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Sample records for genomics developing tools

  1. Coral Reef Genomics: Developing tools for functional genomics ofcoral symbiosis

    SciTech Connect

    Schwarz, Jodi; Brokstein, Peter; Manohar, Chitra; Coffroth, MaryAlice; Szmant, Alina; Medina, Monica

    2005-03-01

    Symbioses between cnidarians and dinoflagellates in the genus Symbiodinium are widespread in the marine environment. The importance of this symbiosis to reef-building corals and reef nutrient and carbon cycles is well documented, but little is known about the mechanisms by which the partners establish and regulate the symbiosis. Because the dinoflagellate symbionts live inside the cells of their host coral, the interactions between the partners occur on cellular and molecular levels, as each partner alters the expression of genes and proteins to facilitate the partnership. These interactions can examined using high-throughput techniques that allow thousands of genes to be examined simultaneously. We are developing the groundwork so that we can use DNA microarray profiling to identify genes involved in the Montastraea faveolata and Acropora palmata symbioses. Here we report results from the initial steps in this microarray initiative, that is, the construction of cDNA libraries from 4 of 16 target stages, sequencing of 3450 cDNA clones to generate Expressed Sequenced Tags (ESTs), and annotation of the ESTs to identify candidate genes to include in the microarrays. An understanding of how the coral-dinoflagellate symbiosis is regulated will have implications for atmospheric and ocean sciences, conservation biology, the study and diagnosis of coral bleaching and disease, and comparative studies of animal-protest interactions.

  2. Development of peanut expessed sequence tag-based genomic resources and tools

    Technology Transfer Automated Retrieval System (TEKTRAN)

    U.S. Peanut Genome Initiative (PGI) has widely recognized the need for peanut genome tools and resources development for mitigating peanut allergens and food safety. Genomics such as Expressed Sequence Tag (EST), microarray technologies, and whole genome sequencing provides robotic tools for profili...

  3. Development of peanut EST (expressed sequence tag)-based genomic resources and tools

    Technology Transfer Automated Retrieval System (TEKTRAN)

    U.S. Peanut Genome Initiative (PGI) has widely recognized the need for peanut genome tools and resources development for mitigating peanut allergens and food safety. Genomics such as Expressed Sequence Tag (EST), microarray technologies, and whole genome sequencing provides robotic tools for profili...

  4. Genomic tools for developing markers for postharvest disease resistance in Rosaceae fruit crops

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A wealth of new plant genomic information and molecular tools have been developed over the past ten years and now the challenge is to learn how to apply this information to address critical production problems, such as disease resistance and abiotic stress tolerance. Malus sieversii, an apple speci...

  5. Recent advances in developing molecular tools for targeted genome engineering of mammalian cells.

    PubMed

    Lim, Kwang-il

    2015-01-01

    Various biological molecules naturally existing in diversified species including fungi, bacteria, and bacteriophage have functionalities for DNA binding and processing. The biological molecules have been recently actively engineered for use in customized genome editing of mammalian cells as the molecule-encoding DNA sequence information and the underlying mechanisms how the molecules work are unveiled. Excitingly, multiple novel methods based on the newly constructed artificial molecular tools have enabled modifications of specific endogenous genetic elements in the genome context at efficiencies that are much higher than that of the conventional homologous recombination based methods. This minireview introduces the most recently spotlighted molecular genome engineering tools with their key features and ongoing modifications for better performance. Such ongoing efforts have mainly focused on the removal of the inherent DNA sequence recognition rigidity from the original molecular platforms, the addition of newly tailored targeting functions into the engineered molecules, and the enhancement of their targeting specificity. Effective targeted genome engineering of mammalian cells will enable not only sophisticated genetic studies in the context of the genome, but also widely-applicable universal therapeutics based on the pinpointing and correction of the disease-causing genetic elements within the genome in the near future.

  6. Recent advances in developing molecular tools for targeted genome engineering of mammalian cells.

    PubMed

    Lim, Kwang-il

    2015-01-01

    Various biological molecules naturally existing in diversified species including fungi, bacteria, and bacteriophage have functionalities for DNA binding and processing. The biological molecules have been recently actively engineered for use in customized genome editing of mammalian cells as the molecule-encoding DNA sequence information and the underlying mechanisms how the molecules work are unveiled. Excitingly, multiple novel methods based on the newly constructed artificial molecular tools have enabled modifications of specific endogenous genetic elements in the genome context at efficiencies that are much higher than that of the conventional homologous recombination based methods. This minireview introduces the most recently spotlighted molecular genome engineering tools with their key features and ongoing modifications for better performance. Such ongoing efforts have mainly focused on the removal of the inherent DNA sequence recognition rigidity from the original molecular platforms, the addition of newly tailored targeting functions into the engineered molecules, and the enhancement of their targeting specificity. Effective targeted genome engineering of mammalian cells will enable not only sophisticated genetic studies in the context of the genome, but also widely-applicable universal therapeutics based on the pinpointing and correction of the disease-causing genetic elements within the genome in the near future. PMID:25104401

  7. Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring

    PubMed Central

    2011-01-01

    Background The Manila clam, Ruditapes philippinarum, is one of the major aquaculture species in the world and a potential sentinel organism for monitoring the status of marine ecosystems. However, genomic resources for R. philippinarum are still extremely limited. Global analysis of gene expression profiles is increasingly used to evaluate the biological effects of various environmental stressors on aquatic animals under either artificial conditions or in the wild. Here, we report on the development of a transcriptomic platform for global gene expression profiling in the Manila clam. Results A normalized cDNA library representing a mixture of adult tissues was sequenced using a ultra high-throughput sequencing technology (Roche 454). A database consisting of 32,606 unique transcripts was constructed, 9,747 (30%) of which could be annotated by similarity. An oligo-DNA microarray platform was designed and applied to profile gene expression of digestive gland and gills. Functional annotation of differentially expressed genes between different tissues was performed by enrichment analysis. Expression of Natural Antisense Transcripts (NAT) analysis was also performed and bi-directional transcription appears a common phenomenon in the R. philippinarum transcriptome. A preliminary study on clam samples collected in a highly polluted area of the Venice Lagoon demonstrated the applicability of genomic tools to environmental monitoring. Conclusions The transcriptomic platform developed for the Manila clam confirmed the high level of reproducibility of current microarray technology. Next-generation sequencing provided a good representation of the clam transcriptome. Despite the known limitations in transcript annotation and sequence coverage for non model species, sufficient information was obtained to identify a large set of genes potentially involved in cellular response to environmental stress. PMID:21569398

  8. Development of Genomic and Genetic Tools for Foxtail Millet, and Use of These Tools in the Improvement of Biomass Production for Bioenergy Crops

    SciTech Connect

    Doust, Andrew, N.

    2011-11-11

    The overall aim of this research was to develop genomic and genetic tools in foxtail millet that will be useful in improving biomass production in bioenergy crops such as switchgrass, napier grass, and pearl millet. A variety of approaches have been implemented, and our lab has been primarily involved in genome analysis and quantitative genetic analysis. Our progress in these activities has been substantially helped by the genomic sequence of foxtail millet produced by the Joint Genome Institute (Bennetzen et al., in prep). In particular, the annotation and analysis of candidate genes for architecture, biomass production and flowering has led to new insights into the control of branching and flowering time, and has shown how closely related flowering time is to vegetative architectural development and biomass accumulation. The differences in genetic control identified at high and low density plantings have direct relevance to the breeding of bioenergy grasses that are tolerant of high planting densities. The developmental analyses have shown how plant architecture changes over time and may indicate which genes may best be manipulated at various times during development to obtain required biomass characteristics. This data contributes to the overall aim of significantly improving genetic and genomic tools in foxtail millet that can be directed to improvement of bioenergy grasses such as switchgrass, where it is important to maximize vegetative growth for greatest biomass production.

  9. Applied genomics: Tools ranging from genomic prediction to bioconservation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This invited presentation will provide an overview of the development of genomic tools in cattle and goats, and how these approaches and methodologies can be adapted for bioconservation of endangered ruminant species....

  10. Development of Genome Engineering Tools from Plant-Specific PPR Proteins Using Animal Cultured Cells.

    PubMed

    Kobayashi, Takehito; Yagi, Yusuke; Nakamura, Takahiro

    2016-01-01

    The pentatricopeptide repeat (PPR) motif is a sequence-specific RNA/DNA-binding module. Elucidation of the RNA/DNA recognition mechanism has enabled engineering of PPR motifs as new RNA/DNA manipulation tools in living cells, including for genome editing. However, the biochemical characteristics of PPR proteins remain unknown, mostly due to the instability and/or unfolding propensities of PPR proteins in heterologous expression systems such as bacteria and yeast. To overcome this issue, we constructed reporter systems using animal cultured cells. The cell-based system has highly attractive features for PPR engineering: robust eukaryotic gene expression; availability of various vectors, reagents, and antibodies; highly efficient DNA delivery ratio (>80 %); and rapid, high-throughput data production. In this chapter, we introduce an example of such reporter systems: a PPR-based sequence-specific translational activation system. The cell-based reporter system can be applied to characterize plant genes of interested and to PPR engineering.

  11. Developing tools for the study of molluscan immunity: The sequencing of the genome of the eastern oyster, Crassostrea virginica.

    PubMed

    Gómez-Chiarri, Marta; Warren, Wesley C; Guo, Ximing; Proestou, Dina

    2015-09-01

    The eastern oyster, Crassostrea virginica, provides important ecological and economical services, making it the target of restoration projects and supporting a significant fishery/aquaculture industry with landings valued at more than $100 million in 2012 in the United States of America. Due to the impact of infectious diseases on wild, restored, and cultured populations, the eastern oyster has been the focus of studies on host-pathogen interactions and immunity, as well as the target of selective breeding efforts for disease resistant oyster lines. Despite these efforts, relatively little is known about the genetic basis of resistance to diseases or environmental stress, not only in eastern oyster, but also in other molluscan species of commercial interest worldwide. In order to develop tools and resources to assist in the elucidation of the genomic basis of traits of commercial, biological, and ecological interest in oysters, a team of genome and bioinformatics experts, in collaboration with the oyster research community, is sequencing, assembling, and annotating the first reference genome for the eastern oyster and producing an exhaustive transcriptome from a variety of oyster developmental stages and tissues in response to a diverse set of environmentally-relevant stimuli. These transcriptomes and reference genome for the eastern oyster, added to the already available genome and transcriptomes for the Pacific oyster (Crassostrea gigas) and other bivalve species, will be an essential resource for the discovery of candidate genes and markers associated with traits of commercial, biological, and ecologic importance in bivalve molluscs, including those related to host-pathogen interactions and immunity.

  12. Developing tools for the study of molluscan immunity: The sequencing of the genome of the eastern oyster, Crassostrea virginica.

    PubMed

    Gómez-Chiarri, Marta; Warren, Wesley C; Guo, Ximing; Proestou, Dina

    2015-09-01

    The eastern oyster, Crassostrea virginica, provides important ecological and economical services, making it the target of restoration projects and supporting a significant fishery/aquaculture industry with landings valued at more than $100 million in 2012 in the United States of America. Due to the impact of infectious diseases on wild, restored, and cultured populations, the eastern oyster has been the focus of studies on host-pathogen interactions and immunity, as well as the target of selective breeding efforts for disease resistant oyster lines. Despite these efforts, relatively little is known about the genetic basis of resistance to diseases or environmental stress, not only in eastern oyster, but also in other molluscan species of commercial interest worldwide. In order to develop tools and resources to assist in the elucidation of the genomic basis of traits of commercial, biological, and ecological interest in oysters, a team of genome and bioinformatics experts, in collaboration with the oyster research community, is sequencing, assembling, and annotating the first reference genome for the eastern oyster and producing an exhaustive transcriptome from a variety of oyster developmental stages and tissues in response to a diverse set of environmentally-relevant stimuli. These transcriptomes and reference genome for the eastern oyster, added to the already available genome and transcriptomes for the Pacific oyster (Crassostrea gigas) and other bivalve species, will be an essential resource for the discovery of candidate genes and markers associated with traits of commercial, biological, and ecologic importance in bivalve molluscs, including those related to host-pathogen interactions and immunity. PMID:25982405

  13. Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies

    PubMed Central

    McKerrell, Thomas; Moreno, Thaidy; Ponstingl, Hannes; Bolli, Niccolo; Dias, João M. L.; Tischler, German; Colonna, Vincenza; Manasse, Bridget; Bench, Anthony; Bloxham, David; Herman, Bram; Fletcher, Danielle; Park, Naomi; Quail, Michael A.; Manes, Nicla; Hodkinson, Clare; Baxter, Joanna; Sierra, Jorge; Foukaneli, Theodora; Warren, Alan J.; Chi, Jianxiang; Costeas, Paul; Rad, Roland; Huntly, Brian; Grove, Carolyn; Ning, Zemin; Tyler-Smith, Chris; Varela, Ignacio; Scott, Mike; Nomdedeu, Josep; Mustonen, Ville

    2016-01-01

    The diagnosis of hematologic malignancies relies on multidisciplinary workflows involving morphology, flow cytometry, cytogenetic, and molecular genetic analyses. Advances in cancer genomics have identified numerous recurrent mutations with clear prognostic and/or therapeutic significance to different cancers. In myeloid malignancies, there is a clinical imperative to test for such mutations in mainstream diagnosis; however, progress toward this has been slow and piecemeal. Here we describe Karyogene, an integrated targeted resequencing/analytical platform that detects nucleotide substitutions, insertions/deletions, chromosomal translocations, copy number abnormalities, and zygosity changes in a single assay. We validate the approach against 62 acute myeloid leukemia, 50 myelodysplastic syndrome, and 40 blood DNA samples from individuals without evidence of clonal blood disorders. We demonstrate robust detection of sequence changes in 49 genes, including difficult-to-detect mutations such as FLT3 internal-tandem and mixed-lineage leukemia (MLL) partial-tandem duplications, and clinically significant chromosomal rearrangements including MLL translocations to known and unknown partners, identifying the novel fusion gene MLL-DIAPH2 in the process. Additionally, we identify most significant chromosomal gains and losses, and several copy neutral loss-of-heterozygosity mutations at a genome-wide level, including previously unreported changes such as homozygosity for DNMT3A R882 mutations. Karyogene represents a dependable genomic diagnosis platform for translational research and for the clinical management of myeloid malignancies, which can be readily adapted for use in other cancers. PMID:27121471

  14. Malaria vaccines: using models of immunity and functional genomics tools to accelerate the development of vaccines against Plasmodium falciparum.

    PubMed

    Duffy, Patrick E; Krzych, Urszula; Francis, Susan; Fried, Michal

    2005-03-18

    Naturally acquired immunity and immunity acquired after immunization with attenuated parasites indicate that a vaccine against malaria is feasible. Several obstacles have stymied malaria vaccine development, among them our poor understanding of protective immunity and technical difficulties for studying gene and protein expression in the Plasmodium falciparum parasite. Pregnancy malaria offers a model approach for vaccine development: recent findings have elucidated the basis for disease pathogenesis and protective immunity in this syndrome, and this understanding has focused the effort to identify the optimal antigens for a pregnancy malaria vaccine. In parallel, functional genomics tools are overcoming several of the obstacles for studying protein expression in the malaria parasite, vastly accelerating the pace for antigen discovery. Together, these conceptual and technological advances allow a rational approach to vaccine antigen selection, in which a finite number of antigens are selected from the entire genome by merit of the expression patterns and specific features. These candidate antigens are then subjected to detailed studies according to criteria established by the understanding of pathogenesis and protective immunity, to identify the optimal antigens for inclusion in subunit vaccines.

  15. Unraveling the 3D genome: genomics tools for multiscale exploration.

    PubMed

    Risca, Viviana I; Greenleaf, William J

    2015-07-01

    A decade of rapid method development has begun to yield exciting insights into the 3D architecture of the metazoan genome and the roles it may play in regulating transcription. Here we review core methods and new tools in the modern genomicist's toolbox at three length scales, ranging from single base pairs to megabase-scale chromosomal domains, and discuss the emerging picture of the 3D genome that these tools have revealed. Blind spots remain, especially at intermediate length scales spanning a few nucleosomes, but thanks in part to new technologies that permit targeted alteration of chromatin states and time-resolved studies, the next decade holds great promise for hypothesis-driven research into the mechanisms that drive genome architecture and transcriptional regulation.

  16. Comparative genomics tools applied to bioterrorism defence.

    PubMed

    Slezak, Tom; Kuczmarski, Tom; Ott, Linda; Torres, Clinton; Medeiros, Dan; Smith, Jason; Truitt, Brian; Mulakken, Nisha; Lam, Marisa; Vitalis, Elizabeth; Zemla, Adam; Zhou, Carol Ecale; Gardner, Shea

    2003-06-01

    Rapid advances in the genomic sequencing of bacteria and viruses over the past few years have made it possible to consider sequencing the genomes of all pathogens that affect humans and the crops and livestock upon which our lives depend. Recent events make it imperative that full genome sequencing be accomplished as soon as possible for pathogens that could be used as weapons of mass destruction or disruption. This sequence information must be exploited to provide rapid and accurate diagnostics to identify pathogens and distinguish them from harmless near-neighbours and hoaxes. The Chem-Bio Non-Proliferation (CBNP) programme of the US Department of Energy (DOE) began a large-scale effort of pathogen detection in early 2000 when it was announced that the DOE would be providing bio-security at the 2002 Winter Olympic Games in Salt Lake City, Utah. Our team at the Lawrence Livermore National Lab (LLNL) was given the task of developing reliable and validated assays for a number of the most likely bioterrorist agents. The short timeline led us to devise a novel system that utilised whole-genome comparison methods to rapidly focus on parts of the pathogen genomes that had a high probability of being unique. Assays developed with this approach have been validated by the Centers for Disease Control (CDC). They were used at the 2002 Winter Olympics, have entered the public health system, and have been in continual use for non-publicised aspects of homeland defence since autumn 2001. Assays have been developed for all major threat list agents for which adequate genomic sequence is available, as well as for other pathogens requested by various government agencies. Collaborations with comparative genomics algorithm developers have enabled our LLNL team to make major advances in pathogen detection, since many of the existing tools simply did not scale well enough to be of practical use for this application. It is hoped that a discussion of a real-life practical application of

  17. Strategies and tools for whole genome alignments

    SciTech Connect

    Couronne, Olivier; Poliakov, Alexander; Bray, Nicolas; Ishkhanov,Tigran; Ryaboy, Dmitriy; Rubin, Edward; Pachter, Lior; Dubchak, Inna

    2002-11-25

    The availability of the assembled mouse genome makespossible, for the first time, an alignment and comparison of two largevertebrate genomes. We have investigated different strategies ofalignment for the subsequent analysis of conservation of genomes that areeffective for different quality assemblies. These strategies were appliedto the comparison of the working draft of the human genome with the MouseGenome Sequencing Consortium assembly, as well as other intermediatemouse assemblies. Our methods are fast and the resulting alignmentsexhibit a high degree of sensitivity, covering more than 90 percent ofknown coding exons in the human genome. We have obtained such coveragewhile preserving specificity. With a view towards the end user, we havedeveloped a suite of tools and websites for automatically aligning, andsubsequently browsing and working with whole genome comparisons. Wedescribe the use of these tools to identify conserved non-coding regionsbetween the human and mouse genomes, some of which have not beenidentified by other methods.

  18. DEVELOPMENT OF GENOMIC AND GENETIC TOOLS FOR FOXTAIL MILLET, AND USE OF THESE TOOLS IN THE IMPROVEMENT OF BIOMASS PRODUCTION FOR BIOENERGY CROPS

    SciTech Connect

    Chen, Xinlu; Zale, Janice; Chen, Feng

    2013-01-22

    Foxtail millet (Setaria italica L.) is a warm-season, C4 annual crop commonly grown for grain and forage worldwide. It has a relatively short generation time, yet produces hundreds of seeds per inflorescence. The crop is inbred and it has a small-size genome (~500 Mb). These features make foxtail millet an attractive grass model, especially for bioenergy crops. While a number of genomic tools have been established for foxtail millet, including a fully sequenced genome and molecular markers, the objectives of this project were to develop a tissue culture system, determine the best explant(s) for tissue culture, optimize transient gene expression, and establish a stable transformation system for foxtail millet cultivar Yugu1. In optimizing a tissue culture medium for the induction of calli and somatic embryos from immature inflorescences and mature seed explants, Murashige and Skoog medium containing 2.5 mg l-1 2,4-dichlorophenoxyacetic acid and 0.6 mg l-1 6- benzylaminopurine was determined to be optimal for callus induction of foxtail millet. The efficiency of callus induction from explants of immature inflorescences was significantly higher at 76% compared to that of callus induction from mature seed explants at 68%. The calli induced from this medium were regenerated into plants at high frequency (~100%) using 0.2 mg l-1 kinetin in the regeneration media. For performing transient gene expression, immature embryos were first isolated from inflorescences. Transient expression of the GUS reporter gene in immature embryos was significantly increased after sonication, a vacuum treatment, centrifugation and the addition of L-cysteine and dithiothreitol, which led to the efficiency of transient expression at levels greater than 70% after Agrobacterium inoculation. Inoculation with Agrobacterium was also tested with germinated seeds. The radicals of germinated seeds were pierced with needles and dipped into Agrobacterium solution. This method achieved a 10% transient

  19. Bioinformatics tools for small genomes, such as hepatitis B virus.

    PubMed

    Bell, Trevor G; Kramvis, Anna

    2015-02-01

    DNA sequence analysis is undertaken in many biological research laboratories. The workflow consists of several steps involving the bioinformatic processing of biological data. We have developed a suite of web-based online bioinformatic tools to assist with processing, analysis and curation of DNA sequence data. Most of these tools are genome-agnostic, with two tools specifically designed for hepatitis B virus sequence data. Tools in the suite are able to process sequence data from Sanger sequencing, ultra-deep amplicon resequencing (pyrosequencing) and chromatograph (trace files), as appropriate. The tools are available online at no cost and are aimed at researchers without specialist technical computer knowledge. The tools can be accessed at http://hvdr.bioinf.wits.ac.za/SmallGenomeTools, and the source code is available online at https://github.com/DrTrevorBell/SmallGenomeTools. PMID:25690798

  20. DCODE.ORG Anthology of Comparative Genomic Tools

    SciTech Connect

    Loots, G G; Ovcharenko, I

    2005-01-11

    Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to deciphering the noncoding encryption of gene regulation across genomes. To facilitate the use of comparative genomics to practical applications in genetics and genomics we have developed several analytical and visualization tools for the analysis of arbitrary sequences and whole genomes. These tools include two alignment tools: zPicture and Mulan; a phylogenetic shadowing tool: eShadow for identifying lineage- and species-specific functional elements; two evolutionary conserved transcription factor analysis tools: rVista and multiTF; a tool for extracting cis-regulatory modules governing the expression of co-regulated genes, CREME; and a dynamic portal to multiple vertebrate and invertebrate genome alignments, the ECR Browser. Here we briefly describe each one of these tools and provide specific examples on their practical applications. All the tools are publicly available at the http://www.dcode.org/ web site.

  1. Galaxy tools to study genome diversity

    PubMed Central

    2013-01-01

    Background Intra-species genetic variation can be used to investigate population structure, selection, and gene flow in non-model vertebrates; and due to the plummeting costs for genome sequencing, it is now possible for small labs to obtain full-genome variation data from their species of interest. However, those labs may not have easy access to, and familiarity with, computational tools to analyze those data. Results We have created a suite of tools for the Galaxy web server aimed at handling nucleotide and amino-acid polymorphisms discovered by full-genome sequencing of several individuals of the same species, or using a SNP genotyping microarray. In addition to providing user-friendly tools, a main goal is to make published analyses reproducible. While most of the examples discussed in this paper deal with nuclear-genome diversity in non-human vertebrates, we also illustrate the application of the tools to fungal genomes, human biomedical data, and mitochondrial sequences. Conclusions This project illustrates that a small group can design, implement, test, document, and distribute a Galaxy tool collection to meet the needs of a particular community of biologists. PMID:24377391

  2. Dcode.org anthology of comparative genomic tools.

    PubMed

    Loots, Gabriela G; Ovcharenko, Ivan

    2005-07-01

    Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to deciphering the non-coding encryption of gene regulation across genomes. To facilitate the practical application of comparative sequence analysis to genetics and genomics, we have developed several analytical and visualization tools for the analysis of arbitrary sequences and whole genomes. These tools include two alignment tools, zPicture and Mulan; a phylogenetic shadowing tool, eShadow for identifying lineage- and species-specific functional elements; two evolutionary conserved transcription factor analysis tools, rVista and multiTF; a tool for extracting cis-regulatory modules governing the expression of co-regulated genes, Creme 2.0; and a dynamic portal to multiple vertebrate and invertebrate genome alignments, the ECR Browser. Here, we briefly describe each one of these tools and provide specific examples on their practical applications. All the tools are publicly available at the http://www.dcode.org/ website.

  3. Tools for sea urchin genomic analysis.

    PubMed

    Cameron, R Andrew

    2014-01-01

    The Sea Urchin Genome Project Web site, SpBase ( http://SpBase.org ), in association with a suite of publicly available sequence comparison tools provides a platform from which to analyze genes and genomic sequences of sea urchin. This information system is specifically designed to support laboratory bench studies in cell and molecular biology. In particular these tools and datasets have supported the description of the gene regulatory networks of the purple sea urchin S. purpuratus. This chapter details methods to undertake in the first steps to find genes and noncoding regulatory sequences for further analysis.

  4. Bovine Genome Database: new tools for gleaning function from the Bos taurus genome.

    PubMed

    Elsik, Christine G; Unni, Deepak R; Diesh, Colin M; Tayal, Aditi; Emery, Marianne L; Nguyen, Hung N; Hagen, Darren E

    2016-01-01

    We report an update of the Bovine Genome Database (BGD) (http://BovineGenome.org). The goal of BGD is to support bovine genomics research by providing genome annotation and data mining tools. We have developed new genome and annotation browsers using JBrowse and WebApollo for two Bos taurus genome assemblies, the reference genome assembly (UMD3.1.1) and the alternate genome assembly (Btau_4.6.1). Annotation tools have been customized to highlight priority genes for annotation, and to aid annotators in selecting gene evidence tracks from 91 tissue specific RNAseq datasets. We have also developed BovineMine, based on the InterMine data warehousing system, to integrate the bovine genome, annotation, QTL, SNP and expression data with external sources of orthology, gene ontology, gene interaction and pathway information. BovineMine provides powerful query building tools, as well as customized query templates, and allows users to analyze and download genome-wide datasets. With BovineMine, bovine researchers can use orthology to leverage the curated gene pathways of model organisms, such as human, mouse and rat. BovineMine will be especially useful for gene ontology and pathway analyses in conjunction with GWAS and QTL studies.

  5. Genomic Tools in Groundnut Breeding Program: Status and Perspectives

    PubMed Central

    Janila, P.; Variath, Murali T.; Pandey, Manish K.; Desmae, Haile; Motagi, Babu N.; Okori, Patrick; Manohar, Surendra S.; Rathnakumar, A. L.; Radhakrishnan, T.; Liao, Boshou; Varshney, Rajeev K.

    2016-01-01

    Groundnut, a nutrient-rich food legume, is cultivated world over. It is valued for its good quality cooking oil, energy and protein rich food, and nutrient-rich fodder. Globally, groundnut improvement programs have developed varieties to meet the preferences of farmers, traders, processors, and consumers. Enhanced yield, tolerance to biotic and abiotic stresses and quality parameters have been the target traits. Spurt in genetic information of groundnut was facilitated by development of molecular markers, genetic, and physical maps, generation of expressed sequence tags (EST), discovery of genes, and identification of quantitative trait loci (QTL) for some important biotic and abiotic stresses and quality traits. The first groundnut variety developed using marker assisted breeding (MAB) was registered in 2003. Since then, USA, China, Japan, and India have begun to use genomic tools in routine groundnut improvement programs. Introgression lines that combine foliar fungal disease resistance and early maturity were developed using MAB. Establishment of marker-trait associations (MTA) paved way to integrate genomic tools in groundnut breeding for accelerated genetic gain. Genomic Selection (GS) tools are employed to improve drought tolerance and pod yield, governed by several minor effect QTLs. Draft genome sequence and low cost genotyping tools such as genotyping by sequencing (GBS) are expected to accelerate use of genomic tools to enhance genetic gains for target traits in groundnut. PMID:27014312

  6. A functional genomics tool for the Pacific bluefin tuna: Development of a 44K oligonucleotide microarray from whole-genome sequencing data for global transcriptome analysis.

    PubMed

    Yasuike, Motoshige; Fujiwara, Atushi; Nakamura, Yoji; Iwasaki, Yuki; Nishiki, Issei; Sugaya, Takuma; Shimizu, Akio; Sano, Motohiko; Kobayashi, Takanori; Ototake, Mitsuru

    2016-02-01

    Bluefin tunas are one of the most important fishery resources worldwide. Because of high market values, bluefin tuna farming has been rapidly growing during recent years. At present, the most common form of the tuna farming is based on the stocking of wild-caught fish. Therefore, concerns have been raised about the negative impact of the tuna farming on wild stocks. Recently, the Pacific bluefin tuna (PBT), Thunnus orientalis, has succeeded in completing the reproduction cycle under aquaculture conditions, but production bottlenecks remain to be solved because of very little biological information on bluefin tunas. Functional genomics approaches promise to rapidly increase our knowledge on biological processes in the bluefin tuna. Here, we describe the development of the first 44K PBT oligonucleotide microarray (oligo-array), based on whole-genome shotgun (WGS) sequencing and large-scale expressed sequence tags (ESTs) data. In addition, we also introduce an initial 44K PBT oligo-array experiment using in vitro grown peripheral blood leukocytes (PBLs) stimulated with immunostimulants such as lipopolysaccharide (LPS: a cell wall component of Gram-negative bacteria) or polyinosinic:polycytidylic acid (poly I:C: a synthetic mimic of viral infection). This pilot 44K PBT oligo-array analysis successfully addressed distinct immune processes between LPS- and poly I:C- stimulated PBLs. Thus, we expect that this oligo-array will provide an excellent opportunity to analyze global gene expression profiles for a better understanding of diseases and stress, as well as for reproduction, development and influence of nutrition on tuna aquaculture production.

  7. Computational tools for Brassica-Arabidopsis comparative genomics.

    PubMed

    Beckett, Paul; Bancroft, Ian; Trick, Martin

    2005-01-01

    Recent advances, such as the availability of extensive genome survey sequence (GSS) data and draft physical maps, are radically transforming the means by which we can dissect Brassica genome structure and systematically relate it to the Arabidopsis model. Hitherto, our view of the co-linearities between these closely related genomes had been largely inferred from comparative RFLP data, necessitating substantial interpolation and expert interpretation. Sequencing of the Brassica rapa genome by the Multinational Brassica Genome Project will, however, enable an entirely computational approach to this problem. Meanwhile we have been developing databases and bioinformatics tools to support our work in Brassica comparative genomics, including a recently completed draft physical map of B. rapa integrated with anchor probes derived from the Arabidopsis genome sequence. We are also exploring new ways to display the emerging Brassica-Arabidopsis sequence homology data. We have mapped all publicly available Brassica sequences in silico to the Arabidopsis TIGR v5 genome sequence and published this in the ATIDB database that uses Generic Genome Browser (GBrowse). This in silico approach potentially identifies all paralogous sequences and so we colour-code the significance of the mappings and offer an integrated, real-time multiple alignment tool to partition them into paralogous groups. The MySQL database driving GBrowse can also be directly interrogated, using the powerful API offered by the Perl BioColon, two colonsDBColon, two colonsGFF methods, facilitating a wide range of data-mining possibilities.

  8. The UCSC genome browser and associated tools.

    PubMed

    Kuhn, Robert M; Haussler, David; Kent, W James

    2013-03-01

    The UCSC Genome Browser (http://genome.ucsc.edu) is a graphical viewer for genomic data now in its 13th year. Since the early days of the Human Genome Project, it has presented an integrated view of genomic data of many kinds. Now home to assemblies for 58 organisms, the Browser presents visualization of annotations mapped to genomic coordinates. The ability to juxtapose annotations of many types facilitates inquiry-driven data mining. Gene predictions, mRNA alignments, epigenomic data from the ENCODE project, conservation scores from vertebrate whole-genome alignments and variation data may be viewed at any scale from a single base to an entire chromosome. The Browser also includes many other widely used tools, including BLAT, which is useful for alignments from high-throughput sequencing experiments. Private data uploaded as Custom Tracks and Data Hubs in many formats may be displayed alongside the rich compendium of precomputed data in the UCSC database. The Table Browser is a full-featured graphical interface, which allows querying, filtering and intersection of data tables. The Saved Session feature allows users to store and share customized views, enhancing the utility of the system for organizing multiple trains of thought. Binary Alignment/Map (BAM), Variant Call Format and the Personal Genome Single Nucleotide Polymorphisms (SNPs) data formats are useful for visualizing a large sequencing experiment (whole-genome or whole-exome), where the differences between the data set and the reference assembly may be displayed graphically. Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting. PMID:22908213

  9. The UCSC genome browser and associated tools

    PubMed Central

    Haussler, David; Kent, W. James

    2013-01-01

    The UCSC Genome Browser (http://genome.ucsc.edu) is a graphical viewer for genomic data now in its 13th year. Since the early days of the Human Genome Project, it has presented an integrated view of genomic data of many kinds. Now home to assemblies for 58 organisms, the Browser presents visualization of annotations mapped to genomic coordinates. The ability to juxtapose annotations of many types facilitates inquiry-driven data mining. Gene predictions, mRNA alignments, epigenomic data from the ENCODE project, conservation scores from vertebrate whole-genome alignments and variation data may be viewed at any scale from a single base to an entire chromosome. The Browser also includes many other widely used tools, including BLAT, which is useful for alignments from high-throughput sequencing experiments. Private data uploaded as Custom Tracks and Data Hubs in many formats may be displayed alongside the rich compendium of precomputed data in the UCSC database. The Table Browser is a full-featured graphical interface, which allows querying, filtering and intersection of data tables. The Saved Session feature allows users to store and share customized views, enhancing the utility of the system for organizing multiple trains of thought. Binary Alignment/Map (BAM), Variant Call Format and the Personal Genome Single Nucleotide Polymorphisms (SNPs) data formats are useful for visualizing a large sequencing experiment (whole-genome or whole-exome), where the differences between the data set and the reference assembly may be displayed graphically. Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting. PMID:22908213

  10. VISTA - computational tools for comparative genomics

    SciTech Connect

    Frazer, Kelly A.; Pachter, Lior; Poliakov, Alexander; Rubin,Edward M.; Dubchak, Inna

    2004-01-01

    Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.lbl.gov/VISTA/ was launched in the summer of 2000 and was designed to align long genomic sequences and visualize these alignments with associated functional annotations. Currently the VISTA site includes multiple comparative genomics tools and provides users with rich capabilities to browse pre-computed whole-genome alignments of large vertebrate genomes and other groups of organisms with VISTA Browser, submit their own sequences of interest to several VISTA servers for various types of comparative analysis, and obtain detailed comparative analysis results for a set of cardiovascular genes. We illustrate capabilities of the VISTA site by the analysis of a 180 kilobase (kb) interval on human chromosome 5 that encodes for the kinesin family member3A (KIF3A) protein.

  11. VISTA: computational tools for comparative genomics.

    PubMed

    Frazer, Kelly A; Pachter, Lior; Poliakov, Alexander; Rubin, Edward M; Dubchak, Inna

    2004-07-01

    Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here, we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.lbl.gov/vista/ was launched in the summer of 2000 and was designed to align long genomic sequences and visualize these alignments with associated functional annotations. Currently the VISTA site includes multiple comparative genomics tools and provides users with rich capabilities to browse pre-computed whole-genome alignments of large vertebrate genomes and other groups of organisms with VISTA Browser, to submit their own sequences of interest to several VISTA servers for various types of comparative analysis and to obtain detailed comparative analysis results for a set of cardiovascular genes. We illustrate capabilities of the VISTA site by the analysis of a 180 kb interval on human chromosome 5 that encodes for the kinesin family member 3A (KIF3A) protein.

  12. Bioinformatics tools for analysing viral genomic data.

    PubMed

    Orton, R J; Gu, Q; Hughes, J; Maabar, M; Modha, S; Vattipally, S B; Wilkie, G S; Davison, A J

    2016-04-01

    The field of viral genomics and bioinformatics is experiencing a strong resurgence due to high-throughput sequencing (HTS) technology, which enables the rapid and cost-effective sequencing and subsequent assembly of large numbers of viral genomes. In addition, the unprecedented power of HTS technologies has enabled the analysis of intra-host viral diversity and quasispecies dynamics in relation to important biological questions on viral transmission, vaccine resistance and host jumping. HTS also enables the rapid identification of both known and potentially new viruses from field and clinical samples, thus adding new tools to the fields of viral discovery and metagenomics. Bioinformatics has been central to the rise of HTS applications because new algorithms and software tools are continually needed to process and analyse the large, complex datasets generated in this rapidly evolving area. In this paper, the authors give a brief overview of the main bioinformatics tools available for viral genomic research, with a particular emphasis on HTS technologies and their main applications. They summarise the major steps in various HTS analyses, starting with quality control of raw reads and encompassing activities ranging from consensus and de novo genome assembly to variant calling and metagenomics, as well as RNA sequencing.

  13. GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.

    PubMed

    Gremme, Gordon; Steinbiss, Sascha; Kurtz, Stefan

    2013-01-01

    Genome annotations are often published as plain text files describing genomic features and their subcomponents by an implicit annotation graph. In this paper, we present the GenomeTools, a convenient and efficient software library and associated software tools for developing bioinformatics software intended to create, process or convert annotation graphs. The GenomeTools strictly follow the annotation graph approach, offering a unified graph-based representation. This gives the developer intuitive and immediate access to genomic features and tools for their manipulation. To process large annotation sets with low memory overhead, we have designed and implemented an efficient pull-based approach for sequential processing of annotations. This allows to handle even the largest annotation sets, such as a complete catalogue of human variations. Our object-oriented C-based software library enables a developer to conveniently implement their own functionality on annotation graphs and to integrate it into larger workflows, simultaneously accessing compressed sequence data if required. The careful C implementation of the GenomeTools does not only ensure a light-weight memory footprint while allowing full sequential as well as random access to the annotation graph, but also facilitates the creation of bindings to a variety of script programming languages (like Python and Ruby) sharing the same interface. PMID:24091398

  14. GenomePeek—an online tool for prokaryotic genome and metagenome analysis

    DOE PAGES

    McNair, Katelyn; Edwards, Robert A.

    2015-06-16

    As increases in prokaryotic sequencing take place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping errormore » rates low, as well as offering unique data visualization options.« less

  15. GenomePeek—an online tool for prokaryotic genome and metagenome analysis

    SciTech Connect

    McNair, Katelyn; Edwards, Robert A.

    2015-06-16

    As increases in prokaryotic sequencing take place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.

  16. Genephony: a knowledge management tool for genome-wide research

    PubMed Central

    Nuzzo, Angelo; Riva, Alberto

    2009-01-01

    Background One of the consequences of the rapid and widespread adoption of high-throughput experimental technologies is an exponential increase of the amount of data produced by genome-wide experiments. Researchers increasingly need to handle very large volumes of heterogeneous data, including both the data generated by their own experiments and the data retrieved from publicly available repositories of genomic knowledge. Integration, exploration, manipulation and interpretation of data and information therefore need to become as automated as possible, since their scale and breadth are, in general, beyond the limits of what individual researchers and the basic data management tools in normal use can handle. This paper describes Genephony, a tool we are developing to address these challenges. Results We describe how Genephony can be used to manage large datesets of genomic information, integrating them with existing knowledge repositories. We illustrate its functionalities with an example of a complex annotation task, in which a set of SNPs coming from a genotyping experiment is annotated with genes known to be associated to a phenotype of interest. We show how, thanks to the modular architecture of Genephony and its user-friendly interface, this task can be performed in a few simple steps. Conclusion Genephony is an online tool for the manipulation of large datasets of genomic information. It can be used as a browser for genomic data, as a high-throughput annotation tool, and as a knowledge discovery tool. It is designed to be easy to use, flexible and extensible. Its knowledge management engine provides fine-grained control over individual data elements, as well as efficient operations on large datasets. PMID:19728881

  17. Genome editing strategies: potential tools for eradicating HIV-1/AIDS

    PubMed Central

    Khalili, Kamel; Gordon, Jennifer; Cosentino, Laura; Hu, Wenhui

    2015-01-01

    Current therapy for controlling HIV-1 infection and preventing AIDS progression has profoundly decreased viral replication in cells susceptible to HIV-1 infection, but it does not eliminate the low level of viral replication in latently infected cells which contain integrated copies of HIV-1 proviral DNA. There is an urgent need for the development of HIV-1 genome eradication strategies that will lead to a permanent or “sterile” cure of HIV-1/AIDS. In the past few years, novel nuclease-initiated genome editing tools have been developing rapidly, including ZFNs, TALENs, and the CRISPR/Cas9 system. These surgical knives, which can excise any genome, provide a great opportunity to eradicate the HIV-1 genome by targeting highly conserved regions of the HIV-1 long terminal repeats or essential viral genes. Given the time consuming and costly engineering of target-specific ZFNs and TALENs, the RNA-guided endonuclease Cas9 technology has emerged as a simpler and more versatile technology to allow permanent removal of integrated HIV-1 proviral DNA in eukaryotic cells, and hopefully animal models or human patients. The major unmet challenges of this approach at present include inefficient nuclease gene delivery, potential off-target cleavage, and cell-specific genome targeting. Nanoparticle or lentivirus-mediated delivery of next generation Cas9 technologies including nickase or RNA-guided FokI nuclease (RFN) will further improve the potential for genome editing to become a promising approach for curing HIV-1/AIDS. PMID:25716921

  18. Healthcare, molecular tools and applied genome research.

    PubMed

    Groves, M

    2000-11-01

    Biotechnology 2000 offered a rare opportunity for scientists from academia and industry to present and discuss data in fields as diverse as environmental biotechnology and applied genome research. The healthcare section of the meeting encompassed a number of gene therapy delivery systems that are successfully treating genetic disorders. Beta-thalassemia is being corrected in mice by continous erythropoeitin delivery from engineered muscles cells, and from naked DNA electrotransfer into muscles, as described by Dr JM Heard (Institut Pasteur, Paris, France). Dr Reszka (Max-Delbrueck-Centrum fuer Molekulare Medizin, Berlin, Germany), meanwhile, described a treatment for liver metastasis in the form of a drug carrier emolization system, DCES (Max-Delbrueck-Centrum fuer Molekulare Medizin), composed of surface modified liposomes and a substance for chemo-occlusion, which drastically reduces the blood supply to the tumor and promotes apoptosis, necrosis and antiangiogenesis. In the molecular tools section, Willem Stemmer (Maxygen Inc, Redwood City, CA, USA) gave an insight into the importance that techniques, such as molecular breeding (DNA shuffling), have in the evolution of molecules with improved function, over a range of fields including pharmaceuticals, vaccines, agriculture and chemicals. Technologies, such as ribosome display, which can incorporate the evolution and the specific enrichment of proteins/peptides in cycles of selection, could play an enormous role in the production of novel therapeutics and diagnostics in future years, as explained by Andreas Plückthun (Institute of Biochemistry, University of Zurich, Switzerland). Applied genome research offered technologies, such as the 'in vitro expression cloning', described by Dr Zwick (Promega Corp, Madison, WI, USA), are providing a functional analysis for the overwhelming flow of data emerging from high-throughput sequencing of genomes and from high-density gene expression microarrays (DNA chips). The

  19. Unraveling the 3D genome: genomics tools for multi-scale exploration

    PubMed Central

    Risca, Viviana I.; Greenleaf, William J.

    2015-01-01

    A decade of rapid method development has begun to yield exciting insights into the three-dimensional architecture of the metazoan genome and the roles it may play in regulating transcription. We review here core methods and new tools in the modern genomicist’s toolbox at three length scales, ranging from single base pair to megabase scale chromosomal domains, and discuss the emerging picture of the 3D genome that these tools have revealed. Blind spots remain, especially at intermediate length scales spanning a few nucleosomes, but thanks in part to new technologies that permit targeted alteration of chromatin states and time-resolved studies, the next decade holds great promise for hypothesis-driven research into the mechanisms that drive genome architecture and transcriptional regulation. PMID:25887733

  20. A web-based genomic sequence database for the Streptomycetaceae: a tool for systematics and genome mining

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ARS Microbial Genome Sequence Database (http://199.133.98.43), a web-based database server, was established utilizing the BIGSdb (Bacterial Isolate Genomics Sequence Database) software package, developed at Oxford University, as a tool to manage multi-locus sequence data for the family Streptomy...

  1. GAViT: Genome Assembly Visualization Tool for Short Read Data

    SciTech Connect

    Syed, Aijazuddin; Shapiro, Harris; Tu, Hank; Pangilinan, Jasmyn; Trong, Stephan

    2008-03-14

    It is a challenging job for genome analysts to accurately debug, troubleshoot, and validate genome assembly results. Genome analysts rely on visualization tools to help validate and troubleshoot assembly results, including such problems as mis-assemblies, low-quality regions, and repeats. Short read data adds further complexity and makes it extremely challenging for the visualization tools to scale and to view all needed assembly information. As a result, there is a need for a visualization tool that can scale to display assembly data from the new sequencing technologies. We present Genome Assembly Visualization Tool (GAViT), a highly scalable and interactive assembly visualization tool developed at the DOE Joint Genome Institute (JGI).

  2. Cytoscape: the network visualization tool for GenomeSpace workflows.

    PubMed

    Demchak, Barry; Hull, Tim; Reich, Michael; Liefeld, Ted; Smoot, Michael; Ideker, Trey; Mesirov, Jill P

    2014-01-01

    Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013. PMID:25165537

  3. CucCAP - Developing genomic resources for the cucurbit community

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The U.S. cucurbit community has initiated a USDA-SCRI funded cucurbit genomics project, CucCAP: Leveraging applied genomics to increase disease resistance in cucurbit crops. Our primary objectives are: develop genomic and bioinformatic breeding tool kits for accelerated crop improvement across the...

  4. Endonucleases: new tools to edit the mouse genome.

    PubMed

    Wijshake, Tobias; Baker, Darren J; van de Sluis, Bart

    2014-10-01

    Mouse transgenesis has been instrumental in determining the function of genes in the pathophysiology of human diseases and modification of genes by homologous recombination in mouse embryonic stem cells remains a widely used technology. However, this approach harbors a number of disadvantages, as it is time-consuming and quite laborious. Over the last decade a number of new genome editing technologies have been developed, including zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas). These systems are characterized by a designed DNA binding protein or RNA sequence fused or co-expressed with a non-specific endonuclease, respectively. The engineered DNA binding protein or RNA sequence guides the nuclease to a specific target sequence in the genome to induce a double strand break. The subsequent activation of the DNA repair machinery then enables the introduction of gene modifications at the target site, such as gene disruption, correction or insertion. Nuclease-mediated genome editing has numerous advantages over conventional gene targeting, including increased efficiency in gene editing, reduced generation time of mutant mice, and the ability to mutagenize multiple genes simultaneously. Although nuclease-driven modifications in the genome are a powerful tool to generate mutant mice, there are concerns about off-target cleavage, especially when using the CRISPR/Cas system. Here, we describe the basic principles of these new strategies in mouse genome manipulation, their inherent advantages, and their potential disadvantages compared to current technologies used to study gene function in mouse models. This article is part of a Special Issue entitled: From Genome to Function.

  5. Genomic Tools in Pea Breeding Programs: Status and Perspectives

    PubMed Central

    Tayeh, Nadim; Aubert, Grégoire; Pilet-Nayel, Marie-Laure; Lejeune-Hénaut, Isabelle; Warkentin, Thomas D.; Burstin, Judith

    2015-01-01

    Pea (Pisum sativum L.) is an annual cool-season legume and one of the oldest domesticated crops. Dry pea seeds contain 22–25% protein, complex starch and fiber constituents, and a rich array of vitamins, minerals, and phytochemicals which make them a valuable source for human consumption and livestock feed. Dry pea ranks third to common bean and chickpea as the most widely grown pulse in the world with more than 11 million tons produced in 2013. Pea breeding has achieved great success since the time of Mendel's experiments in the mid-1800s. However, several traits still require significant improvement for better yield stability in a larger growing area. Key breeding objectives in pea include improving biotic and abiotic stress resistance and enhancing yield components and seed quality. Taking advantage of the diversity present in the pea genepool, many mapping populations have been constructed in the last decades and efforts have been deployed to identify loci involved in the control of target traits and further introgress them into elite breeding materials. Pea now benefits from next-generation sequencing and high-throughput genotyping technologies that are paving the way for genome-wide association studies and genomic selection approaches. This review covers the significant development and deployment of genomic tools for pea breeding in recent years. Future prospects are discussed especially in light of current progress toward deciphering the pea genome. PMID:26640470

  6. Elucidating the molecular responses of apple rootstock resistant to ARD pathogens: challenges and opportunities for development of genomics-assisted breeding tools

    PubMed Central

    Zhu, Yanmin; Fazio, Gennaro; Mazzola, Mark

    2014-01-01

    may lead to different outcomes between rootstocks in response to invasion by necrotrophic pathogens. Elucidation of host defense mechanisms is critical in developing molecular tools for genomics-assisted breeding of resistant apple rootstocks. Due to their perennial nature, use of resistant rootstocks as a component for disease management might offer a durable and cost-effective benefit to tree performance than the standard practice of soil fumigation for control of ARD. PMID:26504547

  7. CRISPR/Cas9: an advanced tool for editing plant genomes.

    PubMed

    Samanta, Milan Kumar; Dey, Avishek; Gayen, Srimonta

    2016-10-01

    To meet current challenges in agriculture, genome editing using sequence-specific nucleases (SSNs) is a powerful tool for basic and applied plant biology research. Here, we describe the principle and application of available genome editing tools, including zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeat associated CRISPR/Cas9 system. Among these SSNs, CRISPR/Cas9 is the most recently characterized and rapidly developing genome editing technology, and has been successfully utilized in a wide variety of organisms. This review specifically illustrates the power of CRISPR/Cas9 as a tool for plant genome engineering, and describes the strengths and weaknesses of the CRISPR/Cas9 technology compared to two well-established genome editing tools, ZFNs and TALENs. PMID:27012546

  8. Application of Genomics Tools to Animal Breeding

    PubMed Central

    Dekkers, Jack C.M.

    2012-01-01

    The main goal in animal breeding is to select individuals that have high breeding values for traits of interest as parents to produce the next generation and to do so as quickly as possible. To date, most programs rely on statistical analysis of large data bases with phenotypes on breeding populations by linear mixed model methodology to estimate breeding values on selection candidates. However, there is a long history of research on the use of genetic markers to identify quantitative trait loci and their use in marker-assisted selection but with limited implementation in practical breeding programs. The advent of high-density SNP genotyping, combined with novel statistical methods for the use of this data to estimate breeding values, has resulted in the recent extensive application of genomic or whole-genome selection in dairy cattle and research to implement genomic selection in other livestock species is underway. The high-density SNP data also provides opportunities to detect QTL and to encover the genetic architecture of quantitative traits, in terms of the distribution of the size of genetic effects that contribute to trait differences in a population. Results show that this genetic architecture differs between traits but that for most traits, over 50% of the genetic variation resides in genomic regions with small effects that are of the order of magnitude that is expected under a highly polygenic model of inheritance. PMID:23115522

  9. Fine-Tuning Next-Generation Genome Editing Tools.

    PubMed

    Kanchiswamy, Chidananda Nagamangala; Maffei, Massimo; Malnoy, Mickael; Velasco, Riccardo; Kim, Jin-Soo

    2016-07-01

    The availability of genome sequences of numerous organisms and the revolution brought about by genome editing tools (e.g., ZFNs, TALENs, and CRISPR/Cas9 or RGENs) has provided a breakthrough in introducing targeted genetic changes both to explore emergent phenotypes and to introduce new functionalities. However, the wider application of these tools in biology, agriculture, medicine, and biotechnology is limited by off-target mutation effects. In this review, we compare available methods for detecting, measuring, and analyzing off-target mutations. Furthermore, we particularly focus on CRISPR/Cas9 regarding various methods, tweaks, and software tools available to nullify off-target effects. PMID:27167723

  10. Groundnut improvement: use of genetic and genomic tools

    PubMed Central

    Janila, Pasupuleti; Nigam, S. N.; Pandey, Manish K.; Nagesh, P.; Varshney, Rajeev K.

    2013-01-01

    Groundnut (Arachis hypogaea L.), a self-pollinated legume is an important crop cultivated in 24 million ha world over for extraction of edible oil and food uses. The kernels are rich in oil (48–50%) and protein (25–28%), and are source of several vitamins, minerals, antioxidants, biologically active polyphenols, flavonoids, and isoflavones. Improved varieties of groundnut with high yield potential were developed and released for cultivation world over. The improved varieties belong to different maturity durations and possess resistance to diseases, tolerance to drought, enhanced oil content, and improved quality traits for food uses. Conventional breeding procedures along with the tools for phenotyping were largely used in groundnut improvement programs. Mutations were used to induce variability and wide hybridization was attempted to tap variability from wild species. Low genetic variability has been a bottleneck for groundnut improvement. The vast potential of wild species, reservoir of new alleles remains under-utilized. Development of linkage maps of groundnut during the last decade was followed by identification of markers and quantitative trait loci for the target traits. Consequently, the last decade has witnessed the deployment of molecular breeding approaches to complement the ongoing groundnut improvement programs in USA, China, India, and Japan. The other potential advantages of molecular breeding are the feasibility to target multiple traits for improvement and provide tools to tap new alleles from wild species. The first groundnut variety developed through marker-assisted back-crossing is a root-knot nematode-resistant variety, NemaTAM in USA. The uptake of molecular breeding approaches in groundnut improvement programs by NARS partners in India and many African countries is slow or needs to be initiated in part due to inadequate infrastructure, high genotyping costs, and human capacities. Availability of draft genome sequence for diploid (AA and

  11. Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.

    PubMed

    Karp, Peter D; Latendresse, Mario; Paley, Suzanne M; Krummenacker, Markus; Ong, Quang D; Billington, Richard; Kothari, Anamika; Weaver, Daniel; Lee, Thomas; Subhraveti, Pallavi; Spaulding, Aaron; Fulcher, Carol; Keseler, Ingrid M; Caspi, Ron

    2016-09-01

    Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms.

  12. Development of genome viewer (Web Omics Viewer) for managing databases of cucumber genome

    NASA Astrophysics Data System (ADS)

    Wojcieszek, M.; RóŻ, P.; Pawełkowicz, M.; Nowak, R.; Przybecki, Z.

    Cucumber is an important plant in horticulture and science world. Sequencing projects of C. sativus genome enable new methodological aproaches in further investigation of this species. Accessibility is crucial to fully exploit obtained information about detail structure of genes, markers and other characteristic features such contigs, scaffolds and chromosomes. Genome viewer is one of tools providing plain and easy way for presenting genome data for users and for databases administration. Gbrowse - the main viewer has several very useful features but lacks in managing simplicity. Our group developed new genome browser Web Omics Viewer (WOV), keeping functionality but improving utilization and accessibility to cucumber genome data.

  13. The Plant Ontology: A Tool for Plant Genomics.

    PubMed

    Cooper, Laurel; Jaiswal, Pankaj

    2016-01-01

    The use of controlled, structured vocabularies (ontologies) has become a critical tool for scientists in the post-genomic era of massive datasets. Adoption and integration of common vocabularies and annotation practices enables cross-species comparative analyses and increases data sharing and reusability. The Plant Ontology (PO; http://www.plantontology.org/ ) describes plant anatomy, morphology, and the stages of plant development, and offers a database of plant genomics annotations associated to the PO terms. The scope of the PO has grown from its original design covering only rice, maize, and Arabidopsis, and now includes terms to describe all green plants from angiosperms to green algae.This chapter introduces how the PO and other related ontologies are constructed and organized, including languages and software used for ontology development, and provides an overview of the key features. Detailed instructions illustrate how to search and browse the PO database and access the associated annotation data. Users are encouraged to provide input on the ontology through the online term request form and contribute datasets for integration in the PO database.

  14. GREAT: a web portal for Genome Regulatory Architecture Tools.

    PubMed

    Bouyioukos, Costas; Bucchini, François; Elati, Mohamed; Képès, François

    2016-07-01

    GREAT (Genome REgulatory Architecture Tools) is a novel web portal for tools designed to generate user-friendly and biologically useful analysis of genome architecture and regulation. The online tools of GREAT are freely accessible and compatible with essentially any operating system which runs a modern browser. GREAT is based on the analysis of genome layout -defined as the respective positioning of co-functional genes- and its relation with chromosome architecture and gene expression. GREAT tools allow users to systematically detect regular patterns along co-functional genomic features in an automatic way consisting of three individual steps and respective interactive visualizations. In addition to the complete analysis of regularities, GREAT tools enable the use of periodicity and position information for improving the prediction of transcription factor binding sites using a multi-view machine learning approach. The outcome of this integrative approach features a multivariate analysis of the interplay between the location of a gene and its regulatory sequence. GREAT results are plotted in web interactive graphs and are available for download either as individual plots, self-contained interactive pages or as machine readable tables for downstream analysis. The GREAT portal can be reached at the following URL https://absynth.issb.genopole.fr/GREAT and each individual GREAT tool is available for downloading.

  15. GREAT: a web portal for Genome Regulatory Architecture Tools

    PubMed Central

    Bouyioukos, Costas; Bucchini, François; Elati, Mohamed; Képès, François

    2016-01-01

    GREAT (Genome REgulatory Architecture Tools) is a novel web portal for tools designed to generate user-friendly and biologically useful analysis of genome architecture and regulation. The online tools of GREAT are freely accessible and compatible with essentially any operating system which runs a modern browser. GREAT is based on the analysis of genome layout -defined as the respective positioning of co-functional genes- and its relation with chromosome architecture and gene expression. GREAT tools allow users to systematically detect regular patterns along co-functional genomic features in an automatic way consisting of three individual steps and respective interactive visualizations. In addition to the complete analysis of regularities, GREAT tools enable the use of periodicity and position information for improving the prediction of transcription factor binding sites using a multi-view machine learning approach. The outcome of this integrative approach features a multivariate analysis of the interplay between the location of a gene and its regulatory sequence. GREAT results are plotted in web interactive graphs and are available for download either as individual plots, self-contained interactive pages or as machine readable tables for downstream analysis. The GREAT portal can be reached at the following URL https://absynth.issb.genopole.fr/GREAT and each individual GREAT tool is available for downloading. PMID:27151196

  16. GREAT: a web portal for Genome Regulatory Architecture Tools.

    PubMed

    Bouyioukos, Costas; Bucchini, François; Elati, Mohamed; Képès, François

    2016-07-01

    GREAT (Genome REgulatory Architecture Tools) is a novel web portal for tools designed to generate user-friendly and biologically useful analysis of genome architecture and regulation. The online tools of GREAT are freely accessible and compatible with essentially any operating system which runs a modern browser. GREAT is based on the analysis of genome layout -defined as the respective positioning of co-functional genes- and its relation with chromosome architecture and gene expression. GREAT tools allow users to systematically detect regular patterns along co-functional genomic features in an automatic way consisting of three individual steps and respective interactive visualizations. In addition to the complete analysis of regularities, GREAT tools enable the use of periodicity and position information for improving the prediction of transcription factor binding sites using a multi-view machine learning approach. The outcome of this integrative approach features a multivariate analysis of the interplay between the location of a gene and its regulatory sequence. GREAT results are plotted in web interactive graphs and are available for download either as individual plots, self-contained interactive pages or as machine readable tables for downstream analysis. The GREAT portal can be reached at the following URL https://absynth.issb.genopole.fr/GREAT and each individual GREAT tool is available for downloading. PMID:27151196

  17. Improved criteria and comparative genomics tool provide new insights into grass paleogenomics.

    PubMed

    Salse, Jerome; Abrouk, Michael; Murat, Florent; Quraishi, Umar Masood; Feuillet, Catherine

    2009-11-01

    In the past decade, a number of bioinformatics tools have been developed to perform comparative genomics studies in plants and animals. However, most of the publicly available and user friendly tools lack common standards for the identification of robust orthologous relationships between genomes leading non-specialists to often over interpret the results of large scale comparative sequence analyses. Recently, we have established a number of improved parameters and tools to define significant relationships between genomes as a basis to develop paleogenomics studies in grasses. Here, we describe our approaches and propose the development of community-based standards that can be used in comparative genomic studies to (i) identify robust sets of orthologous gene pairs, (ii) derive complete sets of chromosome to chromosome relationships within and between genomes and (iii) model common paleo-ancestor genome structures. The rice and sorghum genome sequences are used to exemplify step-by-step a methodology that should allow users to perform accurate comparative genome analyses in their favourite species. Finally, we describe two applications for accurate gene annotation and synteny-based cloning of agronomically important traits.

  18. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

    PubMed Central

    Thorvaldsdottir, Helga; Liefeld, Ted; Ocana, Marco; Borges-Rivera, Diego; Pochet, Nathalie; Robinson, James T.; Demchak, Barry; Hull, Tim; Ben-Artzi, Gil; Blankenberg, Daniel; Barber, Galt P.; Lee, Brian T.; Kuhn, Robert M.; Nekrutenko, Anton; Segal, Eran; Ideker, Trey; Reich, Michael; Regev, Aviv; Chang, Howard Y.; Mesirov, Jill P.

    2015-01-01

    Integrative analysis of multiple data types to address complex biomedical questions requires the use of multiple software tools in concert and remains an enormous challenge for most of the biomedical research community. Here we introduce GenomeSpace (http://www.genomespace.org), a cloud-based, cooperative community resource. Seeded as a collaboration of six of the most popular genomics analysis tools, GenomeSpace now supports the streamlined interaction of 20 bioinformatics tools and data resources. To facilitate the ability of non-programming users’ to leverage GenomeSpace in integrative analysis, it offers a growing set of ‘recipes’, short workflows involving a few tools and steps to guide investigators through high utility analysis tasks. PMID:26780094

  19. Public data and open source tools for multi-assay genomic investigation of disease

    PubMed Central

    Kannan, Lavanya; Ramos, Marcel; Re, Angela; El-Hachem, Nehme; Safikhani, Zhaleh; Gendoo, Deena M.A.; Davis, Sean; Gomez-Cabrero, David; Castelo, Robert; Hansen, Kasper D.; Carey, Vincent J.; Morgan, Martin; Culhane, Aedín C.; Haibe-Kains, Benjamin

    2016-01-01

    Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods. PMID:26463000

  20. Turbine Aerodynamics Design Tool Development

    NASA Technical Reports Server (NTRS)

    Huber, Frank W.; Turner, James E. (Technical Monitor)

    2001-01-01

    This paper presents the Marshal Space Flight Center Fluids Workshop on Turbine Aerodynamic design tool development. The topics include: (1) Meanline Design/Off-design Analysis; and (2) Airfoil Contour Generation and Analysis. This paper is in viewgraph form.

  1. Genome Calligrapher: A Web Tool for Refactoring Bacterial Genome Sequences for de Novo DNA Synthesis.

    PubMed

    Christen, Matthias; Deutsch, Samuel; Christen, Beat

    2015-08-21

    Recent advances in synthetic biology have resulted in an increasing demand for the de novo synthesis of large-scale DNA constructs. Any process improvement that enables fast and cost-effective streamlining of digitized genetic information into fabricable DNA sequences holds great promise to study, mine, and engineer genomes. Here, we present Genome Calligrapher, a computer-aided design web tool intended for whole genome refactoring of bacterial chromosomes for de novo DNA synthesis. By applying a neutral recoding algorithm, Genome Calligrapher optimizes GC content and removes obstructive DNA features known to interfere with the synthesis of double-stranded DNA and the higher order assembly into large DNA constructs. Subsequent bioinformatics analysis revealed that synthesis constraints are prevalent among bacterial genomes. However, a low level of codon replacement is sufficient for refactoring bacterial genomes into easy-to-synthesize DNA sequences. To test the algorithm, 168 kb of synthetic DNA comprising approximately 20 percent of the synthetic essential genome of the cell-cycle bacterium Caulobacter crescentus was streamlined and then ordered from a commercial supplier of low-cost de novo DNA synthesis. The successful assembly into eight 20 kb segments indicates that Genome Calligrapher algorithm can be efficiently used to refactor difficult-to-synthesize DNA. Genome Calligrapher is broadly applicable to recode biosynthetic pathways, DNA sequences, and whole bacterial genomes, thus offering new opportunities to use synthetic biology tools to explore the functionality of microbial diversity. The Genome Calligrapher web tool can be accessed at https://christenlab.ethz.ch/GenomeCalligrapher  .

