGFβ receptor organization, multimerization, and function, providing new insight into the mechanisms that integrate biochemical and physical cues.

  7. [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

  8. Spatial Patterns of Soil Organic Carbon and Total Nitrogen in Mesquite Coppice Dunes

    Science.gov (United States)

    Ebbs, L. M.; Throop, H. L.

    2008-12-01

    Woody encroachment, an increase in woody plant abundance in formerly grass-dominated ecosystems, has occurred in semi-arid and arid systems worldwide over the past century. Woody encroachment has emerged as a potentially important, but highly uncertain, component of the North American carbon sink. The effects of woody plant encroachment on soil organic carbon (SOC) and total nitrogen (TN) relative to Prosopis velutina have been explored in the Sonoran Desert, where strong spatial patterns in SOC and TN based on shrub size and subcanopy location exist. Encroachment of Prosopis glandulosa in sandy soils in the Chihuahuan Desert leads to coppice dune formation. We applied spatially-intensive soil sampling methods around P. glandulosa dunes in the Chihuahuan Desert to see how spatial patterns differed from patterns in the Sonoran Desert, where dunes do not form. Approximately 15 soil cores were taken from within and around each of 13 dunes and analyzed for bulk density, SOC, and TN. The aboveground biomass of P. glandulosa in coppice dunes was also collected for a comparison of aboveground biomass and SOC pools. Intercanopy soils had greater bulk density than soils within dunes (Pglandulosa coppice dunes does not require information on individual dune size or spatial position. The differences in SOC and TN accumulation patterns beneath P. velutina and P. glandulosa may result from differences in shrub morphology and its consequences for patterns of aeolian erosion and deposition.

  9. 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.

  10. 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

  11. Assessment of Homodyned K Distribution Modeling Ultrasonic Speckles from Scatterers with Varying Spatial Organizations

    Directory of Open Access Journals (Sweden)

    Xiao Hu

    2017-01-01

    Full Text Available Objective. This paper presents an assessment of physical meanings of parameter and goodness of fit for homodyned K (HK distribution modeling ultrasonic speckles from scatterer distributions with wide-varying spatial organizations. Methods. A set of 3D scatterer phantoms based on gamma distributions is built to be implemented from the clustered to random to uniform scatterer distributions continuously. The model parameters are obtained by maximum likelihood estimation (MLE from statistical histograms of the ultrasonic envelope data and then compared with those by the optimally fitting models chosen from three single distributions. Results show that the parameters of the HK distribution still present their respective physical meanings of independent contributions in the scatterer distributions. Moreover, the HK distribution presents better goodness of fit with a maximum relative MLE difference of 6.23% for random or clustered scatterers with a well-organized periodic structure. Experiments based on ultrasonic envelope data from common carotid arterial B-mode images of human subjects validate the modeling performance of HK distribution. Conclusion. We conclude that the HK model for ultrasonic speckles is a better choice for characterizing tissue with a wide variety of spatial organizations, especially the emphasis on the goodness of fit for the tissue in practical applications.

  12. Quality and reactivity of dissolved organic matter in a Mediterranean river across hydrological and spatial gradients.

    Science.gov (United States)

    Ejarque, Elisabet; Freixa, Anna; Vazquez, Eusebi; Guarch, Alba; Amalfitano, Stefano; Fazi, Stefano; Romaní, Anna M; Butturini, Andrea

    2017-12-01

    Understanding DOM transport and reactivity in rivers is essential to having a complete picture of the global carbon cycle. In this study, we explore the effects of hydrological variability and downstream transport on dissolved organic matter (DOM) dynamics in a Mediterranean river. We sampled the main stem of the river Tordera from the source to the sea, over a range of fifteen hydrological conditions including extreme events (flood and drought). By exploring spatial and temporal gradients of DOM fluorescence properties, river hydrology was found to be a significant predictor of DOM spatial heterogeneity. An additional space-resolved mass balance analysis performed on four contrasting hydrological conditions revealed that this was due to a shift in the biogeochemical function of the river. Flood conditions caused a conservative transport of DOM, generating a homogeneous, humic-like spatial profile of DOM quality. Lower flows induced a non-conservative, reactive transport of DOM, which enhanced the spatial heterogeneity of DOM properties. Moreover, the downstream evolution of DOM chemostatic behaviour revealed that the role of hydrology in regulating DOM properties increased gradually downstream, indicating an organised inter-dependency between the spatial and the temporal dimensions. Overall, our findings reveal that riverine DOM dynamics is in constant change owing to varying hydrological conditions, and emphasize that in order to fully understand the role of rivers in the global carbon cycle, it is necessary to take into account the full range of hydrological variability, from floods to droughts. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  13. Highly spatially- and seasonally-resolved predictive contamination maps for persistent organic pollutants: development and validation.

    Science.gov (United States)

    Ballabio, Cristiano; Guazzoni, Niccoló; Comolli, Roberto; Tremolada, Paolo

    2013-08-01

    A reliable spatial assessment of the POPs contamination in soils is essential for burden studies and flux evaluations. Soil characteristics and properties vary enormously even within small spatial scale and over time; therefore soil capacity of accumulating POPs varies greatly. In order to include this very high spatial and temporal variability, models can be used for assessing soil accumulation capacity in a specific time and space and, from it, the spatial distribution and temporal trends of POPs concentrations. In this work, predictive contamination maps of the accumulation capacity of soils were developed at a space resolution of 1×1m with a time frame of one day, in a study area located in the central Alps. Physical algorithms for temperature and organic carbon estimation along the soil profile and across the year were fitted to estimate the horizontal, vertical and seasonal distribution of the contamination potential for PCBs in soil (Ksa maps). The resulting maps were cross-validated with an independent set of PCB contamination data, showing very good agreement (e.g. for CB-153, R(2)=0.80, p-value≤2.2·10(-06)). Slopes of the regression between predicted Ksa and experimental concentrations were used to map the soil contamination for the whole area, taking into account soil characteristics and temperature conditions. These maps offer the opportunity to evaluate burden (concentration maps) and fluxes (emission maps) with highly resolved temporal and spatial detail. In addition, in order to explain the observed low autumn PCB concentrations in soil related to the high Ksa values of this period, a dynamic model of seasonal variation of soil concentrations was developed basing on rate parameters fitted on measured concentrations. The model was able to describe, at least partially, the observed different behavior between the quite rapid discharge phase in summer and the slow recharge phase in autumn. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Effects of cell spatial organization and size distribution on ultrasound backscattering.

    Science.gov (United States)

    Saha, Ratan K; Kolios, Michael C

    2011-10-01

    In ultrasound tissue characterization dealing with cellular aggregates (such as tumors), it can be hypothesized that cell microstructure and spatial distribution dominate the backscatter signal. Effects of spatial organization and size distribution of nuclei in cell aggregates on ultrasound backscatter are examined in this work using 2-D computer simulations. The nuclei embedded in cytoplasm were assumed to be weak scatterers of incident ultrasound waves, and therefore multiple scattering could be neglected. The fluid sphere model was employed to obtain the scattering amplitude for each nucleus and the backscatter echo was generated by summing scattered signals originating from many nuclei. A Monte Carlo algorithm was implemented to generate realizations of cell aggregates. It was found that the integrated backscattering coefficient (IBSC) computed between 10 and 30 MHz increased by about 27 dB for a spatially random distribution of mono-disperse nuclei (radius = 4.5 μm) compared with that of a sample of periodically positioned mono-disperse nuclei. The IBSC also increased by nearly 7 dB (between 10 and 30 MHz) for a spatially random distribution of poly-disperse nuclei (mean radius ± SD = 4.5 ± 1.54 μm) compared with that of a spatially random distribution of mono-disperse nuclei. Two different Gaussian pulses with center frequencies 5 and 25 MHz were employed to study the backscatter envelope statistics. An 80% bandwidth was chosen for each case with approximately 0.32 mm as the full-width at half-maximum (FWHM) for the first pulse and 0.06 mm for the second. The incident beam was approximated as a Gaussian beam (FWHM = 2.11 and 1.05 mm for those pulses, respectively). The backscatter signal envelope histograms generally followed the Rayleigh distribution for mono-disperse and poly-disperse samples. However, for samples with partially ordered nuclei, if the irradiating pulse contained a frequency for which ultrasound wavelength and scatter periodicity became

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

    DEFF Research Database (Denmark)

    Zhang, Xiuqing; Yang, Huanming; Yu, Jun

    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...

  16. DGGE with genomic DNA: suitable for detection of numerically important organisms but not for identification of the most abundant organisms.

    Science.gov (United States)

    de Araújo, Juliana Calábria; Schneider, René Peter

    2008-12-01

    Identification of all important community members as well as of the numerically dominant members of a community are key aspects of microbial community analysis of bioreactor samples. A systematic study was conducted with artificial consortia to test whether denaturing gradient gel electrophoresis (DGGE) is a reliable technique to obtain such community data under conditions where results would not be affected by differences in DNA extraction efficiency from cells. A total of 27 consortia were established by mixing DNA extracted from Escherichia coli K12, Burkholderia cepacia and Stenotrophomonas maltophilia in different proportions. Concentrations of DNA of single organisms in the consortia were either 0.04, 0.4 or 4ng/microl. DGGE-PCR of genomic DNA with primer sets targeted at the V3 and V6-V8 regions of the 16S rDNA failed to detect the three community members in only 7% of consortia, but provided incorrect information about dominance or co-dominance for 85% and 89% of consortia with the primer sets for the V6-V8 and V3 regions, respectively. The high failure rate in detection of dominant B. cepacia with the primers for the V6-V8 region was attributable to a single nucleotide primer mismatch in the target sequences of both, the forward and reverse primer. Amplification bias in PCR of E. coli and S. maltophilia for the V6-V8 region and for all three organisms for the V3 region occurred due to interference of genomic DNA in PCR-DGGE, since a nested PCR approach, where PCR-DGGE was started from mixtures of 16S rRNA genes of the organisms, provided correct information about the relative abundance of original DNA in the sample. Multiple bands were not observed in pure culture amplicons produced with the V6-V8 primer pair, but pure culture V3 DGGE profiles of E. coli, S. maltophilia and B. cepacia contained 5, 3 and 3 bands, respectively. These results demonstrate DGGE was suitable for identification of all important community members in the three-membered artificial

  17. The Spatial Variability of Organic Matter and Decomposition Processes at the Marsh Scale

    Science.gov (United States)

    Yousefi Lalimi, Fateme; Silvestri, Sonia; D'Alpaos, Andrea; Roner, Marcella; Marani, Marco

    2017-04-01

    Coastal salt marshes sequester carbon as they respond to the local Rate of Relative Sea Level Rise (RRSLR) and their accretion rate is governed by inorganic soil deposition, organic soil production, and soil organic matter (SOM) decomposition. It is generally recognized that SOM plays a central role in marsh vertical dynamics, but while existing limited observations and modelling results suggest that SOME varies widely at the marsh scale, we lack systematic observations aimed at understanding how SOM production is modulated spatially as a result of biomass productivity and decomposition rate. Marsh topography and distance to the creek can affect biomass and SOM production, while a higher topographic elevation increases drainage, evapotranspiration, aeration, thereby likely inducing higher SOM decomposition rates. Data collected in salt marshes in the northern Venice Lagoon (Italy) show that, even though plant productivity decreases in the lower areas of a marsh located farther away from channel edges, the relative contribution of organic soil production to the overall vertical soil accretion tends to remain constant as the distance from the channel increases. These observations suggest that the competing effects between biomass production and aeration/decomposition determine a contribution of organic soil to total accretion which remains approximately constant with distance from the creek, in spite of the declining plant productivity. Here we test this hypothesis using new observations of SOM and decomposition rates from marshes in North Carolina. The objective is to fill the gap in our understanding of the spatial distribution, at the marsh scale, of the organic and inorganic contributions to marsh accretion in response to RRSLR.

  18. 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.

  19. Tracking changes in land-use and drainage status of organic soils using heterogeneous spatial datasets

    Science.gov (United States)

    Untenecker, Johanna; Tiemeyer, Bärbel; Freibauer, Annette; Laggner, Andreas; Luterbacher, Jürg

    2016-04-01

    Tracking land-use since 1990 is one of the major challenges in greenhouse gas (GHG) reporting under the United Nations Framework Convention on Climate Change (UNFCCC) and the Kyoto Protocol, as the data availability, especially for the base year 1990, is often poor. Even if data is available, spatial and thematic resolution will often change over time or differ even within one country. Such inconsistencies will cause a strong overestimation of land use change (LUC) if not adequately accounted for. Using different spatial datasets, we present a method that allows tracking changes in land-use and drainage status of organic soils. The drainage status is relevant for the Kyoto activities grazing land management (GM) and wetland drainage and rewetting (WDR) as the GHG emissions of organic soils strongly depend on the groundwater level. We used datasets that are already used for the German national inventory report (Digital Landscape Model of official cadastre data) and high resolution spatial datasets (CIR aerial photography) derived for biodiversity monitoring of six federal states in North and East Germany. This data is combined with the legal protection status such as nature conservation areas. To create a consistent time series, we developed a translation key which allows quantifying gross and net LUC in a spatially explicit manner. The developed method fills the lack of data for 1990 and allows GHG accounting on higher Tier levels as soon as detailed emission factors are ready to be implemented. LUC can be stratified by the protection status. Areas without a protection status show a trend towards both intensification of land-use and drier conditions. Highly protected areas show an opposite trend while a moderate protection level (e.g. by nature parks) did only have very weak effects. Furthermore, there are major differences between federal states. In Schleswig-Holstein, known as a federal state of high agricultural production, organic soils tend to become drier and

  20. 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

    2008-02-05

    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. 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. 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 the advancement of comparative

  1. 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

  2. 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

  3. Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome

    Directory of Open Access Journals (Sweden)

    Bringaud Frédéric

    2009-05-01

    major differences. The SIDER1 subfamily is more heterogeneous and shows an evolutionary link with vestigial DIRE retroposons as previously observed for the ingi/RIME and L1Tc/NARTc couples identified in the T. brucei and T. cruzi genomes, whereas no identified DIREs are related to SIDER2 sequences. Although SIDER1s and SIDER2s display equivalent genomic distribution globally, the varying degrees of sequence conservation, preferential genomic disposition, and differential association to orthologous genes allude to an intricate web of SIDER assimilation in these parasitic organisms.

  4. 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 reten...

  5. 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.

  6. DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

    Science.gov (United States)

    Anselmetti, Yoann; Patterson, Murray; Ponty, Yann; B�rard, S�verine; Chauve, Cedric; Scornavacca, Celine; Daubin, Vincent; Tannier, Eric

    2017-01-01

    DeCoSTAR is a software that aims at reconstructing the organization of ancestral genes or genomes in the form of sets of neighborhood relations (adjacencies) between pairs of ancestral genes or gene domains. It can also improve the assembly of fragmented genomes by proposing evolutionary-induced adjacencies between scaffolding fragments. Ancestral genes or domains are deduced from reconciled phylogenetic trees under an evolutionary model that considers gains, losses, speciations, duplications, and transfers as possible events for gene evolution. Reconciliations are either given as input or computed with the ecceTERA package, into which DeCoSTAR is integrated. DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann–Gibbs distribution centered around parsimonious solutions, and statistical supports on ancestral and extant adjacencies are provided. DeCoSTAR supports the features of previously contributed tools that reconstruct ancestral adjacencies, namely DeCo, DeCoLT, ART-DeCo, and DeClone. In a few minutes, DeCoSTAR can reconstruct the evolutionary history of domains inside genes, of gene fusion and fission events, or of gene order along chromosomes, for large data sets including dozens of whole genomes from all kingdoms of life. We illustrate the potential of DeCoSTAR with several applications: ancestral reconstruction of gene orders for Anopheles mosquito genomes, multidomain proteins in Drosophila, and gene fusion and fission detection in Actinobacteria. Availability: http://pbil.univ-lyon1.fr/software/DeCoSTAR (Last accessed April 24, 2017). PMID:28402423

  7. 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.

  8. 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

  9. 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

    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...... of quantitative studies conducted across the world have shown that internal fragmentation, conflicts and alliances between armed groups played a crucial role in explaining the onset and diffusion of internecine violence (Bakke et al. 2012; Cunningham et al. 2012) and the often elusive quest for peace settlements...... 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...

  10. 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

  11. 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.

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

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    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.

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

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    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).

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

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    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

  15. Biogenic gradients in algal density affect the emergent properties of spatially self-organized mussel beds.

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    Liu, Quan-Xing; Weerman, Ellen J; Gupta, Rohit; Herman, Peter M J; Olff, Han; van de Koppel, Johan

    2014-07-06

    Theoretical models highlight that spatially self-organized patterns can have important emergent effects on the functioning of ecosystems, for instance by increasing productivity and affecting the vulnerability to catastrophic shifts. However, most theoretical studies presume idealized homogeneous conditions, which are rarely met in real ecosystems. Using self-organized mussel beds as a case study, we reveal that spatial heterogeneity, resulting from the large-scale effects of mussel beds on their environment, significantly alters the emergent properties predicted by idealized self-organization models that assume homogeneous conditions. The proposed model explicitly considers that the suspended algae, the prime food for the mussels, are supplied by water flow from the seaward boundary of the bed, which causes in combination with consumption a gradual depletion of algae over the simulated domain. Predictions of the model are consistent with properties of natural mussel patterns observed in the field, featuring a decline in mussel biomass and a change in patterning. Model analyses reveal a fundamental change in ecosystem functioning when this self-induced algal depletion gradient is included in the model. First, no enhancement of secondary productivity of the mussels comparing with non-patterns states is predicted, irrespective of parameter setting; the equilibrium amount of mussels is entirely set by the input of algae. Second, alternate stable states, potentially present in the original (no algal gradient) model, are absent when gradual depletion of algae in the overflowing water layer is allowed. Our findings stress the importance of including sufficiently realistic environmental conditions when assessing the emergent properties of self-organized ecosystems.

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

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    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.

  17. A gene regulatory network for apical organ neurogenesis and its spatial control in sea star embryos.

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    Cheatle Jarvela, Alys M; Yankura, Kristen A; Hinman, Veronica F

    2016-11-15

    How neural stem cells generate the correct number and type of differentiated neurons in appropriate places remains an important question. Although nervous systems are diverse across phyla, in many taxa the larva forms an anterior concentration of serotonergic neurons, or apical organ. The sea star embryo initially has a pan-neurogenic ectoderm, but the genetic mechanism that directs a subset of these cells to generate serotonergic neurons in a particular location is unresolved. We show that neurogenesis in sea star larvae begins with soxc-expressing multipotent progenitors. These give rise to restricted progenitors that express lhx2/9 soxc- and lhx2/9-expressing cells can undergo both asymmetric divisions, allowing for progression towards a particular neural fate, and symmetric proliferative divisions. We show that nested concentric domains of gene expression along the anterior-posterior (AP) axis, which are observed in a great diversity of metazoans, control neurogenesis in the sea star larva by promoting particular division modes and progression towards becoming a neuron. This work explains how spatial patterning in the ectoderm controls progression of neurogenesis in addition to providing spatial cues for neuron location. Modification to the sizes of these AP territories provides a simple mechanism to explain the diversity of neuron number among apical organs. © 2016. Published by The Company of Biologists Ltd.

  18. Spatial variation in concentration and sources of organic carbon in the Lena River, Siberia

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    Kutscher, Liselott; Mörth, Carl-Magnus; Porcelli, Don; Hirst, Catherine; Maximov, Trofim C.; Petrov, Roman E.; Andersson, Per S.

    2017-08-01

    Global warming in permafrost areas is expected to change fluxes of riverine organic carbon (OC) to the Arctic Ocean. Here OC concentrations, stable carbon isotope signatures (δ13C), and carbon-nitrogen ratios (C/N) are presented from 22 sampling stations in the Lena River and 40 of its tributaries. Sampling was conducted during two expeditions: the first in July 2012 in the south and southeastern region and the second in June 2013 in the northern region of the Lena basin. The data showed significant spatial differences in concentrations and major sources of OC. Mean subcatchment slopes were correlated with OC concentrations, implying that mountainous areas in general had lower concentrations than lowland areas. δ13C and C/N data from tributaries originating in mountainous areas indicated that both dissolved and particulate OC (DOC and POC) were mainly derived from soil organic matter (SOM). In contrast, tributaries originating in lowland areas had larger contributions from fresh vegetation to DOC, while aquatically produced OC was the major source of POC. We suggest that these differences in dominant sources indicated differences in dominant flow pathways. Tributaries with larger influence of fresh vegetation probably had surficial flow pathways, while tributaries with more SOM influence had deeper water flow pathways. Thus, the future export of OC to the Arctic Ocean will likely be controlled by changes in spatial patterns in hydroclimatology and the depth of the active layers influencing the dominant water flow pathways in Arctic river basins.

  19. Explore the Spatial-Temporal Interrelation between Groundwater and Surface Water by Self-Organizing Map

    Science.gov (United States)

    Chen, I. T.; Chang, L. C.; Chang, F. J.

    2016-12-01

    Groundwater is one of important water resources in Taiwan. Due to the indirect impacts of changes in rainfall characteristics and geomorphological limitation on groundwater recharge, it is imperative to investigate the variation of groundwater resources for making effective management strategies on groundwater resources. This study investigated the spatio-temporal interactive mechanism between surface water and groundwater over the whole river basin by using the self-organizing map (SOM). The Gaoping River basin in Taiwan is the study case and its long-term regional data sets are used for analysis. By applying the self-organizing map (SOM) technology, the variation of groundwater level and topology distribution characteristics can distinctly appear in temporal and spatial way. The results showed: (1) The trend of groundwater movement is from the east area to the west area. In the east area, the groundwater easily recharged from precipitation and discharged to streams since its high permeability is high. There are different types of water movement in the four aquifers. (2) In the second and third aquifers, the seasonal variations of groundwater are larger than others. (3) The spatio-temporal variations of surface water and groundwater were nicely classified by using the SOM model. The level variations of spatial distribution and seasonal variations have been comprehensively linked, which visually displayed topology characteristics of each classification of groundwater level.

  20. 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.

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    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.

  1. Spatial variability and stocks of soil organic carbon in the Gobi desert of Northwestern China.

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    Pingping Zhang

    Full Text Available Soil organic carbon (SOC plays an important role in improving soil properties and the C global cycle. Limited attention, though, has been given to assessing the spatial patterns and stocks of SOC in desert ecosystems. In this study, we quantitatively evaluated the spatial variability of SOC and its influencing factors and estimated SOC storage in a region (40 km2 of the Gobi desert. SOC exhibited a log-normal depth distribution with means of 1.6, 1.5, 1.4, and 1.4 g kg(-1 for the 0-10, 10-20, 20-30, and 30-40 cm layers, respectively, and was moderately variable according to the coefficients of variation (37-42%. Variability of SOC increased as the sampling area expanded and could be well parameterized as a power function of the sampling area. Significant correlations were detected between SOC and soil physical properties, i.e. stone, sand, silt, and clay contents and soil bulk density. The relatively coarse fractions, i.e. sand, silt, and stone contents, had the largest effects on SOC variability. Experimental semivariograms of SOC were best fitted by exponential models. Nugget-to-sill ratios indicated a strong spatial dependence for SOC concentrations at all depths in the study area. The surface layer (0-10 cm had the largest spatial dependency compared with the other layers. The mapping revealed a decreasing trend of SOC concentrations from south to north across this region of the Gobi desert, with higher levels close to an oasis and lower levels surrounded by mountains and near the desert. SOC density to depths of 20 and 40 cm for this 40 km2 area was estimated at 0.42 and 0.68 kg C m(-2, respectively. This study provides an important contribution to understanding the role of the Gobi desert in the global carbon cycle.

  2. The Importance of Facial Features and Their Spatial Organization for Attractiveness is Modulated by Gender

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    D Gill

    2011-04-01

    Full Text Available Many studies suggest that facial attractiveness signals mate quality. Fewer studies argue that the preference criteria emerge as a by-product of cortical processes. One way or the other, preference criteria should not be necessarily identical between female and male observers because either their preferences may have different evolutionary roles or they may even be due to known differences in visiospatial skills and brain function lateralization (ie, advantages favoring males' inability to determine spatial relations despite distracting information. The goal of this study was to assess sex differences in face attractiveness judgments by estimating the importance of facial features and their spatial organization. To this end, semipartial correlations were measured between intact-face preferences and preferences based on specific facial parts (eyes, nose, mouth, and hairstyle or preferences based more on configuration (as reflected by low spatial frequency images. The results show strategy modulations by both observers' and faces' genders. In general, the association between intact-face preferences and parts-based preferences was significantly higher for female compared with male participants. For female faces, males' preferences were more strongly associated with their low spatial frequency preferences than were those of females. The two genders' strategies were more similar when judging male faces, and males performed more criteria modifications across face gender. The similarities between sexes regarding male faces are in line with previous studies that showed higher assignment of importance among men to attractiveness. Moreover, the results may suggest that men adjust their strategy to assess the danger of other males as potential rivals for mates.

