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Sample records for genomics developing tools

  1. Technology developments in biological tools for targeted genome surgery.

    PubMed

    Teimourian, Shahram; Abdollahzadeh, Rasoul

    2015-01-01

    Different biological tools for targeted genome engineering have recently appeared and these include tools like meganucleases, zinc-finger nucleases and newer technologies including TALENs and CRISPR/Cas systems. transcription activator-like effector nucleases (TALENs) have greatly improved genome editing efficiency by making site-specific DNA double-strand breaks. Several studies have shown the prominence of TALENs in comparison to the meganucleases and zinc-finger nucleases. The most important feature of TALENs that makes them suitable tools for targeted genome editing is the modularity of central repeat domains, meaning that they can be designed to recognize any desirable DNA sequence. In this review, we present a comprehensive and concise description of TALENs technology developments for targeted genome surgery with to the point description and comparison of other tools.

  2. Genomics and public health: development of Web-based training tools for increasing genomic awareness.

    PubMed

    Bodzin, Jennifer; Kardia, Sharon L R; Goldenberg, Aaron; Raup, Sarah F; Bach, Janice V; Citrin, Toby

    2005-04-01

    In 2001, the Centers for Disease Control and Prevention funded three Centers for Genomics and Public Health to develop training tools for increasing genomic awareness. Over the past three years, the centers, working together with the Centers for Disease Control and Prevention's Office of Genomics and Disease Prevention, have developed tools to increase awareness of the impact genomics will have on public health practice, to provide a foundation for understanding basic genomic advances, and to translate the relevance of that information to public health practitioners' own work. These training tools serve to communicate genomic advances and their potential for integration into public heath practice. This paper highlights two of these training tools: 1) Genomics for Public Health Practitioners: The Practical Application of Genomics in Public Health Practice, a Web-based introduction to genomics, and 2) Six Weeks to Genomic Awareness, an in-depth training module on public health genomics. This paper focuses on the processes and collaborative efforts by which these live presentations were developed and delivered as Web-based training sessions.

  3. 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.

  4. 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...

  5. 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...

  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.

  7. An Analysis of Adenovirus Genomes Using Whole Genome Software Tools

    PubMed Central

    Mahadevan, Padmanabhan

    2016-01-01

    The evolution of sequencing technology has lead to an enormous increase in the number of genomes that have been sequenced. This is especially true in the field of virus genomics. In order to extract meaningful biological information from these genomes, whole genome data mining software tools must be utilized. Hundreds of tools have been developed to analyze biological sequence data. However, only some of these tools are user-friendly to biologists. Several of these tools that have been successfully used to analyze adenovirus genomes are described here. These include Artemis, EMBOSS, pDRAW, zPicture, CoreGenes, GeneOrder, and PipMaker. These tools provide functionalities such as visualization, restriction enzyme analysis, alignment, and proteome comparisons that are extremely useful in the bioinformatics analysis of adenovirus genomes. PMID:28293072

  8. Integrative genomics--a basic and essential tool for the development of molecular medicine.

    PubMed

    Ostrowski, Jerzy

    2008-01-01

    Understanding the molecular mechanisms of disease requires the introduction of molecular diagnostics into medical practice. Current medicine employs only elements of molecular diagnostics, and usually on the scale of single genes. Medicine in the post-genomic era will utilize thousands of molecular markers associated with disease that are provided by high-throughput sequencing and functional genomic, proteomic and metabolomic studies. Such a spectrum of techniques will link clinical medicine based on molecularly oriented diagnostics with the prediction and prevention of disease. To achieve this task, large-scale and genome-wide biological and medical data must be combined with biostatistical analyses and bioinformatic modeling of biological systems. The collecting, cataloging and comparison of data from molecular studies and the subsequent development of conclusions create the fundamentals of systems biology. This highly complex analytical process reflects a new scientific paradigm called integrative genomics.

  9. 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.

  10. Computational Tools for Genomic Studies in Plants.

    PubMed

    Martinez, Manuel

    2016-12-01

    In recent years, the genomic sequence of numerous plant species including the main crop species has been determined. Computational tools have been developed to deal with the issue of which plant has been sequenced and where is the sequence hosted. In this mini-review, the databases for genome projects, the databases created to host species/clade projects and the databases developed to perform plant comparative genomics are revised. Because of their importance in modern research, an in-depth analysis of the plant comparative genomics databases has been performed. This comparative analysis is focused in the common and specific computational tools developed to achieve the particular objectives of each database. Besides, emerging high-performance bioinformatics tools specific for plant research are commented. What kind of computational approaches should be implemented in next years to efficiently analyze plant genomes is discussed.

  11. Genome Exploitation and Bioinformatics Tools

    NASA Astrophysics Data System (ADS)

    de Jong, Anne; van Heel, Auke J.; Kuipers, Oscar P.

    Bioinformatic tools can greatly improve the efficiency of bacteriocin screening efforts by limiting the amount of strains. Different classes of bacteriocins can be detected in genomes by looking at different features. Finding small bacteriocins can be especially challenging due to low homology and because small open reading frames (ORFs) are often omitted from annotations. In this chapter, several bioinformatic tools/strategies to identify bacteriocins in genomes are discussed.

  12. Development of 5006 Full-Length CDNAs in Barley: A Tool for Accessing Cereal Genomics Resources

    PubMed Central

    Sato, Kazuhiro; Shin-I, Tadasu; Seki, Motoaki; Shinozaki, Kazuo; Yoshida, Hideya; Takeda, Kazuyoshi; Yamazaki, Yukiko; Conte, Matthieu; Kohara, Yuji

    2009-01-01

    A collection of 5006 full-length (FL) cDNA sequences was developed in barley. Fifteen mRNA samples from various organs and treatments were pooled to develop a cDNA library using the CAP trapper method. More than 60% of the clones were confirmed to have complete coding sequences, based on comparison with rice amino acid and UniProt sequences. Blastn homologies (E<1E-5) to rice genes and Arabidopsis genes were 89 and 47%, respectively. Of the 5028 possible amino acid sequences derived from the 5006 FLcDNAs, 4032 (80.2%) were classified into 1678 GreenPhyl multigenic families. There were 555 cDNAs showing low homology to both rice and Arabidopsis. Gene ontology annotation by InterProScan indicated that many of these cDNAs (71%) have no known molecular functions and may be unique to barley. The cDNAs showed high homology to Barley 1 GeneChip oligo probes (81%) and the wheat gene index (84%). The high homology between FLcDNAs (27%) and mapped barley expressed sequence tag enabled assigning linkage map positions to 151–233 FLcDNAs on each of the seven barley chromosomes. These comprehensive barley FLcDNAs provide strong platform to connect pre-existing genomic and genetic resources and accelerate gene identification and genome analysis in barley and related species. PMID:19150987

  13. Application of Genomic Tools in Plant Breeding

    PubMed Central

    Pérez-de-Castro, A.M.; Vilanova, S.; Cañizares, J.; Pascual, L.; Blanca, J.M.; Díez, M.J.; Prohens, J.; Picó, B.

    2012-01-01

    Plant breeding has been very successful in developing improved varieties using conventional tools and methodologies. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic information. The analysis of NGS data by means of bioinformatics developments allows discovering new genes and regulatory sequences and their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Genomic approaches include TILLING and EcoTILLING, which make possible to screen mutant and germplasm collections for allelic variants in target genes. Re-sequencing of genomes is very useful for the genome-wide discovery of markers amenable for high-throughput genotyping platforms, like SSRs and SNPs, or the construction of high density genetic maps. All these tools and resources facilitate studying the genetic diversity, which is important for germplasm management, enhancement and use. Also, they allow the identification of markers linked to genes and QTLs, using a diversity of techniques like bulked segregant analysis (BSA), fine genetic mapping, or association mapping. These new markers are used for marker assisted selection, including marker assisted backcross selection, ‘breeding by design’, or new strategies, like genomic selection. In conclusion, advances in genomics are providing breeders with new tools and methodologies that allow a great leap forward in plant breeding, including the ‘superdomestication’ of crops and the genetic dissection and breeding for complex traits. PMID:23115520

  14. 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.

  15. From plant genomes to protein families: computational tools

    PubMed Central

    Martinez, Manuel

    2013-01-01

    The development of new high-throughput sequencing technologies has increased dramatically the number of successful genomic projects. Thus, draft genomic sequences of more than 60 plant species are currently available. Suitable bioinformatics tools are being developed to assemble, annotate and analyze the enormous number of sequences produced. In this context, specific plant comparative genomic databases are become powerful tools for gene family annotation in plant clades. In this mini-review, the current state-of-art of genomic projects is glossed. Besides, the computational tools developed to compare genomic data are compiled. PMID:24688740

  16. 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

  17. 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

  18. Data management tools for genomic applications: A progress report

    SciTech Connect

    Markowitz, V.M.; Chen, I-Min A.

    1993-09-01

    We report in this paper on the development of data management tools that allow scientist to construct and manipulate genomic data bases in terms of application-specific objects and protocols. We are developing tools for specifying genomic database structures, as well as for entering, changing, maintaining, browsing and querying data in genomic data bases. These tools are based on the Object-protocol Model (OPM) developed by us and target commercial relational database management systems which are widely used in molecular biology laboratories. OPM allows scientists to interact with genomic databases in terms of their own frame or reference, namely genomic objects and protocols. Databases developed using the data management tools are easier to use, manage, and adapt.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. PanGeT: Pan-genomics tool.

    PubMed

    Yuvaraj, Iyyappan; Sridhar, Jayavel; Michael, Daliah; Sekar, Kanagaraj

    2017-02-05

    A decade after the concept of Pan-genome was first introduced; research in this field has spread its tentacles to areas such as pathogenesis of diseases, bacterial evolutionary studies and drug resistance. Gene content-based differentiation of virulent and a virulent strains of bacteria and identification of pathogen specific genes is imperative to understand their physiology and gain insights into the mechanism of genome evolution. Subsequently, this will aid in identifying diagnostic targets and in developing and selecting vaccines. The root of pan-genomic studies, however, is to identify the core genes, dispensable genes and strain specific genes across the genomes belonging to a clade. To this end, we have developed a tool, "PanGeT - Pan-genomics Tool" to compute the 'pan-genome' based on comparisons at the genome as well as the proteome levels. This automated tool is implemented using LaTeX libraries for effective visualization of overall pan-genome through graphical plots. Links to retrieve sequence information and functional annotations have also been provided. PanGeT can be downloaded from http://pranag.physics.iisc.ernet.in/PanGeT/ or https://github.com/PanGeTv1/PanGeT.

  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

    2016-01-04

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

    PubMed

    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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. Rapid SAW Sensor Development Tools

    NASA Technical Reports Server (NTRS)

    Wilson, William C.; Atkinson, Gary M.

    2007-01-01

    The lack of integrated design tools for Surface Acoustic Wave (SAW) devices has led us to develop tools for the design, modeling, analysis, and automatic layout generation of SAW devices. These tools enable rapid development of wireless SAW sensors. The tools developed have been designed to integrate into existing Electronic Design Automation (EDA) tools to take advantage of existing 3D modeling, and Finite Element Analysis (FEA). This paper presents the SAW design, modeling, analysis, and automated layout generation tools.

  14. 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

  15. [Tale nucleases--new tool for genome editing].

    PubMed

    Glazkova, D V; Shipulin, G A

    2014-01-01

    The ability to introduce targeted changes in the genome of living cells or entire organisms enables researchers to meet the challenges of basic life sciences, biotechnology and medicine. Knockdown of target genes in the zygotes gives the opportunity to investigate the functions of these genes in different organisms. Replacement of single nucleotide in the DNA sequence allows to correct mutations in genes and thus to cure hereditary diseases. Adding transgene to specific genomic.loci can be used in biotechnology for generation of organisms with certain properties or cell lines for biopharmaceutical production. Such manipulations of gene sequences in their natural chromosomal context became possible after the emergence of the technology called "genome editing". This technology is based on the induction of a double-strand break in a specific genomic target DNA using endonucleases that recognize the unique sequences in the genome and on subsequent recovery of DNA integrity through the use of cellular repair mechanisms. A necessary tool for the genome editing is a custom-designed endonuclease which is able to recognize selected sequences. The emergence of a new type of programmable endonucleases, which were constructed on the basis of bacterial proteins--TAL-effectors (Transcription activators like effector), has become an important stage in the development of technology and promoted wide spread of the genome editing. This article reviews the history of the discovery of TAL effectors and creation of TALE nucleases, and describes their advantages over zinc finger endonucleases that appeared earlier. A large section is devoted to description of genetic modifications that can be performed using the genome editing.

  16. 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...

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

    PubMed

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

    2015-06-01

    Current therapy for controlling human immunodeficiency virus (HIV-1) infection and preventing acquired immunodeficiency syndrome (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 zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (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.

  18. 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).

  19. Cytoscape: the network visualization tool for GenomeSpace workflows

    PubMed Central

    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

  20. 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...

  1. 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.

  2. 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

  3. Bovine Genome Database: integrated tools for genome annotation and discovery.

    PubMed

    Childers, Christopher P; Reese, Justin T; Sundaram, Jaideep P; Vile, Donald C; Dickens, C Michael; Childs, Kevin L; Salih, Hanni; Bennett, Anna K; Hagen, Darren E; Adelson, David L; Elsik, Christine G

    2011-01-01

    The Bovine Genome Database (BGD; http://BovineGenome.org) strives to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages. Genome browsers, available for both scaffold and chromosome coordinate systems, display the bovine Official Gene Set (OGS), RefSeq and Ensembl gene models, non-coding RNA, repeats, pseudogenes, single-nucleotide polymorphism, markers, QTL and alignments to complementary DNAs, ESTs and protein homologs. The Bovine QTL viewer is connected to the BGD Chromosome GBrowse, allowing for the identification of candidate genes underlying QTL. The Apollo Annotation Editor connects directly to the BGD Chado database to provide researchers with remote access to gene evidence in a graphical interface that allows editing and creating new gene models. Researchers may upload their annotations to the BGD server for review and integration into the subsequent release of the OGS. Gene pages display information for individual OGS gene models, including gene structure, transcript variants, functional descriptions, gene symbols, Gene Ontology terms, annotator comments and links to National Center for Biotechnology Information and Ensembl. Each gene page is linked to a wiki page to allow input from the research community.

  4. 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

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

    PubMed

    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.

  6. 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.

  7. Serine recombinases as tools for genome engineering.

    PubMed

    Brown, William R A; Lee, Nicholas C O; Xu, Zhengyao; Smith, Margaret C M

    2011-04-01

    The serine recombinases differ mechanistically from the tyrosine recombinases and include proteins such as ϕC31 integrase which, unlike Cre and Flp, promote unidirectional reactions. The serine recombinase family is large and includes many other proteins besides ϕC31 integrase with the potential to be widely used in genome engineering. Here we review the details of the mechanism of the reactions promoted by the serine recombinases and discuss how these not only limit the utility of this class of recombinase but also creates opportunities for the engineering of new enzymes. We discuss the unanswered questions posed by genome engineering experiments in a variety of systems in which the serine recombinases have been used and finally describe more recently discovered serine recombinases that have the potential to be used in genome engineering.

  8. FDA Bioinformatics Tool for Microbial Genomics Research on Molecular Characterization of Bacterial Foodborne Pathogens Using Microarrays

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Advances in microbial genomics and bioinformatics are offering greater insights into the emergence and spread of foodborne pathogens in outbreak scenarios. The Food and Drug Administration (FDA) has developed the genomics tool ArrayTrackTM, which provides extensive functionalities to man...

  9. Patenting genome research tools and the law.

    PubMed

    Eisenberg, Rebecca

    2003-01-01

    Patenting genes encoding therapeutic proteins was relatively uncontroversial in the early days of biotechnology. Controversy arose in the era of high-throughput DNA sequencing, when gene patents started to look less like patents on drugs and more like patents on scientific information. Evolving scientific and business strategies for exploiting genomic information raised concerns that patents might slow subsequent research. The trend towards stricter enforcement of the utility and disclosure requirements by the patent offices should help clarify the current confusion.

  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. First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species, Pinus halepensis Mill.

    PubMed

    Pinosio, S; González-Martínez, S C; Bagnoli, F; Cattonaro, F; Grivet, D; Marroni, F; Lorenzo, Z; Pausas, J G; Verdú, M; Vendramin, G G

    2014-07-01

    Aleppo pine (Pinus halepensis Mill.) is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. In this study, we performed Illumina next-generation sequencing of two phenotypically divergent Aleppo pine accessions with the aims of (i) characterizing the transcriptome through Illumina RNA-Seq on trees phenotypically divergent for adaptive traits linked to fire adaptation and drought, (ii) performing a functional annotation of the assembled transcriptome, (iii) identifying genes with accelerated evolutionary rates, (iv) studying the expression levels of the annotated genes and (v) developing gene-based markers for population genomic and association genetic studies. The assembled transcriptome consisted of 48,629 contigs and covered about 54.6 Mbp. The comparison of Aleppo pine transcripts to Picea sitchensis protein-coding sequences resulted in the detection of 34,014 SNPs across species, with a Ka /Ks average value of 0.216, suggesting that the majority of the assembled genes are under negative selection. Several genes were differentially expressed across the two pine accessions with contrasted phenotypes, including a glutathione-s-transferase, a cellulose synthase and a cobra-like protein. A large number of new markers (3334 amplifiable SSRs and 28,236 SNPs) have been identified which should facilitate future population genomics and association genetics in this species. A 384-SNP Oligo Pool Assay for genotyping with the Illumina VeraCode technology has been designed which showed an high overall SNP conversion rate (76.6%). Our results showed that Illumina next-generation sequencing is a valuable technology to obtain an extensive overview on whole transcriptomes of nonmodel species with large genomes.

  12. 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.

  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

    2016-07-08

    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. 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

  16. 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

  17. 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  .

  18. 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

  19. 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.

  20. Frageria vesca, a useful tool for Rosaceae Genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The diploid woodland strawberry, Fragaria vesca subsp. vesca forma semperflorens, has many characteristics that make it an ideal plant for strawberry genomics research. A brief review of some of the tools available for using this plant as a reference for studying gene function in strawberry and oth...

  1. Developing the Advising "Tool Kit."

    ERIC Educational Resources Information Center

    Kelly, James J.

    1988-01-01

    Developing an inventory consisting of each and every item that contributes to a total advising program is suggested. The point to be made by developing a campus "Advising Tool Kit" such as Penn State's is that advising and advisors are becoming increasingly integral to the entire educational mission of colleges and universities. (MLW)

  2. 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…

  3. GAPIT: genome association and prediction integrated tool

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Advances in high throughput sequencing have improved the detection of genes underlying important traits as well as the prediction accuracy of disease risk and breeding value of crop or livestock. Software programs developed to perform statistical genetic analysis that support these activities should...

  4. 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

  5. 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

  6. Databases and Web Tools for Cancer Genomics Study

    PubMed Central

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

    2015-01-01

    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

  7. 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

  8. 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.

  9. Virome genomics: a tool for defining the human virome.

    PubMed

    Wylie, Kristine M; Weinstock, George M; Storch, Gregory A

    2013-08-01

    High throughput, deep sequencing assays are powerful tools for gaining insights into virus-host interactions. Sequencing assays can discover novel viruses and describe the genomes of novel and known viruses. Genomic information can predict viral proteins that can be characterized, describe important genes in the host that control infections, and evaluate gene expression of viruses and hosts during infection. Sequencing can also describe variation and evolution of viruses during replication and transmission. This review recounts some of the major advances in the studies of virus-host interactions from the last two years, and discusses the uses of sequencing technologies relating to these studies.

  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. Genomic Tools in Pearl Millet Breeding for Drought Tolerance: Status and Prospects

    PubMed Central

    Serba, Desalegn D.; Yadav, Rattan S.

    2016-01-01

    Pearl millet [Penisetum glaucum (L) R. Br.] is a hardy cereal crop grown in the arid and semiarid tropics where other cereals are likely to fail to produce economic yields due to drought and heat stresses. Adaptive evolution, a form of natural selection shaped the crop to grow and yield satisfactorily with limited moisture supply or under periodic water deficits in the soil. Drought tolerance is a complex polygenic trait that various morphological and physiological responses are controlled by 100s of genes and significantly influenced by the environment. The development of genomic tools will have enormous potential to improve the efficiency and precision of conventional breeding. The apparent independent domestication events, highly outcrossing nature and traditional cultivation in stressful environments maintained tremendous amount of polymorphism in pearl millet. This high polymorphism of the crop has been revealed by genome mapping that in turn stimulated the mapping and tagging of genomic regions controlling important traits such as drought tolerance. Mapping of a major QTL for terminal drought tolerance in independent populations envisaged the prospect for the development of molecular breeding in pearl millet. To accelerate genetic gains for drought tolerance targeted novel approaches such as establishment of marker-trait associations, genomic selection tools, genome sequence and genotyping-by-sequencing are still limited. Development and application of high throughput genomic tools need to be intensified to improve the breeding efficiency of pearl millet to minimize the impact of climate change on its production. PMID:27920783

  12. Genomic Tools in Pearl Millet Breeding for Drought Tolerance: Status and Prospects.

    PubMed

    Serba, Desalegn D; Yadav, Rattan S

    2016-01-01

    Pearl millet [Penisetum glaucum (L) R. Br.] is a hardy cereal crop grown in the arid and semiarid tropics where other cereals are likely to fail to produce economic yields due to drought and heat stresses. Adaptive evolution, a form of natural selection shaped the crop to grow and yield satisfactorily with limited moisture supply or under periodic water deficits in the soil. Drought tolerance is a complex polygenic trait that various morphological and physiological responses are controlled by 100s of genes and significantly influenced by the environment. The development of genomic tools will have enormous potential to improve the efficiency and precision of conventional breeding. The apparent independent domestication events, highly outcrossing nature and traditional cultivation in stressful environments maintained tremendous amount of polymorphism in pearl millet. This high polymorphism of the crop has been revealed by genome mapping that in turn stimulated the mapping and tagging of genomic regions controlling important traits such as drought tolerance. Mapping of a major QTL for terminal drought tolerance in independent populations envisaged the prospect for the development of molecular breeding in pearl millet. To accelerate genetic gains for drought tolerance targeted novel approaches such as establishment of marker-trait associations, genomic selection tools, genome sequence and genotyping-by-sequencing are still limited. Development and application of high throughput genomic tools need to be intensified to improve the breeding efficiency of pearl millet to minimize the impact of climate change on its production.

  13. DivStat: A User-Friendly Tool for Single Nucleotide Polymorphism Analysis of Genomic Diversity

    PubMed Central

    Soares, Inês; Moleirinho, Ana; Oliveira, Gonçalo N. P.; Amorim, António

    2015-01-01

    Recent developments have led to an enormous increase of publicly available large genomic data, including complete genomes. The 1000 Genomes Project was a major contributor, releasing the results of sequencing a large number of individual genomes, and allowing for a myriad of large scale studies on human genetic variation. However, the tools currently available are insufficient when the goal concerns some analyses of data sets encompassing more than hundreds of base pairs and when considering haplotype sequences of single nucleotide polymorphisms (SNPs). Here, we present a new and potent tool to deal with large data sets allowing the computation of a variety of summary statistics of population genetic data, increasing the speed of data analysis. PMID:25756185

  14. Bioinformatics tools and databases for whole genome sequence analysis of Mycobacterium tuberculosis.

    PubMed

    Faksri, Kiatichai; Tan, Jun Hao; Chaiprasert, Angkana; Teo, Yik-Ying; Ong, Rick Twee-Hee

    2016-11-01

    Tuberculosis (TB) is an infectious disease of global public health importance caused by Mycobacterium tuberculosis complex (MTC) in which M. tuberculosis (Mtb) is the major causative agent. Recent advancements in genomic technologies such as next generation sequencing have enabled high throughput cost-effective generation of whole genome sequence information from Mtb clinical isolates, providing new insights into the evolution, genomic diversity and transmission of the Mtb bacteria, including molecular mechanisms of antibiotic resistance. The large volume of sequencing data generated however necessitated effective and efficient management, storage, analysis and visualization of the data and results through development of novel and customized bioinformatics software tools and databases. In this review, we aim to provide a comprehensive survey of the current freely available bioinformatics software tools and publicly accessible databases for genomic analysis of Mtb for identifying disease transmission in molecular epidemiology and in rapid determination of the antibiotic profiles of clinical isolates for prompt and optimal patient treatment.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. BioViews: Java-Based Tools for Genomic Data Visualization

    PubMed Central

    Helt, Gregg A.; Lewis, Suzanna; Loraine, Ann E.; Rubin, Gerald M.

    1998-01-01

    Visualization tools for bioinformatics ideally should provide universal access to the most current data in an interactive and intuitive graphical user interface. Since the introduction of Java, a language designed for distributed programming over the Web, the technology now exists to build a genomic data visualization tool that meets these requirements. Using Java we have developed a prototype genome browser applet (BioViews) that incorporates a three-level graphical view of genomic data: a physical map, an annotated sequence map, and a DNA sequence display. Annotated biological features are displayed on the physical and sequence-based maps, and the different views are interconnected. The applet is linked to several databases and can retrieve features and display hyperlinked textual data on selected features. In addition to browsing genomic data, different types of analyses can be performed interactively and the results of these analyses visualized alongside prior annotations. Our genome browser is built on top of extensible, reusable graphic components specifically designed for bioinformatics. Other groups can (and do) reuse this work in various ways. Genome centers can reuse large parts of the genome browser with minor modifications, bioinformatics groups working on sequence analysis can reuse components to build front ends for analysis programs, and biology laboratories can reuse components to publish results as dynamic Web documents. PMID:9521932

  20. FEATnotator: A tool for integrated annotation of sequence features and variation, facilitating interpretation in genomics experiments.

