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Sample records for building large genomic

  1. LARGE BUILDING HVAC SIMULATION

    Science.gov (United States)

    The report discusses the monitoring and collection of data relating to indoor pressures and radon concentrations under several test conditions in a large school building in Bartow, Florida. The Florida Solar Energy Center (FSEC) used an integrated computational software, FSEC 3.0...

  2. Radon in large buildings

    International Nuclear Information System (INIS)

    Wilson, D.L.; Dudney, C.S.; Gammage, R.B.

    1993-01-01

    Over the past several years, considerable research has been devoted by the U.S. Environmental Protection Agency (USEPA) and others to develop radon sampling protocols for single family residences and schools. However, very little research has been performed on measuring radon in the work place. To evaluate possible sampling protocols, 833 buildings throughout the United States were selected for extensive radon testing. The buildings tested (warehouses, production plants and office buildings) were representative of commercial buildings across the country both in design, size and use. Based on the results, preliminary radon sampling protocols for the work place have been developed. (orig.). (5 refs., 3 figs.)

  3. Multidimensional scaling for large genomic data sets

    Directory of Open Access Journals (Sweden)

    Lu Henry

    2008-04-01

    Full Text Available Abstract Background Multi-dimensional scaling (MDS is aimed to represent high dimensional data in a low dimensional space with preservation of the similarities between data points. This reduction in dimensionality is crucial for analyzing and revealing the genuine structure hidden in the data. For noisy data, dimension reduction can effectively reduce the effect of noise on the embedded structure. For large data set, dimension reduction can effectively reduce information retrieval complexity. Thus, MDS techniques are used in many applications of data mining and gene network research. However, although there have been a number of studies that applied MDS techniques to genomics research, the number of analyzed data points was restricted by the high computational complexity of MDS. In general, a non-metric MDS method is faster than a metric MDS, but it does not preserve the true relationships. The computational complexity of most metric MDS methods is over O(N2, so that it is difficult to process a data set of a large number of genes N, such as in the case of whole genome microarray data. Results We developed a new rapid metric MDS method with a low computational complexity, making metric MDS applicable for large data sets. Computer simulation showed that the new method of split-and-combine MDS (SC-MDS is fast, accurate and efficient. Our empirical studies using microarray data on the yeast cell cycle showed that the performance of K-means in the reduced dimensional space is similar to or slightly better than that of K-means in the original space, but about three times faster to obtain the clustering results. Our clustering results using SC-MDS are more stable than those in the original space. Hence, the proposed SC-MDS is useful for analyzing whole genome data. Conclusion Our new method reduces the computational complexity from O(N3 to O(N when the dimension of the feature space is far less than the number of genes N, and it successfully

  4. Phylogenetic distribution of large-scale genome patchiness

    Directory of Open Access Journals (Sweden)

    Hackenberg Michael

    2008-04-01

    Full Text Available Abstract Background The phylogenetic distribution of large-scale genome structure (i.e. mosaic compositional patchiness has been explored mainly by analytical ultracentrifugation of bulk DNA. However, with the availability of large, good-quality chromosome sequences, and the recently developed computational methods to directly analyze patchiness on the genome sequence, an evolutionary comparative analysis can be carried out at the sequence level. Results The local variations in the scaling exponent of the Detrended Fluctuation Analysis are used here to analyze large-scale genome structure and directly uncover the characteristic scales present in genome sequences. Furthermore, through shuffling experiments of selected genome regions, computationally-identified, isochore-like regions were identified as the biological source for the uncovered large-scale genome structure. The phylogenetic distribution of short- and large-scale patchiness was determined in the best-sequenced genome assemblies from eleven eukaryotic genomes: mammals (Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, and Canis familiaris, birds (Gallus gallus, fishes (Danio rerio, invertebrates (Drosophila melanogaster and Caenorhabditis elegans, plants (Arabidopsis thaliana and yeasts (Saccharomyces cerevisiae. We found large-scale patchiness of genome structure, associated with in silico determined, isochore-like regions, throughout this wide phylogenetic range. Conclusion Large-scale genome structure is detected by directly analyzing DNA sequences in a wide range of eukaryotic chromosome sequences, from human to yeast. In all these genomes, large-scale patchiness can be associated with the isochore-like regions, as directly detected in silico at the sequence level.

  5. Airflow and radon transport modeling in four large buildings

    International Nuclear Information System (INIS)

    Fan, J.B.; Persily, A.K.

    1995-01-01

    Computer simulations of multizone airflow and contaminant transport were performed in four large buildings using the program CONTAM88. This paper describes the physical characteristics of the buildings and their idealizations as multizone building airflow systems. These buildings include a twelve-story multifamily residential building, a five-story mechanically ventilated office building with an atrium, a seven-story mechanically ventilated office building with an underground parking garage, and a one-story school building. The air change rates and interzonal airflows of these buildings are predicted for a range of wind speeds, indoor-outdoor temperature differences, and percentages of outdoor air intake in the supply air Simulations of radon transport were also performed in the buildings to investigate the effects of indoor-outdoor temperature difference and wind speed on indoor radon concentrations

  6. GDC 2: Compression of large collections of genomes.

    Science.gov (United States)

    Deorowicz, Sebastian; Danek, Agnieszka; Niemiec, Marcin

    2015-06-25

    The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid in the personalized medicine. One of the significant side effects of this change is a necessity of storage and transfer of huge amounts of genomic data. In this paper we deal with the problem of compression of large collections of complete genomic sequences. We propose an algorithm that is able to compress the collection of 1092 human diploid genomes about 9,500 times. This result is about 4 times better than what is offered by the other existing compressors. Moreover, our algorithm is very fast as it processes the data with speed 200 MB/s on a modern workstation. In a consequence the proposed algorithm allows storing the complete genomic collections at low cost, e.g., the examined collection of 1092 human genomes needs only about 700 MB when compressed, what can be compared to about 6.7 TB of uncompressed FASTA files. The source code is available at http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=gdc&subpage=about.

  7. Building Very Large Neighbour-Joining Trees

    DEFF Research Database (Denmark)

    Simonsen, Martin; Mailund, Thomas; Pedersen, Christian Nørgaard Storm

    2010-01-01

    , and the NJ method in general, becomes a problem when inferring phylogenies with 10000+ taxa. In this paper we present two extentions of RapidNJ which reduce memory requirements and enable RapidNJ to infer very large phylogenetic trees efficiently. We also present an improved search heuristic for Rapid...

  8. Thuringische builds large PET plant in Germany

    International Nuclear Information System (INIS)

    Alperowicz, N.

    1993-01-01

    East Germany fibers producer Thuringische Faser AG Schwarza (TFS; Rudolstadt) is entering the polyethylene terephthalate (PET) business. The company, owned by India's Dalmia Group (New Delhi), is building an 80,000-m.t./year PET granulate plant, one of the largest in Europe, for completion at the end of 1995. The product will be used to make PET bottles and film for food packaging. TFS will need to buy 70,000 m.t./year of purified terephthalic acid and 27,000 m.t./year of ethylene glycol to feed the new plant. When acquiring TFS, Dalmia's chairman, Sanjay Dalmia, pledged to invest DM150 million ($95.4 million) in the Germany firm and keep 1,200 of the 3,000 workers. John Brown Deutsche Engineering (Essen) has been awarded a contract covering engineering, know-how, and turnkey supply of the complete plant, and will share of the complete plant, and will share the work with Austrian associate, Voest John Brown Industrieanlagenbau (Linz). The company, which completed against Zimmer (Frankfurt), will use its own technology. TFS, with 1992 sales of DM120 million, has capacities to produce 20,000 m.t/year of viscose staple fiber, 18,000 m.t./year of nylon-6 filament yarn, and 6,300 m.t./year of textile-grade polyester granulate, which will be converted to produce bottle-grade PET

  9. Mixing Metaphors: Building Infrastructure for Large Scale School Turnaround

    Science.gov (United States)

    Peurach, Donald J.; Neumerski, Christine M.

    2015-01-01

    The purpose of this analysis is to increase understanding of the possibilities and challenges of building educational infrastructure--the basic, foundational structures, systems, and resources--to support large-scale school turnaround. Building educational infrastructure often exceeds the capacity of schools, districts, and state education…

  10. ACTIVE SOIL DEPRESSURIZATION (ASD) DEMONSTRATION IN A LARGE BUILDING

    Science.gov (United States)

    The report gives results of an evaluation of the feasibility of implementing radon resistant construction techniques -- especially active soil depressurization (ASD) -- in new large buildings in Florida. Indoor radon concentrations and radon entry were monitored in a finished bui...

  11. Large N saddle formulation of quadratic building block theories

    International Nuclear Information System (INIS)

    Halpern, M.B.

    1980-01-01

    I develop a large N saddle point formulation for the broad class of 'theories of quadratic building blocks'. Such theories are those on which the sums over internal indices are contained in quadratic building blocks, e.g. PHI 2 = Σsup(N)sub(a-1)PHi sup(a)sup(a). The formulation applies as well to fermions, derivative coupling and non-polynomial interactions. In a related development, closed Schwinger-Dyson equations for Green functions of the building blocks are derived and solved for large N. (orig.)

  12. Genome size variation affects song attractiveness in grasshoppers: evidence for sexual selection against large genomes.

    Science.gov (United States)

    Schielzeth, Holger; Streitner, Corinna; Lampe, Ulrike; Franzke, Alexandra; Reinhold, Klaus

    2014-12-01

    Genome size is largely uncorrelated to organismal complexity and adaptive scenarios. Genetic drift as well as intragenomic conflict have been put forward to explain this observation. We here study the impact of genome size on sexual attractiveness in the bow-winged grasshopper Chorthippus biguttulus. Grasshoppers show particularly large variation in genome size due to the high prevalence of supernumerary chromosomes that are considered (mildly) selfish, as evidenced by non-Mendelian inheritance and fitness costs if present in high numbers. We ranked male grasshoppers by song characteristics that are known to affect female preferences in this species and scored genome sizes of attractive and unattractive individuals from the extremes of this distribution. We find that attractive singers have significantly smaller genomes, demonstrating that genome size is reflected in male courtship songs and that females prefer songs of males with small genomes. Such a genome size dependent mate preference effectively selects against selfish genetic elements that tend to increase genome size. The data therefore provide a novel example of how sexual selection can reinforce natural selection and can act as an agent in an intragenomic arms race. Furthermore, our findings indicate an underappreciated route of how choosy females could gain indirect benefits. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  13. Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes.

    Science.gov (United States)

    Hirsch, Cory D; Evans, Joseph; Buell, C Robin; Hirsch, Candice N

    2014-07-01

    Technology and software improvements in the last decade now provide methodologies to access the genome sequence of not only a single accession, but also multiple accessions of plant species. This provides a means to interrogate species diversity at the genome level. Ample diversity among accessions in a collection of species can be found, including single-nucleotide polymorphisms, insertions and deletions, copy number variation and presence/absence variation. For species with small, non-repetitive rich genomes, re-sequencing of query accessions is robust, highly informative, and economically feasible. However, for species with moderate to large sized repetitive-rich genomes, technical and economic barriers prevent en masse genome re-sequencing of accessions. Multiple approaches to access a focused subset of loci in species with larger genomes have been developed, including reduced representation sequencing, exome capture and transcriptome sequencing. Collectively, these approaches have enabled interrogation of diversity on a genome scale for large plant genomes, including crop species important to worldwide food security. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  14. EUPAN enables pan-genome studies of a large number of eukaryotic genomes.

    Science.gov (United States)

    Hu, Zhiqiang; Sun, Chen; Lu, Kuang-Chen; Chu, Xixia; Zhao, Yue; Lu, Jinyuan; Shi, Jianxin; Wei, Chaochun

    2017-08-01

    Pan-genome analyses are routinely carried out for bacteria to interpret the within-species gene presence/absence variations (PAVs). However, pan-genome analyses are rare for eukaryotes due to the large sizes and higher complexities of their genomes. Here we proposed EUPAN, a eukaryotic pan-genome analysis toolkit, enabling automatic large-scale eukaryotic pan-genome analyses and detection of gene PAVs at a relatively low sequencing depth. In the previous studies, we demonstrated the effectiveness and high accuracy of EUPAN in the pan-genome analysis of 453 rice genomes, in which we also revealed widespread gene PAVs among individual rice genomes. Moreover, EUPAN can be directly applied to the current re-sequencing projects primarily focusing on single nucleotide polymorphisms. EUPAN is implemented in Perl, R and C ++. It is supported under Linux and preferred for a computer cluster with LSF and SLURM job scheduling system. EUPAN together with its standard operating procedure (SOP) is freely available for non-commercial use (CC BY-NC 4.0) at http://cgm.sjtu.edu.cn/eupan/index.html . ccwei@sjtu.edu.cn or jianxin.shi@sjtu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  15. GACT: a Genome build and Allele definition Conversion Tool for SNP imputation and meta-analysis in genetic association studies.

    Science.gov (United States)

    Sulovari, Arvis; Li, Dawei

    2014-07-19

    Genome-wide association studies (GWAS) have successfully identified genes associated with complex human diseases. Although much of the heritability remains unexplained, combining single nucleotide polymorphism (SNP) genotypes from multiple studies for meta-analysis will increase the statistical power to identify new disease-associated variants. Meta-analysis requires same allele definition (nomenclature) and genome build among individual studies. Similarly, imputation, commonly-used prior to meta-analysis, requires the same consistency. However, the genotypes from various GWAS are generated using different genotyping platforms, arrays or SNP-calling approaches, resulting in use of different genome builds and allele definitions. Incorrect assumptions of identical allele definition among combined GWAS lead to a large portion of discarded genotypes or incorrect association findings. There is no published tool that predicts and converts among all major allele definitions. In this study, we have developed a tool, GACT, which stands for Genome build and Allele definition Conversion Tool, that predicts and inter-converts between any of the common SNP allele definitions and between the major genome builds. In addition, we assessed several factors that may affect imputation quality, and our results indicated that inclusion of singletons in the reference had detrimental effects while ambiguous SNPs had no measurable effect. Unexpectedly, exclusion of genotypes with missing rate > 0.001 (40% of study SNPs) showed no significant decrease of imputation quality (even significantly higher when compared to the imputation with singletons in the reference), especially for rare SNPs. GACT is a new, powerful, and user-friendly tool with both command-line and interactive online versions that can accurately predict, and convert between any of the common allele definitions and between genome builds for genome-wide meta-analysis and imputation of genotypes from SNP-arrays or deep

  16. Comfort Study of Office Buildings with Large Glazed Areas

    Directory of Open Access Journals (Sweden)

    Violeta Motuzienė

    2017-09-01

    Full Text Available In the buildings with large glazed areas the biggest problem is the space overheating during the warm season. This causes increased energy demand for cooling. The survey was carried out during the warm and cold seasons in two office buildings with large glazed areas. The methodology was prepared for evaluating indoor climate parameters using objective and subjective evaluation. The measurements have shown that there are problems with lighting in workplaces of both buildings during both the warm and cold seasons. The biggest problem is too dry air during the cold period, an acceptable temperature is also not always in the building No. 2. The survey has shown that some employees are dissatisfied with the indoor climate in the workplace, the bigger dissatisfaction is in building No. 2. Assessing according to the O. Fanger methodology was obtained that the number of PPD is in the normal range during the cold period, whereas close to the limit when the building can not be operated in the warm period.

  17. Dose reduction factors from a radioactive cloud for large buildings

    International Nuclear Information System (INIS)

    Grand, J. le; Roux, Y.

    1986-01-01

    A set of complex and accurate computer codes has been established to determine the transport of photons emitted from a radioactive cloud through various media. The geometrical and physical description of large buildings with various numbers of floors and rooms can be done by the user. The codes can calculate, in any room or apartment, the characteristics of the photon fields (photon flux, energy flux and distribution, direction distribution) and whole-body absorbed dose rates in a phantom standing or lying on the floor. The dose reduction factor is then the quotient of the mean absorbed dose rate in the apartment to the absorbed dose rate in the phantom standing on the ground outdoors. Applications to several modern multistorey buildings are presented. The results show the influence of various parameters such as density and composition of building materials, the fraction of the external building surface containing apertures and initial photon energy. (author)

  18. Kernel methods for large-scale genomic data analysis

    Science.gov (United States)

    Xing, Eric P.; Schaid, Daniel J.

    2015-01-01

    Machine learning, particularly kernel methods, has been demonstrated as a promising new tool to tackle the challenges imposed by today’s explosive data growth in genomics. They provide a practical and principled approach to learning how a large number of genetic variants are associated with complex phenotypes, to help reveal the complexity in the relationship between the genetic markers and the outcome of interest. In this review, we highlight the potential key role it will have in modern genomic data processing, especially with regard to integration with classical methods for gene prioritizing, prediction and data fusion. PMID:25053743

  19. Indexes of large genome collections on a PC.

    Directory of Open Access Journals (Sweden)

    Agnieszka Danek

    Full Text Available The availability of thousands of individual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key operation useful in such analyses is aligning sequencing reads against a collection of genomes, which is costly with the use of existing algorithms due to their large memory requirements. We present MuGI, Multiple Genome Index, which reports all occurrences of a given pattern, in exact and approximate matching model, against a collection of thousand(s genomes. Its unique feature is the small index size, which is customisable. It fits in a standard computer with 16-32 GB, or even 8 GB, of RAM, for the 1000GP collection of 1092 diploid human genomes. The solution is also fast. For example, the exact matching queries (of average length 150 bp are handled in average time of 39 µs and with up to 3 mismatches in 373 µs on the test PC with the index size of 13.4 GB. For a smaller index, occupying 7.4 GB in memory, the respective times grow to 76 µs and 917 µs. Software is available at http://sun.aei.polsl.pl/mugi under a free license. Data S1 is available at PLOS One online.

  20. Large Scale Software Building with CMake in ATLAS

    Science.gov (United States)

    Elmsheuser, J.; Krasznahorkay, A.; Obreshkov, E.; Undrus, A.; ATLAS Collaboration

    2017-10-01

    The offline software of the ATLAS experiment at the Large Hadron Collider (LHC) serves as the platform for detector data reconstruction, simulation and analysis. It is also used in the detector’s trigger system to select LHC collision events during data taking. The ATLAS offline software consists of several million lines of C++ and Python code organized in a modular design of more than 2000 specialized packages. Because of different workflows, many stable numbered releases are in parallel production use. To accommodate specific workflow requests, software patches with modified libraries are distributed on top of existing software releases on a daily basis. The different ATLAS software applications also require a flexible build system that strongly supports unit and integration tests. Within the last year this build system was migrated to CMake. A CMake configuration has been developed that allows one to easily set up and build the above mentioned software packages. This also makes it possible to develop and test new and modified packages on top of existing releases. The system also allows one to detect and execute partial rebuilds of the release based on single package changes. The build system makes use of CPack for building RPM packages out of the software releases, and CTest for running unit and integration tests. We report on the migration and integration of the ATLAS software to CMake and show working examples of this large scale project in production.

  1. Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences.

    Science.gov (United States)

    Zhang, Jianwei; Kudrna, Dave; Mu, Ting; Li, Weiming; Copetti, Dario; Yu, Yeisoo; Goicoechea, Jose Luis; Lei, Yang; Wing, Rod A

    2016-10-15

    Next generation sequencing technologies have revolutionized our ability to rapidly and affordably generate vast quantities of sequence data. Once generated, raw sequences are assembled into contigs or scaffolds. However, these assemblies are mostly fragmented and inaccurate at the whole genome scale, largely due to the inability to integrate additional informative datasets (e.g. physical, optical and genetic maps). To address this problem, we developed a semi-automated software tool-Genome Puzzle Master (GPM)-that enables the integration of additional genomic signposts to edit and build 'new-gen-assemblies' that result in high-quality 'annotation-ready' pseudomolecules. With GPM, loaded datasets can be connected to each other via their logical relationships which accomplishes tasks to 'group,' 'merge,' 'order and orient' sequences in a draft assembly. Manual editing can also be performed with a user-friendly graphical interface. Final pseudomolecules reflect a user's total data package and are available for long-term project management. GPM is a web-based pipeline and an important part of a Laboratory Information Management System (LIMS) which can be easily deployed on local servers for any genome research laboratory. The GPM (with LIMS) package is available at https://github.com/Jianwei-Zhang/LIMS CONTACTS: jzhang@mail.hzau.edu.cn or rwing@mail.arizona.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  2. Large scale software building with CMake in ATLAS

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00218447; The ATLAS collaboration; Elmsheuser, Johannes; Obreshkov, Emil; Undrus, Alexander

    2017-01-01

    The offline software of the ATLAS experiment at the LHC (Large Hadron Collider) serves as the platform for detector data reconstruction, simulation and analysis. It is also used in the detector trigger system to select LHC collision events during data taking. ATLAS offline software consists of several million lines of C++ and Python code organized in a modular design of more than 2000 specialized packages. Because of different workflows many stable numbered releases are in parallel production use. To accommodate specific workflow requests, software patches with modified libraries are distributed on top of existing software releases on a daily basis. The different ATLAS software applications require a flexible build system that strongly supports unit and integration tests. Within the last year this build system was migrated to CMake. A CMake configuration has been developed that allows one to easily set up and build the mentioned software packages. This also makes it possible to develop and test new and modifi...

  3. Large Scale Software Building with CMake in ATLAS

    CERN Document Server

    Elmsheuser, Johannes; The ATLAS collaboration; Obreshkov, Emil; Undrus, Alexander

    2016-01-01

    The offline software of the ATLAS experiment at the LHC (Large Hadron Collider) serves as the platform for detector data reconstruction, simulation and analysis. It is also used in the detector trigger system to select LHC collision events during data taking. ATLAS offline software consists of several million lines of C++ and Python code organized in a modular design of more than 2000 specialized packages. Because of different workflows many stable numbered releases are in parallel production use. To accommodate specific workflow requests, software patches with modified libraries are distributed on top of existing software releases on a daily basis. The different ATLAS software applications require a flexible build system that strongly supports unit and integration tests. Within the last year this build system was migrated to CMake. A CMake configuration has been developed that allows one to easily set up and build the mentioned software packages. This also makes it possible to develop and test new and modifi...

  4. Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences

    Directory of Open Access Journals (Sweden)

    Shade Larry L

    2006-06-01

    Full Text Available Abstract Background Approximately 11 Mb of finished high quality genomic sequences were sampled from cattle, dog and human to estimate genomic divergences and their regional variation among these lineages. Results Optimal three-way multi-species global sequence alignments for 84 cattle clones or loci (each >50 kb of genomic sequence were constructed using the human and dog genome assemblies as references. Genomic divergences and substitution rates were examined for each clone and for various sequence classes under different functional constraints. Analysis of these alignments revealed that the overall genomic divergences are relatively constant (0.32–0.37 change/site for pairwise comparisons among cattle, dog and human; however substitution rates vary across genomic regions and among different sequence classes. A neutral mutation rate (2.0–2.2 × 10(-9 change/site/year was derived from ancestral repetitive sequences, whereas the substitution rate in coding sequences (1.1 × 10(-9 change/site/year was approximately half of the overall rate (1.9–2.0 × 10(-9 change/site/year. Relative rate tests also indicated that cattle have a significantly faster rate of substitution as compared to dog and that this difference is about 6%. Conclusion This analysis provides a large-scale and unbiased assessment of genomic divergences and regional variation of substitution rates among cattle, dog and human. It is expected that these data will serve as a baseline for future mammalian molecular evolution studies.

  5. Large-Scale Sequencing: The Future of Genomic Sciences Colloquium

    Energy Technology Data Exchange (ETDEWEB)

    Margaret Riley; Merry Buckley

    2009-01-01

    Genetic sequencing and the various molecular techniques it has enabled have revolutionized the field of microbiology. Examining and comparing the genetic sequences borne by microbes - including bacteria, archaea, viruses, and microbial eukaryotes - provides researchers insights into the processes microbes carry out, their pathogenic traits, and new ways to use microorganisms in medicine and manufacturing. Until recently, sequencing entire microbial genomes has been laborious and expensive, and the decision to sequence the genome of an organism was made on a case-by-case basis by individual researchers and funding agencies. Now, thanks to new technologies, the cost and effort of sequencing is within reach for even the smallest facilities, and the ability to sequence the genomes of a significant fraction of microbial life may be possible. The availability of numerous microbial genomes will enable unprecedented insights into microbial evolution, function, and physiology. However, the current ad hoc approach to gathering sequence data has resulted in an unbalanced and highly biased sampling of microbial diversity. A well-coordinated, large-scale effort to target the breadth and depth of microbial diversity would result in the greatest impact. The American Academy of Microbiology convened a colloquium to discuss the scientific benefits of engaging in a large-scale, taxonomically-based sequencing project. A group of individuals with expertise in microbiology, genomics, informatics, ecology, and evolution deliberated on the issues inherent in such an effort and generated a set of specific recommendations for how best to proceed. The vast majority of microbes are presently uncultured and, thus, pose significant challenges to such a taxonomically-based approach to sampling genome diversity. However, we have yet to even scratch the surface of the genomic diversity among cultured microbes. A coordinated sequencing effort of cultured organisms is an appropriate place to begin

  6. BFAST: an alignment tool for large scale genome resequencing.

    Directory of Open Access Journals (Sweden)

    Nils Homer

    2009-11-01

    Full Text Available The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation.We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels.We compare BFAST to a selection of large-scale alignment tools -- BLAT, MAQ, SHRiMP, and SOAP -- in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at (http://bfast.sourceforge.net.

  7. Application issues for large-area electrochromic windows incommercial buildings

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Eleanor S.; DiBartolomeo, D.L.

    2000-05-01

    Projections of performance from small-area devices to large-area windows and enterprise marketing have created high expectations for electrochromic glazings. As a result, this paper seeks to precipitate an objective dialog between material scientists and building-application scientists to determine whether actual large-area electrochromic devices will result in significant performance benefits and what material improvements are needed, if any, to make electrochromics more practical for commercial building applications. Few in-situ tests have been conducted with large-area electrochromic windows applied in buildings. This study presents monitored results from a full-scale field test of large-area electrochromic windows to illustrate how this technology will perform in commercial buildings. The visible transmittance (Tv) of the installed electrochromic ranged from 0.11 to 0.38. The data are limited to the winter period for a south-east-facing window. The effect of actual device performance on lighting energy use, direct sun control, discomfort glare, and interior illumination is discussed. No mechanical system loads were monitored. These data demonstrate the use of electrochromics in a moderate climate and focus on the most restrictive visual task: computer use in offices. Through this small demonstration, we were able to determine that electrochromic windows can indeed provide unmitigated transparent views and a level of dynamic illumination control never before seen in architectural glazing materials. Daily lighting energy use was 6-24 percent less compared to the 11 percent-glazing, with improved interior brightness levels. Daily lighting energy use was 3 percent less to 13 percent more compared to the 38 percent-glazing, with improved window brightness control. The electrochromic window may not be able to fulfill both energy-efficiency and visual comfort objectives when low winter direct sun is present, particularly for computer tasks using cathode-ray tube (CRT

  8. Building the sequence map of the human pan-genome

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Li, Yingrui; Zheng, Hancheng

    2010-01-01

    analysis of predicted genes indicated that the novel sequences contain potentially functional coding regions. We estimate that a complete human pan-genome would contain approximately 19-40 Mb of novel sequence not present in the extant reference genome. The extensive amount of novel sequence contributing...

  9. Targeted sequencing of large genomic regions with CATCH-Seq.

    Directory of Open Access Journals (Sweden)

    Kenneth Day

    Full Text Available Current target enrichment systems for large-scale next-generation sequencing typically require synthetic oligonucleotides used as capture reagents to isolate sequences of interest. The majority of target enrichment reagents are focused on gene coding regions or promoters en masse. Here we introduce development of a customizable targeted capture system using biotinylated RNA probe baits transcribed from sheared bacterial artificial chromosome clone templates that enables capture of large, contiguous blocks of the genome for sequencing applications. This clone adapted template capture hybridization sequencing (CATCH-Seq procedure can be used to capture both coding and non-coding regions of a gene, and resolve the boundaries of copy number variations within a genomic target site. Furthermore, libraries constructed with methylated adapters prior to solution hybridization also enable targeted bisulfite sequencing. We applied CATCH-Seq to diverse targets ranging in size from 125 kb to 3.5 Mb. Our approach provides a simple and cost effective alternative to other capture platforms because of template-based, enzymatic probe synthesis and the lack of oligonucleotide design costs. Given its similarity in procedure, CATCH-Seq can also be performed in parallel with commercial systems.

  10. The detection of large deletions or duplications in genomic DNA.

    Science.gov (United States)

    Armour, J A L; Barton, D E; Cockburn, D J; Taylor, G R

    2002-11-01

    While methods for the detection of point mutations and small insertions or deletions in genomic DNA are well established, the detection of larger (>100 bp) genomic duplications or deletions can be more difficult. Most mutation scanning methods use PCR as a first step, but the subsequent analyses are usually qualitative rather than quantitative. Gene dosage methods based on PCR need to be quantitative (i.e., they should report molar quantities of starting material) or semi-quantitative (i.e., they should report gene dosage relative to an internal standard). Without some sort of quantitation, heterozygous deletions and duplications may be overlooked and therefore be under-ascertained. Gene dosage methods provide the additional benefit of reporting allele drop-out in the PCR. This could impact on SNP surveys, where large-scale genotyping may miss null alleles. Here we review recent developments in techniques for the detection of this type of mutation and compare their relative strengths and weaknesses. We emphasize that comprehensive mutation analysis should include scanning for large insertions and deletions and duplications. Copyright 2002 Wiley-Liss, Inc.

  11. Genomic characterization of large heterochromatic gaps in the human genome assembly.

    Directory of Open Access Journals (Sweden)

    Nicolas Altemose

    2014-05-01

    Full Text Available The largest gaps in the human genome assembly correspond to multi-megabase heterochromatic regions composed primarily of two related families of tandem repeats, Human Satellites 2 and 3 (HSat2,3. The abundance of repetitive DNA in these regions challenges standard mapping and assembly algorithms, and as a result, the sequence composition and potential biological functions of these regions remain largely unexplored. Furthermore, existing genomic tools designed to predict consensus-based descriptions of repeat families cannot be readily applied to complex satellite repeats such as HSat2,3, which lack a consistent repeat unit reference sequence. Here we present an alignment-free method to characterize complex satellites using whole-genome shotgun read datasets. Utilizing this approach, we classify HSat2,3 sequences into fourteen subfamilies and predict their chromosomal distributions, resulting in a comprehensive satellite reference database to further enable genomic studies of heterochromatic regions. We also identify 1.3 Mb of non-repetitive sequence interspersed with HSat2,3 across 17 unmapped assembly scaffolds, including eight annotated gene predictions. Finally, we apply our satellite reference database to high-throughput sequence data from 396 males to estimate array size variation of the predominant HSat3 array on the Y chromosome, confirming that satellite array sizes can vary between individuals over an order of magnitude (7 to 98 Mb and further demonstrating that array sizes are distributed differently within distinct Y haplogroups. In summary, we present a novel framework for generating initial reference databases for unassembled genomic regions enriched with complex satellite DNA, and we further demonstrate the utility of these reference databases for studying patterns of sequence variation within human populations.

  12. Building a genome database using an object-oriented approach.

    Science.gov (United States)

    Barbasiewicz, Anna; Liu, Lin; Lang, B Franz; Burger, Gertraud

    2002-01-01

    GOBASE is a relational database that integrates data associated with mitochondria and chloroplasts. The most important data in GOBASE, i. e., molecular sequences and taxonomic information, are obtained from the public sequence data repository at the National Center for Biotechnology Information (NCBI), and are validated by our experts. Maintaining a curated genomic database comes with a towering labor cost, due to the shear volume of available genomic sequences and the plethora of annotation errors and omissions in records retrieved from public repositories. Here we describe our approach to increase automation of the database population process, thereby reducing manual intervention. As a first step, we used Unified Modeling Language (UML) to construct a list of potential errors. Each case was evaluated independently, and an expert solution was devised, and represented as a diagram. Subsequently, the UML diagrams were used as templates for writing object-oriented automation programs in the Java programming language.

  13. Tokamak building-design considerations for a large tokamak device

    International Nuclear Information System (INIS)

    Barrett, R.J.; Thomson, S.L.

    1981-01-01

    Design and construction of a satisfactory tokamak building to support FED appears feasible. Further, a pressure vessel building does not appear necessary to meet the plant safety requirements. Some of the building functions will require safety class systems to assure reliable and safe operation. A rectangular tokamak building has been selected for FED preconceptual design which will be part of the confinement system relying on ventilation and other design features to reduce the consequences and probability of radioactivity release

  14. Knowledge Sharing Strategies for Large Complex Building Projects.

    Directory of Open Access Journals (Sweden)

    Esra Bektas

    2013-06-01

    Full Text Available The construction industry is a project-based sector with a myriad of actors such as architects, construction companies, consultants, producers of building materials (Anumba et al., 2005. The interaction between the project partners is often quite limited, which leads to insufficient knowledge sharing during the project and knowledge being unavailable for reuse (Fruchter et al. 2002. The result can be a considerable amount of extra work, delays and cost overruns. Design outcomes that are supposed to function as boundary objects across different disciplines can lead to misinterpretation of requirements, project content and objectives. In this research, knowledge is seen as resulting from social interactions; knowledge resides in communities and it is generated through social relationships (Wenger 1998, Olsson et al. 2008. Knowledge is often tacit, intangible and context-dependent and it is articulated in the changing responsibilities, roles, attitudes and values that are present in the work environment (Bresnen et al., 2003. In a project environment, knowledge enables individuals to solve problems, take decisions, and apply these decisions to actions. In order to achieve a shared understanding and minimize the misunderstanding and misinterpretations among project actors, it is necessary to share knowledge (Fong 2003. Sharing knowledge is particularly crucial in large complex building projects (LCBPs in order to accelerate the building process, improve architectural quality and prevent mistakes or undesirable results. However, knowledge sharing is often hampered through professional or organizational boundaries or contractual concerns. When knowledge is seen as an organizational asset, there is little willingness among project organizations to share their knowledge. Individual people may recognize the need to promote knowledge sharing throughout the project, but typically there is no deliberate strategy agreed by all project partners to address

  15. Large scale genomic reorganization of topological domains at the HoxD locus.

    Science.gov (United States)

    Fabre, Pierre J; Leleu, Marion; Mormann, Benjamin H; Lopez-Delisle, Lucille; Noordermeer, Daan; Beccari, Leonardo; Duboule, Denis

    2017-08-07

    The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD genes in developing digits is controlled by regulatory elements located in the centromeric TAD (C-DOM) through long-range contacts. To assess the structure-function relationships underlying such interactions, we measured compaction levels and TAD discreteness using a combination of chromosome conformation capture (4C-seq) and DNA FISH. We assessed the robustness of the TAD architecture by using a series of genomic deletions and inversions that impact the integrity of this chromatin domain and that remodel long-range contacts. We report multi-partite associations between HoxD genes and up to three enhancers. We find that the loss of native chromatin topology leads to the remodeling of TAD structure following distinct parameters. Our results reveal that the recomposition of TAD architectures after large genomic re-arrangements is dependent on a boundary-selection mechanism in which CTCF mediates the gating of long-range contacts in combination with genomic distance and sequence specificity. Accordingly, the building of a recomposed TAD at this locus depends on distinct functional and constitutive parameters.

  16. Building a model: developing genomic resources for common milkweed (Asclepias syriaca with low coverage genome sequencing

    Directory of Open Access Journals (Sweden)

    Weitemier Kevin

    2011-05-01

    Full Text Available Abstract Background Milkweeds (Asclepias L. have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L. could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. Results A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp and 5S rDNA (120 bp sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp, with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae unigenes (median coverage of 0.29× and 66% of single copy orthologs (COSII in asterids (median coverage of 0.14×. From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites and phylogenetics (low-copy nuclear genes studies were developed. Conclusions The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species

  17. Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing.

    Science.gov (United States)

    Straub, Shannon C K; Fishbein, Mark; Livshultz, Tatyana; Foster, Zachary; Parks, Matthew; Weitemier, Kevin; Cronn, Richard C; Liston, Aaron

    2011-05-04

    Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae) unigenes (median coverage of 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed. The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives. This study represents a first

  18. Building online genomics applications using BioPyramid.

    Science.gov (United States)

    Stephenson, Liam; Wakeham, Yoshua; Seidenman, Nick; Choi, Jarny

    2018-03-29

    BioPyramid is a python package, which serves as a scaffold for building an online application for the exploration of gene expression data. It is designed for bioinformaticians wishing to quickly share transformed data and interactive analyses with collaborators. Current R-based tools similarly address the need to quickly share "omics"-data in an exploratory format, but these are generally small-scale, single-dataset solutions. Biopyramid is written in python pyramid framework and scalable to address longer-term or more complex projects. It contains a number of components designed to reduce the time and effort in building such an application from scratch, including gene annotation, dataset models and visualisation tools. Freely available at http://github.com/jarny/biopyramid. Implemented in python and javascript. jarnyc@unimelb.edu.au.

  19. Large-scale parallel genome assembler over cloud computing environment.

    Science.gov (United States)

    Das, Arghya Kusum; Koppa, Praveen Kumar; Goswami, Sayan; Platania, Richard; Park, Seung-Jong

    2017-06-01

    The size of high throughput DNA sequencing data has already reached the terabyte scale. To manage this huge volume of data, many downstream sequencing applications started using locality-based computing over different cloud infrastructures to take advantage of elastic (pay as you go) resources at a lower cost. However, the locality-based programming model (e.g. MapReduce) is relatively new. Consequently, developing scalable data-intensive bioinformatics applications using this model and understanding the hardware environment that these applications require for good performance, both require further research. In this paper, we present a de Bruijn graph oriented Parallel Giraph-based Genome Assembler (GiGA), as well as the hardware platform required for its optimal performance. GiGA uses the power of Hadoop (MapReduce) and Giraph (large-scale graph analysis) to achieve high scalability over hundreds of compute nodes by collocating the computation and data. GiGA achieves significantly higher scalability with competitive assembly quality compared to contemporary parallel assemblers (e.g. ABySS and Contrail) over traditional HPC cluster. Moreover, we show that the performance of GiGA is significantly improved by using an SSD-based private cloud infrastructure over traditional HPC cluster. We observe that the performance of GiGA on 256 cores of this SSD-based cloud infrastructure closely matches that of 512 cores of traditional HPC cluster.

  20. Radon in large buildings: The development of a protocol

    International Nuclear Information System (INIS)

    Wilson, D.L.; Dudney, C.S.; Gammage, R.B.

    1993-01-01

    Over the past several years, considerable research has been devoted by the US Environmental Protection Agency (USEPA) and others to develop radon sampling protocols for single family residences and schools. However, very little research has been performed on measuring radon in the work place. To evaluate possible sampling protocols, 833 buildings throughout the United States were selected for extensive radon testing. The buildings tested (warehouses, production plants and office buildings) were representative of commercial buildings across the country both in design, size and use. Based on the results, preliminary radon sampling protocols for the work place have been developed

  1. Implementing effect of energy efficiency supervision system for government office buildings and large-scale public buildings in China

    International Nuclear Information System (INIS)

    Zhao Jing; Wu Yong; Zhu Neng

    2009-01-01

    The Chinese central government released a document to initiate a task of energy efficiency supervision system construction for government office buildings and large-scale public buildings in 2007, which marks the overall start of existing buildings energy efficiency management in China with the government office buildings and large-scale public buildings as a breakthrough. This paper focused on the implementing effect in the demonstration region all over China for less than one year, firstly introduced the target and path of energy efficiency supervision system, then described the achievements and problems during the implementing process in the first demonstration provinces and cities. A certain data from the energy efficiency public notice in some typical demonstration provinces and cities were analyzed statistically. It can be concluded that different functional buildings have different energy consumption and the average energy consumption of large-scale public buildings is too high in China compared with the common public buildings and residential buildings. The obstacles need to be overcome afterward were summarized and the prospects for the future work were also put forward in the end.

  2. Implementing effect of energy efficiency supervision system for government office buildings and large-scale public buildings in China

    Energy Technology Data Exchange (ETDEWEB)

    Zhao Jing [School of Environmental Science and Engineering, Tianjin University, Tianjin 300072 (China)], E-mail: zhaojing@tju.edu.cn; Wu Yong [Department of Science and Technology, Ministry of Housing and Urban-Rural Development of the People' s Republic of China, Beijing 100835 (China); Zhu Neng [School of Environmental Science and Engineering, Tianjin University, Tianjin 300072 (China)

    2009-06-15

    The Chinese central government released a document to initiate a task of energy efficiency supervision system construction for government office buildings and large-scale public buildings in 2007, which marks the overall start of existing buildings energy efficiency management in China with the government office buildings and large-scale public buildings as a breakthrough. This paper focused on the implementing effect in the demonstration region all over China for less than one year, firstly introduced the target and path of energy efficiency supervision system, then described the achievements and problems during the implementing process in the first demonstration provinces and cities. A certain data from the energy efficiency public notice in some typical demonstration provinces and cities were analyzed statistically. It can be concluded that different functional buildings have different energy consumption and the average energy consumption of large-scale public buildings is too high in China compared with the common public buildings and residential buildings. The obstacles need to be overcome afterward were summarized and the prospects for the future work were also put forward in the end.

  3. Implementing effect of energy efficiency supervision system for government office buildings and large-scale public buildings in China

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Jing; Zhu, Neng [School of Environmental Science and Engineering, Tianjin University, Tianjin 300072 (China); Wu, Yong [Department of Science and Technology, Ministry of Housing and Urban-Rural Development of the People' s Republic of China, Beijing 100835 (China)

    2009-06-15

    The Chinese central government released a document to initiate a task of energy efficiency supervision system construction for government office buildings and large-scale public buildings in 2007, which marks the overall start of existing buildings energy efficiency management in China with the government office buildings and large-scale public buildings as a breakthrough. This paper focused on the implementing effect in the demonstration region all over China for less than one year, firstly introduced the target and path of energy efficiency supervision system, then described the achievements and problems during the implementing process in the first demonstration provinces and cities. A certain data from the energy efficiency public notice in some typical demonstration provinces and cities were analyzed statistically. It can be concluded that different functional buildings have different energy consumption and the average energy consumption of large-scale public buildings is too high in China compared with the common public buildings and residential buildings. The obstacles need to be overcome afterward were summarized and the prospects for the future work were also put forward in the end. (author)

  4. Efficient assembly of de novo human artificial chromosomes from large genomic loci

    Directory of Open Access Journals (Sweden)

    Stromberg Gregory

    2005-07-01

    Full Text Available Abstract Background Human Artificial Chromosomes (HACs are potentially useful vectors for gene transfer studies and for functional annotation of the genome because of their suitability for cloning, manipulating and transferring large segments of the genome. However, development of HACs for the transfer of large genomic loci into mammalian cells has been limited by difficulties in manipulating high-molecular weight DNA, as well as by the low overall frequencies of de novo HAC formation. Indeed, to date, only a small number of large (>100 kb genomic loci have been reported to be successfully packaged into de novo HACs. Results We have developed novel methodologies to enable efficient assembly of HAC vectors containing any genomic locus of interest. We report here the creation of a novel, bimolecular system based on bacterial artificial chromosomes (BACs for the construction of HACs incorporating any defined genomic region. We have utilized this vector system to rapidly design, construct and validate multiple de novo HACs containing large (100–200 kb genomic loci including therapeutically significant genes for human growth hormone (HGH, polycystic kidney disease (PKD1 and ß-globin. We report significant differences in the ability of different genomic loci to support de novo HAC formation, suggesting possible effects of cis-acting genomic elements. Finally, as a proof of principle, we have observed sustained ß-globin gene expression from HACs incorporating the entire 200 kb ß-globin genomic locus for over 90 days in the absence of selection. Conclusion Taken together, these results are significant for the development of HAC vector technology, as they enable high-throughput assembly and functional validation of HACs containing any large genomic locus. We have evaluated the impact of different genomic loci on the frequency of HAC formation and identified segments of genomic DNA that appear to facilitate de novo HAC formation. These genomic loci

  5. Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans

    OpenAIRE

    Jayapal, Karthik P; Lian, Wei; Glod, Frank; Sherman, David H; Hu, Wei-Shou

    2007-01-01

    Abstract Background The genomes of Streptomyces coelicolor and Streptomyces lividans bear a considerable degree of synteny. While S. coelicolor is the model streptomycete for studying antibiotic synthesis and differentiation, S. lividans is almost exclusively considered as the preferred host, among actinomycetes, for cloning and expression of exogenous DNA. We used whole genome microarrays as a comparative genomics tool for identifying the subtle differences between these two chromosomes. Res...

  6. Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea

    DEFF Research Database (Denmark)

    Treusch, Alexander H; Kletzin, Arnulf; Raddatz, Guenter

    2004-01-01

    Complex genomic libraries are increasingly being used to retrieve complete genes, operons or large genomic fragments directly from environmental samples, without the need to cultivate the respective microorganisms. We report on the construction of three large-insert fosmid libraries in total...... (approximately 1% each) have been captured in our libraries. The diversity of putative protein-encoding genes, as reflected by their distribution into different COG clusters, was comparable to that encoded in complete genomes of cultivated microorganisms. A huge variety of genomic fragments has been captured...

  7. Mass spectrometry allows direct identification of proteins in large genomes

    DEFF Research Database (Denmark)

    Küster, B; Mortensen, Peter V.; Andersen, Jens S.

    2001-01-01

    Proteome projects seek to provide systematic functional analysis of the genes uncovered by genome sequencing initiatives. Mass spectrometric protein identification is a key requirement in these studies but to date, database searching tools rely on the availability of protein sequences derived fro...

  8. Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes

    Science.gov (United States)

    Peng, Qian; Alekseyev, Max A.; Tesler, Glenn; Pevzner, Pavel A.

    The existing synteny block reconstruction algorithms use anchors (e.g., orthologous genes) shared over all genomes to construct the synteny blocks for multiple genomes. This approach, while efficient for a few genomes, cannot be scaled to address the need to construct synteny blocks in many mammalian genomes that are currently being sequenced. The problem is that the number of anchors shared among all genomes quickly decreases with the increase in the number of genomes. Another problem is that many genomes (plant genomes in particular) had extensive duplications, which makes decoding of genomic architecture and rearrangement analysis in plants difficult. The existing synteny block generation algorithms in plants do not address the issue of generating non-overlapping synteny blocks suitable for analyzing rearrangements and evolution history of duplications. We present a new algorithm based on the A-Bruijn graph framework that overcomes these difficulties and provides a unified approach to synteny block reconstruction for multiple genomes, and for genomes with large duplications.

  9. A protocol for large scale genomic DNA isolation for cacao genetics ...

    African Journals Online (AJOL)

    Advances in DNA technology, such as marker assisted selection, detection of quantitative trait loci and genomic selection also require the isolation of DNA from a large number of samples and the preservation of tissue samples for future use in cacao genome studies. The present study proposes a method for the ...

  10. Large-scale chromosome folding versus genomic DNA sequences: A discrete double Fourier transform technique.

    Science.gov (United States)

    Chechetkin, V R; Lobzin, V V

    2017-08-07

    Using state-of-the-art techniques combining imaging methods and high-throughput genomic mapping tools leaded to the significant progress in detailing chromosome architecture of various organisms. However, a gap still remains between the rapidly growing structural data on the chromosome folding and the large-scale genome organization. Could a part of information on the chromosome folding be obtained directly from underlying genomic DNA sequences abundantly stored in the databanks? To answer this question, we developed an original discrete double Fourier transform (DDFT). DDFT serves for the detection of large-scale genome regularities associated with domains/units at the different levels of hierarchical chromosome folding. The method is versatile and can be applied to both genomic DNA sequences and corresponding physico-chemical parameters such as base-pairing free energy. The latter characteristic is closely related to the replication and transcription and can also be used for the assessment of temperature or supercoiling effects on the chromosome folding. We tested the method on the genome of E. coli K-12 and found good correspondence with the annotated domains/units established experimentally. As a brief illustration of further abilities of DDFT, the study of large-scale genome organization for bacteriophage PHIX174 and bacterium Caulobacter crescentus was also added. The combined experimental, modeling, and bioinformatic DDFT analysis should yield more complete knowledge on the chromosome architecture and genome organization. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. GEnomes Management Application (GEM.app): a new software tool for large-scale collaborative genome analysis.

    Science.gov (United States)

    Gonzalez, Michael A; Lebrigio, Rafael F Acosta; Van Booven, Derek; Ulloa, Rick H; Powell, Eric; Speziani, Fiorella; Tekin, Mustafa; Schüle, Rebecca; Züchner, Stephan

    2013-06-01

    Novel genes are now identified at a rapid pace for many Mendelian disorders, and increasingly, for genetically complex phenotypes. However, new challenges have also become evident: (1) effectively managing larger exome and/or genome datasets, especially for smaller labs; (2) direct hands-on analysis and contextual interpretation of variant data in large genomic datasets; and (3) many small and medium-sized clinical and research-based investigative teams around the world are generating data that, if combined and shared, will significantly increase the opportunities for the entire community to identify new genes. To address these challenges, we have developed GEnomes Management Application (GEM.app), a software tool to annotate, manage, visualize, and analyze large genomic datasets (https://genomics.med.miami.edu/). GEM.app currently contains ∼1,600 whole exomes from 50 different phenotypes studied by 40 principal investigators from 15 different countries. The focus of GEM.app is on user-friendly analysis for nonbioinformaticians to make next-generation sequencing data directly accessible. Yet, GEM.app provides powerful and flexible filter options, including single family filtering, across family/phenotype queries, nested filtering, and evaluation of segregation in families. In addition, the system is fast, obtaining results within 4 sec across ∼1,200 exomes. We believe that this system will further enhance identification of genetic causes of human disease. © 2013 Wiley Periodicals, Inc.

  12. Building capacity for human genetics and genomics research in Trinidad and Tobago

    Directory of Open Access Journals (Sweden)

    Allana Roach

    Full Text Available Advances in human genetics and genomic sciences and the corresponding explosion of biomedical technologies have deepened current understanding of human health and revolutionized medicine. In developed nations, this has led to marked improvements in disease risk stratification and diagnosis. These advances have also led to targeted intervention strategies aimed at promoting disease prevention, prolonging disease onset, and mitigating symptoms, as in the well-known case of breast cancer and the BRCA1 gene. In contrast, in the developing nation of Trinidad and Tobago, this scientific revolution has not translated into the development and application of effective genomics-based interventions for improving public health. While the reasons for this are multifactorial, the underlying basis may be rooted in the lack of pertinence of internationally driven genomics research to the local public health needs in the country, as well as a lack of relevance of internationally conducted genetics research to the genetic and environmental contexts of the population. Indeed, if Trinidad and Tobago is able to harness substantial public health benefit from genetics/genomics research, then there is a dire need, in the near future, to build local capacity for the conduct and translation of such research. Specifically, it is essential to establish a national human genetics/genomics research agenda in order to build sustainable human capacity through education and knowledge transfer and to generate public policies that will provide the basis for the creation of a mutually beneficial framework (including partnerships with more developed nations that is informed by public health needs and contextual realities of the nation.

  13. Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes

    Directory of Open Access Journals (Sweden)

    Deng Xuemei

    2007-11-01

    Full Text Available Abstract Background Bird genomes have very different compositional structure compared with other warm-blooded animals. The variation in the base skew rules in the vertebrate genomes remains puzzling, but it must relate somehow to large-scale genome evolution. Current research is inclined to relate base skew with mutations and their fixation. Here we wish to explore base skew correlations in bird genomes, to develop methods for displaying and quantifying such correlations at different scales, and to discuss possible explanations for the peculiarities of the bird genomes in skew correlation. Results We have developed a method called Base Skew Double Triangle (BSDT for exhibiting the genome-scale change of AT/CG skew as a two-dimensional square picture, showing base skews at many scales simultaneously in a single image. By this method we found that most chicken chromosomes have high AT/CG skew correlation (symmetry in 2D picture, except for some microchromosomes. No other organisms studied (18 species show such high skew correlations. This visualized high correlation was validated by three kinds of quantitative calculations with overlapping and non-overlapping windows, all indicating that chicken and birds in general have a special genome structure. Similar features were also found in some of the mammal genomes, but clearly much weaker than in chickens. We presume that the skew correlation feature evolved near the time that birds separated from other vertebrate lineages. When we eliminated the repeat sequences from the genomes, the AT and CG skews correlation increased for some mammal genomes, but were still clearly lower than in chickens. Conclusion Our results suggest that BSDT is an expressive visualization method for AT and CG skew and enabled the discovery of the very high skew correlation in bird genomes; this peculiarity is worth further study. Computational analysis indicated that this correlation might be a compositional characteristic

  14. Building accountability in large land acquisitions in Africa | IDRC ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2016-04-20

    Apr 20, 2016 ... Large-scale land deals can bring benefits such as jobs, infrastructure, and access to food and markets. But when badly managed, they can dispossess people in rural communities and spark conflict. Women and other vulnerable groups face the greatest risks. IDRC is funding research in Africa to find ways ...

  15. Energy efficiency supervision strategy selection of Chinese large-scale public buildings

    International Nuclear Information System (INIS)

    Jin Zhenxing; Wu Yong; Li Baizhan; Gao Yafeng

    2009-01-01

    This paper discusses energy consumption, building development and building energy consumption in China, and points that energy efficiency management and maintenance of large-scale public buildings is the breakthrough point of building energy saving in China. Three obstacles are lack of basic statistics data, lack of service market for building energy saving, and lack of effective management measures account for the necessity of energy efficiency supervision for large-scale public buildings. And then the paper introduces the supervision aims, the supervision system and the five basic systems' role in the supervision system, and analyzes the working mechanism of the five basic systems. The energy efficiency supervision system of large-scale public buildings takes energy consumption statistics as a data basis, Energy auditing as a technical support, energy consumption ration as a benchmark of energy saving and price increase beyond ration as a price lever, and energy efficiency public-noticing as an amplifier. The supervision system promotes energy efficiency operation and maintenance of large-scale public building, and drives a comprehensive building energy saving in China.

  16. Energy efficiency supervision strategy selection of Chinese large-scale public buildings

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Zhenxing; Li, Baizhan; Gao, Yafeng [The Faculty of Urban Construction and Environmental Engineering, Chongqing University, Chongqing (China); Key Laboratory of the Three Gorges Reservoir Region' s Eco-Environment, Ministry of Education, Chongqing 400045 (China); Wu, Yong [The Department of Science and Technology, Ministry of Construction, Beijing 100835 (China)

    2009-06-15

    This paper discusses energy consumption, building development and building energy consumption in China, and points that energy efficiency management and maintenance of large-scale public buildings is the breakthrough point of building energy saving in China. Three obstacles are lack of basic statistics data, lack of service market for building energy saving, and lack of effective management measures account for the necessity of energy efficiency supervision for large-scale public buildings. And then the paper introduces the supervision aims, the supervision system and the five basic systems' role in the supervision system, and analyzes the working mechanism of the five basic systems. The energy efficiency supervision system of large-scale public buildings takes energy consumption statistics as a data basis, Energy auditing as a technical support, energy consumption ration as a benchmark of energy saving and price increase beyond ration as a price lever, and energy efficiency public-noticing as an amplifier. The supervision system promotes energy efficiency operation and maintenance of large-scale public building, and drives a comprehensive building energy saving in China. (author)

  17. Energy efficiency supervision strategy selection of Chinese large-scale public buildings

    Energy Technology Data Exchange (ETDEWEB)

    Jin Zhenxing [Faculty of Urban Construction and Environmental Engineering, Chongqing University, Chongqing (China); Key Laboratory of the Three Gorges Reservoir Region' s Eco-Environment, Ministry of Education, Chongqing 400045 (China)], E-mail: jinzhenxing33@sina.com; Wu Yong [Department of Science and Technology, Ministry of Construction, Beijing 100835 (China); Li Baizhan; Gao Yafeng [Faculty of Urban Construction and Environmental Engineering, Chongqing University, Chongqing (China); Key Laboratory of the Three Gorges Reservoir Region' s Eco-Environment, Ministry of Education, Chongqing 400045 (China)

    2009-06-15

    This paper discusses energy consumption, building development and building energy consumption in China, and points that energy efficiency management and maintenance of large-scale public buildings is the breakthrough point of building energy saving in China. Three obstacles are lack of basic statistics data, lack of service market for building energy saving, and lack of effective management measures account for the necessity of energy efficiency supervision for large-scale public buildings. And then the paper introduces the supervision aims, the supervision system and the five basic systems' role in the supervision system, and analyzes the working mechanism of the five basic systems. The energy efficiency supervision system of large-scale public buildings takes energy consumption statistics as a data basis, Energy auditing as a technical support, energy consumption ration as a benchmark of energy saving and price increase beyond ration as a price lever, and energy efficiency public-noticing as an amplifier. The supervision system promotes energy efficiency operation and maintenance of large-scale public building, and drives a comprehensive building energy saving in China.

  18. Energy-efficiency supervision systems for energy management in large public buildings: Necessary choice for China

    International Nuclear Information System (INIS)

    Feng Yanping; Wu Yong; Liu Changbin

    2009-01-01

    Buildings are important contributors to total energy consumption accounting for around 30% of all energy consumed in China. Of this, around two-fifths are consumed within urban homes, one-fifth within public buildings, and two-fifths within rural area. Government office buildings and large-scale public buildings are the dominant energy consumers in cities but their consumption can be largely cut back through improving efficiency. At present, energy management in the large public sector is a particular priority in China. Firstly, this paper discusses how the large public building is defined, and then energy performance in large public buildings is studied. The paper also describes barriers to improving energy efficiency of large public buildings in China and examines the energy-efficiency policies and programs adopted in United States and European Union. The energy-efficiency supervision (EES) systems developed to improve operation and maintenance practices and promote energy efficiency in large public sector are described. The benefits of the EES systems are finally summarized.

  19. Energy-efficiency supervision systems for energy management in large public buildings. Necessary choice for China

    Energy Technology Data Exchange (ETDEWEB)

    Yan-ping, Feng [Beijing Jiaotong University, School of Economics and Management, Jiaoda Donglu18, 5-803, Beijing 100044 (China); Yong, Wu [Ministry of Housing and Urban-Rural Development, Beijing 100835 (China); Chang-bin, Liu [Beijing Institute of Civil Engineering and Architecture, Beijing 100044 (China)

    2009-06-15

    Buildings are important contributors to total energy consumption accounting for around 30% of all energy consumed in China. Of this, around two-fifths are consumed within urban homes, one-fifth within public buildings, and two-fifths within rural area. Government office buildings and large-scale public buildings are the dominant energy consumers in cities but their consumption can be largely cut back through improving efficiency. At present, energy management in the large public sector is a particular priority in China. Firstly, this paper discusses how the large public building is defined, and then energy performance in large public buildings is studied. The paper also describes barriers to improving energy efficiency of large public buildings in China and examines the energy-efficiency policies and programs adopted in United States and European Union. The energy-efficiency supervision (EES) systems developed to improve operation and maintenance practices and promote energy efficiency in large public sector are described. The benefits of the EES systems are finally summarized. (author)

  20. Energy-efficiency supervision systems for energy management in large public buildings: Necessary choice for China

    Energy Technology Data Exchange (ETDEWEB)

    Feng Yanping [Beijing Jiaotong University, School of Economics and Management, Jiaoda Donglu18, 5-803, Beijing 100044 (China)], E-mail: fengyanping10@sohu.com; Wu Yong [Ministry of Housing and Urban-Rural Development, Beijing 100835 (China); Liu Changbin [Beijing Institute of Civil Engineering and Architecture, Beijing 100044 (China)

    2009-06-15

    Buildings are important contributors to total energy consumption accounting for around 30% of all energy consumed in China. Of this, around two-fifths are consumed within urban homes, one-fifth within public buildings, and two-fifths within rural area. Government office buildings and large-scale public buildings are the dominant energy consumers in cities but their consumption can be largely cut back through improving efficiency. At present, energy management in the large public sector is a particular priority in China. Firstly, this paper discusses how the large public building is defined, and then energy performance in large public buildings is studied. The paper also describes barriers to improving energy efficiency of large public buildings in China and examines the energy-efficiency policies and programs adopted in United States and European Union. The energy-efficiency supervision (EES) systems developed to improve operation and maintenance practices and promote energy efficiency in large public sector are described. The benefits of the EES systems are finally summarized.

  1. Structural safety of HDR reactor building during large scale vibration tests

    International Nuclear Information System (INIS)

    Stangenberg, F.; Zinn, R.

    1985-01-01

    In the second phase of the HDR investigations, a high shaker excitation of the building is planned using a large shaker which will be located on the operating floor and will be brought up to speed in a balanced condition and then unbalanced and decoupled from the drive system. With decreasing speed the shaker comes in resonance with the building frequencies and its energy is transferred to the building. In this paper the structural safety of the reactor building during the projected shaker tests is analysed. Dynamic response calculations with coupling between building and shaker by simultaneously integrating the equilibrium equations of both building and shaker are presented. The resulting building stresses, soil pressures etc. are compared with allowable values. (orig.)

  2. Teaching Synthetic Biology, Bioinformatics and Engineering to Undergraduates: The Interdisciplinary Build-a-Genome Course

    Science.gov (United States)

    Dymond, Jessica S.; Scheifele, Lisa Z.; Richardson, Sarah; Lee, Pablo; Chandrasegaran, Srinivasan; Bader, Joel S.; Boeke, Jef D.

    2009-01-01

    A major challenge in undergraduate life science curricula is the continual evaluation and development of courses that reflect the constantly shifting face of contemporary biological research. Synthetic biology offers an excellent framework within which students may participate in cutting-edge interdisciplinary research and is therefore an attractive addition to the undergraduate biology curriculum. This new discipline offers the promise of a deeper understanding of gene function, gene order, and chromosome structure through the de novo synthesis of genetic information, much as synthetic approaches informed organic chemistry. While considerable progress has been achieved in the synthesis of entire viral and prokaryotic genomes, fabrication of eukaryotic genomes requires synthesis on a scale that is orders of magnitude higher. These high-throughput but labor-intensive projects serve as an ideal way to introduce undergraduates to hands-on synthetic biology research. We are pursuing synthesis of Saccharomyces cerevisiae chromosomes in an undergraduate laboratory setting, the Build-a-Genome course, thereby exposing students to the engineering of biology on a genomewide scale while focusing on a limited region of the genome. A synthetic chromosome III sequence was designed, ordered from commercial suppliers in the form of oligonucleotides, and subsequently assembled by students into ∼750-bp fragments. Once trained in assembly of such DNA “building blocks” by PCR, the students accomplish high-yield gene synthesis, becoming not only technically proficient but also constructively critical and capable of adapting their protocols as independent researchers. Regular “lab meeting” sessions help prepare them for future roles in laboratory science. PMID:19015540

  3. On Building and Processing of Large Digitalized Map Archive

    Directory of Open Access Journals (Sweden)

    Milan Simunek

    2011-07-01

    Full Text Available A tall list of problems needs to be solved during a long-time work on a virtual model of Prague aim of which is to show historical development of the city in virtual reality. This paper presents an integrated solution to digitalizing, cataloguing and processing of a large number of maps from different periods and from variety of sources. A specialized (GIS software application was developed to allow for a fast georeferencing (using an evolutionary algorithm, for cataloguing in an internal database, and subsequently for an easy lookup of relevant maps. So the maps could be processed further to serve as a main input for a proper modeling of a changing face of the city through times.

  4. Large-scale trends in the evolution of gene structures within 11 animal genomes.

    Directory of Open Access Journals (Sweden)

    Mark Yandell

    2006-03-01

    Full Text Available We have used the annotations of six animal genomes (Homo sapiens, Mus musculus, Ciona intestinalis, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans together with the sequences of five unannotated Drosophila genomes to survey changes in protein sequence and gene structure over a variety of timescales--from the less than 5 million years since the divergence of D. simulans and D. melanogaster to the more than 500 million years that have elapsed since the Cambrian explosion. To do so, we have developed a new open-source software library called CGL (for "Comparative Genomics Library". Our results demonstrate that change in intron-exon structure is gradual, clock-like, and largely independent of coding-sequence evolution. This means that genome annotations can be used in new ways to inform, corroborate, and test conclusions drawn from comparative genomics analyses that are based upon protein and nucleotide sequence similarities.

  5. Genic regions of a large salamander genome contain long introns and novel genes

    Directory of Open Access Journals (Sweden)

    Bryant Susan V

    2009-01-01

    Full Text Available Abstract Background The basis of genome size variation remains an outstanding question because DNA sequence data are lacking for organisms with large genomes. Sixteen BAC clones from the Mexican axolotl (Ambystoma mexicanum: c-value = 32 × 109 bp were isolated and sequenced to characterize the structure of genic regions. Results Annotation of genes within BACs showed that axolotl introns are on average 10× longer than orthologous vertebrate introns and they are predicted to contain more functional elements, including miRNAs and snoRNAs. Loci were discovered within BACs for two novel EST transcripts that are differentially expressed during spinal cord regeneration and skin metamorphosis. Unexpectedly, a third novel gene was also discovered while manually annotating BACs. Analysis of human-axolotl protein-coding sequences suggests there are 2% more lineage specific genes in the axolotl genome than the human genome, but the great majority (86% of genes between axolotl and human are predicted to be 1:1 orthologs. Considering that axolotl genes are on average 5× larger than human genes, the genic component of the salamander genome is estimated to be incredibly large, approximately 2.8 gigabases! Conclusion This study shows that a large salamander genome has a correspondingly large genic component, primarily because genes have incredibly long introns. These intronic sequences may harbor novel coding and non-coding sequences that regulate biological processes that are unique to salamanders.