  3. Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms

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    Zhong Daibin

    2006-06-01

    Full Text Available Abstract Background HSP90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. HSP90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. In this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in GenBank, and address the diversity, evolution, gene structure, conservation and nomenclature of the HSP90 family of genes across all organisms. Results Twelve new genes and a new type HSP90C2 were identified. The chromosomal location, exon splicing, and prediction of whether they are functional copies were documented, as well as the amino acid length and molecular mass of their polypeptides. The conserved regions across all protein sequences, and signature sequences in each subfamily were determined, and a standardized nomenclature system for this gene family is presented. The proeukaryote HSP90 homologue, HTPG, exists in most Bacteria species but not in Archaea, and it evolved into three lineages (Groups A, B and C via two gene duplication events. None of the organellar-localized HSP90s were derived from endosymbionts of early eukaryotes. Mitochondrial TRAP and endoplasmic reticulum HSP90B separately originated from the ancestors of HTPG Group A in Firmicutes-like organisms very early in the formation of the eukaryotic cell. TRAP is monophyletic and present in all Animalia and some Protista species, while HSP90B is paraphyletic and present in all eukaryotes with the exception of some Fungi species, which appear to have lost it. Both HSP90C (chloroplast HSP90C1 and location-undetermined SP90C2 and cytosolic HSP90A are monophyletic, and originated from HSP90B by independent gene duplications. HSP90C exists only in Plantae, and was duplicated into HSP90C1 and HSP90C2 isoforms in higher plants. HSP90A occurs across all

  4. The influence of spatial organization of the home on inhabitant activity.

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    Bafna, Sonit; Chambers, Earle

    2014-12-01

    We describe a study to test whether the arrangement of rooms in an apartment has any systematic association with the levels of activity of its inhabitants. This study was conducted in a sample of Latino adults living in the Bronx, New York. A convenience sample of 19 apartments was selected within the Bronx, NY and one adult volunteer was selected from each household based on who was present at the time of a home visit conducted to collect information on extent of activities. Floor plans for the apartments were obtained from the city authorities. The paper begins by reasoning about the mechanism by which the organization of space can influence levels of activity in the house, and goes on distinguish, first, habitual from deliberate and planned activity, and second, sedentary from more vigorous activity. It is argued that habitual activity would be more susceptible to the influence of spatial organization, and that such habitual activity is likely to be sedentary activity around the house rather than moderate or intense activity. Furthermore, different types of sedentary activity should respond differentially to spatial organization. Specifically, sedentary activities that are susceptible to social life in the house, or require social participation like watching TV or playing cards, should show a positive association with how closely the rooms are knit together, while sedentary activities such as reading, working on computers, and playing video games, that are better conducted in solitary situations, should not. Bivariate analyses showed that interconnectedness (a modified version of integration) was significantly associated with hours spent in socially susceptible sedentary activities but not with hours spent in sedentary activities that occur in solitary conditions, like using the computer or reading. In multivariate analyses, conducted to control for the effects of age and educational level, interconnectedness was still significantly associated with sedentary

  5. Structural features based genome-wide characterization and prediction of nucleosome organization

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    Gan Yanglan

    2012-03-01

    Full Text Available Abstract Background Nucleosome distribution along chromatin dictates genomic DNA accessibility and thus profoundly influences gene expression. However, the underlying mechanism of nucleosome formation remains elusive. Here, taking a structural perspective, we systematically explored nucleosome formation potential of genomic sequences and the effect on chromatin organization and gene expression in S. cerevisiae. Results We analyzed twelve structural features related to flexibility, curvature and energy of DNA sequences. The results showed that some structural features such as DNA denaturation, DNA-bending stiffness, Stacking energy, Z-DNA, Propeller twist and free energy, were highly correlated with in vitro and in vivo nucleosome occupancy. Specifically, they can be classified into two classes, one positively and the other negatively correlated with nucleosome occupancy. These two kinds of structural features facilitated nucleosome binding in centromere regions and repressed nucleosome formation in the promoter regions of protein-coding genes to mediate transcriptional regulation. Based on these analyses, we integrated all twelve structural features in a model to predict more accurately nucleosome occupancy in vivo than the existing methods that mainly depend on sequence compositional features. Furthermore, we developed a novel approach, named DLaNe, that located nucleosomes by detecting peaks of structural profiles, and built a meta predictor to integrate information from different structural features. As a comparison, we also constructed a hidden Markov model (HMM to locate nucleosomes based on the profiles of these structural features. The result showed that the meta DLaNe and HMM-based method performed better than the existing methods, demonstrating the power of these structural features in predicting nucleosome positions. Conclusions Our analysis revealed that DNA structures significantly contribute to nucleosome organization and influence

  6. [Spatial distribution characteristics of organic carbon in the soil-plant systems in the Yellow River estuary tidal flat wetland].

    Science.gov (United States)

    Dong, Hong-Fang; Yu, Jun-Bao; Sun, Zhi-Gao; Mu, Xiao-Jie; Chen, Xiao-Bing; Mao, Pei-Li; Wu, Chun-Fa; Guan, Bo

    2010-06-01

    Well-understand the organic carbon status in the Yellow River delta is the most important for studying the biogeochemical processes of the muddy-sandy coastal wetland and ecological restoration. The spatial distribution characteristics and its impact factors of organic carbon in the plant-soil systems of new-born tidal flat wetland in the Yellow River estuary were studied. The results showed that the difference of plant organic carbon content in different plant communities were not obvious, however significant difference of the plant organic carbon density was observed. Moreover, the M-shaped spatial distribution of the plant organic carbon density, which was similar to the plant biomass, was found in the study. The organic carbon contents in top soils were varied from 0.75 to 8.35 g x kg(-1), which was much lower than that in the typical freshwater marsh wetlands ecosystem. The spatial distribution trend of soil organic carbon density was similar to the soil organic carbon. The correlation analysis showed that soil organic carbon density was negatively correlated with pH, and positively correlated with TN, C/N and salinity. However, the correlations of plant organic carbon density with the soil organic carbon density, TN, C/N, pH and salinity were not significant.

  7. Spatial heterogeneity of soil organic carbon in a small alpine catchment (Grindelwald, Switzerland)

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    Poppe, U.; Kuhn, N.

    2009-04-01

    Soils represent a major pool in the global carbon cycle. Their behaviour as a carbon reservoir in global climate and environmental issues is far from fully understood. Surface soil organic carbon (SOC) pools and turnover times are particularly sensitive to a range of factors, such as climate, vegetation, topography, soil properties, soil and crop management and other anthropogenic conditions. These factors are important to formulate process-based C cycling models and to evaluate the influence of future land use and climate changes on SOC content. Mountain environments are strongly affected by and highly sensitive to climate change (geomorphology, vegetation), while also experiencing significant land use change. Little attention has so far been given to the spatial heterogeneity of alpine SOC stocks. In mountain environments, relief exerts a strong control on factors which control SOC, e.g. through meso-climatic differences, but surface processes such as mass wasting and water erosion. While the general relationships between environmental variables and SOC are known, there is uncertainty regarding the specific quantitative relationships between SOC and environmental variables. Particularly, the interaction between geomorphic processes, soil thickness and soil carbon storage is not well understood. A priori reasoning suggests that spatial patterns of SOC in mountain areas are closely correlated to the spatial patterns of terrain attributes that influence soil-forming processes. In this study, we examined the relationships between SOC stocks and climate, topography (elevation, slope, curvature,) and land use along an elevation transect from Grindelwald Grund to the ridge of Kleine Scheidegg in the canton of Bern. Soil samples were collected across a range of elevations, slope, curvature, soil texture, vegetation types, and terrain positions. Topographic variables (e.g. elevation, slope, curvature) were extracted from a high resolution digital elevation model. SOC

  8. 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

  9. 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.

  10. 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

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

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    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

  12. 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.

  13. [Spatial Distribution of Stable Isotopes in Particle Organic Matters and Sediments from Baishi Reservoirs].

    Science.gov (United States)

    Guo, Kai; Zhao, Wen; Wang, Shan; Dai, Yu-xin; Zhang, Rong-kun; Li, Dong-ming

    2015-12-01

    Water quality and spatial distribution of stable isotopes in particle organic matters and sediments from Baishi reservoirs were produced in October, 2013. The results revealed that the average concentration of POC, TP and TN were (1.76 ± 0.98), (0.04 ± 0.03) and (1.80 ± 0.08) mg · L⁻¹, respectively. In different water depths, the concentrations of POC and TN in surface were higher than those in deep layer, but the concentration of TP was opposite. The concentrations of POC and TP were reduced gradually from upstream to downstream, but the concentration of TN had no obvious change in horizontal distribution. The δ¹³C and δ ¹⁵N values of small particle organic matters were (-24.6 ± 0.9) per thousand and (4.8 ± 0.4) per thousand, the δ¹³C and δ¹⁵N values of large particle organic matters were (-22.5 ± 0.9) per thousand and (6.7 ± 0.5) per thousand, both of which exhibited significant fluctuations. With the δ¹³C and δ¹⁵N values in small particle organic matters were different between each other of 4.6 per thousand and 2.7 per thousand, and those in large particle organic matters were different between each other of 3.3 per thousand and 1.8 per thousand. The δ¹³C and δ¹⁵N values of sediments were (-24.2 ± 1.2) per thousand and (4.1 ± 0.7) per thousand. The results of correlation analysis indicated that there were positively significantly correlated relationships between the stable isotopes values of large particle organic matters with those of small particle organic matters (P stable isotopes values of particle organic matters with those of sediments (P < 0.05). The δ¹⁵N values of particle organic matters in water surface were higher than those in deep layer. The results of correlation analysis indicated that the δ¹⁵N values of large particle organic matters were positive significantly correlated with the concentration of TN (P < 0.05), and the δ¹⁵N values of particle organic matters were positively significantly

  14. Perceptual Organization Based Upon Spatial Relationships in Alzheimer’s Disease

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    Daniel D. Kurylo

    2003-01-01

    Full Text Available Alzheimer’s disease (AD is often accompanied by impaired object recognition, thereby reducing the ability to recognize common objects and familiar faces. Impaired recognition may stem from decreased efficacy in integrating visual information. Studies of perceptual abnormalities in AD indicate an impairment in organizing elements of the visual scene, thereby confusing components of individual forms. This type of impairment is consistent with the characteristics of neural loss, which impact cortical integration. To examine the extent to which perceptual organization is impaired in AD, psychophysical measurements were made of visual perceptual grouping based upon spatial relationships in a group of AD patients and demographically matched elderly control subjects. A comparison was also made between young and elderly control subjects to evaluate the effects of aging on these capacities. Deficits in perceptual organization were found for a subgroup of AD patients, which corresponded to impairment on facial recognition. A less profound functional decline was found for the elderly control group. The degree of impairment for AD subjects did not correlate to level of dementia, but instead appears to be idiosyncratic to individual patients. These results are consistent with impaired integrative function in AD, the degree of which reflects individual differences in the regional distribution of neuropathological changes.

  15. Genomic organization, phylogenetic and expression analysis of the B-BOX gene family in tomato

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    Zhuan Nan Chu

    2016-10-01

    Full Text Available The B-BOX (BBX proteins encode a class of zinc-finger transcription factors possessing one or two B-BOX domains and in some cases an additional CCT (CO, CO-like, and TOC1 motif, which play important roles in regulating plant growth, development and stress response. Nevertheless, no systematic study of BBX genes has been undertaken in tomato (Solanum lycopersicum. Here we present the results of a genome-wide analysis of the 29 BBX genes in this important vegetable species. Their structures, conserved domains, phylogenetic relationships, subcellular localizations, and promoter cis-regulatory elements were analyzed; their tissue expression profiles and expression patterns under various hormones and stress treatments were also investigated in detail. Tomato BBX genes can be divided into five subfamilies, and thirteen of them were found to be segmentally duplicated. Real-time quantitative PCR analysis showed that most BBX genes exhibited different temporal and spatial expression patterns, such as SlBBX24, which was constitutively expressed with high abundance in nearly all tissues studied, and eight genes (SlBBX4, 5, 6, 11, 16, 18, 19, and 22 showed relatively higher expression levels in vegetative tissues and non-ripening fruits. The expression of most BBX genes can be induced by drought, polyethylene glycol-6000 or heat stress. Some BBX genes were induced strongly by phytohormones such as abscisic acid, gibberellic acid or ethephon. The majority of tomato BBX proteins was predicted to be located in nuclei, and the transient expression assay using Arabidopsis mesophyll protoplasts demonstrated that all the seven BBX members tested (SlBBX5, 7, 15, 17, 20, 22 and 24 were localized in nucleus. Our analysis of tomato BBX genes on the genome scale would provide valuable information for future functional characterization of specific genes in this family.

  16. How the genome folds

    Science.gov (United States)

    Lieberman Aiden, Erez

    2012-02-01

    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  17. Estimating soil organic carbon stocks and spatial patterns with statistical and GIS-based methods.

    Science.gov (United States)

    Zhi, Junjun; Jing, Changwei; Lin, Shengpan; Zhang, Cao; Liu, Qiankun; DeGloria, Stephen D; Wu, Jiaping

    2014-01-01

    Accurately quantifying soil organic carbon (SOC) is considered fundamental to studying soil quality, modeling the global carbon cycle, and assessing global climate change. This study evaluated the uncertainties caused by up-scaling of soil properties from the county scale to the provincial scale and from lower-level classification of Soil Species to Soil Group, using four methods: the mean, median, Soil Profile Statistics (SPS), and pedological professional knowledge based (PKB) methods. For the SPS method, SOC stock is calculated at the county scale by multiplying the mean SOC density value of each soil type in a county by its corresponding area. For the mean or median method, SOC density value of each soil type is calculated using provincial arithmetic mean or median. For the PKB method, SOC density value of each soil type is calculated at the county scale considering soil parent materials and spatial locations of all soil profiles. A newly constructed 1∶50,000 soil survey geographic database of Zhejiang Province, China, was used for evaluation. Results indicated that with soil classification levels up-scaling from Soil Species to Soil Group, the variation of estimated SOC stocks among different soil classification levels was obviously lower than that among different methods. The difference in the estimated SOC stocks among the four methods was lowest at the Soil Species level. The differences in SOC stocks among the mean, median, and PKB methods for different Soil Groups resulted from the differences in the procedure of aggregating soil profile properties to represent the attributes of one soil type. Compared with the other three estimation methods (i.e., the SPS, mean and median methods), the PKB method holds significant promise for characterizing spatial differences in SOC distribution because spatial locations of all soil profiles are considered during the aggregation procedure.

  18. 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.

  19. 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.

  20. 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.

  1. Molecular evolution constraints in the floral organ specification gene regulatory network module across 18 angiosperm genomes.

    Science.gov (United States)

    Davila-Velderrain, Jose; Servin-Marquez, Andres; Alvarez-Buylla, Elena R

    2014-03-01

    The gene regulatory network of floral organ cell fate specification of Arabidopsis thaliana is a robust developmental regulatory module. Although such finding was proposed to explain the overall conservation of floral organ types and organization among angiosperms, it has not been confirmed that the network components are conserved at the molecular level among flowering plants. Using the genomic data that have accumulated, we address the conservation of the genes involved in this network and the forces that have shaped its evolution during the divergence of angiosperms. We recovered the network gene homologs for 18 species of flowering plants spanning nine families. We found that all the genes are highly conserved with no evidence of positive selection. We studied the sequence conservation features of the genes in the context of their known biological function and the strength of the purifying selection acting upon them in relation to their placement within the network. Our results suggest an association between protein length and sequence conservation, evolutionary rates, and functional category. On the other hand, we found no significant correlation between the strength of purifying selection and gene placement. Our results confirm that the studied robust developmental regulatory module has been subjected to strong functional constraints. However, unlike previous studies, our results do not support the notion that network topology plays a major role in constraining evolutionary rates. We speculate that the dynamical functional role of genes within the network and not just its connectivity could play an important role in constraining evolution.

  2. 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.

  3. Genetic and molecular analyses of PEG10 reveal new aspects of genomic organization, transcription and translation.

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    Heike Lux

    Full Text Available The paternally expressed gene PEG10 is a retrotransposon derived gene adapted through mammalian evolution located on human chromosome 7q21. PEG10 codes for at least two proteins, PEG10-RF1 and PEG10-RF1/2, by -1 frameshift translation. Overexpression or reinduced PEG10 expression was seen in malignancies, like hepatocellular carcinoma or B-cell acute and chronic lymphocytic leukemia. PEG10 was also shown to promote adipocyte differentiation. Experimental evidence suggests that the PEG10-RF1 protein is an inhibitor of apoptosis and mediates cell proliferation. Here we present new data on the genomic organization of PEG10 by identifying the major transcription start site, a new splice variant and report the cloning and analysis of 1.9 kb of the PEG10 promoter. Furthermore, we show for the first time that PEG10 translation is initiated at a non-AUG start codon upstream of the previously predicted AUG codon as well as at the AUG codon. The finding that PEG10 translation is initiated at different sides adds a new aspect to the already interesting feature of PEG10's -1 frameshift translation mechanism. It is now important to unravel the cellular functions of the PEG10 protein variants and how they are related to normal or pathological conditions. The generated promoter-reporter constructs can be used for future studies to investigate how PEG10 expression is regulated. In summary, our study provides new data on the genomic organization as well as expression and translation of PEG10, a prerequisite in order to study and understand the role of PEG10 in cancer, embryonic development and normal cell homeostasis.

  4. Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions.

    Science.gov (United States)

    Bellesia, Giovanni; Bales, Benjamin B

    2016-10-01

    We investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been "extended" and considered as a prototype reaction-diffusion system. Our results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes. More generally, the computational approach presented in this work makes the case for the use of spatial stochastic simulation methods for the study of biochemical networks in vivo where the "well-mixed" approximation is invalid and both thermal and intrinsic fluctuations linked to the possible presence of molecular species in low number copies cannot be averaged out.

  5. Spatial and Temporal Volatile Organic Compound Measurements in New England: Key Insight on Sources and Distributions

    Science.gov (United States)

    Sive, B. C.; White, M. L.; Russo, R. S.; Zhou, Y.; Ambrose, J. L.; Haase, K.; Mao, H.; Talbot, R. W.

    2010-12-01

    Volatile organic compounds (VOCs) in the atmosphere act as precursors in the formation of tropospheric ozone and their emissions and oxidation products can contribute to secondary organic aerosol formation and growth. In examining their effects on regional chemistry and pollution events, considerable uncertainties exist in our understanding of the relative contributions from different sources and classes of compounds as well as their transport from other regions. To quantitatively improve VOC emission estimates for New England, such as propane from widespread LPG leakage and biogenic emissions of toluene, we have conducted regional surveys for VOCs in northern New England to map their spatial variability. This has included repeated one-day quarterly sampling trips covering four 250 to 300 mile loops throughout Maine, New Hampshire, Massachusetts and small portions of Vermont, Connecticut, and Rhode Island and more intensive diurnal hourly-sampling at selected locations within the measurement area. Additionally, long-term VOC measurements from the AIRMAP atmospheric monitoring station at Thompson Farm in rural Durham, New Hampshire are utilized to characterize the mixing ratios, seasonal to interannual variability, and sources of VOCs in this region. The combination of the spatial temporal data sets has provided key insight on the various sources (e.g., fossil fuel combustion, gasoline, LPG, fuel or solvent evaporation, industry, biogenic) and distributions of VOCs throughout New England. Nonmethane hydrocarbon emission rate estimates from the regional sampling campaigns and Thompson Farm ranged from ~109-1010 molecules cm-2 s-1. Moreover, emission rates based on our spatial and temporal measurements are compared with the (2002 and 2005) EPA National Emissions Inventory for the northeastern U.S. Finally, details regarding our analytical techniques and long-term calibration scales will be presented for measurements of C2-C10 nonmethane hydrocarbons, C1-C2 halocarbons

  6. 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

  7. 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

  8. 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

  9. 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.

  10. Classification and regression tree and spatial analyses reveal geographic heterogeneity in genome wide linkage study of Indian visceral leishmaniasis.

    Directory of Open Access Journals (Sweden)

    Michaela Fakiola

    2010-12-01

    Full Text Available Genome wide linkage studies (GWLS have provided evidence for loci controlling visceral leishmaniasis on Chromosomes 1p22, 6q27, 22q12 in Sudan and 6q27, 9p21, 17q11-q21 in Brazil. Genome wide studies from the major focus of disease in India have not previously been reported.We undertook a GWLS in India in which a primary ∼10 cM (515 microsatellites scan was carried out in 58 multicase pedigrees (74 nuclear families; 176 affected, 353 total individuals and replication sought in 79 pedigrees (102 nuclear families; 218 affected, 473 total individuals. The primary scan provided evidence (≥2 adjacent markers allele-sharing LOD≥0.59; nominal P≤0.05 for linkage on Chromosomes 2, 5, 6, 7, 8, 10, 11, 20 and X, with peaks at 6p25.3-p24.3 and 8p23.1-p21.3 contributed to largely by 31 Hindu families and at Xq21.1-q26.1 by 27 Muslim families. Refined mapping confirmed linkage across all primary scan families at 2q12.2-q14.1 and 11q13.2-q23.3, but only 11q13.2-q23.3 replicated (combined LOD = 1.59; P = 0.0034. Linkage at 6p25.3-p24.3 and 8p23.1-p21.3, and at Xq21.1-q26.1, was confirmed by refined mapping for primary Hindu and Muslim families, respectively, but only Xq21.1-q26.1 replicated across all Muslim families (combined LOD 1.49; P = 0.0045. STRUCTURE and SMARTPCA did not identify population genetic substructure related to religious group. Classification and regression tree, and spatial interpolation, analyses confirm geographical heterogeneity for linkages at 6p25.3-p24.3, 8p23.1-p21.3 and Xq21.1-q26.1, with specific clusters of families contributing LOD scores of 2.13 (P = 0.0009, 1.75 (P = 0.002 and 1.84 (P = 0.001, respectively.GWLS has identified novel loci that show geographical heterogeneity in their influence on susceptibility to VL in India.

  11. 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

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

    Science.gov (United States)

    Baughman, Carson A.; 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.

  13. The New Epistemic and Theoretical Rationality Governing the Spatial Organization of Urban Systems

    Directory of Open Access Journals (Sweden)

    H. Dadashpoor

    2016-05-01

    Full Text Available By reviewing the literature of spatial organization and analyzing urban systems as an interdisciplinary field, two different paradigms have been recognized: size-based and network-based paradigms. The first one relies on the definition of urban system as a collection of nodes (urban settlements organized based on their internal attributes. This paradigm, while ignoring interaction among them, focuses on the concentration of activities or functions in nodes. In the last few decades and with the emergence of the system approach, defined as “an interdependent national or regional set of cities” as a system, considerable attention has been paid to investigating reciprocal interurban relationships. In this period, the element of interaction became more important in the description of urban systems. Following this, since the position of a given city in the urban system is a function of interurban flows, it is affected by the relationship with others. This approach considers the interurban relationship as horizontal and non-local interactions, which are features of service economies versus industrial economies. Thus, to understand and apply these approaches, first, the theoretical literature on space organization in urban systems and its evolution were reviewed; then, the new dominant theoretical and epistemological rationality, with its attributes and components, was explained, compared and categorized in order to develop new insights for operational research. This article is fundamental in its objective, and has employed descriptive methodology based on contextual data to do a comparative study of theoretical content and ontological basics of traditional approaches versus new ones.

  14. Spatial Organization of "Farmed" Wetlands in Iowa's Prairie Pothole Landscape: Geomorphic and Anthropogenic Controls

    Science.gov (United States)

    Stunkel, K. B.; Basu, N. B.