  2. Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects.

    PubMed

    Pandey, Manish K; Roorkiwal, Manish; Singh, Vikas K; Ramalingam, Abirami; Kudapa, Himabindu; Thudi, Mahendar; Chitikineni, Anu; Rathore, Abhishek; Varshney, Rajeev K

    2016-01-01

    Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gains is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last 5 years. The availability of the draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale genomic resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seems appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries. PMID:27199998

  3. Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects

    PubMed Central

    Pandey, Manish K.; Roorkiwal, Manish; Singh, Vikas K.; Ramalingam, Abirami; Kudapa, Himabindu; Thudi, Mahendar; Chitikineni, Anu; Rathore, Abhishek; Varshney, Rajeev K.

    2016-01-01

    Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gains is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last 5 years. The availability of the draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale genomic resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seems appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries. PMID:27199998

  4. MaGnET: Malaria Genome Exploration Tool

    PubMed Central

    Sharman, Joanna L.; Gerloff, Dietlind L.

    2013-01-01

    Summary: The Malaria Genome Exploration Tool (MaGnET) is a software tool enabling intuitive ‘exploration-style’ visualization of functional genomics data relating to the malaria parasite, Plasmodium falciparum. MaGnET provides innovative integrated graphic displays for different datasets, including genomic location of genes, mRNA expression data, protein–protein interactions and more. Any selection of genes to explore made by the user is easily carried over between the different viewers for different datasets, and can be changed interactively at any point (without returning to a search). Availability and Implementation: Free online use (Java Web Start) or download (Java application archive and MySQL database; requires local MySQL installation) at http://malariagenomeexplorer.org Contact: joanna.sharman@ed.ac.uk or dgerloff@ffame.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23894142

  5. Developing ICALL Tools Using GATE

    ERIC Educational Resources Information Center

    Wood, Peter

    2008-01-01

    This article discusses the use of the General Architecture for Text Engineering (GATE) as a tool for the development of ICALL and NLP applications. It outlines a paradigm shift in software development, which is mainly influenced by projects such as the Free Software Foundation. It looks at standards that have been proposed to facilitate the…

  6. Genomic Tools in Cowpea Breeding Programs: Status and Perspectives.

    PubMed

    Boukar, Ousmane; Fatokun, Christian A; Huynh, Bao-Lam; Roberts, Philip A; Close, Timothy J

    2016-01-01

    Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA). It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds, and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids, and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP) genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS)-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS), promises an increase in the number of improved

  7. Genomic Tools in Cowpea Breeding Programs: Status and Perspectives

    PubMed Central

    Boukar, Ousmane; Fatokun, Christian A.; Huynh, Bao-Lam; Roberts, Philip A.; Close, Timothy J.

    2016-01-01

    Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA). It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds, and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids, and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP) genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS)-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS), promises an increase in the number of improved

  8. Genomic Tools in Cowpea Breeding Programs: Status and Perspectives.

    PubMed

    Boukar, Ousmane; Fatokun, Christian A; Huynh, Bao-Lam; Roberts, Philip A; Close, Timothy J

    2016-01-01

    Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA). It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds, and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids, and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP) genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS)-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS), promises an increase in the number of improved

  9. Emerging Tools for Synthetic Genome Design

    PubMed Central

    Lee, Bo-Rahm; Cho, Suhyung; Song, Yoseb; Kim, Sun Chang; Cho, Byung-Kwan

    2013-01-01

    Synthetic biology is an emerging discipline for designing and synthesizing predictable, measurable, controllable, and transformable biological systems. These newly designed biological systems have great potential for the development of cheaper drugs, green fuels, biodegradable plastics, and targeted cancer therapies over the coming years. Fortunately, our ability to quickly and accurately engineer biological systems that behave predictably has been dramatically expanded by significant advances in DNA-sequencing, DNA-synthesis, and DNA-editing technologies. Here, we review emerging technologies and methodologies in the field of building designed biological systems, and we discuss their future perspectives. PMID:23708771

  10. Employability Skills Assessment Tool Development

    ERIC Educational Resources Information Center

    Rasul, Mohamad Sattar; Rauf, Rose Amnah Abd; Mansor, Azlin Norhaini; Puvanasvaran, A. P.

    2012-01-01

    Research nationally and internationally found that technical graduates are lacking in employability skills. As employability skills are crucial in outcome-based education, the main goal of this research is to develop an Employability Skill Assessment Tool to help students and lecturers produce competent graduates in employability skills needed by…

  11. BEDTools: the Swiss-army tool for genome feature analysis

    PubMed Central

    Quinlan, Aaron R.

    2014-01-01

    Technological advances have enabled the use of DNA sequencing as a flexible tool to characterize genetic variation and to measure the activity of diverse cellular phenomena such as gene isoform expression and transcription factor binding. Extracting biological insight from the experiments enabled by these advances demands the analysis of large, multi-dimensional datasets. This unit describes the use of the BEDTools toolkit for the exploration of high-throughput genomics datasets. I present several protocols for common genomic analyses and demonstrate how simple BEDTools operations may be combined to create bespoke pipelines addressing complex questions. PMID:25199790

  12. Databases and web tools for cancer genomics study.

    PubMed

    Yang, Yadong; Dong, Xunong; Xie, Bingbing; Ding, Nan; Chen, Juan; Li, Yongjun; Zhang, Qian; Qu, Hongzhu; Fang, Xiangdong

    2015-02-01

    Publicly-accessible resources have promoted the advance of scientific discovery. The era of genomics and big data has brought the need for collaboration and data sharing in order to make effective use of this new knowledge. Here, we describe the web resources for cancer genomics research and rate them on the basis of the diversity of cancer types, sample size, omics data comprehensiveness, and user experience. The resources reviewed include data repository and analysis tools; and we hope such introduction will promote the awareness and facilitate the usage of these resources in the cancer research community. PMID:25707591

  13. Biological database of images and genomes: tools for community annotations linking image and genomic information.

    PubMed

    Oberlin, Andrew T; Jurkovic, Dominika A; Balish, Mitchell F; Friedberg, Iddo

    2013-01-01

    Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype-genotype connection linking the two types of data is lagging behind. While there are many types of software that enable the manipulation and analysis of image data and genomic data as separate entities, there is no framework established for linking the two. We present a generic set of software tools, BioDIG, that allows linking of image data to genomic data. BioDIG tools can be applied to a wide range of research problems that require linking images to genomes. BioDIG features the following: rapid construction of web-based workbenches, community-based annotation, user management and web services. By using BioDIG to create websites, researchers and curators can rapidly annotate a large number of images with genomic information. Here we present the BioDIG software tools that include an image module, a genome module and a user management module. We also introduce a BioDIG-based website, MyDIG, which is being used to annotate images of mycoplasmas. PMID:23550062

  14. Biological Database of Images and Genomes: tools for community annotations linking image and genomic information

    PubMed Central

    Oberlin, Andrew T; Jurkovic, Dominika A; Balish, Mitchell F; Friedberg, Iddo

    2013-01-01

    Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype–genotype connection linking the two types of data is lagging behind. While there are many types of software that enable the manipulation and analysis of image data and genomic data as separate entities, there is no framework established for linking the two. We present a generic set of software tools, BioDIG, that allows linking of image data to genomic data. BioDIG tools can be applied to a wide range of research problems that require linking images to genomes. BioDIG features the following: rapid construction of web-based workbenches, community-based annotation, user management and web services. By using BioDIG to create websites, researchers and curators can rapidly annotate a large number of images with genomic information. Here we present the BioDIG software tools that include an image module, a genome module and a user management module. We also introduce a BioDIG-based website, MyDIG, which is being used to annotate images of mycoplasmas. Database URL: BioDIG website: http://biodig.org BioDIG source code repository: http://github.com/FriedbergLab/BioDIG The MyDIG database: http://mydig.biodig.org/ PMID:23550062

  15. Stacks: an analysis tool set for population genomics

    PubMed Central

    CATCHEN, JULIAN; HOHENLOHE, PAUL A.; BASSHAM, SUSAN; AMORES, ANGEL; CRESKO, WILLIAM A.

    2014-01-01

    Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics. PMID:23701397

  16. Genomic Methylation: a Tool for Typing Helicobacter pylori Isolates▿ †

    PubMed Central

    Vale, Filipa F.; Vítor, Jorge M. B.

    2007-01-01

    The genome sequences of three Helicobacter pylori strains revealed an abundant number of putative restriction and modification (R-M) systems within a small genome (1.60 to 1.67 Mb). Each R-M system includes an endonuclease that cleaves a specific DNA sequence and a DNA methyltransferase that methylates either adenosine or cytosine within the same DNA sequence. These are believed to be a defense mechanism, protecting bacteria from foreign DNA. They have been classified as selfish genetic elements; in some instances it has been shown that they are not easily lost from their host cell. Possibly because of this phenomenon, the H. pylori genome is very rich in R-M systems, with considerable variation in potential recognition sequences. For this reason the protective aspect of the methyltransferase gene has been proposed as a tool for typing H. pylori isolates. We studied the expression of H. pylori methyltransferases by digesting the genomic DNAs of 50 strains with 31 restriction endonucleases. We conclude that methyltransferase diversity is sufficiently high to enable the use of the genomic methylation status as a typing tool. The stability of methyltransferase expression was assessed by comparing the methylation status of genomic DNAs from strains that were isolated either from the same patient at different times or from different stomach locations (antrum and corpus). We found a group of five methyltransferases common to all tested strains. These five may be characteristic of the genetic pool analyzed, and their biological role may be important in the host/bacterium interaction. PMID:17483255

  17. Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels.

    PubMed

    Hall, Miquette; Chattaway, Marie A; Reuter, Sandra; Savin, Cyril; Strauch, Eckhard; Carniel, Elisabeth; Connor, Thomas; Van Damme, Inge; Rajakaruna, Lakshani; Rajendram, Dunstan; Jenkins, Claire; Thomson, Nicholas R; McNally, Alan

    2015-01-01

    The genus Yersinia is a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species. Recently, the phylogenetic and population structure of the entire genus was elucidated through the genome sequence data of 241 strains encompassing every known species in the genus. Here we report the mining of this enormous data set to create a multilocus sequence typing-based scheme that can identify Yersinia strains to the species level to a level of resolution equal to that for whole-genome sequencing. Our assay is designed to be able to accurately subtype the important human-pathogenic species Yersinia enterocolitica to whole-genome resolution levels. We also report the validation of the scheme on 386 strains from reference laboratory collections across Europe. We propose that the scheme is an important molecular typing system to allow accurate and reproducible identification of Yersinia isolates to the species level, a process often inconsistent in nonspecialist laboratories. Additionally, our assay is the most phylogenetically informative typing scheme available for Y. enterocolitica.

  18. Use of Whole-Genus Genome Sequence Data To Develop a Multilocus Sequence Typing Tool That Accurately Identifies Yersinia Isolates to the Species and Subspecies Levels

    PubMed Central

    Hall, Miquette; Chattaway, Marie A.; Reuter, Sandra; Savin, Cyril; Strauch, Eckhard; Carniel, Elisabeth; Connor, Thomas; Van Damme, Inge; Rajakaruna, Lakshani; Rajendram, Dunstan; Jenkins, Claire; Thomson, Nicholas R.

    2014-01-01

    The genus Yersinia is a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species. Recently, the phylogenetic and population structure of the entire genus was elucidated through the genome sequence data of 241 strains encompassing every known species in the genus. Here we report the mining of this enormous data set to create a multilocus sequence typing-based scheme that can identify Yersinia strains to the species level to a level of resolution equal to that for whole-genome sequencing. Our assay is designed to be able to accurately subtype the important human-pathogenic species Yersinia enterocolitica to whole-genome resolution levels. We also report the validation of the scheme on 386 strains from reference laboratory collections across Europe. We propose that the scheme is an important molecular typing system to allow accurate and reproducible identification of Yersinia isolates to the species level, a process often inconsistent in nonspecialist laboratories. Additionally, our assay is the most phylogenetically informative typing scheme available for Y. enterocolitica. PMID:25339391

  19. Tetrahymena as a Unicellular Model Eukaryote: Genetic and Genomic Tools.

    PubMed

    Ruehle, Marisa D; Orias, Eduardo; Pearson, Chad G

    2016-06-01

    Tetrahymena thermophila is a ciliate model organism whose study has led to important discoveries and insights into both conserved and divergent biological processes. In this review, we describe the tools for the use of Tetrahymena as a model eukaryote, including an overview of its life cycle, orientation to its evolutionary roots, and methodological approaches to forward and reverse genetics. Recent genomic tools have expanded Tetrahymena's utility as a genetic model system. With the unique advantages that Tetrahymena provide, we argue that it will continue to be a model organism of choice.

  20. Tetrahymena as a Unicellular Model Eukaryote: Genetic and Genomic Tools.

    PubMed

    Ruehle, Marisa D; Orias, Eduardo; Pearson, Chad G

    2016-06-01

    Tetrahymena thermophila is a ciliate model organism whose study has led to important discoveries and insights into both conserved and divergent biological processes. In this review, we describe the tools for the use of Tetrahymena as a model eukaryote, including an overview of its life cycle, orientation to its evolutionary roots, and methodological approaches to forward and reverse genetics. Recent genomic tools have expanded Tetrahymena's utility as a genetic model system. With the unique advantages that Tetrahymena provide, we argue that it will continue to be a model organism of choice. PMID:27270699

  1. Software tool for the analysis and visualization of whole genome alignments

    2011-08-01

    GenomeVISTA is a tool which performs and displays pairwise and multiple whole genome DNA alignments. The tools provides a graphical user interface by which users can navigate alignments and multiple levels of resolution and get imformation about individual aligned regions. Users can load their own sequences into GenomeVISTA or view pre-computed alignments for genomes in the VISTA database.

  2. Correcting Inconsistencies and Errors in Bacterial Genome Metadata Using an Automated Curation Tool in Excel (AutoCurE).

    PubMed

    Schmedes, Sarah E; King, Jonathan L; Budowle, Bruce

    2015-01-01

    Whole-genome data are invaluable for large-scale comparative genomic studies. Current sequencing technologies have made it feasible to sequence entire bacterial genomes with relative ease and time with a substantially reduced cost per nucleotide, hence cost per genome. More than 3,000 bacterial genomes have been sequenced and are available at the finished status. Publically available genomes can be readily downloaded; however, there are challenges to verify the specific supporting data contained within the download and to identify errors and inconsistencies that may be present within the organizational data content and metadata. AutoCurE, an automated tool for bacterial genome database curation in Excel, was developed to facilitate local database curation of supporting data that accompany downloaded genomes from the National Center for Biotechnology Information. AutoCurE provides an automated approach to curate local genomic databases by flagging inconsistencies or errors by comparing the downloaded supporting data to the genome reports to verify genome name, RefSeq accession numbers, the presence of archaea, BioProject/UIDs, and sequence file descriptions. Flags are generated for nine metadata fields if there are inconsistencies between the downloaded genomes and genomes reports and if erroneous or missing data are evident. AutoCurE is an easy-to-use tool for local database curation for large-scale genome data prior to downstream analyses.

  3. Revolutions in Neuroscience: Tool Development.

    PubMed

    Bickle, John

    2016-01-01

    Thomas Kuhn's famous model of the components and dynamics of scientific revolutions is still dominant to this day across science, philosophy, and history. The guiding philosophical theme of this article is that, concerning actual revolutions in neuroscience over the past 60 years, Kuhn's account is wrong. There have been revolutions, and new ones are brewing, but they do not turn on competing paradigms, anomalies, or the like. Instead, they turn exclusively on the development of new experimental tools. I adopt a metascientific approach and examine in detail the development of two recent neuroscience revolutions: the impact of engineered genetically mutated mammals in the search for causal mechanisms of "higher" cognitive functions; and the more recent impact of optogenetics and designer receptors exclusively activated by designer drugs (DREADDs). The two key metascientific concepts, I derive from these case studies are a revolutionary new tool's motivating problem, and its initial and second-phase hook experiments. These concepts hardly exhaust a detailed metascience of tool development experiments in neuroscience, but they get that project off to a useful start and distinguish the subsequent account of neuroscience revolutions clearly from Kuhn's famous model. I close with a brief remark about the general importance of molecular biology for a current philosophical understanding of science, as comparable to the place physics occupied when Kuhn formulated his famous theory of scientific revolutions. PMID:27013992

  4. The CRISPR/Cas Genome-Editing Tool: Application in Improvement of Crops.

    PubMed

    Khatodia, Surender; Bhatotia, Kirti; Passricha, Nishat; Khurana, S M P; Tuteja, Narendra

    2016-01-01

    The Clustered Regularly Interspaced Short Palindromic Repeats associated Cas9/sgRNA system is a novel targeted genome-editing technique derived from bacterial immune system. It is an inexpensive, easy, most user friendly and rapidly adopted genome editing tool transforming to revolutionary paradigm. This technique enables precise genomic modifications in many different organisms and tissues. Cas9 protein is an RNA guided endonuclease utilized for creating targeted double-stranded breaks with only a short RNA sequence to confer recognition of the target in animals and plants. Development of genetically edited (GE) crops similar to those developed by conventional or mutation breeding using this potential technique makes it a promising and extremely versatile tool for providing sustainable productive agriculture for better feeding of rapidly growing population in a changing climate. The emerging areas of research for the genome editing in plants include interrogating gene function, rewiring the regulatory signaling networks and sgRNA library for high-throughput loss-of-function screening. In this review, we have described the broad applicability of the Cas9 nuclease mediated targeted plant genome editing for development of designer crops. The regulatory uncertainty and social acceptance of plant breeding by Cas9 genome editing have also been described. With this powerful and innovative technique the designer GE non-GM plants could further advance climate resilient and sustainable agriculture in the future and maximizing yield by combating abiotic and biotic stresses. PMID:27148329

  5. The CRISPR/Cas Genome-Editing Tool: Application in Improvement of Crops

    PubMed Central

    Khatodia, Surender; Bhatotia, Kirti; Passricha, Nishat; Khurana, S. M. P.; Tuteja, Narendra

    2016-01-01

    The Clustered Regularly Interspaced Short Palindromic Repeats associated Cas9/sgRNA system is a novel targeted genome-editing technique derived from bacterial immune system. It is an inexpensive, easy, most user friendly and rapidly adopted genome editing tool transforming to revolutionary paradigm. This technique enables precise genomic modifications in many different organisms and tissues. Cas9 protein is an RNA guided endonuclease utilized for creating targeted double-stranded breaks with only a short RNA sequence to confer recognition of the target in animals and plants. Development of genetically edited (GE) crops similar to those developed by conventional or mutation breeding using this potential technique makes it a promising and extremely versatile tool for providing sustainable productive agriculture for better feeding of rapidly growing population in a changing climate. The emerging areas of research for the genome editing in plants include interrogating gene function, rewiring the regulatory signaling networks and sgRNA library for high-throughput loss-of-function screening. In this review, we have described the broad applicability of the Cas9 nuclease mediated targeted plant genome editing for development of designer crops. The regulatory uncertainty and social acceptance of plant breeding by Cas9 genome editing have also been described. With this powerful and innovative technique the designer GE non-GM plants could further advance climate resilient and sustainable agriculture in the future and maximizing yield by combating abiotic and biotic stresses. PMID:27148329

  6. Revolutions in Neuroscience: Tool Development

    PubMed Central

    Bickle, John

    2016-01-01

    Thomas Kuhn’s famous model of the components and dynamics of scientific revolutions is still dominant to this day across science, philosophy, and history. The guiding philosophical theme of this article is that, concerning actual revolutions in neuroscience over the past 60 years, Kuhn’s account is wrong. There have been revolutions, and new ones are brewing, but they do not turn on competing paradigms, anomalies, or the like. Instead, they turn exclusively on the development of new experimental tools. I adopt a metascientific approach and examine in detail the development of two recent neuroscience revolutions: the impact of engineered genetically mutated mammals in the search for causal mechanisms of “higher” cognitive functions; and the more recent impact of optogenetics and designer receptors exclusively activated by designer drugs (DREADDs). The two key metascientific concepts, I derive from these case studies are a revolutionary new tool’s motivating problem, and its initial and second-phase hook experiments. These concepts hardly exhaust a detailed metascience of tool development experiments in neuroscience, but they get that project off to a useful start and distinguish the subsequent account of neuroscience revolutions clearly from Kuhn’s famous model. I close with a brief remark about the general importance of molecular biology for a current philosophical understanding of science, as comparable to the place physics occupied when Kuhn formulated his famous theory of scientific revolutions. PMID:27013992

  7. The SickKids Genome Clinic: developing and evaluating a pediatric model for individualized genomic medicine.

    PubMed

    Bowdin, S C; Hayeems, R Z; Monfared, N; Cohn, R D; Meyn, M S

    2016-01-01

    Our increasing knowledge of how genomic variants affect human health and the falling costs of whole-genome sequencing are driving the development of individualized genomic medicine. This new clinical paradigm uses knowledge of an individual's genomic variants to anticipate, diagnose and manage disease. While individualized genetic medicine offers the promise of transformative change in health care, it forces us to reconsider existing ethical, scientific and clinical paradigms. The potential benefits of pre-symptomatic identification of at-risk individuals, improved diagnostics, individualized therapy, accurate prognosis and avoidance of adverse drug reactions coexist with the potential risks of uninterpretable results, psychological harm, outmoded counseling models and increased health care costs. Here we review the challenges, opportunities and limits of integrating genomic analysis into pediatric clinical practice and describe a model for implementing individualized genomic medicine. Our multidisciplinary team of bioinformaticians, health economists, health services and policy researchers, ethicists, geneticists, genetic counselors and clinicians has designed a 'Genome Clinic' research project that addresses multiple challenges in pediatric genomic medicine--ranging from development of bioinformatics tools for the clinical assessment of genomic variants and the discovery of disease genes to health policy inquiries, assessment of clinical care models, patient preference and the ethics of consent.

  8. Whole genome multilocus sequence typing as an epidemiologic tool for Yersinia pestis.

    PubMed

    Kingry, Luke C; Rowe, Lori A; Respicio-Kingry, Laurel B; Beard, Charles B; Schriefer, Martin E; Petersen, Jeannine M

    2016-04-01

    Human plague is a severe and often fatal zoonotic disease caused by Yersinia pestis. For public health investigations of human cases, nonintensive whole genome molecular typing tools, capable of defining epidemiologic relationships, are advantageous. Whole genome multilocus sequence typing (wgMLST) is a recently developed methodology that simplifies genomic analyses by transforming millions of base pairs of sequence into character data for each gene. We sequenced 13 US Y. pestis isolates with known epidemiologic relationships. Sequences were assembled de novo, and multilocus sequence typing alleles were assigned by comparison against 3979 open reading frames from the reference strain CO92. Allele-based cluster analysis accurately grouped the 13 isolates, as well as 9 publicly available Y. pestis isolates, by their epidemiologic relationships. Our findings indicate wgMLST is a simplified, sensitive, and scalable tool for epidemiologic analysis of Y. pestis strains. PMID:26778487

  9. Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum.

    PubMed

    Grativol, Clícia; Regulski, Michael; Bertalan, Marcelo; McCombie, W Richard; da Silva, Felipe Rodrigues; Zerlotini Neto, Adhemar; Vicentini, Renato; Farinelli, Laurent; Hemerly, Adriana Silva; Martienssen, Robert A; Ferreira, Paulo Cavalcanti Gomes

    2014-07-01

    Many economically important crops have large and complex genomes that hamper their sequencing by standard methods such as whole genome shotgun (WGS). Large tracts of methylated repeats occur in plant genomes that are interspersed by hypomethylated gene-rich regions. Gene-enrichment strategies based on methylation profiles offer an alternative to sequencing repetitive genomes. Here, we have applied methyl filtration with McrBC endonuclease digestion to enrich for euchromatic regions in the sugarcane genome. To verify the efficiency of methylation filtration and the assembly quality of sequences submitted to gene-enrichment strategy, we have compared assemblies using methyl-filtered (MF) and unfiltered (UF) libraries. The use of methy filtration allowed a better assembly by filtering out 35% of the sugarcane genome and by producing 1.5× more scaffolds and 1.7× more assembled Mb in length compared with unfiltered dataset. The coverage of sorghum coding sequences (CDS) by MF scaffolds was at least 36% higher than by the use of UF scaffolds. Using MF technology, we increased by 134× the coverage of gene regions of the monoploid sugarcane genome. The MF reads assembled into scaffolds that covered all genes of the sugarcane bacterial artificial chromosomes (BACs), 97.2% of sugarcane expressed sequence tags (ESTs), 92.7% of sugarcane RNA-seq reads and 98.4% of sorghum protein sequences. Analysis of MF scaffolds from encoded enzymes of the sucrose/starch pathway discovered 291 single-nucleotide polymorphisms (SNPs) in the wild sugarcane species, S. spontaneum and S. officinarum. A large number of microRNA genes was also identified in the MF scaffolds. The information achieved by the MF dataset provides a valuable tool for genomic research in the genus Saccharum and for improvement of sugarcane as a biofuel crop.

  10. Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum.

    PubMed

    Grativol, Clícia; Regulski, Michael; Bertalan, Marcelo; McCombie, W Richard; da Silva, Felipe Rodrigues; Zerlotini Neto, Adhemar; Vicentini, Renato; Farinelli, Laurent; Hemerly, Adriana Silva; Martienssen, Robert A; Ferreira, Paulo Cavalcanti Gomes

    2014-07-01

    Many economically important crops have large and complex genomes that hamper their sequencing by standard methods such as whole genome shotgun (WGS). Large tracts of methylated repeats occur in plant genomes that are interspersed by hypomethylated gene-rich regions. Gene-enrichment strategies based on methylation profiles offer an alternative to sequencing repetitive genomes. Here, we have applied methyl filtration with McrBC endonuclease digestion to enrich for euchromatic regions in the sugarcane genome. To verify the efficiency of methylation filtration and the assembly quality of sequences submitted to gene-enrichment strategy, we have compared assemblies using methyl-filtered (MF) and unfiltered (UF) libraries. The use of methy filtration allowed a better assembly by filtering out 35% of the sugarcane genome and by producing 1.5× more scaffolds and 1.7× more assembled Mb in length compared with unfiltered dataset. The coverage of sorghum coding sequences (CDS) by MF scaffolds was at least 36% higher than by the use of UF scaffolds. Using MF technology, we increased by 134× the coverage of gene regions of the monoploid sugarcane genome. The MF reads assembled into scaffolds that covered all genes of the sugarcane bacterial artificial chromosomes (BACs), 97.2% of sugarcane expressed sequence tags (ESTs), 92.7% of sugarcane RNA-seq reads and 98.4% of sorghum protein sequences. Analysis of MF scaffolds from encoded enzymes of the sucrose/starch pathway discovered 291 single-nucleotide polymorphisms (SNPs) in the wild sugarcane species, S. spontaneum and S. officinarum. A large number of microRNA genes was also identified in the MF scaffolds. The information achieved by the MF dataset provides a valuable tool for genomic research in the genus Saccharum and for improvement of sugarcane as a biofuel crop. PMID:24773339

  11. FluGenome: a web tool for genotyping influenza A virus.

    PubMed

    Lu, Guoqing; Rowley, Thaine; Garten, Rebecca; Donis, Ruben O

    2007-07-01

    Influenza A viruses are hosted by numerous avian and mammalian species, which have shaped their evolution into distinct lineages worldwide. The viral genome consists of eight RNA segments that are frequently exchanged between different viruses via a process known as genetic reassortment. A complete genotype nomenclature is essential to describe gene segment reassortment. Specialized bioinformatic tools to analyze reassortment are not available, which hampers progress in understanding its role in host range, virulence and transmissibility of influenza viruses. To meet this need, we have developed a nomenclature to name influenza A genotypes and implemented a web server, FluGenome (http://www.flugenome.org/), for the assignment of lineages and genotypes. FluGenome provides functions for the user to interrogate the database in different modalities and get detailed reports on lineages and genotypes. These features make FluGenome unique in its ability to automatically detect genotype differences attributable to reassortment events in influenza A virus evolution.

  12. The Saccharomyces Genome Database: A Tool for Discovery.

    PubMed

    Cherry, J Michael

    2015-12-01

    The Saccharomyces Genome Database (SGD) is the main community repository of information for the budding yeast, Saccharomyces cerevisiae. The SGD has collected published results on chromosomal features, including genes and their products, and has become an encyclopedia of information on the biology of the yeast cell. This information includes gene and gene product function, phenotype, interactions, regulation, complexes, and pathways. All information has been integrated into a unique web resource, accessible via http://yeastgenome.org. The website also provides custom tools to allow useful searches and visualization of data. The experimentally defined functions of genes, mutant phenotypes, and sequence homologies archived in the SGD provide a platform for understanding many fields of biological research. The mission of SGD is to provide public access to all published experimental results on yeast to aid life science students, educators, and researchers. As such, the SGD has become an essential tool for the design of experiments and for the analysis of experimental results. PMID:26631132

  13. Genome-editing tools for stem cell biology

    PubMed Central

    Vasileva, E A; Shuvalov, O U; Garabadgiu, A V; Melino, G; Barlev, N A

    2015-01-01

    Human pluripotent stem cells provide a versatile platform for regenerative studies, drug testing and disease modeling. That the expression of only four transcription factors, Oct4, Klf4, Sox2 and c-Myc (OKSM), is sufficient for generation of induced pluripotent stem cells (iPSCs) from differentiated somatic cells has revolutionized the field and also highlighted the importance of OKSM as targets for genome editing. A number of novel genome-editing systems have been developed recently. In this review, we focus on successful applications of several such systems for generation of iPSCs. In particular, we discuss genome-editing systems based on zinc-finger fusion proteins (ZFs), transcription activator-like effectors (TALEs) and an RNA-guided DNA-specific nuclease, Cas9, derived from the bacterial defense system against viruses that utilizes clustered regularly interspaced short palindromic repeats (CRISPR). PMID:26203860

  14. Genome-editing tools for stem cell biology.

    PubMed

    Vasileva, E A; Shuvalov, O U; Garabadgiu, A V; Melino, G; Barlev, N A

    2015-01-01

    Human pluripotent stem cells provide a versatile platform for regenerative studies, drug testing and disease modeling. That the expression of only four transcription factors, Oct4, Klf4, Sox2 and c-Myc (OKSM), is sufficient for generation of induced pluripotent stem cells (iPSCs) from differentiated somatic cells has revolutionized the field and also highlighted the importance of OKSM as targets for genome editing. A number of novel genome-editing systems have been developed recently. In this review, we focus on successful applications of several such systems for generation of iPSCs. In particular, we discuss genome-editing systems based on zinc-finger fusion proteins (ZFs), transcription activator-like effectors (TALEs) and an RNA-guided DNA-specific nuclease, Cas9, derived from the bacterial defense system against viruses that utilizes clustered regularly interspaced short palindromic repeats (CRISPR).

  15. Functional Genomics Tools for Haemonchus contortus and Lessons From Other Helminths.

    PubMed

    Britton, C; Roberts, B; Marks, N D

    2016-01-01

    The availability of genome and transcriptome data for parasitic nematodes, including Haemonchus contortus, has highlighted the need to develop functional genomics tools. Comparative genomic analysis, particularly using data from the free-living nematode Caenorhabditis elegans, can help predict gene function. Reliable approaches to study function directly in parasitic nematodes are currently lacking. However, gene knockdown by RNA interference (RNAi) is being successfully used in schistosome and planarian species to define gene functions. Lessons from these systems may be applied to improve RNAi in H. contortus. Previous studies in H. contortus and related nematodes demonstrated reliable RNAi-mediated silencing of some genes, but not others. Current data suggest that susceptibility to RNAi in these nematodes is limited to genes expressed in sites accessible to the environment, such as the gut, amphids and excretory cell. Therefore, RNAi is functional in H. contortus, but improvements are needed to develop this system as a functional genomics platform. Here, we summarize RNAi studies on H. contortus and discuss the optimization of RNA delivery and improvements to culture methods to enhance larval development, protein turnover and the induction of phenotypic effects in vitro. The transgenic delivery of RNA or dominant-negative gene constructs and the recently developed CRISPR/Cas genome-editing technique are considered as potential alternative approaches for gene knockout. This is a key time to devote greater effort in progressing from genome to function, to improve our understanding of the biology of Haemonchus and identify novel targets for parasite control. PMID:27238014

  16. A survey of tools for variant analysis of next-generation genome sequencing data

    PubMed Central

    Pabinger, Stephan; Dander, Andreas; Fischer, Maria; Snajder, Rene; Sperk, Michael; Efremova, Mirjana; Krabichler, Birgit; Speicher, Michael R.; Zschocke, Johannes

    2014-01-01

    Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations relevant for diagnosis and therapy. Specifically, whole-exome sequencing using next-generation sequencing (NGS) technologies is gaining popularity in the human genetics community due to the moderate costs, manageable data amounts and straightforward interpretation of analysis results. While whole-exome and, in the near future, whole-genome sequencing are becoming commodities, data analysis still poses significant challenges and led to the development of a plethora of tools supporting specific parts of the analysis workflow or providing a complete solution. Here, we surveyed 205 tools for whole-genome/whole-exome sequencing data analysis supporting five distinct analytical steps: quality assessment, alignment, variant identification, variant annotation and visualization. We report an overview of the functionality, features and specific requirements of the individual tools. We then selected 32 programs for variant identification, variant annotation and visualization, which were subjected to hands-on evaluation using four data sets: one set of exome data from two patients with a rare disease for testing identification of germline mutations, two cancer data sets for testing variant callers for somatic mutations, copy number variations and structural variations, and one semi-synthetic data set for testing identification of copy number variations. Our comprehensive survey and evaluation of NGS tools provides a valuable guideline for human geneticists working on Mendelian disorders, complex diseases and cancers. PMID:23341494

  17. A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation.

    PubMed

    Aubrey, Wayne; Riley, Michael C; Young, Michael; King, Ross D; Oliver, Stephen G; Clare, Amanda

    2015-01-01

    Many advances in synthetic biology require the removal of a large number of genomic elements from a genome. Most existing deletion methods leave behind markers, and as there are a limited number of markers, such methods can only be applied a fixed number of times. Deletion methods that recycle markers generally are either imprecise (remove untargeted sequences), or leave scar sequences which can cause genome instability and rearrangements. No existing marker recycling method is automation-friendly. We have developed a novel openly available deletion tool that consists of: 1) a method for deleting genomic elements that can be repeatedly used without limit, is precise, scar-free, and suitable for automation; and 2) software to design the method's primers. Our tool is sequence agnostic and could be used to delete large numbers of coding sequences, promoter regions, transcription factor binding sites, terminators, etc in a single genome. We have validated our tool on the deletion of non-essential open reading frames (ORFs) from S. cerevisiae. The tool is applicable to arbitrary genomes, and we provide primer sequences for the deletion of: 90% of the ORFs from the S. cerevisiae genome, 88% of the ORFs from S. pombe genome, and 85% of the ORFs from the L. lactis genome.

  18. A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation.

    PubMed

    Aubrey, Wayne; Riley, Michael C; Young, Michael; King, Ross D; Oliver, Stephen G; Clare, Amanda

    2015-01-01

    Many advances in synthetic biology require the removal of a large number of genomic elements from a genome. Most existing deletion methods leave behind markers, and as there are a limited number of markers, such methods can only be applied a fixed number of times. Deletion methods that recycle markers generally are either imprecise (remove untargeted sequences), or leave scar sequences which can cause genome instability and rearrangements. No existing marker recycling method is automation-friendly. We have developed a novel openly available deletion tool that consists of: 1) a method for deleting genomic elements that can be repeatedly used without limit, is precise, scar-free, and suitable for automation; and 2) software to design the method's primers. Our tool is sequence agnostic and could be used to delete large numbers of coding sequences, promoter regions, transcription factor binding sites, terminators, etc in a single genome. We have validated our tool on the deletion of non-essential open reading frames (ORFs) from S. cerevisiae. The tool is applicable to arbitrary genomes, and we provide primer sequences for the deletion of: 90% of the ORFs from the S. cerevisiae genome, 88% of the ORFs from S. pombe genome, and 85% of the ORFs from the L. lactis genome. PMID:26630677

  19. Genome engineering and gene expression control for bacterial strain development.

    PubMed

    Song, Chan Woo; Lee, Joungmin; Lee, Sang Yup

    2015-01-01

    In recent years, a number of techniques and tools have been developed for genome engineering and gene expression control to achieve desired phenotypes of various bacteria. Here we review and discuss the recent advances in bacterial genome manipulation and gene expression control techniques, and their actual uses with accompanying examples. Genome engineering has been commonly performed based on homologous recombination. During such genome manipulation, the counterselection systems employing SacB or nucleases have mainly been used for the efficient selection of desired engineered strains. The recombineering technology enables simple and more rapid manipulation of the bacterial genome. The group II intron-mediated genome engineering technology is another option for some bacteria that are difficult to be engineered by homologous recombination. Due to the increasing demands on high-throughput screening of bacterial strains having the desired phenotypes, several multiplex genome engineering techniques have recently been developed and validated in some bacteria. Another approach to achieve desired bacterial phenotypes is the repression of target gene expression without the modification of genome sequences. This can be performed by expressing antisense RNA, small regulatory RNA, or CRISPR RNA to repress target gene expression at the transcriptional or translational level. All of these techniques allow efficient and rapid development and screening of bacterial strains having desired phenotypes, and more advanced techniques are expected to be seen.

  20. OmniMapFree: A unified tool to visualise and explore sequenced genomes

    PubMed Central

    2011-01-01

    • Background Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species, a growing volume of additional experimental information is available but this is rarely searchable within the landscape of the entire genome. • Results We have developed a generic software which permits users to view a single genome in entirety either within its chromosome or supercontig context within a single window. This software permits the genome to be displayed at any scales and with any features. Different data types and data sets are displayed onto the genome, which have been acquired from other types of studies including classical genetics, forward and reverse genetics, transcriptomics, proteomics and improved annotation from alternative sources. In each display, different types of information can be overlapped, then retrieved in the desired combinations and scales and used in follow up analyses. The displays generated are of publication quality. • Conclusions OmniMapFree provides a unified, versatile and easy-to-use software tool for studying a single genome in association with all the other datasets and data types available for the organism. PMID:22085540

  1. Learning-Oriented Instructional Development Tools.

    ERIC Educational Resources Information Center

    Merrill, M. David

    1997-01-01

    Discusses design requirements, and advantages and disadvantages of the following learner-centered instructional development tools: information containers; authoring systems; templates, models, or widgets; learning-oriented instructional development tools; and adaptive learning-oriented systems. (AEF)

  2. Genome-Based Genetic Tool Development for Bacillus methanolicus: Theta- and Rolling Circle-Replicating Plasmids for Inducible Gene Expression and Application to Methanol-Based Cadaverine Production

    PubMed Central

    Irla, Marta; Heggeset, Tonje M. B.; Nærdal, Ingemar; Paul, Lidia; Haugen, Tone; Le, Simone B.; Brautaset, Trygve; Wendisch, Volker F.

    2016-01-01

    Bacillus methanolicus is a thermophilic methylotroph able to overproduce amino acids from methanol, a substrate not used for human or animal nutrition. Based on our previous RNA-seq analysis a mannitol inducible promoter and a putative mannitol activator gene mtlR were identified. The mannitol inducible promoter was applied for controlled gene expression using fluorescent reporter proteins and a flow cytometry analysis, and improved by changing the -35 promoter region and by co-expression of the mtlR regulator gene. For independent complementary gene expression control, the heterologous xylose-inducible system from B. megaterium was employed and a two-plasmid gene expression system was developed. Four different replicons for expression vectors were compared with respect to their copy number and stability. As an application example, methanol-based production of cadaverine was shown to be improved from 11.3 to 17.5 g/L when a heterologous lysine decarboxylase gene cadA was expressed from a theta-replicating rather than a rolling-circle replicating vector. The current work on inducible promoter systems and compatible theta- or rolling circle-replicating vectors is an important extension of the poorly developed B. methanolicus genetic toolbox, valuable for genetic engineering and further exploration of this bacterium. PMID:27713731

  3. ECR Browser: A Tool For Visualizing And Accessing Data From Comparisons Of Multiple Vertebrate Genomes

    SciTech Connect

    Loots, G G; Ovcharenko, I; Stubbs, L; Nobrega, M A

    2004-01-06

    The increasing number of vertebrate genomes being sequenced in draft or finished form provide a unique opportunity to study and decode the language of DNA sequence through comparative genome alignments. However, novel tools and strategies are required to accommodate this increasing volume of genomic information and to facilitate experimental annotation of genome function. Here we present the ECR Browser, a tool that provides an easy and dynamic access to whole genome alignments of human, mouse, rat and fish sequences. This web-based tool (http://ecrbrowser.dcode.org) provides the starting point for discovery of novel genes, identification of distant gene regulatory elements and prediction of transcription factor binding sites. The genome alignment portal of the ECR Browser also permits fast and automated alignment of any user-submitted sequence to the genome of choice. The interconnection of the ECR browser with other DNA sequence analysis tools creates a unique portal for studying and exploring vertebrate genomes.

  4. Single cell analytic tools for drug discovery and development

    PubMed Central

    Heath, James R.; Ribas, Antoni; Mischel, Paul S.

    2016-01-01

    The genetic, functional, or compositional heterogeneity of healthy and diseased tissues presents major challenges in drug discovery and development.1-3 In cancers, heterogeneity may be essential for tumor stability,4 but its precise role in tumor biology is poorly resolved. This challenges the design of accurate disease models for use in drug development, and can confound the interpretation of biomarker levels, and of patient responses to specific therapies. The complex nature of heterogeneous tissues has motivated the development of tools for single cell genomic, transcriptomic, and multiplex proteomic analysis. We review these tools, assess their advantages and limitations, and explore their potential applications in drug discovery and development. PMID:26669673

  5. Emerging Imaging and Genomic Tools for Developmental Systems Biology.

    PubMed

    Liu, Zhe; Keller, Philipp J

    2016-03-21

    Animal development is a complex and dynamic process orchestrated by exquisitely timed cell lineage commitment, divisions, migration, and morphological changes at the single-cell level. In the past decade, extensive genetic, stem cell, and genomic studies provided crucial insights into molecular underpinnings and the functional importance of genetic pathways governing various cellular differentiation processes. However, it is still largely unknown how the precise coordination of these pathways is achieved at the whole-organism level and how the highly regulated spatiotemporal choreography of development is established in turn. Here, we discuss the latest technological advances in imaging and single-cell genomics that hold great promise for advancing our understanding of this intricate process. We propose an integrated approach that combines such methods to quantitatively decipher in vivo cellular dynamic behaviors and their underlying molecular mechanisms at the systems level with single-cell, single-molecule resolution. PMID:27003934

  6. Emerging Imaging and Genomic Tools for Developmental Systems Biology.

    PubMed

    Liu, Zhe; Keller, Philipp J

    2016-03-21

    Animal development is a complex and dynamic process orchestrated by exquisitely timed cell lineage commitment, divisions, migration, and morphological changes at the single-cell level. In the past decade, extensive genetic, stem cell, and genomic studies provided crucial insights into molecular underpinnings and the functional importance of genetic pathways governing various cellular differentiation processes. However, it is still largely unknown how the precise coordination of these pathways is achieved at the whole-organism level and how the highly regulated spatiotemporal choreography of development is established in turn. Here, we discuss the latest technological advances in imaging and single-cell genomics that hold great promise for advancing our understanding of this intricate process. We propose an integrated approach that combines such methods to quantitatively decipher in vivo cellular dynamic behaviors and their underlying molecular mechanisms at the systems level with single-cell, single-molecule resolution.

  7. System analysis: Developing tools for the future

    SciTech Connect

    De Jong, K.; clever, J.; Draper, J.V.; Davies, B.; Lonks, A.

    1996-02-01

    This report introduces and evaluates system analysis tools that were developed, or are under development, for the Robotics Technology Development Program (RTDP). Additionally, it discusses system analysis work completed using these tools aimed at completing a system analysis of the retrieval of waste from underground storage tanks on the Hanford Reservation near Richland, Washington. The tools developed and evaluated include a mixture of commercially available tools adapted to RTDP requirements, and some tools developed in house. The tools that are included in this report include: a Process Diagramming Tool, a Cost Modeling Tool, an Amortization Modeling Tool, a graphical simulation linked to the Cost Modeling Tool, a decision assistance tool, and a system thinking tool. Additionally, the importance of performance testing to the RTDP and the results of such testing executed is discussed. Further, the results of the Tank Waste Retrieval (TWR) System Diagram, the TWR Operations Cost Model, and the TWR Amortization Model are presented, and the implication of the results are discussed. Finally, the RTDP system analysis tools are assessed and some recommendations are made regarding continuing development of the tools and process.

  8. The capsicum transcriptome DB: a "hot" tool for genomic research.

    PubMed

    Góngora-Castillo, Elsa; Fajardo-Jaime, Rubén; Fernández-Cortes, Araceli; Jofre-Garfias, Alba E; Lozoya-Gloria, Edmundo; Martínez, Octavio; Ochoa-Alejo, Neftalí; Rivera-Bustamante, Rafael

    2012-01-01

    Chili pepper (Capsicum annuum) is an economically important crop with no available public genome sequence. We describe a genomic resource to facilitate Capsicum annuum research. A collection of Expressed Sequence Tags (ESTs) derived from five C. annuum organs (root, stem, leaf, flower and fruit) were sequenced using the Sanger method and multiple leaf transcriptomes were deeply sampled using with GS-pyrosequencing. A hybrid assembly of 1,324,516 raw reads yielded 32,314 high quality contigs as validated by coverage and identity analysis with existing pepper sequences. Overall, 75.5% of the contigs had significant sequence similarity to entries in nucleic acid and protein databases; 23% of the sequences have not been previously reported for C. annuum and expand sequence resources for this species. A MySQL database and a user-friendly Web interface were constructed with search-tools that permit queries of the ESTs including sequence, functional annotation, Gene Ontology classification, metabolic pathways, and assembly information. The Capsicum Transcriptome DB is free available from http://www.bioingenios.ira.cinvestav.mx:81/Joomla/

  9. Genomes correction and assembling: present methods and tools

    NASA Astrophysics Data System (ADS)

    Wojcieszek, Michał; Pawełkowicz, Magdalena; Nowak, Robert; Przybecki, Zbigniew

    2014-11-01

    Recent rapid development of next generation sequencing (NGS) technologies provided significant impact into genomics field of study enabling implementation of many de novo sequencing projects of new species which was previously confined by technological costs. Along with advancement of NGS there was need for adjustment in assembly programs. New algorithms must cope with massive amounts of data computation in reasonable time limits and processing power and hardware is also an important factor. In this paper, we address the issue of assembly pipeline for de novo genome assembly provided by programs presently available for scientist both as commercial and as open - source software. The implementation of four different approaches - Greedy, Overlap - Layout - Consensus (OLC), De Bruijn and Integrated resulting in variation of performance is the main focus of our discussion with additional insight into issue of short and long reads correction.

  10. Transposon tools: worldwide landscape of intellectual property and technological developments.

    PubMed

    Palazzoli, Fabien; Testu, François-Xavier; Merly, Franck; Bigot, Yves

    2010-03-01

    DNA transposons are considered to be good candidates for developing tools for genome engineering, insertional mutagenesis and gene delivery for therapeutic purposes, as illustrated by the recent first clinical trial of a transposon. In this article we set out to highlight the interest of patent information, and to develop a strategy for the technological development of transposon tools, similar to what has been done in many other fields. We propose a patent landscape for transposon tools, including the changes in international patent applications, and review the leading inventors and applicants. We also provide an overview of the potential patent portfolio for the prokaryotic and eukaryotic transposons that are exploited by spin-off companies. Finally, we discuss the difficulties involved in tracing relevant state-of-the-art of articles and patent documents, based on the example of one of the most promising transposon systems, including all the impacts on the technological development of transposon tools.

  11. Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report

    SciTech Connect

    Nakhleh, Luay

    2014-03-12

    I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbial genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.

  12. VibrioBase: a model for next-generation genome and annotation database development.

    PubMed

    Choo, Siew Woh; Heydari, Hamed; Tan, Tze King; Siow, Cheuk Chuen; Beh, Ching Yew; Wee, Wei Yee; Mutha, Naresh V R; Wong, Guat Jah; Ang, Mia Yang; Yazdi, Amir Hessam

    2014-01-01

    To facilitate the ongoing research of Vibrio spp., a dedicated platform for the Vibrio research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. We present VibrioBase, a useful resource platform, providing all basic features of a sequence database with the addition of unique analysis tools which could be valuable for the Vibrio research community. VibrioBase currently houses a total of 252 Vibrio genomes developed in a user-friendly manner and useful to enable the analysis of these genomic data, particularly in the field of comparative genomics. Besides general data browsing features, VibrioBase offers analysis tools such as BLAST interfaces and JBrowse genome browser. Other important features of this platform include our newly developed in-house tools, the pairwise genome comparison (PGC) tool, and pathogenomics profiling tool (PathoProT). The PGC tool is useful in the identification and comparative analysis of two genomes, whereas PathoProT is designed for comparative pathogenomics analysis of Vibrio strains. Both of these tools will enable researchers with little experience in bioinformatics to get meaningful information from Vibrio genomes with ease. We have tested the validity and suitability of these tools and features for use in the next-generation database development.

  13. Sequencing Single Cell Microbial Genomes with Microfluidic Amplifications Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Quake, Steve [University of Stanford

    2016-07-12

    Stanford University's Steve Quake on "Sequencing Single Cell Microbial Genomes with Microfluidic Amplification Tools" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  14. Single Virus Genomics: A New Tool for Virus Discovery

    PubMed Central

    Allen, Lisa Zeigler; Ishoey, Thomas; Novotny, Mark A.; McLean, Jeffrey S.; Lasken, Roger S.; Williamson, Shannon J.

    2011-01-01

    Whole genome amplification and sequencing of single microbial cells has significantly influenced genomics and microbial ecology by facilitating direct recovery of reference genome data. However, viral genomics continues to suffer due to difficulties related to the isolation and characterization of uncultivated viruses. We report here on a new approach called ‘Single Virus Genomics’, which enabled the isolation and complete genome sequencing of the first single virus particle. A mixed assemblage comprised of two known viruses; E. coli bacteriophages lambda and T4, were sorted using flow cytometric methods and subsequently immobilized in an agarose matrix. Genome amplification was then achieved in situ via multiple displacement amplification (MDA). The complete lambda phage genome was recovered with an average depth of coverage of approximately 437X. The isolation and genome sequencing of uncultivated viruses using Single Virus Genomics approaches will enable researchers to address questions about viral diversity, evolution, adaptation and ecology that were previously unattainable. PMID:21436882

  15. Geptop: A Gene Essentiality Prediction Tool for Sequenced Bacterial Genomes Based on Orthology and Phylogeny

    PubMed Central

    Wei, Wen; Ning, Lu-Wen; Ye, Yuan-Nong; Guo, Feng-Biao

    2013-01-01

    Integrative genomics predictors, which score highly in predicting bacterial essential genes, would be unfeasible in most species because the data sources are limited. We developed a universal approach and tool designated Geptop, based on orthology and phylogeny, to offer gene essentiality annotations. In a series of tests, our Geptop method yielded higher area under curve (AUC) scores in the receiver operating curves than the integrative approaches. In the ten-fold cross-validations among randomly upset samples, Geptop yielded an AUC of 0.918, and in the cross-organism predictions for 19 organisms Geptop yielded AUC scores between 0.569 and 0.959. A test applied to the very recently determined essential gene dataset from the Porphyromonas gingivalis, which belongs to a phylum different with all of the above 19 bacterial genomes, gave an AUC of 0.77. Therefore, Geptop can be applied to any bacterial species whose genome has been sequenced. Compared with the essential genes uniquely identified by the lethal screening, the essential genes predicted only by Gepop are associated with more protein-protein interactions, especially in the three bacteria with lower AUC scores (<0.7). This may further illustrate the reliability and feasibility of our method in some sense. The web server and standalone version of Geptop are available at http://cefg.uestc.edu.cn/geptop/ free of charge. The tool has been run on 968 bacterial genomes and the results are accessible at the website. PMID:23977285

  16. Geptop: a gene essentiality prediction tool for sequenced bacterial genomes based on orthology and phylogeny.

    PubMed

    Wei, Wen; Ning, Lu-Wen; Ye, Yuan-Nong; Guo, Feng-Biao

    2013-01-01

    Integrative genomics predictors, which score highly in predicting bacterial essential genes, would be unfeasible in most species because the data sources are limited. We developed a universal approach and tool designated Geptop, based on orthology and phylogeny, to offer gene essentiality annotations. In a series of tests, our Geptop method yielded higher area under curve (AUC) scores in the receiver operating curves than the integrative approaches. In the ten-fold cross-validations among randomly upset samples, Geptop yielded an AUC of 0.918, and in the cross-organism predictions for 19 organisms Geptop yielded AUC scores between 0.569 and 0.959. A test applied to the very recently determined essential gene dataset from the Porphyromonas gingivalis, which belongs to a phylum different with all of the above 19 bacterial genomes, gave an AUC of 0.77. Therefore, Geptop can be applied to any bacterial species whose genome has been sequenced. Compared with the essential genes uniquely identified by the lethal screening, the essential genes predicted only by Gepop are associated with more protein-protein interactions, especially in the three bacteria with lower AUC scores (<0.7). This may further illustrate the reliability and feasibility of our method in some sense. The web server and standalone version of Geptop are available at http://cefg.uestc.edu.cn/geptop/ free of charge. The tool has been run on 968 bacterial genomes and the results are accessible at the website.

  17. Program Development Tools and Infrastructures

    SciTech Connect

    Schulz, M

    2012-03-12

    Exascale class machines will exhibit a new level of complexity: they will feature an unprecedented number of cores and threads, will most likely be heterogeneous and deeply hierarchical, and offer a range of new hardware techniques (such as speculative threading, transactional memory, programmable prefetching, and programmable accelerators), which all have to be utilized for an application to realize the full potential of the machine. Additionally, users will be faced with less memory per core, fixed total power budgets, and sharply reduced MTBFs. At the same time, it is expected that the complexity of applications will rise sharply for exascale systems, both to implement new science possible at exascale and to exploit the new hardware features necessary to achieve exascale performance. This is particularly true for many of the NNSA codes, which are large and often highly complex integrated simulation codes that push the limits of everything in the system including language features. To overcome these limitations and to enable users to reach exascale performance, users will expect a new generation of tools that address the bottlenecks of exascale machines, that work seamlessly with the (set of) programming models on the target machines, that scale with the machine, that provide automatic analysis capabilities, and that are flexible and modular enough to overcome the complexities and changing demands of the exascale architectures. Further, any tool must be robust enough to handle the complexity of large integrated codes while keeping the user's learning curve low. With the ASC program, in particular the CSSE (Computational Systems and Software Engineering) and CCE (Common Compute Environment) projects, we are working towards a new generation of tools that fulfill these requirements and that provide our users as well as the larger HPC community with the necessary tools, techniques, and methodologies required to make exascale performance a reality.

  18. Optical Whole-Genome Restriction Mapping as a Tool for Rapidly Distinguishing and Identifying Bacterial Contaminants in Clinical Samples

    PubMed Central

    Baldwin, James C.

    2015-01-01

    Introduction Optical restriction genome mapping is a technology in which a genome is linearized on a surface and digested with specific restriction enzymes, giving an arrangement of the genome with gaps whose order and size are unique for a given organism. Current applications of this technology include assisting with the correct scaffolding and ordering of genomes in conjunction with whole-genome sequencing, observation of genetic drift and evolution using comparative genomics and epidemiological monitoring of the spread of infections. Here, we investigated the suitability of genome mapping for use in clinical labs as a potential diagnostic tool. Materials and Methods Using whole genome mapping, we investigated the basic performance of the technology for identifying two bacteria of interest for food-safety (Lactobacilli spp. and Enterohemorrhagic Escherichia coli). We further evaluated the performance for identifying multiple organisms from both simple and complex mixtures. Results We were able to successfully generate optical restriction maps of four Lactobacillus species as well as a strain of Enterohemorrhagic Escherichia coli from within a mixed solution, each distinguished using a common compatible restriction enzyme. Finally, we demonstrated that optical restriction maps were successfully obtained and the correct organism identified within a clinical matrix. Conclusion With additional development, whole genome mapping may be a useful clinical tool for rapid invitro diagnostics. PMID:26435946

  19. Capitalizing on App Development Tools and Technologies

    ERIC Educational Resources Information Center

    Luterbach, Kenneth J.; Hubbell, Kenneth R.

    2015-01-01

    Instructional developers and others creating apps must choose from a wide variety of app development tools and technologies. Some app development tools have incorporated visual programming features, which enable some drag and drop coding and contextual programming. While those features help novices begin programming with greater ease, questions…

  20. MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering.

    PubMed

    Bonde, Mads T; Klausen, Michael S; Anderson, Mads V; Wallin, Annika I N; Wang, Harris H; Sommer, Morten O A

    2014-07-01

    Recombineering and multiplex automated genome engineering (MAGE) offer the possibility to rapidly modify multiple genomic or plasmid sites at high efficiencies. This enables efficient creation of genetic variants including both single mutants with specifically targeted modifications as well as combinatorial cell libraries. Manual design of oligonucleotides for these approaches can be tedious, time-consuming, and may not be practical for larger projects targeting many genomic sites. At present, the change from a desired phenotype (e.g. altered expression of a specific protein) to a designed MAGE oligo, which confers the corresponding genetic change, is performed manually. To address these challenges, we have developed the MAGE Oligo Design Tool (MODEST). This web-based tool allows designing of MAGE oligos for (i) tuning translation rates by modifying the ribosomal binding site, (ii) generating translational gene knockouts and (iii) introducing other coding or non-coding mutations, including amino acid substitutions, insertions, deletions and point mutations. The tool automatically designs oligos based on desired genotypic or phenotypic changes defined by the user, which can be used for high efficiency recombineering and MAGE. MODEST is available for free and is open to all users at http://modest.biosustain.dtu.dk.

  1. Genomic editing tools to model human diseases with isogenic pluripotent stem cells.

    PubMed

    Kim, Huen Suk; Bernitz, Jeffrey M; Lee, Dung-Fang; Lemischka, Ihor R

    2014-11-15

    Patient-specific induced pluripotent stem cells (iPSCs) are considered a versatile resource in the field of biomedicine. As iPSCs are generated on an individual basis, iPSCs may be the optimal cellular material to use for disease modeling, drug discovery, and the development of patient-specific cellular therapies. Recently, to gain an in-depth understanding of human pathologies, patient-specific iPSCs have been used to model human diseases with some iPSC-derived cells recapitulating pathological phenotypes in vitro. However, complex multigenic diseases generally have not resulted in concise conclusions regarding the underlying mechanisms of disease, in large part due to genetic variations between disease-state and control iPSCs. To circumvent this, the use of genomic editing tools to generate perfect isogenic controls is gaining momentum. To date, DNA binding domain-based zinc finger nucleases and transcription activator-like effector nucleases have been utilized to create genetically defined conditions in patient-specific iPSCs, with some examples leading to the successful identification of novel mechanisms of disease. As the feasibility and utility of genomic editing tools in iPSCs improve, along with the introduction of the clustered regularly interspaced short palindromic repeat system, understanding the features and limitations of genomic editing tools and their applications to iPSC technology is critical to expending the field of human disease modeling.

  2. MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering

    PubMed Central

    Bonde, Mads T.; Klausen, Michael S.; Anderson, Mads V.; Wallin, Annika I.N.; Wang, Harris H.; Sommer, Morten O.A.

    2014-01-01

    Recombineering and multiplex automated genome engineering (MAGE) offer the possibility to rapidly modify multiple genomic or plasmid sites at high efficiencies. This enables efficient creation of genetic variants including both single mutants with specifically targeted modifications as well as combinatorial cell libraries. Manual design of oligonucleotides for these approaches can be tedious, time-consuming, and may not be practical for larger projects targeting many genomic sites. At present, the change from a desired phenotype (e.g. altered expression of a specific protein) to a designed MAGE oligo, which confers the corresponding genetic change, is performed manually. To address these challenges, we have developed the MAGE Oligo Design Tool (MODEST). This web-based tool allows designing of MAGE oligos for (i) tuning translation rates by modifying the ribosomal binding site, (ii) generating translational gene knockouts and (iii) introducing other coding or non-coding mutations, including amino acid substitutions, insertions, deletions and point mutations. The tool automatically designs oligos based on desired genotypic or phenotypic changes defined by the user, which can be used for high efficiency recombineering and MAGE. MODEST is available for free and is open to all users at http://modest.biosustain.dtu.dk. PMID:24838561

  3. Developing molecular tools for Chlamydomonas reinhardtii

    NASA Astrophysics Data System (ADS)

    Noor-Mohammadi, Samaneh

    Microalgae have garnered increasing interest over the years for their ability to produce compounds ranging from biofuels to neutraceuticals. A main focus of researchers has been to use microalgae as a natural bioreactor for the production of valuable and complex compounds. Recombinant protein expression in the chloroplasts of green algae has recently become more routine; however, the heterologous expression of multiple proteins or complete biosynthetic pathways remains a significant challenge. To take full advantage of these organisms' natural abilities, sophisticated molecular tools are needed to be able to introduce and functionally express multiple gene biosynthetic pathways in its genome. To achieve the above objective, we have sought to establish a method to construct, integrate and express multigene operons in the chloroplast and nuclear genome of the model microalgae Chlamydomonas reinhardtii. Here we show that a modified DNA Assembler approach can be used to rapidly assemble multiple-gene biosynthetic pathways in yeast and then integrate these assembled pathways at a site-specific location in the chloroplast, or by random integration in the nuclear genome of C. reinhardtii. As a proof of concept, this method was used to successfully integrate and functionally express up to three reporter proteins (AphA6, AadA, and GFP) in the chloroplast of C. reinhardtii and up to three reporter proteins (Ble, AphVIII, and GFP) in its nuclear genome. An analysis of the relative gene expression of the engineered strains showed significant differences in the mRNA expression levels of the reporter genes and thus highlights the importance of proper promoter/untranslated-region selection when constructing a target pathway. In addition, this work focuses on expressing the cofactor regeneration enzyme phosphite dehydrogenase (PTDH) in the chloroplast and nuclear genomes of C. reinhardtii. The PTDH enzyme converts phosphite into phosphate and NAD(P)+ into NAD(P)H. The reduced

  4. Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases

    PubMed Central

    Amos, Christopher I.; Bafna, Vineet; Hauser, Elizabeth R.; Hernandez, Ryan D.; Li, Chun; Liberles, David A.; McAllister, Kimberly; Moore, Jason H.; Paltoo, Dina N.; Papanicolaou, George J.; Peng, Bo; Ritchie, Marylyn D.; Rosenfeld, Gabriel; Witte, John S.

    2014-01-01

    Genetic simulation programs are used to model data under specified assumptions to facilitate the understanding and study of complex genetic systems. Standardized data sets generated using genetic simulation are essential for the development and application of novel analytical tools in genetic epidemiology studies. With continuing advances in high-throughput genomic technologies and generation and analysis of larger, more complex data sets, there is a need for updating current approaches in genetic simulation modeling. To provide a forum to address current and emerging challenges in this area, the National Cancer Institute (NCI) sponsored a workshop, entitled “Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases” at the National Institutes of Health (NIH) in Bethesda, Maryland on March 11-12, 2014. The goals of the workshop were to: (i) identify opportunities, challenges and resource needs for the development and application of genetic simulation models; (ii) improve the integration of tools for modeling and analysis of simulated data; and (iii) foster collaborations to facilitate development and applications of genetic simulation. During the course of the meeting the group identified challenges and opportunities for the science of simulation, software and methods development, and collaboration. This paper summarizes key discussions at the meeting, and highlights important challenges and opportunities to advance the field of genetic simulation. PMID:25371374

  5. Genetic simulation tools for post-genome wide association studies of complex diseases.

    PubMed

    Chen, Huann-Sheng; Hutter, Carolyn M; Mechanic, Leah E; Amos, Christopher I; Bafna, Vineet; Hauser, Elizabeth R; Hernandez, Ryan D; Li, Chun; Liberles, David A; McAllister, Kimberly; Moore, Jason H; Paltoo, Dina N; Papanicolaou, George J; Peng, Bo; Ritchie, Marylyn D; Rosenfeld, Gabriel; Witte, John S; Gillanders, Elizabeth M; Feuer, Eric J

    2015-01-01

    Genetic simulation programs are used to model data under specified assumptions to facilitate the understanding and study of complex genetic systems. Standardized data sets generated using genetic simulation are essential for the development and application of novel analytical tools in genetic epidemiology studies. With continuing advances in high-throughput genomic technologies and generation and analysis of larger, more complex data sets, there is a need for updating current approaches in genetic simulation modeling. To provide a forum to address current and emerging challenges in this area, the National Cancer Institute (NCI) sponsored a workshop, entitled "Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases" at the National Institutes of Health (NIH) in Bethesda, Maryland on March 11-12, 2014. The goals of the workshop were to (1) identify opportunities, challenges, and resource needs for the development and application of genetic simulation models; (2) improve the integration of tools for modeling and analysis of simulated data; and (3) foster collaborations to facilitate development and applications of genetic simulation. During the course of the meeting, the group identified challenges and opportunities for the science of simulation, software and methods development, and collaboration. This paper summarizes key discussions at the meeting, and highlights important challenges and opportunities to advance the field of genetic simulation.