  6. Large-scale building energy efficiency retrofit: Concept, model and control

    International Nuclear Information System (INIS)

    Wu, Zhou; Wang, Bo; Xia, Xiaohua

    2016-01-01

    BEER (Building energy efficiency retrofit) projects are initiated in many nations and regions over the world. Existing studies of BEER focus on modeling and planning based on one building and one year period of retrofitting, which cannot be applied to certain large BEER projects with multiple buildings and multi-year retrofit. In this paper, the large-scale BEER problem is defined in a general TBT (time-building-technology) framework, which fits essential requirements of real-world projects. The large-scale BEER is newly studied in the control approach rather than the optimization approach commonly used before. Optimal control is proposed to design optimal retrofitting strategy in terms of maximal energy savings and maximal NPV (net present value). The designed strategy is dynamically changing on dimensions of time, building and technology. The TBT framework and the optimal control approach are verified in a large BEER project, and results indicate that promising performance of energy and cost savings can be achieved in the general TBT framework. - Highlights: • Energy efficiency retrofit of many buildings is studied. • A TBT (time-building-technology) framework is proposed. • The control system of the large-scale BEER is modeled. • The optimal retrofitting strategy is obtained.

  7. MicroRNAs in large herpesvirus DNA genomes: recent advances.

    Science.gov (United States)

    Sorel, Océane; Dewals, Benjamin G

    2016-08-01

    MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs) that regulate gene expression. They alter mRNA translation through base-pair complementarity, leading to regulation of genes during both physiological and pathological processes. Viruses have evolved mechanisms to take advantage of the host cells to multiply and/or persist over the lifetime of the host. Herpesviridae are a large family of double-stranded DNA viruses that are associated with a number of important diseases, including lymphoproliferative diseases. Herpesviruses establish lifelong latent infections through modulation of the interface between the virus and its host. A number of reports have identified miRNAs in a very large number of human and animal herpesviruses suggesting that these short non-coding transcripts could play essential roles in herpesvirus biology. This review will specifically focus on the recent advances on the functions of herpesvirus miRNAs in infection and pathogenesis.

  8. Large-scale building integrated photovoltaics field trial. First technical report - installation phase

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2004-07-01

    This report summarises the results of the first eighteen months of the Large-Scale Building Integrated Photovoltaic Field Trial focussing on technical aspects. The project aims included increasing awareness and application of the technology, raising the UK capabilities in application of the technology, and assessing the potential for building integrated photovoltaics (BIPV). Details are given of technology choices; project organisation, cost, and status; and the evaluation criteria. Installations of BIPV described include University buildings, commercial centres, and a sports stadium, wildlife park, church hall, and district council building. Lessons learnt are discussed, and a further report covering monitoring aspects is planned.

  9. Large inserts for big data: artificial chromosomes in the genomic era.

    Science.gov (United States)

    Tocchetti, Arianna; Donadio, Stefano; Sosio, Margherita

    2018-05-01

    The exponential increase in available microbial genome sequences coupled with predictive bioinformatic tools is underscoring the genetic capacity of bacteria to produce an unexpected large number of specialized bioactive compounds. Since most of the biosynthetic gene clusters (BGCs) present in microbial genomes are cryptic, i.e. not expressed under laboratory conditions, a variety of cloning systems and vectors have been devised to harbor DNA fragments large enough to carry entire BGCs and to allow their transfer in suitable heterologous hosts. This minireview provides an overview of the vectors and approaches that have been developed for cloning large BGCs, and successful examples of heterologous expression.

  10. Insertion Sequence-Caused Large Scale-Rearrangements in the Genome of Escherichia coli

    Science.gov (United States)

    2016-07-18

    affordable ap- proach to genome-wide characterization of genetic varia - tion in bacterial and eukaryotic genomes (1–3). In addition to small-scale...Paired-End Reads), that uses a graph-based al- gorithm (27) capable of detecting most large-scale varia - tion involving repetitive regions, including novel...Avila,P., Grinsted,J. and De La Cruz,F. (1988) Analysis of the variable endpoints generated by one-ended transposition of Tn21.. J. Bacteriol., 170

  11. Aqueous aerosol may build up large upper tropospheric ice supersaturation

    Science.gov (United States)

    Bogdan, Anatoli; Molina, Mario J.

    2010-05-01

    Keywords: ice supersaturation, upper tropospheric cirrus clouds, freezing of aqueous aerosol. Observations often reveal enhanced and persistent upper tropospheric (UT) ice supersaturation, Si up to 100%, independently of whether cirrus ice clouds are present or not (Krämer et al., 2009; Lawson et al., 2008). However, a water activity criterion (WAC) (Koop et al., 2000) does not allow the formation of Si > ~67% by the homogeneous freezing of aqueous droplets even at the lowest atmospheric temperature of ~185 K. For aqueous aerosol the WAC predicts the existence of a so called homogeneous ice nucleation threshold which, being expressed as Si, is between ~52 and 67% in the temperature range of ~220 - 185 K. The nature of the formation of large Si remains unclear. Since water vapor is the dominant greenhouse gas it is important to know the nature of the accumulation and persistence of water vapor in the UT. We studied the freezing behavior of micrometer-scaled 3-, 4-, and 5-component droplets, which contain different weight fractions of H2O, H2SO4, HNO3, (NH4)2SO4, (NH4)HSO4, NH4NO3, and (NH4)3H(SO4)2. The study was performed between 133 and 278 K at cooling rates of 3, 0.1, and 0.05 K/min using differential scanning calorimetry (DSC) (Bogdan and Molina, 2010). The cooling rates of 0.1 and 0.05 K/min (6 and 3 K/h) are similar to the smallest reported synoptic temperature change of ~2 K/h (Carslaw et al., 1998). Using the measured freezing temperature of ice, Ti, and the thermodynamic E-AIM model of the system of H+ - NH4+ - SO42-- NO3-- H2O (Clegg et al., 1998), we calculated the corresponding clear-sky Si which would be built up immediately prior to the formation of ice cirrus clouds by the homogeneous freezing of aqueous aerosol of similar composition. We found that our calculated values of Si are both larger and smaller than the homogeneous ice nucleation threshold. For example, for the droplets of compositions of 15/10 and 20/10 wt % (NH4)3H(SO4)2/H2SO4, which

  12. Small genomes and large seeds: chromosome numbers, genome size and seed mass in diploid Aesculus species (Sapindaceae).

    Science.gov (United States)

    Krahulcová, Anna; Trávnícek, Pavel; Krahulec, František; Rejmánek, Marcel

    2017-04-01

    Aesculus L. (horse chestnut, buckeye) is a genus of 12-19 extant woody species native to the temperate Northern Hemisphere. This genus is known for unusually large seeds among angiosperms. While chromosome counts are available for many Aesculus species, only one has had its genome size measured. The aim of this study is to provide more genome size data and analyse the relationship between genome size and seed mass in this genus. Chromosome numbers in root tip cuttings were confirmed for four species and reported for the first time for three additional species. Flow cytometric measurements of 2C nuclear DNA values were conducted on eight species, and mean seed mass values were estimated for the same taxa. The same chromosome number, 2 n = 40, was determined in all investigated taxa. Original measurements of 2C values for seven Aesculus species (eight taxa), added to just one reliable datum for A. hippocastanum , confirmed the notion that the genome size in this genus with relatively large seeds is surprisingly low, ranging from 0·955 pg 2C -1 in A. parviflora to 1·275 pg 2C -1 in A. glabra var. glabra. The chromosome number of 2 n = 40 seems to be conclusively the universal 2 n number for non-hybrid species in this genus. Aesculus genome sizes are relatively small, not only within its own family, Sapindaceae, but also within woody angiosperms. The genome sizes seem to be distinct and non-overlapping among the four major Aesculus clades. These results provide an extra support for the most recent reconstruction of Aesculus phylogeny. The correlation between the 2C values and seed masses in examined Aesculus species is slightly negative and not significant. However, when the four major clades are treated separately, there is consistent positive association between larger genome size and larger seed mass within individual lineages. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For

  13. A review of radon mitigation in large buildings in the US

    International Nuclear Information System (INIS)

    Craig, A.B.

    1994-01-01

    The Environmental Protection Agency of the US carried out its initial research on radon mitigation in houses, both existing and new. A review of this work is presented in another paper at this workshop. Four years ago, this work was expanded to include the study of radon in schools, both new and existing, and now includes studies in other large buildings, as well. Factors affecting ease of mitigation of existing schools using active soil depressurisation (ASD) have been identified and quantified. Examination of the building and architectural plans makes it possible to predict the ease of mitigation of a specific building. Many schools can be easily and inexpensively mitigated using ASD. However, examination of a fairly large number of schools has shown that a significant percentage of existing schools will be hard to mitigate with ASD. In some cases, the heating, ventilating, and air conditioning (HVAC) system can be used to pressurise the building and retard radon entry. However, in some cases no central HVAC system exists and the school is difficult and/or expensive to mitigate by any technique. Prevention of radon entry is relatively easy and inexpensive to accomplish during construction of schools and other large buildings. It is also possible to control radon to near ambient levels in new construction, a goal which is much more difficult to approach in existing large buildings. The preferred method of radon prevention in the construction of large buildings is to design the HVAC system for building pressurisation, install a simple ASD system, and seal all entry routes between the sub-slab and the building interior. (author)

  14. Using relational databases for improved sequence similarity searching and large-scale genomic analyses.

    Science.gov (United States)

    Mackey, Aaron J; Pearson, William R

    2004-10-01

    Relational databases are designed to integrate diverse types of information and manage large sets of search results, greatly simplifying genome-scale analyses. Relational databases are essential for management and analysis of large-scale sequence analyses, and can also be used to improve the statistical significance of similarity searches by focusing on subsets of sequence libraries most likely to contain homologs. This unit describes using relational databases to improve the efficiency of sequence similarity searching and to demonstrate various large-scale genomic analyses of homology-related data. This unit describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. These include basic use of the database to generate a novel sequence library subset, how to extend and use seqdb_demo for the storage of sequence similarity search results and making use of various kinds of stored search results to address aspects of comparative genomic analysis.

  15. Learning directed acyclic graphs from large-scale genomics data.

    Science.gov (United States)

    Nikolay, Fabio; Pesavento, Marius; Kritikos, George; Typas, Nassos

    2017-09-20

    In this paper, we consider the problem of learning the genetic interaction map, i.e., the topology of a directed acyclic graph (DAG) of genetic interactions from noisy double-knockout (DK) data. Based on a set of well-established biological interaction models, we detect and classify the interactions between genes. We propose a novel linear integer optimization program called the Genetic-Interactions-Detector (GENIE) to identify the complex biological dependencies among genes and to compute the DAG topology that matches the DK measurements best. Furthermore, we extend the GENIE program by incorporating genetic interaction profile (GI-profile) data to further enhance the detection performance. In addition, we propose a sequential scalability technique for large sets of genes under study, in order to provide statistically significant results for real measurement data. Finally, we show via numeric simulations that the GENIE program and the GI-profile data extended GENIE (GI-GENIE) program clearly outperform the conventional techniques and present real data results for our proposed sequential scalability technique.

  16. A New Perspective on Polyploid Fragaria (Strawberry) Genome Composition Based on Large-Scale, Multi-Locus Phylogenetic Analysis.

    Science.gov (United States)

    Yang, Yilong; Davis, Thomas M

    2017-12-01

    The subgenomic compositions of the octoploid (2n = 8× = 56) strawberry (Fragaria) species, including the economically important cultivated species Fragaria x ananassa, have been a topic of long-standing interest. Phylogenomic approaches utilizing next-generation sequencing technologies offer a new window into species relationships and the subgenomic compositions of polyploids. We have conducted a large-scale phylogenetic analysis of Fragaria (strawberry) species using the Fluidigm Access Array system and 454 sequencing platform. About 24 single-copy or low-copy nuclear genes distributed across the genome were amplified and sequenced from 96 genomic DNA samples representing 16 Fragaria species from diploid (2×) to decaploid (10×), including the most extensive sampling of octoploid taxa yet reported. Individual gene trees were constructed by different tree-building methods. Mosaic genomic structures of diploid Fragaria species consisting of sequences at different phylogenetic positions were observed. Our findings support the presence in octoploid species of genetic signatures from at least five diploid ancestors (F. vesca, F. iinumae, F. bucharica, F. viridis, and at least one additional allele contributor of unknown identity), and questions the extent to which distinct subgenomes are preserved over evolutionary time in the allopolyploid Fragaria species. In addition, our data support divergence between the two wild octoploid species, F. virginiana and F. chiloensis. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

    Energy Technology Data Exchange (ETDEWEB)

    Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, James A.; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang

    2015-02-10

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

  18. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.

    Science.gov (United States)

    Brettin, Thomas; Davis, James J; Disz, Terry; Edwards, Robert A; Gerdes, Svetlana; Olsen, Gary J; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D; Shukla, Maulik; Thomason, James A; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R; Xia, Fangfang

    2015-02-10

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

  19. Low frequency of large genomic rearrangements of BRCA1 and BRCA2 in western Denmark

    DEFF Research Database (Denmark)

    Thomassen, Mads; Gerdes, Anne-Marie; Cruger, Dorthe

    2006-01-01

    Germline mutations in BRCA1 and BRCA2 predispose female carriers to breast and ovarian cancer. The majority of mutations identified are small deletions or insertions or are nonsense mutations. Large genomic rearrangements in BRCA1 are found with varying frequencies in different populations......, but BRCA2 rearrangements have not been investigated thoroughly. The objective in this study was to determine the frequency of large genomic rearrangements in BRCA1 and BRCA2 in a large group of Danish families with increased risk of breast and ovarian cancer. A total of 617 families previously tested...... negative for mutations involving few bases were screened with multiplex ligation-dependent probe amplification (MLPA). Two deletions in BRCA1 were identified in three families; no large rearrangements were detected in BRCA2. The large deletions constitute 3.8% of the BRCA1 mutations identified, which...

  20. What Will the Neighbors Think? Building Large-Scale Science Projects Around the World

    International Nuclear Information System (INIS)

    Jones, Craig; Mrotzek, Christian; Toge, Nobu; Sarno, Doug

    2007-01-01

    Public participation is an essential ingredient for turning the International Linear Collider into a reality. Wherever the proposed particle accelerator is sited in the world, its neighbors -- in any country -- will have something to say about hosting a 35-kilometer-long collider in their backyards. When it comes to building large-scale physics projects, almost every laboratory has a story to tell. Three case studies from Japan, Germany and the US will be presented to examine how community relations are handled in different parts of the world. How do particle physics laboratories interact with their local communities? How do neighbors react to building large-scale projects in each region? How can the lessons learned from past experiences help in building the next big project? These and other questions will be discussed to engage the audience in an active dialogue about how a large-scale project like the ILC can be a good neighbor.

  1. Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma

    NARCIS (Netherlands)

    Cerhan, James R.; Berndt, Sonja I.; Vijai, Joseph; Ghesquières, Hervé; McKay, James; Wang, Sophia S.; Wang, Zhaoming; Yeager, Meredith; Conde, Lucia; De Bakker, Paul I W; Nieters, Alexandra; Cox, David; Burdett, Laurie; Monnereau, Alain; Flowers, Christopher R.; De Roos, Anneclaire J.; Brooks-Wilson, Angela R.; Lan, Qing; Severi, Gianluca; Melbye, Mads; Gu, Jian; Jackson, Rebecca D.; Kane, Eleanor; Teras, Lauren R.; Purdue, Mark P.; Vajdic, Claire M.; Spinelli, John J.; Giles, Graham G.; Albanes, Demetrius; Kelly, Rachel S.; Zucca, Mariagrazia; Bertrand, Kimberly A.; Zeleniuch-Jacquotte, Anne; Lawrence, Charles; Hutchinson, Amy; Zhi, Degui; Habermann, Thomas M.; Link, Brian K.; Novak, Anne J.; Dogan, Ahmet; Asmann, Yan W.; Liebow, Mark; Thompson, Carrie A.; Ansell, Stephen M.; Witzig, Thomas E.; Weiner, George J.; Veron, Amelie S.; Zelenika, Diana; Tilly, Hervé; Haioun, Corinne; Molina, Thierry Jo; Hjalgrim, Henrik; Glimelius, Bengt; Adami, Hans Olov; Bracci, Paige M.; Riby, Jacques; Smith, Martyn T.; Holly, Elizabeth A.; Cozen, Wendy; Hartge, Patricia; Morton, Lindsay M.; Severson, Richard K.; Tinker, Lesley F.; North, Kari E.; Becker, Nikolaus; Benavente, Yolanda; Boffetta, Paolo; Brennan, Paul; Foretova, Lenka; Maynadie, Marc; Staines, Anthony; Lightfoot, Tracy; Crouch, Simon; Smith, Alex; Roman, Eve; Diver, W. Ryan; Offit, Kenneth; Zelenetz, Andrew; Klein, Robert J.; Villano, Danylo J.; Zheng, Tongzhang; Zhang, Yawei; Holford, Theodore R.; Kricker, Anne; Turner, Jenny; Southey, Melissa C.; Clavel, Jacqueline; Virtamo, Jarmo; Weinstein, Stephanie; Riboli, Elio; Vineis, Paolo; Kaaks, Rudolph; Trichopoulos, Dimitrios; Vermeulen, Roel C H; Boeing, Heiner; Tjonneland, Anne; Angelucci, Emanuele; Di Lollo, Simonetta; Rais, Marco; Birmann, Brenda M.; Laden, Francine; Giovannucci, Edward; Kraft, Peter; Huang, Jinyan; Ma, Baoshan; Ye, Yuanqing; Chiu, Brian C H; Sampson, Joshua; Liang, Liming; Park, Ju Hyun; Chung, Charles C.; Weisenburger, Dennis D.; Chatterjee, Nilanjan; Fraumeni, Joseph F.; Slager, Susan L.; Wu, Xifeng; De Sanjose, Silvia; Smedby, Karin E.; Salles, Gilles; Skibola, Christine F.; Rothman, Nathaniel; Chanock, Stephen J.

    2014-01-01

    Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma subtype and is clinically aggressive. To identify genetic susceptibility loci for DLBCL, we conducted a meta-analysis of 3 new genome-wide association studies (GWAS) and 1 previous scan, totaling 3,857 cases and 7,666 controls of

  2. Software engineering the mixed model for genome-wide association studies on large samples

    Science.gov (United States)

    Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample siz...

  3. Experience from large scale use of the EuroGenomics custom SNP chip in cattle

    DEFF Research Database (Denmark)

    Boichard, Didier A; Boussaha, Mekki; Capitan, Aurélien

    2018-01-01

    This article presents the strategy to evaluate candidate mutations underlying QTL or responsible for genetic defects, based upon the design and large-scale use of the Eurogenomics custom SNP chip set up for bovine genomic selection. Some variants under study originated from mapping genetic defect...

  4. Large-eddy simulation of plume dispersion within regular arrays of cubic buildings

    Science.gov (United States)

    Nakayama, H.; Jurcakova, K.; Nagai, H.

    2011-04-01

    There is a potential problem that hazardous and flammable materials are accidentally or intentionally released within populated urban areas. For the assessment of human health hazard from toxic substances, the existence of high concentration peaks in a plume should be considered. For the safety analysis of flammable gas, certain critical threshold levels should be evaluated. Therefore, in such a situation, not only average levels but also instantaneous magnitudes of concentration should be accurately predicted. In this study, we perform Large-Eddy Simulation (LES) of plume dispersion within regular arrays of cubic buildings with large obstacle densities and investigate the influence of the building arrangement on the characteristics of mean and fluctuating concentrations.

  5. Hydrogen behavior in a large-dry pressurized water reactor containment building during a severe accident

    International Nuclear Information System (INIS)

    Hsu Wensheng; Chen Hungpei; Hung Zhenyu; Lin Huichen

    2014-01-01

    Following severe accidents in nuclear power plants, large quantities of hydrogen may be generated after core degradation. If the hydrogen is transported from the reactor vessel into the containment building, an explosion might occur, which might threaten the integrity of the building; this can ultimately cause the release of radioactive materials. During the Fukushima Daiichi nuclear accident in 2011, the primary containment structures remained intact but contaminated fragments broke off the secondary containment structures, which disrupted mitigation activities and triggered subsequent explosions. Therefore, the ability to predict the behavior of hydrogen after severe accidents may facilitate the development of effective nuclear reactor accident management procedures. The present study investigated the behavior of hydrogen in a large-dry pressurized water reactor (PWR). The amount of hydrogen produced was calculated using the Modular Accident Analysis Program. The hydrogen transport behavior and the effect of the explosion on the PWR containment building were simulated using the Flame Acceleration Simulator. The simulation results showed that the average hydrogen volume fraction is approximately 7% in the containment building and that the average temperature is 330 K. The maximum predicted pressure load after ignition is 2.55 bar, which does not endanger the structural integrity of the containment building. The results of this investigation indicate that the hydrogen mitigation system should be arranged on both the upper and lower parts of the containment building to reduce the impact of an explosion. (author)

  6. Genomic profiling of plasmablastic lymphoma using array comparative genomic hybridization (aCGH: revealing significant overlapping genomic lesions with diffuse large B-cell lymphoma

    Directory of Open Access Journals (Sweden)

    Lu Xin-Yan

    2009-11-01

    Full Text Available Abstract Background Plasmablastic lymphoma (PL is a subtype of diffuse large B-cell lymphoma (DLBCL. Studies have suggested that tumors with PL morphology represent a group of neoplasms with clinopathologic characteristics corresponding to different entities including extramedullary plasmablastic tumors associated with plasma cell myeloma (PCM. The goal of the current study was to evaluate the genetic similarities and differences among PL, DLBCL (AIDS-related and non AIDS-related and PCM using array-based comparative genomic hybridization. Results Examination of genomic data in PL revealed that the most frequent segmental gain (> 40% include: 1p36.11-1p36.33, 1p34.1-1p36.13, 1q21.1-1q23.1, 7q11.2-7q11.23, 11q12-11q13.2 and 22q12.2-22q13.3. This correlated with segmental gains occurring in high frequency in DLBCL (AIDS-related and non AIDS-related cases. There were some segmental gains and some segmental loss that occurred in PL but not in the other types of lymphoma suggesting that these foci may contain genes responsible for the differentiation of this lymphoma. Additionally, some segmental gains and some segmental loss occurred only in PL and AIDS associated DLBCL suggesting that these foci may be associated with HIV infection. Furthermore, some segmental gains and some segmental loss occurred only in PL and PCM suggesting that these lesions may be related to plasmacytic differentiation. Conclusion To the best of our knowledge, the current study represents the first genomic exploration of PL. The genomic aberration pattern of PL appears to be more similar to that of DLBCL (AIDS-related or non AIDS-related than to PCM. Our findings suggest that PL may remain best classified as a subtype of DLBCL at least at the genome level.

  7. Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing.

    Science.gov (United States)

    Zhao, Shanrong; Prenger, Kurt; Smith, Lance; Messina, Thomas; Fan, Hongtao; Jaeger, Edward; Stephens, Susan

    2013-06-27

    Technical improvements have decreased sequencing costs and, as a result, the size and number of genomic datasets have increased rapidly. Because of the lower cost, large amounts of sequence data are now being produced by small to midsize research groups. Crossbow is a software tool that can detect single nucleotide polymorphisms (SNPs) in whole-genome sequencing (WGS) data from a single subject; however, Crossbow has a number of limitations when applied to multiple subjects from large-scale WGS projects. The data storage and CPU resources that are required for large-scale whole genome sequencing data analyses are too large for many core facilities and individual laboratories to provide. To help meet these challenges, we have developed Rainbow, a cloud-based software package that can assist in the automation of large-scale WGS data analyses. Here, we evaluated the performance of Rainbow by analyzing 44 different whole-genome-sequenced subjects. Rainbow has the capacity to process genomic data from more than 500 subjects in two weeks using cloud computing provided by the Amazon Web Service. The time includes the import and export of the data using Amazon Import/Export service. The average cost of processing a single sample in the cloud was less than 120 US dollars. Compared with Crossbow, the main improvements incorporated into Rainbow include the ability: (1) to handle BAM as well as FASTQ input files; (2) to split large sequence files for better load balance downstream; (3) to log the running metrics in data processing and monitoring multiple Amazon Elastic Compute Cloud (EC2) instances; and (4) to merge SOAPsnp outputs for multiple individuals into a single file to facilitate downstream genome-wide association studies. Rainbow is a scalable, cost-effective, and open-source tool for large-scale WGS data analysis. For human WGS data sequenced by either the Illumina HiSeq 2000 or HiSeq 2500 platforms, Rainbow can be used straight out of the box. Rainbow is available

  8. The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA

    Directory of Open Access Journals (Sweden)

    Tran Duc

    2010-05-01

    Full Text Available Abstract Background Dunaliella salina Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because D. salina can produce massive amounts of β-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of D. salina have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model green algae Chlamydomonas reinhardtii and Volvox carteri. Results The D. salina organelle genomes are large, circular-mapping molecules with ~60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the D. salina plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: ~1.5 and ~0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the D. salina ptDNA. Conclusions These findings confirm the notion that chlamydomonadalean algae have some of the most extreme organelle genomes of all eukaryotes. They also suggest that the events giving rise to the expanded ptDNA architecture of D. salina and other Chlamydomonadales may have occurred early in the evolution of this lineage. Although interesting from a genome evolution standpoint, the D. salina organelle DNA sequences will aid in the

  9. The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA

    Energy Technology Data Exchange (ETDEWEB)

    Smith, David R.; Lee, Robert W.; Cushman, John C.; Magnuson, Jon K.; Tran, Duc; Polle, Juergen E.

    2010-05-07

    Abstract Background: Dunaliella salina Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because D. salina can produce massive amounts of β-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of D. salina have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model green algae Chlamydomonas reinhardtii and Volvox carteri. Results: The D. salina organelle genomes are large, circular-mapping molecules with ~60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the D. salina plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA) sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: ~1.5 and ~0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the D. salina ptDNA. Conclusions: These findings confirm the notion that chlamydomonadalean algae have some of the most extreme organelle genomes of all eukaryotes. They also suggest that the events giving rise to the expanded ptDNA architecture of D. salina and other Chlamydomonadales may have occurred early in the evolution of this lineage. Although interesting from a genome evolution standpoint, the D. salina organelle DNA sequences will aid in the development of a viable

  10. Wind Power: Building and Connecting Large Wind Power Plants; Vindkraft: bygga och ansluta stoerre vindkraftverk

    Energy Technology Data Exchange (ETDEWEB)

    2007-09-15

    This brochure is written for those who want to build a large wind power plant (1 MW or more) or wind power parks. It describes the process from idea to completed plant. A review of environmental impacts of wind power is also included

  11. Large BRCA1 and BRCA2 genomic rearrangements in Danish high risk breast-ovarian cancer families

    DEFF Research Database (Denmark)

    Hansen, Thomas v O; Jønson, Lars; Albrechtsen, Anders

    2009-01-01

    BRCA1 and BRCA2 germ-line mutations predispose to breast and ovarian cancer. Large genomic rearrangements of BRCA1 account for 0-36% of all disease causing mutations in various populations, while large genomic rearrangements in BRCA2 are more rare. We examined 642 East Danish breast and/or ovaria...

  12. Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets.

    Science.gov (United States)

    Heath, Allison P; Greenway, Matthew; Powell, Raymond; Spring, Jonathan; Suarez, Rafael; Hanley, David; Bandlamudi, Chai; McNerney, Megan E; White, Kevin P; Grossman, Robert L

    2014-01-01

    As large genomics and phenotypic datasets are becoming more common, it is increasingly difficult for most researchers to access, manage, and analyze them. One possible approach is to provide the research community with several petabyte-scale cloud-based computing platforms containing these data, along with tools and resources to analyze it. Bionimbus is an open source cloud-computing platform that is based primarily upon OpenStack, which manages on-demand virtual machines that provide the required computational resources, and GlusterFS, which is a high-performance clustered file system. Bionimbus also includes Tukey, which is a portal, and associated middleware that provides a single entry point and a single sign on for the various Bionimbus resources; and Yates, which automates the installation, configuration, and maintenance of the software infrastructure required. Bionimbus is used by a variety of projects to process genomics and phenotypic data. For example, it is used by an acute myeloid leukemia resequencing project at the University of Chicago. The project requires several computational pipelines, including pipelines for quality control, alignment, variant calling, and annotation. For each sample, the alignment step requires eight CPUs for about 12 h. BAM file sizes ranged from 5 GB to 10 GB for each sample. Most members of the research community have difficulty downloading large genomics datasets and obtaining sufficient storage and computer resources to manage and analyze the data. Cloud computing platforms, such as Bionimbus, with data commons that contain large genomics datasets, are one choice for broadening access to research data in genomics. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  13. Radon prevention in the design and construction of schools and other large buildings

    International Nuclear Information System (INIS)

    Leovic, K.W.; Craig, A.B.; Harris, D.B.

    1991-01-01

    The paper discusses radon prevention in the design and construction of schools and other large buildings. The U.S. EPA's Office of Research and Development (ORD) has started incorporating radon control measures into the design and construction of new schools and other large buildings. The goal of the new designs is twofold: (1) to prevent elevated radon levels in the completed building, and (2) to provide the protection at a fraction of the cost of retrofit systems. ORD's Air and Energy Engineering Research Laboratory (AEERL) has conducted the research necessary to develop viable designs. The Indoor Radon Abatement Act of 1988 set a national long-term goal for indoor radon of 0.5 picocurie per liter (pCi/L)--the same as that typically found in outdoor air. The EPA currently recommends that homeowners take action to reduce radon levels to below 4 pCi/L. To achieve the national goal set in the 1988 Act for new construction in radon-prone areas, AEERL research is using a combination of active subslab depressurization (ASD) and operation of the heating, ventilation, and air-conditioning (HVAC) system to pressurize buildings. These measures are described briefly, along with a case history of one building

  14. Opportunities for low carbon sustainability in large commercial buildings in China

    International Nuclear Information System (INIS)

    Jiang Ping; Keith Tovey, N.

    2009-01-01

    China's building sector consumes one quarter of total energy consumption in the country and plays an important role in long-term ability of the country to achieve sustainable development. This paper discusses a comprehensive approach to achieving low carbon sustainability in large commercial buildings in China incorporating both energy and carbon-reduction strategies. The approach concentrates primarily on three complementary aspects: (a) the introduction of an effective energy management system; (b) the incorporation of relevant advanced energy saving technologies and measures and (c) the promotion of awareness among occupants to make changes in their behaviour towards a more environmental-friendly behaviour. However, reference is also made to the role that renewable energy and offsetting may have in the effective management and environmental performance of buildings. Nine examples of large commercial buildings in Beijing and Shanghai were studied and the average electricity consumption of around 153 kWh/m 2 per annum is about 5 times higher than average electricity use in residential buildings. At the same time the associated green house gas (GHG) emissions are around 158 kg/m 2 per annum.

  15. Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey

    Directory of Open Access Journals (Sweden)

    Varala Kranthi

    2007-05-01

    Full Text Available Abstract Background Extensive computational and database tools are available to mine genomic and genetic databases for model organisms, but little genomic data is available for many species of ecological or agricultural significance, especially those with large genomes. Genome surveys using conventional sequencing techniques are powerful, particularly for detecting sequences present in many copies per genome. However these methods are time-consuming and have potential drawbacks. High throughput 454 sequencing provides an alternative method by which much information can be gained quickly and cheaply from high-coverage surveys of genomic DNA. Results We sequenced 78 million base-pairs of randomly sheared soybean DNA which passed our quality criteria. Computational analysis of the survey sequences provided global information on the abundant repetitive sequences in soybean. The sequence was used to determine the copy number across regions of large genomic clones or contigs and discover higher-order structures within satellite repeats. We have created an annotated, online database of sequences present in multiple copies in the soybean genome. The low bias of pyrosequencing against repeat sequences is demonstrated by the overall composition of the survey data, which matches well with past estimates of repetitive DNA content obtained by DNA re-association kinetics (Cot analysis. Conclusion This approach provides a potential aid to conventional or shotgun genome assembly, by allowing rapid assessment of copy number in any clone or clone-end sequence. In addition, we show that partial sequencing can provide access to partial protein-coding sequences.

  16. Building

    OpenAIRE

    Seavy, Ryan

    2014-01-01

    Building for concrete is temporary. The building of wood and steel stands against the concrete to give form and then gives way, leaving a trace of its existence behind. Concrete is not a building material. One does not build with concrete. One builds for concrete. MARCH

  17. Glass-covering of large building volumes. An interdisciplinary evaluation of a shopping centre

    Energy Technology Data Exchange (ETDEWEB)

    Oeman, R [Royal Inst. of Tech., Stockholm (Sweden). Dept. of Building Technology

    1994-12-31

    Systematized experiences of the function of large glass-covered spaces related to shopping centres, hotels, office buildings etc. are still relatively limited. With the glazed pedestrian precincts of the rebuilt Skaerholmen Centre in Stockholm as the main object of interdisciplinary studies, the aim of this thesis is to provide additional knowledge of large glass-covered spaces (atrium buildings). The studies comprises thermal comfort, temperature conditions, ventilation, energy balance, humidity - mycology, acoustics, operation - maintenance - durability and sociology. To sum up, it is clear that in the Scandinavian climate there is every likelihood of large glass-covered spaces in the public places functioning well from a technical as well as a social point of view. The energy consumption on heating the whole complex, based on theoretical calculations and measurement, is shown to have been reduced by the order of 10%. figs., tabs., refs.

  18. The characteristic of the building damage from historical large earthquakes in Kyoto

    Science.gov (United States)

    Nishiyama, Akihito

    2016-04-01

    The Kyoto city, which is located in the northern part of Kyoto basin in Japan, has a long history of >1,200 years since the city was initially constructed. The city has been a populated area with many buildings and the center of the politics, economy and culture in Japan for nearly 1,000 years. Some of these buildings are now subscribed as the world's cultural heritage. The Kyoto city has experienced six damaging large earthquakes during the historical period: i.e., in 976, 1185, 1449, 1596, 1662, and 1830. Among these, the last three earthquakes which caused severe damage in Kyoto occurred during the period in which the urban area had expanded. These earthquakes are considered to be inland earthquakes which occurred around the Kyoto basin. The damage distribution in Kyoto from historical large earthquakes is strongly controlled by ground condition and earthquakes resistance of buildings rather than distance from estimated source fault. Therefore, it is necessary to consider not only the strength of ground shaking but also the condition of building such as elapsed years since the construction or last repair in order to more accurately and reliably estimate seismic intensity distribution from historical earthquakes in Kyoto. The obtained seismic intensity map would be helpful for reducing and mitigating disaster from future large earthquakes.

  19. Are building users prepared for energy flexible buildings?—A large-scale survey in the Netherlands

    NARCIS (Netherlands)

    Li, Rongling; Dane, G.Z.; Finck, C.J.; Zeiler, W.

    2017-01-01

    Building energy flexibility might play a crucial role in demand side management for integrating intermittent renewables into smart grids. The potential of building energy flexibility depends not only on the physical characteristics of a building but also on occupant behaviour in the building.

  20. Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction.

    Science.gov (United States)

    Wu, Chen; Twort, Victoria G; Crowhurst, Ross N; Newcomb, Richard D; Buckley, Thomas R

    2017-11-16

    Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large genome size in stick insects. The C. hookeri genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest insect genome sequenced and assembled to date. Like the large genome of Locusta migratoria, the genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced insect genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae genome, is the most abundant repeat type in the C. hookeri genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. The evolution of large insect genomes such as L. migratoria and C. hookeri genomes is most likely due to the

  1. Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms.

    Science.gov (United States)

    Ferraro Petrillo, Umberto; Roscigno, Gianluca; Cattaneo, Giuseppe; Giancarlo, Raffaele

    2018-06-01

    Information theoretic and compositional/linguistic analysis of genomes have a central role in bioinformatics, even more so since the associated methodologies are becoming very valuable also for epigenomic and meta-genomic studies. The kernel of those methods is based on the collection of k-mer statistics, i.e. how many times each k-mer in {A,C,G,T}k occurs in a DNA sequence. Although this problem is computationally very simple and efficiently solvable on a conventional computer, the sheer amount of data available now in applications demands to resort to parallel and distributed computing. Indeed, those type of algorithms have been developed to collect k-mer statistics in the realm of genome assembly. However, they are so specialized to this domain that they do not extend easily to the computation of informational and linguistic indices, concurrently on sets of genomes. Following the well-established approach in many disciplines, and with a growing success also in bioinformatics, to resort to MapReduce and Hadoop to deal with 'Big Data' problems, we present KCH, the first set of MapReduce algorithms able to perform concurrently informational and linguistic analysis of large collections of genomic sequences on a Hadoop cluster. The benchmarking of KCH that we provide indicates that it is quite effective and versatile. It is also competitive with respect to the parallel and distributed algorithms highly specialized to k-mer statistics collection for genome assembly problems. In conclusion, KCH is a much needed addition to the growing number of algorithms and tools that use MapReduce for bioinformatics core applications. The software, including instructions for running it over Amazon AWS, as well as the datasets are available at http://www.di-srv.unisa.it/KCH. umberto.ferraro@uniroma1.it. Supplementary data are available at Bioinformatics online.

  2. Large-Eddy Simulation on Plume Dispersion within Regular Arrays of Cubic Buildings

    Science.gov (United States)

    Nakayama, H.; Jurcakova, K.; Nagai, H.

    2010-09-01

    There is a potential problem that hazardous and flammable materials are accidentally or intentionally released into the atmosphere, either within or close to populated urban areas. For the assessment of human health hazard from toxic substances, the existence of high concentration peaks in a plume should be considered. For the safety analysis of flammable gas, certain critical threshold levels should be evaluated. Therefore, in such a situation, not only average levels but also instantaneous magnitudes of concentration should be accurately predicted. However, plume dispersion is an extremely complicated process strongly influenced by the existence of buildings. In complex turbulent flows, such as impinging, separated and circulation flows around buildings, plume behaviors can be no longer accurately predicted using empirical Gaussian-type plume model. Therefore, we perform Large-Eddy Simulations (LES) on turbulent flows and plume dispersions within and over regular arrays of cubic buildings with various roughness densities and investigate the influence of the building arrangement pattern on the characteristics of mean and fluctuation concentrations. The basic equations for the LES model are composed of the spatially filtered continuity equation, Navier-Stokes equation and transport equation of concentration. The standard Smagorinsky model (Smagorinsky, 1963) that has enough potential for environment flows is used and its constant is set to 0.12 for estimating the eddy viscosity. The turbulent Schmidt number is 0.5. In our LES model, two computational regions are set up. One is a driver region for generation of inflow turbulence and the other is a main region for LES of plume dispersion within a regular array of cubic buildings. First, inflow turbulence is generated by using Kataoka's method (2002) in the driver region and then, its data are imposed at the inlet of the main computational region at each time step. In this study, the cubic building arrays with λf=0

  3. Assessment of Retrofitting Measures for a Large Historic Research Facility Using a Building Energy Simulation Model

    Directory of Open Access Journals (Sweden)

    Young Tae Chae

    2016-06-01

    Full Text Available A calibrated building simulation model was developed to assess the energy performance of a large historic research building. The complexity of space functions and operational conditions with limited availability of energy meters makes it hard to understand the end-used energy consumption in detail and to identify appropriate retrofitting options for reducing energy consumption and greenhouse gas (GHG emissions. An energy simulation model was developed to study the energy usage patterns not only at a building level, but also of the internal thermal zones, and system operations. The model was validated using site measurements of energy usage and a detailed audit of the internal load conditions, system operation, and space programs to minimize the discrepancy between the documented status and actual operational conditions. Based on the results of the calibrated model and end-used energy consumption, the study proposed potential energy conservation measures (ECMs for the building envelope, HVAC system operational methods, and system replacement. It also evaluated each ECM from the perspective of both energy and utility cost saving potentials to help retrofitting plan decision making. The study shows that the energy consumption of the building was highly dominated by the thermal requirements of laboratory spaces. Among other ECMs the demand management option of overriding the setpoint temperature is the most cost effective measure.

  4. High-efficiency targeted editing of large viral genomes by RNA-guided nucleases.

    Science.gov (United States)

    Bi, Yanwei; Sun, Le; Gao, Dandan; Ding, Chen; Li, Zhihua; Li, Yadong; Cun, Wei; Li, Qihan

    2014-05-01

    A facile and efficient method for the precise editing of large viral genomes is required for the selection of attenuated vaccine strains and the construction of gene therapy vectors. The type II prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas)) RNA-guided nuclease system can be introduced into host cells during viral replication. The CRISPR-Cas9 system robustly stimulates targeted double-stranded breaks in the genomes of DNA viruses, where the non-homologous end joining (NHEJ) and homology-directed repair (HDR) pathways can be exploited to introduce site-specific indels or insert heterologous genes with high frequency. Furthermore, CRISPR-Cas9 can specifically inhibit the replication of the original virus, thereby significantly increasing the abundance of the recombinant virus among progeny virus. As a result, purified recombinant virus can be obtained with only a single round of selection. In this study, we used recombinant adenovirus and type I herpes simplex virus as examples to demonstrate that the CRISPR-Cas9 system is a valuable tool for editing the genomes of large DNA viruses.

  5. High-efficiency targeted editing of large viral genomes by RNA-guided nucleases.

    Directory of Open Access Journals (Sweden)

    Yanwei Bi

    2014-05-01

    Full Text Available A facile and efficient method for the precise editing of large viral genomes is required for the selection of attenuated vaccine strains and the construction of gene therapy vectors. The type II prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats (CRISPR-associated (Cas RNA-guided nuclease system can be introduced into host cells during viral replication. The CRISPR-Cas9 system robustly stimulates targeted double-stranded breaks in the genomes of DNA viruses, where the non-homologous end joining (NHEJ and homology-directed repair (HDR pathways can be exploited to introduce site-specific indels or insert heterologous genes with high frequency. Furthermore, CRISPR-Cas9 can specifically inhibit the replication of the original virus, thereby significantly increasing the abundance of the recombinant virus among progeny virus. As a result, purified recombinant virus can be obtained with only a single round of selection. In this study, we used recombinant adenovirus and type I herpes simplex virus as examples to demonstrate that the CRISPR-Cas9 system is a valuable tool for editing the genomes of large DNA viruses.

  6. Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories.

    Science.gov (United States)

    Chockalingam, Sriram; Aluru, Maneesha; Aluru, Srinivas

    2016-09-19

    Pre-processing of microarray data is a well-studied problem. Furthermore, all popular platforms come with their own recommended best practices for differential analysis of genes. However, for genome-scale network inference using microarray data collected from large public repositories, these methods filter out a considerable number of genes. This is primarily due to the effects of aggregating a diverse array of experiments with different technical and biological scenarios. Here we introduce a pre-processing pipeline suitable for inferring genome-scale gene networks from large microarray datasets. We show that partitioning of the available microarray datasets according to biological relevance into tissue- and process-specific categories significantly extends the limits of downstream network construction. We demonstrate the effectiveness of our pre-processing pipeline by inferring genome-scale networks for the model plant Arabidopsis thaliana using two different construction methods and a collection of 11,760 Affymetrix ATH1 microarray chips. Our pre-processing pipeline and the datasets used in this paper are made available at http://alurulab.cc.gatech.edu/microarray-pp.

  7. High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak

    Directory of Open Access Journals (Sweden)

    Trout-Yakel Keri M

    2010-02-01

    Full Text Available Abstract Background A large, multi-province outbreak of listeriosis associated with ready-to-eat meat products contaminated with Listeria monocytogenes serotype 1/2a occurred in Canada in 2008. Subtyping of outbreak-associated isolates using pulsed-field gel electrophoresis (PFGE revealed two similar but distinct AscI PFGE patterns. High-throughput pyrosequencing of two L. monocytogenes isolates was used to rapidly provide the genome sequence of the primary outbreak strain and to investigate the extent of genetic diversity associated with a change of a single restriction enzyme fragment during PFGE. Results The chromosomes were collinear, but differences included 28 single nucleotide polymorphisms (SNPs and three indels, including a 33 kbp prophage that accounted for the observed difference in AscI PFGE patterns. The distribution of these traits was assessed within further clinical, environmental and food isolates associated with the outbreak, and this comparison indicated that three distinct, but highly related strains may have been involved in this nationwide outbreak. Notably, these two isolates were found to harbor a 50 kbp putative mobile genomic island encoding translocation and efflux functions that has not been observed in other Listeria genomes. Conclusions High-throughput genome sequencing provided a more detailed real-time assessment of genetic traits characteristic of the outbreak strains than could be achieved with routine subtyping methods. This study confirms that the latest generation of DNA sequencing technologies can be applied during high priority public health events, and laboratories need to prepare for this inevitability and assess how to properly analyze and interpret whole genome sequences in the context of molecular epidemiology.

  8. D-GENIES: dot plot large genomes in an interactive, efficient and simple way.

    Science.gov (United States)

    Cabanettes, Floréal; Klopp, Christophe

    2018-01-01

    Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots, but they are often limited in the input sequence size. D-GENIES is a standalone and web application performing large genome alignments using minimap2 software package and generating interactive dot plots. It enables users to sort query sequences along the reference, zoom in the plot and download several image, alignment or sequence files. D-GENIES is an easy-to-install, open-source software package (GPL) developed in Python and JavaScript. The source code is available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/.

  9. Quantitative linkage genome scan for atopy in a large collection of Caucasian families

    DEFF Research Database (Denmark)

    Webb, BT; van den Oord, E; Akkari, A

    2007-01-01

    adulthood, asthma is frequently associated also with quantitative measures of atopy. Genome wide quantitative multipoint linkage analysis was conducted for serum IgE levels and percentage of positive skin prick test (SPT(per)) using three large groups of families originally ascertained for asthma....... In this report, 438 and 429 asthma families were informative for linkage using IgE and SPT(per) which represents 690 independent families. Suggestive linkage (LOD >/= 2) was found on chromosomes 1, 3, and 8q with maximum LODs of 2.34 (IgE), 2.03 (SPT(per)), and 2.25 (IgE) near markers D1S1653, D3S2322-D3S1764...... represents one of the biggest genome scans so far reported for asthma related phenotypes. This study also demonstrates the utility of increased sample sizes and quantitative phenotypes in linkage analysis of complex disorders....

  10. Biological consequences of ancient gene acquisition and duplication in the large genome soil bacterium, ""solibacter usitatus"" strain Ellin6076

    Energy Technology Data Exchange (ETDEWEB)

    Challacombe, Jean F [Los Alamos National Laboratory; Eichorst, Stephanie A [Los Alamos National Laboratory; Xie, Gary [Los Alamos National Laboratory; Kuske, Cheryl R [Los Alamos National Laboratory; Hauser, Loren [ORNL; Land, Miriam [ORNL

    2009-01-01

    Bacterial genome sizes range from ca. 0.5 to 10Mb and are influenced by gene duplication, horizontal gene transfer, gene loss and other evolutionary processes. Sequenced genomes of strains in the phylum Acidobacteria revealed that 'Solibacter usistatus' strain Ellin6076 harbors a 9.9 Mb genome. This large genome appears to have arisen by horizontal gene transfer via ancient bacteriophage and plasmid-mediated transduction, as well as widespread small-scale gene duplications. This has resulted in an increased number of paralogs that are potentially ecologically important (ecoparalogs). Low amino acid sequence identities among functional group members and lack of conserved gene order and orientation in the regions containing similar groups of paralogs suggest that most of the paralogs were not the result of recent duplication events. The genome sizes of cultured subdivision 1 and 3 strains in the phylum Acidobacteria were estimated using pulsed-field gel electrophoresis to determine the prevalence of the large genome trait within the phylum. Members of subdivision 1 were estimated to have smaller genome sizes ranging from ca. 2.0 to 4.8 Mb, whereas members of subdivision 3 had slightly larger genomes, from ca. 5.8 to 9.9 Mb. It is hypothesized that the large genome of strain Ellin6076 encodes traits that provide a selective metabolic, defensive and regulatory advantage in the variable soil environment.

  11. Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing.

    Science.gov (United States)

    Keinath, Melissa C; Timoshevskiy, Vladimir A; Timoshevskaya, Nataliya Y; Tsonis, Panagiotis A; Voss, S Randal; Smith, Jeramiah J

    2015-11-10

    Vertebrates exhibit substantial diversity in genome size, and some of the largest genomes exist in species that uniquely inform diverse areas of basic and biomedical research. For example, the salamander Ambystoma mexicanum (the Mexican axolotl) is a model organism for studies of regeneration, development and genome evolution, yet its genome is ~10× larger than the human genome. As part of a hierarchical approach toward improving genome resources for the species, we generated 600 Gb of shotgun sequence data and developed methods for sequencing individual laser-captured chromosomes. Based on these data, we estimate that the A. mexicanum genome is ~32 Gb. Notably, as much as 19 Gb of the A. mexicanum genome can potentially be considered single copy, which presumably reflects the evolutionary diversification of mobile elements that accumulated during an ancient episode of genome expansion. Chromosome-targeted sequencing permitted the development of assemblies within the constraints of modern computational platforms, allowed us to place 2062 genes on the two smallest A. mexicanum chromosomes and resolves key events in the history of vertebrate genome evolution. Our analyses show that the capture and sequencing of individual chromosomes is likely to provide valuable information for the systematic sequencing, assembly and scaffolding of large genomes.

  12. Ultra Large Gene Families: A Matter of Adaptation or Genomic Parasites?

    Directory of Open Access Journals (Sweden)

    Philipp H. Schiffer

    2016-08-01

    Full Text Available Gene duplication is an important mechanism of molecular evolution. It offers a fast track to modification, diversification, redundancy or rescue of gene function. However, duplication may also be neutral or (slightly deleterious, and often ends in pseudo-geneisation. Here, we investigate the phylogenetic distribution of ultra large gene families on long and short evolutionary time scales. In particular, we focus on a family of NACHT-domain and leucine-rich-repeat-containing (NLR-genes, which we previously found in large numbers to occupy one chromosome arm of the zebrafish genome. We were interested to see whether such a tight clustering is characteristic for ultra large gene families. Our data reconfirm that most gene family inflations are lineage-specific, but we can only identify very few gene clusters. Based on our observations we hypothesise that, beyond a certain size threshold, ultra large gene families continue to proliferate in a mechanism we term “run-away evolution”. This process might ultimately lead to the failure of genomic integrity and drive species to extinction.

  13. [Indoor air pollution by volatile organic compounds in large buildings: pollution levels and remaining issues after revision of the Act on Maintenance of Sanitation in Buildings in 2002].

    Science.gov (United States)

    Sakai, Kiyoshi; Kamijima, Michihiro; Shibata, Eiji; Ohno, Hiroyuki; Nakajima, Tamie

    2010-09-01

    This study aimed to clarify indoor air pollution levels of volatile organic compounds (VOCs), especially 2-ethyl-1-hexanol (2E1H) in large buildings after revising of the Act on Maintenance of Sanitation in Buildings in 2002. We measured indoor air VOC concentrations in 57 (97%) out of a total of 61 large buildings completed within one year in half of the area of Nagoya, Japan, from 2003 through 2007. Airborne concentrations of 13 carbonyl compounds were determined with diffusion samplers and high-performance liquid chromatography, and of the other 32 VOCs with diffusion samplers and gas chromatography with a mass spectrometer. Formaldehyde was detected in all samples of indoor air but the concentrations were lower than the indoor air quality standard value set in Japan (100 microg/m3). Geometric mean concentrations of the other major VOCs, namely toluene, xylene, ethylbenzene, styrene, p-dichlorobenzene and acetaldehyde were also low. 2E1H was found to be one of the predominating VOCs in indoor air of large buildings. A few rooms in a small number of buildings surveyed showed high concentrations of 2E1H, while low concentrations were observed in most rooms of those buildings as well as in other buildings. It was estimated that about 310 buildings had high indoor air pollution levels of 2E1H, with increase during the 5 years from 2003 in Japan. Indoor air pollution levels of VOCs in new large buildings are generally good, although a few rooms in a small number of buildings showed high concentrations in 2E1H, a possible causative chemical in sick building symptoms. Therefore, 2E1H needs particular attention as an important indoor air pollutant.

  14. Interactive effects of fire and large herbivores on web-building spiders.

    Science.gov (United States)

    Foster, C N; Barton, P S; Wood, J T; Lindenmayer, D B

    2015-09-01

    Altered disturbance regimes are a major driver of biodiversity loss worldwide. Maintaining or re-creating natural disturbance regimes is therefore the focus of many conservation programmes. A key challenge, however, is to understand how co-occurring disturbances interact to affect biodiversity. We experimentally tested for the interactive effects of prescribed fire and large macropod herbivores on the web-building spider assemblage of a eucalypt forest understorey and investigated the role of vegetation in mediating these effects using path analysis. Fire had strong negative effects on the density of web-building spiders, which were partly mediated by effects on vegetation structure, while negative effects of large herbivores on web density were not related to changes in vegetation. Fire amplified the effects of large herbivores on spiders, both via vegetation-mediated pathways and by increasing herbivore activity. The importance of vegetation-mediated pathways and fire-herbivore interactions differed for web density and richness and also differed between web types. Our results demonstrate that for some groups of web-building spiders, the effects of co-occurring disturbance drivers may be mostly additive, whereas for other groups, interactions between drivers can amplify disturbance effects. In our study system, the use of prescribed fire in the presence of high densities of herbivores could lead to reduced densities and altered composition of web-building spiders, with potential cascading effects through the arthropod food web. Our study highlights the importance of considering both the independent and interactive effects of disturbances, as well as the mechanisms driving their effects, in the management of disturbance regimes.

  15. A stochastic de novo assembly algorithm for viral-sized genomes obtains correct genomes and builds consensus

    NARCIS (Netherlands)

    Bucur, Doina

    2017-01-01

    A genetic algorithm with stochastic macro mutation operators which merge, split, move, reverse and align DNA contigs on a scaffold is shown to accurately and consistently assemble raw DNA reads from an accurately sequenced single-read library into a contiguous genome. A candidate solution is a

  16. Technical Support Document: Strategies for 50% Energy Savings in Large Office Buildings

    Energy Technology Data Exchange (ETDEWEB)

    Leach, M.; Lobato, C.; Hirsch, A.; Pless, S.; Torcellini, P.

    2010-09-01

    This Technical Support Document (TSD) documents technical analysis that informs design guidance for designing and constructing large office buildings that achieve 50% net site energy savings over baseline buildings defined by minimal compliance with respect to ANSI/ASHRAE/IESNA Standard 90.1-2004. This report also represents a step toward developing a methodology for using energy modeling in the design process to achieve aggressive energy savings targets. This report documents the modeling and analysis methods used to identify design recommendations for six climate zones that capture the range of U.S. climate variability; demonstrates how energy savings change between ASHRAE Standard 90.1-2007 and Standard 90.1-2004 to determine baseline energy use; uses a four-story 'low-rise' prototype to analyze the effect of building aspect ratio on energy use intensity; explores comparisons between baseline and low-energy building energy use for alternate energy metrics (net source energy, energy emissions, and energy cost); and examines the extent to which glass curtain construction limits achieve energy savings by using a 12-story 'high-rise' prototype.

  17. Impact of a Large San Andreas Fault Earthquake on Tall Buildings in Southern California

    Science.gov (United States)

    Krishnan, S.; Ji, C.; Komatitsch, D.; Tromp, J.

    2004-12-01

    In 1857, an earthquake of magnitude 7.9 occurred on the San Andreas fault, starting at Parkfield and rupturing in a southeasterly direction for more than 300~km. Such a unilateral rupture produces significant directivity toward the San Fernando and Los Angeles basins. The strong shaking in the basins due to this earthquake would have had a significant long-period content (2--8~s). If such motions were to happen today, they could have a serious impact on tall buildings in Southern California. In order to study the effects of large San Andreas fault earthquakes on tall buildings in Southern California, we use the finite source of the magnitude 7.9 2001 Denali fault earthquake in Alaska and map it onto the San Andreas fault with the rupture originating at Parkfield and proceeding southward over a distance of 290~km. Using the SPECFEM3D spectral element seismic wave propagation code, we simulate a Denali-like earthquake on the San Andreas fault and compute ground motions at sites located on a grid with a 2.5--5.0~km spacing in the greater Southern California region. We subsequently analyze 3D structural models of an existing tall steel building designed in 1984 as well as one designed according to the current building code (Uniform Building Code, 1997) subjected to the computed ground motion. We use a sophisticated nonlinear building analysis program, FRAME3D, that has the ability to simulate damage in buildings due to three-component ground motion. We summarize the performance of these structural models on contour maps of carefully selected structural performance indices. This study could benefit the city in laying out emergency response strategies in the event of an earthquake on the San Andreas fault, in undertaking appropriate retrofit measures for tall buildings, and in formulating zoning regulations for new construction. In addition, the study would provide risk data associated with existing and new construction to insurance companies, real estate developers, and

  18. Government regulation and associated innovations in building energy-efficiency supervisory systems for large-scale public buildings in a market economy

    International Nuclear Information System (INIS)

    Dai Xuezhi; Wu Yong; Di Yanqiang; Li Qiaoyan

    2009-01-01

    The supervision of energy efficiency in government office buildings and large-scale public buildings is the main embodiment for government implementation of Public Administration in the fields of resource saving and environmental protection. Aimed at improving the current situation of lack of government administration in building energy efficiency, this paper proposes the concept of 'change and redesign of governmental supervision in building energy efficiency', repositioning the role of government supervision. Based on this theory and other related theories in regulation economic and modern management, this paper analyzes and researches the action and function of all level governments in execution of the supervisory system of building energy efficiency in government office buildings and large-scale public buildings. This paper also defines the importance of government supervision in energy-efficiency system. Finally, this paper analyzes and researches the interaction mechanism between government and owners of different type buildings, government and energy-efficiency service institution with gambling as main features. This paper also presents some measurements to achieve a common benefit community in implementation of building energy-efficiency supervisory system.

  19. Government regulation and associated innovations in building energy-efficiency supervisory systems for large-scale public buildings in a market economy

    Energy Technology Data Exchange (ETDEWEB)

    Dai Xuezhi [China Academy of Building Research, Beijing 100013 (China)], E-mail: daixz9999@126.com; Wu Yong [Ministry of Housing and Urban-Rural Development of the People' s Republic of China, Beijing 100835 (China); Di Yanqiang [China Academy of Building Research, Beijing 100013 (China); Li Qiaoyan [Department of Building, School of Design and Environment, National University of Singapore (Singapore)

    2009-06-15

    The supervision of energy efficiency in government office buildings and large-scale public buildings is the main embodiment for government implementation of Public Administration in the fields of resource saving and environmental protection. Aimed at improving the current situation of lack of government administration in building energy efficiency, this paper proposes the concept of 'change and redesign of governmental supervision in building energy efficiency', repositioning the role of government supervision. Based on this theory and other related theories in regulation economic and modern management, this paper analyzes and researches the action and function of all level governments in execution of the supervisory system of building energy efficiency in government office buildings and large-scale public buildings. This paper also defines the importance of government supervision in energy-efficiency system. Finally, this paper analyzes and researches the interaction mechanism between government and owners of different type buildings, government and energy-efficiency service institution with gambling as main features. This paper also presents some measurements to achieve a common benefit community in implementation of building energy-efficiency supervisory system.

  20. Government regulation and associated innovations in building energy-efficiency supervisory systems for large-scale public buildings in a market economy

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Xuezhi; Di, Yanqiang [China Academy of Building Research, Beijing 100013 (China); Wu, Yong [Ministry of Housing and Urban-Rural Development of the People' s Republic of China, Beijing 100835 (China); Li, Qiaoyan [Department of Building, School of Design and Environment, National University of Singapore (Singapore)

    2009-06-15

    The supervision of energy efficiency in government office buildings and large-scale public buildings is the main embodiment for government implementation of Public Administration in the fields of resource saving and environmental protection. Aimed at improving the current situation of lack of government administration in building energy efficiency, this paper proposes the concept of 'change and redesign of governmental supervision in building energy efficiency', repositioning the role of government supervision. Based on this theory and other related theories in regulation economic and modern management, this paper analyzes and researches the action and function of all level governments in execution of the supervisory system of building energy efficiency in government office buildings and large-scale public buildings. This paper also defines the importance of government supervision in energy-efficiency system. Finally, this paper analyzes and researches the interaction mechanism between government and owners of different type buildings, government and energy-efficiency service institution with gambling as main features. This paper also presents some measurements to achieve a common benefit community in implementation of building energy-efficiency supervisory system. (author)

  1. GRAPHICS-IMAGE MIXED METHOD FOR LARGE-SCALE BUILDINGS RENDERING

    Directory of Open Access Journals (Sweden)

    Y. Zhou

    2018-05-01

    Full Text Available Urban 3D model data is huge and unstructured, LOD and Out-of-core algorithm are usually used to reduce the amount of data that drawn in each frame to improve the rendering efficiency. When the scene is large enough, even the complex optimization algorithm is difficult to achieve better results. Based on the traditional study, a novel idea was developed. We propose a graphics and image mixed method for large-scale buildings rendering. Firstly, the view field is divided into several regions, the graphics-image mixed method used to render the scene on both screen and FBO, then blending the FBO with scree. The algorithm is tested on the huge CityGML model data in the urban areas of New York which contained 188195 public building models, and compared with the Cesium platform. The experiment result shows the system was running smoothly. The experimental results confirm that the algorithm can achieve more massive building scene roaming under the same hardware conditions, and can rendering the scene without vision loss.

  2. Segregation distortion causes large-scale differences between male and female genomes in hybrid ants.

    Science.gov (United States)

    Kulmuni, Jonna; Seifert, Bernhard; Pamilo, Pekka

    2010-04-20

    Hybridization in isolated populations can lead either to hybrid breakdown and extinction or in some cases to speciation. The basis of hybrid breakdown lies in genetic incompatibilities between diverged genomes. In social Hymenoptera, the consequences of hybridization can differ from those in other animals because of haplodiploidy and sociality. Selection pressures differ between sexes because males are haploid and females are diploid. Furthermore, sociality and group living may allow survival of hybrid genotypes. We show that hybridization in Formica ants has resulted in a stable situation in which the males form two highly divergent gene pools whereas all the females are hybrids. This causes an exceptional situation with large-scale differences between male and female genomes. The genotype differences indicate strong transmission ratio distortion depending on offspring sex, whereby the mother transmits some alleles exclusively to her daughters and other alleles exclusively to her sons. The genetic differences between the sexes and the apparent lack of multilocus hybrid genotypes in males can be explained by recessive incompatibilities which cause the elimination of hybrid males because of their haploid genome. Alternatively, differentiation between sexes could be created by prezygotic segregation into male-forming and female-forming gametes in diploid females. Differentiation between sexes is stable and maintained throughout generations. The present study shows a unique outcome of hybridization and demonstrates that hybridization has the potential of generating evolutionary novelties in animals.

  3. The gradient boosting algorithm and random boosting for genome-assisted evaluation in large data sets.

    Science.gov (United States)

    González-Recio, O; Jiménez-Montero, J A; Alenda, R

    2013-01-01

    In the next few years, with the advent of high-density single nucleotide polymorphism (SNP) arrays and genome sequencing, genomic evaluation methods will need to deal with a large number of genetic variants and an increasing sample size. The boosting algorithm is a machine-learning technique that may alleviate the drawbacks of dealing with such large data sets. This algorithm combines different predictors in a sequential manner with some shrinkage on them; each predictor is applied consecutively to the residuals from the committee formed by the previous ones to form a final prediction based on a subset of covariates. Here, a detailed description is provided and examples using a toy data set are included. A modification of the algorithm called "random boosting" was proposed to increase predictive ability and decrease computation time of genome-assisted evaluation in large data sets. Random boosting uses a random selection of markers to add a subsequent weak learner to the predictive model. These modifications were applied to a real data set composed of 1,797 bulls genotyped for 39,714 SNP. Deregressed proofs of 4 yield traits and 1 type trait from January 2009 routine evaluations were used as dependent variables. A 2-fold cross-validation scenario was implemented. Sires born before 2005 were used as a training sample (1,576 and 1,562 for production and type traits, respectively), whereas younger sires were used as a testing sample to evaluate predictive ability of the algorithm on yet-to-be-observed phenotypes. Comparison with the original algorithm was provided. The predictive ability of the algorithm was measured as Pearson correlations between observed and predicted responses. Further, estimated bias was computed as the average difference between observed and predicted phenotypes. The results showed that the modification of the original boosting algorithm could be run in 1% of the time used with the original algorithm and with negligible differences in accuracy

  4. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments

    DEFF Research Database (Denmark)

    Mussmann, Marc; Hu, Fen Z.; Richter, Michael

    2007-01-01

    Beggiatoa to overcome non-overlapping availabilities of electron donors and acceptors while gliding between oxic and sulfidic zones. The first look into the genome of these filamentous sulfur-oxidizing bacteria substantially deepens the understanding of their evolution and their contribution to sulfur......Marine sediments are frequently covered by mats of the filamentous Beggiatoa and other large nitrate-storing bacteria that oxidize hydrogen sulfide using either oxygen or nitrate, which they store in intracellular vacuoles. Despite their conspicuous metabolic properties and their biogeochemical...

  5. Functional Genome Mining for Metabolites Encoded by Large Gene Clusters through Heterologous Expression of a Whole-Genome Bacterial Artificial Chromosome Library in Streptomyces spp.