    2012-12-01

    The Des Moines Lobe landform within North Central Iowa is the southernmost portion of the Prairie Pothole Region (PPR) that extends northwest into Canada. The PPR is a vast landscape dotted with thousands of glacially formed depressional wetlands known as prairie potholes. These potholes provide a wide range of ecological and hydrological services and are notable for their high waterfowl productivity. Within Iowa it is estimated that 95% of the wetlands in the Des Moines Lobe have been drained for agricultural purposes. Wetlands in this region are typically drained by subsurface tile drains in an attempt to lower the water table and increase agricultural productivity. Efforts are also underway in restoring some of these drained wetlands. In order to better understand the hydrological impacts of restoring drained wetlands at the watershed scale, it is important to understand how these depressions are distributed in space throughout the Des Moines Lobe. The overall objective of this study was to (1) understand the size-distribution and spatial organization of depressional features in the Des Moines Lobe as a function of watershed area and landform type; and (2) Explore the role of human impact on the size-distribution and spatial organization by comparing depressions based on 1m LIDAR DEM (surrogate for historic wetlands) with "farmed" wetlands based on National Wetlands Inventory (NWI ) data. It was found that the size-frequency relationship follows a power law regression that varies based on the landform type and the size of the study area. The power law function varies predictably with changes in area, suggesting fractal properties within the watersheds examined. Comparison between the National Wetlands Inventory (NWI) database and the LIDAR images was used to evaluate the effect of human disturbance on the landscape. The LIDAR captures the depressional areas that correspond to wetlands before the landscape was extensively tile-drained, while NWI captures the

  15. 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

  16. 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

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

    Science.gov (United States)

    Schnitzler, Christine E; Pang, Kevin; Powers, Meghan L; Reitzel, Adam M; Ryan, Joseph F; Simmons, David; Tada, Takashi; Park, Morgan; Gupta, Jyoti; Brooks, Shelise Y; Blakesley, Robert W; Yokoyama, Shozo; Haddock, Steven Hd; Martindale, Mark Q; Baxevanis, Andreas D

    2012-12-21

    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. 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 emission, raising the hypothesis that light

  18. Organization and expression of genes in the genomic region surrounding the glutamine synthetase gene Gln1 from Lotus japonicus

    DEFF Research Database (Denmark)

    Thykjaer, T; Danielsen, D; She, Q

    1997-01-01

    The diploid Lotus japonicus was previously suggested as a model for the legume plant family. We present here the nucleotide sequence and the derived gene organization of a small part of the genome in this model plant. Two functional genes with the same transcriptional orientation were identified...

  19. Spatial Organization of NG2 Glial Cells and Astrocytes in Rat Hippocampal CA1 Region

    Science.gov (United States)

    Xu, Guangjin; Wang, Wei; Zhou, Min

    2014-01-01

    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 μm3. 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 post-recording 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. PMID:24339242

  20. 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.

  1. 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

  2. Evolution and comparative genomics of subcellular specializations: EST sequencing of Torpedo electric organ.

    Science.gov (United States)

    Nazarian, Javad; Berry, Deborah L; Sanjari, Salar; Razvi, Mohammed; Brown, Kristy; Hathout, Yetrib; Vertes, Akos; Dadgar, Sherry; Hoffman, Eric P

    2011-03-01

    Uncharacterized open reading frames (ORFs) in human genomic sequence often show a high degree of evolutionary conservation, yet have little or no tissue EST or protein data suggestive of protein product function. The encoded proteins may have highly restricted expression in specialized cells, subcellular specializations, and/or narrow windows during development. One such highly specialized and minute subcellular compartment is the neuromuscular junction (NMJ), where motorneurons contact muscle fibers. The electric Torpedo ray has evolved to expand the NMJ structure to the size of a large organ (electroplax organ), and we hypothesized that Torpedo electroplax proteins would be candidates for human ESTs expressed at the human NMJ. A total of 9719 primary electroplax cDNA clones were sequenced. We identified 44 human ORFs showing high (>63%) amino acid identity to Torpedo electroplax transcripts with enrichment for mRNA splicing motifs (SH2 and pre-mRNA splicing domains), an observation potentially important for the strict nuclear domains maintained by myonuclei underlying the NMJ. We generated antibodies against two uncharacterized human genes (C19orf29 [Drosophila cactin] and C15orf24) and showed that these were indeed expressed at the murine NMJ. Cactin, a member of the Rel transcription factor family in Drosophila, localized to the postsynaptic cytosol of the NMJ and nuclear membrane. C15orf24 protein localized to the murine postsynaptic sarcolemma. We show a novel approach towards identifying proteins expressed at a subcellular specialization using evolutionary diversity of organ function and cross-species mapping. Copyright © 2010 Elsevier B.V. All rights reserved.

  3. 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.

  4. 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.

  5. Organic aerosol spatial/temporal patterns: perspectives of measurements and model.

    Science.gov (United States)

    Pun, Betty K; Seigneur, Christian

    2008-10-01

    Ambient measurements from SEARCH and model results from CMAQ-MADRID are analyzed side by side for the southeastern United States to understand the strengths and weaknesses of an air quality model in reproducing key spatial and temporal patterns related to organic aerosol (OA), with inferences regarding secondary organic aerosol (SOA). The model predicts a larger difference in OA concentrations between an urban (JST) and a rural site (YRK) than indicated by measurements. Modeled OA concentrations at JST and YRK are more strongly correlated than measurements. On average, models may understate urban OA emissions, while overstating urban SOA production; measurements indicate that SOA production takes place on the regional scale. Modeled diurnal fluctuations for OA are stronger than measured, due partially to overestimations of the temperature dependence parameters (deltaH(vap)) for SOA in the model. Urban-rural differences in the composition of SOA, inferred from the variations of estimated deltaH(vap), are not properly captured by the model, which does not represent multiple generations of SOA or varied reaction pathways as a function of chemical regimes. Model results are hampered by day-of-the-week and diurnal allocation issues related to EC and OA emissions. Top quintile (20%) afternoon OA concentrations are observed in both warm and cold seasons at the urban site. The frequency of high OA in the cold season is overstated in the model. The model predicts the warm vs cold season frequency of elevated OA episodes better at YRK than at JST, suggesting that regional emissions, chemistry, and transport are better simulated than urban processes.

  6. Spatial and Temporal Patterns of Dissolved Organic Matter Characteristics in the Upper Willamette River Basin, Oregon

    Science.gov (United States)

    Lee, B. S.; Lajtha, K.

    2014-12-01

    Dissolved organic matter (DOM) leaching through soil affects soil carbon sequestration and the carbon metabolism of receiving water bodies. Improving our understanding of the sources and fate of DOM at varying spatial and temporal patterns is crucial for land management decisions. However, little is known about how DOM sources change with land use types and seasonal flow patterns. In the Willamette River Basin (WRB), which is home to Oregon's major cities including Portland and Salem, forested headwaters transition to agricultural and urban land. The climate of WRB has a distinctive seasonal pattern with dry warm summers and wet winters driven by winter precipitation and snowmelt runoff between November and March. This study examined DOM fluorescence characteristic in stream water from 21 locations collected monthly and 16 locations collected seasonally to identify the sources and fate of DOM in the upper WRB in contrasting land uses. DOC and dissolved organic nitrogen concentrations increased as the flow rate increased during winter precipitation at all sites. This indicates that increased flow rate increased the connectivity between land and nearby water bodies. DOM fluorescent properties varied among land use types. During the first precipitation event after a long dry summer, a microbial DOM signature in agricultural areas increased along with nitrate concentrations. This may be because accumulated nutrients on land during the dry season flowed to nearby streams during the first rain event and promoted microbial growth in the streams. During the month of the highest flow rate in 2014, sampling sites near forest showed evidence of a greater terrestrial DOM signature compared to its signature during the dry season. This indicates fluorescent DOM characteristics in streams vary as the flow connectivity changes even within the same land type.

  7. 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.

  8. Spatial and temporal trends of volatile organic compounds (VOC) in a rural area of northern Spain

    Energy Technology Data Exchange (ETDEWEB)

    Parra, M.A.; Gonzalez, L.; Elustondo, D.; Garrigo, J.; Bermejo, R.; Santamaria, J.M. [Laboratorio Integrado de Calidad Ambiental (LICA), Departamento de Quimica y Edafologia, Facultad de Ciencias, Universidad de Navarra, Irunlarrea s/n, 31080, Pamplona, Navarra (Spain)

    2006-10-15

    Ambient concentrations of volatile organic compounds (VOCs) were measured at 40 rural sampling points in Navarre (northern Spain). Air samples were collected by means of sorbent passive sampling and analyzed by thermal desorption (TD) and gas chromatography/mass-selective detector (GC/MSD). A total of 140 VOCs were identified during the study, which was carried out between May to October 2004 for a total of a 10 biweekly sampling campaigns. Concentrations of benzene, toluene, ethylbenzene, m/p-xylenes, o-xylene (BTEX) and 1,3,5-trimethylbenzene were determined in order to investigate their temporal and spatial distributions. Geostatistical analysis pointed to traffic as the main emission source of these compounds. Supporting this idea, BTEX and nitrogen oxides concentrations were found to be highly significantly correlated (r=0.495, P=0.001), whereas a strong negative correlation between BTEX and ozone was also observed (r=-0.355, P=0.025). The concentrations for the BTEX group were similar to the values that have been previously reported for other rural areas. (author)

  9. Control of the spatial distribution and crystal orientation of self-organized Au nanoparticles.

    Science.gov (United States)

    Yasukawa, Yukiko; Liu, Xiaoxi; Shirsath, Sagar E; Suematsu, Hisayuki; Kotaki, Yukio; Nemoto, Yoshihiro; Takeguchi, Masaki; Morisako, Akimitsu

    2016-09-23

    Ordered, two-dimensional, self-organized Au nanoparticles were fabricated using radiofrequency (RF) magnetron sputtering. The particles were uniformly spherical in shape and ultrafine in size (3-7 nm) and showed an ultrahigh density in the order of ∼10(12) inch(-2). A custom-developed sputtering apparatus that employs low sputtering power density and a minimized sputtering time (1 min) was used to markedly simplify the preparation conditions for Au nanoparticle fabrication. The spatial distribution of Au nanoparticles was rigorously controlled by placing a Ta interfacial layer between the Au nanoparticles and substrate as well as by post-annealing samples in an Ar atmosphere after the formation of Au nanoparticles. The interfacial layer and the post-annealing step caused approximately 40% of the Au nanoparticles on the substrate surface to orient in the (111) direction. This method was shown to produce ultrafine Au nanoparticles showing an ultrahigh surface density. The crystal orientation of the nanoparticles can be precisely controlled with respect to the substrate surface. Therefore, this technique promises to deliver tunable nanostructures for applications in the field of high-performance electronic devices.

  10. Super-Resolution Fluorescence Imaging of Spatial Organization of Proteins and Lipids in Natural Rubber.

    Science.gov (United States)

    Wu, Jinrong; Qu, Wei; Huang, Guangsu; Wang, Siyuan; Huang, Cheng; Liu, Han

    2017-06-12

    Natural rubber (NR) with proteins and lipids has superior mechanical properties to its synthetic counterpart, polyisoprene rubber. However, it is a challenge to unravel the morphology of proteins and lipids. Here we used two-color stochastic optical reconstruction microscopy (STORM) to directly visualize the spatial organization of proteins and lipids in NR. We found that the proteins and lipids form an interdispersed stabilizing layer on the surface of NR latex particles. After drying, the proteins and lipids form aggregates of up to 300 nm in diameter. The aggregates physically interact with the terminal groups of polyisoprene chains, leading to the formation of a network, which contributes to the high elasticity and mechanical property of NR. If we remove proteins in NR, the large phospholipid aggregates disintegrate into small ones. However, it does not decompose the network but rather reduces the effective cross-linking density, thus the deproteinized NR is still elastic-like with decreased mechanical property. Removing both proteins and lipids wholly decomposes the network, thus, results in a liquid-like behavior of the rubber. The STORM measurements in this paper enable more insight into the structure-property relationship of NR, which also shows a great potential of STORM in studying the fine structure of polymeric materials and nanocomposites.

  11. 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…

  12. Complete nucleotide sequence and genome organization of a Cactus virus X strain from Hylocereus undatus (Cactaceae).

    Science.gov (United States)

    Liou, M R; Chen, Y R; Liou, R F

    2004-05-01

    The complete nucleotide sequence of a strain of Cactus virus X (CVX-Hu) isolated from Hylocereus undatus (Cactaceae) has been determined. Excluding the poly(A) tail, the sequence is 6614 nucleotides in length and contains seven open reading frames (ORFs). The genome organization of CVX is similar to that of other potexviruses. ORF1 encodes the putative viral replicase with conserved methyltransferase, helicase, and polymerase motifs. Within ORF1, two other ORFs were located separately in the +2 reading frame, we call these ORF6 and ORF7. ORF2, 3, and 4, which form the "triple gene block" characteristic of the potexviruses, encode proteins with molecular mass of 25, 12, and 7 KDa, respectively. ORF5 encodes the coat protein with an estimated molecular mass of 24 KDa. Sequence analysis indicated that proteins encoded by ORF1-5 display certain degree of homology to the corresponding proteins of other potexviruses. Putative product of ORF6, however, shows no significant similarity to those of other potexviruses. Phylogenetic analyses based on the replicase (the methyltransferase, helicase, and polymerase domains) and coat protein demonstrated a closer relationship of CVX with Bamboo mosaic virus, Cassava common mosaic virus, Foxtail mosaic virus, Papaya mosaic virus, and Plantago asiatica mosaic virus.

  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 and expression of immunoglobulin genes in the Chinese hamster (Cricetulus griseus).

    Science.gov (United States)

    Qin, T; Zhu, H; Wang, D; Hao, H; Du, W

    2015-01-01

    In science, the hamsters are widely used as a model for studying the human diseases because they display many features like humans. The utility of the Chinese hamster as a biology model can be further enhanced by further characterization of the genes encoding components of the immune system. Here, we report the genomic organization and expression of the Chinese hamster immunoglobulin heavy and light chain genes. The Chinese hamster IgH locus contains 268 VH segments (132 potentially functional genes, 12 ORFs and 124 pseudogenes), 4 DH segments, 6 JH segments, four constant region genes (μ, γ, ε and α) and one reverse δ remnant fragment. The Igκ locus contains only a single Cκ gene, 4 Jκ segments and 48 Vκ segments (15 potentially functional genes and 33 pseudogenes), whereas the Igλ locus contains 4 Cλ genes, but only Cλ 3 and Cλ 4 each preceded by a Jλ gene segment. A total of 49 Vλ segments (39 potentially functional genes, 3 ORFs and 7 pseudogenes) were identified. Analysis of junctions of the recombined V(D)J transcripts reveals complex diversity in both expressed H and κ sequences, but the microhomology-directed VJ recombination obviously results in very limited diversity in the Chinese hamster λ gene despite more potential germline-encoded combinatorial diversity. This is the first study to make a comprehensive analysis of the Ig genes in the Chinese hamster, which provides insights into the Ig genes in placental mammals. © 2014 John Wiley & Sons Ltd.

  15. Genomic organization of the mouse fibroblast growth factor receptor 3 (Fgfr3) gene

    Energy Technology Data Exchange (ETDEWEB)

    Perez-Castro, A.V.; Wilson, J.; Altherr, M.R. [Los Alamos National Lab., NM (United States)

    1995-11-20

    The fibroblast growth factor receptor 3 (Fgfr3) protein is a tyrosine kinase receptor involved in the signal transduction of various fibroblast growth factors. Recent studies suggest its important role in normal development. In humans, mutation in Fgfr3 is responsible for growth disorders such as achondroplasia, hypoachondroplasia, and thanatophoric dysplasia. Here, we report the complete genomic organization of the mouse Fgfr3 gene. The murine gene spans approximately 15 kb and consists of 19 exons and 18 introns. One major and one minor transcription initiation site were identified. Position +1 is located 614 nucleotides upstream from the ATG initiation codon. The translation initiation and termination sites are located in exons 2 and 19, respectively. Five Sp1 sites, two AP2 sites, one Zeste site, and one Krox 24 site were observed in the 5{prime}-flanking region. The Fgfr3 promoter appears to be contained within a CpG island and, as is common in genes having multiple Sp1-binding sites, lacks a TATA box. 35 refs., 3 figs., 1 tab.

  16. Genomic organization of the mouse dystrobrevin gene: Comparative analysis with the dystrophin gene

    Energy Technology Data Exchange (ETDEWEB)

    Ambrose, H.J.; Blake, D.J.; Nawrotzki, R.A.; Davies, K.E. [Univ. of Oxford (United Kingdom)

    1997-02-01

    Dystrobrevin, the mammalian orthologue of the Torpedo 87-kDa postsynaptic protein, is a member of the dystrophin gene family with homology to the cysteine-rich carboxy-terminal domain of dystrophin. Torpedo dystrobrevin copurifies with the acetylcholine receptors and is thought to form a complex with dystrophin and syntrophin. This complex is also found at the sarcolemma in vertebrates and defines the cytoplasmic component of the dystrophin-associated protein complex. Previously we have cloned several dystrobrevin isoforms from mouse brain and muscle. Here we show that these transcripts are the products of a single gene located on proximal mouse chromosome 18. To investigate the diversity of dystrobrevin transcripts we have determined that the mouse dystrobrevin gene is organized into 24 coding exons that span between 130 and 170 kb at the genomic level. The gene encodes at least three distinct protein isoforms that are expressed in a tissue-specific manner. Interestingly, although there is only 27% amino acid identity between the homologous regions of dystrobrevin and dystrophin, the positions of 8 of the 15 exon-intron junctions are identical. 47 refs., 4 figs., 2 tabs.

  17. National Human Genome Research Institute

    Science.gov (United States)

    ... the Director Organization Reports & Publications Español The National Human Genome Research Institute conducts genetic and genomic research, funds ... genomic literacy among physicians. Funded by the National Human Genome Research Institute (NHGRI), The Universal Genomics Instructor Handbook ...

  18. 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.

  19. Nucleotide sequence and genome organization of a member of a new and distinct Caulimovirus species from dahlia.

    Science.gov (United States)

    Pappu, H R; Druffel, K L; Miglino, R; van Schadewijk, A R

    2008-01-01

    A distinct caulimovirus, associated with dahlia mosaic, was cloned and sequenced. The caulimovirus, tentatively designated as dahlia common mosaic virus (DCMV), had a double-stranded DNA genome of ca. 8 kb. The genome organization of DCMV was found to be typical of members of the genus Caulimovirus and consisted of six major open reading frames (ORFs), ORFs I-VI, and one minor ORF, ORF VII. Sequence comparisons with the DNA genomes of two known caulimoviruses isolated from dahlia, Dahlia mosaic virus (DMV) and an endogenous caulimovirus, DMV-D10, showed that DCMV is a member of a distinct caulimovirus species, with sequence identities among various ORFs ranging from 25 to 80%.

  20. 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...

  1. 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.

  2. 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

  3. Complete chloroplast genome sequence of poisonous and medicinal plant Datura stramonium: organizations and implications for genetic engineering.

    Directory of Open Access Journals (Sweden)

    Yang Yang

    Full Text Available Datura stramonium is a widely used poisonous plant with great medicinal and economic value. Its chloroplast (cp genome is 155,871 bp in length with a typical quadripartite structure of the large (LSC, 86,302 bp and small (SSC, 18,367 bp single-copy regions, separated by a pair of inverted repeats (IRs, 25,601 bp. The genome contains 113 unique genes, including 80 protein-coding genes, 29 tRNAs and four rRNAs. A total of 11 forward, 9 palindromic and 13 tandem repeats were detected in the D. stramonium cp genome. Most simple sequence repeats (SSR are AT-rich and are less abundant in coding regions than in non-coding regions. Both SSRs and GC content were unevenly distributed in the entire cp genome. All preferred synonymous codons were found to use A/T ending codons. The difference in GC contents of entire genomes and of the three-codon positions suggests that the D. stramonium cp genome might possess different genomic organization, in part due to different mutational pressures. The five most divergent coding regions and four non-coding regions (trnH-psbA, rps4-trnS, ndhD-ccsA, and ndhI-ndhG were identified using whole plastome alignment, which can be used to develop molecular markers for phylogenetics and barcoding studies within the Solanaceae. Phylogenetic analysis based on 68 protein-coding genes supported Datura as a sister to Solanum. This study provides valuable information for phylogenetic and cp genetic engineering studies of this poisonous and medicinal plant.

  4. Complete chloroplast genome sequence of poisonous and medicinal plant Datura stramonium: organizations and implications for genetic engineering.

    Science.gov (United States)

    Yang, Yang; Dang, Yuanye; Yuanye, Dang; Li, Qing; Qing, Li; Lu, Jinjian; Jinjian, Lu; Li, Xiwen; Xiwen, Li; Wang, Yitao; Yitao, Wang

    2014-01-01

    Datura stramonium is a widely used poisonous plant with great medicinal and economic value. Its chloroplast (cp) genome is 155,871 bp in length with a typical quadripartite structure of the large (LSC, 86,302 bp) and small (SSC, 18,367 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,601 bp). The genome contains 113 unique genes, including 80 protein-coding genes, 29 tRNAs and four rRNAs. A total of 11 forward, 9 palindromic and 13 tandem repeats were detected in the D. stramonium cp genome. Most simple sequence repeats (SSR) are AT-rich and are less abundant in coding regions than in non-coding regions. Both SSRs and GC content were unevenly distributed in the entire cp genome. All preferred synonymous codons were found to use A/T ending codons. The difference in GC contents of entire genomes and of the three-codon positions suggests that the D. stramonium cp genome might possess different genomic organization, in part due to different mutational pressures. The five most divergent coding regions and four non-coding regions (trnH-psbA, rps4-trnS, ndhD-ccsA, and ndhI-ndhG) were identified using whole plastome alignment, which can be used to develop molecular markers for phylogenetics and barcoding studies within the Solanaceae. Phylogenetic analysis based on 68 protein-coding genes supported Datura as a sister to Solanum. This study provides valuable information for phylogenetic and cp genetic engineering studies of this poisonous and medicinal plant.

  5. The genomes of two key bumblebee species with primitive eusocial organization

    DEFF Research Database (Denmark)

    Sadd, Ben M.; Barribeau, Seth M.; Bloch, Guy

    2015-01-01

    , and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. RESULTS: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens...

  6. Understanding the spatial distribution of factors controlling topsoil organic carbon content in European soils.

    Science.gov (United States)

    Rial, M; Martínez Cortizas, A; Rodríguez-Lado, L

    2017-12-31

    Soil Organic Carbon (SOC) constitutes the largest terrestrial carbon pool. The understanding of its dynamics and the environmental factors that influence its behaviour as sink or source of atmospheric CO 2 is crucial to quantify the carbon budget at the global scale. At the European scale, most of the existing studies to account for SOC stocks are centred in the fitting of predictive model to ascertain the distribution of SOC. However, the development of methodologies for monitoring and identifying the environmental factors that control SOC storage in Europe remains a key research challenge. Here we present a modelling procedure for mapping and monitoring SOC contents that uses Visible-Near Infrared (VNIR) spectroscopic measurements and a series of environmental covariates to ascertain the key environmental processes that have a major contribution into SOC sequestration processes. Our results show that it follows a geographically non-stationary process in which the influencing environmental factors have different weights depending on the spatial location. This implies that SOC stock modelling should not rely on a single model but on a combination of different statistical models depending on the environmental characteristics of each area. A cluster classification of European soils in relation to those factors resulted in the determination of four groups for which specific models have been obtained. Differences in climate, soil pH, content of coarse fragments or land cover type are the main factors explaining the differences in SOC in topsoil from Europe. We found that climatic conditions are the main driver of SOC storage at the continental scale, but we also found that parameters like land cover type influence SOC content found at the local scales in certain areas. Our methodology developed at continental scale could be used in future research aimed to improve the predictive performance of SOC assessments at European scale. Copyright © 2017 Elsevier B.V. All

  7. Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages

    Science.gov (United States)

    Pett, Walker

    2016-01-01

    Abstract Animal mitochondrial DNA (mtDNA) is commonly described as a small, circular molecule that is conserved in size, gene content, and organization. Data collected in the last decade have challenged this view by revealing considerable diversity in animal mitochondrial genome organization. Much of this diversity has been found in nonbilaterian animals (phyla Cnidaria, Ctenophora, Placozoa, and Porifera), which, from a phylogenetic perspective, form the main branches of the animal tree along with Bilateria. Within these groups, mt-genomes are characterized by varying numbers of both linear and circular chromosomes, extra genes (e.g. atp9, polB, tatC), large variation in the number of encoded mitochondrial transfer RNAs (tRNAs) (0–25), at least seven different genetic codes, presence/absence of introns, tRNA and mRNA editing, fragmented ribosomal RNA genes, translational frameshifting, highly variable substitution rates, and a large range of genome sizes. This newly discovered diversity allows a better understanding of the evolutionary plasticity and conservation of animal mtDNA and provides insights into the molecular and evolutionary mechanisms shaping mitochondrial genomes. PMID:27557826

  8. 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.

  9. 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.