  6. Observation Tools for Professional Development

    ERIC Educational Resources Information Center

    Malu, Kathleen F.

    2015-01-01

    Professional development of teachers, including English language teachers, empowers them to change in ways that improve teaching and learning (Gall and Acheson 2011; Murray 2010). In their seminal research on staff development--professional development in today's terms--Joyce and Showers (2002) identify key factors that promote teacher change.…

  7. The integrated microbial genomes (IMG) system in 2007: datacontent and analysis tool extensions

    SciTech Connect

    Markowitz, Victor M.; Szeto, Ernest; Palaniappan, Krishna; Grechkin, Yuri; Chu, Ken; Chen, I-Min A.; Dubchak, Inna; Anderson, Iain; Lykidis, Athanasios; Mavromatis, Konstantinos; Ivanova, Natalia N.; Kyrpides, Nikos C.

    2007-08-01

    The Integrated Microbial Genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through quarterly releases. IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov.

  8. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

    PubMed Central

    2011-01-01

    Background Second-generation sequencing technologies are precipitating major shifts with regards to what kinds of genomes are being sequenced and how they are annotated. While the first generation of genome projects focused on well-studied model organisms, many of today's projects involve exotic organisms whose genomes are largely terra incognita. This complicates their annotation, because unlike first-generation projects, there are no pre-existing 'gold-standard' gene-models with which to train gene-finders. Improvements in genome assembly and the wide availability of mRNA-seq data are also creating opportunities to update and re-annotate previously published genome annotations. Today's genome projects are thus in need of new genome annotation tools that can meet the challenges and opportunities presented by second-generation sequencing technologies. Results We present MAKER2, a genome annotation and data management tool designed for second-generation genome projects. MAKER2 is a multi-threaded, parallelized application that can process second-generation datasets of virtually any size. We show that MAKER2 can produce accurate annotations for novel genomes where training-data are limited, of low quality or even non-existent. MAKER2 also provides an easy means to use mRNA-seq data to improve annotation quality; and it can use these data to update legacy annotations, significantly improving their quality. We also show that MAKER2 can evaluate the quality of genome annotations, and identify and prioritize problematic annotations for manual review. Conclusions MAKER2 is the first annotation engine specifically designed for second-generation genome projects. MAKER2 scales to datasets of any size, requires little in the way of training data, and can use mRNA-seq data to improve annotation quality. It can also update and manage legacy genome annotation datasets. PMID:22192575

  9. Use of Genomic Tools to Improve Cattle Health in the Context of Infectious Diseases.

    PubMed

    Raszek, Mikolaj M; Guan, Le L; Plastow, Graham S

    2016-01-01

    Although infectious diseases impose a heavy economic burden on the cattle industry, the etiology of many disorders that affect livestock is not fully elucidated, and effective countermeasures are often lacking. The main tools available until now have been vaccines, antibiotics and antiparasitic drugs. Although these have been very successful in some cases, the appearance of parasite and microbial resistance to these treatments is a cause of concern. Next-generation sequencing provides important opportunities to tackle problems associated with pathogenic illnesses. This review describes the rapid gains achieved to track disease progression, identify the pathogens involved, and map pathogen interactions with the host. Use of novel genomic tools subsequently aids in treatment development, as well as successful creation of breeding programs aimed toward less susceptible livestock. These may be important tools for mitigating the long term effects of combating infection and helping reduce the reliance on antibiotic treatment. PMID:27014337

  10. Use of Genomic Tools to Improve Cattle Health in the Context of Infectious Diseases

    PubMed Central

    Raszek, Mikolaj M.; Guan, Le L.; Plastow, Graham S.

    2016-01-01

    Although infectious diseases impose a heavy economic burden on the cattle industry, the etiology of many disorders that affect livestock is not fully elucidated, and effective countermeasures are often lacking. The main tools available until now have been vaccines, antibiotics and antiparasitic drugs. Although these have been very successful in some cases, the appearance of parasite and microbial resistance to these treatments is a cause of concern. Next-generation sequencing provides important opportunities to tackle problems associated with pathogenic illnesses. This review describes the rapid gains achieved to track disease progression, identify the pathogens involved, and map pathogen interactions with the host. Use of novel genomic tools subsequently aids in treatment development, as well as successful creation of breeding programs aimed toward less susceptible livestock. These may be important tools for mitigating the long term effects of combating infection and helping reduce the reliance on antibiotic treatment. PMID:27014337

  11. Development and characterization of genomic and expressed SSRs in citrus by genome-wide analysis.

    PubMed

    Liu, Sheng-Rui; Li, Wen-Yang; Long, Dang; Hu, Chun-Gen; Zhang, Jin-Zhi

    2013-01-01

    Microsatellites or simple sequence repeats (SSRs) are one of the most popular sources of genetic markers and play a significant role in plant genetics and breeding. In this study, we identified citrus SSRs in the genome of Clementine mandarin and analyzed their frequency and distribution in different genomic regions. A total of 80,708 SSRs were detected in the genome with an overall density of 268 SSRs/Mb. While di-nucleotide repeats were the most frequent microsatellites in genomic DNA sequence, tetra-nucleotides, which had more repeat units than any other SSR types, had the highest cumulative sequence length. We identified 6,834 transcripts as containing 8,989 SSRs in 33,929 Clementine mandarin transcripts, among which, tri-nucleotide motifs (36.0%) were the most common, followed by di-nucleotide (26.9%) and hexa-nucleotide motifs (15.1%). The motif AG (16.7%) was most abundant among these SSRs, while motifs AAG (6.6%), AAT (5.0%), and TAG (2.2%) were most common among tri-nucleotides. Functional categorization of transcripts containing SSRs revealed that 5,879 (86.0%) of such transcripts had homology with known proteins, GO and KEGG annotation revealed that transcripts containing SSRs were those implicated in diverse biological processes in plants, including binding, development, transcription, and protein degradation. When 27 genomic and 78 randomly selected SSRs were tested on Clementine mandarin, 95 SSRs revealed polymorphism. These 95 SSRs were further deployed on 18 genotypes of the three generas of Rutaceae for the genetic diversity assessment, genomic SSRs generally show low transferability in comparison to SSRs developed from expressed sequences. These transcript-markers identified in our study may provide a valuable genetic and genomic tool for further genetic research and varietal development in citrus, such as diversity study, QTL mapping, molecular breeding, comparative mapping and other genetic analyses.

  12. Genome-Wide Approaches to Drosophila Heart Development

    PubMed Central

    Frasch, Manfred

    2016-01-01

    The development of the dorsal vessel in Drosophila is one of the first systems in which key mechanisms regulating cardiogenesis have been defined in great detail at the genetic and molecular level. Due to evolutionary conservation, these findings have also provided major inputs into studies of cardiogenesis in vertebrates. Many of the major components that control Drosophila cardiogenesis were discovered based on candidate gene approaches and their functions were defined by employing the outstanding genetic tools and molecular techniques available in this system. More recently, approaches have been taken that aim to interrogate the entire genome in order to identify novel components and describe genomic features that are pertinent to the regulation of heart development. Apart from classical forward genetic screens, the availability of the thoroughly annotated Drosophila genome sequence made new genome-wide approaches possible, which include the generation of massive numbers of RNA interference (RNAi) reagents that were used in forward genetic screens, as well as studies of the transcriptomes and proteomes of the developing heart under normal and experimentally manipulated conditions. Moreover, genome-wide chromatin immunoprecipitation experiments have been performed with the aim to define the full set of genomic binding sites of the major cardiogenic transcription factors, their relevant target genes, and a more complete picture of the regulatory network that drives cardiogenesis. This review will give an overview on these genome-wide approaches to Drosophila heart development and on computational analyses of the obtained information that ultimately aim to provide a description of this process at the systems level. PMID:27294102

  13. Genome Duplication: The Heartbeat of Developing Organisms

    PubMed Central

    DePamphilis, Melvin L.

    2016-01-01

    The mechanism that duplicates the nuclear genome during the trillions of cell divisions required to develop from zygote to adult is the same throughout the eukarya, but the mechanisms that determine where, when and how much nuclear genome duplication occur regulate development and differ among the eukarya. They allow organisms to change the rate of cell proliferation during development, to activate zygotic gene expression independently of DNA replication, and to restrict nuclear DNA replication to once per cell division. They allow specialized cells to exit their mitotic cell cycle and differentiate into polyploid cells, and in some cases, to amplify the number of copies of specific genes. It is genome duplication that drives evolution, by virtue of the errors that inevitably occur when the same process is repeated trillions of times. It is, unfortunately, the same errors that produce age-related genetic disorders such as cancer. PMID:26970621

  14. E-TALEN: a web tool to design TALENs for genome engineering

    PubMed Central

    Heigwer, Florian; Kerr, Grainne; Walther, Nike; Glaeser, Kathrin; Pelz, Oliver; Breinig, Marco; Boutros, Michael

    2013-01-01

    Use of transcription activator-like effector nucleases (TALENs) is a promising new technique in the field of targeted genome engineering, editing and reverse genetics. Its applications span from introducing knockout mutations to endogenous tagging of proteins and targeted excision repair. Owing to this wide range of possible applications, there is a need for fast and user-friendly TALEN design tools. We developed E-TALEN (http://www.e-talen.org), a web-based tool to design TALENs for experiments of varying scale. E-TALEN enables the design of TALENs against a single target or a large number of target genes. We significantly extended previously published design concepts to consider genomic context and different applications. E-TALEN guides the user through an end-to-end design process of de novo TALEN pairs, which are specific to a certain sequence or genomic locus. Furthermore, E-TALEN offers a functionality to predict targeting and specificity for existing TALENs. Owing to the computational complexity of many of the steps in the design of TALENs, particular emphasis has been put on the implementation of fast yet accurate algorithms. We implemented a user-friendly interface, from the input parameters to the presentation of results. An additional feature of E-TALEN is the in-built sequence and annotation database available for many organisms, including human, mouse, zebrafish, Drosophila and Arabidopsis, which can be extended in the future. PMID:24003033

  15. E-TALEN: a web tool to design TALENs for genome engineering.

    PubMed

    Heigwer, Florian; Kerr, Grainne; Walther, Nike; Glaeser, Kathrin; Pelz, Oliver; Breinig, Marco; Boutros, Michael

    2013-11-01

    Use of transcription activator-like effector nucleases (TALENs) is a promising new technique in the field of targeted genome engineering, editing and reverse genetics. Its applications span from introducing knockout mutations to endogenous tagging of proteins and targeted excision repair. Owing to this wide range of possible applications, there is a need for fast and user-friendly TALEN design tools. We developed E-TALEN (http://www.e-talen.org), a web-based tool to design TALENs for experiments of varying scale. E-TALEN enables the design of TALENs against a single target or a large number of target genes. We significantly extended previously published design concepts to consider genomic context and different applications. E-TALEN guides the user through an end-to-end design process of de novo TALEN pairs, which are specific to a certain sequence or genomic locus. Furthermore, E-TALEN offers a functionality to predict targeting and specificity for existing TALENs. Owing to the computational complexity of many of the steps in the design of TALENs, particular emphasis has been put on the implementation of fast yet accurate algorithms. We implemented a user-friendly interface, from the input parameters to the presentation of results. An additional feature of E-TALEN is the in-built sequence and annotation database available for many organisms, including human, mouse, zebrafish, Drosophila and Arabidopsis, which can be extended in the future.

  16. Novel integrative genomic tool for interrogating lithium response in bipolar disorder.

    PubMed

    Hunsberger, J G; Chibane, F L; Elkahloun, A G; Henderson, R; Singh, R; Lawson, J; Cruceanu, C; Nagarajan, V; Turecki, G; Squassina, A; Medeiros, C D; Del Zompo, M; Rouleau, G A; Alda, M; Chuang, D-M

    2015-01-01

    We developed a novel integrative genomic tool called GRANITE (Genetic Regulatory Analysis of Networks Investigational Tool Environment) that can effectively analyze large complex data sets to generate interactive networks. GRANITE is an open-source tool and invaluable resource for a variety of genomic fields. Although our analysis is confined to static expression data, GRANITE has the capability of evaluating time-course data and generating interactive networks that may shed light on acute versus chronic treatment, as well as evaluating dose response and providing insight into mechanisms that underlie therapeutic versus sub-therapeutic doses or toxic doses. As a proof-of-concept study, we investigated lithium (Li) response in bipolar disorder (BD). BD is a severe mood disorder marked by cycles of mania and depression. Li is one of the most commonly prescribed and decidedly effective treatments for many patients (responders), although its mode of action is not yet fully understood, nor is it effective in every patient (non-responders). In an in vitro study, we compared vehicle versus chronic Li treatment in patient-derived lymphoblastoid cells (LCLs) (derived from either responders or non-responders) using both microRNA (miRNA) and messenger RNA gene expression profiling. We present both Li responder and non-responder network visualizations created by our GRANITE analysis in BD. We identified by network visualization that the Let-7 family is consistently downregulated by Li in both groups where this miRNA family has been implicated in neurodegeneration, cell survival and synaptic development. We discuss the potential of this analysis for investigating treatment response and even providing clinicians with a tool for predicting treatment response in their patients, as well as for providing the industry with a tool for identifying network nodes as targets for novel drug discovery. PMID:25646593

  17. Novel integrative genomic tool for interrogating lithium response in bipolar disorder.

    PubMed

    Hunsberger, J G; Chibane, F L; Elkahloun, A G; Henderson, R; Singh, R; Lawson, J; Cruceanu, C; Nagarajan, V; Turecki, G; Squassina, A; Medeiros, C D; Del Zompo, M; Rouleau, G A; Alda, M; Chuang, D-M

    2015-01-01

    We developed a novel integrative genomic tool called GRANITE (Genetic Regulatory Analysis of Networks Investigational Tool Environment) that can effectively analyze large complex data sets to generate interactive networks. GRANITE is an open-source tool and invaluable resource for a variety of genomic fields. Although our analysis is confined to static expression data, GRANITE has the capability of evaluating time-course data and generating interactive networks that may shed light on acute versus chronic treatment, as well as evaluating dose response and providing insight into mechanisms that underlie therapeutic versus sub-therapeutic doses or toxic doses. As a proof-of-concept study, we investigated lithium (Li) response in bipolar disorder (BD). BD is a severe mood disorder marked by cycles of mania and depression. Li is one of the most commonly prescribed and decidedly effective treatments for many patients (responders), although its mode of action is not yet fully understood, nor is it effective in every patient (non-responders). In an in vitro study, we compared vehicle versus chronic Li treatment in patient-derived lymphoblastoid cells (LCLs) (derived from either responders or non-responders) using both microRNA (miRNA) and messenger RNA gene expression profiling. We present both Li responder and non-responder network visualizations created by our GRANITE analysis in BD. We identified by network visualization that the Let-7 family is consistently downregulated by Li in both groups where this miRNA family has been implicated in neurodegeneration, cell survival and synaptic development. We discuss the potential of this analysis for investigating treatment response and even providing clinicians with a tool for predicting treatment response in their patients, as well as for providing the industry with a tool for identifying network nodes as targets for novel drug discovery.

  18. CoryneBase: Corynebacterium genomic resources and analysis tools at your fingertips.

    PubMed

    Heydari, Hamed; Siow, Cheuk Chuen; Tan, Mui Fern; Jakubovics, Nick S; Wee, Wei Yee; Mutha, Naresh V R; Wong, Guat Jah; Ang, Mia Yang; Yazdi, Amir Hessam; Choo, Siew Woh

    2014-01-01

    Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um.edu.my/.

  19. SHARAD Radargram Analysis Tool Development in JMARS

    NASA Astrophysics Data System (ADS)

    Adler, J. B.; Anwar, S.; Dickenshied, S.; Carter, S.

    2016-09-01

    New tools are being developed in JMARS, a free GIS software, for SHARAD radargram viewing and analysis. These capabilities are useful for the polar science community, and for constraining the viability of ice resource deposits for human exploration.

  20. Interactive Tools to Track Child Development

    MedlinePlus

    ... What's this? Submit Button Past Emails CDC Features Interactive Tools to Track Child Development Recommend on Facebook ... maintained by: Office of the Associate Director for Communication, Digital Media Branch, Division of Public Affairs Email ...

  1. Data Mining and Optimization Tools for Developing Engine Parameters Tools

    NASA Technical Reports Server (NTRS)

    Dhawan, Atam P.

    1998-01-01

    This project was awarded for understanding the problem and developing a plan for Data Mining tools for use in designing and implementing an Engine Condition Monitoring System. Tricia Erhardt and I studied the problem domain for developing an Engine Condition Monitoring system using the sparse and non-standardized datasets to be available through a consortium at NASA Lewis Research Center. We visited NASA three times to discuss additional issues related to dataset which was not made available to us. We discussed and developed a general framework of data mining and optimization tools to extract useful information from sparse and non-standard datasets. These discussions lead to the training of Tricia Erhardt to develop Genetic Algorithm based search programs which were written in C++ and used to demonstrate the capability of GA algorithm in searching an optimal solution in noisy, datasets. From the study and discussion with NASA LeRC personnel, we then prepared a proposal, which is being submitted to NASA for future work for the development of data mining algorithms for engine conditional monitoring. The proposed set of algorithm uses wavelet processing for creating multi-resolution pyramid of tile data for GA based multi-resolution optimal search.

  2. Software development tools: A bibliography, appendix C.

    NASA Technical Reports Server (NTRS)

    Riddle, W. E.

    1980-01-01

    A bibliography containing approximately 200 citations on tools which help software developers perform some development task (such as text manipulation, testing, etc.), and which would not necessarily be found as part of a computing facility is given. The bibliography comes from a relatively random sampling of the literature and is not complete. But it is indicative of the nature and range of tools currently being prepared or currently available.

  3. Genomic Landscape of Developing Male Germ Cells

    PubMed Central

    Lee, Tin-Lap; Pang, Alan Lap-Yin; Rennert, Owen M.; Chan, Wai-Yee

    2010-01-01

    Spermatogenesis is a highly orchestrated developmental process by which spermatogonia develop into mature spermatozoa. This process involves many testis- or male germ cell-specific gene products whose expressions are strictly regulated. In the past decade the advent of high-throughput gene expression analytical techniques has made functional genomic studies of this process, particularly in model animals such as mice and rats, feasible and practical. These studies have just begun to reveal the complexity of the genomic landscape of the developing male germ cells. Over 50% of the mouse and rat genome are expressed during testicular development. Among transcripts present in germ cells, 40% – 60% are uncharacterized. A number of genes, and consequently their associated biological pathways, are differentially expressed at different stages of spermatogenesis. Developing male germ cells present a rich repertoire of genetic processes. Tissue-specific as well as spermatogenesis stage-specific alternative splicing of genes exemplifies the complexity of genome expression. In addition to this layer of control, discoveries of abundant presence of antisense transcripts, expressed psuedogenes, non-coding RNAs (ncRNA) including long ncRNAs, microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), and retrogenes all point to the presence of multiple layers of expression and functional regulation in male germ cells. It is anticipated that application of systems biology approaches will further our understanding of the regulatory mechanism of spermatogenesis.† PMID:19306351

  4. Phytozome: a Tool for Green Plant Comparative Genomics

    DOE Data Explorer

    Phytozome is a joint project of the Department of Energy's Joint Genome Institute and the Center for Integrative Genomics to facilitate comparative genomic studies amongst green plants. Clusters of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These clusters allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. As of release v4.0, Phytozome provides access to nine sequenced and annotated green plant genomes, eight of which have been clustered into gene families at six evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are hyper-linked and searchable. [Copied from the Overview at http://www.phytozome.net/Phytozome_info.php

  5. FY06 LDRD Final Report "Development of Computational Techniques For Decoding The Language of Genomes"

    SciTech Connect

    Ovcharenko, I

    2007-01-09

    This project was aimed at developing computational methods and tools to decipher the universal language of gene regulation encoded in genomes. It was proposed to identify and decipher the code and to functionally annotate genomic elements that orchestrate the temporal and spatial dynamics of gene expression in living cells.

  6. The GLOBE 3D Genome Platform - towards a novel system-biological paper tool to integrate the huge complexity of genome organization and function.

    PubMed

    Knoch, Tobias A; Lesnussa, Michael; Kepper, Nick; Eussen, Hubert B; Grosveld, Frank G

    2009-01-01

    Genomes are tremendous co-evolutionary holistic systems for molecular storage, processing and fabrication of information. Their system-biological complexity remains, however, still largely mysterious, despite immense sequencing achievements and huge advances in the understanding of the general sequential, three-dimensional and regulatory organization. Here, we present the GLOBE 3D Genome Platform a completely novel grid based virtual "paper" tool and in fact the first system-biological genome browser integrating the holistic complexity of genomes in a single easy comprehensible platform: Based on a detailed study of biophysical and IT requirements, every architectural level from sequence to morphology of one or several genomes can be approached in a real and in a symbolic representation simultaneously and navigated by continuous scale-free zooming within a unique three-dimensional OpenGL and grid driven environment. In principle an unlimited number of multi-dimensional data sets can be visualized, customized in terms of arrangement, shape, colour, and texture etc. as well as accessed and annotated individually or in groups using internal or external data bases/facilities. Any information can be searched and correlated by importing or calculating simple relations in real-time using grid resources. A general correlation and application platform for more complex correlative analysis and a front-end for system-biological simulations both using again the huge capabilities of grid infrastructures is currently under development. Hence, the GLOBE 3D Genome Platform is an example of a grid based approach towards a virtual desktop for genomic work combining the three fundamental distributed resources: i) visual data representation, ii) data access and management, and iii) data analysis and creation. Thus, the GLOBE 3D Genome Platform is the novel system-biology oriented information system urgently needed to access, present, annotate, and to simulate the holistic genome

  7. The GLOBE 3D Genome Platform - towards a novel system-biological paper tool to integrate the huge complexity of genome organization and function.

    PubMed

    Knoch, Tobias A; Lesnussa, Michael; Kepper, Nick; Eussen, Hubert B; Grosveld, Frank G

    2009-01-01

    Genomes are tremendous co-evolutionary holistic systems for molecular storage, processing and fabrication of information. Their system-biological complexity remains, however, still largely mysterious, despite immense sequencing achievements and huge advances in the understanding of the general sequential, three-dimensional and regulatory organization. Here, we present the GLOBE 3D Genome Platform a completely novel grid based virtual "paper" tool and in fact the first system-biological genome browser integrating the holistic complexity of genomes in a single easy comprehensible platform: Based on a detailed study of biophysical and IT requirements, every architectural level from sequence to morphology of one or several genomes can be approached in a real and in a symbolic representation simultaneously and navigated by continuous scale-free zooming within a unique three-dimensional OpenGL and grid driven environment. In principle an unlimited number of multi-dimensional data sets can be visualized, customized in terms of arrangement, shape, colour, and texture etc. as well as accessed and annotated individually or in groups using internal or external data bases/facilities. Any information can be searched and correlated by importing or calculating simple relations in real-time using grid resources. A general correlation and application platform for more complex correlative analysis and a front-end for system-biological simulations both using again the huge capabilities of grid infrastructures is currently under development. Hence, the GLOBE 3D Genome Platform is an example of a grid based approach towards a virtual desktop for genomic work combining the three fundamental distributed resources: i) visual data representation, ii) data access and management, and iii) data analysis and creation. Thus, the GLOBE 3D Genome Platform is the novel system-biology oriented information system urgently needed to access, present, annotate, and to simulate the holistic genome

  8. Current genome editing tools in gene therapy: new approaches to treat cancer.

    PubMed

    Shuvalov, Oleg; Petukhov, Alexey; Daks, Alexandra; Fedorova, Olga; Ermakov, Alexander; Melino, Gerry; Barlev, Nickolai A

    2015-01-01

    Gene therapy suggests a promising approach to treat genetic diseases by applying genes as pharmaceuticals. Cancer is a complex disease, which strongly depends on a particular genetic make-up and hence can be treated with gene therapy. From about 2,000 clinical trials carried out so far, more than 60% were cancer targeted. Development of precise and effective gene therapy approaches is intimately connected with achievements in the molecular biology techniques. The field of gene therapy was recently revolutionized by the introduction of "programmable" nucleases, including ZFNs, TALENs, and CRISPR, which target specific genomic loci with high efficacy and precision. Furthermore, when combined with DNA transposons for the delivery purposes into cells, these programmable nucleases represent a promising alternative to the conventional viral-mediated gene delivery. In addition to "programmable" nucleases, a new class of TALE- and CRISPR-based "artificial transcription effectors" has been developed to mediate precise regulation of specific genes. In sum, these new molecular tools may be used in a wide plethora of gene therapy strategies. This review highlights the current status of novel genome editing tools and discusses their suitability and perspectives in respect to cancer gene therapy studies.

  9. GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences.

    PubMed

    Gao, Feng; Zhang, Chun-Ting

    2006-07-01

    In order to understand the evolution, structure and function of genomes, it is important to know the general compositional features of DNA sequences. Based on the quadratic divergence, a new segmentation algorithm to partition a given genome or DNA sequence into compositionally distinct domains has been put forward. With the aid of the technique of cumulative GC profile, the distribution of segmentation points can be displayed intuitively. We have therefore developed them into GC-Profile, an interactive web-based software system, which can be used to segment prokaryotic and eukaryotic genomes. GC-Profile provides a quantitative and qualitative view of genome organization. Based on the obtained results, the relationships between the G+C content and other genomic features, such as distributions of genes and CpG islands, can be analyzed in a perceivable manner. It shows that GC-Profile would be an appropriate starting point for analyzing the isochore structure of higher eukaryotic genomes, and an intuitive tool for identifying genomic islands in prokaryotic genomes. GC-Profile is freely available at the website http://tubic.tju.edu.cn/GC-Profile/. In addition, precompiled binaries, together with examples and documentation, can also be freely downloaded for a local execution.

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

    PubMed Central

    2013-01-01

    Background 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. Results 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. Conclusions 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

  11. Computational Tools to Accelerate Commercial Development

    SciTech Connect

    Miller, David C

    2013-01-01

    The goals of the work reported are: to develop new computational tools and models to enable industry to more rapidly develop and deploy new advanced energy technologies; to demonstrate the capabilities of the CCSI Toolset on non-proprietary case studies; and to deploy the CCSI Toolset to industry. Challenges of simulating carbon capture (and other) processes include: dealing with multiple scales (particle, device, and whole process scales); integration across scales; verification, validation, and uncertainty; and decision support. The tools cover: risk analysis and decision making; validated, high-fidelity CFD; high-resolution filtered sub-models; process design and optimization tools; advanced process control and dynamics; process models; basic data sub-models; and cross-cutting integration tools.

  12. Forty years of development in diamond tools

    NASA Astrophysics Data System (ADS)

    The growth of the diamond industry in Western Countries since the First World War is surveyed. The articles described deal specifically with the development of the industrial diamond and diamond tool sector in different countries. All data point to continuing rapid expansion in the diamond tool sector. The West consumes 80 percent of world industrial diamond production. Diamond consumption increased sharply in the U.S. during World War 2. There are 300 diamond manufacturers in the U.S. today. In 1940, there were 25. In Japan, consumption of industrial diamonds has increased several times. In Italy, there has been a 75 fold increase in the production of diamond tools since 1959.

  13. Data Mining and Optimization Tools for Developing Engine Parameters Tools

    NASA Technical Reports Server (NTRS)

    Dhawan, Atam P.

    1998-01-01

    This project was awarded for understanding the problem and developing a plan for Data Mining tools for use in designing and implementing an Engine Condition Monitoring System. From the total budget of $5,000, Tricia and I studied the problem domain for developing ail Engine Condition Monitoring system using the sparse and non-standardized datasets to be available through a consortium at NASA Lewis Research Center. We visited NASA three times to discuss additional issues related to dataset which was not made available to us. We discussed and developed a general framework of data mining and optimization tools to extract useful information from sparse and non-standard datasets. These discussions lead to the training of Tricia Erhardt to develop Genetic Algorithm based search programs which were written in C++ and used to demonstrate the capability of GA algorithm in searching an optimal solution in noisy datasets. From the study and discussion with NASA LERC personnel, we then prepared a proposal, which is being submitted to NASA for future work for the development of data mining algorithms for engine conditional monitoring. The proposed set of algorithm uses wavelet processing for creating multi-resolution pyramid of the data for GA based multi-resolution optimal search. Wavelet processing is proposed to create a coarse resolution representation of data providing two advantages in GA based search: 1. We will have less data to begin with to make search sub-spaces. 2. It will have robustness against the noise because at every level of wavelet based decomposition, we will be decomposing the signal into low pass and high pass filters.

  14. The Developing Child: Tools for Monitoring.

    ERIC Educational Resources Information Center

    D'Agostino, Micheline

    1991-01-01

    This document examines the use of measurement tools to evaluate children's psychological development. The first part of the document discusses the identification and quantification of developmental landmarks and the reasons for evaluation. The second part reviews several evaluation instruments. The Ruth Griffiths mental development scales are used…

  15. UniPrimer: A Web-Based Primer Design Tool for Comparative Analyses of Primate Genomes

    PubMed Central

    Batnyam, Nomin; Lee, Jimin; Lee, Jungnam; Hong, Seung Bok; Oh, Sejong; Han, Kyudong

    2012-01-01

    Whole genome sequences of various primates have been released due to advanced DNA-sequencing technology. A combination of computational data mining and the polymerase chain reaction (PCR) assay to validate the data is an excellent method for conducting comparative genomics. Thus, designing primers for PCR is an essential procedure for a comparative analysis of primate genomes. Here, we developed and introduced UniPrimer for use in those studies. UniPrimer is a web-based tool that designs PCR- and DNA-sequencing primers. It compares the sequences from six different primates (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque) and designs primers on the conserved region across species. UniPrimer is linked to RepeatMasker, Primer3Plus, and OligoCalc softwares to produce primers with high accuracy and UCSC In-Silico PCR to confirm whether the designed primers work. To test the performance of UniPrimer, we designed primers on sample sequences using UniPrimer and manually designed primers for the same sequences. The comparison of the two processes showed that UniPrimer was more effective than manual work in terms of saving time and reducing errors. PMID:22693428

  16. Mudi, a web tool for identifying mutations by bioinformatics analysis of whole-genome sequence.

    PubMed

    Iida, Naoko; Yamao, Fumiaki; Nakamura, Yasukazu; Iida, Tetsushi

    2014-06-01

    In forward genetics, identification of mutations is a time-consuming and laborious process. Modern whole-genome sequencing, coupled with bioinformatics analysis, has enabled fast and cost-effective mutation identification. However, for many experimental researchers, bioinformatics analysis is still a difficult aspect of whole-genome sequencing. To address this issue, we developed a browser-accessible and easy-to-use bioinformatics tool called Mutation discovery (Mudi; http://naoii.nig.ac.jp/mudi_top.html), which enables 'one-click' identification of causative mutations from whole-genome sequence data. In this study, we optimized Mudi for pooled-linkage analysis aimed at identifying mutants in yeast model systems. After raw sequencing data are uploaded, Mudi performs sequential analysis, including mapping, detection of variant alleles, filtering and removal of background polymorphisms, prioritization, and annotation. In an example study of suppressor mutants of ptr1-1 in the fission yeast Schizosaccharomyces pombe, pooled-linkage analysis with Mudi identified mip1(+) , a component of Target of Rapamycin Complex 1 (TORC1), as a novel component involved in RNA interference (RNAi)-related cell-cycle control. The accessibility of Mudi will accelerate systematic mutation analysis in forward genetics.

  17. A decision tool to guide the ethics review of a challenging breed of emerging genomic projects.

    PubMed

    Joly, Yann; So, Derek; Osien, Gladys; Crimi, Laura; Bobrow, Martin; Chalmers, Don; Wallace, Susan E; Zeps, Nikolajs; Knoppers, Bartha

    2016-08-01

    Recent projects conducted by the International Cancer Genome Consortium (ICGC) have raised the important issue of distinguishing quality assurance (QA) activities from research in the context of genomics. Research was historically defined as a systematic effort to expand a shared body of knowledge, whereas QA was defined as an effort to ascertain whether a specific project met desired standards. However, the two categories increasingly overlap due to advances in bioinformatics and the shift toward open science. As few ethics review policies take these changes into account, it is often difficult to determine the appropriate level of review. Mislabeling can result in unnecessary burdens for the investigators or, conversely, in underestimation of the risks to participants. Therefore, it is important to develop a consistent method of selecting the review process for genomics and bioinformatics projects. This paper begins by discussing two case studies from the ICGC, followed by a literature review on the distinction between QA and research and a comparative analysis of ethics review policies from Canada, the United States, the United Kingdom, and Australia. These results are synthesized into a novel two-step decision tool for researchers and policymakers, which uses traditional criteria to sort clearly defined activities while requiring the use of actual risk levels to decide more complex cases. PMID:26785834

  18. CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison.

    PubMed

    Castrignanò, Tiziana; Canali, Alessandro; Grillo, Giorgio; Liuni, Sabino; Mignone, Flavio; Pesole, Graziano

    2004-07-01

    The identification and characterization of genome tracts that are highly conserved across species during evolution may contribute significantly to the functional annotation of whole-genome sequences. Indeed, such sequences are likely to correspond to known or unknown coding exons or regulatory motifs. Here, we present a web server implementing a previously developed algorithm that, by comparing user-submitted genome sequences, is able to identify statistically significant conserved blocks and assess their coding or noncoding nature through the measure of a coding potential score. The web tool, available at http://www.caspur.it/CSTminer/, is dynamically interconnected with the Ensembl genome resources and produces a graphical output showing a map of detected conserved sequences and annotated gene features.

  19. GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics.

    PubMed

    Tabas-Madrid, Daniel; Nogales-Cadenas, Ruben; Pascual-Montano, Alberto

    2012-07-01

    Since its first release in 2007, GeneCodis has become a valuable tool to functionally interpret results from experimental techniques in genomics. This web-based application integrates different sources of information to finding groups of genes with similar biological meaning. This process, known as enrichment analysis, is essential in the interpretation of high-throughput experiments. The frequent feedbacks and the natural evolution of genomics and bioinformatics have allowed the growth of the tool and the development of this third release. In this version, a special effort has been made to remove noisy and redundant output from the enrichment results with the inclusion of a recently reported algorithm that summarizes significantly enriched terms and generates functionally coherent modules of genes and terms. A new comparative analysis has been added to allow the differential analysis of gene sets. To expand the scope of the application, new sources of biological information have been included, such as genetic diseases, drugs-genes interactions and Pubmed information among others. Finally, the graphic section has been renewed with the inclusion of new interactive graphics and filtering options. The application is freely available at http://genecodis.cnb.csic.es.

  20. OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes.

    PubMed

    Jiang, Li-Wei; Lin, Kuang-Lun; Lu, Chin Lung

    2008-07-01

    OGtree is a web-based tool for constructing genome trees of prokaryotic species based on a measure of combining overlapping-gene content and overlapping-gene order in their whole genomes. The overlapping genes (OGs) are defined as adjacent genes whose coding sequences overlap partially or entirely. In fact, OGs are ubiquitous in microbial genomes and more conserved between species than non-OGs. Based on these properties, it has been suggested that OGs can serve as better phylogenetic characters than non-OGs for reconstructing the evolutionary relationships among microbial genomes. OGtree takes the accession numbers of prokaryotic genomes as its input. It then downloads their complete genomes from the National Centre for Biotechnology Information and identifies OGs in each genome and their orthologous OGs in other genomes. Next, OGtree computes an overlapping-gene distance between each pair of input genomes based on a combination of their OG content and orthologous OG order. Finally, it utilizes distance-based methods of building tree to reconstruct the genome trees of input prokaryotic genomes according to their pairwise OG distance. OGtree is available online at http://bioalgorithm.life.nctu.edu.tw/OGtree/.

  1. GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing

    PubMed Central

    Wang, Xuewen; Wang, Le

    2016-01-01

    Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar.

  2. GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing.

    PubMed

    Wang, Xuewen; Wang, Le

    2016-01-01

    Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar.

  3. TALEN and CRISPR/Cas Genome Editing Systems: Tools of Discovery

    PubMed Central

    Nemudryi, A. A.; Valetdinova, K. R.; Medvedev, S. P.; Zakian, S. M.

    2014-01-01

    Precise studies of plant, animal and human genomes enable remarkable opportunities of obtained data application in biotechnology and medicine. However, knowing nucleotide sequences isn’t enough for understanding of particular genomic elements functional relationship and their role in phenotype formation and disease pathogenesis. In post-genomic era methods allowing genomic DNA sequences manipulation, visualization and regulation of gene expression are rapidly evolving. Though, there are few methods, that meet high standards of efficiency, safety and accessibility for a wide range of researchers. In 2011 and 2013 novel methods of genome editing appeared – this are TALEN (Transcription Activator-Like Effector Nucleases) and CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats)/Cas9 systems. Although TALEN and CRISPR/Cas9 appeared recently, these systems have proved to be effective and reliable tools for genome engineering. Here we generally review application of these systems for genome editing in conventional model objects of current biology, functional genome screening, cell-based human hereditary disease modeling, epigenome studies and visualization of cellular processes. Additionally, we review general strategies for designing TALEN and CRISPR/Cas9 and analyzing their activity. We also discuss some obstacles researcher can face using these genome editing tools. PMID:25349712

  4. Development of chloroplast genomic resources for Cynara.

    PubMed

    Curci, Pasquale L; De Paola, Domenico; Sonnante, Gabriella

    2016-03-01

    In this study, new chloroplast (cp) resources were developed for the genus Cynara, using whole cp genomes from 20 genotypes, by means of high-throughput sequencing technologies. Our target species included seven globe artichokes, two cultivated cardoons, eight wild artichokes, and three other wild Cynara species (C. baetica, C. cornigera and C. syriaca). One complete cp genome was isolated using short reads from a whole-genome sequencing project, while the others were obtained by means of long-range PCR, for which primer pairs are provided here. A de novo assembly strategy combined with a reference-based assembly allowed us to reconstruct each cp genome. Comparative analyses among the newly sequenced genotypes and two additional Cynara cp genomes ('Brindisino' artichoke and C. humilis) retrieved from public databases revealed 126 parsimony informative characters and 258 singletons in Cynara, for a total of 384 variable characters. Thirty-nine SSR loci and 34 other INDEL events were detected. After data analysis, 37 primer pairs for SSR amplification were designed, and these molecular markers were subsequently validated in our Cynara genotypes. Phylogenetic analysis based on all cp variable characters provided the best resolution when compared to what was observed using only parsimony informative characters, or only short 'variable' cp regions. The evaluation of the molecular resources obtained from this study led us to support the 'super-barcode' theory and consider the total cp sequence of Cynara as a reliable and valuable molecular marker for exploring species diversity and examining variation below the species level. PMID:26354522

  5. Novel tools for an old lineage: Population genomics for cycads.

    PubMed

    Cibrián-Jaramillo, Angelica; Marler, Thomas E

    2011-07-01

    With a ca. 300 million year-old evolutionary history, cycads are often perceived as "living fossils," relicts of their previously widespread dominance. Patterns of genetic variation for a member of the most basal cycad genus, Cycas micronesica, support the notion that cycads are a dynamic group with ongoing diversification. Herein we hypothesize that cycad's hefty genomes enable rapid adaptive change and facilitate specific beneficial interactions with varying assemblages of symbionts. Characterizing population-level genomic patterns of cycads and their symbionts, pollinators in particular, will enlighten our understanding of these mechanisms and of adaptive variation that underlies cycad evolution. In light of rapid climate and landscape change, cycads are a beacon for understanding the ecological processes that ultimately enable species long-term survival. PMID:21966573

  6. Genomic tools to assist breeding for drought tolerance.

    PubMed

    Langridge, Peter; Reynolds, Matthew P

    2015-04-01

    Water deficit or drought stress is a major limitation to crop production globally. Plant breeders have used a wide range of technologies to successfully breed varieties that perform well under the growth conditions for their target environments but they are always seeking new opportunities to enhance rates of genetic gain. Under drought, yield is determined by the integration of variable levels of water deficit across the developmental life of the crop. Genomics technologies were seen as a path to understand the genetic and environmental complexity of drought stress. To be relevant to breeding programs, genomic studies must consider the nature of drought stress in the target environment and use plant material and phenotyping techniques that relate to field conditions. PMID:25531270

  7. Novel tools for an old lineage: Population genomics for cycads.

    PubMed

    Cibrián-Jaramillo, Angelica; Marler, Thomas E

    2011-07-01

    With a ca. 300 million year-old evolutionary history, cycads are often perceived as "living fossils," relicts of their previously widespread dominance. Patterns of genetic variation for a member of the most basal cycad genus, Cycas micronesica, support the notion that cycads are a dynamic group with ongoing diversification. Herein we hypothesize that cycad's hefty genomes enable rapid adaptive change and facilitate specific beneficial interactions with varying assemblages of symbionts. Characterizing population-level genomic patterns of cycads and their symbionts, pollinators in particular, will enlighten our understanding of these mechanisms and of adaptive variation that underlies cycad evolution. In light of rapid climate and landscape change, cycads are a beacon for understanding the ecological processes that ultimately enable species long-term survival.

  8. Genomic resource development for shellfish of conservation concern.

    PubMed

    Timmins-Schiffman, Emma B; Friedman, Carolyn S; Metzger, Dave C; White, Samuel J; Roberts, Steven B

    2013-03-01

    Effective conservation of threatened species depends on the ability to assess organism physiology and population demography. To develop genomic resources to better understand the dynamics of two ecologically vulnerable species in the Pacific Northwest of the United States, larval transcriptomes were sequenced for the pinto abalone, Haliotis kamtschatkana kamtschatkana, and the Olympia oyster, Ostrea lurida. Based on comparative species analysis the Ostrea lurida transcriptome (41 136 contigs) is relatively complete. These transcriptomes represent the first significant contribution to genomic resources for both species. Genes are described based on biological function with particular attention to those associated with temperature change, oxidative stress and immune function. In addition, transcriptome-derived genetic markers are provided. Together, these resources provide valuable tools for future studies aimed at conservation of Haliotis kamtschatkana kamtschatkana, Ostrea lurida and related species.

  9. Mutagenesis as a Tool in Plant Genetics, Functional Genomics, and Breeding

    PubMed Central

    Sikora, Per; Chawade, Aakash; Larsson, Mikael; Olsson, Johanna; Olsson, Olof

    2011-01-01

    Plant mutagenesis is rapidly coming of age in the aftermath of recent developments in high-resolution molecular and biochemical techniques. By combining the high variation of mutagenised populations with novel screening methods, traits that are almost impossible to identify by conventional breeding are now being developed and characterised at the molecular level. This paper provides a comprehensive overview of the various techniques and workflows available to researchers today in the field of molecular breeding, and how these tools complement the ones already used in traditional breeding. Both genetic (Targeting Induced Local Lesions in Genomes; TILLING) and phenotypic screens are evaluated. Finally, different ways of bridging the gap between genotype and phenotype are discussed. PMID:22315587

  10. Whole genome scanning as a cytogenetic tool in hematologic malignancies

    PubMed Central

    Mufti, Ghulam J.

    2008-01-01

    Over the years, methods of cytogenetic analysis evolved and became part of routine laboratory testing, providing valuable diagnostic and prognostic information in hematologic disorders. Karyotypic aberrations contribute to the understanding of the molecular pathogenesis of disease and thereby to rational application of therapeutic modalities. Most of the progress in this field stems from the application of metaphase cytogenetics (MC), but recently, novel molecular technologies have been introduced that complement MC and overcome many of the limitations of traditional cytogenetics, including a need for cell culture. Whole genome scanning using comparative genomic hybridization and single nucleotide polymorphism arrays (CGH-A; SNP-A) can be used for analysis of somatic or clonal unbalanced chromosomal defects. In SNP-A, the combination of copy number detection and genotyping enables diagnosis of copy-neutral loss of heterozygosity, a lesion that cannot be detected using MC but may have important pathogenetic implications. Overall, whole genome scanning arrays, despite the drawback of an inability to detect balanced translocations, allow for discovery of chromosomal defects in a higher proportion of patients with hematologic malignancies. Newly detected chromosomal aberrations, including somatic uniparental disomy, may lead to more precise prognostic schemes in many diseases. PMID:18505780

  11. Software Tools for Empowering Instructional Developers.

    ERIC Educational Resources Information Center

    Gayeski, Diane M.

    1991-01-01

    Software systems are being created to assist both novice and expert instructional technologists in response to perceived need of organizations to increase their training. Underlying philosophies and goals of instructional developer automation tools and their potential effects upon the organizations who adopt them must be examined so they will help…

  12. Update on SLD Engineering Tools Development

    NASA Technical Reports Server (NTRS)

    Miller, Dean R.; Potapczuk, Mark G.; Bond, Thomas H.

    2004-01-01

    The airworthiness authorities (FAA, JAA, Transport Canada) will be releasing a draft rule in the 2006 timeframe concerning the operation of aircraft in a Supercooled Large Droplet (SLD) environment aloft. The draft rule will require aircraft manufacturers to demonstrate that their aircraft can operate safely in an SLD environment for a period of time to facilitate a safe exit from the condition. It is anticipated that aircraft manufacturers will require a capability to demonstrate compliance with this rule via experimental means (icing tunnels or tankers) and by analytical means (ice prediction codes). Since existing icing research facilities and analytical codes were not developed to account for SLD conditions, current engineering tools are not adequate to support compliance activities in SLD conditions. Therefore, existing capabilities need to be augmented to include SLD conditions. In response to this need, NASA and its partners conceived a strategy or Roadmap for developing experimental and analytical SLD simulation tools. Following review and refinement by the airworthiness authorities and other international research partners, this technical strategy has been crystallized into a project plan to guide the SLD Engineering Tool Development effort. This paper will provide a brief overview of the latest version of the project plan and technical rationale, and provide a status of selected SLD Engineering Tool Development research tasks which are currently underway.

  13. New bioinformatic tool for quick identification of functionally relevant endogenous retroviral inserts in human genome.

    PubMed

    Garazha, Andrew; Ivanova, Alena; Suntsova, Maria; Malakhova, Galina; Roumiantsev, Sergey; Zhavoronkov, Alex; Buzdin, Anton

    2015-01-01

    Endogenous retroviruses (ERVs) and LTR retrotransposons (LRs) occupy ∼8% of human genome. Deep sequencing technologies provide clues to understanding of functional relevance of individual ERVs/LRs by enabling direct identification of transcription factor binding sites (TFBS) and other landmarks of functional genomic elements. Here, we performed the genome-wide identification of human ERVs/LRs containing TFBS according to the ENCODE project. We created the first interactive ERV/LRs database that groups the individual inserts according to their familial nomenclature, number of mapped TFBS and divergence from their consensus sequence. Information on any particular element can be easily extracted by the user. We also created a genome browser tool, which enables quick mapping of any ERV/LR insert according to genomic coordinates, known human genes and TFBS. These tools can be used to easily explore functionally relevant individual ERV/LRs, and for studying their impact on the regulation of human genes. Overall, we identified ∼110,000 ERV/LR genomic elements having TFBS. We propose a hypothesis of "domestication" of ERV/LR TFBS by the genome milieu including subsequent stages of initial epigenetic repression, partial functional release, and further mutation-driven reshaping of TFBS in tight coevolution with the enclosing genomic loci.

  14. New bioinformatic tool for quick identification of functionally relevant endogenous retroviral inserts in human genome

    PubMed Central

    Garazha, Andrew; Ivanova, Alena; Suntsova, Maria; Malakhova, Galina; Roumiantsev, Sergey; Zhavoronkov, Alex; Buzdin, Anton

    2015-01-01

    Abstract Endogenous retroviruses (ERVs) and LTR retrotransposons (LRs) occupy ∼8% of human genome. Deep sequencing technologies provide clues to understanding of functional relevance of individual ERVs/LRs by enabling direct identification of transcription factor binding sites (TFBS) and other landmarks of functional genomic elements. Here, we performed the genome-wide identification of human ERVs/LRs containing TFBS according to the ENCODE project. We created the first interactive ERV/LRs database that groups the individual inserts according to their familial nomenclature, number of mapped TFBS and divergence from their consensus sequence. Information on any particular element can be easily extracted by the user. We also created a genome browser tool, which enables quick mapping of any ERV/LR insert according to genomic coordinates, known human genes and TFBS. These tools can be used to easily explore functionally relevant individual ERV/LRs, and for studying their impact on the regulation of human genes. Overall, we identified ∼110,000 ERV/LR genomic elements having TFBS. We propose a hypothesis of “domestication” of ERV/LR TFBS by the genome milieu including subsequent stages of initial epigenetic repression, partial functional release, and further mutation-driven reshaping of TFBS in tight coevolution with the enclosing genomic loci. PMID:25853282

  15. A genomic regulatory network for development

    NASA Technical Reports Server (NTRS)

    Davidson, Eric H.; Rast, Jonathan P.; Oliveri, Paola; Ransick, Andrew; Calestani, Cristina; Yuh, Chiou-Hwa; Minokawa, Takuya; Amore, Gabriele; Hinman, Veronica; Arenas-Mena, Cesar; Otim, Ochan; Brown, C. Titus; Livi, Carolina B.; Lee, Pei Yun; Revilla, Roger; Rust, Alistair G.; Pan, Zheng jun; Schilstra, Maria J.; Clarke, Peter J C.; Arnone, Maria I.; Rowen, Lee; Cameron, R. Andrew; McClay, David R.; Hood, Leroy; Bolouri, Hamid

    2002-01-01

    Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.

  16. OntoMate: a text-mining tool aiding curation at the Rat Genome Database.

    PubMed

    Liu, Weisong; Laulederkind, Stanley J F; Hayman, G Thomas; Wang, Shur-Jen; Nigam, Rajni; Smith, Jennifer R; De Pons, Jeff; Dwinell, Melinda R; Shimoyama, Mary

    2015-01-01

    The Rat Genome Database (RGD) is the premier repository of rat genomic, genetic and physiologic data. Converting data from free text in the scientific literature to a structured format is one of the main tasks of all model organism databases. RGD spends considerable effort manually curating gene, Quantitative Trait Locus (QTL) and strain information. The rapidly growing volume of biomedical literature and the active research in the biological natural language processing (bioNLP) community have given RGD the impetus to adopt text-mining tools to improve curation efficiency. Recently, RGD has initiated a project to use OntoMate, an ontology-driven, concept-based literature search engine developed at RGD, as a replacement for the PubMed (http://www.ncbi.nlm.nih.gov/pubmed) search engine in the gene curation workflow. OntoMate tags abstracts with gene names, gene mutations, organism name and most of the 16 ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. All listed terms are linked both to data entry boxes and a term browser in the curation tool. OntoMate also provides user-activated filters for species, date and other parameters relevant to the literature search. Using the system for literature search and import has streamlined the process compared to using PubMed. The system was built with a scalable and open architecture, including features specifically designed to accelerate the RGD gene curation process. With the use of bioNLP tools, RGD has added more automation to its curation workflow. Database URL: http://rgd.mcw.edu.

  17. OntoMate: a text-mining tool aiding curation at the Rat Genome Database

    PubMed Central

    Liu, Weisong; Laulederkind, Stanley J. F.; Hayman, G. Thomas; Wang, Shur-Jen; Nigam, Rajni; Smith, Jennifer R.; De Pons, Jeff; Dwinell, Melinda R.; Shimoyama, Mary

    2015-01-01

    The Rat Genome Database (RGD) is the premier repository of rat genomic, genetic and physiologic data. Converting data from free text in the scientific literature to a structured format is one of the main tasks of all model organism databases. RGD spends considerable effort manually curating gene, Quantitative Trait Locus (QTL) and strain information. The rapidly growing volume of biomedical literature and the active research in the biological natural language processing (bioNLP) community have given RGD the impetus to adopt text-mining tools to improve curation efficiency. Recently, RGD has initiated a project to use OntoMate, an ontology-driven, concept-based literature search engine developed at RGD, as a replacement for the PubMed (http://www.ncbi.nlm.nih.gov/pubmed) search engine in the gene curation workflow. OntoMate tags abstracts with gene names, gene mutations, organism name and most of the 16 ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. All listed terms are linked both to data entry boxes and a term browser in the curation tool. OntoMate also provides user-activated filters for species, date and other parameters relevant to the literature search. Using the system for literature search and import has streamlined the process compared to using PubMed. The system was built with a scalable and open architecture, including features specifically designed to accelerate the RGD gene curation process. With the use of bioNLP tools, RGD has added more automation to its curation workflow. Database URL: http://rgd.mcw.edu PMID:25619558

  18. H1640 caster tool development report

    SciTech Connect

    Brown, L.A.

    1997-12-01

    This report describes the development and certification of the H1640 caster tool. This tool is used to rotate swivel caster wheels 90 degrees on bomb hand trucks or shipping containers. The B83 is a heavy bomb system and weighs close to 5,600 pounds for a two-high stack configuration. High castering moments (handle length times the force exerted on handle) are required to caster a wheel for a two-high stack of B83s. The H1640 is available to the DoD (Air Force) through the Special Equipment List (SEL) for the B83 as a replacement for the H631 and H1216 caster tools.

  19. CVTree: a phylogenetic tree reconstruction tool based on whole genomes.

    PubMed

    Qi, Ji; Luo, Hong; Hao, Bailin

    2004-07-01

    Composition Vector Tree (CVTree) implements a systematic method of inferring evolutionary relatedness of microbial organisms from the oligopeptide content of their complete proteomes (http://cvtree.cbi.pku.edu.cn). Since the first bacterial genomes were sequenced in 1995 there have been several attempts to infer prokaryote phylogeny from complete genomes. Most of them depend on sequence alignment directly or indirectly and, in some cases, need fine-tuning and adjustment. The composition vector method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of aligning sequences of essentially different length and gene content. This new method does not contain 'free' parameter and 'fine-tuning'. A bootstrap test for a phylogenetic tree of 139 organisms has shown the stability of the branchings, which support the small subunit ribosomal RNA (SSU rRNA) tree of life in its overall structure and in many details. It may provide a quick reference in prokaryote phylogenetics whenever the proteome of an organism is available, a situation that will become commonplace in the near future.

  20. Gnome View: A tool for visual representation of human genome data

    SciTech Connect

    Pelkey, J.E.; Thomas, G.S.; Thurman, D.A.; Lortz, V.B.; Douthart, R.J.

    1993-02-01

    GnomeView is a tool for exploring data generated by the Human Gemone Project. GnomeView provides both graphical and textural styles of data presentation: employs an intuitive window-based graphical query interface: and integrates its underlying genome databases in such a way that the user can navigate smoothly across databases and between different levels of data. This paper describes GnomeView and discusses how it addresses various genome informatics issues.

  1. CGUG: in silico proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to ca. 1.9 Mb

    PubMed Central

    Mahadevan, Padmanabhan; King, John F; Seto, Donald

    2009-01-01

    Background Viruses and small-genome bacteria (~2 megabases and smaller) comprise a considerable population in the biosphere and are of interest to many researchers. These genomes are now sequenced at an unprecedented rate and require complementary computational tools to analyze. "CoreGenesUniqueGenes" (CGUG) is an in silico genome data mining tool that determines a "core" set of genes from two to five organisms with genomes in this size range. Core and unique genes may reflect similar niches and needs, and may be used in classifying organisms. Findings CGUG is available at as a web-based on-the-fly tool that performs iterative BLASTP analyses using a reference genome and up to four query genomes to provide a table of genes common to these genomes. The result is an in silico display of genomes and their proteomes, allowing for further analysis. CGUG can be used for "genome annotation by homology", as demonstrated with Chlamydophila and Francisella genomes. Conclusion CGUG is used to reanalyze the ICTV-based classifications of bacteriophages, to reconfirm long-standing relationships and to explore new classifications. These genomes have been problematic in the past, due largely to horizontal gene transfers. CGUG is validated as a tool for reannotating small genome bacteria using more up-to-date annotations by similarity or homology. These serve as an entry point for wet-bench experiments to confirm the functions of these "hypothetical" and "unknown" proteins. PMID:19706165

  2. Kvik: three-tier data exploration tools for flexible analysis of genomic data in epidemiological studies

    PubMed Central

    Fjukstad, Bjørn; Standahl Olsen, Karina; Jareid, Mie; Lund, Eiliv; Bongo, Lars Ailo

    2015-01-01

    Kvik is an open-source framework that we developed for explorative analysis of functional genomics data from large epidemiological studies. Creating such studies requires a significant amount of time and resources. It is therefore usual to reuse the data from one study for several research projects. Often each project requires implementing new analysis code, integration with specific knowledge bases, and specific visualizations. Although existing data exploration tools are available for single study data exploration, no tool provides all the required functionality for multistudy data exploration. We have therefore used the Kvik framework to develop Kvik Pathways, an application for exploring gene expression data in the context of biological pathways. We have used Kvik Pathways to explore data from both a cross-sectional study design and a case-control study within the Norwegian Women and Cancer (NOWAC) cohort. Kvik Pathways follows the three-tier architecture in web applications using a powerful back-end for statistical analyses and retrieval of metadata.In this note, we describe how we used the Kvik framework to develop the Kvik Pathways application. Kvik Pathways was used by our team of epidemiologists toexplore gene expression data from healthy women with high and low plasma ratios of essential fatty acids. PMID:26425340

  3. Kvik: three-tier data exploration tools for flexible analysis of genomic data in epidemiological studies.

    PubMed

    Fjukstad, Bjørn; Standahl Olsen, Karina; Jareid, Mie; Lund, Eiliv; Bongo, Lars Ailo

    2015-01-01

    Kvik is an open-source framework that we developed for explorative analysis of functional genomics data from large epidemiological studies. Creating such studies requires a significant amount of time and resources. It is therefore usual to reuse the data from one study for several research projects. Often each project requires implementing new analysis code, integration with specific knowledge bases, and specific visualizations. Although existing data exploration tools are available for single study data exploration, no tool provides all the required functionality for multistudy data exploration. We have therefore used the Kvik framework to develop Kvik Pathways, an application for exploring gene expression data in the context of biological pathways. We have used Kvik Pathways to explore data from both a cross-sectional study design and a case-control study within the Norwegian Women and Cancer (NOWAC) cohort. Kvik Pathways follows the three-tier architecture in web applications using a powerful back-end for statistical analyses and retrieval of metadata.In this note, we describe how we used the Kvik framework to develop the Kvik Pathways application. Kvik Pathways was used by our team of epidemiologists toexplore gene expression data from healthy women with high and low plasma ratios of essential fatty acids. PMID:26425340

  4. Kvik: three-tier data exploration tools for flexible analysis of genomic data in epidemiological studies.

    PubMed

    Fjukstad, Bjørn; Standahl Olsen, Karina; Jareid, Mie; Lund, Eiliv; Bongo, Lars Ailo

    2015-01-01

    Kvik is an open-source framework that we developed for explorative analysis of functional genomics data from large epidemiological studies. Creating such studies requires a significant amount of time and resources. It is therefore usual to reuse the data from one study for several research projects. Often each project requires implementing new analysis code, integration with specific knowledge bases, and specific visualizations. Although existing data exploration tools are available for single study data exploration, no tool provides all the required functionality for multistudy data exploration. We have therefore used the Kvik framework to develop Kvik Pathways, an application for exploring gene expression data in the context of biological pathways. We have used Kvik Pathways to explore data from both a cross-sectional study design and a case-control study within the Norwegian Women and Cancer (NOWAC) cohort. Kvik Pathways follows the three-tier architecture in web applications using a powerful back-end for statistical analyses and retrieval of metadata.In this note, we describe how we used the Kvik framework to develop the Kvik Pathways application. Kvik Pathways was used by our team of epidemiologists toexplore gene expression data from healthy women with high and low plasma ratios of essential fatty acids.

  5. Development of a HT seismic downhole tool.

    SciTech Connect

    Maldonado, Frank P.; Greving, Jeffrey J.; Henfling, Joseph Anthony; Chavira, David J.; Uhl, James Eugene; Polsky, Yarom

    2009-06-01

    Enhanced Geothermal Systems (EGS) require the stimulation of the drilled well, likely through hydraulic fracturing. Whether fracturing of the rock occurs by shear destabilization of natural fractures or by extensional failure of weaker zones, control of the fracture process will be required to create the flow paths necessary for effective heat mining. As such, microseismic monitoring provides one method for real-time mapping of the fractures created during the hydraulic fracturing process. This monitoring is necessary to help assess stimulation effectiveness and provide the information necessary to properly create the reservoir. In addition, reservoir monitoring of the microseismic activity can provide information on reservoir performance and evolution over time. To our knowledge, no seismic tool exists that will operate above 125 C for the long monitoring durations that may be necessary. Replacing failed tools is costly and introduces potential errors such as depth variance, etc. Sandia has designed a high temperature seismic tool for long-term deployment in geothermal applications. It is capable of detecting microseismic events and operating continuously at temperatures up to 240 C. This project includes the design and fabrication of two High Temperature (HT) seismic tools that will have the capability to operate in both temporary and long-term monitoring modes. To ensure the developed tool meets industry requirements for high sampling rates (>2ksps) and high resolution (24-bit Analog-to-Digital Converter) two electronic designs will be implemented. One electronic design will utilize newly developed 200 C electronic components. The other design will use qualified Silicon-on-Insulator (SOI) devices and will have a continuous operating temperature of 240 C.

  6. Development of wavelet analysis tools for turbulence

    NASA Technical Reports Server (NTRS)

    Bertelrud, A.; Erlebacher, G.; Dussouillez, PH.; Liandrat, M. P.; Liandrat, J.; Bailly, F. Moret; Tchamitchian, PH.

    1992-01-01

    Presented here is the general framework and the initial results of a joint effort to derive novel research tools and easy to use software to analyze and model turbulence and transition. Given here is a brief review of the issues, a summary of some basic properties of wavelets, and preliminary results. Technical aspects of the implementation, the physical conclusions reached at this time, and current developments are discussed.

  7. Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing

    PubMed Central

    Tacutu, Robi; Craig, Thomas; Budovsky, Arie; Wuttke, Daniel; Lehmann, Gilad; Taranukha, Dmitri; Costa, Joana; Fraifeld, Vadim E.; de Magalhães, João Pedro

    2013-01-01

    The Human Ageing Genomic Resources (HAGR, http://genomics.senescence.info) is a freely available online collection of research databases and tools for the biology and genetics of ageing. HAGR features now several databases with high-quality manually curated data: (i) GenAge, a database of genes associated with ageing in humans and model organisms; (ii) AnAge, an extensive collection of longevity records and complementary traits for >4000 vertebrate species; and (iii) GenDR, a newly incorporated database, containing both gene mutations that interfere with dietary restriction-mediated lifespan extension and consistent gene expression changes induced by dietary restriction. Since its creation about 10 years ago, major efforts have been undertaken to maintain the quality of data in HAGR, while further continuing to develop, improve and extend it. This article briefly describes the content of HAGR and details the major updates since its previous publications, in terms of both structure and content. The completely redesigned interface, more intuitive and more integrative of HAGR resources, is also presented. Altogether, we hope that through its improvements, the current version of HAGR will continue to provide users with the most comprehensive and accessible resources available today in the field of biogerontology. PMID:23193293

  8. Human Ageing Genomic Resources: integrated databases and tools for the biology and genetics of ageing.

    PubMed

    Tacutu, Robi; Craig, Thomas; Budovsky, Arie; Wuttke, Daniel; Lehmann, Gilad; Taranukha, Dmitri; Costa, Joana; Fraifeld, Vadim E; de Magalhães, João Pedro

    2013-01-01

    The Human Ageing Genomic Resources (HAGR, http://genomics.senescence.info) is a freely available online collection of research databases and tools for the biology and genetics of ageing. HAGR features now several databases with high-quality manually curated data: (i) GenAge, a database of genes associated with ageing in humans and model organisms; (ii) AnAge, an extensive collection of longevity records and complementary traits for >4000 vertebrate species; and (iii) GenDR, a newly incorporated database, containing both gene mutations that interfere with dietary restriction-mediated lifespan extension and consistent gene expression changes induced by dietary restriction. Since its creation about 10 years ago, major efforts have been undertaken to maintain the quality of data in HAGR, while further continuing to develop, improve and extend it. This article briefly describes the content of HAGR and details the major updates since its previous publications, in terms of both structure and content. The completely redesigned interface, more intuitive and more integrative of HAGR resources, is also presented. Altogether, we hope that through its improvements, the current version of HAGR will continue to provide users with the most comprehensive and accessible resources available today in the field of biogerontology.