    Science.gov (United States)

    Xu, Min; Wang, Yemin; Zhao, Zhilong; Gao, Guixi; Huang, Sheng-Xiong; Kang, Qianjin; He, Xinyi; Lin, Shuangjun; Pang, Xiuhua; Deng, Zixin

    2016-01-01

    ABSTRACT Genome sequencing projects in the last decade revealed numerous cryptic biosynthetic pathways for unknown secondary metabolites in microbes, revitalizing drug discovery from microbial metabolites by approaches called genome mining. In this work, we developed a heterologous expression and functional screening approach for genome mining from genomic bacterial artificial chromosome (BAC) libraries in Streptomyces spp. We demonstrate mining from a strain of Streptomyces rochei, which is known to produce streptothricins and borrelidin, by expressing its BAC library in the surrogate host Streptomyces lividans SBT5, and screening for antimicrobial activity. In addition to the successful capture of the streptothricin and borrelidin biosynthetic gene clusters, we discovered two novel linear lipopeptides and their corresponding biosynthetic gene cluster, as well as a novel cryptic gene cluster for an unknown antibiotic from S. rochei. This high-throughput functional genome mining approach can be easily applied to other streptomycetes, and it is very suitable for the large-scale screening of genomic BAC libraries for bioactive natural products and the corresponding biosynthetic pathways. IMPORTANCE Microbial genomes encode numerous cryptic biosynthetic gene clusters for unknown small metabolites with potential biological activities. Several genome mining approaches have been developed to activate and bring these cryptic metabolites to biological tests for future drug discovery. Previous sequence-guided procedures relied on bioinformatic analysis to predict potentially interesting biosynthetic gene clusters. In this study, we describe an efficient approach based on heterologous expression and functional screening of a whole-genome library for the mining of bioactive metabolites from Streptomyces. The usefulness of this function-driven approach was demonstrated by the capture of four large biosynthetic gene clusters for metabolites of various chemical types, including

  6. Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study

    DEFF Research Database (Denmark)

    de Vries, Paul S; Sabater-Lleal, Maria; Chasman, Daniel I

    2017-01-01

    An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In...

  7. Techniques for Large-Scale Bacterial Genome Manipulation and Characterization of the Mutants with Respect to In Silico Metabolic Reconstructions.

    Science.gov (United States)

    diCenzo, George C; Finan, Turlough M

    2018-01-01

    The rate at which all genes within a bacterial genome can be identified far exceeds the ability to characterize these genes. To assist in associating genes with cellular functions, a large-scale bacterial genome deletion approach can be employed to rapidly screen tens to thousands of genes for desired phenotypes. Here, we provide a detailed protocol for the generation of deletions of large segments of bacterial genomes that relies on the activity of a site-specific recombinase. In this procedure, two recombinase recognition target sequences are introduced into known positions of a bacterial genome through single cross-over plasmid integration. Subsequent expression of the site-specific recombinase mediates recombination between the two target sequences, resulting in the excision of the intervening region and its loss from the genome. We further illustrate how this deletion system can be readily adapted to function as a large-scale in vivo cloning procedure, in which the region excised from the genome is captured as a replicative plasmid. We next provide a procedure for the metabolic analysis of bacterial large-scale genome deletion mutants using the Biolog Phenotype MicroArray™ system. Finally, a pipeline is described, and a sample Matlab script is provided, for the integration of the obtained data with a draft metabolic reconstruction for the refinement of the reactions and gene-protein-reaction relationships in a metabolic reconstruction.

  8. Building Participation in Large-scale Conservation: Lessons from Belize and Panama

    Directory of Open Access Journals (Sweden)

    Jesse Guite Hastings

    2015-01-01

    Full Text Available Motivated by biogeography and a desire for alignment with the funding priorities of donors, the twenty-first century has seen big international NGOs shifting towards a large-scale conservation approach. This shift has meant that even before stakeholders at the national and local scale are involved, conservation programmes often have their objectives defined and funding allocated. This paper uses the experiences of Conservation International′s Marine Management Area Science (MMAS programme in Belize and Panama to explore how to build participation at the national and local scale while working within the bounds of the current conservation paradigm. Qualitative data about MMAS was gathered through a multi-sited ethnographic research process, utilising document review, direct observation, and semi-structured interviews with 82 informants in Belize, Panama, and the United States of America. Results indicate that while a large-scale approach to conservation disadvantages early national and local stakeholder participation, this effect can be mediated through focusing engagement efforts, paying attention to context, building horizontal and vertical partnerships, and using deliberative processes that promote learning. While explicit consideration of geopolitics and local complexity alongside biogeography in the planning phase of a large-scale conservation programme is ideal, actions taken by programme managers during implementation can still have a substantial impact on conservation outcomes.

  9. Large Eddy Simulation of Unstably Stratified Turbulent Flow over Urban-Like Building Arrays

    Directory of Open Access Journals (Sweden)

    Bobin Wang

    2013-01-01

    Full Text Available Thermal instability induced by solar radiation is the most common condition of urban atmosphere in daytime. Compared to researches under neutral conditions, only a few numerical works studied the unstable urban boundary layer and the effect of buoyancy force is unclear. In this paper, unstably stratified turbulent boundary layer flow over three-dimensional urban-like building arrays with ground heating is simulated. Large eddy simulation is applied to capture main turbulence structures and the effect of buoyancy force on turbulence can be investigated. Lagrangian dynamic subgrid scale model is used for complex flow together with a wall function, taking into account the large pressure gradient near buildings. The numerical model and method are verified with the results measured in wind tunnel experiment. The simulated results satisfy well with the experiment in mean velocity and temperature, as well as turbulent intensities. Mean flow structure inside canopy layer varies with thermal instability, while no large secondary vortex is observed. Turbulent intensities are enhanced, as buoyancy force contributes to the production of turbulent kinetic energy.

  10. Estimating demographic parameters from large-scale population genomic data using Approximate Bayesian Computation

    Directory of Open Access Journals (Sweden)

    Li Sen

    2012-03-01

    Full Text Available Abstract Background The Approximate Bayesian Computation (ABC approach has been used to infer demographic parameters for numerous species, including humans. However, most applications of ABC still use limited amounts of data, from a small number of loci, compared to the large amount of genome-wide population-genetic data which have become available in the last few years. Results We evaluated the performance of the ABC approach for three 'population divergence' models - similar to the 'isolation with migration' model - when the data consists of several hundred thousand SNPs typed for multiple individuals by simulating data from known demographic models. The ABC approach was used to infer demographic parameters of interest and we compared the inferred values to the true parameter values that was used to generate hypothetical "observed" data. For all three case models, the ABC approach inferred most demographic parameters quite well with narrow credible intervals, for example, population divergence times and past population sizes, but some parameters were more difficult to infer, such as population sizes at present and migration rates. We compared the ability of different summary statistics to infer demographic parameters, including haplotype and LD based statistics, and found that the accuracy of the parameter estimates can be improved by combining summary statistics that capture different parts of information in the data. Furthermore, our results suggest that poor choices of prior distributions can in some circumstances be detected using ABC. Finally, increasing the amount of data beyond some hundred loci will substantially improve the accuracy of many parameter estimates using ABC. Conclusions We conclude that the ABC approach can accommodate realistic genome-wide population genetic data, which may be difficult to analyze with full likelihood approaches, and that the ABC can provide accurate and precise inference of demographic parameters from

  11. Potential advantages and disadvantages of sequentially building small nuclear units instead of a large nuclear plant

    International Nuclear Information System (INIS)

    Feretic, D.; Cavlina, N.; Grgic, D.

    2008-01-01

    Renewal of nuclear power programs in countries with modest electricity consumptions and weak electrical grid interconnections has raised the question of optimal nuclear power plants sizes for such countries. The same question would be also valid for isolated or weakly connected regions within a large country. Building large size nuclear power plant could be prevented by technical or financial limits. Research programs have been initiated in the International Atomic Energy Agency and in the USA (within the framework of the Global Nuclear Energy Partnership (GNEP) program) with the aim to inspect under which circumstances small and medium reactors could be the preferred option compared to large nuclear plants. The economy of scale is a clear advantage of large plants. This paper compares, by using probabilistic methods, the net cash flow of large and medium size plants, taking as example a large nuclear plant (around 1200 MW) and four sequentially built smaller plants (300 MW). Potential advantages and disadvantageous of both options have been considered. Main advantages of the sequential construction of several identical small units could be the reduced investor risk and reduced investment costs due to the learning effect. This analysis is a part of studies for the Croatian power generating system development. (orig.)

  12. Dynamic classification system in large-scale supervision of energy efficiency in buildings

    International Nuclear Information System (INIS)

    Kiluk, S.

    2014-01-01

    Highlights: • Rough set approximation of classification improves energy efficiency prediction. • Dynamic features of diagnostic classification allow for its precise prediction. • Indiscernibility in large population enhances identification of process features. • Diagnostic information can be refined by dynamic references to local neighbourhood. • We introduce data exploration validation based on system dynamics and uncertainty. - Abstract: Data mining and knowledge discovery applied to the billing data provide the diagnostic instruments for the evaluation of energy use in buildings connected to a district heating network. To ensure the validity of an algorithm-based classification system, the dynamic properties of a sequence of partitions for consecutive detected events were investigated. The information regarding the dynamic properties of the classification system refers to the similarities between the supervised objects and migrations that originate from the changes in the building energy use and loss similarity to their neighbourhood and thus represents the refinement of knowledge. In this study, we demonstrate that algorithm-based diagnostic knowledge has dynamic properties that can be exploited with a rough set predictor to evaluate whether the implementation of classification for supervision of energy use aligns with the dynamics of changes of district heating-supplied building properties. Moreover, we demonstrate the refinement of the current knowledge with the previous findings and we present the creation of predictive diagnostic systems based on knowledge dynamics with a satisfactory level of classification errors, even for non-stationary data

  13. NAVIGATION IN LARGE-FORMAT BUILDINGS BASED ON RFID SENSORS AND QR AND AR MARKERS

    Directory of Open Access Journals (Sweden)

    Tomasz Szymczyk

    2016-09-01

    Full Text Available The authors address the problem of passive navigation in large buildings. Based on the example of several interconnected buildings housing departments of the Lublin University of Technology, as well as the conceptual navigation system, the paper presents one of the possible ways of leading the user from the entrance of the building to a particular room. An analysis of different types of users is made and different (best for them ways of navigating the intricate corridors are proposed. Three ways of user localisation are suggested: RFID, AR and QR markers. A graph of connections between specific rooms was made and weights proposed, representing “the difficulty of covering a given distance”. In the process of navigation Dijkstra’s algorithm was used. The road is indicated as multimedia information: a voice-over or animated arrow showing the direction displayed on the smart phone screen with proprietary software installed. It is also possible to inform the user of the position of the location in which he currently is, based on the static information stored in the QR code.

  14. Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications.

    Science.gov (United States)

    Christen, Matthias; Del Medico, Luca; Christen, Heinz; Christen, Beat

    2017-01-01

    Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.

  15. Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications.

    Directory of Open Access Journals (Sweden)

    Matthias Christen

    Full Text Available Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.

  16. First Insights into the Large Genome of Epimedium sagittatum (Sieb. et Zucc Maxim, a Chinese Traditional Medicinal Plant

    Directory of Open Access Journals (Sweden)

    Gong Xiao

    2013-06-01

    Full Text Available Epimedium sagittatum (Sieb. et Zucc Maxim is a member of the Berberidaceae family of basal eudicot plants, widely distributed and used as a traditional medicinal plant in China for therapeutic effects on many diseases with a long history. Recent data shows that E. sagittatum has a relatively large genome, with a haploid genome size of ~4496 Mbp, divided into a small number of only 12 diploid chromosomes (2n = 2x = 12. However, little is known about Epimedium genome structure and composition. Here we present the analysis of 691 kb of high-quality genomic sequence derived from 672 randomly selected plasmid clones of E. sagittatum genomic DNA, representing ~0.0154% of the genome. The sampled sequences comprised at least 78.41% repetitive DNA elements and 2.51% confirmed annotated gene sequences, with a total GC% content of 39%. Retrotransposons represented the major class of transposable element (TE repeats identified (65.37% of all TE repeats, particularly LTR (Long Terminal Repeat retrotransposons (52.27% of all TE repeats. Chromosome analysis and Fluorescence in situ Hybridization of Gypsy-Ty3 retrotransposons were performed to survey the E. sagittatum genome at the cytological level. Our data provide the first insights into the composition and structure of the E. sagittatum genome, and will facilitate the functional genomic analysis of this valuable medicinal plant.

  17. First Insights into the Large Genome of Epimedium sagittatum (Sieb. et Zucc) Maxim, a Chinese Traditional Medicinal Plant

    Science.gov (United States)

    Liu, Di; Zeng, Shao-Hua; Chen, Jian-Jun; Zhang, Yan-Jun; Xiao, Gong; Zhu, Lin-Yao; Wang, Ying

    2013-01-01

    Epimedium sagittatum (Sieb. et Zucc) Maxim is a member of the Berberidaceae family of basal eudicot plants, widely distributed and used as a traditional medicinal plant in China for therapeutic effects on many diseases with a long history. Recent data shows that E. sagittatum has a relatively large genome, with a haploid genome size of ~4496 Mbp, divided into a small number of only 12 diploid chromosomes (2n = 2x = 12). However, little is known about Epimedium genome structure and composition. Here we present the analysis of 691 kb of high-quality genomic sequence derived from 672 randomly selected plasmid clones of E. sagittatum genomic DNA, representing ~0.0154% of the genome. The sampled sequences comprised at least 78.41% repetitive DNA elements and 2.51% confirmed annotated gene sequences, with a total GC% content of 39%. Retrotransposons represented the major class of transposable element (TE) repeats identified (65.37% of all TE repeats), particularly LTR (Long Terminal Repeat) retrotransposons (52.27% of all TE repeats). Chromosome analysis and Fluorescence in situ Hybridization of Gypsy-Ty3 retrotransposons were performed to survey the E. sagittatum genome at the cytological level. Our data provide the first insights into the composition and structure of the E. sagittatum genome, and will facilitate the functional genomic analysis of this valuable medicinal plant. PMID:23807511

  18. Large scale rooftop photovoltaics grid connected system at Charoenphol-Rama I green building

    Energy Technology Data Exchange (ETDEWEB)

    Ketjoy, N.; Rakwichian, W. [School of Renewable Energy Technology (SERT) (Thailand); Wongchupan, V. [Panya Consultants Co., Ltd (Thailand); Sankarat, T. [Tesco Lotus, Ek-Chai Distribution System Co., Ltd. (Thailand)

    2004-07-01

    This paper presents a technical feasibility study project for the large scale rooftop photovoltaics (PV) grid connected system at Charoenphol-Rama I green building super store of TESCO LOTUS (TL) in Thailand. The objective of this project is (i) to study the technical feasibility of installation 350 kWp PV systems on the top of the roof in this site (ii) and to determine the energy produce from this system. The technical factors are examined using a computerized PVS 2000 simulation and assessment tool. This super store building located in Bangkok, with latitude 14 N, longitude 100 E and the building direction is 16 from North direction. The building roof area is 14,000 m2; with 3 degree face East and 3 degree face West pitch. Average daily solar energy in this area is approximately 5.0 kWh. The study team for this project consists of educational institution as School of Renewable Energy Technology (SERT) and private institution as Panya Consultants (PC). TL is the project owner, PC is responsible for project management, and SERT is a third party and responsible for PV system study, conceptual design and all technical process. In this feasibility studies SERT will identify the most attractive scenarios of photovoltaic cell technology (mono, poly-crystalline or thin film amorphous), system design concepts for owners (TL) and determine possibility of the energy yield of the system from different module orientation and tilt angle. The result of this study is a guide to help TL to make decision to select proper rooftop PV system option for this store with proper technology view. The economic view will not be considered in this study. (orig.)

  19. PGen: large-scale genomic variations analysis workflow and browser in SoyKB.

    Science.gov (United States)

    Liu, Yang; Khan, Saad M; Wang, Juexin; Rynge, Mats; Zhang, Yuanxun; Zeng, Shuai; Chen, Shiyuan; Maldonado Dos Santos, Joao V; Valliyodan, Babu; Calyam, Prasad P; Merchant, Nirav; Nguyen, Henry T; Xu, Dong; Joshi, Trupti

    2016-10-06

    With the advances in next-generation sequencing (NGS) technology and significant reductions in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scale genetic variations and to apply the knowledge towards improvements in traits. To efficiently facilitate large-scale NGS resequencing data analysis of genomic variations, we have developed "PGen", an integrated and optimized workflow using the Extreme Science and Engineering Discovery Environment (XSEDE) high-performance computing (HPC) virtual system, iPlant cloud data storage resources and Pegasus workflow management system (Pegasus-WMS). The workflow allows users to identify single nucleotide polymorphisms (SNPs) and insertion-deletions (indels), perform SNP annotations and conduct copy number variation analyses on multiple resequencing datasets in a user-friendly and seamless way. We have developed both a Linux version in GitHub ( https://github.com/pegasus-isi/PGen-GenomicVariations-Workflow ) and a web-based implementation of the PGen workflow integrated within the Soybean Knowledge Base (SoyKB), ( http://soykb.org/Pegasus/index.php ). Using PGen, we identified 10,218,140 single-nucleotide polymorphisms (SNPs) and 1,398,982 indels from analysis of 106 soybean lines sequenced at 15X coverage. 297,245 non-synonymous SNPs and 3330 copy number variation (CNV) regions were identified from this analysis. SNPs identified using PGen from additional soybean resequencing projects adding to 500+ soybean germplasm lines in total have been integrated. These SNPs are being utilized for trait improvement using genotype to phenotype prediction approaches developed in-house. In order to browse and access NGS data easily, we have also developed an NGS resequencing data browser ( http://soykb.org/NGS_Resequence/NGS_index.php ) within SoyKB to provide easy access to SNP and downstream analysis results for soybean researchers. PGen workflow has been optimized for the most

  20. Optimization of a hybrid electric power system design for large commercial buildings: An application design guide

    Science.gov (United States)

    Lee, Keun

    with the optimization of the hybrid system design (which consists of PV panels and/or wind turbines and/or storage devices for building applications) by developing an algorithm designed to make the system cost effective and energy efficient. Input data includes electrical load demand profile of the buildings, buildings' structural and geographical characteristics, real time pricing of electricity, and the costs of hybrid systems and storage devices. When the electrical load demand profile of a building that is being studied is available, a measured demand profile is directly used as input data. However, if that information is not available, a building's electric load demand is estimated using a developed algorithm based on three large data sources from a public domain, and used as input data. Using the acquired input data, the algorithm of this research is designed and programmed in order to determine the size of renewable components and to minimize the total yearly net cost. This dissertation also addresses the parametric sensitivity analysis to determine which factors are more significant and are expected to produce useful guidelines in the decision making process. An engineered and more practical, simplified solution has been provided for the optimized design process.

  1. Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core.

    Directory of Open Access Journals (Sweden)

    Rachel A Mann

    Full Text Available The plant pathogen Erwinia amylovora can be divided into two host-specific groupings; strains infecting a broad range of hosts within the Rosaceae subfamily Spiraeoideae (e.g., Malus, Pyrus, Crataegus, Sorbus and strains infecting Rubus (raspberries and blackberries. Comparative genomic analysis of 12 strains representing distinct populations (e.g., geographic, temporal, host origin of E. amylovora was used to describe the pan-genome of this major pathogen. The pan-genome contains 5751 coding sequences and is highly conserved relative to other phytopathogenic bacteria comprising on average 89% conserved, core genes. The chromosomes of Spiraeoideae-infecting strains were highly homogeneous, while greater genetic diversity was observed between Spiraeoideae- and Rubus-infecting strains (and among individual Rubus-infecting strains, the majority of which was attributed to variable genomic islands. Based on genomic distance scores and phylogenetic analysis, the Rubus-infecting strain ATCC BAA-2158 was genetically more closely related to the Spiraeoideae-infecting strains of E. amylovora than it was to the other Rubus-infecting strains. Analysis of the accessory genomes of Spiraeoideae- and Rubus-infecting strains has identified putative host-specific determinants including variation in the effector protein HopX1(Ea and a putative secondary metabolite pathway only present in Rubus-infecting strains.

  2. Towards Building a High Performance Spatial Query System for Large Scale Medical Imaging Data.

    Science.gov (United States)

    Aji, Ablimit; Wang, Fusheng; Saltz, Joel H

    2012-11-06

    Support of high performance queries on large volumes of scientific spatial data is becoming increasingly important in many applications. This growth is driven by not only geospatial problems in numerous fields, but also emerging scientific applications that are increasingly data- and compute-intensive. For example, digital pathology imaging has become an emerging field during the past decade, where examination of high resolution images of human tissue specimens enables more effective diagnosis, prediction and treatment of diseases. Systematic analysis of large-scale pathology images generates tremendous amounts of spatially derived quantifications of micro-anatomic objects, such as nuclei, blood vessels, and tissue regions. Analytical pathology imaging provides high potential to support image based computer aided diagnosis. One major requirement for this is effective querying of such enormous amount of data with fast response, which is faced with two major challenges: the "big data" challenge and the high computation complexity. In this paper, we present our work towards building a high performance spatial query system for querying massive spatial data on MapReduce. Our framework takes an on demand index building approach for processing spatial queries and a partition-merge approach for building parallel spatial query pipelines, which fits nicely with the computing model of MapReduce. We demonstrate our framework on supporting multi-way spatial joins for algorithm evaluation and nearest neighbor queries for microanatomic objects. To reduce query response time, we propose cost based query optimization to mitigate the effect of data skew. Our experiments show that the framework can efficiently support complex analytical spatial queries on MapReduce.

  3. Should we build more large dams? The actual costs of hydropower megaproject development

    International Nuclear Information System (INIS)

    Ansar, Atif; Flyvbjerg, Bent; Budzier, Alexander; Lunn, Daniel

    2014-01-01

    A brisk building boom of hydropower mega-dams is underway from China to Brazil. Whether benefits of new dams will outweigh costs remains unresolved despite contentious debates. We investigate this question with the “outside view” or “reference class forecasting” based on literature on decision-making under uncertainty in psychology. We find overwhelming evidence that budgets are systematically biased below actual costs of large hydropower dams—excluding inflation, substantial debt servicing, environmental, and social costs. Using the largest and most reliable reference data of its kind and multilevel statistical techniques applied to large dams for the first time, we were successful in fitting parsimonious models to predict cost and schedule overruns. The outside view suggests that in most countries large hydropower dams will be too costly in absolute terms and take too long to build to deliver a positive risk-adjusted return unless suitable risk management measures outlined in this paper can be affordably provided. Policymakers, particularly in developing countries, are advised to prefer agile energy alternatives that can be built over shorter time horizons to energy megaprojects. - Highlights: • We investigate ex post outcomes of schedule and cost estimates of hydropower dams. • We use the “outside view” based on Kahneman and Tversky's research in psychology. • Estimates are systematically and severely biased below actual values. • Projects that take longer have greater cost overruns; bigger projects take longer. • Uplift required to de-bias systematic cost underestimation for large dams is +99%

  4. Analysis of impact of large commercial aircraft on a prestressed containment building

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Kyoungsoo, E-mail: kylee@pvamu.edu [Center for Energy and Environmental Sustainability, Prairie View A and M University, Prairie view, TX, 77446 (United States); Han, Sang Eul, E-mail: hsang@inha.ac.kr [Department of Architectural Engineering, School of Architecture, Inha University, 253 Yonghyundong Nam-gu, Incheon, 402-751 (Korea, Republic of); Hong, Jung-Wuk, E-mail: j.hong@kaist.ac.kr [Department of Civil and Environmental Engineering, KAIST, 373-1 Guseon-dong, Yuseong-gu, Daejeon, 305-701 (Korea, Republic of)

    2013-12-15

    Highlights: • Aircraft impact analyses are performed using the missile–target interaction method. • A large commercial B747 aircraft is considered with erosion effect. • The rigid wall impact test shows the validity of the developed aircraft model. • The parametric studies on the fictitious containment building are performed. • The plastic failure of the target is governed by the impulse of aircraft at the first momentum peak. - Abstract: In this paper, the results of nonlinear dynamic analyses of a concrete containment building under extreme loads are presented. The impact of a large commercial B747 airliner is investigated as the extreme load, and a rigid wall impact test is performed using commercial nonlinear finite element codes. The impact forces exerted by the aircraft are verified compared with the time-dependent impact force provided by OECD/NEA (2002), which was calculated based on the so-called Riera method. The rigid wall impact analysis shows that the finite element model of a B747 is appropriate for the purpose of the aircraft crash analysis exposed to the external hazard of “Beyond Design-Basis Events” defined by U.S. Nuclear Regulatory Commission. Finally, the applicability of this methodology is further studied and verified by conducting parametric studies on the critical infrastructures of nuclear power plant containment structures.

  5. Analysis of impact of large commercial aircraft on a prestressed containment building

    International Nuclear Information System (INIS)

    Lee, Kyoungsoo; Han, Sang Eul; Hong, Jung-Wuk

    2013-01-01

    Highlights: • Aircraft impact analyses are performed using the missile–target interaction method. • A large commercial B747 aircraft is considered with erosion effect. • The rigid wall impact test shows the validity of the developed aircraft model. • The parametric studies on the fictitious containment building are performed. • The plastic failure of the target is governed by the impulse of aircraft at the first momentum peak. - Abstract: In this paper, the results of nonlinear dynamic analyses of a concrete containment building under extreme loads are presented. The impact of a large commercial B747 airliner is investigated as the extreme load, and a rigid wall impact test is performed using commercial nonlinear finite element codes. The impact forces exerted by the aircraft are verified compared with the time-dependent impact force provided by OECD/NEA (2002), which was calculated based on the so-called Riera method. The rigid wall impact analysis shows that the finite element model of a B747 is appropriate for the purpose of the aircraft crash analysis exposed to the external hazard of “Beyond Design-Basis Events” defined by U.S. Nuclear Regulatory Commission. Finally, the applicability of this methodology is further studied and verified by conducting parametric studies on the critical infrastructures of nuclear power plant containment structures

  6. Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and Tulipa

    Directory of Open Access Journals (Sweden)

    Shahin Arwa

    2012-11-01

    Full Text Available Abstract Background Bulbous flowers such as lily and tulip (Liliaceae family are monocot perennial herbs that are economically very important ornamental plants worldwide. However, there are hardly any genetic studies performed and genomic resources are lacking. To build genomic resources and develop tools to speed up the breeding in both crops, next generation sequencing was implemented. We sequenced and assembled transcriptomes of four lily and five tulip genotypes using 454 pyro-sequencing technology. Results Successfully, we developed the first set of 81,791 contigs with an average length of 514 bp for tulip, and enriched the very limited number of 3,329 available ESTs (Expressed Sequence Tags for lily with 52,172 contigs with an average length of 555 bp. The contigs together with singletons covered on average 37% of lily and 39% of tulip estimated transcriptome. Mining lily and tulip sequence data for SSRs (Simple Sequence Repeats showed that di-nucleotide repeats were twice more abundant in UTRs (UnTranslated Regions compared to coding regions, while tri-nucleotide repeats were equally spread over coding and UTR regions. Two sets of single nucleotide polymorphism (SNP markers suitable for high throughput genotyping were developed. In the first set, no SNPs flanking the target SNP (50 bp on either side were allowed. In the second set, one SNP in the flanking regions was allowed, which resulted in a 2 to 3 fold increase in SNP marker numbers compared with the first set. Orthologous groups between the two flower bulbs: lily and tulip (12,017 groups and among the three monocot species: lily, tulip, and rice (6,900 groups were determined using OrthoMCL. Orthologous groups were screened for common SNP markers and EST-SSRs to study synteny between lily and tulip, which resulted in 113 common SNP markers and 292 common EST-SSR. Lily and tulip contigs generated were annotated and described according to Gene Ontology terminology. Conclusions

  7. Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and Tulipa.

    Science.gov (United States)

    Shahin, Arwa; van Kaauwen, Martijn; Esselink, Danny; Bargsten, Joachim W; van Tuyl, Jaap M; Visser, Richard G F; Arens, Paul

    2012-11-20

    Bulbous flowers such as lily and tulip (Liliaceae family) are monocot perennial herbs that are economically very important ornamental plants worldwide. However, there are hardly any genetic studies performed and genomic resources are lacking. To build genomic resources and develop tools to speed up the breeding in both crops, next generation sequencing was implemented. We sequenced and assembled transcriptomes of four lily and five tulip genotypes using 454 pyro-sequencing technology. Successfully, we developed the first set of 81,791 contigs with an average length of 514 bp for tulip, and enriched the very limited number of 3,329 available ESTs (Expressed Sequence Tags) for lily with 52,172 contigs with an average length of 555 bp. The contigs together with singletons covered on average 37% of lily and 39% of tulip estimated transcriptome. Mining lily and tulip sequence data for SSRs (Simple Sequence Repeats) showed that di-nucleotide repeats were twice more abundant in UTRs (UnTranslated Regions) compared to coding regions, while tri-nucleotide repeats were equally spread over coding and UTR regions. Two sets of single nucleotide polymorphism (SNP) markers suitable for high throughput genotyping were developed. In the first set, no SNPs flanking the target SNP (50 bp on either side) were allowed. In the second set, one SNP in the flanking regions was allowed, which resulted in a 2 to 3 fold increase in SNP marker numbers compared with the first set. Orthologous groups between the two flower bulbs: lily and tulip (12,017 groups) and among the three monocot species: lily, tulip, and rice (6,900 groups) were determined using OrthoMCL. Orthologous groups were screened for common SNP markers and EST-SSRs to study synteny between lily and tulip, which resulted in 113 common SNP markers and 292 common EST-SSR. Lily and tulip contigs generated were annotated and described according to Gene Ontology terminology. Two transcriptome sets were built that are valuable

  8. SWAP-Assembler 2: Optimization of De Novo Genome Assembler at Large Scale

    Energy Technology Data Exchange (ETDEWEB)

    Meng, Jintao; Seo, Sangmin; Balaji, Pavan; Wei, Yanjie; Wang, Bingqiang; Feng, Shengzhong

    2016-08-16

    In this paper, we analyze and optimize the most time-consuming steps of the SWAP-Assembler, a parallel genome assembler, so that it can scale to a large number of cores for huge genomes with the size of sequencing data ranging from terabyes to petabytes. According to the performance analysis results, the most time-consuming steps are input parallelization, k-mer graph construction, and graph simplification (edge merging). For the input parallelization, the input data is divided into virtual fragments with nearly equal size, and the start position and end position of each fragment are automatically separated at the beginning of the reads. In k-mer graph construction, in order to improve the communication efficiency, the message size is kept constant between any two processes by proportionally increasing the number of nucleotides to the number of processes in the input parallelization step for each round. The memory usage is also decreased because only a small part of the input data is processed in each round. With graph simplification, the communication protocol reduces the number of communication loops from four to two loops and decreases the idle communication time. The optimized assembler is denoted as SWAP-Assembler 2 (SWAP2). In our experiments using a 1000 Genomes project dataset of 4 terabytes (the largest dataset ever used for assembling) on the supercomputer Mira, the results show that SWAP2 scales to 131,072 cores with an efficiency of 40%. We also compared our work with both the HipMER assembler and the SWAP-Assembler. On the Yanhuang dataset of 300 gigabytes, SWAP2 shows a 3X speedup and 4X better scalability compared with the HipMer assembler and is 45 times faster than the SWAP-Assembler. The SWAP2 software is available at https://sourceforge.net/projects/swapassembler.

  9. Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database.

    Science.gov (United States)

    Allard, Marc W; Strain, Errol; Melka, David; Bunning, Kelly; Musser, Steven M; Brown, Eric W; Timme, Ruth

    2016-08-01

    The FDA has created a United States-based open-source whole-genome sequencing network of state, federal, international, and commercial partners. The GenomeTrakr network represents a first-of-its-kind distributed genomic food shield for characterizing and tracing foodborne outbreak pathogens back to their sources. The GenomeTrakr network is leading investigations of outbreaks of foodborne illnesses and compliance actions with more accurate and rapid recalls of contaminated foods as well as more effective monitoring of preventive controls for food manufacturing environments. An expanded network would serve to provide an international rapid surveillance system for pathogen traceback, which is critical to support an effective public health response to bacterial outbreaks. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  10. Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies.

    Science.gov (United States)

    Sharma, Deepak K; Solbrig, Harold R; Tao, Cui; Weng, Chunhua; Chute, Christopher G; Jiang, Guoqian

    2017-06-05

    Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning when data are exchanged between heterogeneous computer systems. To better support clinical cancer data capturing and reporting, there is an emerging need to develop informatics solutions for standards-based clinical models in cancer study domains. The objective of the study is to develop and evaluate a cancer genome study metadata management system that serves as a key infrastructure in supporting clinical information modeling in cancer genome study domains. We leveraged a Semantic Web-based metadata repository enhanced with both ISO11179 metadata standard and Clinical Information Modeling Initiative (CIMI) Reference Model. We used the common data elements (CDEs) defined in The Cancer Genome Atlas (TCGA) data dictionary, and extracted the metadata of the CDEs using the NCI Cancer Data Standards Repository (caDSR) CDE dataset rendered in the Resource Description Framework (RDF). The ITEM/ITEM_GROUP pattern defined in the latest CIMI Reference Model is used to represent reusable model elements (mini-Archetypes). We produced a metadata repository with 38 clinical cancer genome study domains, comprising a rich collection of mini-Archetype pattern instances. We performed a case study of the domain "clinical pharmaceutical" in the TCGA data dictionary and demonstrated enriched data elements in the metadata repository are very useful in support of building detailed clinical models. Our informatics approach leveraging Semantic Web technologies provides an effective way to build a CIMI-compliant metadata repository that would facilitate the detailed clinical modeling to support use cases beyond TCGA in clinical cancer study domains.

  11. Quantitative linkage genome scan for atopy in a large collection of Caucasian families

    DEFF Research Database (Denmark)

    Webb, BT; van den Oord, E; Akkari, A

    2007-01-01

    Quantitative phenotypes correlated with a complex disorder offer increased power to detect linkage in comparison to affected-unaffected classifications. Asthma is a complex disorder characterized by periods of bronchial obstruction and increased bronchial hyper reactivity. In childhood and early...... adulthood, asthma is frequently associated also with quantitative measures of atopy. Genome wide quantitative multipoint linkage analysis was conducted for serum IgE levels and percentage of positive skin prick test (SPT(per)) using three large groups of families originally ascertained for asthma....... In this report, 438 and 429 asthma families were informative for linkage using IgE and SPT(per) which represents 690 independent families. Suggestive linkage (LOD >/= 2) was found on chromosomes 1, 3, and 8q with maximum LODs of 2.34 (IgE), 2.03 (SPT(per)), and 2.25 (IgE) near markers D1S1653, D3S2322-D3S1764...

  12. Software engineering the mixed model for genome-wide association studies on large samples.

    Science.gov (United States)

    Zhang, Zhiwu; Buckler, Edward S; Casstevens, Terry M; Bradbury, Peter J

    2009-11-01

    Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample size and number of markers used for GWAS is increasing dramatically, resulting in greater statistical power to detect those associations. The use of mixed models with increasingly large data sets depends on the availability of software for analyzing those models. While multiple software packages implement the mixed model method, no single package provides the best combination of fast computation, ability to handle large samples, flexible modeling and ease of use. Key elements of association analysis with mixed models are reviewed, including modeling phenotype-genotype associations using mixed models, population stratification, kinship and its estimation, variance component estimation, use of best linear unbiased predictors or residuals in place of raw phenotype, improving efficiency and software-user interaction. The available software packages are evaluated, and suggestions made for future software development.

  13. BUSINESS STRATEGY OF LARGE CONTRACTORS IN ADOPTING INDUSTRIALISED BUILDING SYSTEM (IBS: THE MALAYSIAN CASE

    Directory of Open Access Journals (Sweden)

    FRANKY AMBON

    2012-12-01

    Full Text Available Industrialised Building System (IBS is the term coined by the government and industry in Malaysia to represent the construction industry and the application of prefabrication method in building construction. The purpose of this exploratory research paper is to highlight business strategy being pursued by large Malaysian contractors in adopting IBS. The paper uses case study as research method. The analysis is based primarily on cross-case analysis and pattern matching technique. The paper observes contractors which involved in IBS are part of larger holding companies in a corporate set-up include design and manufacturing subsidiaries. The companies positioned themselves as one-stop total solution provider for IBS and offer a wider range of services from design, production, and installation to clients. To become competitive and able to create total solution, contractors need to establish cluster and consortium of integrated project team by creating a partnership when and where it is needed. A vendor development programme modelled along the lines of the development of automotive industry should also be established. Future empirical studies should extensively examine these areas, especially the development of business model for contractors. The availability of this model could help to accelerate the uptake of IBS among contractors.

  14. Small genomes and large seeds: chromosome numbers, genome size and seed mass in diploid Aesculus species (Sapindaceae)

    Czech Academy of Sciences Publication Activity Database

    Krahulcová, Anna; Trávníček, Pavel; Krahulec, František; Rejmánek, M.

    2017-01-01

    Roč. 119, č. 6 (2017), s. 957-964 ISSN 0305-7364 Institutional support: RVO:67985939 Keywords : Aesculus * chromosome number * genome size * phylogeny * seed mass Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 4.041, year: 2016

  15. Axiomatic design in large systems complex products, buildings and manufacturing systems

    CERN Document Server

    Suh, Nam

    2016-01-01

    This book provides a synthesis of recent developments in Axiomatic Design theory and its application in large complex systems. Introductory chapters provide concise tutorial materials for graduate students and new practitioners, presenting the fundamentals of Axiomatic Design and relating its key concepts to those of model-based systems engineering. A mathematical exposition of design axioms is also provided. The main body of the book, which represents a concentrated treatment of several applications, is divided into three parts covering work on: complex products; buildings; and manufacturing systems. The book shows how design work in these areas can benefit from the scientific and systematic underpinning provided by Axiomatic Design, and in so doing effectively combines the state of the art in design research with practice. All contributions were written by an international group of leading proponents of Axiomatic Design. The book concludes with a call to action motivating further research into the engineeri...

  16. Task Phase Recognition for Highly Mobile Workers in Large Building Complexes

    DEFF Research Database (Denmark)

    Stisen, Allan; Mathisen, Andreas; Krogh, Søren

    2016-01-01

    requirements on the accuracy of the indoor positioning, and thus come with low deployment and maintenance effort in real-world settings. We evaluated the proposed methods in a large hospital complex, where the highly mobile workers were recruited among the non-clinical workforce. The evaluation is based......-scale indoor work environments, namely from a WiFi infrastructure providing coarse grained indoor positioning, from inertial sensors in the workers’ mobile phones, and from a task management system yielding information about the scheduled tasks’ start and end locations. The methods presented have low...... on manually labelled real-world data collected over 4 days of regular work life of the mobile workforce. The collected data yields 83 tasks in total involving 8 different orderlies from a major university hospital with a building area of 160, 000 m2. The results show that the proposed methods can distinguish...

  17. Open-loop groundwater heat pumps development for large buildings. A case study

    Energy Technology Data Exchange (ETDEWEB)

    Lo Russo, Stefano; Civita, Massimo Vincenzo [Politecnico di Torino, Dipartimento di Ingegneria del Territorio, dell' Ambiente e delle Geotecnologie (DITAG), Corso Duca degli Abruzzi, 24 - 10129 Torino (Italy)

    2009-09-15

    A study of the feasibility of providing the heating and cooling needs of the new, large commercial building near Turin, Italy, by means of an open-loop indirect groundwater heat pump (GWHP) system is described. A finite element subsurface flow and transport simulator (FEFLOW) was used to investigate possible configurations of extraction and injection wells for five different scenarios. Modelling results confirmed the hydrogeological capacity of the site to provide the necessary amount of groundwater and associated energy with limited environmental impact. Injection of warmer (or cooler) water in the aquifer creates a thermal plume whose dimensions and geometry depend on the properties of the subsurface formations, particularly their thermal dispersivity values. The study suggests that there are several possible well configurations that could support the GWHP system without adversely affecting the aquifer. (author)

  18. Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes.

    Science.gov (United States)

    Kumar, Ajay; Seetan, Raed; Mergoum, Mohamed; Tiwari, Vijay K; Iqbal, Muhammad J; Wang, Yi; Al-Azzam, Omar; Šimková, Hana; Luo, Ming-Cheng; Dvorak, Jan; Gu, Yong Q; Denton, Anne; Kilian, Andrzej; Lazo, Gerard R; Kianian, Shahryar F

    2015-10-16

    The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence (retention) vs. absence (deletion) marker assay. In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 bi-parental populations, 2) a RH map of the D-genome of reference hexaploid wheat 'Chinese Spring', and 3) two SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical map and draft sequence of the D-genome of Ae. tauschii. A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR) or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609 mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average

  19. 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...

  20. Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.

    KAUST Repository

    Bayer, Till; Aranda, Manuel; Sunagawa, Shinichi; Yum, Lauren K; Desalvo, Michael K; Lindquist, Erika; Coffroth, Mary Alice; Voolstra, Christian R.; Medina, Mó nica

    2012-01-01

    Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance

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

    Science.gov (United States)

    Ishihama, Akira

    2018-01-15

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

  2. Building on the Past, Shaping the Future: The Environmental Mutagenesis and Genomics Society

    Science.gov (United States)

    In late 2012 the members of the Environmental Mutagen Society voted to change its name to the Environmental Mutagenesis and Genomics Society. Here we describe the thought process that led to adoption of the new name, which both respects the rich history of a Society founded in 19...

  3. Analysis Methods for Extracting Knowledge from Large-Scale WiFi Monitoring to Inform Building Facility Planning

    DEFF Research Database (Denmark)

    Ruiz-Ruiz, Antonio; Blunck, Henrik; Prentow, Thor Siiger

    2014-01-01

    realistic data to inform facility planning. In this paper, we propose analysis methods to extract knowledge from large sets of network collected WiFi traces to better inform facility management and planning in large building complexes. The analysis methods, which build on a rich set of temporal and spatial......The optimization of logistics in large building com- plexes with many resources, such as hospitals, require realistic facility management and planning. Current planning practices rely foremost on manual observations or coarse unverified as- sumptions and therefore do not properly scale or provide....... Spatio-temporal visualization tools built on top of these methods enable planners to inspect and explore extracted information to inform facility-planning activities. To evaluate the methods, we present results for a large hospital complex covering more than 10 hectares. The evaluation is based on Wi...

  4. Quantification of fossil fuel CO2 at the building/street level for large US cities

    Science.gov (United States)

    Gurney, K. R.; Razlivanov, I. N.; Song, Y.

    2012-12-01

    Quantification of fossil fuel CO2 emissions from the bottom-up perspective is a critical element in emerging plans on a global, integrated, carbon monitoring system (CMS). A space/time explicit emissions data product can act as both a verification and planning system. It can verify atmospheric CO2 measurements (in situ and remote) and offer detailed mitigation information to management authorities in order to optimize the mix of mitigation efforts. Here, we present the Hestia Project, an effort aimed at building a high resolution (eg. building and road link-specific, hourly) fossil fuel CO2 emissions data product for the urban domain as a pilot effort to a CMS. A complete data product has been built for the city of Indianapolis and preliminary quantification has been completed for Los Angeles and Phoenix (see figure). The effort in Indianapolis is now part of a larger effort aimed at a convergent top-down/bottom-up assessment of greenhouse gas emissions, called INFLUX. Our urban-level quantification relies on a mixture of data and modeling structures. We start with the sector-specific Vulcan Project estimate at the mix of geocoded and county-wide levels. The Hestia aim is to distribute the Vulcan result in space and time. Two components take the majority of effort: buildings and onroad emissions. In collaboration with our INFLUX colleagues, we are transporting these high resolution emissions through an atmospheric transport model for a forward comparison of the Hestia data product with atmospheric measurements, collected on aircraft and cell towers. In preparation for a formal urban-scale inversion, these forward comparisons offer insights into both improving our emissions data product and measurement strategies. A key benefit of the approach taken in this study is the tracking and archiving of fuel and process-level detail (eg. combustion process, other pollutants), allowing for a more thorough understanding and analysis of energy throughputs in the urban

  5. Building large collections of Chinese and English medical terms from semi-structured and encyclopedia websites.

    Science.gov (United States)

    Xu, Yan; Wang, Yining; Sun, Jian-Tao; Zhang, Jianwen; Tsujii, Junichi; Chang, Eric

    2013-01-01

    To build large collections of medical terms from semi-structured information sources (e.g. tables, lists, etc.) and encyclopedia sites on the web. The terms are classified into the three semantic categories, Medical Problems, Medications, and Medical Tests, which were used in i2b2 challenge tasks. We developed two systems, one for Chinese and another for English terms. The two systems share the same methodology and use the same software with minimum language dependent parts. We produced large collections of terms by exploiting billions of semi-structured information sources and encyclopedia sites on the Web. The standard performance metric of recall (R) is extended to three different types of Recall to take the surface variability of terms into consideration. They are Surface Recall (R(S)), Object Recall (R(O)), and Surface Head recall (R(H)). We use two test sets for Chinese. For English, we use a collection of terms in the 2010 i2b2 text. Two collections of terms, one for English and the other for Chinese, have been created. The terms in these collections are classified as either of Medical Problems, Medications, or Medical Tests in the i2b2 challenge tasks. The English collection contains 49,249 (Problems), 89,591 (Medications) and 25,107 (Tests) terms, while the Chinese one contains 66,780 (Problems), 101,025 (Medications), and 15,032 (Tests) terms. The proposed method of constructing a large collection of medical terms is both efficient and effective, and, most of all, independent of language. The collections will be made publicly available.

  6. GIGGLE: a search engine for large-scale integrated genome analysis

    Science.gov (United States)

    Layer, Ryan M; Pedersen, Brent S; DiSera, Tonya; Marth, Gabor T; Gertz, Jason; Quinlan, Aaron R

    2018-01-01

    GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is over three orders of magnitude faster than existing methods. Its speed extends the accessibility and utility of resources such as ENCODE, Roadmap Epigenomics, and GTEx by facilitating data integration and hypothesis generation. PMID:29309061

  7. GIGGLE: a search engine for large-scale integrated genome analysis.

    Science.gov (United States)

    Layer, Ryan M; Pedersen, Brent S; DiSera, Tonya; Marth, Gabor T; Gertz, Jason; Quinlan, Aaron R

    2018-02-01

    GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is over three orders of magnitude faster than existing methods. Its speed extends the accessibility and utility of resources such as ENCODE, Roadmap Epigenomics, and GTEx by facilitating data integration and hypothesis generation.

  8. Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study.

    Directory of Open Access Journals (Sweden)

    Paul S de Vries

    Full Text Available An increasing number of genome-wide association (GWA studies are now using the higher resolution 1000 Genomes Project reference panel (1000G for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G imputation, while 29 loci were associated using both HapMap and 1000G imputation. One locus identified using HapMap imputation was not significant using 1000G imputation. The genome-wide significance threshold of 5×10-8 is based on the number of independent statistical tests using HapMap imputation, and 1000G imputation may lead to further independent tests that should be corrected for. When using a stricter Bonferroni correction for the 1000G GWA study (P-value < 2.5×10-8, the number of loci significant only using HapMap imputation increased to 4 while the number of loci significant only using 1000G decreased to 5. In conclusion, 1000G imputation enabled the identification of 20% more loci than HapMap imputation, although the advantage of 1000G imputation became less clear when a stricter Bonferroni correction was used. More generally, our results provide insights that are applicable to the implementation of other dense reference panels that are under development.

  9. Genomic similarity and kernel methods I: advancements by building on mathematical and statistical foundations.

    Science.gov (United States)

    Schaid, Daniel J

    2010-01-01

    Measures of genomic similarity are the basis of many statistical analytic methods. We review the mathematical and statistical basis of similarity methods, particularly based on kernel methods. A kernel function converts information for a pair of subjects to a quantitative value representing either similarity (larger values meaning more similar) or distance (smaller values meaning more similar), with the requirement that it must create a positive semidefinite matrix when applied to all pairs of subjects. This review emphasizes the wide range of statistical methods and software that can be used when similarity is based on kernel methods, such as nonparametric regression, linear mixed models and generalized linear mixed models, hierarchical models, score statistics, and support vector machines. The mathematical rigor for these methods is summarized, as is the mathematical framework for making kernels. This review provides a framework to move from intuitive and heuristic approaches to define genomic similarities to more rigorous methods that can take advantage of powerful statistical modeling and existing software. A companion paper reviews novel approaches to creating kernels that might be useful for genomic analyses, providing insights with examples [1]. Copyright © 2010 S. Karger AG, Basel.

  10. Conservation genomics of natural and managed populations: building a conceptual and practical framework.

    Science.gov (United States)

    Benestan, Laura Marilyn; Ferchaud, Anne-Laure; Hohenlohe, Paul A; Garner, Brittany A; Naylor, Gavin J P; Baums, Iliana Brigitta; Schwartz, Michael K; Kelley, Joanna L; Luikart, Gordon

    2016-07-01

    The boom of massive parallel sequencing (MPS) technology and its applications in conservation of natural and managed populations brings new opportunities and challenges to meet the scientific questions that can be addressed. Genomic conservation offers a wide range of approaches and analytical techniques, with their respective strengths and weaknesses that rely on several implicit assumptions. However, finding the most suitable approaches and analysis regarding our scientific question are often difficult and time-consuming. To address this gap, a recent workshop entitled 'ConGen 2015' was held at Montana University in order to bring together the knowledge accumulated in this field and to provide training in conceptual and practical aspects of data analysis applied to the field of conservation and evolutionary genomics. Here, we summarize the expertise yield by each instructor that has led us to consider the importance of keeping in mind the scientific question from sampling to management practices along with the selection of appropriate genomics tools and bioinformatics challenges. © 2016 John Wiley & Sons Ltd.

  11. Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families

    NARCIS (Netherlands)

    Seidl, M.F.; Ackerveken, van den G.; Govers, F.; Snel, B.

    2012-01-01

    The taxonomic class of oomycetes contains numerous pathogens of plants and animals but is related to nonpathogenic diatoms and brown algae. Oomycetes have flexible genomes comprising large gene families that play roles in pathogenicity. The evolutionary processes that shaped the gene content have

  12. High proportion of large genomic deletions and a genotype phenotype update in 80 unrelated families with juvenile polyposis syndrome

    DEFF Research Database (Denmark)

    Aretz, S; Stienen, D; Uhlhaas, S

    2007-01-01

    BACKGROUND: In patients with juvenile polyposis syndrome (JPS) the frequency of large genomic deletions in the SMAD4 and BMPR1A genes was unknown. METHODS: Mutation and phenotype analysis was used in 80 unrelated patients of whom 65 met the clinical criteria for JPS (typical JPS) and 15 were susp...

  13. Comparative genome analysis identifies two large deletions in the genome of highly-passaged attenuated Streptococcus agalactiae strain YM001 compared to the parental pathogenic strain HN016.

    Science.gov (United States)

    Wang, Rui; Li, Liping; Huang, Yan; Luo, Fuguang; Liang, Wanwen; Gan, Xi; Huang, Ting; Lei, Aiying; Chen, Ming; Chen, Lianfu

    2015-11-04

    Streptococcus agalactiae (S. agalactiae), also known as group B Streptococcus (GBS), is an important pathogen for neonatal pneumonia, meningitis, bovine mastitis, and fish meningoencephalitis. The global outbreaks of Streptococcus disease in tilapia cause huge economic losses and threaten human food hygiene safety as well. To investigate the mechanism of S. agalactiae pathogenesis in tilapia and develop attenuated S. agalactiae vaccine, this study sequenced and comparatively analyzed the whole genomes of virulent wild-type S. agalactiae strain HN016 and its highly-passaged attenuated strain YM001 derived from tilapia. We performed Illumina sequencing of DNA prepared from strain HN016 and YM001. Sequencedreads were assembled and nucleotide comparisons, single nucleotide polymorphism (SNP) , indels were analyzed between the draft genomes of HN016 and YM001. Clustered regularly interspaced short palindromic repeats (CRISPRs) and prophage were detected and analyzed in different S. agalactiae strains. The genome of S. agalactiae YM001 was 2,047,957 bp with a GC content of 35.61 %; it contained 2044 genes and 88 RNAs. Meanwhile, the genome of S. agalactiae HN016 was 2,064,722 bp with a GC content of 35.66 %; it had 2063 genes and 101 RNAs. Comparative genome analysis indicated that compared with HN016, YM001 genome had two significant large deletions, at the sizes of 5832 and 11,116 bp respectively, resulting in the deletion of three rRNA and ten tRNA genes, as well as the deletion and functional damage of ten genes related to metabolism, transport, growth, anti-stress, etc. Besides these two large deletions, other ten deletions and 28 single nucleotide variations (SNVs) were also identified, mainly affecting the metabolism- and growth-related genes. The genome of attenuated S. agalactiae YM001 showed significant variations, resulting in the deletion of 10 functional genes, compared to the parental pathogenic strain HN016. The deleted and mutated functional genes all

  14. Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines.

    Directory of Open Access Journals (Sweden)

    Mark Eppinger

    2006-07-01

    Full Text Available Helicobacter pylori infection of humans is so old that its population genetic structure reflects that of ancient human migrations. A closely related species, Helicobacter acinonychis, is specific for large felines, including cheetahs, lions, and tigers, whereas hosts more closely related to humans harbor more distantly related Helicobacter species. This observation suggests a jump between host species. But who ate whom and when did it happen? In order to resolve this question, we determined the genomic sequence of H. acinonychis strain Sheeba and compared it to genomes from H. pylori. The conserved core genes between the genomes are so similar that the host jump probably occurred within the last 200,000 (range 50,000-400,000 years. However, the Sheeba genome also possesses unique features that indicate the direction of the host jump, namely from early humans to cats. Sheeba possesses an unusually large number of highly fragmented genes, many encoding outer membrane proteins, which may have been destroyed in order to bypass deleterious responses from the feline host immune system. In addition, the few Sheeba-specific genes that were found include a cluster of genes encoding sialylation of the bacterial cell surface carbohydrates, which were imported by horizontal genetic exchange and might also help to evade host immune defenses. These results provide a genomic basis for elucidating molecular events that allow bacteria to adapt to novel animal hosts.

  15. Measurements of indoor thermal environment and energy analysis in a large space building in typical seasons

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Chen; Zou, Zhijun; Li, Meiling; Wang, Xin; Huang, Wugang; Yang, Jiangang [University of Shanghai for Science and Technology, Shanghai (China); Li, Wei; Xiao, Xueqin [Shanghai International Gymnastics Stadium, Shanghai (China)

    2007-05-15

    Shanghai International Gymnastics Stadium is the selected object for site-measurement. The site-measurements have been carried out during summer, winter, and the transitional seasons. Their indoor thermal environments were controlled by continuous air-conditioning, intermittent air-conditioning and natural ventilation, respectively. The site-measurement includes outdoor environment (the weather conditions and peripheral hallway), indoor air temperature distribution (the occupant zone temperature, radial temperature near upper openings and the vertical temperature distributions, etc.), and the heat balance of air-conditioning system, etc. It is found that temperature stratification in winter with air-conditioning is most obvious. The maximum difference of vertical temperature is 15{sup o}C in winter. The second largest one is 12{sup o}C in summer, and less than 2{sup o}C in the transitional season. The results of measurements indicate that it is different in the characteristics on energy saving of upper openings during the different seasons. With heat balance measurements, it is discovered that the roof load and ventilated and infiltrated load account for larger percentages in terms of cooling and heating load. In this paper, many discussions on the results of site measurements show some characteristics and regulations of indoor thermal environment in large space building. (author)

  16. Electrooptic converter to control linear displacements of the large structures of the buildings and facilities

    Science.gov (United States)

    Vasilev, Aleksandr S.; Konyakhin, Igor A.; Timofeev, Alexander N.; Lashmanov, Oleg U.; Molev, Fedor V.

    2015-05-01

    The paper analyzes the construction matters and metrological parameters of the electrooptic converter to control linear displacements of the large structures of the buildings and facilities. The converter includes the base module, the processing module and a set of the reference marks. The base module is the main unit of the system, it includes the receiving optical system and the CMOS photodetector array that realizes the instrument coordinate system that controls the mark coordinates in the space. The methods of the frame-to-frame difference, adaptive threshold filtration, binarization and objects search by the tied areas to detect the marks against accidental contrast background is the basis of the algorithm. The entire algorithm is performed during one image reading stage and is based on the FPGA. The developed and manufactured converter experimental model was tested in laboratory conditions at the metrological bench at the distance between the base module and the mark 50±0.2 m. The static characteristic was read during the experiment of the reference mark displacement at the pitch of 5 mm in the horizontal and vertical directions for the displacement range 400 mm. The converter experimental model error not exceeding ±0.5 mm was obtained in the result of the experiment.

  17. Environmental assessment for the proposed construction and operation of a Genome Sequencing Facility in Building 64 at Lawrence Berkeley Laboratory, Berkeley, California

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-04-01

    This document is an Environmental Assessment (EA) for a proposed project to modify 14,900 square feet of an existing building (Building 64) at Lawrence Berkeley Laboratory (LBL) to operate as a Genome Sequencing Facility. This EA addresses the potential environmental impacts from the proposed modifications to Building 64 and operation of the Genome Sequencing Facility. The proposed action is to modify Building 64 to provide space and equipment allowing LBL to demonstrate that the Directed DNA Sequencing Strategy can be scaled up from the current level of 750,000 base pairs per year to a facility that produces over 6,000,000 base pairs per year, while still retaining its efficiency.

  18. ENERGY DEMANDS OF THE EXISTING COLLECTIVE BUILDINGS WITH BEARING STRUCTURE OF LARGE PRECAST CONCRETE PANELS FROM TIMISOARA

    Directory of Open Access Journals (Sweden)

    Pescari S.

    2015-05-01

    Full Text Available One of the targets of EU Directives on the energy performance of buildings is to reduce the energy consumption of the existing buildings by finding efficient solutions for thermal rehabilitation. In order to find the adequate solutions, the first step is to establish the current state of the buildings and to determine their actual energy consumption. The current paper aims to present the energy demands of the existing buildings with bearing structure of large precast concrete panels in the city of Timisoara. Timisoara is one of the most important cities in the west side of Romania, being on the third place in terms of size and economic development. The Census of Population and Housing of 2011 states that Timisoara has about 127841 private dwellings and 60 percent of them are collective buildings. Energy demand values of the existing buildings with bearing structure of large precast concrete panels in Timisoara, in their current condition, are higher than the accepted values provided in the Romanian normative, C107. The difference between these two values can reach up to 300 percent.

  19. Large Genomic Deletions in CACNA1A Cause Episodic Ataxia Type 2

    Directory of Open Access Journals (Sweden)

    Jijun eWan

    2011-09-01

    Full Text Available Episodic ataxia (EA syndromes are heritable diseases characterized by dramatic episodes of imbalance and incoordination. Episodic ataxia type 2 (EA2, the most common and the best characterized subtype, is caused by mostly nonsense, splice site, small indel and sometimes missense mutations in CACNA1A. Direct sequencing of CACNA1A fails to identify mutations in some patients with EA2-like features, possibly due to incomplete interrogation of CACNA1A or defects in other EA genes not yet defined. Previous reports described genomic deletions between 4-40kb in EA2. In 47 subjects with EA (26 with EA2-like features who tested negative for mutations in the known EA genes, we used Multiplex Ligation-dependent Probe Amplification (MLPA to analyze CACNA1A for exonic copy number variations. Breakpoints were further defined by long-range PCR. We identified distinct multi-exonic deletions in three probands with classic EA2-like features: episodes of prolonged vertigo and ataxia triggered by stress and fatigue, interictal nystagmus, with onset during infancy or early childhood. The breakpoints in all three probands are located in Alu sequences, indicating errors in homologous recombination of Alu sequences as the underlying mechanism. The smallest deletion spanned exons 39 and 40, while the largest deletion spanned 200kb, missing all but the first three exons. One deletion involving exons 39 through 47 arose spontaneously. The search for mutations in CACNA1A appears most fruitful in EA patients with interictal nystagmus and onset early in life. The finding of large heterozygous deletions suggests haploinsufficiency as a possible pathomechanism of EA2.

  20. Selection for Unequal Densities of Sigma70 Promoter-like Signalsin Different Regions of Large Bacterial Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Huerta, Araceli M.; Francino, M. Pilar; Morett, Enrique; Collado-Vides, Julio

    2006-03-01

    distribution of promoter-like signals between regulatory and nonregulatory regions detected in large bacterial genomes confers a significant, although small, fitness advantage. This study paves the way for further identification of the specific types of selective constraints that affect the organization of regulatory regions and the overall distribution of promoter-like signals through more detailed comparative analyses among closely-related bacterial genomes.

  1. Genomic Selection Using Extreme Phenotypes and Pre-Selection of SNPs in Large Yellow Croaker (Larimichthys crocea).

    Science.gov (United States)

    Dong, Linsong; Xiao, Shijun; Chen, Junwei; Wan, Liang; Wang, Zhiyong

    2016-10-01

    Genomic selection (GS) is an effective method to improve predictive accuracies of genetic values. However, high cost in genotyping will limit the application of this technology in some species. Therefore, it is necessary to find some methods to reduce the genotyping costs in genomic selection. Large yellow croaker is one of the most commercially important marine fish species in southeast China and Eastern Asia. In this study, genotyping-by-sequencing was used to construct the libraries for the NGS sequencing and find 29,748 SNPs in the genome. Two traits, eviscerated weight (EW) and the ratio between eviscerated weight and whole body weight (REW), were chosen to study. Two strategies to reduce the costs were proposed as follows: selecting extreme phenotypes (EP) for genotyping in reference population or pre-selecting SNPs to construct low-density marker panels in candidates. Three methods of pre-selection of SNPs, i.e., pre-selecting SNPs by absolute effects (SE), by single marker analysis (SMA), and by fixed intervals of sequence number (EL), were studied. The results showed that using EP was a feasible method to save the genotyping costs in reference population. Heritability did not seem to have obvious influences on the predictive abilities estimated by EP. Using SMA was the most feasible method to save the genotyping costs in candidates. In addition, the combination of EP and SMA in genomic selection also showed good results, especially for trait of REW. We also described how to apply the new methods in genomic selection and compared the genotyping costs before and after using the new methods. Our study may not only offer a reference for aquatic genomic breeding but also offer a reference for genomic prediction in other species including livestock and plants, etc.

  2. CFD analysis of natural ventilation in large semi-enclosed buildings - case study: Amsterdam ArenA football stadium

    NARCIS (Netherlands)

    Hooff, van T.A.J.; Blocken, B.J.E.; Strachan, P.A.; Kelly, N.J.; Kummert, M.

    2009-01-01

    Large modern sports stadia are often multifunctional buildings that are not only used for sports purposes but also for other events such as concerts, conferences and festivities. Some of the stadia that have been built in recent years in north-western Europe are equipped with a semi-transparent roof

  3. An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus

    Directory of Open Access Journals (Sweden)

    Lemieux Claude

    2007-05-01

    Full Text Available Abstract Background The Streptophyta comprises all land plants and six groups of charophycean green algae. The scaly biflagellate Mesostigma viride (Mesostigmatales and the sarcinoid Chlorokybus atmophyticus (Chlorokybales represent the earliest diverging lineages of this phylum. In trees based on chloroplast genome data, these two charophycean green algae are nested in the same clade. To validate this relationship and gain insight into the ancestral state of the mitochondrial genome in the Charophyceae, we sequenced the mitochondrial DNA (mtDNA of Chlorokybus and compared this genome sequence with those of three other charophycean green algae and the bryophytes Marchantia polymorpha and Physcomitrella patens. Results The Chlorokybus genome differs radically from its 42,424-bp Mesostigma counterpart in size, gene order, intron content and density of repeated elements. At 201,763-bp, it is the largest mtDNA yet reported for a green alga. The 70 conserved genes represent 41.4% of the genome sequence and include nad10 and trnL(gag, two genes reported for the first time in a streptophyte mtDNA. At the gene order level, the Chlorokybus genome shares with its Chara, Chaetosphaeridium and bryophyte homologues eight to ten gene clusters including about 20 genes. Notably, some of these clusters exhibit gene linkages not previously found outside the Streptophyta, suggesting that they originated early during streptophyte evolution. In addition to six group I and 14 group II introns, short repeated sequences accounting for 7.5% of the genome were identified. Mitochondrial trees were unable to resolve the correct position of Mesostigma, due to analytical problems arising from accelerated sequence evolution in this lineage. Conclusion The Chlorokybus and Mesostigma mtDNAs exemplify the marked fluidity of the mitochondrial genome in charophycean green algae. The notion that the mitochondrial genome was constrained to remain compact during charophycean

  4. Demand Shifting With Thermal Mass in Large Commercial Buildings:Field Tests, Simulation and Audits

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Peng; Haves, Philip; Piette, Mary Ann; Zagreus, Leah

    2005-09-01

    The principle of pre-cooling and demand limiting is to pre-cool buildings at night or in the morning during off-peak hours, storing cooling in the building thermal mass and thereby reducing cooling loads and reducing or shedding related electrical demand during the peak periods. Cost savings are achieved by reducing on-peak energy and demand charges. The potential for utilizing building thermal mass for load shifting and peak demand reduction has been demonstrated in a number of simulation, laboratory, and field studies (Braun 1990, Ruud et al. 1990, Conniff 1991, Andresen and Brandemuehl 1992, Mahajan et al. 1993, Morris et al. 1994, Keeney and Braun 1997, Becker and Paciuk 2002, Xu et al. 2003). This technology appears to have significant potential for demand reduction if applied within an overall demand response program. The primary goal associated with this research is to develop information and tools necessary to assess the viability of and, where appropriate, implement demand response programs involving building thermal mass in buildings throughout California. The project involves evaluating the technology readiness, overall demand reduction potential, and customer acceptance for different classes of buildings. This information can be used along with estimates of the impact of the strategies on energy use to design appropriate incentives for customers.

  5. Government management and implementation of national real-time energy monitoring system for China large-scale public building

    International Nuclear Information System (INIS)

    Na Wei; Wu Yong; Song Yan; Dong Zhongcheng

    2009-01-01

    The supervision of energy efficiency in government office buildings and large-scale public buildings (GOBLPB) is the main embodiment for government implementation of Public Administration in the fields of resource saving and environmental protection. It is significant for China government to achieve the target: reducing building energy consumption by 11 million ton standard coal before 2010. In the framework of a national demonstration project concerning the energy management system, Shenzhen Municipality has been selected for the implementation of the system. A data acquisition system and a methodology concerning the energy consumption of the GOBLPB have been developed. This paper summarizes the various features of the system incorporated into identifying the building consumes and energy saving potential. This paper also defines the methods to achieve the real-time monitoring and diagnosis: the meters installed at each building, the data transmitted through internet to a center server, the analysis and unification at the center server and the publication through web. Furthermore, this paper introduces the plans to implement the system and to extend countrywide. Finally, this paper presents some measurements to achieve a common benefit community in implementation of building energy efficiency supervisory system on GOBLPB in its construction, reconstruction or operation stages.