    PubMed

    Podicheti, Ram; Mockaitis, Keithanne

    2015-06-01

    As approaches are sought for more efficient and democratized uses of non-model and expanded model genomics references, ease of integration of genomic feature datasets is especially desirable in multidisciplinary research communities. Valuable conclusions are often missed or slowed when researchers refer experimental results to a single reference sequence that lacks integrated pan-genomic and multi-experiment data in accessible formats. Association of genomic positional information, such as results from an expansive variety of next-generation sequencing experiments, with annotated reference features such as genes or predicted protein binding sites, provides the context essential for conclusions and ongoing research. When the experimental system includes polymorphic genomic inputs, rapid calculation of gene structural and protein translational effects of sequence variation from the reference can be invaluable. Here we present FEATnotator, a lightweight, fast and easy to use open source software program that integrates and reports overlap and proximity in genomic information from any user-defined datasets including those from next generation sequencing applications. We illustrate use of the tool by summarizing whole genome sequence variation of a widely used natural isolate of Arabidopsis thaliana in the context of gene models of the reference accession. Previous discovery of a protein coding deletion influencing root development is replicated rapidly. Appropriate even in investigations of a single gene or genic regions such as QTL, comprehensive reports provided by FEATnotator better prepare researchers for interpretation of their experimental results. The tool is available for download at http://featnotator.sourceforge.net.

  1. DFAST and DAGA: web-based integrated genome annotation tools and resources

    PubMed Central

    TANIZAWA, Yasuhiro; FUJISAWA, Takatomo; KAMINUMA, Eli; NAKAMURA, Yasukazu; ARITA, Masanori

    2016-01-01

    Quality assurance and correct taxonomic affiliation of data submitted to public sequence databases have been an everlasting problem. The DDBJ Fast Annotation and Submission Tool (DFAST) is a newly developed genome annotation pipeline with quality and taxonomy assessment tools. To enable annotation of ready-to-submit quality, we also constructed curated reference protein databases tailored for lactic acid bacteria. DFAST was developed so that all the procedures required for DDBJ submission could be done seamlessly online. The online workspace would be especially useful for users not familiar with bioinformatics skills. In addition, we have developed a genome repository, DFAST Archive of Genome Annotation (DAGA), which currently includes 1,421 genomes covering 179 species and 18 subspecies of two genera, Lactobacillus and Pediococcus, obtained from both DDBJ/ENA/GenBank and Sequence Read Archive (SRA). All the genomes deposited in DAGA were annotated consistently and assessed using DFAST. To assess the taxonomic position based on genomic sequence information, we used the average nucleotide identity (ANI), which showed high discriminative power to determine whether two given genomes belong to the same species. We corrected mislabeled or misidentified genomes in the public database and deposited the curated information in DAGA. The repository will improve the accessibility and reusability of genome resources for lactic acid bacteria. By exploiting the data deposited in DAGA, we found intraspecific subgroups in Lactobacillus gasseri and Lactobacillus jensenii, whose variation between subgroups is larger than the well-accepted ANI threshold of 95% to differentiate species. DFAST and DAGA are freely accessible at https://dfast.nig.ac.jp. PMID:27867804

  2. DFAST and DAGA: web-based integrated genome annotation tools and resources.

    PubMed

    Tanizawa, Yasuhiro; Fujisawa, Takatomo; Kaminuma, Eli; Nakamura, Yasukazu; Arita, Masanori

    2016-01-01

    Quality assurance and correct taxonomic affiliation of data submitted to public sequence databases have been an everlasting problem. The DDBJ Fast Annotation and Submission Tool (DFAST) is a newly developed genome annotation pipeline with quality and taxonomy assessment tools. To enable annotation of ready-to-submit quality, we also constructed curated reference protein databases tailored for lactic acid bacteria. DFAST was developed so that all the procedures required for DDBJ submission could be done seamlessly online. The online workspace would be especially useful for users not familiar with bioinformatics skills. In addition, we have developed a genome repository, DFAST Archive of Genome Annotation (DAGA), which currently includes 1,421 genomes covering 179 species and 18 subspecies of two genera, Lactobacillus and Pediococcus, obtained from both DDBJ/ENA/GenBank and Sequence Read Archive (SRA). All the genomes deposited in DAGA were annotated consistently and assessed using DFAST. To assess the taxonomic position based on genomic sequence information, we used the average nucleotide identity (ANI), which showed high discriminative power to determine whether two given genomes belong to the same species. We corrected mislabeled or misidentified genomes in the public database and deposited the curated information in DAGA. The repository will improve the accessibility and reusability of genome resources for lactic acid bacteria. By exploiting the data deposited in DAGA, we found intraspecific subgroups in Lactobacillus gasseri and Lactobacillus jensenii, whose variation between subgroups is larger than the well-accepted ANI threshold of 95% to differentiate species. DFAST and DAGA are freely accessible at https://dfast.nig.ac.jp.

  3. [Genome Editing Tools and their Application in Experimental Ophthalmology].

    PubMed

    Yanik, M; Wende, W; Stieger, K

    2017-01-23

    New genome editing tools in molecular biology are revolutionising precise genome surgery and have greatly influenced experimental ophthalmology too. Aside from the commonly used nuclease-based platforms, such as the zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN), CRISPR/Cas systems, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes, perform very efficiently in site-specific DNA cleavage within living cells. DNA double strand breaks (DSB) are repaired through two different conserved repair pathways: NHEJ (non-homologous end joining) and HDR (homology directed repair). By using the correct DNA templates, these repair pathways can be used to knock out defective genes or to repair mutations. Genome editing technology lays the ground for new strategies in basic science, biotechnology, and biomedical science, as well as clinical studies with genome editing. Therapeutic gene editing strategies are now concentrating on diseases in the retina, due to the comparatively easy accessibility of the eye and with local application in vivo.

  4. Molecular Tools for Exploring Polyploid Genomes in Plants

    PubMed Central

    Aversano, Riccardo; Ercolano, Maria Raffaella; Caruso, Immacolata; Fasano, Carlo; Rosellini, Daniele; Carputo, Domenico

    2012-01-01

    Polyploidy is a very common phenomenon in the plant kingdom, where even diploid species are often described as paleopolyploids. The polyploid condition may bring about several advantages compared to the diploid state. Polyploids often show phenotypes that are not present in their diploid progenitors or exceed the range of the contributing species. Some of these traits may play a role in heterosis or could favor adaptation to new ecological niches. Advances in genomics and sequencing technology may create unprecedented opportunities for discovering and monitoring the molecular effects of polyploidization. Through this review, we provide an overview of technologies and strategies that may allow an in-depth analysis of polyploid genomes. After introducing some basic aspects on the origin and genetics of polyploids, we highlight the main tools available for genome and gene expression analysis and summarize major findings. In the last part of this review, the implications of next generation sequencing are briefly discussed. The accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists to understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement. PMID:22949863

  5. GAPIT Version 2: An Enhanced Integrated Tool for Genomic Association and Prediction.

    PubMed

    Tang, You; Liu, Xiaolei; Wang, Jiabo; Li, Meng; Wang, Qishan; Tian, Feng; Su, Zhongbin; Pan, Yuchun; Liu, Di; Lipka, Alexander E; Buckler, Edward S; Zhang, Zhiwu

    2016-07-01

    Most human diseases and agriculturally important traits are complex. Dissecting their genetic architecture requires continued development of innovative and powerful statistical methods. Corresponding advances in computing tools are critical to efficiently use these statistical innovations and to enhance and accelerate biomedical and agricultural research and applications. The genome association and prediction integrated tool (GAPIT) was first released in 2012 and became widely used for genome-wide association studies (GWAS) and genomic prediction. The GAPIT implemented computationally efficient statistical methods, including the compressed mixed linear model (CMLM) and genomic prediction by using genomic best linear unbiased prediction (gBLUP). New state-of-the-art statistical methods have now been implemented in a new, enhanced version of GAPIT. These methods include factored spectrally transformed linear mixed models (FaST-LMM), enriched CMLM (ECMLM), FaST-LMM-Select, and settlement of mixed linear models under progressively exclusive relationship (SUPER). The genomic prediction methods implemented in this new release of the GAPIT include gBLUP based on CMLM, ECMLM, and SUPER. Additionally, the GAPIT was updated to improve its existing output display features and to add new data display and evaluation functions, including new graphing options and capabilities, phenotype simulation, power analysis, and cross-validation. These enhancements make the GAPIT a valuable resource for determining appropriate experimental designs and performing GWAS and genomic prediction. The enhanced R-based GAPIT software package uses state-of-the-art methods to conduct GWAS and genomic prediction. The GAPIT also provides new functions for developing experimental designs and creating publication-ready tabular summaries and graphs to improve the efficiency and application of genomic research.

  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. CRISPR-Cas9: Tool for Qualitative and Quantitative Plant Genome Editing

    PubMed Central

    Noman, Ali; Aqeel, Muhammad; He, Shuilin

    2016-01-01

    Recent developments in genome editing techniques have aroused substantial excitement among agricultural scientists. These techniques offer new opportunities for developing improved plant lines with addition of important traits or removal of undesirable traits. Increased adoption of genome editing has been geared by swiftly developing Clustered regularly interspaced short palindromic repeats (CRISPR). This is appearing as driving force for innovative utilization in diverse branches of plant biology. CRISPR-Cas9 mediated genome editing is being used for rapid, easy and efficient alteration of genes among diverse plant species. With approximate completion of conceptual work about CRISPR-Cas9, plant scientists are applying this genome editing tool for crop attributes enhancement. The capability of this system for performing targeted and efficient modifications in genome sequence as well as gene expression will certainly spur novel developments not only in model plants but in crop and ornamental plants as well. Additionally, due to non-involvement of foreign DNA, this technique may help alleviating regulatory issues associated with genetically modified plants. We expect that prevailing challenges in plant science like genomic region manipulation, crop specific vectors etc. will be addressed along with sustained growth of this genome editing tool. In this review, recent progress of CRISPR-Cas9 technology in plants has been summarized and discussed. We reviewed significance of CRISPR-Cas9 for specific and non-traditional aspects of plant life. It also covers strengths of this technique in comparison with other genome editing techniques, e.g., Zinc finger nucleases, Transcription activator-like effector nucleases and potential challenges in coming decades have been described. PMID:27917188

  8. CRISPR-Cas9: Tool for Qualitative and Quantitative Plant Genome Editing.

    PubMed

    Noman, Ali; Aqeel, Muhammad; He, Shuilin

    2016-01-01

    Recent developments in genome editing techniques have aroused substantial excitement among agricultural scientists. These techniques offer new opportunities for developing improved plant lines with addition of important traits or removal of undesirable traits. Increased adoption of genome editing has been geared by swiftly developing Clustered regularly interspaced short palindromic repeats (CRISPR). This is appearing as driving force for innovative utilization in diverse branches of plant biology. CRISPR-Cas9 mediated genome editing is being used for rapid, easy and efficient alteration of genes among diverse plant species. With approximate completion of conceptual work about CRISPR-Cas9, plant scientists are applying this genome editing tool for crop attributes enhancement. The capability of this system for performing targeted and efficient modifications in genome sequence as well as gene expression will certainly spur novel developments not only in model plants but in crop and ornamental plants as well. Additionally, due to non-involvement of foreign DNA, this technique may help alleviating regulatory issues associated with genetically modified plants. We expect that prevailing challenges in plant science like genomic region manipulation, crop specific vectors etc. will be addressed along with sustained growth of this genome editing tool. In this review, recent progress of CRISPR-Cas9 technology in plants has been summarized and discussed. We reviewed significance of CRISPR-Cas9 for specific and non-traditional aspects of plant life. It also covers strengths of this technique in comparison with other genome editing techniques, e.g., Zinc finger nucleases, Transcription activator-like effector nucleases and potential challenges in coming decades have been described.

  9. 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.

  10. The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows

    PubMed Central

    O'Connor, Brian D.; Yuen, Denis; Chung, Vincent; Duncan, Andrew G.; Liu, Xiang Kun; Patricia, Janice; Paten, Benedict; Stein, Lincoln; Ferretti, Vincent

    2017-01-01

    As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing. If run locally, an operation at this scale would have monopolized a typical academic data centre for many months, and would have presented major challenges for data storage and distribution. However, this scale is increasingly typical for genomics projects and necessitates a rethink of how analytical tools are packaged and moved to the data. For PCAWG, we embraced the use of highly portable Docker images for encapsulating and sharing complex alignment and variant calling workflows across highly variable environments. While successful, this endeavor revealed a limitation in Docker containers, namely the lack of a standardized way to describe and execute the tools encapsulated inside the container. As a result, we created the Dockstore ( https://dockstore.org), a project that brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within. This service greatly improves the sharing and reuse of genomics tools and promotes interoperability with similar projects through emerging web service standards developed by the Global Alliance for Genomics and Health (GA4GH). PMID:28344774

  11. The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows.

    PubMed

    O'Connor, Brian D; Yuen, Denis; Chung, Vincent; Duncan, Andrew G; Liu, Xiang Kun; Patricia, Janice; Paten, Benedict; Stein, Lincoln; Ferretti, Vincent

    2017-01-01

    As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing. If run locally, an operation at this scale would have monopolized a typical academic data centre for many months, and would have presented major challenges for data storage and distribution. However, this scale is increasingly typical for genomics projects and necessitates a rethink of how analytical tools are packaged and moved to the data. For PCAWG, we embraced the use of highly portable Docker images for encapsulating and sharing complex alignment and variant calling workflows across highly variable environments. While successful, this endeavor revealed a limitation in Docker containers, namely the lack of a standardized way to describe and execute the tools encapsulated inside the container. As a result, we created the Dockstore ( https://dockstore.org), a project that brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within. This service greatly improves the sharing and reuse of genomics tools and promotes interoperability with similar projects through emerging web service standards developed by the Global Alliance for Genomics and Health (GA4GH).

  12. Transcription activator-like effector nucleases (TALENs): a highly efficient and versatile tool for genome editing.

    PubMed

    Sun, Ning; Zhao, Huimin

    2013-07-01

    Transcription activator-like effector (TALE) nucleases (TALENs) have recently emerged as a revolutionary genome editing tool in many different organisms and cell types. The site-specific chromosomal double-strand breaks introduced by TALENs significantly increase the efficiency of genomic modification. The modular nature of the TALE central repeat domains enables researchers to tailor DNA recognition specificity with ease and target essentially any desired DNA sequence. Here, we comprehensively review the development of TALEN technology in terms of scaffold optimization, DNA recognition, and repeat array assembly. In addition, we provide some perspectives on the future development of this technology.

  13. Single-cell analysis tools for drug discovery and development.

    PubMed

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

    2016-03-01

    The genetic, functional or compositional heterogeneity of healthy and diseased tissues presents major challenges in drug discovery and development. Such heterogeneity hinders the design of accurate disease models and can confound the interpretation of biomarker levels and of patient responses to specific therapies. The complex nature of virtually all tissues has motivated the development of tools for single-cell genomic, transcriptomic and multiplex proteomic analyses. Here, we review these tools and assess their advantages and limitations. Emerging applications of single cell analysis tools in drug discovery and development, particularly in the field of oncology, are discussed.

  14. A comparison of tools for the simulation of genomic next-generation sequencing data

    PubMed Central

    Escalona, Merly; Rocha, Sara; Posada, David

    2017-01-01

    Computer simulation of genomic data has become increasingly popular for assessing and validating biological models or to gain understanding about specific datasets. Multiple computational tools for the simulation of next-generation sequencing (NGS) data have been developed in recent years, which could be used to compare existing and new NGS analytical pipelines. Here we review 23 of these tools, highlighting their distinct functionality, requirements and potential applications. We also provide a decision tree for the informed selection of an appropriate NGS simulation tool for the specific question at hand. PMID:27320129

  15. A comparison of tools for the simulation of genomic next-generation sequencing data.

    PubMed

    Escalona, Merly; Rocha, Sara; Posada, David

    2016-08-01

    Computer simulation of genomic data has become increasingly popular for assessing and validating biological models or for gaining an understanding of specific data sets. Several computational tools for the simulation of next-generation sequencing (NGS) data have been developed in recent years, which could be used to compare existing and new NGS analytical pipelines. Here we review 23 of these tools, highlighting their distinct functionality, requirements and potential applications. We also provide a decision tree for the informed selection of an appropriate NGS simulation tool for the specific question at hand.

  16. 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.

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

    PubMed Central

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

    2015-01-01

    SUMMARY Many economically important crops have large and complex genomes, which hampers sequencing of their genome by standard methods such as WGS. Large tracts of methylated repeats occur at plant genomes interspersed by hypomethylated gene-rich regions. Gene enrichment strategies based on methylation profile offer an alternative to sequencing repetitive genomes. Here, we have applied methyl filtration (MF) with McrBC digestion to enrich for euchromatic regions of sugarcane genome. To verify the efficiency of MF and the assembly quality of sequences submitted to gene-enrichment strategy, we have compared assemblies using MF and unfiltered (UF) libraries. The MF allowed the achievement of a better assembly by filtering out 35% of the sugarcane genome and by producing 1.5 times more scaffolds and 1.7 times more assembled Mb compared to unfiltered scaffolds. The coverage of sorghum CDS by MF scaffolds was at least 36% higher than by UF scaffolds. Using MF technology, we increased by 134X the coverage of genic regions of the monoploid sugarcane genome. The MF reads assembled into scaffolds covering all genes at sugarcane BACs, 97.2% of sugarcane ESTs, 92.7% of sugarcane RNA-seq reads and 98.4% of sorghum protein sequences. Analysis of MF scaffolds encoding enzymes of the sucrose/starch pathway discovered 291 SNPs in the wild sugarcane species, S. spontaneum and S. officinarum. A large number of microRNA genes were 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 improvement of sugarcane as a biofuel crop. PMID:24773339

  18. ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing

    PubMed Central

    Francis, Felix; Dumas, Michael D.; Wisser, Randall J.

    2017-01-01

    Isolating and sequencing specific regions in a genome is a cornerstone of molecular biology. This has been facilitated by computationally encoding the thermodynamics of DNA hybridization for automated design of hybridization and priming oligonucleotides. However, the repetitive composition of genomes challenges the identification of target-specific oligonucleotides, which limits genetics and genomics research on many species. Here, a tool called ThermoAlign was developed that ensures the design of target-specific primer pairs for DNA amplification. This is achieved by evaluating the thermodynamics of hybridization for full-length oligonucleotide-template alignments — thermoalignments — across the genome to identify primers predicted to bind specifically to the target site. For amplification-based resequencing of regions that cannot be amplified by a single primer pair, a directed graph analysis method is used to identify minimum amplicon tiling paths. Laboratory validation by standard and long-range polymerase chain reaction and amplicon resequencing with maize, one of the most repetitive genomes sequenced to date (≈85% repeat content), demonstrated the specificity-by-design functionality of ThermoAlign. ThermoAlign is released under an open source license and bundled in a dependency-free container for wide distribution. It is anticipated that this tool will facilitate multiple applications in genetics and genomics and be useful in the workflow of high-throughput targeted resequencing studies. PMID:28300202

  19. Primer: genomic and proteomic tools for the molecular dissection of disease.

    PubMed

    Walker, Erin J; Siminovitch, Katherine A

    2007-10-01

    Completion of the Human Genome Project has been rapidly followed by the emergence of high-throughput technologies that combine automation, miniaturization, and many other strategies and tools to enable systematic surveys of genome composition and gene expression. Of particular relevance to the prevention and management of disease are technologies such as high-throughput DNA genotyping, microarray-based gene-expression profiling, and mass spectrometry-facilitated protein profiling--platforms that collectively support the comprehensive analysis of DNA sequence variants across the genome and the global gene and protein expression changes that distinguish health from disease. Now used extensively in all facets of biomedical investigation, genomic and proteomic tools are already beginning to pinpoint molecular variants that influence risk and outcome in common diseases, and to thereby inform and direct development of novel molecular biomarkers and drug targets. As evidenced by recent advances in DNA sequencing methods, continued improvements in the scope, power, and cost efficiency of genomic and proteomic technologies should ensure their capacity to provide the scale and depth of knowledge required for translating genome sequence information into major medical impact.

  20. 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

  1. 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.

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

    PubMed Central

    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

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

    PubMed Central

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

    2015-01-01

    Novel genes are now identified at a rapid pace for many Mendelian disorders, and increasingly, for genetically complex phenotypes. However, new challenges have also become evident: (1) effectively managing larger exome and/or genome datasets, especially for smaller labs; (2) direct hands-on analysis and contextual interpretation of variant data in large genomic datasets; and (3) many small and medium-sized clinical and research-based investigative teams around the world are generating data that, if combined and shared, will significantly increase the opportunities for the entire community to identify new genes. To address these challenges we have developed GEnomes Management Application (GEM.app), a software tool to annotate, manage, visualize, and analyze large genomic datasets (https://genomics.med.miami.edu/). GEM.app currently contains ~1,600 whole exomes from 50 different phenotypes studied by 40 principal investigators from 15 different countries. The focus of GEM.app is on user-friendly analysis for non-bioinformaticians to make NGS data directly accessible. Yet, GEM.app provides powerful and flexible filter options, including single family filtering, across family/phenotype queries, nested filtering, and evaluation of segregation in families. In addition, the system is fast, obtaining results within 4 seconds across ~1,200 exomes. We believe that this system will further enhance identification of genetic causes of human disease. PMID:23463597

  4. 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.

  5. 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)

  6. 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

  7. 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

    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.

  8. Family history in public health practice: a genomic tool for disease prevention and health promotion.

    PubMed

    Valdez, Rodolfo; Yoon, Paula W; Qureshi, Nadeem; Green, Ridgely Fisk; Khoury, Muin J

    2010-01-01

    Family history is a risk factor for many chronic diseases, including cancer, cardiovascular disease, and diabetes. Professional guidelines usually include family history to assess health risk, initiate interventions, and motivate behavioral changes. The advantages of family history over other genomic tools include a lower cost, greater acceptability, and a reflection of shared genetic and environmental factors. However, the utility of family history in public health has been poorly explored. To establish family history as a public health tool, it needs to be evaluated within the ACCE framework (analytical validity; clinical validity; clinical utility; and ethical, legal, and social issues). Currently, private and public organizations are developing tools to collect standardized family histories of many diseases. Their goal is to create family history tools that have decision support capabilities and are compatible with electronic health records. These advances will help realize the potential of family history as a public health tool.

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

    PubMed Central

    2011-01-01

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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. CrossMap: a versatile tool for coordinate conversion between genome assemblies

    PubMed Central

    Zhao, Hao; Sun, Zhifu; Wang, Jing; Huang, Haojie; Kocher, Jean-Pierre; Wang, Liguo

    2014-01-01

    Motivation: Reference genome assemblies are subject to change and refinement from time to time. Generally, researchers need to convert the results that have been analyzed according to old assemblies to newer versions, or vice versa, to facilitate meta-analysis, direct comparison, data integration and visualization. Several useful conversion tools can convert genome interval files in browser extensible data or general feature format, but none have the functionality to convert files in sequence alignment map or BigWig format. This is a significant gap in computational genomics tools, as these formats are the ones most widely used for representing high-throughput sequencing data, such as RNA-seq, chromatin immunoprecipitation sequencing, DNA-seq, etc. Results: Here we developed CrossMap, a versatile and efficient tool for converting genome coordinates between assemblies. CrossMap supports most of the commonly used file formats, including BAM, sequence alignment map, Wiggle, BigWig, browser extensible data, general feature format, gene transfer format and variant call format. Availability and implementation: CrossMap is written in Python and C. Source code and a comprehensive user’s manual are freely available at: http://crossmap.sourceforge.net/. Contact: Kocher.JeanPierre@mayo.edu or wang.liguo@mayo.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24351709

  15. 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/

  16. Flight Awareness Collaboration Tool Development

    NASA Technical Reports Server (NTRS)

    Mogford, Richard

    2016-01-01

    This is a PowerPoint presentation covering airline operations center (AOC) research. It reviews a dispatcher decision support tool called the Flight Awareness Collaboration Tool (FACT). FACT gathers information about winter weather onto one screen and includes predictive abilities. FACT should prove to be useful for airline dispatchers and airport personnel when they manage winter storms and their effect on air traffic. This material is very similar to other previously approved presentations.

  17. 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.

  18. 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.

  19. The hidden perils of read mapping as a quality assessment tool in genome sequencing

    PubMed Central

    Lehri, B.; Seddon, A. M.; Karlyshev, A. V.

    2017-01-01

    This article provides a comparative analysis of the various methods of genome sequencing focusing on verification of the assembly quality. The results of a comparative assessment of various de novo assembly tools, as well as sequencing technologies, are presented using a recently completed sequence of the genome of Lactobacillus fermentum 3872. In particular, quality of assemblies is assessed by using CLC Genomics Workbench read mapping and Optical mapping developed by OpGen. Over-extension of contigs without prior knowledge of contig location can lead to misassembled contigs, even when commonly used quality indicators such as read mapping suggest that a contig is well assembled. Precautions must also be undertaken when using long read sequencing technology, which may also lead to misassembled contigs. PMID:28225089

  20. FilooT: a visualization tool for exploring genomic data

    NASA Astrophysics Data System (ADS)

    Zeinaly, Mahshid; Soltangheis, Mina; Shaw, Chris D.