  9. GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture

    PubMed Central

    Guðbjartsson, Hákon; Georgsson, Guðmundur Fr.; Guðjónsson, Sigurjón A.; Valdimarsson, Ragnar þór; Sigurðsson, Jóhann H.; Stefánsson, Sigmar K.; Másson, Gísli; Magnússon, Gísli; Pálmason, Vilmundur; Stefánsson, Kári

    2016-01-01

    Motivation: Our aim was to create a general-purpose relational data format and analysis tools to provide an efficient and coherent framework for working with large volumes of DNA sequence data. Results: For this purpose we developed the GORpipe software system. It is based on a genomic ordered architecture and uses a declarative query language that combines features from SQL and shell pipe syntax in a novel manner. The system can for instance be used to annotate sequence variants, find genomic spatial overlap between various types of genomic features, filter and aggregate them in various ways. Availability and Implementation: The GORpipe software is freely available for non-commercial academic usage and can be downloaded from www.nextcode.com/gorpipe. Contact: hakon@wuxinextcode.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27339714

  10. nWayComp: a genome-wide sequence comparison tool for multiple strains/species of phylogenetically related microorganisms.

    PubMed

    Yao, Jiqiang; Lin, Hong; Doddapaneni, Harshavardhan; Civerolo, Edwin L

    2007-01-01

    The increasing number of whole genomic sequences of microorganisms has led to the complexity of genome-wide annotation and gene sequence comparison among multiple microorganisms. To address this problem, we have developed nWayComp software that compares DNA and protein sequences of phylogenetically-related microorganisms. This package integrates a series of bioinformatics tools such as BLAST, ClustalW, ALIGN, PHYLIP and PRIMER3 for sequence comparison. It searches for homologous sequences among multiple organisms and identifies genes that are unique to a particular organism. The homologous gene sets are then ranked in the descending order of the sequence similarity. For each set of homologous sequences, a table of sequence identity among homologous genes along with sequence variations such as SNPs and INDELS is developed, and a phylogenetic tree is constructed. In addition, a common set of primers that can amplify all the homologous sequences are generated. The nWayComp package provides users with a quick and convenient tool to compare genomic sequences among multiple organisms at the whole-genome level. PMID:17688445

  11. MAAP: a versatile and universal tool for genome analysis.

    PubMed

    Caetano-Anollés, G

    1994-09-01

    Multiple arbitrary amplicon profiling (MAAP) uses one or more oligonucleotide primers (> or = 5 nt) of arbitrary sequence to initiate DNA amplification and generate characteristic fingerprints from anonymous genomes or DNA templates. MAAP markers can be used in general fingerprinting as well as in mapping applications, either directly or as sequence-characterized amplified regions (SCARs). MAAP profiles can be tailored in the number of monomorphic and/or polymorphic products. For example, multiple endonuclease digestion of template DNA or the use of mini-hairpin primers can enhance detection of polymorphic DNA. Comparison of the expected and actual number of amplification products produced with primers differing in length, sequence and GC content from templates of varying complexity reveal severe departures from theoretical formulations with interesting implications in primer-template interaction. Extensive primer-template mismatching can occur when using templates of low complexity or long primers. Primer annealing and extension appears directed by an 8 nt 3'-terminal primer domain, requires sites with perfect homology to the first 5-6 nt fom the 3' terminus, and involves direct physical interaction between amplicon annealing sites.

  12. Fernald Silo Remote Retrieval Tool Development

    SciTech Connect

    Varma, V.K.

    2004-05-18

    A long-reach tool was developed to remove discrete objects from the silos at the Fernald Environmental Management Project in Ohio. If they are not removed, these objects can potentially cause problems during the retrieval and transfer of waste from the silos. Most of the objects are on top of the Bentogrout cap inside the silos at or near the primary opening into the tank and will therefore require only vertical lifting. The objects are located about 20 ft from the top of the silo. Although most of the objects can be retrieved from 20 ft, the long-reach tool was designed to for a reach up to 40 ft in case objects roll towards the walls of the tank or need to be removed during heel retrieval operations. This report provides a detailed description of the tool that was developed, tested, and demonstrated at the Tanks Technology Cold Test Facility at Oak Ridge National Laboratory. Scaffolding was erected over two experimental cells to simulate the 40-ft maximum working depth anticipated in the silos at Fernald. Plastic bottles and plastic sheeting simulated the debris that could be encountered during waste retrieval operations.

  13. Mapping by sequencing the Pneumocystis genome using the ordering DNA sequences V3 tool.

    PubMed

    Xu, Zheng; Lance, Britton; Vargas, Claudia; Arpinar, Budak; Bhandarkar, Suchendra; Kraemer, Eileen; Kochut, Krys J; Miller, John A; Wagner, Jeff R; Weise, Michael J; Wunderlich, John K; Stringer, James; Smulian, George; Cushion, Melanie T; Arnold, Jonathan

    2003-04-01

    A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits an integrated genome map to be stored, retrieved, viewed, and queried in a stand-alone capacity, in a client/server relationship with the Fungal Genome Database (FGDB), and as a web-browsing tool for the FGDB. In that ODS3 is programmed in Java, the tool promotes platform independence and supports export of integrated genome-mapping data in the extensible markup language (XML) for data interchange with other genome information systems. The tool ODS3 is used to create an initial integrated genome map of the AIDS-related fungal pathogen, Pneumocystis carinii. Contig dynamics would indicate that this physical map is approximately 50% complete with approximately 200 contigs. A total of 10 putative multigene families were found. Two of these putative families were previously characterized in P. carinii, namely the major surface glycoproteins (MSGs) and HSP70 proteins; three of these putative families (not previously characterized in P. carinii) were found to be similar to families encoding the HSP60 in Schizosaccharomyces pombe, the heat-shock psi protein in S. pombe, and the RNA synthetase family (i.e., MES1) in Saccharomyces cerevisiae. Physical mapping data are consistent with the 16S, 5.8S, and 26S rDNA genes being single copy in P. carinii. No other fungus outside this genus is known to have the rDNA genes in single copy.

  14. PIPEMicroDB: microsatellite database and primer generation tool for pigeonpea genome.

    PubMed

    Sarika; Arora, Vasu; Iquebal, M A; Rai, Anil; Kumar, Dinesh

    2013-01-01

    Molecular markers play a significant role for crop improvement in desirable characteristics, such as high yield, resistance to disease and others that will benefit the crop in long term. Pigeonpea (Cajanus cajan L.) is the recently sequenced legume by global consortium led by ICRISAT (Hyderabad, India) and been analysed for gene prediction, synteny maps, markers, etc. We present PIgeonPEa Microsatellite DataBase (PIPEMicroDB) with an automated primer designing tool for pigeonpea genome, based on chromosome wise as well as location wise search of primers. Total of 123 387 Short Tandem Repeats (STRs) were extracted from pigeonpea genome, available in public domain using MIcroSAtellite tool (MISA). The database is an online relational database based on 'three-tier architecture' that catalogues information of microsatellites in MySQL and user-friendly interface is developed using PHP. Search for STRs may be customized by limiting their location on chromosome as well as number of markers in that range. This is a novel approach and is not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of selected markers with left and right flankings of size up to 500 bp. This will enable researchers to select markers of choice at desired interval over the chromosome. Furthermore, one can use individual STRs of a targeted region over chromosome to narrow down location of gene of interest or linked Quantitative Trait Loci (QTLs). Although it is an in silico approach, markers' search based on characteristics and location of STRs is expected to be beneficial for researchers. Database URL: http://cabindb.iasri.res.in/pigeonpea/ PMID:23396298

  15. Spatial Genome Organization and Its Emerging Role as a Potential Diagnosis Tool

    PubMed Central

    Meaburn, Karen J.

    2016-01-01

    In eukaryotic cells the genome is highly spatially organized. Functional relevance of higher order genome organization is implied by the fact that specific genes, and even whole chromosomes, alter spatial position in concert with functional changes within the nucleus, for example with modifications to chromatin or transcription. The exact molecular pathways that regulate spatial genome organization and the full implication to the cell of such an organization remain to be determined. However, there is a growing realization that the spatial organization of the genome can be used as a marker of disease. While global genome organization patterns remain largely conserved in disease, some genes and chromosomes occupy distinct nuclear positions in diseased cells compared to their normal counterparts, with the patterns of reorganization differing between diseases. Importantly, mapping the spatial positioning patterns of specific genomic loci can distinguish cancerous tissue from benign with high accuracy. Genome positioning is an attractive novel biomarker since additional quantitative biomarkers are urgently required in many cancer types. Current diagnostic techniques are often subjective and generally lack the ability to identify aggressive cancer from indolent, which can lead to over- or under-treatment of patients. Proof-of-principle for the use of genome positioning as a diagnostic tool has been provided based on small scale retrospective studies. Future large-scale studies are required to assess the feasibility of bringing spatial genome organization-based diagnostics to the clinical setting and to determine if the positioning patterns of specific loci can be useful biomarkers for cancer prognosis. Since spatial reorganization of the genome has been identified in multiple human diseases, it is likely that spatial genome positioning patterns as a diagnostic biomarker may be applied to many diseases. PMID:27507988

  16. Process-Based Quality (PBQ) Tools Development

    SciTech Connect

    Cummins, J.L.

    2001-12-03

    The objective of this effort is to benchmark the development of process-based quality tools for application in CAD (computer-aided design) model-based applications. The processes of interest are design, manufacturing, and quality process applications. A study was commissioned addressing the impact, current technologies, and known problem areas in application of 3D MCAD (3-dimensional mechanical computer-aided design) models and model integrity on downstream manufacturing and quality processes. The downstream manufacturing and product quality processes are profoundly influenced and dependent on model quality and modeling process integrity. The goal is to illustrate and expedite the modeling and downstream model-based technologies for available or conceptual methods and tools to achieve maximum economic advantage and advance process-based quality concepts.

  17. Applying genomic and bioinformatic resources to human adenovirus genomes for use in vaccine development and for applications in vector development for gene delivery.

    PubMed

    Seto, Jason; Walsh, Michael P; Mahadevan, Padmanabhan; Zhang, Qiwei; Seto, Donald

    2010-01-01

    Technological advances and increasingly cost-effect methodologies in DNA sequencing and computational analysis are providing genome and proteome data for human adenovirus research. Applying these tools, data and derived knowledge to the development of vaccines against these pathogens will provide effective prophylactics. The same data and approaches can be applied to vector development for gene delivery in gene therapy and vaccine delivery protocols. Examination of several field strain genomes and their analyses provide examples of data that are available using these approaches. An example of the development of HAdV-B3 both as a vaccine and also as a vector is presented.

  18. Bioinformatic tools for using whole genome sequencing as a rapid high resolution diagnostic typing tool when tracing bioterror organisms in the food and feed chain.

    PubMed

    Segerman, Bo; De Medici, Dario; Ehling Schulz, Monika; Fach, Patrick; Fenicia, Lucia; Fricker, Martina; Wielinga, Peter; Van Rotterdam, Bart; Knutsson, Rickard

    2011-03-01

    The rapid technological development in the field of parallel sequencing offers new opportunities when tracing and tracking microorganisms in the food and feed chain. If a bioterror organism is deliberately spread it is of crucial importance to get as much information as possible regarding the strain as fast as possible to aid the decision process and select suitable controls, tracing and tracking tools. A lot of efforts have been made to sequence multiple strains of potential bioterror organisms so there is a relatively large set of reference genomes available. This study is focused on how to use parallel sequencing for rapid phylogenomic analysis and screen for genetic modifications. A bioinformatic methodology has been developed to rapidly analyze sequence data with minimal post-processing. Instead of assembling the genome, defining genes, defining orthologous relations and calculating distances, the present method can achieve a similar high resolution directly from the raw sequence data. The method defines orthologous sequence reads instead of orthologous genes and the average similarity of the core genome (ASC) is calculated. The sequence reads from the core and from the non-conserved genomic regions can also be separated for further analysis. Finally, the comparison algorithm is used to visualize the phylogenomic diversity of the bacterial bioterror organisms Bacillus anthracis and Clostridium botulinum using heat plot diagrams.

  19. Genetic and Genomic Tools for the Marine Annelid Platynereis dumerilii

    PubMed Central

    Zantke, Juliane; Bannister, Stephanie; Rajan, Vinoth Babu Veedin; Raible, Florian; Tessmar-Raible, Kristin

    2014-01-01

    The bristle worm Platynereis dumerilii displays many interesting biological characteristics. These include its reproductive timing, which is synchronized to the moon phase, its regenerative capacity that is hormonally controlled, and a slow rate of evolution, which permits analyses of ancestral genes and cell types. As a marine annelid, Platynereis is also representative of the marine ecosystem, as well as one of the three large animal subphyla, the Lophotrochozoa. Here, we provide an overview of the molecular resources, functional techniques, and behavioral assays that have recently been established for the bristle worm. This combination of tools now places Platynereis in an excellent position to advance research at the frontiers of neurobiology, chronobiology, evo-devo, and marine biology. PMID:24807110

  20. Developing a mapping tool for tablets

    NASA Astrophysics Data System (ADS)

    Vaughan, Alan; Collins, Nathan; Krus, Mike

    2014-05-01

    Digital field mapping offers significant benefits when compared with traditional paper mapping techniques in that it provides closer integration with downstream geological modelling and analysis. It also provides the mapper with the ability to rapidly integrate new data with existing databases without the potential degradation caused by repeated manual transcription of numeric, graphical and meta-data. In order to achieve these benefits, a number of PC-based digital mapping tools are available which have been developed for specific communities, eg the BGS•SIGMA project, Midland Valley's FieldMove®, and a range of solutions based on ArcGIS® software, which can be combined with either traditional or digital orientation and data collection tools. However, with the now widespread availability of inexpensive tablets and smart phones, a user led demand for a fully integrated tablet mapping tool has arisen. This poster describes the development of a tablet-based mapping environment specifically designed for geologists. The challenge was to deliver a system that would feel sufficiently close to the flexibility of paper-based geological mapping while being implemented on a consumer communication and entertainment device. The first release of a tablet-based geological mapping system from this project is illustrated and will be shown as implemented on an iPad during the poster session. Midland Valley is pioneering tablet-based mapping and, along with its industrial and academic partners, will be using the application in field based projects throughout this year and will be integrating feedback in further developments of this technology.

  1. CRISPR/Cas9-based tools for targeted genome editing and replication control of HBV.

    PubMed

    Peng, Cheng; Lu, Mengji; Yang, Dongliang

    2015-10-01

    Hepatitis B virus (HBV) infection remains a major global health problem because current therapies rarely eliminate HBV infections to achieve a complete cure. A different treatment paradigm to effectively clear HBV infection and eradicate latent viral reservoirs is urgently required. In recent years, the development of a new RNA-guided gene-editing tool, the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease 9) system, has greatly facilitated site-specific mutagenesis and represents a very promising potential therapeutic tool for diseases, including for eradication of invasive pathogens such as HBV. Here, we review recent advances in the use of CRISPR/Cas9, which is designed to target HBV specific DNA sequences to inhibit HBV replication and to induce viral genome mutation, in cell lines or animal models. Advantages, limitations and possible solutions, and proposed directions for future research are discussed to highlight the opportunities and challenges of CRISPR/Cas9 as a new, potentially curative therapy for chronic hepatitis B infection.

  2. Development of a lightning activity nowcasting tool

    NASA Astrophysics Data System (ADS)

    Karagiannidis, Athanassios; Lagouvardos, Kostas; Kotroni, Vassiliki

    2015-04-01

    Electrical phenomena inside thunderstorm clouds are a significant threat to numerous activities. Summertime convective activity is usually associated to local thermal instability, which is hard to predict using numerical weather prediction models. Despite their relatively small areal extend, these thunderstorms can be violent, resulting to infrastructure damage and loss of life. In the frame of TALOS project the National Observatory of Athens has developed a lightning activity nowcasting tool. This tool uses as sole inputs: (i) real time infrared Meteosat Second Generation (MSG) imagery and (ii) real time flashes provided by the VLF lightning detection system ZEUS, which is operated by the National Observatory of Athens. The MSG SEVIRI 10.8 and 6.2μm channels data are utilized to produce 3 Interest Fields (IFs). These fields are the TB10.8 brightness temperature (indicative of the cloud top glaciation), the TB6.2-TB10.8 difference (indicative of the cloud depth) and the TB10.8 15 minute trend, which will be referenced as "TB10.8trend" (indicative of the cloud growth rate). The latter is defined as the difference between two successive 15 minutes images of the TB10.8. When a predefined threshold value is surpassed, the delimited area is considered to be favorable for lightning activity. A statistical procedure is employed to identify the optimum threshold values for the three IFs, based on the performance of each one. The assessment of their efficiency showed that these three IFs can be used independently as predictors of lightning activity. However, in an effort to improve the tool's efficiency a combined estimation is performed. When all three IFs agree that lightning activity is expected over an area, then a Warning Level 3 (WL3) is issued. When 2 or 1 IFs indicate upcoming activity then a WL2 or WL1 is issued. The assessment of the efficiency of the combined IF tool showed that the combined estimation is more skillful than the individual IFs estimations. In a

  3. Synonymous Virus Genome Recoding as a Tool to Impact Viral Fitness.

    PubMed

    Martínez, Miguel Angel; Jordan-Paiz, Ana; Franco, Sandra; Nevot, Maria

    2016-02-01

    Synthetic genome recoding is a novel method of generating viruses with altered phenotypes, whereby many synonymous mutations are introduced into the protein coding region of the virus genome without altering the encoded proteins. Virus genome recoding with large numbers of slightly deleterious mutations has produced attenuated forms of several RNA viruses. Virus genome recoding can also aid in investigating virus interactions with innate immune responses, identifying functional virus genome structures, strategically ameliorating cis-inhibitory signaling sequences related to complex viral functions, to unravel the relevance of codon usage for the temporal regulation of viral gene expression and improving our knowledge of virus mutational robustness and adaptability. The present review discusses the impacts of synonymous genome recoding with regard to expanding our comprehension of virus biology, and the development of new and better therapeutic strategies.

  4. Uterine smooth muscle tumor analysis by comparative genomic hybridization: a useful diagnostic tool in challenging lesions.

    PubMed

    Croce, Sabrina; Ribeiro, Agnes; Brulard, Celine; Noel, Jean-Christophe; Amant, Frederic; Stoeckle, Eberhard; Devouassoux-Shisheborah, Mojgan; Floquet, Anne; Arnould, Laurent; Guyon, Frederic; Mishellany, Florence; Garbay, Delphine; Cuppens, Tine; Zikan, Michal; Leroux, Agnès; Frouin, Eric; Duvillard, Pierre; Terrier, Philippe; Farre, Isabelle; Valo, Isabelle; MacGrogan, Gaetan M; Chibon, Frederic

    2015-07-01

    The diagnosis and management of uterine smooth muscle tumors with uncertain malignant potential (STUMP) is often challenging, and genomic data on these lesions as well as on uterine smooth muscle lesions are limited. We tested the hypothesis that genomic profile determination by array-CGH could split STUMP into a benign group with scarce chromosomal alterations akin to leiomyoma and a malignant group with high chromosomal instability akin to leiomyosarcoma. Array-CGH genomic profile analysis was conducted for a series of 29 cases of uterine STUMP. A group of ten uterine leiomyomas and ten uterine leiomyosarcomas served as controls. The mean age was 50 years (range, 24-85) and the follow-up ranged from 12 to 156 months (average 70 months). Since STUMP is a heterogenous group of tumors with genomic profiles that can harbor few to many chromosomal alterations, we compared genomic indices in leiomyomas and leiomyosarcomas and set a genomic index=10 threshold. Tumors with a genomic index <10 were classified as nonrecurring STUMPs and those with a genomic index >10 represented STUMPs with recurrences and unfavorable outcomes. Hence, the genomic index threshold splits the STUMP category into two groups of tumors with different outcomes: a group comparable to leiomyomas and another similar to leiomyosarcomas, but more indolent. In our STUMP series, genomic analysis by array-CGH is an innovative diagnostic tool for problematic smooth muscle uterine lesions, complementary to the morphological evaluation approach. We provide an improved classification method for distinguishing truly malignant tumors from benign lesions within the category of STUMP, especially those with equivocal morphological features.

  5. CRISPR-Cas: From the Bacterial Adaptive Immune System to a Versatile Tool for Genome Engineering.

    PubMed

    Kirchner, Marion; Schneider, Sabine

    2015-11-01

    The field of biology has been revolutionized by the recent advancement of an adaptive bacterial immune system as a universal genome engineering tool. Bacteria and archaea use repetitive genomic elements termed clustered regularly interspaced short palindromic repeats (CRISPR) in combination with an RNA-guided nuclease (CRISPR-associated nuclease: Cas) to target and destroy invading DNA. By choosing the appropriate sequence of the guide RNA, this two-component system can be used to efficiently modify, target, and edit genomic loci of interest in plants, insects, fungi, mammalian cells, and whole organisms. This has opened up new frontiers in genome engineering, including the potential to treat or cure human genetic disorders. Now the potential risks as well as the ethical, social, and legal implications of this powerful new technique move into the limelight. PMID:26382836

  6. CRISPR-Cas: From the Bacterial Adaptive Immune System to a Versatile Tool for Genome Engineering.

    PubMed

    Kirchner, Marion; Schneider, Sabine

    2015-11-01

    The field of biology has been revolutionized by the recent advancement of an adaptive bacterial immune system as a universal genome engineering tool. Bacteria and archaea use repetitive genomic elements termed clustered regularly interspaced short palindromic repeats (CRISPR) in combination with an RNA-guided nuclease (CRISPR-associated nuclease: Cas) to target and destroy invading DNA. By choosing the appropriate sequence of the guide RNA, this two-component system can be used to efficiently modify, target, and edit genomic loci of interest in plants, insects, fungi, mammalian cells, and whole organisms. This has opened up new frontiers in genome engineering, including the potential to treat or cure human genetic disorders. Now the potential risks as well as the ethical, social, and legal implications of this powerful new technique move into the limelight.

  7. Accelerating Genome Editing in CHO Cells Using CRISPR Cas9 and CRISPy, a Web-Based Target Finding Tool

    PubMed Central

    Ronda, Carlotta; Pedersen, Lasse Ebdrup; Hansen, Henning Gram; Kallehauge, Thomas Beuchert; Betenbaugh, Michael J; Nielsen, Alex Toftgaard; Kildegaard, Helene Faustrup

    2014-01-01

    Chinese hamster ovary (CHO) cells are widely used in the biopharmaceutical industry as a host for the production of complex pharmaceutical proteins. Thus genome engineering of CHO cells for improved product quality and yield is of great interest. Here, we demonstrate for the first time the efficacy of the CRISPR Cas9 technology in CHO cells by generating site-specific gene disruptions in COSMC and FUT8, both of which encode proteins involved in glycosylation. The tested single guide RNAs (sgRNAs) created an indel frequency up to 47.3% in COSMC, while an indel frequency up to 99.7% in FUT8 was achieved by applying lectin selection. All eight sgRNAs examined in this study resulted in relatively high indel frequencies, demonstrating that the Cas9 system is a robust and efficient genome-editing methodology in CHO cells. Deep sequencing revealed that 85% of the indels created by Cas9 resulted in frameshift mutations at the target sites, with a strong preference for single base indels. Finally, we have developed a user-friendly bioinformatics tool, named “CRISPy” for rapid identification of sgRNA target sequences in the CHO-K1 genome. The CRISPy tool identified 1,970,449 CRISPR targets divided into 27,553 genes and lists the number of off-target sites in the genome. In conclusion, the proven functionality of Cas9 to edit CHO genomes combined with our CRISPy database have the potential to accelerate genome editing and synthetic biology efforts in CHO cells. Biotechnol. Bioeng. 2014; 111: 1604–1616. © 2014 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc. PMID:24827782

  8. Accelerating genome editing in CHO cells using CRISPR Cas9 and CRISPy, a web-based target finding tool.

    PubMed

    Ronda, Carlotta; Pedersen, Lasse Ebdrup; Hansen, Henning Gram; Kallehauge, Thomas Beuchert; Betenbaugh, Michael J; Nielsen, Alex Toftgaard; Kildegaard, Helene Faustrup

    2014-08-01

    Chinese hamster ovary (CHO) cells are widely used in the biopharmaceutical industry as a host for the production of complex pharmaceutical proteins. Thus genome engineering of CHO cells for improved product quality and yield is of great interest. Here, we demonstrate for the first time the efficacy of the CRISPR Cas9 technology in CHO cells by generating site-specific gene disruptions in COSMC and FUT8, both of which encode proteins involved in glycosylation. The tested single guide RNAs (sgRNAs) created an indel frequency up to 47.3% in COSMC, while an indel frequency up to 99.7% in FUT8 was achieved by applying lectin selection. All eight sgRNAs examined in this study resulted in relatively high indel frequencies, demonstrating that the Cas9 system is a robust and efficient genome-editing methodology in CHO cells. Deep sequencing revealed that 85% of the indels created by Cas9 resulted in frameshift mutations at the target sites, with a strong preference for single base indels. Finally, we have developed a user-friendly bioinformatics tool, named "CRISPy" for rapid identification of sgRNA target sequences in the CHO-K1 genome. The CRISPy tool identified 1,970,449 CRISPR targets divided into 27,553 genes and lists the number of off-target sites in the genome. In conclusion, the proven functionality of Cas9 to edit CHO genomes combined with our CRISPy database have the potential to accelerate genome editing and synthetic biology efforts in CHO cells.

  9. Accelerating genome editing in CHO cells using CRISPR Cas9 and CRISPy, a web-based target finding tool.

    PubMed

    Ronda, Carlotta; Pedersen, Lasse Ebdrup; Hansen, Henning Gram; Kallehauge, Thomas Beuchert; Betenbaugh, Michael J; Nielsen, Alex Toftgaard; Kildegaard, Helene Faustrup

    2014-08-01

    Chinese hamster ovary (CHO) cells are widely used in the biopharmaceutical industry as a host for the production of complex pharmaceutical proteins. Thus genome engineering of CHO cells for improved product quality and yield is of great interest. Here, we demonstrate for the first time the efficacy of the CRISPR Cas9 technology in CHO cells by generating site-specific gene disruptions in COSMC and FUT8, both of which encode proteins involved in glycosylation. The tested single guide RNAs (sgRNAs) created an indel frequency up to 47.3% in COSMC, while an indel frequency up to 99.7% in FUT8 was achieved by applying lectin selection. All eight sgRNAs examined in this study resulted in relatively high indel frequencies, demonstrating that the Cas9 system is a robust and efficient genome-editing methodology in CHO cells. Deep sequencing revealed that 85% of the indels created by Cas9 resulted in frameshift mutations at the target sites, with a strong preference for single base indels. Finally, we have developed a user-friendly bioinformatics tool, named "CRISPy" for rapid identification of sgRNA target sequences in the CHO-K1 genome. The CRISPy tool identified 1,970,449 CRISPR targets divided into 27,553 genes and lists the number of off-target sites in the genome. In conclusion, the proven functionality of Cas9 to edit CHO genomes combined with our CRISPy database have the potential to accelerate genome editing and synthetic biology efforts in CHO cells. PMID:24827782

  10. Cryogenic Propellant Feed System Analytical Tool Development

    NASA Technical Reports Server (NTRS)

    Lusby, Brian S.; Miranda, Bruno M.; Collins, Jacob A.

    2011-01-01

    The Propulsion Systems Branch at NASA s Lyndon B. Johnson Space Center (JSC) has developed a parametric analytical tool to address the need to rapidly predict heat leak into propellant distribution lines based on insulation type, installation technique, line supports, penetrations, and instrumentation. The Propellant Feed System Analytical Tool (PFSAT) will also determine the optimum orifice diameter for an optional thermodynamic vent system (TVS) to counteract heat leak into the feed line and ensure temperature constraints at the end of the feed line are met. PFSAT was developed primarily using Fortran 90 code because of its number crunching power and the capability to directly access real fluid property subroutines in the Reference Fluid Thermodynamic and Transport Properties (REFPROP) Database developed by NIST. A Microsoft Excel front end user interface was implemented to provide convenient portability of PFSAT among a wide variety of potential users and its ability to utilize a user-friendly graphical user interface (GUI) developed in Visual Basic for Applications (VBA). The focus of PFSAT is on-orbit reaction control systems and orbital maneuvering systems, but it may be used to predict heat leak into ground-based transfer lines as well. PFSAT is expected to be used for rapid initial design of cryogenic propellant distribution lines and thermodynamic vent systems. Once validated, PFSAT will support concept trades for a variety of cryogenic fluid transfer systems on spacecraft, including planetary landers, transfer vehicles, and propellant depots, as well as surface-based transfer systems. The details of the development of PFSAT, its user interface, and the program structure will be presented.

  11. CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering.

    PubMed

    Labun, Kornel; Montague, Tessa G; Gagnon, James A; Thyme, Summer B; Valen, Eivind

    2016-07-01

    In just 3 years CRISPR genome editing has transformed biology, and its popularity and potency continue to grow. New CRISPR effectors and rules for locating optimum targets continue to be reported, highlighting the need for computational CRISPR targeting tools to compile these rules and facilitate target selection and design. CHOPCHOP is one of the most widely used web tools for CRISPR- and TALEN-based genome editing. Its overarching principle is to provide an intuitive and powerful tool that can serve both novice and experienced users. In this major update we introduce tools for the next generation of CRISPR advances, including Cpf1 and Cas9 nickases. We support a number of new features that improve the targeting power, usability and efficiency of CHOPCHOP. To increase targeting range and specificity we provide support for custom length sgRNAs, and we evaluate the sequence composition of the whole sgRNA and its surrounding region using models compiled from multiple large-scale studies. These and other new features, coupled with an updated interface for increased usability and support for a continually growing list of organisms, maintain CHOPCHOP as one of the leading tools for CRISPR genome editing. CHOPCHOP v2 can be found at http://chopchop.cbu.uib.no. PMID:27185894

  12. CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering

    PubMed Central

    Labun, Kornel; Montague, Tessa G.; Gagnon, James A.; Thyme, Summer B.; Valen, Eivind

    2016-01-01

    In just 3 years CRISPR genome editing has transformed biology, and its popularity and potency continue to grow. New CRISPR effectors and rules for locating optimum targets continue to be reported, highlighting the need for computational CRISPR targeting tools to compile these rules and facilitate target selection and design. CHOPCHOP is one of the most widely used web tools for CRISPR- and TALEN-based genome editing. Its overarching principle is to provide an intuitive and powerful tool that can serve both novice and experienced users. In this major update we introduce tools for the next generation of CRISPR advances, including Cpf1 and Cas9 nickases. We support a number of new features that improve the targeting power, usability and efficiency of CHOPCHOP. To increase targeting range and specificity we provide support for custom length sgRNAs, and we evaluate the sequence composition of the whole sgRNA and its surrounding region using models compiled from multiple large-scale studies. These and other new features, coupled with an updated interface for increased usability and support for a continually growing list of organisms, maintain CHOPCHOP as one of the leading tools for CRISPR genome editing. CHOPCHOP v2 can be found at http://chopchop.cbu.uib.no PMID:27185894

  13. D-peaks: a visual tool to display ChIP-seq peaks along the genome.

    PubMed

    Brohée, Sylvain; Bontempi, Gianluca

    2012-01-01

    ChIP-sequencing is a method of choice to localize the positions of protein binding sites on DNA on a whole genomic scale. The deciphering of the sequencing data produced by this novel technique is challenging and it is achieved by their rigorous interpretation using dedicated tools and adapted visualization programs. Here, we present a bioinformatics tool (D-peaks) that adds several possibilities (including, user-friendliness, high-quality, relative position with respect to the genomic features) to the well-known visualization browsers or databases already existing. D-peaks is directly available through its web interface http://rsat.ulb.ac.be/dpeaks/ as well as a command line tool.

  14. Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses

    PubMed Central

    Zhaxybayeva, Olga; Gogarten, J Peter

    2002-01-01

    Background Horizontal gene transfer (HGT) played an important role in shaping microbial genomes. In addition to genes under sporadic selection, HGT also affects housekeeping genes and those involved in information processing, even ribosomal RNA encoding genes. Here we describe tools that provide an assessment and graphic illustration of the mosaic nature of microbial genomes. Results We adapted the Maximum Likelihood (ML) mapping to the analyses of all detected quartets of orthologous genes found in four genomes. We have automated the assembly and analyses of these quartets of orthologs given the selection of four genomes. We compared the ML-mapping approach to more rigorous Bayesian probability and Bootstrap mapping techniques. The latter two approaches appear to be more conservative than the ML-mapping approach, but qualitatively all three approaches give equivalent results. All three tools were tested on mitochondrial genomes, which presumably were inherited as a single linkage group. Conclusions In some instances of interphylum relationships we find nearly equal numbers of quartets strongly supporting the three possible topologies. In contrast, our analyses of genome quartets containing the cyanobacterium Synechocystis sp. indicate that a large part of the cyanobacterial genome is related to that of low GC Gram positives. Other groups that had been suggested as sister groups to the cyanobacteria contain many fewer genes that group with the Synechocystis orthologs. Interdomain comparisons of genome quartets containing the archaeon Halobacterium sp. revealed that Halobacterium sp. shares more genes with Bacteria that live in the same environment than with Bacteria that are more closely related based on rRNA phylogeny . Many of these genes encode proteins involved in substrate transport and metabolism and in information storage and processing. The performed analyses demonstrate that relationships among prokaryotes cannot be accurately depicted by or inferred from

  15. Recent updates and developments to plant genome size databases.

    PubMed

    Garcia, Sònia; Leitch, Ilia J; Anadon-Rosell, Alba; Canela, Miguel Á; Gálvez, Francisco; Garnatje, Teresa; Gras, Airy; Hidalgo, Oriane; Johnston, Emmeline; Mas de Xaxars, Gemma; Pellicer, Jaume; Siljak-Yakovlev, Sonja; Vallès, Joan; Vitales, Daniel; Bennett, Michael D

    2014-01-01

    Two plant genome size databases have been recently updated and/or extended: the Plant DNA C-values database (http://data.kew.org/cvalues), and GSAD, the Genome Size in Asteraceae database (http://www.asteraceaegenomesize.com). While the first provides information on nuclear DNA contents across land plants and some algal groups, the second is focused on one of the largest and most economically important angiosperm families, Asteraceae. Genome size data have numerous applications: they can be used in comparative studies on genome evolution, or as a tool to appraise the cost of whole-genome sequencing programs. The growing interest in genome size and increasing rate of data accumulation has necessitated the continued update of these databases. Currently, the Plant DNA C-values database (Release 6.0, Dec. 2012) contains data for 8510 species, while GSAD has 1219 species (Release 2.0, June 2013), representing increases of 17 and 51%, respectively, in the number of species with genome size data, compared with previous releases. Here we provide overviews of the most recent releases of each database, and outline new features of GSAD. The latter include (i) a tool to visually compare genome size data between species, (ii) the option to export data and (iii) a webpage containing information about flow cytometry protocols.

  16. From the genome to the phenome: tools to understand the basic biology of Plasmodium falciparum.

    PubMed

    Webster, Wesley A J; McFadden, Geoffrey I

    2014-01-01

    Malaria plagues one out of every 30 humans and contributes to almost a million deaths, and the problem could worsen. Our current therapeutic options are compromised by emerging resistance by the parasite to our front line drugs. It is thus imperative to better understand the basic biology of the parasite and develop novel drugs to stem this disease. The most facile approach to analyse a gene's function is to remove it from the genome or inhibit its activity. Although genetic manipulation of the human malaria parasite Plasmodium falciparum is a relatively standard procedure, there is no optimal method to perturb genes essential to the intraerythrocytic development cycle--the part of the life cycle that produces the clinical manifestation of malaria. This is a severe impediment to progress because the phenotype we wish to study is exactly the one that is so elusive. In the absence of any utilitarian way to conditionally delete essential genes, we are prevented from investigating the parasite's most vulnerable points. This review aims to focus on the development of tools identifying essential genes of P. falciparum and our ability to elicit phenotypic mutation.

  17. Development of a collision risk assessment tool

    NASA Astrophysics Data System (ADS)

    Alarcon Rodriguez, J.; Martinez Fadrique, F.; Klinkrad, H.

    The avoidance of near misses and catastrophic collisions is of particular interest to manned missions and to valuable assets at densely populated altitude regions. GMV has developed a software tool for ESOC, ESA's European Space Operations Centre, which forecasts close conjunctions of selected spacecraft with over 8,000 objects included in the USSPACECOM catalog. The Collision Risk Assessment Tool (CRASS) generates collision risk estimates and collision warnings based on collision probability for a time span on the order of one week. In the framework of this activity, several collision probability algorithms have been implemented and tested. Considerable effort has also been placed in the characterisation of orbit determination errors and covariance propagation. The direct comparison of orbits of several spacecraft against a large catalog is an extremely computation intensive task. As a consequence, pre-filtering and parallel computing techniques have been proposed and used in the past as a means to reduce the computing time. However, the "smart sieve" algorithm devised and implemented by GMV retains the reliability of a "direct" method while drastically reducing the computing time. Therefore, the "smart sieve" is far more reliable than traditional pre-filtering techniques with no need for parallel computing. Besides, the method presents no constraints or singularities for any terrestrial orbit, as it is not based on simplifying assumptions. In summary, the method's main characteristics are general applicability, high reliability, and high computing efficiency. As a result of the increased efficiency, the field of application of the tool can be extended to other challenging problems. For instance, all to all comparisons of objects within a large catalog, or comparisons of a single spacecraft against a complete catalog over long periods of time can be completed in a reasonable time.

  18. Getting trichy: tools and approaches to interrogating Trichomonas vaginalis in a post-genome world

    PubMed Central

    Conrad, Melissa D.; Bradic, Martina; Warring, Sally D.; Gorman, Andrew W.; Carlton, Jane M.

    2012-01-01

    Trichomonas vaginalis is a parasite of the urogenital tract in men and women, with a worldwide presence and significant implications for global public health. T. vaginalis research entered the age of genomics with the publication of the first genome sequence in 2007, yet subsequent utilization of other ‘omics’ technologies and methods has been slow. Here, we review some of the tools and approaches available to interrogate T. vaginalis biology, with an emphasis on recent advances and current limitations, and draw attention to areas where further efforts are needed to effectively examine the complex and intriguing biology of the parasite. PMID:23219217

  19. Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools

    PubMed Central

    Fierst, Janna L.

    2015-01-01

    Modern high-throughput DNA sequencing has made it possible to inexpensively produce genome sequences, but in practice many of these draft genomes are fragmented and incomplete. Genetic linkage maps based on recombination rates between physical markers have been used in biology for over 100 years and a linkage map, when paired with a de novo sequencing project, can resolve mis-assemblies and anchor chromosome-scale sequences. Here, I summarize the methodology behind integrating de novo assemblies and genetic linkage maps, outline the current challenges, review the available software tools, and discuss new mapping technologies. PMID:26150829

  20. GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing.

    PubMed

    Wang, Xuewen; Wang, Le

    2016-01-01

    Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar. PMID:27679641

  1. GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing

    PubMed Central

    Wang, Xuewen; Wang, Le

    2016-01-01

    Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar. PMID:27679641

  2. Development of the SOFIA Image Processing Tool

    NASA Technical Reports Server (NTRS)

    Adams, Alexander N.

    2011-01-01

    The Stratospheric Observatory for Infrared Astronomy (SOFIA) is a Boeing 747SP carrying a 2.5 meter infrared telescope capable of operating between at altitudes of between twelve and fourteen kilometers, which is above more than 99 percent of the water vapor in the atmosphere. The ability to make observations above most water vapor coupled with the ability to make observations from anywhere, anytime, make SOFIA one of the world s premiere infrared observatories. SOFIA uses three visible light CCD imagers to assist in pointing the telescope. The data from these imagers is stored in archive files as is housekeeping data, which contains information such as boresight and area of interest locations. A tool that could both extract and process data from the archive files was developed.

  3. Genetics and genomics of flower initiation and development in roses

    PubMed Central

    Bendahmane, Mohammed

    2013-01-01

    Roses hold high symbolic value and great cultural importance in different societies throughout human history. They are widely used as garden ornamental plants, as cut flowers, and for the production of essential oils for the perfume and cosmetic industries. Domestication of roses has a long and complex history, and the rose species have been hybridized across vast geographic areas such as Europe, Asia, and the Middle East. The domestication processes selected several flower characters affecting floral quality, such as recurrent flowering, double flowers, petal colours, and fragrance. The molecular and genetic events that determine some of these flower characters cannot be studied using model species such as Arabidopsis thaliana, or at least only in a limited manner. In this review, we comment on the recent development of genetic, genomic, and transcriptomic tools for roses, and then focus on recent advances that have helped unravel the molecular mechanisms underlying several rose floral traits. PMID:23364936

  4. Genetics and genomics of flower initiation and development in roses.

    PubMed

    Bendahmane, Mohammed; Dubois, Annick; Raymond, Olivier; Bris, Manuel Le

    2013-02-01

    Roses hold high symbolic value and great cultural importance in different societies throughout human history. They are widely used as garden ornamental plants, as cut flowers, and for the production of essential oils for the perfume and cosmetic industries. Domestication of roses has a long and complex history, and the rose species have been hybridized across vast geographic areas such as Europe, Asia, and the Middle East. The domestication processes selected several flower characters affecting floral quality, such as recurrent flowering, double flowers, petal colours, and fragrance. The molecular and genetic events that determine some of these flower characters cannot be studied using model species such as Arabidopsis thaliana, or at least only in a limited manner. In this review, we comment on the recent development of genetic, genomic, and transcriptomic tools for roses, and then focus on recent advances that have helped unravel the molecular mechanisms underlying several rose floral traits.

  5. Solar Array Verification Analysis Tool (SAVANT) Developed

    NASA Technical Reports Server (NTRS)

    Bailey, Sheila G.; Long, KIenwyn J.; Curtis, Henry B.; Gardner, Barbara; Davis, Victoria; Messenger, Scott; Walters, Robert

    1999-01-01

    Modeling solar cell performance for a specific radiation environment to obtain the end-of-life photovoltaic array performance has become both increasingly important and, with the rapid advent of new types of cell technology, more difficult. For large constellations of satellites, a few percent difference in the lifetime prediction can have an enormous economic impact. The tool described here automates the assessment of solar array on-orbit end-of-life performance and assists in the development and design of ground test protocols for different solar cell designs. Once established, these protocols can be used to calculate on-orbit end-of-life performance from ground test results. The Solar Array Verification Analysis Tool (SAVANT) utilizes the radiation environment from the Environment Work Bench (EWB) model developed by the NASA Lewis Research Center s Photovoltaic and Space Environmental Effects Branch in conjunction with Maxwell Technologies. It then modifies and combines this information with the displacement damage model proposed by Summers et al. (ref. 1) of the Naval Research Laboratory to determine solar cell performance during the course of a given mission. The resulting predictions can then be compared with flight data. The Environment WorkBench (ref. 2) uses the NASA AE8 (electron) and AP8 (proton) models of the radiation belts to calculate the trapped radiation flux. These fluxes are integrated over the defined spacecraft orbit for the duration of the mission to obtain the total omnidirectional fluence spectra. Components such as the solar cell coverglass, adhesive, and antireflective coatings can slow and attenuate the particle fluence reaching the solar cell. In SAVANT, a continuous slowing down approximation is used to model this effect.

  6. Whole Genome Sequence Analysis Using JSpecies Tool Establishes Clonal Relationships between Listeria monocytogenes Strains from Epidemiologically Unrelated Listeriosis Outbreaks.

    PubMed

    Burall, Laurel S; Grim, Christopher J; Mammel, Mark K; Datta, Atin R

    2016-01-01

    In an effort to build a comprehensive genomic approach to food safety challenges, the FDA has implemented a whole genome sequencing effort, GenomeTrakr, which involves the sequencing and analysis of genomes of foodborne pathogens. As a part of this effort, we routinely sequence whole genomes of Listeria monocytogenes (Lm) isolates associated with human listeriosis outbreaks, as well as those isolated through other sources. To rapidly establish genetic relatedness of these genomes, we evaluated tetranucleotide frequency analysis via the JSpecies program to provide a cursory analysis of strain relatedness. The JSpecies tetranucleotide (tetra) analysis plots standardized (z-score) tetramer word frequencies of two strains against each other and uses linear regression analysis to determine similarity (r2). This tool was able to validate the close relationships between outbreak related strains from four different outbreaks. Included in this study was the analysis of Lm strains isolated during the recent caramel apple outbreak and stone fruit incident in 2014. We identified that many of the isolates from these two outbreaks shared a common 4b variant (4bV) serotype, also designated as IVb-v1, using a qPCR protocol developed in our laboratory. The 4bV serotype is characterized by the presence of a 6.3 Kb DNA segment normally found in serotype 1/2a, 3a, 1/2c and 3c strains but not in serotype 4b or 1/2b strains. We decided to compare these strains at a genomic level using the JSpecies Tetra tool. Specifically, we compared several 4bV and 4b isolates and identified a high level of similarity between the stone fruit and apple 4bV strains, but not the 4b strains co-identified in the caramel apple outbreak or other 4b or 4bV strains in our collection. This finding was further substantiated by a SNP-based analysis. Additionally, we were able to identify close relatedness between isolates from clinical cases from 1993-1994 and a single case from 2011 as well as links between two

  7. Whole Genome Sequence Analysis Using JSpecies Tool Establishes Clonal Relationships between Listeria monocytogenes Strains from Epidemiologically Unrelated Listeriosis Outbreaks

    PubMed Central

    Burall, Laurel S.; Grim, Christopher J.; Mammel, Mark K.; Datta, Atin R.

    2016-01-01

    In an effort to build a comprehensive genomic approach to food safety challenges, the FDA has implemented a whole genome sequencing effort, GenomeTrakr, which involves the sequencing and analysis of genomes of foodborne pathogens. As a part of this effort, we routinely sequence whole genomes of Listeria monocytogenes (Lm) isolates associated with human listeriosis outbreaks, as well as those isolated through other sources. To rapidly establish genetic relatedness of these genomes, we evaluated tetranucleotide frequency analysis via the JSpecies program to provide a cursory analysis of strain relatedness. The JSpecies tetranucleotide (tetra) analysis plots standardized (z-score) tetramer word frequencies of two strains against each other and uses linear regression analysis to determine similarity (r2). This tool was able to validate the close relationships between outbreak related strains from four different outbreaks. Included in this study was the analysis of Lm strains isolated during the recent caramel apple outbreak and stone fruit incident in 2014. We identified that many of the isolates from these two outbreaks shared a common 4b variant (4bV) serotype, also designated as IVb-v1, using a qPCR protocol developed in our laboratory. The 4bV serotype is characterized by the presence of a 6.3 Kb DNA segment normally found in serotype 1/2a, 3a, 1/2c and 3c strains but not in serotype 4b or 1/2b strains. We decided to compare these strains at a genomic level using the JSpecies Tetra tool. Specifically, we compared several 4bV and 4b isolates and identified a high level of similarity between the stone fruit and apple 4bV strains, but not the 4b strains co-identified in the caramel apple outbreak or other 4b or 4bV strains in our collection. This finding was further substantiated by a SNP-based analysis. Additionally, we were able to identify close relatedness between isolates from clinical cases from 1993–1994 and a single case from 2011 as well as links between

  8. Genome editing: intellectual property and product development in plant biotechnology.

    PubMed

    Schinkel, Helga; Schillberg, Stefan

    2016-07-01

    Genome editing is a revolutionary technology in molecular biology. While scientists are fascinated with the unlimited possibilities provided by directed and controlled changes in DNA in eukaryotes and have eagerly adopted such tools for their own experiments, an understanding of the intellectual property (IP) implications involved in bringing genome editing-derived products to market is often lacking. Due to the ingenuity of genome editing, the time between new product conception and its actual existence can be relatively short; therefore knowledge about IP of the various genome editing methods is relevant. This point must be regarded in a national framework as patents are instituted nationally. Therefore, when designing scientific work that could lead to a product, it is worthwhile to consider the different methods used for genome editing not only for their scientific merits but also for their compatibility with a speedy and reliable launch into the desired market.

  9. Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser

    PubMed Central

    Stenger, Judith E; Xu, Hong; Haynes, Carol; Hauser, Elizabeth R; Pericak-Vance, Margaret; Goldschmidt-Clermont, Pascal J; Vance, Jeffery M

    2005-01-01

    Background To facilitate efficient selection and the prioritization of candidate complex disease susceptibility genes for association analysis, increasingly comprehensive annotation tools are essential to integrate, visualize and analyze vast quantities of disparate data generated by genomic screens, public human genome sequence annotation and ancillary biological databases. We have developed a plug-in package for Ensembl called "Statistical Viewer" that facilitates the analysis of genomic features and annotation in the regions of interest defined by linkage analysis. Results Statistical Viewer is an add-on package to the open-source Ensembl Genome Browser and Annotation System that displays disease study-specific linkage and/or association data as 2 dimensional plots in new panels in the context of Ensembl's Contig View and Cyto View pages. An enhanced upload server facilitates the upload of statistical data, as well as additional feature annotation to be displayed in DAS tracts, in the form of Excel Files. The Statistical View panel, drawn directly under the ideogram, illustrates lod score values for markers from a study of interest that are plotted against their position in base pairs. A module called "Get Map" easily converts the genetic locations of markers to genomic coordinates. The graph is placed under the corresponding ideogram features a synchronized vertical sliding selection box that is seamlessly integrated into Ensembl's Contig- and Cyto- View pages to choose the region to be displayed in Ensembl's "Overview" and "Detailed View" panels. To resolve Association and Fine mapping data plots, a "Detailed Statistic View" plot corresponding to the "Detailed View" may be displayed underneath. Conclusion Features mapping to regions of linkage are accentuated when Statistic View is used in conjunction with the Distributed Annotation System (DAS) to display supplemental laboratory information such as differentially expressed disease genes in private data tracks

  10. A Guide to Computational Tools and Design Strategies for Genome Editing Experiments in Zebrafish Using CRISPR/Cas9.

    PubMed

    Prykhozhij, Sergey V; Rajan, Vinothkumar; Berman, Jason N

    2016-02-01

    The development of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology for mainstream biotechnological use based on its discovery as an adaptive immune mechanism in bacteria has dramatically improved the ability of molecular biologists to modify genomes of model organisms. The zebrafish is highly amenable to applications of CRISPR/Cas9 for mutation generation and a variety of DNA insertions. Cas9 protein in complex with a guide RNA molecule recognizes where to cut the homologous DNA based on a short stretch of DNA termed the protospacer-adjacent motif (PAM). Rapid and efficient identification of target sites immediately preceding PAM sites, quantification of genomic occurrences of similar (off target) sites and predictions of cutting efficiency are some of the features where computational tools play critical roles in CRISPR/Cas9 applications. Given the rapid advent and development of this technology, it can be a challenge for researchers to remain up to date with all of the important technological developments in this field. We have contributed to the armamentarium of CRISPR/Cas9 bioinformatics tools and trained other researchers in the use of appropriate computational programs to develop suitable experimental strategies. Here we provide an in-depth guide on how to use CRISPR/Cas9 and other relevant computational tools at each step of a host of genome editing experimental strategies. We also provide detailed conceptual outlines of the steps involved in the design and execution of CRISPR/Cas9-based experimental strategies, such as generation of frameshift mutations, larger chromosomal deletions and inversions, homology-independent insertion of gene cassettes and homology-based knock-in of defined point mutations and larger gene constructs.

  11. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

    DOE PAGES

    Kang, Dongwan D.; Froula, Jeff; Egan, Rob; Wang, Zhong

    2015-01-01

    Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Because of the complex nature of these communities, existing metagenome binning methods often miss a large number of microbial species. In addition, most of the tools are not scalable to large datasets. Here we introduce automated software called MetaBAT that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning. MetaBAT outperforms alternative methods in accuracy and computational efficiency on both synthetic and real metagenome datasets. Lastly, it automatically formsmore » hundreds of high quality genome bins on a very large assembly consisting millions of contigs in a matter of hours on a single node. MetaBAT is open source software and available at https://bitbucket.org/berkeleylab/metabat.« less

  12. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

    SciTech Connect

    Kang, Dongwan D.; Froula, Jeff; Egan, Rob; Wang, Zhong

    2015-01-01

    Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Because of the complex nature of these communities, existing metagenome binning methods often miss a large number of microbial species. In addition, most of the tools are not scalable to large datasets. Here we introduce automated software called MetaBAT that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning. MetaBAT outperforms alternative methods in accuracy and computational efficiency on both synthetic and real metagenome datasets. Lastly, it automatically forms hundreds of high quality genome bins on a very large assembly consisting millions of contigs in a matter of hours on a single node. MetaBAT is open source software and available at https://bitbucket.org/berkeleylab/metabat.

  13. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide...

  14. SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges.

    PubMed

    Lin, Ying Chih; Lu, Chin Lung; Liu, Ying-Chuan; Tang, Chuan Yi

    2006-07-01

    SPRING (http://algorithm.cs.nthu.edu.tw/tools/SPRING/) is a tool for the analysis of genome rearrangement between two chromosomal genomes using reversals and/or block-interchanges. SPRING takes two or more chromosomes as its input and then computes a minimum series of reversals and/or block-interchanges between any two input chromosomes for transforming one chromosome into another. The input of SPRING can be either bacterial-size sequences or gene/landmark orders. If the input is a set of chromosomal sequences then the SPRING will automatically search for identical landmarks, which are homologous/conserved regions shared by all input sequences. In particular, SPRING also computes the breakpoint distance between any pair of two chromosomes, which can be used to compare with the rearrangement distance to confirm whether they are correlated or not. In addition, SPRING shows phylogenetic trees that are reconstructed based on the rearrangement and breakpoint distance matrixes.

  15. Development of Advanced Tools for Cryogenic Integration

    NASA Astrophysics Data System (ADS)

    Bugby, D. C.; Marland, B. C.; Stouffer, C. J.; Kroliczek, E. J.

    2004-06-01

    This paper describes four advanced devices (or tools) that were developed to help solve problems in cryogenic integration. The four devices are: (1) an across-gimbal nitrogen cryogenic loop heat pipe (CLHP); (2) a miniaturized neon CLHP; (3) a differential thermal expansion (DTE) cryogenic thermal switch (CTSW); and (4) a dual-volume nitrogen cryogenic thermal storage unit (CTSU). The across-gimbal CLHP provides a low torque, high conductance solution for gimbaled cryogenic systems wishing to position their cryocoolers off-gimbal. The miniaturized CLHP combines thermal transport, flexibility, and thermal switching (at 35 K) into one device that can be directly mounted to both the cooler cold head and the cooled component. The DTE-CTSW, designed and successfully tested in a previous program using a stainless steel tube and beryllium (Be) end-pieces, was redesigned with a polymer rod and high-purity aluminum (Al) end-pieces to improve performance and manufacturability while still providing a miniaturized design. Lastly, the CTSU was designed with a 6063 Al heat exchanger and integrally welded, segmented, high purity Al thermal straps for direct attachment to both a cooler cold head and a Be component whose peak heat load exceeds its average load by 2.5 times. For each device, the paper will describe its development objective, operating principles, heritage, requirements, design, test data and lessons learned.

  16. Genome-based approaches to develop vaccines against bacterial pathogens.

    PubMed

    Serruto, Davide; Serino, Laura; Masignani, Vega; Pizza, Mariagrazia

    2009-05-26

    Bacterial infectious diseases remain the single most important threat to health worldwide. Although conventional vaccinology approaches were successful in conferring protection against several diseases, they failed to provide efficacious solutions against many others. The advent of whole-genome sequencing changed the way to think about vaccine development, enabling the targeting of possible vaccine candidates starting from the genomic information of a single bacterial isolate, with a process named reverse vaccinology. As the genomic era progressed, reverse vaccinology has evolved with a pan-genome approach and multi-strain genome analysis became fundamental for the design of universal vaccines. This review describes the applications of genome-based approaches in the development of new vaccines against bacterial pathogens.

  17. After genomics, what proteomics tools could help us understand the antimicrobial resistance of Escherichia coli?

    PubMed

    Radhouani, Hajer; Pinto, Luís; Poeta, Patrícia; Igrejas, Gilberto

    2012-06-01

    Proteomic approaches have been considerably improved during the past decade and have been used to investigate the differences in protein expression profiles of cells grown under a broad spectrum of growth conditions and with different stress factors including antibiotics. In Europe, the most significant disease threat remains the presence of microorganisms that have become resistant to antimicrobials and so it is important that different scientific tools are combined to achieve the largest amount of knowledge in this area of expertise. The emergence and spread of the antibiotic-resistant Gram-negative pathogens, such as Escherichia coli, can lead to serious problem public health in humans. E. coli, a very well described prokaryote, has served as a model organism for several biological and biotechnological studies increasingly so since the completion of the E. coli genome-sequencing project. The purpose of this review is to present an overview of the different proteomic approaches to antimicrobial-resistant E. coli that will be helpful to obtain a better knowledge of the antibiotic-resistant mechanism(s). This can also aid to understand the molecular determinants involved with pathogenesis, which is essential for the development of effective strategies to combat infection and to reveal new therapeutic targets. This article is part of a Special Issue entitled: Proteomics: The clinical link.

  18. Dissecting diabetes/metabolic disease mechanisms using pluripotent stem cells and genome editing tools

    PubMed Central

    Teo, Adrian Kee Keong; Gupta, Manoj K.; Doria, Alessandro; Kulkarni, Rohit N.

    2015-01-01

    Background Diabetes and metabolic syndromes are chronic, devastating diseases with increasing prevalence. Human pluripotent stem cells are gaining popularity in their usage for human in vitro disease modeling. With recent rapid advances in genome editing tools, these cells can now be genetically manipulated with relative ease to study how genes and gene variants contribute to diabetes and metabolic syndromes. Scope of review We highlight the diabetes and metabolic genes and gene variants, which could potentially be studied, using two powerful technologies – human pluripotent stem cells (hPSCs) and genome editing tools – to aid the elucidation of yet elusive mechanisms underlying these complex diseases. Major conclusions hPSCs and the advancing genome editing tools appear to be a timely and potent combination for probing molecular mechanism(s) underlying diseases such as diabetes and metabolic syndromes. The knowledge gained from these hiPSC-based disease modeling studies can potentially be translated into the clinics by guiding clinicians on the appropriate type of medication to use for each condition based on the mechanism of action of the disease. PMID:26413465

  19. Microarray-based genomic profiling as a diagnostic tool in acute lymphoblastic leukemia.

    PubMed

    Simons, Annet; Stevens-Kroef, Marian; El Idrissi-Zaynoun, Najat; van Gessel, Sabine; Weghuis, Daniel Olde; van den Berg, Eva; Waanders, Esmé; Hoogerbrugge, Peter; Kuiper, Roland; van Kessel, Ad Geurts

    2011-12-01

    In acute lymphoblastic leukemia (ALL) specific genomic abnormalities provide important clinical information. In most routine clinical diagnostic laboratories conventional karyotyping, in conjunction with targeted screens using e.g., fluorescence in situ hybridization (FISH), is currently considered as the gold standard to detect such aberrations. Conventional karyotyping, however, is limited in its resolution and yield, thus hampering the genetic diagnosis of ALL. We explored whether microarray-based genomic profiling would be feasible as an alternative strategy in a routine clinical diagnostic setting. To this end, we compared conventional karyotypes with microarray-deduced copy number aberration (CNA) karyotypes in 60 ALL cases. Microarray-based genomic profiling resulted in a CNA detection rate of 90%, whereas for conventional karyotyping this was 61%. In addition, many small (< 5 Mb) genetic lesions were encountered, frequently harboring clinically relevant ALL-related genes such as CDKN2A/B, ETV6, PAX5, and IKZF1. From our data we conclude that microarray-based genomic profiling serves as a robust tool in the genetic diagnosis of ALL, outreaching conventional karyotyping in CNA detection both in terms of sensitivity and specificity. We also propose a practical workflow for a comprehensive and objective interpretation of CNAs obtained through microarray-based genomic profiling, thereby facilitating its application in a routine clinical diagnostic setting.

  20. Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond.

    PubMed

    Mascher, Martin; Richmond, Todd A; Gerhardt, Daniel J; Himmelbach, Axel; Clissold, Leah; Sampath, Dharanya; Ayling, Sarah; Steuernagel, Burkhard; Pfeifer, Matthias; D'Ascenzo, Mark; Akhunov, Eduard D; Hedley, Pete E; Gonzales, Ana M; Morrell, Peter L; Kilian, Benjamin; Blattner, Frank R; Scholz, Uwe; Mayer, Klaus F X; Flavell, Andrew J; Muehlbauer, Gary J; Waugh, Robbie; Jeddeloh, Jeffrey A; Stein, Nils

    2013-11-01

    Advanced resources for genome-assisted research in barley (Hordeum vulgare) including a whole-genome shotgun assembly and an integrated physical map have recently become available. These have made possible studies that aim to assess genetic diversity or to isolate single genes by whole-genome resequencing and in silico variant detection. However such an approach remains expensive given the 5 Gb size of the barley genome. Targeted sequencing of the mRNA-coding exome reduces barley genomic complexity more than 50-fold, thus dramatically reducing this heavy sequencing and analysis load. We have developed and employed an in-solution hybridization-based sequence capture platform to selectively enrich for a 61.6 megabase coding sequence target that includes predicted genes from the genome assembly of the cultivar Morex as well as publicly available full-length cDNAs and de novo assembled RNA-Seq consensus sequence contigs. The platform provides a highly specific capture with substantial and reproducible enrichment of targeted exons, both for cultivated barley and related species. We show that this exome capture platform provides a clear path towards a broader and deeper understanding of the natural variation residing in the mRNA-coding part of the barley genome and will thus constitute a valuable resource for applications such as mapping-by-sequencing and genetic diversity analyzes.

  1. Development of a Raman lidar simulation tool

    NASA Technical Reports Server (NTRS)

    Grasso, R. J.; Hummel, J. R.

    1992-01-01

    Raman Lidar is a useful and powerful tool for remote probing of the atmosphere. With Raman Lidars, one can accurately determine the identity and concentration of a particular molecular specie present in the atmosphere. We present the results from a program to develop a simulation capability of Raman Lidar systems for the remote detection of atmospheric gases and/or air polluting hydrocarbons. Our model, which integrates remote Raman spectroscopy with SPARTA's BACKSCAT atmospheric lidar simulation package, permits accurate determination of the performance of a Raman Lidar system. The accuracy with which our model operates is due to the accurate calculation, at any given excitation wavelength, of the differential scattering cross section for the molecular specie under investigation. We show excellent correlation of our calculated cross section data with experimental data from the published literature. In addition, the use of our BACKSCAT package, which provides a user friendly environment to define the operating conditions, provides an accurate calculation of the atmospheric extinction at both the excitation and Raman shifted wavelengths. Our code can be used to accurately predict the performance of a Raman Lidar system, the concentration and identification of a specie in the atmosphere, or the feasibility of making Raman measurements.

  2. MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands.

    PubMed

    Ou, Hong-Yu; He, Xinyi; Harrison, Ewan M; Kulasekara, Bridget R; Thani, Ali Bin; Kadioglu, Aras; Lory, Stephen; Hinton, Jay C D; Barer, Michael R; Deng, Zixin; Rajakumar, Kumar

    2007-07-01

    MobilomeFINDER (http://mml.sjtu.edu.cn/MobilomeFINDER) is an interactive online tool that facilitates bacterial genomic island or 'mobile genome' (mobilome) discovery; it integrates the ArrayOme and tRNAcc software packages. ArrayOme utilizes a microarray-derived comparative genomic hybridization input data set to generate 'inferred contigs' produced by merging adjacent genes classified as 'present'. Collectively these 'fragments' represent a hypothetical 'microarray-visualized genome (MVG)'. ArrayOme permits recognition of discordances between physical genome and MVG sizes, thereby enabling identification of strains rich in microarray-elusive novel genes. Individual tRNAcc tools facilitate automated identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites and other integration hotspots in closely related sequenced genomes. Accessory tools facilitate design of hotspot-flanking primers for in silico and/or wet-science-based interrogation of cognate loci in unsequenced strains and analysis of islands for features suggestive of foreign origins; island-specific and genome-contextual features are tabulated and represented in schematic and graphical forms. To date we have used MobilomeFINDER to analyse several Enterobacteriaceae, Pseudomonas aeruginosa and Streptococcus suis genomes. MobilomeFINDER enables high-throughput island identification and characterization through increased exploitation of emerging sequence data and PCR-based profiling of unsequenced test strains; subsequent targeted yeast recombination-based capture permits full-length sequencing and detailed functional studies of novel genomic islands.