  10. 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…

  11. Seasonal and spatial contrasts of sedimentary organic carbon in floodplain lakes of the central Amazon basin.

    Science.gov (United States)

    Sobrinho, Rodrigo; Kim, Jung-Hyun; Abril, Gwenaël; Zell, Claudia; Moreira-Turcq, Patricia; Mortillaro, Jean-Michel; Meziane, Tarik; Damsté, Jaap; Bernardes, Marcelo

    2014-05-01

    Three-quarters of the area of flooded land in the world are temporary wetlands (Downing, 2009), which play a significant role in the global carbon cycle(Einsele et al., 2001; Cole et al., 2007; Battin et al., 2009; Abril et al., 2013). Previous studies of the Amazonian floodplain lakes (várzeas), one important compartment of wetlands, showed that the sedimentation of organic carbon (OC) in the floodplain lakes is strongly linked to the periodical floods and to the biogeography from upstream to downstream(Victoria et al., 1992; Martinelli et al., 2003). However, the main sources of sedimentary OC remain uncertain. Hence, the study of the sources of OC buried in floodplain lake sediments can enhance our understanding of the carbon balance of the Amazon ecosystems. In this study, we investigated the seasonal and spatial pattern of sedimentary organic matter in five floodplain lakes of the central Amazon basin (Cabaliana, Janauaca, Canaçari, Miratuba, and Curuai) which have different morphologies, hydrodynamics and vegetation coverage. 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 geochemical tracers such as C:N ratio and stable isotopic composition of organic carbon (δ13COC). These results were compared with lignin-phenol parameters as an indicator of vascular plant detritus (Hedges and Ertel, 1982) and branched glycerol dialkyl glycerol tetraethers (brGDGTs) to trace the soil OC from land to the aquatic settings (Hopmans et al., 2004). Our data showed that during the RW and FW seasons, the concentration of lignin and brGDGTs were higher in comparison to other seasons. Our study also indicated that floodplain lake sediments primarily consisted of a mixture of C3 plant detritus and soil OC. However, a downstream increase in C4 plant-derived OC contribution was observed along the gradient of increasingly open waters, i

  12. Metabolic potential of the organic-solvent tolerant Pseudomonas putida DOT-T1E deduced from its annotated genome

    Science.gov (United States)

    Udaondo, Zulema; Molina, Lazaro; Daniels, Craig; Gómez, Manuel J; Molina-Henares, María A; Matilla, Miguel A; Roca, Amalia; Fernández, Matilde; Duque, Estrella; Segura, Ana; Ramos, Juan Luis

    2013-01-01

    Summary Pseudomonas putida DOT-T1E is an organic solvent tolerant strain capable of degrading aromatic hydrocarbons. Here we report the DOT-T1E genomic sequence (6 394 153 bp) and its metabolic atlas based on the classification of enzyme activities. The genome encodes for at least 1751 enzymatic reactions that account for the known pattern of C, N, P and S utilization by this strain. Based on the potential of this strain to thrive in the presence of organic solvents and the subclasses of enzymes encoded in the genome, its metabolic map can be drawn and a number of potential biotransformation reactions can be deduced. This information may prove useful for adapting desired reactions to create value-added products. This bioengineering potential may be realized via direct transformation of substrates, or may require genetic engineering to block an existing pathway, or to re-organize operons and genes, as well as possibly requiring the recruitment of enzymes from other sources to achieve the desired transformation. Funding Information Work in our laboratory was supported by Fondo Social Europeo and Fondos FEDER from the European Union, through several projects (BIO2010-17227, Consolider-Ingenio CSD2007-00005, Excelencia 2007 CVI-3010, Excelencia 2011 CVI-7391 and EXPLORA BIO2011-12776-E). PMID:23815283

  13. Metabolic potential of the organic-solvent tolerant Pseudomonas putida DOT-T1E deduced from its annotated genome.

    Science.gov (United States)

    Udaondo, Zulema; Molina, Lazaro; Daniels, Craig; Gómez, Manuel J; Molina-Henares, María A; Matilla, Miguel A; Roca, Amalia; Fernández, Matilde; Duque, Estrella; Segura, Ana; Ramos, Juan Luis

    2013-09-01

    Pseudomonas putida DOT-T1E is an organic solvent tolerant strain capable of degrading aromatic hydrocarbons. Here we report the DOT-T1E genomic sequence (6,394,153 bp) and its metabolic atlas based on the classification of enzyme activities. The genome encodes for at least 1751 enzymatic reactions that account for the known pattern of C, N, P and S utilization by this strain. Based on the potential of this strain to thrive in the presence of organic solvents and the subclasses of enzymes encoded in the genome, its metabolic map can be drawn and a number of potential biotransformation reactions can be deduced. This information may prove useful for adapting desired reactions to create value-added products. This bioengineering potential may be realized via direct transformation of substrates, or may require genetic engineering to block an existing pathway, or to re-organize operons and genes, as well as possibly requiring the recruitment of enzymes from other sources to achieve the desired transformation. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  14. Higher-order genome organization in platypus and chicken sperm and repositioning of sex chromosomes during mammalian evolution.

    Science.gov (United States)

    Tsend-Ayush, Enkhjargal; Dodge, Natasha; Mohr, Julia; Casey, Aaron; Himmelbauer, Heinz; Kremitzki, Colin L; Schatzkamer, Kyriena; Graves, Tina; Warren, Wesley C; Grützner, Frank

    2009-02-01

    In mammals, chromosomes occupy defined positions in sperm, whereas previous work in chicken showed random chromosome distribution. Monotremes (platypus and echidnas) are the most basal group of living mammals. They have elongated sperm like chicken and a complex sex chromosome system with homology to chicken sex chromosomes. We used platypus and chicken genomic clones to investigate genome organization in sperm. In chicken sperm, about half of the chromosomes investigated are organized non-randomly, whereas in platypus chromosome organization in sperm is almost entirely non-random. The use of genomic clones allowed us to determine chromosome orientation and chromatin compaction in sperm. We found that in both species chromosomes maintain orientation of chromosomes in sperm independent of random or non-random positioning along the sperm nucleus. The distance of loci correlated with the total length of sperm nuclei, suggesting that chromatin extension depends on sperm elongation. In platypus, most sex chromosomes cluster in the posterior region of the sperm nucleus, presumably the result of postmeiotic association of sex chromosomes. Chicken and platypus autosomes sharing homology with the human X chromosome located centrally in both species suggesting that this is the ancestral position. This suggests that in some therian mammals a more anterior position of the X chromosome has evolved independently.

  15. Spatial distribution of particulate organic matter pools, quantified and characterized by mid-infrared spectroscopy

    Science.gov (United States)

    Bornemann, L.; Welp, G.; Amelung, W.

    2009-04-01

    Comprising more than 60 % of the terrestrial carbon pool, soil organic carbon (SOC) is one of the principal factors regulating the global C-cycle. Against the background of worldwide increasing CO2 emissions, much effort has been put to the modelling of soil-C turnover in order to evaluate its potential for mitigation of climate change. Soil organic matter is an ever changing assemblage of various organic components that interact with the mineral matrix and in dependence of its ecological environment. Carbon storage is thereby assumed to propagate by hierarchical saturation of different carbon pools. A homogeneous distribution of the respective pools within natural environments is unlikely as the controlling soil parameters are subject to spatial and temporal heterogeneity. Several attempts to operationalize this complex soil compartment have been proposed, most of them resting upon a concept of pools with different stability and varying turnover times. Among these pools, particulate organic matter (POM) is considered to be most sensitive to environmental changes and has been shown to explain major parts of the SOC variations. Until today, rather laborious physical and physico-chemical fractionation procedures are most commonly applied for the initialization and validation of POM in C-turnover models. Mid-infrared spectroscopy (MIRS) in combination with partial least squares regression (PLSR) could overcome this problem. The technique is fast, cheap, and requires little sample preparation. All the same, it is an appropriate technique not only for the determination of gross parameters like total soil organic carbon contents, but also for the determination and characterization of minor constituents like black carbon in soils. Basically, the infrared radiation is absorbed by molecules that express a dipole-moment during vibration. As virtually all constituents of soil organic matter and also a multitude of inorganic soil constituents express such a dipole

  16. Advances in porcine genomics and proteomics - a toolbox for developing the pig as a model organism for molecular biomedical research

    DEFF Research Database (Denmark)

    Bendixen, Emøke; Danielsen, Marianne; Larsen, Knud

    2010-01-01

    Our current knowledge of human biology is often based on studying a wide range of animal species. In particular, for understanding human diseases, the development of adequate animal models is of immediate importance. Although genetic strains and transgenic animal model organisms like fruit fly...... the pig into a novel model organism for biomedical research. This toolbox includes the near completion of the pig genome, catalogues of genes and genetic variation in pigs, extensive characterization of pig proteomes and transcriptomes, as well as the development of transgenic disease models. The aim...

  17. Genomic organization of Tropomodulins 2 and 4 and unusual intergenic and intraexonic splicing of YL-1 and Tropomodulin 4

    Directory of Open Access Journals (Sweden)

    Zoghbi Huda Y

    2001-10-01

    Full Text Available Abstract Background The tropomodulins (TMODs are a family of proteins that cap the pointed ends of actin filaments. Four TMODs have been identified in humans, with orthologs in mice. Mutations in actin or actin-binding proteins have been found to cause several human diseases, ranging from hypertrophic cardiomyopathy to immunodefiencies such as Wiskott-Aldrich syndrome. We had previously mapped Tropomodulin 2 (TMOD2 to the genomic region containing the gene for amyotrophic lateral sclerosis 5 (ALS5. We determined the genomic structure of Tmod2 in order to better analyze patient DNA for mutations; we also determined the genomic structure of Tropomodulin 4 (TMOD4. Results In this study, we determined the genomic structure of TMOD2 and TMOD4 and found the organization of both genes to be similar. Sequence analysis of TMOD2 revealed no mutations or polymorphisms in ALS5 patients or controls. Interestingly, we discovered that another gene, YL-1, intergenically splices into TMOD4. YL-1 encodes six exons, the last of which is 291 bp from a 5' untranslated exon of TMOD4. We used 5' RACE and RT-PCR from TMOD4 to identify several intergenic RACE products. YL-1 was also found to undergo unconventional splicing using non-canonical splice sites within exons (intraexonic splicing to produce several alternative transcripts. Conclusions The genomic structure of TMOD2 and TMOD4 have been delineated. This should facilitate future mutational analysis of these genes. In addition, intergenic splicing at TMOD4/YL-1 was discovered, demonstrating yet another level of complexity of gene organization and regulation.

  18. T4-Like Genome Organization of the Escherichia coli O157:H7 Lytic Phage AR1▿†

    Science.gov (United States)

    Liao, Wei-Chao; Ng, Wailap Victor; Lin, I-Hsuan; Syu, Wan-Jr; Liu, Tze-Tze; Chang, Chuan-Hsiung

    2011-01-01

    We report the genome organization and analysis of the first completely sequenced T4-like phage, AR1, of Escherichia coli O157:H7. Unlike most of the other sequenced phages of O157:H7, which belong to the temperate Podoviridae and Siphoviridae families, AR1 is a T4-like phage known to efficiently infect this pathogenic bacterial strain. The 167,435-bp AR1 genome is currently the largest among all the sequenced E. coli O157:H7 phages. It carries a total of 281 potential open reading frames (ORFs) and 10 putative tRNA genes. Of these, 126 predicted proteins could be classified into six viral orthologous group categories, with at least 18 proteins of the structural protein category having been detected by tandem mass spectrometry. Comparative genomic analysis of AR1 and four other completely sequenced T4-like genomes (RB32, RB69, T4, and JS98) indicated that they share a well-organized and highly conserved core genome, particularly in the regions encoding DNA replication and virion structural proteins. The major diverse features between these phages include the modules of distal tail fibers and the types and numbers of internal proteins, tRNA genes, and mobile elements. Codon usage analysis suggested that the presence of AR1-encoded tRNAs may be relevant to the codon usage of structural proteins. Furthermore, protein sequence analysis of AR1 gp37, a potential receptor binding protein, indicated that eight residues in the C terminus are unique to O157:H7 T4-like phages AR1 and PP01. These residues are known to be located in the T4 receptor recognition domain, and they may contribute to specificity for adsorption to the O157:H7 strain. PMID:21507986

  19. 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.

  20. Spatial variability of organic matter molecular composition and elemental geochemistry in surface sediments of a small boreal Swedish lake

    Science.gov (United States)

    Tolu, Julie; Rydberg, Johan; Meyer-Jacob, Carsten; Gerber, Lorenz; Bindler, Richard

    2017-04-01

    The composition of sediment organic matter (OM) exerts a strong control on biogeochemical processes in lakes, such as those involved in the fate of carbon, nutrients and trace metals. While between-lake spatial variability of OM quality is increasingly investigated, we explored in this study how the molecular composition of sediment OM varies spatially within a single lake and related this variability to physical parameters and elemental geochemistry. Surface sediment samples (0-10 cm) from 42 locations in Härsvatten - a small boreal forest lake with a complex basin morphometry - were analyzed for OM molecular composition using pyrolysis gas chromatography mass spectrometry for the contents of 23 major and trace elements and biogenic silica. We identified 162 organic compounds belonging to different biochemical classes of OM (e.g., carbohydrates, lignin and lipids). Close relationships were found between the spatial patterns of sediment OM molecular composition and elemental geochemistry. Differences in the source types of OM (i.e., terrestrial, aquatic plant and algal) were linked to the individual basin morphometries and chemical status of the lake. The variability in OM molecular composition was further driven by the degradation status of these different source pools, which appeared to be related to sedimentary physicochemical parameters (e.g., redox conditions) and to the molecular structure of the organic compounds. Given the high spatial variation in OM molecular composition within Härsvatten and its close relationship with elemental geochemistry, the potential for large spatial variability across lakes should be considered when studying biogeochemical processes involved in the cycling of carbon, nutrients and trace elements or when assessing lake budgets.

  1. 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.

  2. 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.

  3. VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

    Directory of Open Access Journals (Sweden)

    Peterson Elena S

    2012-04-01

    Full Text Available Abstract Background The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq, global microarrays, and tandem mass spectrometry (MS/MS-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. Results VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric and transcriptomics (probe or RNA-Seq data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002 to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. Conclusions VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis

  4. VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

    Science.gov (United States)

    2012-01-01

    Background The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. Results VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. Conclusions VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic

  5. The role of terrestrial bromeliads in determining the spatial organization of plant life forms in a tropical coastal forest

    Directory of Open Access Journals (Sweden)

    Celio M. Lopes

    Full Text Available ABSTRACT The interplay between plant-plant interactions and light heterogeneity in the understory of tropical forests has rarely been examined. We aimed to identify the relative importance of the understory light environment and terrestrial bromeliads in explaining the abundance and spatial organization of different plant life forms along a coastal forest gradient from seashore inland in southeastern Brazil. We estimated the abundance of various life forms (herbs, woody plants, bromeliads, climbers, and palms and the degree of light availability using hemispherical photographs in 165 plots (1 m2 within a 1.75 ha site. We used ordination methods, partial redundancy analysis (pRDA, spatial filtering using Moran’s eigenvector mapping, and Moran’s I splines. Forest cover was highly heterogeneous, but did not explain variation in abundance of life forms. Spatially, bromeliads were negatively associated with woody saplings, herbs and climbing plants at scales between 5-20 m, while the distance to seashore was found to be unrelated to these patterns. Our findings revealed that terrestrial bromeliads play an important role in the spatial organization of various life forms near the forest floor. Overall, the presence of terrestrial bromeliads and the plant area index better explained the understory vegetation than forest cover and distance to seashore.

  6. 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

  7. 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

    contamination) and variation in environmental, physiological, and ecological parameters included within the model. Finally, the model was used to explore interactions between spatial heterogeneity in water and sediment contaminant concentrations and theoretical movement profiles of different fish species...... 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...

  8. 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.

  9. 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.

  10. 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

    Members of a triple-species 3-(3,4-dichlorophenyl)-1-methoxy-1-methyl urea (linuron)-mineralizing consortium, i.e. the linuron- and 3,4-dichloroaniline-degrading Variovorax sp. WDL1, the 3,4-dichloroaniline-degrading Comamonas testosteroni WDL7 and the N,O-dimethylhydroxylamine-degrading Hyphomic....... These observations indicate that the spatial organization in the linuron-fed consortium biofilm reflected the metabolic interactions within the consortium....

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

    Science.gov (United States)

    Oppel, Henning; Schumann, Andreas

    2017-08-01

    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.

  12. 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.

  13. Organization of repeated DNA elements in the genome of the cichlid fish Cichla kelberi and its contributions to the knowledge of fish genomes.

    Science.gov (United States)

    Teixeira, W G; Ferreira, I A; Cabral-de-Mello, D C; Mazzuchelli, J; Valente, G T; Pinhal, D; Poletto, A B; Venere, P C; Martins, C

    2009-01-01

    Repeated DNA elements have been extensively applied as physical chromosome markers in comparative studies for the identification of chromosomal rearrangements, the identification of sex chromosomes, chromosome evolution analysis and applied genetics. Here, we report the characterization of the transposable elements (TE) Tc1, Rex1, Rex3 and Rex6 and a new element called RCk in the genome of the South American cichlid fish Cichla kelberi using nucleotide sequence analysis and hybridization to metaphase chromosomes. The analysis of the repeated elements demonstrated that they are, in most cases, compartmentalized in heterochromatic regions, as has been observed in several other vertebrates. On the other hand, the elements Rex1 and Rex3 were also observed spanning extensive euchromatic regions on 2 chromosome pairs. The RCk element exhibits a wide distribution among fishes and also in amphibians, and it was spread throughout the chromosomes of C. kelberi. Our results have demonstrated that the compartmentalization of repeated elements is not restricted to heterochromatic segments, which has provided new concepts with regard to the genomic organization of transposons. Copyright 2009 S. Karger AG, Basel.

  14. 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.

  15. 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.

  16. The complete mitochondrial genome sequence and gene organization of the rainbow runner (Elagatis bipinnulata) (Perciformes: Carangidae).

    Science.gov (United States)

    Ma, Chunyan; Ma, Hongyu; Zhang, Heng; Feng, Chunlei; Wei, Hongqing; Wang, Wei; Chen, Wei; Zhang, Fengying; Ma, Lingbo

    2017-01-01

    The complete mitochondrial genome information can play an important role in species identification, phylogeny, evolution research, genetic differentiation, and diversity. Here we determined the complete mitochondrial genome sequence of Elagatis bipinnulata (Perciformes: Carangidae). This circular genome was 16 542 bp in length, and included all 37 typical mitochondrial genes, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a putative control region. The gene order of E. bipinnulata was identical to that observed in most other vertebrates. Of 37 genes, 28 were encoded by heavy strand, while the other ones were encoded by light strand. According to the phylogenetic analysis based on 13 concatenated protein-coding genes, E. bipinnulata was genetically closer to the species of genus Seriola compared with any other species within Perciformes. This work can provide helpful data for further studies on population genetic diversity and molecular evolution.

  17. 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

  18. The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota

    DEFF Research Database (Denmark)

    Chen, L.M.; Brugger, K.; Skovgaard, Marie

    2005-01-01

    tokodaii. The S. acidocaldarius genome contains an integrated, and probably encaptured, pARN-type conjugative plasmid which may facilitate intercellular chromosomal gene exchange in S. acidocaldarius. Moreover, it contains genes for a characteristic restriction modification system, a UV damage excision...... repair system, thermopsin, and an aromatic ring dioxygenase, all of which are absent from genomes of other Sulfolobus species. However, it lacks genes for some of their sugar transporters, consistent with it growing on a more limited range of carbon sources. These results, together with the many newly...

  19. Spatial and Functional Organization of Pig Trade in Different European Production Systems: Implications for Disease Prevention and Control.

    Science.gov (United States)

    Relun, Anne; Grosbois, Vladimir; Sánchez-Vizcaíno, José Manuel; Alexandrov, Tsviatko; Feliziani, Francesco; Waret-Szkuta, Agnès; Molia, Sophie; Etter, Eric Marcel Charles; Martínez-López, Beatriz

    2016-01-01

    Understanding the complexity of live pig trade organization is a key factor to predict and control major infectious diseases, such as classical swine fever (CSF) or African swine fever (ASF). Whereas the organization of pig trade has been described in several European countries with indoor commercial production systems, little information is available on this organization in other systems, such as outdoor or small-scale systems. The objective of this study was to describe and compare the spatial and functional organization of live pig trade in different European countries and different production systems. Data on premise characteristics and pig movements between premises were collected during 2011 from Bulgaria, France, Italy, and Spain, which swine industry is representative of most of the production systems in Europe (i.e., commercial vs. small-scale and outdoor vs. indoor). Trade communities were identified in each country using the Walktrap algorithm. Several descriptive and network metrics were generated at country and community levels. Pig trade organization showed heterogeneous spatial and functional organization. Trade communities mostly composed of indoor commercial premises were identified in western France, northern Italy, northern Spain, and north-western Bulgaria. They covered large distances, overlapped in space, demonstrated both scale-free and small-world properties, with a role of trade operators and multipliers as key premises. Trade communities involving outdoor commercial premises were identified in western Spain, south-western and central France. They were more spatially clustered, demonstrated scale-free properties, with multipliers as key premises. Small-scale communities involved the majority of premises in Bulgaria and in central and Southern Italy. They were spatially clustered and had scale-free properties, with key premises usually being commercial production premises. These results indicate that a disease might spread very differently

  20. Phase separation explains a new class of self-organized spatial patterns in ecological systems

    NARCIS (Netherlands)

    Liu, Q.X.; Doelman, A.; Rottschäfer, V.; de Jager, M.; Herman, P.M.J.; Rietkerk, M.; van de Koppel, J.

    2013-01-01

    The origin of regular spatial patterns in ecological systems has long fascinated researchers. Turing's activator-inhibitor principle is considered the central paradigm to explain such patterns. According to this principle, local activation combined with long-range inhibition of growth and survival

  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. 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

  3. 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

  4. Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi.

    Science.gov (United States)

    Cornell, Michael J; Alam, Intikhab; Soanes, Darren M; Wong, Han Min; Hedeler, Cornelia; Paton, Norman W; Rattray, Magnus; Hubbard, Simon J; Talbot, Nicholas J; Oliver, Stephen G

    2007-12-01

    The recent proliferation of genome sequencing in diverse fungal species has provided the first opportunity for comparative genome analysis across a eukaryotic kingdom. Here, we report a comparative study of 34 complete fungal genome sequences, representing a broad diversity of Ascomycete, Basidiomycete, and Zygomycete species. We have clustered all predicted protein-encoding gene sequences from these species to provide a means of investigating gene innovations, gene family expansions, protein family diversification, and the conservation of essential gene functions-empirically determined in Saccharomyces cerevisiae-among the fungi. The results are presented with reference to a phylogeny of the 34 fungal species, based on 29 universally conserved protein-encoding gene sequences. We contrast this phylogeny with one based on gene presence and absence and show that, while the two phylogenies are largely in agreement, there are differences in the positioning of some species. We have investigated levels of gene duplication and demonstrate that this varies greatly between fungal species, although there are instances of coduplication in distantly related fungi. We have also investigated the extent of orthology for protein families and demonstrate unexpectedly high levels of diversity among genes involved in lipid metabolism. These analyses have been collated in the e-Fungi data warehouse, providing an online resource for comparative genomic analysis of the fungi.

  5. Genomic organization of the human T-cell antigen-receptor alpha/delta locus

    NARCIS (Netherlands)

    Satyanarayana, K.; Hata, S.; Devlin, P.; Roncarolo, M. G.; de Vries, J. E.; Spits, H.; Strominger, J. L.; Krangel, M. S.

    1988-01-01

    Two clusters of overlapping cosmid clones comprising about 100 kilobases (kb) at the human T-cell antigen-receptor alpha/delta locus were isolated from a genomic library. The structure of the germ-line V delta 1 variable gene segment was determined. V delta 1 is located 8.5 kb downstream of the V

  6. Complete nucleotide sequence and genome organization of a novel allexivirus from alfalfa (Medicago sativa)

    Science.gov (United States)

    A new species of the family Alphaflexiviridae provisionally named Alfalfa virus S (AVS) was diagnosed in alfalfa samples originating from Sudan. A complete nucleotide sequence of the viral genome consisting of 8,349 nucleotides excluding the 3’ poly(A) tail was determined by Illumina NGS technology ...

  7. Spatial Patterns and Topographic Controls of Post-settlement Deposition and Soil Organic Carbon Storage in Depressional Landscapes of Minnesota

    Science.gov (United States)

    Wu, A.; Bell, J.; Nater, E.

    2013-12-01

    Agriculture-enhanced erosion and deposition affect soil organic carbon (SOC) dynamics and storage on hillslopes. Because soil is the largest terrestrial C inventory, such SOC change can have significant impacts on global C cycling. The downslope deposition and burial of C-rich topsoils in depressional landscapes are likely to sequester SOC, but our understanding of the spatial patterns and mechanisms behind it is still limited. In this study, we aim to identify spatial distribution of post-settlement deposition and SOC and to understand its physical impact on soil C storage in depressional landscapes on the Des Moines Lobe in Minnesota. The specific objectives for this study are to: 1) understand the distribution and thickness of post-settlement deposition by building spatial soil-landscape models using local and upslope dependence area terrain attributes; 2) develop soil C models for various profile depths; and 3) identify the spatial relation between post-settlement deposition and SOC. Using a 1-m LiDAR-based digital elevation model, we apply upslope dependence (contributing areas) and local (3-by-3 cell window) terrain attributes in spatial modeling because topographic features are key factors controlling landscape-scale soil processes. Upslope dependence terrain drives the waterflow-relevant soil processes such as soil erosion production, and local terrain controls redeposition. We predict the spatially-explicit probability of post-settlement deposition presence using logistic regression, and employ multiple linear regressions for the prediction of its thickness. Because the depth distribution of SOC in soil is affected by biological activities and topographic controls, we interpolated and mapped the spatial distribution of SOC in five fixed-depth layers (0-10cm, 10-30cm, 30-60cm, 60-90cm, and 90-120cm) and reported full depth composite values after individual layer modeling. The resulting SOC (kg/m2) map will be overlayed with post-settlement deposition maps

  8. Spatial and Temporal Trends of Persistent Organic Chemicals with Emphasis on Brominated Flame Retardants

    Science.gov (United States)

    Rapid growth in chemical and agrochemical industries during the past century have resulted in the release of large numbers of persistent organic chemicals (POCs) into the environment. Since POCs are prevalent in air, water, soil and tissue of organisms throughout the world and r...