  6. Merlin: Computer-Aided Oligonucleotide Design for Large Scale Genome Engineering with MAGE.

    Science.gov (United States)

    Quintin, Michael; Ma, Natalie J; Ahmed, Samir; Bhatia, Swapnil; Lewis, Aaron; Isaacs, Farren J; Densmore, Douglas

    2016-06-17

    Genome engineering technologies now enable precise manipulation of organism genotype, but can be limited in scalability by their design requirements. Here we describe Merlin ( http://merlincad.org ), an open-source web-based tool to assist biologists in designing experiments using multiplex automated genome engineering (MAGE). Merlin provides methods to generate pools of single-stranded DNA oligonucleotides (oligos) for MAGE experiments by performing free energy calculation and BLAST scoring on a sliding window spanning the targeted site. These oligos are designed not only to improve recombination efficiency, but also to minimize off-target interactions. The application further assists experiment planning by reporting predicted allelic replacement rates after multiple MAGE cycles, and enables rapid result validation by generating primer sequences for multiplexed allele-specific colony PCR. Here we describe the Merlin oligo and primer design procedures and validate their functionality compared to OptMAGE by eliminating seven AvrII restriction sites from the Escherichia coli genome.

  7. Large Scale Sequencing of Dothideomycetes Provides Insights into Genome Evolution and Adaptation

    Energy Technology Data Exchange (ETDEWEB)

    Haridas, Sajeet; Crous, Pedro; Binder, Manfred; Spatafora, Joseph; Grigoriev, Igor

    2015-03-16

    Dothideomycetes is the largest and most diverse class of ascomycete fungi with 23 orders 110 families, 1300 genera and over 19,000 known species. We present comparative analysis of 70 Dothideomycete genomes including over 50 that we sequenced and are as yet unpublished. This extensive sampling has almost quadrupled the previous study of 18 species and uncovered a 10 fold range of genome sizes. We were able to clarify the phylogenetic positions of several species whose origins were unclear in previous morphological and sequence comparison studies. We analyzed selected gene families including proteases, transporters and small secreted proteins and show that major differences in gene content is influenced by speciation.

  8. Large scale analysis of small repeats via mining of the human genome

    NARCIS (Netherlands)

    van den Berg, I.; Bosnacki, D.; Hilbers, P.A.J.

    2009-01-01

    Small repetitive sequences, called tandem repeats, are abundant throughout the human genome, both in coding and in non-coding regions. Their role is still mostly unknown, but at least 20 of those repetitive sequences have been related to neurodegenerative disorders. The mutational process that is

  9. Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species.

    Science.gov (United States)

    Kim, Jae-Heup; Antunes, Agostinho; Luo, Shu-Jin; Menninger, Joan; Nash, William G; O'Brien, Stephen J; Johnson, Warren E

    2006-02-01

    Translocation of cymtDNA into the nuclear genome, also referred to as numt, has been reported in many species, including several closely related to the domestic cat (Felis catus). We describe the recent transposition of 12,536 bp of the 17 kb mitochondrial genome into the nucleus of the common ancestor of the five Panthera genus species: tiger, P. tigris; snow leopard, P. uncia; jaguar, P. onca; leopard, P. pardus; and lion, P. leo. This nuclear integration, representing 74% of the mitochondrial genome, is one of the largest to be reported in eukaryotes. The Panthera genus numt differs from the numt previously described in the Felis genus in: (1) chromosomal location (F2-telomeric region vs. D2-centromeric region), (2) gene make up (from the ND5 to the ATP8 vs. from the CR to the COII), (3) size (12.5 vs. 7.9 kb), and (4) structure (single monomer vs. tandemly repeated in Felis). These distinctions indicate that the origin of this large numt fragment in the nuclear genome of the Panthera species is an independent insertion from that of the domestic cat lineage, which has been further supported by phylogenetic analyses. The tiger cymtDNA shared around 90% sequence identity with the homologous numt sequence, suggesting an origin for the Panthera numt at around 3.5 million years ago, prior to the radiation of the five extant Panthera species.

  10. Multi-objective and multidisciplinary design optimization of large sports building envelopes : A case study

    NARCIS (Netherlands)

    Yang, D.; Sun, Y.; Turrin, M.; von Buelow, P.; Paul, J.C.

    2015-01-01

    Currently, in the conceptual envelope design of sports facilities, multiple engineering performance feedbacks (e.g. daylight, energy and structural performance) are expected to assist architectural design decision-making. In general, it is known as Building Performance Optimization in the conceptual

  11. Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.

    KAUST Repository

    Bayer, Till

    2012-04-18

    Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance, little is known about the genetics of dinoflagellates in general and Symbiodinium in particular. Here, we used 454 sequencing to generate transcriptome data from two Symbiodinium species from different clades (clade A and clade B). With more than 56,000 assembled sequences per species, these data represent the largest transcriptomic resource for dinoflagellates to date. Our results corroborate previous observations that dinoflagellates possess the complete nucleosome machinery. We found a complete set of core histones as well as several H3 variants and H2A.Z in one species. Furthermore, transcriptome analysis points toward a low number of transcription factors in Symbiodinium spp. that also differ in the distribution of DNA-binding domains relative to other eukaryotes. In particular the cold shock domain was predominant among transcription factors. Additionally, we found a high number of antioxidative genes in comparison to non-symbiotic but evolutionary related organisms. These findings might be of relevance in the context of the role that Symbiodinium spp. play as coral symbionts.Our data represent the most comprehensive dinoflagellate EST data set to date. This study provides a comprehensive resource to further analyze the genetic makeup, metabolic capacities, and gene repertoire of Symbiodinium and dinoflagellates. Overall, our findings indicate that Symbiodinium possesses some unique characteristics, in particular the transcriptional regulation in Symbiodinium may differ from the currently known mechanisms of eukaryotic gene regulation.

  12. Research Guidelines in the Era of Large-scale Collaborations: An Analysis of Genome-wide Association Study Consortia

    Science.gov (United States)

    Austin, Melissa A.; Hair, Marilyn S.; Fullerton, Stephanie M.

    2012-01-01

    Scientific research has shifted from studies conducted by single investigators to the creation of large consortia. Genetic epidemiologists, for example, now collaborate extensively for genome-wide association studies (GWAS). The effect has been a stream of confirmed disease-gene associations. However, effects on human subjects oversight, data-sharing, publication and authorship practices, research organization and productivity, and intellectual property remain to be examined. The aim of this analysis was to identify all research consortia that had published the results of a GWAS analysis since 2005, characterize them, determine which have publicly accessible guidelines for research practices, and summarize the policies in these guidelines. A review of the National Human Genome Research Institute’s Catalog of Published Genome-Wide Association Studies identified 55 GWAS consortia as of April 1, 2011. These consortia were comprised of individual investigators, research centers, studies, or other consortia and studied 48 different diseases or traits. Only 14 (25%) were found to have publicly accessible research guidelines on consortia websites. The available guidelines provide information on organization, governance, and research protocols; half address institutional review board approval. Details of publication, authorship, data-sharing, and intellectual property vary considerably. Wider access to consortia guidelines is needed to establish appropriate research standards with broad applicability to emerging forms of large-scale collaboration. PMID:22491085

  13. Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed.

    Science.gov (United States)

    Schiavo, G; Galimberti, G; Calò, D G; Samorè, A B; Bertolini, F; Russo, V; Gallo, M; Buttazzoni, L; Fontanesi, L

    2016-04-01

    In this study, we investigated at the genome-wide level if 20 years of artificial directional selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n = 192), born from 1992 (the beginning of the selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni  selection program. The obtained results indicated that the genome of the Italian Large White pigs was shaped by a directional selection program derived by the application of methodologies assuming the infinitesimal model that captured a continuous trend of allele frequency changes in the boar population. © 2015 Stichting International Foundation for Animal Genetics.

  14. Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island

    Directory of Open Access Journals (Sweden)

    Bonten Marc JM

    2010-04-01

    Full Text Available Abstract Background The Gram-positive bacterium Enterococcus faecium is an important cause of nosocomial infections in immunocompromized patients. Results We present a pyrosequencing-based comparative genome analysis of seven E. faecium strains that were isolated from various sources. In the genomes of clinical isolates several antibiotic resistance genes were identified, including the vanA transposon that confers resistance to vancomycin in two strains. A functional comparison between E. faecium and the related opportunistic pathogen E. faecalis based on differences in the presence of protein families, revealed divergence in plant carbohydrate metabolic pathways and oxidative stress defense mechanisms. The E. faecium pan-genome was estimated to be essentially unlimited in size, indicating that E. faecium can efficiently acquire and incorporate exogenous DNA in its gene pool. One of the most prominent sources of genomic diversity consists of bacteriophages that have integrated in the genome. The CRISPR-Cas system, which contributes to immunity against bacteriophage infection in prokaryotes, is not present in the sequenced strains. Three sequenced isolates carry the esp gene, which is involved in urinary tract infections and biofilm formation. The esp gene is located on a large pathogenicity island (PAI, which is between 64 and 104 kb in size. Conjugation experiments showed that the entire esp PAI can be transferred horizontally and inserts in a site-specific manner. Conclusions Genes involved in environmental persistence, colonization and virulence can easily be aquired by E. faecium. This will make the development of successful treatment strategies targeted against this organism a challenge for years to come.

  15. Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome.

    Directory of Open Access Journals (Sweden)

    Tim van Opijnen

    2016-09-01

    Full Text Available The interaction between an antibiotic and bacterium is not merely restricted to the drug and its direct target, rather antibiotic induced stress seems to resonate through the bacterium, creating selective pressures that drive the emergence of adaptive mutations not only in the direct target, but in genes involved in many different fundamental processes as well. Surprisingly, it has been shown that adaptive mutations do not necessarily have the same effect in all species, indicating that the genetic background influences how phenotypes are manifested. However, to what extent the genetic background affects the manner in which a bacterium experiences antibiotic stress, and how this stress is processed is unclear. Here we employ the genome-wide tool Tn-Seq to construct daptomycin-sensitivity profiles for two strains of the bacterial pathogen Streptococcus pneumoniae. Remarkably, over half of the genes that are important for dealing with antibiotic-induced stress in one strain are dispensable in another. By confirming over 100 genotype-phenotype relationships, probing potassium-loss, employing genetic interaction mapping as well as temporal gene-expression experiments we reveal genome-wide conditionally important/essential genes, we discover roles for genes with unknown function, and uncover parts of the antibiotic's mode-of-action. Moreover, by mapping the underlying genomic network for two query genes we encounter little conservation in network connectivity between strains as well as profound differences in regulatory relationships. Our approach uniquely enables genome-wide fitness comparisons across strains, facilitating the discovery that antibiotic responses are complex events that can vary widely between strains, which suggests that in some cases the emergence of resistance could be strain specific and at least for species with a large pan-genome less predictable.

  16. Building local capacity for genomics research in Africa: recommendations from analysis of publications in Sub-Saharan Africa from 2004 to 2013.

    Science.gov (United States)

    Adedokun, Babatunde O; Olopade, Christopher O; Olopade, Olufunmilayo I

    2016-01-01

    The poor genomics research capacity of Sub-Saharan Africa (SSA) could prevent maximal benefits from the applications of genomics in the practice of medicine and research. The objective of this study is to examine the author affiliations of genomic epidemiology publications in order to make recommendations for building local genomics research capacity in SSA. SSA genomic epidemiology articles published between 2004 and 2013 were extracted from the Human Genome Epidemiology (HuGE) database. Data on authorship details, country of population studied, and phenotype or disease were extracted. Factors associated with the first author, who has an SSA institution affiliation (AIAFA), were determined using a Chi-square test and multiple logistic regression analysis. The most commonly studied population was South Africa, accounting for 31.1%, followed by Ghana (10.6%) and Kenya (7.5%). About one-tenth of the papers were related to non-communicable diseases (NCDs) such as cancer (6.1%) and cardiovascular diseases (CVDs) (4.3%). Fewer than half of the first authors (46.9%) were affiliated with an African institution. Among the 238 articles with an African first author, over three-quarters (79.8%) belonged to a university or medical school, 16.8% were affiliated with a research institute, and 3.4% had affiliations with other institutions. Significant disparities currently exist among SSA countries in genomics research capacity. South Africa has the highest genomics research output, which is reflected in the investments made in its genomics and biotechnology sector. These findings underscore the need to focus on developing local capacity, especially among those affiliated with SSA universities where there are more opportunities for teaching and research.

  17. Multiple recent horizontal transfers of a large genomic region in cheese making fungi.

    Science.gov (United States)

    Cheeseman, Kevin; Ropars, Jeanne; Renault, Pierre; Dupont, Joëlle; Gouzy, Jérôme; Branca, Antoine; Abraham, Anne-Laure; Ceppi, Maurizio; Conseiller, Emmanuel; Debuchy, Robert; Malagnac, Fabienne; Goarin, Anne; Silar, Philippe; Lacoste, Sandrine; Sallet, Erika; Bensimon, Aaron; Giraud, Tatiana; Brygoo, Yves

    2014-01-01

    While the extent and impact of horizontal transfers in prokaryotes are widely acknowledged, their importance to the eukaryotic kingdom is unclear and thought by many to be anecdotal. Here we report multiple recent transfers of a huge genomic island between Penicillium spp. found in the food environment. Sequencing of the two leading filamentous fungi used in cheese making, P. roqueforti and P. camemberti, and comparison with the penicillin producer P. rubens reveals a 575 kb long genomic island in P. roqueforti--called Wallaby--present as identical fragments at non-homologous loci in P. camemberti and P. rubens. Wallaby is detected in Penicillium collections exclusively in strains from food environments. Wallaby encompasses about 250 predicted genes, some of which are probably involved in competition with microorganisms. The occurrence of multiple recent eukaryotic transfers in the food environment provides strong evidence for the importance of this understudied and probably underestimated phenomenon in eukaryotes.

  18. Computed versus measured response of HDR reactor building in large scale shaking tests

    International Nuclear Information System (INIS)

    Werkle, H.; Waas, G.

    1987-01-01

    The earthquake resistant design of NPP structures and their installations is commonly based on linear analysis methods. Nonlinear effects, which may occur during strong earthquakes, are approximately accounted for in the analysis by adjusting the structural damping values. Experimental investigations of nonlinear effects were performed with an extremely heavy shaker at the decommissioned HDR reactor building in West Germany. The tests were directed by KfK (Nuclear Research Center Karlsruhe, West Germany) and supported by several companies and institutes from West Germany, Switzerland and the USA. The objective was the dynamic repsonse behaviour of the structure, piping and components to strong earthquake-like shaking including nonlinear effects. This paper presents some results of safety analyses and measurements, which were performed prior and during the test series. It was intended to shake the building up to a level where only a marginal safety against global structural failure was left

  19. Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae.

    OpenAIRE

    Enyenihi, Akon H; Saunders, William S

    2003-01-01

    We have used a single-gene deletion mutant bank to identify the genes required for meiosis and sporulation among 4323 nonessential Saccharomyces cerevisiae annotated open reading frames (ORFs). Three hundred thirty-four sporulation-essential genes were identified, including 78 novel ORFs and 115 known genes without previously described sporulation defects in the comprehensive Saccharomyces Genome (SGD) or Yeast Proteome (YPD) phenotype databases. We have further divided the uncharacterized sp...

  20. Building Capacity: Challenges and Opportunities in Large Class Pedagogy (LCP) in Sub-Saharan Africa

    Science.gov (United States)

    Foley, Alan R.; Masingila, Joanna O.

    2014-01-01

    Over the past 20 years most countries, particularly developing countries, have seen a large increase in the number of students seeking higher education. A consequence of this growth is increasing pressure on teaching staff and institutions, usually resulting in, among other effects, increased class size. Large classes of between 300 and 1,000, and…

  1. Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence

    Directory of Open Access Journals (Sweden)

    Edgar E. Lara-Ramírez

    2014-01-01

    Full Text Available The increasing number of dengue virus (DENV genome sequences available allows identifying the contributing factors to DENV evolution. In the present study, the codon usage in serotypes 1–4 (DENV1–4 has been explored for 3047 sequenced genomes using different statistics methods. The correlation analysis of total GC content (GC with GC content at the three nucleotide positions of codons (GC1, GC2, and GC3 as well as the effective number of codons (ENC, ENCp versus GC3 plots revealed mutational bias and purifying selection pressures as the major forces influencing the codon usage, but with distinct pressure on specific nucleotide position in the codon. The correspondence analysis (CA and clustering analysis on relative synonymous codon usage (RSCU within each serotype showed similar clustering patterns to the phylogenetic analysis of nucleotide sequences for DENV1–4. These clustering patterns are strongly related to the virus geographic origin. The phylogenetic dependence analysis also suggests that stabilizing selection acts on the codon usage bias. Our analysis of a large scale reveals new feature on DENV genomic evolution.

  2. Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence

    Science.gov (United States)

    Lara-Ramírez, Edgar E.; Salazar, Ma Isabel; López-López, María de Jesús; Salas-Benito, Juan Santiago; Sánchez-Varela, Alejandro

    2014-01-01

    The increasing number of dengue virus (DENV) genome sequences available allows identifying the contributing factors to DENV evolution. In the present study, the codon usage in serotypes 1–4 (DENV1–4) has been explored for 3047 sequenced genomes using different statistics methods. The correlation analysis of total GC content (GC) with GC content at the three nucleotide positions of codons (GC1, GC2, and GC3) as well as the effective number of codons (ENC, ENCp) versus GC3 plots revealed mutational bias and purifying selection pressures as the major forces influencing the codon usage, but with distinct pressure on specific nucleotide position in the codon. The correspondence analysis (CA) and clustering analysis on relative synonymous codon usage (RSCU) within each serotype showed similar clustering patterns to the phylogenetic analysis of nucleotide sequences for DENV1–4. These clustering patterns are strongly related to the virus geographic origin. The phylogenetic dependence analysis also suggests that stabilizing selection acts on the codon usage bias. Our analysis of a large scale reveals new feature on DENV genomic evolution. PMID:25136631

  3. A novel common large genomic deletion and two new missense mutations identified in the Romanian phenylketonuria population.

    Science.gov (United States)

    Gemperle-Britschgi, Corinne; Iorgulescu, Daniela; Mager, Monica Alina; Anton-Paduraru, Dana; Vulturar, Romana; Thöny, Beat

    2016-01-15

    The mutation spectrum for the phenylalanine hydroxylase (PAH) gene was investigated in a cohort of 84 hyperphenylalaninemia (HPA) patients from Romania identified through newborn screening or neurometabolic investigations. Differential diagnosis identified 81 patients with classic PAH deficiency while 3 had tetrahydropterin-cofactor deficiency and/or remained uncertain due to insufficient specimen. PAH-genetic analysis included a combination of Sanger sequencing of exons and exon–intron boundaries, MLPA and NGS with genomic DNA, and cDNA analysis from immortalized lymphoblasts. A diagnostic efficiency of 99.4% was achieved, as for one allele (out of a total of 162 alleles) no mutation could be identified. The most prevalent mutation was p.Arg408Trp which was found in ~ 38% of all PKU alleles. Three novel mutations were identified, including the two missense mutations p.Gln226Lys and p.Tyr268Cys that were both disease causing by prediction algorithms, and the large genomic deletion EX6del7831 (c.509 + 4140_706 + 510del7831) that resulted in skipping of exon 6 based on PAH-cDNA analysis in immortalized lymphocytes. The genomic deletion was present in a heterozygous state in 12 patients, i.e. in ~ 8% of all the analyzed PKU alleles, and might have originated from a Romanian founder.

  4. Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species

    NARCIS (Netherlands)

    Legault, Boris A.; Lopez-Lopez, Arantxa; Alba-Casado, Jose Carlos; Doolittle, W. Ford; Bolhuis, Henk; Rodriguez-Valera, Francisco; Papke, R. Thane

    2006-01-01

    Background: Mature saturated brine (crystallizers) communities are largely dominated (> 80% of cells) by the square halophilic archaeon "Haloquadratum walsbyi". The recent cultivation of the strain HBSQ001 and thesequencing of its genome allows comparison with the metagenome of this taxonomically

  5. Perspectives on Clinical Informatics: Integrating Large-Scale Clinical, Genomic, and Health Information for Clinical Care

    Directory of Open Access Journals (Sweden)

    In Young Choi

    2013-12-01

    Full Text Available The advances in electronic medical records (EMRs and bioinformatics (BI represent two significant trends in healthcare. The widespread adoption of EMR systems and the completion of the Human Genome Project developed the technologies for data acquisition, analysis, and visualization in two different domains. The massive amount of data from both clinical and biology domains is expected to provide personalized, preventive, and predictive healthcare services in the near future. The integrated use of EMR and BI data needs to consider four key informatics areas: data modeling, analytics, standardization, and privacy. Bioclinical data warehouses integrating heterogeneous patient-related clinical or omics data should be considered. The representative standardization effort by the Clinical Bioinformatics Ontology (CBO aims to provide uniquely identified concepts to include molecular pathology terminologies. Since individual genome data are easily used to predict current and future health status, different safeguards to ensure confidentiality should be considered. In this paper, we focused on the informatics aspects of integrating the EMR community and BI community by identifying opportunities, challenges, and approaches to provide the best possible care service for our patients and the population.

  6. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach.

    Directory of Open Access Journals (Sweden)

    Simon Boitard

    2016-03-01

    Full Text Available Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey, PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles.

  7. Field demonstration of automated demand response for both winter and summer events in large buildings in the Pacific Northwest

    Energy Technology Data Exchange (ETDEWEB)

    Piette, M.A.; Kiliccote, S.; Dudley, J.H. [Lawrence Berkeley National Laboratory, Berkeley, CA (United States)

    2013-11-15

    There are growing strains on the electric grid as cooling peaks grow and equipment ages. Increased penetration of renewables on the grid is also straining electricity supply systems and the need for flexible demand is growing. This paper summarizes results of a series of field test of automated demand response systems in large buildings in the Pacific Northwest. The objective of the research was twofold. One objective was to evaluate the use demand response automation technologies. A second objective was to evaluate control strategies that could change the electric load shape in both winter and summer conditions. Winter conditions focused on cold winter mornings, a time when the electric grid is often stressed. The summer test evaluated DR strategies in the afternoon. We found that we could automate both winter and summer control strategies with the open automated demand response communication standard. The buildings were able to provide significant demand response in both winter and summer events.

  8. The analysis of energy consumption and greenhouse gas emissions of a large-scale commercial building in Shanghai, China

    Directory of Open Access Journals (Sweden)

    Xin Wang

    2016-02-01

    Full Text Available Reasonable test, diagnosis, and analysis are meaningful for building energy efficiency retrofit and management. Energy consumption and greenhouse gas emission of a large-scale commercial building are described in this article. Basic information about energy consumption equipment is included in the investigation. Further diagnoses about the operational state of air-conditioning water systems, and ducted systems were implemented. Energy consumption decreased 200 kWh/m2 per year from 2007 to 2009 after energy-saving reconstruction in 2006. Next, a carbon audit was carried out; this comprised CO2 emission statistics associated with the energy use and categorization and structural analysis (categorization refers to energy categorization and structural analysis means the composition and its proportion relationship of all kinds of primary energy and secondary energy in energy production or consumption. Greenhouse gas emissions could be less than 150 kg/m2 per year from 2007 to 2009. An analysis of the correlation between CO2 emissions, building gross domestic product, and energy efficiency is also presented. This article makes an analysis on the energy utilization and energy-saving reconstruction of a public commercial building in Shanghai and then makes an analysis of carbon audit about greenhouse gas emissions related to energy utilization (it analyzes the status of building’s energy utilization and greenhouse gas emissions, to have a more comprehensive understanding on the internal relationship between energy consumption and its greenhouse gas emissions and provide researchful reference data for the development with reduction strategies of greenhouse gas emission in future building.

  9. The influence of local mechanisms on large scale seismic vulnerability estimation of masonry building aggregates

    Science.gov (United States)

    Formisano, Antonio; Chieffo, Nicola; Milo, Bartolomeo; Fabbrocino, Francesco

    2016-12-01

    The current paper deals with the seismic vulnerability evaluation of masonry constructions grouped in aggregates through an "ad hoc" quick vulnerability form based on new assessment parameters considering local collapse mechanisms. First, a parametric kinematic analysis on masonry walls with different height (h) / thickness (t) ratios has been developed with the purpose of identifying the collapse load multiplier for activation of the main four first-order failure mechanisms. Subsequently, a form initially conceived for building aggregates suffering second-mode collapse mechanisms, has been expanded on the basis of the achieved results. Tre proposed quick vulnerability technique has been applied to one case study within the territory of Arsita (Teramo, Italy) and, finally, it has been also validated by the comparison of results with those deriving from application of the well-known FaMIVE procedure.

  10. Genomic characterization of a large outbreak of Legionella pneumophila serogroup 1 strains in Quebec City, 2012.

    Directory of Open Access Journals (Sweden)

    Simon Lévesque

    Full Text Available During the summer of 2012, a major Legionella pneumophila serogroup 1 outbreak occurred in Quebec City, Canada, which caused 182 declared cases of Legionnaire's disease and included 13 fatalities. Legionella pneumophila serogroup 1 isolates from 23 patients as well as from 32 cooling towers located in the vicinity of the outbreak were recovered for analysis. In addition, 6 isolates from the 1996 Quebec City outbreak and 4 isolates from patients unrelated to both outbreaks were added to allow comparison. We characterized the isolates using pulsed-field gel electrophoresis, sequence-based typing, and whole genome sequencing. The comparison of patients-isolated strains to cooling tower isolates allowed the identification of the tower that was the source of the outbreak. Legionella pneumophila strain Quebec 2012 was identified as a ST-62 by sequence-based typing methodology. Two new Legionellaceae plasmids were found only in the epidemic strain. The LVH type IV secretion system was found in the 2012 outbreak isolates but not in the ones from the 1996 outbreak and only in half of the contemporary human isolates. The epidemic strains replicated more efficiently and were more cytotoxic to human macrophages than the environmental strains tested. At least four Icm/Dot effectors in the epidemic strains were absent in the environmental strains suggesting that some effectors could impact the intracellular replication in human macrophages. Sequence-based typing and pulsed-field gel electrophoresis combined with whole genome sequencing allowed the identification and the analysis of the causative strain including its likely environmental source.

  11. Querying and reasoning over large scale building data sets : an outline of a performance benchmark

    NARCIS (Netherlands)

    Pauwels, P.; Mendes de Farias, T.; Zhang, C.; Roxin, A.; Beetz, J.; De Roo, J.; Nicolle, C.

    2016-01-01

    The architectural design and construction domains work on a daily basis with massive amounts of data. Properly managing, exchanging and exploiting these data is an ever ongoing challenge in this domain. This has resulted in large semantic RDF graphs that are to be combined with a significant number

  12. Building calculations

    DEFF Research Database (Denmark)

    Jensen, Bjarne Christian; Hansen, Svend Ole

    Textbook on design of large panel building including rules on robustness and a method for producing the Statical documentattion......Textbook on design of large panel building including rules on robustness and a method for producing the Statical documentattion...

  13. Evaluation of Various Retrofitting Concepts of Building Envelope for Offices Equipped with Large Radiant Ceiling Panels by Dynamic Simulations

    Directory of Open Access Journals (Sweden)

    Sabina Jordan

    2015-09-01

    Full Text Available In order to achieve significant savings in energy and an improved level of thermal comfort in retrofitted existing buildings, specific retrofitting concepts that combine new technologies and design need to be developed and implemented. Large radiant surfaces systems are now among the most promising future technologies to be used both in retrofitted and in new low-energy buildings. These kinds of systems have been the topic of several studies dealing with thermal comfort and energy utilization, but some specific issues concerning their possible use in various concepts for retrofitting are still poorly understood. In the present paper, some results of dynamic simulations, with the transient system simulation tool (TRNSYS model, of the retrofitted offices equipped with radiant ceiling panels are presented and thoroughly analysed. Based on a precise comparison of the results of these simulations with actual measurements in the offices, certain input data for the model were added, so that the model was consequently validated. The model was then applied to the evaluation of various concepts of building envelopes for office retrofitting. By means of dynamic simulations of indoor environment it was possible to determine the benefits and limitations of individual retrofitting concepts. Some specific parameters, which are relevant to these concepts, were also identified.

  14. The build up of the correlation between halo spin and the large-scale structure

    Science.gov (United States)

    Wang, Peng; Kang, Xi

    2018-01-01

    Both simulations and observations have confirmed that the spin of haloes/galaxies is correlated with the large-scale structure (LSS) with a mass dependence such that the spin of low-mass haloes/galaxies tend to be parallel with the LSS, while that of massive haloes/galaxies tend to be perpendicular with the LSS. It is still unclear how this mass dependence is built up over time. We use N-body simulations to trace the evolution of the halo spin-LSS correlation and find that at early times the spin of all halo progenitors is parallel with the LSS. As time goes on, mass collapsing around massive halo is more isotropic, especially the recent mass accretion along the slowest collapsing direction is significant and it brings the halo spin to be perpendicular with the LSS. Adopting the fractional anisotropy (FA) parameter to describe the degree of anisotropy of the large-scale environment, we find that the spin-LSS correlation is a strong function of the environment such that a higher FA (more anisotropic environment) leads to an aligned signal, and a lower anisotropy leads to a misaligned signal. In general, our results show that the spin-LSS correlation is a combined consequence of mass flow and halo growth within the cosmic web. Our predicted environmental dependence between spin and large-scale structure can be further tested using galaxy surveys.

  15. Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?

    Directory of Open Access Journals (Sweden)

    Harrington Eoghan D

    2008-07-01

    Full Text Available Abstract Background Across the fully sequenced microbial genomes there are thousands of examples of overlapping genes. Many of these are only a few nucleotides long and are thought to function by permitting the coordinated regulation of gene expression. However, there should also be selective pressure against long overlaps, as the existence of overlapping reading frames increases the risk of deleterious mutations. Here we examine the longest overlaps and assess whether they are the product of special functional constraints or of erroneous annotation. Results We analysed the genes that overlap by 60 bps or more among 338 fully-sequenced prokaryotic genomes. The likely functional significance of an overlap was determined by comparing each of the genes to its respective orthologs. If a gene showed a significantly different length from its orthologs it was considered unlikely to be functional and therefore the result of an error either in sequencing or gene prediction. Focusing on 715 co-directional overlaps longer than 60 bps, we classified the erroneous ones into five categories: i 5'-end extension of the downstream gene due to either a mispredicted start codon or a frameshift at 5'-end of the gene (409 overlaps, ii fragmentation of a gene caused by a frameshift (163, iii 3'-end extension of the upstream gene due to either a frameshift at 3'-end of a gene or point mutation at the stop codon (68, iv Redundant gene predictions (4, v 5' & 3'-end extension which is a combination of i and iii (71. We also studied 75 divergent overlaps that could be classified as misannotations of group i. Nevertheless we found some convergent long overlaps (54 that might be true overlaps, although an important part of convergent overlaps could be classified as group iii (124. Conclusion Among the 968 overlaps larger than 60 bps which we analysed, we did not find a single real one among the co-directional and divergent orientations and concluded that there had been an

  16. Building flexibility and managing complexity in community mental health: lessons learned in a large urban centre.

    Science.gov (United States)

    Stergiopoulos, Vicky; Saab, Dima; Francombe Pridham, Kate; Aery, Anjana; Nakhost, Arash

    2018-01-24

    Across many jurisdictions, adults with complex mental health and social needs face challenges accessing appropriate supports due to system fragmentation and strict eligibility criteria of existing services. To support this underserviced population, Toronto's local health authority launched two novel community mental health models in 2014, inspired by Flexible Assertive Community Team principles. This study explores service user and provider perspectives on the acceptability of these services, and lessons learned during early implementation. We purposively sampled 49 stakeholders (staff, physicians, service users, health systems stakeholders) and conducted 17 semi-structured qualitative interviews and 5 focus groups between October 23, 2014 and March 2, 2015, exploring stakeholder perspectives on the newly launched team based models, as well as activities and strategies employed to support early implementation. Interviews and focus groups were audio recorded, transcribed verbatim and analyzed using thematic analysis. Findings revealed wide-ranging endorsement for the two team-based models' success in engaging the target population of adults with complex service needs. Implementation strengths included the broad recognition of existing service gaps, the use of interdisciplinary teams and experienced service providers, broad partnerships and collaboration among various service sectors, training and team building activities. Emerging challenges included lack of complementary support services such as suitable housing, organizational contexts reluctant to embrace change and risk associated with complexity, as well as limited service provider and organizational capacity to deliver evidence-based interventions. Findings identified implementation drivers at the practitioner, program, and system levels, specific to the implementation of community mental health interventions for adults with complex health and social needs. These can inform future efforts to address the health

  17. Large clusters of co-expressed genes in the Drosophila genome.

    Science.gov (United States)

    Boutanaev, Alexander M; Kalmykova, Alla I; Shevelyov, Yuri Y; Nurminsky, Dmitry I

    2002-12-12

    Clustering of co-expressed, non-homologous genes on chromosomes implies their co-regulation. In lower eukaryotes, co-expressed genes are often found in pairs. Clustering of genes that share aspects of transcriptional regulation has also been reported in higher eukaryotes. To advance our understanding of the mode of coordinated gene regulation in multicellular organisms, we performed a genome-wide analysis of the chromosomal distribution of co-expressed genes in Drosophila. We identified a total of 1,661 testes-specific genes, one-third of which are clustered on chromosomes. The number of clusters of three or more genes is much higher than expected by chance. We observed a similar trend for genes upregulated in the embryo and in the adult head, although the expression pattern of individual genes cannot be predicted on the basis of chromosomal position alone. Our data suggest that the prevalent mechanism of transcriptional co-regulation in higher eukaryotes operates with extensive chromatin domains that comprise multiple genes.

  18. Contribution of Large Genomic Rearrangements in Italian Lynch Syndrome Patients: Characterization of a Novel Alu-Mediated Deletion

    Directory of Open Access Journals (Sweden)

    Francesca Duraturo

    2013-01-01

    Full Text Available Lynch syndrome is associated with germ-line mutations in the DNA mismatch repair (MMR genes, mainly MLH1 and MSH2. Most of the mutations reported in these genes to date are point mutations, small deletions, and insertions. Large genomic rearrangements in the MMR genes predisposing to Lynch syndrome also occur, but the frequency varies depending on the population studied on average from 5 to 20%. The aim of this study was to examine the contribution of large rearrangements in the MLH1 and MSH2 genes in a well-characterised series of 63 unrelated Southern Italian Lynch syndrome patients who were negative for pathogenic point mutations in the MLH1, MSH2, and MSH6 genes. We identified a large novel deletion in the MSH2 gene, including exon 6 in one of the patients analysed (1.6% frequency. This deletion was confirmed and localised by long-range PCR. The breakpoints of this rearrangement were characterised by sequencing. Further analysis of the breakpoints revealed that this rearrangement was a product of Alu-mediated recombination. Our findings identified a novel Alu-mediated rearrangement within MSH2 gene and showed that large deletions or duplications in MLH1 and MSH2 genes are low-frequency mutational events in Southern Italian patients with an inherited predisposition to colon cancer.

  19. Importation, Mitigation, and Genomic Epidemiology of Candida auris at a Large Teaching Hospital.

    Science.gov (United States)

    Lesho, Emil P; Bronstein, Melissa Z; McGann, Patrick; Stam, Jason; Kwak, Yoon; Maybank, Rosslyn; McNamara, Jodi; Callahan, Megan; Campbell, Jean; Hinkle, Mary K; Walsh, Edward E

    2018-01-01

    OBJECTIVE Candida auris (CA) is an emerging multidrug-resistant pathogen associated with increased mortality. The environment may play a role, but transmission dynamics remain poorly understood. We sought to limit environmental and patient CA contamination following a sustained unsuspected exposure. DESIGN Quasi-experimental observation. SETTING A 528-bed teaching hospital. PATIENTS The index case patient and 17 collocated ward mates. INTERVENTION Immediately after confirmation of CA in the bloodstream and urine of a patient admitted 6 days previously, active surveillance, enhanced transmission-based precautions, environmental cleaning with peracetic acid-hydrogen peroxide and ultraviolet light, and patient relocation were undertaken. Pre-existing agreements and foundational relationships among internal multidisciplinary teams and external partners were leveraged to bolster detection and mitigation efforts and to provide genomic epidemiology. RESULTS Candida auris was isolated from 3 of 132 surface samples on days 8, 9, and 15 of ward occupancy, and from no patient samples (0 of 48). Environmental and patient isolates were genetically identical (4-8 single-nucleotide polymorphisms [SNPs]) and most closely related to the 2013 India CA-6684 strain (~200 SNPs), supporting the epidemiological hypothesis that the source of environmental contamination was the index case patient, who probably acquired the South Asian strain from another New York hospital. All isolates contained a mutation associated with azole resistance (K163R) found in the India 2105 VPCI strain but not in CA-6684. The index patient remained colonized until death. No surfaces were CA-positive 1 month later. CONCLUSION Compared to previous descriptions, CA dissemination was minimal. Immediate access to rapid CA diagnostics facilitates early containment strategies and outbreak investigations. Infect Control Hosp Epidemiol 2018;39:53-57.

  20. Building an Undergraduate Book Approval Plan for a Large Academic Library

    Directory of Open Access Journals (Sweden)

    Denise Koufogiannakis

    2007-05-01

    Full Text Available The University of Alberta Libraries (UAL, working with two book vendors, created large-scale undergraduate book approval plans to deliver new publications. Detailed selections profiles were created for many subject areas, designed to deliver books that would have been obvious choices by subject selectors. More than 5800 monographs were received through the book approval plans during the pilot period. These volumes proved to be highly relevant to users, showing twice as much circulation as other monographs acquired during the same time period. Goals achieved through this project include: release of selectors’ time from routine work, systematic acquisition of a broadly based high-demand undergraduate collection and faster delivery of undergraduate materials. This successful program will be expanded and incorporated into UAL’s normal acquisitions processes for undergraduate materials.

  1. The anti corrosive design of structural metallic elements in buildings with large exploitation period

    International Nuclear Information System (INIS)

    Avila Ayon, V.; Rodriguez Quesada, A. L.

    2009-01-01

    The corrosion deterioration in metallic structural elements, with the consistent loss of his physical and mechanical properties, is cause by errors in the design or fabrication, that allows the accumulation of humidity and contaminants in the surfaces, or acceleration zones of the corrosion processes, as the bimetalics pairs. The aggressiveness of the environment and the productive processes that develop in industrial installations, causes the apparition of premature failures that engage the edification use. The identification of design errors is the first step in the conservation of these structures. the elimination and made a project adapted to the proper installations conditions, is essential procedures to prolong the edification useful life with an optimum and rational use of the resources that destined for this end. The investigation is about the results obtained in the diagnostic and the conservation of industrial installment, with large exploitation periods, in which existed evidences of failures by corrosion, specifically to the elimination of errors of design. (Author) 12 refs

  2. Building an Undergraduate Book Approval Plan for a Large Academic Library

    Directory of Open Access Journals (Sweden)

    Denise Koufogiannakis

    2007-03-01

    Full Text Available The University of Alberta Libraries (UAL, working with two book vendors,created large-scale undergraduate book approval plans to deliver newpublications. Detailed selections profiles were created for many subject areas,designed to deliver books that would have been obvious choices by subjectselectors. More than 5800 monographs were received through the book approvalplans during the pilot period. These volumes proved to be highly relevant tousers, showing twice as much circulation as other monographs acquired duringthe same time period. Goals achieved through this project include: release ofselectors’ time from routine work, systematic acquisition of a broadly based highdemandundergraduate collection and faster delivery of undergraduate materials.This successful program will be expanded and incorporated into UAL’s normalacquisitions processes for undergraduate materials.

  3. Reducing Plug and Process Loads for a Large Scale, Low Energy Office Building: NREL's Research Support Facility; Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Lobato, C.; Pless, S.; Sheppy, M.; Torcellini, P.

    2011-02-01

    This paper documents the design and operational plug and process load energy efficiency measures needed to allow a large scale office building to reach ultra high efficiency building goals. The appendices of this document contain a wealth of documentation pertaining to plug and process load design in the RSF, including a list of equipment was selected for use.

  4. A genome-wide association study to detect QTL for commercially important traits in Swiss Large White boars.

    Directory of Open Access Journals (Sweden)

    Doreen Becker

    Full Text Available The improvement of meat quality and production traits has high priority in the pork industry. Many of these traits show a low to moderate heritability and are difficult and expensive to measure. Their improvement by targeted breeding programs is challenging and requires knowledge of the genetic and molecular background. For this study we genotyped 192 artificial insemination boars of a commercial line derived from the Swiss Large White breed using the PorcineSNP60 BeadChip with 62,163 evenly spaced SNPs across the pig genome. We obtained 26 estimated breeding values (EBVs for various traits including exterior, meat quality, reproduction, and production. The subsequent genome-wide association analysis allowed us to identify four QTL with suggestive significance for three of these traits (p-values ranging from 4.99×10⁻⁶ to 2.73×10⁻⁵. Single QTL for the EBVs pH one hour post mortem (pH1 and carcass length were on pig chromosome (SSC 14 and SSC 2, respectively. Two QTL for the EBV rear view hind legs were on SSC 10 and SSC 16.

  5. Large-scale experiments for the vulnerability analysis of buildings impacted and intruded by fluviatile torrential hazard processes

    Science.gov (United States)

    Sturm, Michael; Gems, Bernhard; Fuchs, Sven; Mazzorana, Bruno; Papathoma-Köhle, Maria; Aufleger, Markus

    2016-04-01

    In European mountain regions, losses due to torrential hazards are still considerable high despite the ongoing debate on an overall increasing or decreasing trend. Recent events in Austria severely revealed that due to technical and economic reasons, an overall protection of settlements in the alpine environment against torrential hazards is not feasible. On the side of the hazard process, events with unpredictable intensities may represent overload scenarios for existent protection structures in the torrent catchments. They bear a particular risk of significant losses in the living space. Although the importance of vulnerability is widely recognised, there is still a research gap concerning its assessment. Currently, potential losses at buildings due to torrential hazards and their comparison with reinstatement costs are determined by the use of empirical functions. Hence, relations of process intensities and the extent of losses, gathered by the analysis of historic hazard events and the information of object-specific restoration values, are used. This approach does not represent a physics-based and integral concept since relevant and often crucial processes, as the intrusion of the fluid-sediment-mixture into elements at risk, are not considered. Based on these findings, our work is targeted at extending these findings and models of present risk research in the context of an integral, more physics-based vulnerability analysis concept. Fluviatile torrential hazard processes and their impacts on the building envelope are experimentally modelled. Material intrusion processes are thereby explicitly considered. Dynamic impacts are gathered quantitatively and spatially distributed by the use of a large set of force transducers. The experimental tests are accomplished with artificial, vertical and skewed plates, including also openings for material intrusion. Further, the impacts on specific buildings within the test site of the work, the fan apex of the Schnannerbach

  6. Integrating large-scale functional genomics data to dissect metabolic networks for hydrogen production

    Energy Technology Data Exchange (ETDEWEB)

    Harwood, Caroline S

    2012-12-17

    The goal of this project is to identify gene networks that are critical for efficient biohydrogen production by leveraging variation in gene content and gene expression in independently isolated Rhodopseudomonas palustris strains. Coexpression methods were applied to large data sets that we have collected to define probabilistic causal gene networks. To our knowledge this a first systems level approach that takes advantage of strain-to strain variability to computationally define networks critical for a particular bacterial phenotypic trait.

  7. Sampling in schools and large institutional buildings: Implications for regulations, exposure and management of lead and copper.

    Science.gov (United States)

    Doré, Evelyne; Deshommes, Elise; Andrews, Robert C; Nour, Shokoufeh; Prévost, Michèle

    2018-04-21

    Legacy lead and copper components are ubiquitous in plumbing of large buildings including schools that serve children most vulnerable to lead exposure. Lead and copper samples must be collected after varying stagnation times and interpreted in reference to different thresholds. A total of 130 outlets (fountains, bathroom and kitchen taps) were sampled for dissolved and particulate lead as well as copper. Sampling was conducted at 8 schools and 3 institutional (non-residential) buildings served by municipal water of varying corrosivity, with and without corrosion control (CC), and without a lead service line. Samples included first draw following overnight stagnation (>8h), partial (30 s) and fully (5 min) flushed, and first draw after 30 min of stagnation. Total lead concentrations in first draw samples after overnight stagnation varied widely from 0.07 to 19.9 μg Pb/L (median: 1.7 μg Pb/L) for large buildings served with non-corrosive water. Higher concentrations were observed in schools with corrosive water without CC (0.9-201 μg Pb/L, median: 14.3 μg Pb/L), while levels in schools with CC ranged from 0.2 to 45.1 μg Pb/L (median: 2.1 μg Pb/L). Partial flushing (30 s) and full flushing (5 min) reduced concentrations by 88% and 92% respectively for corrosive waters without CC. Lead concentrations were 45% than values in 1st draw samples collected after overnight stagnation. Concentrations of particulate Pb varied widely (≥0.02-846 μg Pb/L) and was found to be the cause of very high total Pb concentrations in the 2% of samples exceeding 50 μg Pb/L. Pb levels across outlets within the same building varied widely (up to 1000X) especially in corrosive water (0.85-851 μg Pb/L after 30MS) confirming the need to sample at each outlet to identify high risk taps. Based on the much higher concentrations observed in first draw samples, even after a short stagnation, the first 250mL should be discarded unless no sources

  8. Large-Scale Isolation of Microsatellites from Chinese Mitten Crab Eriocheir sinensis via a Solexa Genomic Survey

    Directory of Open Access Journals (Sweden)

    Qun Wang

    2012-12-01

    Full Text Available Microsatellites are simple sequence repeats with a high degree of polymorphism in the genome; they are used as DNA markers in many molecular genetic studies. Using traditional methods such as the magnetic beads enrichment method, only a few microsatellite markers have been isolated from the Chinese mitten crab Eriocheir sinensis, as the crab genome sequence information is unavailable. Here, we have identified a large number of microsatellites from the Chinese mitten crab by taking advantage of Solexa genomic surveying. A total of 141,737 SSR (simple sequence repeats motifs were identified via analysis of 883 Mb of the crab genomic DNA information, including mono-, di-, tri-, tetra-, penta- and hexa-nucleotide repeat motifs. The number of di-nucleotide repeat motifs was 82,979, making this the most abundant type of repeat motif (58.54%; the second most abundant were the tri-nucleotide repeats (42,657, 30.11%. Among di-nucleotide repeats, the most frequent repeats were AC motifs, accounting for 67.55% of the total number. AGG motifs were the most frequent (59.32% of the tri-nucleotide motifs. A total of 15,125 microsatellite loci had a flanking sequence suitable for setting the primer of a polymerase chain reaction (PCR. To verify the identified SSRs, a subset of 100 primer pairs was randomly selected for PCR. Eighty two primer sets (82% produced strong PCR products matching expected sizes, and 78% were polymorphic. In an analysis of 30 wild individuals from the Yangtze River with 20 primer sets, the number of alleles per locus ranged from 2–14 and the mean allelic richness was 7.4. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy-Weinberg equilibrium test showed significant deviation in four of the 20 microsatellite loci after sequential Bonferroni corrections. This method is cost- and time-effective in comparison to traditional approaches for the isolation of microsatellites.

  9. Large-Scale Science Observatories: Building on What We Have Learned from USArray

    Science.gov (United States)

    Woodward, R.; Busby, R.; Detrick, R. S.; Frassetto, A.

    2015-12-01

    With the NSF-sponsored EarthScope USArray observatory, the Earth science community has built the operational capability and experience to tackle scientific challenges at the largest scales, such as a Subduction Zone Observatory. In the first ten years of USArray, geophysical instruments were deployed across roughly 2% of the Earth's surface. The USArray operated a rolling deployment of seismic stations that occupied ~1,700 sites across the USA, made co-located atmospheric observations, occupied hundreds of sites with magnetotelluric sensors, expanded a backbone reference network of seismic stations, and provided instruments to PI-led teams that deployed thousands of additional seismic stations. USArray included a comprehensive outreach component that directly engaged hundreds of students at over 50 colleges and universities to locate station sites and provided Earth science exposure to roughly 1,000 landowners who hosted stations. The project also included a comprehensive data management capability that received, archived and distributed data, metadata, and data products; data were acquired and distributed in real time. The USArray project was completed on time and under budget and developed a number of best practices that can inform other large-scale science initiatives that the Earth science community is contemplating. Key strategies employed by USArray included: using a survey, rather than hypothesis-driven, mode of observation to generate comprehensive, high quality data on a large-scale for exploration and discovery; making data freely and openly available to any investigator from the very onset of the project; and using proven, commercial, off-the-shelf systems to ensure a fast start and avoid delays due to over-reliance on unproven technology or concepts. Scope was set ambitiously, but managed carefully to avoid overextending. Configuration was controlled to ensure efficient operations while providing consistent, uniform observations. Finally, community

  10. Building the Foundations for a Large-Scale, Cross-Sector Collaboration for a Sustainable and Permanent Return to the Lunar Surface

    Science.gov (United States)

    Kapoglou, A.

    2017-10-01

    This presentation will describe how to build the foundations needed for a large scale, cross-industry collaboration to enable a sustainable and permanent return to the Moon based on system leadership, cross-sector partnership, and inclusive business.

  11. Analysis of Large Genomic Data in Silico: The EPICNorfolk Study of Obesity

    DEFF Research Database (Denmark)

    Zhao, Jing Hua; Luan, Jian'an; Tan, Qihua

    In human genetics, large-scale data are now available with advances in genotyping technologies and international collaborative projects. Our ongoing study of obesity involves Affymetrix 500k genechips on approximately 7000 individuals from the European Prospective Investigation of Cancer (EPIC......) Norfolk study. Although the scale of our data is well beyond the ability of many software systems, we have successfully performed the analysis using the statistical analysis system (SAS) software. Our implementation trades memory with computing time and requires moderate hardware configuration. By using...

  12. Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array

    Directory of Open Access Journals (Sweden)

    Settles Matthew L

    2009-05-01

    Full Text Available Abstract Background Natural antisense transcripts (NATs are transcripts of the opposite DNA strand to the sense-strand either at the same locus (cis-encoded or a different locus (trans-encoded. They can affect gene expression at multiple stages including transcription, RNA processing and transport, and translation. NATs give rise to sense-antisense transcript pairs and the number of these identified has escalated greatly with the availability of DNA sequencing resources and public databases. Traditionally, NATs were identified by the alignment of full-length cDNAs or expressed sequence tags to genome sequences, but an alternative method for large-scale detection of sense-antisense transcript pairs involves the use of microarrays. In this study we developed a novel protocol to assay sense- and antisense-strand transcription on the 55 K Affymetrix GeneChip Wheat Genome Array, which is a 3' in vitro transcription (3'IVT expression array. We selected five different tissue types for assay to enable maximum discovery, and used the 'Chinese Spring' wheat genotype because most of the wheat GeneChip probe sequences were based on its genomic sequence. This study is the first report of using a 3'IVT expression array to discover the expression of natural sense-antisense transcript pairs, and may be considered as proof-of-concept. Results By using alternative target preparation schemes, both the sense- and antisense-strand derived transcripts were labeled and hybridized to the Wheat GeneChip. Quality assurance verified that successful hybridization did occur in the antisense-strand assay. A stringent threshold for positive hybridization was applied, which resulted in the identification of 110 sense-antisense transcript pairs, as well as 80 potentially antisense-specific transcripts. Strand-specific RT-PCR validated the microarray observations, and showed that antisense transcription is likely to be tissue specific. For the annotated sense

  13. Evolution of the Banana Genome (Musa acuminata) Is Impacted by Large Chromosomal Translocations.

    Science.gov (United States)

    Martin, Guillaume; Carreel, Françoise; Coriton, Olivier; Hervouet, Catherine; Cardi, Céline; Derouault, Paco; Roques, Danièle; Salmon, Frédéric; Rouard, Mathieu; Sardos, Julie; Labadie, Karine; Baurens, Franc-Christophe; D'Hont, Angélique

    2017-09-01

    Most banana cultivars are triploid seedless parthenocarpic clones derived from hybridization between Musa acuminata subspecies and sometimes M. balbisiana. M. acuminata subspecies were suggested to differ by a few large chromosomal rearrangements based on chromosome pairing configurations in intersubspecies hybrids. We searched for large chromosomal rearrangements in a seedy M. acuminata ssp. malaccensis banana accession through mate-pair sequencing, BAC-FISH, targeted PCR and marker (DArTseq) segregation in its progeny. We identified a heterozygous reciprocal translocation involving two distal 3 and 10 Mb segments from chromosomes 01 and 04, respectively, and showed that it generated high segregation distortion, reduced recombination and linkage between chromosomes 01 and 04 in its progeny. The two chromosome structures were found to be mutually exclusive in gametes and the rearranged structure was preferentially transmitted to the progeny. The rearranged chromosome structure was frequently found in triploid cultivars but present only in wild malaccensis ssp. accessions, thus suggesting that this rearrangement occurred in M. acuminata ssp. malaccensis. We propose a mechanism for the spread of this rearrangement in Musa diversity and suggest that this rearrangement could have played a role in the emergence of triploid cultivars. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  14. Identification of a large genomic region in UV-irradiated human cells which has fewer cyclobutane pyrimidine dimers than most genomic regions

    International Nuclear Information System (INIS)

    Kantor, G.J.; Deiss-Tolbert, D.M.

    1995-01-01

    Size separation after UV-endonuclease digestion of DNA from UV-irradiated human cells using denaturing conditions fractionates the genome based on cyclobutane pyrimidine dimer content. We have examined the largest molecules available (50-80 kb; about 5% of the DNA) after fractionation and those of average size (5-15 kb) for content of some specific genes. We find that the largest molecules are not a representative sampling of the genome. Three contiguous genes located in a G+C-rich isochore (tyrosine hydroxylase, insulin, insulin-like growth factor II) have concentrations two to three times greater in the largest molecules. This shows that this genomic region has fewer pyrimidine dimers than most other genomic regions. In contrast, the β-actin genomic region, which has a similar G+C content, has an equal concentration in both fractions as do the p53 and β-globin genomic regions, which are A+T-rich. These data show that DNA damage in the form of cyclobutane pyrimidine dimers occurs with different probabilities in specific isochores. Part of the reason may be the relative G-C content, but other factors must play a significant role. We also report that the transcriptionally inactive insulin region is repaired at the genome-overall rate in normal cells and is not repaired in xeroderma pigmentosum complementation group C cells. (author)

  15. Fragmentation of the large subunit ribosomal RNA gene in oyster mitochondrial genomes

    Directory of Open Access Journals (Sweden)

    Milbury Coren A

    2010-09-01

    Full Text Available Abstract Background Discontinuous genes have been observed in bacteria, archaea, and eukaryotic nuclei, mitochondria and chloroplasts. Gene discontinuity occurs in multiple forms: the two most frequent forms result from introns that are spliced out of the RNA and the resulting exons are spliced together to form a single transcript, and fragmented gene transcripts that are not covalently attached post-transcriptionally. Within the past few years, fragmented ribosomal RNA (rRNA genes have been discovered in bilateral metazoan mitochondria, all within a group of related oysters. Results In this study, we have characterized this fragmentation with comparative analysis and experimentation. We present secondary structures, modeled using comparative sequence analysis of the discontinuous mitochondrial large subunit rRNA genes of the cupped oysters C. virginica, C. gigas, and C. hongkongensis. Comparative structure models for the large subunit rRNA in each of the three oyster species are generally similar to those for other bilateral metazoans. We also used RT-PCR and analyzed ESTs to determine if the two fragmented LSU rRNAs are spliced together. The two segments are transcribed separately, and not spliced together although they still form functional rRNAs and ribosomes. Conclusions Although many examples of discontinuous ribosomal genes have been documented in bacteria and archaea, as well as the nuclei, chloroplasts, and mitochondria of eukaryotes, oysters are some of the first characterized examples of fragmented bilateral animal mitochondrial rRNA genes. The secondary structures of the oyster LSU rRNA fragments have been predicted on the basis of previous comparative metazoan mitochondrial LSU rRNA structure models.

  16. Implementation and testing of a fault detection software tool for improving control system performance in a large commercial building

    Energy Technology Data Exchange (ETDEWEB)

    Salsbury, T.I.; Diamond, R.C.

    2000-05-01

    This paper describes a model-based, feedforward control scheme that can detect faults in the controlled process and improve control performance over traditional PID control. The tool uses static simulation models of the system under control to generate feed-forward control action, which acts as a reference of correct operation. Faults that occur in the system cause discrepancies between the feedforward models and the controlled process. The scheme facilitates detection of faults by monitoring the level of these discrepancies. We present results from the first phase of tests on a dual-duct air-handling unit installed in a large office building in San Francisco. We demonstrate the ability of the tool to detect a number of preexisting faults in the system and discuss practical issues related to implementation.

  17. Long-term performance of ETICS on external walls of large-panel buildings; Dauerbestaendigkeit von WDVS auf Plattenbau - Fassaden

    Energy Technology Data Exchange (ETDEWEB)

    Reuschel, M. [Materialforschungs- und Pruefungsanstalt fuer Bauwesen Leipzig (Germany)

    1997-12-31

    Urgently required renovation work on external walls of large panel buildings makes novel demands on thermal insulation composites. In the quest for a practice-oriented test method, a pilot project was carried out. Separate parts of a completely renovated housefront were covered with different thermal insulation composites in a way permitting to carry out investigations for a period of several years. The test methods used and the installed thermal insulation composites are described. The results are pointed out. (MSK) [Deutsch] Die dringend erforderlichen Fassadeninstandsetzungen von Plattenbauten stellen an Waermedaemmverbundsysteme neue Anforderungen. Auf der Suche nach einer praxisgerechten Pruefmethode wurde ein Demopruefstand errichtet, der es ermoeglicht im Rahmen einer Komplettsanierung einen separaten Fassadenbereich mit unterschiedlichen Waermedaemmverbundsystemen so zu bekleiden, dass Untersuchungen ueber mehrere Jahre durchgefuehrt werden koennen. Im Folgenden werden die angewendeten Pruefmethoden und die installierten WDV-Systeme erlaeutert. Die einzelnen Ergebnisse werden aufgezeigt.

  18. Big Data Analytics for Genomic Medicine.

    Science.gov (United States)

    He, Karen Y; Ge, Dongliang; He, Max M

    2017-02-15

    Genomic medicine attempts to build individualized strategies for diagnostic or therapeutic decision-making by utilizing patients' genomic information. Big Data analytics uncovers hidden patterns, unknown correlations, and other insights through examining large-scale various data sets. While integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs) on a Big Data infrastructure exhibit challenges, they also provide a feasible opportunity to develop an efficient and effective approach to identify clinically actionable genetic variants for individualized diagnosis and therapy. In this paper, we review the challenges of manipulating large-scale next-generation sequencing (NGS) data and diverse clinical data derived from the EHRs for genomic medicine. We introduce possible solutions for different challenges in manipulating, managing, and analyzing genomic and clinical data to implement genomic medicine. Additionally, we also present a practical Big Data toolset for identifying clinically actionable genetic variants using high-throughput NGS data and EHRs.

  19. Big Data Analytics for Genomic Medicine

    Science.gov (United States)

    He, Karen Y.; Ge, Dongliang; He, Max M.

    2017-01-01

    Genomic medicine attempts to build individualized strategies for diagnostic or therapeutic decision-making by utilizing patients’ genomic information. Big Data analytics uncovers hidden patterns, unknown correlations, and other insights through examining large-scale various data sets. While integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs) on a Big Data infrastructure exhibit challenges, they also provide a feasible opportunity to develop an efficient and effective approach to identify clinically actionable genetic variants for individualized diagnosis and therapy. In this paper, we review the challenges of manipulating large-scale next-generation sequencing (NGS) data and diverse clinical data derived from the EHRs for genomic medicine. We introduce possible solutions for different challenges in manipulating, managing, and analyzing genomic and clinical data to implement genomic medicine. Additionally, we also present a practical Big Data toolset for identifying clinically actionable genetic variants using high-throughput NGS data and EHRs. PMID:28212287

  20. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species

    Directory of Open Access Journals (Sweden)

    Messeguer Xavier

    2006-10-01

    Full Text Available Abstract Background Due to recent advances in whole genome shotgun sequencing and assembly technologies, the financial cost of decoding an organism's DNA has been drastically reduced, resulting in a recent explosion of genomic sequencing projects. This increase in related genomic data will allow for in depth studies of evolution in closely related species through multiple whole genome comparisons. Results To facilitate such comparisons, we present an interactive multiple genome comparison and alignment tool, M-GCAT, that can efficiently construct multiple genome comparison frameworks in closely related species. M-GCAT is able to compare and identify highly conserved regions in up to 20 closely related bacterial species in minutes on a standard computer, and as many as 90 (containing 75 cloned genomes from a set of 15 published enterobacterial genomes in an hour. M-GCAT also incorporates a novel comparative genomics data visualization interface allowing the user to globally and locally examine and inspect the conserved regions and gene annotations. Conclusion M-GCAT is an interactive comparative genomics tool well suited for quickly generating multiple genome comparisons frameworks and alignments among closely related species. M-GCAT is freely available for download for academic and non-commercial use at: http://alggen.lsi.upc.es/recerca/align/mgcat/intro-mgcat.html.

  1. Grass genomes

    OpenAIRE

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  2. A genome-wide association study in a large F2-cross of laying hens reveals novel genomic regions associated with feather pecking and aggressive pecking behavior.

    Science.gov (United States)

    Lutz, Vanessa; Stratz, Patrick; Preuß, Siegfried; Tetens, Jens; Grashorn, Michael A; Bessei, Werner; Bennewitz, Jörn

    2017-02-03

    Feather pecking and aggressive pecking in laying hens are serious economic and welfare issues. In spite of extensive research on feather pecking during the last decades, the motivation for this behavior is still not clear. A small to moderate heritability has frequently been reported for these traits. Recently, we identified several single-nucleotide polymorphisms (SNPs) associated with feather pecking by mapping selection signatures in two divergent feather pecking lines. Here, we performed a genome-wide association analysis (GWAS) for feather pecking and aggressive pecking behavior, then combined the results with those from the recent selection signature experiment, and linked them to those obtained from a differential gene expression study. A large F2 cross of 960 F2 hens was generated using the divergent lines as founders. Hens were phenotyped for feather pecks delivered (FPD), aggressive pecks delivered (APD), and aggressive pecks received (APR). Individuals were genotyped with the Illumina 60K chicken Infinium iSelect chip. After data filtering, 29,376 SNPs remained for analyses. Single-marker GWAS was performed using a Poisson model. The results were combined with those from the selection signature experiment using Fisher's combined probability test. Numerous significant SNPs were identified for all traits but with low false discovery rates. Nearly all significant SNPs were located in clusters that spanned a maximum of 3 Mb and included at least two significant SNPs. For FPD, four clusters were identified, which increased to 13 based on the meta-analysis (FPD meta ). Seven clusters were identified for APD and three for APR. Eight genes (of the 750 investigated genes located in the FPD meta clusters) were significantly differentially-expressed in the brain of hens from both lines. One gene, SLC12A9, and the positional candidate gene for APD, GNG2, may be linked to the monomanine signaling pathway, which is involved in feather pecking and aggressive behavior

  3. A Genome-Wide Association Study in Large White and Landrace Pig Populations for Number Piglets Born Alive

    Science.gov (United States)

    Bergfelder-Drüing, Sarah; Grosse-Brinkhaus, Christine; Lind, Bianca; Erbe, Malena; Schellander, Karl; Simianer, Henner; Tholen, Ernst

    2015-01-01

    The number of piglets born alive (NBA) per litter is one of the most important traits in pig breeding due to its influence on production efficiency. It is difficult to improve NBA because the heritability of the trait is low and it is governed by a high number of loci with low to moderate effects. To clarify the biological and genetic background of NBA, genome-wide association studies (GWAS) were performed using 4,012 Large White and Landrace pigs from herdbook and commercial breeding companies in Germany (3), Austria (1) and Switzerland (1). The animals were genotyped with the Illumina PorcineSNP60 BeadChip. Because of population stratifications within and between breeds, clusters were formed using the genetic distances between the populations. Five clusters for each breed were formed and analysed by GWAS approaches. In total, 17 different significant markers affecting NBA were found in regions with known effects on female reproduction. No overlapping significant chromosome areas or QTL between Large White and Landrace breed were detected. PMID:25781935

  4. A genome-wide association study in large white and landrace pig populations for number piglets born alive.

    Directory of Open Access Journals (Sweden)

    Sarah Bergfelder-Drüing

    Full Text Available The number of piglets born alive (NBA per litter is one of the most important traits in pig breeding due to its influence on production efficiency. It is difficult to improve NBA because the heritability of the trait is low and it is governed by a high number of loci with low to moderate effects. To clarify the biological and genetic background of NBA, genome-wide association studies (GWAS were performed using 4,012 Large White and Landrace pigs from herdbook and commercial breeding companies in Germany (3, Austria (1 and Switzerland (1. The animals were genotyped with the Illumina PorcineSNP60 BeadChip. Because of population stratifications within and between breeds, clusters were formed using the genetic distances between the populations. Five clusters for each breed were formed and analysed by GWAS approaches. In total, 17 different significant markers affecting NBA were found in regions with known effects on female reproduction. No overlapping significant chromosome areas or QTL between Large White and Landrace breed were detected.

  5. Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data.