    2013-12-01

    In order to enhance analysis of synthetic health data of the IEEE VAST Challenge 2010, we introduce an interactive Visual Analytics tool called FilooT designed as a part of the Interactive Multi-genomic Analysis System (IMAS) project. In this paper, we describe different interactive views of FilooT: the Tabular View for exploring and comparing genetic sequences, the Matrix View for sorting sequences according to the values of different characteristics, the P-value View for finding the most important mutations across a family of sequences, the Graph View for finding related sequences and the Group View to group them for further investigation. We followed the Nested Process Model framework throughout the design process and the evaluation. To understand the tool's design capabilities for target domain analysts, we conducted a User Experience scenario-based study followed by an informal interview. The findings indicated how analysts employ each of the visualization and interaction designs in their Bioinformatics task-analysis process. The critical analysis of the results inspired design informing suggestions.

  1. Cpf1 Is A Versatile Tool for CRISPR Genome Editing Across Diverse Species of Cyanobacteria

    PubMed Central

    Ungerer, Justin; Pakrasi, Himadri B.

    2016-01-01

    Cyanobacteria are the ideal organisms for the production of a wide range of bioproducts as they can convert CO2 directly into the desired end product using solar energy. Unfortunately, the engineering of cyanobacteria to create efficient cell factories has been impaired by the cumbersome genetic tools that are currently available for these organisms; especially when trying to accumulate multiple modifications. We sought to construct an efficient and precise tool for generating numerous markerless modifications in cyanobacteria using CRISPR technology and the alternative nuclease, Cpf1. In this study we demonstrate rapid engineering of markerless knock-ins, knock-outs and point mutations in each of three model cyanobacteria; Synechococcus, Synechocystis and Anabaena. The markerless nature of cpf1 genome editing will allow for complex genome modification that was not possible with previously existing technology while facilitating the development of cyanobacteria as highly modified biofactories. PMID:28000776

  2. Cpf1 Is A Versatile Tool for CRISPR Genome Editing Across Diverse Species of Cyanobacteria.

    PubMed

    Ungerer, Justin; Pakrasi, Himadri B

    2016-12-21

    Cyanobacteria are the ideal organisms for the production of a wide range of bioproducts as they can convert CO2 directly into the desired end product using solar energy. Unfortunately, the engineering of cyanobacteria to create efficient cell factories has been impaired by the cumbersome genetic tools that are currently available for these organisms; especially when trying to accumulate multiple modifications. We sought to construct an efficient and precise tool for generating numerous markerless modifications in cyanobacteria using CRISPR technology and the alternative nuclease, Cpf1. In this study we demonstrate rapid engineering of markerless knock-ins, knock-outs and point mutations in each of three model cyanobacteria; Synechococcus, Synechocystis and Anabaena. The markerless nature of cpf1 genome editing will allow for complex genome modification that was not possible with previously existing technology while facilitating the development of cyanobacteria as highly modified biofactories.

  3. 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.

  4. 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.

  5. 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

  6. 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…

  7. Molecular tools for functional genomics in filamentous fungi: recent advances and new strategies.

    PubMed

    Jiang, Dewei; Zhu, Wei; Wang, Yunchuan; Sun, Chang; Zhang, Ke-Qin; Yang, Jinkui

    2013-12-01

    Advances in genetic transformation techniques have made important contributions to molecular genetics. Various molecular tools and strategies have been developed for functional genomic analysis of filamentous fungi since the first DNA transformation was successfully achieved in Neurospora crassa in 1973. Increasing amounts of genomic data regarding filamentous fungi are continuously reported and large-scale functional studies have become common in a wide range of fungal species. In this review, various molecular tools used in filamentous fungi are compared and discussed, including methods for genetic transformation (e.g., protoplast transformation, electroporation, and microinjection), the construction of random mutant libraries (e.g., restriction enzyme mediated integration, transposon arrayed gene knockout, and Agrobacterium tumefaciens mediated transformation), and the analysis of gene function (e.g., RNA interference and transcription activator-like effector nucleases). We also focused on practical strategies that could enhance the efficiency of genetic manipulation in filamentous fungi, such as choosing a proper screening system and marker genes, assembling target-cassettes or vectors effectively, and transforming into strains that are deficient in the nonhomologous end joining pathway. In summary, we present an up-to-date review on the different molecular tools and latest strategies that have been successfully used in functional genomics in filamentous fungi.

  8. 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

  9. 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

  10. Probing the impact of chromatin conformation on genome editing tools

    PubMed Central

    Chen, Xiaoyu; Rinsma, Marrit; Janssen, Josephine M.; Liu, Jin; Maggio, Ignazio; Gonçalves, Manuel A.F.V.

    2016-01-01

    Transcription activator-like effector nucleases (TALENs) and RNA-guided nucleases derived from clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 systems have become ubiquitous genome editing tools. Despite this, the impact that distinct high-order chromatin conformations have on these sequence-specific designer nucleases is, presently, ill-defined. The same applies to the relative performance of TALENs and CRISPR/Cas9 nucleases at isogenic target sequences subjected to different epigenetic modifications. Here, to address these gaps in our knowledge, we have implemented quantitative cellular systems based on genetic reporters in which the euchromatic and heterochromatic statuses of designer nuclease target sites are stringently controlled by small-molecule drug availability. By using these systems, we demonstrate that TALENs and CRISPR/Cas9 nucleases are both significantly affected by the high-order epigenetic context of their target sequences. In addition, this outcome could also be ascertained for S. pyogenes CRISPR/Cas9 complexes harbouring Cas9 variants whose DNA cleaving specificities are superior to that of the wild-type Cas9 protein. Thus, the herein investigated cellular models will serve as valuable functional readouts for screening and assessing the role of chromatin on designer nucleases based on different platforms or with different architectures or compositions. PMID:27280977

  11. 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.…

  12. 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.

  13. 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

  14. 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

  15. The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists

    PubMed Central

    Kang, Fan; Angiuoli, Samuel V.; White, Owen; Botstein, David; Dolinski, Kara

    2007-01-01

    Many biological databases that provide comparative genomics information and tools are now available on the internet. While certainly quite useful, to our knowledge none of the existing databases combine results from multiple comparative genomics methods with manually curated information from the literature. Here we describe the Princeton Protein Orthology Database (P-POD, http://ortholog.princeton.edu), a user-friendly database system that allows users to find and visualize the phylogenetic relationships among predicted orthologs (based on the OrthoMCL method) to a query gene from any of eight eukaryotic organisms, and to see the orthologs in a wider evolutionary context (based on the Jaccard clustering method). In addition to the phylogenetic information, the database contains experimental results manually collected from the literature that can be compared to the computational analyses, as well as links to relevant human disease and gene information via the OMIM, model organism, and sequence databases. Our aim is for the P-POD resource to be extremely useful to typical experimental biologists wanting to learn more about the evolutionary context of their favorite genes. P-POD is based on the commonly used Generic Model Organism Database (GMOD) schema and can be downloaded in its entirety for installation on one's own system. Thus, bioinformaticians and software developers may also find P-POD useful because they can use the P-POD database infrastructure when developing their own comparative genomics resources and database tools. PMID:17712414

  16. Recent Advances in Algal Genetic Tool Development

    SciTech Connect

    R. Dahlin, Lukas; T. Guarnieri, Michael

    2016-06-24

    The goal of achieving cost-effective biofuels and bioproducts derived from algal biomass will require improvements along the entire value chain, including identification of robust, high-productivity strains and development of advanced genetic tools. Though there have been modest advances in development of genetic systems for the model alga Chlamydomonas reinhardtii, progress in development of algal genetic tools, especially as applied to non-model algae, has generally lagged behind that of more commonly utilized laboratory and industrial microbes. This is in part due to the complex organellar structure of algae, including robust cell walls and intricate compartmentalization of target loci, as well as prevalent gene silencing mechanisms, which hinder facile utilization of conventional genetic engineering tools and methodologies. However, recent progress in global tool development has opened the door for implementation of strain-engineering strategies in industrially-relevant algal strains. Here, we review recent advances in algal genetic tool development and applications in eukaryotic microalgae.

  17. 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.

  18. Genetic resources offer efficient tools for rice functional genomics research.

    PubMed

    Lo, Shuen-Fang; Fan, Ming-Jen; Hsing, Yue-Ie; Chen, Liang-Jwu; Chen, Shu; Wen, Ien-Chie; Liu, Yi-Lun; Chen, Ku-Ting; Jiang, Mirng-Jier; Lin, Ming-Kuang; Rao, Meng-Yen; Yu, Lin-Chih; Ho, Tuan-Hua David; Yu, Su-May

    2016-05-01

    Rice is an important crop and major model plant for monocot functional genomics studies. With the establishment of various genetic resources for rice genomics, the next challenge is to systematically assign functions to predicted genes in the rice genome. Compared with the robustness of genome sequencing and bioinformatics techniques, progress in understanding the function of rice genes has lagged, hampering the utilization of rice genes for cereal crop improvement. The use of transfer DNA (T-DNA) insertional mutagenesis offers the advantage of uniform distribution throughout the rice genome, but preferentially in gene-rich regions, resulting in direct gene knockout or activation of genes within 20-30 kb up- and downstream of the T-DNA insertion site and high gene tagging efficiency. Here, we summarize the recent progress in functional genomics using the T-DNA-tagged rice mutant population. We also discuss important features of T-DNA activation- and knockout-tagging and promoter-trapping of the rice genome in relation to mutant and candidate gene characterizations and how to more efficiently utilize rice mutant populations and datasets for high-throughput functional genomics and phenomics studies by forward and reverse genetics approaches. These studies may facilitate the translation of rice functional genomics research to improvements of rice and other cereal crops.

  19. 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

  20. 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.

  1. 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

  2. Development and Application of Camelid Molecular Cytogenetic Tools

    PubMed Central

    Avila, Felipe; Das, Pranab J.; Kutzler, Michelle; Owens, Elaine; Perelman, Polina; Rubes, Jiri; Hornak, Miroslav; Johnson, Warren E.

    2014-01-01

    Cytogenetic chromosome maps offer molecular tools for genome analysis and clinical cytogenetics and are of particular importance for species with difficult karyotypes, such as camelids (2n = 74). Building on the available human–camel zoo-fluorescence in situ hybridization (FISH) data, we developed the first cytogenetic map for the alpaca (Lama pacos, LPA) genome by isolating and identifying 151 alpaca bacterial artificial chromosome (BAC) clones corresponding to 44 specific genes. The genes were mapped by FISH to 31 alpaca autosomes and the sex chromosomes; 11 chromosomes had 2 markers, which were ordered by dual-color FISH. The STS gene mapped to Xpter/Ypter, demarcating the pseudoautosomal region, whereas no markers were assigned to chromosomes 14, 21, 22, 28, and 36. The chromosome-specific markers were applied in clinical cytogenetics to identify LPA20, the major histocompatibility complex (MHC)-carrying chromosome, as a part of an autosomal translocation in a sterile male llama (Lama glama, LGL; 2n = 73,XY). FISH with LPAX BACs and LPA36 paints, as well as comparative genomic hybridization, were also used to investigate the origin of the minute chromosome, an abnormally small LPA36 in infertile female alpacas. This collection of cytogenetically mapped markers represents a new tool for camelid clinical cytogenetics and has applications for the improvement of the alpaca genome map and sequence assembly. PMID:23109720

  3. CoryneBase: Corynebacterium Genomic Resources and Analysis Tools at Your Fingertips

    PubMed Central

    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/. PMID:24466021

  4. Quality Assurance Project Plan Development Tool

    EPA Pesticide Factsheets

    This tool contains information designed to assist in developing a Quality Assurance (QA) Project Plan that meets EPA requirements for projects that involve surface or groundwater monitoring and/or the collection and analysis of water samples.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. Development of a transportation planning tool

    SciTech Connect

    Funkhouser, B.R.; Moyer, J.W.; Ballweg, E.L.

    1994-07-01

    This paper describes the application of simulation modeling and logistics techniques to the development of a planning tool for the Department of Energy (DOE). The focus of the Transportation Planning Model (TPM) tool is to aid DOE and Sandia analysts in the planning of future fleet sizes, driver and support personnel sizes, base site locations, and resource balancing among the base sites. The design approach is to develop a rapid modeling environment which will allow analysts to easily set up a shipment scenario and perform multiple ``what if`` evaluations. The TPM is being developed on personal computers using commercial off-the shelf (COTS) software tools under the WINDOWS{reg_sign} operating environment. Prototype development of the TPM has been completed.

  16. BACs as tools for the study of genomic imprinting.

    PubMed

    Tunster, S J; Van De Pette, M; John, R M

    2011-01-01

    Genomic imprinting in mammals results in the expression of genes from only one parental allele. Imprinting occurs as a consequence of epigenetic marks set down either in the father's or the mother's germ line and affects a very specific category of mammalian gene. A greater understanding of this distinctive phenomenon can be gained from studies using large genomic clones, called bacterial artificial chromosomes (BACs). Here, we review the important applications of BACs to imprinting research, covering physical mapping studies and the use of BACs as transgenes in mice to study gene expression patterns, to identify imprinting centres, and to isolate the consequences of altered gene dosage. We also highlight the significant and unique advantages that rapid BAC engineering brings to genomic imprinting research.

  17. Recent Advances in Algal Genetic Tool Development

    DOE PAGES

    R. Dahlin, Lukas; T. Guarnieri, Michael

    2016-06-24

    The goal of achieving cost-effective biofuels and bioproducts derived from algal biomass will require improvements along the entire value chain, including identification of robust, high-productivity strains and development of advanced genetic tools. Though there have been modest advances in development of genetic systems for the model alga Chlamydomonas reinhardtii, progress in development of algal genetic tools, especially as applied to non-model algae, has generally lagged behind that of more commonly utilized laboratory and industrial microbes. This is in part due to the complex organellar structure of algae, including robust cell walls and intricate compartmentalization of target loci, as well asmore » prevalent gene silencing mechanisms, which hinder facile utilization of conventional genetic engineering tools and methodologies. However, recent progress in global tool development has opened the door for implementation of strain-engineering strategies in industrially-relevant algal strains. Here, we review recent advances in algal genetic tool development and applications in eukaryotic microalgae.« less

  18. Tools to Develop or Convert MOVES Inputs

    EPA Pesticide Factsheets

    The following tools are designed to help users develop inputs to MOVES and post-process the output. With the release of MOVES2014, EPA strongly encourages state and local agencies to develop local inputs based on MOVES fleet and activity categories.

  19. 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…

  20. MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data.

    PubMed

    Schmid, Christoph D; Sengstag, Thierry; Bucher, Philipp; Delorenzi, Mauro

    2007-07-01

    A recurring task in the analysis of mass genome annotation data from high-throughput technologies is the identification of peaks or clusters in a noisy signal profile. Examples of such applications are the definition of promoters on the basis of transcription start site profiles, the mapping of transcription factor binding sites based on ChIP-chip data and the identification of quantitative trait loci (QTL) from whole genome SNP profiles. Input to such an analysis is a set of genome coordinates associated with counts or intensities. The output consists of a discrete number of peaks with respective volumes, extensions and center positions. We have developed for this purpose a flexible one-dimensional clustering tool, called MADAP, which we make available as a web server and as standalone program. A set of parameters enables the user to customize the procedure to a specific problem. The web server, which returns results in textual and graphical form, is useful for small to medium-scale applications, as well as for evaluation and parameter tuning in view of large-scale applications, requiring a local installation. The program written in C++ can be freely downloaded from ftp://ftp.epd.unil.ch/pub/software/unix/madap. The MADAP web server can be accessed at http://www.isrec.isb-sib.ch/madap/.

  1. Use of genome-editing tools to treat sickle cell disease.

    PubMed

    Tasan, Ipek; Jain, Surbhi; Zhao, Huimin

    2016-09-01

    Recent advances in genome-editing techniques have made it possible to modify any desired DNA sequence by employing programmable nucleases. These next-generation genome-modifying tools are the ideal candidates for therapeutic applications, especially for the treatment of genetic disorders like sickle cell disease (SCD). SCD is an inheritable monogenic disorder which is caused by a point mutation in the β-globin gene. Substantial success has been achieved in the development of supportive therapeutic strategies for SCD, but unfortunately there is still a lack of long-term universal cure. The only existing curative treatment is based on allogeneic stem cell transplantation from healthy donors; however, this treatment is applicable to a limited number of patients only. Hence, a universally applicable therapy is highly desirable. In this review, we will discuss the three programmable nucleases that are commonly used for genome-editing purposes: zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9). We will continue by exemplifying uses of these methods to correct the sickle cell mutation. Additionally, we will present induction of fetal globin expression as an alternative approach to cure sickle cell disease. We will conclude by comparing the three methods and explaining the concerns about their use in therapy.

  2. 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.

  3. DECIDE: a Decision Support Tool to Facilitate Parents' Choices Regarding Genome-Wide Sequencing.

    PubMed

    Birch, Patricia; Adam, S; Bansback, N; Coe, R R; Hicklin, J; Lehman, A; Li, K C; Friedman, J M

    2016-12-01

    We describe the rationale, development, and usability testing for an integrated e-learning tool and decision aid for parents facing decisions about genome-wide sequencing (GWS) for their children with a suspected genetic condition. The online tool, DECIDE, is designed to provide decision-support and to promote high quality decisions about undergoing GWS with or without return of optional incidental finding results. DECIDE works by integrating educational material with decision aids. Users may tailor their learning by controlling both the amount of information and its format - text and diagrams and/or short videos. The decision aid guides users to weigh the importance of various relevant factors in their own lives and circumstances. After considering the pros and cons of GWS and return of incidental findings, DECIDE summarizes the user's responses and apparent preferred choices. In a usability study of 16 parents who had already chosen GWS after conventional genetic counselling, all participants found DECIDE to be helpful. Many would have been satisfied to use it alone to guide their GWS decisions, but most would prefer to have the option of consulting a health care professional as well to aid their decision. Further testing is necessary to establish the effectiveness of using DECIDE as an adjunct to or instead of conventional pre-test genetic counselling for clinical genome-wide sequencing.

  4. Population genomics as a new tool for wildlife management.

    PubMed

    Gompert, Zachariah

    2012-04-01

    Admixture and introgression have varied effects on population viability and fitness. Admixture might be an important source of new alleles, particularly for small, geographically isolated populations. However, admixture might also cause outbreeding depression if populations are adapted to different ecological or climatic conditions. Because of the emerging use of translocation and admixture as a conservation and wildlife management strategy to reduce genetic load (termed genetic rescue), the possible effects of admixture have practical consequences (Bouzat et al. 2009; Hedrick & Fredrickson 2010). Importantly, genetic load and local adaptation are properties of individual loci and epistatic interactions among loci rather than properties of genomes. Likewise, the outcome and consequences of genetic rescue depend on the fitness effects of individual introduced alleles. In this issue of Molecular Ecology, Miller et al. (2012) use model-based, population genomic analyses to document locus-specific effects of a recent genetic rescue in the bighorn sheep population within the National Bison Range wildlife refuge (NBR; Montana, USA). They find a subset of introduced alleles associated with increased fitness in NBR bighorn sheep, some of which experienced accelerated introgression following their introduction. These loci mark regions of the genome that could constitute the genetic basis of the successful NBR bighorn sheep genetic rescue. Although population genomic analyses are frequently used to study local adaptation and selection (e.g. Hohenlohe et al. 2010; Lawniczak et al. 2010), this study constitutes a novel application of this analytical framework for wildlife management. Moreover, the detailed demographic data available for the NBR bighorn sheep population provide a rare and powerful source of information and allow more robust population genomic inference than is often possible.

  5. 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.

  6. 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

  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. 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

  9. Genomics tools for the unraveling of chromosome architecture

    PubMed Central

    van Steensel, Bas; Dekker, Job

    2010-01-01

    The spatial organization of chromosomes inside the cell nucleus is still poorly understood. This organization is guided by intra- and interchromosomal contacts and by interactions of specific chromosomal loci with relatively fixed nuclear “landmarks” such as the nuclear envelope and the nucleolus. New molecular genome-wide mapping techniques have begun to uncover both types of molecular interactions, providing insights into the fundamental principles of interphase chromosome folding. PMID:20944601

  10. 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.

  11. Cost-Effective Cloud Computing: A Case Study Using the Comparative Genomics Tool, Roundup

    PubMed Central

    Kudtarkar, Parul; DeLuca, Todd F.; Fusaro, Vincent A.; Tonellato, Peter J.; Wall, Dennis P.

    2010-01-01

    Background Comparative genomics resources, such as ortholog detection tools and repositories are rapidly increasing in scale and complexity. Cloud computing is an emerging technological paradigm that enables researchers to dynamically build a dedicated virtual cluster and may represent a valuable alternative for large computational tools in bioinformatics. In the present manuscript, we optimize the computation of a large-scale comparative genomics resource—Roundup—using cloud computing, describe the proper operating principles required to achieve computational efficiency on the cloud, and detail important procedures for improving cost-effectiveness to ensure maximal computation at minimal costs. Methods Utilizing the comparative genomics tool, Roundup, as a case study, we computed orthologs among 902 fully sequenced genomes on Amazon’s Elastic Compute Cloud. For managing the ortholog processes, we designed a strategy to deploy the web service, Elastic MapReduce, and maximize the use of the cloud while simultaneously minimizing costs. Specifically, we created a model to estimate cloud runtime based on the size and complexity of the genomes being compared that determines in advance the optimal order of the jobs to be submitted. Results We computed orthologous relationships for 245,323 genome-to-genome comparisons on Amazon’s computing cloud, a computation that required just over 200 hours and cost $8,000 USD, at least 40% less than expected under a strategy in which genome comparisons were submitted to the cloud randomly with respect to runtime. Our cost savings projections were based on a model that not only demonstrates the optimal strategy for deploying RSD to the cloud, but also finds the optimal cluster size to minimize waste and maximize usage. Our cost-reduction model is readily adaptable for other comparative genomics tools and potentially of significant benefit to labs seeking to take advantage of the cloud as an alternative to local computing

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

    PubMed

    Chang, Yi-Feng; Chang, Chuan-Hsiung

    2011-01-01

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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. Kapteyn Package: Tools for developing astronomical applications

    NASA Astrophysics Data System (ADS)

    Terlouw, J. P.; Vogelaar, M. G. R.

    2016-11-01

    The Kapteyn Package provides tools for the development of astronomical applications with Python. It handles spatial and spectral coordinates, WCS projections and transformations between different sky systems; spectral translations (e.g., between frequencies and velocities) and mixed coordinates are also supported. Kapteyn offers versatile tools for writing small and dedicated applications for the inspection of FITS headers, the extraction and display of (FITS) data, interactive inspection of this data (color editing) and for the creation of plots with world coordinate information. It includes utilities for use with matplotlib such as obtaining coordinate information from plots, interactively modifiable colormaps and timer events (module mplutil); tools for parsing and interpreting coordinate information entered by the user (module positions); a function to search for gaussian components in a profile (module profiles); and a class for non-linear least squares fitting (module kmpfit).

  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. Iterative ACORN as a high throughput tool in structural genomics.

    PubMed

    Selvanayagam, S; Velmurugan, D; Yamane, T

    2006-08-01

    High throughput macromolecular structure determination is very essential in structural genomics as the available number of sequence information far exceeds the number of available 3D structures. ACORN, a freely available resource in the CCP4 suite of programs is a comprehensive and efficient program for phasing in the determination of protein structures, when atomic resolution data are available. ACORN with the automatic model-building program ARP/wARP and refinement program REFMAC is a suitable combination for the high throughput structural genomics. ACORN can also be run with secondary structural elements like helices and sheets as inputs with high resolution data. In situations, where ACORN phasing is not sufficient for building the protein model, the fragments (incomplete model/dummy atoms) can again be used as a starting input. Iterative ACORN is proved to work efficiently in the subsequent model building stages in congerin (PDB-ID: lis3) and catalase (PDB-ID: 1gwe) for which models are available.

  20. CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes

    PubMed Central

    2014-01-01

    Background The relationships between bacterial genomes are complicated by rampant horizontal gene transfer, varied selection pressures, acquisition of new genes, loss of genes, and divergence of genes, even in closely related lineages. As more and more bacterial genomes are sequenced, organizing and interpreting the incredible amount of relational information that connects them becomes increasingly difficult. Results We have developed CodaChrome (http://www.sourceforge.com/p/codachrome), a one-versus-all proteome comparison tool that allows the user to visually investigate the relationship between a bacterial proteome of interest and the proteomes encoded by every other bacterial genome recorded in GenBank in a massive interactive heat map. This tool has allowed us to rapidly identify the most highly conserved proteins encoded in the bacterial pan-genome, fast-clock genes useful for subtyping of bacterial species, the evolutionary history of an indel in the Sphingobium lineage, and an example of horizontal gene transfer from a member of the genus Enterococcus to a recent ancestor of Helicobacter pylori. Conclusion CodaChrome is a user-friendly and powerful tool for simultaneously visualizing relationships between thousands of proteomes. PMID:24460813

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. Computational and molecular tools for scalable rAAV-mediated genome editing

    PubMed Central

    Stoimenov, Ivaylo; Ali, Muhammad Akhtar; Pandzic, Tatjana; Sjöblom, Tobias

    2015-01-01

    The rapid discovery of potential driver mutations through large-scale mutational analyses of human cancers generates a need to characterize their cellular phenotypes. Among the techniques for genome editing, recombinant adeno-associated virus (rAAV)-mediated gene targeting is suited for knock-in of single nucleotide substitutions and to a lesser degree for gene knock-outs. However, the generation of gene targeting constructs and the targeting process is time-consuming and labor-intense. To facilitate rAAV-mediated gene targeting, we developed the first software and complementary automation-friendly vector tools to generate optimized targeting constructs for editing human protein encoding genes. By computational approaches, rAAV constructs for editing ∼71% of bases in protein-coding exons were designed. Similarly, ∼81% of genes were predicted to be targetable by rAAV-mediated knock-out. A Gateway-based cloning system for facile generation of rAAV constructs suitable for robotic automation was developed and used in successful generation of targeting constructs. Together, these tools enable automated rAAV targeting construct design, generation as well as enrichment and expansion of targeted cells with desired integrations. PMID:25488813

  7. 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

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

    PubMed Central

    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

    2003-01-01

    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. PMID:12702676

  9. 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.