  3. Meta-tools for software development and knowledge acquisition

    NASA Technical Reports Server (NTRS)

    Eriksson, Henrik; Musen, Mark A.

    1992-01-01

    The effectiveness of tools that provide support for software development is highly dependent on the match between the tools and their task. Knowledge-acquisition (KA) tools constitute a class of development tools targeted at knowledge-based systems. Generally, KA tools that are custom-tailored for particular application domains are more effective than are general KA tools that cover a large class of domains. The high cost of custom-tailoring KA tools manually has encouraged researchers to develop meta-tools for KA tools. Current research issues in meta-tools for knowledge acquisition are the specification styles, or meta-views, for target KA tools used, and the relationships between the specification entered in the meta-tool and other specifications for the target program under development. We examine different types of meta-views and meta-tools. Our current project is to provide meta-tools that produce KA tools from multiple specification sources--for instance, from a task analysis of the target application.

  4. Novel genomic tools for specific and real-time detection of biothreat and frequently encountered foodborne pathogens.

    PubMed

    Woubit, Abdela; Yehualaeshet, Teshome; Habtemariam, Tsegaye; Samuel, Temesgen

    2012-04-01

    The bacterial genera Escherichia, Salmonella, Shigella, Vibrio, Yersinia, and Francisella include important food safety and biothreat agents. By extensive mining of the whole genome and protein databases of diverse, closely and distantly related bacterial species and strains, we have identified novel genome regions, which we utilized to develop a rapid detection platform for these pathogens. The specific genomic targets we have identified to design the primers in Francisella tularensis subsp. tularensis, F. tularensis subsp. novicida, Shigella dysenteriae, Salmonella enterica serovar Typhimurium, Vibrio cholerae, Yersinia pestis, and Yersinia pseudotuberculosis contained either known genes or putative proteins. Primer sets were designed from the target regions for use in real-time PCR assays to detect specific biothreat pathogens at species or strain levels. The primer sets were first tested by in silico PCR against whole-genome sequences of different species, subspecies, or strains and then by in vitro PCR against genomic DNA preparations from 23 strains representing six biothreat agents (Escherichia coli O157:H7 strain EDL 933, Shigella dysenteriae, S. enterica serovar Typhi, F. tularensis subsp. tularensis, V. cholerae, and Y. pestis) and six foodborne pathogens (Salmonella Typhimurium, Salmonella Saintpaul, Shigella sonnei, F. tularensis subsp. novicida, Vibrio parahaemolyticus, and Y. pseudotuberculosis). Each pathogen was specifically identifiable at the genus and species levels. Sensitivity assays performed with purified DNA showed the lowest detection limit of 128 fg of DNA/μl for F. tularensis subsp. tularensis. A preliminary test to detect Shigella organisms in a milk matrix also enabled the detection of 6 to 60 CFU/ml. These new tools could ultimately be used to develop platforms to simultaneously detect these pathogens. PMID:22488053

  5. The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes.

    PubMed

    Bracken-Grissom, Heather; Collins, Allen G; Collins, Timothy; Crandall, Keith; Distel, Daniel; Dunn, Casey; Giribet, Gonzalo; Haddock, Steven; Knowlton, Nancy; Martindale, Mark; Medina, Mónica; Messing, Charles; O'Brien, Stephen J; Paulay, Gustav; Putnam, Nicolas; Ravasi, Timothy; Rouse, Greg W; Ryan, Joseph F; Schulze, Anja; Wörheide, Gert; Adamska, Maja; Bailly, Xavier; Breinholt, Jesse; Browne, William E; Diaz, M Christina; Evans, Nathaniel; Flot, Jean-François; Fogarty, Nicole; Johnston, Matthew; Kamel, Bishoy; Kawahara, Akito Y; Laberge, Tammy; Lavrov, Dennis; Michonneau, François; Moroz, Leonid L; Oakley, Todd; Osborne, Karen; Pomponi, Shirley A; Rhodes, Adelaide; Santos, Scott R; Satoh, Nori; Thacker, Robert W; Van de Peer, Yves; Voolstra, Christian R; Welch, David Mark; Winston, Judith; Zhou, Xin

    2014-01-01

    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 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 (http://giga.nova.edu) has been launched to facilitate this collaborative venture.

  6. The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

    PubMed Central

    2014-01-01

    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 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 (http://giga.nova.edu) has been launched to facilitate this collaborative venture. PMID:24336862

  7. The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes.

    PubMed

    Bracken-Grissom, Heather; Collins, Allen G; Collins, Timothy; Crandall, Keith; Distel, Daniel; Dunn, Casey; Giribet, Gonzalo; Haddock, Steven; Knowlton, Nancy; Martindale, Mark; Medina, Mónica; Messing, Charles; O'Brien, Stephen J; Paulay, Gustav; Putnam, Nicolas; Ravasi, Timothy; Rouse, Greg W; Ryan, Joseph F; Schulze, Anja; Wörheide, Gert; Adamska, Maja; Bailly, Xavier; Breinholt, Jesse; Browne, William E; Diaz, M Christina; Evans, Nathaniel; Flot, Jean-François; Fogarty, Nicole; Johnston, Matthew; Kamel, Bishoy; Kawahara, Akito Y; Laberge, Tammy; Lavrov, Dennis; Michonneau, François; Moroz, Leonid L; Oakley, Todd; Osborne, Karen; Pomponi, Shirley A; Rhodes, Adelaide; Santos, Scott R; Satoh, Nori; Thacker, Robert W; Van de Peer, Yves; Voolstra, Christian R; Welch, David Mark; Winston, Judith; Zhou, Xin

    2014-01-01

    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 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 (http://giga.nova.edu) has been launched to facilitate this collaborative venture. PMID:24336862

  8. Patient-derived cell models as preclinical tools for genome-directed targeted therapy

    PubMed Central

    Jang, Jiryeon; Park, Kyunghee; Yi, Jun Ho; Hong, Mineui; Ahn, Taejin; Rath, Oliver; Schueler, Julia; Kim, Seung Tae; Do, In-Gu; Lee, Sujin; Park, Se Hoon; Ji, Yong Ick; Kim, Dukwhan; Park, Joon Oh; Park, Young Suk; Kang, Won Ki; Kim, Kyoung-Mee; Park, Woong-Yang; Lim, Ho Yeong; Lee, Jeeyun

    2015-01-01

    Background In this study, we established patient-derived tumor cell (PDC) models using tissues collected from patients with metastatic cancer and assessed whether these models could be used as a tool for genome-based cancer treatment. Methods PDCs were isolated and cultured from malignant effusions including ascites and pleural fluid. Pathological examination, immunohistochemical analysis, and genomic profiling were performed to compare the histological and genomic features of primary tumors, PDCs. An exploratory gene expression profiling assay was performed to further characterize PDCs. Results From January 2012 to May 2013, 176 samples from patients with metastatic cancer were collected. PDC models were successfully established in 130 (73.6%) samples. The median time from specimen collection to passage 1 (P1) was 3 weeks (range, 0.5–4 weeks), while that from P1 to P2 was 2.5 weeks (range, 0.5–5 weeks). Sixteen paired samples of genomic alterations were highly concordant between each primary tumor and progeny PDCs, with an average variant allele frequency (VAF) correlation of 0.878. We compared genomic profiles of the primary tumor (P0), P1 cells, P2 cells, and patient-derived xenografts (PDXs) derived from P2 cells and found that three samples (P0, P1, and P2 cells) were highly correlated (0.99–1.00). Moreover, PDXs showed more than 100 variants, with correlations of only 0.6–0.8 for the other samples. Drug responses of PDCs were reflective of the clinical response to targeted agents in selected patient PDC lines. Conclusion(s) Our results provided evidence that our PDC model was a promising model for preclinical experiments and closely resembled the patient tumor genome and clinical response. PMID:26296973

  9. Developing genomic resources for the apiaceae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Apiaceae family includes carrot, celery, cilantro, dill, fennel and numerous other spice and medicinal crops. Carrot is the most economically important member of the Apiaceae with an annual value of $600 M in the United States alone. There are few genomic resources for carrot or other Apiaceae, ...

  10. Genome-wide microsatellite characterization and marker development in the sequenced Brassica crop species.

    PubMed

    Shi, Jiaqin; Huang, Shunmou; Zhan, Jiepeng; Yu, Jingyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

    2014-02-01

    Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species.

  11. Genome-Wide Microsatellite Characterization and Marker Development in the Sequenced Brassica Crop Species

    PubMed Central

    Shi, Jiaqin; Huang, Shunmou; Zhan, Jiepeng; Yu, Jingyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

    2014-01-01

    Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species. PMID:24130371

  12. Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data.

    PubMed

    Bolser, Dan; Staines, Daniel M; Pritchard, Emily; Kersey, Paul

    2016-01-01

    Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for a growing number of sequenced plant species (currently 33). Data provided includes genome sequence, gene models, functional annotation, and polymorphic loci. Various additional information are provided for variation data, including population structure, individual genotypes, linkage, and phenotype data. In each release, comparative analyses are performed on whole genome and protein sequences, and genome alignments and gene trees are made available that show the implied evolutionary history of each gene family. Access to the data is provided through a genome browser incorporating many specialist interfaces for different data types, and through a variety of additional methods for programmatic access and data mining. These access routes are consistent with those offered through the Ensembl interface for the genomes of non-plant species, including those of plant pathogens, pests, and pollinators.Ensembl Plants is updated 4-5 times a year and is developed in collaboration with our international partners in the Gramene ( http://www.gramene.org ) and transPLANT projects ( http://www.transplantdb.org ).

  13. Engineering plastid genomes: methods, tools, and applications in basic research and biotechnology.

    PubMed

    Bock, Ralph

    2015-01-01

    The small bacterial-type genome of the plastid (chloroplast) can be engineered by genetic transformation, generating cells and plants with transgenic plastid genomes, also referred to as transplastomic plants. The transformation process relies on homologous recombination, thereby facilitating the site-specific alteration of endogenous plastid genes as well as the precisely targeted insertion of foreign genes into the plastid DNA. The technology has been used extensively to analyze chloroplast gene functions and study plastid gene expression at all levels in vivo. Over the years, a large toolbox has been assembled that is now nearly comparable to the techniques available for plant nuclear transformation and that has enabled new applications of transplastomic technology in basic and applied research. This review describes the state of the art in engineering the plastid genomes of algae and land plants (Embryophyta). It provides an overview of the existing tools for plastid genome engineering, discusses current technological limitations, and highlights selected applications that demonstrate the immense potential of chloroplast transformation in several key areas of plant biotechnology. PMID:25494465

  14. Engineering plastid genomes: methods, tools, and applications in basic research and biotechnology.

    PubMed

    Bock, Ralph

    2015-01-01

    The small bacterial-type genome of the plastid (chloroplast) can be engineered by genetic transformation, generating cells and plants with transgenic plastid genomes, also referred to as transplastomic plants. The transformation process relies on homologous recombination, thereby facilitating the site-specific alteration of endogenous plastid genes as well as the precisely targeted insertion of foreign genes into the plastid DNA. The technology has been used extensively to analyze chloroplast gene functions and study plastid gene expression at all levels in vivo. Over the years, a large toolbox has been assembled that is now nearly comparable to the techniques available for plant nuclear transformation and that has enabled new applications of transplastomic technology in basic and applied research. This review describes the state of the art in engineering the plastid genomes of algae and land plants (Embryophyta). It provides an overview of the existing tools for plastid genome engineering, discusses current technological limitations, and highlights selected applications that demonstrate the immense potential of chloroplast transformation in several key areas of plant biotechnology.

  15. Next generation genome-wide association tool: Design and coverage of a high-throughput European-optimized SNP array

    PubMed Central

    Hoffmann, Thomas J.; Kvale, Mark N.; Hesselson, Stephanie E.; Zhan, Yiping; Aquino, Christine; Cao, Yang; Cawley, Simon; Chung, Elaine; Connell, Sheryl; Eshragh, Jasmin; Ewing, Marcia; Gollub, Jeremy; Henderson, Mary; Hubbell, Earl; Iribarren, Carlos; Kaufman, Jay; Lao, Richard Z.; Lu, Yontao; Ludwig, Dana; Mathauda, Gurpreet K.; McGuire, William; Mei, Gangwu; Miles, Sunita; Purdy, Matthew M.; Quesenberry, Charles; Ranatunga, Dilrini; Rowell, Sarah; Sadler, Marianne; Shapero, Michael H.; Shen, Ling; Shenoy, Tanushree R.; Smethurst, David; Van den Eeden, Stephen K.; Walter, Larry; Wan, Eunice; Wearley, Reid; Webster, Teresa; Wen, Christopher C.; Weng, Li; Whitmer, Rachel A.; Williams, Alan; Wong, Simon C.; Zau, Chia; Finn, Andrea; Schaefer, Catherine; Kwok, Pui-Yan; Risch, Neil

    2011-01-01

    The success of genome-wide association studies has paralleled the development of efficient genotyping technologies. We describe the development of a next-generation microarray based on the new highly-efficient Affymetrix Axiom genotyping technology that we are using to genotype individuals of European ancestry from the Kaiser Permanente Research Program on Genes, Environment and Health (RPGEH). The array contains 674,517 SNPs, and provides excellent genome-wide as well as gene-based and candidate-SNP coverage. Coverage was calculated using an approach based on imputation and cross validation. Preliminary results for the first 80,301 saliva-derived DNA samples from the RPGEH demonstrate very high quality genotypes, with sample success rates above 94% and over 98% of successful samples having SNP call rates exceeding 98%. At steady state, we have produced 462 million genotypes per week for each Axiom system. The new array provides a valuable addition to the repertoire of tools for large scale genome-wide association studies. PMID:21565264

  16. ANItools web: a web tool for fast genome comparison within multiple bacterial strains

    PubMed Central

    Han, Na; Qiang, Yujun; Zhang, Wen

    2016-01-01

    Background: Early classification of prokaryotes was based solely on phenotypic similarities, but modern prokaryote characterization has been strongly influenced by advances in genetic methods. With the fast development of the sequencing technology, the ever increasing number of genomic sequences per species offers the possibility for developing distance determinations based on whole-genome information. The average nucleotide identity (ANI), calculated from pair-wise comparisons of all sequences shared between two given strains, has been proposed as the new metrics for bacterial species definition and classification. Results: In this study, we developed the web version of ANItools (http://ani.mypathogen.cn/), which helps users directly get ANI values from online sources. A database covering ANI values of any two strains in a genus was also included (2773 strains, 1487 species and 668 genera). Importantly, ANItools web can automatically run genome comparison between the input genomic sequence and data sequences (Genus and Species levels), and generate a graphical report for ANI calculation results. Conclusion: ANItools web is useful for defining the relationship between bacterial strains, further contributing to the classification and identification of bacterial species using genome data. Database URL: http://ani.mypathogen.cn/ PMID:27270714

  17. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality.

    PubMed

    Kamvar, Zhian N; Brooks, Jonah C; Grünwald, Niklaus J

    2015-01-01

    To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations is crucial. Plant pathogen populations are often clonal or partially clonal which requires different analytical tools. With the advent of high throughput sequencing technologies, obtaining genome-wide population genetic data has become easier than ever before. We previously contributed the R package poppr specifically addressing issues with analysis of clonal populations. In this paper we provide several significant extensions to poppr with a focus on large, genome-wide SNP data. Specifically, we provide several new functionalities including the new function mlg.filter to define clone boundaries allowing for inspection and definition of what is a clonal lineage, minimum spanning networks with reticulation, a sliding-window analysis of the index of association, modular bootstrapping of any genetic distance, and analyses across any level of hierarchies. PMID:26113860

  18. Use of genome editing tools in human stem cell-based disease modeling and precision medicine.

    PubMed

    Yuda, Wei; Shuang, Li; Gaigai, Liu; Yongxian, Zhang; Qiurong, Ding

    2015-10-01

    Precision medicine emerges as a new approach that takes into account individual variability. The successful conduct of precision medicine requires the use of precise disease models. Human pluripotent stem cells (hPSCs), as well as adult stem cells, can be differentiated into a variety of human somatic cell types that can be used for research and drug screening. The development of genome editing technology over the past few years, especially the CRISPR/Cas system, has made it feasible to precisely and efficiently edit the genetic background. Therefore, disease modeling by using a combination of human stem cells and genome editing technology has offered a new platform to generate " personalized " disease models, which allow the study of the contribution of individual genetic variabilities to disease progression and the development of precise treatments. In this review, recent advances in the use of genome editing in human stem cells and the generation of stem cell models for rare diseases and cancers are discussed.

  19. Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila.

    PubMed

    Port, Fillip; Chen, Hui-Min; Lee, Tzumin; Bullock, Simon L

    2014-07-22

    The type II clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system has emerged recently as a powerful method to manipulate the genomes of various organisms. Here, we report a toolbox for high-efficiency genome engineering of Drosophila melanogaster consisting of transgenic Cas9 lines and versatile guide RNA (gRNA) expression plasmids. Systematic evaluation reveals Cas9 lines with ubiquitous or germ-line-restricted patterns of activity. We also demonstrate differential activity of the same gRNA expressed from different U6 snRNA promoters, with the previously untested U6:3 promoter giving the most potent effect. An appropriate combination of Cas9 and gRNA allows targeting of essential and nonessential genes with transmission rates ranging from 25-100%. We also demonstrate that our optimized CRISPR/Cas tools can be used for offset nicking-based mutagenesis. Furthermore, in combination with oligonucleotide or long double-stranded donor templates, our reagents allow precise genome editing by homology-directed repair with rates that make selection markers unnecessary. Last, we demonstrate a novel application of CRISPR/Cas-mediated technology in revealing loss-of-function phenotypes in somatic cells following efficient biallelic targeting by Cas9 expressed in a ubiquitous or tissue-restricted manner. Our CRISPR/Cas tools will facilitate the rapid evaluation of mutant phenotypes of specific genes and the precise modification of the genome with single-nucleotide precision. Our results also pave the way for high-throughput genetic screening with CRISPR/Cas. PMID:25002478

  20. Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila.

    PubMed

    Port, Fillip; Chen, Hui-Min; Lee, Tzumin; Bullock, Simon L

    2014-07-22

    The type II clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system has emerged recently as a powerful method to manipulate the genomes of various organisms. Here, we report a toolbox for high-efficiency genome engineering of Drosophila melanogaster consisting of transgenic Cas9 lines and versatile guide RNA (gRNA) expression plasmids. Systematic evaluation reveals Cas9 lines with ubiquitous or germ-line-restricted patterns of activity. We also demonstrate differential activity of the same gRNA expressed from different U6 snRNA promoters, with the previously untested U6:3 promoter giving the most potent effect. An appropriate combination of Cas9 and gRNA allows targeting of essential and nonessential genes with transmission rates ranging from 25-100%. We also demonstrate that our optimized CRISPR/Cas tools can be used for offset nicking-based mutagenesis. Furthermore, in combination with oligonucleotide or long double-stranded donor templates, our reagents allow precise genome editing by homology-directed repair with rates that make selection markers unnecessary. Last, we demonstrate a novel application of CRISPR/Cas-mediated technology in revealing loss-of-function phenotypes in somatic cells following efficient biallelic targeting by Cas9 expressed in a ubiquitous or tissue-restricted manner. Our CRISPR/Cas tools will facilitate the rapid evaluation of mutant phenotypes of specific genes and the precise modification of the genome with single-nucleotide precision. Our results also pave the way for high-throughput genetic screening with CRISPR/Cas.

  1. Tool Forces Developed During Friction Stir Welding

    NASA Technical Reports Server (NTRS)

    Melendez, M.; Tang, W.; Schmidt, C.; McClure, J. C.; Nunes, A. C.; Murr, L. E.

    2003-01-01

    This paper will describe a technique for measuring the various forces and the torque that exist on the Friction Stir Welding pin tool. Results for various plunge depths, weld speeds, rotational speed, and tool configurations will be presented. Welds made on 6061 aluminum with typical welding conditions require a downward force of 2800 lbs. (12.5 kN) a longitudinal force in the direction of motion of 300 lbs (1.33 kN), a transverse force in the omega x v direction of 30 lbs (135 N). Aluminum 2195 under typical weld conditions requires a downward force of 3100 lbs. (1.38 kN), a longitudinal force of 920 lbs. (4.1 kN), and a transverse force of 45 lbs. (200 N) in the omega x v direction.

  2. Computational Tools for Accelerating Carbon Capture Process Development

    SciTech Connect

    Miller, David; Sahinidis, N V; Cozad, A; Lee, A; Kim, H; Morinelly, J; Eslick, J; Yuan, Z

    2013-06-04

    This presentation reports development of advanced computational tools to accelerate next generation technology development. These tools are to develop an optimized process using rigorous models. They include: Process Models; Simulation-Based Optimization; Optimized Process; Uncertainty Quantification; Algebraic Surrogate Models; and Superstructure Optimization (Determine Configuration).

  3. Algal Functional Annotation Tool from the DOE-UCLA Institute for Genomics and Proteomics

    DOE Data Explorer

    Lopez, David

    The Algal Functional Annotation Tool is a bioinformatics resource to visualize pathway maps, identify enriched biological terms, or convert gene identifiers to elucidate biological function in silico. These types of analysis have been catered to support lists of gene identifiers, such as those coming from transcriptome gene expression analysis. By analyzing the functional annotation of an interesting set of genes, common biological motifs may be elucidated and a first-pass analysis can point further research in the right direction. Currently, the following databases have been parsed, processed, and added to the tool: 1( Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways Database, 2) MetaCyc Encyclopedia of Metabolic Pathways, 3) Panther Pathways Database, 4) Reactome Pathways Database, 5) Gene Ontology, 6) MapMan Ontology, 7) KOG (Eukaryotic Clusters of Orthologous Groups), 5)Pfam, 6) InterPro.

  4. Developing A SPOT CRM Debriefing Tool

    NASA Technical Reports Server (NTRS)

    Martin, Lynne; Villeda, Eric; Orasanu, Judith; Connors, Mary M. (Technical Monitor)

    1998-01-01

    In a study of CRM LOFT briefings published in 1997, Dismukes, McDonnell & Jobe reported that briefings were not being utilized as fully as they could be and that crews may not be getting the full benefit from LOFT that is possible. On the basis of their findings, they suggested a set of general guidelines for briefings for the industry. Our work builds on this study to try to provide a specific debriefing tool which provides a focus for the strategies that Dismukes et al suggest.

  5. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

    PubMed Central

    Paley, Suzanne M.; Krummenacker, Markus; Latendresse, Mario; Dale, Joseph M.; Lee, Thomas J.; Kaipa, Pallavi; Gilham, Fred; Spaulding, Aaron; Popescu, Liviu; Altman, Tomer; Paulsen, Ian; Keseler, Ingrid M.; Caspi, Ron

    2010-01-01

    Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry. PMID:19955237

  6. A new tool called DISSECT for analysing large genomic data sets using a Big Data approach

    PubMed Central

    Canela-Xandri, Oriol; Law, Andy; Gray, Alan; Woolliams, John A.; Tenesa, Albert

    2015-01-01

    Large-scale genetic and genomic data are increasingly available and the major bottleneck in their analysis is a lack of sufficiently scalable computational tools. To address this problem in the context of complex traits analysis, we present DISSECT. DISSECT is a new and freely available software that is able to exploit the distributed-memory parallel computational architectures of compute clusters, to perform a wide range of genomic and epidemiologic analyses, which currently can only be carried out on reduced sample sizes or under restricted conditions. We demonstrate the usefulness of our new tool by addressing the challenge of predicting phenotypes from genotype data in human populations using mixed-linear model analysis. We analyse simulated traits from 470,000 individuals genotyped for 590,004 SNPs in ∼4 h using the combined computational power of 8,400 processor cores. We find that prediction accuracies in excess of 80% of the theoretical maximum could be achieved with large sample sizes. PMID:26657010

  7. Hordeum chilense genome, a useful tool to investigate the endosperm yellow pigment content in the Triticeae

    PubMed Central

    2012-01-01

    Background The wild barley Hordeum chilense fulfills some requirements for being a useful tool to investigate the endosperm yellow pigment content (YPC) in the Triticeae including its diploid constitution, the availability of genetic resources (addition and deletion stocks and a high density genetic map) and, especially, its high seed YPC not silenced in tritordeums (amphiploids derived from H. chilense and wheat). Thus, the aim of this work was to test the utility of the H. chilense genome for investigating the YPC in the Triticeae. Results Twelve genes related to endosperm carotenoid content and/or YPC in grasses (Dxr, Hdr [synonym ispH], Ggpps1, Psy2, Psy3, Pds, Zds, e-Lcy, b-Lcy, Hyd3, Ccd1 and Ppo1) were identified, and mapped in H. chilense using rice genes to identify orthologs from barley, wheat, sorghum and maize. Macrocolinearity studies revealed that gene positions were in agreement in H. vulgare and H. chilense. Additionally, three main regions associated with YPC were identified in chromosomes 2Hch, 3Hch and 7Hch in H. chilense, the former being the most significant one. Conclusions The results obtained are consistent with previous findings in wheat and suggest that Ggpps1, Zds and Hyd3 on chromosome 2Hch may be considered candidate genes in wheat for further studies in YPC improvement. Considering the syntenic location of carotenoid genes in H. chilense, we have concluded that the Hch genome may constitute a valuable tool for YPC studies in the Triticeae. PMID:23122232

  8. Applying CASE Tools for On-Board Software Development

    NASA Astrophysics Data System (ADS)

    Brammer, U.; Hönle, A.

    For many space projects the software development is facing great pressure with respect to quality, costs and schedule. One way to cope with these challenges is the application of CASE tools for automatic generation of code and documentation. This paper describes two CASE tools: Rhapsody (I-Logix) featuring UML and ISG (BSSE) that provides modeling of finite state machines. Both tools have been used at Kayser-Threde in different space projects for the development of on-board software. The tools are discussed with regard to the full software development cycle.

  9. Developing LIGO Detector Characterization Tools and Methods

    NASA Astrophysics Data System (ADS)

    Costa, Cesar

    2010-10-01

    Laser Interferometric Gravitational-Wave Observatory (LIGO) has been in constant process of improvement to achieve its main goal: the detection of gravitational waves (GWs). For the current science run (S6), improved control systems have been installed in order to increase the instrument sensitivity. The LIGO Detector Characterization (DetChar) Group works to understand how such devices and environmental sources could affect the GW channel, specially when they contaminate measurements by introducing spurious signals. To decrease false alarm rates DetChar monitors several auxiliary channels in order to diagnose environmental and instrumental glitches which can produce GW signal-like events. This improves the data quality for GW searches, and also informs commissioners about instrumental issues. This talk describes the methodology that we have been applying to LIGO Detector Characterization, specially glitch hunting and monitoring tools.

  10. A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing of 240 Eucalyptus tree genomes across 12 species.

    PubMed

    Silva-Junior, Orzenil B; Faria, Danielle A; Grattapaglia, Dario

    2015-06-01

    We used whole genome resequencing of pooled individuals to develop a high-density single-nucleotide polymorphism (SNP) chip for Eucalyptus. Genomes of 240 trees of 12 species were sequenced at 3.5× each, and 46 997 586 raw SNP variants were subject to multivariable filtering metrics toward a multispecies, genome-wide distributed chip content. Of the 60 904 SNPs on the chip, 59 222 were genotyped and 51 204 were polymorphic across 14 Eucalyptus species, providing a 96% genome-wide coverage with 1 SNP/12-20 kb, and 47 069 SNPs at ≤ 10 kb from 30 444 of the 33 917 genes in the Eucalyptus genome. Given the EUChip60K multi-species genotyping flexibility, we show that both the sample size and taxonomic composition of cluster files impact heterozygous call specificity and sensitivity by benchmarking against 'gold standard' genotypes derived from deeply sequenced individual tree genomes. Thousands of SNPs were shared across species, likely representing ancient variants arisen before the split of these taxa, hinting to a recent eucalypt radiation. We show that the variable SNP filtering constraints allowed coverage of the entire site frequency spectrum, mitigating SNP ascertainment bias. The EUChip60K represents an outstanding tool with which to address population genomics questions in Eucalyptus and to empower genomic selection, GWAS and the broader study of complex trait variation in eucalypts.

  11. Empowered genome community: leveraging a bioinformatics platform as a citizen-scientist collaboration tool.

    PubMed

    Wendelsdorf, Katherine; Shah, Sohela

    2015-09-01

    There is on-going effort in the biomedical research community to leverage Next Generation Sequencing (NGS) technology to identify genetic variants that affect our health. The main challenge facing researchers is getting enough samples from individuals either sick or healthy - to be able to reliably identify the few variants that are causal for a phenotype among all other variants typically seen among individuals. At the same time, more and more individuals are having their genome sequenced either out of curiosity or to identify the cause of an illness. These individuals may benefit from of a way to view and understand their data. QIAGEN's Ingenuity Variant Analysis is an online application that allows users with and without extensive bioinformatics training to incorporate information from published experiments, genetic databases, and a variety of statistical models to identify variants, from a long list of candidates, that are most likely causal for a phenotype as well as annotate variants with what is already known about them in the literature and databases. Ingenuity Variant Analysis is also an information sharing platform where users may exchange samples and analyses. The Empowered Genome Community (EGC) is a new program in which QIAGEN is making this on-line tool freely available to any individual who wishes to analyze their own genetic sequence. EGC members are then able to make their data available to other Ingenuity Variant Analysis users to be used in research. Here we present and describe the Empowered Genome Community in detail. We also present a preliminary, proof-of-concept study that utilizes the 200 genomes currently available through the EGC. The goal of this program is to allow individuals to access and understand their own data as well as facilitate citizen-scientist collaborations that can drive research forward and spur quality scientific dialogue in the general public. PMID:27054071

  12. Empowered genome community: leveraging a bioinformatics platform as a citizen-scientist collaboration tool.

    PubMed

    Wendelsdorf, Katherine; Shah, Sohela

    2015-09-01

    There is on-going effort in the biomedical research community to leverage Next Generation Sequencing (NGS) technology to identify genetic variants that affect our health. The main challenge facing researchers is getting enough samples from individuals either sick or healthy - to be able to reliably identify the few variants that are causal for a phenotype among all other variants typically seen among individuals. At the same time, more and more individuals are having their genome sequenced either out of curiosity or to identify the cause of an illness. These individuals may benefit from of a way to view and understand their data. QIAGEN's Ingenuity Variant Analysis is an online application that allows users with and without extensive bioinformatics training to incorporate information from published experiments, genetic databases, and a variety of statistical models to identify variants, from a long list of candidates, that are most likely causal for a phenotype as well as annotate variants with what is already known about them in the literature and databases. Ingenuity Variant Analysis is also an information sharing platform where users may exchange samples and analyses. The Empowered Genome Community (EGC) is a new program in which QIAGEN is making this on-line tool freely available to any individual who wishes to analyze their own genetic sequence. EGC members are then able to make their data available to other Ingenuity Variant Analysis users to be used in research. Here we present and describe the Empowered Genome Community in detail. We also present a preliminary, proof-of-concept study that utilizes the 200 genomes currently available through the EGC. The goal of this program is to allow individuals to access and understand their own data as well as facilitate citizen-scientist collaborations that can drive research forward and spur quality scientific dialogue in the general public.

  13. Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting)

    SciTech Connect

    Goldberg, Robert

    2012-03-21

    Robert Goldberg of UCLA presents "Using Genomics to Dissect Seed Development" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  14. Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting)

    ScienceCinema

    Goldberg, Robert [UCLA

    2016-07-12

    Robert Goldberg of UCLA presents "Using Genomics to Dissect Seed Development" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  15. Development of Asset Management Decision Support Tools for Power Equipment

    NASA Astrophysics Data System (ADS)

    Okamoto, Tatsuki; Takahashi, Tsuguhiro

    Development of asset management decision support tools become very intensive in order to reduce maintenance cost of power equipment due to the liberalization of power business. This article reviews some aspects of present status of asset management decision support tools development for power equipment based on the papers published in international conferences, domestic conventions, and several journals.

  16. SNPTracker: A Swift Tool for Comprehensive Tracking and Unifying dbSNP rs IDs and Genomic Coordinates of Massive Sequence Variants.

    PubMed

    Deng, Jia-En; Sham, Pak C; Li, Miao-Xin

    2015-11-19

    The reference single nucleotide polymorphism (rs) ID in dbSNP (http://www.ncbi.nlm.nih.gov/SNP/) is a key resource identifier, which is widely used in human genetics and genomics studies. However, its application is often complicated by the varied IDs of different versions. Here, we developed a user-friendly tool, SNPTracker, for comprehensively tracking and unifying the rs IDs and genomic coordinates of massive sequence variants at a time. It worked perfectly, and had much higher accuracy and capacity than two alternative utilities in our proof-of-principle examples. SNPTracker will greatly facilitate genetic data exchange and integration in the postgenome-wide association study era.

  17. Development of a Geometric Spatial Visualization Tool

    ERIC Educational Resources Information Center

    Ganesh, Bibi; Wilhelm, Jennifer; Sherrod, Sonya

    2009-01-01

    This paper documents the development of the Geometric Spatial Assessment. We detail the development of this instrument which was designed to identify middle school students' strategies and advancement in understanding of four geometric concept domains (geometric spatial visualization, spatial projection, cardinal directions, and periodic patterns)…

  18. CLIPS interface development tools and their application

    NASA Technical Reports Server (NTRS)

    Engel, Bernard A.; Rewerts, Chris C.; Srinivasan, Raghavan; Rogers, Joseph B.; Jones, Don D.

    1990-01-01

    A package of C-based PC user interface development functions has been developed and integrated into CLIPS. The primary function is ASK which provides a means to ask the user questions via multiple choice menus or the keyboard and then returns the user response to CLIPS. A parameter-like structure supplies information for the interface. Another function, SHOW, provides a means to paginate and display text. A third function, TITLE, formats and displays title screens. A similar set of C-based functions that are more general and thus will run on UNIX and machines have also been developed. Seven expert system applications were transformed from commercial development environments into CLIPS and utilize ASK, SHOW, and TITLE. Development of numerous new expert system applications using CLIPS and these interface functions has started. These functions greatly reduce the time required to build interfaces for CLIPS applications.

  19. [COMETE: a tool to develop psychosocial competences in patient education].

    PubMed

    Saugeron, Benoit; Sonnier, Pierre; Marchais, Stéphanie

    2016-01-01

    This article presents a detailed description of the development and use of the COMETE tool. The COMETE tool is designed to help medical teams identify, develop or evaluate psychosocial skills in patient education and counselling. This tool, designed in the form of a briefcase, proposes methodological activities and cards that assess psychosocial skills during a shared educational assessment, group meetings or during an individual evaluation. This tool is part of a support approach for medical teams caring for patients with chronic diseases. PMID:27392049

  20. Developing a 300C Analog Tool for EGS

    SciTech Connect

    Normann, Randy

    2015-03-23

    This paper covers the development of a 300°C geothermal well monitoring tool for supporting future EGS (enhanced geothermal systems) power production. This is the first of 3 tools planed. This is an analog tool designed for monitoring well pressure and temperature. There is discussion on 3 different circuit topologies and the development of the supporting surface electronics and software. There is information on testing electronic circuits and component. One of the major components is the cable used to connect the analog tool to the surface.

  1. DEVELOPING A TOOL FOR ENVIRONMENTALLY PREFERABLE PURCHASING

    EPA Science Inventory

    LCA-based guidance was developed by EPA under the Framework for Responsible Environmental Decision Making (FRED) effort to demonstrate how to conduct a relative comparison between product types to determine environmental preferability. It identifies data collection needs and iss...

  2. DEVELOPMENT OF SOLUBILITY PRODUCT VISUALIZATION TOOLS

    SciTech Connect

    T.F. Turner; A.T. Pauli; J.F. Schabron

    2004-05-01

    Western Research Institute (WRI) has developed software for the visualization of data acquired from solubility tests. The work was performed in conjunction with AB Nynas Petroleum, Nynashamn, Sweden who participated as the corporate cosponsor for this Jointly Sponsored Research (JSR) task. Efforts in this project were split between software development and solubility test development. The Microsoft Windows-compatible software developed inputs up to three solubility data sets, calculates the parameters for six solid body types to fit the data, and interactively displays the results in three dimensions. Several infrared spectroscopy techniques have been examined for potential use in determining bitumen solubility in various solvents. Reflectance, time-averaged absorbance, and transmittance techniques were applied to bitumen samples in single and binary solvent systems. None of the techniques were found to have wide applicability.

  3. Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes

    PubMed Central

    2013-01-01

    Background Lettuce (Lactuca sativa L.) is the major crop from the group of leafy vegetables. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers. Results Testing of newly developed markers on a set of 36 Lactuca accession (33 L. sativa, and one of each L. serriola L., L. saligna L., and L. virosa L.) revealed that both the genetic heterozygosity (UHe = 0.56) and the number of loci per SSR (Na = 5.50) are significantly higher for genomic SSR markers than for previously developed EST-based SSR markers (UHe = 0.32, Na = 3.56). Fifty-four genomic SSR markers were placed on the molecular linkage map of lettuce. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. Analysis of molecular variance (AMOVA) of L. sativa accessions showed that approximately 3% of genetic diversity was within accessions, 79% among accessions, and 18% among horticultural types. Conclusions The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping of genes. PMID:23339733

  4. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple.

    PubMed

    Chagné, David; Crowhurst, Ross N; Troggio, Michela; Davey, Mark W; Gilmore, Barbara; Lawley, Cindy; Vanderzande, Stijn; Hellens, Roger P; Kumar, Satish; Cestaro, Alessandro; Velasco, Riccardo; Main, Dorrie; Rees, Jasper D; Iezzoni, Amy; Mockler, Todd; Wilhelm, Larry; Van de Weg, Eric; Gardiner, Susan E; Bassil, Nahla; Peace, Cameron

    2012-01-01

    As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of 'Golden Delicious', SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple.

  5. Genome-wide linkage analysis is a powerful prenatal diagnostic tool in families with unknown genetic defects.

    PubMed

    Arélin, Maria; Schulze, Bernt; Müller-Myhsok, Bertram; Horn, Denise; Diers, Alexander; Uhlenberg, Birgit; Nürnberg, Peter; Nürnberg, Gudrun; Becker, Christian; Mundlos, Stefan; Lindner, Tom H; Sperling, Karl; Hoffmann, Katrin

    2013-04-01

    Genome-wide linkage analysis is an established tool to map inherited diseases. To our knowledge it has not been used in prenatal diagnostics of any genetic disorder. We present a family with a severe recessive mental retardation syndrome, where the mother wished pregnancy termination to avoid delivering another affected child. By genome-wide scanning using the Affymetrix (Santa Clara, CA, USA) 10k chip we were able to establish the disease haplotype. Without knowing the exact genetic defect, we excluded the condition in the fetus. The woman finally gave birth to a healthy baby. We suggest that genome-wide linkage analysis--based on either SNP mapping or full-genome sequencing--is a very useful tool in prenatal diagnostics of diseases.

  6. MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis

    PubMed Central

    Moyer, Eric; Hagenauer, Megan; Lesko, Matthew; Francis, Felix; Rodriguez, Oscar; Nagarajan, Vijayaraj; Huser, Vojtech; Busby, Ben

    2016-01-01

    Network analysis can make variant analysis better. There are existing tools like HotNet2 and dmGWAS that can provide various analytical methods. We developed a prototype of a pipeline called MetaNetVar that allows execution of multiple tools. The code is published at https://github.com/NCBI-Hackathons/Network_SNPs. A working prototype is published as an Amazon Machine Image - ami-4510312f . PMID:27158457

  7. 78 FR 68459 - Medical Device Development Tools; Draft Guidance for Industry, Tool Developers, and Food and Drug...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-14

    ... guidance to FDA staff, industry, healthcare providers, researchers, and patient and consumer groups on a... HUMAN SERVICES Food and Drug Administration Medical Device Development Tools; Draft Guidance for Industry, Tool Developers, and Food and Drug Administration Staff; Availability AGENCY: Food and...

  8. Microcomputers: Tools for Developing Technological Literacy.

    ERIC Educational Resources Information Center

    Liao, Thomas T.

    1983-01-01

    Describes a course in which undergraduate students learn to program microcomputers while learning about its applications and ramifications. Descriptions of software developed for the course are also provided. These include yellow light (traffic flow), domestic electrical energy use/cost, water pollution, and supermarket automation. (CN)

  9. Tools for Nanotechnology Education Development Program

    SciTech Connect

    Dorothy Moore

    2010-09-27

    The overall focus of this project was the development of reusable, cost-effective educational modules for use with the table top scanning electron microscope (TTSEM). The goal of this project's outreach component was to increase students' exposure to the science and technology of nanoscience.

  10. Developments in multicavity hot runner tooling.

    PubMed

    Glendenning, P

    2009-01-01

    Technological developments in specific areas of multicavity hot runner systems are improving quality control and repeatability and reducing cycle times. Advances such as closed loop filling control of multicavity moulds within the mould itself, servo-actuated valve gates and synchronised valve stems are discussed.

  11. Appreciative Inquiry as an Organizational Development Tool.

    ERIC Educational Resources Information Center

    Martinetz, Charles F.

    2002-01-01

    Defines appreciative inquiry as a change model that uses traditional organizational development processes (team building, strategic planning, business process redesign, management audits) in a new way, both as a philosophy and as a process. Emphasizes collaboration, participation of all voices, and changing the organization rather than the people.…

  12. Surrogate Analysis and Index Developer (SAID) tool

    USGS Publications Warehouse

    Domanski, Marian M.; Straub, Timothy D.; Landers, Mark N.

    2015-10-01

    The regression models created in SAID can be used in utilities that have been developed to work with the USGS National Water Information System (NWIS) and for the USGS National Real-Time Water Quality (NRTWQ) Web site. The real-time dissemination of predicted SSC and prediction intervals for each time step has substantial potential to improve understanding of sediment-related water quality and associated engineering and ecological management decisions.

  13. Entering the Public Health Genomics Era: Why Must Health Educators Develop Genomic Competencies?

    ERIC Educational Resources Information Center

    Chen, Lei-Shih; Goodson, Patricia

    2007-01-01

    Although the completion of the Human Genome Project will offer new insight into diseases and help develop efficient, personalized treatment or prevention programs, it will also raise new and non-trivial public health issues. Many of these issues fall under the professional purview of public health workers. As members of the public health…

  14. Genome Elimination: Translating Basic Research into a Future Tool for Plant Breeding

    PubMed Central

    Comai, Luca

    2014-01-01

    During the course of our history, humankind has been through different periods of agricultural improvement aimed at enhancing our food supply and the performance of food crops. In recent years, it has become apparent that future crop improvement efforts will require new approaches to address the local challenges of farmers while empowering discovery across industry and academia. New plant breeding approaches are needed to meet this challenge to help feed a growing world population. Here I discuss how a basic research discovery is being translated into a potential future tool for plant breeding, and share the story of researcher Simon Chan, who recognized the potential application of this new approach—genome elimination—for the breeding of staple food crops in Africa and South America. PMID:24915001

  15. The capsicum transcriptome DB: a “hot” tool for genomic research

    PubMed Central

    Góngora-Castillo, Elsa; Fajardo-Jaime, Rubén; Fernández-Cortes, Araceli; Jofre-Garfias, Alba E; Lozoya-Gloria, Edmundo; Martínez, Octavio; Ochoa-Alejo, Neftalí; Rivera-Bustamante, Rafael

    2012-01-01

    Chili pepper (Capsicum annuum) is an economically important crop with no available public genome sequence. We describe a genomic resource to facilitate Capsicum annuum research. A collection of Expressed Sequence Tags (ESTs) derived from five C. annuum organs (root, stem, leaf, flower and fruit) were sequenced using the Sanger method and multiple leaf transcriptomes were deeply sampled using with GS-pyrosequencing. A hybrid assembly of 1,324,516 raw reads yielded 32,314 high quality contigs as validated by coverage and identity analysis with existing pepper sequences. Overall, 75.5% of the contigs had significant sequence similarity to entries in nucleic acid and protein databases; 23% of the sequences have not been previously reported for C. annuum and expand sequence resources for this species. A MySQL database and a user-friendly Web interface were constructed with search-tools that permit queries of the ESTs including sequence, functional annotation, Gene Ontology classification, metabolic pathways, and assembly information. The Capsicum Transcriptome DB is free available from http://www.bioingenios.ira.cinvestav.mx:81/Joomla/ PMID:22359434

  16. Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing.

    PubMed

    Thoendel, Matthew; Jeraldo, Patricio R; Greenwood-Quaintance, Kerryl E; Yao, Janet Z; Chia, Nicholas; Hanssen, Arlen D; Abdel, Matthew P; Patel, Robin

    2016-08-01

    Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus. Using spiked uninfected sonicate fluid there was a 6-fold enrichment of bacterial DNA with the NEBNext kit and 76-fold enrichment with the MolYsis kit. Metagenomic whole genome sequencing of sonicate fluid revealed 13- to 85-fold enrichment of bacterial DNA using the NEBNext enrichment kit. The MolYsis approach achieved 481- to 9580-fold enrichment, resulting in 7 to 59% of sequencing reads being from the pathogens known to be present in the samples. These results demonstrate the usefulness of these tools when testing clinical samples with low microbial burden using next generation sequencing. PMID:27237775

  17. User Studies: Developing Learning Strategy Tool Software for Children.

    ERIC Educational Resources Information Center

    Fitzgerald, Gail E.; Koury, Kevin A.; Peng, Hsinyi

    This paper is a report of user studies for developing learning strategy tool software for children. The prototype software demonstrated is designed for children with learning and behavioral disabilities. The tools consist of easy-to-use templates for creating organizational, memory, and learning approach guides for use in classrooms and at home.…

  18. Genomic-based tools for the risk assessment, management, and prevention of type 2 diabetes

    PubMed Central

    Johansen Taber, Katherine A; Dickinson, Barry D

    2015-01-01

    Type 2 diabetes (T2D) is a common and serious disorder and is a significant risk factor for the development of cardiovascular disease, neuropathy, nephropathy, retinopathy, periodontal disease, and foot ulcers and amputations. The burden of disease associated with T2D has led to an emphasis on early identification of the millions of individuals at high risk so that management and intervention strategies can be effectively implemented before disease progression begins. With increasing knowledge about the genetic basis of T2D, several genomic-based strategies have been tested for their ability to improve risk assessment, management and prevention. Genetic risk scores have been developed with the intent to more accurately identify those at risk for T2D and to potentially improve motivation and adherence to lifestyle modification programs. In addition, evidence is building that oral antihyperglycemic medications are subject to pharmacogenomic variation in a substantial number of patients, suggesting genomics may soon play a role in determining the most effective therapies. T2D is a complex disease that affects individuals differently, and risk prediction and treatment may be challenging for health care providers. Genomic approaches hold promise for their potential to improve risk prediction and tailor management for individual patients and to contribute to better health outcomes for those with T2D. PMID:25609992

  19. Genomic-based tools for the risk assessment, management, and prevention of type 2 diabetes.

    PubMed

    Johansen Taber, Katherine A; Dickinson, Barry D

    2015-01-01

    Type 2 diabetes (T2D) is a common and serious disorder and is a significant risk factor for the development of cardiovascular disease, neuropathy, nephropathy, retinopathy, periodontal disease, and foot ulcers and amputations. The burden of disease associated with T2D has led to an emphasis on early identification of the millions of individuals at high risk so that management and intervention strategies can be effectively implemented before disease progression begins. With increasing knowledge about the genetic basis of T2D, several genomic-based strategies have been tested for their ability to improve risk assessment, management and prevention. Genetic risk scores have been developed with the intent to more accurately identify those at risk for T2D and to potentially improve motivation and adherence to lifestyle modification programs. In addition, evidence is building that oral antihyperglycemic medications are subject to pharmacogenomic variation in a substantial number of patients, suggesting genomics may soon play a role in determining the most effective therapies. T2D is a complex disease that affects individuals differently, and risk prediction and treatment may be challenging for health care providers. Genomic approaches hold promise for their potential to improve risk prediction and tailor management for individual patients and to contribute to better health outcomes for those with T2D.

  20. Black raspberry genetic and genomic resources development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study incorporates field and laboratory components to advance and streamline identification of a variety of traits of economic interest and to develop molecular markers for marker assisted breeding of black raspberry (Rubus occidentalis). A lack of adapted, disease resistant cultivars has led t...

  1. Developing black raspberry genetic and genomic resources

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study incorporates field and laboratory components to advance and streamline identification of a variety of traits of economic interest and to develop molecular markers for marker assisted breeding of black raspberry (Rubus occidentalis). A lack of adapted, disease resistant cultivars has led t...

  2. Thyroid insufficiency in developing rat brain: A genomic analysis.

    EPA Science Inventory

    Thyroid Insufficiency in the Developing Rat Brain: A Genomic Analysis. JE Royland and ME Gilbert, Neurotox. Div., U.S. EPA, RTP, NC, USA. Endocrine disruption (ED) is an area of major concern in environmental neurotoxicity. Severe deficits in thyroid hormone (TH) levels have bee...

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

    PubMed Central

    Bouskila, Amos; Chorev, Michal; Carmel, Liran; Mishmar, Dan

    2015-01-01

    RNA-seq is becoming a preferred tool for genomics studies of model and non-model organisms. However, DNA-based analysis of organisms lacking sequenced genomes cannot rely on RNA-seq data alone to isolate most genes of interest, as DNA codes both exons and introns. With this in mind, we designed a novel tool, LEMONS, that exploits the evolutionary conservation of both exon/intron boundary positions and splice junction recognition signals to produce high throughput splice-junction predictions in the absence of a reference genome. When tested on multiple annotated vertebrate mRNA data, LEMONS accurately identified 87% (average) of the splice-junctions. LEMONS was then applied to our updated Mediterranean chameleon transcriptome, which lacks a reference genome, and predicted a total of 90,820 exon-exon junctions. We experimentally verified these splice-junction predictions by amplifying and sequencing twenty randomly selected genes from chameleon DNA templates. Exons and introns were detected in 19 of 20 of the positions predicted by LEMONS. To the best of our knowledge, LEMONS is currently the only experimentally verified tool that can accurately predict splice-junctions in organisms that lack a reference genome. PMID:26606265

  4. FOCAL: an experimental design tool for systematizing metabolic discoveries and model development.

    PubMed

    Tervo, Christopher J; Reed, Jennifer L

    2012-12-13

    Current computational tools can generate and improve genome-scale models based on existing data; however, for many organisms, the data needed to test and refine such models are not available. To facilitate model development, we created the forced coupling algorithm, FOCAL, to identify genetic and environmental conditions such that a reaction becomes essential for an experimentally measurable phenotype. This reaction's conditional essentiality can then be tested experimentally to evaluate whether network connections occur or to create strains with desirable phenotypes. FOCAL allows network connections to be queried, which improves our understanding of metabolism and accuracy of developed models.

  5. DEVELOPMENT OF REMOTE HANFORD CONNECTOR GASKET REPLACEMENT TOOLING FOR DWPF

    SciTech Connect

    Krementz, D.; Coughlin, Jeffrey

    2009-05-05

    The Defense Waste Processing Facility (DWPF) requested the Savannah River National Laboratory (SRNL) to develop tooling and equipment to remotely replace gaskets in mechanical Hanford connectors to reduce personnel radiation exposure as compared to the current hands-on method. It is also expected that radiation levels will continually increase with future waste streams. The equipment is operated in the Remote Equipment Decontamination Cell (REDC), which is equipped with compressed air, two master-slave manipulators (MSM's) and an electro-mechanical manipulator (EMM) arm for operation of the remote tools. The REDC does not provide access to electrical power, so the equipment must be manually or pneumatically operated. The MSM's have a load limit at full extension of ten pounds, which limited the weight of the installation tool. In order to remotely replace Hanford connector gaskets several operations must be performed remotely, these include: removal of the spent gasket and retaining ring (retaining ring is also called snap ring), loading the new snap ring and gasket into the installation tool and installation of the new gasket into the Hanford connector. SRNL developed and tested tools that successfully perform all of the necessary tasks. Removal of snap rings from horizontal and vertical connectors is performed by separate air actuated retaining ring removal tools and is manipulated in the cell by the MSM. In order install a new gasket, the snap ring loader is used to load a new snap ring into a groove in the gasket installation tool. A new gasket is placed on the installation tool and retained by custom springs. An MSM lifts the installation tool and presses the mounted gasket against the connector block. Once the installation tool is in position, the gasket and snap ring are installed onto the connector by pneumatic actuation. All of the tools are located on a custom work table with a pneumatic valve station that directs compressed air to the desired tool and

  6. The development and demonstration of the metric assessment tool

    NASA Astrophysics Data System (ADS)

    Campbell, Cynthia A.; Gutterman, Gregory M.

    1993-09-01

    This study reflects the development and demonstration of the metric assessment tool. The purpose of the tool was to provide individuals the means to assess metrics and make improvements to the process measurement. The tool was developed using two critical attributes: customer satisfaction and process improvement. Once the tool was developed, a metric assessment process was designed to demonstrate the tool. Two metrics were selected from the Aeronautical Systems Center (ASC) and individuals with a working knowledge of the metric and process were selected for the demonstrations. Using a group support system at Armstrong Laboratory, Wright Patterson AFB, the group was asked to identify behaviors which might be motivated from the metric. Once the behaviors were identified, the group evaluated the behaviors against the critical attributes. From this assessment, behaviors were placed on the metric assessment tool. This tool clearly identified deficient behaviors and how they might distort the process measurement. From this information, the group was asked to generate improvement actions which would serve to eliminate or control deficient behaviors. With the elimination or control of deficient behaviors, the process measurement is improved and the organizational objective is better served.

  7. Limited resources of genome sequencing in developing countries: Challenges and solutions.

    PubMed

    Helmy, Mohamed; Awad, Mohamed; Mosa, Kareem A

    2016-06-01

    The differences between countries in national income, growth, human development and many other factors are used to classify countries into developed and developing countries. There are several classification systems that use different sets of measures and criteria. The most common classifications are the United Nations (UN) and the World Bank (WB) systems. The UN classification system uses the UN Human Development Index (HDI), an indicator that uses statistic of life expectancy, education, and income per capita for countries' classification. While the WB system uses gross national income (GNI) per capita that is calculated using the World Bank Atlas method. According to the UN and WB classification systems, there are 151 and 134 developing countries, respectively, with 89% overlap between the two systems. Developing countries have limited human development, and limited expenditure in education and research, among several other limitations. The biggest challenge facing genomic researchers and clinicians is limited resources. As a result, genomic tools, specifically genome sequencing technologies, which are rapidly becoming indispensable, are not widely available. In this report, we explore the current status of sequencing technologies in developing countries, describe the associated challenges and emphasize potential solutions. PMID:27354935

  8. Limited resources of genome sequencing in developing countries: Challenges and solutions.

    PubMed

    Helmy, Mohamed; Awad, Mohamed; Mosa, Kareem A

    2016-06-01

    The differences between countries in national income, growth, human development and many other factors are used to classify countries into developed and developing countries. There are several classification systems that use different sets of measures and criteria. The most common classifications are the United Nations (UN) and the World Bank (WB) systems. The UN classification system uses the UN Human Development Index (HDI), an indicator that uses statistic of life expectancy, education, and income per capita for countries' classification. While the WB system uses gross national income (GNI) per capita that is calculated using the World Bank Atlas method. According to the UN and WB classification systems, there are 151 and 134 developing countries, respectively, with 89% overlap between the two systems. Developing countries have limited human development, and limited expenditure in education and research, among several other limitations. The biggest challenge facing genomic researchers and clinicians is limited resources. As a result, genomic tools, specifically genome sequencing technologies, which are rapidly becoming indispensable, are not widely available. In this report, we explore the current status of sequencing technologies in developing countries, describe the associated challenges and emphasize potential solutions.

  9. Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.

    PubMed

    Popova, Tatiana; Manié, Elodie; Stoppa-Lyonnet, Dominique; Rigaill, Guillem; Barillot, Emmanuel; Stern, Marc Henri

    2009-01-01

    We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured with single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. Assignments were verified by DNA indexes of primary tumors and karyotypes of cell lines. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes.

  10. Consumer acceptance of food crops developed by genome editing.

    PubMed

    Ishii, Tetsuya; Araki, Motoko

    2016-07-01

    One of the major problems regarding consumer acceptance of genetically modified organisms (GMOs) is the possibility that their transgenes could have adverse effects on the environment and/or human health. Genome editing, represented by the CRISPR/Cas9 system, can efficiently achieve transgene-free gene modifications and is anticipated to generate a wide spectrum of plants. However, the public attitude against GMOs suggests that people will initially be unlikely to accept these plants. We herein explored the bottlenecks of consumer acceptance of transgene-free food crops developed by genome editing and made some recommendations. People should not pursue a zero-risk bias regarding such crops. Developers are encouraged to produce cultivars with a trait that would satisfy consumer needs. Moreover, they should carefully investigate off-target mutations in resultant plants and initially refrain from agricultural use of multiplex genome editing for better risk-benefit communication. The government must consider their regulatory status and establish appropriate regulations if necessary. The government also should foster communication between the public and developers. If people are informed of the benefits of genome editing-mediated plant breeding and trust in the relevant regulations, and if careful risk-benefit communication and sincere considerations for the right to know approach are guaranteed, then such transgene-free crops could gradually be integrated into society. PMID:27038939

  11. Consumer acceptance of food crops developed by genome editing.

    PubMed

    Ishii, Tetsuya; Araki, Motoko

    2016-07-01

    One of the major problems regarding consumer acceptance of genetically modified organisms (GMOs) is the possibility that their transgenes could have adverse effects on the environment and/or human health. Genome editing, represented by the CRISPR/Cas9 system, can efficiently achieve transgene-free gene modifications and is anticipated to generate a wide spectrum of plants. However, the public attitude against GMOs suggests that people will initially be unlikely to accept these plants. We herein explored the bottlenecks of consumer acceptance of transgene-free food crops developed by genome editing and made some recommendations. People should not pursue a zero-risk bias regarding such crops. Developers are encouraged to produce cultivars with a trait that would satisfy consumer needs. Moreover, they should carefully investigate off-target mutations in resultant plants and initially refrain from agricultural use of multiplex genome editing for better risk-benefit communication. The government must consider their regulatory status and establish appropriate regulations if necessary. The government also should foster communication between the public and developers. If people are informed of the benefits of genome editing-mediated plant breeding and trust in the relevant regulations, and if careful risk-benefit communication and sincere considerations for the right to know approach are guaranteed, then such transgene-free crops could gradually be integrated into society.

  12. Participant Satisfaction With a Preference-Setting Tool for the Return of Individual Research Results in Pediatric Genomic Research.

    PubMed

    Holm, Ingrid A; Iles, Brittany R; Ziniel, Sonja I; Bacon, Phoebe L; Savage, Sarah K; Christensen, Kurt D; Weitzman, Elissa R; Green, Robert C; Huntington, Noelle L

    2015-10-01

    The perceived benefit of return of individual research results (IRRs) in accordance to participants' preferences in genomic biobank research is unclear. We developed an online preference-setting tool for return of IRRs based on the preventability and severity of a condition, which included an opt-out option for IRRs for mental illness, developmental disorders, childhood-onset degenerative conditions, and adult-onset conditions. Parents of patients <18 years of age at Boston Children's Hospital were randomized to the hypothetical scenario that their child was enrolled in one of four biobanks with different policies for IRRs to receive (a) "None," (b) "All," (c) "Binary"--choice to receive all or none, and (d) "Granular"--use the preference-setting tool to choose categories of IRRs. Parents were given a hypothetical IRRs report for their child. The survey was sent to 11,391 parents and completed by 2,718. The Granular group was the most satisfied with the process, biobank, and hypothetical IRRs received. The None group was least satisfied and least likely to agree that the biobank was beneficial (p < .001). The response to the statement that the biobank was harmful was not different between groups. Our data suggest that the ability to designate preferences leads to greater satisfaction and may increase biobank participation.

  13. Participant Satisfaction With a Preference-Setting Tool for the Return of Individual Research Results in Pediatric Genomic Research.

    PubMed

    Holm, Ingrid A; Iles, Brittany R; Ziniel, Sonja I; Bacon, Phoebe L; Savage, Sarah K; Christensen, Kurt D; Weitzman, Elissa R; Green, Robert C; Huntington, Noelle L

    2015-10-01

    The perceived benefit of return of individual research results (IRRs) in accordance to participants' preferences in genomic biobank research is unclear. We developed an online preference-setting tool for return of IRRs based on the preventability and severity of a condition, which included an opt-out option for IRRs for mental illness, developmental disorders, childhood-onset degenerative conditions, and adult-onset conditions. Parents of patients <18 years of age at Boston Children's Hospital were randomized to the hypothetical scenario that their child was enrolled in one of four biobanks with different policies for IRRs to receive (a) "None," (b) "All," (c) "Binary"--choice to receive all or none, and (d) "Granular"--use the preference-setting tool to choose categories of IRRs. Parents were given a hypothetical IRRs report for their child. The survey was sent to 11,391 parents and completed by 2,718. The Granular group was the most satisfied with the process, biobank, and hypothetical IRRs received. The None group was least satisfied and least likely to agree that the biobank was beneficial (p < .001). The response to the statement that the biobank was harmful was not different between groups. Our data suggest that the ability to designate preferences leads to greater satisfaction and may increase biobank participation. PMID:26376753

  14. Host-Brucella interactions and the Brucella genome as tools for subunit antigen discovery and immunization against brucellosis

    PubMed Central

    Gomez, Gabriel; Adams, Leslie G.; Rice-Ficht, Allison; Ficht, Thomas A.

    2013-01-01

    Vaccination is the most important approach to counteract infectious diseases. Thus, the development of new and improved vaccines for existing, emerging, and re-emerging diseases is an area of great interest to the scientific community and general public. Traditional approaches to subunit antigen discovery and vaccine development lack consideration for the critical aspects of public safety and activation of relevant protective host immunity. The availability of genomic sequences for pathogenic Brucella spp. and their hosts have led to development of systems-wide analytical tools that have provided a better understanding of host and pathogen physiology while also beginning to unravel the intricacies at the host-pathogen interface. Advances in pathogen biology, host immunology, and host-agent interactions have the potential to serve as a platform for the design and implementation of better-targeted antigen discovery approaches. With emphasis on Brucella spp., we probe the biological aspects of host and pathogen that merit consideration in the targeted design of subunit antigen discovery and vaccine development. PMID:23720712

  15. Development of a Safety Management Web Tool for Horse Stables

    PubMed Central

    Leppälä, Jarkko; Kolstrup, Christina Lunner; Pinzke, Stefan; Rautiainen, Risto; Saastamoinen, Markku; Särkijärvi, Susanna

    2015-01-01

    Simple Summary A new web tool for equine activities, InnoHorse, was developed to support horse stable managers in business, safety, pasture and manure management. The aim of the safety section of the web tool was to raise awareness of safety issues in daily horse stable activities. This section contains a safety checklist, stable safety map and good practices to support human health and horse welfare and to prevent injuries in horse-related activities. Reviews of the literature and statistics, empirical horse stable case studies, expert panel workshops and stakeholder interviews were utilized in designing the web tool. Abstract Managing a horse stable involves risks, which can have serious consequences for the stable, employees, clients, visitors and horses. Existing industrial or farm production risk management tools are not directly applicable to horse stables and they need to be adapted for use by managers of different types of stables. As a part of the InnoEquine project, an innovative web tool, InnoHorse, was developed to support horse stable managers in business, safety, pasture and manure management. A literature review, empirical horse stable case studies, expert panel workshops and stakeholder interviews were carried out to support the design. The InnoHorse web tool includes a safety section containing a horse stable safety map, stable safety checklists, and examples of good practices in stable safety, horse handling and rescue planning. This new horse stable safety management tool can also help in organizing work processes in horse stables in general. PMID:26569319

  16. SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals

    PubMed Central

    Damienikan, Aliaksandr U.

    2016-01-01

    The majority of bacterial genome annotations are currently automated and based on a ‘gene by gene’ approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn’t fit with regulatory information allowed us to correct product and gene names for over 300 loci. PMID:27257541

  17. SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals.

    PubMed

    Nikolaichik, Yevgeny; Damienikan, Aliaksandr U

    2016-01-01

    The majority of bacterial genome annotations are currently automated and based on a 'gene by gene' approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn't fit with regulatory information allowed us to correct product and gene names for over 300 loci.