    Science.gov (United States)

    Bhaskar, Anand; Wang, Y X Rachel; Song, Yun S

    2015-02-01

    With the recent increase in study sample sizes in human genetics, there has been growing interest in inferring historical population demography from genomic variation data. Here, we present an efficient inference method that can scale up to very large samples, with tens or hundreds of thousands of individuals. Specifically, by utilizing analytic results on the expected frequency spectrum under the coalescent and by leveraging the technique of automatic differentiation, which allows us to compute gradients exactly, we develop a very efficient algorithm to infer piecewise-exponential models of the historical effective population size from the distribution of sample allele frequencies. Our method is orders of magnitude faster than previous demographic inference methods based on the frequency spectrum. In addition to inferring demography, our method can also accurately estimate locus-specific mutation rates. We perform extensive validation of our method on simulated data and show that it can accurately infer multiple recent epochs of rapid exponential growth, a signal that is difficult to pick up with small sample sizes. Lastly, we use our method to analyze data from recent sequencing studies, including a large-sample exome-sequencing data set of tens of thousands of individuals assayed at a few hundred genic regions. © 2015 Bhaskar et al.; Published by Cold Spring Harbor Laboratory Press.

  6. Genomic structure and promoter functional analysis of GnRH3 gene in large yellow croaker (Larimichthys crocea).

    Science.gov (United States)

    Huang, Wei; Zhang, Jianshe; Liao, Zhi; Lv, Zhenming; Wu, Huifei; Zhu, Aiyi; Wu, Changwen

    2016-01-15

    Gonadotropin-releasing hormone III (GnRH3) is considered to be a key neurohormone in fish reproduction control. In the present study, the cDNA and genomic sequences of GnRH3 were cloned and characterized from large yellow croaker Larimichthys crocea. The cDNA encoded a protein of 99 amino acids with four functional motifs. The full-length genome sequence was composed of 3797 nucleotides, including four exons and three introns. Higher identities of amino acid sequences and conserved exon-intron organizations were found between LcGnRH3 and other GnRH3 genes. In addition, some special features of the sequences were detected in partial species. For example, two specific residues (V and A) were found in the family Sciaenidae, and the unique 75-72 bp type of the open reading frame 2 and 3 existed in the family Cyprinidae. Analysis of the 2576 bp promoter fragment of LcGnRH3 showed a number of transcription factor binding sites, such as AP1, CREB, GATA-1, HSF, FOXA2, and FOXL1. Promoter functional analysis using an EGFP reporter fusion in zebrafish larvae presented positive signals in the brain, including the olfactory region, the terminal nerve ganglion, the telencephalon, and the hypothalamus. The expression pattern was generally consistent with the endogenous GnRH3 GFP-expressing transgenic zebrafish lines, but the details were different. These results indicate that the structure and function of LcGnRH3 are generally similar to the other teleost GnRH3 genes, but there exist some distinctions among them. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Large-scale genome-wide association studies and meta-analyses of longitudinal change in adult lung function.

    Directory of Open Access Journals (Sweden)

    Wenbo Tang

    Full Text Available Genome-wide association studies (GWAS have identified numerous loci influencing cross-sectional lung function, but less is known about genes influencing longitudinal change in lung function.We performed GWAS of the rate of change in forced expiratory volume in the first second (FEV1 in 14 longitudinal, population-based cohort studies comprising 27,249 adults of European ancestry using linear mixed effects model and combined cohort-specific results using fixed effect meta-analysis to identify novel genetic loci associated with longitudinal change in lung function. Gene expression analyses were subsequently performed for identified genetic loci. As a secondary aim, we estimated the mean rate of decline in FEV1 by smoking pattern, irrespective of genotypes, across these 14 studies using meta-analysis.The overall meta-analysis produced suggestive evidence for association at the novel IL16/STARD5/TMC3 locus on chromosome 15 (P  =  5.71 × 10(-7. In addition, meta-analysis using the five cohorts with ≥3 FEV1 measurements per participant identified the novel ME3 locus on chromosome 11 (P  =  2.18 × 10(-8 at genome-wide significance. Neither locus was associated with FEV1 decline in two additional cohort studies. We confirmed gene expression of IL16, STARD5, and ME3 in multiple lung tissues. Publicly available microarray data confirmed differential expression of all three genes in lung samples from COPD patients compared with controls. Irrespective of genotypes, the combined estimate for FEV1 decline was 26.9, 29.2 and 35.7 mL/year in never, former, and persistent smokers, respectively.In this large-scale GWAS, we identified two novel genetic loci in association with the rate of change in FEV1 that harbor candidate genes with biologically plausible functional links to lung function.

  8. Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS

    Directory of Open Access Journals (Sweden)

    You Frank M

    2010-06-01

    Full Text Available Abstract Background Physical maps employing libraries of bacterial artificial chromosome (BAC clones are essential for comparative genomics and sequencing of large and repetitive genomes such as those of the hexaploid bread wheat. The diploid ancestor of the D-genome of hexaploid wheat (Triticum aestivum, Aegilops tauschii, is used as a resource for wheat genomics. The barley diploid genome also provides a good model for the Triticeae and T. aestivum since it is only slightly larger than the ancestor wheat D genome. Gene co-linearity between the grasses can be exploited by extrapolating from rice and Brachypodium distachyon to Ae. tauschii or barley, and then to wheat. Results We report the use of Ae. tauschii for the construction of the physical map of a large distal region of chromosome arm 3DS. A physical map of 25.4 Mb was constructed by anchoring BAC clones of Ae. tauschii with 85 EST on the Ae. tauschii and barley genetic maps. The 24 contigs were aligned to the rice and B. distachyon genomic sequences and a high density SNP genetic map of barley. As expected, the mapped region is highly collinear to the orthologous chromosome 1 in rice, chromosome 2 in B. distachyon and chromosome 3H in barley. However, the chromosome scale of the comparative maps presented provides new insights into grass genome organization. The disruptions of the Ae. tauschii-rice and Ae. tauschii-Brachypodium syntenies were identical. We observed chromosomal rearrangements between Ae. tauschii and barley. The comparison of Ae. tauschii physical and genetic maps showed that the recombination rate across the region dropped from 2.19 cM/Mb in the distal region to 0.09 cM/Mb in the proximal region. The size of the gaps between contigs was evaluated by comparing the recombination rate along the map with the local recombination rates calculated on single contigs. Conclusions The physical map reported here is the first physical map using fingerprinting of a complete

  9. Large eddy simulation of pollutant gas dispersion with buoyancy ejected from building into an urban street canyon.

    Science.gov (United States)

    Hu, L H; Xu, Y; Zhu, W; Wu, L; Tang, F; Lu, K H

    2011-09-15

    The dispersion of buoyancy driven smoke soot and carbon monoxide (CO) gas, which was ejected out from side building into an urban street canyon with aspect ratio of 1 was investigated by large eddy simulation (LES) under a perpendicular wind flow. Strong buoyancy effect, which has not been revealed before, on such pollution dispersion in the street canyon was studied. The buoyancy release rate was 5 MW. The wind speed concerned ranged from 1 to 7.5m/s. The characteristics of flow pattern, distribution of smoke soot and temperature, CO concentration were revealed by the LES simulation. Dimensionless Froude number (Fr) was firstly introduced here to characterize the pollutant dispersion with buoyancy effect counteracting the wind. It was found that the flow pattern can be well categorized into three regimes. A regular characteristic large vortex was shown for the CO concentration contour when the wind velocity was higher than the critical re-entrainment value. A new formula was theoretically developed to show quantitatively that the critical re-entrainment wind velocities, u(c), for buoyancy source at different floors, were proportional to -1/3 power of the characteristic height. LES simulation results agreed well with theoretical analysis. The critical Froude number was found to be constant of 0.7. Copyright © 2010 Elsevier B.V. All rights reserved.

  10. Implementation of genomic recursions in single-step genomic best linear unbiased predictor for US Holsteins with a large number of genotyped animals.

    Science.gov (United States)

    Masuda, Y; Misztal, I; Tsuruta, S; Legarra, A; Aguilar, I; Lourenco, D A L; Fragomeni, B O; Lawlor, T J

    2016-03-01

    The objectives of this study were to develop and evaluate an efficient implementation in the computation of the inverse of genomic relationship matrix with the recursion algorithm, called the algorithm for proven and young (APY), in single-step genomic BLUP. We validated genomic predictions for young bulls with more than 500,000 genotyped animals in final score for US Holsteins. Phenotypic data included 11,626,576 final scores on 7,093,380 US Holstein cows, and genotypes were available for 569,404 animals. Daughter deviations for young bulls with no classified daughters in 2009, but at least 30 classified daughters in 2014 were computed using all the phenotypic data. Genomic predictions for the same bulls were calculated with single-step genomic BLUP using phenotypes up to 2009. We calculated the inverse of the genomic relationship matrix GAPY(-1) based on a direct inversion of genomic relationship matrix on a small subset of genotyped animals (core animals) and extended that information to noncore animals by recursion. We tested several sets of core animals including 9,406 bulls with at least 1 classified daughter, 9,406 bulls and 1,052 classified dams of bulls, 9,406 bulls and 7,422 classified cows, and random samples of 5,000 to 30,000 animals. Validation reliability was assessed by the coefficient of determination from regression of daughter deviation on genomic predictions for the predicted young bulls. The reliabilities were 0.39 with 5,000 randomly chosen core animals, 0.45 with the 9,406 bulls, and 7,422 cows as core animals, and 0.44 with the remaining sets. With phenotypes truncated in 2009 and the preconditioned conjugate gradient to solve mixed model equations, the number of rounds to convergence for core animals defined by bulls was 1,343; defined by bulls and cows, 2,066; and defined by 10,000 random animals, at most 1,629. With complete phenotype data, the number of rounds decreased to 858, 1,299, and at most 1,092, respectively. Setting up GAPY(-1

  11. The large-scale blast score ratio (LS-BSR pipeline: a method to rapidly compare genetic content between bacterial genomes

    Directory of Open Access Journals (Sweden)

    Jason W. Sahl

    2014-04-01

    Full Text Available Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the rapid, large-scale, full-genome comparative analyses carried out by LS-BSR.Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 min using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in 27–57 h, depending upon the alignment method, using 16 processors.Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated

  12. Insights into the Pathogenesis of Anaplastic Large-Cell Lymphoma through Genome-wide DNA Methylation Profiling

    Directory of Open Access Journals (Sweden)

    Melanie R. Hassler

    2016-10-01

    Full Text Available Aberrant DNA methylation patterns in malignant cells allow insight into tumor evolution and development and can be used for disease classification. Here, we describe the genome-wide DNA methylation signatures of NPM-ALK-positive (ALK+ and NPM-ALK-negative (ALK− anaplastic large-cell lymphoma (ALCL. We find that ALK+ and ALK− ALCL share common DNA methylation changes for genes involved in T cell differentiation and immune response, including TCR and CTLA-4, without an ALK-specific impact on tumor DNA methylation in gene promoters. Furthermore, we uncover a close relationship between global ALCL DNA methylation patterns and those in distinct thymic developmental stages and observe tumor-specific DNA hypomethylation in regulatory regions that are enriched for conserved transcription factor binding motifs such as AP1. Our results indicate similarity between ALCL tumor cells and thymic T cell subsets and a direct relationship between ALCL oncogenic signaling and DNA methylation through transcription factor induction and occupancy.

  13. GRIMP: A web- and grid-based tool for high-speed analysis of large-scale genome-wide association using imputed data.

    NARCIS (Netherlands)

    K. Estrada Gil (Karol); A. Abuseiris (Anis); F.G. Grosveld (Frank); A.G. Uitterlinden (André); T.A. Knoch (Tobias); F. Rivadeneira Ramirez (Fernando)

    2009-01-01

    textabstractThe current fast growth of genome-wide association studies (GWAS) combined with now common computationally expensive imputation requires the online access of large user groups to high-performance computing resources capable of analyzing rapidly and efficiently millions of genetic

  14. Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species

    Directory of Open Access Journals (Sweden)

    Bolhuis Henk

    2006-07-01

    Full Text Available Abstract Background Mature saturated brine (crystallizers communities are largely dominated (>80% of cells by the square halophilic archaeon "Haloquadratum walsbyi". The recent cultivation of the strain HBSQ001 and thesequencing of its genome allows comparison with the metagenome of this taxonomically simplified environment. Similar studies carried out in other extreme environments have revealed very little diversity in gene content among the cell lineages present. Results The metagenome of the microbial community of a crystallizer pond has been analyzed by end sequencing a 2000 clone fosmid library and comparing the sequences obtained with the genome sequence of "Haloquadratum walsbyi". The genome of the sequenced strain was retrieved nearly complete within this environmental DNA library. However, many ORF's that could be ascribed to the "Haloquadratum" metapopulation by common genome characteristics or scaffolding to the strain genome were not present in the specific sequenced isolate. Particularly, three regions of the sequenced genome were associated with multiple rearrangements and the presence of different genes from the metapopulation. Many transposition and phage related genes were found within this pool which, together with the associated atypical GC content in these areas, supports lateral gene transfer mediated by these elements as the most probable genetic cause of this variability. Additionally, these sequences were highly enriched in putative regulatory and signal transduction functions. Conclusion These results point to a large pan-genome (total gene repertoire of the genus/species even in this highly specialized extremophile and at a single geographic location. The extensive gene repertoire is what might be expected of a population that exploits a diverse nutrient pool, resulting from the degradation of biomass produced at lower salinities.

  15. Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease

    NARCIS (Netherlands)

    Nalls, Mike A.; Pankratz, Nathan; Lill, Christina M.; Do, Chuong B.; Hernandez, Dena G.; Saad, Mohamad; DeStefano, Anita L.; Kara, Eleanna; Bras, Jose; Sharma, Manu; Schulte, Claudia; Keller, Margaux F.; Arepalli, Sampath; Letson, Christopher; Edsall, Connor; Stefansson, Hreinn; Liu, Xinmin; Pliner, Hannah; Lee, Joseph H.; Cheng, Rong; Ikram, M. Arfan; Ioannidis, John P. A.; Hadjigeorgiou, Georgios M.; Bis, Joshua C.; Martinez, Maria; Perlmutter, Joel S.; Goate, Alison; Marder, Karen; Fiske, Brian; Sutherland, Margaret; Xiromerisiou, Georgia; Myers, Richard H.; Clark, Lorraine N.; Stefansson, Kari; Hardy, John A.; Heutink, Peter; Chen, Honglei; Wood, Nicholas W.; Houlden, Henry; Payami, Haydeh; Brice, Alexis; Scott, William K.; Gasser, Thomas; Bertram, Lars; Eriksson, Nicholas; Foroud, Tatiana; Singleton, Andrew B.; Plagnol, Vincent; Sheerin, Una-Marie; Simón-Sánchez, Javier; Lesage, Suzanne; Sveinbjörnsdóttir, Sigurlaug; Barker, Roger; Ben-Shlomo, Yoav; Berendse, Henk W.; Berg, Daniela; Bhatia, Kailash; de Bie, Rob M. A.; Biffi, Alessandro; Bloem, Bas; Bochdanovits, Zoltan; Bonin, Michael; Bras, Jose M.; Brockmann, Kathrin; Brooks, Janet; Burn, David J.; Charlesworth, Gavin; Chinnery, Patrick F.; Chong, Sean; Clarke, Carl E.; Cookson, Mark R.; Cooper, J. Mark; Corvol, Jean Christophe; Counsell, Carl; Damier, Philippe; Dartigues, Jean-François; Deloukas, Panos; Deuschl, Günther; Dexter, David T.; van Dijk, Karin D.; Dillman, Allissa; Durif, Frank; Dürr, Alexandra; Edkins, Sarah; Evans, Jonathan R.; Foltynie, Thomas; Dong, Jing; Gardner, Michelle; Gibbs, J. Raphael; Gray, Emma; Guerreiro, Rita; Harris, Clare; van Hilten, Jacobus J.; Hofman, Albert; Hollenbeck, Albert; Holton, Janice; Hu, Michele; Huang, Xuemei; Wurster, Isabel; Mätzler, Walter; Hudson, Gavin; Hunt, Sarah E.; Huttenlocher, Johanna; Illig, Thomas; Jónsson, Pálmi V.; Lambert, Jean-Charles; Langford, Cordelia; Lees, Andrew; Lichtner, Peter; Limousin, Patricia; Lopez, Grisel; Lorenz, Delia; McNeill, Alisdair; Moorby, Catriona; Moore, Matthew; Morris, Huw R.; Morrison, Karen E.; Mudanohwo, Ese; O'Sullivan, Sean S.; Pearson, Justin; Pétursson, Hjörvar; Pollak, Pierre; Post, Bart; Potter, Simon; Ravina, Bernard; Revesz, Tamas; Riess, Olaf; Rivadeneira, Fernando; Rizzu, Patrizia; Ryten, Mina; Sawcer, Stephen; Schapira, Anthony; Scheffer, Hans; Shaw, Karen; Shoulson, Ira; Sidransky, Ellen; Smith, Colin; Spencer, Chris C. A.; Stefánsson, Hreinn; Bettella, Francesco; Stockton, Joanna D.; Strange, Amy; Talbot, Kevin; Tanner, Carlie M.; Tashakkori-Ghanbaria, Avazeh; Tison, François; Trabzuni, Daniah; Traynor, Bryan J.; Uitterlinden, André G.; Velseboer, Daan; Vidailhet, Marie; Walker, Robert; van de Warrenburg, Bart; Wickremaratchi, Mirdhu; Williams, Nigel; Williams-Gray, Caroline H.; Winder-Rhodes, Sophie; Stefánsson, Kári; Hardy, John; Factor, S.; Higgins, D.; Evans, S.; Shill, H.; Stacy, M.; Danielson, J.; Marlor, L.; Williamson, K.; Jankovic, J.; Hunter, C.; Simon, D.; Ryan, P.; Scollins, L.; Saunders-Pullman, R.; Boyar, K.; Costan-Toth, C.; Ohmann, E.; Sudarsky, L.; Joubert, C.; Friedman, J.; Chou, K.; Fernandez, H.; Lannon, M.; Galvez-Jimenez, N.; Podichetty, A.; Thompson, K.; Lewitt, P.; Deangelis, M.; O'Brien, C.; Seeberger, L.; Dingmann, C.; Judd, D.; Marder, K.; Fraser, J.; Harris, J.; Bertoni, J.; Peterson, C.; Rezak, M.; Medalle, G.; Chouinard, S.; Panisset, M.; Hall, J.; Poiffaut, H.; Calabrese, V.; Roberge, P.; Wojcieszek, J.; Belden, J.; Jennings, D.; Marek, K.; Mendick, S.; Reich, S.; Dunlop, B.; Jog, M.; Horn, C.; Uitti, R.; Turk, M.; Ajax, T.; Mannetter, J.; Sethi, K.; Carpenter, J.; Dill, B.; Hatch, L.; Ligon, K.; Narayan, S.; Blindauer, K.; Abou-Samra, K.; Petit, J.; Elmer, L.; Aiken, E.; Davis, K.; Schell, C.; Wilson, S.; Velickovic, M.; Koller, W.; Phipps, S.; Feigin, A.; Gordon, M.; Hamann, J.; Licari, E.; Marotta-Kollarus, M.; Shannon, B.; Winnick, R.; Simuni, T.; Videnovic, A.; Kaczmarek, A.; Williams, K.; Wolff, M.; Rao, J.; Cook, M.; Fernandez, M.; Kostyk, S.; Hubble, J.; Campbell, A.; Reider, C.; Seward, A.; Camicioli, R.; Carter, J.; Nutt, J.; Andrews, P.; Morehouse, S.; Stone, C.; Mendis, T.; Grimes, D.; Alcorn-Costa, C.; Gray, P.; Haas, K.; Vendette, J.; Sutton, J.; Hutchinson, B.; Young, J.; Rajput, A.; Klassen, L.; Shirley, T.; Manyam, B.; Simpson, P.; Whetteckey, J.; Wulbrecht, B.; Truong, D.; Pathak, M.; Frei, K.; Luong, N.; Tra, T.; Tran, A.; Vo, J.; Lang, A.; Kleiner- Fisman, G.; Nieves, A.; Johnston, L.; So, J.; Podskalny, G.; Giffin, L.; Atchison, P.; Allen, C.; Martin, W.; Wieler, M.; Suchowersky, O.; Furtado, S.; Klimek, M.; Hermanowicz, N.; Niswonger, S.; Shults, C.; Fontaine, D.; Aminoff, M.; Christine, C.; Diminno, M.; Hevezi, J.; Dalvi, A.; Kang, U.; Richman, J.; Uy, S.; Sahay, A.; Gartner, M.; Schwieterman, D.; Hall, D.; Leehey, M.; Culver, S.; Derian, T.; Demarcaida, T.; Thurlow, S.; Rodnitzky, R.; Dobson, J.; Lyons, K.; Pahwa, R.; Gales, T.; Thomas, S.; Shulman, L.; Weiner, W.; Dustin, K.; Singer, C.; Zelaya, L.; Tuite, P.; Hagen, V.; Rolandelli, S.; Schacherer, R.; Kosowicz, J.; Gordon, P.; Werner, J.; Serrano, C.; Roque, S.; Kurlan, R.; Berry, D.; Gardiner, I.; Hauser, R.; Sanchez-Ramos, J.; Zesiewicz, T.; Delgado, H.; Price, K.; Rodriguez, P.; Wolfrath, S.; Pfeiffer, R.; Davis, L.; Pfeiffer, B.; Dewey, R.; Hayward, B.; Johnson, A.; Meacham, M.; Estes, B.; Walker, F.; Hunt, V.; O'Neill, C.; Racette, B.; Swisher, L.; Dijamco, Cheri; Conley, Emily Drabant; Dorfman, Elizabeth; Tung, Joyce Y.; Hinds, David A.; Mountain, Joanna L.; Wojcicki, Anne; Lew, M.; Klein, C.; Golbe, L.; Growdon, J.; Wooten, G. F.; Watts, R.; Guttman, M.; Goldwurm, S.; Saint-Hilaire, M. H.; Baker, K.; Litvan, I.; Nicholson, G.; Nance, M.; Drasby, E.; Isaacson, S.; Burn, D.; Pramstaller, P.; Al-hinti, J.; Moller, A.; Sherman, S.; Roxburgh, R.; Slevin, J.; Perlmutter, J.; Mark, M. H.; Huggins, N.; Pezzoli, G.; Massood, T.; Itin, I.; Corbett, A.; Chinnery, P.; Ostergaard, K.; Snow, B.; Cambi, F.; Kay, D.; Samii, A.; Agarwal, P.; Roberts, J. W.; Higgins, D. S.; Molho, Eric; Rosen, Ami; Montimurro, J.; Martinez, E.; Griffith, A.; Kusel, V.; Yearout, D.; Zabetian, C.; Clark, L. N.; Liu, X.; Lee, J. H.; Taub, R. Cheng; Louis, E. D.; Cote, L. J.; Waters, C.; Ford, B.; Fahn, S.; Vance, Jeffery M.; Beecham, Gary W.; Martin, Eden R.; Nuytemans, Karen; Pericak-Vance, Margaret A.; Haines, Jonathan L.; DeStefano, Anita; Seshadri, Sudha; Choi, Seung Hoan; Frank, Samuel; Psaty, Bruce M.; Rice, Kenneth; Longstreth, W. T.; Ton, Thanh G. N.; Jain, Samay; van Duijn, Cornelia M.; Verlinden, Vincent J.; Koudstaal, Peter J.; Singleton, Andrew; Cookson, Mark; Hernandez, Dena; Nalls, Michael; Zonderman, Alan; Ferrucci, Luigi; Johnson, Robert; Longo, Dan; O'Brien, Richard; Traynor, Bryan; Troncoso, Juan; van der Brug, Marcel; Zielke, Ronald; Weale, Michael; Ramasamy, Adaikalavan; Dardiotis, Efthimios; Tsimourtou, Vana; Spanaki, Cleanthe; Plaitakis, Andreas; Bozi, Maria; Stefanis, Leonidas; Vassilatis, Dimitris; Koutsis, Georgios; Panas, Marios; Lunnon, Katie; Lupton, Michelle; Powell, John; Parkkinen, Laura; Ansorge, Olaf

    2014-01-01

    We conducted a meta-analysis of Parkinson's disease genome-wide association studies using a common set of 7,893,274 variants across 13,708 cases and 95,282 controls. Twenty-six loci were identified as having genome-wide significant association; these and 6 additional previously reported loci were

  16. Assessment of technical and economical viability for large-scale conversion of single family residential buildings into zero energy buildings in Brazil: Climatic and cultural considerations

    International Nuclear Information System (INIS)

    Pacheco, Miguel; Lamberts, Roberto

    2013-01-01

    This paper addresses the viability of converting single-family residential buildings in Brazil into zero energy buildings (ZEBs). The European Union and the United States aim ZEBs implementation to address ‘peak oil’ and environmental concerns. However, literature shows no agreement on a consensual definition of ZEB. Seeking a Brazilian ZEB definition, this paper addresses PassivHaus and thermal comfort standards for hot climates, source metrics for ZEB, Brazil′s energy mix, residential energy end uses and Brazilian legal framework for residential photovoltaic (PV) generation. Internal Rate of Return for PV systems in two Brazilian cities is calculated under various scenarios. It shows grid parity was reached from April 2012 to November 2012 assuming residential electric tariffs of that period and the financial conditions given by the Brazilian government for the construction of new dams in the Amazon and the lowest rates offered by Brazilian banks to private individuals. Governmental decision to lower electric residential tariffs in November 2012 reduced the scope of grid parity. Later revocation of a tax exemption in April 2013 ended grid parity in Brazil. It concludes, conversely to developed countries, it is the volatile Brazilian energy policy, instead of economical barriers, the main obstacle for ZEB viability in Brazil. - Highlights: • Critique on super insolated buildings as a good solution for hot climates. • PV parity already reached in some parts of Brazil. • Proposal for a zero energy building definition for Brazil. • Critique of the source metric for energy balance in zero energy buildings. • Average roof area in Brazil enough for PV array to meet average energy consumption

  17. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)-A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes.

    Science.gov (United States)

    Chwialkowska, Karolina; Korotko, Urszula; Kosinska, Joanna; Szarejko, Iwona; Kwasniewski, Miroslaw

    2017-01-01

    Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare . However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop

  18. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq—A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

    Directory of Open Access Journals (Sweden)

    Karolina Chwialkowska

    2017-11-01

    Full Text Available Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq. We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation

  19. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)—A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

    Science.gov (United States)

    Chwialkowska, Karolina; Korotko, Urszula; Kosinska, Joanna; Szarejko, Iwona; Kwasniewski, Miroslaw

    2017-01-01

    Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop

  20. Are building users prepared for energy flexible buildings—A large-scale survey in the Netherlands

    DEFF Research Database (Denmark)

    Li, Rongling; Dane, Gamze; Finck, Christian

    2017-01-01

    Building energy flexibility might play a crucial role in demand side management for integrating intermittent renewables into smart grids. The potential of building energy flexibility depends not only on the physical characteristics of a building but also on occupant behaviour in the building. Bui...... incentives such as financial rewards....... never heard of smart grids. However, unfamiliarity with smart grids increased with age, and half of the respondents aged 20–29 years old were aware of the concept. Monetary incentives were identified as the biggest motivating factor for adoption of smart grid technologies. It was also found that people...

  1. EFFECTIVE KEYED CONNECTIONS OF HOLLOW-CORE FLOOR SLABS WITH WALLS IN MODERN LARGE-PANEL HOUSE BUILDING

    Directory of Open Access Journals (Sweden)

    O. A. Dovzhenko

    2018-01-01

    Full Text Available The paper considers large-panel constructive system of multi-storey buildings and its industrial basis creates conditions for intensive volume growth in house construction. Application of hollow-core panels are recommended as floor slabs that allows to increase a distance between bearing walls, to improve planning solutions, and also significantly to increase thermal and sound protection properties of floor discs (coatings. Keyed joints having the highest resistance to shearing forces are used to ensure joint action of the slabs with wall panels. A supporting unit of floor elements in the precast-monolithic constructive system ARKOS by means of concrete keys is considered as a prototype of the considered joint. In order to increase a bearing capacity and improve reliability of joints it is envisaged to reinforce keys with space frames. Improvement of joint units is possible to carry out with due account of total number of the factors influencing on strength. Poltava National Technical University named after Yuri Kondratyuk has developed a general methodology for assessment of bearing capacity in keyed joints which is based on the variational method in the theory of concrete plasticity and reflects specificity of stress-strain state of the failure zone. For experimental verification of this methodology investigations have been carried out with the purpose to test operation of keys when they are reinforced in mid-height and reinforcement is distributed in two tiers. The observed experimental fracture pattern in the specimens has confirmed kinematic schemes accepted for calculations and comparative analysis of experimental and theoretical values points to their closeness. Two-level reinforcement significantly improves plastic properties of concrete keys and excludes brittle failure. The proposed design of the joint unit for floor slabs with wall panels is characterized by the ratio of key dimensions and shape of reinforcing cages in the form of

  2. Building the genomic nation: ‘Homo Brasilis’ and the ‘Genoma Mexicano’ in comparative cultural perspective

    Science.gov (United States)

    Kent, Michael; García-Deister, Vivette; López-Beltrán, Carlos; Santos, Ricardo Ventura; Schwartz-Marín, Ernesto; Wade, Peter

    2015-01-01

    This article explores the relationship between genetic research, nationalism and the construction of collective social identities in Latin America. It makes a comparative analysis of two research projects – the ‘Genoma Mexicano’ and the ‘Homo Brasilis’ – both of which sought to establish national and genetic profiles. Both have reproduced and strengthened the idea of their respective nations of focus, incorporating biological elements into debates on social identities. Also, both have placed the unifying figure of the mestizo/mestiço at the heart of national identity constructions, and in so doing have displaced alternative identity categories, such as those based on race. However, having been developed in different national contexts, these projects have had distinct scientific and social trajectories: in Mexico, the genomic mestizo is mobilized mainly in relation to health, while in Brazil the key arena is that of race. We show the importance of the nation as a frame for mobilizing genetic data in public policy debates, and demonstrate how race comes in and out of focus in different Latin American national contexts of genomic research, while never completely disappearing. PMID:27479999

  3. Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta).

    Science.gov (United States)

    Cremen, Ma Chiela M; Leliaert, Frederik; Marcelino, Vanessa R; Verbruggen, Heroen

    2018-04-01

    Chloroplast genomes have undergone tremendous alterations through the evolutionary history of the green algae (Chloroplastida). This study focuses on the evolution of chloroplast genomes in the siphonous green algae (order Bryopsidales). We present five new chloroplast genomes, which along with existing sequences, yield a data set representing all but one families of the order. Using comparative phylogenetic methods, we investigated the evolutionary dynamics of genomic features in the order. Our results show extensive variation in chloroplast genome architecture and intron content. Variation in genome size is accounted for by the amount of intergenic space and freestanding open reading frames that do not show significant homology to standard plastid genes. We show the diversity of these nonstandard genes based on their conserved protein domains, which are often associated with mobile functions (reverse transcriptase/intron maturase, integrases, phage- or plasmid-DNA primases, transposases, integrases, ligases). Investigation of the introns showed proliferation of group II introns in the early evolution of the order and their subsequent loss in the core Halimedineae, possibly through RT-mediated intron loss.

  4. Methodological Considerations in Estimation of Phenotype Heritability Using Genome-Wide SNP Data, Illustrated by an Analysis of the Heritability of Height in a Large Sample of African Ancestry Adults.

    Directory of Open Access Journals (Sweden)

    Fang Chen

    Full Text Available Height has an extremely polygenic pattern of inheritance. Genome-wide association studies (GWAS have revealed hundreds of common variants that are associated with human height at genome-wide levels of significance. However, only a small fraction of phenotypic variation can be explained by the aggregate of these common variants. In a large study of African-American men and women (n = 14,419, we genotyped and analyzed 966,578 autosomal SNPs across the entire genome using a linear mixed model variance components approach implemented in the program GCTA (Yang et al Nat Genet 2010, and estimated an additive heritability of 44.7% (se: 3.7% for this phenotype in a sample of evidently unrelated individuals. While this estimated value is similar to that given by Yang et al in their analyses, we remain concerned about two related issues: (1 whether in the complete absence of hidden relatedness, variance components methods have adequate power to estimate heritability when a very large number of SNPs are used in the analysis; and (2 whether estimation of heritability may be biased, in real studies, by low levels of residual hidden relatedness. We addressed the first question in a semi-analytic fashion by directly simulating the distribution of the score statistic for a test of zero heritability with and without low levels of relatedness. The second question was addressed by a very careful comparison of the behavior of estimated heritability for both observed (self-reported height and simulated phenotypes compared to imputation R2 as a function of the number of SNPs used in the analysis. These simulations help to address the important question about whether today's GWAS SNPs will remain useful for imputing causal variants that are discovered using very large sample sizes in future studies of height, or whether the causal variants themselves will need to be genotyped de novo in order to build a prediction model that ultimately captures a large fraction of the

  5. Mobilisation and remobilisation of a large archetypal pathogenicity island of uropathogenic Escherichia coli in vitro support the role of conjugation for horizontal transfer of genomic islands

    Directory of Open Access Journals (Sweden)

    Hochhut Bianca

    2011-09-01

    Full Text Available Abstract Background A substantial amount of data has been accumulated supporting the important role of genomic islands (GEIs - including pathogenicity islands (PAIs - in bacterial genome plasticity and the evolution of bacterial pathogens. Their instability and the high level sequence similarity of different (partial islands suggest an exchange of PAIs between strains of the same or even different bacterial species by horizontal gene transfer (HGT. Transfer events of archetypal large genomic islands of enterobacteria which often lack genes required for mobilisation or transfer have been rarely investigated so far. Results To study mobilisation of such large genomic regions in prototypic uropathogenic E. coli (UPEC strain 536, PAI II536 was supplemented with the mobRP4 region, an origin of replication (oriVR6K, an origin of transfer (oriTRP4 and a chloramphenicol resistance selection marker. In the presence of helper plasmid RP4, conjugative transfer of the 107-kb PAI II536 construct occured from strain 536 into an E. coli K-12 recipient. In transconjugants, PAI II536 existed either as a cytoplasmic circular intermediate (CI or integrated site-specifically into the recipient's chromosome at the leuX tRNA gene. This locus is the chromosomal integration site of PAI II536 in UPEC strain 536. From the E. coli K-12 recipient, the chromosomal PAI II536 construct as well as the CIs could be successfully remobilised and inserted into leuX in a PAI II536 deletion mutant of E. coli 536. Conclusions Our results corroborate that mobilisation and conjugal transfer may contribute to evolution of bacterial pathogens through horizontal transfer of large chromosomal regions such as PAIs. Stabilisation of these mobile genetic elements in the bacterial chromosome result from selective loss of mobilisation and transfer functions of genomic islands.

  6. Life-cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga Ostreococcus tauri.

    Directory of Open Access Journals (Sweden)

    Evelyne Derelle

    Full Text Available Large DNA viruses are ubiquitous, infecting diverse organisms ranging from algae to man, and have probably evolved from an ancient common ancestor. In aquatic environments, such algal viruses control blooms and shape the evolution of biodiversity in phytoplankton, but little is known about their biological functions. We show that Ostreococcus tauri, the smallest known marine photosynthetic eukaryote, whose genome is completely characterized, is a host for large DNA viruses, and present an analysis of the life-cycle and 186,234 bp long linear genome of OtV5. OtV5 is a lytic phycodnavirus which unexpectedly does not degrade its host chromosomes before the host cell bursts. Analysis of its complete genome sequence confirmed that it lacks expected site-specific endonucleases, and revealed the presence of 16 genes whose predicted functions are novel to this group of viruses. OtV5 carries at least one predicted gene whose protein closely resembles its host counterpart and several other host-like sequences, suggesting that horizontal gene transfers between host and viral genomes may occur frequently on an evolutionary scale. Fifty seven percent of the 268 predicted proteins present no similarities with any known protein in Genbank, underlining the wealth of undiscovered biological diversity present in oceanic viruses, which are estimated to harbour 200Mt of carbon.

  7. Large-scale building scenes reconstruction from close-range images based on line and plane feature

    Science.gov (United States)

    Ding, Yi; Zhang, Jianqing

    2007-11-01

    Automatic generate 3D models of buildings and other man-made structures from images has become a topic of increasing importance, those models may be in applications such as virtual reality, entertainment industry and urban planning. In this paper we address the main problems and available solution for the generation of 3D models from terrestrial images. We first generate a coarse planar model of the principal scene planes and then reconstruct windows to refine the building models. There are several points of novelty: first we reconstruct the coarse wire frame model use the line segments matching with epipolar geometry constraint; Secondly, we detect the position of all windows in the image and reconstruct the windows by established corner points correspondences between images, then add the windows to the coarse model to refine the building models. The strategy is illustrated on image triple of college building.

  8. Analysis of Various Inflow Turbulence Generation Methods in Large Eddy Simulation Approach for Prediction of Pollutant Dispersion around Model Buildings

    Directory of Open Access Journals (Sweden)

    F. Bazdidi Tehrani

    2017-02-01

    of windward wall of the second building. Among the various inflow turbulence generation methods, the vortex method is the most precise method and no-inlet perturbation method is the least precise method.

  9. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource.

    Science.gov (United States)

    Sharpton, Thomas J; Jospin, Guillaume; Wu, Dongying; Langille, Morgan G I; Pollard, Katherine S; Eisen, Jonathan A

    2012-10-13

    New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of protein diversity. We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences. We implemented fully automated and high-throughput procedures to de novo cluster proteins into families based upon global alignment similarity. Our approach employs an iterative clustering strategy in which homologs of known families are sifted out of the search for new families. The resulting reduction in computational complexity enables us to rapidly identify novel protein families found in new genomes and to perform efficient, automated updates that keep pace with genome sequencing. We refer to protein families identified through this approach as "Sifting Families," or SFams. Our analysis of ~10.5 million protein sequences from 2,928 genomes identified 436,360 SFams, many of which are not represented in other protein family databases. We validated the quality of SFam clustering through statistical as well as network topology-based analyses. We describe the rapid identification of SFams and demonstrate how they can be used to annotate genomes and metagenomes. The SFam database catalogs protein-family quality metrics, multiple sequence alignments, hidden Markov models, and phylogenetic trees. Our source code and database are publicly available and will be subject to frequent updates (http://edhar.genomecenter.ucdavis.edu/sifting_families/).

  10. 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.

  11. Large meta-analysis of genome-wide association studies identifies five loci for lean body mass

    DEFF Research Database (Denmark)

    Zillikens, M Carola; Demissie, Serkalem; Hsu, Yi-Hsiang

    2017-01-01

    Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorpt...... a meta-analysis of genome-wide association studies for whole body lean body mass and find five novel genetic loci to be significantly associated.......-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p 

  12. Partial loss of heterozygosity events at the mutated gene in tumors from MLH1/MSH2 large genomic rearrangement carriers

    Energy Technology Data Exchange (ETDEWEB)

    Zavodna, Katarina; Krivulcik, Tomas; Bujalkova, Maria Gerykova [Laboratory of Cancer Genetics, Cancer Research Institute of Slovak Academy of Sciences, Vlarska 7, 833 91 Bratislava (Slovakia); Slamka, Tomas; Martinicky, David; Ilencikova, Denisa [National Cancer Institute, Department of Oncologic Genetics, Klenova 1, 833 01 Bratislava (Slovakia); Bartosova, Zdena [Laboratory of Cancer Genetics, Cancer Research Institute of Slovak Academy of Sciences, Vlarska 7, 833 91 Bratislava (Slovakia)

    2009-11-20

    Depending on the population studied, large genomic rearrangements (LGRs) of the mismatch repair (MMR) genes constitute various proportions of the germline mutations that predispose to hereditary non-polyposis colorectal cancer (HNPCC). It has been reported that loss of heterozygosity (LOH) at the LGR region occurs through a gene conversion mechanism in tumors from MLH1/MSH2 deletion carriers; however, the converted tracts were delineated only by extragenic microsatellite markers. We sought to determine the frequency of LGRs in Slovak HNPCC patients and to study LOH in tumors from LGR carriers at the LGR region, as well as at other heterozygous markers within the gene to more precisely define conversion tracts. The main MMR genes responsible for HNPCC, MLH1, MSH2, MSH6, and PMS2, were analyzed by MLPA (multiplex ligation-dependent probe amplification) in a total of 37 unrelated HNPCC-suspected patients whose MLH1/MSH2 genes gave negative results in previous sequencing experiments. An LOH study was performed on six tumors from LGR carriers by combining MLPA to assess LOH at LGR regions and sequencing to examine LOH at 28 SNP markers from the MLH1 and MSH2 genes. We found six rearrangements in the MSH2 gene (five deletions and dup5-6), and one aberration in the MLH1 gene (del5-6). The MSH2 deletions were of three types (del1, del1-3, del1-7). We detected LOH at the LGR region in the single MLH1 case, which was determined in a previous study to be LOH-negative in the intragenic D3S1611 marker. Three tumors displayed LOH of at least one SNP marker, including two cases that were LOH-negative at the LGR region. LGRs accounted for 25% of germline MMR mutations identified in 28 Slovakian HNPCC families. A high frequency of LGRs among the MSH2 mutations provides a rationale for a MLPA screening of the Slovakian HNPCC families prior scanning by DNA sequencing. LOH at part of the informative loci confined to the MLH1 or MSH2 gene (heterozygous LGR region, SNP, or

  13. Partial loss of heterozygosity events at the mutated gene in tumors from MLH1/MSH2 large genomic rearrangement carriers

    Directory of Open Access Journals (Sweden)

    Ilencikova Denisa

    2009-11-01

    Full Text Available Abstract Background Depending on the population studied, large genomic rearrangements (LGRs of the mismatch repair (MMR genes constitute various proportions of the germline mutations that predispose to hereditary non-polyposis colorectal cancer (HNPCC. It has been reported that loss of heterozygosity (LOH at the LGR region occurs through a gene conversion mechanism in tumors from MLH1/MSH2 deletion carriers; however, the converted tracts were delineated only by extragenic microsatellite markers. We sought to determine the frequency of LGRs in Slovak HNPCC patients and to study LOH in tumors from LGR carriers at the LGR region, as well as at other heterozygous markers within the gene to more precisely define conversion tracts. Methods The main MMR genes responsible for HNPCC, MLH1, MSH2, MSH6, and PMS2, were analyzed by MLPA (multiplex ligation-dependent probe amplification in a total of 37 unrelated HNPCC-suspected patients whose MLH1/MSH2 genes gave negative results in previous sequencing experiments. An LOH study was performed on six tumors from LGR carriers by combining MLPA to assess LOH at LGR regions and sequencing to examine LOH at 28 SNP markers from the MLH1 and MSH2 genes. Results We found six rearrangements in the MSH2 gene (five deletions and dup5-6, and one aberration in the MLH1 gene (del5-6. The MSH2 deletions were of three types (del1, del1-3, del1-7. We detected LOH at the LGR region in the single MLH1 case, which was determined in a previous study to be LOH-negative in the intragenic D3S1611 marker. Three tumors displayed LOH of at least one SNP marker, including two cases that were LOH-negative at the LGR region. Conclusion LGRs accounted for 25% of germline MMR mutations identified in 28 Slovakian HNPCC families. A high frequency of LGRs among the MSH2 mutations provides a rationale for a MLPA screening of the Slovakian HNPCC families prior scanning by DNA sequencing. LOH at part of the informative loci confined to the MLH1

  14. Partial loss of heterozygosity events at the mutated gene in tumors from MLH1/MSH2 large genomic rearrangement carriers

    International Nuclear Information System (INIS)

    Zavodna, Katarina; Krivulcik, Tomas; Bujalkova, Maria Gerykova; Slamka, Tomas; Martinicky, David; Ilencikova, Denisa; Bartosova, Zdena

    2009-01-01

    Depending on the population studied, large genomic rearrangements (LGRs) of the mismatch repair (MMR) genes constitute various proportions of the germline mutations that predispose to hereditary non-polyposis colorectal cancer (HNPCC). It has been reported that loss of heterozygosity (LOH) at the LGR region occurs through a gene conversion mechanism in tumors from MLH1/MSH2 deletion carriers; however, the converted tracts were delineated only by extragenic microsatellite markers. We sought to determine the frequency of LGRs in Slovak HNPCC patients and to study LOH in tumors from LGR carriers at the LGR region, as well as at other heterozygous markers within the gene to more precisely define conversion tracts. The main MMR genes responsible for HNPCC, MLH1, MSH2, MSH6, and PMS2, were analyzed by MLPA (multiplex ligation-dependent probe amplification) in a total of 37 unrelated HNPCC-suspected patients whose MLH1/MSH2 genes gave negative results in previous sequencing experiments. An LOH study was performed on six tumors from LGR carriers by combining MLPA to assess LOH at LGR regions and sequencing to examine LOH at 28 SNP markers from the MLH1 and MSH2 genes. We found six rearrangements in the MSH2 gene (five deletions and dup5-6), and one aberration in the MLH1 gene (del5-6). The MSH2 deletions were of three types (del1, del1-3, del1-7). We detected LOH at the LGR region in the single MLH1 case, which was determined in a previous study to be LOH-negative in the intragenic D3S1611 marker. Three tumors displayed LOH of at least one SNP marker, including two cases that were LOH-negative at the LGR region. LGRs accounted for 25% of germline MMR mutations identified in 28 Slovakian HNPCC families. A high frequency of LGRs among the MSH2 mutations provides a rationale for a MLPA screening of the Slovakian HNPCC families prior scanning by DNA sequencing. LOH at part of the informative loci confined to the MLH1 or MSH2 gene (heterozygous LGR region, SNP, or

  15. SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints

    Science.gov (United States)

    2014-01-01

    Background Genomic disorders are caused by copy number changes that may exhibit recurrent breakpoints processed by nonallelic homologous recombination. However, region-specific disease-associated copy number changes have also been observed which exhibit non-recurrent breakpoints. The mechanisms underlying these non-recurrent copy number changes have not yet been fully elucidated. Results We analyze large NF1 deletions with non-recurrent breakpoints as a model to investigate the full spectrum of causative mechanisms, and observe that they are mediated by various DNA double strand break repair mechanisms, as well as aberrant replication. Further, two of the 17 NF1 deletions with non-recurrent breakpoints, identified in unrelated patients, occur in association with the concomitant insertion of SINE/variable number of tandem repeats/Alu (SVA) retrotransposons at the deletion breakpoints. The respective breakpoints are refractory to analysis by standard breakpoint-spanning PCRs and are only identified by means of optimized PCR protocols designed to amplify across GC-rich sequences. The SVA elements are integrated within SUZ12P intron 8 in both patients, and were mediated by target-primed reverse transcription of SVA mRNA intermediates derived from retrotranspositionally active source elements. Both SVA insertions occurred during early postzygotic development and are uniquely associated with large deletions of 1 Mb and 867 kb, respectively, at the insertion sites. Conclusions Since active SVA elements are abundant in the human genome and the retrotranspositional activity of many SVA source elements is high, SVA insertion-associated large genomic deletions encompassing many hundreds of kilobases could constitute a novel and as yet under-appreciated mechanism underlying large-scale copy number changes in the human genome. PMID:24958239

  16. The variability of the large genomic segment of Tahyna orthobunyavirus and an all-atom exploration of its anti-viral drug resistance

    Czech Academy of Sciences Publication Activity Database

    Kilian, Patrik; Valdés, James J.; Lecina-Casas, D.; Chrudimský, T.; Růžek, Daniel

    2013-01-01

    Roč. 20, 2013-Dec (2013), s. 304-311 ISSN 1567-1348 R&D Projects: GA ČR GAP502/11/2116; GA MŠk(CZ) EE2.3.30.0032 Institutional support: RVO:60077344 Keywords : Tahyna virus * Orthobunyavirus * California complex * Genetic variability * Large genomic segment Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.264, year: 2013

  17. Glass-covering of large building volumes. An interdisciplinary evaluation of a shopping centre; Oeverglasning av stora byggnadsvolymer; En tvaervetenskaplig utvaerdering av ett koepcentrum

    Energy Technology Data Exchange (ETDEWEB)

    Oeman, R. [Royal Inst. of Tech., Stockholm (Sweden). Dept. of Building Technology

    1993-11-01

    Systematized experiences of the function of large glass- covered spaces related to shopping centres, hotels, office buildings etc. are still relatively limited. With the glazed pedestrian precincts of the rebuilt Skaerholmen Centre in Stockholm as the main object of interdisciplinary studies, the aim of this thesis is to provide additional knowledge of large glass-covered spaces (atrium buildings). The studies comprises thermal comfort, temperature conditions, ventilation, energy balance, humidity - mycology, acoustics, operation - maintenance - durability and sociology. To sum up, it is clear that in the Scandinavian climate there is every likelihood of large glass-covered spaces in the public places functioning well from a technical as well as a social point of view. The energy consumption on heating the whole complex, based on theoretical calculations and measurement, is shown to have been reduced by the order of 10%. (author) figs., tabs., 101 refs

  18. Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species

    OpenAIRE

    Kim, Jae-Heup; Antunes, Agostinho; Luo, Shu-Jin; Menninger, Joan; Nash, William G.; O’Brien, Stephen J.; Johnson, Warren E.

    2005-01-01

    Translocation of cymtDNA into the nuclear genome, also referred to as numt, has been reported in many species, including several closely related to the domestic cat (Felis catus). We describe the recent transposition of 12,536 bp of the 17 kb mitochondrial genome into the nucleus of the common ancestor of the five Panthera genus species: tiger, P. tigris; snow leopard, P. uncia; jaguar, P. onca; leopard, P. pardus; and lion, P. leo. This nuclear integration, representing 74% of the mitochondr...

  19. Design of intelligent power consumption optimization and visualization management platform for large buildings based on internet of things

    Directory of Open Access Journals (Sweden)

    Gong Shulan

    2017-01-01

    Full Text Available The buildings provide a significant contribution to total energy consumption and CO2 emission. It has been estimated that the development of an intelligent power consumption monitor and control system will result in about 30% savings in energy consumption. This design innovatively integrates the advanced technologies such as the internet of things, the internet, intelligent buildings and intelligent electricity which can offer open, efficient, convenient energy consumption detection platform in demand side and visual management demonstration application platform in power enterprises side. The system was created to maximize the effective and efficient the use of energy resource. It was development around sensor networks and intelligent gateway and the monitoring center software. This will realize the highly integration and comprehensive application in energy and information to meet the needs with intelligent buildings

  20. The effect of plasma minor-radius expansion in the current build-up phase of a large tokamak

    International Nuclear Information System (INIS)

    Kobayashi, Tomofumi; Tazima, Teruhiko; Tani, Keiji; Tamura, Sanae

    1977-03-01

    A plasma simulation code has been developed to study the plasma current build-up process in JT-60. Plasma simulation is made with a model which represents well overall plasma behavior of the present-day tokamaks. The external electric circuit is taken into consideration in simulation calculation. An emphasis is placed on the simulation of minor-radius expansion of the plasma and behavior of neutral particles in the plasma during current build-up. A calculation with typical parameters of JT-60 shows a week skin distribution in the current density and the electron temperature, if the minor radius of the plasma expands with build-up of the plasma current. (auth.)

  1. Large scale experiments simulating hydrogen distribution in a spent fuel pool building during a hypothetical fuel uncovery accident scenario

    Energy Technology Data Exchange (ETDEWEB)

    Mignot, Guillaume; Paranjape, Sidharth; Paladino, Domenico; Jaeckel, Bernd; Rydl, Adolf [Paul Scherrer Institute, Villigen (Switzerland)

    2016-08-15

    Following the Fukushima accident and its extended station blackout, attention was brought to the importance of the spent fuel pools' (SFPs) behavior in case of a prolonged loss of the cooling system. Since then, many analytical works have been performed to estimate the timing of hypothetical fuel uncovery for various SFP types. Experimentally, however, little was done to investigate issues related to the formation of a flammable gas mixture, distribution, and stratification in the SFP building itself and to some extent assess the capability for the code to correctly predict it. This paper presents the main outcomes of the Experiments on Spent Fuel Pool (ESFP) project carried out under the auspices of Swissnuclear (Framework 2012–2013) in the PANDA facility at the Paul Scherrer Institut in Switzerland. It consists of an experimental investigation focused on hydrogen concentration build-up into a SFP building during a predefined scaled scenario for different venting positions. Tests follow a two-phase scenario. Initially steam is released to mimic the boiling of the pool followed by a helium/steam mixture release to simulate the deterioration of the oxidizing spent fuel. Results shows that while the SFP building would mainly be inerted by the presence of a high concentration of steam, the volume located below the level of the pool in adjacent rooms would maintain a high air content. The interface of the two-gas mixture presents the highest risk of flammability. Additionally, it was observed that the gas mixture could become stagnant leading locally to high hydrogen concentration while steam condenses. Overall, the experiments provide relevant information for the potentially hazardous gas distribution formed in the SFP building and hints on accident management and on eventual retrofitting measures to be implemented in the SFP building.

  2. Large meta-analysis of genome-wide association studies identifies five loci for lean body mass

    NARCIS (Netherlands)

    Zillikens, M.C.; Demissie, Serkalem; Hsu, Yi Hsiang; Yerges-Armstrong, Laura M.; Chou, Wen Chi; Stolk, Lisette; Livshits, Gregory; Broer, Linda; Johnson, Toby; Koller, Daniel L.; Kutalik, Zoltán; Luan, J.A.; Malkin, Ida; Ried, Janina S.; Smith, Albert V.; Thorleifsson, Gudmar; Vandenput, Liesbeth; Hua Zhao, Jing; Zhang, Weihua; Aghdassi, Ali; Åkesson, Kristina; Amin, Najaf; Baier, Leslie J.; Barroso, Inês; Bennett, David A.; Bertram, Lars; Biffar, Rainer; Bochud, Murielle; Boehnke, Michael; Borecki, Ingrid B.; Buchman, Aron S.; Byberg, Liisa; Campbell, Harry; Campos Obanda, Natalia; Cauley, Jane A.; Cawthon, Peggy M.; Cederberg, Henna; Chen, Zhao; Cho, Nam H.; Jin Choi, Hyung; Claussnitzer, Melina; Collins, Francis; Cummings, Steven R.; Jager, De Philip L.; Demuth, Ilja; Dhonukshe-Rutten, Rosalie A.M.; DIatchenko, Luda; Eiriksdottir, Gudny; Enneman, Anke W.; Erdos, Mike; Eriksson, Johan G.; Eriksson, Joel; Estrada, Karol; Evans, Daniel S.; Feitosa, Mary F.; Fu, Mao; Garcia, Melissa; Gieger, Christian; Girke, Thomas; Glazer, Nicole L.; Grallert, Harald; Grewal, Jagvir; Han, Bok Ghee; Hanson, Robert L.; Hayward, Caroline; Hofman, Albert; Hoffman, Eric P.; Homuth, Georg; Hsueh, Wen Chi; Hubal, Monica J.; Hubbard, Alan; Huffman, Kim M.; Husted, Lise B.; Illig, Thomas; Ingelsson, Erik; Ittermann, Till; Jansson, John Olov; Jordan, Joanne M.; Jula, Antti; Karlsson, Magnus; Khaw, Kay Tee; Kilpelaïnen, Tuomas O.; Klopp, Norman; Kloth, Jacqueline S.L.; Koistinen, Heikki A.; Kraus, William E.; Kritchevsky, Stephen; Kuulasmaa, Teemu; Kuusisto, Johanna; Laakso, Markku; Lahti, Jari; Lang, Thomas; Langdahl, Bente L.; Launer, Lenore J.; Lee, Jong Young; Lerch, Markus M.; Lewis, Joshua R.; Lind, Lars; Lindgren, Cecilia M.; Liu, Yongmei; Liu, Tian; Liu, Youfang; Ljunggren, Östen; Lorentzon, Mattias; Luben, Robert N.; Maixner, William; McGuigan, Fiona E.; Medina-Gomez, Carolina; Meitinger, Thomas; Melhus, Håkan; Mellström, Dan; Melov, Simon; Michaëlsson, Karl; Mitchell, Braxton D.; Morris, Andrew P.; Mosekilde, Leif; Newman, Anne; Nielson, Carrie M.; O'Connell, Jeffrey R.; Oostra, Ben A.; Orwoll, Eric S.; Palotie, Aarno; Parker, Stephan; Peacock, Munro; Perola, Markus; Peters, Annette; Polasek, Ozren; Prince, Richard L.; Raïkkönen, Katri; Ralston, Stuart H.; Ripatti, Samuli; Robbins, John A.; Rotter, Jerome I.; Rudan, Igor; Salomaa, Veikko; Satterfield, Suzanne; Schadt, Eric E.; Schipf, Sabine; Scott, Laura; Sehmi, Joban; Shen, Jian; Soo Shin, Chan; Sigurdsson, Gunnar; Smith, Shad; Soranzo, Nicole; Stančáková, Alena; Steinhagen-Thiessen, Elisabeth; Streeten, Elizabeth A.; Styrkarsdottir, Unnur; Swart, Karin M.A.; Tan, Sian Tsung; Tarnopolsky, Mark A.; Thompson, Patricia; Thomson, Cynthia A.; Thorsteinsdottir, Unnur; Tikkanen, Emmi; Tranah, Gregory J.; Tuomilehto, Jaakko; Schoor, van Natasja M.; Verma, Arjun; Vollenweider, Peter; Völzke, Henry; Wactawski-Wende, Jean; Walker, Mark; Weedon, Michael N.; Welch, Ryan; Wichman, H.E.; Widen, Elisabeth; Williams, Frances M.K.; Wilson, James F.; Wright, Nicole C.; Xie, Weijia; Yu, Lei; Zhou, Yanhua; Chambers, John C.; Döring, Angela; Duijn, Van Cornelia M.; Econs, Michael J.; Gudnason, Vilmundur; Kooner, Jaspal S.; Psaty, Bruce M.; Spector, Timothy D.; Stefansson, Kari; Rivadeneira, Fernando; Uitterlinden, André G.; Wareham, Nicholas J.; Ossowski, Vicky; Waterworth, Dawn M.; Loos, Ruth J.F.; Karasik, David; Harris, Tamara B.; Ohlsson, Claes; Kiel, Douglas P.

    2017-01-01

    Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray

  3. Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework.

    Science.gov (United States)

    Li, Miaoxin; Li, Jiang; Li, Mulin Jun; Pan, Zhicheng; Hsu, Jacob Shujui; Liu, Dajiang J; Zhan, Xiaowei; Wang, Junwen; Song, Youqiang; Sham, Pak Chung

    2017-05-19

    Whole genome sequencing (WGS) is a promising strategy to unravel variants or genes responsible for human diseases and traits. However, there is a lack of robust platforms for a comprehensive downstream analysis. In the present study, we first proposed three novel algorithms, sequence gap-filled gene feature annotation, bit-block encoded genotypes and sectional fast access to text lines to address three fundamental problems. The three algorithms then formed the infrastructure of a robust parallel computing framework, KGGSeq, for integrating downstream analysis functions for whole genome sequencing data. KGGSeq has been equipped with a comprehensive set of analysis functions for quality control, filtration, annotation, pathogenic prediction and statistical tests. In the tests with whole genome sequencing data from 1000 Genomes Project, KGGSeq annotated several thousand more reliable non-synonymous variants than other widely used tools (e.g. ANNOVAR and SNPEff). It took only around half an hour on a small server with 10 CPUs to access genotypes of ∼60 million variants of 2504 subjects, while a popular alternative tool required around one day. KGGSeq's bit-block genotype format used 1.5% or less space to flexibly represent phased or unphased genotypes with multiple alleles and achieved a speed of over 1000 times faster to calculate genotypic correlation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. An Atypical Human Induced Pluripotent Stem Cell Line With a Complex, Stable, and Balanced Genomic Rearrangement Including a Large De Novo 1q Uniparental Disomy

    Science.gov (United States)

    Steichen, Clara; Maluenda, Jérôme; Tosca, Lucie; Luce, Eléanor; Pineau, Dominique; Dianat, Noushin; Hannoun, Zara; Tachdjian, Gérard; Melki, Judith

    2015-01-01

    Human induced pluripotent stem cells (hiPSCs) hold great promise for cell therapy through their use as vital tools for regenerative and personalized medicine. However, the genomic integrity of hiPSCs still raises some concern and is one of the barriers limiting their use in clinical applications. Numerous articles have reported the occurrence of aneuploidies, copy number variations, or single point mutations in hiPSCs, and nonintegrative reprogramming strategies have been developed to minimize the impact of the reprogramming process on the hiPSC genome. Here, we report the characterization of an hiPSC line generated by daily transfections of modified messenger RNAs, displaying several genomic abnormalities. Karyotype analysis showed a complex genomic rearrangement, which remained stable during long-term culture. Fluorescent in situ hybridization analyses were performed on the hiPSC line showing that this karyotype is balanced. Interestingly, single-nucleotide polymorphism analysis revealed the presence of a large 1q region of uniparental disomy (UPD), demonstrating for the first time that UPD can occur in a noncompensatory context during nonintegrative reprogramming of normal fibroblasts. PMID:25650439

  5. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource

    Directory of Open Access Journals (Sweden)

    Sharpton Thomas J

    2012-10-01

    Full Text Available Abstract Background New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of protein diversity. We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences. Results We implemented fully automated and high-throughput procedures to de novo cluster proteins into families based upon global alignment similarity. Our approach employs an iterative clustering strategy in which homologs of known families are sifted out of the search for new families. The resulting reduction in computational complexity enables us to rapidly identify novel protein families found in new genomes and to perform efficient, automated updates that keep pace with genome sequencing. We refer to protein families identified through this approach as “Sifting Families,” or SFams. Our analysis of ~10.5 million protein sequences from 2,928 genomes identified 436,360 SFams, many of which are not represented in other protein family databases. We validated the quality of SFam clustering through statistical as well as network topology–based analyses. Conclusions We describe the rapid identification of SFams and demonstrate how they can be used to annotate genomes and metagenomes. The SFam database catalogs protein-family quality metrics, multiple sequence alignments, hidden Markov models, and phylogenetic trees. Our source code and database are publicly available and will be subject to frequent updates (http://edhar.genomecenter.ucdavis.edu/sifting_families/.

  6. Coral life history and symbiosis: Functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata

    Directory of Open Access Journals (Sweden)

    Szmant Alina M

    2008-02-01

    -scleractinian cnidarians Nematostella vectensis and Hydra magnipapillata. Conclusion Partial sequencing of 5 cDNA libraries each for A. palmata and M. faveolata has produced a rich set of candidate genes (4,980 genes from A. palmata, and 1,732 genes from M. faveolata that we can use as a starting point for examining the life history and symbiosis of these two species, as well as to further expand the dataset of cnidarian genes for comparative genomics and evolutionary studies.

  7. Coral life history and symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata.

    Science.gov (United States)

    Schwarz, Jodi A; Brokstein, Peter B; Voolstra, Christian; Terry, Astrid Y; Manohar, Chitra F; Miller, David J; Szmant, Alina M; Coffroth, Mary Alice; Medina, Mónica

    2008-02-25

    Hydra magnipapillata. Partial sequencing of 5 cDNA libraries each for A. palmata and M. faveolata has produced a rich set of candidate genes (4,980 genes from A. palmata, and 1,732 genes from M. faveolata) that we can use as a starting point for examining the life history and symbiosis of these two species, as well as to further expand the dataset of cnidarian genes for comparative genomics and evolutionary studies.

  8. Genomics With Cloud Computing

    OpenAIRE

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

    Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

  9. Large meta-analysis of genome-wide association studies identifies five loci for lean body mass

    OpenAIRE

    Zillikens, Carola M.; Demissie, Serkalem; Hsu, Yi-Hsiang; Yerges-Armstrong, Laura M.; Chou, Wen-Chi; Stolk, Lisette; Demuth, Ilja; Steinhagen-Thiessen, Elisabeth [u.v.m.

    2017-01-01

    We acknowledge the essential role of the Cohorts for Heart and Aging Research in Genome Epidemiology (CHARGE) Consortium in development and support of this manuscript. CHARGE members include the Netherland’s Rotterdam Study (RS), Framingham Heart Study (FHS), Cardiovascular Health Study (CHS), the NHLBI’s Atherosclerosis Risk in Communities (ARIC) Study, and Iceland’s Age, Gene/Environment Susceptibility (AGES) Reykjavik Study. Age, Gene/Environment Susceptibility Reykjavik Study (AGES-Reykja...

  10. Genome wide analysis of drug-induced torsades de pointes: lack of common variants with large effect sizes.

    Directory of Open Access Journals (Sweden)

    Elijah R Behr

    Full Text Available Marked prolongation of the QT interval on the electrocardiogram associated with the polymorphic ventricular tachycardia Torsades de Pointes is a serious adverse event during treatment with antiarrhythmic drugs and other culprit medications, and is a common cause for drug relabeling and withdrawal. Although clinical risk factors have been identified, the syndrome remains unpredictable in an individual patient. Here we used genome-wide association analysis to search for common predisposing genetic variants. Cases of drug-induced Torsades de Pointes (diTdP, treatment tolerant controls, and general population controls were ascertained across multiple sites using common definitions, and genotyped on the Illumina 610k or 1M-Duo BeadChips. Principal Components Analysis was used to select 216 Northwestern European diTdP cases and 771 ancestry-matched controls, including treatment-tolerant and general population subjects. With these sample sizes, there is 80% power to detect a variant at genome-wide significance with minor allele frequency of 10% and conferring an odds ratio of ≥2.7. Tests of association were carried out for each single nucleotide polymorphism (SNP by logistic regression adjusting for gender and population structure. No SNP reached genome wide-significance; the variant with the lowest P value was rs2276314, a non-synonymous coding variant in C18orf21 (p  =  3×10(-7, odds ratio = 2, 95% confidence intervals: 1.5-2.6. The haplotype formed by rs2276314 and a second SNP, rs767531, was significantly more frequent in controls than cases (p  =  3×10(-9. Expanding the number of controls and a gene-based analysis did not yield significant associations. This study argues that common genomic variants do not contribute importantly to risk for drug-induced Torsades de Pointes across multiple drugs.