  10. SE Requirements Development Tool User Guide

    SciTech Connect

    Benson, Faith Ann

    2016-05-13

    The LANL Systems Engineering Requirements Development Tool (SERDT) is a data collection tool created in InfoPath for use with the Los Alamos National Laboratory’s (LANL) SharePoint sites. Projects can fail if a clear definition of the final product requirements is not performed. For projects to be successful requirements must be defined early in the project and those requirements must be tracked during execution of the project to ensure the goals of the project are met. Therefore, the focus of this tool is requirements definition. The content of this form is based on International Council on Systems Engineering (INCOSE) and Department of Defense (DoD) process standards and allows for single or collaborative input. The “Scoping” section is where project information is entered by the project team prior to requirements development, and includes definitions and examples to assist the user in completing the forms. The data entered will be used to define the requirements and once the form is filled out, a “Requirements List” is automatically generated and a Word document is created and saved to a SharePoint document library. SharePoint also includes the ability to download the requirements data defined in the InfoPath from into an Excel spreadsheet. This User Guide will assist you in navigating through the data entry process.

  11. ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia.

    PubMed

    Arnaiz, Olivier; Sperling, Linda

    2011-01-01

    ParameciumDB is a community model organism database built with the GMOD toolkit to integrate the genome and biology of the ciliate Paramecium tetraurelia. Over the last four years, post-genomic data from proteome and transcriptome studies has been incorporated along with predicted orthologs in 33 species, annotations from the community and publications from the scientific literature. Available tools include BioMart for complex queries, GBrowse2 for genome browsing, the Apollo genome editor for expert curation of gene models, a Blast server, a motif finder, and a wiki for protocols, nomenclature guidelines and other documentation. In-house tools have been developed for ontology browsing and evaluation of off-target RNAi matches. Now ready for next-generation deep sequencing data and the genomes of other Paramecium species, this open-access resource is available at http://paramecium.cgm.cnrs-gif.fr.

  12. 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

  13. Developing Decontamination Tools and Approaches to ...

    EPA Pesticide Factsheets

    Developing Decontamination Tools and Approaches to Address Indoor Pesticide Contamination from Improper Bed Bug Treatments The National Exposure Research Laboratory (NERL) Human Exposure and Atmospheric Sciences Division (HEASD) conducts research in support of EPA mission to protect human health and the environment. HEASD research program supports Goal 1 (Clean Air) and Goal 4 (Healthy People) of EPA strategic plan. More specifically, our division conducts research to characterize the movement of pollutants from the source to contact with humans. Our multidisciplinary research program produces Methods, Measurements, and Models to identify relationships between and characterize processes that link source emissions, environmental concentrations, human exposures, and target-tissue dose. The impact of these tools is improved regulatory programs and policies for EPA.

  14. 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.

  15. Genetic and genomic tools for the marine annelid Platynereis dumerilii.

    PubMed

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

    2014-05-01

    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.

  16. 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

  17. Excisable cassettes: new tools for functional analysis of Streptomyces genomes.

    PubMed

    Raynal, Alain; Karray, Fatma; Tuphile, Karine; Darbon-Rongère, Emmanuelle; Pernodet, Jean-Luc

    2006-07-01

    The functional analysis of microbial genomes often requires gene inactivation. We constructed a set of cassettes consisting of single antibiotic resistance genes flanked by the attL and attR sites resulting from site-specific integration of the Streptomyces pSAM2 element. These cassettes can easily be used to inactivate genes by in-frame deletion in Streptomyces by a three-step strategy. In the first step, in Escherichia coli, the cassette is inserted into a cloned copy of the gene to be inactivated. In the second step, the gene is replaced by homologous recombination in Streptomyces, allowing substitution of the wild-type target gene with its inactivated counterpart. In the third step, the cassette can be removed by expression of the pSAM2 genes xis and int. The resulting strains are marker-free and contain an "attB-like" sequence of 33, 34, or 35 bp with no stop codon if the cassette is correctly chosen. Thus, a gene can be disrupted by creating an in-frame deletion, avoiding polar effects if downstream genes are cotranscribed with the target gene. A set of cassettes was constructed to contain a hygromycin or gentamicin resistance gene flanked by the attL and attR sites. The initial constructions carrying convenient cloning sites allow the insertion of any other marker gene. We tested insertion and excision by inserting a cassette into orf3, the third gene of an operon involved in spiramycin biosynthesis. We verified that the cassette exerted a polar effect on the transcription of downstream genes but that, after excision, complementation with orf3 alone restored spiramycin production.

  18. Excisable Cassettes: New Tools for Functional Analysis of Streptomyces Genomes

    PubMed Central

    Raynal, Alain; Karray, Fatma; Tuphile, Karine; Darbon-Rongère, Emmanuelle; Pernodet, Jean-Luc

    2006-01-01

    The functional analysis of microbial genomes often requires gene inactivation. We constructed a set of cassettes consisting of single antibiotic resistance genes flanked by the attL and attR sites resulting from site-specific integration of the Streptomyces pSAM2 element. These cassettes can easily be used to inactivate genes by in-frame deletion in Streptomyces by a three-step strategy. In the first step, in Escherichia coli, the cassette is inserted into a cloned copy of the gene to be inactivated. In the second step, the gene is replaced by homologous recombination in Streptomyces, allowing substitution of the wild-type target gene with its inactivated counterpart. In the third step, the cassette can be removed by expression of the pSAM2 genes xis and int. The resulting strains are marker-free and contain an “attB-like” sequence of 33, 34, or 35 bp with no stop codon if the cassette is correctly chosen. Thus, a gene can be disrupted by creating an in-frame deletion, avoiding polar effects if downstream genes are cotranscribed with the target gene. A set of cassettes was constructed to contain a hygromycin or gentamicin resistance gene flanked by the attL and attR sites. The initial constructions carrying convenient cloning sites allow the insertion of any other marker gene. We tested insertion and excision by inserting a cassette into orf3, the third gene of an operon involved in spiramycin biosynthesis. We verified that the cassette exerted a polar effect on the transcription of downstream genes but that, after excision, complementation with orf3 alone restored spiramycin production. PMID:16820478

  19. Genomic tools to improve progress and preserve variation for future generations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Use of genomic tools has greatly decreased generation intervals and increased genetic progress in dairy cattle, but faster selection cycles can also increase rates of inbreeding per unit of time. Average pedigree inbreeding of Holstein cows increased from 4.6% in 2000 to 5.6% in 2009 to 6.6% in 201...

  20. EPICS simulation tools for control system development

    SciTech Connect

    Wright, R.M.; Kerstiens, D.M.; Vaughn, G.D.; Weiss, R.E.

    1994-09-01

    When developing control system software there are many times when the ability to simulate the response of the instrumentation can be very useful. Examples are: (i) when the operator interface is being designed and the users want an idea of what the finished system might took like; (ii) when the interface hardware is not yet available; (iii) when the reaction of the control system to an error condition must be tested, but the actual occurrence of such an error would cause undesirable side effects; (iv) when operators are being trained to use the system; (v) when an improvement or bug fix needs to be tested, but the running system cannot be shut down for long. The Experimental Physics and Industrial Control System (EPICS) provides tools for building simple simulations and interfacing to more complex simulations of accelerator hardware. At the lowest level an individual data channel can be switched to take its input from either a simulated data location or from the actual hardware. At a slightly higher level, sequences can be run on the real-time interface processor so that output to the hardware is intercepted and an appropriate substitute value is provided for the corresponding read-back records. At a still higher level a program can use the Channel Access software bus facility of EPICS to control some global aspect of an accelerator or can interface to an external accelerator simulation instead of the actual accelerator. The goal of testing control system software using simulated hardware is to minimize the changes required in shifting between the simulated system and the real system. The degree of success of the EPICS tools in meeting the minimum change goal will be addressed with suggestions for improvements. The implementation of simulated responses using EPICS tools will be discussed and examples of experience using the EPICS tools to create and interface to simulations will be given.

  1. 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

  2. Development of a language identification tool.

    PubMed

    Davies, Charlotte; Milligan, Frank

    Service improvement is an important aspect of healthcare practice. Practitioners need to identify improvements in processes to free up time and resources for patient care. The obligation to do this falls to all staff, from students to chief executives. The project described in this article was led by a nursing student at the University of Bedfordshire, Luton, as part of the final-year assessment requirement of the pre-registration nursing degree programme. The project involved the development of a language identification tool to address communication barriers in the emergency department.

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

    PubMed

    Kirchner, Marion; Schneider, Sabine

    2015-11-09

    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.

  4. 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

  5. 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.

  6. Decoding the genome with an integrative analysis tool: combinatorial CRM Decoder.

    PubMed

    Kang, Keunsoo; Kim, Joomyeong; Chung, Jae Hoon; Lee, Daeyoup

    2011-09-01

    The identification of genome-wide cis-regulatory modules (CRMs) and characterization of their associated epigenetic features are fundamental steps toward the understanding of gene regulatory networks. Although integrative analysis of available genome-wide information can provide new biological insights, the lack of novel methodologies has become a major bottleneck. Here, we present a comprehensive analysis tool called combinatorial CRM decoder (CCD), which utilizes the publicly available information to identify and characterize genome-wide CRMs in a species of interest. CCD first defines a set of the epigenetic features which is significantly associated with a set of known CRMs as a code called 'trace code', and subsequently uses the trace code to pinpoint putative CRMs throughout the genome. Using 61 genome-wide data sets obtained from 17 independent mouse studies, CCD successfully catalogued ∼12 600 CRMs (five distinct classes) including polycomb repressive complex 2 target sites as well as imprinting control regions. Interestingly, we discovered that ∼4% of the identified CRMs belong to at least two different classes named 'multi-functional CRM', suggesting their functional importance for regulating spatiotemporal gene expression. From these examples, we show that CCD can be applied to any potential genome-wide datasets and therefore will shed light on unveiling genome-wide CRMs in various species.

  7. 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.

  8. 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

  9. Recent updates and developments to plant genome size databases

    PubMed Central

    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. PMID:24288377

  10. 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.

  11. Suite of tools for statistical N-gram language modeling for pattern mining in whole genome sequences.

    PubMed

    Ganapathiraju, Madhavi K; Mitchell, Asia D; Thahir, Mohamed; Motwani, Kamiya; Ananthasubramanian, Seshan

    2012-12-01

    Genome sequences contain a number of patterns that have biomedical significance. Repetitive sequences of various kinds are a primary component of most of the genomic sequence patterns. We extended the suffix-array based Biological Language Modeling Toolkit to compute n-gram frequencies as well as n-gram language-model based perplexity in windows over the whole genome sequence to find biologically relevant patterns. We present the suite of tools and their application for analysis on whole human genome sequence.

  12. Developing a biomonitoring tool for fine sediment

    NASA Astrophysics Data System (ADS)

    Turley, Matt; Bilotta, Gary; Brazier, Richard; Extence, Chris

    2014-05-01

    Sediment is an essential component of freshwater ecosystems; however anthropogenic activities can lead to elevated sediment delivery which can impact on the physical, chemical and biological characteristics of these ecosystems. Ultimately, this can result in a loss of ecosystem services worth more than 1.7 trillion per annum. As such it is important that sediment, which is one of the most commonly attributed causes of water quality impairment globally, is managed in order to minimise these impacts. The current EU environmental quality standard for sediment (monitored in the form of suspended solids) is 25 mg L-1 for all environments. It is widely recognised that this standard is unsuitable and not ecologically relevant. Furthermore, it requires a substantial resource investment to monitor sediment in this form as part of national and international water resource legislation. In recognition of this the development of sediment-specific biomonitoring tools is receiving increasing attention. The Proportion of Sediment-Sensitive Invertebrates (PSI) index is one such tool that is designed to indicate levels of fine sediment (

  13. Cas-analyzer: an online tool for assessing genome editing results using NGS data.

    PubMed

    Park, Jeongbin; Lim, Kayeong; Kim, Jin-Soo; Bae, Sangsu

    2017-01-15

    Genome editing with programmable nucleases has been widely adopted in research and medicine. Next generation sequencing (NGS) platforms are now widely used for measuring the frequencies of mutations induced by CRISPR-Cas9 and other programmable nucleases. Here, we present an online tool, Cas-Analyzer, a JavaScript-based implementation for NGS data analysis. Because Cas-Analyzer is completely used at a client-side web browser on-the-fly, there is no need to upload very large NGS datasets to a server, a time-consuming step in genome editing analysis. Currently, Cas-Analyzer supports various programmable nucleases, including single nucleases and paired nucleases.

  14. 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

  15. 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

  16. 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.

  17. 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

  18. Developing academic-practice partnerships to enhance the integration of genomics into public health.

    PubMed

    Raup, Sarah F; Oehlke, Kristin Peterson; Edwards, Karen L

    2005-04-01

    The sequencing of the human genome has provided tools to gain a better understanding of the role of genes and their interaction with environmental factors in the development of disease. However, much work remains in translating discoveries into new opportunities for disease prevention and health promotion. Both public health academia and practice have important roles to play in bridging the gap between the growth in knowledge stemming from the Human Genome Project and its application in public health. Recognizing this, the Centers for Disease Control and Prevention, through the Association of Schools of Public Health, established Centers for Genomics and Public Health at three schools of public health in 2001: the University of Michigan, the University of North Carolina, and the University of Washington. This paper describes the experience of the University of Washington Center for Genomics and Public Health in forging partnerships with public health practitioners to translate genomic advances into public health practice.

  19. 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.

  20. 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.

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

    DOE PAGES

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

    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

  2. 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...

  3. Immersive virtual environment technology: a promising tool for future social and behavioral genomics research and practice.

    PubMed

    Persky, Susan; McBride, Colleen M

    2009-12-01

    Social and behavioral research needs to get started now if scientists are to direct genomic discoveries to address pressing public health problems. Advancing social and behavioral science will require innovative and rigorous communication methodologies that move researchers beyond reliance on traditional tools and their inherent limitations. One such emerging research tool is immersive virtual environment technology (virtual reality), a methodology that gives researchers the ability to maintain high experimental control and mundane realism of scenarios; portray and manipulate complex, abstract objects and concepts; and implement innovative implicit behavioral measurement. This report suggests the role that immersive virtual environment technology can play in furthering future research in genomics-related education, decision making, test intentions, behavior change, and health-care provider behaviors. Practical implementation and challenges are also discussed.

  4. Complete genome sequence of cyanobacterium Fischerella sp. NIES-3754, providing thermoresistant optogenetic tools.

    PubMed

    Hirose, Yuu; Fujisawa, Takatomo; Ohtsubo, Yoshiyuki; Katayama, Mitsunori; Misawa, Naomi; Wakazuki, Sachiko; Shimura, Yohei; Nakamura, Yasukazu; Kawachi, Masanobu; Yoshikawa, Hirofumi; Eki, Toshihiko; Kanesaki, Yu

    2016-02-20

    Cyanobacterial phytochrome-class photosensors are recently emerging optogenetic tools. We isolated Fischerella sp. strain NIES-3754 from hotspring at Suwa-shrine, Suwa, Nagano, Japan. We determined complete genome sequence of the NIES-3754 strain, which is composed of one chromosome and two putative replicons (total 5,826,863bp containing no gaps). We identified photosensor genes of 5 phytochromes and 9 cyanobacteriochromes, which will facilitate optogenetics of thermophile.

  5. genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools.

    PubMed

    Lemieux Perreault, Louis-Philippe; Legault, Marc-André; Asselin, Géraldine; Dubé, Marie-Pierre

    2016-12-01

    Genotype imputation is now commonly performed following genome-wide genotyping experiments. Imputation increases the density of analyzed genotypes in the dataset, enabling fine-mapping across the genome. However, the process of imputation using the most recent publicly available reference datasets can require considerable computation power and the management of hundreds of large intermediate files. We have developed genipe, a complete genome-wide imputation pipeline which includes automatic reporting, imputed data indexing and management, and a suite of statistical tests for imputed data commonly used in genetic epidemiology (Sequence Kernel Association Test, Cox proportional hazards for survival analysis, and linear mixed models for repeated measurements in longitudinal studies).

  6. EggLib: processing, analysis and simulation tools for population genetics and genomics

    PubMed Central

    2012-01-01

    Background With the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity. In particular, in the field of population genetics, there is a strong need for automated and reliable procedures to conduct repeatable and rapid polymorphism analyses, coalescent simulations, data manipulation and estimation of demographic parameters under a variety of scenarios. Results In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the egglib script which provides direct access to pre-programmed Python applications. Conclusions EggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website http://egglib.sourceforge.net/ where a full documentation and a manual can also be found and downloaded. PMID:22494792

  7. 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

  8. DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool.

    PubMed

    Motion, Graham B; Howden, Andrew J M; Huitema, Edgar; Jones, Susan

    2015-12-15

    There are currently 151 plants with draft genomes available but levels of functional annotation for putative protein products are low. Therefore, accurate computational predictions are essential to annotate genomes in the first instance, and to provide focus for the more costly and time consuming functional assays that follow. DNA-binding proteins are an important class of proteins that require annotation, but current computational methods are not applicable for genome wide predictions in plant species. Here, we explore the use of species and lineage specific models for the prediction of DNA-binding proteins in plants. We show that a species specific support vector machine model based on Arabidopsis sequence data is more accurate (accuracy 81%) than a generic model (74%), and based on this we develop a plant specific model for predicting DNA-binding proteins. We apply this model to the tomato proteome and demonstrate its ability to perform accurate high-throughput prediction of DNA-binding proteins. In doing so, we have annotated 36 currently uncharacterised proteins by assigning a putative DNA-binding function. Our model is publically available and we propose it be used in combination with existing tools to help increase annotation levels of DNA-binding proteins encoded in plant genomes.

  9. The use of retroviruses as pharmaceutical tools for target discovery and validation in the field of functional genomics.

    PubMed

    Lorens, J B; Sousa, C; Bennett, M K; Molineaux, S M; Payan, D G

    2001-12-01

    Retrovirally mediated functional genomics enables identification of physiologically relevant cellular therapeutic targets. Unique properties of retroviruses make them ideal tools for the introduction of large and diverse libraries of potential genetic effectors to a variety of cell types. The identification and recovery of intracellular library elements responsible for altered disease responses establishes a direct basis for pharmaceutical development. Recent innovations in retroviral infection efficiency and expression control have broadened application of the methodology to include libraries of mutagenized cDNAs, peptides and ribozyme genetic effectors.

  10. 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

    ... 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 Drug Administration, HHS. ACTION: Notice. SUMMARY: The Food and Drug Administration (FDA) is announcing...

  11. Stage Separation CFD Tool Development and Evaluation

    NASA Technical Reports Server (NTRS)

    Droege, Alan; Gomez, Reynaldo; Wang, Ten-See

    2002-01-01

    This viewgraph presentation evaluates CFD (Computational Fluid Dynamics) tools for solving stage separation problems. The demonstration and validation of the tools is for a second generation RLV (Reusable Launch Vehicle) stage separation. The flow solvers are: Cart3D; Overflow/Overflow-D; Unic.

  12. Developments in applications of PCD tooling

    NASA Astrophysics Data System (ADS)

    Heath, Peter J.

    1991-06-01

    The performance of tooling based on polycrystalline diamond (PCD) has been quantified in the machining of two types of aluminum-based metal matrix composites (MMCs), where the reinforcing phase was either silicon carbide particles or alumina fibers. The machinability of these MMCs was compared with that of a hypereutectic aluminum 20 percent silicon alloy when using both cemented-carbide and PCD cutting edges. It is found that PCD is a most suitable tool material for the machining of aluminum-silicon carbide MMCs, and that cutting speeds should be in the 50-150 m/min range. Feed rates and depths of cut should be adjusted to suit the component being machined and the surface finish required. At low cutting speeds, cemented carbide cutting tools can be used on aluminum-silicon carbide MMCs, but the tool life is very low and the amount of subsurface damage produced is greater than that produced by PCD tools.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees.

    PubMed

    Wang, Qinghua; Arighi, Cecilia N; King, Benjamin L; Polson, Shawn W; Vincent, James; Chen, Chuming; Huang, Hongzhan; Kingham, Brewster F; Page, Shallee T; Rendino, Marc Farnum; Thomas, William Kelley; Udwary, Daniel W; Wu, Cathy H

    2012-01-01

    Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome.

  18. Genomic Tools for Customized Recovery and Detection of Foodborne Shiga Toxigenic Escherichia coli.

    PubMed

    Knowles, Michael; Stinson, Sara; Lambert, Dominic; Carrillo, Catherine; Koziol, Adam; Gauthier, Martine; Blais, Burton

    2016-12-01

    Genomic antimicrobial resistance (AMR) prediction tools have the potential to support foodborne illness outbreak investigations through their application in the analysis of bacterial genomes from causative strains. The AMR marker profile of a strain of interest, initially identified in outbreak-associated clinical samples, may serve as the basis for customization of selective enrichment media, facilitating its recovery from samples in a food safety investigation. Different possibilities for AMR analyses include the use of comprehensive AMR gene databases such as the Comprehensive Antibiotic Resistance Database, which can be mined with in-house bioinformatics alignment tools (e.g., Antimicrobial Resistance Marker Identifier), or publicly available tools based on clinically relevant acquired AMR gene databases (e.g., ResFinder). In combination with a previously reported pipeline (SigSeekr) designed to identify specific DNA sequences associated with a particular strain for its rapid identification by PCR, it should be possible to deploy custom recovery and identification tools for the efficient detection of priority pathogens such as Shiga toxigenic Escherichia coli (STEC) outbreak strains within the time frame of an active investigation. Using a laboratory STEC strain as a model, trimethoprim resistance identified by both Antimicrobial Resistance Marker Identifier and ResFinder was used as the basis for its selective recovery against a background of commensal E. coli bacteria in ground beef samples. Enrichment in modified tryptic soy broth containing trimethoprim greatly enhanced the recovery of low numbers of model strain cells inoculated in ground beef samples, as verified by the enumeration of colonies on plating media using a strain-specific PCR method to determine the recovery efficiency for the target strain. We discuss the relative merits of different AMR marker prediction tools for this purpose and describe how such tools can be utilized to good effect in a

  19. Plant Aquaporins: Genome-Wide Identification, Transcriptomics, Proteomics, and Advanced Analytical Tools

    PubMed Central

    Deshmukh, Rupesh K.; Sonah, Humira; Bélanger, Richard R.

    2016-01-01

    Aquaporins (AQPs) are channel-forming integral membrane proteins that facilitate the movement of water and many other small molecules. Compared to animals, plants contain a much higher number of AQPs in their genome. Homology-based identification of AQPs in sequenced species is feasible because of the high level of conservation of protein sequences across plant species. Genome-wide characterization of AQPs has highlighted several important aspects such as distribution, genetic organization, evolution and conserved features governing solute specificity. From a functional point of view, the understanding of AQP transport system has expanded rapidly with the help of transcriptomics and proteomics data. The efficient analysis of enormous amounts of data generated through omic scale studies has been facilitated through computational advancements. Prediction of protein tertiary structures, pore architecture, cavities, phosphorylation sites, heterodimerization, and co-expression networks has become more sophisticated and accurate with increasing computational tools and pipelines. However, the effectiveness of computational approaches is based on the understanding of physiological and biochemical properties, transport kinetics, solute specificity, molecular interactions, sequence variations, phylogeny and evolution of aquaporins. For this purpose, tools like Xenopus oocyte assays, yeast expression systems, artificial proteoliposomes, and lipid membranes have been efficiently exploited to study the many facets that influence solute transport by AQPs. In the present review, we discuss genome-wide identification of AQPs in plants in relation with recent advancements in analytical tools, and their availability and technological challenges as they apply to AQPs. An exhaustive review of omics resources available for AQP research is also provided in order to optimize their efficient utilization. Finally, a detailed catalog of computational tools and analytical pipelines is

  20. 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.

  1. 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

  2. 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, ...

  3. 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.

  4. 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 ).

  5. 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.

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

    PubMed Central

    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

  7. Stakeholder engagement in policy development: challenges and opportunities for human genomics.

    PubMed

    Lemke, Amy A; Harris-Wai, Julie N

    2015-12-01

    Along with rapid advances in human genomics, policies governing genomic data and clinical technologies have proliferated. Stakeholder engagement is widely lauded as an important methodology for improving clinical, scientific, and public health policy decision making. The purpose of this paper is to examine how stakeholder engagement is used to develop policies in genomics research and public health areas, as well as to identify future priorities for conducting evidence-based stakeholder engagements. We focus on exemplars in biobanking and newborn screening to illustrate a variety of current stakeholder engagement in policy-making efforts. Each setting provides an important context for examining the methods of obtaining and integrating informed stakeholder voices into the policy-making process. While many organizations have an interest in engaging stakeholders with regard to genomic policy issues, there is broad divergence with respect to the stakeholders involved, the purpose of engagements, when stakeholders are engaged during policy development, methods of engagement, and the outcomes reported. Stakeholder engagement in genomics policy development is still at a nascent stage. Several challenges of using stakeholder engagement as a tool for genomics policy development remain, and little evidence regarding how to best incorporate stakeholder feedback into policy-making processes is currently available.