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Genomic organization of a receptor from sea anemones, structurally and evolutionary related to glycoprotein hormone receptors from mamals

    DEFF Research Database (Denmark)

    Vibede, N; Hauser, Frank; Williamson, M

    1998-01-01

    Abstract Cnidarians (e.g., sea anemones and corals) are the lowest animal group having a nervous system. Previously, we cloned a receptor from sea anemones that showed a strong structural similarity to the glycoprotein hormone (TSH, FSH, LH/CG) receptors from mammals. Here, we determine the genomic...... organization of this sea anemone receptor. The receptor gene contains eight introns that are all localized within a region coding for the large extracellular N terminus. These introns occur at the same positions and have the same intron phasing as eight introns in the genes coding for the mammalian...

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Origin of spatial organization of DNA-polymer in bacterial chromosomes

    Science.gov (United States)

    Agarwal, Tejal; Manjunath, G. P.; Habib, Farhat; Chatterji, Apratim

    2018-01-01

    In vivo DNA organization at large length scales (∼100 \\text{nm}) is highly debated and polymer models have proved useful to understand the principles of DNA organization. Here, we show that extracted from contact maps of bacterial DNA. We are able to predict the structure of 2 DNAs (E. coli and Caulobacter crescentus) using Monte Carlo simulations of the bead-spring polymer with cross-links at these special positions. Simulations with cross-links at random positions along the chain show that the organization of the polymer is different in nature from the previous case. We provide some direct and some indirect experimental validation for our predicted organization of DNA-polymers.

  3. Spatial and functional organization of pig trade in different european production systems: implications for disease prevention and control

    Directory of Open Access Journals (Sweden)

    Anne eRelun

    2016-02-01

    Full Text Available Understanding the complexity of live pig trade organization is a key factor to predict and control major infectious diseases such as Classical or African swine fever. Whereas the organization of pig trade has been described in several European countries with indoor commercial production systems, little information is available on this organisation in other systems like outdoor or small-scale systems. The objective of this study was to describe and compare the spatial and functional organisation of live pig trade in different European countries and different production systems. Data on premise characteristics and pig movements between premises were collected during 2011 from Bulgaria, France, Italy and Spain, which swine industry is representative of most of the production systems in Europe (i.e. commercial vs small-scale; outdoor vs indoor. Trade communities were identified in each country using the Walktrap algorithm. Several descriptive and network metrics were generated at country and community level. Pig trade organization showed heterogeneous spatial and functional organization. Trade communities mostly composed of indoor commercial premises were identified in Western France, Northern Italy, Northern Spain and North-Western Bulgaria. They covered large distances, overlapped in space, demonstrated both scale-free and small-world properties, with a role of trade operators and multipliers as key premises. Trade communities involving outdoor commercial premises were identified in Western Spain, South-Western and Central France. They were more spatially clustered, demonstrated scale-free properties, with multipliers as key premises. Small-scale communities involved the majority of premises in Bulgaria and in central and Southern Italy. They were spatially clustered and had scale-free properties, with key premises usually being commercial production premises. These results indicate that a disease might spread very differently according to the

  4. Transmission of methicillin-resistant Staphylococcus aureus infection through solid organ transplantation: confirmation via whole genome sequencing.

    Science.gov (United States)

    Wendt, J M; Kaul, D; Limbago, B M; Ramesh, M; Cohle, S; Denison, A M; Driebe, E M; Rasheed, J K; Zaki, S R; Blau, D M; Paddock, C D; McDougal, L K; Engelthaler, D M; Keim, P S; Roe, C C; Akselrod, H; Kuehnert, M J; Basavaraju, S V

    2014-11-01

    We describe two cases of donor-derived methicillin-resistant Staphylococcus aureus (MRSA) bacteremia that developed after transplantation of organs from a common donor who died from acute MRSA endocarditis. Both recipients developed recurrent MRSA infection despite appropriate antibiotic therapy, and required prolonged hospitalization and hospital readmission. Comparison of S. aureus whole genome sequence of DNA extracted from fixed donor tissue and recipients' isolates confirmed donor-derived transmission. Current guidelines emphasize the risk posed by donors with bacteremia from multidrug-resistant organisms. This investigation suggests that, particularly in the setting of donor endocarditis, even a standard course of prophylactic antibiotics may not be sufficient to prevent donor-derived infection. © Copyright 2014 The American Society of Transplantation and the American Society of Transplant Surgeons.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. The Emerging Spatial Organization of the Metropolis: Zones of Diversity and Minority Enclaves in Chicago.

    Science.gov (United States)

    Zhang, Wenquan; Logan, John R

    2017-07-01

    The rapid growth of Asian and Hispanic populations in urban areas is superceding traditional classifications of neighborhoods (for example as white, transitional, or minority). The "global neighborhood" that includes all groups (white, black, Hispanic and Asian) is one important new category. We examine the emerging spatial pattern of racial/ethnic composition in the Chicago metropolis, documenting an expansion of all-minority neighborhoods in the city and just beyond its borders, a shrinking set of all-white neighborhoods in the outer suburbs, and more diverse neighborhoods including whites mainly in between. The most novel element of this pattern is how large the zone of diversity has become and how far it extends into suburbia, upending the old dichotomy of "chocolate city" and "vanilla suburbs." In addition to comparing the distance of different kinds of neighborhoods from the urban core, we also analyze their adjacency to neighborhoods of the same type or other types. There is a strong tendency toward spatial clustering of each neighborhood type and also for transitions on the boundaries of clusters either to expand or to contract their territory.

  12. Application of a graded Sorensen test evokes spatially organized lumbar muscle fatigue.

    Science.gov (United States)

    Kurz, Eduard; Scholle, Hans-Christoph; Schenk, Philipp; Anders, Christoph

    2016-04-27

    The Sorensen test is commonly used to assess back muscle endurance capacity. However, the clinical value of this test, requiring compensation of the entire upper body mass, is limited if pain occurs. Therefore, a test variant using only portions of upper body mass could be an alternative. This study aimed to determine fatigue characteristics in lumbar muscles during a modified Sorensen test utilizing only 50% of the upper body mass and asked if localization-related effects of surface electrodes in the assessment of lumbar muscle fatigue should be considered. Thirty-two young (20-29 years) symptom-free men were enrolled and asked to maintain only 50% upper body mass for 10 minutes. Fatigue characteristics were bilaterally derived from four different lumbar levels using Surface EMG. Side-specific and SEMG parameter-independent repeated measures (four lumbar levels, nine time points) analyses of variance were conducted. All participants were able to complete the test. Over time, a spatial effect of fatigue-related amplitude alterations at the respective segments could be observed. By using this modified Sorensen test, muscular fatigue can be evoked. Electrophysiological assessment of lumbar fatigue should consider spatial differences.

  13. Automated feature extraction and spatial organization of seafloor pockmarks, Belfast Bay, Maine, USA

    Science.gov (United States)

    Andrews, Brian D.; Brothers, Laura L.; Barnhardt, Walter A.

    2010-01-01

    Seafloor pockmarks occur worldwide and may represent millions of m3 of continental shelf erosion, but few numerical analyses of their morphology and spatial distribution of pockmarks exist. We introduce a quantitative definition of pockmark morphology and, based on this definition, propose a three-step geomorphometric method to identify and extract pockmarks from high-resolution swath bathymetry. We apply this GIS-implemented approach to 25 km2 of bathymetry collected in the Belfast Bay, Maine USA pockmark field. Our model extracted 1767 pockmarks and found a linear pockmark depth-to-diameter ratio for pockmarks field-wide. Mean pockmark depth is 7.6 m and mean diameter is 84.8 m. Pockmark distribution is non-random, and nearly half of the field's pockmarks occur in chains. The most prominent chains are oriented semi-normal to the steepest gradient in Holocene sediment thickness. A descriptive model yields field-wide spatial statistics indicating that pockmarks are distributed in non-random clusters. Results enable quantitative comparison of pockmarks in fields worldwide as well as similar concave features, such as impact craters, dolines, or salt pools.

  14. 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.

  15. 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.

  16. 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)

  17. 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.

  18. 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

  19. 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...

  20. The genome of tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster.

    Directory of Open Access Journals (Sweden)

    Kathryn E Bushley

    2013-06-01

    Full Text Available 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

  1. Link between spatial structure of microbial communities and degradation of a complex mixture of volatile organic compounds in peat biofilters.

    Science.gov (United States)

    Khammar, N; Malhautier, L; Degrange, V; Lensi, R; Godon, J-J; Fanlo, J-L

    2005-01-01

    To investigate the relationships between the operation of the volatile organic compound (VOC) removal biofilter and the structure of microbial communities, and to study the impact on degradation activities and the structuring of microbial communities of biofilter malfunctions related to the qualitative composition of the polluted air. A microbiological study and a measurement of biodegradation activities were simultaneously carried out on two identical peat-packed columns, seeded with two different inocula, treating polluted air containing 11 VOCs. For both reactors, the spatial structure of the microbial communities was investigated by means of single-strand conformation polymorphism (SSCP) analysis. For both reactors, stratification of degradation activities in function of depth was observed. Oxygenated compounds were removed at the top of the column and aromatics at the bottom. Comparison of SSCP patterns clearly showed a shift in community structure in function of depth inside both biofilters. This distribution of biodegradation activities correlates with the spatialization of microbial density and diversity. Although the operating conditions of both reactors were identical and the biodegradation activities similar, the composition of microflora differed for biofilters A and B. Subdivision of biofilter B into two independent parts supplied with polluted air containing the complex VOC mixture showed that the microflora having colonized the bottom of biofilter B retained their potential for degrading oxygenated compounds. This work highlights the spatialization of biodegradation functions in a biofilter treating a complex mixture of VOCs. This distribution of biodegradation activities correlates with the spatialization of microbial density and diversity. This vertical structure of microbial communities must be taken into consideration when dealing with the malfunctioning of bioreactors. These results are also useful information about changes in microbial

  2. Spatial and Dosimetric Variability of Organs at Risk in Head-and-Neck Intensity-Modulated Radiotherapy

    International Nuclear Information System (INIS)

    Robar, James L.; Day, Allan Nova; Clancey, James; Kelly, Robin; Yewondwossen, Mammo; Hollenhorst, Helmut; Rajaraman, Murali; Wilke, Derek

    2007-01-01

    Purpose: The accuracy of intensity-modulated radiotherapy (IMRT) delivery may be compromised by random spatial error and systematic anatomic changes during the treatment course. We present quantitative measurements of the spatial variability of head-and-neck organs-at-risk and demonstrate the resultant dosimetric effects. Methods and Materials: Fifteen consecutive patients were imaged weekly using computed tomography during the treatment course. Three-dimensional displacements were calculated for the superior and inferior brainstem; C1, C6, and T2 spinal cord; as well as the lateral and medial aspects of the parotid glands. The data were analyzed to show distributions of spatial error and to track temporal changes. The treatment plan was recalculated on all computed tomography sets, and the dosimetric error was quantified in terms of the maximal dose difference (brainstem and spinal cord) or the mean dose difference and the volume receiving 26 Gy (parotid glands). Results: The mean three-dimensional displacement was 2.9 mm for the superior brainstem, 3.4 mm for the inferior brainstem, 3.5 mm for the C1 spine, 5.6 mm for the C6 spine and 6.0 mm for the T2 spine. The lateral aspects of both parotid glands showed a medial translation of 0.85 mm/wk, and glands shrank by 4.9%/wk. The variability of the maximal dose difference was described by standard deviations ranging from 5.6% (upper cord) to 8.0% (lower cord.) The translation of the left parotid resulted in an increase of the mean dose and the volume receiving 26 Gy. Conclusion: Random spatial and dosimetric variability is predominant for the brainstem and spinal cord and increases at more inferior locations. In contrast, the parotid glands demonstrated a systematic medial translation during the treatment course and thus sparing may be compromised

  3. Spatial patterns and environmental controls of particulate organic carbon in surface waters in the conterminous United States

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Qichun; Zhang, Xuesong; Xu, Xingya; Asrar, Ghassem R.; Smith, Richard A.; Shih, Jhih-Shyang; Duan, Shuiwang

    2016-06-01

    Carbon stocks and fluxes in inland waters have been identified as important, but poorly constrained components of the global carbon cycle. In this study, we compile and analyze particulate organic carbon (POC) concentration data from 1145 U.S. Geological Survey (USGS) hydrologic stations to investigate the spatial variability and environmental controls of POC concentration. We observe substantial spatial variability in POC concentration (1.43 ± 2.56 mg C/ L, Mean ± Standard Deviation), with the Upper Mississippi River basin and the Piedmont region in the eastern U.S. having the highest POC concentration. Further, we employ generalized linear regression models to analyze the impacts of sediment transport and algae growth as well as twenty-one other environmental factors on the POC variability. Suspended sediment and chlorophyll-a explain 26% and 17% of the variability in POC concentration, respectively. At the national level, the twenty-one selected environmental factors combined can explain ca. 40% of the spatial variance in POC concentration. Overall, urban area and soil clay content show significant negative correlation with POC concentration, while soil water content and soil bulk density correlate positively with POC. In addition, total phosphorus concentration and dam density covariate positively with POC concentration. Furthermore, regional scale analyses reveal substantial variation in environmental controls determining POC concentration across the 18 major water resource regions in the U.S. The POC concentration and associated environmental controls also vary non-monotonically with river order. These findings indicate complex interactions among multiple factors in regulating POC production over different spatial scales and across various sections of the river networks. This complexity together with the large unexplained uncertainty highlight the need for consideration of non-linear processes that control them and developing appropriate methodologies to

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. Molecular cloning and genomic organization of a second probable allatostatin receptor from Drosophila melanogaster

    DEFF Research Database (Denmark)

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

    2000-01-01

    We (C. Lenz et al. (2000) Biochem. Biophys. Res. Commun. 269, 91-96) and others (N. Birgül et al. (1999) EMBO J. 18, 5892-5900) have recently cloned a Drosophila receptor that was structurally related to the mammalian galanin receptors, but turned out to be a receptor for a Drosophila peptide...... with a Drosophila genomic database clone that contained a DNA sequence coding for a protein having, again, structural similarities with the rat galanin receptors. Using PCR with primers coding for the presumed exons of this second Drosophila receptor gene, 5'- and 3'-RACE, and Drosophila cDNA as template, we...

  9. Comparative Genomics

    Indian Academy of Sciences (India)

    An important hallmark of biological research is the aspect of 'comparisons'. As the complete genome sequences of numerous organisms have become available, the emphasis in biology has shifted to comparisons at the genome level. Indeed, the last few years have witnessed an exponential rise in the number of ...

  10. Hydrologic controls on aperiodic spatial organization of the ridge–slough patterned landscape

    Directory of Open Access Journals (Sweden)

    S. T. Casey

    2016-11-01

    Full Text Available A century of hydrologic modification has altered the physical and biological drivers of landscape processes in the Everglades (Florida, USA. Restoring the ridge–slough patterned landscape, a dominant feature of the historical system, is a priority but requires an understanding of pattern genesis and degradation mechanisms. Physical experiments to evaluate alternative pattern formation mechanisms are limited by the long timescales of peat accumulation and loss, necessitating model-based comparisons, where support for a particular mechanism is based on model replication of extant patterning and trajectories of degradation. However, multiple mechanisms yield a central feature of ridge–slough patterning (patch elongation in the direction of historical flow, limiting the utility of that characteristic for discriminating among alternatives. Using data from vegetation maps, we investigated the statistical features of ridge–slough spatial patterning (ridge density, patch perimeter, elongation, patch size distributions, and spatial periodicity to establish more rigorous criteria for evaluating model performance and to inform controls on pattern variation across the contemporary system. Mean water depth explained significant variation in ridge density, total perimeter, and length : width ratios, illustrating an important pattern response to existing hydrologic gradients. Two independent analyses (2-D periodograms and patch size distributions provide strong evidence against regular patterning, with the landscape exhibiting neither a characteristic wavelength nor a characteristic patch size, both of which are expected under conditions that produce regular patterns. Rather, landscape properties suggest robust scale-free patterning, indicating genesis from the coupled effects of local facilitation and a global negative feedback operating uniformly at the landscape scale. Critically, this challenges widespread invocation of scale-dependent negative

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. The spatial and logical organization of devices in an advanced industrial robot system

    Science.gov (United States)

    Ruoff, C. F.

    1980-01-01

    This paper describes the geometrical and device organization of a robot system which is based in part upon transformations of Cartesian frames and exchangeable device tree structures. It discusses coordinate frame transformations, geometrical device representation and solution degeneracy along with the data structures which support the exchangeable logical-physical device assignments. The system, which has been implemented in a minicomputer, supports vision, force, and other sensors. It allows tasks to be instantiated with logically equivalent devices and it allows tasks to be defined relative to appropriate frames. Since these frames are, in turn, defined relative other frames this organization provides a significant simplification in task specification and a high degree of system modularity.

  16. Spatial organization of ecologically-relevant high order flow properties and implications for river habitat assessment

    OpenAIRE

    Trinci, Giuditta

    2017-01-01

    The turbulent properties of flow in rivers are of fundamental importance to aquatic organisms yet are rarely quantified during routine river habitat assessment surveys or the design of restoration schemes due to their complex nature. This thesis uses a detailed review of the literature to highlight the various ways in which plants and animals modify the flow field, how this can deliver beneficial effects; and how turbulence can also generate threats to growth and survival. The thesis then pre...

  17. 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.

  18. Directional reflectance factors for monitoring spatial changes in soil surface structure and soil organic matter erosion in agricultural systems

    Science.gov (United States)

    Croft, H.; Anderson, K.

    2012-04-01

    Soils can experience rapid structural degradation in response to land cover changes, resulting in reduced soil productivity, increased erodibility and a loss of soil organic matter (SOM). The breakdown of soil aggregates through slaking and raindrop impact is linked to organic matter turnover, with subsequently eroded material often displaying proportionally more SOM. A reduction in aggregate stability is reflected in a decline in soil surface roughness (SSR), indicating that a soil structural change can be used to highlight soil vulnerability to SOM loss through mineralisation or erosion. Accurate, spatially-continuous measurements of SSR are therefore needed at a variety of spatial and temporal scales to understand the spatial nature of SOM erosion and deposition. Remotely-sensed data can provide a cost-effective means of monitoring changes in soil surface condition over broad spatial extents. Previous work has demonstrated the ability of directional reflectance factors to monitor soil crusting within a controlled laboratory experiment, due to changes in the levels of self-shadowing effects by soil aggregates. However, further research is needed to test this approach in situ, where other soil variables may affect measured reflectance factors and to investigate the use of directional reflectance factors for monitoring soil erosion processes. This experiment assesses the potential of using directional reflectance factors to monitor changes in SSR, aggregate stability and soil organic carbon (SOC) content for two agricultural conditions. Five soil plots representing tilled and seedbed soils were subjected to different durations of natural rainfall, producing a range of different levels of SSR. Directional reflectance factors were measured concomitantly with sampling for soil structural and biochemical tests at each soil plot. Soil samples were taken to measure aggregate stability (wet sieving), SOC (loss on ignition) and soil moisture (gravimetric method). SSM

  19. A Secreted BMP Antagonist, Cer1, Fine Tunes the Spatial Organization of the Ureteric Bud Tree during Mouse Kidney Development

    Science.gov (United States)

    Chi, Lijun; Saarela, Ulla; Railo, Antti; Prunskaite-Hyyryläinen, Renata; Skovorodkin, Ilya; Anthony, Shelagh; Katsu, Kenjiro; Liu, Yu; Shan, Jingdong; Salgueiro, Ana Marisa; Belo, José António; Davies, Jamie; Yokouchi, Yuji; Vainio, Seppo J.

    2011-01-01

    The epithelial ureteric bud is critical for mammalian kidney development as it generates the ureter and the collecting duct system that induces nephrogenesis in dicrete locations in the kidney mesenchyme during its emergence. We show that a secreted Bmp antagonist Cerberus homologue (Cer1) fine tunes the organization of the ureteric tree during organogenesis in the mouse embryo. Both enhanced ureteric expression of Cer1 and Cer1 knock out enlarge kidney size, and these changes are associated with an altered three-dimensional structure of the ureteric tree as revealed by optical projection tomography. Enhanced Cer1 expression changes the ureteric bud branching programme so that more trifid and lateral branches rather than bifid ones develop, as seen in time-lapse organ culture. These changes may be the reasons for the modified spatial arrangement of the ureteric tree in the kidneys of Cer1+ embryos. Cer1 gain of function is associated with moderately elevated expression of Gdnf and Wnt11, which is also induced in the case of Cer1 deficiency, where Bmp4 expression is reduced, indicating the dependence of Bmp expression on Cer1. Cer1 binds at least Bmp2/4 and antagonizes Bmp signalling in cell culture. In line with this, supplementation of Bmp4 restored the ureteric bud tip number, which was reduced by Cer1+ to bring it closer to the normal, consistent with models suggesting that Bmp signalling inhibits ureteric bud development. Genetic reduction of Wnt11 inhibited the Cer1-stimulated kidney development, but Cer1 did not influence Wnt11 signalling in cell culture, although it did inhibit the Wnt3a-induced canonical Top Flash reporter to some extent. We conclude that Cer1 fine tunes the spatial organization of the ureteric tree by coordinating the activities of the growth-promoting ureteric bud signals Gndf and Wnt11 via Bmp-mediated antagonism and to some degree via the canonical Wnt signalling involved in branching. PMID:22114682

  20. 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

  1. 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 ...

  2. Decadal climate variability and the spatial organization of deep hydrological drought

    Science.gov (United States)

    Barros, Ana P.; Hodes, Jared L.; Arulraj, Malarvizhi

    2017-10-01

    Empirical Orthogonal Function (EOF), wavelet, and wavelet coherence analysis of baseflow time-series from 126 streamgauges (record-length > 50 years; small and mid-size watersheds) in the US South Atlantic (USSA) region reveal three principal modes of space-time variability: (1) a region-wide dominant mode tied to annual precipitation that exhibits non-stationary decadal variability after the mid 1990s concurrent with the warming of the AMO (Atlantic Multidecadal Oscillation); (2) two spatial modes, east and west of the Blue Ridge, exhibiting nonstationary seasonal to sub-decadal variability before and after 1990 attributed to complex nonlinear interactions between ENSO and AMO impacting precipitation and recharge; and (3) deep (decadal) and shallow (predictability of hydrological drought in small and mid-size watersheds, where baseflow is a robust indicator of nonstationary yield capacity of the underlying groundwater basins. Predictive associations between climate mode indices and deep baseflow (e.g. persistent decreases of the decadal-scale components of baseflow during the cold phase of the AMO in the USSA) can be instrumental toward improving forecast lead-times and long-range mitigation of severe drought.

  3. 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

  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...... insect allatostatins. This resulted in alignment with a DNA sequence coding for some Drosophila allatostatins (drostatins). Using PCR with oligonucleotide primers directed against the presumed exons of this Drosophila allatostatin gene and subsequent 3'- and 5'-RACE, we were able to clone its c......DNA. The Drosophila allatostatin preprohormone contains four amino acid sequences that after processing would give rise to four Drosophila allatostatins: Val-Glu-Arg-Tyr-Ala-Phe-Gly-Leu-NH(2) (drostatin-1), Leu-Pro-Val-Tyr-Asn-Phe-Gly-Leu-NH(2) (drostatin-2), Ser-Arg-Pro-Tyr-Ser-Phe-Gly-Leu-NH(2) (drostatin-3...