  11. Large meta-analysis of genome-wide association studies identifies five loci for lean body mass.

    Science.gov (United States)

    Zillikens, M Carola; Demissie, Serkalem; Hsu, Yi-Hsiang; Yerges-Armstrong, Laura M; Chou, Wen-Chi; Stolk, Lisette; Livshits, Gregory; Broer, Linda; Johnson, Toby; Koller, Daniel L; Kutalik, Zoltán; Luan, Jian'an; Malkin, Ida; Ried, Janina S; Smith, Albert V; Thorleifsson, Gudmar; Vandenput, Liesbeth; Hua Zhao, Jing; Zhang, Weihua; Aghdassi, Ali; Åkesson, Kristina; Amin, Najaf; Baier, Leslie J; Barroso, Inês; Bennett, David A; Bertram, Lars; Biffar, Rainer; Bochud, Murielle; Boehnke, Michael; Borecki, Ingrid B; Buchman, Aron S; Byberg, Liisa; Campbell, Harry; Campos Obanda, Natalia; Cauley, Jane A; Cawthon, Peggy M; Cederberg, Henna; Chen, Zhao; Cho, Nam H; Jin Choi, Hyung; Claussnitzer, Melina; Collins, Francis; Cummings, Steven R; De Jager, Philip L; Demuth, Ilja; Dhonukshe-Rutten, Rosalie A M; Diatchenko, Luda; Eiriksdottir, Gudny; Enneman, Anke W; Erdos, Mike; Eriksson, Johan G; Eriksson, Joel; Estrada, Karol; Evans, Daniel S; Feitosa, Mary F; Fu, Mao; Garcia, Melissa; Gieger, Christian; Girke, Thomas; Glazer, Nicole L; Grallert, Harald; Grewal, Jagvir; Han, Bok-Ghee; Hanson, Robert L; Hayward, Caroline; Hofman, Albert; Hoffman, Eric P; Homuth, Georg; Hsueh, Wen-Chi; Hubal, Monica J; Hubbard, Alan; Huffman, Kim M; Husted, Lise B; Illig, Thomas; Ingelsson, Erik; Ittermann, Till; Jansson, John-Olov; Jordan, Joanne M; Jula, Antti; Karlsson, Magnus; Khaw, Kay-Tee; Kilpeläinen, Tuomas O; Klopp, Norman; Kloth, Jacqueline S L; Koistinen, Heikki A; Kraus, William E; Kritchevsky, Stephen; Kuulasmaa, Teemu; Kuusisto, Johanna; Laakso, Markku; Lahti, Jari; Lang, Thomas; Langdahl, Bente L; Launer, Lenore J; Lee, Jong-Young; Lerch, Markus M; Lewis, Joshua R; Lind, Lars; Lindgren, Cecilia; Liu, Yongmei; Liu, Tian; Liu, Youfang; Ljunggren, Östen; Lorentzon, Mattias; Luben, Robert N; Maixner, William; McGuigan, Fiona E; Medina-Gomez, Carolina; Meitinger, Thomas; Melhus, Håkan; Mellström, Dan; Melov, Simon; Michaëlsson, Karl; Mitchell, Braxton D; Morris, Andrew P; Mosekilde, Leif; Newman, Anne; Nielson, Carrie M; O'Connell, Jeffrey R; Oostra, Ben A; Orwoll, Eric S; Palotie, Aarno; Parker, Stephen C J; Peacock, Munro; Perola, Markus; Peters, Annette; Polasek, Ozren; Prince, Richard L; Räikkönen, Katri; Ralston, Stuart H; Ripatti, Samuli; Robbins, John A; Rotter, Jerome I; Rudan, Igor; Salomaa, Veikko; Satterfield, Suzanne; Schadt, Eric E; Schipf, Sabine; Scott, Laura; Sehmi, Joban; Shen, Jian; Soo Shin, Chan; Sigurdsson, Gunnar; Smith, Shad; Soranzo, Nicole; Stančáková, Alena; Steinhagen-Thiessen, Elisabeth; Streeten, Elizabeth A; Styrkarsdottir, Unnur; Swart, Karin M A; Tan, Sian-Tsung; Tarnopolsky, Mark A; Thompson, Patricia; Thomson, Cynthia A; Thorsteinsdottir, Unnur; Tikkanen, Emmi; Tranah, Gregory J; Tuomilehto, Jaakko; van Schoor, Natasja M; Verma, Arjun; Vollenweider, Peter; Völzke, Henry; Wactawski-Wende, Jean; Walker, Mark; Weedon, Michael N; Welch, Ryan; Wichmann, H-Erich; Widen, Elisabeth; Williams, Frances M K; Wilson, James F; Wright, Nicole C; Xie, Weijia; Yu, Lei; Zhou, Yanhua; Chambers, John C; Döring, Angela; van Duijn, Cornelia M; Econs, Michael J; Gudnason, Vilmundur; Kooner, Jaspal S; Psaty, Bruce M; Spector, Timothy D; Stefansson, Kari; Rivadeneira, Fernando; Uitterlinden, André G; Wareham, Nicholas J; Ossowski, Vicky; Waterworth, Dawn; Loos, Ruth J F; Karasik, David; Harris, Tamara B; Ohlsson, Claes; Kiel, Douglas P

    2017-07-19

    Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p lean body mass and in 45,090 (42,360 of European ancestry) subjects from 25 cohorts for appendicular lean body mass was successful for five single-nucleotide polymorphisms in/near HSD17B11, VCAN, ADAMTSL3, IRS1, and FTO for total lean body mass and for three single-nucleotide polymorphisms in/near VCAN, ADAMTSL3, and IRS1 for appendicular lean body mass. Our findings provide new insight into the genetics of lean body mass.Lean body mass is a highly heritable trait and is associated with various health conditions. Here, Kiel and colleagues perform a meta-analysis of genome-wide association studies for whole body lean body mass and find five novel genetic loci to be significantly associated.

  12. SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets.

    Science.gov (United States)

    Mao, Hongliang; Wang, Hao

    2017-03-01

    Short Interspersed Nuclear Elements (SINEs) are transposable elements (TEs) that amplify through a copy-and-paste mode via RNA intermediates. The computational identification of new SINEs are challenging because of their weak structural signals and rapid diversification in sequences. Here we report SINE_Scan, a highly efficient program to predict SINE elements in genomic DNA sequences. SINE_Scan integrates hallmark of SINE transposition, copy number and structural signals to identify a SINE element. SINE_Scan outperforms the previously published de novo SINE discovery program. It shows high sensitivity and specificity in 19 plant and animal genome assemblies, of which sizes vary from 120 Mb to 3.5 Gb. It identifies numerous new families and substantially increases the estimation of the abundance of SINEs in these genomes. The code of SINE_Scan is freely available at http://github.com/maohlzj/SINE_Scan , implemented in PERL and supported on Linux. wangh8@fudan.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  13. Building 2000

    International Nuclear Information System (INIS)

    Den Ouden, C.; Steemers, T.C.

    1992-01-01

    This is the first volume of Building 2000, a pilot project of the Commission's R and D-programme 'Solar Energy Applications to Buildings' with the purpose of encouraging the adoption of solar architecture in large buildings. In this first rich illustrated volume the results of the design studies illustrating passive solar architecture in buildings in the European Community are presented in particular for the building categories as mentioned in the subtitle. In a second volume, a similar series of studies is presented for the building categories: office buildings, public buildings and hotels and holiday complexes. Several Design Support Workshops were organized during the Building 2000 programme during which Building 2000 design teams could directly exchange ideas with the various design advice experts represented at these workshops. In the second part of the Building 2000 final report a summary of a selection of many reports is presented (15 papers), as produced by Design Support experts. Most of the design support activities resulted in changes of the various designs, as have been reported by the design teams in the brochures presented in the first part of this book. It is to be expected that design aids and simulation tools for passive solar options, daylighting concepts, comfort criteria etc., will be utilized more frequently in the future. This will result in a better exchange of information between the actual design practitioners and the European R and D community. This technology transfer will result in buildings with a higher quality with respect to energy and environmental issues

  14. Building 2000

    Energy Technology Data Exchange (ETDEWEB)

    Den Ouden, C [EGM Engineering BV, Dordrecht (Netherlands); Steemers, T C [Commission of the European Communities, Brussels (Belgium)

    1992-01-01

    This is the first volume of Building 2000, a pilot project of the Commission's R and D-programme 'Solar Energy Applications to Buildings' with the purpose of encouraging the adoption of solar architecture in large buildings. In this first rich illustrated volume the results of the design studies illustrating passive solar architecture in buildings in the European Community are presented in particular for the building categories as mentioned in the subtitle. In a second volume, a similar series of studies is presented for the building categories: office buildings, public buildings and hotels and holiday complexes. Several Design Support Workshops were organized during the Building 2000 programme during which Building 2000 design teams could directly exchange ideas with the various design advice experts represented at these workshops. In the second part of the Building 2000 final report a summary of a selection of many reports is presented (15 papers), as produced by Design Support experts. Most of the design support activities resulted in changes of the various designs, as have been reported by the design teams in the brochures presented in the first part of this book. It is to be expected that design aids and simulation tools for passive solar options, daylighting concepts, comfort criteria etc., will be utilized more frequently in the future. This will result in a better exchange of information between the actual design practitioners and the European R and D community. This technology transfer will result in buildings with a higher quality with respect to energy and environmental issues.

  15. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies

    Energy Technology Data Exchange (ETDEWEB)

    Catfish Genome Consortium; Wang, Shaolin; Peatman, Eric; Abernathy, Jason; Waldbieser, Geoff; Lindquist, Erika; Richardson, Paul; Lucas, Susan; Wang, Mei; Li, Ping; Thimmapuram, Jyothi; Liu, Lei; Vullaganti, Deepika; Kucuktas, Huseyin; Murdock, Christopher; Small, Brian C; Wilson, Melanie; Liu, Hong; Jiang, Yanliang; Lee, Yoona; Chen, Fei; Lu, Jianguo; Wang, Wenqi; Xu, Peng; Somridhivej, Benjaporn; Baoprasertkul, Puttharat; Quilang, Jonas; Sha, Zhenxia; Bao, Baolong; Wang, Yaping; Wang, Qun; Takano, Tomokazu; Nandi, Samiran; Liu, Shikai; Wong, Lilian; Kaltenboeck, Ludmilla; Quiniou, Sylvie; Bengten, Eva; Miller, Norman; Trant, John; Rokhsar, Daniel; Liu, Zhanjiang

    2010-03-23

    Background-Through the Community Sequencing Program, a catfish EST sequencing project was carried out through a collaboration between the catfish research community and the Department of Energy's Joint Genome Institute. Prior to this project, only a limited EST resource from catfish was available for the purpose of SNP identification. Results-A total of 438,321 quality ESTs were generated from 8 channel catfish (Ictalurus punctatus) and 4 blue catfish (Ictalurus furcatus) libraries, bringing the number of catfish ESTs to nearly 500,000. Assembly of all catfish ESTs resulted in 45,306 contigs and 66,272 singletons. Over 35percent of the unique sequences had significant similarities to known genes, allowing the identification of 14,776 unique genes in catfish. Over 300,000 putative SNPs have been identified, of which approximately 48,000 are high-quality SNPs identified from contigs with at least four sequences and the minor allele presence of at least two sequences in the contig. The EST resource should be valuable for identification of microsatellites, genome annotation, large-scale expression analysis, and comparative genome analysis. Conclusions-This project generated a large EST resource for catfish that captured the majority of the catfish transcriptome. The parallel analysis of ESTs from two closely related Ictalurid catfishes should also provide powerful means for the evaluation of ancient and recent gene duplications, and for the development of high-density microarrays in catfish. The inter- and intra-specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies.

  16. The development of large-scale de-identified biomedical databases in the age of genomics-principles and challenges.

    Science.gov (United States)

    Dankar, Fida K; Ptitsyn, Andrey; Dankar, Samar K

    2018-04-10

    Contemporary biomedical databases include a wide range of information types from various observational and instrumental sources. Among the most important features that unite biomedical databases across the field are high volume of information and high potential to cause damage through data corruption, loss of performance, and loss of patient privacy. Thus, issues of data governance and privacy protection are essential for the construction of data depositories for biomedical research and healthcare. In this paper, we discuss various challenges of data governance in the context of population genome projects. The various challenges along with best practices and current research efforts are discussed through the steps of data collection, storage, sharing, analysis, and knowledge dissemination.

  17. Systematic CpT (ApG) Depletion and CpG Excess Are Unique Genomic Signatures of Large DNA Viruses Infecting Invertebrates

    Science.gov (United States)

    Upadhyay, Mohita; Sharma, Neha; Vivekanandan, Perumal

    2014-01-01

    Differences in the relative abundance of dinucleotides, if any may provide important clues on host-driven evolution of viruses. We studied dinucleotide frequencies of large DNA viruses infecting vertebrates (n = 105; viruses infecting mammals = 99; viruses infecting aves = 6; viruses infecting reptiles = 1) and invertebrates (n = 88; viruses infecting insects = 84; viruses infecting crustaceans = 4). We have identified systematic depletion of CpT(ApG) dinucleotides and over-representation of CpG dinucleotides as the unique genomic signature of large DNA viruses infecting invertebrates. Detailed investigation of this unique genomic signature suggests the existence of invertebrate host-induced pressures specifically targeting CpT(ApG) and CpG dinucleotides. The depletion of CpT dinucleotides among large DNA viruses infecting invertebrates is at least in part, explained by non-canonical DNA methylation by the infected host. Our findings highlight the role of invertebrate host-related factors in shaping virus evolution and they also provide the necessary framework for future studies on evolution, epigenetics and molecular biology of viruses infecting this group of hosts. PMID:25369195

  18. Assessment of biological effects resulting from large scale applications of coal power plant wastes in building technology in Poland

    International Nuclear Information System (INIS)

    Pensko, J.; Geisler, J.

    1980-01-01

    Some of the building materials commonly used in Poland contain natural radioactive elements and some contain radioactive industrial wastes. It has been shown that these building materials could induce additional annual doses to the inhabitants of the order of 0.4 mGy gamma radiation to the whole body and about 13 mSv alpha radiation to the critical tissues of the respiratory tract. On the basis of these dosimetric data and demographic and forecasting data, the number of severe genetic effects and cancer deaths caused by the additional radiation doses in dwellings were assessed for the population of Poland for the period 1951-2010. It was estimated that additional somatic effects in six consecutive decades will result in approximately 31,200 cancer deaths, including about 26,300 deaths caused by lung cancer. The expected number of severe genetic effects resulting from additional doses of ionizing radiation absorbed by parents indoors will amount to about 260 cases in the first generation and about 7500 cases in succeeding generations. (H.K.)

  19. Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.

    LENUS (Irish Health Repository)

    Sklar, Pamela

    2011-10-01

    We conducted a combined genome-wide association study (GWAS) of 7,481 individuals with bipolar disorder (cases) and 9,250 controls as part of the Psychiatric GWAS Consortium. Our replication study tested 34 SNPs in 4,496 independent cases with bipolar disorder and 42,422 independent controls and found that 18 of 34 SNPs had P < 0.05, with 31 of 34 SNPs having signals with the same direction of effect (P = 3.8 × 10(-7)). An analysis of all 11,974 bipolar disorder cases and 51,792 controls confirmed genome-wide significant evidence of association for CACNA1C and identified a new intronic variant in ODZ4. We identified a pathway comprised of subunits of calcium channels enriched in bipolar disorder association intervals. Finally, a combined GWAS analysis of schizophrenia and bipolar disorder yielded strong association evidence for SNPs in CACNA1C and in the region of NEK4-ITIH1-ITIH3-ITIH4. Our replication results imply that increasing sample sizes in bipolar disorder will confirm many additional loci.

  20. Genomics With Cloud Computing

    Directory of Open Access Journals (Sweden)

    Sukhamrit Kaur

    2015-04-01

    Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

  1. Building foundations for transcatheter intervascular anastomoses: 3D anatomy of the great vessels in large experimental animals

    NARCIS (Netherlands)

    Sizarov, Aleksander; de Bakker, Bernadette S.; Klein, Karina; Ohlerth, Stefanie

    2014-01-01

    To provide comprehensive illustrations of anatomy of the relevant vessels in large experimental animals in an interactive format as preparation for developing an effective and safe transcatheter technique of aortopulmonary and bidirectional cavopulmonary intervascular anastomoses. Computed

  2. Genomic profiling using array comparative genomic hybridization define distinct subtypes of diffuse large b-cell lymphoma: a review of the literature

    Directory of Open Access Journals (Sweden)

    Tirado Carlos A

    2012-09-01

    Full Text Available Abstract Diffuse large B-cell lymphoma (DLBCL is the most common type of non-Hodgkin Lymphoma comprising of greater than 30% of adult non-Hodgkin Lymphomas. DLBCL represents a diverse set of lymphomas, defined as diffuse proliferation of large B lymphoid cells. Numerous cytogenetic studies including karyotypes and fluorescent in situ hybridization (FISH, as well as morphological, biological, clinical, microarray and sequencing technologies have attempted to categorize DLBCL into morphological variants, molecular and immunophenotypic subgroups, as well as distinct disease entities. Despite such efforts, most lymphoma remains undistinguishable and falls into DLBCL, not otherwise specified (DLBCL-NOS. The advent of microarray-based studies (chromosome, RNA, gene expression, etc has provided a plethora of high-resolution data that could potentially facilitate the finer classification of DLBCL. This review covers the microarray data currently published for DLBCL. We will focus on these types of data; 1 array based CGH; 2 classical CGH; and 3 gene expression profiling studies. The aims of this review were three-fold: (1 to catalog chromosome loci that are present in at least 20% or more of distinct DLBCL subtypes; a detailed list of gains and losses for different subtypes was generated in a table form to illustrate specific chromosome loci affected in selected subtypes; (2 to determine common and distinct copy number alterations among the different subtypes and based on this information, characteristic and similar chromosome loci for the different subtypes were depicted in two separate chromosome ideograms; and, (3 to list re-classified subtypes and those that remained indistinguishable after review of the microarray data. To the best of our knowledge, this is the first effort to compile and review available literatures on microarray analysis data and their practical utility in classifying DLBCL subtypes. Although conventional cytogenetic methods such

  3. Chromosome-wise Protein Interaction Patterns and Their Impact on Functional Implications of Large-Scale Genomic Aberrations

    DEFF Research Database (Denmark)

    Kirk, Isa Kristina; Weinhold, Nils; Belling, Kirstine González-Izarzugaza

    2017-01-01

    Gene copy-number changes influence phenotypes through gene-dosage alteration and subsequent changes of protein complex stoichiometry. Human trisomies where gene copy numbers are increased uniformly over entire chromosomes provide generic cases for studying these relationships. In most trisomies......, gene and protein level alterations have fatal consequences. We used genome-wide protein-protein interaction data to identify chromosome-specific patterns of protein interactions. We found that some chromosomes encode proteins that interact infrequently with each other, chromosome 21 in particular. We...... combined the protein interaction data with transcriptome data from human brain tissue to investigate how this pattern of global interactions may affect cellular function. We identified highly connected proteins that also had coordinated gene expression. These proteins were associated with important...

  4. Genome Writing: Current Progress and Related Applications

    Directory of Open Access Journals (Sweden)

    Yueqiang Wang

    2018-02-01

    Full Text Available The ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic writing technologies are required to build such an artificial genome. Recently, the partially-completed synthetic yeast genome project represents a milestone in this field. In this mini review, we briefly introduce the techniques for de novo genome synthesis and genome editing. Furthermore, we summarize recent research progresses and highlight several applications in the synthetic genome field. Finally, we discuss current challenges and future prospects. Keywords: Synthetic biology, Genome writing, Genome editing, Bioethics, Biosafety

  5. Building 2000

    International Nuclear Information System (INIS)

    Den Ouden, C.; Steemers, T.C.

    1992-01-01

    This is the second volume of Building 2000, a pilot project of the Commission's R and D-programme 'Solar Energy Applications to Buildings' with the purpose of encouraging the adoption of solar architecture in large buildings. In this second rich illustrated volume the results of the design studies illustrating passive solar architecture in buildings in the European Community are presented in particular for the building categories as mentioned in the subtitle. In the first volume, a similar series of studies is presented for the building categories: schools, laboratories and universities, and sports and educational centres. Several Design Support Workshops were organized during the Building 2000 programme during which Building 2000 design teams could directly exchange ideas with the various design advice experts represented at these workshops. In the second part of the Building 2000 final report a summary of a selection of many reports is presented (11 papers), as produced by Design Support experts. Most of the design support activities resulted in changes of the various designs, as have been reported by the design teams in the brochures presented in the first part of this book. It is to be expected that design aids and simulation tools for passive solar options, daylighting concepts, comfort criteria etc., will be utilized more frequently in the future. This will result in a better exchange of information between the actual design practitioners and the European R and D community. This technology transfer will result in buildings with a higher quality with respect to energy and environmental issues

  6. Building 2000

    Energy Technology Data Exchange (ETDEWEB)

    Den Ouden, C [EGM Engineering BV, Dordrecht (Netherlands); Steemers, T C [Commission of the European Communities, Brussels (Belgium)

    1992-01-01

    This is the second volume of Building 2000, a pilot project of the Commission's R and D-programme 'Solar Energy Applications to Buildings' with the purpose of encouraging the adoption of solar architecture in large buildings. In this second rich illustrated volume the results of the design studies illustrating passive solar architecture in buildings in the European Community are presented in particular for the building categories as mentioned in the subtitle. In the first volume, a similar series of studies is presented for the building categories: schools, laboratories and universities, and sports and educational centres. Several Design Support Workshops were organized during the Building 2000 programme during which Building 2000 design teams could directly exchange ideas with the various design advice experts represented at these workshops. In the second part of the Building 2000 final report a summary of a selection of many reports is presented (11 papers), as produced by Design Support experts. Most of the design support activities resulted in changes of the various designs, as have been reported by the design teams in the brochures presented in the first part of this book. It is to be expected that design aids and simulation tools for passive solar options, daylighting concepts, comfort criteria etc., will be utilized more frequently in the future. This will result in a better exchange of information between the actual design practitioners and the European R and D community. This technology transfer will result in buildings with a higher quality with respect to energy and environmental issues.

  7. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  8. MONJU experimental data analysis and its feasibility evaluation to build up the standard data base for large FBR nuclear core design

    International Nuclear Information System (INIS)

    Sugino, K.; Iwai, T.

    2006-01-01

    MONJU experimental data analysis was performed by using the detailed calculation scheme for fast reactor cores developed in Japan. Subsequently, feasibility of the MONJU integral data was evaluated by the cross-section adjustment technique for the use of FBR nuclear core design. It is concluded that the MONJU integral data is quite valuable for building up the standard data base for large FBR nuclear core design. In addition, it is found that the application of the updated data base has a possibility to considerably improve the prediction accuracy of neutronic parameters for MONJU. (authors)

  9. Large-scale genomic analysis shows association between homoplastic genetic variation in Mycobacterium tuberculosis genes and meningeal or pulmonary tuberculosis.

    NARCIS (Netherlands)

    Ruesen, Carolien; Chaidir, Lidya; van Laarhoven, Arjan; Dian, Sofiati; Ganiem, Ahmad Rizal; Nebenzahl-Guimaraes, Hanna; Huynen, Martijn A; Alisjahbana, Bachti; Dutilh, Bas E; van Crevel, Reinout

    2018-01-01

    Meningitis is the most severe manifestation of tuberculosis. It is largely unknown why some people develop pulmonary TB (PTB) and others TB meningitis (TBM); we examined if the genetic background of infecting M. tuberculosis strains may be relevant.

  10. KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation.

    Science.gov (United States)

    Wang, Dapeng; Xu, Jiayue; Yu, Jun

    2015-09-16

    The K-mer approach, treating genomic sequences as simple characters and counting the relative abundance of each string upon a fixed K, has been extensively applied to phylogeny inference for genome assembly, annotation, and comparison. To meet increasing demands for comparing large genome sequences and to promote the use of the K-mer approach, we develop a versatile database, KGCAK ( http://kgcak.big.ac.cn/KGCAK/ ), containing ~8,000 genomes that include genome sequences of diverse life forms (viruses, prokaryotes, protists, animals, and plants) and cellular organelles of eukaryotic lineages. It builds phylogeny based on genomic elements in an alignment-free fashion and provides in-depth data processing enabling users to compare the complexity of genome sequences based on K-mer distribution. We hope that KGCAK becomes a powerful tool for exploring relationship within and among groups of species in a tree of life based on genomic data.

  11. Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses.

    Science.gov (United States)

    Clark, Shaunna L; McClay, Joseph L; Adkins, Daniel E; Aberg, Karolina A; Kumar, Gaurav; Nerella, Sri; Xie, Linying; Collins, Ann L; Crowley, James J; Quakenbush, Corey R; Hillard, Christopher E; Gao, Guimin; Shabalin, Andrey A; Peterson, Roseann E; Copeland, William E; Silberg, Judy L; Maes, Hermine; Sullivan, Patrick F; Costello, Elizabeth J; van den Oord, Edwin J

    2016-05-01

    Genome-wide association study meta-analyses have robustly implicated three loci that affect susceptibility for smoking: CHRNA5\\CHRNA3\\CHRNB4, CHRNB3\\CHRNA6 and EGLN2\\CYP2A6. Functional follow-up studies of these loci are needed to provide insight into biological mechanisms. However, these efforts have been hampered by a lack of knowledge about the specific causal variant(s) involved. In this study, we prioritized variants in terms of the likelihood they account for the reported associations. We employed targeted capture of the CHRNA5\\CHRNA3\\CHRNB4, CHRNB3\\CHRNA6, and EGLN2\\CYP2A6 loci and flanking regions followed by next-generation deep sequencing (mean coverage 78×) to capture genomic variation in 363 individuals. We performed single locus tests to determine if any single variant accounts for the association, and examined if sets of (rare) variants that overlapped with biologically meaningful annotations account for the associations. In total, we investigated 963 variants, of which 71.1% were rare (minor allele frequency < 0.01), 6.02% were insertion/deletions, and 51.7% were catalogued in dbSNP141. The single variant results showed that no variant fully accounts for the association in any region. In the variant set results, CHRNB4 accounts for most of the signal with significant sets consisting of directly damaging variants. CHRNA6 explains most of the signal in the CHRNB3\\CHRNA6 locus with significant sets indicating a regulatory role for CHRNA6. Significant sets in CYP2A6 involved directly damaging variants while the significant variant sets suggested a regulatory role for EGLN2. We found that multiple variants implicating multiple processes explain the signal. Some variants can be prioritized for functional follow-up. © The Author 2015. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Hazard-to-Risk: High-Performance Computing Simulations of Large Earthquake Ground Motions and Building Damage in the Near-Fault Region

    Science.gov (United States)

    Miah, M.; Rodgers, A. J.; McCallen, D.; Petersson, N. A.; Pitarka, A.

    2017-12-01

    We are running high-performance computing (HPC) simulations of ground motions for large (magnitude, M=6.5-7.0) earthquakes in the near-fault region (steel moment frame buildings throughout the near-fault domain. For ground motions, we are using SW4, a fourth order summation-by-parts finite difference time-domain code running on 10,000-100,000's of cores. Earthquake ruptures are generated using the Graves and Pitarka (2017) method. We validated ground motion intensity measurements against Ground Motion Prediction Equations. We considered two events (M=6.5 and 7.0) for vertical strike-slip ruptures with three-dimensional (3D) basin structures, including stochastic heterogeneity. We have also considered M7.0 scenarios for a Hayward Fault rupture scenario which effects the San Francisco Bay Area and northern California using both 1D and 3D earth structure. Dynamic, inelastic response of canonical buildings is computed with the NEVADA, a nonlinear, finite-deformation finite element code. Canonical buildings include 3-, 9-, 20- and 40-story steel moment frame buildings. Damage potential is tracked by the peak inter-story drift (PID) ratio, which measures the maximum displacement between adjacent floors of the building and is strongly correlated with damage. PID ratios greater 1.0 generally indicate non-linear response and permanent deformation of the structure. We also track roof displacement to identify permanent deformation. PID (damage) for a given earthquake scenario (M, slip distribution, hypocenter) is spatially mapped throughout the SW4 domain with 1-2 km resolution. Results show that in the near fault region building damage is correlated with peak ground velocity (PGV), while farther away (> 20 km) it is better correlated with peak ground acceleration (PGA). We also show how simulated ground motions have peaks in the response spectra that shift to longer periods for larger magnitude events and for locations of forward directivity, as has been reported by

  13. Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action

    Directory of Open Access Journals (Sweden)

    Dusica eVidovic

    2014-09-01

    Full Text Available The Library of Integrated Network-based Cellular Signatures (LINCS project is a large-scale coordinated effort to build a comprehensive systems biology reference resource. The goals of the program include the generation of a very large multidimensional data matrix and informatics and computational tools to integrate, analyze, and make the data readily accessible. LINCS data include genome-wide transcriptional signatures, biochemical protein binding profiles, cellular phenotypic response profiles and various other datasets for a wide range of cell model systems and molecular and genetic perturbations. Here we present a partial survey of this data facilitated by data standards and in particular a robust compound standardization workflow; we integrated several types of LINCS signatures and analyzed the results with a focus on mechanism of action and chemical compounds. We illustrate how kinase targets can be related to disease models and relevant drugs. We identified some fundamental trends that appear to link Kinome binding profiles and transcriptional signatures to chemical information and biochemical binding profiles to transcriptional responses independent of chemical similarity. To fill gaps in the datasets we developed and applied predictive models. The results can be interpreted at the systems level as demonstrated based on a large number of signaling pathways. We can identify clear global relationships, suggesting robustness of cellular responses to chemical perturbation. Overall, the results suggest that chemical similarity is a useful measure at the systems level, which would support phenotypic drug optimization efforts. With this study we demonstrate the potential of such integrated analysis approaches and suggest prioritizing further experiments to fill the gaps in the current data.

  14. Energy performance strategies for the large scale introduction of geothermal energy in residential and industrial buildings: The GEO.POWER project

    International Nuclear Information System (INIS)

    Giambastiani, B.M.S.; Tinti, F.; Mendrinos, D.; Mastrocicco, M.

    2014-01-01

    Use of shallow geothermal energy, in terms of ground coupled heat pumps (GCHP) for heating and cooling purposes, is an environmentally-friendly and cost-effective alternative with potential to replace fossil fuels and help mitigate global warming. Focusing on the recent results of the GEO.POWER project, this paper aims at examining the energy performance strategies and the future regional and national financial instruments for large scale introduction of geothermal energy and GCHP systems in both residential and industrial buildings. After a transferability assessment to evaluate the reproducibility of some outstanding examples of systems currently existing in Europe for the utilisation of shallow geothermal energy, a set of regulatory, economic and technical actions is proposed to encourage the GCHP market development and support geothermal energy investments in the frame of the existing European normative platforms. This analysis shows that many European markets are changing from a new GCHP market to growth market. However some interventions are still required, such as incentives, regulatory framework, certification schemes and training activities in order to accelerate the market uptake and achieve the main European energy and climate targets. - Highlights: • Potentiality of geothermal applications for heating and cooling in buildings. • Description of the GEO.POWER project and its results. • Local strategies for the large scale introduction of GCHPs

  15. Building a large-area GEM-based readout chamber for the upgrade of the ALICE TPC

    CERN Document Server

    Gasik, Piotr

    2017-01-01

    A large Time Projection Chamber (TPC) is the main device for tracking and charged-particle identification in the ALICE experiment at the CERN LHC. After the second long shutdown in 2019-2020, the LHC will deliver Pb beams colliding at an interaction rate up to 50 kHz, which is about a factor of 100 above the present read-out rate of the TPC. To fully exploit the LHC potential the TPC will be upgraded based on the Gas Electron Multiplier (GEM) technology. A prototype of an ALICE TPC Outer Read-Out Chamber (OROC) was equipped with twelve large-size GEM foils as amplification stage to demonstrate the feasibility of replacing the current Multi Wire Proportional Chambers with the new technology. With a total area of $\\sim$0.76 m$^2$ it is the largest GEM-based detector built to date. The GEM OROC was installed within a test field cage and commissioned with radioactive sources.

  16. Building a large-area GEM-based readout chamber for the upgrade of the ALICE TPC

    Energy Technology Data Exchange (ETDEWEB)

    Gasik, P. [Physik Department E62, Technische Universität München, Garching (Germany); Excellence Cluster ‘Origin and Structure of the Universe’, Garching (Germany)

    2017-02-11

    A large Time Projection Chamber (TPC) is the main device for tracking and charged-particle identification in the ALICE experiment at the CERN LHC. After the second long shutdown in 2019–2020, the LHC will deliver Pb beams colliding at an interaction rate up to 50 kHz, which is about a factor of 100 above the present read-out rate of the TPC. To fully exploit the LHC potential the TPC will be upgraded based on the Gas Electron Multiplier (GEM) technology. A prototype of an ALICE TPC Outer Read-Out Chamber (OROC) was equipped with twelve large-size GEM foils as amplification stage to demonstrate the feasibility of replacing the current Multi Wire Proportional Chambers with the new technology. With a total area of ∼0.76 m{sup 2} it is the largest GEM-based detector built to date. The GEM OROC was installed within a test field cage and commissioned with radioactive sources.

  17. Building a large-area GEM-based readout chamber for the upgrade of the ALICE TPC

    International Nuclear Information System (INIS)

    Gasik, P.

    2017-01-01

    A large Time Projection Chamber (TPC) is the main device for tracking and charged-particle identification in the ALICE experiment at the CERN LHC. After the second long shutdown in 2019–2020, the LHC will deliver Pb beams colliding at an interaction rate up to 50 kHz, which is about a factor of 100 above the present read-out rate of the TPC. To fully exploit the LHC potential the TPC will be upgraded based on the Gas Electron Multiplier (GEM) technology. A prototype of an ALICE TPC Outer Read-Out Chamber (OROC) was equipped with twelve large-size GEM foils as amplification stage to demonstrate the feasibility of replacing the current Multi Wire Proportional Chambers with the new technology. With a total area of ∼0.76 m 2 it is the largest GEM-based detector built to date. The GEM OROC was installed within a test field cage and commissioned with radioactive sources.

  18. Comparative Genomics of Chrysochromulina Ericina Virus and Other Microalga-Infecting Large DNA Viruses Highlights Their Intricate Evolutionary Relationship with the Established Mimiviridae Family.

    Science.gov (United States)

    Gallot-Lavallée, Lucie; Blanc, Guillaume; Claverie, Jean-Michel

    2017-07-15

    Chrysochromulina ericina virus CeV-01B (CeV) was isolated from Norwegian coastal waters in 1998. Its icosahedral particle is 160 nm in diameter and encloses a 474-kb double-stranded DNA (dsDNA) genome. This virus, although infecting a microalga (the haptophyceae Haptolina ericina , formerly Chrysochromulina ericina ), is phylogenetically related to members of the Mimiviridae family, initially established with the acanthamoeba-infecting mimivirus and megavirus as prototypes. This family was later split into two genera ( Mimivirus and Cafeteriavirus ) following the characterization of a virus infecting the heterotrophic stramenopile Cafeteria roenbergensis (CroV). CeV, as well as two of its close relatives, which infect the unicellular photosynthetic eukaryotes Phaeocystis globosa (Phaeocystis globosa virus [PgV]) and Aureococcus anophagefferens (Aureococcus anophagefferens virus [AaV]), are currently unclassified by the International Committee on Viral Taxonomy (ICTV). The detailed comparative analysis of the CeV genome presented here confirms the phylogenetic affinity of this emerging group of microalga-infecting viruses with the Mimiviridae but argues in favor of their classification inside a distinct clade within the family. Although CeV, PgV, and AaV share more common features among them than with the larger Mimiviridae , they also exhibit a large complement of unique genes, attesting to their complex evolutionary history. We identified several gene fusion events and cases of convergent evolution involving independent lateral gene acquisitions. Finally, CeV possesses an unusual number of inteins, some of which are closely related despite being inserted in nonhomologous genes. This appears to contradict the paradigm of allele-specific inteins and suggests that the Mimiviridae are especially efficient in spreading inteins while enlarging their repertoire of homing genes. IMPORTANCE Although it infects the microalga Chrysochromulina ericina , CeV is more closely

  19. 'You should at least ask'. The expectations, hopes and fears of rare disease patients on large-scale data and biomaterial sharing for genomics research.

    Science.gov (United States)

    McCormack, Pauline; Kole, Anna; Gainotti, Sabina; Mascalzoni, Deborah; Molster, Caron; Lochmüller, Hanns; Woods, Simon

    2016-10-01

    Within the myriad articles about participants' opinions of genomics research, the views of a distinct group - people with a rare disease (RD) - are unknown. It is important to understand if their opinions differ from the general public by dint of having a rare disease and vulnerabilities inherent in this. Here we document RD patients' attitudes to participation in genomics research, particularly around large-scale, international data and biosample sharing. This work is unique in exploring the views of people with a range of rare disorders from many different countries. The authors work within an international, multidisciplinary consortium, RD-Connect, which has developed an integrated platform connecting databases, registries, biobanks and clinical bioinformatics for RD research. Focus groups were conducted with 52 RD patients from 16 countries. Using a scenario-based approach, participants were encouraged to raise topics relevant to their own experiences, rather than these being determined by the researcher. Issues include wide data sharing, and consent for new uses of historic samples and for children. Focus group members are positively disposed towards research and towards allowing data and biosamples to be shared internationally. Expressions of trust and attitudes to risk are often affected by the nature of the RD which they have experience of, as well as regulatory and cultural practices in their home country. Participants are concerned about data security and misuse. There is an acute recognition of the vulnerability inherent in having a RD and the possibility that open knowledge of this could lead to discrimination.

  20. Annotation Of Novel And Conserved MicroRNA Genes In The Build 10 Sus scrofa Reference Genome And Determination Of Their Expression Levels In Ten Different Tissues

    DEFF Research Database (Denmark)

    Thomsen, Bo; Nielsen, Mathilde; Hedegaard, Jakob

    The DNA template used in the pig genome sequencing project was provided by a Duroc pig named TJ Tabasco. In an effort to annotate microRNA (miRNA) genes in the reference genome we have conducted deep sequencing to determine the miRNA transcriptomes in ten different tissues isolated from Pinky......, a genetically identical clone of TJ Tabasco. The purpose was to generate miRNA sequences that are highly homologous to the reference genome sequence, which along with computational prediction will improve confidence in the genomic annotation of miRNA genes. Based on homology searches of the sequence data...... against miRBase, we identified more than 600 conserved known miRNA/miRNA*, which is a significant increase relative to the 211 porcine miRNA/miRNA* deposited in the current version of miRBase. Furthermore, the genome-wide transcript profiles provided important information on the relative abundance...

  1. A New Perspective on Polyploid Fragaria (Strawberry) Genome Composition Based on Large-Scale, Multi-Locus Phylogenetic Analysis

    OpenAIRE

    Yang, Yilong; Davis, Thomas M

    2017-01-01

    Abstract The subgenomic compositions of the octoploid (2n = 8× = 56) strawberry (Fragaria) species, including the economically important cultivated species Fragaria x ananassa, have been a topic of long-standing interest. Phylogenomic approaches utilizing next-generation sequencing technologies offer a new window into species relationships and the subgenomic compositions of polyploids. We have conducted a large-scale phylogenetic analysis of Fragaria (strawberry) species using the Fluidigm Ac...

  2. Planning and Building Qualifiable Embedded Systems: Safety and Risk Properties Assessment for a Large and Complex System with Embedded Subsystems

    Science.gov (United States)

    Silva, N.; Lopes, R.; Barbosa, R.

    2012-01-01

    Systems based on embedded components and applications are today used in all markets. They are planned and developed by all types of institutions with different types of background experience, multidisciplinary teams and all types of capability and maturity levels. Organisational/engineering maturity has an impact on all aspects of the engineering of large and complex systems. An embedded system is a specific computer system designed to perform one or more dedicated functions, usually with real-time constraints. It is generally integrated as part of a more complex device typically composed of specific hardware such as sensors and actuators. This article presents an experimented technique to evaluate the organisation, processes, system and software engineering practices, methods, tools and the planned/produced artefacts themselves, leading towards certification/qualification. The safety and risk assessment of such core and complex systems is explained, described on a step-by- step manner, while presenting the main results and conclusions of the application of the technique to a real case study.

  3. Building rainfall thresholds for large-scales landslides by extracting occurrence time of landslides from seismic records

    Science.gov (United States)

    Yen, Hsin-Yi; Lin, Guan-Wei

    2017-04-01

    Understanding the rainfall condition which triggers mass moment on hillslope is the key to forecast rainfall-induced slope hazards, and the exact time of landslide occurrence is one of the basic information for rainfall statistics. In the study, we focused on large-scale landslides (LSLs) with disturbed area larger than 10 ha and conducted a string of studies including the recognition of landslide-induced ground motions and the analyses of different terms of rainfall thresholds. More than 10 heavy typhoons during the periods of 2005-2014 in Taiwan induced more than hundreds of LSLs and provided the opportunity to characterize the rainfall conditions which trigger LSLs. A total of 101 landslide-induced seismic signals were identified from the records of Taiwan seismic network. These signals exposed the occurrence time of landslide to assess rainfall conditions. Rainfall analyses showed that LSLs occurred when cumulative rainfall exceeded 500 mm. The results of rainfall-threshold analyses revealed that it is difficult to distinct LSLs from small-scale landslides (SSLs) by the I-D and R-D methods, but the I-R method can achieve the discrimination. Besides, an enhanced three-factor threshold considering deep water content was proposed as the rainfall threshold for LSLs.

  4. Moving into a new era of periodontal genetic studies: relevance of large case-control samples using severe phenotypes for genome-wide association studies.

    Science.gov (United States)

    Vaithilingam, R D; Safii, S H; Baharuddin, N A; Ng, C C; Cheong, S C; Bartold, P M; Schaefer, A S; Loos, B G

    2014-12-01

    Studies to elucidate the role of genetics as a risk factor for periodontal disease have gone through various phases. In the majority of cases, the initial 'hypothesis-dependent' candidate-gene polymorphism studies did not report valid genetic risk loci. Following a large-scale replication study, these initially positive results are believed to be caused by type 1 errors. However, susceptibility genes, such as CDKN2BAS (Cyclin Dependend KiNase 2B AntiSense RNA; alias ANRIL [ANtisense Rna In the Ink locus]), glycosyltransferase 6 domain containing 1 (GLT6D1) and cyclooxygenase 2 (COX2), have been reported as conclusive risk loci of periodontitis. The search for genetic risk factors accelerated with the advent of 'hypothesis-free' genome-wide association studies (GWAS). However, despite many different GWAS being performed for almost all human diseases, only three GWAS on periodontitis have been published - one reported genome-wide association of GLT6D1 with aggressive periodontitis (a severe phenotype of periodontitis), whereas the remaining two, which were performed on patients with chronic periodontitis, were not able to find significant associations. This review discusses the problems faced and the lessons learned from the search for genetic risk variants of periodontitis. Current and future strategies for identifying genetic variance in periodontitis, and the importance of planning a well-designed genetic study with large and sufficiently powered case-control samples of severe phenotypes, are also discussed. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  5. Studies on learning by detecting impasse and by resulting it for building large scale knowledge base for autonomous plant

    International Nuclear Information System (INIS)

    Sawaragi, Tetsuo

    1997-03-01

    The acquisition of knowledge from human experts in an exhaustive way is extremely difficult, and even if it were possible, the maintenance of such a large knowledge base for realtime operation is not an easy task. The autonomous system having just incomplete knowledge would face with so many problems that contradicts with the system's current beliefs and/or are novel or unknown to the system. Experienced humans can manage to do with such novelty due to their generalizing ability and analogical inference based on the repertoire of precedents, even if they with new problems. Moreover, through experiencing such breakdowns and impasse, they can acquire some novel knowledge by their proactive attempts to interpret a provided problem as well as by updating their beliefs and contents and organization of their prior knowledge. We call such a style of learning as impasse-driven learning, meaning that learning dose occur being motivated by facing with contradiction and impasse. The related studies concerning with such a style of leaning have been studied within a field of machine learning of artificial intelligence so far as well as within a cognitive science field. In this paper, we at first summarize an outline of machine learning methodologies, and then, we detail about the impasse-driven learning. We discuss that from two different perspective of learning, one is from deductive and analogical learning and the other one is from inductive conceptual learning (i.e., concept formation or generalization-based memory). The former mainly discuss about how the learning system updates its prior beliefs and knowledge so that it can explain away the current contradiction using some meta-cognition heuristics. The latter attempts to assimilate a contradicting problem into its prior memory structure by dynamically reorganizing a collection of the precedents. We present those methodologies, and finally we introduce a case study of concept formation for plant anomalies and its usage for

  6. Whole-genome sequence, SNP chips and pedigree structure: building demographic profiles in domestic dog breeds to optimize genetic-trait mapping

    Science.gov (United States)

    Dreger, Dayna L.; Rimbault, Maud; Davis, Brian W.; Bhatnagar, Adrienne; Parker, Heidi G.

    2016-01-01

    ABSTRACT In the decade following publication of the draft genome sequence of the domestic dog, extraordinary advances with application to several fields have been credited to the canine genetic system. Taking advantage of closed breeding populations and the subsequent selection for aesthetic and behavioral characteristics, researchers have leveraged the dog as an effective natural model for the study of complex traits, such as disease susceptibility, behavior and morphology, generating unique contributions to human health and biology. When designing genetic studies using purebred dogs, it is essential to consider the unique demography of each population, including estimation of effective population size and timing of population bottlenecks. The analytical design approach for genome-wide association studies (GWAS) and analysis of whole-genome sequence (WGS) experiments are inextricable from demographic data. We have performed a comprehensive study of genomic homozygosity, using high-depth WGS data for 90 individuals, and Illumina HD SNP data from 800 individuals representing 80 breeds. These data were coupled with extensive pedigree data analyses for 11 breeds that, together, allowed us to compute breed structure, demography, and molecular measures of genome diversity. Our comparative analyses characterize the extent, formation and implication of breed-specific diversity as it relates to population structure. These data demonstrate the relationship between breed-specific genome dynamics and population architecture, and provide important considerations influencing the technological and cohort design of association and other genomic studies. PMID:27874836

  7. Large palindromes in the lambda phage genome are preserved in a rec/sup +/ host by inhibiting lambda DNA replication

    Energy Technology Data Exchange (ETDEWEB)

    Shurvinton, C.E.; Stahl, M.M.; Stahl, F.W.

    1987-03-01

    A large palindrome carried by phage lambda has been shown to prevent growth of the phage on a rec/sup +/ strain of Escherichia coli. The phage do form plaques on recBC sbcB strains, but the palindrome is not stable - deletions that either destroy the palindrome or diminish its size overgrow the original engineered palindrome-containing phage. The authors have prepared stocks of lambda carrying a palindrome that is 2 x 4200 base pairs long. lambda phage were density labeled by UV induction of lysogens grown in minimal medium containing (/sup 13/C) glucose and /sup 15/NH/sub 4/Cl. These phage stocks are produced by induction of a lysogen in which the two halves of the palindrome are stored at opposite ends of the prophage and are of sufficient titer (10/sup 9/ phage per ml) to enable one-step growth experiments with replication-blocked phage. They find that the large palindrome as well as a lesser palindrome of 2 x 265 base pairs are recovered intact among particles carrying unreplicated chromosomes following such an infection of a rec/sup +/ host. they propose that DNA replication drives the extrusion of palindromic sequences in vivo, forming secondary structures that are substrates for the recBC and sbcB gene products.

  8. CNV analysis in Tourette syndrome implicates large genomic rearrangements in COL8A1 and NRXN1.

    Directory of Open Access Journals (Sweden)

    Abhishek Nag

    Full Text Available Tourette syndrome (TS is a neuropsychiatric disorder with a strong genetic component. However, the genetic architecture of TS remains uncertain. Copy number variation (CNV has been shown to contribute to the genetic make-up of several neurodevelopmental conditions, including schizophrenia and autism. Here we describe CNV calls using SNP chip genotype data from an initial sample of 210 TS cases and 285 controls ascertained in two Latin American populations. After extensive quality control, we found that cases (N = 179 have a significant excess (P = 0.006 of large CNV (>500 kb calls compared to controls (N = 234. Amongst 24 large CNVs seen only in the cases, we observed four duplications of the COL8A1 gene region. We also found two cases with ∼400 kb deletions involving NRXN1, a gene previously implicated in neurodevelopmental disorders, including TS. Follow-up using multiplex ligation-dependent probe amplification (and including 53 more TS cases validated the CNV calls and identified additional patients with rearrangements in COL8A1 and NRXN1, but none in controls. Examination of available parents indicates that two out of three NRXN1 deletions detected in the TS cases are de-novo mutations. Our results are consistent with the proposal that rare CNVs play a role in TS aetiology and suggest a possible role for rearrangements in the COL8A1 and NRXN1 gene regions.

  9. CNV analysis in Tourette syndrome implicates large genomic rearrangements in COL8A1 and NRXN1.

    Science.gov (United States)

    Nag, Abhishek; Bochukova, Elena G; Kremeyer, Barbara; Campbell, Desmond D; Muller, Heike; Valencia-Duarte, Ana V; Cardona, Julio; Rivas, Isabel C; Mesa, Sandra C; Cuartas, Mauricio; Garcia, Jharley; Bedoya, Gabriel; Cornejo, William; Herrera, Luis D; Romero, Roxana; Fournier, Eduardo; Reus, Victor I; Lowe, Thomas L; Farooqi, I Sadaf; Mathews, Carol A; McGrath, Lauren M; Yu, Dongmei; Cook, Ed; Wang, Kai; Scharf, Jeremiah M; Pauls, David L; Freimer, Nelson B; Plagnol, Vincent; Ruiz-Linares, Andrés

    2013-01-01

    Tourette syndrome (TS) is a neuropsychiatric disorder with a strong genetic component. However, the genetic architecture of TS remains uncertain. Copy number variation (CNV) has been shown to contribute to the genetic make-up of several neurodevelopmental conditions, including schizophrenia and autism. Here we describe CNV calls using SNP chip genotype data from an initial sample of 210 TS cases and 285 controls ascertained in two Latin American populations. After extensive quality control, we found that cases (N = 179) have a significant excess (P = 0.006) of large CNV (>500 kb) calls compared to controls (N = 234). Amongst 24 large CNVs seen only in the cases, we observed four duplications of the COL8A1 gene region. We also found two cases with ∼400 kb deletions involving NRXN1, a gene previously implicated in neurodevelopmental disorders, including TS. Follow-up using multiplex ligation-dependent probe amplification (and including 53 more TS cases) validated the CNV calls and identified additional patients with rearrangements in COL8A1 and NRXN1, but none in controls. Examination of available parents indicates that two out of three NRXN1 deletions detected in the TS cases are de-novo mutations. Our results are consistent with the proposal that rare CNVs play a role in TS aetiology and suggest a possible role for rearrangements in the COL8A1 and NRXN1 gene regions.

  10. Equivalent full-load hours for assessing climate change impact on building cooling and heating energy consumption in large Asian cities

    International Nuclear Information System (INIS)

    Spandagos, Constantinos; Ng, Tze Ling

    2017-01-01

    Highlights: • EFLH for estimating cooling/heating energy demand in Asian buildings are provided. • Net increases in building energy consumption over the next 30 years are predicted. • Switching to more efficient AC devices can offset much of the increases. - Abstract: Estimating cooling and heating energy requirements is an integral part of designing and managing buildings. Further, as buildings are among the largest energy consumers in cities, the estimates are important for formulating effective energy conservation strategies. Where complex hourly simulation models are not favored, such estimates may be derived by simplified methods that are less computationally intensive but still provide results that are reasonably close to those obtained from the more complicated approach. The equivalent full load hours (EFLH) method is a simplified energy estimation method that has recently gained popularity. It offers a straightforward means of evaluating energy efficiency programs. However, to date, easily accessible EFLH data exist only for a very limited number of countries in North America and Europe, but not Asia. This current work provides previously unavailable monthly EFLH data for building cooling and heating in three large Asian cities, viz. Hong Kong, Seoul and Tokyo. To assess the effects of changing temperature over the course of decades on building cooling and heating energy consumption, EFLH data are calculated for three time periods: past (1983–2005), present (2006–2014) and future (2015–2044). The projections for the future time period are based on the climate scenarios Representative Concentration Pathways (RCPs) 4.5 and 8.5 of the Intergovernmental Panel on Climate Change (IPCC) Fifth Assessment Report. RCP-4.5 assumes a stabilization of future greenhouse gas (GHG) emissions followed by a reduction, while RCP-8.5 assumes their further increase. From the EFLH data, considering just the effects of ambient temperature changes, it is projected the

  11. Screening for large genomic rearrangements in the FANCA gene reveals extensive deletion in a Finnish breast cancer family.

    Science.gov (United States)

    Solyom, Szilvia; Winqvist, Robert; Nikkilä, Jenni; Rapakko, Katrin; Hirvikoski, Pasi; Kokkonen, Hannaleena; Pylkäs, Katri

    2011-03-28

    A portion of familial breast cancer cases are caused by mutations in the same genes that are inactivated in the downstream part of Fanconi anemia (FA) signaling pathway. Here we have assessed the FANCA gene for breast cancer susceptibility by examining blood DNA for aberrations from 100 Northern Finnish breast cancer families using the MLPA method. We identified a novel heterozygous deletion, removing the promoter and 12 exons of the gene in one family. This allele was absent from 124 controls. We conclude that FANCA deletions might contribute to breast cancer susceptibility, potentially in combination with other germline mutations. To our knowledge, this is the first study reporting a large deletion in an upstream FA gene in familial breast cancer. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  12. Modern frame structure buildings

    Directory of Open Access Journals (Sweden)

    В. М. Першаков

    2013-07-01

    Full Text Available The article deals with the design, construction and implementation of reinforced concrete frame structures with span 18, 21 m for agricultural production buildings, hall-premises of public buildings and buildings of agricultural aviation. Structures are prefabricated frame buildings and have such advantages as large space inside the structure and lower cost compared with other facilities with same purpose

  13. The Mitochondrial Genome of the Prasinophyte Prasinoderma coloniale Reveals Two Trans-Spliced Group I Introns in the Large Subunit rRNA Gene

    Science.gov (United States)

    Pombert, Jean-François; Otis, Christian; Turmel, Monique; Lemieux, Claude

    2013-01-01

    Organelle genes are often interrupted by group I and or group II introns. Splicing of these mobile genetic occurs at the RNA level via serial transesterification steps catalyzed by the introns'own tertiary structures and, sometimes, with the help of external factors. These catalytic ribozymes can be found in cis or trans configuration, and although trans-arrayed group II introns have been known for decades, trans-spliced group I introns have been reported only recently. In the course of sequencing the complete mitochondrial genome of the prasinophyte picoplanktonic green alga Prasinoderma coloniale CCMP 1220 (Prasinococcales, clade VI), we uncovered two additional cases of trans-spliced group I introns. Here, we describe these introns and compare the 54,546 bp-long mitochondrial genome of Prasinoderma with those of four other prasinophytes (clades II, III and V). This comparison underscores the highly variable mitochondrial genome architecture in these ancient chlorophyte lineages. Both Prasinoderma trans-spliced introns reside within the large subunit rRNA gene (rnl) at positions where cis-spliced relatives, often containing homing endonuclease genes, have been found in other organelles. In contrast, all previously reported trans-spliced group I introns occur in different mitochondrial genes (rns or coxI). Each Prasinoderma intron is fragmented into two pieces, forming at the RNA level a secondary structure that resembles those of its cis-spliced counterparts. As observed for other trans-spliced group I introns, the breakpoint of the first intron maps to the variable loop L8, whereas that of the second is uniquely located downstream of P9.1. The breakpoint In each Prasinoderma intron corresponds to the same region where the open reading frame (ORF) occurs when present in cis-spliced orthologs. This correlation between the intron breakpoint and the ORF location in cis-spliced orthologs also holds for other trans-spliced introns; we discuss the possible implications

  14. The mitochondrial genome of the prasinophyte Prasinoderma coloniale reveals two trans-spliced group I introns in the large subunit rRNA gene.

    Directory of Open Access Journals (Sweden)

    Jean-François Pombert

    Full Text Available Organelle genes are often interrupted by group I and or group II introns. Splicing of these mobile genetic occurs at the RNA level via serial transesterification steps catalyzed by the introns'own tertiary structures and, sometimes, with the help of external factors. These catalytic ribozymes can be found in cis or trans configuration, and although trans-arrayed group II introns have been known for decades, trans-spliced group I introns have been reported only recently. In the course of sequencing the complete mitochondrial genome of the prasinophyte picoplanktonic green alga Prasinoderma coloniale CCMP 1220 (Prasinococcales, clade VI, we uncovered two additional cases of trans-spliced group I introns. Here, we describe these introns and compare the 54,546 bp-long mitochondrial genome of Prasinoderma with those of four other prasinophytes (clades II, III and V. This comparison underscores the highly variable mitochondrial genome architecture in these ancient chlorophyte lineages. Both Prasinoderma trans-spliced introns reside within the large subunit rRNA gene (rnl at positions where cis-spliced relatives, often containing homing endonuclease genes, have been found in other organelles. In contrast, all previously reported trans-spliced group I introns occur in different mitochondrial genes (rns or coxI. Each Prasinoderma intron is fragmented into two pieces, forming at the RNA level a secondary structure that resembles those of its cis-spliced counterparts. As observed for other trans-spliced group I introns, the breakpoint of the first intron maps to the variable loop L8, whereas that of the second is uniquely located downstream of P9.1. The breakpoint In each Prasinoderma intron corresponds to the same region where the open reading frame (ORF occurs when present in cis-spliced orthologs. This correlation between the intron breakpoint and the ORF location in cis-spliced orthologs also holds for other trans-spliced introns; we discuss the

  15. Molecular epidemiology of Staphylococcus aureus bacteremia in a single large Minnesota medical center in 2015 as assessed using MLST, core genome MLST and spa typing.

    Directory of Open Access Journals (Sweden)

    Kyung-Hwa Park

    Full Text Available Staphylococcus aureus is a leading cause of bacteremia in hospitalized patients. Whether or not S. aureus bacteremia (SAB is associated with clonality, implicating potential nosocomial transmission, has not, however, been investigated. Herein, we examined the epidemiology of SAB using whole genome sequencing (WGS. 152 SAB isolates collected over the course of 2015 at a single large Minnesota medical center were studied. Staphylococcus protein A (spa typing was performed by PCR/Sanger sequencing; multilocus sequence typing (MLST and core genome MLST (cgMLST were determined by WGS. Forty-eight isolates (32% were methicillin-resistant S. aureus (MRSA. The isolates encompassed 66 spa types, clustered into 11 spa clonal complexes (CCs and 10 singleton types. 88% of 48 MRSA isolates belonged to spa CC-002 or -008. Methicillin-susceptible S. aureus (MSSA isolates were more genotypically diverse, with 61% distributed across four spa CCs (CC-002, CC-012, CC-008 and CC-084. By MLST, there was 31 sequence types (STs, including 18 divided into 6 CCs and 13 singleton STs. Amongst MSSA isolates, the common MLST clones were CC5 (23%, CC30 (19%, CC8 (15% and CC15 (11%. Common MRSA clones were CC5 (67% and CC8 (25%; there were no MRSA isolates in CC45 or CC30. By cgMLST analysis, there were 9 allelic differences between two isolates, with the remaining 150 isolates differing from each other by over 40 alleles. The two isolates were retroactively epidemiologically linked by medical record review. Overall, cgMLST analysis resulted in higher resolution epidemiological typing than did multilocus sequence or spa typing.

  16. Genome-wide association analysis for heat tolerance at flowering detected a large set of genes involved in adaptation to thermal and other stresses.

    Directory of Open Access Journals (Sweden)

    Tanguy Lafarge

    Full Text Available Fertilization sensitivity to heat in rice is a major issue within climate change scenarios in the tropics. A panel of 167 indica landraces and improved varieties was phenotyped for spikelet sterility (SPKST under 38°C during anthesis and for several secondary traits potentially affecting panicle micro-climate and thus the fertilization process. The panel was genotyped with an average density of one marker per 29 kb using genotyping by sequencing. Genome-wide association analyses (GWAS were conducted using three methods based on single marker regression, haplotype regression and simultaneous fitting of all markers, respectively. Fourteen loci significantly associated with SPKST under at least two GWAS methods were detected. A large number of associations was also detected for the secondary traits. Analysis of co-localization of SPKST associated loci with QTLs detected in progenies of bi-parental crosses reported in the literature allowed to narrow -down the position of eight of those QTLs, including the most documented one, qHTSF4.1. Gene families underlying loci associated with SPKST corresponded to functions ranging from sensing abiotic stresses and regulating plant response, such as wall-associated kinases and heat shock proteins, to cell division and gametophyte development. Analysis of diversity at the vicinity of loci associated with SPKST within the rice three thousand genomes, revealed widespread distribution of the favourable alleles across O. sativa genetic groups. However, few accessions assembled the favourable alleles at all loci. Effective donors included the heat tolerant variety N22 and some Indian and Taiwanese varieties. These results provide a basis for breeding for heat tolerance during anthesis and for functional validation of major loci governing this trait.

  17. Genomic prediction using subsampling

    OpenAIRE

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-01-01

    Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

  18. Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management.

    Science.gov (United States)

    Grossmann, Sebastian; Nowak, Piotr; Neogi, Ujjwal

    2015-01-01

    HIV-1 near full-length genome (HIV-NFLG) sequencing from plasma is an attractive multidimensional tool to apply in large-scale population-based molecular epidemiological studies. It also enables genotypic resistance testing (GRT) for all drug target sites allowing effective intervention strategies for control and prevention in high-risk population groups. Thus, the main objective of this study was to develop a simplified subtype-independent, cost- and labour-efficient HIV-NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies. Plasma samples (n=30) were obtained from HIV-1B (n=10), HIV-1C (n=10), CRF01_AE (n=5) and CRF01_AG (n=5) infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV-NFLG. GRT was validated against ViroSeq™ HIV-1 Genotyping System. After excluding four plasma samples with low-quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92%) samples with the lowest viral load being 3000 copies/ml. High (>99%) concordance was observed between HIV-NFLG and ViroSeq™ when determining the drug resistance mutations (DRMs). The N384I connection mutation was additionally detected by NFLG in two samples. Our high efficiency subtype-independent HIV-NFLG is a simple and promising approach to be used in large-scale molecular epidemiological studies. It will facilitate the understanding of the HIV-1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay.

  19. Sustainable Buildings

    DEFF Research Database (Denmark)

    Tommerup, Henrik M.; Elle, Morten

    The scientific community agrees that: all countries must drastically and rapidly reduce their CO2 emissions and that energy efficient houses play a decisive role in this. The general attitude at the workshop on Sustainable Buildings was that we face large and serious climate change problems...

  20. Co-Circulation and Genomic Recombination of Coxsackievirus A16 and Enterovirus 71 during a Large Outbreak of Hand, Foot, and Mouth Disease in Central China

    Science.gov (United States)

    Liu, Weiyong; Wu, Shimin; Xiong, Ying; Li, Tongya; Wen, Zhou; Yan, Mingzhe; Qin, Kai; Liu, Yingle; Wu, Jianguo

    2014-01-01

    A total of 1844 patients with hand, foot, and mouth disease (HFMD), most of them were children of age 1–3-year-old, in Central China were hospitalized from 2011 to 2012. Among them, 422 were infected with coxsackievirus A16 (CVA16), 334 were infected with enterovirus 71 (EV71), 38 were co-infected with EV71 and CVA16, and 35 were infected with other enteroviruses. Molecular epidemiology analysis revealed that EV71 and CVA16 were detected year-round, but EV71 circulated mainly in July and CVA16 circulated predominantly in November, and incidence of HFMD was reduced in January and February and increased in March. Clinical data showed that hyperglycemia and neurologic complications were significantly higher in EV71-infected patients, while upper respiratory tract infection and C-reactive protein were significantly higher in CVA16-associated patients. 124 EV71 and 80 CVA16 strains were isolated, among them 56 and 68 EV71 strains were C4a and C4b, while 25 and 55 CVA16 strains were B1a and B1b, respectively. Similarity plots and bootscan analyses based on entire genomic sequences revealed that the three C4a sub-genotype EV71 strains were recombinant with C4b sub-genotype EV71 in 2B–2C region, and the three CVA16 strains were recombinant with EV71 in 2A–2B region. Thus, CVA16 and EV71 were the major causative agents in a large HFMD outbreak in Central China. HFMD incidence was high for children among household contact and was detected year-round, but outbreak was seasonal dependent. CVA16 B1b and EV71 C4b reemerged and caused a large epidemic in China after a quiet period of many years. Moreover, EV71 and CVA16 were co-circulated during the outbreak, which may have contributed to the genomic recombination between the pathogens. It should gain more attention as there may be an upward trend in co-circulation of the two pathogens globally and the new role recombination plays in the emergence of new enterovirus variants. PMID:24776922

  1. Co-circulation and genomic recombination of coxsackievirus A16 and enterovirus 71 during a large outbreak of hand, foot, and mouth disease in Central China.