  8. ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

    PubMed Central

    Gupta, Sushim Kumar; Padmanabhan, Babu Roshan; Diene, Seydina M.; Lopez-Rojas, Rafael; Kempf, Marie; Landraud, Luce

    2014-01-01

    ARG-ANNOT (Antibiotic Resistance Gene-ANNOTation) is a new bioinformatic tool that was created to detect existing and putative new antibiotic resistance (AR) genes in bacterial genomes. ARG-ANNOT uses a local BLAST program in Bio-Edit software that allows the user to analyze sequences without a Web interface. All AR genetic determinants were collected from published works and online resources; nucleotide and protein sequences were retrieved from the NCBI GenBank database. After building a database that includes 1,689 antibiotic resistance genes, the software was tested in a blind manner using 100 random sequences selected from the database to verify that the sensitivity and specificity were at 100% even when partial sequences were queried. Notably, BLAST analysis results obtained using the rmtF gene sequence (a new aminoglycoside-modifying enzyme gene sequence that is not included in the database) as a query revealed that the tool was able to link this sequence to short sequences (17 to 40 bp) found in other genes of the rmt family with significant E values. Finally, the analysis of 178 Acinetobacter baumannii and 20 Staphylococcus aureus genomes allowed the detection of a significantly higher number of AR genes than the Resfinder gene analyzer and 11 point mutations in target genes known to be associated with AR. The average time for the analysis of a genome was 3.35 ± 0.13 min. We have created a concise database for BLAST using a Bio-Edit interface that can detect AR genetic determinants in bacterial genomes and can rapidly and easily discover putative new AR genetic determinants. PMID:24145532

  9. Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification.

    PubMed

    Bao, Yiming; Chetvernin, Vyacheslav; Tatusova, Tatiana

    2014-12-01

    The number of viral genome sequences in the public databases is increasing dramatically, and these sequences are playing an important role in virus classification. Pairwise sequence comparison is a sequence-based virus classification method. A program using this method calculates the pairwise identities of virus sequences within a virus family and displays their distribution, and visual analysis helps to determine demarcations at different taxonomic levels such as strain, species, genus and subfamily. Subsequent comparison of new sequences against existing ones allows viruses from which the new sequences were derived to be classified. Although this method cannot be used as the only criterion for virus classification in some cases, it is a quantitative method and has many advantages over conventional virus classification methods. It has been applied to several virus families, and there is an increasing interest in using this method for other virus families/groups. The Pairwise Sequence Comparison (PASC) classification tool was created at the National Center for Biotechnology Information. The tool's database stores pairwise identities for complete genomes/segments of 56 virus families/groups. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database. The web interface of the tool ( http://www.ncbi.nlm.nih.gov/sutils/pasc/ ) makes it easy to navigate and perform analyses. Multiple new viral genome sequences can be tested simultaneously with this system to suggest the taxonomic position of virus isolates in a specific family. PASC eliminates potential discrepancies in the results caused by different algorithms and/or different data used by researchers.

  10. MAVEN: a tool for visualization and functional analysis of genome-wide association results

    PubMed Central

    Narayanan, Kanchana; Li, Jing

    2010-01-01

    Summary: We describe the features and implementation of a web application tool named MAVEN—for Management, Analysis, Visualization and rEsults shariNg of genome-wide association data using cutting edge technologies. Main capabilities include user data uploading and management, queries using a variety of criteria, visualization of results, interactive selections and seamless integration of users' data with databases at the National Center for Biotechnology Information (NCBI) for functional annotations of single nucleotide polymorphisms (SNPs) and genes. Availability: http://cbc.case.edu/maven Contact: jingli@case.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19933166

  11. 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.

  12. Hull Form Design and Optimization Tool Development

    DTIC Science & Technology

    2012-07-01

    Combatants • Unconventional Surface Combatants • Twin - Screw , Open-Stern, UNREP and Auxiliary • Single- Screw , Closed-Stern, UNREP and Auxiliary • Single...Waterplane Area Twin Hull TriSWACH – Trimaran Small Waterplane Area Center Hull UI – User Interface UNREP – Underway Replenishment Naval Surface...resistance prediction tool for SWATH (Small Waterplane Area Twin Hull) ships. An example of a SWATH ship is shown in Figure 11. The input files

  13. 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).

  14. 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.

  15. Reverse Vaccinology: Developing Vaccines in the Era of Genomics

    PubMed Central

    Sette, Alessandro; Rappuoli, Rino

    2012-01-01

    The sequence of microbial genomes made all potential antigens of each pathogen available for vaccine development. This increased by orders of magnitude potential vaccine targets in bacteria, parasites, and large viruses and revealed virtually all their CD4+ and CD8+ T cell epitopes. The genomic information was first used for the development of a vaccine against serogroup B meningococcus, and it is now being used for several other bacterial vaccines. In this review, we will first summarize the impact that genome sequencing has had on vaccine development, and then we will analyze how the genomic information can help further our understanding of immunity to infection or vaccination and lead to the design of better vaccines by diving into the world of T cell immunity. PMID:21029963

  16. 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.

  17. Different whole-genome amplification methods as a preamplification tool in Y-chromosome Loci analysis.

    PubMed

    Maciejewska, Agnieszka; Jakubowska, Joanna; Pawłowski, Ryszard

    2014-06-01

    Degraded and low template DNA is often analyzed in forensic genetics laboratories. Reliable analysis of degraded and low template DNA is of great importance, because its results impact the quality and reliability of expert testimonies. Recently, a number of whole-genome amplification (WGA) methods have been proposed as preamplification tools improving quantity and quality of DNA. We chose, investigated, and compared 7 WGA methods to evaluate their ability to "recover" degraded and nondegraded DNA. These methods include degenerate oligonucleotide primed polymerase chain reaction, primer extension preamplification (PEP) polymerase chain reaction, GenomePlex WGA (Sigma), multiple displacement amplification, GenomiPhi Amplification Kit (Amersham Biosciences), restriction and circularization aided rolling circle amplification, and blunt-end ligation-mediated WGA. Recently, we have described the comparison of these methods' efficiency and reliability using SGMPlus kit. However, Y-chromosome profiling is also often used in analysis of both nondegraded and degraded DNA. This includes criminal cases and investigation of kinship in male linage. Here we demonstrate the impact of WGA methods on Y-chromosome loci (Yfiler) reactivation.The best results for nondegraded DNA were obtained with GenomiPhi kit and PEP method. In the case of degraded DNA (200 base pairs), the most complete profiles were obtained with GenomePlex kit and PEP method. None of the analyzed methods allowed full reactivation of degraded (200 base pairs) DNA in terms of Y-chromosome loci profiling.

  18. PentaPlot: A software tool for the illustration of genome mosaicism

    PubMed Central

    Hamel, Lutz; Zhaxybayeva, Olga; Gogarten, J Peter

    2005-01-01

    Background Dekapentagonal maps depict the phylogenetic relationships of five genomes in a visually appealing diagram and can be viewed as an alternative to a single evolutionary consensus tree. In particular, the generated maps focus attention on those gene families that significantly deviate from the consensus or plurality phylogeny. PentaPlot is a software tool that computes such dekapentagonal maps given an appropriate probability support matrix. Results The visualization with dekapentagonal maps critically depends on the optimal layout of unrooted tree topologies representing different evolutionary relationships among five organisms along the vertices of the dekapentagon. This is a difficult optimization problem given the large number of possible layouts. At its core our tool utilizes a genetic algorithm with demes and a local search strategy to search for the optimal layout. The hybrid genetic algorithm performs satisfactorily even in those cases where the chosen genomes are so divergent that little phylogenetic information has survived in the individual gene families. Conclusion PentaPlot is being made publicly available as an open source project at . PMID:15938752

  19. 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.

  20. Development of CAM System for Multi-Tasking Machine Tools

    NASA Astrophysics Data System (ADS)

    Kubota, Koji; Kotani, Takashi; Nakamoto, Keiichi; Ishida, Tohru; Takeuchi, Yoshimi

    Multi-tasking machine tools are very useful to manufacture complicated workpiece efficiently. However, it is very difficult to generate NC data when an operator uses multi-tasking machine tools. Currently, there are some CAM systems for multi-tasking machine tools. However, there are such problems as the manual allocation of parts to generate tool paths, the difficulty of self-interference recognition without a simulator, and so on. Therefore, this study deals with the development of CAM system which can recognize part configurations, calculate tool paths automatically for turning and milling operations, and sort them in machining order, based on 3-D CAD data of workpieces.

  1. 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.

  2. 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.

  3. 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.

  4. Developing a Statewide Student Tracking Tool

    ERIC Educational Resources Information Center

    Pai, Wendell; Moschos, Marina; Detlev, Angela; Robinson, Ophelia; Lanneau, Sumi

    2008-01-01

    This chapter describes the development of a state-level student tracking system that enables the state and institutions to follow various cohort types of students across institutional boundaries. The system was developed by the Policy Research and Data Warehousing section of the State Council of Higher Education for Virginia (SCHEV). SCHEV is the…

  5. 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)…

  6. 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.

  7. 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.

  8. 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...

  9. 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.

  10. Computational tools and resources for prediction and analysis of gene regulatory regions in the chick genome.

    PubMed

    Khan, Mohsin A F; Soto-Jimenez, Luz Mayela; Howe, Timothy; Streit, Andrea; Sosinsky, Alona; Stern, Claudio D

    2013-05-01

    The discovery of cis-regulatory elements is a challenging problem in bioinformatics, owing to distal locations and context-specific roles of these elements in controlling gene regulation. Here we review the current bioinformatics methodologies and resources available for systematic discovery of cis-acting regulatory elements and conserved transcription factor binding sites in the chick genome. In addition, we propose and make available, a novel workflow using computational tools that integrate CTCF analysis to predict putative insulator elements, enhancer prediction, and TFBS analysis. To demonstrate the usefulness of this computational workflow, we then use it to analyze the locus of the gene Sox2 whose developmental expression is known to be controlled by a complex array of cis-acting regulatory elements. The workflow accurately predicts most of the experimentally verified elements along with some that have not yet been discovered. A web version of the CTCF tool, together with instructions for using the workflow can be accessed from http://toolshed.g2.bx.psu.edu/view/mkhan1980/ctcf_analysis. For local installation of the tool, relevant Perl scripts and instructions are provided in the directory named "code" in the supplementary materials.

  11. Computational tools and resources for prediction and analysis of gene regulatory regions in the chick genome

    PubMed Central

    Khan, Mohsin A. F.; Soto-Jimenez, Luz Mayela; Howe, Timothy; Streit, Andrea; Sosinsky, Alona; Stern, Claudio D.

    2013-01-01

    The discovery of cis-regulatory elements is a challenging problem in bioinformatics, owing to distal locations and context-specific roles of these elements in controlling gene regulation. Here we review the current bioinformatics methodologies and resources available for systematic discovery of cis-acting regulatory elements and conserved transcription factor binding sites in the chick genome. In addition, we propose and make available, a novel workflow using computational tools that integrate CTCF analysis to predict putative insulator elements, enhancer prediction and TFBS analysis. To demonstrate the usefulness of this computational workflow, we then use it to analyze the locus of the gene Sox2 whose developmental expression is known to be controlled by a complex array of cis-acting regulatory elements. The workflow accurately predicts most of the experimentally verified elements along with some that have not yet been discovered. A web version of the CTCF tool, together with instructions for using the workflow can be accessed from http://toolshed.g2.bx.psu.edu/view/mkhan1980/ctcf_analysis. For local installation of the tool, relevant Perl scripts and instructions are provided in the directory named “code” in the supplementary materials. PMID:23355428

  12. 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.…

  13. 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.

  14. 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)

  15. The development of tool manufacture in humans: what helps young children make innovative tools?

    PubMed

    Chappell, Jackie; Cutting, Nicola; Apperly, Ian A; Beck, Sarah R

    2013-11-19

    We know that even young children are proficient tool users, but until recently, little was known about how they make tools. Here, we will explore the concepts underlying tool making, and the kinds of information and putative cognitive abilities required for children to manufacture novel tools. We will review the evidence for novel tool manufacture from the comparative literature and present a growing body of data from children suggesting that innovation of the solution to a problem by making a tool is a much more challenging task than previously thought. Children's difficulty with these kinds of tasks does not seem to be explained by perseveration with unmodified tools, difficulty with switching to alternative strategies, task pragmatics or issues with permission. Rather, making novel tools (without having seen an example of the required tool within the context of the task) appears to be hard, because it is an example of an 'ill-structured problem'. In this type of ill-structured problem, the starting conditions and end goal are known, but the transformations and/or actions required to get from one to the other are not specified. We will discuss the implications of these findings for understanding the development of problem-solving in humans and other animals.

  16. 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.

  17. Development of Machine Learning Tools in ROOT

    NASA Astrophysics Data System (ADS)

    Gleyzer, S. V.; Moneta, L.; Zapata, Omar A.

    2016-10-01

    ROOT is a framework for large-scale data analysis that provides basic and advanced statistical methods used by the LHC experiments. These include machine learning algorithms from the ROOT-integrated Toolkit for Multivariate Analysis (TMVA). We present several recent developments in TMVA, including a new modular design, new algorithms for variable importance and cross-validation, interfaces to other machine-learning software packages and integration of TMVA with Jupyter, making it accessible with a browser.

  18. 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…

  19. New tools for experimental diabetes research: Cellular reprogramming and genome editing

    PubMed Central

    2016-01-01

    Isolated human islets are a rare and precious material for diabetes research. However, their availability is limited, and it is impossible to obtain them from patients with specific genotypes. Human pluripotent stem cells provide an alternative. Induced pluripotent stem cells can be generated from any individual’s somatic cells and differentiated into pancreatic cells. Currently, this approach is limited by the immaturity of the islet-like cells derived from stem cells. However, this approach can already be used to model developmental defects, and the possibilities for studying insulin secretion are continuously improving. In addition, genome editing using the CRISPR/Cas9 technology provides powerful possibilities to study the impact of specific genotypes. The same technology can also be used for transcriptional regulation in order to improve the functional maturation of stem cell-derived islets. These tools are today becoming available for tomorrow’s translational diabetes research. PMID:27007444

  20. Genome elimination: translating basic research into a future tool for plant breeding.

    PubMed

    Comai, Luca

    2014-06-01

    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.

  1. 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

  2. Evaluating IMU communication skills training programme: assessment tool development.

    PubMed

    Yeap, R; Beevi, Z; Lukman, H

    2008-08-01

    This article describes the development of four assessment tools designed to evaluate the communication skills training (CST) programme at the International Medical University (IMU). The tools measure pre-clinical students' 1) perceived competency in basic interpersonal skills, 2) attitude towards patient-centred communication, 3) conceptual knowledge on doctor-patient communication, and 4) acceptance of the CST programme.

  3. The Development and Demonstration of The Metric Assessment Tool

    DTIC Science & Technology

    1993-09-01

    APIT/GCM/LAS/93S-3 A04 Ai 7.5 4 . " . THE DEVELOPMENT AND DEMONSTRATION OF THE METRIC ASSESSMENT TOOL THESIS Cynthia A. Campbell, GS-13, USAF and...Av•JI:a)iity Ccdes Avaii "•tc, or Dist 6pi-claI * iiV AFIT/GCM/LAS/93S-3 THE DEVELOPMENT AND DEMONSTRATION OF THE METRIC ASSESSMENT TOOL THESIS...thesis was to develop and demonstrate a Metric Assessment Tool for the purpose of evaluating and improving process measurements. We narrowed our study

  4. Plasmid vectors and molecular building blocks for the development of genetic manipulation tools for Trypanosoma cruzi.

    PubMed

    Bouvier, León A; Cámara, María de los Milagros; Canepa, Gaspar E; Miranda, Mariana R; Pereira, Claudio A

    2013-01-01

    The post genomic era revealed the need for developing better performing, easier to use and more sophisticated genetic manipulation tools for the study of Trypanosoma cruzi, the etiological agent of Chagas disease. In this work a series of plasmids that allow genetic manipulation of this protozoan parasite were developed. First of all we focused on useful tools to establish selection strategies for different strains and which can be employed as expression vectors. On the other hand molecular building blocks in the form of diverse selectable markers, modifiable fluorescent protein and epitope-tag coding sequences were produced. Both types of modules were harboured in backbone molecules conceived to offer multiple construction and sub-cloning strategies. These can be used to confer new properties to already available genetic manipulation tools or as starting points for whole novel designs. The performance of each plasmid and building block was determined independently. For illustration purposes, some simple direct practical applications were conducted.

  5. Enhancers as information integration hubs in development: lessons from genomics

    PubMed Central

    Buecker, Christa; Wysocka, Joanna

    2016-01-01

    Transcriptional enhancers are the primary determinants of tissue-specific gene expression. Although the majority of our current knowledge of enhancer elements comes from detailed analyses of individual loci, recent progress in epigenomics has led to the development of methods for comprehensive and conservation-independent annotation of cell type-specific enhancers. Here, we discuss the advantages and limitations of different genomic approaches to enhancer mapping and summarize observations that have been afforded by the genome-wide views of enhancer landscapes, with a focus on development. We propose that enhancers serve as information integration hubs, at which instructions encoded by the genome are read in the context of a specific cellular state, signaling milieu and chromatin environment, allowing for exquisitely precise spatiotemporal control of gene expression during embryogenesis. PMID:22487374

  6. Organoid development in cancer genome discovery.

    PubMed

    Gao, Dong; Chen, Yu

    2015-02-01

    The tumor response to most therapeutic agents in cancer is highly unpredictable. Cancer models which can adequately represent tumor heterogeneity and predict in vivo drug sensitivity are intense areas of investigation. Cancer cell lines and patient-derived xenograft models are the most frequently used models in cancer research and anticancer drug screening. Recently, cancer 'organoid' culture conditions have been developed to establish in vitro growth of patient-derived samples at higher efficiency and they are very promising for large scale drug screening and fundamental cancer biology research. Here, we leverage our experience in prostate cancer to discuss the advantages and limitations of these cancer models and summarize the development of cancer organoid culture--a development which may provide a new path towards personalized medicine in the future.

  7. 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...

  8. 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...

  9. netview p: a network visualization tool to unravel complex population structure using genome-wide SNPs.

    PubMed

    Steinig, Eike J; Neuditschko, Markus; Khatkar, Mehar S; Raadsma, Herman W; Zenger, Kyall R

    2016-01-01

    Network-based approaches are emerging as valuable tools for the analysis of complex genetic structure in wild and captive populations. netview p combines data quality control with the construction of population networks through mutual k-nearest neighbours thresholds applied to genome-wide SNPs. The program is cross-platform compatible, open-source and efficiently operates on data ranging from hundreds to hundreds of thousands of SNPs. The pipeline was used for the analysis of pedigree data from simulated (n = 750, SNPs = 1279) and captive silver-lipped pearl oysters (n = 415, SNPs = 1107), wild populations of the European hake from the Atlantic and Mediterranean (n = 834, SNPs = 380) and grey wolves from North America (n = 239, SNPs = 78 255). The population networks effectively visualize large- and fine-scale genetic structure within and between populations, including family-level structure and relationships. netview p comprises a network-based addition to other population analysis tools and provides user-friendly access to a complex network analysis pipeline through implementation in python.

  10. Artificial zinc finger DNA binding domains: versatile tools for genome engineering and modulation of gene expression.

    PubMed

    Hossain, Mir A; Barrow, Joeva J; Shen, Yong; Haq, Md Imdadul; Bungert, Jörg

    2015-11-01

    Genome editing and alteration of gene expression by synthetic DNA binding activities gained a lot of momentum over the last decade. This is due to the development of new DNA binding molecules with enhanced binding specificity. The most commonly used DNA binding modules are zinc fingers (ZFs), TALE-domains, and the RNA component of the CRISPR/Cas9 system. These binding modules are fused or linked to either nucleases that cut the DNA and induce DNA repair processes, or to protein domains that activate or repress transcription of genes close to the targeted site in the genome. This review focuses on the structure, design, and applications of ZF DNA binding domains (ZFDBDs). ZFDBDs are relatively small and have been shown to penetrate the cell membrane without additional tags suggesting that they could be delivered to cells without a DNA or RNA intermediate. Advanced algorithms that are based on extensive knowledge of the mode of ZF/DNA interactions are used to design the amino acid composition of ZFDBDs so that they bind to unique sites in the genome. Off-target binding has been a concern for all synthetic DNA binding molecules. Thus, increasing the specificity and affinity of ZFDBDs will have a significant impact on their use in analytical or therapeutic settings.

  11. Surveying the maize community for their diversity and pedigree visualization needs to prioritize tool development and curation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Maize Genetics and Genomics Database (MaizeGDB) team prepared a survey to identify breeders’ needs for visualizing pedigrees, diversity data, and haplotypes in order to prioritize tool development and curation efforts at MaizeGDB. The survey was distributed to the maize research community on beh...

  12. 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...

  13. Genomic Perspectives of Transcriptional Regulation in Forebrain Development

    PubMed Central

    Nord, Alex S.; Pattabiraman, Kartik; Visel, Axel; Rubenstein, John L. R.

    2015-01-01

    The forebrain is the seat of higher order brain functions, and many human neuropsychiatric disorders are due to genetic defects affecting forebrain development, making it imperative to understand the underlying genetic circuitry. Recent progress now makes it possible to begin fully elucidating the genomic regulatory mechanisms that control forebrain gene expression. Herein, we discuss the current knowledge of how transcription factors drive gene expression programs through their interactions with cis-acting genomic elements, such as enhancers; how analyses of chromatin and DNA modifications provide insights into gene expression states; and how these approaches yield insights into the evolution of the human brain. PMID:25569346

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a commun...

  20. Tnt1 Retrotransposon Mutagenesis: A Tool for Soybean Functional Genomics1[W][OA

    PubMed Central

    Cui, Yaya; Barampuram, Shyam; Stacey, Minviluz G.; Hancock, C. Nathan; Findley, Seth; Mathieu, Melanie; Zhang, Zhanyuan; Parrott, Wayne A.; Stacey, Gary

    2013-01-01

    Insertional mutagenesis is a powerful tool for determining gene function in both model and crop plant species. Tnt1, the transposable element of tobacco (Nicotiana tabacum) cell type 1, is a retrotransposon that replicates via an RNA copy that is reverse transcribed and integrated elsewhere in the plant genome. Based on studies in a variety of plants, Tnt1 appears to be inactive in normal plant tissue but can be reactivated by tissue culture. Our goal was to evaluate the utility of the Tnt1 retrotransposon as a mutagenesis strategy in soybean (Glycine max). Experiments showed that the Tnt1 element was stably transformed into soybean plants by Agrobacterium tumefaciens-mediated transformation. Twenty-seven independent transgenic lines carrying Tnt1 insertions were generated. Southern-blot analysis revealed that the copy number of transposed Tnt1 elements ranged from four to 19 insertions, with an average of approximately eight copies per line. These insertions showed Mendelian segregation and did not transpose under normal growth conditions. Analysis of 99 Tnt1 flanking sequences revealed insertions into 62 (62%) annotated genes, indicating that the element preferentially inserts into protein-coding regions. Tnt1 insertions were found in all 20 soybean chromosomes, indicating that Tnt1 transposed throughout the soybean genome. Furthermore, fluorescence in situ hybridization experiments validated that Tnt1 inserted into multiple chromosomes. Passage of transgenic lines through two different tissue culture treatments resulted in Tnt1 transposition, significantly increasing the number of insertions per line. Thus, our data demonstrate the Tnt1 retrotransposon to be a powerful system that can be used for effective large-scale insertional mutagenesis in soybean. PMID:23124322

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

    PubMed

    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.

  2. 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

  3. 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

  4. 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.

  5. Developing and Validating a New Classroom Climate Observation Assessment Tool

    PubMed Central

    Leff, Stephen S.; Thomas, Duane E.; Shapiro, Edward S.; Paskewich, Brooke; Wilson, Kim; Necowitz-Hoffman, Beth; Jawad, Abbas F.

    2011-01-01

    The climate of school classrooms, shaped by a combination of teacher practices and peer processes, is an important determinant for children’s psychosocial functioning and is a primary factor affecting bullying and victimization. Given that there are relatively few theoretically-grounded and validated assessment tools designed to measure the social climate of classrooms, our research team developed an observation tool through participatory action research (PAR). This article details how the assessment tool was designed and preliminarily validated in 18 third-, fourth-, and fifth-grade classrooms in a large urban public school district. The goals of this study are to illustrate the feasibility of a PAR paradigm in measurement development, ascertain the psychometric properties of the assessment tool, and determine associations with different indices of classroom levels of relational and physical aggression. PMID:21643447

  6. Developing and Validating a New Classroom Climate Observation Assessment Tool.

    PubMed

    Leff, Stephen S; Thomas, Duane E; Shapiro, Edward S; Paskewich, Brooke; Wilson, Kim; Necowitz-Hoffman, Beth; Jawad, Abbas F

    2011-01-01

    The climate of school classrooms, shaped by a combination of teacher practices and peer processes, is an important determinant for children's psychosocial functioning and is a primary factor affecting bullying and victimization. Given that there are relatively few theoretically-grounded and validated assessment tools designed to measure the social climate of classrooms, our research team developed an observation tool through participatory action research (PAR). This article details how the assessment tool was designed and preliminarily validated in 18 third-, fourth-, and fifth-grade classrooms in a large urban public school district. The goals of this study are to illustrate the feasibility of a PAR paradigm in measurement development, ascertain the psychometric properties of the assessment tool, and determine associations with different indices of classroom levels of relational and physical aggression.

  7. 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.

  8. 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

  9. 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.