  5. DMRT gene cluster analysis in the platypus: new insights into genomic organization and regulatory regions.

    Science.gov (United States)

    El-Mogharbel, Nisrine; Wakefield, Matthew; Deakin, Janine E; Tsend-Ayush, Enkhjargal; Grützner, Frank; Alsop, Amber; Ezaz, Tariq; Marshall Graves, Jennifer A

    2007-01-01

    We isolated and characterized a cluster of platypus DMRT genes and compared their arrangement, location, and sequence across vertebrates. The DMRT gene cluster on human 9p24.3 harbors, in order, DMRT1, DMRT3, and DMRT2, which share a DM domain. DMRT1 is highly conserved and involved in sexual development in vertebrates, and deletions in this region cause sex reversal in humans. Sequence comparisons of DMRT genes between species have been valuable in identifying exons, control regions, and conserved nongenic regions (CNGs). The addition of platypus sequences is expected to be particularly valuable, since monotremes fill a gap in the vertebrate genome coverage. We therefore isolated and fully sequenced platypus BAC clones containing DMRT3 and DMRT2 as well as DMRT1 and then generated multispecies alignments and ran prediction programs followed by experimental verification to annotate this gene cluster. We found that the three genes have 58-66% identity to their human orthologues, lie in the same order as in other vertebrates, and colocate on 1 of the 10 platypus sex chromosomes, X5. We also predict that optimal annotation of the newly sequenced platypus genome will be challenging. The analysis of platypus sequence revealed differences in structure and sequence of the DMRT gene cluster. Multispecies comparison was particularly effective for detecting CNGs, revealing several novel potential regulatory regions within DMRT3 and DMRT2 as well as DMRT1. RT-PCR indicated that platypus DMRT1 and DMRT3 are expressed specifically in the adult testis (and not ovary), but DMRT2 has a wider expression profile, as it does for other mammals. The platypus DMRT1 expression pattern, and its location on an X chromosome, suggests an involvement in monotreme sexual development.

  6. 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.

  7. Spatially organized aggregation of misfolded proteins as cellular stress defense strategy.

    Science.gov (United States)

    Miller, Stephanie B M; Mogk, Axel; Bukau, Bernd

    2015-04-10

    An evolutionary conserved response of cells to proteotoxic stress is the organized sequestration of misfolded proteins into subcellular deposition sites. In Saccharomyces cerevisiae, three major sequestration sites for misfolded proteins exist, IPOD (insoluble protein deposit), INQ (intranuclear quality control compartment) [former JUNQ (juxtanuclear quality control compartment)] and CytoQ. IPOD is perivacuolar and predominantly sequesters amyloidogenic proteins. INQ and CytoQs are stress-induced deposits for misfolded proteins residing in the nucleus and the cytosol, respectively, and requiring cell-compartment-specific aggregases, nuclear Btn2 and cytosolic Hsp42 for formation. The organized aggregation of misfolded proteins is proposed to serve several purposes collectively increasing cellular fitness and survival under proteotoxic stress. These include (i) shielding of cellular processes from interference by toxic protein conformers, (ii) reducing the substrate burden for protein quality control systems upon immediate stress, (iii) orchestrating chaperone and protease functions for efficient repair or degradation of damaged proteins [this involves initial extraction of aggregated molecules via the Hsp70/Hsp104 bi-chaperone system followed by either refolding or proteasomal degradation or removal of entire aggregates by selective autophagy (aggrephagy) involving the adaptor protein Cue5] and (iv) enabling asymmetric retention of protein aggregates during cell division, thereby allowing for damage clearance in daughter cells. Regulated protein aggregation thus serves cytoprotective functions vital for the maintenance of cell integrity and survival even under adverse stress conditions and during aging. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Genomic organization of the human PAX 3 gene: DNA sequence analysis of the region disrupted in alveolar rhabdomyosarcoma

    Energy Technology Data Exchange (ETDEWEB)

    Macina, R.A.; Galili, N.; Riethman, H.C. [Wistar Inst., Philadelphia, PA (United States)] [and others

    1995-03-01

    Mutations in the human PAX3 gene have previously been associated with two distinct diseases, Waardenburg syndrome and alveolar rhabdomyosarcoma. In this report the authors establish that the normal human PAX3 gene is encoded by 8 exons. Intron-exon boundary sequences were obtained for PAX 3 exons 5, 6, 7, and 8 and together with previous work provide the complete genomic sequence organization for PAX3. Difficulties in obtaining overlapping genomic clone coverage of PAX3 were circumvented in part by RARE cleavage mapping, which showed that the entire PAX3 gene spans 100 kb of chromosome 2. Sequence analysis of the last intron of PAX3, which contains the previously mapped t(2;13)(q35;q14) translocation breakpoints of alveolar rhabdomyosarcoma, revealed the presence of a pair of inverted Alu repeats and a pair of inverted (GT){sub n}-rich microsatellite repeats with in a 5k-kb region. This work establishes the complete structure of PAX 3 and will permit high-resolution analyses of this locus for mutations associated with Waardenburg syndrome, alveolar rhabdomyosarcoma, and other phenotypes for which PAX3 may be a candidate locus.31 refs., 5 figs., 1 tab.

  9. Temporal and spatial variability of trace volatile organic compounds in rainwater.

    Science.gov (United States)

    Mullaugh, Katherine M; Hamilton, Joanna M; Avery, G Brooks; Felix, J David; Mead, Ralph N; Willey, Joan D; Kieber, Robert J

    2015-09-01

    This study presents the first detailed concentration profile of trace VOCs in atmospheric waters. Analytes were detected and quantified in 111 unique rain events in Wilmington, NC, USA over a one-year period. Headspace solid phase microextraction was optimized for detection of these compounds at sub-nanomolar levels. Distinct seasonality in both the occurrence and concentration of compounds was observed with the lowest abundance occurring during low irradiance winter months. In contrast to other rainwater components studied at this location, VOCs did not show any correlation between rainfall amount and concentrations. There was significant spatial variation with regards to air-mass back-trajectory for methyfuran with higher concentrations observed in terrestrial events during the growing season. Air mass back trajectory also impacted CCl4 concentrations in rainwater with evidence of a possible oceanic input. However there was no significant impact of air-mass back-trajectory on the concentration of BTEX observed in rain indicating that storm origin is not the controlling factor driving concentrations of these analytes in precipitation. Members of the BTEX family did, however, have significant correlations with each other occurring in ratios aligned closely with ratios reported in the literature for gas-phase BTEX. Using available gas-phase data from locations with similar anthropogenic sources and Henry's Law constants, calculated concentrations agreed with VOC levels found in Wilmington rain. Results of this study indicate local gas-phase scavenging is the major source of VOCs in rain and wet deposition is not an efficient removal mechanism (<0.1%) of VOCs from the atmosphere. Copyright © 2015 Elsevier Ltd. All rights reserved.

  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. SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter.

    Science.gov (United States)

    Landry, Zachary; Swan, Brandon K; Herndl, Gerhard J; Stepanauskas, Ramunas; Giovannoni, Stephen J

    2017-04-18

    Deep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg of dissolved organic matter (DOM), much of which persists for thousands of years. It is thought that bacteria oxidize DOM until it is too dilute or refractory to support microbial activity. We analyzed five single-amplified genomes (SAGs) from the abundant SAR202 clade of dark-ocean bacterioplankton and found they encode multiple families of paralogous enzymes involved in carbon catabolism, including several families of oxidative enzymes that we hypothesize participate in the degradation of cyclic alkanes. The five partial genomes encoded 152 flavin mononucleotide/F420-dependent monooxygenases (FMNOs), many of which are predicted to be type II Baeyer-Villiger monooxygenases (BVMOs) that catalyze oxygen insertion into semilabile alicyclic alkanes. The large number of oxidative enzymes, as well as other families of enzymes that appear to play complementary roles in catabolic pathways, suggests that SAR202 might catalyze final steps in the biological oxidation of relatively recalcitrant organic compounds to refractory compounds that persist. IMPORTANCE Carbon in the ocean is massively sequestered in a complex mixture of biologically refractory molecules that accumulate as the chemical end member of biological oxidation and diagenetic change. However, few details are known about the biochemical machinery of carbon sequestration in the deep ocean. Reconstruction of the metabolism of a deep-ocean microbial clade, SAR202, led to postulation of new biochemical pathways that may be the penultimate stages of DOM oxidation to refractory forms that persist. These pathways are tied to a proliferation of oxidative enzymes. This research illuminates dark-ocean biochemistry that is broadly consequential for reconstructing the global carbon cycle. Copyright © 2017 Landry et al.

  13. 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.

  14. A temporally and spatially resolved validation of emission inventories by measurements of ambient volatile organic compounds in Beijing, China

    Science.gov (United States)

    Wang, M.; Shao, M.; Chen, W.; Yuan, B.; Lu, S.; Zhang, Q.; Zeng, L.; Wang, Q.

    2014-06-01

    Understanding the sources of volatile organic compounds (VOCs) is essential for ground-level ozone and secondary organic aerosol (SOA) abatement measures. We made VOC measurements at 27 sites and online observations at an urban site in Beijing from July 2009 to January 2012. Based on these measurement data, we determined the spatial and temporal distribution of VOCs, estimated their annual emission strengths based on their emission ratios relative to carbon monoxide (CO), and quantified the relative contributions of various sources using the chemical mass balance (CMB) model. These results from ambient measurements were compared with existing emission inventories to evaluate the spatial distribution, species-specific emissions, and source structure of VOCs in Beijing. The measured VOC distributions revealed a hotspot in the southern suburban area of Beijing, whereas current emission inventories suggested that VOC emissions were concentrated in downtown areas. Compared with results derived from ambient measurements, the annual inventoried emissions of oxygenated VOC (OVOC) species and C2-C4 alkanes may be underestimated, while the emissions of styrene and 1,3-butadiene may be overestimated by current inventories. Source apportionment using the CMB model identified vehicular exhaust as the most important VOC source, with the relative contribution of 49%, in good agreement with the 40-51% estimated by emission inventories. The relative contribution of paint and solvent utilization obtained from the CMB model was 14%, significantly lower than the value of 32% reported by one existing inventory. Meanwhile, the relative contribution of liquefied petroleum gas (LPG) usage calculated using the CMB model was 6%, whereas LPG usage contribution was not reported by current emission inventories. These results suggested that VOC emission strengths in southern suburban area of Beijing, annual emissions of C2-C4 alkanes, OVOCs and some alkenes, and the contributions of solvent and

  15. Spatial distribution of soil organic carbon and its influencing factors in desert grasslands of the Hexi Corridor, northwest China.

    Science.gov (United States)

    Wang, Min; Su, Yongzhong; Yang, Xiao

    2014-01-01

    Knowledge of the distribution patterns of soil organic carbon (SOC) and factors that influence these patterns is crucial for understanding the carbon cycle. The objectives of this study were to determine the spatial distribution pattern of soil organic carbon density (SOCD) and the controlling factors in arid desert grasslands of northwest China. The above- and belowground biomass and SOCD in 260 soil profiles from 52 sites over 2.7×10(4) km2 were investigated. Combined with a satellite-based dataset of an enhanced vegetation index during 2011-2012 and climatic factors at different sites, the relationships between SOCD and biotic and abiotic factors were identified. The results indicated that the mean SOCD was 1.20 (SD:+/- 0.85), 1.73 (SD:+/- 1.20), and 2.69 (SD:+/- 1.91) kg m(-2) at soil depths of 0-30 cm, 0-50 cm, and 0-100 cm, respectively, which was smaller than other estimates in temperate grassland, steppe, and desert-grassland ecosystems. The spatial distribution of SOCD gradually decreased from the southeast to the northwest, corresponding to the precipitation gradient. SOCD increased significantly with vegetation biomass, annual precipitation, soil moisture, clay and silt content, and decreased with mean annual temperature and sand content. The correlation between BGB and SOCD was closer than the correlation between AGB and SOCD. Variables could together explain about 69.8%, 74.4%, and 78.9% of total variation in SOCD at 0-30 cm, 0-50 cm, and 0-100 cm, respectively. In addition, we found that mean annual temperature is more important than other abiotic factors in determining SOCD in arid desert grasslands in our study area. The information obtained in this study provides a basis for accurately estimating SOC stocks and assessing carbon (C) sequestration potential in the desert grasslands of northwest China.

  16. Spatial distribution of soil organic carbon and its influencing factors in desert grasslands of the Hexi Corridor, northwest China.

    Directory of Open Access Journals (Sweden)

    Min Wang

    Full Text Available Knowledge of the distribution patterns of soil organic carbon (SOC and factors that influence these patterns is crucial for understanding the carbon cycle. The objectives of this study were to determine the spatial distribution pattern of soil organic carbon density (SOCD and the controlling factors in arid desert grasslands of northwest China. The above- and belowground biomass and SOCD in 260 soil profiles from 52 sites over 2.7×10(4 km2 were investigated. Combined with a satellite-based dataset of an enhanced vegetation index during 2011-2012 and climatic factors at different sites, the relationships between SOCD and biotic and abiotic factors were identified. The results indicated that the mean SOCD was 1.20 (SD:+/- 0.85, 1.73 (SD:+/- 1.20, and 2.69 (SD:+/- 1.91 kg m(-2 at soil depths of 0-30 cm, 0-50 cm, and 0-100 cm, respectively, which was smaller than other estimates in temperate grassland, steppe, and desert-grassland ecosystems. The spatial distribution of SOCD gradually decreased from the southeast to the northwest, corresponding to the precipitation gradient. SOCD increased significantly with vegetation biomass, annual precipitation, soil moisture, clay and silt content, and decreased with mean annual temperature and sand content. The correlation between BGB and SOCD was closer than the correlation between AGB and SOCD. Variables could together explain about 69.8%, 74.4%, and 78.9% of total variation in SOCD at 0-30 cm, 0-50 cm, and 0-100 cm, respectively. In addition, we found that mean annual temperature is more important than other abiotic factors in determining SOCD in arid desert grasslands in our study area. The information obtained in this study provides a basis for accurately estimating SOC stocks and assessing carbon (C sequestration potential in the desert grasslands of northwest China.

  17. 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.

  18. 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

    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...

  19. 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...

  20. Spatial and Temporal Distribution of Particulate Organic Carbon in the Winisk River, Northern Ontario

    Science.gov (United States)

    Glasauer, S.; Smith, P.; Smith, R. W.

    2016-12-01

    The Winisk River begins in the Precambrian rock of the Canadian Shield in Ontario and traverses the Hudson Bay Lowlands before terminating in Hudson Bay. It drains an area of 67,300 km2that is sparsely populated, with remote communities that depend on natural resources. Accelerated decomposition of organic carbon (OC) in the area due to climate change is supported by higher inputs of particulate and dissolved OC to surface waters (Amon et al, 2012). The Winisk River is a particularly important source of OC to Hudson Bay, shown by high rates of lignin accumulation near the mouth of the river (Kuzyk et al., 2008). Webequie First Nation (WFN) is a small community located on Eastwood Island in Winisk Lake. It is the closest community to the proposed massive development of the "Ring of Fire" chromite and other mineral deposits in the James Bay Lowlands. Mine-related developments can be expected to impact water flows, water chemistry, and carbon cycling in the region. We sampled water and sediment at the major inlets to the lake and at the northern outlet within the territorial boundaries to characterize water chemistry, relate lignin compositional patterns to C and N isotopic signatures, and interpret temporal patterns in advance of development and future climate change. Organic C in the sediments ranged from around 1% to around 30%. Samples were analyzed for lignin compounds using a CuO digestion method coupled to GC-MS to identify lignin-phenol monomers, benzoic acids, and p-hydroxy acid. Ratios of 3,5-dihydroxybenzoic acid, P-hydroxy phenols and cinnamyl phenols to total vanillyl phenols indicate that gymnosperm wood and sphagnum peat dominate the OC pool, although the proportions of gymnosperm- and sphagnum-derived material vary between sites. Stable isotope analysis (δ13C, δ15N) suggests that other inputs of OC may be present that are consistent with OM derived from the erosion of older marine sediments. The results support that the proportion of sphagnum mosses

  1. 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.

  2. Amount, determining factors and spatial distribution of soil organic carbon storage in the Dano catchment (Southwest Burkina-Faso)

    Science.gov (United States)

    Hounkpatin, O.; Op de Hipt, F.; Bossa, A. Y.; Welp, G.; Amelung, W.

    2015-12-01

    The ability to project and to mitigate the impacts of climate change is closely related to the evaluation of soil organic carbon (SOC) content and stock across different types of land use and soil groups. Therefore, this study aimed at estimating the surface and subsoil organic carbon stocks in different land use systems and across various soil groups. A further aim was to assess the spatial variability of SOC content and stocks and how this is controlled by climate and site properties. The Random Forest (RF) modelling was used and compared to Ordinary Kriging interpolation (OK) for the topsoil SOC and stock. About 70 soil profiles were described along 16 transects with 197 samples collected from different horizons up to 1 m depth where possible. In addition, 1205 samples were collected within an intensive auger grid mapping. Mid-infrared spectroscopy and partial least-squares analysis were used as a fast and low-cost technique to handle the large amount of samples for the SOC estimation. The natural/semi natural vegetation recorded the highest SOC stock in the topsoil (28.6 t C ha-1) as compared to the cropland (25.5 t C ha-1). Over 1 m depth, Gleysols (87.4 t C ha-1) stored the highest amount of SOC stock followed by the Cambisols (76. t C ha-1) and the Plinthosols (73.1 t C ha-1) while the lowest were found in the Lixisols (57.8 t C ha-1). For the topsoil, the RF model revealed soil properties such as cation exchange capacity (CEC) and stone content as main factors affecting SOC content variability while CEC and bulk density were the major drivers for the subsoil. The carbon stock variability was mainly affected by the CEC and the reference soil group in the topsoil while horizon thickness and bulk density constituted the main factors for the subsoil. The geostatistical evaluation proved that the SOC content in the Dano catchment has a moderate spatial autocorrelation while the carbon stock was strongly spatially dependent. The RF gave a better prediction for

  3. How well do food distributions predict spatial distributions of shorebirds with different degrees of self-organization?

    Science.gov (United States)

    Folmer, Eelke O; Olff, Han; Piersma, Theunis

    2010-07-01

    1. Habitat selection models usually assume that the spatial distributions of animals depend positively on the distributions of resources and negatively on interference. However, the presence of conspecifics at a given location also signals safety and the availability of resources. This may induce followers to select contiguous patches and causes animals to cluster. Resource availability, interference and attraction therefore jointly lead to self-organized patterns in foraging animals. 2. We analyse the distribution of foraging shorebirds at landscape level on the basis of a resource-based model to establish, albeit indirectly, the importance of conspecific attraction and interference. 3. At 23 intertidal sites with a mean area of 170 ha spread out over the Dutch Wadden Sea, the spatial distribution of six abundant shorebird species was determined. The location of individuals and groups was mapped using a simple method based on projective geometry, enabling fast mapping of low-tide foraging shorebird distributions. We analysed the suitability of these 23 sites in terms of food availability and travel distances to high tide roosts. 4. We introduce an interference sensitivity scale which maps interference as a function of inter-individual distance. We thus obtain interference-insensitive species, which are only sensitive to interference at short inter-individual distances (and may thus pack densely) and interference-sensitive species which interfere over greater inter-individual distances (and thus form sparse flocks). 5. We found that interference-insensitive species like red knot (Calidris canutus) and dunlins (Calidris alpina) are more clustered than predicted by the spatial distribution of their food resources. This suggests that these species follow each other when selecting foraging patches. In contrast, curlew (Numenius arquata) and grey plover (Pluvialis squatarola), known to be sensitive to interference, form sparse flocks. Hence, resource-based models have

  4. High-resolution mapping and spatial variability of soil organic carbon storage of permafrost-affected soils

    Science.gov (United States)

    Siewert, Matthias; Hugelius, Gustaf

    2017-04-01

    Permafrost-affected soils store large amounts of soil organic carbon (SOC). Mapping of this SOC provides a first order spatial input variable for research that relates carbon stored in permafrost regions to carbon cycle dynamics. High-resolution satellite imagery is becoming increasingly available even in circum-polar regions. The presented research highlights findings of high-resolution mapping efforts of SOC from five study areas in the northern circum-polar permafrost region. These study areas are located in Siberia (Kytalyk, Spasskaya Pad /Neleger, Lena delta), Northern Sweden (Abisko) and Northwestern Canada (Herschel Island). Our high spatial resolution analyses show how geomorphology has a strong influence on the distribution of SOC. This is organized at different spatial scales. Periglacial landforms and processes dictate local scale SOC distribution due to patterned ground. Such landforms are non-sorted circles and ice-wedge polygons of different age and scale. Palsas and peat plateaus are formed and can cover larger areas in Sub-Arctic environments. Study areas that have not been affected by Pleistocene glaciation feature ice-rich Yedoma sediments that dominate the local relief through thermokarst formation and create landscape scale macro environments that dictate the distribution of SOC. A general trend indicates higher SOC storage in Arctic tundra soils compared to forested Boreal or Sub-Arctic taiga soils. Yet, due to the shallower active layer depth in the Arctic, much of the SOC may be permanently frozen and thus not be available to ecosystem processes. Significantly more SOC is stored in soils compared to vegetation, indicating that vegetation growth and incorporation of the carbon into the plant phytomass alone will not be able to offset SOC released from permafrost. This contribution also addresses advances in thematic mapping methods and digital soil mapping of SOC in permafrost terrain. In particular machine-learning methods, such as support

  5. 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.

  6. 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.

  7. 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

  8. Monitoring of organ transplants through genomic analyses of circulating cell-free DNA

    Science.gov (United States)

    de Vlaminck, Iwijn

    Solid-organ transplantation is the preferred treatment for patients with end-stage organ diseases, but complications due to infection and acute rejection undermine its long-term benefits. While clinicians strive to carefully monitor transplant patients, diagnostic options are currently limited. My colleagues and I in the lab of Stephen Quake have found that a combination of next-generation sequencing with a phenomenon called circulating cell-free DNA enables non-invasive diagnosis of both infection and rejection in transplantation. A substantial amount of small fragments of cell-free DNA circulate in blood that are the debris of dead cells. We discovered that donor specific DNA is released in circulation during injury to the transplant organ and we show that the proportion of donor DNA in plasma is predictive of acute rejection in heart and lung transplantation. We profiled viral and bacterial DNA sequences in plasma of transplant patients and discovered that the relative representation of different viruses and bacteria is informative of immunosuppression. This discovery suggested a novel biological measure of a person's immune strength, a finding that we have more recently confirmed via B-cell repertoire sequencing. Lastly, our studies highlight applications of shotgun sequencing of cell-free DNA in the broad, hypothesis free diagnosis of infection.

  9. 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

    2015-02-01

    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.

  10. 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

  11. Spatial Controls on the Persistence and Vulnerability of Soil Organic Carbon

    Science.gov (United States)

    Smith, A. P.; Bond-Lamberty, B. P.; Tfaily, M. M.; Heredia-Langner, A.; Bailey, V. L.

    2016-12-01

    Soluble soil organic carbon (C) can be protected from microbial degradation through physical occlusion in fine-pore spaces, but how such protection mechanisms shift in response to environmental change, such as antecedent drought, rewetting direction (precipitation versus groundwater rise), and physical disturbance remains unclear. We coupled core-scale greenhouse gas measurements with pore-scale C chemistry to test the combined effects of drought, rewetting direction, and soil structure on C cycling. We subjected both intact and homogenized soil cores to drought or constant field moisture conditions, and then simulated groundwater rise or precipitation; soil CO2 and CH4 emissions were then monitored over 24 hours. Soil pore water was extracted from each core using different suction strengths to sample water retained by pore throats of different sizes and characterized by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. The effects of soil disturbance, rewetting direction, and their interaction altered CO2 emissions, with greater C-CO2 losses from homogenized cores subjected to groundwater rise compared to intact cores subjected to precipitation. We observed an increase in the nominal oxidation state of C in pore waters from homogenized cores compared to intact cores indicating C released from homogenization are reactive and thermodynamically available for microbial degradation. FT-ICR features were associated with metabolic and degradative processes in the pore waters from intact cores and synthesis-associated compounds in the homogenized cores. We also observed more aromatic compounds in the soil water collected at higher suction strengths, i.e. finer, more constricted pore spaces. These results suggest that physically protected C is more chemically complex than freely accessible C, and linked to biological processes that may be constrained by soil structure. A breakdown in physical protection releases these compounds into active C pools

  12. Influence of land use and land cover on the spatial variability of dissolved organic matter in multiple aquatic environments.