  18. SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals.

    PubMed

    Nikolaichik, Yevgeny; Damienikan, Aliaksandr U

    2016-01-01

    The majority of bacterial genome annotations are currently automated and based on a 'gene by gene' approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn't fit with regulatory information allowed us to correct product and gene names for over 300 loci. PMID:27257541

  19. Computational Tools for Accelerating Carbon Capture Process Development

    SciTech Connect

    Miller, David

    2013-01-01

    The goals of the work reported are: to develop new computational tools and models to enable industry to more rapidly develop and deploy new advanced energy technologies; to demonstrate the capabilities of the CCSI Toolset on non-proprietary case studies; and to deploy the CCSI Toolset to industry. Challenges of simulating carbon capture (and other) processes include: dealing with multiple scales (particle, device, and whole process scales); integration across scales; verification, validation, and uncertainty; and decision support. The tools cover: risk analysis and decision making; validated, high-fidelity CFD; high-resolution filtered sub-models; process design and optimization tools; advanced process control and dynamics; process models; basic data sub-models; and cross-cutting integration tools.

  20. The environment power system analysis tool development program

    NASA Technical Reports Server (NTRS)

    Jongeward, Gary A.; Kuharski, Robert A.; Kennedy, Eric M.; Stevens, N. John; Putnam, Rand M.; Roche, James C.; Wilcox, Katherine G.

    1990-01-01

    The Environment Power System Analysis Tool (EPSAT) is being developed to provide space power system design engineers with an analysis tool for determining system performance of power systems in both naturally occurring and self-induced environments. The program is producing an easy to use computer aided engineering (CAE) tool general enough to provide a vehicle for technology transfer from space scientists and engineers to power system design engineers. The results of the project after two years of a three year development program are given. The EPSAT approach separates the CAE tool into three distinct functional units: a modern user interface to present information, a data dictionary interpreter to coordinate analysis; and a data base for storing system designs and results of analysis.

  1. The environment power system analysis tool development program

    NASA Astrophysics Data System (ADS)

    Jongeward, Gary A.; Kuharski, Robert A.; Kennedy, Eric M.; Stevens, N. John; Putnam, Rand M.; Roche, James C.; Wilcox, Katherine G.

    1990-12-01

    The Environment Power System Analysis Tool (EPSAT) is being developed to provide space power system design engineers with an analysis tool for determining system performance of power systems in both naturally occurring and self-induced environments. The program is producing an easy to use computer aided engineering (CAE) tool general enough to provide a vehicle for technology transfer from space scientists and engineers to power system design engineers. The results of the project after two years of a three year development program are given. The EPSAT approach separates the CAE tool into three distinct functional units: a modern user interface to present information, a data dictionary interpreter to coordinate analysis; and a data base for storing system designs and results of analysis.

  2. Open source tools for ATR development and performance evaluation

    NASA Astrophysics Data System (ADS)

    Baumann, James M.; Dilsavor, Ronald L.; Stubbles, James; Mossing, John C.

    2002-07-01

    Early in almost every engineering project, a decision must be made about tools; should I buy off-the-shelf tools or should I develop my own. Either choice can involve significant cost and risk. Off-the-shelf tools may be readily available, but they can be expensive to purchase and to maintain licenses, and may not be flexible enough to satisfy all project requirements. On the other hand, developing new tools permits great flexibility, but it can be time- (and budget-) consuming, and the end product still may not work as intended. Open source software has the advantages of both approaches without many of the pitfalls. This paper examines the concept of open source software, including its history, unique culture, and informal yet closely followed conventions. These characteristics influence the quality and quantity of software available, and ultimately its suitability for serious ATR development work. We give an example where Python, an open source scripting language, and OpenEV, a viewing and analysis tool for geospatial data, have been incorporated into ATR performance evaluation projects. While this case highlights the successful use of open source tools, we also offer important insight into risks associated with this approach.

  3. DEVELOPMENT OF A WIRELINE CPT SYSTEM FOR MULTIPLE TOOL USAGE

    SciTech Connect

    Stephen P. Farrington; Martin L. Gildea; J. Christopher Bianchi

    1999-08-01

    The first phase of development of a wireline cone penetrometer system for multiple tool usage was completed under DOE award number DE-AR26-98FT40366. Cone penetrometer technology (CPT) has received widespread interest and is becoming more commonplace as a tool for environmental site characterization activities at several Department of Energy (DOE) facilities. Although CPT already offers many benefits for site characterization, the wireline system can improve CPT technology by offering greater utility and increased cost savings. Currently the use of multiple CPT tools during a site characterization (i.e. piezometric cone, chemical sensors, core sampler, grouting tool) must be accomplished by withdrawing the entire penetrometer rod string to change tools. This results in multiple penetrations being required to collect the data and samples that may be required during characterization of a site, and to subsequently seal the resulting holes with grout. The wireline CPT system allows multiple CPT tools to be interchanged during a single penetration, without withdrawing the CPT rod string from the ground. The goal of the project is to develop and demonstrate a system by which various tools can be placed at the tip of the rod string depending on the type of information or sample desired. Under the base contract, an interchangeable piezocone and grouting tool was designed, fabricated, and evaluated. The results of the evaluation indicate that success criteria for the base contract were achieved. In addition, the wireline piezocone tool was validated against ASTM standard cones, the depth capability of the system was found to compare favorably with that of conventional CPT, and the reliability and survivability of the system were demonstrated.

  4. A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy.

    PubMed

    Brenton, Zachary W; Cooper, Elizabeth A; Myers, Mathew T; Boyles, Richard E; Shakoor, Nadia; Zielinski, Kelsey J; Rauh, Bradley L; Bridges, William C; Morris, Geoffrey P; Kresovich, Stephen

    2016-09-01

    With high productivity and stress tolerance, numerous grass genera of the Andropogoneae have emerged as candidates for bioenergy production. To optimize these candidates, research examining the genetic architecture of yield, carbon partitioning, and composition is required to advance breeding objectives. Significant progress has been made developing genetic and genomic resources for Andropogoneae, and advances in comparative and computational genomics have enabled research examining the genetic basis of photosynthesis, carbon partitioning, composition, and sink strength. To provide a pivotal resource aimed at developing a comparative understanding of key bioenergy traits in the Andropogoneae, we have established and characterized an association panel of 390 racially, geographically, and phenotypically diverse Sorghum bicolor accessions with 232,303 genetic markers. Sorghum bicolor was selected because of its genomic simplicity, phenotypic diversity, significant genomic tools, and its agricultural productivity and resilience. We have demonstrated the value of sorghum as a functional model for candidate gene discovery for bioenergy Andropogoneae by performing genome-wide association analysis for two contrasting phenotypes representing key components of structural and non-structural carbohydrates. We identified potential genes, including a cellulase enzyme and a vacuolar transporter, associated with increased non-structural carbohydrates that could lead to bioenergy sorghum improvement. Although our analysis identified genes with potentially clear functions, other candidates did not have assigned functions, suggesting novel molecular mechanisms for carbon partitioning traits. These results, combined with our characterization of phenotypic and genetic diversity and the public accessibility of each accession and genomic data, demonstrate the value of this resource and provide a foundation for future improvement of sorghum and related grasses for bioenergy production.

  5. A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy

    PubMed Central

    Brenton, Zachary W.; Cooper, Elizabeth A.; Myers, Mathew T.; Boyles, Richard E.; Shakoor, Nadia; Zielinski, Kelsey J.; Rauh, Bradley L.; Bridges, William C.; Morris, Geoffrey P.; Kresovich, Stephen

    2016-01-01

    With high productivity and stress tolerance, numerous grass genera of the Andropogoneae have emerged as candidates for bioenergy production. To optimize these candidates, research examining the genetic architecture of yield, carbon partitioning, and composition is required to advance breeding objectives. Significant progress has been made developing genetic and genomic resources for Andropogoneae, and advances in comparative and computational genomics have enabled research examining the genetic basis of photosynthesis, carbon partitioning, composition, and sink strength. To provide a pivotal resource aimed at developing a comparative understanding of key bioenergy traits in the Andropogoneae, we have established and characterized an association panel of 390 racially, geographically, and phenotypically diverse Sorghum bicolor accessions with 232,303 genetic markers. Sorghum bicolor was selected because of its genomic simplicity, phenotypic diversity, significant genomic tools, and its agricultural productivity and resilience. We have demonstrated the value of sorghum as a functional model for candidate gene discovery for bioenergy Andropogoneae by performing genome-wide association analysis for two contrasting phenotypes representing key components of structural and non-structural carbohydrates. We identified potential genes, including a cellulase enzyme and a vacuolar transporter, associated with increased non-structural carbohydrates that could lead to bioenergy sorghum improvement. Although our analysis identified genes with potentially clear functions, other candidates did not have assigned functions, suggesting novel molecular mechanisms for carbon partitioning traits. These results, combined with our characterization of phenotypic and genetic diversity and the public accessibility of each accession and genomic data, demonstrate the value of this resource and provide a foundation for future improvement of sorghum and related grasses for bioenergy production

  6. A Tool for Developing Adaptive Electronic Textbooks on WWW.

    ERIC Educational Resources Information Center

    Brusilovsky, Peter; Schwarz, Elmar; Weber, Gerhard

    This paper describes an approach for developing adaptive electronic textbooks and presents InterBook, an authoring tool based on this approach which simplifies the development of adaptive electronic textbooks on the World Wide Web. The following topics are discussed: (1) content structuring, including the domain and user models, the glossary, and…

  7. The Portfolio: A Tool for Workplace Learning and Development.

    ERIC Educational Resources Information Center

    Brown, Judith O.

    This paper explores and explains the validity and value of the experiential learning portfolio as an effective tool for workplace learning and development. Qualitative and survey methods of inquiry were used to produce data on the portfolio in workplace learning. Eight workers who developed experiential learning portfolios as a component of their…

  8. Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses

    PubMed Central

    Yun, Sang-Im; Song, Byung-Hak; Kim, Jin-Kyoung; Lee, Young-Min

    2015-01-01

    Reverse genetics, an approach to rescue infectious virus entirely from a cloned cDNA, has revolutionized the field of positive-strand RNA viruses, whose genomes have the same polarity as cellular mRNA. The cDNA-based reverse genetics system is a seminal method that enables direct manipulation of the viral genomic RNA, thereby generating recombinant viruses for molecular and genetic studies of both viral RNA elements and gene products in viral replication and pathogenesis. It also provides a valuable platform that allows the development of genetically defined vaccines and viral vectors for the delivery of foreign genes. For many positive-strand RNA viruses such as Japanese encephalitis virus (JEV), however, the cloned cDNAs are unstable, posing a major obstacle to the construction and propagation of the functional cDNA. Here, the present report describes the strategic considerations in creating and amplifying a genetically stable full-length infectious JEV cDNA as a bacterial artificial chromosome (BAC) using the following general experimental procedures: viral RNA isolation, cDNA synthesis, cDNA subcloning and modification, assembly of a full-length cDNA, cDNA linearization, in vitro RNA synthesis, and virus recovery. This protocol provides a general methodology applicable to cloning full-length cDNA for a range of positive-strand RNA viruses, particularly those with a genome of >10 kb in length, into a BAC vector, from which infectious RNAs can be transcribed in vitro with a bacteriophage RNA polymerase. PMID:26780115

  9. The SOFG Anatomy Entry List (SAEL): An Annotation Tool for Functional Genomics Data

    PubMed Central

    Parkinson, Helen; Aitken, Stuart; Baldock, Richard A.; Bard, Jonathan B. L.; Burger, Albert; Hayamizu, Terry F.; Rector, Alan; Ringwald, Martin; Rogers, Jeremy; Rosse, Cornelius; Stoeckert, Christian J.

    2004-01-01

    A great deal of data in functional genomics studies needs to be annotated with low-resolution anatomical terms. For example, gene expression assays based on manually dissected samples (microarray, SAGE, etc.) need high-level anatomical terms to describe sample origin. First-pass annotation in high-throughput assays (e.g. large-scale in situ gene expression screens or phenotype screens) and bibliographic applications, such as selection of keywords, would also benefit from a minimum set of standard anatomical terms. Although only simple terms are required, the researcher faces serious practical problems of inconsistency and confusion, given the different aims and the range of complexity of existing anatomy ontologies. A Standards and Ontologies for Functional Genomics (SOFG) group therefore initiated discussions between several of the major anatomical ontologies for higher vertebrates. As we report here, one result of these discussions is a simple, accessible, controlled vocabulary of gross anatomical terms, the SOFG Anatomy Entry List (SAEL). The SAEL is available from http://www.sofg.org and is intended as a resource for biologists, curators, bioinformaticians and developers of software supporting functional genomics. It can be used directly for annotation in the contexts described above. Importantly, each term is linked to the corresponding term in each of the major anatomy ontologies. Where the simple list does not provide enough detail or sophistication, therefore, the researcher can use the SAEL to choose the appropriate ontology and move directly to the relevant term as an entry point. The SAEL links will also be used to support computational access to the respective ontologies. PMID:18629134

  10. GOES-R AWG GLM Val Tool Development

    NASA Technical Reports Server (NTRS)

    Bateman, Monte; Mach, Douglas; Goodman, Steve; Blakeslee, Richard; Koshak, William

    2012-01-01

    We are developing tools needed to enable the validation of the Geostationary Lightning Mapper (GLM). In order to develop and test these tools, we have need of a robust, high-fidelity set of GLM proxy data. Many steps have been taken to ensure that the proxy data are high quality. LIS is the closest analog that exists for GLM, so it has been used extensively in developing the GLM proxy. We have verified the proxy data both statistically and algorithmically. The proxy data are pixel (event) data, called Level 1B. These data were then clustered into flashes by the Lightning Cluster-Filter Algorithm (LCFA), generating proxy Level 2 data. These were then compared with the data used to generate the proxy, and both the proxy data and the LCFA were validated. We have developed tools to allow us to visualize and compare the GLM proxy data with several other sources of lightning and other meteorological data (the so-called shallow-dive tool). The shallow-dive tool shows storm-level data and can ingest many different ground-based lightning detection networks, including: NLDN, LMA, WWLLN, and ENTLN. These are presented in a way such that it can be seen if the GLM is properly detecting the lightning in location and time comparable to the ground-based networks. Currently in development is the deep-dive tool, which will allow us to dive into the GLM data, down to flash, group and event level. This will allow us to assess performance in comparison with other data sources, and tell us if there are detection, timing, or geolocation problems. These tools will be compatible with the GLM Level-2 data format, so they can be used beginning on Day 0.

  11. Geochip: A high throughput genomic tool for linking community structure to functions

    SciTech Connect

    Van Nostrand, Joy D.; Liang, Yuting; He, Zhili; Li, Guanghe; Zhou, Jizhong

    2009-01-30

    GeoChip is a comprehensive functional gene array that targets key functional genes involved in the geochemical cycling of N, C, and P, sulfate reduction, metal resistance and reduction, and contaminant degradation. Studies have shown the GeoChip to be a sensitive, specific, and high-throughput tool for microbial community analysis that has the power to link geochemical processes with microbial community structure. However, several challenges remain regarding the development and applications of microarrays for microbial community analysis.

  12. piggyBac-based insertional mutagenesis and enhancer detection as a tool for functional insect genomics.

    PubMed Central

    Horn, Carsten; Offen, Nils; Nystedt, Sverker; Häcker, Udo; Wimmer, Ernst A

    2003-01-01

    Transposon mutagenesis provides a fundamental tool for functional genomics. Here we present a non-species-specific, combined enhancer detection and binary expression system based on the transposable element piggyBac: For the different components of this insertional mutagenesis system, we used widely applicable transposons and distinguishable broad-range transformation markers, which should enable this system to be operational in nonmodel arthropods. In a pilot screen in Drosophila melanogaster, piggyBac mutator elements on the X chromosome were mobilized in males by a Hermes-based jumpstarter element providing piggyBac transposase activity under control of the alpha1-tubulin promoter. As primary reporters in the piggyBac mutator elements, we employed the heterologous transactivators GAL4delta or tTA. To identify larval and adult enhancer detectors, strains carrying UASp-EYFP or TRE-EYFP as secondary reporter elements were used. Tissue-specific enhancer activities were readily observed in the GAL4delta/UASp-based systems, but only rarely in the tTA/TRE system. Novel autosomal insertions were recovered with an average jumping rate of 80%. Of these novel insertions, 3.8% showed homozygous lethality, which was reversible by piggyBac excision. Insertions were found in both coding and noncoding regions of characterized genes and also in noncharacterized and non-P-targeted CG-number genes. This indicates that piggyBac will greatly facilitate the intended saturation mutagenesis in Drosophila. PMID:12618403

  13. Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.

    PubMed

    Pavlopoulos, Georgios A; Malliarakis, Dimitris; Papanikolaou, Nikolas; Theodosiou, Theodosis; Enright, Anton J; Iliopoulos, Ioannis

    2015-01-01

    "Α picture is worth a thousand words." This widely used adage sums up in a few words the notion that a successful visual representation of a concept should enable easy and rapid absorption of large amounts of information. Although, in general, the notion of capturing complex ideas using images is very appealing, would 1000 words be enough to describe the unknown in a research field such as the life sciences? Life sciences is one of the biggest generators of enormous datasets, mainly as a result of recent and rapid technological advances; their complexity can make these datasets incomprehensible without effective visualization methods. Here we discuss the past, present and future of genomic and systems biology visualization. We briefly comment on many visualization and analysis tools and the purposes that they serve. We focus on the latest libraries and programming languages that enable more effective, efficient and faster approaches for visualizing biological concepts, and also comment on the future human-computer interaction trends that would enable for enhancing visualization further.

  14. Small-molecule tools for dissecting the roles of SSB/protein interactions in genome maintenance

    SciTech Connect

    Lu, Duo; Bernstein, Douglas A.; Satyshur, Kenneth A.; Keck, James L.

    2010-09-03

    Bacterial single-stranded DNA-binding proteins (SSBs) help to recruit a diverse array of genome maintenance enzymes to their sites of action through direct protein interactions. For all cases examined to date, these interactions are mediated by the evolutionarily conserved C terminus of SSB (SSB-Ct). The essential nature of SSB protein interactions makes inhibitors that block SSB complex formation valuable biochemical tools and attractive potential antibacterial agents. Here, we identify four small molecules that disrupt complexes formed between Escherichia coli SSB and Exonuclease I (ExoI), a well-studied SSB-interacting enzyme. Each compound disrupts ExoI/SSB-Ct peptide complexes and abrogates SSB stimulation of ExoI nuclease activity. Structural and biochemical studies support a model for three of the compounds in which they compete with SSB for binding to ExoI. The fourth appears to rely on an allosteric mechanism to disrupt ExoI/SSB complexes. Subsets of the inhibitors block SSB-Ct complex formation with two other SSB-interaction partners as well, which highlights their utility as reagents for investigating the roles of SSB/protein interactions in diverse DNA replication, recombination, and repair reactions.

  15. Blast2GO goes grid: developing a grid-enabled prototype for functional genomics analysis.

    PubMed

    Aparicio, G; Götz, S; Conesa, A; Segrelles, D; Blanquer, I; García, J M; Hernandez, V; Robles, M; Talon, M

    2006-01-01

    The vast amount in complexity of data generated in Genomic Research implies that new dedicated and powerful computational tools need to be developed to meet their analysis requirements. Blast2GO (B2G) is a bioinformatics tool for Gene Ontology-based DNA or protein sequence annotation and function-based data mining. The application has been developed with the aim of affering an easy-to-use tool for functional genomics research. Typical B2G users are middle size genomics labs carrying out sequencing, ETS and microarray projects, handling datasets up to several thousand sequences. In the current version of B2G. The power and analytical potential of both annotation and function data-mining is somehow restricted to the computational power behind each particular installation. In order to be able to offer the possibility of an enhanced computational capacity within this bioinformatics application, a Grid component is being developed. A prototype has been conceived for the particular problem of speeding up the Blast searches to obtain fast results for large datasets. Many efforts have been done in the literature concerning the speeding up of Blast searches, but few of them deal with the use of large heterogeneous production Grid Infrastructures. These are the infrastructures that could reach the largest number of resources and the best load balancing for data access. The Grid Service under development will analyse requests based on the number of sequences, splitting them accordingly to the available resources. Lower-level computation will be performed through MPIBLAST. The software architecture is based on the WSRF standard.

  16. Development and testing of the autobiographical memory coding tool.

    PubMed

    Kovach, C R

    1993-04-01

    Development and testing of the autobiographical memory coding tool (AMCT) is detailed. The tool uses quantitative content analysis procedures to code interpretations of autobiographical memories as validating or lamenting. Development of a system of measuring autobiographical memories from transcribed reminiscence interviews involved defining the units of analysis, defining the categories and themes, constructing a codebook, assessing content validity, assessing reliability and making revisions. Thirty-nine transcripts of reminiscence interviews were used for tool development and testing. The AMCT contains a series of step-by-step guidelines for conducting the analysis and includes an autobiographical memory thematic dictionary and descriptions of range and variations in each theme to assist with coding data. Intercoder reliability estimates were 0.93, 0.93 and 0.95. Test-retest reliability was 1.00.

  17. Development of a Safety Management Web Tool for Horse Stables.

    PubMed

    Leppälä, Jarkko; Kolstrup, Christina Lunner; Pinzke, Stefan; Rautiainen, Risto; Saastamoinen, Markku; Särkijärvi, Susanna

    2015-01-01

    Managing a horse stable involves risks, which can have serious consequences for the stable, employees, clients, visitors and horses. Existing industrial or farm production risk management tools are not directly applicable to horse stables and they need to be adapted for use by managers of different types of stables. As a part of the InnoEquine project, an innovative web tool, InnoHorse, was developed to support horse stable managers in business, safety, pasture and manure management. A literature review, empirical horse stable case studies, expert panel workshops and stakeholder interviews were carried out to support the design. The InnoHorse web tool includes a safety section containing a horse stable safety map, stable safety checklists, and examples of good practices in stable safety, horse handling and rescue planning. This new horse stable safety management tool can also help in organizing work processes in horse stables in general. PMID:26569319

  18. Development of a Safety Management Web Tool for Horse Stables.

    PubMed

    Leppälä, Jarkko; Kolstrup, Christina Lunner; Pinzke, Stefan; Rautiainen, Risto; Saastamoinen, Markku; Särkijärvi, Susanna

    2015-11-12

    Managing a horse stable involves risks, which can have serious consequences for the stable, employees, clients, visitors and horses. Existing industrial or farm production risk management tools are not directly applicable to horse stables and they need to be adapted for use by managers of different types of stables. As a part of the InnoEquine project, an innovative web tool, InnoHorse, was developed to support horse stable managers in business, safety, pasture and manure management. A literature review, empirical horse stable case studies, expert panel workshops and stakeholder interviews were carried out to support the design. The InnoHorse web tool includes a safety section containing a horse stable safety map, stable safety checklists, and examples of good practices in stable safety, horse handling and rescue planning. This new horse stable safety management tool can also help in organizing work processes in horse stables in general.

  19. Using competences and competence tools in workforce development.

    PubMed

    Green, Tess; Dickerson, Claire; Blass, Eddie

    The NHS Knowledge and Skills Framework (KSF) has been a driving force in the move to competence-based workforce development in the NHS. Skills for Health has developed national workforce competences that aim to improve behavioural performance, and in turn increase productivity. This article describes five projects established to test Skills for Health national workforce competences, electronic tools and products in different settings in the NHS. Competences and competence tools were used to redesign services, develop job roles, identify skills gaps and develop learning programmes. Reported benefits of the projects included increased clarity and a structured, consistent and standardized approach to workforce development. Findings from the evaluation of the tools were positive in terms of their overall usefulness and provision of related training/support. Reported constraints of using the competences and tools included issues relating to their availability, content and organization. It is recognized that a highly skilled and flexible workforce is important to the delivery of high-quality health care. These projects suggest that Skills for Health competences can be used as a 'common currency' in workforce development in the UK health sector. This would support the need to adapt rapidly to changing service needs.

  20. Using competences and competence tools in workforce development.

    PubMed

    Green, Tess; Dickerson, Claire; Blass, Eddie

    The NHS Knowledge and Skills Framework (KSF) has been a driving force in the move to competence-based workforce development in the NHS. Skills for Health has developed national workforce competences that aim to improve behavioural performance, and in turn increase productivity. This article describes five projects established to test Skills for Health national workforce competences, electronic tools and products in different settings in the NHS. Competences and competence tools were used to redesign services, develop job roles, identify skills gaps and develop learning programmes. Reported benefits of the projects included increased clarity and a structured, consistent and standardized approach to workforce development. Findings from the evaluation of the tools were positive in terms of their overall usefulness and provision of related training/support. Reported constraints of using the competences and tools included issues relating to their availability, content and organization. It is recognized that a highly skilled and flexible workforce is important to the delivery of high-quality health care. These projects suggest that Skills for Health competences can be used as a 'common currency' in workforce development in the UK health sector. This would support the need to adapt rapidly to changing service needs. PMID:21072016

  1. A draft genome of field pennycress (Thlaspi arvense) provides tools for the domestication of a new winter biofuel crop.

    PubMed

    Dorn, Kevin M; Fankhauser, Johnathon D; Wyse, Donald L; Marks, M David

    2015-04-01

    Field pennycress (Thlaspi arvense L.) is being domesticated as a new winter cover crop and biofuel species for the Midwestern United States that can be double-cropped between corn and soybeans. A genome sequence will enable the use of new technologies to make improvements in pennycress. To generate a draft genome, a hybrid sequencing approach was used to generate 47 Gb of DNA sequencing reads from both the Illumina and PacBio platforms. These reads were used to assemble 6,768 genomic scaffolds. The draft genome was annotated using the MAKER pipeline, which identified 27,390 predicted protein-coding genes, with almost all of these predicted peptides having significant sequence similarity to Arabidopsis proteins. A comprehensive analysis of pennycress gene homologues involved in glucosinolate biosynthesis, metabolism, and transport pathways revealed high sequence conservation compared with other Brassicaceae species, and helps validate the assembly of the pennycress gene space in this draft genome. Additional comparative genomic analyses indicate that the knowledge gained from years of basic Brassicaceae research will serve as a powerful tool for identifying gene targets whose manipulation can be predicted to result in improvements for pennycress.

  2. Phonological assessment and analysis tools for Tagalog: Preliminary development.

    PubMed

    Chen, Rachelle Kay; Bernhardt, B May; Stemberger, Joseph P

    2016-01-01

    Information and assessment tools concerning Tagalog phonological development are minimally available. The current study thus sets out to develop elicitation and analysis tools for Tagalog. A picture elicitation task was designed with a warm-up, screener and two extension lists, one with more complex and one with simpler words. A nonlinear phonological analysis form was adapted from English (Bernhardt & Stemberger, 2000) to capture key characteristics of Tagalog. The tools were piloted on a primarily Tagalog-speaking 4-year-old boy living in a Canadian-English-speaking environment. The data provided initial guidance for revision of the elicitation tool (available at phonodevelopment.sites.olt.ubc.ca). The analysis provides preliminary observations about possible expectations for primarily Tagalog-speaking 4-year-olds in English-speaking environments: Lack of mastery for tap/trill 'r', and minor mismatches for vowels, /l/, /h/ and word stress. Further research is required in order to develop the tool into a norm-referenced instrument for Tagalog in both monolingual and multilingual environments. PMID:27096390

  3. Soybean Genomics: Developments through the Use of Cultivar “Forrest”

    PubMed Central

    Lightfoot, David A.

    2008-01-01

    Legume crops are particularly important due to their ability to support symbiotic nitrogen fixation, a key to sustainable crop production and reduced carbon emissions. Soybean (Glycine max) has a special position as a major source of increased protein and oil production in the common grass-legume rotation. The cultivar “Forrest” has saved US growers billions of dollars in crop losses due to resistances programmed into the genome. Moreover, since Forrest grows well in the north-south transition zone, breeders have used this cultivar as a bridge between the southern and northern US gene pools. Investment in Forrest genomics resulted in the development of the following research tools: (i) a genetic map, (ii) three RIL populations (96 > n > 975), (iii) ∼200 NILs, (iv) 115 220 BACs and BIBACs, (v) a physical map, (vi) 4 different minimum tiling path (MTP) sets, (vii) 25 123 BAC end sequences (BESs) that encompass 18.5 Mbp spaced out from the MTPs, and 2 000 microsatellite markers within them (viii) a map of 2408 regions each found at a single position in the genome and 2104 regions found in 2 or 4 similar copies at different genomic locations (each of >150 kbp), (ix) a map of homoeologous regions among both sets of regions, (x) a set of transcript abundance measurements that address biotic stress resistance, (xi) methods for transformation, (xii) methods for RNAi, (xiii) a TILLING resource for directed mutant isolation, and (xiv) analyses of conserved synteny with other sequenced genomes. The SoyGD portal at sprovides access to the data. To date these resources assisted in the genomic analysis of soybean nodulation and disease resistance. This review summarizes the resources and their uses. PMID:18483614

  4. An assessment tool for developing healthcare managerial skills and roles.

    PubMed

    Guo, Kristina L

    2003-01-01

    This article is based on a study to identify, and by doing so help develop, the skills and roles of senior-level healthcare managers related to the needs of the current healthcare environment. To classify these roles and skills, a qualitative study was conducted to examine the literature on forces in the healthcare environment and their impact on managers. Ten senior managers were interviewed, revealing six roles as the most crucial to their positions along with the skills necessary to perform those roles. A pilot study was conducted with these senior managers to produce a final assessment tool. This assessment tool helps managers to identify strengths and weaknesses, develop in deficient areas, and promote competence in all areas as demanded by the market and organization. This tool can be used by organizations in the recruitment process and in the training process.

  5. Development of a green remediation tool in Japan.

    PubMed

    Yasutaka, Tetsuo; Zhang, Hong; Murayama, Koki; Hama, Yoshihito; Tsukada, Yasuhisa; Furukawa, Yasuhide

    2016-09-01

    The green remediation assessment tool for Japan (GRATJ) presented in this study is a spreadsheet-based software package developed to facilitate comparisons of the environmental impacts associated with various countermeasures against contaminated soil in Japan. This tool uses a life-cycle assessment-based model to calculate inventory inputs/outputs throughout the activity life cycle during remediation. Processes of 14 remediation methods for heavy metal contamination and 12 for volatile organic compound contamination are built into the tool. This tool can evaluate 130 inventory inputs/outputs and easily integrate those inputs/outputs into 9 impact categories, 4 integrated endpoints, and 1 index. Comparative studies can be performed by entering basic data associated with a target site. The integrated results can be presented in a simpler and clearer manner than the results of an inventory analysis. As a case study, an arsenic-contaminated soil remediation site was examined using this tool. Results showed that the integrated environmental impacts were greater with onsite remediation methods than with offsite ones. Furthermore, the contributions of CO2 to global warming, SO2 to urban air pollution, and crude oil to resource consumption were greater than other inventory inputs/outputs. The GRATJ has the potential to improve green remediation and can serve as a valuable tool for decision makers and practitioners in selecting countermeasures in Japan. PMID:26803220

  6. Development of a green remediation tool in Japan.

    PubMed

    Yasutaka, Tetsuo; Zhang, Hong; Murayama, Koki; Hama, Yoshihito; Tsukada, Yasuhisa; Furukawa, Yasuhide

    2016-09-01

    The green remediation assessment tool for Japan (GRATJ) presented in this study is a spreadsheet-based software package developed to facilitate comparisons of the environmental impacts associated with various countermeasures against contaminated soil in Japan. This tool uses a life-cycle assessment-based model to calculate inventory inputs/outputs throughout the activity life cycle during remediation. Processes of 14 remediation methods for heavy metal contamination and 12 for volatile organic compound contamination are built into the tool. This tool can evaluate 130 inventory inputs/outputs and easily integrate those inputs/outputs into 9 impact categories, 4 integrated endpoints, and 1 index. Comparative studies can be performed by entering basic data associated with a target site. The integrated results can be presented in a simpler and clearer manner than the results of an inventory analysis. As a case study, an arsenic-contaminated soil remediation site was examined using this tool. Results showed that the integrated environmental impacts were greater with onsite remediation methods than with offsite ones. Furthermore, the contributions of CO2 to global warming, SO2 to urban air pollution, and crude oil to resource consumption were greater than other inventory inputs/outputs. The GRATJ has the potential to improve green remediation and can serve as a valuable tool for decision makers and practitioners in selecting countermeasures in Japan.

  7. Low voltage resist processes developed for MAPPER tool first exposures

    NASA Astrophysics Data System (ADS)

    Rio, D.; Constancias, C.; van Nieuwstadt, J.; Vijverberg, J.; Derrough, S.; Icard, B.; Pain, L.

    2010-05-01

    The FP7 European project MAGIC [1] aims at designing a multi electron beam machine. In the frame of this project, LETI evaluates a multibeam tool from MAPPER lithography [2]. Each beam has an acceleration voltage of 5kV. A tool has been installed in LETI premises in July 2009. In order to prepare its evaluation, preliminary work was performed on Gaussian beam tools down to 5kV. It aimed at the determination of a stable and robust resist process allowing high resolution at 5kV. Then those results were used to characterize MAPPER tool performances. Meeting the requirements of high resolution and low roughness at low voltage, Dow Corningmolecular glass HSQ (hydrogen silsesquioxane) and MicroChem PMMA (polymethylmethacrylate) were used to test MAPPER tool as negative and positive tone resist references. We did exposures at beam acceleration voltages from 5 kV up to 100 kV. Different post application bake (PAB) temperatures were applied to resist. Several developer concentrations were also tested. The impact of those three parameters on contrast and resolution was checked. Resists chemical characterization was performed with FTIR (Fourier transform infra red) spectroscopy in order to understand the mechanisms leading to the observed variations of contrast and exposure dose as process parameters are changed. The main purpose of this work was to show that high resolution can be achieved at 5kV. First exposures performed with MAPER tool confirmed those results.

  8. Infinity: An In-Silico Tool for Genome-Wide Prediction of Specific DNA Matrices in miRNA Genomic Loci

    PubMed Central

    Garibaldi, Francesca; Manni, Isabella; Filligoi, Giancarlo; Piaggio, Giulia; Gurtner, Aymone

    2016-01-01

    Motivation miRNAs are potent regulators of gene expression and modulate multiple cellular processes in physiology and pathology. Deregulation of miRNAs expression has been found in various cancer types, thus, miRNAs may be potential targets for cancer therapy. However, the mechanisms through which miRNAs are regulated in cancer remain unclear. Therefore, the identification of transcriptional factor–miRNA crosstalk is one of the most update aspects of the study of miRNAs regulation. Results In the present study we describe the development of a fast and user-friendly software, named infinity, able to find the presence of DNA matrices, such as binding sequences for transcriptional factors, on ~65kb (kilobase) of 939 human miRNA genomic sequences, simultaneously. Of note, the power of this software has been validated in vivo by performing chromatin immunoprecipitation assays on a subset of new in silico identified target sequences (CCAAT) for the transcription factor NF-Y on colon cancer deregulated miRNA loci. Moreover, for the first time, we have demonstrated that NF-Y, through its CCAAT binding activity, regulates the expression of miRNA-181a, -181b, -21, -17, -130b, -301b in colon cancer cells. Conclusions The infinity software that we have developed is a powerful tool to underscore new TF/miRNA regulatory networks. Availability and Implementation Infinity was implemented in pure Java using Eclipse framework, and runs on Linux and MS Windows machine, with MySQL database. The software is freely available on the web at https://github.com/bio-devel/infinity. The website is implemented in JavaScript, PHP and HTML with all major browsers supported. PMID:27082112

  9. Expression genomics and drug development: towards predictive pharmacology.

    PubMed

    Liu, Edison T

    2005-02-01

    Expression genomics can be defined as the study of the dynamic transciptome and its regulatory elements. Technologies are available that can assess transcripts on a genome-wide scale over time and across many samples. This comprehensive and dynamic database is being used to decipher signalling pathways and to identify new biomarkers and targets. Biomarkers emerging from these studies have prognostic potential and can be used to predict therapeutic outcome. The multiplex nature of this approach not only telescopes the time to discovery, but also allows for detection of complex interactions. Taken together, these capabilities, if carefully used, can speed drug development, enhance the identification of potent drug combinations and identify patient populations that will benefit from these new drugs. PMID:15814022

  10. Implications of enterotoxigenic Escherichia coli genomics for vaccine development.

    PubMed

    Sjöling, Åsa; von Mentzer, Astrid; Svennerholm, Ann-Mari

    2015-04-01

    Enterotoxigenic Escherichia coli (ETEC) is a major cause of morbidity and mortality caused by diarrhea in children less than 5 years of age in low- and middle-income countries. Despite a wealth of research elucidating the mechanisms of disease, the immunological responses and vaccine development, ETEC is still relatively uncharacterized when it comes to regulation of virulence and detailed immune mechanisms. The recent emergence of next-generation sequencing now offers the possibility to screen genomes of ETEC strains isolated globally to identify novel vaccine targets in addition to those already established. In this review, we discuss how recent findings on ETEC genomics using novel sequencing techniques will aid in finding novel protective antigens that can be used in vaccine approaches. PMID:25540974

  11. Implications of enterotoxigenic Escherichia coli genomics for vaccine development.

    PubMed

    Sjöling, Åsa; von Mentzer, Astrid; Svennerholm, Ann-Mari

    2015-04-01

    Enterotoxigenic Escherichia coli (ETEC) is a major cause of morbidity and mortality caused by diarrhea in children less than 5 years of age in low- and middle-income countries. Despite a wealth of research elucidating the mechanisms of disease, the immunological responses and vaccine development, ETEC is still relatively uncharacterized when it comes to regulation of virulence and detailed immune mechanisms. The recent emergence of next-generation sequencing now offers the possibility to screen genomes of ETEC strains isolated globally to identify novel vaccine targets in addition to those already established. In this review, we discuss how recent findings on ETEC genomics using novel sequencing techniques will aid in finding novel protective antigens that can be used in vaccine approaches.

  12. The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

    PubMed Central

    Cooper, Laurel; Walls, Ramona L.; Elser, Justin; Gandolfo, Maria A.; Stevenson, Dennis W.; Smith, Barry; Preece, Justin; Athreya, Balaji; Mungall, Christopher J.; Rensing, Stefan; Hiss, Manuel; Lang, Daniel; Reski, Ralf; Berardini, Tanya Z.; Li, Donghui; Huala, Eva; Schaeffer, Mary; Menda, Naama; Arnaud, Elizabeth; Shrestha, Rosemary; Yamazaki, Yukiko; Jaiswal, Pankaj

    2013-01-01

    The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary (‘ontology’) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. PMID:23220694

  13. The plant ontology as a tool for comparative plant anatomy and genomic analyses.

    PubMed

    Cooper, Laurel; Walls, Ramona L; Elser, Justin; Gandolfo, Maria A; Stevenson, Dennis W; Smith, Barry; Preece, Justin; Athreya, Balaji; Mungall, Christopher J; Rensing, Stefan; Hiss, Manuel; Lang, Daniel; Reski, Ralf; Berardini, Tanya Z; Li, Donghui; Huala, Eva; Schaeffer, Mary; Menda, Naama; Arnaud, Elizabeth; Shrestha, Rosemary; Yamazaki, Yukiko; Jaiswal, Pankaj

    2013-02-01

    The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. PMID:23220694

  14. Injury outcome indicators: the development of a validation tool

    PubMed Central

    Cryer, C; Langley, J; Jarvis, S; Mackenzie, S; Stephenson, S; Heywood, P; on, b

    2005-01-01

    Background: Researchers have previously expressed concern about some national indicators of injury incidence and have argued that indicators should be validated before their introduction. Aims: To develop a tool to assess the validity of indicators of injury incidence and to carry out initial testing of the tool to explore consistency on application. Methods: Previously proposed criteria were shared for comment with members of the International Collaborative Effort on Injury Statistics (ICE) Injury Indicators Group over a period of six months. Immediately after, at a meeting of Injury ICE in Washington, DC in April 2001, revised criteria were agreed over two days of meetings. The criteria were applied, by three raters, to six non-fatal indicators that underpin the national road safety targets for Canada, New Zealand, and the United Kingdom. Consistency of ratings were judged. Consensus outcome: The development process resulted in a validation tool that comprised criteria relating to: (1) case definition, (2) a focus on serious injury, (3) unbiased case ascertainment, (4) source data for the indicator being representative of the target population, (5) availability of data to generate the indicator, and (6) the existence of a full written specification for the indicator. On application of these criteria to the six road safety indicators, some problems of agreement between raters were identified. Conclusion: This paper has presented an early step in the development of a tool for validating injury indicators, as well as some directions that can be taken in its further development. PMID:15691991

  15. Sharpening a Tool for Teaching: The Zone of Proximal Development

    ERIC Educational Resources Information Center

    Wass, Rob; Golding, Clinton

    2014-01-01

    Vygotsky's Zone of Proximal Development (ZPD) provides an important understanding of learning, but its implications for teachers are often unclear or limited and could be further explored. We use conceptual analysis to sharpen the ZPD as a teaching tool, illustrated with examples from teaching critical thinking in zoology. Our conclusions are…

  16. The Development of a Literacy Diagnostic Tool for Maltese Children

    ERIC Educational Resources Information Center

    Xuereb, Rachael; Grech, Helen; Dodd, Barbara

    2011-01-01

    This article focuses on the development of a Literacy Assessment Battery for the diagnosis of Maltese children with specific learning difficulties. It forms part of a wider research study involving testing of 549 children in Malta as well as standardisation of the tool. Results of the children's performance and psychometric validation go beyond…

  17. Developing an Intranet: Tool Selection and Management Issues.

    ERIC Educational Resources Information Center

    Chou, David C.

    1998-01-01

    Moving corporate systems onto an intranet will increase the data traffic within the corporate network, which necessitates a high-quality management process to the intranet. Discusses costs and benefits of adopting an intranet, tool availability and selection criteria, and management issues for developing an intranet. (Author/AEF)

  18. Developing a Decision Support System: The Software and Hardware Tools.

    ERIC Educational Resources Information Center

    Clark, Phillip M.

    1989-01-01

    Describes some of the available software and hardware tools that can be used to develop a decision support system implemented on microcomputers. Activities that should be supported by software are discussed, including data entry, data coding, finding and combining data, and data compatibility. Hardware considerations include speed, storage…

  19. Development of a Psychotropic PRN Medication Evaluative Tool

    ERIC Educational Resources Information Center

    Silk, Larry; Watt, Jackie; Pilon, Nancy; Draper, Chad

    2013-01-01

    This article describes a psychotropic PRN Evaluative Tool developed by interprofessional clinicians to address inconsistent reporting and assessment of the effectiveness of PRN medications used for people who are developmentally disabled. Fifty-nine participants (37 males, 22 females), ages 16 to 60 years, were included in the review, all…

  20. The Word Processor as a Tool for Developing Young Writers.

    ERIC Educational Resources Information Center

    Schrader, Carol Taylor

    A study investigated how young children use the word processor as a tool in their development as writers. Forty children, ages 4 through 7, from a university laboratory school in a small midwestern community, participated in the study. Videotapings and audiotapings during writing events served as the primary means of data collection. These were…

  1. Development of a New Measurement Tool for Individualism and Collectivism

    ERIC Educational Resources Information Center

    Shulruf, Boaz; Hattie, John; Dixon, Robyn

    2007-01-01

    A new measurement tool for individualism and collectivism has been developed to address critical methodological issues in this field of social psychology. This new measure, the Auckland Individualism and Collectivism Scale (AICS), defines three dimensions of individualism: (a) responsibility (acknowledging one's responsibility for one's actions),…

  2. Writing for Publication as a Tool in Teacher Development

    ERIC Educational Resources Information Center

    Rathert, Stefan; Okan, Zühal

    2015-01-01

    Writing is widely accepted as a tool in the personal and professional development of teachers. Among other forms of teacher writing, writing for publication is rather unusual as it requires courage to share ideas and unfavourable working conditions prevent teachers from finding time and space to write for publication in the first place. In this…

  3. Measurement Learning Trajectories: A Tool for Professional Development

    ERIC Educational Resources Information Center

    McCool, Jenni K.

    2009-01-01

    This study investigated the ways in which a teacher developed conceptions of measurement teaching and learning as she collaborated with a researcher to learn and implement a measurement learning trajectory with two of her students. Teachers need tools that effectively address the content area of measurement and can be used to improve their…

  4. DEVELOPMENT OF THE METAL FINISHING FACILITY RISK SCREENING TOOL (MFFRST)

    EPA Science Inventory

    Recently the US EPA completed the development of the first version of the Metal Finishing Facility Risk Screening Tool (MFFRST) and has made this product available to the general public. MFFRST calculates the air emissions from a metal plating line and determines the risk to bot...

  5. Chips: A Tool for Developing Software Interfaces Interactively.

    ERIC Educational Resources Information Center

    Cunningham, Robert E.; And Others

    This report provides a detailed description of Chips, an interactive tool for developing software employing graphical/computer interfaces on Xerox Lisp machines. It is noted that Chips, which is implemented as a collection of customizable classes, provides the programmer with a rich graphical interface for the creation of rich graphical…

  6. Developing a Benchmark Tool for Sustainable Consumption: An Iterative Process

    ERIC Educational Resources Information Center

    Heiskanen, E.; Timonen, P.; Nissinen, A.; Gronroos, J.; Honkanen, A.; Katajajuuri, J. -M.; Kettunen, J.; Kurppa, S.; Makinen, T.; Seppala, J.; Silvenius, F.; Virtanen, Y.; Voutilainen, P.

    2007-01-01

    This article presents the development process of a consumer-oriented, illustrative benchmarking tool enabling consumers to use the results of environmental life cycle assessment (LCA) to make informed decisions. LCA provides a wealth of information on the environmental impacts of products, but its results are very difficult to present concisely…

  7. Software tools for developing parallel applications. Part 1: Code development and debugging

    SciTech Connect

    Brown, J.; Geist, A.; Pancake, C.; Rover, D.

    1997-04-01

    Developing an application for parallel computers can be a lengthy and frustrating process making it a perfect candidate for software tool support. Yet application programmers are often the last to hear about new tools emerging from R and D efforts. This paper provides an overview of two focuses of tool support: code development and debugging. Each is discussed in terms of the programmer needs addressed, the extent to which representative current tools meet those needs, and what new levels of tool support are important if parallel computing is to become more widespread.

  8. PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny

    PubMed Central

    Lei, Runhua; Rowley, Thaine W.; Zhu, Lifeng; Bailey, Carolyn A.; Engberg, Shannon E.; Wood, Mindy L.; Christman, Mary C.; Perry, George H.; Louis, Edward E.; Lu, Guoqing

    2012-01-01

    Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker through comparison of partial genomes of Microcebus and Otolemur. In experimental tests of 20 randomly selected markers, nine markers were successfully amplified by PCR and directly sequenced in all 17 nominal Microcebus species. Phylogenetic analyses of the sequence data obtained for 17 taxa and nine markers confirmed the distinct lineage inferred from previous mtDNA data. PhyloMarker has also been used by other projects including the herons (Ardeidae, Aves) phylogeny and the Wood mice (Muridae, Mammalia) phylogeny. All source code and sample data are made available at http://bioinfo-srv1.awh.unomaha.edu/phylomarker/.

  9. CyMATE: a new tool for methylation analysis of plant genomic DNA after bisulphite sequencing.

    PubMed

    Hetzl, Jennifer; Foerster, Andrea M; Raidl, Günther; Mittelsten Scheid, Ortrun

    2007-08-01

    Cytosine methylation is a hallmark of epigenetic information in the DNA of many fungi, vertebrates and plants. The technique of bisulphite genomic sequencing reveals the methylation state of every individual cytosine in a sequence, and thereby provides high-resolution data on epigenetic diversity; however, the manual evaluation and documentation of large amounts of data is laborious and error-prone. While some software is available for facilitating the analysis of mammalian DNA methylation, which is found nearly exclusively at CG sites, there is no software optimally suited for data from DNA with significant non-CG methylation. We describe CyMATE (Cytosine Methylation Analysis Tool for Everyone) for in silico analysis of DNA sequences after bisulphite conversion of plant DNA, in which methylation is more divergent with respect to sequence context and biological relevance. From aligned sequences, CyMATE includes and distinguishes methylation at CG, CHG and CHH (where H = A, C or T), and can extract both quantitative and qualitative data regarding general and pattern-specific methylation per sequence and per position, i.e. data for individual sites in a sequence and the epigenetic divergence within a sample. In addition, it can provide graphical output from alignments in either an overview or a 'zoom-in' view as pdf files. Detailed information, including a quality control of the sequencing data, is provided in text format. We applied CyMATE to the analysis of DNA methylation at transcriptionally silenced promoters in diploid and polyploid Arabidopsis and found significant hypermethylation, high stability of the methylated state independent of chromosome number, and non-redundant patterns of mC distribution. CyMATE is freely available for non-commercial use at http://www.gmi.oeaw.ac.at/CyMATE. PMID:17559516

  10. Development and characterization of genomic SSR markers in Cynodon transvaalensis Burtt-Davy.

    PubMed

    Tan, Chengcheng; Wu, Yanqi; Taliaferro, Charles M; Bell, Greg E; Martin, Dennis L; Smith, Mike W

    2014-08-01

    Simple sequence repeat (SSR) markers are a major molecular tool for genetic and genomic research that have been extensively developed and used in major crops. However, few are available in African bermudagrass (Cynodon transvaalensis Burtt-Davy), an economically important warm-season turfgrass species. African bermudagrass is mainly used for hybridizations with common bermudagrass [C. dactylon var. dactylon (L.) Pers.] in the development of superior interspecific hybrid turfgrass cultivars. Accordingly, the major objective of this study was to develop and characterize a large set of SSR markers. Genomic DNA of C. transvaalensis '4200TN 24-2' from an Oklahoma State University (OSU) turf nursery was extracted for construction of four SSR genomic libraries enriched with [CA](n), [GA](n), [AAG](n), and [AAT](n) as core repeat motifs. A total of 3,064 clones were sequenced at the OSU core facility. The sequences were categorized into singletons and contiguous sequences to exclude redundancy. From the two sequence categories, 1,795 SSR loci were identified. After excluding duplicate SSRs by comparison with previously developed SSR markers using a nucleotide basic local alignment tool, 1,426 unique primer pairs (PPs) were designed. Out of the 1,426 designed PPs, 981 (68.8 %) amplified alleles of the expected size in the donor DNA. Polymorphisms of the SSR PPs tested in eight C. transvaalensis plants were 93 % polymorphic with 544 markers effective in all genotypes. Inheritance of the SSRs was examined in six F(1) progeny of African parents 'T577' × 'Uganda', indicating 917 markers amplified heritable alleles. The SSR markers developed in the study are the first large set of co-dominant markers in African bermudagrass and should be highly valuable for molecular and traditional breeding research.

  11. Identification of Gene Expression Pattern Related to Breast Cancer Survival Using Integrated TCGA Datasets and Genomic Tools

    PubMed Central

    Huang, Zhenzhen; Duan, Huilong; Li, Haomin

    2015-01-01

    Several large-scale human cancer genomics projects such as TCGA offered huge genomic and clinical data for researchers to obtain meaningful genomics alterations which intervene in the development and metastasis of the tumor. A web-based TCGA data analysis platform called TCGA4U was developed in this study. TCGA4U provides a visualization solution for this study to illustrate the relationship of these genomics alternations with clinical data. A whole genome screening of the survival related gene expression patterns in breast cancer was studied. The gene list that impacts the breast cancer patient survival was divided into two patterns. Gene list of each of these patterns was separately analyzed on DAVID. The result showed that mitochondrial ribosomes play a more crucial role in the cancer development. We also reported that breast cancer patients with low HSPA2 expression level had shorter overall survival time. This is widely different to findings of HSPA2 expression pattern in other cancer types. TCGA4U provided a new perspective for the TCGA datasets. We believe it can inspire more biomedical researchers to study and explain the genomic alterations in cancer development and discover more targeted therapies to help more cancer patients. PMID:26576432

  12. Using Modern Design Tools for Digital Avionics Development

    NASA Technical Reports Server (NTRS)

    Hyde, David W.; Lakin, David R., II; Asquith, Thomas E.

    2000-01-01

    Using Modem Design Tools for Digital Avionics Development Shrinking development time and increased complexity of new avionics forces the designer to use modem tools and methods during hardware development. Engineers at the Marshall Space Flight Center have successfully upgraded their design flow and used it to develop a Mongoose V based radiation tolerant processor board for the International Space Station's Water Recovery System. The design flow, based on hardware description languages, simulation, synthesis, hardware models, and full functional software model libraries, allowed designers to fully simulate the processor board from reset, through initialization before any boards were built. The fidelity of a digital simulation is limited to the accuracy of the models used and how realistically the designer drives the circuit's inputs during simulation. By using the actual silicon during simulation, device modeling errors are reduced. Numerous design flaws were discovered early in the design phase when they could be easily fixed. The use of hardware models and actual MIPS software loaded into full functional memory models also provided checkout of the software development environment. This paper will describe the design flow used to develop the processor board and give examples of errors that were found using the tools. An overview of the processor board firmware will also be covered.

  13. Preliminary Development of an Object-Oriented Optimization Tool

    NASA Technical Reports Server (NTRS)

    Pak, Chan-gi

    2011-01-01

    The National Aeronautics and Space Administration Dryden Flight Research Center has developed a FORTRAN-based object-oriented optimization (O3) tool that leverages existing tools and practices and allows easy integration and adoption of new state-of-the-art software. The object-oriented framework can integrate the analysis codes for multiple disciplines, as opposed to relying on one code to perform analysis for all disciplines. Optimization can thus take place within each discipline module, or in a loop between the central executive module and the discipline modules, or both. Six sample optimization problems are presented. The first four sample problems are based on simple mathematical equations; the fifth and sixth problems consider a three-bar truss, which is a classical example in structural synthesis. Instructions for preparing input data for the O3 tool are presented.

  14. Development of Design Tools for Flow-Control Actuators

    NASA Technical Reports Server (NTRS)

    Mathew, Jose; Gallas, Quentin; Cattafesta, Louis N., III

    2003-01-01

    This report discusses the: 1. Development coupled electro/fluid/structural lumped-element model (LEM) of a prototypical flow-control actuator. 2. Validation the coupled electro/fluid/structural dynamics lumped-element models. 3. Development simple, yet effective, design tools for actuators. 4. Development structural dynamic models that accurately characterize the dynamic response of piezoelectric flap actuators using the Finite Element Method (FEW as well as analytical methods. 5. Perform a parametric study of a piezo-composite flap actuator. 6.Develop an optimization scheme for maximizing the actuator performance.

  15. SNPTracker: A Swift Tool for Comprehensive Tracking and Unifying dbSNP rs IDs and Genomic Coordinates of Massive Sequence Variants.

    PubMed

    Deng, Jia-En; Sham, Pak C; Li, Miao-Xin

    2016-01-01

    The reference single nucleotide polymorphism (rs) ID in dbSNP (http://www.ncbi.nlm.nih.gov/SNP/) is a key resource identifier, which is widely used in human genetics and genomics studies. However, its application is often complicated by the varied IDs of different versions. Here, we developed a user-friendly tool, SNPTracker, for comprehensively tracking and unifying the rs IDs and genomic coordinates of massive sequence variants at a time. It worked perfectly, and had much higher accuracy and capacity than two alternative utilities in our proof-of-principle examples. SNPTracker will greatly facilitate genetic data exchange and integration in the postgenome-wide association study era. PMID:26585827

  16. Current Developments in Prokaryotic Single Cell Whole Genome Amplification

    SciTech Connect

    Goudeau, Danielle; Nath, Nandita; Ciobanu, Doina; Cheng, Jan-Fang; Malmstrom, Rex

    2014-03-14

    Our approach to prokaryotic single-cell Whole Genome Amplification at the JGI continues to evolve. To increase both the quality and number of single-cell genomes produced, we explore all aspects of the process from cell sorting to sequencing. For example, we now utilize specialized reagents, acoustic liquid handling, and reduced reaction volumes eliminate non-target DNA contamination in WGA reactions. More specifically, we use a cleaner commercial WGA kit from Qiagen that employs a UV decontamination procedure initially developed at the JGI, and we use the Labcyte Echo for tip-less liquid transfer to set up 2uL reactions. Acoustic liquid handling also dramatically reduces reagent costs. In addition, we are exploring new cell lysis methods including treatment with Proteinase K, lysozyme, and other detergents, in order to complement standard alkaline lysis and allow for more efficient disruption of a wider range of cells. Incomplete lysis represents a major hurdle for WGA on some environmental samples, especially rhizosphere, peatland, and other soils. Finding effective lysis strategies that are also compatible with WGA is challenging, and we are currently assessing the impact of various strategies on genome recovery.

  17. National Energy Audit Tool for Multifamily Buildings Development Plan

    SciTech Connect

    Malhotra, Mini; MacDonald, Michael; Accawi, Gina K; New, Joshua Ryan; Im, Piljae

    2012-03-01

    The U.S. Department of Energy's (DOE's) Weatherization Assistance Program (WAP) enables low-income families to reduce their energy costs by providing funds to make their homes more energy efficient. In addition, the program funds Weatherization Training and Technical Assistance (T and TA) activities to support a range of program operations. These activities include measuring and documenting performance, monitoring programs, promoting advanced techniques and collaborations to further improve program effectiveness, and training, including developing tools and information resources. The T and TA plan outlines the tasks, activities, and milestones to support the weatherization network with the program implementation ramp up efforts. Weatherization of multifamily buildings has been recognized as an effective way to ramp up weatherization efforts. To support this effort, the 2009 National Weatherization T and TA plan includes the task of expanding the functionality of the Weatherization Assistant, a DOE-sponsored family of energy audit computer programs, to perform audits for large and small multifamily buildings This report describes the planning effort for a new multifamily energy audit tool for DOE's WAP. The functionality of the Weatherization Assistant is being expanded to also perform energy audits of small multifamily and large multifamily buildings. The process covers an assessment of needs that includes input from national experts during two national Web conferences. The assessment of needs is then translated into capability and performance descriptions for the proposed new multifamily energy audit, with some description of what might or should be provided in the new tool. The assessment of needs is combined with our best judgment to lay out a strategy for development of the multifamily tool that proceeds in stages, with features of an initial tool (version 1) and a more capable version 2 handled with currently available resources. Additional development in the

  18. Tools for regulatory assessment of occupational exposure: development and challenges.

    PubMed

    Tielemans, Erik; Warren, Nick; Schneider, Thomas; Tischer, Martin; Ritchie, Peter; Goede, Henk; Kromhout, Hans; Van Hemmen, Joop; Cherrie, John W

    2007-12-01

    REACH (Registration, Evaluation and Authorization of CHemicals) requires improved exposure models that can be incorporated into screening tools and refined assessment tools. These are referred to as tier 1 and 2 models, respectively. There are a number of candidate in tier 1 models that could be used with REACH. Tier 2 models, producing robust and realistic exposure assessments, are currently not available. A research programme is proposed in this paper that will result in a new, advanced exposure assessment tool for REACH. In addition, issues related to variability and uncertainty are discussed briefly, and some examples of tier 1 screening tools are presented. The proposed framework for the tier 2 tool is based on a Bayesian approach, and makes full use of mechanistically modelled estimates and any relevant measurements of exposure. The new approach will preclude the necessity to conduct of case-by-case exposure measurements for each chemical and scenario, since the system will allow for the use of analogous exposure data from relatively comparable scenarios. The development of the new approach requires substantial effort in the area of mechanistic modelling, database development and Bayesian statistical techniques. In this paper, the data gaps and areas for future research are identified to help realise and further improve this type of approach within REACH. A structured data collection and storage system is a central element of the research programme and the availability of this type of tool may also facilitate the sharing of exposure data down and up the supply chain. In addition, new data that are stored according to the proposed structure could enable the validation of any exposure model and thus this programme enhances the exposure assessment field as a whole.

  19. JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes

    PubMed Central

    Richter, Michael; Lombardot, Thierry; Kostadinov, Ivaylo; Kottmann, Renzo; Duhaime, Melissa Beth; Peplies, Jörg; Glöckner, Frank Oliver

    2008-01-01

    Background Current sequencing technologies give access to sequence information for genomes and metagenomes at a tremendous speed. Subsequent data processing is mainly performed by automatic pipelines provided by the sequencing centers. Although, standardised workflows are desirable and useful in many respects, rational data mining, comparative genomics, and especially the interpretation of the sequence information in the biological context, demands for intuitive, flexible, and extendable solutions. Results The JCoast software tool was primarily designed to analyse and compare (meta)genome sequences of prokaryotes. Based on a pre-computed GenDB database project, JCoast offers a flexible graphical user interface (GUI), as well as an application programming interface (API) that facilitates back-end data access. JCoast offers individual, cross genome-, and metagenome analysis, and assists the biologist in exploration of large and complex datasets. Conclusion JCoast combines all functions required for the mining, annotation, and interpretation of (meta)genomic data. The lightweight software solution allows the user to easily take advantage of advanced back-end database structures by providing a programming and graphical user interface to answer biological questions. JCoast is available at the project homepage. PMID:18380896

  20. The plant ontology as a tool for comparative plant anatomy and genomic analyses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant science is now a major player in the fields of genomics, gene expression analysis, phenomics and metabolomics. Recent advances in sequencing technologies have led to a windfall of data, with new species being added rapidly to the list of species whose genomes have been decoded. The Plant Ontol...

  1. solGS: a web-based tool for genomic selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic selection (GS) promises to improve accuracy in estimating breeding values and genetic gain for quantitative traits compared to traditional breeding methods. Its reliance on high-throughput genome-wide markers and statistical complexity, however, is a serious challenge in data management, ana...

  2. Parallel continuous flow: a parallel suffix tree construction tool for whole genomes.

    PubMed

    Comin, Matteo; Farreras, Montse

    2014-04-01

    The construction of suffix trees for very long sequences is essential for many applications, and it plays a central role in the bioinformatic domain. With the advent of modern sequencing technologies, biological sequence databases have grown dramatically. Also the methodologies required to analyze these data have become more complex everyday, requiring fast queries to multiple genomes. In this article, we present parallel continuous flow (PCF), a parallel suffix tree construction method that is suitable for very long genomes. We tested our method for the suffix tree construction of the entire human genome, about 3GB. We showed that PCF can scale gracefully as the size of the input genome grows. Our method can work with an efficiency of 90% with 36 processors and 55% with 172 processors. We can index the human genome in 7 minutes using 172 processes.

  3. Development of a Custom-Designed, Pan Genomic DNA Microarray to Characterize Strain-Level Diversity among Cronobacter spp.

    PubMed Central

    Tall, Ben Davies; Gangiredla, Jayanthi; Gopinath, Gopal R.; Yan, Qiongqiong; Chase, Hannah R.; Lee, Boram; Hwang, Seongeun; Trach, Larisa; Park, Eunbi; Yoo, YeonJoo; Chung, TaeJung; Jackson, Scott A.; Patel, Isha R.; Sathyamoorthy, Venugopal; Pava-Ripoll, Monica; Kotewicz, Michael L.; Carter, Laurenda; Iversen, Carol; Pagotto, Franco; Stephan, Roger; Lehner, Angelika; Fanning, Séamus; Grim, Christopher J.

    2015-01-01

    Cronobacter species cause infections in all age groups; however neonates are at highest risk and remain the most susceptible age group for life-threatening invasive disease. The genus contains seven species:Cronobacter sakazakii, Cronobacter malonaticus, Cronobacter turicensis, Cronobacter muytjensii, Cronobacter dublinensis, Cronobacter universalis, and Cronobacter condimenti. Despite an abundance of published genomes of these species, genomics-based epidemiology of the genus is not well established. The gene content of a diverse group of 126 unique Cronobacter and taxonomically related isolates was determined using a pan genomic-based DNA microarray as a genotyping tool and as a means to identify outbreak isolates for food safety, environmental, and clinical surveillance purposes. The microarray constitutes 19,287 independent genes representing 15 Cronobacter genomes and 18 plasmids and 2,371 virulence factor genes of phylogenetically related Gram-negative bacteria. The Cronobacter microarray was able to distinguish the seven Cronobacter species from one another and from non-Cronobacter species; and within each species, strains grouped into distinct clusters based on their genomic diversity. These results also support the phylogenic divergence of the genus and clearly highlight the genomic diversity among each member of the genus. The current study establishes a powerful platform for further genomics research of this diverse genus, an important prerequisite toward the development of future countermeasures against this foodborne pathogen in the food safety and clinical arenas. PMID:25984509

  4. Advanced Vibration Analysis Tool Developed for Robust Engine Rotor Designs

    NASA Technical Reports Server (NTRS)

    Min, James B.