  10. Case Studies of Software Development Tools for Parallel Architectures

    DTIC Science & Technology

    1993-06-01

    RL-TR-93-114 Final Technical Report AD-A269 193I M N11 Nal I U l iE rr ll Hllll CASE STUDIES OF SOFTWARE DEVELOPMENT TOOLS FOR PARALLEL ARCHITECTURES...65 Om ega/ PegaSys ..................................................................................... 66 PARET...Pisces Rn BALSA II TANGO PARET VMMP Omega/ PegaSys PSG POKER ISSOS Unity -4- PADWB Schedule Tool Degn Graph= Alg I/gr- Sol Pormbil- Ptform Pan/don Debug

  11. Development of highly efficient, low-cost lignocellulolytic enzyme systems in the post-genomic era.

    PubMed

    Liu, Guodong; Qin, Yuqi; Li, Zhonghai; Qu, Yinbo

    2013-11-01

    The current high cost of lignocellulolytic enzymes is a major bottleneck in the economic bioconversion of lignocellulosic biomass to fuels and chemicals. Fungal lignocellulolytic enzyme systems are secreted at high levels, making them the most promising starting points for further development of highly efficient lignocellulolytic enzyme systems. In this paper, recent advances in improvement of fungal lignocellulolytic enzyme systems are reviewed, with an emphasis on the achievements made using genomic approaches. A general strategy for lignocellulolytic enzyme system development is proposed, including the improvement of the hydrolysis efficiencies and productivities of current enzyme systems. The applications of genomic, transcriptomic and proteomic analysis methods in examining the composition of native enzyme systems, discovery of novel enzymes and synergistic proteins from natural sources, and understanding of regulatory mechanisms for lignocellulolytic enzyme biosynthesis are summarized. By combining systems biology and synthetic biology tools, engineered fungal strains are expected to produce high levels of optimized lignocellulolytic enzyme systems.

  12. 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.

  13. 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.

  14. USER-FRIENDLY GIS: HELPFUL TOOLS FOR CROP DEVELOPMENT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Geographic Information System (GIS) applications provide a wide range of tools that can increase the efficiency of developing new crops. Thanks to the growth of applications that are user-friendly and relatively inexpensive, scientists developing new crops can capitalize on the technology without ne...

  15. Narrative Inquiry: Research Tool and Medium for Professional Development.

    ERIC Educational Resources Information Center

    Conle, Carola

    2000-01-01

    Describes the development of narrative inquiry, highlighting one institutional setting, and discussing how narrative inquiry moved from being a research tool to a vehicle for curriculum within both graduate and preservice teacher development. After discussing theoretical resources for narrative inquiry, the paper examines criteria and terms…

  16. 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

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

    PubMed

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

    2015-12-29

    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.

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. Development and validation of microsatellite markers for Brachiaria ruziziensis obtained by partial genome assembly of Illumina single-end reads

    PubMed Central

    2013-01-01

    Background Brachiaria ruziziensis is one of the most important forage species planted in the tropics. The application of genomic tools to aid the selection of superior genotypes can provide support to B. ruziziensis breeding programs. However, there is a complete lack of information about the B. ruziziensis genome. Also, the availability of genomic tools, such as molecular markers, to support B. ruziziensis breeding programs is rather limited. Recently, next-generation sequencing technologies have been applied to generate sequence data for the identification of microsatellite regions and primer design. In this study, we present a first validated set of SSR markers for Brachiaria ruziziensis, selected from a de novo partial genome assembly of single-end Illumina reads. Results A total of 85,567 perfect microsatellite loci were detected in contigs with a minimum 10X coverage. We selected a set of 500 microsatellite loci identified in contigs with minimum 100X coverage for primer design and synthesis, and tested a subset of 269 primer pairs, 198 of which were polymorphic on 11 representative B. ruziziensis accessions. Descriptive statistics for these primer pairs are presented, as well as estimates of marker transferability to other relevant brachiaria species. Finally, a set of 11 multiplex panels containing the 30 most informative markers was validated and proposed for B. ruziziensis genetic analysis. Conclusions We show that the detection and development of microsatellite markers from genome assembled Illumina single-end DNA sequences is highly efficient. The developed markers are readily suitable for genetic analysis and marker assisted selection of Brachiaria ruziziensis. The use of this approach for microsatellite marker development is promising for species with limited genomic information, whose breeding programs would benefit from the use of genomic tools. To our knowledge, this is the first set of microsatellite markers developed for this important species

  4. Genomic Grade Index: An important tool for assessing breast cancer tumor grade and prognosis.

    PubMed

    Metzger Filho, Otto; Ignatiadis, Michail; Sotiriou, Christos

    2011-01-01

    Different multi-gene expression signatures have been shown to outperform classic histopathologic variables and therefore represent an important step towards personalizing breast cancer treatment. In particular, gene profiles overcome many of the limitations observed with classic histopathologic variables. The Genomic Grade Index (GGI) is a gene expression signature developed to better define histologic grade assessment. GGI divides classic histologic grade into low and high risk, instead of grades 1, 2 and 3. The ability of GGI to predict response to chemotherapy and separate hormone receptor positive breast cancer subtypes has also been demonstrated. This article critically reviews the limitations inherent in classic histologic grade evaluation; it also reviews the process of gene signature development in general and then focuses on GGI, its biologic significance, comparison with different gene signatures, and its applicability to clinical practise.

  5. 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.

  6. 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.

  7. MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations.

    PubMed

    Campbell, Michael S; Law, MeiYee; Holt, Carson; Stein, Joshua C; Moghe, Gaurav D; Hufnagel, David E; Lei, Jikai; Achawanantakun, Rujira; Jiao, Dian; Lawrence, Carolyn J; Ware, Doreen; Shiu, Shin-Han; Childs, Kevin L; Sun, Yanni; Jiang, Ning; Yandell, Mark

    2014-02-01

    We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts. New features include better parallelization for large repeat-rich plant genomes, noncoding RNA annotation capabilities, and support for pseudogene identification. We have benchmarked the resulting software tool kit, MAKER-P, using the Arabidopsis (Arabidopsis thaliana) and maize (Zea mays) genomes. Here, we demonstrate the ability of the MAKER-P tool kit to automatically update, extend, and revise the Arabidopsis annotations in light of newly available data and to annotate pseudogenes and noncoding RNAs absent from The Arabidopsis Informatics Resource 10 build. Our results demonstrate that MAKER-P can be used to manage and improve the annotations of even Arabidopsis, perhaps the best-annotated plant genome. We have also installed and benchmarked MAKER-P on the Texas Advanced Computing Center. We show that this public resource can de novo annotate the entire Arabidopsis and maize genomes in less than 3 h and produce annotations of comparable quality to those of the current The Arabidopsis Information Resource 10 and maize V2 annotation builds.

  8. 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.

  9. 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.

  10. Recent developments in genomics, bioinformatics and drug discovery to combat emerging drug-resistant tuberculosis.

    PubMed

    Swaminathan, Soumya; Sundaramurthi, Jagadish Chandrabose; Palaniappan, Alangudi Natarajan; Narayanan, Sujatha

    2016-12-01

    Emergence of drug-resistant tuberculosis (DR-TB) is a big challenge in TB control. The delay in diagnosis of DR-TB leads to its increased transmission, and therefore prevalence. Recent developments in genomics have enabled whole genome sequencing (WGS) of Mycobacterium tuberculosis (M. tuberculosis) from 3-day-old liquid culture and directly from uncultured sputa, while new bioinformatics tools facilitate to determine DR mutations rapidly from the resulting sequences. The present drug discovery and development pipeline is filled with candidate drugs which have shown efficacy against DR-TB. Furthermore, some of the FDA-approved drugs are being evaluated for repurposing, and this approach appears promising as several drugs are reported to enhance efficacy of the standard TB drugs, reduce drug tolerance, or modulate the host immune response to control the growth of intracellular M. tuberculosis. Recent developments in genomics and bioinformatics along with new drug discovery collectively have the potential to result in synergistic impact leading to the development of a rapid protocol to determine the drug resistance profile of the infecting strain so as to provide personalized medicine. Hence, in this review, we discuss recent developments in WGS, bioinformatics and drug discovery to perceive how they would transform the management of tuberculosis in a timely manner.

  11. MEMS product engineering using fabrication process development tools

    NASA Astrophysics Data System (ADS)

    Hahn, K.; Schmidt, T.; Ortloff, D.; Popp, J.; Wagener, A.; Brück, R.

    2008-12-01

    The development of MEMS devices differs substantially from product engineering methods used in more traditional industries. The approach is characterized by a close customer involvement and product specific fabrication processes. A large number interdependencies between device design on the one hand and manufacturing process development on the other hand make product engineering in the MEMS area a rather tedious and complicated task. In this paper we discuss a comprehensive customer-oriented MEMS product engineering methodology. Both MEMS design and fabrication process development are analyzed with regard to procedures and interfaces used in order to develop an appropriate CAD support either in terms of existing tools or by specifying individual tools to be implemented. The manufacturing process development is part of this holistic approach and is supported by a CAD environment for the management and the design of thin-film MEMS fabrication processes. This environment has been developed by the authors and became recently commercially available.

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

    PubMed Central

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

    2015-01-01

    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. PMID:25632110

  13. Functional genomics of root growth and development in Arabidopsis.

    PubMed

    Iyer-Pascuzzi, Anjali; Simpson, June; Herrera-Estrella, Luis; Benfey, Philip N

    2009-04-01

    Roots are vital for the uptake of water and nutrients, and for anchorage in the soil. They are highly plastic, able to adapt developmentally and physiologically to changing environmental conditions. Understanding the molecular mechanisms behind this growth and development requires knowledge of root transcriptomics, proteomics, and metabolomics. Genomics approaches, including the recent publication of a root expression map, root proteome, and environment-specific root expression studies, are uncovering complex transcriptional and post-transcriptional networks underlying root development. The challenge is in further capitalizing on the information in these datasets to understand the fundamental principles of root growth and development. In this review, we highlight progress researchers have made toward this goal.

  14. Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population.

    PubMed

    Bowden, Rory; MacFie, Tammie S; Myers, Simon; Hellenthal, Garrett; Nerrienet, Eric; Bontrop, Ronald E; Freeman, Colin; Donnelly, Peter; Mundy, Nicholas I

    2012-01-01

    In spite of its evolutionary significance and conservation importance, the population structure of the common chimpanzee, Pan troglodytes, is still poorly understood. An issue of particular controversy is whether the proposed fourth subspecies of chimpanzee, Pan troglodytes ellioti, from parts of Nigeria and Cameroon, is genetically distinct. Although modern high-throughput SNP genotyping has had a major impact on our understanding of human population structure and demographic history, its application to ecological, demographic, or conservation questions in non-human species has been extremely limited. Here we apply these tools to chimpanzee population structure, using ∼700 autosomal SNPs derived from chimpanzee genomic data and a further ∼100 SNPs from targeted re-sequencing. We demonstrate conclusively the existence of P. t. ellioti as a genetically distinct subgroup. We show that there is clear differentiation between the verus, troglodytes, and ellioti populations at the SNP and haplotype level, on a scale that is greater than that separating continental human populations. Further, we show that only a small set of SNPs (10-20) is needed to successfully assign individuals to these populations. Tellingly, use of only mitochondrial DNA variation to classify individuals is erroneous in 4 of 54 cases, reinforcing the dangers of basing demographic inference on a single locus and implying that the demographic history of the species is more complicated than that suggested analyses based solely on mtDNA. In this study we demonstrate the feasibility of developing economical and robust tests of individual chimpanzee origin as well as in-depth studies of population structure. These findings have important implications for conservation strategies and our understanding of the evolution of chimpanzees. They also act as a proof-of-principle for the use of cheap high-throughput genomic methods for ecological questions.

  15. Genomic Tools for Evolution and Conservation in the Chimpanzee: Pan troglodytes ellioti Is a Genetically Distinct Population

    PubMed Central

    Myers, Simon; Hellenthal, Garrett; Nerrienet, Eric; Bontrop, Ronald E.; Freeman, Colin; Donnelly, Peter; Mundy, Nicholas I.

    2012-01-01

    In spite of its evolutionary significance and conservation importance, the population structure of the common chimpanzee, Pan troglodytes, is still poorly understood. An issue of particular controversy is whether the proposed fourth subspecies of chimpanzee, Pan troglodytes ellioti, from parts of Nigeria and Cameroon, is genetically distinct. Although modern high-throughput SNP genotyping has had a major impact on our understanding of human population structure and demographic history, its application to ecological, demographic, or conservation questions in non-human species has been extremely limited. Here we apply these tools to chimpanzee population structure, using ∼700 autosomal SNPs derived from chimpanzee genomic data and a further ∼100 SNPs from targeted re-sequencing. We demonstrate conclusively the existence of P. t. ellioti as a genetically distinct subgroup. We show that there is clear differentiation between the verus, troglodytes, and ellioti populations at the SNP and haplotype level, on a scale that is greater than that separating continental human populations. Further, we show that only a small set of SNPs (10–20) is needed to successfully assign individuals to these populations. Tellingly, use of only mitochondrial DNA variation to classify individuals is erroneous in 4 of 54 cases, reinforcing the dangers of basing demographic inference on a single locus and implying that the demographic history of the species is more complicated than that suggested analyses based solely on mtDNA. In this study we demonstrate the feasibility of developing economical and robust tests of individual chimpanzee origin as well as in-depth studies of population structure. These findings have important implications for conservation strategies and our understanding of the evolution of chimpanzees. They also act as a proof-of-principle for the use of cheap high-throughput genomic methods for ecological questions. PMID:22396655

  16. 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

  17. Thermal shock as a carbide grade development tool

    SciTech Connect

    Merten, C.W.; von Turkovich, B.F.

    1984-01-01

    Objective improvement of quality through the maximization of signal to noise ratios is discussed. It is proposed that the signal to noise ratio concept also be applied to grade development of carbide tools for intermittent cutting. Thermal shock resistance is identified as a tool material property which might serve as a practical indicator of tool life for certain cutting conditions. Carbide specimens were subjected to single cycle thermal shock and statistical methods for the analysis of the resulting data are presented. Parameters for monitoring signal shift and signal to noise ratio are identified for the Weibull distribution. These parameters are then utilized for grade selection or grade prediction according to a proposed grade development strategy.

  18. Development of culturally sensitive dialog tools in diabetes education

    PubMed Central

    Hempler, Nana Folmann; Ewers, Bettina

    2015-01-01

    Person-centeredness is a goal in diabetes education, and cultural influences are important to consider in this regard. This report describes the use of a design-based research approach to develop culturally sensitive dialog tools to support person-centered dietary education targeting Pakistani immigrants in Denmark with type 2 diabetes. The approach appears to be a promising method to develop dialog tools for patient education that are culturally sensitive, thereby increasing their acceptability among ethnic minority groups. The process also emphasizes the importance of adequate training and competencies in the application of dialog tools and of alignment between researchers and health care professionals with regards to the educational philosophy underlying their use. PMID:25593850

  19. 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

  20. Development of a Public Health Assessment Tool to Prevent Lyme Disease: Tool Construction and Validation

    PubMed Central

    Garvin, Jennifer Hornung; Gordon, Thomas F; Haignere, Clara; DuCette, Joseph P

    2005-01-01

    This study involved the design and validation of a new Lyme disease risk assessment instrument. The study was funded in part by a research grant from the American Health Information Management Association (AHIMA) Foundation on Research and Education (FORE). The resulting instrument measured theoretical constructs such as attitudes, behaviors, beliefs, skills, and knowledge relative to Lyme disease. The survey assessment tool is described here, and the tool development process, the validation and reliability process, and results are presented. The assessment tool was created by using a standard instrument development process that first involved constructing possible items (questions) based on several health behavior theories and known health risk behaviors. These items were then further refined by using focus groups, a small pilot study, factor analysis, and a large-scale pilot study. Validity and reliability indices were established with a test-retest reliability coefficient of .66, and finally the tool was used among a population living in a Lyme-disease-endemic area. Cronbach's alpha coefficients of .737 for behavioral items, .573 for cognitive items, and .331 for environmental items were established. PMID:18066379

  1. 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.

  2. 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

  3. 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…

  4. 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),…

  5. 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…

  6. 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…

  7. 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…

  8. 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

  9. Practitioner-Oriented Research as a Tool for Professional Development

    ERIC Educational Resources Information Center

    Johansson, Inge; Sandberg, Anette; Vuorinen, Tuula

    2007-01-01

    The aim of this study was to analyse how a model for practitioner-oriented research can be used as a tool for professional development in the preschool. The focus of interest is the type of knowledge that is formed when researchers and preschool staff cooperate on local projects, and what this new knowledge means for the images of professional…

  10. 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…

  11. 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…

  12. 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…

  13. 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…

  14. Collection Development in Public Health: A Guide to Selection Tools

    ERIC Educational Resources Information Center

    Wallis, Lisa C.

    2004-01-01

    Public health librarians face many challenges in collection development because the field is multidisciplinary, the collection's users have varied needs, and many of the essential resources are grey literature materials. Further, little has been published about public health selection tools. However, librarians responsible for these areas have a…

  15. Reflective Journaling: A Tool for Teacher Professional Development

    ERIC Educational Resources Information Center

    Dreyer, Lorna M.

    2015-01-01

    This qualitative study explores the introduction of postgraduate education students to reflective journaling as a tool for professional development. Students were purposefully selected to keep a weekly journal in which they reflected in and on the activities (methodologies, techniques, strategies) they engaged in while executing a workplace…

  16. 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.

  17. The potential of comparative genomic hybridization as a tool in the differential diagnosis of matrix-producing bone lesions.

    PubMed

    Gebert, Carsten; Brinkschmidt, Christian; Bielack, Stefan; Bernhardt, Thomas; Jürgens, Heribert; Böcker, Werner; Winkelmann, Winfried; Bürger, Horst; Gosheger, Georg

    2006-07-01

    Matrix-producing bone lesions consist of a wide variety of benign and malignant conditions. With respect to morphology, an overlap exists between benign and malignant bone tumors that causes difficulties in the final determination of the tumor. This study was conducted to show the potential of comparative genomic hybridization as a tool in the differential diagnosis of matrix-producing bone lesions. Thirty benign bone tumors were evaluated by conventional comparative genomic hybridization. To test its diagnostic reliability, 5 additional cases were analyzed, all with differential diagnostic difficulties related to morphology and radiology. All were ultimately diagnosed as malignant sarcomas, and unbalanced alterations were detected. In contrast benign tumors or tumor-like lesions did not reveal any chromosomal alterations. Comparative genomic hybridization is a useful adjunct in the complicated differential diagnostic algorithms of matrix-producing bone tumors.

  18. MetaSpark: a spark-based distributed processing tool to recruit metagenomic reads to reference genomes.

    PubMed

    Zhou, Wei; Li, Ruilin; Yuan, Shuo; Liu, ChangChun; Yao, Shaowen; Luo, Jing; Niu, Beifang

    2017-01-08

    With the advent of next-generation sequencing, traditional bioinformatics tools are challenged by massive raw metagenomic datasets. One of the bottlenecks of metagenomic studies is lack of large-scale and cloud computing suitable data analysis tools. In this paper, we proposed a Spark -: based tool, called MetaSpark, to recruit metagenomic reads to reference genomes. MetaSpark benefits from the distributed data set (RDD) of Spark, which makes it able to cache data set in memory across cluster nodes and scale well with the datasets. Compared with previous metagenomics recruitment tools, MetaSpark recruited significantly more reads than many programs such as SOAP2, BWA and LAST and increased recruited reads by ∼4% compared with FR-HIT when there were 1 million reads and 0.75 GB references. Different test cases demonstrate MetaSpark's scalability and overall high performance.

  19. Developing an assessment tool for evaluating community involvement

    PubMed Central

    South, Jane; Fairfax, Pat; Green, Eleanor

    2005-01-01

    Abstract Background  Current UK policy has resulted in greater requirements for public and patient participation in health service planning and decision making. Organizations and services need to be able to monitor and evaluate the effectiveness and quality of their community involvement processes, but there are few appropriate evaluation tools or sets of indicators available. This paper reports on work within Bradford Health Action Zone to develop a self‐assessment tool for organizations on community involvement. Methods  A multi‐agency working group developed the tool. A literature search was undertaken and evaluation resources were reviewed. A set of benchmarks for community involvement in regeneration was utilized in developing the assessment areas. A range of individuals with expertise on community involvement practice and performance management was consulted. The tool was then piloted in two primary care trusts prior to final modifications. Results  The process resulted in the production of Well Connected – a self‐assessment tool on community involvement designed for organizations to assess their progress and identify areas for improvement. A scoring system assesses evidence of a strategic approach to community involvement, good practice throughout the organization, and a range of opportunities and support. Feedback from the pilots revealed that the tool had facilitated assessment of the strengths and weaknesses of organizational practices. Conclusion  The paper discusses some of the methodological challenges pertaining to the measurement of community involvement. Notwithstanding those challenges, it is argued that Well Connected provides a robust and practical framework that health organizations and their partners can use to assess practice. PMID:15713172

  20. 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.

  1. Screen and clean: a tool for identifying interactions in genome-wide association studies.

    PubMed

    Wu, Jing; Devlin, Bernie; Ringquist, Steven; Trucco, Massimo; Roeder, Kathryn

    2010-04-01

    Epistasis could be an important source of risk for disease. How interacting loci might be discovered is an open question for genome-wide association studies (GWAS). Most researchers limit their statistical analyses to testing individual pairwise interactions (i.e., marginal tests for association). A more effective means of identifying important predictors is to fit models that include many predictors simultaneously (i.e., higher-dimensional models). We explore a procedure called screen and clean (SC) for identifying liability loci, including interactions, by using the lasso procedure, which is a model selection tool for high-dimensional regression. We approach the problem by using a varying dictionary consisting of terms to include in the model. In the first step the lasso dictionary includes only main effects. The most promising single-nucleotide polymorphisms (SNPs) are identified using a screening procedure. Next the lasso dictionary is adjusted to include these main effects and the corresponding interaction terms. Again, promising terms are identified using lasso screening. Then significant terms are identified through the cleaning process. Implementation of SC for GWAS requires algorithms to explore the complex model space induced by the many SNPs genotyped and their interactions. We propose and explore a set of algorithms and find that SC successfully controls Type I error while yielding good power to identify risk loci and their interactions. When the method is applied to data obtained from the Wellcome Trust Case Control Consortium study of Type 1 Diabetes it uncovers evidence supporting interaction within the HLA class II region as well as within Chromosome 12q24.

  2. Screen and Clean: a tool for identifying interactions in genome-wide association studies

    PubMed Central

    Wu, Jing; Devlin, Bernie; Ringquist, Steven; Trucco, Massimo; Roeder, Kathryn

    2010-01-01

    Epistasis could be an important source of risk for disease. How interacting loci might be discovered is an open question for genome-wide association studies (GWAS). Most researchers limit their statistical analyses to testing individual pairwise interactions (i.e., marginal tests for association). A more effective means of identifying important predictors is to fit models that include many predictors simultaneously (i.e., higher dimensional models). We explore a procedure called screen and clean (SC) for identifying liability loci, including interactions, by using the lasso procedure, which is a model selection tool for high dimensional regression. We approach the problem by using a varying dictionary consisting of terms to include in the model. In the first step the lasso dictionary includes only main effects. The most promising SNPs are identified using a screening procedure. Next the lasso dictionary is adjusted to include these main effects and the corresponding interaction terms. Again, promising terms are identified using lasso screening. Then significant terms are identified through the cleaning process. Implementation of SC for GWAS requires algorithms to explore the complex model space induced by the many SNPs genotyped and their interactions. We propose and explore a set of algorithms and find that SC successfully controls Type I error while yielding good power to identify risk loci and their interactions. When the method is applied to data obtained from the Wellcome Trust Case Control Consortium study of Type 1 Diabetes it uncovers evidence supporting interaction within the HLA class II region as well as within Chromosome 12q24. PMID:20088021

  3. 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.

  4. 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

  5. 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.

  6. The development of an obstetric triage acuity tool.

    PubMed

    Paisley, Kathleen S; Wallace, Ruth; DuRant, Patricia G

    2011-01-01

    The purpose of this article is to describe the journey a multicampus hospital system took to improve the obstetric triage process. A review of literature revealed no current comprehensive obstetric acuity tool, and thus our team developed a tool with a patient flow process, revised and updated triage nurse competencies, and then educated the nurses about the new tool and process. Data were collected to assess the functionality of the new process in assigning acuity upon patient arrival, conveying appropriate acuities based on patient complaints, and initiating the medical screening examination, all within prescribed time intervals. Initially data indicated that processes were still not optimal, and re-education was provided for all triage nurses. This improved all data points. The result of this QI project is that our patients are now seen based on their acuity within designated time frames.

  7. Development of a Simulation Tool for 3D Braiding Architectures

    NASA Astrophysics Data System (ADS)

    Tolosana, N.; Lomov, S.; Stüve, J.; Miravete, A.

    2007-04-01

    The usage of textile technologies for composites is widely extended in aeronautic applications. They provide an improvement on mechanical properties in the thickness direction, and offer some other advantages in comparison with prepreg technology regarding production. Nowadays 3D-braiding machines do not only enable the production of solid profiles but enable also the production of complex near-net-shape reinforcement structures with changing cross section geometry. In order to attain a full understanding on structure of 3d braids to be able to predict mechanical properties, simulation tools including machine operation are needed. A simulation tool is being developed as a part of the EU project "Integrated Tool for Simulation of Textile Composites", starting from 3d braiding machinery description and operation. This information is required to reproduce yarn paths in the produced unit cell, based on the interlacing pattern of the braid.

  8. 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.

  9. 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

  10. Development of a site analysis tool for distributed wind projects

    SciTech Connect

    Shaw, Shawn

    2012-02-28

    The Cadmus Group, Inc., in collaboration with the National Renewable Energy Laboratory (NREL) and Encraft, was awarded a grant from the Department of Energy (DOE) to develop a site analysis tool for distributed wind technologies. As the principal investigator for this project, Mr. Shawn Shaw was responsible for overall project management, direction, and technical approach. The product resulting from this project is the Distributed Wind Site Analysis Tool (DSAT), a software tool for analyzing proposed sites for distributed wind technology (DWT) systems. This user-friendly tool supports the long-term growth and stability of the DWT market by providing reliable, realistic estimates of site and system energy output and feasibility. DSAT-which is accessible online and requires no purchase or download of software-is available in two account types; Standard: This free account allows the user to analyze a limited number of sites and to produce a system performance report for each; and Professional: For a small annual fee users can analyze an unlimited number of sites, produce system performance reports, and generate other customizable reports containing key information such as visual influence and wind resources. The tool’s interactive maps allow users to create site models that incorporate the obstructions and terrain types present. Users can generate site reports immediately after entering the requisite site information. Ideally, this tool also educates users regarding good site selection and effective evaluation practices.