    Directory of Open Access Journals (Sweden)

    Weiyong Liu

    Full Text Available A total of 1844 patients with hand, foot, and mouth disease (HFMD, most of them were children of age 1-3-year-old, in Central China were hospitalized from 2011 to 2012. Among them, 422 were infected with coxsackievirus A16 (CVA16, 334 were infected with enterovirus 71 (EV71, 38 were co-infected with EV71 and CVA16, and 35 were infected with other enteroviruses. Molecular epidemiology analysis revealed that EV71 and CVA16 were detected year-round, but EV71 circulated mainly in July and CVA16 circulated predominantly in November, and incidence of HFMD was reduced in January and February and increased in March. Clinical data showed that hyperglycemia and neurologic complications were significantly higher in EV71-infected patients, while upper respiratory tract infection and C-reactive protein were significantly higher in CVA16-associated patients. 124 EV71 and 80 CVA16 strains were isolated, among them 56 and 68 EV71 strains were C4a and C4b, while 25 and 55 CVA16 strains were B1a and B1b, respectively. Similarity plots and bootscan analyses based on entire genomic sequences revealed that the three C4a sub-genotype EV71 strains were recombinant with C4b sub-genotype EV71 in 2B-2C region, and the three CVA16 strains were recombinant with EV71 in 2A-2B region. Thus, CVA16 and EV71 were the major causative agents in a large HFMD outbreak in Central China. HFMD incidence was high for children among household contact and was detected year-round, but outbreak was seasonal dependent. CVA16 B1b and EV71 C4b reemerged and caused a large epidemic in China after a quiet period of many years. Moreover, EV71 and CVA16 were co-circulated during the outbreak, which may have contributed to the genomic recombination between the pathogens. It should gain more attention as there may be an upward trend in co-circulation of the two pathogens globally and the new role recombination plays in the emergence of new enterovirus variants.

  2. Mortality during a Large-Scale Heat Wave by Place, Demographic Group, Internal and External Causes of Death, and Building Climate Zone.

    Science.gov (United States)

    Joe, Lauren; Hoshiko, Sumi; Dobraca, Dina; Jackson, Rebecca; Smorodinsky, Svetlana; Smith, Daniel; Harnly, Martha

    2016-03-09

    Mortality increases during periods of elevated heat. Identification of vulnerable subgroups by demographics, causes of death, and geographic regions, including deaths occurring at home, is needed to inform public health prevention efforts. We calculated mortality relative risks (RRs) and excess deaths associated with a large-scale California heat wave in 2006, comparing deaths during the heat wave with reference days. For total (all-place) and at-home mortality, we examined risks by demographic factors, internal and external causes of death, and building climate zones. During the heat wave, 582 excess deaths occurred, a 5% increase over expected (RR = 1.05, 95% confidence interval (CI) 1.03-1.08). Sixty-six percent of excess deaths were at home (RR = 1.12, CI 1.07-1.16). Total mortality risk was higher among those aged 35-44 years than ≥ 65, and among Hispanics than whites. Deaths from external causes increased more sharply (RR = 1.18, CI 1.10-1.27) than from internal causes (RR = 1.04, CI 1.02-1.07). Geographically, risk varied by building climate zone; the highest risks of at-home death occurred in the northernmost coastal zone (RR = 1.58, CI 1.01-2.48) and the southernmost zone of California's Central Valley (RR = 1.43, CI 1.21-1.68). Heat wave mortality risk varied across subpopulations, and some patterns of vulnerability differed from those previously identified. Public health efforts should also address at-home mortality, non-elderly adults, external causes, and at-risk geographic regions.

  3. DNA Sequence Patterns – A Successful Example of Grid Computing in Genome Research and Building Virtual Super-Computers for the Research Commons of e-Societies

    NARCIS (Netherlands)

    T.A. Knoch (Tobias); A. Abuseiris (Anis); M. Lesnussa (Michael); F.N. Kepper (Nick); R.M. de Graaf (Rob); F.G. Grosveld (Frank)

    2011-01-01

    textabstractThe amount of information is growing exponentially with ever-new technologies emerging and is believed to be always at the limit. In contrast, huge resources are obviously available, which are underused in the IT sector, similar as e.g. in the renewable energy sector. Genome research is

  4. A systematic search for linkage with nonsyndromic recessive deafness in two large Middle Eastern inbred kindreds excludes more than 30% of the genome

    Energy Technology Data Exchange (ETDEWEB)

    Weiss, S.; Korostishevsky, M. [Sackler Faculty of Medicine, Ramat-Aviv (Israel); Frydman, M. [Haim Sheba Medical Center, Tel-Hashomer (Israel)] [and others

    1994-09-01

    It has been estimated that as many as 35 loci may individually cause autosomal recessive non-syndromic deafness. The extreme genetic heterogeneity, limited clinical differentiation and phenotypic assortative mating in many western countries make many families unsuitable for genetic linkage studies. Recently the first of those loci was mapped (to 13q) in two consanguineous families from northern Tunisia. We are studying two large highly consanguineous Middle Eastern kindreds (a total of 26 deaf in 98 sampled individuals). Examination in each family showed no evidence of clinical heterogeneity and indicated an uncomplicated profound bilateral sensorineural deafness. We have been able to exclude the 13q locus as the cause of deafness in each kindred and have also excluded such `candidate` loci as regions as those causing Usher`s syndrome type 1 (11q13)(11p), Usher`s syndrome type II (1q32-q41), Waardenburg syndrome type I (2q37), branchio-oto-renal syndrome (8q12-q13), Monge`s deafness (5q31), and Treacher Collins syndrome (5q31.3-q33.3). To date, no lod scores greater than 1 have been obtained in either kindred using 150 RFLT`s, VNTR`s and highly polymorphic microsatellite markers (CA repeats and tetranucleotides). By Morton`s criterion a minimum of 30% of the autosomal genome can be excluded for each kindred separately.

  5. A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes

    Directory of Open Access Journals (Sweden)

    Fontanesi Luca

    2012-11-01

    Full Text Available Abstract Background Carcass fatness is an important trait in most pig breeding programs. Following market requests, breeding plans for fresh pork consumption are usually designed to reduce carcass fat content and increase lean meat deposition. However, the Italian pig industry is mainly devoted to the production of Protected Designation of Origin dry cured hams: pigs are slaughtered at around 160 kg of live weight and the breeding goal aims at maintaining fat coverage, measured as backfat thickness to avoid excessive desiccation of the hams. This objective has shaped the genetic pool of Italian heavy pig breeds for a few decades. In this study we applied a selective genotyping approach within a population of ~ 12,000 performance tested Italian Large White pigs. Within this population, we selectively genotyped 304 pigs with extreme and divergent backfat thickness estimated breeding value by the Illumina PorcineSNP60 BeadChip and performed a genome wide association study to identify loci associated to this trait. Results We identified 4 single nucleotide polymorphisms with P≤5.0E-07 and additional 119 ones with 5.0E-07 Conclusions Further investigations are needed to evaluate the effects of the identified single nucleotide polymorphisms associated with backfat thickness on other traits as a pre-requisite for practical applications in breeding programs. Reported results could improve our understanding of the biology of fat metabolism and deposition that could also be relevant for other mammalian species including humans, confirming the role of neuronal genes on obesity.

  6. Long- and short-term outcomes in renal allografts with deceased donors: A large recipient and donor genome-wide association study.

    Science.gov (United States)

    Hernandez-Fuentes, Maria P; Franklin, Christopher; Rebollo-Mesa, Irene; Mollon, Jennifer; Delaney, Florence; Perucha, Esperanza; Stapleton, Caragh; Borrows, Richard; Byrne, Catherine; Cavalleri, Gianpiero; Clarke, Brendan; Clatworthy, Menna; Feehally, John; Fuggle, Susan; Gagliano, Sarah A; Griffin, Sian; Hammad, Abdul; Higgins, Robert; Jardine, Alan; Keogan, Mary; Leach, Timothy; MacPhee, Iain; Mark, Patrick B; Marsh, James; Maxwell, Peter; McKane, William; McLean, Adam; Newstead, Charles; Augustine, Titus; Phelan, Paul; Powis, Steve; Rowe, Peter; Sheerin, Neil; Solomon, Ellen; Stephens, Henry; Thuraisingham, Raj; Trembath, Richard; Topham, Peter; Vaughan, Robert; Sacks, Steven H; Conlon, Peter; Opelz, Gerhard; Soranzo, Nicole; Weale, Michael E; Lord, Graham M

    2018-02-01

    Improvements in immunosuppression have modified short-term survival of deceased-donor allografts, but not their rate of long-term failure. Mismatches between donor and recipient HLA play an important role in the acute and chronic allogeneic immune response against the graft. Perfect matching at clinically relevant HLA loci does not obviate the need for immunosuppression, suggesting that additional genetic variation plays a critical role in both short- and long-term graft outcomes. By combining patient data and samples from supranational cohorts across the United Kingdom and European Union, we performed the first large-scale genome-wide association study analyzing both donor and recipient DNA in 2094 complete renal transplant-pairs with replication in 5866 complete pairs. We studied deceased-donor grafts allocated on the basis of preferential HLA matching, which provided some control for HLA genetic effects. No strong donor or recipient genetic effects contributing to long- or short-term allograft survival were found outside the HLA region. We discuss the implications for future research and clinical application. © 2018 The Authors. American Journal of Transplantation published by Wiley Periodicals, Inc. on behalf of The American Society of Transplantation and the American Society of Transplant Surgeons.

  7. A review of genomic data warehousing systems.

    Science.gov (United States)

    Triplet, Thomas; Butler, Gregory

    2014-07-01

    To facilitate the integration and querying of genomics data, a number of generic data warehousing frameworks have been developed. They differ in their design and capabilities, as well as their intended audience. We provide a comprehensive and quantitative review of those genomic data warehousing frameworks in the context of large-scale systems biology. We reviewed in detail four genomic data warehouses (BioMart, BioXRT, InterMine and PathwayTools) freely available to the academic community. We quantified 20 aspects of the warehouses, covering the accuracy of their responses, their computational requirements and development efforts. Performance of the warehouses was evaluated under various hardware configurations to help laboratories optimize hardware expenses. Each aspect of the benchmark may be dynamically weighted by scientists using our online tool BenchDW (http://warehousebenchmark.fungalgenomics.ca/benchmark/) to build custom warehouse profiles and tailor our results to their specific needs.

  8. A Large-Scale Multi-ancestry Genome-wide Study Accounting for Smoking Behavior Identifies Multiple Significant Loci for Blood Pressure

    DEFF Research Database (Denmark)

    Sung, Yun J; Winkler, Thomas W; de Las Fuentes, Lisa

    2018-01-01

    Genome-wide association analysis advanced understanding of blood pressure (BP), a major risk factor for vascular conditions such as coronary heart disease and stroke. Accounting for smoking behavior may help identify BP loci and extend our knowledge of its genetic architecture. We performed genom...

  9. JGI Plant Genomics Gene Annotation Pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Shu, Shengqiang; Rokhsar, Dan; Goodstein, David; Hayes, David; Mitros, Therese

    2014-07-14

    Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.

  10. New Perspectives for Old Clusters: Anderson-Evans Anions as Building Blocks of Large Polyoxometalate Frameworks in a Series of Heterometallic 3 d-4 f Species.

    Science.gov (United States)

    Artetxe, Beñat; Reinoso, Santiago; San Felices, Leire; Lezama, Luis; Gutiérrez-Zorrilla, Juan M; Vicent, Cristian; Haso, Fadi; Liu, Tianbo

    2016-03-18

    A series of nine [Sb7W36O133Ln3M2(OAc)(H2O)8](17-) heterometallic anions (Ln3M2; Ln=La-Gd, M=Co; Ln=Ce, M=Ni and Zn) have been obtained by reacting 3 d metal disubstituted Krebs-type tungstoantimonates(III) with early lanthanides. Their unique tetrameric structure contains a novel {MW9O33} capping unit formed by a planar {MW6O24} fragment to which three {WO2} groups are condensed to form a tungstate skeleton identical to that of a hypothetical trilacunary derivative of the ɛ-Keggin cluster. It is shown, for the first time, that classical Anderson-Evans {MW6O24} anions can act as building blocks to construct purely inorganic large frameworks. Unprecedented reactivity in the outer ring of these disk-shaped species is also revealed. The Ln3M2 anions possess chirality owing to a {Sb4O4} cluster being encapsulated in left- or right-handed orientations. Their ability to self-associate in blackberry-type vesicles in solution has been assessed for the Ce3Co2 derivative. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Building Integrated Photovoltaics - A State-of-the-Art Review, Future Research Opportunities and Large-Scale Experimental Wind-Driven Rain Exposure Investigations

    OpenAIRE

    Breivik, Christer

    2012-01-01

    This work consists of three scientific journal articles on the subject building integrated photovoltaics (BIPVs), and was initiated by a student project work which consisted of a major revision and extension of an article on BIPVs (appendix A). BIPVs are photovoltaic materials that replace conventional building materials in parts of the building envelopes, such as the roof covering or facades. BIPV systems may represent a powerful and versatile tool for achieving the ever increasing demand fo...

  12. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine.

    Science.gov (United States)

    Stenson, Peter D; Mort, Matthew; Ball, Edward V; Shaw, Katy; Phillips, Andrew; Cooper, David N

    2014-01-01

    The Human Gene Mutation Database (HGMD®) is a comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. By June 2013, the database contained over 141,000 different lesions detected in over 5,700 different genes, with new mutation entries currently accumulating at a rate exceeding 10,000 per annum. HGMD was originally established in 1996 for the scientific study of mutational mechanisms in human genes. However, it has since acquired a much broader utility as a central unified disease-oriented mutation repository utilized by human molecular geneticists, genome scientists, molecular biologists, clinicians and genetic counsellors as well as by those specializing in biopharmaceuticals, bioinformatics and personalized genomics. The public version of HGMD (http://www.hgmd.org) is freely available to registered users from academic institutions/non-profit organizations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via BIOBASE GmbH.

  13. Assembly and Multiplex Genome Integration of Metabolic Pathways in Yeast Using CasEMBLR

    DEFF Research Database (Denmark)

    Jakočiūnas, Tadas; Jensen, Emil D.; Jensen, Michael Krogh

    2018-01-01

    and marker-free integration of the carotenoid pathway from 15 exogenously supplied DNA parts into three targeted genomic loci. As a second proof-of-principle, a total of ten DNA parts were assembled and integrated in two genomic loci to construct a tyrosine production strain, and at the same time knocking......Genome integration is a vital step for implementing large biochemical pathways to build a stable microbial cell factory. Although traditional strain construction strategies are well established for the model organism Saccharomyces cerevisiae, recent advances in CRISPR/Cas9-mediated genome...... engineering allow much higher throughput and robustness in terms of strain construction. In this chapter, we describe CasEMBLR, a highly efficient and marker-free genome engineering method for one-step integration of in vivo assembled expression cassettes in multiple genomic sites simultaneously. Cas...

  14. Functional genomic mRNA profiling of a large cancer data base demonstrates mesothelin overexpression in a broad range of tumor types.

    Science.gov (United States)

    Lamberts, Laetitia E; de Groot, Derk Jan A; Bense, Rico D; de Vries, Elisabeth G E; Fehrmann, Rudolf S N

    2015-09-29

    The membrane bound glycoprotein mesothelin (MSLN) is a highly specific tumor marker, which is currently exploited as target for drugs. There are only limited data available on MSLN expression by human tumors. Therefore we determined overexpression of MSLN across different tumor types with Functional Genomic mRNA (FGM) profiling of a large cancer database. Results were compared with data in articles reporting immunohistochemical (IHC) MSLN tumor expression. FGM profiling is a technique that allows prediction of biologically relevant overexpression of proteins from a robust data set of mRNA microarrays. This technique was used in a database comprising 19,746 tumors to identify for 41 tumor types the percentage of samples with an overexpression of MSLN compared to a normal background. A literature search was performed to compare the FGM profiling data with studies reporting IHC MSLN tumor expression. FGM profiling showed MSLN overexpression in gastrointestinal (12-36%) and gynecological tumors (20-66%), non-small cell lung cancer (21%) and synovial sarcomas (30%). The overexpression found in thyroid cancers (5%) and renal cell cancers (10%) was not yet reported with IHC analyses. We observed that MSLN amplification rate within esophageal cancer depends on the histotype (31% for adenocarcinomas versus 3% for squamous-cell carcinomas). Subset analysis in breast cancer showed MSLN amplification rates of 28% in triple-negative breast cancer (TNBC) and 33% in basal-like breast cancer. Further subtype analysis of TNBCs showed the highest amplification rate (42%) in the basal-like 1 subtype and the lowest amplification rate (9%) in the luminal androgen receptor subtype.

  15. Genomic diversity of Mycobacterium tuberculosis Beijing strains isolated in Tuscany, Italy, based on large sequence deletions, SNPs in putative DNA repair genes and MIRU-VNTR polymorphisms.

    Science.gov (United States)

    Garzelli, Carlo; Lari, Nicoletta; Rindi, Laura

    2016-03-01

    The Beijing genotype of Mycobacterium tuberculosis is cause of global concern as it is rapidly spreading worldwide, is considered hypervirulent, and is most often associated to massive spread of MDR/XDR TB, although these epidemiological or pathological properties have not been confirmed for all strains and in all geographic settings. In this paper, to gain new insights into the biogeographical heterogeneity of the Beijing family, we investigated a global sample of Beijing strains (22% from Italian-born, 78% from foreign-born patients) by determining large sequence polymorphism of regions RD105, RD181, RD150 and RD142, single nucleotide polymorphism of putative DNA repair genes mutT4 and mutT2 and MIRU-VNTR profiles based on 11 discriminative loci. We found that, although our sample of Beijing strains showed a considerable genomic heterogeneity, yielding both ancient and recent phylogenetic strains, the prevalent successful Beijing subsets were characterized by deletions of RD105 and RD181 and by one nucleotide substitution in one or both mutT genes. MIRU-VNTR analysis revealed 47 unique patterns and 9 clusters including a total of 33 isolates (41% of total isolates); the relatively high proportion of Italian-born Beijing TB patients, often occurring in mixed clusters, supports the possibility of an ongoing cross-transmission of the Beijing genotype to autochthonous population. High rates of extra-pulmonary localization and drug-resistance, particularly MDR, frequently reported for Beijing strains in other settings, were not observed in our survey. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Genomic Variability of Mycobacterium tuberculosis Strains of the Euro-American Lineage Based on Large Sequence Deletions and 15-Locus MIRU-VNTR Polymorphism

    Science.gov (United States)

    Rindi, Laura; Medici, Chiara; Bimbi, Nicola; Buzzigoli, Andrea; Lari, Nicoletta; Garzelli, Carlo

    2014-01-01

    A sample of 260 Mycobacterium tuberculosis strains assigned to the Euro-American family was studied to identify phylogenetically informative genomic regions of difference (RD). Mutually exclusive deletions of regions RD115, RD122, RD174, RD182, RD183, RD193, RD219, RD726 and RD761 were found in 202 strains; the RDRio deletion was detected exclusively among the RD174-deleted strains. Although certain deletions were found more frequently in certain spoligotype families (i.e., deletion RD115 in T and LAM, RD174 in LAM, RD182 in Haarlem, RD219 in T and RD726 in the “Cameroon” family), the RD-defined sublineages did not specifically match with spoligotype-defined families, thus arguing against the use of spoligotyping for establishing exact phylogenetic relationships between strains. Notably, when tested for katG463/gyrA95 polymorphism, all the RD-defined sublineages belonged to Principal Genotypic Group (PGG) 2, except sublineage RD219 exclusively belonging to PGG3; the 58 Euro-American strains with no deletion were of either PGG2 or 3. A representative sample of 197 isolates was then analyzed by standard 15-locus MIRU-VNTR typing, a suitable approach to independently assess genetic relationships among the strains. Analysis of the MIRU-VNTR typing results by using a minimum spanning tree (MST) and a classical dendrogram showed groupings that were largely concordant with those obtained by RD-based analysis. Isolates of a given RD profile show, in addition to closely related MIRU-VNTR profiles, related spoligotype profiles that can serve as a basis for better spoligotype-based classification. PMID:25197794

  17. Building and calibrating a large-extent and high resolution coupled groundwater-land surface model using globally available data-sets

    Science.gov (United States)

    Sutanudjaja, E. H.; Van Beek, L. P.; de Jong, S. M.; van Geer, F.; Bierkens, M. F.

    2012-12-01

    The current generation of large-scale hydrological models generally lacks a groundwater model component simulating lateral groundwater flow. Large-scale groundwater models are rare due to a lack of hydro-geological data required for their parameterization and a lack of groundwater head data required for their calibration. In this study, we propose an approach to develop a large-extent fully-coupled land surface-groundwater model by using globally available datasets and calibrate it using a combination of discharge observations and remotely-sensed soil moisture data. The underlying objective is to devise a collection of methods that enables one to build and parameterize large-scale groundwater models in data-poor regions. The model used, PCR-GLOBWB-MOD, has a spatial resolution of 1 km x 1 km and operates on a daily basis. It consists of a single-layer MODFLOW groundwater model that is dynamically coupled to the PCR-GLOBWB land surface model. This fully-coupled model accommodates two-way interactions between surface water levels and groundwater head dynamics, as well as between upper soil moisture states and groundwater levels, including a capillary rise mechanism to sustain upper soil storage and thus to fulfill high evaporation demands (during dry conditions). As a test bed, we used the Rhine-Meuse basin, where more than 4000 groundwater head time series have been collected for validation purposes. The model was parameterized using globally available data-sets on surface elevation, drainage direction, land-cover, soil and lithology. Next, the model was calibrated using a brute force approach and massive parallel computing, i.e. by running the coupled groundwater-land surface model for more than 3000 different parameter sets. Here, we varied minimal soil moisture storage and saturated conductivities of the soil layers as well as aquifer transmissivities. Using different regularization strategies and calibration criteria we compared three calibration scenarios

  18. Clinical implication of genome-wide profiling in diffuse large B-cell lymphoma and other subtypes of B-cell lymphoma

    DEFF Research Database (Denmark)

    Iqbal, Javeed; Joshi, Shantaram; Patel, Kavita N

    2007-01-01

    of Lymphoid Neoplasms (REAL) and World Health Organization (WHO) classifications. These classification methods were based on histological, immunophenotypic and cytogenetic markers and widely accepted by pathologists and oncologists worldwide. During last several decades, great progress has been made...... technology. The genome-wide transcriptional measurement, also called gene expression profile (GEP) can accurately define the biological phenotype of the tumor. In this review, important discoveries made by genome-wide GEP in understanding the biology of lymphoma and additionally the diagnostic and prognostic...

  19. Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics.

    Science.gov (United States)

    Aoki, Koh; Yano, Kentaro; Suzuki, Ayako; Kawamura, Shingo; Sakurai, Nozomu; Suda, Kunihiro; Kurabayashi, Atsushi; Suzuki, Tatsuya; Tsugane, Taneaki; Watanabe, Manabu; Ooga, Kazuhide; Torii, Maiko; Narita, Takanori; Shin-I, Tadasu; Kohara, Yuji; Yamamoto, Naoki; Takahashi, Hideki; Watanabe, Yuichiro; Egusa, Mayumi; Kodama, Motoichiro; Ichinose, Yuki; Kikuchi, Mari; Fukushima, Sumire; Okabe, Akiko; Arie, Tsutomu; Sato, Yuko; Yazawa, Katsumi; Satoh, Shinobu; Omura, Toshikazu; Ezura, Hiroshi; Shibata, Daisuke

    2010-03-30

    The Solanaceae family includes several economically important vegetable crops. The tomato (Solanum lycopersicum) is regarded as a model plant of the Solanaceae family. Recently, a number of tomato resources have been developed in parallel with the ongoing tomato genome sequencing project. In particular, a miniature cultivar, Micro-Tom, is regarded as a model system in tomato genomics, and a number of genomics resources in the Micro-Tom-background, such as ESTs and mutagenized lines, have been established by an international alliance. To accelerate the progress in tomato genomics, we developed a collection of fully-sequenced 13,227 Micro-Tom full-length cDNAs. By checking redundant sequences, coding sequences, and chimeric sequences, a set of 11,502 non-redundant full-length cDNAs (nrFLcDNAs) was generated. Analysis of untranslated regions demonstrated that tomato has longer 5'- and 3'-untranslated regions than most other plants but rice. Classification of functions of proteins predicted from the coding sequences demonstrated that nrFLcDNAs covered a broad range of functions. A comparison of nrFLcDNAs with genes of sixteen plants facilitated the identification of tomato genes that are not found in other plants, most of which did not have known protein domains. Mapping of the nrFLcDNAs onto currently available tomato genome sequences facilitated prediction of exon-intron structure. Introns of tomato genes were longer than those of Arabidopsis and rice. According to a comparison of exon sequences between the nrFLcDNAs and the tomato genome sequences, the frequency of nucleotide mismatch in exons between Micro-Tom and the genome-sequencing cultivar (Heinz 1706) was estimated to be 0.061%. The collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies. The nrFLcDNA sequences will help annotation of the tomato whole-genome sequence and aid in tomato functional

  20. Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum cultivar Micro-Tom, a reference system for the Solanaceae genomics

    Directory of Open Access Journals (Sweden)

    Kikuchi Mari

    2010-03-01

    Full Text Available Abstract Background The Solanaceae family includes several economically important vegetable crops. The tomato (Solanum lycopersicum is regarded as a model plant of the Solanaceae family. Recently, a number of tomato resources have been developed in parallel with the ongoing tomato genome sequencing project. In particular, a miniature cultivar, Micro-Tom, is regarded as a model system in tomato genomics, and a number of genomics resources in the Micro-Tom-background, such as ESTs and mutagenized lines, have been established by an international alliance. Results To accelerate the progress in tomato genomics, we developed a collection of fully-sequenced 13,227 Micro-Tom full-length cDNAs. By checking redundant sequences, coding sequences, and chimeric sequences, a set of 11,502 non-redundant full-length cDNAs (nrFLcDNAs was generated. Analysis of untranslated regions demonstrated that tomato has longer 5'- and 3'-untranslated regions than most other plants but rice. Classification of functions of proteins predicted from the coding sequences demonstrated that nrFLcDNAs covered a broad range of functions. A comparison of nrFLcDNAs with genes of sixteen plants facilitated the identification of tomato genes that are not found in other plants, most of which did not have known protein domains. Mapping of the nrFLcDNAs onto currently available tomato genome sequences facilitated prediction of exon-intron structure. Introns of tomato genes were longer than those of Arabidopsis and rice. According to a comparison of exon sequences between the nrFLcDNAs and the tomato genome sequences, the frequency of nucleotide mismatch in exons between Micro-Tom and the genome-sequencing cultivar (Heinz 1706 was estimated to be 0.061%. Conclusion The collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies. The nrFLcDNA sequences will help annotation of the

  1. Successful application of FTA Classic Card technology and use of bacteriophage phi29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomes.

    Science.gov (United States)

    Owor, Betty E; Shepherd, Dionne N; Taylor, Nigel J; Edema, Richard; Monjane, Adérito L; Thomson, Jennifer A; Martin, Darren P; Varsani, Arvind

    2007-03-01

    Leaf samples from 155 maize streak virus (MSV)-infected maize plants were collected from 155 farmers' fields in 23 districts in Uganda in May/June 2005 by leaf-pressing infected samples onto FTA Classic Cards. Viral DNA was successfully extracted from cards stored at room temperature for 9 months. The diversity of 127 MSV isolates was analysed by PCR-generated RFLPs. Six representative isolates having different RFLP patterns and causing either severe, moderate or mild disease symptoms, were chosen for amplification from FTA cards by bacteriophage phi29 DNA polymerase using the TempliPhi system. Full-length genomes were inserted into a cloning vector using a unique restriction enzyme site, and sequenced. The 1.3-kb PCR product amplified directly from FTA-eluted DNA and used for RFLP analysis was also cloned and sequenced. Comparison of cloned whole genome sequences with those of the original PCR products indicated that the correct virus genome had been cloned and that no errors were introduced by the phi29 polymerase. This is the first successful large-scale application of FTA card technology to the field, and illustrates the ease with which large numbers of infected samples can be collected and stored for downstream molecular applications such as diversity analysis and cloning of potentially new virus genomes.

  2. Genomic research in Eucalyptus.

    Science.gov (United States)

    Poke, Fiona S; Vaillancourt, René E; Potts, Brad M; Reid, James B

    2005-09-01

    Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.

  3. Sustainable Building Operation

    DEFF Research Database (Denmark)

    Jensen, Jesper Ole

    2009-01-01

    of sustainable building operation and a survey amongst building administrators from the private and the social housing sector. Our results show that there are many good examples on sustainable building operation in Danish housing estates, where local building managers, residents etc. have gained impressive......Energy-savings in the existing building stock have becomes a main goal in national and international policies. Often focus is on building-renovations, whereas the potential of sustainable building operation to a large extent has been neglected. Nevertheless, international research as well...... as practical experiences from Danish housing estates indicates that there are large potentials for energy savings by focusing on the operation of the buildings. We suggest that in order to achieve sustainability in the existing housing, renovation and operations should be seen as integrated parts...

  4. The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

    KAUST Repository

    Bracken-Grissom, Heather; Collins, Allen G.; Collins, Timothy; Crandall, Keith; Distel, Daniel; Dunn, Casey; Giribet, Gonzalo; Haddock, Steven; Knowlton, Nancy; Martindale, Mark; Medina, Monica; Messing, Charles; O'Brien, Stephen J.; Paulay, Gustav; Putnam, Nicolas; Ravasi, Timothy; Rouse, Greg W.; Ryan, Joseph F.; Schulze, Anja; Worheide, Gert; Adamska, Maja; Bailly, Xavier; Breinholt, Jesse; Browne, William E.; Diaz, M. Christina; Evans, Nathaniel; Flot, Jean-Francois; Fogarty, Nicole; Johnston, Matthew; Kamel, Bishoy; Kawahara, Akito Y.; Laberge, Tammy; Lavrov, Dennis; Michonneau, Francois; Moroz, Leonid L.; Oakley, Todd; Osborne, Karen; Pomponi, Shirley A.; Rhodes, Adelaide; Rodriguez-Lanetty, Mauricio; Santos, Scott R.; Satoh, Nori; Thacker, Robert W.; Van de Peer, Yves; Voolstra, Christian R.; Welch, David Mark; Winston, Judith; Zhou, Xin

    2013-01-01

    Over 95% of all metazoan (animal) species comprise the invertebrates, but very few genomes from these organisms have been sequenced. We have, therefore, formed a Global Invertebrate Genomics Alliance (GIGA). Our intent is to build a collaborative

  5. Rice Genome Research: Current Status and Future Perspectives

    Directory of Open Access Journals (Sweden)

    Bin Han

    2008-11-01

    Full Text Available Rice ( L. is the leading genomics system among the crop plants. The sequence of the rice genome, the first cereal plant genome, was published in 2005. This review summarizes progress made in rice genome annotations, comparative genomics, and functional genomics researches. It also maps out the status of rice genomics globally and provides a vision of future research directions and resource building.

  6. The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

    KAUST Repository

    Bracken-Grissom, Heather

    2013-12-12

    Over 95% of all metazoan (animal) species comprise the invertebrates, but very few genomes from these organisms have been sequenced. We have, therefore, formed a Global Invertebrate Genomics Alliance (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site () has been launched to facilitate this collaborative venture.

  7. Building 431 fire tests

    International Nuclear Information System (INIS)

    Alvares, N.J.; Beason, D.G.; Ford, H.W.; Magee, M.W.

    1977-01-01

    An extensive discussion of considerations for fire protection in the LLL mirror fusion test facility (MFTF) is presented. Because of the large volume and high bays of the building, sufficient data on fire detection is unavailable. Results of fire detection tests using controlled fire sources in the building are presented. Extensive data concerning the behavior of the building atmosphere are included. Candidate fire detection instrumentation and extinguishing systems for use in the building are briefly reviewed

  8. Changes in respiratory and non-respiratory symptoms in occupants of a large office building over a period of moisture damage remediation attempts

    Science.gov (United States)

    Cho, Sook Ja; White, Sandra K.; Cox-Ganser, Jean M.

    2018-01-01

    There is limited information on the natural history of building occupants’ health in relation to attempts to remediate moisture damage. We examined changes in respiratory and non-respiratory symptoms in 1,175 office building occupants over seven years with multiple remediation attempts. During each of four surveys, we categorized participants using a severity score: 0 = asymptomatic; 1 = mild, symptomatic in the last 12 months, but not frequently in the last 4 weeks; 2 = severe, symptomatic at least once weekly in the last 4 weeks. Building-related symptoms were defined as improving away from the building. We used random intercept models adjusted for demographics, smoking, building tenure, and microbial exposures to estimate temporal changes in the odds of building-related symptoms or severity scores independent of the effect of microbial exposures. Trend analyses of combined mild/severe symptoms showed no changes in the odds of respiratory symptoms but significant improvement in non-respiratory symptoms over time. Separate analyses showed increases in the odds of severe respiratory symptoms (odds ratio/year = 1.15‒1.16, p-valuesremediation efforts might not be effective in improving occupants’ health. PMID:29324816

  9. Validation of rice genome sequence by optical mapping

    Directory of Open Access Journals (Sweden)

    Pape Louise

    2007-08-01

    Full Text Available Abstract Background Rice feeds much of the world, and possesses the simplest genome analyzed to date within the grass family, making it an economically relevant model system for other cereal crops. Although the rice genome is sequenced, validation and gap closing efforts require purely independent means for accurate finishing of sequence build data. Results To facilitate ongoing sequencing finishing and validation efforts, we have constructed a whole-genome SwaI optical restriction map of the rice genome. The physical map consists of 14 contigs, covering 12 chromosomes, with a total genome size of 382.17 Mb; this value is about 11% smaller than original estimates. 9 of the 14 optical map contigs are without gaps, covering chromosomes 1, 2, 3, 4, 5, 7, 8 10, and 12 in their entirety – including centromeres and telomeres. Alignments between optical and in silico restriction maps constructed from IRGSP (International Rice Genome Sequencing Project and TIGR (The Institute for Genomic Research genome sequence sources are comprehensive and informative, evidenced by map coverage across virtually all published gaps, discovery of new ones, and characterization of sequence misassemblies; all totalling ~14 Mb. Furthermore, since optical maps are ordered restriction maps, identified discordances are pinpointed on a reliable physical scaffold providing an independent resource for closure of gaps and rectification of misassemblies. Conclusion Analysis of sequence and optical mapping data effectively validates genome sequence assemblies constructed from large, repeat-rich genomes. Given this conclusion we envision new applications of such single molecule analysis that will merge advantages offered by high-resolution optical maps with inexpensive, but short sequence reads generated by emerging sequencing platforms. Lastly, map construction techniques presented here points the way to new types of comparative genome analysis that would focus on discernment of

  10. Energy-oriented and structural modernisation of industrial large-panel buildings, type ``Hoyerswerda``; Energetische und bautechnische Sanierung von industriellen Wohnbauten der Wohnbauserie Typ ``Hoyerswerda``

    Energy Technology Data Exchange (ETDEWEB)

    Loeber, H.; Derlig, R. [Hochschule fuer Technik, Wirtschaft und Sozialwesen Zittau/Goerlitz, Zittau (Germany); Sprenger, S. [Wohnungsgenossenschaft Hoyerswerda e.G. (Germany)

    1997-12-31

    The condition of the building prior to redevelopment is described with the following regards: layout of the building, construction material specifications and layers of structural components, condition of the thermally insulating shell of the building and condition of its technical equipment. Executed modernization measures are discussed. Heat energy consumption before and after modernization is compared and put in relation to external temperature. Finally, area-specific heat energy consumption and ventilation are discussed in detail. Information as to the cost of modernization rounds off the report. (MSK.) [Deutsch] Der Gebaeudezustand vor der Sanierung wird in folgenden Punkten beschrieben: Bausystem, Baustoffdaten und Schichtaufbau der Bauteile, Bauzustand der waermedaemmenden Gebaeudehuelle sowie Bauzustand der technischen Gebaeudeausruestung. Die Sanierungsmassnahmen werden erlaeutert. Der Heiwaermeverbrauch vor und nach der Sanierung wird verglichen und in Beziehung zur Aussentemperatur gesetzt. Ausserdem werden der flaechenspezifische Heizwaermeverbrauch und die Wohnungslueftung naeher erlaeutert. Angaben zu den Sanierungskosten schliessen den Bericht ab.

  11. The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study

    NARCIS (Netherlands)

    T.W. Winkler (Thomas W.); A.E. Justice (Anne); M.J. Graff (Maud J.L.); Barata, L. (Llilda); M.F. Feitosa (Mary Furlan); Chu, S. (Su); J. Czajkowski (Jacek); T. Esko (Tõnu); M. Fall (Magnus); T.O. Kilpeläinen (Tuomas); Y. Lu (Yingchang); R. Mägi (Reedik); E. Mihailov (Evelin); T.H. Pers (Tune); Rüeger, S. (Sina); A. Teumer (Alexander); G.B. Ehret (Georg); T. Ferreira (Teresa); N.L. Heard-Costa (Nancy); J. Karjalainen (Juha); V. Lagou (Vasiliki); A. Mahajan (Anubha); Neinast, M.D. (Michael D.); I. Prokopenko (Inga); J. Simino (Jeannette); T.M. Teslovich (Tanya M.); R. Jansen; H.J. Westra (Harm-Jan); C.C. White (Charles); D. Absher (Devin); T.S. Ahluwalia (Tarunveer Singh); S. Ahmad (Shafqat); E. Albrecht (Eva); A.C. Alves (Alexessander Couto); Bragg-Gresham, J.L. (Jennifer L.); A.J. de Craen (Anton); J.C. Bis (Joshua); A. Bonnefond (Amélie); G. Boucher (Gabrielle); G. Cadby (Gemma); Y.-C. Cheng (Yu-Ching); Chiang, C.W. (Charleston W K); G. Delgado; A. Demirkan (Ayşe); N. Dueker (Nicole); N. Eklund (Niina); G. Eiriksdottir (Gudny); J. Eriksson (Joel); B. Feenstra (Bjarke); K. Fischer (Krista); F. Frau (Francesca); T.E. Galesloot (Tessel); F. Geller (Frank); A. Goel (Anuj); M. Gorski (Mathias); T.B. Grammer (Tanja); S. Gustafsson (Stefan); Haitjema, S. (Saskia); J.J. Hottenga (Jouke Jan); J.E. Huffman (Jennifer); A.U. Jackson (Anne); K.B. Jacobs (Kevin); A. Johansson (Åsa); M. Kaakinen (Marika); M.E. Kleber (Marcus); J. Lahti (Jari); I.M. Leach (Irene Mateo); Lehne, B. (Benjamin); Liu, Y. (Youfang); K.S. Lo; M. Lorentzon (Mattias); J. Luan (Jian'An); P.A. Madden (Pamela); M. Mangino (Massimo); B. McKnight (Barbara); Medina-Gomez, C. (Carolina); K.L. Monda (Keri); M.E. Montasser (May E.); G. Müller (Gabriele); M. Müller-Nurasyid (Martina); I.M. Nolte (Ilja); Panoutsopoulou, K. (Kalliope); L. Pascoe (Laura); L. Paternoster (Lavinia); N.W. Rayner (Nigel William); F. Renström (Frida); Rizzi, F. (Federica); L.M. Rose (Lynda); Ryan, K.A. (Kathy A.); P. Salo (Perttu); S. Sanna (Serena); H. Scharnagl (Hubert); Shi, J. (Jianxin); A.V. Smith (Albert Vernon); L. Southam (Lorraine); A. Stancáková (Alena); V. Steinthorsdottir (Valgerdur); R.J. Strawbridge (Rona); Sung, Y.J. (Yun Ju); I. Tachmazidou (Ioanna); T. Tanaka (Toshiko); G. Thorleifsson (Gudmar); S. Trompet (Stella); N. Pervjakova (Natalia); J.P. Tyrer (Jonathan); L. Vandenput (Liesbeth); S.W. Van Der Laan (Sander W.); N. van der Velde (Nathalie); J. van Setten (Jessica); J.V. van Vliet-Ostaptchouk (Jana); N. Verweij (Niek); E. Vlachopoulou (Efthymia); L. Waite (Lindsay); S.R. Wang (Sophie); Z. Wang (Zhaoming); S.H. Wild (Sarah); C. Willenborg (Christina); J.F. Wilson (James); A. Wong (Andrew); Yang, J. (Jian); L. Yengo (Loic); L.M. Yerges-Armstrong (Laura); Yu, L. (Lei); W. Zhang (Weihua); Zhao, J.H. (Jing Hua); E.A. Andersson (Ehm Astrid); S.J.L. Bakker (Stephan); D. Baldassarre (Damiano); Banasik, K. (Karina); Barcella, M. (Matteo); Barlassina, C. (Cristina); C. Bellis (Claire); P. Benaglio (Paola); J. Blangero (John); M. Blüher (Matthias); Bonnet, F. (Fabrice); L.L. Bonnycastle (Lori); H.A. Boyd (Heather); M. Bruinenberg (M.); Buchman, A.S. (Aron S.); H. Campbell (Harry); Y.D. Chen (Y.); P.S. Chines (Peter); S. Claudi-Boehm (Simone); J.W. Cole (John W.); F.S. Collins (Francis); E.J.C. de Geus (Eco); L.C.P.G.M. de Groot (Lisette); M. Dimitriou (Maria); J. Duan (Jubao); S. Enroth (Stefan); E. Eury (Elodie); A.-E. Farmaki (Aliki-Eleni); N.G. Forouhi (Nita); N. Friedrich (Nele); P.V. Gejman (Pablo); B. Gigante (Bruna); N. Glorioso (Nicola); A. Go (Attie); R.F. Gottesman (Rebecca); J. Gräßler (Jürgen); H. Grallert (Harald); N. Grarup (Niels); Gu, Y.-M. (Yu-Mei); L. Broer (Linda); A.C. Ham (Annelies); T. Hansen (T.); T.B. Harris (Tamara); C.A. Hartman (Catharina A.); Hassinen, M. (Maija); N. Hastie (Nick); A.T. Hattersley (Andrew); A.C. Heath (Andrew); A.K. Henders (Anjali); D.G. Hernandez (Dena); H.L. Hillege (Hans); O.L. Holmen (Oddgeir); G.K. Hovingh (Kees); J. Hui (Jennie); Husemoen, L.L. (Lise L.); Hutri-Kähönen, N. (Nina); P.G. Hysi (Pirro); T. Illig (Thomas); P.L. de Jager (Philip); S. Jalilzadeh (Shapour); T. Jorgensen (Torben); J.W. Jukema (Jan Wouter); Juonala, M. (Markus); S. Kanoni (Stavroula); M. Karaleftheri (Maria); K.T. Khaw; L. Kinnunen (Leena); T. Kittner (Thomas); W. Koenig (Wolfgang); I. Kolcic (Ivana); P. Kovacs (Peter); Krarup, N.T. (Nikolaj T.); W. Kratzer (Wolfgang); Krüger, J. (Janine); Kuh, D. (Diana); M. Kumari (Meena); T. Kyriakou (Theodosios); C. Langenberg (Claudia); L. Lannfelt (Lars); C. Lanzani (Chiara); V. Lotay (Vaneet); L.J. Launer (Lenore); K. Leander (Karin); J. Lindström (Jaana); A. Linneberg (Allan); Liu, Y.-P. (Yan-Ping); S. Lobbens (Stéphane); R.N. Luben (Robert); V. Lyssenko (Valeriya); S. Männistö (Satu); P.K. Magnusson (Patrik); W.L. McArdle (Wendy); C. Menni (Cristina); S. Merger (Sigrun); L. Milani (Lili); Montgomery, G.W. (Grant W.); A.P. Morris (Andrew); N. Narisu (Narisu); M. Nelis (Mari); K.K. Ong (Ken); A. Palotie (Aarno); L. Perusse (Louis); I. Pichler (Irene); M.G. Pilia (Maria Grazia); A. Pouta (Anneli); Rheinberger, M. (Myriam); Ribel-Madsen, R. (Rasmus); Richards, M. (Marcus); K.M. Rice (Kenneth); T.K. Rice (Treva K.); C. Rivolta (Carlo); V. Salomaa (Veikko); A.R. Sanders (Alan); M.A. Sarzynski (Mark A.); S. Scholtens (Salome); R.A. Scott (Robert); W.R. Scott (William R.); S. Sebert (Sylvain); S. Sengupta (Sebanti); B. Sennblad (Bengt); T. Seufferlein (Thomas); A. Silveira (Angela); P.E. Slagboom (Eline); J.H. Smit (Jan); T. Sparsø (Thomas); K. Stirrups (Kathy); R.P. Stolk (Ronald); H.M. Stringham (Heather); Swertz, M.A. (Morris A.); A.J. Swift (Amy); A.C. Syvänen; S.-T. Tan (Sian-Tsung); B. Thorand (Barbara); A. Tönjes (Anke); Tremblay, A. (Angelo); E. Tsafantakis (Emmanouil); P.J. van der Most (Peter); U. Völker (Uwe); M.-C. Vohl (Marie-Claude); J.M. Vonk (Judith); M. Waldenberger (Melanie); Walker, R.W. (Ryan W.); R. Wennauer (Roman); E. Widen; G.A.H.M. Willemsen (Gonneke); T. Wilsgaard (Tom); A.F. Wright (Alan); M.C. Zillikens (Carola); S. Van Dijk (Suzanne); N.M. van Schoor (Natasja); F.W. Asselbergs (Folkert); P.I.W. de Bakker (Paul); J.S. Beckmann (Jacques); J.P. Beilby (John); D.A. Bennett (David A.); R.N. Bergman (Richard); S.M. Bergmann (Sven); C.A. Böger (Carsten); B.O. Boehm (Bernhard); E.A. Boerwinkle (Eric); D.I. Boomsma (Dorret); S.R. Bornstein (Stefan); E.P. Bottinger (Erwin); C. Bouchard (Claude); J.C. Chambers (John); S.J. Chanock (Stephen); D.I. Chasman (Daniel); F. Cucca (Francesco); D. Cusi (Daniele); G.V. Dedoussis (George); J. Erdmann (Jeanette); K. Hagen (Knut); D. Evans; U. de Faire (Ulf); M. Farrall (Martin); L. Ferrucci (Luigi); I. Ford (Ian); L. Franke (Lude); P.W. Franks (Paul); P. Froguel (Philippe); R.T. Gansevoort (Ron); C. Gieger (Christian); H. Grönberg (Henrik); V. Gudnason (Vilmundur); U. Gyllensten (Ulf); P. Hall (Per); A. Hamsten (Anders); P. van der Harst (Pim); C. Hayward (Caroline); M. Heliovaara (Markku); C. Hengstenberg (Christian); A.A. Hicks (Andrew); A. Hingorani (Aroon); A. Hofman (Albert); Hu, F. (Frank); H.V. Huikuri (Heikki); K. Hveem (Kristian); A. James (Alan); Jordan, J.M. (Joanne M.); A. Jula (Antti); M. Kähönen (Mika); E. Kajantie (Eero); S. Kathiresan (Sekar); L.A.L.M. Kiemeney (Bart); M. Kivimaki (Mika); P. Knekt; H. Koistinen (Heikki); J.S. Kooner (Jaspal S.); S. Koskinen (Seppo); J. Kuusisto (Johanna); W. Maerz (Winfried); N.G. Martin (Nicholas); M. Laakso (Markku); T.A. Lakka (Timo); T. Lehtimäki (Terho); G. Lettre (Guillaume); D.F. Levinson (Douglas); W.H.L. Kao (Wen); M.L. Lokki; Mäntyselkä, P. (Pekka); M. Melbye (Mads); A. Metspalu (Andres); B.D. Mitchell (Braxton); F.L. Moll (Frans); J.C. Murray (Jeffrey); A.W. Musk (Arthur); M.S. Nieminen (Markku); I. Njølstad (Inger); C. Ohlsson (Claes); A.J. Oldehinkel (Albertine); B.A. Oostra (Ben); C. Palmer (Cameron); J.S. Pankow (James); G. Pasterkamp (Gerard); N.L. Pedersen (Nancy); O. Pedersen (Oluf); B.W.J.H. Penninx (Brenda); M. Perola (Markus); A. Peters (Annette); O. Polasek (Ozren); P.P. Pramstaller (Peter Paul); Psaty, B.M. (Bruce M.); Qi, L. (Lu); T. Quertermous (Thomas); Raitakari, O.T. (Olli T.); T. Rankinen (Tuomo); R. Rauramaa (Rainer); P.M. Ridker (Paul); J.D. Rioux (John); F. Rivadeneira Ramirez (Fernando); J.I. Rotter (Jerome I.); I. Rudan (Igor); H.M. den Ruijter (Hester ); J. Saltevo (Juha); N. Sattar (Naveed); Schunkert, H. (Heribert); P.E.H. Schwarz (Peter); A.R. Shuldiner (Alan); J. Sinisalo (Juha); H. Snieder (Harold); T.I.A. Sørensen (Thorkild); T.D. Spector (Timothy); Staessen, J.A. (Jan A.); Stefania, B. (Bandinelli); U. Thorsteinsdottir (Unnur); M. Stumvoll (Michael); J.-C. Tardif (Jean-Claude); E. Tremoli (Elena); J. Tuomilehto (Jaakko); A.G. Uitterlinden (André); M. Uusitupa (Matti); A.L.M. Verbeek; S.H.H.M. Vermeulen (Sita); J. Viikari (Jorma); Vitart, V. (Veronique); H. Völzke (Henry); P. Vollenweider (Peter); G. Waeber (Gérard); M. Walker (Mark); H. Wallaschofski (Henri); N.J. Wareham (Nick); H. Watkins (Hugh); E. Zeggini (Eleftheria); A. Chakravarti (Aravinda); Clegg, D.J. (Deborah J.); L.A. Cupples (Adrienne); P. Gordon-Larsen (Penny); C.E. Jaquish (Cashell); D.C. Rao (Dabeeru C.); Abecasis, G.R. (Goncalo R.); T.L. Assimes (Themistocles); I.E. Barroso (Inês); S.I. Berndt (Sonja); M. Boehnke (Michael); P. Deloukas (Panagiotis); C.S. Fox (Caroline); L. Groop (Leif); D. Hunter (David); E. Ingelsson (Erik); R.C. Kaplan (Robert); McCarthy, M.I. (Mark I.); K.L. Mohlke (Karen); J.R. O´Connell; Schlessinger, D. (David); D.P. Strachan (David); J-A. Zwart (John-Anker); C.M. van Duijn (Cornelia); J.N. Hirschhorn (Joel); C.M. Lindgren (Cecilia M.); I.M. Heid (Iris); K.E. North (Kari); I.B. Borecki (Ingrid); Z. Kutalik (Zoltán); R.J.F. Loos (Ruth)

    2015-01-01

    textabstractGenome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ

  12. SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints

    NARCIS (Netherlands)

    J. Vogt (Julia); K. Bengesser (Kathrin); K.B.M. Claes (Kathleen B.M.); K. Wimmer (Katharina); V.-F. Mautner (Victor-Felix); R. van Minkelen (Rick); E. Legius (Eric); H. Brems (Hilde); M. Upadhyaya (Meena); J. Högel (Josef); C. Lazaro (Conxi); T. Rosenbaum (Thorsten); S. Bammert (Simone); L. Messiaen (Ludwine); D.N. Cooper (David); H. Kehrer-Sawatzki (Hildegard)

    2014-01-01

    textabstractBackground: Genomic disorders are caused by copy number changes that may exhibit recurrent breakpoints processed by nonallelic homologous recombination. However, region-specific disease-associated copy number changes have also been observed which exhibit non-recurrent breakpoints. The

  13. A Large-Scale Multi-ancestry Genome-wide Study Accounting for Smoking Behavior Identifies Multiple Significant Loci for Blood Pressure

    NARCIS (Netherlands)

    Sung, Yun J.; Winkler, Thomas W.; de las Fuentes, Lisa; Bentley, Amy R.; Brown, Michael R.; Kraja, Aldi T.; Schwander, Karen; Ntalla, Ioanna; Guo, Xiuqing; Franceschini, Nora; Lu, Yingchang; Cheng, Ching-Yu; Sim, Xueling; Vojinovic, Dina; Marten, Jonathan; Musani, Solomon K.; Li, Changwei; Feitosa, Mary F.; Kilpelainen, Tuomas O.; Richard, Melissa A.; Noordam, Raymond; Aslibekyan, Stella; Aschard, Hugues; Bartz, Traci M.; Dorajoo, Rajkumar; Liu, Yongmei; Manning, Alisa K.; Rankinen, Tuomo; Smith, Albert Vernon; Tajuddin, Salman M.; Tayo, Bamidele O.; Warren, Helen R.; Zhao, Wei; Zhou, Yanhua; Matoba, Nana; Sofer, Tamar; Alver, Maris; Amini, Marzyeh; Boissel, Mathilde; Chai, Jin Fang; Chen, Xu; Divers, Jasmin; Gandin, Ilaria; Gao, Chuan; Giulianini, Franco; Goel, Anuj; Harris, Sarah E.; Hartwig, Fernando Pires; Horimoto, Andrea R. V. R.; Hsu, Fang-Chi; Jackson, Anne U.; Kahonen, Mika; Kasturiratne, Anuradhani; Kuhnel, Brigitte; Leander, Karin; Lee, Wen-Jane; Lin, Keng-Hung; Luan, Jian' an; McKenzie, Colin A.; He Meian,; Nelson, Christopher P.; Rauramaa, Rainer; Schupf, Nicole; Scott, Robert A.; Sheu, Wayne H. H.; Stancakova, Alena; Takeuchi, Fumihiko; van der Most, Peter J.; Varga, Tibor V.; Wang, Heming; Wang, Yajuan; Ware, Erin B.; Weiss, Stefan; Wen, Wanqing; Yanek, Lisa R.; Zhang, Weihua; Zhao, Jing Hua; Afaq, Saima; Alfred, Tamuno; Amin, Najaf; Arking, Dan; Aung, Tin; Barr, R. Graham; Bielak, Lawrence F.; Boerwinkle, Eric; Bottinger, Erwin P.; Braund, Peter S.; Brody, Jennifer A.; Broeckel, Ulrich; Cabrera, Claudia P.; Cade, Brian; Yu Caizheng,; Campbell, Archie; Canouil, Mickael; Chakravarti, Aravinda; Chauhan, Ganesh; Christensen, Kaare; Cocca, Massimiliano; Collins, Francis S.; Connell, John M.; de Mutsert, Renee; de Silva, H. Janaka; Debette, Stephanie; Dorr, Marcus; Duan, Qing; Eaton, Charles B.; Ehret, Georg; Evangelou, Evangelos; Faul, Jessica D.; Fisher, Virginia A.; Forouhi, Nita G.; Franco, Oscar H.; Friedlander, Yechiel; Gao, He; Gigante, Bruna; Graff, Misa; Gu, C. Charles; Gu, Dongfeng; Gupta, Preeti; Hagenaars, Saskia P.; Harris, Tamara B.; He, Jiang; Heikkinen, Sami; Heng, Chew-Kiat; Hirata, Makoto; Hofman, Albert; Howard, Barbara V.; Hunt, Steven; Irvin, Marguerite R.; Jia, Yucheng; Joehanes, Roby; Justice, Anne E.; Katsuya, Tomohiro; Kaufman, Joel; Kerrison, Nicola D.; Khor, Chiea Chuen; Koh, Woon-Puay; Koistinen, Heikki A.; Komulainen, Pirjo; Kooperberg, Charles; Krieger, Jose E.; Kubo, Michiaki; Kuusisto, Johanna; Langefeld, Carl D.; Langenberg, Claudia; Launer, Lenore J.; Lehne, Benjamin; Lewis, Cora E.; Li, Yize; Lim, Sing Hui; Lin, Shiow; Liu, Ching-Ti; Liu, Jianjun; Liu, Jingmin; Liu, Kiang; Liu, Yeheng; Loh, Marie; Lohman, Kurt K.; Long, Jirong; Louie, Tin; Magi, Reedik; Mahajan, Anubha; Meitinger, Thomas; Metspalu, Andres; Milani, Lili; Momozawa, Yukihide; Morris, Andrew P.; Mosley, Thomas H.; Munson, Peter; Murray, Alison D.; Nalls, Mike A.; Nasri, Ubaydah; Norris, Jill M.; North, Kari; Ogunniyi, Adesola; Padmanabhan, Sandosh; Palmas, Walter R.; Palmer, Nicholette D.; Pankow, James S.; Pedersen, Nancy L.; Peters, Annette; Peyser, Patricia A.; Polasek, Ozren; Raitakari, Olli T.; Renstrom, Frida; Rice, Treva K.; Ridker, Paul M.; Robino, Antonietta; Robinson, Jennifer G.; Rose, Lynda M.; Rudan, Igor; Sabanayagam, Charumathi; Salako, Babatunde L.; Sandow, Kevin; Schmidt, Carsten O.; Schreiner, Pamela J.; Scott, William R.; Seshadri, Sudha; Sever, Peter; Sitlani, Colleen M.; Smith, Jennifer A.; Snieder, Harold; Starr, John M.; Strauch, Konstantin; Tang, Hua; Taylor, Kent D.; Teo, Yik Ying; Tham, Yih Chung; Ultterlinden, Andre G.; Waldenberger, Melanie; Wang, Lihua; Wang, Ya X.; Bin Wei, Wen; Williams, Christine; Wilson, Gregory; Wojczynski, Mary K.; Yao, Jie; Yuan, Jian-Min; Zonderman, Alan B.; Becker, Diane M.; Boehnke, Michael; Bowden, Donald W.; Chambers, John C.; Chen, Yii-Der Ida; de Faire, Ulf; Deary, Ian J.; Esko, Tonu; Farrall, Martin; Forrester, Terrence; Franks, Paul W.; Freedman, Barry I.; Froguel, Philippe; Gasparini, Paolo; Gieger, Christian; Horta, Bernardo Lessa; Hung, Yi-Jen; Jonas, Jost B.; Kato, Norihiro; Kooner, Jaspal S.; Laakso, Markku; Lehtimaki, Terho; Liang, Kae-Woei; Magnusson, Patrik K. E.; Newman, Anne B.; Oldehinkel, Albertine J.; Pereira, Alexandre C.; Redline, Susan; Rettig, Rainer; Samani, Nilesh J.; Scott, James; Shu, Xiao-Ou; van der Harst, Pim; Wagenknecht, Lynne E.; Wareham, Nicholas J.; Watkins, Hugh; Weir, David R.; Wickremasinghe, Ananda R.; Wu, Tangchun; Zheng, Wei; Kamatani, Yoichiro; Laurie, Cathy C.; Bouchard, Claude; Cooper, Richard S.; Evans, Michele K.; Gudnason, Vilmundur; Kardia, Sharon L. R.; Kritchevsky, Stephen B.; Levy, Daniel; O'Connell, Jeff R.; Psaty, Bruce M.; van Dam, Rob M.; Sims, Mario; Arnett, Donna K.; Mook-Kanamori, Dennis O.; Kelly, Tanika N.; Fox, Ervin R.; Hayward, Caroline; Fornage, Myriam; Rotimi, Charles N.; Province, Michael A.; van Duijn, Cornelia M.; Tai, E. Shyong; Wong, Tien Yin; Loos, Ruth J. F.; Reiner, Alex P.; Rotter, Jerome I.; Zhu, Xiaofeng; Bierut, Laura J.; Gauderman, W. James; Caulfield, Mark J.; Elliott, Paul; Rice, Kenneth; Munroe, Patricia B.; Morrison, Alanna C.; Cupples, L. Adrienne; Rao, Dabeeru C.; Chasman, Daniel I.; Study, Lifelines Cohort

    2018-01-01

    Genome-wide association analysis advanced understanding of blood pressure (BP), a major risk factor for vascular conditions such as coronary heart disease and stroke. Accounting for smoking behavior may help identify BP loci and extend our knowledge of its genetic architecture. We performed

  14. Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with conjunctivitis versus the deep nasopharynx of asymptomatic cattle

    Science.gov (United States)

    Moraxella bovoculi is a recently described bacterium that is associated with infectious bovine keratoconjunctivitis (IBK) or "pinkeye" in cattle. In this study, closed circularized genomes were generated for seven M. bovoculi isolates: three that originated from the eyes of clinical IBK bovine case...

  15. Changes in respiratory and non-respiratory symptoms in occupants of a large office building over a period of moisture damage remediation attempts.

    Science.gov (United States)

    Park, Ju-Hyeong; Cho, Sook Ja; White, Sandra K; Cox-Ganser, Jean M

    2018-01-01

    There is limited information on the natural history of building occupants' health in relation to attempts to remediate moisture damage. We examined changes in respiratory and non-respiratory symptoms in 1,175 office building occupants over seven years with multiple remediation attempts. During each of four surveys, we categorized participants using a severity score: 0 = asymptomatic; 1 = mild, symptomatic in the last 12 months, but not frequently in the last 4 weeks; 2 = severe, symptomatic at least once weekly in the last 4 weeks. Building-related symptoms were defined as improving away from the building. We used random intercept models adjusted for demographics, smoking, building tenure, and microbial exposures to estimate temporal changes in the odds of building-related symptoms or severity scores independent of the effect of microbial exposures. Trend analyses of combined mild/severe symptoms showed no changes in the odds of respiratory symptoms but significant improvement in non-respiratory symptoms over time. Separate analyses showed increases in the odds of severe respiratory symptoms (odds ratio/year = 1.15‒1.16, p-values<0.05) and severity scores (0.02/year, p-values<0.05) for wheezing and shortness of breath on exertion, due to worsening of participants in the mild symptom group. For non-respiratory symptoms, we found no changes in the odds of severe symptoms but improvement in severity scores (-0.04‒-0.01/year, p-values<0.05) and the odds for mild fever and chills, excessive fatigue, headache, and throat symptoms (0.65-0.79/year, p-values<0.05). Our study suggests that after the onset of respiratory and severe non-respiratory symptoms associated with dampness/mold, remediation efforts might not be effective in improving occupants' health.

  16. Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Roz Laing

    Full Text Available The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid

  17. Assembly and Multiplex Genome Integration of Metabolic Pathways in Yeast Using CasEMBLR.

    Science.gov (United States)

    Jakočiūnas, Tadas; Jensen, Emil D; Jensen, Michael K; Keasling, Jay D

    2018-01-01

    Genome integration is a vital step for implementing large biochemical pathways to build a stable microbial cell factory. Although traditional strain construction strategies are well established for the model organism Saccharomyces cerevisiae, recent advances in CRISPR/Cas9-mediated genome engineering allow much higher throughput and robustness in terms of strain construction. In this chapter, we describe CasEMBLR, a highly efficient and marker-free genome engineering method for one-step integration of in vivo assembled expression cassettes in multiple genomic sites simultaneously. CasEMBLR capitalizes on the CRISPR/Cas9 technology to generate double-strand breaks in genomic loci, thus prompting native homologous recombination (HR) machinery to integrate exogenously derived homology templates. As proof-of-principle for microbial cell factory development, CasEMBLR was used for one-step assembly and marker-free integration of the carotenoid pathway from 15 exogenously supplied DNA parts into three targeted genomic loci. As a second proof-of-principle, a total of ten DNA parts were assembled and integrated in two genomic loci to construct a tyrosine production strain, and at the same time knocking out two genes. This new method complements and improves the field of genome engineering in S. cerevisiae by providing a more flexible platform for rapid and precise strain building.

  18. Buildings interoperability landscape - Draft

    Energy Technology Data Exchange (ETDEWEB)

    Hardin, Dave B. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Stephan, Eric G. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Wang, Weimin [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Corbin, Charles D. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Widergren, Steven E. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

    2015-02-01

    Buildings are an integral part of our nation’s energy economy. The advancement in information and communications technology (ICT) has revolutionized energy management in industrial facilities and large commercial buildings. As ICT costs decrease and capabilities increase, buildings automation and energy management features are transforming the small-medium commercial and residential buildings sectors. A vision of a connected world in which equipment and systems within buildings coordinate with each other to efficiently meet their owners’ and occupants’ needs, and where buildings regularly transact business with other buildings and service providers (such as gas and electric service providers) is emerging. However, while the technology to support this collaboration has been demonstrated at various degrees of maturity, the integration frameworks and ecosystems of products that support the ability to easily install, maintain, and evolve building systems and their equipment components are struggling to nurture the fledging business propositions of their proponents.

  19. Genome size analyses of Pucciniales reveal the largest fungal genomes.

    Science.gov (United States)

    Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

    2014-01-01

    Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

  20. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)—A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

    OpenAIRE

    Karolina Chwialkowska; Urszula Korotko; Joanna Kosinska; Iwona Szarejko; Miroslaw Kwasniewski

    2017-01-01

    Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing ...

  1. Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity--a large-scale system analysis of decoded bacterial genomes.