    2005-01-01

    The primary objective of this research program is to develop vibration analysis tools, design tools, and design strategies to significantly improve the safety and robustness of turbine engine rotors. Bladed disks in turbine engines always feature small, random blade-to-blade differences, or mistuning. Mistuning can lead to a dramatic increase in blade forced-response amplitudes and stresses. Ultimately, this results in high-cycle fatigue, which is a major safety and cost concern. In this research program, the necessary steps will be taken to transform a state-of-the-art vibration analysis tool, the Turbo- Reduce forced-response prediction code, into an effective design tool by enhancing and extending the underlying modeling and analysis methods. Furthermore, novel techniques will be developed to assess the safety of a given design. In particular, a procedure will be established for using natural-frequency curve veerings to identify ranges of operating conditions (rotational speeds and engine orders) in which there is a great risk that the rotor blades will suffer high stresses. This work also will aid statistical studies of the forced response by reducing the necessary number of simulations. Finally, new strategies for improving the design of rotors will be pursued.

  5. Developing Electronic Cooperation Tools: A Case From Norwegian Health Care

    PubMed Central

    Mydske, Per Kristen

    2013-01-01

    Background Many countries aim to create electronic cooperational tools in health care, but the progress is rather slow. Objective The study aimed to uncover how the authoritys’ financing policies influence the development of electronic cooperational tools within public health care. Methods An interpretative approach was used in this study. We performed 30 semistructured interviews with vendors, policy makers, and public authorities. Additionally, we conducted an extensive documentation study and participated in 18 workshops concerning information and communication technology (ICT) in Norwegian health care. Results We found that the interorganizational communication in sectors like health care, that have undergone an independent development of their internal information infrastructure would find it difficult to create electronic services that interconnect the organizations because such connections would affect all interconnected organizations within the heterogenic structure. The organizations would, to a large extent, depend on new functionality in existing information systems. Electronic patient records play a central role in all parts of the health care sector and therefore dependence is established to the information systems and theirs vendors. The Norwegian government authorities, which run more than 80% of the Norwegian health care, have not taken extraordinary steps to compensate for this dependency–the government's political philosophy is that each health care institution should pay for further electronic patient record development. However, cooperational tools are complex due to the number of players involved and the way they are intertwined with the overall workflow. The customers are not able to buy new functionalities on the drawing table, while the electronic patient record vendors are not willing to take the economic risk in developing cooperational tools. Thus, the market mechanisms in the domain are challenged. We also found that public projects

  6. Microsystem design framework based on tool adaptations and library developments

    NASA Astrophysics Data System (ADS)

    Karam, Jean Michel; Courtois, Bernard; Rencz, Marta; Poppe, Andras; Szekely, Vladimir

    1996-09-01

    Besides foundry facilities, Computer-Aided Design (CAD) tools are also required to move microsystems from research prototypes to an industrial market. This paper describes a Computer-Aided-Design Framework for microsystems, based on selected existing software packages adapted and extended for microsystem technology, assembled with libraries where models are available in the form of standard cells described at different levels (symbolic, system/behavioral, layout). In microelectronics, CAD has already attained a highly sophisticated and professional level, where complete fabrication sequences are simulated and the device and system operation is completely tested before manufacturing. In comparison, the art of microsystem design and modelling is still in its infancy. However, at least for the numerical simulation of the operation of single microsystem components, such as mechanical resonators, thermo-elements, elastic diaphragms, reliable simulation tools are available. For the different engineering disciplines (like electronics, mechanics, optics, etc) a lot of CAD-tools for the design, simulation and verification of specific devices are available, but there is no CAD-environment within which we could perform a (micro-)system simulation due to the different nature of the devices. In general there are two different approaches to overcome this limitation: the first possibility would be to develop a new framework tailored for microsystem-engineering. The second approach, much more realistic, would be to use the existing CAD-tools which contain the most promising features, and to extend these tools so that they can be used for the simulation and verification of microsystems and of the devices involved. These tools are assembled with libraries in a microsystem design environment allowing a continuous design flow. The approach is driven by the wish to make microsystems accessible to a large community of people, including SMEs and non-specialized academic institutions.

  7. Development of the Sasquatch Drop Test Footprint Tool

    NASA Technical Reports Server (NTRS)

    Bledsoe, Kristin J.

    2011-01-01

    The Crew Exploration Vehicle Parachute Assembly System (CPAS) is the parachute system for NASA s Orion spacecraft. CPAS is currently in the design and testing phase of development. The test program consists of numerous drop tests, wherein a test article rigged with parachutes is extracted or released from an aircraft. During such tests, range safety is paramount, as is the recoverability of the parachutes and test article. It is crucial to establish an aircraft release point that will ensure that the article and all items released from it will land in safe locations. Early in the CPAS project, a legacy tool (previously used on the X-38 project) was used to determine a safe release point and to predict the landing locations (the footprint) of the payload and all released objects. Due to increasing test complexity and the need for a more flexible tool, a new footprint predictor tool, called Sasquatch, was created in MATLAB. This tool takes in a simulated trajectory for the test article, information about all released objects, and atmospheric wind data (simulated or actual) to calculate the trajectories of the released objects. Dispersions are applied to the landing locations of those objects, taking into account the variability of winds, aircraft release point, and object descent rate. A safe aircraft release point is determined based on the landing locations of the payload and released objects. The release point, landing locations, and dispersions are plotted on a simple map of the drop zone for easy reference. To date, Sasquatch has been used for thirteen drop tests. Comparing the predictions with actual test results has allowed for significant improvements in the tool s predictive capabilities, especially the incorporation of a well-correlated horizontal throw model. Intended future improvements to the tool include tighter dispersions on the landing locations, Monte Carlo capability, direct input from trajectory simulations, and a graphical user interface.

  8. JGI Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  9. Genomic Encyclopedia of Fungi

    SciTech Connect

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  10. Development of an Extensible Computational Framework for Centralized Storage and Distributed Curation and Analysis of Genomic Data Genome-scale Metabolic Models

    SciTech Connect

    Stevens, Rick

    2010-08-01

    The DOE funded KBase project of the Stevens group at the University of Chicago was focused on four high-level goals: (i) improve extensibility, accessibility, and scalability of the SEED framework for genome annotation, curation, and analysis; (ii) extend the SEED infrastructure to support transcription regulatory network reconstructions (2.1), metabolic model reconstruction and analysis (2.2), assertions linked to data (2.3), eukaryotic annotation (2.4), and growth phenotype prediction (2.5); (iii) develop a web-API for programmatic remote access to SEED data and services; and (iv) application of all tools to bioenergy-related genomes and organisms. In response to these goals, we enhanced and improved the ModelSEED resource within the SEED to enable new modeling analyses, including improved model reconstruction and phenotype simulation. We also constructed a new website and web-API for the ModelSEED. Further, we constructed a comprehensive web-API for the SEED as a whole. We also made significant strides in building infrastructure in the SEED to support the reconstruction of transcriptional regulatory networks by developing a pipeline to identify sets of consistently expressed genes based on gene expression data. We applied this pipeline to 29 organisms, computing regulons which were subsequently stored in the SEED database and made available on the SEED website (http://pubseed.theseed.org). We developed a new pipeline and database for the use of kmers, or short 8-residue oligomer sequences, to annotate genomes at high speed. Finally, we developed the PlantSEED, or a new pipeline for annotating primary metabolism in plant genomes. All of the work performed within this project formed the early building blocks for the current DOE Knowledgebase system, and the kmer annotation pipeline, plant annotation pipeline, and modeling tools are all still in use in KBase today.

  11. The teaching portfolio as a professional development tool for anaesthetists.

    PubMed

    Sidhu, N S

    2015-05-01

    A teaching portfolio (TP) is a document containing a factual description of a teacher's teaching strengths and accomplishments, allowing clinicians to display them for examination by others. The primary aim of a TP is to improve quality of teaching by providing a structure for self-reflection, which in turn aids professional development in medical education. Contents typically include a personal statement on teaching, an overview of teaching accomplishments and activities, feedback from colleagues and learners, a reflective component and some examples of teaching material. Electronic portfolios are more portable and flexible compared to paper portfolios. Clinicians gain the most benefit from a TP when it is used as a tool for self-reflection of their teaching practice and not merely as a list of activities and achievements. This article explains why and how anaesthetists might use a TP as a tool for professional development in medical education. PMID:25943606

  12. The teaching portfolio as a professional development tool for anaesthetists.

    PubMed

    Sidhu, N S

    2015-05-01

    A teaching portfolio (TP) is a document containing a factual description of a teacher's teaching strengths and accomplishments, allowing clinicians to display them for examination by others. The primary aim of a TP is to improve quality of teaching by providing a structure for self-reflection, which in turn aids professional development in medical education. Contents typically include a personal statement on teaching, an overview of teaching accomplishments and activities, feedback from colleagues and learners, a reflective component and some examples of teaching material. Electronic portfolios are more portable and flexible compared to paper portfolios. Clinicians gain the most benefit from a TP when it is used as a tool for self-reflection of their teaching practice and not merely as a list of activities and achievements. This article explains why and how anaesthetists might use a TP as a tool for professional development in medical education.

  13. An overview of bioinformatics tools for epitope prediction: implications on vaccine development.

    PubMed

    Soria-Guerra, Ruth E; Nieto-Gomez, Ricardo; Govea-Alonso, Dania O; Rosales-Mendoza, Sergio

    2015-02-01

    Exploitation of recombinant DNA and sequencing technologies has led to a new concept in vaccination in which isolated epitopes, capable of stimulating a specific immune response, have been identified and used to achieve advanced vaccine formulations; replacing those constituted by whole pathogen-formulations. In this context, bioinformatics approaches play a critical role on analyzing multiple genomes to select the protective epitopes in silico. It is conceived that cocktails of defined epitopes or chimeric protein arrangements, including the target epitopes, may provide a rationale design capable to elicit convenient humoral or cellular immune responses. This review presents a comprehensive compilation of the most advantageous online immunological software and searchable, in order to facilitate the design and development of vaccines. An outlook on how these tools are supporting vaccine development is presented. HIV and influenza have been taken as examples of promising developments on vaccination against hypervariable viruses. Perspectives in this field are also envisioned.

  14. Malaria vaccines: high-throughput tools for antigens discovery with potential for their development.

    PubMed

    Céspedes, Nora; Vallejo, Andrés; Arévalo-Herrera, Myriam; Herrera, Sócrates

    2013-04-01

    Malaria is a disease induced by parasites of the Plasmodium genus, which are transmitted by Anopheles mosquitoes and represents a great socio-economic burden Worldwide. Plasmodium vivax is the second species of malaria Worldwide, but it is the most prevalent in Latin America and other regions of the planet. It is currently considered that vaccines represent a cost-effective strategy for controlling transmissible diseases and could complement other malaria control measures; however, the chemical and immunological complexity of the parasite has hindered development of effective vaccines. Recent availability of several genomes of Plasmodium species, as well as bioinformatic tools are allowing the selection of large numbers of proteins and analysis of their immune potential. Herein, we review recently developed strategies for discovery of novel antigens with potential for malaria vaccine development.

  15. Continued Development of Expert System Tools for NPSS Engine Diagnostics

    NASA Technical Reports Server (NTRS)

    Lewandowski, Henry

    1996-01-01

    The objectives of this grant were to work with previously developed NPSS (Numerical Propulsion System Simulation) tools and enhance their functionality; explore similar AI systems; and work with the High Performance Computing Communication (HPCC) K-12 program. Activities for this reporting period are briefly summarized and a paper addressing the implementation, monitoring and zooming in a distributed jet engine simulation is included as an attachment.

  16. Decision tables in process control: a powerful development tool.

    PubMed

    Nixon, J S; McMullen, W L

    1986-01-01

    An automation and control systems development methodology based on the use of decision tables and its major analysis, design, and documentation technique will be discussed. Decision tables are a powerful facility for expressing complex procedures, programs, and control strategies to be implemented in computer-based systems. Their characteristics and advantages will be discussed, and examples of their use will be compared to other traditional tools. Two industrial plant automation projects employing decision tables will be cited.

  17. Genome-wide characterization of microsatellites and marker development in the carcinogenic liver fluke Clonorchis sinensis.

    PubMed

    Nguyen, Thao T B; Arimatsu, Yuji; Hong, Sung-Jong; Brindley, Paul J; Blair, David; Laha, Thewarach; Sripa, Banchob

    2015-06-01

    Clonorchis sinensis is an important carcinogenic human liver fluke endemic in East and Southeast Asia. There are several conventional molecular markers that have been used for identification and genetic diversity; however, no information about microsatellites of this liver fluke is published so far. We here report microsatellite characterization and marker development for a genetic diversity study in C. sinensis, using a genome-wide bioinformatics approach. Based on our search criteria, a total of 256,990 microsatellites (≥12 base pairs) were identified from a genome database of C. sinensis, with hexanucleotide motif being the most abundant (51%) followed by pentanucleotide (18.3%) and trinucleotide (12.7%). The tetranucleotide, dinucleotide, and mononucleotide motifs accounted for 9.75, 7.63, and 0.14%, respectively. The total length of all microsatellites accounts for 0. 72% of 547 Mb of the whole genome size, and the frequency of microsatellites was found to be one microsatellite in every 2.13 kb of DNA. For the di-, tri-, and tetranucleotide, the repeat numbers redundant are six (28%), four (45%), and three (76%), respectively. The ATC repeat is the most abundant microsatellites followed by AT, AAT, and AC, respectively. Within 40 microsatellite loci developed, 24 microsatellite markers showed potential to differentiate between C. sinensis and Opisthorchis viverrini. Seven out of 24 loci showed to be heterozygous with observed heterozygosity that ranged from 0.467 to 1. Four primer sets could amplify both C. sinensis and O. viverrini DNA with different sizes. This study provides basic information of C. sinensis microsatellites, and the genome-wide markers developed may be a useful tool for the genetic study of C. sinensis. PMID:25782682

  18. Genome-wide characterization of microsatelittes and marker development in the carcinogenic liver fluke Clonorchis sinensis

    PubMed Central

    Nguyen, Thao T.B.; Arimatsu, Yuji; Hong, Sung-Jong; Brindley, Paul J.; Blair, David; Laha, Thewarach; Sripa, Banchob

    2015-01-01

    Clonorchis sinensis is an important carcinogenic human liver fluke endemic in East and Southeast Asia. There are several conventional molecular markers have been used for identification and genetic diversity, however, no information about microsatellites of this liver fluke published so far. We here report microsatellite characterization and marker development for genetic diversity study in C. sinensis using genome-wide bioinformatics approach. Based on our search criteria, a total of 256,990 microsatellites (≥ 12 base pairs) were identified from genome database of C. sinensis with hexa-nucleotide motif being the most abundant (51%) followed by penta-nucleotide (18.3%) and tri-nucleotide (12.7%). The tetra-nucleotide, di-nucleotide and mononucleotide motifs accounted for 9.75 %, 7.63% and 0.14%, respectively. The total length of all microsatellites accounts for 0. 72 % of 547 Mb of the whole genome size and the frequency of microsatellites were found to be one microsatellite in every 2.13 kb of DNA. For the di-, tri, and tetra-nucleotide, the repeat numbers redundant are six (28%), four (45%) and three (76%), respectively. The ATC repeat is the most abundant microsatellites followed by AT, AAT and AC, respectively. Within 40 microsatellite loci developed, 24 microsatellite markers showed potential to differentiate between C. sinensis and O. viverrini. Seven out of 24 loci showed heterozygous with observed heterozygosity ranged from 0.467 to 1. Four-primer sets could amplify both C. sinensis and O. viverrini DNA with different sizes. This study provides basic information of C. sinensis microsatellites and the genome-wide markers developed may be a useful tool for genetic study of C. sinensis. PMID:25782682

  19. Developing an interaction-centered evaluation tool for distance education.

    PubMed

    Perrine, John A; Logan, Judith R

    2004-01-01

    Web-based distance instruction is growing in popularity. As more courses and programs go online, instructional methods and technologies are changing to meet new demands. These courses and instructional methods need be evaluated to determine their quality and to aid in their development. An instrument that measures the quality of student interaction within courses could play a useful role in this evaluation. The objective of this project was to produce an interaction-centered evaluation tool for distance education. We developed items for the evaluation tool based on a review of the literature and interviews with distance education faculty. We then conducted a measurement study to determine the instrument's validity and reliability. Fifty-five students in seven medical informatics courses participated in this study. Questionnaire items were included or rejected based on their fit with underlying theoretical constructs. In conclusion, the Web-based evaluation tool developed in this project measures student perception of quality of course interactions with demonstrated validity and reliability.

  20. Collaborative socioeconomic tool development to address management and planning needs

    USGS Publications Warehouse

    Richardson, Leslie A.; Huber, Christopher; Cullinane Thomas, Catherine; Donovan, Elizabeth; Koontz, Lynne M.

    2014-01-01

    Public lands and resources managed by the National Park Service (NPS) and other land management agencies provide a wide range of social and economic benefits to both nearby local communities and society as a whole, ranging from job creation, to access to unique recreational opportunities, to subsistence and tribal uses of the land. Over the years, there has been an increased need to identify and analyze the socioeconomic effects of the public’s use of NPS lands and resources, and the wide range of NPS land management decisions. This need stems from laws such as the National Environmental Policy Act (NEPA), increased litigation and appeals on NPS management decisions, as well as an overall need to demonstrate how parks benefit communities and the American public. To address these needs, the U.S. Geological Survey (USGS) and NPS have an ongoing partnership to collaboratively develop socioeconomic tools to support planning needs and resource management. This article discusses two such tools. The first, Assessing Socioeconomic Planning Needs (ASPN), was developed to help NPS planners and managers identify key social and economic issues that can arise as a result of land management actions. The second tool, the Visitor Spending Effects (VSE) model, provides a specific example of a type of analysis that may be recommended by ASPN. The remainder of this article discusses the development, main features, and plans for future versions and applications of both ASPN and the VSE.

  1. Comparative genetics and genomics of nematodes: genome structure, development, and lifestyle.

    PubMed

    Sommer, Ralf J; Streit, Adrian

    2011-01-01

    Nematodes are found in virtually all habitats on earth. Many of them are parasites of plants and animals, including humans. The free-living nematode, Caenorhabditis elegans, is one of the genetically best-studied model organisms and was the first metazoan whose genome was fully sequenced. In recent years, the draft genome sequences of another six nematodes representing four of the five major clades of nematodes were published. Compared to mammalian genomes, all these genomes are very small. Nevertheless, they contain almost the same number of genes as the human genome. Nematodes are therefore a very attractive system for comparative genetic and genomic studies, with C. elegans as an excellent baseline. Here, we review the efforts that were made to extend genetic analysis to nematodes other than C. elegans, and we compare the seven available nematode genomes. One of the most striking findings is the unexpectedly high incidence of gene acquisition through horizontal gene transfer (HGT). PMID:21721943

  2. Support Tools in Formulation Development for Poorly Soluble Drugs.

    PubMed

    Fridgeirsdottir, Gudrun A; Harris, Robert; Fischer, Peter M; Roberts, Clive J

    2016-08-01

    The need for solubility enhancement through formulation is a well-known but still problematic issue because of the numbers of poorly water-soluble drugs in development. There are several possible routes that can be taken to increase the bioavailability of drugs intended for immediate-release oral formulation. The best formulation strategy for any given drug will depend on numerous factors, including required dose, shelf life, manufacturability, and the properties of the active pharmaceutical ingredient (API). Choosing an optimal formulation and manufacturing route for a new API is therefore not a straightforward process. Currently, there are several approaches that are used in the pharmaceutical industry to select the best formulation strategy. These differ in complexity and efficiency, but most try to predict which route will best suit the API based on selected molecular parameters such as molecular weight, lipophilicity (logP), and solubility. These methods range from using no tools, trial and error methods through a variety of complex tools from small in vitro or in vivo experiments or high throughput screening, guidance maps, and decision trees to the most complex methods based on computational modelling tools. This review aims to list available support tools and explain how they are used. PMID:27368122

  3. Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci.

    PubMed

    Rasmussen, L H; Dargis, R; Højholt, K; Christensen, J J; Skovgaard, O; Justesen, U S; Rosenvinge, F S; Moser, C; Lukjancenko, O; Rasmussen, S; Nielsen, X C

    2016-10-01

    Identification of Mitis group streptococci (MGS) to the species level is challenging for routine microbiology laboratories. Correct identification is crucial for the diagnosis of infective endocarditis, identification of treatment failure, and/or infection relapse. Eighty MGS from Danish patients with infective endocarditis were whole genome sequenced. We compared the phylogenetic analyses based on single genes (recA, sodA, gdh), multigene (MLSA), SNPs, and core-genome sequences. The six phylogenetic analyses generally showed a similar pattern of six monophyletic clusters, though a few differences were observed in single gene analyses. Species identification based on single gene analysis showed their limitations when more strains were included. In contrast, analyses incorporating more sequence data, like MLSA, SNPs and core-genome analyses, provided more distinct clustering. The core-genome tree showed the most distinct clustering. PMID:27325438

  4. Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci.

    PubMed

    Rasmussen, L H; Dargis, R; Højholt, K; Christensen, J J; Skovgaard, O; Justesen, U S; Rosenvinge, F S; Moser, C; Lukjancenko, O; Rasmussen, S; Nielsen, X C

    2016-10-01

    Identification of Mitis group streptococci (MGS) to the species level is challenging for routine microbiology laboratories. Correct identification is crucial for the diagnosis of infective endocarditis, identification of treatment failure, and/or infection relapse. Eighty MGS from Danish patients with infective endocarditis were whole genome sequenced. We compared the phylogenetic analyses based on single genes (recA, sodA, gdh), multigene (MLSA), SNPs, and core-genome sequences. The six phylogenetic analyses generally showed a similar pattern of six monophyletic clusters, though a few differences were observed in single gene analyses. Species identification based on single gene analysis showed their limitations when more strains were included. In contrast, analyses incorporating more sequence data, like MLSA, SNPs and core-genome analyses, provided more distinct clustering. The core-genome tree showed the most distinct clustering.

  5. The discrepancies in the results of bioinformatics tools for genomic structural annotation

    NASA Astrophysics Data System (ADS)

    Pawełkowicz, Magdalena; Nowak, Robert; Osipowski, Paweł; Rymuszka, Jacek; Świerkula, Katarzyna; Wojcieszek, Michał; Przybecki, Zbigniew

    2014-11-01

    A major focus of sequencing project is to identify genes in genomes. However it is necessary to define the variety of genes and the criteria for identifying them. In this work we present discrepancies and dependencies from the application of different bioinformatic programs for structural annotation performed on the cucumber data set from Polish Consortium of Cucumber Genome Sequencing. We use Fgenesh, GenScan and GeneMark to automated structural annotation, the results have been compared to reference annotation.

  6. QCanvas: An Advanced Tool for Data Clustering and Visualization of Genomics Data.

    PubMed

    Kim, Nayoung; Park, Herin; He, Ningning; Lee, Hyeon Young; Yoon, Sukjoon

    2012-12-01

    We developed a user-friendly, interactive program to simultaneously cluster and visualize omics data, such as DNA and protein array profiles. This program provides diverse algorithms for the hierarchical clustering of two-dimensional data. The clustering results can be interactively visualized and optimized on a heatmap. The present tool does not require any prior knowledge of scripting languages to carry out the data clustering and visualization. Furthermore, the heatmaps allow the selective display of data points satisfying user-defined criteria. For example, a clustered heatmap of experimental values can be differentially visualized based on statistical values, such as p-values. Including diverse menu-based display options, QCanvas provides a convenient graphical user interface for pattern analysis and visualization with high-quality graphics.

  7. PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences

    PubMed Central

    2011-01-01

    Background Periodic spacing of short adenine or thymine runs phased with DNA helical period of ~10.5 bp is associated with intrinsic DNA curvature and deformability, which play important roles in DNA-protein interactions and in the organization of chromosomes in both eukaryotes and prokaryotes. Local differences in DNA sequence periodicity have been linked to differences in gene expression in some organisms. Despite the significance of these periodic patterns, there are virtually no publicly accessible tools for their analysis. Results We present novel tools suitable for assessments of DNA curvature-related sequence periodicity in nucleotide sequences at the genome scale. Utility of the present software is demonstrated on a comparison of sequence periodicities in the genomes of Haemophilus influenzae, Methanocaldococcus jannaschii, Saccharomyces cerevisiae, and Arabidopsis thaliana. The software can be accessed through a web interface and the programs are also available for download. Conclusions The present software is suitable for comparing DNA curvature-related sequence periodicity among different genomes as well as for analysis of intrachromosomal heterogeneity of the sequence periodicity. It provides a quick and convenient way to detect anomalous regions of chromosomes that could have unusual structural and functional properties and/or distinct evolutionary history. PMID:22587738

  8. Development of tools, technologies, and methodologies for imaging sensor testing

    NASA Astrophysics Data System (ADS)

    Lowry, H.; Bynum, K.; Steely, S.; Nicholson, R.; Horne, H.

    2013-05-01

    Ground testing of space- and air-borne imaging sensor systems is supported by Vis-to-LWIR imaging sensor calibration and characterization, as well as hardware-in-the-loop (HWIL) simulation with high-fidelity complex scene projection to validate sensor mission performance. To accomplish this successfully, there must be the development of tools, technologies, and methodologies that are used in space simulation chambers for such testing. This paper provides an overview of such efforts being investigated and implemented at Arnold Engineering Development Complex (AEDC).

  9. Project 1: Microbial Genomes: A Genomic Approach to Understanding the Evolution of Virulence. Project 2: From Genomes to Life: Drosophilia Development in Space and Time

    SciTech Connect

    Robert DeSalle

    2004-09-10

    This project seeks to use the genomes of two close relatives, A. actinomycetemcomitans and H. aphrophilus, to understand the evolutionary changes that take place in a genome to make it more or less virulent. Our primary specific aim of this project was to sequence, annotate, and analyze the genomes of Actinobacillus actinomycetemcomitans (CU1000, serotype f) and Haemophilus aphrophilus. With these genome sequences we have then compared the whole genome sequences to each other and to the current Aa (HK1651 www.genome.ou.edu) genome project sequence along with other fully sequenced Pasteurellaceae to determine inter and intra species differences that may account for the differences and similarities in disease. We also propose to create and curate a comprehensive database where sequence information and analysis for the Pasteurellaceae (family that includes the genera Actinobacillus and Haemophilus) are readily accessible. And finally we have proposed to develop phylogenetic techniques that can be used to efficiently and accurately examine the evolution of genomes. Below we report on progress we have made on these major specific aims. Progress on the specific aims is reported below under two major headings--experimental approaches and bioinformatics and systematic biology approaches.

  10. Development of a burn prevention teaching tool for Amish children.

    PubMed

    Rieman, Mary T; Kagan, Richard J

    2012-01-01

    Although there are inherent risks for burn injury associated with the Amish lifestyle, burn prevention is not taught in Amish schools. The purpose of this study was to develop a burn prevention teaching tool for Amish children. An anonymous parental survey was designed to explore the content and acceptability of a teaching tool within an Old Order Amish community. After institutional review board approval, the Amish teacher distributed surveys to 16 families of the 30 children attending the one-room school. Fourteen (88%) of the families responded to identify these burn risks in and around their homes, barns, and shops: lighters, wood and coal stoves, kerosene heaters, gasoline-powered engines, and hot liquids used for canning, butchering, mopping, washing clothes, and making lye soap. All respondents were in favor of teaching familiar safety precautions, fire escape plans, burn first aid, and emergency care to the children. There was some minor objection to more modern devices such as bath tub thermometers (25%), fire extinguishers (19%), and smoke detectors (6%). The teacher was interested in a magnetic teaching board depicting Amish children and typical objects in their home environment. Movable pieces could afford the opportunity to identify hazards and to rearrange them for a safer situation. This survey served to introduce burn prevention to one Amish community and to develop an appropriate teaching tool for the school. It is anticipated that community participation would support its acceptance and eventual utilization within this tenaciously traditional culture.

  11. The role of customized computational tools in product development.

    SciTech Connect

    Heinstein, Martin Wilhelm; Kempka, Steven Norman; Tikare, Veena

    2005-06-01

    Model-based computer simulations have revolutionized product development in the last 10 to 15 years. Technologies that have existed for many decades or even centuries have been improved with the aid of computer simulations. Everything from low-tech consumer goods such as detergents, lubricants and light bulb filaments to the most advanced high-tech products such as airplane wings, wireless communication technologies and pharmaceuticals is engineered with the aid of computer simulations today. In this paper, we present a framework for describing computational tools and their application within the context of product engineering. We examine a few cases of product development that integrate numerical computer simulations into the development stage. We will discuss how the simulations were integrated into the development process, what features made the simulations useful, the level of knowledge and experience that was necessary to run meaningful simulations and other details of the process. Based on this discussion, recommendations for the incorporation of simulations and computational tools into product development will be made.

  12. ANALYTICAL TOOL DEVELOPMENT FOR AFTERTREATMENT SUB-SYSTEMS INTEGRATION

    SciTech Connect

    Bolton, B; Fan, A; Goney, K; Pavlova-MacKinnon, Z; Sisken, K; Zhang, H

    2003-08-24

    The stringent emissions standards of 2007 and beyond require complex engine, aftertreatment and vehicle systems with a high degree of sub-system interaction and flexible control solutions. This necessitates a system-based approach to technology development, in addition to individual sub-system optimization. Analytical tools can provide an effective means to evaluate and develop such complex technology interactions as well as understand phenomena that is either too expensive or impossible to study with conventional experimental means. The analytical effort can also guide experimental development and thus lead to efficient utilization of available experimental resources.A suite of analytical models has been developed to represent PM and NOx aftertreatment sub-systems. These models range from computationally inexpensive zero-dimensional models for real-time control applications to CFD-based, multi-dimensional models with detailed temporal and spatial resolution. Such models in conjunction with well established engine modeling tools such as engine cycle simulation, engine controls modeling, CFD models of non-combusting and combusting flow, and vehicle models provide a comprehensive analytical toolbox for complete engine, aftertreatment and vehicle sub-systems development and system integration applications. However, the fidelity of aftertreatment models and application going forward is limited by the lack of fundamental kinetic data.

  13. Confluence of genes, environment, development, and behavior in a post Genome-Wide Association Study world.

    PubMed

    Vrieze, Scott I; Iacono, William G; McGue, Matt

    2012-11-01

    This article serves to outline a research paradigm to investigate main effects and interactions of genes, environment, and development on behavior and psychiatric illness. We provide a historical context for candidate gene studies and genome-wide association studies, including benefits, limitations, and expected payoffs. Using substance use and abuse as our driving example, we then turn to the importance of etiological psychological theory in guiding genetic, environmental, and developmental research, as well as the utility of refined phenotypic measures, such as endophenotypes, in the pursuit of etiological understanding and focused tests of genetic and environmental associations. Phenotypic measurement has received considerable attention in the history of psychology and is informed by psychometrics, whereas the environment remains relatively poorly measured and is often confounded with genetic effects (i.e., gene-environment correlation). Genetically informed designs, which are no longer limited to twin and adoption studies thanks to ever-cheaper genotyping, are required to understand environmental influences. Finally, we outline the vast amount of individual difference in structural genomic variation, most of which remains to be leveraged in genetic association tests. Although the genetic data can be massive and burdensome (tens of millions of variants per person), we argue that improved understanding of genomic structure and function will provide investigators with new tools to test specific a priori hypotheses derived from etiological psychological theory, much like current candidate gene research but with less confusion and more payoff than candidate gene research has to date. PMID:23062291

  14. New Developments of RNAi in Paracoccidioides brasiliensis: Prospects for High-Throughput, Genome-Wide, Functional Genomics

    PubMed Central

    Goes, Tercio; Bailão, Elisa Flavia L. C.; Correa, Cristiane R.; Bozzi, Adriana; Santos, Luara I.; Gomes, Dawidson A.; Soares, Celia M. A.; Goes, Alfredo M.

    2014-01-01

    Background The Fungal Genome Initiative of the Broad Institute, in partnership with the Paracoccidioides research community, has recently sequenced the genome of representative isolates of this human-pathogen dimorphic fungus: Pb18 (S1), Pb03 (PS2) and Pb01. The accomplishment of future high-throughput, genome-wide, functional genomics will rely upon appropriate molecular tools and straightforward techniques to streamline the generation of stable loss-of-function phenotypes. In the past decades, RNAi has emerged as the most robust genetic technique to modulate or to suppress gene expression in diverse eukaryotes, including fungi. These molecular tools and techniques, adapted for RNAi, were up until now unavailable for P. brasiliensis. Methodology/Principal Findings In this paper, we report Agrobacterium tumefaciens mediated transformation of yeast cells for high-throughput applications with which higher transformation frequencies of 150±24 yeast cell transformants per 1×106 viable yeast cells were obtained. Our approach is based on a bifunctional selective marker fusion protein consisted of the Streptoalloteichus hindustanus bleomycin-resistance gene (Shble) and the intrinsically fluorescent monomeric protein mCherry which was codon-optimized for heterologous expression in P. brasiliensis. We also report successful GP43 gene knock-down through the expression of intron-containing hairpin RNA (ihpRNA) from a Gateway-adapted cassette (cALf) which was purpose-built for gene silencing in a high-throughput manner. Gp43 transcript levels were reduced by 73.1±22.9% with this approach. Conclusions/Significance We have a firm conviction that the genetic transformation technique and the molecular tools herein described will have a relevant contribution in future Paracoccidioides spp. functional genomics research. PMID:25275433

  15. Developments in the Tools and Methodologies of Synthetic Biology

    PubMed Central

    Kelwick, Richard; MacDonald, James T.; Webb, Alexander J.; Freemont, Paul

    2014-01-01

    Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices, or systems. However, biological systems are generally complex and unpredictable, and are therefore, intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a “body of knowledge” from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled, and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled, and its functionality tested. At each stage of the design cycle, an expanding repertoire of tools is being developed. In this review, we highlight several of these tools in terms of their applications and benefits to the synthetic biology community. PMID:25505788

  16. Development Life Cycle and Tools for XML Content Models

    SciTech Connect

    Kulvatunyou, Boonserm; Morris, Katherine; Buhwan, Jeong; Goyal, Puja

    2004-11-01

    Many integration projects today rely on shared semantic models based on standards represented using Extensible Mark up Language (XML) technologies. Shared semantic models typically evolve and require maintenance. In addition, to promote interoperability and reduce integration costs, the shared semantics should be reused as much as possible. Semantic components must be consistent and valid in terms of agreed upon standards and guidelines. In this paper, we describe an activity model for creation, use, and maintenance of a shared semantic model that is coherent and supports efficient enterprise integration. We then use this activity model to frame our research and the development of tools to support those activities. We provide overviews of these tools primarily in the context of the W3C XML Schema. At the present, we focus our work on the W3C XML Schema as the representation of choice, due to its extensive adoption by industry.

  17. [From random mutagenesis to precise genome editing: the development and evolution of genome editing techniques in Drosophila].

    PubMed

    Su, Fang; Huang, Zongliang; Guo, Yawen; Jiao, Renjie; Zi, Li; Chen, Jianming; Liu, Jiyong

    2016-01-01

    Drosophila melanogaster, an important model organism for studying life science, has contributed more to the research of genetics, developmental biology and biomedicine with the development of genome editing techniques. Drosophila genome-editing techniques have evolved from random mutagenesis to precise genome editing and from simple mutant construction to diverse genome editing methods since the 20th century. Chemical mutagenesis, using Ethyl methanesulfonate (EMS), is an important technique to study gene function in forward genetics, however, the precise knockout of Drosophila genes could not be achieved. The gene targeting technology, based on homologous recombination, has accomplished the precise editing of Drosophila genome for the first time, but with low efficiency. The CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein)-mediated precise genome editing is simple, fast and highly efficient compared with the gene targeting technology in Drosophila. In this review, we focus on Drosophila gene knockout, and summarize the evolution of genome editing techniques in Drosophila, emphasizing the development and applications of gene targeting, zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) and CRISPR/Cas9 techniques. PMID:26787520

  18. The development of a tool to predict team performance.

    PubMed

    Sinclair, M A; Siemieniuch, C E; Haslam, R A; Henshaw, M J D C; Evans, L

    2012-01-01

    The paper describes the development of a tool to predict quantitatively the success of a team when executing a process. The tool was developed for the UK defence industry, though it may be useful in other domains. It is expected to be used by systems engineers in initial stages of systems design, when concepts are still fluid, including the structure of the team(s) which are expected to be operators within the system. It enables answers to be calculated for questions such as "What happens if I reduce team size?" and "Can I reduce the qualifications necessary to execute this process and still achieve the required level of success?". The tool has undergone verification and validation; it predicts fairly well and shows promise. An unexpected finding is that the tool creates a good a priori argument for significant attention to Human Factors Integration in systems projects. The simulations show that if a systems project takes full account of human factors integration (selection, training, process design, interaction design, culture, etc.) then the likelihood of team success will be in excess of 0.95. As the project derogates from this state, the likelihood of team success will drop as low as 0.05. If the team has good internal communications and good individuals in key roles, the likelihood of success rises towards 0.25. Even with a team comprising the best individuals, p(success) will not be greater than 0.35. It is hoped that these results will be useful for human factors professionals involved in systems design.

  19. Continued development of modeling tools and theory for RF heating

    SciTech Connect

    1998-12-01

    Mission Research Corporation (MRC) is pleased to present the Department of Energy (DOE) with its renewal proposal to the Continued Development of Modeling Tools and Theory for RF Heating program. The objective of the program is to continue and extend the earlier work done by the proposed principal investigator in the field of modeling (Radio Frequency) RF heating experiments in the large tokamak fusion experiments, particularly the Tokamak Fusion Test Reactor (TFTR) device located at Princeton Plasma Physics Laboratory (PPPL). An integral part of this work is the investigation and, in some cases, resolution of theoretical issues which pertain to accurate modeling. MRC is nearing the successful completion of the specified tasks of the Continued Development of Modeling Tools and Theory for RF Heating project. The following tasks are either completed or nearing completion. (1) Anisotropic temperature and rotation upgrades; (2) Modeling for relativistic ECRH; (3) Further documentation of SHOOT and SPRUCE. As a result of the progress achieved under this project, MRC has been urged to continue this effort. Specifically, during the performance of this project two topics were identified by PPPL personnel as new applications of the existing RF modeling tools. These two topics concern (a) future fast-wave current drive experiments on the large tokamaks including TFTR and (c) the interpretation of existing and future RF probe data from TFTR. To address each of these topics requires some modification or enhancement of the existing modeling tools, and the first topic requires resolution of certain theoretical issues to produce self-consistent results. This work falls within the scope of the original project and is more suited to the project`s renewal than to the initiation of a new project.

  20. Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing

    NASA Astrophysics Data System (ADS)

    Lu, Xia; Luan, Sheng; Kong, Jie; Hu, Longyang; Mao, Yong; Zhong, Shengping

    2015-12-01

    The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization and distribution of simple sequence repeats (SSRs) remains ambiguous and the use of SSR markers in genomic studies and marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide SSR markers in M. japonicus by genome survey sequencing for application in comparative genomics and breeding. A total of 326 945 perfect SSRs were identifi ed, among which dinucleotide repeats were the most frequent class (44.08%), followed by mononucleotides (29.67%), trinucleotides (18.96%), tetranucleotides (5.66%), hexanucleotides (1.07%), and pentanucleotides (0.56%). In total, 151 541 SSR loci primers were successfully designed. A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population, of which 27 loci (90.0%) were successfully amplifi ed with specifi c products and 24 (80.0%) were polymorphic. For the amplifi ed polymorphic loci, the alleles ranged from 5 to 17 (with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing sequences had signifi cant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identifi ed SSRs signifi cantly contribute to the M. japonicus genomic resources and will facilitate a number of genetic and genomic studies, including high density linkage mapping, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution.

  1. COSTMODL - AN AUTOMATED SOFTWARE DEVELOPMENT COST ESTIMATION TOOL

    NASA Technical Reports Server (NTRS)

    Roush, G. B.

    1994-01-01

    The cost of developing computer software consumes an increasing portion of many organizations' budgets. As this trend continues, the capability to estimate the effort and schedule required to develop a candidate software product becomes increasingly important. COSTMODL is an automated software development estimation tool which fulfills this need. Assimilating COSTMODL to any organization's particular environment can yield significant reduction in the risk of cost overruns and failed projects. This user-customization capability is unmatched by any other available estimation tool. COSTMODL accepts a description of a software product to be developed and computes estimates of the effort required to produce it, the calendar schedule required, and the distribution of effort and staffing as a function of the defined set of development life-cycle phases. This is accomplished by the five cost estimation algorithms incorporated into COSTMODL: the NASA-developed KISS model; the Basic, Intermediate, and Ada COCOMO models; and the Incremental Development model. This choice affords the user the ability to handle project complexities ranging from small, relatively simple projects to very large projects. Unique to COSTMODL is the ability to redefine the life-cycle phases of development and the capability to display a graphic representation of the optimum organizational structure required to develop the subject project, along with required staffing levels and skills. The program is menu-driven and mouse sensitive with an extensive context-sensitive help system that makes it possible for a new user to easily install and operate the program and to learn the fundamentals of cost estimation without having prior training or separate documentation. The implementation of these functions, along with the customization feature, into one program makes COSTMODL unique within the industry. COSTMODL was written for IBM PC compatibles, and it requires Turbo Pascal 5.0 or later and Turbo

  2. Application of Genomic and Quantitative Genetic Tools to Identify Candidate Resistance Genes for Brown Rot Resistance in Peach

    PubMed Central

    Martínez-García, Pedro J.; Parfitt, Dan E.; Bostock, Richard M.; Fresnedo-Ramírez, Jonathan; Vazquez-Lobo, Alejandra; Ogundiwin, Ebenezer A.; Gradziel, Thomas M.; Crisosto, Carlos H.

    2013-01-01

    The availability of a complete peach genome assembly and three different peach genome sequences created by our group provide new opportunities for application of genomic data and can improve the power of the classical Quantitative Trait Loci (QTL) approaches to identify candidate genes for peach disease resistance. Brown rot caused by Monilinia spp., is the most important fungal disease of stone fruits worldwide. Improved levels of peach fruit rot resistance have been identified in some cultivars and advanced selections developed in the UC Davis and USDA breeding programs. Whole genome sequencing of the Pop-DF parents lead to discovery of high-quality SNP markers for QTL genome scanning in this experimental population. Pop-DF created by crossing a brown rot moderately resistant cultivar ‘Dr. Davis’ and a brown rot resistant introgression line, ‘F8,1–42’, derived from an initial almond × peach interspecific hybrid, was evaluated for brown rot resistance in fruit of harvest maturity over three seasons. Using the SNP linkage map of Pop-DF and phenotypic data collected with inoculated fruit, a genome scan for QTL identified several SNP markers associated with brown rot resistance. Two of these QTLs were placed on linkage group 1, covering a large (physical) region on chromosome 1. The genome scan for QTL and SNP effects predicted several candidate genes associated with disease resistance responses in other host-pathogen systems. Two potential candidate genes, ppa011763m and ppa026453m, may be the genes primarily responsible for M. fructicola recognition in peach, activating both PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI) responses. Our results provide a foundation for further genetic dissection, marker assisted breeding for brown rot resistance, and development of peach cultivars resistant to brown rot. PMID:24244329

  3. Sugarcane Functional Genomics: Gene Discovery for Agronomic Trait Development

    PubMed Central

    Menossi, M.; Silva-Filho, M. C.; Vincentz, M.; Van-Sluys, M.-A.; Souza, G. M.

    2008-01-01

    Sugarcane is a highly productive crop used for centuries as the main source of sugar and recently to produce ethanol, a renewable bio-fuel energy source. There is increased interest in this crop due to the impending need to decrease fossil fuel usage. Sugarcane has a highly polyploid genome. Expressed sequence tag (EST) sequencing has significantly contributed to gene discovery and expression studies used to associate function with sugarcane genes. A significant amount of data exists on regulatory events controlling responses to herbivory, drought, and phosphate deficiency, which cause important constraints on yield and on endophytic bacteria, which are highly beneficial. The means to reduce drought, phosphate deficiency, and herbivory by the sugarcane borer have a negative impact on the environment. Improved tolerance for these constraints is being sought. Sugarcane's ability to accumulate sucrose up to 16% of its culm dry weight is a challenge for genetic manipulation. Genome-based technology such as cDNA microarray data indicates genes associated with sugar content that may be used to develop new varieties improved for sucrose content or for traits that restrict the expansion of the cultivated land. The genes can also be used as molecular markers of agronomic traits in traditional breeding programs. PMID:18273390

  4. Demonstration of Decision Support Tools for Sustainable Development

    SciTech Connect

    Shropshire, David Earl; Jacobson, Jacob Jordan; Berrett, Sharon; Cobb, D. A.; Worhach, P.

    2000-11-01

    The Demonstration of Decision Support Tools for Sustainable Development project integrated the Bechtel/Nexant Industrial Materials Exchange Planner and the Idaho National Engineering and Environmental Laboratory System Dynamic models, demonstrating their capabilities on alternative fuel applications in the Greater Yellowstone-Teton Park system. The combined model, called the Dynamic Industrial Material Exchange, was used on selected test cases in the Greater Yellow Teton Parks region to evaluate economic, environmental, and social implications of alternative fuel applications, and identifying primary and secondary industries. The test cases included looking at compressed natural gas applications in Teton National Park and Jackson, Wyoming, and studying ethanol use in Yellowstone National Park and gateway cities in Montana. With further development, the system could be used to assist decision-makers (local government, planners, vehicle purchasers, and fuel suppliers) in selecting alternative fuels, vehicles, and developing AF infrastructures. The system could become a regional AF market assessment tool that could help decision-makers understand the behavior of the AF market and conditions in which the market would grow. Based on this high level market assessment, investors and decision-makers would become more knowledgeable of the AF market opportunity before developing detailed plans and preparing financial analysis.

  5. Development of the Space Operations Incident Reporting Tool (SOIRT)

    NASA Technical Reports Server (NTRS)

    Minton, Jacquie

    1997-01-01

    The space operations incident reporting tool (SOIRT) is an instrument used to record information about an anomaly occurring during flight which may have been due to insufficient and/or inappropriate application of human factors knowledge. We originally developed the SOIRT form after researching other incident reporting systems of this type. We modified the form after performing several in-house reviews and a pilot test to access usability. Finally, crew members from Space Shuttle flights participated in a usability test of the tool after their missions. Since the National Aeronautics and Space Administration (NASA) currently has no system for continuous collection of this type of information, the SOIRT was developed to report issues such as reach envelope constraints, control operation difficulties, and vision impairments. However, if the SOIRT were to become a formal NASA process, information from crew members could be collected in a database and made available to individuals responsible for improving in-flight safety and productivity. Potential benefits include documentation to justify the redesign or development of new equipment/systems, provide the mission planners with a method for identifying past incidents, justify the development of timelines and mission scenarios, and require the creation of more appropriate work/rest cycles.

  6. Measuring vaccine hesitancy: The development of a survey tool.

    PubMed

    Larson, Heidi J; Jarrett, Caitlin; Schulz, William S; Chaudhuri, Mohuya; Zhou, Yuqing; Dube, Eve; Schuster, Melanie; MacDonald, Noni E; Wilson, Rose

    2015-08-14

    In March 2012, the SAGE Working Group on Vaccine Hesitancy was convened to define the term "vaccine hesitancy", as well as to map the determinants of vaccine hesitancy and develop tools to measure and address the nature and scale of hesitancy in settings where it is becoming more evident. The definition of vaccine hesitancy and a matrix of determinants guided the development of a survey tool to assess the nature and scale of hesitancy issues. Additionally, vaccine hesitancy questions were piloted in the annual WHO-UNICEF joint reporting form, completed by National Immunization Managers globally. The objective of characterizing the nature and scale of vaccine hesitancy issues is to better inform the development of appropriate strategies and policies to address the concerns expressed, and to sustain confidence in vaccination. The Working Group developed a matrix of the determinants of vaccine hesitancy informed by a systematic review of peer reviewed and grey literature, and by the expertise of the working group. The matrix mapped the key factors influencing the decision to accept, delay or reject some or all vaccines under three categories: contextual, individual and group, and vaccine-specific. These categories framed the menu of survey questions presented in this paper to help diagnose and address vaccine hesitancy.

  7. Assessment of COTS IR image simulation tools for ATR development

    NASA Astrophysics Data System (ADS)

    Seidel, Heiko; Stahl, Christoph; Bjerkeli, Frode; Skaaren-Fystro, Paal

    2005-05-01

    Following the tendency of increased use of imaging sensors in military aircraft, future fighter pilots will need onboard artificial intelligence e.g. ATR for aiding them in image interpretation and target designation. The European Aeronautic Defence and Space Company (EADS) in Germany has developed an advanced method for automatic target recognition (ATR) which is based on adaptive neural networks. This ATR method can assist the crew of military aircraft like the Eurofighter in sensor image monitoring and thereby reduce the workload in the cockpit and increase the mission efficiency. The EADS ATR approach can be adapted for imagery of visual, infrared and SAR sensors because of the training-based classifiers of the ATR method. For the optimal adaptation of these classifiers they have to be trained with appropriate and sufficient image data. The training images must show the target objects from different aspect angles, ranges, environmental conditions, etc. Incomplete training sets lead to a degradation of classifier performance. Additionally, ground truth information i.e. scenario conditions like class type and position of targets is necessary for the optimal adaptation of the ATR method. In Summer 2003, EADS started a cooperation with Kongsberg Defence & Aerospace (KDA) from Norway. The EADS/KDA approach is to provide additional image data sets for training-based ATR through IR image simulation. The joint study aims to investigate the benefits of enhancing incomplete training sets for classifier adaptation by simulated synthetic imagery. EADS/KDA identified the requirements of a commercial-off-the-shelf IR simulation tool capable of delivering appropriate synthetic imagery for ATR development. A market study of available IR simulation tools and suppliers was performed. After that the most promising tool was benchmarked according to several criteria e.g. thermal emission model, sensor model, targets model, non-radiometric image features etc., resulting in a

  8. Genome-wide screening and identification of antigens for rickettsial vaccine development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The capacity to identify immunogens for vaccine development by genome-wide screening has been markedly enhanced by the availability of complete microbial genome sequences coupled to rapid proteomic and bioinformatic analysis. Critical to this genome-wide screening is in vivo testing in the context o...

  9. ON DEVELOPING TOOLS AND METHODS FOR ENVIRONMENTALLY BENIGN PROCESSES

    EPA Science Inventory

    Two types of tools are generally needed for designing processes and products that are cleaner from environmental impact perspectives. The first kind is called process tools. Process tools are based on information obtained from experimental investigations in chemistry., material s...

  10. Adapting functional genomic tools to metagenomic analyses: investigating the role of gut bacteria in relation to obesity.

    PubMed

    Liu, Yuanhua; Zhang, Chenhong; Zhao, Liping; Nardini, Christine

    2010-12-01

    With the expanding availability of sequencing technologies, research previously centered on the human genome can now afford to include the study of humans' internal ecosystem (human microbiome). Given the scale of the data involved in this metagenomic research (two orders of magnitude larger than the human genome) and their importance in relation to human health, it is crucial to guarantee (along with the appropriate data collection and taxonomy) proper tools for data analysis. We propose to adapt the approaches defined for the analysis of gene-expression microarray in order to infer information in metagenomics. In particular, we applied SAM, a broadly used tool for the identification of differentially expressed genes among different samples classes, to a reported dataset on a research model with mice of two genotypes (a high density lipoprotein knockout mouse and its wild-type counterpart). The data contain two different diets (high-fat or normal-chow) to ensure the onset of obesity, prodrome of metabolic syndromes (MS). By using 16S rRNA gene as a genomic diversity marker, we illustrate how this approach can identify bacterial populations differentially enriched among different genetic and dietary conditions of the host. This approach faithfully reproduces highly-relevant results from phylogenetic and standard statistical analyses, used to explain the role of the gut microbiome in relation to obesity. This represents a promising proof-of-principle for using functional genomic approaches in the fast growing area of metagenomics, and warrants the availability of a large body of thoroughly tested and theoretically sound methodologies to this exciting new field.

  11. Biomedical informatics: development of a comprehensive data warehouse for clinical and genomic breast cancer research.

    PubMed

    Hu, Hai; Brzeski, Henry; Hutchins, Joe; Ramaraj, Mohan; Qu, Long; Xiong, Richard; Kalathil, Surendran; Kato, Rand; Tenkillaya, Santhosh; Carney, Jerry; Redd, Rosann; Arkalgudvenkata, Sheshkumar; Shahzad, Kashif; Scott, Richard; Cheng, Hui; Meadow, Stephen; McMichael, John; Sheu, Shwu-Lin; Rosendale, David; Kvecher, Leonid; Ahern, Stephen; Yang, Song; Zhang, Yonghong; Jordan, Rick; Somiari, Stella B; Hooke, Jeffrey; Shriver, Craig D; Somiari, Richard I; Liebman, Michael N

    2004-10-01

    The Windber Research Institute is an integrated high-throughput research center employing clinical, genomic and proteomic platforms to produce terabyte levels of data. We use biomedical informatics technologies to integrate all of these operations. This report includes information on a multi-year, multi-phase hybrid data warehouse project currently under development in the Institute. The purpose of the warehouse is to host the terabyte-level of internal experimentally generated data as well as data from public sources. We have previously reported on the phase I development, which integrated limited internal data sources and selected public databases. Currently, we are completing phase II development, which integrates our internal automated data sources and develops visualization tools to query across these data types. This paper summarizes our clinical and experimental operations, the data warehouse development, and the challenges we have faced. In phase III we plan to federate additional manual internal and public data sources and then to develop and adapt more data analysis and mining tools. We expect that the final implementation of the data warehouse will greatly facilitate biomedical informatics research.

  12. COSTMODL: An automated software development cost estimation tool

    NASA Technical Reports Server (NTRS)

    Roush, George B.

    1991-01-01

    The cost of developing computer software continues to consume an increasing portion of many organizations' total budgets, both in the public and private sector. As this trend develops, the capability to produce reliable estimates of the effort and schedule required to develop a candidate software product takes on increasing importance. The COSTMODL program was developed to provide an in-house capability to perform development cost estimates for NASA software projects. COSTMODL is an automated software development cost estimation tool which incorporates five cost estimation algorithms including the latest models for the Ada language and incrementally developed products. The principal characteristic which sets COSTMODL apart from other software cost estimation programs is its capacity to be completely customized to a particular environment. The estimation equations can be recalibrated to reflect the programmer productivity characteristics demonstrated by the user's organization, and the set of significant factors which effect software development costs can be customized to reflect any unique properties of the user's development environment. Careful use of a capability such as COSTMODL can significantly reduce the risk of cost overruns and failed projects.

  13. Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness

    SciTech Connect

    Wu, L.; Liu, X.; Fields, M.W.; Thompson, D.K.; Bagwell, C.E.; Tiedje, J. M.; Hazen, T.C.; Zhou, J.

    2008-01-15

    The definition and delineation of microbial species are of great importance and challenge due to the extent of evolution and diversity. Whole-genome DNA-DNA hybridization is the cornerstone for defining procaryotic species relatedness, but obtaining pairwise DNA-DNA reassociation values for a comprehensive phylogenetic analysis of procaryotes is tedious and time consuming. A previously described microarray format containing whole-genomic DNA (the community genome array or CGA) was rigorously evaluated as a high-throughput alternative to the traditional DNA-DNA reassociation approach for delineating procaryotic species relationships. DNA similarities for multiple bacterial strains obtained with the CGA-based hybridization were comparable to those obtained with various traditional whole-genome hybridization methods (r=0.87, P<0.01). Significant linear relationships were also observed between the CGA-based genome similarities and those derived from small subunit (SSU) rRNA gene sequences (r=0.79, P<0.0001), gyrB sequences (r=0.95, P<0.0001) or REP- and BOX-PCR fingerprinting profiles (r=0.82, P<0.0001). The CGA hybridization-revealed species relationships in several representative genera, including Pseudomonas, Azoarcus and Shewanella, were largely congruent with previous classifications based on various conventional whole-genome DNA-DNA reassociation, SSU rRNA and/or gyrB analyses. These results suggest that CGA-based DNA-DNA hybridization could serve as a powerful, high-throughput format for determining species relatedness among microorganisms.

  14. FGF: a web tool for Fishing Gene Family in a whole genome database.

    PubMed

    Zheng, Hongkun; Shi, Junjie; Fang, Xiaodong; Li, Yuan; Vang, Søren; Fan, Wei; Wang, Junyi; Zhang, Zhang; Wang, Wen; Kristiansen, Karsten; Wang, Jun

    2007-07-01

    Gene duplication is an important process in evolution. The availability of genome sequences of a number of organisms has made it possible to conduct comprehensive searches for duplicated genes enabling informative studies of their evolution. We have established the FGF (Fishing Gene Family) program to efficiently search for and identify gene families. The FGF output displays the results as visual phylogenetic trees including information on gene structure, chromosome position, duplication fate and selective pressure. It is particularly useful to identify pseudogenes and detect changes in gene structure. FGF is freely available on a web server at http://fgf.genomics.org.cn/

  15. Development and Validation of an Oral Anticoagulation Knowledge Tool (AKT)

    PubMed Central

    Obamiro, Kehinde O.; Chalmers, Leanne; Bereznicki, Luke R. E.

    2016-01-01

    Background Assessing and improving patients’ anticoagulation knowledge can lead to better treatment outcomes. While validated knowledge instruments exist for use in people taking warfarin, these tools are not necessarily applicable to patients taking direct-acting oral anticoagulants. Objective To develop and validate an oral anticoagulation knowledge instrument that is applicable to all oral anticoagulant medications. Methods Ten anticoagulation experts participated in the development of the Anticoagulation Knowledge Tool to ensure content validity. The knowledge instrument was administered to three groups of participants comprising of 44 pharmacists, 50 patients and 50 members of the general public. A subgroup of participants in the patient and pharmacist group were retested approximately 2–3 months after the initial testing. Statistical tests were conducted to determine the validity and reliability of the scale, and item analysis was used to determine the performance of individual questions. Results The 28-item instrument developed had a scale content validity index of 0.92, supporting content validity. The pharmacist group’s mean score was significantly higher than that of the patient group, and the patient group scored significantly higher than the general public group (94% vs 62% vs 20%, respectively; p<0.001), supporting construct validity. Internal consistency reliability was acceptable with a Cronbach’s α value of > 0.7 across the three groups, and the test–retest reliability was confirmed with a Pearson’s correlation coefficient of 0.72 and 0.78 for the pharmacist and patient groups, respectively. Conclusion The Anticoagulation Knowledge Tool is a valid and reliable instrument that can be used in routine clinical practice to assess patients’ anticoagulation knowledge. PMID:27351746

  16. NEEMO 20: Science Training, Operations, and Tool Development

    NASA Technical Reports Server (NTRS)

    Graff, T.; Miller, M.; Rodriguez-Lanetty, M.; Chappell, S.; Naids, A.; Hood, A.; Coan, D.; Abell, P.; Reagan, M.; Janoiko, B.

    2016-01-01

    The 20th mission of the National Aeronautics and Space Administration (NASA) Extreme Environment Mission Operations (NEEMO) was a highly integrated evaluation of operational protocols and tools designed to enable future exploration beyond low-Earth orbit. NEEMO 20 was conducted from the Aquarius habitat off the coast of Key Largo, FL in July 2015. The habitat and its surroundings provide a convincing analog for space exploration. A crew of six (comprised of astronauts, engineers, and habitat technicians) lived and worked in and around the unique underwater laboratory over a mission duration of 14-days. Incorporated into NEEMO 20 was a diverse Science Team (ST) comprised of geoscientists from the Astromaterials Research and Exploration Science (ARES/XI) Division from the Johnson Space Center (JSC), as well as marine scientists from the Department of Biological Sciences at Florida International University (FIU). This team trained the crew on the science to be conducted, defined sampling techniques and operational procedures, and planned and coordinated the science focused Extra Vehicular Activities (EVAs). The primary science objectives of NEEMO 20 was to study planetary sampling techniques and tools in partial gravity environments under realistic mission communication time delays and operational pressures. To facilitate these objectives two types of science sites were employed 1) geoscience sites with available rocks and regolith for testing sampling procedures and tools and, 2) marine science sites dedicated to specific research focused on assessing the photosynthetic capability of corals and their genetic connectivity between deep and shallow reefs. These marine sites and associated research objectives included deployment of handheld instrumentation, context descriptions, imaging, and sampling; thus acted as a suitable proxy for planetary surface exploration activities. This abstract briefly summarizes the scientific training, scientific operations, and tool

  17. The development of a neonatal communication intervention tool.

    PubMed

    Strasheim, Esedra; Kritzinger, Alta; Louw, Brenda

    2011-10-01

    Neonatal communication intervention is important in South Africa, which has an increased prevalence of infants born with risks for disabilities and where the majority of infants live in poverty. Local literature showed a dearth of information on the current service delivery and roles of speech-language therapists (SLTs) and audiologists in neonatal nurseries in the South African context. SLTs have the opportunity to provide the earliest intervention, provided that intervention is well-timed in the neonatal nursery context. The aim of the research was to compile a locally relevant neonatal communication intervention instrument/tool for use by SLTs in neonatal nurseries of public hospitals. The study entailed descriptive, exploratory research. During phase 1, a survey was received from 39 SLTs and 2 audiologists in six provinces. The data revealed that participants performed different roles in neonatal nurseries, which depended on the environment, tools, materials and instrumentation available to them. Many participants were inexperienced, but resourceful in their attempts to adapt tools/materials. Participants expressed needs for culturally appropriate and user-friendly instruments for parent guidance and staff/team training on the topic of developmental care. During phase 2, a tool for parent guidance titled Neonatal communication intervention programme for parents was compiled in English and isiZulu. The programme was piloted by three participants. Suggestions for enhancements of the programme were made, such as providing a glossary of terms, adapting the programme's language and terminology, and providing more illustrations. SLTs and audiologists must contribute to neonatal care of high-risk infants to facilitate development and to support families.

  18. Development and Evaluation of a Riparian Buffer Mapping Tool

    USGS Publications Warehouse

    Milheim, Lesley E.; Claggett, Peter R.

    2008-01-01

    Land use and land cover within riparian areas greatly affect the conditions of adjacent water features. In particular, riparian forests provide many environmental benefits, including nutrient uptake, bank stabilization, steam shading, sediment trapping, aquatic and terrestrial habitat, and stream organic matter. In contrast, residential and commercial development and associated transportation infrastructure increase pollutant and nutrient loading and change the hydrologic characteristics of the landscape, thereby affecting both water quality and habitat. Restoring riparian areas is a popular and cost effective restoration technique to improve and protect water quality. Recognizing this, the Chesapeake Executive Council committed to restoring 10,000 miles of riparian forest buffers throughout the Chesapeake Bay watershed by the year 2010. In 2006, the Chesapeake Executive Council further committed to 'using the best available...tools to identify areas where retention and expansion of forests is most needed to protect water quality'. The Chesapeake Bay watershed encompasses 64,000 square miles, including portions of six States and Washington, D.C. Therefore, the interpretation of remotely sensed imagery provides the only effective technique for comprehensively evaluating riparian forest protection and restoration opportunities throughout the watershed. Although 30-meter-resolution land use and land cover data have proved useful on a regional scale, they have not been equally successful at providing the detail required for local-scale assessment of riparian area characteristics. Use of high-resolution imagery (HRI) provides sufficient detail for local-scale assessments, although at greater cost owing to the cost of the imagery and the skill and time required to process the data. To facilitate the use of HRI for monitoring the extent of riparian forest buffers, the U.S. Forest Service and the U.S. Geological Survey Eastern Geographic Science Center funded the

  19. Development of Doppler Global Velocimetry as a Flow Diagnostics Tool

    NASA Technical Reports Server (NTRS)

    Meyers, James F.

    1995-01-01

    The development of Doppler global velocimetry is described from its inception to its use as a flow diagnostics tool. Its evolution is traced from an elementary one-component laboratory prototype, to a full three-component configuration operating in a wind tunnel at focal distances exceeding 15 m. As part of the developmental process, several wind tunnel flow field investigations were conducted. These included supersonic flow measurements about an oblique shock, subsonic and supersonic measurements of the vortex flow above a delta wing, and three-component measurements of a high-speed jet.

  20. Development of a laboratory extreme-ultraviolet lithography tool

    SciTech Connect

    Tichenor, D.A.; Kubiak, G.D.; Malinowski, M.E.; Stulen, R.H.; Haney, S.J.; Berger, K.W.; Nissen, R.P.; Wilkerson, G.A.; Paul, P.H.; Birtola, S.R.; Jin, P.S.; Arling, R.W.; Ray-Chaudhuri, A.K.; Sweatt, W.C.; Chow, W.W.; Bjorkholm, J.E.; Freeman, R.R.; Himel, M.D.; MacDowell, A.A.; Tennant, D.M.; Fetter, L.A.; Wood, O.R. II; Waskiewicz, W.K.; White, D.L.; Windt, D.L.; Jewell, T.E.