  11. 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.

  12. MISIS-2: A bioinformatics tool for in-depth analysis of small RNAs and representation of consensus master genome in viral quasispecies.

    PubMed

    Seguin, Jonathan; Otten, Patricia; Baerlocher, Loïc; Farinelli, Laurent; Pooggin, Mikhail M

    2016-07-01

    In most eukaryotes, small RNA (sRNA) molecules such as miRNAs, siRNAs and piRNAs regulate gene expression and repress transposons and viruses. AGO/PIWI family proteins sort functional sRNAs based on size, 5'-nucleotide and other sequence features. In plants and some animals, viral sRNAs are extremely diverse and cover the entire viral genome sequences, which allows for de novo reconstruction of a complete viral genome by deep sequencing and bioinformatics analysis of viral sRNAs. Previously, we have developed a tool MISIS to view and analyze sRNA maps of viruses and cellular genome regions which spawn multiple sRNAs. Here we describe a new release of MISIS, MISIS-2, which enables to determine and visualize a consensus sequence and count sRNAs of any chosen sizes and 5'-terminal nucleotide identities. Furthermore we demonstrate the utility of MISIS-2 for identification of single nucleotide polymorphisms (SNPs) at each position of a reference sequence and reconstruction of a consensus master genome in evolving viral quasispecies. MISIS-2 is a Java standalone program. It is freely available along with the source code at the website http://www.fasteris.com/apps.

  13. 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...

  14. 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...

  15. Endonuclease mediated genome editing in drug discovery and development: promises and challenges.

    PubMed

    Prabhu, Vidya; Xu, Han

    Site specific genome editing has been gradually employed in drug discovery and development process over the past few decades. Recent development of CRISPR technology has significantly accelerated the incorporation of genome editing in the bench side to bedside process. In this review, we summarize examples of applications of genome editing in the drug discovery and development process. We also discuss current hurdles and solutions of genome editing.

  16. Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes

    PubMed Central

    Farreras, Montse

    2014-01-01

    Abstract 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. PMID:24597675

  17. 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.

  18. Development of simulation tools for virus shell assembly. Final report

    SciTech Connect

    Berger, Bonnie

    2001-01-05

    Prof. Berger's major areas of research have been in applying computational and mathematical techniques to problems in biology, and more specifically to problems in protein folding and genomics. Significant progress has been made in the following areas relating to virus shell assembly: development has been progressing on a second-generation self-assembly simulator which provides a more versatile and physically realistic model of assembly; simulations are being developed and applied to a variety of problems in virus assembly; and collaborative efforts have continued with experimental biologists to verify and inspire the local rules theory and the simulator. The group has also worked on applications of the techniques developed here to other self-assembling structures in the material and biological sciences. Some of this work has been conducted in conjunction with Dr. Sorin Istrail when he was at Sandia National Labs.

  19. 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.

  20. 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

  1. Developing a tool for assessing public health law in countries.

    PubMed

    Kim, So Yoon; Lee, Yuri; Sohn, Myongsei; Hahm, Ki-Hyun

    2012-09-01

    At present, the World Health Organization (WHO) is in the process of developing a tool designed to assess the status of public health legislation in a given country. An Expert Consultation on Public Health Law was convened in Manila, Philippines, in May 2011. The participants agreed that the tool could serve as a guide for a regional approach to assist Member States in assessing the scope, completeness, and adequacy of their public health law. Given the broad definition of "public health" and the laws that affect health, directly or indirectly, the participants further agreed to narrow the field to 4 areas based on significant WHO works/policies, each organized into an independent module: (1) International Digest on Health Law, (2) Primary Health Care, (3) International Health Regulations 2005, and (4) Framework Convention on Tobacco Control. The tool would be drafted in a questionnaire format that asks the respondent to determine whether primary and/or subsidiary legislation exists in the country on a specific topic and, if so, to cite the relevant law, describe the pertinent points, and attach and/or link to the full text where available. The participants agreed that the respondents should include government officials and/or academics with legal competency. Version 1 of the tool was piloted in the Philippines, the Republic of Korea, Samoa, and Vanuatu. At a 2nd Expert Consultation on Public Health Law, convened in Incheon, Republic of Korea, in October 2011, in conjunction with the 43rd Conference of the Asia-Pacific Academic Consortium on Public Health, the participants determined that the tool was generally usable, certain concerns notwithstanding, such as the risk of standardizing compliance with WHO policies. The agreed next step is to finalize the analysis tool by August 2012, marking the end of stage I in the development process. Stage II will consist of team building and networking of responsible officers and/or professionals in the countries. The tool

  2. 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.

  3. Genomic imprinting in development, growth, behavior and stem cells.

    PubMed

    Plasschaert, Robert N; Bartolomei, Marisa S

    2014-05-01

    Genes that are subject to genomic imprinting in mammals are preferentially expressed from a single parental allele. This imprinted expression of a small number of genes is crucial for normal development, as these genes often directly regulate fetal growth. Recent work has also demonstrated intricate roles for imprinted genes in the brain, with important consequences on behavior and neuronal function. Finally, new studies have revealed the importance of proper expression of specific imprinted genes in induced pluripotent stem cells and in adult stem cells. As we review here, these findings highlight the complex nature and developmental importance of imprinted genes.

  4. 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.

  5. 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.

  6. Space mission scenario development and performance analysis tool

    NASA Technical Reports Server (NTRS)

    Kordon, Mark; Baker, John; Gilbert, John; Hanks, David

    2004-01-01

    This paper discusses a new and innovative approach for a rapid spacecraft multi-disciplinary performance analysis using a tool called the Mission Scenario Development Workbench (MSDW). To meet the needs of new classes of space missions, analysis tools with proven models were developed and integrated into a framework to enable rapid trades and analyses between spacecraft designs and operational scenarios during the formulation phase of a mission. Generally speaking, spacecraft resources are highly constrained on deep space missions and this approach makes it possible to maximize the use of existing resources to attain the best possible science return. This approach also has the potential benefit of reducing the risk of costly design changes made later in the design cycle necessary to meet the mission requirements by understanding system design sensitivities early and adding appropriate margins. This paper will describe the approach used by the Mars Science Laboratory Project to accomplish this result.

  7. 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.

  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 a Program Manager/User Communication Evaluation Tool.

    DTIC Science & Technology

    1987-09-01

    TECHNOLOGY Wright-Patterson Air Force Base , Ohio * ~ I IBUON STATEMEN2T AL Appra~id for public r.eaa. . .1. ... Ty..IU..4 6*..IP AFIT/GLM/LSM/87S-8 ~El...managers construct messages based on what the program manager feels is important and not necessarily what is important to the receiver. A communications...Manager/User Communication .. ......... 5- 5 Develop a Program Manager/User Communication Evaluation Tool, Based Upon the Attributes of Communications

  11. Developing Battery Computer Aided Engineering Tools for Military Vehicles

    DTIC Science & Technology

    2013-12-01

    Solid Electrolyte Interphase (SEI) layer decomposition 80 2 Anode — electrolyte 100 3 Cathode — electrolyte 130 4 Electrolyte decomposition 180...performance, NREL and the University of Colorado at Boulder coded and linked a solid mechanics model to explore mechanical phenomena in lithium -ion...electrified military vehicles. Particularly, TARDEC’s objective was the development of tools to accelerate comparative analysis of alternative lithium -ion

  12. 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.

  13. On transform coding tools under development for VP10

    NASA Astrophysics Data System (ADS)

    Parker, Sarah; Chen, Yue; Han, Jingning; Liu, Zoe; Mukherjee, Debargha; Su, Hui; Wang, Yongzhe; Bankoski, Jim; Li, Shunyao

    2016-09-01

    Google started the WebM Project in 2010 to develop open source, royaltyfree video codecs designed specifically for media on the Web. The second generation codec released by the WebM project, VP9, is currently served by YouTube, and enjoys billions of views per day. Realizing the need for even greater compression efficiency to cope with the growing demand for video on the web, the WebM team embarked on an ambitious project to develop a next edition codec, VP10, that achieves at least a generational improvement in coding efficiency over VP9. Starting from VP9, a set of new experimental coding tools have already been added to VP10 to achieve decent coding gains. Subsequently, Google joined a consortium of major tech companies called the Alliance for Open Media to jointly develop a new codec AV1. As a result, the VP10 effort is largely expected to merge with AV1. In this paper, we focus primarily on new tools in VP10 that improve coding of the prediction residue using transform coding techniques. Specifically, we describe tools that increase the flexibility of available transforms, allowing the codec to handle a more diverse range or residue structures. Results are presented on a standard test set.

  14. Human Performance Tool Development and Analysis Support. FY15 Task: Early Manpower Assessment Tool (EMAT) for STAMPS

    DTIC Science & Technology

    2015-10-01

    1 Annual Progress Report (A003) for Human Performance Tool Development and Analysis Support FY15 Task: EARLY MANPOWER ASSESSMENT TOOL (EMAT...00-2015 to 00-00-2015 4. TITLE AND SUBTITLE Human Performance Tool Development and Analysis Support 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c...for the development and maintenance of the U.S. Navy’s Leading Edge Architecture got Prototyping Systems (LEAPS) Integrated Digital Environment

  15. 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.

  16. Global nutrient profiling by Phenotype MicroArrays: a tool complementing genomic and proteomic studies in conidial fungi*

    PubMed Central

    Atanasova, Lea; Druzhinina, Irina S.

    2010-01-01

    Conidial fungi or molds and mildews are widely used in modern biotechnology as producers of antibiotics and other secondary metabolites, industrially important enzymes, chemicals and food. They are also important pathogens of animals including humans and agricultural crops. These various applications and extremely versatile natural phenotypes have led to the constantly growing list of complete genomes which are now available. Functional genomics and proteomics widely exploit the genomic information to study the cell-wide impact of altered genes on the phenotype of an organism and its function. This allows for global analysis of the information flow from DNA to RNA to protein, but it is usually not sufficient for the description of the global phenotype of an organism. More recently, Phenotype MicroArray (PM) technology has been introduced as a tool to characterize the metabolism of a (wild) fungal strain or a mutant. In this article, we review the background of PM applications for fungi and the methodic requirements to obtain reliable results. We also report examples of the versatility of this tool. PMID:20205302

  17. 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

  18. Developing Tools and Technologies to Meet MSR Planetary Protection Requirements

    NASA Technical Reports Server (NTRS)

    Lin, Ying

    2013-01-01

    This paper describes the tools and technologies that need to be developed for a Caching Rover mission in order to meet the overall Planetary Protection requirements for future Mars Sample Return (MSR) campaign. This is the result of an eight-month study sponsored by the Mars Exploration Program Office. The goal of this study is to provide a future MSR project with a focused technology development plan for achieving the necessary planetary protection and sample integrity capabilities for a Mars Caching Rover mission.

  19. Development of proteasome inhibitors as research tools and cancer drugs

    PubMed Central

    2012-01-01

    The proteasome is the primary site for protein degradation in mammalian cells, and proteasome inhibitors have been invaluable tools in clarifying its cellular functions. The anticancer agent bortezomib inhibits the major peptidase sites in the proteasome’s 20S core particle. It is a “blockbuster drug” that has led to dramatic improvements in the treatment of multiple myeloma, a cancer of plasma cells. The development of proteasome inhibitors illustrates the unpredictability, frustrations, and potential rewards of drug development but also emphasizes the dependence of medical advances on basic biological research. PMID:23148232

  20. 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.

  1. PGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine typing

    PubMed Central

    Liu, Yen-Yi; Chiou, Chien-Shun; Chen, Chih-Chieh

    2016-01-01

    With the advance of next generation sequencing techniques, whole genome sequencing (WGS) is expected to become the optimal method for molecular subtyping of bacterial isolates. To use WGS as a general subtyping method for disease outbreak investigation and surveillance, the layout of WGS-based typing must be comparable among laboratories. Whole genome multilocus sequence typing (wgMLST) is an approach that achieves this requirement. To apply wgMLST as a standard subtyping approach, a pan-genome allele database (PGAdb) for the population of a bacterial organism must first be established. We present a free web service tool, PGAdb-builder (http://wgmlstdb.imst.nsysu.edu.tw), for the construction of bacterial PGAdb. The effectiveness of PGAdb-builder was tested by constructing a pan-genome allele database for Salmonella enterica serovar Typhimurium, with the database being applied to create a wgMLST tree for a panel of epidemiologically well-characterized S. Typhimurium isolates. The performance of the wgMLST-based approach was as high as that of the SNP-based approach in Leekitcharoenphon’s study used for discerning among epidemiologically related and non-related isolates. PMID:27824078

  2. 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.

  3. Development and testing of a community flood resilience measurement tool

    NASA Astrophysics Data System (ADS)

    Keating, Adriana; Campbell, Karen; Szoenyi, Michael; McQuistan, Colin; Nash, David; Burer, Meinrad

    2017-01-01

    Given the increased attention on resilience strengthening in international humanitarian and development work, there is a growing need to invest in its measurement and the overall accountability of resilience strengthening initiatives. The purpose of this article is to present our framework and tool for measuring community-level resilience to flooding and generating empirical evidence and to share our experience in the application of the resilience concept. At the time of writing the tool is being tested in 75 communities across eight countries. Currently 88 potential sources of resilience are measured at the baseline (initial state) and end line (final state) approximately 2 years later. If a flood occurs in the community during the study period, resilience outcome measures are recorded. By comparing pre-flood characteristics to post-flood outcomes, we aim to empirically verify sources of resilience, something which has never been done in this field. There is an urgent need for the continued development of theoretically anchored, empirically verified, and practically applicable disaster resilience measurement frameworks and tools so that the field may (a) deepen understanding of the key components of disaster resilience in order to better target resilience-enhancing initiatives, and (b) enhance our ability to benchmark and measure disaster resilience over time, and (c) compare how resilience changes as a result of different capacities, actions and hazards.

  4. 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.

  5. 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.

  6. Development of forensic-quality full mtGenome haplotypes: success rates with low template specimens.

    PubMed

    Just, Rebecca S; Scheible, Melissa K; Fast, Spence A; Sturk-Andreaggi, Kimberly; Higginbotham, Jennifer L; Lyons, Elizabeth A; Bush, Jocelyn M; Peck, Michelle A; Ring, Joseph D; Diegoli, Toni M; Röck, Alexander W; Huber, Gabriela E; Nagl, Simone; Strobl, Christina; Zimmermann, Bettina; Parson, Walther; Irwin, Jodi A

    2014-05-01

    Forensic mitochondrial DNA (mtDNA) testing requires appropriate, high quality reference population data for estimating the rarity of questioned haplotypes and, in turn, the strength of the mtDNA evidence. Available reference databases (SWGDAM, EMPOP) currently include information from the mtDNA control region; however, novel methods that quickly and easily recover mtDNA coding region data are becoming increasingly available. Though these assays promise to both facilitate the acquisition of mitochondrial genome (mtGenome) data and maximize the general utility of mtDNA testing in forensics, the appropriate reference data and database tools required for their routine application in forensic casework are lacking. To address this deficiency, we have undertaken an effort to: (1) increase the large-scale availability of high-quality entire mtGenome reference population data, and (2) improve the information technology infrastructure required to access/search mtGenome data and employ them in forensic casework. Here, we describe the application of a data generation and analysis workflow to the development of more than 400 complete, forensic-quality mtGenomes from low DNA quantity blood serum specimens as part of a U.S. National Institute of Justice funded reference population databasing initiative. We discuss the minor modifications made to a published mtGenome Sanger sequencing protocol to maintain a high rate of throughput while minimizing manual reprocessing with these low template samples. The successful use of this semi-automated strategy on forensic-like samples provides practical insight into the feasibility of producing complete mtGenome data in a routine casework environment, and demonstrates that large (>2kb) mtDNA fragments can regularly be recovered from high quality but very low DNA quantity specimens. Further, the detailed empirical data we provide on the amplification success rates across a range of DNA input quantities will be useful moving forward as PCR

  7. 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.

  8. Development and testing of the codependency assessment tool.

    PubMed

    Hughes-Hammer, C; Martsolf, D S; Zeller, R A

    1998-10-01

    Codependency constitutes a significant health risk, particularly for women, because codependent women are often involved in abusive and potentially harmful relationships. Individuals who are identified as codependent can engage in therapy and gain knowledge and freedom from such relationships. However, there is no reliable and valid measure of codependency that is consistently used to identify these individuals. This article describes the development and testing of the Codependency Assessment Tool, a multivariate tool that conceptualizes codependency as a construct comprising five factors: (1) Other Focus/Self-Neglect, (2) Low Self-Worth, (3) Hiding Self, (4) Medical Problems, and (5) Family of Origin Issues. The instrument has excellent reliability and validity. Its test-retest reliabilities = .78 to .94; Cronbach's alpha = .78 to .91. Criterion validity was determined to be established by using known groups; construct validity was established by comparing the codependency dimensions with depression.

  9. 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

  10. [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.

  11. 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.

  12. 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

  13. 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

    2017-01-01

    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 identified, 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 amplified with specific products and 24 (80.0%) were polymorphic. For the amplified 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 significant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identified SSRs significantly 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.

  14. Application of genomic and quantitative genetic tools to identify candidate resistance genes for brown rot resistance in peach.

    PubMed

    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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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...

  1. 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...

  2. 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.

  3. CRISPR-Cas9 System as a Versatile Tool for Genome Engineering in Human Cells

    PubMed Central

    Wang, Xuelian; Huang, Xiumin; Fang, Xiuli; Zhang, Youzhong; Wang, Wanpeng

    2016-01-01

    Targeted nucleases are influential instruments for intervening in genome revision with great accuracy. RNA-guided Cas9 nucleases produced from clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have noticeably altered the means to modify the genomes of distinct organisms. They can be notably used to facilitate effective genome manipulation in eukaryotic cells by clearly detailing a 20-nt targeting sequence inside its directed RNA. We discuss the most recent advancements in the molecular basis of the type II CRISPR/Cas system and encapsulate applications and elements affecting its use in human cells. We also propose possible applications covering its uses ranging from basic science to implementation in the clinic. PMID:27845770

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. Development of the Liverpool Adverse Drug Reaction Avoidability Assessment Tool

    PubMed Central

    Bracken, Louise E.; Nunn, Anthony J.; Kirkham, Jamie J.; Peak, Matthew; Arnott, Janine; Smyth, Rosalind L.; Pirmohamed, Munir; Turner, Mark A.

    2017-01-01

    Aim To develop and test a new tool to assess the avoidability of adverse drug reactions that is suitable for use in paediatrics but which is also applicable to a variety of other settings. Methods The study involved multiple phases. Preliminary work involved using the Hallas scale and a modification of the existing Hallas scale, to assess two different sets of adverse drug reaction (ADR) case reports. Phase 1 defined, modified and refined a new tool using multidisciplinary teams. Phase 2 involved the assessment of 50 ADR case reports from a prospective study of paediatric inpatients by individual assessors. Phase 3 compared assessments with the new tool for individuals and groups in comparison to the ‘gold standard’ (the avoidability outcome set by a panel of senior investigators: an experienced clinical pharmacologist, paediatrician and pharmacist). Main Outcome Measures Inter-rater reliability (IRR), measure of disagreement and utilization of avoidability categories. Results Preliminary work—Pilot phase: results for the original Hallas cases were fair and pairwise kappa scores ranged from 0.21 to 0.36. Results for the modified Hallas cases were poor, pairwise kappa scores ranged from 0.06 to 0.16. Phase 1: on initial use of the new tool, agreement between the two multidisciplinary groups was found on 13/20 cases with a kappa score of 0.29 (95% CI -0.04 to 0.62). Phase 2: the assessment of 50 ADR case reports by six individual reviewers yielded pairwise kappa scores ranging from poor to good 0.12 to 0.75 and percentage exact agreement (%EA) ranged from 52–90%. Phase 3: Percentage exact agreement ranged from 35–70%. Overall, individuals had better agreement with the ‘gold standard’. Conclusion Avoidability assessment is feasible but needs careful attention to methods. The Liverpool ADR avoidability assessment tool showed mixed IRR. We have developed and validated a method for assessing the avoidability of ADRs that is transparent, more objective than

  9. 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

  10. Ex Vivo Metrics, a preclinical tool in new drug development.

    PubMed

    Curtis, C Gerald; Bilyard, Kevin; Stephenson, Hugo

    2008-01-23

    Among the challenges facing translational medicine today is the need for greater productivity and safety during the drug development process. To meet this need, practitioners of translational medicine are developing new technologies that can facilitate decision making during the early stages of drug discovery and clinical development. Ex Vivo Metrics is an emerging technology that addresses this need by using intact human organs ethically donated for research. After hypothermic storage, the organs are reanimated by blood perfusion, providing physiologically and biochemically stable preparations. In terms of emulating human exposure to drugs, Ex Vivo Metrics is the closest biological system available for clinical trials. Early application of this tool for evaluating drug targeting, efficacy, and toxicity could result in better selection among promising drug candidates, greater drug productivity, and increased safety.

  11. Development of New Modeling and Analysis Tools for Solar Sails

    NASA Technical Reports Server (NTRS)

    Lou, Michael; Fang, Houfei; Yang, Bingen

    2004-01-01

    Existing finite-element-based structural analysis codes are ineffective in treating deployable gossamer space systems, including solar sails that are formed by long space-deployable booms and extremely large thin-film membrane apertures. Recognizing this, the NASA Space transportation Technology Program has initiated and sponsored a focused research effort to develop new and computationally efficient structural modeling and analysis tools for solar sails. The technical approach of this ongoing effort will be described. Two solution methods, the Distributed Transfer Function Method and the Parameter-Variation-Principle method, based on which the technical approach was formatted are also discussed.

  12. 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.

  13. Astronaut tool development: An orbital replaceable unit-portable handhold

    NASA Technical Reports Server (NTRS)

    Redmon, John W., Jr.

    1989-01-01

    A tool to be used during astronaut Extra-Vehicular Activity (EVA) replacement of spent or defective electrical/electronic component boxes is described. The generation of requirements and design philosophies are detailed, as well as specifics relating to mechanical development, interface verifications, testing, and astronaut feedback. Findings are presented in the form of: (1) a design which is universally applicable to spacecraft component replacement, and (2) guidelines that the designer of orbital replacement units might incorporate to enhance spacecraft on-orbit maintainability and EVA mission safety.

  14. 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 ...

  15. Molecular typing tools: from pattern recognition to genome-based algorithms.

    PubMed

    Sachse, Konrad; Moebius, Petra

    2015-01-01

    In the present chapter, we discuss DNA-based typing methods for microbial pathogens that were frequently used in the past two decades and their essential features, as well as virtues and downsides. We conclude with an outlook on the fundamental changes that can be expected in the era of high-throughput genomics.

  16. 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...

  17. 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...

  18. Agrobacterium rhizogenes-induced cotton hairy root culture as an alternative tool for cotton functional genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although well-accepted as the ultimate method for cotton functional genomics, Agrobacterium tumefaciens-mediated cotton transformation is not widely used for functional analyses of cotton genes and their promoters since regeneration of cotton in tissue culture is lengthy and labor intensive. In cer...

  19. Development of simple sequence repeat (SSR) markers of sesame (Sesamum indicum) from a genome survey.

    PubMed

    Wei, Xin; Wang, Linhai; Zhang, Yanxin; Qi, Xiaoqiong; Wang, Xiaoling; Ding, Xia; Zhang, Jing; Zhang, Xiurong

    2014-04-22

    Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world's population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding.

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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.

  5. RNAi--a tool for target finding in new drug development.

    PubMed

    Gomase, Virendra S; Tagore, Somnath

    2008-03-01

    RNAi (RNA interference) refers to the introduction of homologous double stranded RNA (dsRNA) to specifically target a gene's product, resulting in null or hypomorphic phenotypes. Long double-stranded RNAs (dsRNAs; typically >200 nt) can be used to silence the expression of target genes in a variety of organisms and cell types (e.g., worms, fruit flies, and plants). The long dsRNAs enter a cellular pathway that is commonly referred to as the RNA interference (RNAi) pathway. RNAi is being considered as an important tool not only for functional genomics, but also for gene-specific therapeutic activities that target the mRNAs of disease-related genes. RNAi plays a very important role in endogenous cellular processes, such as heterochromatin formation, developmental control and serves as an antiviral defense mechanism. RNAi has shown great potential for use as a tool for target finding in new drug development, molecular biological discovery, analysis and therapeutics. RNAi pathway is involved in post-transcription silencing, transcriptional silencing and epigenetic silencing as well as its use as a tool for forward genetics and therapeutics.

  6. Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

    PubMed Central

    Prigent, Sylvain; Frioux, Clémence; Dittami, Simon M.; Larhlimi, Abdelhalim; Collet, Guillaume; Gutknecht, Fabien; Got, Jeanne; Eveillard, Damien; Bourdon, Jérémie; Plewniak, Frédéric; Tonon, Thierry; Siegel, Anne

    2017-01-01

    Increasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. Forecasting trends in NASA flight software development tools

    NASA Technical Reports Server (NTRS)

    Garman, J. R.