    Science.gov (United States)

    Singh, Shatrughan; Dash, Padmanava; Silwal, Saurav; Feng, Gary; Adeli, Ardeshir; Moorhead, Robert J

    2017-06-01

    Water quality of lakes, estuaries, and coastal areas serves as an indicator of the overall health of aquatic ecosystems as well as the health of the terrestrial ecosystem that drains to the water body. Land use and land cover plays not only a significant role in controlling the quantity of the exported dissolved organic matter (DOM) but also influences the quality of DOM via various biogeochemical and biodegradation processes. We examined the characteristics and spatial distribution of DOM in five major lakes, in an estuary, and in the coastal waters of the Mississippi, USA, and investigated the influence of the land use and land cover of their watersheds on the DOM composition. We employed absorption and fluorescence spectroscopy including excitation-emission matrix (EEM) combined with parallel factor (PARAFAC) analysis modeling techniques to determine optical properties of DOM and its characteristics in this study. We developed a site-specific PARAFAC model to evaluate DOM characteristics resulting in five diverse DOM compositions that included two terrestrial humic-like (C1 and C3), two microbial humic-like (C2 and C5), and one protein-like (C4) DOM. Our results showed elevated fluorescence levels of microbial humic-like or protein-like DOM in the lakes and coastal waters, while the estuarine waters showed relatively high fluorescence levels of terrestrial humic-like DOM. The results also showed that percent forest and wetland coverage explained 68 and 82% variability, respectively, in terrestrial humic-like DOM exports, while 87% variability in microbially derived humiclike DOM was explained by percent agricultural lands. Strong correlations between microbial humic-like DOM and fluorescence-derived DOM indices such as biological index (BIX) and fluorescence index (FI) indicated autochthonous characteristics in the lakes, while the estuary showed largely allochthonous DOM of terrestrial origin. We also observed higher concentrations of total dissolved

  13. Spatial distribution of organic carbon and humic substances in irrigated soils under different management systems in a semi-arid zone in Ceará, Brazil

    Directory of Open Access Journals (Sweden)

    Antônia Arleudina Barros de Melo

    2016-08-01

    Full Text Available Spatial distribution of organic carbon and humic substances in irrigated soils under different management systems in a semi-arid zone in Ceará, Brazil Knowledge of the spatial variability in soil properties can contribute to effective use and management. This study was conducted to evaluate the spatial distribution of the levels of total organic carbon (TOC and humic substances (humic acid (C-FAH, fulvic acid fraction (C-FAF, and humin fraction (C-HUM in an Ultisol under different land uses, located in the irrigated perimeter of Baixo Acaraú-CE, transition to semiarid Ceará. The distribution and spatial dependence of the humic fractions were evaluated using descriptive statistics, including semivariogram analysis and data interpolation (kriging. The TOC showed a pure nugget effect, whereas the other fractions showed moderate spatial dependence. Forested and banana cultivation areas showed similar distributions of C-FAH and C-FAF, due to the high input of organic matter (leaves and pseudostems in the area of banana cultivation and the absence of soil disturbance in the forested area. Data interpolation (kriging and mapping were useful tools to assess the distribution and spatial dependence of soil attributes.

  14. 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.

  15. 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

  16. 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.

  17. Identification of the HSP70-II gene in Leishmania braziliensis HSP70 locus: genomic organization and UTRs characterization

    Directory of Open Access Journals (Sweden)

    Puerta Concepción J

    2011-08-01

    Full Text Available Abstract Background The heat stress suffered by Leishmania sp during its digenetic life-cycle is a key trigger for its stage differentiation. In Leishmania subgenera two classes of HSP70 genes differing in their 3' UTR were described. Although the presence of HSP70-I genes was previously suggested in Leishmania (Viannia braziliensis, HSP70-II genes had been reluctant to be uncovered. Results Here, we report the existence of two types of HSP70 genes in L. braziliensis and the genomic organization of the HSP70 locus. RT-PCR experiments were used to map the untranslated regions (UTR of both types of genes. The 3' UTR-II has a low sequence identity (55-57% when compared with this region in other Leishmania species. In contrast, the 5' UTR, common to both types of genes, and the 3' UTR-I were found to be highly conserved among all Leishmania species (77-81%. Southern blot assays suggested that L. braziliensis HSP70 gene cluster may contain around 6 tandemly-repeated HSP70-I genes followed by one HSP70-II gene, located at chromosome 28. Northern blot analysis indicated that levels of both types of mRNAs are not affected by heat shock. Conclusions This study has led to establishing the composition and structure of the HSP70 locus of L. braziliensis, complementing the information available in the GeneDB genome database for this species. L. braziliensis HSP70 gene regulation does not seem to operate by mRNA stabilization as occurs in other Leishmania species.

  18. Genomic organization and transcription of satellite DNA in the ant Aphaenogaster subterranea (Hymenoptera, Formicidae).

    Science.gov (United States)

    Lorite, P; Renault, S; Rouleux-Bonnin, F; Bigot, S; Periquet, G; Palomeque, T

    2002-08-01

    A satellite DNA family (APSU) was isolated and characterized in the ant Aphaenogaster subterranea. This satellite DNA is organized in tandem repeats of 162 bp and is relatively AT rich (51.9%). Sequence analysis showed a high level of homogeneity between monomers. Loss of satellite DNA has been detected in queens in relation to workers, because the amount of satellite DNA in queens is about 25% of the amount found in workers. Restriction analysis of the total DNA with methylation-sensitive enzymes suggests that this DNA is not methylated. Analysis of the electrophoretic mobility of satellite DNA on non-denaturing polyacrylamide showed that this satellite DNA is only very lightly curved. Their possible transcription was analyzed using reverse transcription and polymerase chain reaction (RT-PCR). The satellite DNA is transcribed on the two DNA strands at the same level in worker and queen pupae, as well as in worker adults.

  19. Sequence, genomic organization and expression of two channel catfish, Ictalurus punctatus, ghrelin receptors.

    Science.gov (United States)

    Small, Brian C; Quiniou, Sylvie M A; Kaiya, Hiroyuki

    2009-12-01

    Two ghrelin receptor (GHS-R) genes were isolated from channel catfish tissue and a bacterial artificial chromosome (BAC) library. The two receptors were characterized by determining tissue distribution, ontogeny of receptor mRNA expression, and effects of exogenous homologous ghrelin administration on target tissue mRNA expression. Analysis of sequence similarities indicated two genes putatively encoding GHS-R1 and GHS-R2, respectively, which have been known to be present in zebrafish. Organization and tissue expression of the GHS-R1 gene was similar to that reported for other species, and likewise yielded two detectable mRNA products as a result of alternative splicing. Expression of both full-length, GHS-R1a, and splice variant, GHS-R1b, mRNA was highest in the pituitary. Gene organization of GHS-R2 was similar to GHS-R1, but no splice variant was identified. Expression of GHS-R2a mRNA was highest in the Brockmann bodies. GHS-R1a mRNA was detected in unfertilized eggs and throughout embryogenesis, whereas GHR-R2a mRNA was not expressed in unfertilized eggs or early developing embryos and was the highest at the time of hatching. Catfish intraperitoneally injected with catfish ghrelin-Gly had greater mRNA expression of GHS-R1a in pituitaries at 2 h and Brockmann bodies at 4 h, and of GHS-R2a in Brockmann bodies at 6 h post injection. Amidated catfish ghrelin (ghrelin-amide) had no observable effect on expression of either pituitary receptor; however, GHS-R1a and GHS-R2a mRNA expression levels were increased 4 h post injection of ghrelin-amide in Brockmann bodies. This is the first characterization of GHS-R2a and suggests regulatory and functional differences between the two catfish receptors.

  20. New Insights into the Genome Organization of Yeast Killer Viruses Based on “Atypical” Killer Strains Characterized by High-Throughput Sequencing

    Directory of Open Access Journals (Sweden)

    Manuel Ramírez

    2017-09-01

    Full Text Available Viral M-dsRNAs encoding yeast killer toxins share similar genomic organization, but no overall sequence identity. The dsRNA full-length sequences of several known M-viruses either have yet to be completed, or they were shorter than estimated by agarose gel electrophoresis. High-throughput sequencing was used to analyze some M-dsRNAs previously sequenced by traditional techniques, and new dsRNAs from atypical killer strains of Saccharomyces cerevisiae and Torulaspora delbrueckii. All dsRNAs expected to be present in a given yeast strain were reliably detected and sequenced, and the previously-known sequences were confirmed. The few discrepancies between viral variants were mostly located around the central poly(A region. A continuous sequence of the ScV-M2 genome was obtained for the first time. M1 virus was found for the first time in wine yeasts, coexisting with Mbarr-1 virus in T. delbrueckii. Extra 5′- and 3′-sequences were found in all M-genomes. The presence of repeated short sequences in the non-coding 3′-region of most M-genomes indicates that they have a common phylogenetic origin. High identity between amino acid sequences of killer toxins and some unclassified proteins of yeast, bacteria, and wine grapes suggests that killer viruses recruited some sequences from the genome of these organisms, or vice versa, during evolution.

  1. New Insights into the Genome Organization of Yeast Killer Viruses Based on "Atypical" Killer Strains Characterized by High-Throughput Sequencing.

    Science.gov (United States)

    Ramírez, Manuel; Velázquez, Rocío; López-Piñeiro, Antonio; Naranjo, Belén; Roig, Francisco; Llorens, Carlos

    2017-09-19

    Viral M-dsRNAs encoding yeast killer toxins share similar genomic organization, but no overall sequence identity. The dsRNA full-length sequences of several known M-viruses either have yet to be completed, or they were shorter than estimated by agarose gel electrophoresis. High-throughput sequencing was used to analyze some M-dsRNAs previously sequenced by traditional techniques, and new dsRNAs from atypical killer strains of Saccharomyces cerevisiae and Torulaspora delbrueckii . All dsRNAs expected to be present in a given yeast strain were reliably detected and sequenced, and the previously-known sequences were confirmed. The few discrepancies between viral variants were mostly located around the central poly(A) region. A continuous sequence of the ScV-M2 genome was obtained for the first time. M1 virus was found for the first time in wine yeasts, coexisting with Mbarr-1 virus in T. delbrueckii . Extra 5'- and 3'-sequences were found in all M-genomes. The presence of repeated short sequences in the non-coding 3'-region of most M-genomes indicates that they have a common phylogenetic origin. High identity between amino acid sequences of killer toxins and some unclassified proteins of yeast, bacteria, and wine grapes suggests that killer viruses recruited some sequences from the genome of these organisms, or vice versa, during evolution.

  2. The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes.

    Science.gov (United States)

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

    2016-01-01

    The dynamic three-dimensional chromatin architecture of genomes and its co-evolutionary connection to its function-the storage, expression, and replication of genetic information-is still one of the central issues in biology. Here, we describe the much debated 3D architecture of the human and mouse genomes from the nucleosomal to the megabase pair level by a novel approach combining selective high-throughput high-resolution chromosomal interaction capture ( T2C ), polymer simulations, and scaling analysis of the 3D architecture and the DNA sequence. The genome is compacted into a chromatin quasi-fibre with ~5 ± 1 nucleosomes/11 nm, folded into stable ~30-100 kbp loops forming stable loop aggregates/rosettes connected by similar sized linkers. Minor but significant variations in the architecture are seen between cell types and functional states. The architecture and the DNA sequence show very similar fine-structured multi-scaling behaviour confirming their co-evolution and the above. This architecture, its dynamics, and accessibility, balance stability and flexibility ensuring genome integrity and variation enabling gene expression/regulation by self-organization of (in)active units already in proximity. Our results agree with the heuristics of the field and allow "architectural sequencing" at a genome mechanics level to understand the inseparable systems genomic properties.

  3. 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

  4. Genomic organization and expression of the human fatty aldehyde dehydrogenase gene (FALDH)

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, G.R.; Markova, N.G.; Compton, J.G. [National Institutes of Health, Bethesda, MD (United States)] [and others

    1997-01-15

    Mutations in the fatty aldehyde dehydrogenase (FALDH) gene cause Sjoegren-Larsson syndrome (SLS) - a disease characterized by mental retardation, spasticity, and congenital ichthyosis. To facilitate mutation analysis in SLS and to study the pathogenesis of FALDH deficiency, we have determined the structural organization and characterized expression of the FALDH (proposed designation ALDH10) gene. The gene consists of 10 exons spanning about 30.5 kb. A TATA-less promoter is associated with the major transcription initiation site found to be 258 hp upstream of the ATG codon. The G4C-rich sequences surrounding the transcription initiation site encompassed regulatory elements that interacted with proteins in HeLa nuclear extracts and were able to promote transcription in vitro. FALDH is widely expressed as three transcripts of 2, 3.8, and 4.0 kb, which originate from multiple polyadenylation signals in the 3{prime} UTR. An alternatively spliced mRNA was detected that contains an extra exon and encodes an enzyme that is likely to have altered membrane-binding properties. The FALDH gene lies only 50-85 kb from ALDH3, an aldehyde dehydrogenase gene that has homologous sequence and intron/exon structure. 25 refs., 4 figs., 1 tab.

  5. Spatially confined folding of chromatin in the interphase nucleus

    NARCIS (Netherlands)

    Mateos-Langerak, J.; Bohn, M.; de Leeuw, W.; Giromus, O.; Manders, E.M.M.; Verschure, P.J.; Indemans, M.H.G.; Gierman, H.J.; Heermann, D.W.; van Driel, R.; Goetze, S.

    2009-01-01

    Genome function in higher eukaryotes involves major changes in the spatial organization of the chromatin fiber. Nevertheless, our understanding of chromatin folding is remarkably limited. Polymer models have been used to describe chromatin folding. However, none of the proposed models gives a

  6. 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

  7. 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

  8. Positive circuits and d-dimensional spatial differentiation: application to the formation of sense organs in Drosophila.

    Science.gov (United States)

    Crumière, Anne; Sablik, Mathieu

    2008-01-01

    We discuss a rule proposed by the biologist Thomas according to which the possibility for a genetic network (represented by a signed directed graph called a regulatory graph) to have several stable states implies the existence of a positive circuit. This result is already known for different models, differential or discrete formalism, but always with a network of genes contained in a single cell. Thus, we can ask about the validity of this rule for a system containing several cells and with intercellular genetic interactions. In this paper, we consider the genetic interactions between several cells located on a d-dimensional lattice, i.e., each point of lattice represents a cell to which we associate the expression level of n genes contained in this cell. With this configuration, we show that the existence of a positive circuit is a necessary condition for a specific form of multistationarity, which naturally corresponds to spatial differentiation. We then illustrate this theorem through the example of the formation of sense organs in Drosophila.

  9. 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.

  10. Geochemistry of Dissolved Organic Matter in a Spatially Highly Resolved Groundwater Petroleum Hydrocarbon Plume Cross-Section.

    Science.gov (United States)

    Dvorski, Sabine E-M; Gonsior, Michael; Hertkorn, Norbert; Uhl, Jenny; Müller, Hubert; Griebler, Christian; Schmitt-Kopplin, Philippe

    2016-06-07

    At numerous groundwater sites worldwide, natural dissolved organic matter (DOM) is quantitatively complemented with petroleum hydrocarbons. To date, research has been focused almost exclusively on the contaminants, but detailed insights of the interaction of contaminant biodegradation, dominant redox processes, and interactions with natural DOM are missing. This study linked on-site high resolution spatial sampling of groundwater with high resolution molecular characterization of DOM and its relation to groundwater geochemistry across a petroleum hydrocarbon plume cross-section. Electrospray- and atmospheric pressure photoionization (ESI, APPI) ultrahigh resolution mass spectrometry (FT-ICR-MS) revealed a strong interaction between DOM and reactive sulfur species linked to microbial sulfate reduction, i.e., the key redox process involved in contaminant biodegradation. Excitation emission matrix (EEM) fluorescence spectroscopy in combination with Parallel Factor Analysis (PARAFAC) modeling attributed DOM samples to specific contamination traits. Nuclear magnetic resonance (NMR) spectroscopy evaluated the aromatic compounds and their degradation products in samples influenced by the petroleum contamination and its biodegradation. Our orthogonal high resolution analytical approach enabled a comprehensive molecular level understanding of the DOM with respect to in situ petroleum hydrocarbon biodegradation and microbial sulfate reduction. The role of natural DOM as potential cosubstrate and detoxification reactant may improve future bioremediation strategies.

  11. 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.

  12. The GLOBE 3D Genome Platform : Towards a novel System-Biological Paper-Tool to integrate the Huge Complexity of Genome Organization and Function - Presentation

    NARCIS (Netherlands)

    T.A. Knoch (Tobias); M. Lesnussa (Michael); F.N. Kepper (Nick); H.J.F.M.M. Eussen (Bert); F.G. Grosveld (Frank)

    2009-01-01

    textabstractThe combination of genome sequence and structure, its annotation and experimental data in an accessible and comprehensible way is a major challenge. Increasingly, there are a large number of extremely divergent data sets: the sequence itself, genes, regulatory regions, various

  13. 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.

  14. 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.

  15. Spatial and seasonal variation and source apportionment of volatile organic compounds (VOCs) in a heavily industrialized region

    Science.gov (United States)

    Dumanoglu, Yetkin; Kara, Melik; Altiok, Hasan; Odabasi, Mustafa; Elbir, Tolga; Bayram, Abdurrahman

    2014-12-01

    Source apportionment is generally applied to a time series of pollutant concentrations measured at a single site. However, in a complex airshed having multiple pollutant sources, it may be helpful to collect samples from several sites to ensure that some of them have low contributions from specific sources. Ambient air samples (n = 160) were collected by passive sampling during four seasons in 2009 and 2010 at forty different sites in Aliaga, Turkey to determine the spatial, seasonal variations and possible sources of volatile organic compounds (VOCs). Fifty-eight VOCs (Σ58VOC) were detected. Σ58VOC concentrations ranged between 0.1 and 1770 μg m-3 (avg ± SD, 67 ± 193 μg m-3). Aliphatic hydrocarbons were generally predominant with a high percentage of contribution (31%-88%) at all sites. Aromatic VOCs were the second highest group (8-50%), followed by halogenated VOCs (1-24%) and oxygenated VOCs (0.04-5.9%). Highly variable spatial distribution of ambient VOC concentrations suggested that the major sources in this region were industrial plants. Generally, VOC concentrations were higher in summer than in winter probably due to increased volatilization from their sources at higher ambient temperatures. However, high atmospheric VOC concentrations were also observed in winter and fall near the petroleum refinery and petrochemical complex, probably due to the calm conditions and high atmospheric stability that is commonly encountered during the winter months in the area, restricting the dilution of pollutants. The newest version of EPA PMF (V5.0) (Positive Matrix Factorization) having the capability of handling multiple site data was used for source apportionment. Refinery and petroleum products, petrochemical industry, solvent use and industrial processes, and vehicle exhaust were the identified VOC sources in the study area, contributing 56%, 22%, 12%, and 10%, respectively to the Σ58VOC concentrations. Carcinogenic risks due to lifetime exposure to seven VOCs

  16. Spatial Variation of Soil Organic Carbon and Total Nitrogen in the Coastal Area of Mid-Eastern China

    Science.gov (United States)

    Pu, Lijie; Liao, Qilin; Zhu, Ming; Yu, Xue; Mao, Tianying; Xu, Chenxing

    2017-01-01

    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. PMID:28708078

  17. Layer specific geostatistical coregionalisation of soil organic carbon utilising terrain attributes and spatial patterns of soil redistribution

    Science.gov (United States)

    Dlugoß, V.; Fiener, P.; Schneider, K.

    2009-04-01

    High-resolution soil organic carbon (SOC) maps are a major prerequisite for many environmental studies dealing with carbon stocks and fluxes as well as for biogeochemical modelling. Hence, the development of time and cost effective mapping methods is an important issue. In most cases these maps are interpolated based on measured point SOC data with different horizontal resolution, whereas additional secondary (terrain) information is often utilised. In this study the potential of external drift kriging (EDK) to improve the soil layer specific (I: 0-0.25 m, II: 0.25-0.5 m and III: 0.5-0.9 m) interpolation of SOC concentrations in a hilly 4.2 ha agriculturally used catchment was tested using three different input data densities (6, 16.9, and 37.9 soil samples/ha). A number of covariables were used in EDK with a special focus on those representing processes of soil moisture distribution and soil redistribution. The later was, among others, represented by the results of a relatively simple and robust water and tillage erosion model (WaTEM/SEDEM). With the EDK method a significant improvement of the precision of SOC maps derived from different input data densities was observed particularly for deeper soil layers. While in the plough layer only slight improvements could be found, covariables representing soil moisture distribution and especially soil redistribution substantially improved predictions in the two subsoil layers. A maximum relative improvement of 15.5% was found for soil layer III (16.9 soil samples/ha; Root Mean Square Error 0.153% kg kg-1). Comparing EDK results of medium and low resolution SOC input data (16.9 and 6 samples/ha) with OK results of high resolution inputs (37.9 samples/ha) shows a similar or even improved precision for soil layers I and III, while the reduction of input data density could not be fully compensated utilising covariables in soil layer II. In general, the results indicate the potential of EDK to improve SOC maps and to reduce

  18. 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.

  19. 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

  20. 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...

  1. Quantification of centimeter-scale spatial variation in PAH, glucose and benzoic acid mineralization and soil organic matter in road-side soil.

    Science.gov (United States)

    Hybholt, Trine K; Aamand, Jens; Johnsen, Anders R

    2011-05-01

    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 14C-labeled organic compounds in deep-well microplates and thereby compile mineralization curves for 348 soil samples of 0.2-cm3. 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 (7×11cm) 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. Copyright © 2011 Elsevier Ltd. All rights reserved.

  2. Constrained spherical deconvolution-based tractography and tract-based spatial statistics show abnormal microstructural organization in Asperger syndrome.

    Science.gov (United States)

    Roine, Ulrika; Salmi, Juha; Roine, Timo; Wendt, Taina Nieminen-von; Leppämäki, Sami; Rintahaka, Pertti; Tani, Pekka; Leemans, Alexander; Sams, Mikko

    2015-01-01

    The aim of this study was to investigate potential differences in neural structure in individuals with Asperger syndrome (AS), high-functioning individuals with autism spectrum disorder (ASD). The main symptoms of AS are severe impairments in social interactions and restricted or repetitive patterns of behaviors, interests or activities. Diffusion weighted magnetic resonance imaging data were acquired for 14 adult males with AS and 19 age, sex and IQ-matched controls. Voxelwise group differences in fractional anisotropy (FA) were studied with tract-based spatial statistics (TBSS). Based on the results of TBSS, a tract-level comparison was performed with constrained spherical deconvolution (CSD)-based tractography, which is able to detect complex (for example, crossing) fiber configurations. In addition, to investigate the relationship between the microstructural changes and the severity of symptoms, we looked for correlations between FA and the Autism Spectrum Quotient (AQ), Empathy Quotient and Systemizing Quotient. TBSS revealed widely distributed local increases in FA bilaterally in individuals with AS, most prominent in the temporal part of the superior longitudinal fasciculus, corticospinal tract, splenium of corpus callosum, anterior thalamic radiation, inferior fronto-occipital fasciculus (IFO), posterior thalamic radiation, uncinate fasciculus and inferior longitudinal fasciculus (ILF). CSD-based tractography also showed increases in the FA in multiple tracts. However, only the difference in the left ILF was significant after a Bonferroni correction. These results were not explained by the complexity of microstructural organization, measured using the planar diffusion coefficient. In addition, we found a correlation between AQ and FA in the right IFO in the whole group. Our results suggest that there are local and tract-level abnormalities in white matter (WM) microstructure in our homogenous and carefully characterized group of adults with AS, most

  3. The impact of dissolved organic carbon on the spatial variability of methanogenic archaea communities in natural wetland ecosystems across China.

    Science.gov (United States)

    Liu, Deyan; Ding, Weixin; Jia, Zhongjun; Cai, Zucong

    2012-10-01

    Significant spatial variation in CH(4) emissions is a well-established feature of natural wetland ecosystems. To understand the key factors affecting CH(4) production, the variation in community structure of methanogenic archaea, in relation to substrate and external environmental influences, was investigated in selected wetlands across China, using denaturing gradient gel electrophoresis. Case study areas were the subtropical Poyang wetland, the warm-temperate Hongze wetland, the cold-temperate Sanjiang marshes, and the alpine Ruoergai peatland on the Qinghai-Tibetan Plateau. The topsoil layer in the Hongze wetland exhibited the highest population of methanogens; the lowest was found in the Poyang wetland. Maximum CH(4) production occurred in the topsoil layer of the Sanjiang Carex lasiocarpa marsh, the minimum was observed in the Ruoergai peatland. CH(4) production potential was significantly correlated with the dissolved organic carbon (DOC) concentration but not with the abundance or diversity indices of methanogenic archaea. Phylogenetic analysis and DOC concentration indicated a shift in the dominant methanogen from the hydrogenotrophic Methanobacteriales in DOC-rich wetlands to Methanosarcinaceae with a low affinity in wetlands with relatively high DOC and then to the acetotrophic methanogen Methanosaetaceae with a high affinity in wetlands with low DOC, or with high DOC but rich sulfate-reducing bacteria. Therefore, it is proposed that the dominant methanogen type in wetlands is primarily influenced by available DOC concentration. In turn, the variation in CH(4) production potential in the wetlands of eastern China is attributable to differences in the DOC content and the dominant type of methanogen present.