    Science.gov (United States)

    Shestov, Maksim; Ontañón, Santiago; Tozeren, Aydin

    2015-10-13

    Bacterial infections comprise a global health challenge as the incidences of antibiotic resistance increase. Pathogenic potential of bacteria has been shown to be context dependent, varying in response to environment and even within the strains of the same genus. We used the KEGG repository and extensive literature searches to identify among the 2527 bacterial genomes in the literature those implicated as pathogenic to the host, including those which show pathogenicity in a context dependent manner. Using data on the gene contents of these genomes, we identified sets of genes highly abundant in pathogenic but relatively absent in commensal strains and vice versa. In addition, we carried out genome comparison within a genus for the seventeen largest genera in our genome collection. We projected the resultant lists of ortholog genes onto KEGG bacterial pathways to identify clusters and circuits, which can be linked to either pathogenicity or synergy. Gene circuits relatively abundant in nonpathogenic bacteria often mediated biosynthesis of antibiotics. Other synergy-linked circuits reduced drug-induced toxicity. Pathogen-abundant gene circuits included modules in one-carbon folate, two-component system, type-3 secretion system, and peptidoglycan biosynthesis. Antibiotics-resistant bacterial strains possessed genes modulating phagocytosis, vesicle trafficking, cytoskeletal reorganization, and regulation of the inflammatory response. Our study also identified bacterial genera containing a circuit, elements of which were previously linked to Alzheimer's disease. Present study produces for the first time, a signature, in the form of a robust list of gene circuitry whose presence or absence could potentially define the pathogenicity of a microbiome. Extensive literature search substantiated a bulk majority of the commensal and pathogenic circuitry in our predicted list. Scanning microbiome libraries for these circuitry motifs will provide further insights into the complex

  2. A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence.

    Science.gov (United States)

    Drost, Derek R; Novaes, Evandro; Boaventura-Novaes, Carolina; Benedict, Catherine I; Brown, Ryan S; Yin, Tongming; Tuskan, Gerald A; Kirst, Matias

    2009-06-01

    Microarrays have demonstrated significant power for genome-wide analyses of gene expression, and recently have also revolutionized the genetic analysis of segregating populations by genotyping thousands of loci in a single assay. Although microarray-based genotyping approaches have been successfully applied in yeast and several inbred plant species, their power has not been proven in an outcrossing species with extensive genetic diversity. Here we have developed methods for high-throughput microarray-based genotyping in such species using a pseudo-backcross progeny of 154 individuals of Populus trichocarpa and P. deltoides analyzed with long-oligonucleotide in situ-synthesized microarray probes. Our analysis resulted in high-confidence genotypes for 719 single-feature polymorphism (SFP) and 1014 gene expression marker (GEM) candidates. Using these genotypes and an established microsatellite (SSR) framework map, we produced a high-density genetic map comprising over 600 SFPs, GEMs and SSRs. The abundance of gene-based markers allowed us to localize over 35 million base pairs of previously unplaced whole-genome shotgun (WGS) scaffold sequence to putative locations in the genome of P. trichocarpa. A high proportion of sampled scaffolds could be verified for their placement with independently mapped SSRs, demonstrating the previously un-utilized power that high-density genotyping can provide in the context of map-based WGS sequence reassembly. Our results provide a substantial contribution to the continued improvement of the Populus genome assembly, while demonstrating the feasibility of microarray-based genotyping in a highly heterozygous population. The strategies presented are applicable to genetic mapping efforts in all plant species with similarly high levels of genetic diversity.

  3. The Genome of a Tortoise Herpesvirus (Testudinid Herpesvirus 3) Has a Novel Structure and Contains a Large Region That Is Not Required for Replication In Vitro or Virulence In Vivo

    Science.gov (United States)

    Gandar, Frédéric; Wilkie, Gavin S.; Gatherer, Derek; Kerr, Karen; Marlier, Didier; Diez, Marianne; Marschang, Rachel E.; Mast, Jan; Dewals, Benjamin G.

    2015-01-01

    ABSTRACT Testudinid herpesvirus 3 (TeHV-3) is the causative agent of a lethal disease affecting several tortoise species. The threat that this virus poses to endangered animals is focusing efforts on characterizing its properties, in order to enable the development of prophylactic methods. We have sequenced the genomes of the two most studied TeHV-3 strains (1976 and 4295). TeHV-3 strain 1976 has a novel genome structure and is most closely related to a turtle herpesvirus, thus supporting its classification into genus Scutavirus, subfamily Alphaherpesvirinae, family Herpesviridae. The sequence of strain 1976 also revealed viral counterparts of cellular interleukin-10 and semaphorin, which have not been described previously in members of subfamily Alphaherpesvirinae. TeHV-3 strain 4295 is a mixture of three forms (m1, m2, and M), in which, in comparison to strain 1976, the genomes exhibit large, partially overlapping deletions of 12.5 to 22.4 kb. Viral subclones representing these forms were isolated by limiting dilution assays, and each replicated in cell culture comparably to strain 1976. With the goal of testing the potential of the three forms as attenuated vaccine candidates, strain 4295 was inoculated intranasally into Hermann's tortoises (Testudo hermanni). All inoculated subjects died, and PCR analyses demonstrated the ability of the m2 and M forms to spread and invade the brain. In contrast, the m1 form was detected in none of the organs tested, suggesting its potential as the basis of an attenuated vaccine candidate. Our findings represent a major step toward characterizing TeHV-3 and developing prophylactic methods against it. IMPORTANCE Testudinid herpesvirus 3 (TeHV-3) causes a lethal disease in tortoises, several species of which are endangered. We have characterized the viral genome and used this information to take steps toward developing an attenuated vaccine. We have sequenced the genomes of two strains (1976 and 4295), compared their growth in

  4. The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.

    Directory of Open Access Journals (Sweden)

    Mark Ravinet

    2018-05-01

    Full Text Available Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus and the Japan Sea stickleback (G. nipponicus, which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.

  5. The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.

    Science.gov (United States)

    Ravinet, Mark; Yoshida, Kohta; Shigenobu, Shuji; Toyoda, Atsushi; Fujiyama, Asao; Kitano, Jun

    2018-05-01

    Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus) and the Japan Sea stickleback (G. nipponicus), which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.

  6. Conserved cis-regulatory regions in a large genomic landscape control SHH and BMP-regulated Gremlin1 expression in mouse limb buds

    Directory of Open Access Journals (Sweden)

    Zuniga Aimée

    2012-08-01

    Full Text Available Abstract Background Mouse limb bud is a prime model to study the regulatory interactions that control vertebrate organogenesis. Major aspects of limb bud development are controlled by feedback loops that define a self-regulatory signalling system. The SHH/GREM1/AER-FGF feedback loop forms the core of this signalling system that operates between the posterior mesenchymal organiser and the ectodermal signalling centre. The BMP antagonist Gremlin1 (GREM1 is a critical node in this system, whose dynamic expression is controlled by BMP, SHH, and FGF signalling and key to normal progression of limb bud development. Previous analysis identified a distant cis-regulatory landscape within the neighbouring Formin1 (Fmn1 locus that is required for Grem1 expression, reminiscent of the genomic landscapes controlling HoxD and Shh expression in limb buds. Results Three highly conserved regions (HMCO1-3 were identified within the previously defined critical genomic region and tested for their ability to regulate Grem1 expression in mouse limb buds. Using a combination of BAC and conventional transgenic approaches, a 9 kb region located ~70 kb downstream of the Grem1 transcription unit was identified. This region, termed Grem1 Regulatory Sequence 1 (GRS1, is able to recapitulate major aspects of Grem1 expression, as it drives expression of a LacZ reporter into the posterior and, to a lesser extent, in the distal-anterior mesenchyme. Crossing the GRS1 transgene into embryos with alterations in the SHH and BMP pathways established that GRS1 depends on SHH and is modulated by BMP signalling, i.e. integrates inputs from these pathways. Chromatin immunoprecipitation revealed interaction of endogenous GLI3 proteins with the core cis-regulatory elements in the GRS1 region. As GLI3 is a mediator of SHH signal transduction, these results indicated that SHH directly controls Grem1 expression through the GRS1 region. Finally, all cis-regulatory regions within the Grem1

  7. Development, implementation and evaluation of a clinical research engagement and leadership capacity building program in a large Australian health care service.

    Science.gov (United States)

    Misso, Marie L; Ilic, Dragan; Haines, Terry P; Hutchinson, Alison M; East, Christine E; Teede, Helena J

    2016-01-14

    Health professionals need to be integrated more effectively in clinical research to ensure that research addresses clinical needs and provides practical solutions at the coal face of care. In light of limited evidence on how best to achieve this, evaluation of strategies to introduce, adapt and sustain evidence-based practices across different populations and settings is required. This project aims to address this gap through the co-design, development, implementation, evaluation, refinement and ultimately scale-up of a clinical research engagement and leadership capacity building program in a clinical setting with little to no co-ordinated approach to clinical research engagement and education. The protocol is based on principles of research capacity building and on a six-step framework, which have previously led to successful implementation and long-term sustainability. A mixed methods study design will be used. Methods will include: (1) a review of the literature about strategies that engage health professionals in research through capacity building and/or education in research methods; (2) a review of existing local research education and support elements; (3) a needs assessment in the local clinical setting, including an online cross-sectional survey and semi-structured interviews; (4) co-design and development of an educational and support program; (5) implementation of the program in the clinical environment; and (6) pre- and post-implementation evaluation and ultimately program scale-up. The evaluation focuses on research activity and knowledge, attitudes and preferences about clinical research, evidence-based practice and leadership and post implementation, about their satisfaction with the program. The investigators will evaluate the feasibility and effect of the program according to capacity building measures and will revise where appropriate prior to scale-up. It is anticipated that this clinical research engagement and leadership capacity building

  8. Building Languages

    Science.gov (United States)

    ... Glossary Contact Information Information For… Media Policy Makers Building Languages Recommend on Facebook Tweet Share Compartir Communicating ... any speech and only very loud sounds. Close × “Building Blocks” “Building Blocks” refers to the different skills ...

  9. The Sequenced Angiosperm Genomes and Genome Databases.

    Science.gov (United States)

    Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

    2018-01-01

    Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

  10. Between Two Fern Genomes

    Science.gov (United States)

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  11. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  12. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  13. Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies

    Science.gov (United States)

    2011-01-01

    Background Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus dominates continental shelf waters in the northwest Pacific Ocean and plays an important role in the local ecosystem by linking primary production to higher trophic levels. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. As they are genome-level informative, mitochondrial DNA sequences can be used as markers for population genetic studies and phylogenetic studies. Results The mitochondrial genome of C. sinicus is distinct from other arthropods owing to the concurrence of multiple non-coding regions and a reshuffled gene arrangement. Further particularities in the mitogenome of C. sinicus include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes atp6 and atp8 relative to other copepods. The monophyletic Copepoda should be placed within the Vericrustacea. The close affinity between Cyclopoida and Poecilostomatoida suggests reassigning the latter as subordinate to the former. Monophyly of Maxillopoda is rejected. Within the alignment of 11 C. sinicus mitogenomes, there are 397 variable sites harbouring three 'hotspot' variable sites and three microsatellite loci. Conclusion The occurrence of the circular subgenomic fragment during laboratory assays suggests that special caution should be taken when sequencing mitogenomes using long PCR. Such a phenomenon may provide additional evidence of mitochondrial DNA recombination, which appears to have been a prerequisite for shaping the present mitochondrial profile of C. sinicus during its evolution. The lack of synapomorphic gene arrangements among copepods has cast doubt on the utility of gene order as a useful molecular marker for deep phylogenetic analysis. However, mitochondrial genomic sequences have been valuable markers for

  14. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes

    DEFF Research Database (Denmark)

    Zeggini, Eleftheria; Scott, Laura J; Saxena, Richa

    2008-01-01

    analyses had limited power to identify variants with modest effects, we carried out meta-analysis of three T2D GWA scans comprising 10,128 individuals of European descent and approximately 2.2 million SNPs (directly genotyped and imputed), followed by replication testing in an independent sample......Genome-wide association (GWA) studies have identified multiple loci at which common variants modestly but reproducibly influence risk of type 2 diabetes (T2D). Established associations to common and rare variants explain only a small proportion of the heritability of T2D. As previously published...

  15. The influence of age and sex on genetic associations with adult body size and shape: a large-scale genome-wide interaction study

    OpenAIRE

    Winkler, Thomas W.; Heid, Iris M.; Gorski, Mathias

    2015-01-01

    Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age-and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of Eur...

  16. Detailed data set of a large administration building as a validation model for DIN V18599-software; Umfangreicher Validierungsdatensatz eines grossen Verwaltungsgebaeudes fuer Software zur DIN V 18599

    Energy Technology Data Exchange (ETDEWEB)

    Hoettges, Kirsten; Woessner, Simon; de Boer, Jan; Erhorn, Hans [Fraunhofer-Institut fuer Bauphysik (IBP), Abt. Energiesysteme, Kassel (Germany); Fraunhofer-Institut fuer Bauphysik (IBP), Stuttgart (Germany)

    2009-04-15

    The calculation method of DIN V 18599 represents a very complex model for the estimation of the energy efficiency of buildings. The method is used for certificates too, thus, the number of users is quite high. This fact and the complexity of the method causes high demands on the related software products. Most of the end user software tools work with the calculation engine ibp18599kernel developed by Fraunhofer-Institut for Building Physics. There is a continuous quality control for both, the kernel and the user interfaces, i.e. the end user software. This paper gives an overview of the process of quality control as well as a documentation of a validation model used within this process, i.e. a complex administration building as a sample. (Abstract Copyright [2009], Wiley Periodicals, Inc.) [German] Mit dem Berechnungsverfahren der DIN V 18599 liegt ein umfassendes Berechnungsmodell fuer die energetische Bewertung von Gebaeuden vor. Der grosse Umfang der Verfahren stellt auch an die softwaretechnischen Umsetzungen fuer die Planungspraxis hohe Anforderungen. Das Fraunhofer-Institut fuer Bauphysik hat hierzu den Rechenkern ibp18599kernel entwickelt, der zwischenzeit-lich von zahlreichen Softwarehaeusern fuer Endanwendungsprogramme zur energetischen Bewertung und Erstellung von Energieausweisen eingesetzt wird. Dieser ''Rechenmotor'' unterliegt einer steten Qualitaetskontrolle zur Sicherstellung der Berechnungsgenauigkeit. Der vorliegende Aufsatz stellt den Prozess der Qualitaetssicherung anhand eines neuen Validierungsbeispiels in Form eines komplexen Verwaltungsgebaeudes vor. Die Fallstudie kann auch zur Validierung anderer Berechnungssysteme, die nicht auf dem Rechenkern basieren, genutzt werden. (Abstract Copyright [2009], Wiley Periodicals, Inc.)

  17. Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)].

    Science.gov (United States)

    Pandey, Garima; Misra, Gopal; Kumari, Kajal; Gupta, Sarika; Parida, Swarup Kumar; Chattopadhyay, Debasis; Prasad, Manoj

    2013-04-01

    The availability of well-validated informative co-dominant microsatellite markers and saturated genetic linkage map has been limited in foxtail millet (Setaria italica L.). In view of this, we conducted a genome-wide analysis and identified 28 342 microsatellite repeat-motifs spanning 405.3 Mb of foxtail millet genome. The trinucleotide repeats (∼48%) was prevalent when compared with dinucleotide repeats (∼46%). Of the 28 342 microsatellites, 21 294 (∼75%) primer pairs were successfully designed, and a total of 15 573 markers were physically mapped on 9 chromosomes of foxtail millet. About 159 markers were validated successfully in 8 accessions of Setaria sp. with ∼67% polymorphic potential. The high percentage (89.3%) of cross-genera transferability across millet and non-millet species with higher transferability percentage in bioenergy grasses (∼79%, Switchgrass and ∼93%, Pearl millet) signifies their importance in studying the bioenergy grasses. In silico comparative mapping of 15 573 foxtail millet microsatellite markers against the mapping data of sorghum (16.9%), maize (14.5%) and rice (6.4%) indicated syntenic relationships among the chromosomes of foxtail millet and target species. The results, thus, demonstrate the immense applicability of developed microsatellite markers in germplasm characterization, phylogenetics, construction of genetic linkage map for gene/quantitative trait loci discovery, comparative mapping in foxtail millet, including other millets and bioenergy grass species.

  18. Analysis of the impact of large scale seismic retrofitting strategies through the application of a vulnerability-based approach on traditional masonry buildings

    Science.gov (United States)

    Ferreira, Tiago Miguel; Maio, Rui; Vicente, Romeu

    2017-04-01

    The buildings' capacity to maintain minimum structural safety levels during natural disasters, such as earthquakes, is recognisably one of the aspects that most influence urban resilience. Moreover, the public investment in risk mitigation strategies is fundamental, not only to promote social and urban and resilience, but also to limit consequent material, human and environmental losses. Despite the growing awareness of this issue, there is still a vast number of traditional masonry buildings spread throughout many European old city centres that lacks of adequate seismic resistance, requiring therefore urgent retrofitting interventions in order to both reduce their seismic vulnerability and to cope with the increased seismic requirements of recent code standards. Thus, this paper aims at contributing to mitigate the social and economic impacts of earthquake damage scenarios through the development of vulnerability-based comparative analysis of some of the most popular retrofitting techniques applied after the 1998 Azores earthquake. The influence of each technique individually and globally studied resorting to a seismic vulnerability index methodology integrated into a GIS tool and damage and loss scenarios are constructed and critically discussed. Finally, the economic balance resulting from the implementation of that techniques are also examined.

  19. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

    Science.gov (United States)

    Machado, Henrique; Gram, Lone

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

  20. The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study.

    Directory of Open Access Journals (Sweden)

    Thomas W Winkler

    2015-10-01

    Full Text Available Genome-wide association studies (GWAS have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI, a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age- and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT Consortium. Each study tested the association of up to ~2.8M SNPs with BMI and WHRadjBMI in four strata (men ≤50y, men >50y, women ≤50y, women >50y and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE, sex-specific effects (G x SEX or age-specific effects that differed between men and women (G x AGE x SEX. For BMI, we identified 15 loci (11 previously established for main effects, four novel that showed significant (FDR<5% age-specific effects, of which 11 had larger effects in younger (<50y than in older adults (≥50y. No sex-dependent effects were identified for BMI. For WHRadjBMI, we identified 44 loci (27 previously established for main effects, 17 novel with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHRadjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHRadjBMI. These results may provide further insights into the biology that underlies weight change with age or the sexually dimorphism of body shape.

  1. Reducing Data Center Loads for a Large-Scale, Low-Energy Office Building: NREL's Research Support Facility (Book)

    Energy Technology Data Exchange (ETDEWEB)

    Sheppy, M.; Lobato, C.; Van Geet, O.; Pless, S.; Donovan, K.; Powers, C.

    2011-12-01

    This publication detailing the design, implementation strategies, and continuous performance monitoring of NREL's Research Support Facility data center. Data centers are energy-intensive spaces that facilitate the transmission, receipt, processing, and storage of digital data. These spaces require redundancies in power and storage, as well as infrastructure, to cool computing equipment and manage the resulting waste heat (Tschudi, Xu, Sartor, and Stein, 2003). Data center spaces can consume more than 100 times the energy of standard office spaces (VanGeet 2011). The U.S. Environmental Protection Agency (EPA) reported that data centers used 61 billion kilowatt-hours (kWh) in 2006, which was 1.5% of the total electricity consumption in the U.S. (U.S. EPA, 2007). Worldwide, data centers now consume more energy annually than Sweden (New York Times, 2009). Given their high energy consumption and conventional operation practices, there is a potential for huge energy savings in data centers. The National Renewable Energy Laboratory (NREL) is world renowned for its commitment to green building construction. In June 2010, the laboratory finished construction of a 220,000-square-foot (ft{sup 2}), LEED Platinum, Research Support Facility (RSF), which included a 1,900-ft{sup 2} data center. The RSF will expand to 360,000 ft{sup 2} with the opening of an additional wing December, 2011. The project's request for proposals (RFP) set a whole-building demand-side energy use requirement of a nominal 35 kBtu/ft{sup 2} per year. On-site renewable energy generation will offset the annual energy consumption. To support the RSF's energy goals, NREL's new data center was designed to minimize its energy footprint without compromising service quality. Several implementation challenges emerged during the design, construction, and first 11 months of operation of the RSF data center. This document highlights these challenges and describes in detail how NREL successfully

  2. COGNAT: a web server for comparative analysis of genomic neighborhoods.

    Science.gov (United States)

    Klimchuk, Olesya I; Konovalov, Kirill A; Perekhvatov, Vadim V; Skulachev, Konstantin V; Dibrova, Daria V; Mulkidjanian, Armen Y

    2017-11-22

    In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-transcribed genes. Those genes that evolved from a common ancestral gene by speciation (i.e. orthologs) are expected to have similar genomic neighborhoods in different organisms, whereas those copies of the gene that are responsible for dissimilar functions (i.e. paralogs) could be found in dissimilar genomic contexts. Comparative analysis of genomic neighborhoods facilitates the prediction of co-regulated genes and helps to discern different functions in large protein families. We intended, building on the attribution of gene sequences to the clusters of orthologous groups of proteins (COGs), to provide a method for visualization and comparative analysis of genomic neighborhoods of evolutionary related genes, as well as a respective web server. Here we introduce the COmparative Gene Neighborhoods Analysis Tool (COGNAT), a web server for comparative analysis of genomic neighborhoods. The tool is based on the COG database, as well as the Pfam protein families database. As an example, we show the utility of COGNAT in identifying a new type of membrane protein complex that is formed by paralog(s) of one of the membrane subunits of the NADH:quinone oxidoreductase of type 1 (COG1009) and a cytoplasmic protein of unknown function (COG3002). This article was reviewed by Drs. Igor Zhulin, Uri Gophna and Igor Rogozin.

  3. How big is too big or how many partners are needed to build a large project which still can be managed successfully?

    Science.gov (United States)

    Henkel, Daniela; Eisenhauer, Anton

    2017-04-01

    During the last decades, the number of large research projects has increased and therewith the requirement for multidisciplinary, multisectoral collaboration. Such complex and large-scale projects pose new competencies to form, manage, and use large, diverse teams as a competitive advantage. For complex projects the effort is magnified because multiple large international research consortia involving academic and non-academic partners, including big industries, NGOs, private and public bodies, all with cultural differences, individually discrepant expectations on teamwork and differences in the collaboration between national and multi-national administrations and research organisations, challenge the organisation and management of such multi-partner research consortia. How many partners are needed to establish and conduct collaboration with a multidisciplinary and multisectoral approach? How much personnel effort and what kinds of management techniques are required for such projects. This presentation identifies advantages and challenges of large research projects based on the experiences made in the context of an Innovative Training Network (ITN) project within Marie Skłodowska-Curie Actions of the European HORIZON 2020 program. Possible strategies are discussed to circumvent and avoid conflicts already at the beginning of the project.

  4. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  5. Genomics: Looking at Life in New Ways

    Energy Technology Data Exchange (ETDEWEB)

    Adams, Mark D. (Case-Western Reserve University)

    2003-10-22

    The availability of complete or nearly complete mouse, human, and rat genomes (in addition to those from many other species) has resulted in a series of new and powerful opportunities to apply the technologies and approaches developed for large-scale genome sequencing to the study of disease. New approaches to biological problems are being explored that involve concepts from computer science such as systems theory and modern large scale computing techniques. A recent project at Celera Genomics involved sequencing protein coding regions from several humans and a chimpanzee. Computational models of evolutionary divergence enabled us to identify genes with unique evolutionary signatures. These genes give us some insight into features that may be uniquely human. The laboratory mouse and rat have long been favorite mammalian models of human disease. Integrated approaches to the study of disease that combine genetics, DNA sequence analysis, and careful analysis of phenotype at a molecular level are becoming more common and powerful. In addition, evaluation of the variation inherent in normal populations is now being used to build networks to describe heart function based on the interaction of multiple phenotypes in randomized populations using a factorial design.

  6. An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database

    International Nuclear Information System (INIS)

    Kobayashi, Naohiro; Harano, Yoko; Tochio, Naoya; Nakatani, Eiichi; Kigawa, Takanori; Yokoyama, Shigeyuki; Mading, Steve; Ulrich, Eldon L.; Markley, John L.; Akutsu, Hideo; Fujiwara, Toshimichi

    2012-01-01

    Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including 1 H, 13 C and 15 N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001–2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies.

  7. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  8. Genomics Portals: integrative web-platform for mining genomics data.

    Science.gov (United States)

    Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

    2010-01-13

    A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  9. Genomics Portals: integrative web-platform for mining genomics data

    Directory of Open Access Journals (Sweden)

    Ghosh Krishnendu

    2010-01-01

    Full Text Available Abstract Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc, and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  10. Development of local-scale high-resolution atmospheric dispersion model using large-eddy simulation. Part 3: turbulent flow and plume dispersion in building arrays

    Czech Academy of Sciences Publication Activity Database

    Nakayama, H.; Jurčáková, Klára; Nagai, H.

    2013-01-01

    Roč. 50, č. 5 (2013), s. 503-519 ISSN 0022-3131 Institutional support: RVO:61388998 Keywords : local-scale high-resolution dispersion model * nuclear emergency response system * large-eddy simulation * spatially developing turbulent boundary layer flow Subject RIV: DG - Athmosphere Sciences, Meteorology Impact factor: 1.452, year: 2013

  11. Development of Tandem Amorphous/Microcrystalline Silicon Thin-Film Large-Area See-Through Color Solar Panels with Reflective Layer and 4-Step Laser Scribing for Building-Integrated Photovoltaic Applications

    Directory of Open Access Journals (Sweden)

    Chin-Yi Tsai

    2014-01-01

    Full Text Available In this work, tandem amorphous/microcrystalline silicon thin-film large-area see-through color solar modules were successfully designed and developed for building-integrated photovoltaic applications. Novel and key technologies of reflective layers and 4-step laser scribing were researched, developed, and introduced into the production line to produce solar panels with various colors, such as purple, dark blue, light blue, silver, golden, orange, red wine, and coffee. The highest module power is 105 W and the highest visible light transmittance is near 20%.

  12. Residential and commercial buildings

    Energy Technology Data Exchange (ETDEWEB)

    Svendsen, Svend; Furbo, S.

    2012-11-15

    Low-energy buildings can make a major contribution to general sustainable development by providing a solution to problems related to the use of fossil fuels. The EPBD (EU Directive on Energy Performance of Buildings) requirements that by 2020 new building shall be constructed to use nearly zero energy, and no fossil fuels, can be accomplished by combining low-energy buildings with renewable energy via low-temperature district heating in cities and suburbs, and via heat pumps for low-density settlements. Based on experience with passive houses, low-energy buildings meeting the energy performance requirements of 2020 are expected to cost only a few percent more than conventional buildings. The very large and rapid changes needed in the energy performance of buildings is a challenge for the building sector, but one that can be overcome by better methods of developing products and designing, constructing and operating buildings. Simulation-based analysis and optimisation, and considerations of durability, will be important here. Building may thus be transformed from an experience-based sector to one based on knowledge and research, with high-quality sustainable products and good business opportunities. (Author)

  13. Development of Bioinformatics Infrastructure for Genomics Research.

    Science.gov (United States)

    Mulder, Nicola J; Adebiyi, Ezekiel; Adebiyi, Marion; Adeyemi, Seun; Ahmed, Azza; Ahmed, Rehab; Akanle, Bola; Alibi, Mohamed; Armstrong, Don L; Aron, Shaun; Ashano, Efejiro; Baichoo, Shakuntala; Benkahla, Alia; Brown, David K; Chimusa, Emile R; Fadlelmola, Faisal M; Falola, Dare; Fatumo, Segun; Ghedira, Kais; Ghouila, Amel; Hazelhurst, Scott; Isewon, Itunuoluwa; Jung, Segun; Kassim, Samar Kamal; Kayondo, Jonathan K; Mbiyavanga, Mamana; Meintjes, Ayton; Mohammed, Somia; Mosaku, Abayomi; Moussa, Ahmed; Muhammd, Mustafa; Mungloo-Dilmohamud, Zahra; Nashiru, Oyekanmi; Odia, Trust; Okafor, Adaobi; Oladipo, Olaleye; Osamor, Victor; Oyelade, Jellili; Sadki, Khalid; Salifu, Samson Pandam; Soyemi, Jumoke; Panji, Sumir; Radouani, Fouzia; Souiai, Oussama; Tastan Bishop, Özlem

    2017-06-01

    Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community. H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis. Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for

  14. Large Scale Genome Analysis Shows that the Epitopes for Broadly Cross-Reactive Antibodies Are Predominant in the Pandemic 2009 Influenza Virus A H1N1 Strain

    Directory of Open Access Journals (Sweden)

    Edgar E. Lara-Ramírez

    2013-11-01

    Full Text Available The past pandemic strain H1N1 (A (H1N1pdm09 has now become a common component of current seasonal influenza viruses. It has changed the pre-existing immunity of the human population to succeeding infections. In the present study, a total of 14,210 distinct sequences downloaded from National Center for Biotechnology Information (NCBI database were used for the analysis. The epitope compositions in A (H1N1pdm09, classic seasonal strains, swine strains as well as highly virulent avian strain H5N1, identified with the aid of the Immune Epitope DataBase (IEDB, were compared at genomic level. The result showed that A (H1N1 pdm09 contains the 90% of B-cell epitopes for broadly cross-reactive antibodies (EBCA, which is in consonance with the recent reports on the experimental identification of new epitopes or antibodies for this virus and the binding tests with influenza virus protein HA of different subtypes. Our analysis supports that high proportional EBCA depends on the epitope pattern of A (H1N1pdm09 virus. This study may be helpful for better understanding of A (H1N1pdm09 and the production of new influenza vaccines.

  15. Impact of production systems on swine confinement buildings bioaerosols.

    Science.gov (United States)

    Létourneau, Valérie; Nehmé, Benjamin; Mériaux, Anne; Massé, Daniel; Duchaine, Caroline

    2010-02-01

    Hog production has been substantially intensified in Eastern Canada. Hogs are now fattened in swine confinement buildings with controlled ventilation systems and high animal densities. Newly designed buildings are equipped with conventional manure handling and management systems, shallow or deep litter systems, or source separation systems to manage the large volumes of waste. However, the impacts of those alternative production systems on bioaerosol concentrations within the barns have never been evaluated. Bioaerosols were characterized in 18 modern swine confinement buildings, and the differences in bioaerosol composition in the three different production systems were evaluated. Total dust, endotoxins, culturable actinomycetes, fungi, and bacteria were collected with various apparatuses. The total DNA of the air samples was extracted, and quantitative polymerase chain reaction (PCR) was used to assess the total number of bacterial genomes, as a total (culturable and nonculturable) bacterial assessment. The measured total dust and endotoxin concentrations were not statistically different in the three studied production systems. In buildings with sawdust beds, actinomycetes and molds were found in higher concentrations than in the conventional barns. Aspergillus, Cladosporium, Penicillium, and Scopulariopsis species were identified in all the studied swine confinement buildings. A. flavus, A. terreus, and A. versicolor were abundantly present in the facilities with sawdust beds. Thermotolerant A. fumigatus and Mucor were usually found in all the buildings. The culturable bacteria concentrations were higher in the barns with litters than in the conventional buildings, while real-time PCR revealed nonstatistically different concentrations of total bacteria in all the studied swine confinement buildings. In terms of workers' respiratory health, barns equipped with a solid/liquid separation system may offer better air quality than conventional buildings or barns with

  16. Building America

    Energy Technology Data Exchange (ETDEWEB)

    Brad Oberg

    2010-12-31

    IBACOS researched the constructability and viability issues of using high performance windows as one component of a larger approach to building houses that achieve the Building America 70% energy savings target.

  17. Big Data Analysis of Human Genome Variations

    KAUST Repository

    Gojobori, Takashi

    2016-01-01

    Since the human genome draft sequence was in public for the first time in 2000, genomic analyses have been intensively extended to the population level. The following three international projects are good examples for large-scale studies of human

  18. Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

    KAUST Repository

    Neave, Matthew J.

    2017-01-17

    Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.

  19. Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

    KAUST Repository

    Neave, Matthew J.; Michell, Craig; Apprill, Amy; Voolstra, Christian R.

    2017-01-01

    Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.

  20. Solar building

    OpenAIRE

    Zhang, Luxin

    2014-01-01

    In my thesis I describe the utilization of solar energy and solar energy with building integration. In introduction it is also mentioned how the solar building works, trying to make more people understand and accept the solar building. The thesis introduces different types of solar heat collectors. I compared the difference two operation modes of solar water heating system and created examples of solar water system selection. I also introduced other solar building applications. It is conv...

  1. Building envelope

    CSIR Research Space (South Africa)

    Gibberd, Jeremy T

    2009-01-01

    Full Text Available for use in the building. This is done through photovoltaic and solar water heating panels and wind turbines. Ideally these are integrated in the design of the building envelope to improve the aesthetic quality of the building and minimise material... are naturally ventilated. Renewable energy The building envelope includes renewable energy generation such as photovoltaics, wind turbines and solar water heaters and 10% of the building’s energy requirements are generated from these sources. Views All...

  2. Genomic selection: genome-wide prediction in plant improvement.

    Science.gov (United States)

    Desta, Zeratsion Abera; Ortiz, Rodomiro

    2014-09-01

    Association analysis is used to measure relations between markers and quantitative trait loci (QTL). Their estimation ignores genes with small effects that trigger underpinning quantitative traits. By contrast, genome-wide selection estimates marker effects across the whole genome on the target population based on a prediction model developed in the training population (TP). Whole-genome prediction models estimate all marker effects in all loci and capture small QTL effects. Here, we review several genomic selection (GS) models with respect to both the prediction accuracy and genetic gain from selection. Phenotypic selection or marker-assisted breeding protocols can be replaced by selection, based on whole-genome predictions in which phenotyping updates the model to build up the prediction accuracy. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Identification of relevant drugable targets in diffuse large B-cell lymphoma using a genome-wide unbiased CD20 guilt-by association approach

    NARCIS (Netherlands)

    de Jong, Mathilde R. W.; Visser, Lydia; Huls, Gerwin; Diepstra, Arjan; van Vugt, Marcel; Ammatuna, Emanuele; van Rijn, Rozemarijn S.; Vellenga, Edo; van den Berg, Anke; Fehrmann, Rudolf S. N.; van Meerten, Tom

    2018-01-01

    Forty percent of patients with diffuse large B-cell lymphoma (DLBCL) show resistant disease to standard chemotherapy (CHOP) in combination with the anti-CD20 monoclonal antibody rituximab (R). Although many new anti-cancer drugs were developed in the last years, it is unclear which of these drugs

  4. Moving into a new era of periodontal genetic studies: relevance of large case-control samples using severe phenotypes for genome-wide association studies

    NARCIS (Netherlands)

    Vaithilingam, R.D.; Saffi, S.H.; Baharuddin, N.A.; Ng, C.C.; Cheong, S.C.; Bartold, P.M.; Schaefer, A.S.; Loos, B.G.

    2014-01-01

    Studies to elucidate the role of genetics as a risk factor for periodontal disease have gone through various phases. In the majority of cases, the initial ‘hypothesis-dependent’ candidate-gene polymorphism studies did not report valid genetic risk loci. Following a large-scale replication study,

  5. Auxiliary buildings

    International Nuclear Information System (INIS)

    Lakner, I.; Lestyan, E.

    1979-01-01

    The nuclear power station represents a complicated and a particular industrial project. Consequently, the design of the auxiliary buildings serving the power station (offices, kitchen, refreshment room, workshops, depots, water treatment plant building, boiler houses, etc.) requires more attention than usual. This chapter gives a short survey of the auxiliary buildings already completed and discusses the problems of their design, location and structure. (author)

  6. Identification of genomic biomarkers for concurrent diagnosis of drug-induced renal tubular injury using a large-scale toxicogenomics database

    International Nuclear Information System (INIS)

    Kondo, Chiaki; Minowa, Yohsuke; Uehara, Takeki; Okuno, Yasushi; Nakatsu, Noriyuki; Ono, Atsushi; Maruyama, Toshiyuki; Kato, Ikuo; Yamate, Jyoji; Yamada, Hiroshi; Ohno, Yasuo; Urushidani, Tetsuro

    2009-01-01

    Drug-induced renal tubular injury is one of the major concerns in preclinical safety evaluations. Toxicogenomics is becoming a generally accepted approach for identifying chemicals with potential safety problems. In the present study, we analyzed 33 nephrotoxicants and 8 non-nephrotoxic hepatotoxicants to elucidate time- and dose-dependent global gene expression changes associated with proximal tubular toxicity. The compounds were administered orally or intravenously once daily to male Sprague-Dawley rats. The animals were exposed to four different doses of the compounds, and kidney tissues were collected on days 4, 8, 15, and 29. Gene expression profiles were generated from kidney RNA by using Affymetrix GeneChips and analyzed in conjunction with the histopathological changes. We used the filter-type gene selection algorithm based on t-statistics conjugated with the SVM classifier, and achieved a sensitivity of 90% with a selectivity of 90%. Then, 92 genes were extracted as the genomic biomarker candidates that were used to construct the classifier. The gene list contains well-known biomarkers, such as Kidney injury molecule 1, Ceruloplasmin, Clusterin, Tissue inhibitor of metallopeptidase 1, and also novel biomarker candidates. Most of the genes involved in tissue remodeling, the immune/inflammatory response, cell adhesion/proliferation/migration, and metabolism were predominantly up-regulated. Down-regulated genes participated in cell adhesion/proliferation/migration, membrane transport, and signal transduction. Our classifier has better prediction accuracy than any of the well-known biomarkers. Therefore, the toxicogenomics approach would be useful for concurrent diagnosis of renal tubular injury.

  7. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

    OpenAIRE

    Henrique Machado; Henrique Machado; Lone Gram

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationship...

  8. Development of a unified sizing method for gas radiation heating facilities used in large-volume buildings; Developpement d'une methode de dimensionnement unifiee d'installations de chauffage radiant gaz pour les batiments de grand volume

    Energy Technology Data Exchange (ETDEWEB)

    Jimenez, M.; Bego, L.; Douls, Y.; Le Dean, P.; Paradowski, V. [Gaz de France, GDF, Dir. de la Recherche, 75 - Paris (France)

    2000-07-01

    Builders now have perfect command of the natural gas heating technique used for large-volume buildings. However, the sizing of heating facilities still leaves grounds for discussion, whatever the energies actually used. Accordingly, between 1997 and 1999, the ATG (technical association of the Gas industry in France), seven French manufacturers of 'large volume' heating equipment, the Chaleur Et Rayonnement (CER) association and Gaz de France decided to collaborate and develop a 'unified sizing method' for heating facilities using radiating emitters. During the first year of the study, the above partners worked on the said method (theoretical thermal study of the radiative phenomena, and then adaptation to the methods currently used by the various manufacturers). In 1998, with the support of the ADEME (the French environment and energy control agency), the partners tested the method on five industrial buildings (studying the thermal behavior and making air renewal measurements with search gases). This work made it possible to either confirm or adapt the theoretical evaluations which had been made originally. In 1999, a software program was produced to make the developed method more user friendly. The program can be used to determine the power to be installed, but also to assess the quality of the chosen configuration of the emitters (unit power, inclination, orientation) for optimum customer comfort. (authors)

  9. The challenge of building large area, high precision small-strip Thin Gap Trigger Chambers for the upgrade of the ATLAS experiment

    CERN Document Server

    Maleev, Victor; The ATLAS collaboration

    2015-01-01

    The current innermost stations of the ATLAS muon endcap system must be upgraded in 2018 and 2019 to retain the good precision tracking and trigger capabilities in the high background environment expected with the upcoming luminosity increase of the LHC. Large area small-strip Thin Gap Chambers (sTGC) up to 2 m2 in size and totaling an active area of 1200 m2 will be employed for fast and precise triggering. The precision reconstruction of tracks requires a spatial resolution of about 100 μm to allow the Level-1 trigger track segments to be reconstructed with an angular resolution of 1mrad. The upgraded detector will consist of eight layers each of Micromegas and sTGC’s detectors together forming the ATLAS New Small Wheels. The position of each strip must be known with an accuracy of 30 µm along the precision coordinate and 80 µm along the beam. On such large area detectors, the mechanical precision is a key point and then must be controlled and monitored all along the process of construction and integrati...

  10. The Challenge of Building Large Area, High Precision Small-Strip Thin Gap Trigger Chambers for the Upgrade of the ATLAS Experiment

    CERN Document Server

    Maleev, Victor; The ATLAS collaboration

    2015-01-01

    The current innermost stations of the ATLAS muon end-cap system must be upgraded in 2018 and 2019 to retain the good precision tracking and trigger capabilities in the high background environment expected with the upcoming luminosity increase of the LHC. Large area small-strip Thin Gap Chambers (sTGC) up to 2 $m^2$ in size and totaling an active area of 1200 $m^2$ will be employed for fast and precise triggering. The precision reconstruction of tracks requires a spatial resolution of about 100 $\\mu m$ while the Level-1 trigger track segments need to be reconstructed with an angular resolution of 1 mrad. The upgraded detector will consist of eight layers each of Micromegas and sTGC’s detectors together forming the ATLAS New Small Wheels. The position of each strip must be known with an accuracy of 40 $\\mu m$ along the precision coordinate and 80 $\\mu m$ along the beam. On such large area detectors, the mechanical precision is a key point and then must be controlled and monitored all along the process of cons...

  11. Ensembl 2002: accommodating comparative genomics.

    Science.gov (United States)

    Clamp, M; Andrews, D; Barker, D; Bevan, P; Cameron, G; Chen, Y; Clark, L; Cox, T; Cuff, J; Curwen, V; Down, T; Durbin, R; Eyras, E; Gilbert, J; Hammond, M; Hubbard, T; Kasprzyk, A; Keefe, D; Lehvaslaiho, H; Iyer, V; Melsopp, C; Mongin, E; Pettett, R; Potter, S; Rust, A; Schmidt, E; Searle, S; Slater, G; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Stupka, E; Ureta-Vidal, A; Vastrik, I; Birney, E

    2003-01-01

    The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

  12. The Ensembl genome database project.

    Science.gov (United States)

    Hubbard, T; Barker, D; Birney, E; Cameron, G; Chen, Y; Clark, L; Cox, T; Cuff, J; Curwen, V; Down, T; Durbin, R; Eyras, E; Gilbert, J; Hammond, M; Huminiecki, L; Kasprzyk, A; Lehvaslaiho, H; Lijnzaad, P; Melsopp, C; Mongin, E; Pettett, R; Pocock, M; Potter, S; Rust, A; Schmidt, E; Searle, S; Slater, G; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Stupka, E; Ureta-Vidal, A; Vastrik, I; Clamp, M

    2002-01-01

    The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

  13. The anti corrosive design of structural metallic elements in buildings with large exploitation period; El diseno anticorrovio de elementos estructurales metalicos en edificaciones con periodos prolongados de explotacion

    Energy Technology Data Exchange (ETDEWEB)

    Avila Ayon, V.; Rodriguez Quesada, A. L.

    2009-07-01

    The corrosion deterioration in metallic structural elements, with the consistent loss of his physical and mechanical properties, is cause by errors in the design or fabrication, that allows the accumulation of humidity and contaminants in the surfaces, or acceleration zones of the corrosion processes, as the bimetalics pairs. The aggressiveness of the environment and the productive processes that develop in industrial installations, causes the apparition of premature failures that engage the edification use. The identification of design errors is the first step in the conservation of these structures. the elimination and made a project adapted to the proper installations conditions, is essential procedures to prolong the edification useful life with an optimum and rational use of the resources that destined for this end. The investigation is about the results obtained in the diagnostic and the conservation of industrial installment, with large exploitation periods, in which existed evidences of failures by corrosion, specifically to the elimination of errors of design. (Author) 12 refs.

  14. [Ethical considerations in genomic cohort study].

    Science.gov (United States)

    Choi, Eun Kyung; Kim, Ock-Joo

    2007-03-01

    During the last decade, genomic cohort study has been developed in many countries by linking health data and genetic data in stored samples. Genomic cohort study is expected to find key genetic components that contribute to common diseases, thereby promising great advance in genome medicine. While many countries endeavor to build biobank systems, biobank-based genome research has raised important ethical concerns including genetic privacy, confidentiality, discrimination, and informed consent. Informed consent for biobank poses an important question: whether true informed consent is possible in population-based genomic cohort research where the nature of future studies is unforeseeable when consent is obtained. Due to the sensitive character of genetic information, protecting privacy and keeping confidentiality become important topics. To minimize ethical problems and achieve scientific goals to its maximum degree, each country strives to build population-based genomic cohort research project, by organizing public consultation, trying public and expert consensus in research, and providing safeguards to protect privacy and confidentiality.

  15. Advanced DInSAR analysis for building damage assessment in large urban areas: an application to the city of Roma, Italy

    Science.gov (United States)

    D'Aranno, Peppe J. V.; Marsella, Maria; Scifoni, Silvia; Scutti, Marianna; Sonnessa, Alberico; Bonano, Manuela

    2015-10-01

    Remote sensing data play an important role for the environmental monitoring because they allow to provide systematic information on very large areas and for a long period of time. Such information must be analyzed, validated and incorporated into proper modeling tools in order to become useful for performing risk assessment analysis. These approaches has been already applied in the field of natural hazard evaluation (i.e. for monitoring seismic, volcanic areas and landslides). However, not enough attention has been devoted to the development of validated methods for implementing quantitative analysis on civil structures. This work is dedicated to the comprehensive utilization of ERS / ENVISAT data store ESA SAR used to detect deformation trends and perform back-analysis of the investigated structures useful to calibrate the damage assessment models. After this preliminary analysis, SAR data of the new satellite mission (ie Cosmo SkyMed) were adopted to monitor the evolution of existent surface deformation processes and to detect new occurrence. The specific objective was to set up a data processing and data analysis chain tailored on a service that sustains the safe maintenance of the built-up environment, including critical construction such as public (schools, hospital, etc), strategic (dam, highways, etc) and also the cultural heritage sites. The analysis of the test area, in the southeastern sector of Roma, has provided three different levels and sub-levels of products from metropolitan area scale (territorial analysis), settlement scale (aggregated analysis) to single structure scale (damage degree associated to the structure).

  16. Vertically building Zn2SnO4 nanowire arrays on stainless steel mesh toward fabrication of large-area, flexible dye-sensitized solar cells.

    Science.gov (United States)

    Li, Zhengdao; Zhou, Yong; Bao, Chunxiong; Xue, Guogang; Zhang, Jiyuan; Liu, Jianguo; Yu, Tao; Zou, Zhigang

    2012-06-07

    Zn(2)SnO(4) nanowire arrays were for the first time grown onto a stainless steel mesh (SSM) in a binary ethylenediamine (En)/water solvent system using a solvothermal route. The morphology evolution following this reaction was carefully followed to understand the formation mechanism. The SSM-supported Zn(2)SnO(4) nanowire was utilized as a photoanode for fabrication of large-area (10 cm × 5 cm size as a typical sample), flexible dye-sensitized solar cells (DSSCs). The synthesized Zn(2)SnO(4) nanowires exhibit great bendability and flexibility, proving potential advantage over other metal oxide nanowires such as TiO(2), ZnO, and SnO(2) for application in flexible solar cells. Relative to the analogous Zn(2)SnO(4) nanoparticle-based flexible DSSCs, the nanowire geometry proves to enhance solar energy conversion efficiency through enhancement of electron transport. The bendable nature of the DSSCs without obvious degradation of efficiency and facile scale up gives the as-made flexible solar cell device potential for practical application.

  17. Somatic mutation of EZH2 (Y641) in follicular and diffuse large B-cell lymphomas of germinal center origin | Office of Cancer Genomics

    Science.gov (United States)

    Morin et al. describe recurrent somatic mutations in EZH2, a polycomb group oncogene. The mutation, found in the SET domain of this gene encoding a histone methyltransferase, is found only in a subset of lymphoma samples. Specifically, EZH2 mutations are found in about 12% of follicular lymphomas (FL) and almost 23% of diffuse large B-cell lymphomas (DLBCL) of germinal center origin. This paper goes on to demonstrate that altered EZH2 proteins, corresponding to the most frequent mutations found in human lymphomas, have reduced activity using in vitro histone methylation assays.

  18. Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy.

    Science.gov (United States)

    Rittmann, Bruce E; Krajmalnik-Brown, Rosa; Halden, Rolf U

    2008-08-01

    Microorganisms can produce renewable energy in large quantities and without damaging the environment or disrupting food supply. The microbial communities must be robust and self-stabilizing, and their essential syntrophies must be managed. Pre-genomic, genomic and post-genomic tools can provide crucial information about the structure and function of these microbial communities. Applying these tools will help accelerate the rate at which microbial bioenergy processes move from intriguing science to real-world practice.

  19. H3Africa and the African life sciences ecosystem: building sustainable innovation.

    Science.gov (United States)

    Dandara, Collet; Huzair, Farah; Borda-Rodriguez, Alexander; Chirikure, Shadreck; Okpechi, Ikechi; Warnich, Louise; Masimirembwa, Collen

    2014-12-01

    Interest in genomics research in African populations is experiencing exponential growth. This enthusiasm stems in part from the recognition that the genomic diversity of African populations is a window of opportunity for innovations in postgenomics medicine, ecology, and evolutionary biology. The recently launched H3Africa initiative, for example, captures the energy and momentum of this interest. This interdisciplinary socio-technical analysis highlights the challenges that have beset previous genomics research activities in Africa, and looking ahead, suggests constructive ways H3Africa and similar large scale science efforts could usefully chart a new era of genomics and life sciences research in Africa that is locally productive and globally competitive. As independent African scholars and social scientists, we propose that any serious global omics science effort, including H3Africa, aiming to build genomics research capacity and capability in Africa, needs to fund the establishment of biobanks and the genomic analyses platforms within Africa. Equally they need to prioritize community engagement and bioinformatics capability and the training of African scientists on these platforms. Historically, the financial, technological, and skills imbalance between Africa and developed countries has created exploitative frameworks of collaboration where African researchers have become merely facilitators of Western funded and conceived research agendas involving offshore expatriation of samples. Not surprisingly, very little funding was allocated to infrastructure and human capital development in the past. Moving forward, capacity building should materialize throughout the entire knowledge co-production trajectory: idea generation (e.g., brainstorming workshops for innovative hypotheses development by African scientists), data generation (e.g., genome sequencing), and high-throughput data analysis and contextualization. Additionally, building skills for political science

  20. Risk of a large amount of high-radioactive contaminated water leaking into the reactor building basement of Fukushima Daiichi nuclear power station

    International Nuclear Information System (INIS)

    Ebisawa, Toru; Sawai, Masako

    2013-01-01

    In November 2012 about one and half year after the accident at units 1, 2 and 3 of Fukushima Daiichi nuclear power station, some 405 m 3 /day cooling water was being injected into the melt damaged core and leaked as highly-radioactive contaminated water from damaged lower part of containment into the basement of turbine hall. To treat a large amount of contaminated water in the basement, waste processing plant to remove cesium was installed in June 2011 with desalination plant, which produced clean water for circulating coolant system of damaged nuclear fuel while the rest went to storage. Radioactivity of contaminated water in the basement accumulated at initial almost 80 days of the accident was evaluated about 20% for Cs-137 of core inventory of units 1, 2 and 3 and 2.3% for Sr-90 of core inventory of units 2 and 3. Sr-90 from unit 1 was not released into the basement and almost remained at suppression chamber. By November 2012, Cs-137 released into the basement was evaluated to total about 40% of core inventory and stored contaminated water amounted to about 360 kilotons, while Cs-137 released into the atmosphere was estimated about 3.6% of core inventory with its one third contributed for land contamination. Sr-90 released into the basement was estimated as 6.3% or 4.4% of core inventory based on Sr-90 measured activity of treated water in December or September 2011 with stored contaminated water of 300 kilotons. Cs-137 and Sr-90 contaminated water kept continuously releasing into the basement as long as melt damaged core existed and cooling water washed out Cs-137 and Sr-90 attached on containment walls. Safe store of released radioactivity was highly important and acquired important data was recommended to publish for check and review. (T. Tanaka)

  1. Consumer Central Energy Flexibility in Office Buildings

    DEFF Research Database (Denmark)

    Billanes, Joy Dalmacio; Ma, Zheng; Jørgensen, Bo Nørregaard

    2017-01-01

    Energy flexibility in buildings will play an important role in the smart energy system. Office buildings have more potentials to provide energy flexibility to the grid compared to other types of buildings, due to the existing building management, control systems and large energy consumption....... Consumers in office buildings (building owners/managers and occupants) take a main role for adopting and engaging in building energy flexibility. In this paper provides a systematic review of consumer central energy flexibility in office buildings with the discussion of social, technical and business...... can boost energy flexibility in the office buildings....

  2. Personalized medicine: new genomics, old lessons

    OpenAIRE

    Offit, Kenneth

    2011-01-01

    Personalized medicine uses traditional, as well as emerging concepts of the genetic and environmental basis of disease to individualize prevention, diagnosis and treatment. Personalized genomics plays a vital, but not exclusive role in this evolving model of personalized medicine. The distinctions between genetic and genomic medicine are more quantitative than qualitative. Personalized genomics builds on principles established by the integration of genetics into medical practice. Principles s...

  3. Laboratory Building

    Energy Technology Data Exchange (ETDEWEB)

    Herrera, Joshua M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-03-01

    This report is an analysis of the means of egress and life safety requirements for the laboratory building. The building is located at Sandia National Laboratories (SNL) in Albuquerque, NM. The report includes a prescriptive-based analysis as well as a performance-based analysis. Following the analysis are appendices which contain maps of the laboratory building used throughout the analysis. The top of all the maps is assumed to be north.

  4. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

    DEFF Research Database (Denmark)

    Machado, Henrique; Gram, Lone

    2017-01-01

    was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.......Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand...... the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two...

  5. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  6. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  7. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  8. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  9. A comparison of accuracy validation methods for genomic and pedigree-based predictions of swine litter size traits using Large White and simulated data.

    Science.gov (United States)

    Putz, A M; Tiezzi, F; Maltecca, C; Gray, K A; Knauer, M T

    2018-02-01

    The objective of this study was to compare and determine the optimal validation method when comparing accuracy from single-step GBLUP (ssGBLUP) to traditional pedigree-based BLUP. Field data included six litter size traits. Simulated data included ten replicates designed to mimic the field data in order to determine the method that was closest to the true accuracy. Data were split into training and validation sets. The methods used were as follows: (i) theoretical accuracy derived from the prediction error variance (PEV) of the direct inverse (iLHS), (ii) approximated accuracies from the accf90(GS) program in the BLUPF90 family of programs (Approx), (iii) correlation between predictions and the single-step GEBVs from the full data set (GEBV Full ), (iv) correlation between predictions and the corrected phenotypes of females from the full data set (Y c ), (v) correlation from method iv divided by the square root of the heritability (Y ch ) and (vi) correlation between sire predictions and the average of their daughters' corrected phenotypes (Y cs ). Accuracies from iLHS increased from 0.27 to 0.37 (37%) in the Large White. Approximation accuracies were very consistent and close in absolute value (0.41 to 0.43). Both iLHS and Approx were much less variable than the corrected phenotype methods (ranging from 0.04 to 0.27). On average, simulated data showed an increase in accuracy from 0.34 to 0.44 (29%) using ssGBLUP. Both iLHS and Y ch approximated the increase well, 0.30 to 0.46 and 0.36 to 0.45, respectively. GEBV Full performed poorly in both data sets and is not recommended. Results suggest that for within-breed selection, theoretical accuracy using PEV was consistent and accurate. When direct inversion is infeasible to get the PEV, correlating predictions to the corrected phenotypes divided by the square root of heritability is adequate given a large enough validation data set. © 2017 Blackwell Verlag GmbH.

  10. Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

    Directory of Open Access Journals (Sweden)

    Enis Afgan

    Full Text Available Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise.We designed and implemented the Genomics Virtual Laboratory (GVL as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic.This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints

  11. Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

    Science.gov (United States)

    Afgan, Enis; Sloggett, Clare; Goonasekera, Nuwan; Makunin, Igor; Benson, Derek; Crowe, Mark; Gladman, Simon; Kowsar, Yousef; Pheasant, Michael; Horst, Ron; Lonie, Andrew

    2015-01-01

    Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s) enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise. We designed and implemented the Genomics Virtual Laboratory (GVL) as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook) or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au) and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic. This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints, and explore the

  12. Genomics and the human genome project: implications for psychiatry

    OpenAIRE

    Kelsoe, J R

    2004-01-01

    In the past decade the Human Genome Project has made extraordinary strides in understanding of fundamental human genetics. The complete human genetic sequence has been determined, and the chromosomal location of almost all human genes identified. Presently, a large international consortium, the HapMap Project, is working to identify a large portion of genetic variation in different human populations and the structure and relationship of these variants to each other. The Human Genome Project h...

  13. Building a capacity building manual

    CSIR Research Space (South Africa)

    Clinton, DD

    2010-02-01

    Full Text Available Organizations 2010 Building a capacity building manual Daniel D. Clinton, Jr., P.E., F.NSPE Chair, WFEO Capacity Building Committee Dr Andrew Cleland, FIPENZ, Chief Executive, IPENZ, NZ Eng David Botha, FSAICE, Executive Director, SAICE, SA Dawit... 2010 Tertiary level University curricula Coaches and mentors Facilities EXCeeD Remuneration of Academics Experiential training Outreach to Students Students chapters Young members forum World Federation of Engineering Organizations 2010 Post...

  14. Playing with heart and soul…and genomes: sports implications and applications of personal genomics.

    Science.gov (United States)

    Wagner, Jennifer K

    2013-01-01

    Whether the integration of genetic/omic technologies in sports contexts will facilitate player success, promote player safety, or spur genetic discrimination depends largely upon the game rules established by those currently designing genomic sports medicine programs. The integration has already begun, but there is not yet a playbook for best practices. Thus far discussions have focused largely on whether the integration would occur and how to prevent the integration from occurring, rather than how it could occur in such a way that maximizes benefits, minimizes risks, and avoids the exacerbation of racial disparities. Previous empirical research has identified members of the personal genomics industry offering sports-related DNA tests, and previous legal research has explored the impact of collective bargaining in professional sports as it relates to the employment protections of the Genetic Information Nondiscrimination Act (GINA). Building upon that research and upon participant observations with specific sports-related DNA tests purchased from four direct-to-consumer companies in 2011 and broader personal genomics (PGx) services, this anthropological, legal, and ethical (ALE) discussion highlights fundamental issues that must be addressed by those developing personal genomic sports medicine programs, either independently or through collaborations with commercial providers. For example, the vulnerability of student-athletes creates a number of issues that require careful, deliberate consideration. More broadly, however, this ALE discussion highlights potential sports-related implications (that ultimately might mitigate or, conversely, exacerbate racial disparities among athletes) of whole exome/genome sequencing conducted by biomedical researchers and clinicians for non-sports purposes. For example, the possibility that exome/genome sequencing of individuals who are considered to be non-patients, asymptomatic, normal, etc. will reveal the presence of variants of

  15. Cloud computing for comparative genomics

    Directory of Open Access Journals (Sweden)

    Pivovarov Rimma

    2010-05-01

    Full Text Available Abstract Background Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastructures are likely to become prohibitive with the increase, especially as the breadth of questions continues to rise. Alternative computing architectures, in particular cloud computing environments, may help alleviate this increasing pressure and enable fast, large-scale, and cost-effective comparative genomics strategies going forward. To test this, we redesigned a typical comparative genomics algorithm, the reciprocal smallest distance algorithm (RSD, to run within Amazon's Elastic Computing Cloud (EC2. We then employed the RSD-cloud for ortholog calculations across a wide selection of fully sequenced genomes. Results We ran more than 300,000 RSD-cloud processes within the EC2. These jobs were farmed simultaneously to 100 high capacity compute nodes using the Amazon Web Service Elastic Map Reduce and included a wide mix of large and small genomes. The total computation time took just under 70 hours and cost a total of $6,302 USD. Conclusions The effort to transform existing comparative genomics algorithms from local compute infrastructures is not trivial. However, the speed and flexibility of cloud computing environments provides a substantial boost with manageable cost. The procedure designed to transform the RSD algorithm into a cloud-ready application is readily adaptable to similar comparative genomics problems.

  16. Cloud computing for comparative genomics.

    Science.gov (United States)

    Wall, Dennis P; Kudtarkar, Parul; Fusaro, Vincent A; Pivovarov, Rimma; Patil, Prasad; Tonellato, Peter J

    2010-05-18

    Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastructures are likely to become prohibitive with the increase, especially as the breadth of questions continues to rise. Alternative computing architectures, in particular cloud computing environments, may help alleviate this increasing pressure and enable fast, large-scale, and cost-effective comparative genomics strategies going forward. To test this, we redesigned a typical comparative genomics algorithm, the reciprocal smallest distance algorithm (RSD), to run within Amazon's Elastic Computing Cloud (EC2). We then employed the RSD-cloud for ortholog calculations across a wide selection of fully sequenced genomes. We ran more than 300,000 RSD-cloud processes within the EC2. These jobs were farmed simultaneously to 100 high capacity compute nodes using the Amazon Web Service Elastic Map Reduce and included a wide mix of large and small genomes. The total computation time took just under 70 hours and cost a total of $6,302 USD. The effort to transform existing comparative genomics algorithms from local compute infrastructures is not trivial. However, the speed and flexibility of cloud computing environments provides a substantial boost with manageable cost. The procedure designed to transform the RSD algorithm into a cloud-ready application is readily adaptable to similar comparative genomics problems.

  17. Cost-effective cloud computing: a case study using the comparative genomics tool, roundup.

    Science.gov (United States)

    Kudtarkar, Parul; Deluca, Todd F; Fusaro, Vincent A; Tonellato, Peter J; Wall, Dennis P

    2010-12-22

    Comparative genomics resources, such as ortholog detection tools and repositories are rapidly increasing in scale and complexity. Cloud computing is an emerging technological paradigm that enables researchers to dynamically build a dedicated virtual cluster and may represent a valuable alternative for large computational tools in bioinformatics. In the present manuscript, we optimize the computation of a large-scale comparative genomics resource-Roundup-using cloud computing, describe the proper operating principles required to achieve computational efficiency on the cloud, and detail important procedures for improving cost-effectiveness to ensure maximal computation at minimal costs. Utilizing the comparative genomics tool, Roundup, as a case study, we computed orthologs among 902 fully sequenced genomes on Amazon's Elastic Compute Cloud. For managing the ortholog processes, we designed a strategy to deploy the web service, Elastic MapReduce, and maximize the use of the cloud while simultaneously minimizing costs. Specifically, we created a model to estimate cloud runtime based on the size and complexity of the genomes being compared that determines in advance the optimal order of the jobs to be submitted. We computed orthologous relationships for 245,323 genome-to-genome comparisons on Amazon's computing cloud, a computation that required just over 200 hours and cost $8,000 USD, at least 40% less than expected under a strategy in which genome comparisons were submitted to the cloud randomly with respect to runtime. Our cost savings projections were based on a model that not only demonstrates the optimal strategy for deploying RSD to the cloud, but also finds the optimal cluster size to minimize waste and maximize usage. Our cost-reduction model is readily adaptable for other comparative genomics tools and potentially of significant benefit to labs seeking to take advantage of the cloud as an alternative to local computing infrastructure.

  18. Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.

    Directory of Open Access Journals (Sweden)

    Jiang Du

    2009-07-01

    Full Text Available The goal of human genome re-sequencing is obtaining an accurate assembly of an individual's genome. Recently, there has been great excitement in the development of many technologies for this (e.g. medium and short read sequencing from companies such as 454 and SOLiD, and high-density oligo-arrays from Affymetrix and NimbelGen, with even more expected to appear. The costs and sensitivities of these technologies differ considerably from each other. As an important goal of personal genomics is to reduce the cost of re-sequencing to an affordable point, it is worthwhile to consider optimally integrating technologies. Here, we build a simulation toolbox that will help us optimally combine different technologies for genome re-sequencing, especially in reconstructing large structural variants (SVs. SV reconstruction is considered the most challenging step in human genome re-sequencing. (It is sometimes even harder than de novo assembly of small genomes because of the duplications and repetitive sequences in the human genome. To this end, we formulate canonical problems that are representative of issues in reconstruction and are of small enough scale to be computationally tractable and simulatable. Using semi-realistic simulations, we show how we can combine different technologies to optimally solve the assembly at low cost. With mapability maps, our simulations efficiently handle the inhomogeneous repeat-containing structure of the human genome and the computational complexity of practical assembly algorithms. They quantitatively show how combining different read lengths is more cost-effective than using one length, how an optimal mixed sequencing strategy for reconstructing large novel SVs usually also gives accurate detection of SNPs/indels, how paired-end reads can improve reconstruction efficiency, and how adding in arrays is more efficient than just sequencing for disentangling some complex SVs. Our strategy should facilitate the sequencing of

  19. Building the green way.

    Science.gov (United States)

    Lockwood, Charles

    2006-06-01

    Just five or six years ago, the term "green building" evoked visions of barefoot, tie-dyed, granola-munching denizens. There's been a large shift in perception. Of course, green buildings are still known for conserving natural resources by, for example, minimizing on-site grading, using alternative materials, and recycling construction waste. But people now see the financial advantages as well. Well-designed green buildings yield lower utility costs, greater employee productivity, less absenteeism, and stronger attraction and retention of workers than standard buildings do. Green materials, mechanical systems, and furnishings have become more widely available and considerably less expensive than they used to be-often cheaper than their standard counterparts. So building green is no longer a pricey experiment; just about any company can do it on a standard budget by following the ten rules outlined by the author. Reliable building-rating systems like the U.S. Green Building Council's rigorous Leadership in Energy and Environmental Design (LEED) program have done much to underscore the benefits of green construction. LEED evaluates buildings and awards points in several areas, such as water efficiency and indoor environmental quality. Other rating programs include the UK's BREEAM (Building Research Establishment's Environmental Assessment Method) and Australia's Green Star. Green construction is not simply getting more respect; it is rapidly becoming a necessity as corporations push it fully into the mainstream over the next five to ten years. In fact, the author says, the owners of standard buildings face massive obsolescence. To avoid this problem, they should carry out green renovations. Corporations no longer have an excuse for eschewing environmental and economic sustainability. They have at their disposal tools proven to lower overhead costs, improve productivity, and strengthen the bottom line.

  20. The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects.

    Science.gov (United States)

    Papanicolaou, Alexie

    2016-01-01

    Many research programs on non-model species biology have been empowered by genomics. In turn, genomics is underpinned by a reference sequence and ancillary information created by so-called "genome projects". The most reliable genome projects are the ones created as part of an active research program and designed to address specific questions but their life extends past publication. In this opinion paper I outline four key insights that have facilitated maintaining genomic communities: the key role of computational capability, the iterative process of building genomic resources, the value of community participation and the importance of manual curation. Taken together, these ideas can and do ensure the longevity of genome projects and the growing non-model species community can use them to focus a discussion with regards to its future genomic infrastructure.

  1. Reactor building

    International Nuclear Information System (INIS)

    Ebata, Sakae.

    1990-01-01

    At least one valve rack is disposed in a reactor building, on which pipeways to a main closure valve, valves and bypasses of turbines are placed and contained. The valve rack is fixed to the main body of the building or to a base mat. Since the reactor building is designed as class A earthquake-proofness and for maintaining the S 1 function, the valve rack can be fixed to the building main body or to the base mat. With such a constitution, the portions for maintaining the S 1 function are concentrated to the reactor buildi