    1994-04-01

    The development of a laboratory EUV lithography tool based on a laser plasma source, a 10x Schwarzchild camera, and a magnetically levitated wafer stage is presented. Interferometric measurements of the camera aberrations are incorporated into physical-optics simulations to estimate the EUV imaging performance of the camera. Experimental results demonstrate the successful matching of five multilayer reflecting surfaces, coated to specification for a wide range of figure and incidence angle requirements. High-resolution, 10x-reduction images of a reflection mask are shown.

  1. The Maize TFome – development of a transcription factor open reading frame collection for functional genomics

    PubMed Central

    Burdo, Brett; Gray, John; Goetting-Minesky, Mary P; Wittler, Bettina; Hunt, Matthew; Li, Tai; Velliquette, David; Thomas, Julie; Gentzel, Irene; Brito, Michael dos Santos; Mejía-Guerra, Maria Katherine; Connolly, Layne N; Qaisi, Dalya; Li, Wei; Casas, Maria I; Doseff, Andrea I; Grotewold, Erich

    2014-01-01

    Establishing the architecture of the gene regulatory networks (GRNs) responsible for controlling the transcription of all genes in an organism is a natural development that follows elucidation of the genome sequence. Reconstruction of the GRN requires the availability of a series of molecular tools and resources that so far have been limited to a few model organisms. One such resource consists of collections of transcription factor (TF) open reading frames (ORFs) cloned into vectors that facilitate easy expression in plants or microorganisms. In this study, we describe the development of a publicly available maize TF ORF collection (TFome) of 2034 clones corresponding to 2017 unique gene models in recombination-ready vectors that make possible the facile mobilization of the TF sequences into a number of different expression vectors. The collection also includes several hundred co-regulators (CoREGs), which we classified into well-defined families, and for which we propose here a standard nomenclature, as we have previously done for TFs. We describe the strategies employed to overcome the limitations associated with cloning ORFs from a genome that remains incompletely annotated, with a partial full-length cDNA set available, and with many TF/CoREG genes lacking experimental support. In many instances this required the combination of genome-wide expression data with gene synthesis approaches. The strategies developed will be valuable for developing similar resources for other agriculturally important plants. Information on all the clones generated is available through the GRASSIUS knowledgebase (http://grassius.org/). PMID:25053252

  2. Genomics Tools Available For Unravelling Mechanisms Underlying Agronomical Traits in Strawberry With More To Come

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the last few years, high-throughput genomics promised to bridge the gap between plant physiology and plant sciences. In addition, high-throughput genotyping technologies facilitate marker-based selection for better performing genotypes. In strawberry, Fragaria vesca was the first reference sequen...

  3. Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the last few years, high-throughput genomics promised to bridge the gap between plant physiology and plant sciences. In addition, high-throughput genotyping technologies facilitate marker-based selection for better performing genotypes. In strawberry, Fragaria vesca was the first reference sequen...

  4. Candidate fire blight resistance genes in Malus identified with the use of genomic tools and approaches

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The goal of this research is to utilize current advances in Rosaceae genomics to identify DNA markers for use in marker-assisted selection of durable resistance to fire blight. Candidate fire blight resistance genes were selected and ranked based upon differential expression after inoculation with ...

  5. The Qatar genome: a population-specific tool for precision medicine in the Middle East

    PubMed Central

    Fakhro, Khalid A; Staudt, Michelle R; Ramstetter, Monica Denise; Robay, Amal; Malek, Joel A; Badii, Ramin; Al-Marri, Ajayeb Al-Nabet; Khalil, Charbel Abi; Al-Shakaki, Alya; Chidiac, Omar; Stadler, Dora; Zirie, Mahmoud; Jayyousi, Amin; Salit, Jacqueline; Mezey, Jason G; Crystal, Ronald G; Rodriguez-Flores, Juan L

    2016-01-01

    Reaching the full potential of precision medicine depends on the quality of personalized genome interpretation. In order to facilitate precision medicine in regions of the Middle East and North Africa (MENA), a population-specific genome for the indigenous Arab population of Qatar (QTRG) was constructed by incorporating allele frequency data from sequencing of 1,161 Qataris, representing 0.4% of the population. A total of 20.9 million single nucleotide polymorphisms (SNPs) and 3.1 million indels were observed in Qatar, including an average of 1.79% novel variants per individual genome. Replacement of the GRCh37 standard reference with QTRG in a best practices genome analysis workflow resulted in an average of 7* deeper coverage depth (an improvement of 23%) and 756,671 fewer variants on average, a reduction of 16% that is attributed to common Qatari alleles being present in QTRG. The benefit for using QTRG varies across ancestries, a factor that should be taken into consideration when selecting an appropriate reference for analysis. PMID:27408750

  6. Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico.

    PubMed

    Silva-Zolezzi, Irma; Hidalgo-Miranda, Alfredo; Estrada-Gil, Jesus; Fernandez-Lopez, Juan Carlos; Uribe-Figueroa, Laura; Contreras, Alejandra; Balam-Ortiz, Eros; del Bosque-Plata, Laura; Velazquez-Fernandez, David; Lara, Cesar; Goya, Rodrigo; Hernandez-Lemus, Enrique; Davila, Carlos; Barrientos, Eduardo; March, Santiago; Jimenez-Sanchez, Gerardo

    2009-05-26

    Mexico is developing the basis for genomic medicine to improve healthcare of its population. The extensive study of genetic diversity and linkage disequilibrium structure of different populations has made it possible to develop tagging and imputation strategies to comprehensively analyze common genetic variation in association studies of complex diseases. We assessed the benefit of a Mexican haplotype map to improve identification of genes related to common diseases in the Mexican population. We evaluated genetic diversity, linkage disequilibrium patterns, and extent of haplotype sharing using genomewide data from Mexican Mestizos from regions with different histories of admixture and particular population dynamics. Ancestry was evaluated by including 1 Mexican Amerindian group and data from the HapMap. Our results provide evidence of genetic differences between Mexican subpopulations that should be considered in the design and analysis of association studies of complex diseases. In addition, these results support the notion that a haplotype map of the Mexican Mestizo population can reduce the number of tag SNPs required to characterize common genetic variation in this population. This is one of the first genomewide genotyping efforts of a recently admixed population in Latin America.

  7. Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico

    PubMed Central

    Silva-Zolezzi, Irma; Hidalgo-Miranda, Alfredo; Estrada-Gil, Jesus; Fernandez-Lopez, Juan Carlos; Uribe-Figueroa, Laura; Contreras, Alejandra; Balam-Ortiz, Eros; del Bosque-Plata, Laura; Velazquez-Fernandez, David; Lara, Cesar; Goya, Rodrigo; Hernandez-Lemus, Enrique; Davila, Carlos; Barrientos, Eduardo; March, Santiago; Jimenez-Sanchez, Gerardo

    2009-01-01

    Mexico is developing the basis for genomic medicine to improve healthcare of its population. The extensive study of genetic diversity and linkage disequilibrium structure of different populations has made it possible to develop tagging and imputation strategies to comprehensively analyze common genetic variation in association studies of complex diseases. We assessed the benefit of a Mexican haplotype map to improve identification of genes related to common diseases in the Mexican population. We evaluated genetic diversity, linkage disequilibrium patterns, and extent of haplotype sharing using genomewide data from Mexican Mestizos from regions with different histories of admixture and particular population dynamics. Ancestry was evaluated by including 1 Mexican Amerindian group and data from the HapMap. Our results provide evidence of genetic differences between Mexican subpopulations that should be considered in the design and analysis of association studies of complex diseases. In addition, these results support the notion that a haplotype map of the Mexican Mestizo population can reduce the number of tag SNPs required to characterize common genetic variation in this population. This is one of the first genomewide genotyping efforts of a recently admixed population in Latin America. PMID:19433783

  8. Development of Next Generation Multiphase Pipe Flow Prediction Tools

    SciTech Connect

    Cem Sarica; Holden Zhang

    2006-05-31

    The developments of oil and gas fields in deep waters (5000 ft and more) will become more common in the future. It is inevitable that production systems will operate under multiphase flow conditions (simultaneous flow of gas, oil and water possibly along with sand, hydrates, and waxes). Multiphase flow prediction tools are essential for every phase of hydrocarbon recovery from design to operation. Recovery from deep-waters poses special challenges and requires accurate multiphase flow predictive tools for several applications, including the design and diagnostics of the production systems, separation of phases in horizontal wells, and multiphase separation (topside, seabed or bottom-hole). It is crucial for any multiphase separation technique, either at topside, seabed or bottom-hole, to know inlet conditions such as flow rates, flow patterns, and volume fractions of gas, oil and water coming into the separation devices. Therefore, the development of a new generation of multiphase flow predictive tools is needed. The overall objective of the proposed study is to develop a unified model for gas-oil-water three-phase flow in wells, flow lines, and pipelines to predict flow characteristics such as flow patterns, phase distributions, and pressure gradient encountered during petroleum production at different flow conditions (pipe diameter and inclination, fluid properties and flow rates). In the current multiphase modeling approach, flow pattern and flow behavior (pressure gradient and phase fractions) prediction modeling are separated. Thus, different models based on different physics are employed, causing inaccuracies and discontinuities. Moreover, oil and water are treated as a pseudo single phase, ignoring the distinct characteristics of both oil and water, and often resulting in inaccurate design that leads to operational problems. In this study, a new model is being developed through a theoretical and experimental study employing a revolutionary approach. The

  9. Advanced Reach Tool (ART): development of the mechanistic model.

    PubMed

    Fransman, Wouter; Van Tongeren, Martie; Cherrie, John W; Tischer, Martin; Schneider, Thomas; Schinkel, Jody; Kromhout, Hans; Warren, Nick; Goede, Henk; Tielemans, Erik

    2011-11-01

    This paper describes the development of the mechanistic model within a collaborative project, referred to as the Advanced REACH Tool (ART) project, to develop a tool to model inhalation exposure for workers sharing similar operational conditions across different industries and locations in Europe. The ART mechanistic model is based on a conceptual framework that adopts a source receptor approach, which describes the transport of a contaminant from the source to the receptor and defines seven independent principal modifying factors: substance emission potential, activity emission potential, localized controls, segregation, personal enclosure, surface contamination, and dispersion. ART currently differentiates between three different exposure types: vapours, mists, and dust (fumes, fibres, and gases are presently excluded). Various sources were used to assign numerical values to the multipliers to each modifying factor. The evidence used to underpin this assessment procedure was based on chemical and physical laws. In addition, empirical data obtained from literature were used. Where this was not possible, expert elicitation was applied for the assessment procedure. Multipliers for all modifying factors were peer reviewed by leading experts from industry, research institutes, and public authorities across the globe. In addition, several workshops with experts were organized to discuss the proposed exposure multipliers. The mechanistic model is a central part of the ART tool and with advancing knowledge on exposure, determinants will require updates and refinements on a continuous basis, such as the effect of worker behaviour on personal exposure, 'best practice' values that describe the maximum achievable effectiveness of control measures, the intrinsic emission potential of various solid objects (e.g. metal, glass, plastics, etc.), and extending the applicability domain to certain types of exposures (e.g. gas, fume, and fibre exposure).

  10. PrimerDesign-M: A multiple-alignment based multiple-primer design tool for walking across variable genomes

    SciTech Connect

    Yoon, Hyejin; Leitner, Thomas

    2014-12-17

    Analyses of entire viral genomes or mtDNA requires comprehensive design of many primers across their genomes. In addition, simultaneous optimization of several DNA primer design criteria may improve overall experimental efficiency and downstream bioinformatic processing. To achieve these goals, we developed PrimerDesign-M. It includes several options for multiple-primer design, allowing researchers to efficiently design walking primers that cover long DNA targets, such as entire HIV-1 genomes, and that optimizes primers simultaneously informed by genetic diversity in multiple alignments and experimental design constraints given by the user. PrimerDesign-M can also design primers that include DNA barcodes and minimize primer dimerization. PrimerDesign-M finds optimal primers for highly variable DNA targets and facilitates design flexibility by suggesting alternative designs to adapt to experimental conditions.

  11. PrimerDesign-M: A multiple-alignment based multiple-primer design tool for walking across variable genomes

    DOE PAGES

    Yoon, Hyejin; Leitner, Thomas

    2014-12-17

    Analyses of entire viral genomes or mtDNA requires comprehensive design of many primers across their genomes. In addition, simultaneous optimization of several DNA primer design criteria may improve overall experimental efficiency and downstream bioinformatic processing. To achieve these goals, we developed PrimerDesign-M. It includes several options for multiple-primer design, allowing researchers to efficiently design walking primers that cover long DNA targets, such as entire HIV-1 genomes, and that optimizes primers simultaneously informed by genetic diversity in multiple alignments and experimental design constraints given by the user. PrimerDesign-M can also design primers that include DNA barcodes and minimize primer dimerization. PrimerDesign-Mmore » finds optimal primers for highly variable DNA targets and facilitates design flexibility by suggesting alternative designs to adapt to experimental conditions.« less

  12. Development of a Logging Tool for Muon Radiography

    NASA Astrophysics Data System (ADS)

    Suenaga, H.; Kiho, K.; Miyakawa, K.; Tanaka, H.

    2012-04-01

    A research for high level radioactive waste disposal should investigate geological structure and saturation change of rock mass around a disposal cavern. In the CO2 geological storage and the underground storage of crude oil, natural gas or liquefied petroleum gas (LPG), it is necessary to monitor an upward migration of a gaseous fluid which is stored in underground. For an investigation of slope stability, it is effective to evaluate a high saturation area in the ground's pore space as the area should be the same as that of a rainfall infiltration. Since these phenomena could be evaluated by a measurement of a density variation in underground rock, an application of muon radiography is highly prospective. The Central Research Institute of Electric Power Industry (CRIEPI) has a plan to conduct a field experiment to evaluate an applicability of the muon radiography to engineering geology in cooperation with Electric Power Development Co., Ltd. (J-POWER). The field experiment will be performed this year in slope topography. If the applicability will be revealed as a result of the field experiment, CRIEPI will start a research on development of a logging tool which can measure muon in a borehole. We plan to build a prototype of the logging tool in around three years and will put it into practical use in around five years.

  13. Development of the Central Dogma Concept Inventory (CDCI) Assessment Tool

    PubMed Central

    Newman, Dina L.; Snyder, Christopher W.; Fisk, J. Nick; Wright, L. Kate

    2016-01-01

    Scientific teaching requires scientifically constructed, field-tested instruments to accurately evaluate student thinking and gauge teacher effectiveness. We have developed a 23-question, multiple select–format assessment of student understanding of the essential concepts of the central dogma of molecular biology that is appropriate for all levels of undergraduate biology. Questions for the Central Dogma Concept Inventory (CDCI) tool were developed and iteratively revised based on student language and review by experts. The ability of the CDCI to discriminate between levels of understanding of the central dogma is supported by field testing (N = 54), and large-scale beta testing (N = 1733). Performance on the assessment increased with experience in biology; scores covered a broad range and showed no ceiling effect, even with senior biology majors, and pre/posttesting of a single class focused on the central dogma showed significant improvement. The multiple-select format reduces the chances of correct answers by random guessing, allows students at different levels to exhibit the extent of their knowledge, and provides deeper insight into the complexity of student thinking on each theme. To date, the CDCI is the first tool dedicated to measuring student thinking about the central dogma of molecular biology, and version 5 is ready to use. PMID:27055775

  14. Simulation of spin dynamics: a tool in MRI system development

    NASA Astrophysics Data System (ADS)

    Stöcker, Tony; Vahedipour, Kaveh; Shah, N. Jon

    2011-05-01

    Magnetic Resonance Imaging (MRI) is a routine diagnostic tool in the clinics and the method of choice in soft-tissue contrast medical imaging. It is an important tool in neuroscience to investigate structure and function of the living brain on a systemic level. The latter is one of the driving forces to further develop MRI technology, as neuroscience especially demands higher spatiotemporal resolution which is to be achieved through increasing the static main magnetic field, B0. Although standard MRI is a mature technology, ultra high field (UHF) systems, at B0 >= 7 T, offer space for new technical inventions as the physical conditions dramatically change. This work shows that the development strongly benefits from computer simulations of the measurement process on the basis of a semi-classical, nuclear spin-1/2 treatment given by the Bloch equations. Possible applications of such simulations are outlined, suggesting new solutions to the UHF-specific inhomogeneity problems of the static main field as well as the high-frequency transmit field.

  15. Development of the Central Dogma Concept Inventory (CDCI) Assessment Tool.

    PubMed

    Newman, Dina L; Snyder, Christopher W; Fisk, J Nick; Wright, L Kate

    2016-01-01

    Scientific teaching requires scientifically constructed, field-tested instruments to accurately evaluate student thinking and gauge teacher effectiveness. We have developed a 23-question, multiple select-format assessment of student understanding of the essential concepts of the central dogma of molecular biology that is appropriate for all levels of undergraduate biology. Questions for the Central Dogma Concept Inventory (CDCI) tool were developed and iteratively revised based on student language and review by experts. The ability of the CDCI to discriminate between levels of understanding of the central dogma is supported by field testing (N= 54), and large-scale beta testing (N= 1733). Performance on the assessment increased with experience in biology; scores covered a broad range and showed no ceiling effect, even with senior biology majors, and pre/posttesting of a single class focused on the central dogma showed significant improvement. The multiple-select format reduces the chances of correct answers by random guessing, allows students at different levels to exhibit the extent of their knowledge, and provides deeper insight into the complexity of student thinking on each theme. To date, the CDCI is the first tool dedicated to measuring student thinking about the central dogma of molecular biology, and version 5 is ready to use. PMID:27055775

  16. Developer Tools for Evaluating Multi-Objective Algorithms

    NASA Technical Reports Server (NTRS)

    Giuliano, Mark E.; Johnston, Mark D.

    2011-01-01

    Multi-objective algorithms for scheduling offer many advantages over the more conventional single objective approach. By keeping user objectives separate instead of combined, more information is available to the end user to make trade-offs between competing objectives. Unlike single objective algorithms, which produce a single solution, multi-objective algorithms produce a set of solutions, called a Pareto surface, where no solution is strictly dominated by another solution for all objectives. From the end-user perspective a Pareto-surface provides a tool for reasoning about trade-offs between competing objectives. From the perspective of a software developer multi-objective algorithms provide an additional challenge. How can you tell if one multi-objective algorithm is better than another? This paper presents formal and visual tools for evaluating multi-objective algorithms and shows how the developer process of selecting an algorithm parallels the end-user process of selecting a solution for execution out of the Pareto-Surface.

  17. Developing Tools and Techniques to Increase Communication Effectiveness

    NASA Technical Reports Server (NTRS)

    Hayes, Linda A.; Peterson, Doug

    1997-01-01

    The Public Affairs Office (PAO) of the Johnson Space Center (JSC) is responsible for communicating current JSC Space Program activities as well as goals and objectives to the American Public. As part of the 1996 Strategic Communications Plan, a review of PAO' s current communication procedures was conducted. The 1996 Summer Faculty Fellow performed research activities to support this effort by reviewing current research concerning NASA/JSC's customers' perceptions and interests, developing communications tools which enable PAO to more effectively inform JSC customers about the Space Program, and proposing a process for developing and using consistent messages throughout PAO. Note that this research does not attempt to change or influence customer perceptions or interests but, instead, incorporates current customer interests into PAO's communication process.

  18. The Development of NASA's Low Thrust Trajectory Tool Set

    NASA Technical Reports Server (NTRS)

    Sims, Jon; Artis, Gwen; Kos, Larry

    2006-01-01

    Highly efficient electric propulsion systems can enable interesting classes of missions; unfortunately, they provide only a limited amount of thrust. Low-thrust (LT) trajectories are much more difficult to design than impulsive-type (chemical propulsion) trajectories. Previous low-thrust (LT) trajectory optimization software was often difficult to use, often had difficulties converging, and was somewhat limited in the types of missions it could support. A new state-of-the-art suite (toolbox) of low-thrust (LT) tools along with improved algorithms and methods was developed by NASA's MSFC, JPL, JSC, and GRC to address the needs of our customers to help foster technology development in the areas of advanced LT propulsion systems, and to facilitate generation of similar results by different analysts.

  19. Environmental epigenetics: A promising venue for developing next-generation pollution biomonitoring tools in marine invertebrates.

    PubMed

    Suarez-Ulloa, Victoria; Gonzalez-Romero, Rodrigo; Eirin-Lopez, Jose M

    2015-09-15

    Environmental epigenetics investigates the cause-effect relationships between specific environmental factors and the subsequent epigenetic modifications triggering adaptive responses in the cell. Given the dynamic and potentially reversible nature of the different types of epigenetic marks, environmental epigenetics constitutes a promising venue for developing fast and sensible biomonitoring programs. Indeed, several epigenetic biomarkers have been successfully developed and applied in traditional model organisms (e.g., human and mouse). Nevertheless, the lack of epigenetic knowledge in other ecologically and environmentally relevant organisms has hampered the application of these tools in a broader range of ecosystems, most notably in the marine environment. Fortunately, that scenario is now changing thanks to the growing availability of complete reference genome sequences along with the development of high-throughput DNA sequencing and bioinformatic methods. Altogether, these resources make the epigenetic study of marine organisms (and more specifically marine invertebrates) a reality. By building on this knowledge, the present work provides a timely perspective highlighting the extraordinary potential of environmental epigenetic analyses as a promising source of rapid and sensible tools for pollution biomonitoring, using marine invertebrates as sentinel organisms. This strategy represents an innovative, groundbreaking approach, improving the conservation and management of natural resources in the oceans.

  20. Molecular confirmation of the genomic constitution of Douglasdeweya (Triticeae: Poaceae): demonstration of the utility of the 5S rDNA sequence as a tool for haplome identification.

    PubMed

    Baum, Bernard R; Johnson, Douglas A

    2008-06-01

    A new genus Douglasdeweya containing the two species, Douglasdeweya deweyi and D. wangii was published in 2005 by Yen et al. based upon the results of cytogenetical and morphological findings. The genome constitution of Douglasdeweya-PPStSt-allowed its segregation from the genus Pseudoroegneria which contains the StSt or StStStSt genomes. Our previous work had demonstrated the utility of using 5S rDNA units, especially the non-transcribed spacer sequence variation, for the resolution of genomes (haplomes) previously established by cytology. Here, we show that sequence analysis of the 5S DNA units from these species strongly supports the proposed species relationships of Yen et al. (Can J Bot 83:413-419, 2005), i.e., the PP genome from Agropyron and the StSt genome from Pseudoroegneria. Analysis of the 5S rDNA units constitutes a powerful tool for genomic research especially in the Triticeae. PMID:18421479

  1. Comparative Genome Analysis in the Integrated Microbial Genomes(IMG) System

    SciTech Connect

    Kyrpides, Nikos C.; Markowitz, Victor M.

    2006-03-01

    Comparative genome analysis is critical for the effectiveexploration of a rapidly growing number of complete and draft sequencesfor microbial genomes. The Integrated Microbial Genomes (IMG) system(img.jgi.doe.gov) has been developed as a community resource thatprovides support for comparative analysis of microbial genomes in anintegrated context. IMG allows users to navigate the multidimensionalmicrobial genome data space and focus their analysis on a subset ofgenes, genomes, and functions of interest. IMG provides graphicalviewers, summaries and occurrence profile tools for comparing genes,pathways and functions (terms) across specific genomes. Genes can befurther examined using gene neighborhoods and compared with sequencealignment tools.

  2. T346Hunter: a novel web-based tool for the prediction of type III, type IV and type VI secretion systems in bacterial genomes.

    PubMed

    Martínez-García, Pedro Manuel; Ramos, Cayo; Rodríguez-Palenzuela, Pablo

    2015-01-01

    T346Hunter (Type Three, Four and Six secretion system Hunter) is a web-based tool for the identification and localisation of type III, type IV and type VI secretion systems (T3SS, T4SS and T6SS, respectively) clusters in bacterial genomes. Non-flagellar T3SS (NF-T3SS) and T6SS are complex molecular machines that deliver effector proteins from bacterial cells into the environment or into other eukaryotic or prokaryotic cells, with significant implications for pathogenesis of the strains encoding them. Meanwhile, T4SS is a more functionally diverse system, which is involved in not only effector translocation but also conjugation and DNA uptake/release. Development of control strategies against bacterial-mediated diseases requires genomic identification of the virulence arsenal of pathogenic bacteria, with T3SS, T4SS and T6SS being major determinants in this regard. Therefore, computational methods for systematic identification of these specialised machines are of particular interest. With the aim of facilitating this task, T346Hunter provides a user-friendly web-based tool for the prediction of T3SS, T4SS and T6SS clusters in newly sequenced bacterial genomes. After inspection of the available scientific literature, we constructed a database of hidden Markov model (HMM) protein profiles and sequences representing the various components of T3SS, T4SS and T6SS. T346Hunter performs searches of such a database against user-supplied bacterial sequences and localises enriched regions in any of these three types of secretion systems. Moreover, through the T346Hunter server, users can visualise the predicted clusters obtained for approximately 1700 bacterial chromosomes and plasmids. T346Hunter offers great help to researchers in advancing their understanding of the biological mechanisms in which these sophisticated molecular machines are involved. T346Hunter is freely available at http://bacterial-virulence-factors.cbgp.upm.es/T346Hunter.

  3. Development of Nylon Based FDM Filament for Rapid Tooling Application

    NASA Astrophysics Data System (ADS)

    Singh, R.; Singh, S.

    2014-04-01

    There has been critical need for development of cost effective nylon based wire to be used as feed stock filament for fused deposition modelling (FDM) machine. But hitherto, very less work has been reported for development of alternate solution of acrylonitrile butadiene styrene (ABS) based wire which is presently used in most of FDM machines. The present research work is focused on development of nylon based wire as an alternative of ABS wire (which is to be used as feedstock filament on FDM) without changing any hardware or software of machine. For the present study aluminium oxide (Al2O3) as additive in different proportion has been used with nylon fibre. Single screw extruder was used for wire preparation and wire thus produced was tested on FDM. Mechanical properties i.e. tensile strength and percentage elongation of finally developed wire have been optimized by Taguchi L9 technique. The work represented major development in reducing cost and time in rapid tooling applications.

  4. A CROSS-SPECIES APPROACH TO USING GENOMICS TOOLS IN AQUATIC TOXICOLOGY

    EPA Science Inventory

    Microarray technology has proven to be a useful tool for analyzing the transcriptome of various organisms representing conditions such as disease states, developmental stages, and responses to chemical exposure. Most commercially available arrays are limited to organisms that ha...

  5. MosaicSolver: a tool for determining recombinants of viral genomes from pileup data

    PubMed Central

    Wood, Graham R.; Ryabov, Eugene V.; Fannon, Jessica M.; Moore, Jonathan D.; Evans, David J.; Burroughs, Nigel

    2014-01-01

    Viral recombination is a key evolutionary mechanism, aiding escape from host immunity, contributing to changes in tropism and possibly assisting transmission across species barriers. The ability to determine whether recombination has occurred and to locate associated specific recombination junctions is thus of major importance in understanding emerging diseases and pathogenesis. This paper describes a method for determining recombinant mosaics (and their proportions) originating from two parent genomes, using high-throughput sequence data. The method involves setting the problem geometrically and the use of appropriately constrained quadratic programming. Recombinants of the honeybee deformed wing virus and the Varroa destructor virus-1 are inferred to illustrate the method from both siRNAs and reads sampling the viral genome population (cDNA library); our results are confirmed experimentally. Matlab software (MosaicSolver) is available. PMID:25120266

  6. MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models.

    PubMed

    Aurich, Maike K; Fleming, Ronan M T; Thiele, Ines

    2016-01-01

    Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. With the MetaboTools, we make our methods available to the broader scientific community. The MetaboTools consist of a protocol, a toolbox, and tutorials of two use cases. The protocol describes, in a step-wise manner, the workflow of data integration, and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorials explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, the MetaboTools constitute a comprehensive guide to the intra-model analysis of extracellular metabolomic data from microbial, plant, or human cells. This computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community. PMID:27536246

  7. MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models

    PubMed Central

    Aurich, Maike K.; Fleming, Ronan M. T.; Thiele, Ines

    2016-01-01

    Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. With the MetaboTools, we make our methods available to the broader scientific community. The MetaboTools consist of a protocol, a toolbox, and tutorials of two use cases. The protocol describes, in a step-wise manner, the workflow of data integration, and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorials explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, the MetaboTools constitute a comprehensive guide to the intra-model analysis of extracellular metabolomic data from microbial, plant, or human cells. This computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community. PMID:27536246

  8. MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models

    DOE PAGES

    Aurich, Maike K.; Fleming, Ronan M. T.; Thiele, Ines

    2016-08-03

    Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. With the MetaboTools, we make our methods available to the broader scientific community. The MetaboTools consist of a protocol, a toolbox, and tutorials of two use cases. The protocol describes, in a step-wise manner, the workflow of data integration, and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorialsmore » explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, the MetaboTools constitute a comprehensive guide to the intra-model analysis of extracellular metabolomic data from microbial, plant, or human cells. In conclusion, this computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community.« less

  9. Infectious diseases of marine molluscs and host responses as revealed by genomic tools.

    PubMed

    Guo, Ximing; Ford, Susan E

    2016-03-01

    More and more infectious diseases affect marine molluscs. Some diseases have impacted commercial species including MSX and Dermo of the eastern oyster, QPX of hard clams, withering syndrome of abalone and ostreid herpesvirus 1 (OsHV-1) infections of many molluscs. Although the exact transmission mechanisms are not well understood, human activities and associated environmental changes often correlate with increased disease prevalence. For instance, hatcheries and large-scale aquaculture create high host densities, which, along with increasing ocean temperature, might have contributed to OsHV-1 epizootics in scallops and oysters. A key to understanding linkages between the environment and disease is to understand how the environment affects the host immune system. Although we might be tempted to downplay the role of immunity in invertebrates, recent advances in genomics have provided insights into host and parasite genomes and revealed surprisingly sophisticated innate immune systems in molluscs. All major innate immune pathways are found in molluscs with many immune receptors, regulators and effectors expanded. The expanded gene families provide great diversity and complexity in innate immune response, which may be key to mollusc's defence against diverse pathogens in the absence of adaptive immunity. Further advances in host and parasite genomics should improve our understanding of genetic variation in parasite virulence and host disease resistance. PMID:26880838

  10. Crosscutting Development- EVA Tools and Geology Sample Acquisition

    NASA Technical Reports Server (NTRS)

    2011-01-01

    Exploration to all destinations has at one time or another involved the acquisition and return of samples and context data. Gathered at the summit of the highest mountain, the floor of the deepest sea, or the ice of a polar surface, samples and their value (both scientific and symbolic) have been a mainstay of Earthly exploration. In manned spaceflight exploration, the gathering of samples and their contextual information has continued. With the extension of collecting activities to spaceflight destinations comes the need for geology tools and equipment uniquely designed for use by suited crew members in radically different environments from conventional field geology. Beginning with the first Apollo Lunar Surface Extravehicular Activity (EVA), EVA Geology Tools were successfully used to enable the exploration and scientific sample gathering objectives of the lunar crew members. These early designs were a step in the evolution of Field Geology equipment, and the evolution continues today. Contemporary efforts seek to build upon and extend the knowledge gained in not only the Apollo program but a wealth of terrestrial field geology methods and hardware that have continued to evolve since the last lunar surface EVA. This paper is presented with intentional focus on documenting the continuing evolution and growing body of knowledge for both engineering and science team members seeking to further the development of EVA Geology. Recent engineering development and field testing efforts of EVA Geology equipment for surface EVA applications are presented, including the 2010 Desert Research and Technology Studies (Desert RATs) field trial. An executive summary of findings will also be presented, detailing efforts recommended for exotic sample acquisition and pre-return curation development regardless of planetary or microgravity destination.

  11. Developing improved durum wheat germplasm by altering the cytoplasmic genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In eukaryotic organisms, nuclear and cytoplasmic genomes interact to drive cellular functions. These genomes have co-evolved to form specific nuclear-cytoplasmic interactions that are essential to the origin, success, and evolution of diploid and polyploid species. Hundreds of genetic diseases in h...

  12. Child Development and Structural Variation in the Human Genome

    ERIC Educational Resources Information Center

    Zhang, Ying; Haraksingh, Rajini; Grubert, Fabian; Abyzov, Alexej; Gerstein, Mark; Weissman, Sherman; Urban, Alexander E.

    2013-01-01

    Structural variation of the human genome sequence is the insertion, deletion, or rearrangement of stretches of DNA sequence sized from around 1,000 to millions of base pairs. Over the past few years, structural variation has been shown to be far more common in human genomes than previously thought. Very little is currently known about the effects…

  13. Experimental Stage Separation Tool Development in NASA Langley's Aerothermodynamics Laboratory

    NASA Technical Reports Server (NTRS)

    Murphy, Kelly J.; Scallion, William I.

    2005-01-01

    As part of the research effort at NASA in support of the stage separation and ascent aerothermodynamics research program, proximity testing of a generic bimese wing-body configuration was conducted in NASA Langley's Aerothermodynamics Laboratory in the 20-Inch Mach 6 Air Tunnel. The objective of this work is the development of experimental tools and testing methodologies to apply to hypersonic stage separation problems for future multi-stage launch vehicle systems. Aerodynamic force and moment proximity data were generated at a nominal Mach number of 6 over a small range of angles of attack. The generic bimese configuration was tested in a belly-to-belly and back-to-belly orientation at 86 relative proximity locations. Over 800 aerodynamic proximity data points were taken to serve as a database for code validation. Longitudinal aerodynamic data generated in this test program show very good agreement with viscous computational predictions. Thus a framework has been established to study separation problems in the hypersonic regime using coordinated experimental and computational tools.

  14. Genomics of CpG methylation in developing and developed zebrafish.

    PubMed

    McGaughey, David M; Abaan, Hatice Ozel; Miller, Ryan M; Kropp, Peter A; Brody, Lawrence C

    2014-05-01

    DNA methylation is a dynamic process through which specific chromatin modifications can be stably transmitted from parent to daughter cells. A large body of work has suggested that DNA methylation influences gene expression by silencing gene promoters. However, these conclusions were drawn from data focused mostly on promoter regions. Regarding the entire genome, it is unclear how methylation and gene transcription patterns are related during vertebrate development. To identify the genome-wide distribution of CpG methylation, we created series of high-resolution methylome maps of Danio rerio embryos during development and in mature, differentiated tissues. We found that embryonic and terminal tissues have unique methylation signatures in CpG islands and repetitive sequences. Fully differentiated tissues have increased CpG and LTR methylation and decreased SINE methylation relative to embryonic tissues. Unsupervised clustering analyses reveal that the embryonic and terminal tissues can be classified solely by their methylation patterning. Novel analyses also identify a previously undescribed genome-wide exon methylation signature. We also compared whole genome methylation with genome-wide mRNA expression levels using publicly available RNA-seq datasets. These comparisons revealed previously unrecognized relationships between gene expression, alternative splicing, and exon methylation. Surprisingly, we found that exonic methylation is a better predictor of mRNA expression level than promoter methylation. We also found that transcriptionally skipped exons have significantly less methylation than retained exons. Our integrative analyses reveal highly complex interplay between gene expression, alternative splicing, development, and methylation patterning in zebrafish. PMID:24657902

  15. Developing tools and strategies for communicating climate change

    NASA Astrophysics Data System (ADS)

    Bader, D.; Yam, E. M.; Perkins, L.

    2011-12-01

    Research indicates that the public views zoos and aquariums as reliable and trusted sources for information on conservation. Additionally, visiting zoos and aquariums helps people reconsider their connections to conservation issues and solutions. The Aquarium of the Pacific, an AZA-accredited institution that serves the most ethnically diverse population of all aquariums in the nation, is using exhibit space, technology, public programming, and staff professional development to present a model for how aquariums can promote climate literacy. Our newest galleries and programs are designed to immerse our visitors in experiences that connect our live animal collection to larger themes on ocean change. The Aquarium is supporting our new programming with a multifaceted staff professional development that exposes our interpretive staff to current climate science and researchers as well as current social science on public perception of climate science. Our staff also leads workshops for scientists; these sessions allow us to examine learning theory and develop tools to communicate science and controversial subjects effectively. Through our partnerships in the science, social science, and informal science education communities, we are working to innovate and develop best practices in climate communication.

  16. Gene prediction and annotation in Penstemon (Plantaginaceae): A workflow for marker development from extremely low-coverage genome sequencing1

    PubMed Central

    Blischak, Paul D.; Wenzel, Aaron J.; Wolfe, Andrea D.

    2014-01-01

    • Premise of the study: Penstemon (Plantaginaceae) is a large and diverse genus endemic to North America. However, determining the phylogenetic relationships among its 280 species has been difficult due to its recent evolutionary radiation. The development of a large, multilocus data set can help to resolve this challenge. • Methods: Using both previously sequenced genomic libraries and our own low-coverage whole-genome shotgun sequencing libraries, we used the MAKER2 Annotation Pipeline to identify gene regions for the development of sequencing loci from six extremely low-coverage Penstemon genomes (∼0.005×–0.007×). We also compared this approach to BLAST searches, and conducted analyses to characterize sequence divergence across the species sequenced. • Results: Annotations and gene predictions were successfully added to more than 10,000 contigs for potential use in downstream primer design. Primers were then designed for chloroplast, mitochondrial, and nuclear loci from these annotated sequences. MAKER2 identified longer gene regions in all six Penstemon genomes when compared with BLASTN and BLASTX searches. The average level of sequence divergence among the six species was 7.14%. • Discussion: Combining bioinformatics tools into a workflow that produces annotations can be useful for creating potential phylogenetic markers from thousands of sequences even when genome coverage is extremely low and reference data are only available from distant relatives. Furthermore, the output from MAKER2 contains information about important gene features, such as exon boundaries, and can be easily integrated with visualization tools to facilitate the process of marker development. PMID:25506519

  17. Rotary Percussive Sample Acquisition Tool (SAT): Hardware Development and Testing

    NASA Technical Reports Server (NTRS)

    Klein, Kerry; Badescu, Mircea; Haddad, Nicolas; Shiraishi, Lori; Walkemeyer, Phillip

    2012-01-01

    In support of a potential Mars Sample Return (MSR) mission an Integrated Mars Sample Acquisition and Handling (IMSAH) architecture has been proposed to provide a means for Rover-based end-to-end sample capture and caching. A key enabling feature of the architecture is the use of a low mass sample Acquisition Tool (SAT) that is capable of drilling and capturing rock cores directly within a sample tube in order to maintain sample integrity and prevent contamination across the sample chain. As such, this paper will describe the development and testing of a low mass rotary percussive SAT that has been shown to provide a means for core generation, fracture, and capture.

  18. Genomic Variants and Variations in Malformations of Cortical Development

    PubMed Central

    Jamuar, Saumya S.; Walsh, Christopher A.

    2015-01-01

    Malformations of cortical development (MCD) are a common cause of neurodevelopmental delay and epilepsy and are caused by disruptions in the normal development of the cerebral cortex. Advances in genetic tools have expanded our understanding of the genetics of these malformations over the past few years, with a number of new causative genes identified in patients with MCD. In addition, there has been a vast expansion in the phenotypic characterization of the known genes, with a wide range as well as severity of malformations being reported. There is increasing evidence of role of de novo mutations, including those occurring post fertilization, in MCD. These “somatic” mutations may not be detectable by traditional methods of genetic testing performed on blood DNA. Identification of the genetic etiology can help in guiding families in future pregnancies. Recent work has highlighted how elucidation of key molecular pathway can also allow for targeted therapeutic interventions. PMID:26022163

  19. New genome sequence data and molecular tools promote the use of photosynthetic and edible cyanobacteria in bioregenerative systems to support human space exploration.

    NASA Astrophysics Data System (ADS)

    Leys, Natalie; Morin, Nicolas; Janssen, Paul; Mergeay, Max

    Cyanobacteria are daily used as nutritional supplements (e.g. Spirulina) and are considered for promising applications beyond Earth, in space, where they can play a crucial role in closed miniaturised biological waste recycling systems that are currently developed to support future long-term space missions. Cyanobacteria can be cultured with artificial light in controllable photobioreactors, and used for the efficient removal of CO2 from and production of O2 in the at-mosphere of the confined spacecraft, for removal of nitrate from waste water that is recycled to potable water, and as complementary food source. In this context, the filamentous cyanobac-terium Arthrospira sp. PCC 8005 was selected as part of the bio-regenerative life-support system MELiSSA from the European Space Agency. For bioprocess control and optimisation, the access to its genetic information and the development of molecular tools is crucial. Here we report on our efforts to determine the full genome of the cyanobacterium Arthrospira sp. PCC 8005. The obtained sequence data were analysed in detail to gain a better insight in the photosynthetic, nutritive, or potential toxic potential of this strain. In addition, the sensitivity of PCC 8005 to ionizing radiation was investigated because prolonged exposure of PCC 8005 to cosmic radiation in space might have a deleterious effect on its metabolism and oxygenic properties. To our knowledge, of the 6 different research groups across the globe trying to sequence Arthrospira strains, none of them, including us, were yet able to obtain a complete genome sequence. For Arthrospira sp. strain PCC 8005, we obtained 119 contigs (assembled in 16 scaffolds), representing 6,3 Mb, with 5,856 predicted protein-coding sequences (CDSs) and 176 genes encoding RNA. The PCC 8005 genome displays an unusual high number of large repeated sequences, covering around 8% of the genome, which likely hampered the sequenc-ing. The PCC 8005 genome is also ridden by mobile

  20. Developing an integration tool for soil contamination assessment

    NASA Astrophysics Data System (ADS)

    Anaya-Romero, Maria; Zingg, Felix; Pérez-Álvarez, José Miguel; Madejón, Paula; Kotb Abd-Elmabod, Sameh

    2015-04-01

    In the last decades, huge soil areas have been negatively influenced or altered in multiples forms. Soils and, consequently, underground water, have been contaminated by accumulation of contaminants from agricultural activities (fertilizers and pesticides) industrial activities (harmful material dumping, sludge, flying ashes) and urban activities (hydrocarbon, metals from vehicle traffic, urban waste dumping). In the framework of the RECARE project, local partners across Europe are focusing on a wide range of soil threats, as soil contamination, and aiming to develop effective prevention, remediation and restoration measures by designing and applying targeted land management strategies (van Lynden et al., 2013). In this context, the Guadiamar Green Corridor (Southern Spain) was used as a case study, aiming to obtain soil data and new information in order to assess soil contamination. The main threat in the Guadiamar valley is soil contamination after a mine spill occurred on April 1998. About four hm3 of acid waters and two hm3 of mud, rich in heavy metals, were released into the Agrio and Guadiamar rivers affecting more than 4,600 ha of agricultural and pasture land. Main trace elements contaminating soil and water were As, Cd, Cu, Pb, Tl and Zn. The objective of the present research is to develop informatics tools that integrate soil database, models and interactive platforms for soil contamination assessment. Preliminary results were obtained related to the compilation of harmonized databases including geographical, hydro-meteorological, soil and socio-economic variables based on spatial analysis and stakeholder's consultation. Further research will be modellization and upscaling at the European level, in order to obtain a scientifically-technical predictive tool for the assessment of soil contamination.

  1. Development of Antimicrobial Peptide Prediction Tool for Aquaculture Industries.

    PubMed

    Gautam, Aditi; Sharma, Asuda; Jaiswal, Sarika; Fatma, Samar; Arora, Vasu; Iquebal, M A; Nandi, S; Sundaray, J K; Jayasankar, P; Rai, Anil; Kumar, Dinesh

    2016-09-01

    Microbial diseases in fish, plant, animal and human are rising constantly; thus, discovery of their antidote is imperative. The use of antibiotic in aquaculture further compounds the problem by development of resistance and consequent consumer health risk by bio-magnification. Antimicrobial peptides (AMPs) have been highly promising as natural alternative to chemical antibiotics. Though AMPs are molecules of innate immune defense of all advance eukaryotic organisms, fish being heavily dependent on their innate immune defense has been a good source of AMPs with much wider applicability. Machine learning-based prediction method using wet laboratory-validated fish AMP can accelerate the AMP discovery using available fish genomic and proteomic data. Earlier AMP prediction servers are based on multi-phyla/species data, and we report here the world's first AMP prediction server in fishes. It is freely accessible at http://webapp.cabgrid.res.in/fishamp/ . A total of 151 AMPs related to fish collected from various databases and published literature were taken for this study. For model development and prediction, N-terminus residues, C-terminus residues and full sequences were considered. Best models were with kernels polynomial-2, linear and radial basis function with accuracy of 97, 99 and 97 %, respectively. We found that performance of support vector machine-based models is superior to artificial neural network. This in silico approach can drastically reduce the time and cost of AMP discovery. This accelerated discovery of lead AMP molecules having potential wider applications in diverse area like fish and human health as substitute of antibiotics, immunomodulator, antitumor, vaccine adjuvant and inactivator, and also for packaged food can be of much importance for industries.

  2. Development of Antimicrobial Peptide Prediction Tool for Aquaculture Industries.

    PubMed

    Gautam, Aditi; Sharma, Asuda; Jaiswal, Sarika; Fatma, Samar; Arora, Vasu; Iquebal, M A; Nandi, S; Sundaray, J K; Jayasankar, P; Rai, Anil; Kumar, Dinesh

    2016-09-01

    Microbial diseases in fish, plant, animal and human are rising constantly; thus, discovery of their antidote is imperative. The use of antibiotic in aquaculture further compounds the problem by development of resistance and consequent consumer health risk by bio-magnification. Antimicrobial peptides (AMPs) have been highly promising as natural alternative to chemical antibiotics. Though AMPs are molecules of innate immune defense of all advance eukaryotic organisms, fish being heavily dependent on their innate immune defense has been a good source of AMPs with much wider applicability. Machine learning-based prediction method using wet laboratory-validated fish AMP can accelerate the AMP discovery using available fish genomic and proteomic data. Earlier AMP prediction servers are based on multi-phyla/species data, and we report here the world's first AMP prediction server in fishes. It is freely accessible at http://webapp.cabgrid.res.in/fishamp/ . A total of 151 AMPs related to fish collected from various databases and published literature were taken for this study. For model development and prediction, N-terminus residues, C-terminus residues and full sequences were considered. Best models were with kernels polynomial-2, linear and radial basis function with accuracy of 97, 99 and 97 %, respectively. We found that performance of support vector machine-based models is superior to artificial neural network. This in silico approach can drastically reduce the time and cost of AMP discovery. This accelerated discovery of lead AMP molecules having potential wider applications in diverse area like fish and human health as substitute of antibiotics, immunomodulator, antitumor, vaccine adjuvant and inactivator, and also for packaged food can be of much importance for industries. PMID:27141850

  3. Development of Wet-Etching Tools for Precision Optical Figuring

    SciTech Connect

    Rushford, M C; Dixit, S N; Hyde, R; Britten, J A; Nissen, J; Aasen, M; Toeppen, J; Hoaglan, C; Nelson, C; Summers, L; Thomas, I

    2004-01-27

    This FY03 final report on Wet Etch Figuring involves a 2D thermal tool. Its purpose is to flatten (0.3 to 1 mm thickness) sheets of glass faster thus cheaper than conventional sub aperture tools. An array of resistors on a circuit board was used to heat acid over the glass Optical Path Difference (OPD) thick spots and at times this heating extended over the most of the glass aperture. Where the acid is heated on the glass it dissolves faster. A self-referencing interferometer measured the glass thickness, its design taking advantage of the parallel nature and thinness of these glass sheets. This measurement is used in close loop control of the heating patterns of the circuit board thus glass and acid. Only the glass and acid were to be moved to make the tool logistically simple to use in mass production. A set of 4-circuit board, covering 80 x 80-cm aperture was ordered, but only one 40 x 40-cm board was put together and tested for this report. The interferometer measurement of glass OPD was slower than needed on some glass profiles. Sometimes the interference fringes were too fine to resolve which would alias the sign of the glass thickness profile. This also caused the phase unwrapping code (FLYNN) to struggle thus run slowly at times taking hours, for a 10 inch square area. We did extensive work to improve the speed of this code. We tried many different phase unwrapping codes. Eventually running (FLYNN) on a farm of networked computers. Most of the work reported here is therefore limited to a 10-inch square aperture. Researched into fabricating a better interferometer lens from Plexiglas so to have less of the scattered light issues of Fresnel lens groves near field scattering patterns, this set the Nyquest limit. There was also a problem with the initial concept of wetting the 1737 glass on its bottom side with acid. The wetted 1737 glass developed an Achromatic AR coating, spoiling the reflection needed to see glass thickness interference fringes. In response

  4. A Thermoelastic Hydraulic Fracture Design Tool for Geothermal Reservoir Development

    SciTech Connect

    Ahmad Ghassemi

    2003-06-30

    Geothermal energy is recovered by circulating water through heat exchange areas within a hot rock mass. Geothermal reservoir rock masses generally consist of igneous and metamorphic rocks that have low matrix permeability. Therefore, cracks and fractures play a significant role in extraction of geothermal energy by providing the major pathways for fluid flow and heat exchange. Thus, knowledge of conditions leading to formation of fractures and fracture networks is of paramount importance. Furthermore, in the absence of natural fractures or adequate connectivity, artificial fracture are created in the reservoir using hydraulic fracturing. At times, the practice aims to create a number of parallel fractures connecting a pair of wells. Multiple fractures are preferred because of the large size necessary when using only a single fracture. Although the basic idea is rather simple, hydraulic fracturing is a complex process involving interactions of high pressure fluid injections with a stressed hot rock mass, mechanical interaction of induced fractures with existing natural fractures, and the spatial and temporal variations of in-situ stress. As a result it is necessary to develop tools that can be used to study these interactions as an integral part of a comprehensive approach to geothermal reservoir development, particularly enhanced geothermal systems. In response to this need we have set out to develop advanced thermo-mechanical models for design of artificial fractures and rock fracture research in geothermal reservoirs. These models consider the significant hydraulic and thermo-mechanical processes and their interaction with the in-situ stress state. Wellbore failure and fracture initiation is studied using a model that fully couples poro-mechanical and thermo-mechanical effects. The fracture propagation model is based on a complex variable and regular displacement discontinuity formulations. In the complex variable approach the displacement discontinuities are

  5. The Web Interface Template System (WITS), a software developer`s tool

    SciTech Connect

    Lauer, L.J.; Lynam, M.; Muniz, T.

    1995-11-01

    The Web Interface Template System (WITS) is a tool for software developers. WITS is a three-tiered, object-oriented system operating in a Client/Server environment. This tool can be used to create software applications that have a Web browser as the user interface and access a Sybase database. Development, modification, and implementation are greatly simplified because the developer can change and test definitions immediately, without writing or compiling any code. This document explains WITS functionality, the system structure and components of WITS, and how to obtain, install, and use the software system.

  6. Reactive services for supporting tool integration in a development environment

    SciTech Connect

    Amouroux, R.

    1995-12-31

    This paper proposes and discusses an approach to build cooperative tool environments in a flexible and incremental way. The approach is based on a storage system that provides powerful services to manage data sharing and cooperation between the tools. The storage system provides an object model to describe {open_quotes}resources{close_quotes} (objects of any nature manipulated by the different tools) augmented with the capability of reacting to various kinds of events. The paper shows how these reactions can be used to easily and effectively implement cooperation among the tools as well as to flexibly integrate new tools as the environment evolves.

  7. Development and commissioning of decision support tools for sewerage management.

    PubMed

    Manic, G; Printemps, C; Zug, M; Lemoine, C

    2006-01-01

    Managing sewerage systems is a highly complex task due to the dynamic nature of the facilities. Their performance strongly depends on the know-how applied by the operators. In order to define optimal operational settings, two decision support tools based on mathematical models have been developed. Moreover, easy-to-use interfaces have been created as well, aiding operators who presumably do not have the necessary skills to use modelling software. The two developed programs simulate the behaviour of both wastewater treatment plants (WWTP) and sewer network systems, respectively. They have essentially the same structure, including raw data management and statistical analysis, a simulation layer using the application programming interface of the applied software and a layer responsible for the representation of the obtained results. Four user modes are provided in the two software including the simulation of historical data using the applied and novel operational settings, as well as modes concerning prediction of possible operation periods and updates. Concerning the WWTP software, it was successfully installed in Nantes (France) in June 2004. Moreover, the one managing sewer networks has been deployed in Saint-Malo (France) in January 2005. This paper presents the structure of the developed software and the first results obtained during the commissioning phase.

  8. Development of AN All-Purpose Free Photogrammetric Tool

    NASA Astrophysics Data System (ADS)

    González-Aguilera, D.; López-Fernández, L.; Rodriguez-Gonzalvez, P.; Guerrero, D.; Hernandez-Lopez, D.; Remondino, F.; Menna, F.; Nocerino, E.; Toschi, I.; Ballabeni, A.; Gaiani, M.

    2016-06-01

    Photogrammetry is currently facing some challenges and changes mainly related to automation, ubiquitous processing and variety of applications. Within an ISPRS Scientific Initiative a team of researchers from USAL, UCLM, FBK and UNIBO have developed an open photogrammetric tool, called GRAPHOS (inteGRAted PHOtogrammetric Suite). GRAPHOS allows to obtain dense and metric 3D point clouds from terrestrial and UAV images. It encloses robust photogrammetric and computer vision algorithms with the following aims: (i) increase automation, allowing to get dense 3D point clouds through a friendly and easy-to-use interface; (ii) increase flexibility, working with any type of images, scenarios and cameras; (iii) improve quality, guaranteeing high accuracy and resolution; (iv) preserve photogrammetric reliability and repeatability. Last but not least, GRAPHOS has also an educational component reinforced with some didactical explanations about algorithms and their performance. The developments were carried out at different levels: GUI realization, image pre-processing, photogrammetric processing with weight parameters, dataset creation and system evaluation. The paper will present in detail the developments of GRAPHOS with all its photogrammetric components and the evaluation analyses based on various image datasets. GRAPHOS is distributed for free for research and educational needs.

  9. Facilities as teaching tools: A transformative participatory professional development experience

    NASA Astrophysics Data System (ADS)

    Wilson, Eric A.

    Resource consumption continues to increase as the population grows. In order to secure a sustainable future, society must educate the next generation to become "sustainability natives." Schools play a pivotal role in educating a sustainability-literate society. However, a disconnect exists between the hidden curriculum of the built environment and the enacted curriculum. This study employs a transformative participatory professional development model to instruct teachers on how to use their school grounds as teaching tools for the purpose of helping students make explicit choices in energy consumption, materials use, and sustainable living. Incorporating a phenomenological perspective, this study considers the lived experience of two sustainability coordinators. Grounded theory provides an interpretational context for the participants' interactions with each other and the professional development process. Through a year long professional development experience - commencing with an intense, participatory two-day workshop -the participants discussed challenges they faced with integrating facilities into school curriculum and institutionalizing a culture of sustainability. Two major needs were identified in this study. For successful sustainability initiatives, a hybrid model that melds top-down and bottom-up approaches offers the requisite mix of administrative support, ground level buy-in, and excitement vis-a-vis sustainability. Second, related to this hybrid approach, K-12 sustainability coordinators ideally need administrative capabilities with access to decision making, while remaining connected to students in a meaningful way, either directly in the classroom, as a mentor, or through work with student groups and projects.

  10. Application of the genome editing tool CRISPR/Cas9 in non-human primates.

    PubMed

    Luo, Xin; Li, Min; Su, Bing

    2016-07-18

    In the past three years, RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system has been used to facilitate efficient genome editing in many model and non-model animals. However, its application in nonhuman primates is still at the early stage, though in view of the similarities in anatomy, physiology, behavior and genetics, closely related nonhuman primates serve as optimal models for human biology and disease studies. In this review, we summarize the current proceedings of gene editing using CRISPR/Cas9 in nonhuman primates. PMID:27469252

  11. Genomic tools in Acute Myeloid Leukemia: from the bench to the bedside

    PubMed Central

    White, Brian S.; DiPersio, John F.

    2014-01-01

    Following its use in the initial characterization of an acute myeloid leukemia (AML) genome, next generation sequencing (NGS) has continued to molecularly refine the disease. Here we review the spectrum of NGS applications that have subsequently delineated the prognostic significance and biological consequences of these mutations. Further, we discuss the technology’s role in providing a high-resolution glimpse of AML clonal heterogeneity, which may inform future choice of targeted therapy. Though obstacles remain in applying these techniques clinically, they have already impacted patient care. PMID:24474533

  12. An automated graphics tool for comparative genomics: the Coulson plot generator

    PubMed Central

    2013-01-01

    Background Comparative analysis is an essential component to biology. When applied to genomics for example, analysis may require comparisons between the predicted presence and absence of genes in a group of genomes under consideration. Frequently, genes can be grouped into small categories based on functional criteria, for example membership of a multimeric complex, participation in a metabolic or signaling pathway or shared sequence features and/or paralogy. These patterns of retention and loss are highly informative for the prediction of function, and hence possible biological context, and can provide great insights into the evolutionary history of cellular functions. However, representation of such information in a standard spreadsheet is a poor visual means from which to extract patterns within a dataset. Results We devised the Coulson Plot, a new graphical representation that exploits a matrix of pie charts to display comparative genomics data. Each pie is used to describe a complex or process from a separate taxon, and is divided into sectors corresponding to the number of proteins (subunits) in a complex/process. The predicted presence or absence of proteins in each complex are delineated by occupancy of a given sector; this format is visually highly accessible and makes pattern recognition rapid and reliable. A key to the identity of each subunit, plus hierarchical naming of taxa and coloring are included. A java-based application, the Coulson plot generator (CPG) automates graphic production, with a tab or comma-delineated text file as input and generating an editable portable document format or svg file. Conclusions CPG software may be used to rapidly convert spreadsheet data to a graphical matrix pie chart format. The representation essentially retains all of the information from the spreadsheet but presents a graphically rich format making comparisons and identification of patterns significantly clearer. While the Coulson plot format is highly useful in

  13. Application of the genome editing tool CRISPR/Cas9 in non-human primates

    PubMed Central

    LUO, Xin; LI, Min; SU, Bing

    2016-01-01

    In the past three years, RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system has been used to facilitate efficient genome editing in many model and non-model animals. However, its application in nonhuman primates is still at the early stage, though in view of the similarities in anatomy, physiology, behavior and genetics, closely related nonhuman primates serve as optimal models for human biology and disease studies. In this review, we summarize the current proceedings of gene editing using CRISPR/Cas9 in nonhuman primates. PMID:27469252

  14. Application of the genome editing tool CRISPR/Cas9 in non-human primates.

    PubMed

    Luo, Xin; Li, Min; Su, Bing

    2016-07-18

    In the past three years, RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system has been used to facilitate efficient genome editing in many model and non-model animals. However, its application in nonhuman primates is still at the early stage, though in view of the similarities in anatomy, physiology, behavior and genetics, closely related nonhuman primates serve as optimal models for human biology and disease studies. In this review, we summarize the current proceedings of gene editing using CRISPR/Cas9 in nonhuman primates.

  15. Goldilocks: a tool for identifying genomic regions that are ‘just right’

    PubMed Central

    Nicholls, Samuel M.; Clare, Amanda; Randall, Joshua C.

    2016-01-01

    Summary: We present Goldilocks: a Python package providing functionality for collecting summary statistics, identifying shifts in variation, discovering outlier regions and locating and extracting interesting regions from one or more arbitrary genomes for further analysis, for a user-provided definition of interesting. Availability and implementation: Goldilocks is freely available open-source software distributed under the MIT licence. Source code is hosted publicly at https://github.com/SamStudio8/goldilocks and the package may also be installed using pip install goldilocks. Documentation can be found at https://goldilocks.readthedocs.org. Contact: msn@aber.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153673

  16. MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes.

    PubMed

    Neph, Shane; Tompa, Martin

    2006-07-01

    Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of homologous regulatory regions, usually collected from multiple species. It does so by identifying the most conserved motifs in those homologous regions. This note describes web software that has been designed specifically for this purpose in prokaryotic genomes, making use of the phylogenetic relationships among the homologous sequences in order to make more accurate predictions. The software is called MicroFootPrinter and is available at http://bio.cs.washington.edu/software.html.

  17. The development of a two-component force dynamometer and tool control system for dynamic machine tool research

    NASA Technical Reports Server (NTRS)

    Sutherland, I. A.

    1973-01-01

    The development is presented of a tooling system that makes a controlled sinusoidal oscillation simulating a dynamic chip removal condition. It also measures the machining forces in two mutually perpendicular directions without any cross sensitivity.

  18. Development of Next Generation Multiphase Pipe Flow Prediction Tools

    SciTech Connect

    Tulsa Fluid Flow

    2008-08-31

    The developments of fields in deep waters (5000 ft and more) is a common occurrence. It is inevitable that production systems will operate under multiphase flow conditions (simultaneous flow of gas-oil-and water possibly along with sand, hydrates, and waxes). Multiphase flow prediction tools are essential for every phase of the hydrocarbon recovery from design to operation. The recovery from deep-waters poses special challenges and requires accurate multiphase flow predictive tools for several applications including the design and diagnostics of the production systems, separation of phases in horizontal wells, and multiphase separation (topside, seabed or bottom-hole). It is very crucial to any multiphase separation technique that is employed either at topside, seabed or bottom-hole to know inlet conditions such as the flow rates, flow patterns, and volume fractions of gas, oil and water coming into the separation devices. The overall objective was to develop a unified model for gas-oil-water three-phase flow in wells, flow lines, and pipelines to predict the flow characteristics such as flow patterns, phase distributions, and pressure gradient encountered during petroleum production at different flow conditions (pipe diameter and inclination, fluid properties and flow rates). The project was conducted in two periods. In Period 1 (four years), gas-oil-water flow in pipes were investigated to understand the fundamental physical mechanisms describing the interaction between the gas-oil-water phases under flowing conditions, and a unified model was developed utilizing a novel modeling approach. A gas-oil-water pipe flow database including field and laboratory data was formed in Period 2 (one year). The database was utilized in model performance demonstration. Period 1 primarily consisted of the development of a unified model and software to predict the gas-oil-water flow, and experimental studies of the gas-oil-water project, including flow behavior description and

  19. Laminin A chain: expression during Drosophila development and genomic sequence.

    PubMed Central

    Kusche-Gullberg, M; Garrison, K; MacKrell, A J; Fessler, L I; Fessler, J H

    1992-01-01

    A Drosophila laminin A chain gene was characterized as a 14 kb genomic nucleotide sequence which encodes an open reading frame of 3712 amino acids in 15 exons. Overall, this A chain is similar to its vertebrate counterparts, especially in its N- and C-terminal globular domains, but the sequence that forms the laminin A short arm is quite different and larger. Laminin messages appear in newly formed mesoderm and are later prominently expressed in hemocytes, which also synthesize basement membrane collagen IV. The composition of Drosophila basement membranes changes with development. A novel method of tandemly fused RNA probes showed that developmental increases of laminin mRNAs were primarily associated with periods of morphogenesis, and preceded those of collagen IV, a protein strongly expressed during growth. The ratio of A:B1:B2 mRNAs varied little during embryogenesis, with less mRNA for A than B chains. Staining of embryos with antibodies confirmed and extended the information provided by in situ hybridization. Homologs of the G-subdomains of this A chain, which occur in interacting regions of agrin, perlecan, laminin and sex steroid binding protein, may be involved in protein associations. Images PMID:1425586

  20. Laser metrology — a diagnostic tool in automotive development processes

    NASA Astrophysics Data System (ADS)

    Beeck, Manfred-Andreas; Hentschel, Werner

    2000-08-01

    Laser measurement techniques are widely used in automotive development processes. Applications at Volkswagen are presented where laser metrology works as a diagnostic tool for analysing and optimising complex coupled processes inside and between automotive components and structures such as the reduction of a vehicle's interior or outer acoustic noise, including brake noise, and the combustion analysis for diesel and gasoline engines to further reduce fuel consumption and pollution. Pulsed electronic speckle pattern interferometry (ESPI) and holographic interferometry are used for analysing the knocking behaviour of modern engines and for correct positioning of knocking sensors. Holographic interferometry shows up the vibrational behaviour of brake components and their interaction during braking, and allows optimisation for noise-free brake systems. Scanning laser vibrometry analyses structure-born noise of a whole car body for the optimisation of its interior acoustical behaviour.Modern engine combustion concepts such as in direct-injection (DI) gasoline and diesel engines benefit from laser diagnostic tools which permit deeper insight into the in-cylinder processes such as flow generation, fuel injection and spray formation, atomisation and mixing, ignition and combustion, and formation and reduction of pollutants. The necessary optical access inside a cylinder is realised by so-called 'transparent engines' allowing measurements nearly during the whole engine cycle. Measurement techniques and results on double-pulse particle image velocimetry (PIV) with a frequency-doubled YAG laser for in-cylinder flow analysis are presented, as well as Mie-scattering on droplets using a copper vapour laser combined with high-speed filming, and laser-induced fluorescence (LIF) with an excimer laser for spray and fuel vapour analysis.