  4. Hypolithic Biocrust in the Larsemann Hills of East Antarctica: Spatial Patterns, Organic Matter Stabilization, Comparison with Endolithic Systems

    Science.gov (United States)

    Mergelov, Nikita; Dolgikh, Andrey; Shorkunov, Ilya; Zazovskaya, Elya; Shishkov, Vasily; Pochikalov, Alexander

    2017-04-01

    The survey conducted in the Larsemann Hills oasis of East Antarctica (69°24'S, 76°14'E) revealed that hypolithic and endolithic bio-abiotic systems occupy from 20 to 60% of the wet valleys floors and slopes area. As in many other parts of Antarctica a significant portion of organic matter in Larsemann Hills is produced in cryptic niches inside the fissure network of hard rocks or under the stone pavements on loose sediments. The dominant autotrophic components of such ecosystems are cyanobacteria and green algae, mainly in the form of biofilms. However moss dominated communities could form distinct patterns within hypolithic biocrust. The spatial distribution of various types of hypolithic biocrusts, its thickness, moisture content, carbon and nitrogen content/stocks, as well as C/N ratios were studied at a detailed scale at several key sites along the grid of 10x10 m with a step of 1 m (121 sampling points each). The data received are evident that microbial and cryptogamic photoautotrophs activity in hidden habitats under the stone pavements could lead to the substantial organic matter accumulation in extreme environment of East Antarctica - up to 5% of C and 0.4% of N. However the radiocarbon data indicate that in many cases the values of fraction modern (F14C) exceed "1" which means that organic matter in hypolithic biocrust is not preserved in a long-term period. This contrasts with 14C "ages" of endolithic systems on surrounding slopes of the valley exceeding 500 and sometimes 1000 yr BP. We found that once hypolithic organogenous material is buried under sand and gravel 2-5 cm deeper than common hypolithic biocrust it could preserve for a dramatically longer periods and have the 14C "age" up to 1100 yr BP. As evidenced by optical and scanning electron microscopy with EDX this old organogenous material of hypolithic origin still retains clear filamentous structure of cyanobacteria biofilm as well as remnants of EPS stabilized mainly by amorphous Si and Al

  5. Cloning, genomic organization and expression of two glycosyl hydrolase family 10 (GHF10) genes from golden apple snail (Pomacea canaliculata).

    Science.gov (United States)

    Imjongjirak, Chanprapa; Amparyup, Piti; Sittipraneed, Siriporn

    2008-06-01

    Two cellulase cDNAs (GHF10-Pc1 and GHF10-Pc3) belonging to glycoside hydrolase family 10 (GHF10) were successfully isolated and characterized from stomach tissue of golden apple snail (Pomacea canaliculata), a kind of herbivorous mollusca. Sequencing analysis revealed full-length cDNAs of 1300 and 1277 bp in length, respectively. The open reading frame (ORF) of cellulase cDNA was 1188 and 1191 bp, encoding 395 and 396 amino acid, respectively. Sequence alignment revealed that GHF10-Pc1 and GHF10-Pc3 shared high identity with glycosyl hydrolase family 10 (GHF10) and had an overall similarity of 98 and 82% to those of Ampullaria crossean cellulase EGX. A neighbour-joining tree showed a clear differentiation between each species and also indicated that GHF10-Pc1 and GHF10-Pc3 from P. canaliculata and A. crossean EGX are closely related phylogenetically. The genomic organization of cellulase GHF10-Pc1 and GHF10-Pc3 genes was also investigated. The GHF10-Pc1 and GHF10-Pc3 genes spanned over 4937 and 4512 bp, respectively. Both genes contained 9 exons interrupted by eight introns. The result verified the endogenous origin of the GHF10-Pc1 and GHF10-Pc3 genes. Analysis of RNA by RT-PCR from several ages of P. canaliculata revealed that neither gene was expressed in eggs. GHF10-Pc1 was also expressed in 1- and 10-day-old juvenile snails whereas GHF10-Pc3 was expressed only in 1-day-old juvenile snails. The result showed that two GHF10-Pc transcripts were developmentally expressed.

  6. Analysis of Genome Content Evolution in PVC Bacterial Super-Phylum: Assessment of Candidate Genes Associated with Cellular Organization and Lifestyle

    Science.gov (United States)

    Kamneva, Olga K.; Knight, Stormy J.; Liberles, David A.; Ward, Naomi L.

    2012-01-01

    The Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) super-phylum contains bacteria with either complex cellular organization or simple cell structure; it also includes organisms of different lifestyles (pathogens, mutualists, commensal, and free-living). Genome content evolution of this group has not been studied in a systematic fashion, which would reveal genes underlying the emergence of PVC-specific phenotypes. Here, we analyzed the evolutionary dynamics of 26 PVC genomes and several outgroup species. We inferred HGT, duplications, and losses by reconciliation of 27,123 gene trees with the species phylogeny. We showed that genome expansion and contraction have driven evolution within Planctomycetes and Chlamydiae, respectively, and balanced each other in Verrucomicrobia and Lentisphaerae. We also found that for a large number of genes in PVC genomes the most similar sequences are present in Acidobacteria, suggesting past and/or current ecological interaction between organisms from these groups. We also found evidence of shared ancestry between carbohydrate degradation genes in the mucin-degrading human intestinal commensal Akkermansia muciniphila and sequences from Acidobacteria and Bacteroidetes, suggesting that glycoside hydrolases are transferred laterally between gut microbes and that the process of carbohydrate degradation is crucial for microbial survival within the human digestive system. Further, we identified a highly conserved genetic module preferentially present in compartmentalized PVC species and possibly associated with the complex cell plan in these organisms. This conserved machinery is likely to be membrane targeted and involved in electron transport, although its exact function is unknown. These genes represent good candidates for future functional studies. PMID:23221607

  7. MARINE-EXPRESS: taking advantage of high throughput cloning and expression strategies for the post-genomic analysis of marine organisms

    Directory of Open Access Journals (Sweden)

    Power Déborah

    2010-06-01

    Full Text Available Abstract Background The production of stable and soluble proteins is one of the most important steps prior to structural and functional studies of biological importance. We investigated the parallel production in a medium throughput strategy of genes coding for proteins from various marine organisms, using protocols that involved recombinatorial cloning, protein expression screening and batch purification. This strategy was applied in order to respond to the need for post-genomic validation of the recent success of a large number of marine genomic projects. Indeed, the upcoming challenge is to go beyond the bioinformatic data, since the bias introduced through the genomes of the so called model organisms leads to numerous proteins of unknown function in the still unexplored world of the oceanic organisms. Results We present here the results of expression tests for 192 targets using a 96-well plate format. Genes were PCR amplified and cloned in parallel into expression vectors pFO4 and pGEX-4T-1, in order to express proteins N-terminally fused to a six-histidine-tag and to a GST-tag, respectively. Small-scale expression and purification permitted isolation of 84 soluble proteins and 34 insoluble proteins, which could also be used in refolding assays. Selected examples of proteins expressed and purified to a larger scale are presented. Conclusions The objective of this program was to get around the bottlenecks of soluble, active protein expression and crystallization for post-genomic validation of a number of proteins that come from various marine organisms. Multiplying the constructions, vectors and targets treated in parallel is important for the success of a medium throughput strategy and considerably increases the chances to get rapid access to pure and soluble protein samples, needed for the subsequent biochemical characterizations. Our set up of a medium throughput strategy applied to genes from marine organisms had a mean success rate of 44

  8. MARINE-EXPRESS: taking advantage of high throughput cloning and expression strategies for the post-genomic analysis of marine organisms.

    Science.gov (United States)

    Groisillier, Agnès; Hervé, Cécile; Jeudy, Alexandra; Rebuffet, Etienne; Pluchon, Pierre F; Chevolot, Yann; Flament, Didier; Geslin, Claire; Morgado, Isabel M; Power, Déborah; Branno, Margherita; Moreau, Hervé; Michel, Gurvan; Boyen, Catherine; Czjzek, Mirjam

    2010-06-14

    The production of stable and soluble proteins is one of the most important steps prior to structural and functional studies of biological importance. We investigated the parallel production in a medium throughput strategy of genes coding for proteins from various marine organisms, using protocols that involved recombinatorial cloning, protein expression screening and batch purification. This strategy was applied in order to respond to the need for post-genomic validation of the recent success of a large number of marine genomic projects. Indeed, the upcoming challenge is to go beyond the bioinformatic data, since the bias introduced through the genomes of the so called model organisms leads to numerous proteins of unknown function in the still unexplored world of the oceanic organisms. We present here the results of expression tests for 192 targets using a 96-well plate format. Genes were PCR amplified and cloned in parallel into expression vectors pFO4 and pGEX-4T-1, in order to express proteins N-terminally fused to a six-histidine-tag and to a GST-tag, respectively. Small-scale expression and purification permitted isolation of 84 soluble proteins and 34 insoluble proteins, which could also be used in refolding assays. Selected examples of proteins expressed and purified to a larger scale are presented. The objective of this program was to get around the bottlenecks of soluble, active protein expression and crystallization for post-genomic validation of a number of proteins that come from various marine organisms. Multiplying the constructions, vectors and targets treated in parallel is important for the success of a medium throughput strategy and considerably increases the chances to get rapid access to pure and soluble protein samples, needed for the subsequent biochemical characterizations. Our set up of a medium throughput strategy applied to genes from marine organisms had a mean success rate of 44% soluble protein expression from marine bacteria, archaea

  9. Functional annotation, genome organization and phylogeny of the grapevine (Vitis vinifera) terpene synthase gene family based on genome assembly, FLcDNA cloning, and enzyme assays.

    Science.gov (United States)

    Martin, Diane M; Aubourg, Sébastien; Schouwey, Marina B; Daviet, Laurent; Schalk, Michel; Toub, Omid; Lund, Steven T; Bohlmann, Jörg

    2010-10-21

    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. 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. 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 about gene structure and phylogeny for the entire currently

  10. The Chloroplast Genome ofPassiflora edulis(Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales.

    Science.gov (United States)

    Cauz-Santos, Luiz A; Munhoz, Carla F; Rodde, Nathalie; Cauet, Stephane; Santos, Anselmo A; Penha, Helen A; Dornelas, Marcelo C; Varani, Alessandro M; Oliveira, Giancarlo C X; Bergès, Hélène; Vieira, Maria Lucia C

    2017-01-01

    The family Passifloraceae consists of some 700 species classified in around 16 genera. Almost all its members belong to the genus Passiflora . In Brazil, the yellow passion fruit ( Passiflora edulis ) is of considerable economic importance, both for juice production and consumption as fresh fruit. The availability of chloroplast genomes (cp genomes) and their sequence comparisons has led to a better understanding of the evolutionary relationships within plant taxa. In this study, we obtained the complete nucleotide sequence of the P. edulis chloroplast genome, the first entirely sequenced in the Passifloraceae family. We determined its structure and organization, and also performed phylogenomic studies on the order Malpighiales and the Fabids clade. The P. edulis chloroplast genome is characterized by the presence of two copies of an inverted repeat sequence (IRA and IRB) of 26,154 bp, each separating a small single copy region of 13,378 bp and a large single copy (LSC) region of 85,720 bp. The annotation resulted in the identification of 105 unique genes, including 30 tRNAs, 4 rRNAs, and 71 protein coding genes. Also, 36 repetitive elements and 85 SSRs (microsatellites) were identified. The structure of the complete cp genome of P. edulis differs from that of other species because of rearrangement events detected by means of a comparison based on 22 members of the Malpighiales. The rearrangements were three inversions of 46,151, 3,765 and 1,631 bp, located in the LSC region. Phylogenomic analysis resulted in strongly supported trees, but this could also be a consequence of the limited taxonomic sampling used. Our results have provided a better understanding of the evolutionary relationships in the Malpighiales and the Fabids, confirming the potential of complete chloroplast genome sequences in inferring evolutionary relationships and the utility of long sequence reads for generating very accurate biological information.

  11. Genome cartography: charting the apicomplexan genome.

    Science.gov (United States)

    Kissinger, Jessica C; DeBarry, Jeremy

    2011-08-01

    Genes reside in particular genomic contexts that can be mapped at many levels. Historically, 'genetic maps' were used primarily to locate genes. Recent technological advances in the determination of genome sequences have made the analysis and comparison of whole genomes possible and increasingly tractable. What do we see if we shift our focus from gene content (the 'inventory' of genes contained within a genome) to the composition and organization of a genome? This review examines what has been learned about the evolution of the apicomplexan genome as well as the significance and impact of genomic location on our understanding of the eukaryotic genome and parasite biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Spatial distributions and sequestrations of organic carbon and black carbon in soils from the Chinese Loess Plateau.

    Science.gov (United States)

    Zhan, Changlin; Cao, Junji; Han, Yongming; Huang, Shaopeng; Tu, Xiaming; Wang, Ping; An, Zhisheng

    2013-11-01

    Concentrations of soil organic carbon (SOC), black carbon (BC), char, and soot in topsoils (0-20 cm) and vertical soil profiles (0-100 cm) from the Chinese Loess Plateau (CLP) were investigated. Objectives of the study were to establish the spatial distributions and estimate the sequestrations of these substances. The SOC, BC, char and soot concentrations were higher in the eastern and southeastern parts of the plateau and lower in the north, which is consistent with the patterns of economic development and energy consumption. The highest average SOC concentration was found in the clayey loess zone, followed by the loess and sandy loess zones. Similar trends were observed for BC, char and soot, suggesting interactions with clay and silt are potentially important influences on OC and BC. The SOC contents in topsoils varied from 0.31 to 51.81 g kg(-1), with a mean value of 6.54 g kg(-1), while BC and char concentrations were 0.02 to 5.5 g kg(-1) and 0.003 to 4.19 g kg(-1), respectively, and soot ranged from 0.01 to 1.32 g kg(-1). Unlike SOC, both BC and char decreased with soil depth, whereas soot showed little variation with depth. BC and char were correlated in the topsoils, and both correlated moderately well with SOC (R(2)=0.60) and soot (R(2)=0.53). The SOC pools sequestered in the 0 to 20 cm and 0 to 100 cm depths were estimated to be 0.741 and 3.63 Pg, respectively, and the BC pools sequestered in the 0 to 20 cm and 0 to 100 cm depths were 0.073 and 0.456 Pg, respectively. Therefore the quantity of carbon stored in the sediments of the CLP evidently exceeds 10(9) tons. The char contained in the upper 20 cm layer was 0.053 Pg, which amounted to 72.5% of the BC in that layer. Copyright © 2012 Elsevier B.V. All rights reserved.

  18. 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

  19. 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

  20. Confocal Raman microscopy as a tool to describe different mineral and organic phases at high spatial resolution within marine biogenic carbonates: case study on Nerita undata (Gastropoda, Neritopsina)

    Science.gov (United States)

    Nehrke, G.; Nouet, J.

    2011-06-01

    Marine biogenic carbonates formed by invertebrates (e.g. corals and mollusk shells) represent complex composites of one or more mineral phases and organic molecules. This complexity ranges from the macroscopic structures observed with the naked eye down to sub micrometric structures only revealed by micro analytical techniques. Understanding to what extent and how organisms can control the formation of these structures requires that the mineral and organic phases can be identified and their spatial distribution related. Here we demonstrate the capability of confocal Raman microscopy applied to cross sections of a shell of Nerita undata to describe the distribution of calcite and aragonite including their crystallographic orientation with high lateral resolution (∼300 nm). Moreover, spatial distribution of functional groups of organic compounds can be simultaneously acquired, allowing to specifically relate them to the observed microstructures. The data presented in this case study highlights the possible new contributions of this method to the description of modalities of Nerita undata shell formation, and what could be expected of its application to other marine biogenic carbonates. Localization of areas of interest would also allow further investigations using more localized methods, such as TEM that would provide complementary information on the relation between organic molecules and crystallographic lattice.

  1. Riparian zone hydrology and soil water total organic carbon (TOC: implications for spatial variability and upscaling of lateral riparian TOC exports

    Directory of Open Access Journals (Sweden)

    T. Grabs

    2012-10-01

    Full Text Available Groundwater flowing from hillslopes through riparian (near-stream soils often undergoes chemical transformations that can substantially influence stream water chemistry. We used landscape analysis to predict total organic carbon (TOC concentration profiles and groundwater levels measured in the riparian zone (RZ of a 67 km2 catchment in Sweden. TOC exported laterally from 13 riparian soil profiles was then estimated based on the riparian flow–concentration integration model (RIM. Much of the observed spatial variability of riparian TOC concentrations in this system could be predicted from groundwater levels and the topographic wetness index (TWI. Organic riparian peat soils in forested areas emerged as hotspots exporting large amounts of TOC. These TOC fluxes were subject to considerable temporal variations caused by a combination of variable flow conditions and changing soil water TOC concentrations. Mineral riparian gley soils, on the other hand, were related to rather small TOC export rates and were characterized by relatively time-invariant TOC concentration profiles. Organic and mineral soils in RZs constitute a heterogeneous landscape mosaic that potentially controls much of the spatial variability of stream water TOC. We developed an empirical regression model based on the TWI to move beyond the plot scale and to predict spatially variable riparian TOC concentration profiles for RZs underlain by glacial till.

  2. Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate.

    Science.gov (United States)

    Chong, Teik Min; Chen, Jian-Woon; See-Too, Wah-Seng; Yu, Choo-Yee; Ang, Geik-Yong; Lim, Yan Lue; Yin, Wai-Fong; Grandclément, Catherine; Faure, Denis; Dessaux, Yves; Chan, Kok-Gan

    2017-12-01

    Root exudates are chemical compounds that are released from living plant roots and provide significant energy, carbon, nitrogen and phosphorus sources for microbes inhabiting the rhizosphere. The exudates shape the microflora associated with the plant, as well as influences the plant health and productivity. Therefore, a better understanding of the trophic link that is established between the plant and the associated bacteria is necessary. In this study, a comprehensive survey on the utilization of grapevine and rootstock related organic acids were conducted on a vineyard soil isolate which is Pseudomonas mendocina strain S5.2. Phenotype microarray analysis has demonstrated that this strain can utilize several organic acids including lactic acid, succinic acid, malic acid, citric acid and fumaric acid as sole growth substrates. Complete genome analysis using single molecule real-time technology revealed that the genome consists of a 5,120,146 bp circular chromosome and a 252,328 bp megaplasmid. A series of genetic determinants associated with the carbon utilization signature of the strain were subsequently identified in the chromosome. Of note, the coexistence of genes encoding several iron-sulfur cluster independent isoenzymes in the genome indicated the importance of these enzymes in the events of iron deficiency. Synteny and comparative analysis have also unraveled the unique features of D-lactate dehydrogenase of strain S5.2 in the study. Collective information of this work has provided insights on the metabolic role of this strain in vineyard soil rhizosphere.

  3. 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 (Austri...... in this white paper......., 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...

  4. 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.

  5. 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.

  6. Spatial distribution of pH and organic matter in urban soils and its implications on site-specific land uses in Xuzhou, China.

    Science.gov (United States)

    Mao, Yingming; Sang, Shuxun; Liu, Shiqi; Jia, Jinlong

    2014-05-01

    The spatial variation of soil pH and soil organic matter (SOM) in the urban area of Xuzhou, China, was investigated in this study. Conventional statistics, geostatistics, and a geographical information system (GIS) were used to produce spatial distribution maps and to provide information about land use types. A total of 172 soil samples were collected based on grid method in the study area. Soil pH ranged from 6.47 to 8.48, with an average of 7.62. SOM content was very variable, ranging from 3.51 g/kg to 17.12 g/kg, with an average of 8.26 g/kg. Soil pH followed a normal distribution, while SOM followed a log-normal distribution. The results of semi-variograms indicated that soil pH and SOM had strong (21%) and moderate (44%) spatial dependence, respectively. The variogram model was spherical for soil pH and exponential for SOM. The spatial distribution maps were achieved using kriging interpolation. The high pH and high SOM tended to occur in the mixed forest land cover areas such as those in the southwestern part of the urban area, while the low values were found in the eastern and the northern parts, probably due to the effect of industrial and human activities. In the central urban area, the soil pH was low, but the SOM content was high, which is mainly attributed to the disturbance of regional resident activities and urban transportation. Furthermore, anthropogenic organic particles are possible sources of organic matter after entering the soil ecosystem in urban areas. These maps provide useful information for urban planning and environmental management. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  7. The Genome of Sulfolobus acidocaldarius, a Model Organism of the Crenarchaeota

    DEFF Research Database (Denmark)

    Chen, Lanming; Brügger, Kim; Skovgaard, M.

    2005-01-01

    tokodaii. The S. acidocaldarius genome contains an integrated, and probably encaptured, pARN-type conjugative plasmid which may facilitate intercellular chromosomal gene exchange in S. acidocaldarius. Moreover, it contains genes for a characteristic restriction modification system, a UV damage excision...... repair system, thermopsin, and an aromatic ring dioxygenase, all of which are absent from genomes of other Sulfolobus species. However, it lacks genes for some of their sugar transporters, consistent with it growing on a more limited range of carbon sources. These results, together with the many newly...

  8. Spatial distribution of soil organic carbon and total nitrogen based on GIS and geostatistics in a small watershed in a hilly area of northern China.

    Science.gov (United States)

    Peng, Gao; Bing, Wang; Guangpo, Geng; Guangcan, Zhang

    2013-01-01

    The spatial variability of soil organic carbon (SOC) and total nitrogen (STN) levels is important in both global carbon-nitrogen cycle and climate change research. There has been little research on the spatial distribution of SOC and STN at the watershed scale based on geographic information systems (GIS) and geostatistics. Ninety-seven soil samples taken at depths of 0-20 cm were collected during October 2010 and 2011 from the Matiyu small watershed (4.2 km(2)) of a hilly area in Shandong Province, northern China. The impacts of different land use types, elevation, vegetation coverage and other factors on SOC and STN spatial distributions were examined using GIS and a geostatistical method, regression-kriging. The results show that the concentration variations of SOC and STN in the Matiyu small watershed were moderate variation based on the mean, median, minimum and maximum, and the coefficients of variation (CV). Residual values of SOC and STN had moderate spatial autocorrelations, and the Nugget/Sill were 0.2% and 0.1%, respectively. Distribution maps of regression-kriging revealed that both SOC and STN concentrations in the Matiyu watershed decreased from southeast to northwest. This result was similar to the watershed DEM trend and significantly correlated with land use type, elevation and aspect. SOC and STN predictions with the regression-kriging method were more accurate than those obtained using ordinary kriging. This research indicates that geostatistical characteristics of SOC and STN concentrations in the watershed were closely related to both land-use type and spatial topographic structure and that regression-kriging is suitable for investigating the spatial distributions of SOC and STN in the complex topography of the watershed.

  9. 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

    Directory of Open Access Journals (Sweden)

    Lemieux Claude

    2006-04-01

    Full Text Available Abstract 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

  10. 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

  11. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics.......Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  12. 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

  13. Novel insights in the genomic organization and hotspots of recombination in the human KIR locus through analysis of intergenic regions

    NARCIS (Netherlands)

    Vendelbosch, S.; de Boer, M.; van Leeuwen, K.; Pourfarzad, F.; Geissler, J.; van den Berg, T. K.; Kuijpers, T. W.

    2015-01-01

    The Killer Immunoglobulin-like Receptor (KIR) proteins constitute a family of highly homologous surface receptors involved in the regulation of the innate cytotoxicity of natural killer (NK) cells. Within the human genome, 17 KIR genes are present, many of which show large variation across the

  14. 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...

  15. Spatial prediction of Soil Organic Carbon contents in croplands, grasslands and forests using environmental covariates and Generalized Additive Models (Southern Belgium)

    Science.gov (United States)

    Chartin, Caroline; Stevens, Antoine; van Wesemael, Bas

    2015-04-01

    Providing spatially continuous Soil Organic Carbon data (SOC) is needed to support decisions regarding soil management, and inform the political debate with quantified estimates of the status and change of the soil resource. Digital Soil Mapping techniques are based on relations existing between a soil parameter (measured at different locations in space at a defined period) and relevant covariates (spatially continuous data) that are factors controlling soil formation and explaining the spatial variability of the target variable. This study aimed at apply DSM techniques to recent SOC content measurements (2005-2013) in three different landuses, i.e. cropland, grassland, and forest, in the Walloon region (Southern Belgium). For this purpose, SOC databases of two regional Soil Monitoring Networks (CARBOSOL for croplands and grasslands, and IPRFW for forests) were first harmonized, totalising about 1,220 observations. Median values of SOC content for croplands, grasslands, and forests, are respectively of 12.8, 29.0, and 43.1 g C kg-1. Then, a set of spatial layers were prepared with a resolution of 40 meters and with the same grid topology, containing environmental covariates such as, landuses, Digital Elevation Model and its derivatives, soil texture, C factor, carbon inputs by manure, and climate. Here, in addition to the three classical texture classes (clays, silt, and sand), we tested the use of clays + fine silt content (particles agricultural soils and forests was for the first time computed for the Walloon region.

  16. 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...... hand, organic soil frequency was positively correlated to the corresponding DOC concentrations. Croplands also had a significant influence but with weaker correlations. For our case study we conclude that the fractions of coarse textured and organic soils have a major influence on N and DOC export...

  17. 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 T