    1983-01-01

    The experience gained in the design and development of Shuttle flight and ground support embedded software systems along with projections of increasing role and size of software in the proposed Space Station and other future NASA projects provides the basis for forecasting substantial changes in the tools and methodologies by which embedded software systems are developed and acquired. Similar changes in software architectures and operator interfaces will lead to substantial changes in the approach and techniques involved in software test and system integration. Increasing commonality among different flight systems and between flight and supporting ground systems is projected, along with a more distributed approach to software acquisition in highly complex projects such as Space Station.

  12. 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.

  13. 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.

  14. RNA-CODE: a noncoding RNA classification tool for short reads in NGS data lacking reference genomes.

    PubMed

    Yuan, Cheng; Sun, Yanni

    2013-01-01

    The number of transcriptomic sequencing projects of various non-model organisms is still accumulating rapidly. As non-coding RNAs (ncRNAs) are highly abundant in living organism and play important roles in many biological processes, identifying fragmentary members of ncRNAs in small RNA-seq data is an important step in post-NGS analysis. However, the state-of-the-art ncRNA search tools are not optimized for next-generation sequencing (NGS) data, especially for very short reads. In this work, we propose and implement a comprehensive ncRNA classification tool (RNA-CODE) for very short reads. RNA-CODE is specifically designed for ncRNA identification in NGS data that lack quality reference genomes. Given a set of short reads, our tool classifies the reads into different types of ncRNA families. The classification results can be used to quantify the expression levels of different types of ncRNAs in RNA-seq data and ncRNA composition profiles in metagenomic data, respectively. The experimental results of applying RNA-CODE to RNA-seq of Arabidopsis and a metagenomic data set sampled from human guts demonstrate that RNA-CODE competes favorably in both sensitivity and specificity with other tools. The source codes of RNA-CODE can be downloaded at http://www.cse.msu.edu/~chengy/RNA_CODE.

  15. 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...

  16. 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.

  17. Development of a CRISPR-Cas9 Tool Kit for Comprehensive Engineering of Bacillus subtilis

    PubMed Central

    Westbrook, Adam W.; Moo-Young, Murray

    2016-01-01

    ABSTRACT The establishment of a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system for strain construction in Bacillus subtilis is essential for its progression toward industrial utility. Here we outline the development of a CRISPR-Cas9 tool kit for comprehensive genetic engineering in B. subtilis. In addition to site-specific mutation and gene insertion, our approach enables continuous genome editing and multiplexing and is extended to CRISPR interference (CRISPRi) for transcriptional modulation. Our tool kit employs chromosomal expression of Cas9 and chromosomal transcription of guide RNAs (gRNAs) using a gRNA transcription cassette and counterselectable gRNA delivery vectors. Our design obviates the need for multicopy plasmids, which can be unstable and impede cell viability. Efficiencies of up to 100% and 85% were obtained for single and double gene mutations, respectively. Also, a 2.9-kb hyaluronic acid (HA) biosynthetic operon was chromosomally inserted with an efficiency of 69%. Furthermore, repression of a heterologous reporter gene was achieved, demonstrating the versatility of the tool kit. The performance of our tool kit is comparable with those of systems developed for Escherichia coli and Saccharomyces cerevisiae, which rely on replicating vectors to implement CRISPR-Cas9 machinery. IMPORTANCE In this paper, as the first approach, we report implementation of the CRISPR-Cas9 system in Bacillus subtilis, which is recognized as a valuable host system for biomanufacturing. The study enables comprehensive engineering of B. subtilis strains with virtually any desired genotypes/phenotypes and biochemical properties for extensive industrial application. PMID:27260361

  18. 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.

  19. Drama: an appropriate tool in development support communication.

    PubMed

    Moyo, F F

    1997-01-01

    Because it supports progress, drama embodies development and, thus, can be used to support development communication. In fact, drama is the most appropriate medium for effecting change for development because it 1) involves interpersonal communication; 2) broadens the meaning of development; 3) challenges assumptions, demands accountability, suggests remedies, and evaluates the totality of performance; 4) exploits the politics of possibility; 5) is inherently dialogue; 6) allows the target community to participation during the exposition, the conflict, and the resolution; 7) is easy to assimilate; and 8) provides access to any medium. Drama is especially appropriate in South Africa because children carry on a tradition of play-acting, South Africans exhibit politeness to strangers that makes them passively aggressive in resisting change, it allows the temporary removal of cultural barriers among members of households, and it resembles the oral tradition that was pervasive in the culture. Drama can impart greater legitimacy to topics originating from the community or fuse a totally new concept with local culture. It can be used as a tool to criticize political mismanagement, comment on social problems, question culture, debate religious matters, examine economic society, assist educational programs, assist health efforts, raise people's awareness about conservation, and help spread technological advancements. Drama allows more to be done than said and allows communities to be involved in development efforts.

  20. MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models

    SciTech Connect

    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. 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. In conclusion, this computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community.

  1. 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

  2. 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

  3. 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.

  4. Applying Genomic and Genetic Tools to Understand and Mitigate Damage from Exposure to Toxins

    DTIC Science & Technology

    2011-10-01

    donepezil (brand name Aricept) are all water-soluble AChEIs that are currently approved by the FDA for the treatment of Alzheimer’s disease and have...Huang da, B. T. Sherman, R. A. Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4...large gene lists . Nucleic Acids Res 37, 1 (Jan, 2009). 13. T. Whistler et al., Impaired immune function in Gulf War Illness. BMC Med Genomics 2, 12

  5. Infectious diseases of marine molluscs and host responses as revealed by genomic tools

    PubMed Central

    Ford, Susan E.

    2016-01-01

    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

  6. Infectious diseases of marine molluscs and host responses as revealed by genomic tools.

    PubMed

    Guo, Ximing; Ford, Susan E

    2016-03-05

    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.

  7. A new genome-mining tool redefines the lasso peptide biosynthetic landscape.

    PubMed

    Tietz, Jonathan I; Schwalen, Christopher J; Patel, Parth S; Maxson, Tucker; Blair, Patricia M; Tai, Hua-Chia; Zakai, Uzma I; Mitchell, Douglas A

    2017-02-28

    Ribosomally synthesized and post-translationally modified peptide (RiPP) natural products are attractive for genome-driven discovery and re-engineering, but limitations in bioinformatic methods and exponentially increasing genomic data make large-scale mining of RiPP data difficult. We report RODEO (Rapid ORF Description and Evaluation Online), which combines hidden-Markov-model-based analysis, heuristic scoring, and machine learning to identify biosynthetic gene clusters and predict RiPP precursor peptides. We initially focused on lasso peptides, which display intriguing physicochemical properties and bioactivities, but their hypervariability renders them challenging prospects for automated mining. Our approach yielded the most comprehensive mapping to date of lasso peptide space, revealing >1,300 compounds. We characterized the structures and bioactivities of six lasso peptides, prioritized based on predicted structural novelty, including one with an unprecedented handcuff-like topology and another with a citrulline modification exceptionally rare among bacteria. These combined insights significantly expand the knowledge of lasso peptides and, more broadly, provide a framework for future genome-mining efforts.

  8. 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.

  9. Development of molecular tools to monitor conjugative transfer in rhizobia.

    PubMed

    Tejerizo, Gonzalo Torres; Bañuelos, Luis Alfredo; Cervantes, Laura; Gaytán, Paul; Pistorio, Mariano; Romero, David; Brom, Susana

    2015-10-01

    Evolution of bacterial populations has been extensively driven by horizontal transfer events. Conjugative plasmid transfer is considered the principal contributor to gene exchange among bacteria. Several conjugative and mobilizable plasmids have been identified in rhizobia, and two major molecular mechanisms that regulate their transfer have been described, under laboratory conditions. The knowledge of rhizobial plasmid transfer regulation in natural environments is very poor. In this work we developed molecular tools to easily monitor the conjugative plasmid transfer in rhizobia by flow cytometry (FC) or microscopy. 24 cassettes were constructed by combining a variety of promotors, fluorescent proteins and antibiotic resistance genes, and used to tag plasmids and chromosome of donor strains. We were able to detect plasmid transfer after conversion of non-fluorescent recipients into fluorescent transconjugants. Flow cytometry (FC) was optimized to count donor, recipient and transconjugant strains to determine conjugative transfer frequencies. Results were similar, when determined either by FC or by viable counts. Our constructions also allowed the visualization of transconjugants in crosses performed on bean roots. The tools presented here may also be used for other purposes, such as analysis of transcriptional fusions or single-cell tagging. Application of the system will allow the survey of how different environmental conditions or other regulators modulate plasmid transfer in rhizobia.

  10. Developing Tools for Computation of Basin Topographic Parameters in GIS

    NASA Astrophysics Data System (ADS)

    Gökgöz, T.; Yayla, Y.; Yaman, M. B.; Güvenç, H.; Kaya, S.

    2016-10-01

    Although water use has been increasing day by day depending on fast population increase, urbanization and industrialization in the world, potential of usable water resources remains stable. On the other side, expansion of agricultural activities, industrialization, urbanization, global warming and climate change create a big pressure on current water resources. Therefore, management of water resources is one of the most significant problems of today that is required to be solved and `'Integrated Basin Management'' has gained importance in the world in terms of decreasing environmental problems by more efficiently using current water resources. In order to achieve integrated basin management, it is needed to determine basin boundaries with sufficient accuracy and precision and encode them systematically. In various analyses to be done on the basis of basin, topographic parameters are also needed such as shape factor, bifurcation ratio, drainage frequency, drainage density, length of the main flow path, harmonic slope, average slope, time of concentration, hypsometric curve and maximum elevation difference. Nowadays, basin boundaries are obtained with digital elevation models in geographical information systems. However, tools developed for topographic parameters are not available. In this study, programs were written in Python programming language for afore-mentioned topographic parameters and each turned into a geographical information system tool. Therefore, a significant contribution has been made to the subject by completing the deficiency in the geographical information system devoted to the topographic parameters that are needed in almost every analyses concerning to the hydrology.

  11. Development of environmental tools for anopheline larval control

    PubMed Central

    2011-01-01

    Background Malaria mosquitoes spend a considerable part of their life in the aquatic stage, rendering them vulnerable to interventions directed to aquatic habitats. Recent successes of mosquito larval control have been reported using environmental and biological tools. Here, we report the effects of shading by plants and biological control agents on the development and survival of anopheline and culicine mosquito larvae in man-made natural habitats in western Kenya. Trials consisted of environmental manipulation using locally available plants, the introduction of predatory fish and/or the use of Bacillus thuringiensis var. israelensis (Bti) in various combinations. Results Man-made habitats provided with shade from different crop species produced significantly fewer larvae than those without shade especially for the malaria vector Anopheles gambiae. Larval control of the African malaria mosquito An. gambiae and other mosquito species was effective in habitats where both predatory fish and Bti were applied, than where the two biological control agents were administered independently. Conclusion We conclude that integration of environmental management techniques using shade-providing plants and predatory fish and/or Bti are effective and sustainable tools for the control of malaria and other mosquito-borne disease vectors. PMID:21733150

  12. 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.

  13. 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...

  14. 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…

  15. Development of a Mass Casualty Triage Performance Assessment Tool

    DTIC Science & Technology

    2015-02-01

    Assessment, Triage, Performance measurement, BCT performance, Feedback , Tasks, Task analysis, Military police 16. SECURITY...assessment and provided feedback for further refinement. Findings: The assessment tool comprises six cases. Each case includes a scenario...Tool Feedback ..................................................................................................... 11 Procedure

  16. 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.

  17. Non-genomic actions of thyroid hormone in brain development.

    PubMed

    Leonard, Jack L

    2008-10-01

    Thyroid hormone (TH) is essential for neuronal migration and synaptogenesis in the developing brain. Assembly of neuronal circuits depends on guidance cues provided by the extracellular matrix. These cues are interpreted by the migrating neuron and its growing neurites through transmembrane signaling proteins anchored in place by the actin cytoskeleton. One of the best examples of a non-genomic action of thyroid hormone is its dynamic regulation of the number and quantity of actin fibers in astrocytes. Thyroxine (T4) and its transcriptionally inactive metabolite, 3',5',3-triiodothyronine (reverse T3) are responsible for modulating microfilament organization, while the transcriptional activator, 3',3,5-triiodothyronine (T3) is inert. The biological consequence of the loss of the actin filaments in astrocytes is the inability of the cell to anchor laminin, to its cell surface, and the loss of this key guidance molecule interrupts neurite pathfinding and neuronal migration. These data provide the essentials to construct a physiological pathway where TH-dependent regulation of the polymerization state of actin in the astrocyte and the developing neuron modulates the production and recognition of guidance cues--cues that if disrupted lead to abnormal neuronal migration and neuronal process formation--and lead to the morphological deficits observed in the cretinous brain.

  18. 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

  19. 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.

  20. RATT: Rapid Annotation Transfer Tool

    PubMed Central

    Otto, Thomas D.; Dillon, Gary P.; Degrave, Wim S.; Berriman, Matthew

    2011-01-01

    Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, de novo assembly or visualization, genome annotation remains a challenge. We have developed a method to rapidly provide accurate annotation for new genomes using previously annotated genomes as a reference. The method, implemented in a tool called RATT (Rapid Annotation Transfer Tool), transfers annotations from a high-quality reference to a new genome on the basis of conserved synteny. We demonstrate that a Mycobacterium tuberculosis genome or a single 2.5 Mb chromosome from a malaria parasite can be annotated in less than five minutes with only modest computational resources. RATT is available at http://ratt.sourceforge.net. PMID:21306991

  1. 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.

  2. Development and psychometric testing of the clinical networks engagement tool

    PubMed Central

    Hecker, Kent G.; Rabatach, Leora; Noseworthy, Tom W.; White, Deborah E.

    2017-01-01

    Background Clinical networks are being used widely to facilitate large system transformation in healthcare, by engagement of stakeholders throughout the health system. However, there are no available instruments that measure engagement in these networks. Methods The study purpose was to develop and assess the measurement properties of a multiprofessional tool to measure engagement in clinical network initiatives. Based on components of the International Association of Public Participation Spectrum and expert panel review, we developed 40 items for testing. The draft instrument was distributed to 1,668 network stakeholders across different governance levels (leaders, members, support, frontline stakeholders) in 9 strategic clinical networks in Alberta (January to July 2014). With data from 424 completed surveys (25.4% response rate), descriptive statistics, exploratory and confirmatory factor analysis, Pearson correlations, linear regression, multivariate analysis, and Cronbach alpha were conducted to assess reliability and validity of the scores. Results Sixteen items were retained in the instrument. Exploratory factor analysis indicated a four-factor solution and accounted for 85.7% of the total variance in engagement with clinical network initiatives: global engagement, inform (provided with information), involve (worked together to address concerns), and empower (given final decision-making authority). All subscales demonstrated acceptable reliability (Cronbach alpha 0.87 to 0.99). Both the confirmatory factor analysis and regression analysis confirmed that inform, involve, and empower were all significant predictors of global engagement, with involve as the strongest predictor. Leaders had higher mean scores than frontline stakeholders, while members and support staff did not differ in mean scores. Conclusions This study provided foundational evidence for the use of this tool for assessing engagement in clinical networks. Further work is necessary to evaluate

  3. Progress on EUV-source development, tool integration and applications

    NASA Astrophysics Data System (ADS)

    Lebert, Rainer; Jagle, Bernhard; Wies, Christian; Stamm, Uwe; Kleinschmidt, Juergen; Gaebel, Kai; Schriever, Guido; Pankert, Joseph; Bergmann, Klaus; Neff, Willi; Egbert, Andre

    2005-06-01

    In EUV lithography, extreme ultraviolet radiation of 13.5 nm wavelength is used to print feature with resolutions consis-tent with the requirements of the 45 nm technology node or below. EUV is produced by heating xenon, tin, or other ele-ments to a plasma state, using either magnetic compression or laser irradiation. The key concerns-identified at the third EUV-Symposium-are the ability to supply defect-free masks and to increase source component lifetimes to meet the wafer throughput requirements for high volume manufacturing. Source availability and performance, however, made steady progress within the last years on two lines of actions: High power sources for high volume production and medium and low power sources for allowing in-house metrology and performance studies on EUV-mask-blanks, EUV-Masks, photoresists and optical elements. For "volume production sources" 50 W of collected EUV powers are already available by various suppliers. Compact discharge sources of medium power in the range of 10-100 mW / sr / 2% bandwidth and low power EUV-tubes of low-est cost of ownership and superior stability are ideal for peripheral metrology on components for EUV-Lithography. These low power sources supplement beamlines at storage rings by transferring EUV-applications to individual R&D labs. Proceeding integration of those EUV sources into tools for technology development like open frame and micro-exposers, and in tools for actinic metrology is the best proof of the progress. As of today, the first EUV sources and measurement equipment are available to be used for EUV system, mask, optics and component as well as lithography process development. With the commercial availability of EUV-plasma sources other applications using short wave-length, XUV-radiation will be feasible in a laboratory environment. Some examples of XUV applications are discussed.

  4. 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.

  5. 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

  6. VOSED: a tool for the characterization of developing planetary systems

    NASA Astrophysics Data System (ADS)

    Solano, E.; Gutiérrez, R.; Delgado, A.; Sarro, L. M.; Merín, B.

    2007-08-01

    The transition phase from optically thick disks around young pre-main sequence stars to optically thin debris disks around Vega type stars is not well understood and plays an important role in the theory of planet formation. One of the most promising methods to characterize this process is the fitting of the observed SED with disk models. However, despite its potential, this technique is affected by two major problems if a non-VO methodology is used: on the one hand, SEDs building requires accessing to a variety of astronomical services which provide, in most of the cases, heterogeneous information. On the other hand, model fitting demands a tremendous amount of work and time which makes it very inefficient even for a modest dataset. This is an important issue considering the large volume of data that missions like Spitzer is producing. In the framework of the Spanish Virtual Observatory (SVO) we have developed VOSED an application that permits to characterize the protoplanetary disks around young stars taking advantage of the already existing VO standards and tools. The application allows the user to gather photometric and spectroscopic information from a number of VO services, trace the SED, and fit the photospheric contribution with a stellar model and the IR excess with a disk model. The Kurucz models described in Castelli et al. (1997, A&A, 318, 841) are used to reproduce the photospheric contribution whereas the grid of models of accretion disks irradiated by their central stars developed by D'Alessio et al. (2005, ) is used for the disk contribution. In both cases, the models are retrieved from the SVO Theoretical Model Web Server using the TSAP protocol. As pointed out before, model fitting constitutes a fundamental step in the analysis process. VOSED includes a tool to estimate the model parameters (both stellar and disk) based on bayesian inference. The main aim of the tool

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Iterative Development of an Online Dietary Recall Tool: INTAKE24.

    PubMed

    Simpson, Emma; Bradley, Jennifer; Poliakov, Ivan; Jackson, Dan; Olivier, Patrick; Adamson, Ashley J; Foster, Emma

    2017-02-09

    Collecting large-scale population data on dietary intake is challenging, particularly when resources and funding are constrained. Technology offers the potential to develop novel ways of collecting large amounts of dietary information while making it easier, more convenient, intuitive, and engaging for users. INTAKE24 is an online multiple pass 24 h dietary recall tool developed for use in national food and nutrition surveys. The development of INTAKE24 was a four-stage iterative process of user interaction and evaluation with the intended end users, 11-24 years old. A total of 80 11-24 years old took part in the evaluation, 20 at each stage. Several methods were used to elicit feedback from the users including, 'think aloud', 'eye tracking', semi-structured interviews, and a system usability scale. Each participant completed an interviewer led recall post system completion. Key system developments generated from the user feedback included a 'flat' interface, which uses only a single interface screen shared between all of the various activities (e.g., free text entry, looking up foods in the database, portion size estimation). Improvements to the text entry, search functionality, and navigation around the system were also influenced through feedback from users at each stage. The time to complete a recall using INTAKE24 almost halved from the initial prototype to the end system, while the agreement with an interviewer led recall improved. Further developments include testing the use of INTAKE24 with older adults and translation into other languages for international use. Our future aim is to validate the system with recovery biomarkers.

  15. Iterative Development of an Online Dietary Recall Tool: INTAKE24

    PubMed Central

    Simpson, Emma; Bradley, Jennifer; Poliakov, Ivan; Jackson, Dan; Olivier, Patrick; Adamson, Ashley J.; Foster, Emma

    2017-01-01

    Collecting large-scale population data on dietary intake is challenging, particularly when resources and funding are constrained. Technology offers the potential to develop novel ways of collecting large amounts of dietary information while making it easier, more convenient, intuitive, and engaging for users. INTAKE24 is an online multiple pass 24 h dietary recall tool developed for use in national food and nutrition surveys. The development of INTAKE24 was a four-stage iterative process of user interaction and evaluation with the intended end users, 11–24 years old. A total of 80 11–24 years old took part in the evaluation, 20 at each stage. Several methods were used to elicit feedback from the users including, ‘think aloud’, ‘eye tracking’, semi-structured interviews, and a system usability scale. Each participant completed an interviewer led recall post system completion. Key system developments generated from the user feedback included a ‘flat’ interface, which uses only a single interface screen shared between all of the various activities (e.g., free text entry, looking up foods in the database, portion size estimation). Improvements to the text entry, search functionality, and navigation around the system were also influenced through feedback from users at each stage. The time to complete a recall using INTAKE24 almost halved from the initial prototype to the end system, while the agreement with an interviewer led recall improved. Further developments include testing the use of INTAKE24 with older adults and translation into other languages for international use. Our future aim is to validate the system with recovery biomarkers. PMID:28208763

  16. Whole-Genome Mapping as a Novel High-Resolution Typing Tool for Legionella pneumophila.

    PubMed

    Bosch, Thijs; Euser, Sjoerd M; Landman, Fabian; Bruin, Jacob P; IJzerman, Ed P; den Boer, Jeroen W; Schouls, Leo M

    2015-10-01

    Legionella is the causative agent for Legionnaires' disease (LD) and is responsible for several large outbreaks in the world. More than 90% of LD cases are caused by Legionella pneumophila, and studies on the origin and transmission routes of this pathogen rely on adequate molecular characterization of isolates. Current typing of L. pneumophila mainly depends on sequence-based typing (SBT). However, studies have shown that in some outbreak situations, SBT does not have sufficient discriminatory power to distinguish between related and nonrelated L. pneumophila isolates. In this study, we used a novel high-resolution typing technique, called whole-genome mapping (WGM), to differentiate between epidemiologically related and nonrelated L. pneumophila isolates. Assessment of the method by various validation experiments showed highly reproducible results, and WGM was able to confirm two well-documented Dutch L. pneumophila outbreaks. Comparison of whole-genome maps of the two outbreaks together with WGMs of epidemiologically nonrelated L. pneumophila isolates showed major differences between the maps, and WGM yielded a higher discriminatory power than SBT. In conclusion, WGM can be a valuable alternative to perform outbreak investigations of L. pneumophila in real time since the turnaround time from culture to comparison of the L. pneumophila maps is less than 24 h.

  17. 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

  18. Variation in salamanders: an essay on genomes, development, and evolution.

    PubMed

    Brockes, Jeremy P

    2015-01-01

    Regeneration is studied in a few model species of salamanders, but the ten families of salamanders show considerable variation, and this has implications for our understanding of salamander biology. The most recent classification of the families identifies the cryptobranchoidea as the basal group which diverged in the early Jurassic. Variation in the sizes of genomes is particularly obvious, and reflects a major contribution from transposable elements which is already present in the basal group.Limb development has been a focus for evodevo studies, in part because of the variable property of pre-axial dominance which distinguishes salamanders from other tetrapods. This is thought to reflect the selective pressures that operate on a free-living aquatic larva, and might also be relevant for the evolution of limb regeneration. Recent fossil evidence suggests that both pre-axial dominance and limb regeneration were present 300 million years ago in larval temnospondyl amphibians that lived in mountain lakes. A satisfying account of regeneration in salamanders may need to address all these different aspects in the future.

  19. Reactive metabolites in early drug development: predictive in vitro tools.

    PubMed

    Pelkonen, Olavi; Pasanen, Markku; Tolonen, Ari; Koskinen, Mikko; Hakkola, Jukka; Abass, Khaled; Laine, Jaana; Hakkinen, Merja; Juvonen, Risto; Auriola, Seppo; Storvik, Markus; Huuskonen, Pasi; Rousu, Timo; Rahikkala, Maiju

    2015-01-01

    Drug metabolism can result in the formation of highly reactive metabolites that are known to play a role in toxicity resulting in a significant proportion of attrition during drug development and clinical use. Thus, the earlier such reactivity was detected, the better. This review summarizes our multi-year project, together with pertinent literature, to examine a battery of in vitro tests capable of detecting the formation of reactive metabolites. Principal prerequisites for such tests were delineated: chemicals known/not known to cause tissue injury and produce reactive metabolites, activation system (mainly human-derived), small- and large-molecular targets (small-molecular trappers, peptides, proteins), analytical techniques (mass spectrometry), and cellular toxicity biomarkers. The current status of in vitro tools to detect reactive intermediates is the following: 1. Small-molecular trapping agents such glutathione or cyanide detect the production of reactive species with high sensitivity by proper MS technique. However, it seems that also putative "negatives" give rise to corresponding adducts. 2. Results from peptide and dG (DNA targeting) trapper studies are generally in line with those of small-molecular trappers, although also important differences exist. These two trapping platforms do not overlap. 3. It is anticipated that the in vitro adduct studies could be fully interpreted only in conjunction with toxicity biomarker (such as the Nrf2 pathway) information from whole cells or tissues. However, while there are tools to characterize the chemical liability and there are correlation between individual/integrated endpoints and toxicity, there are still severe gaps in understanding the mechanisms behind the link between reactive metabolites and adverse effects.

  20. The development of a spreadsheet-aided-engineering design tool for parachutes

    SciTech Connect

    Waye, D.E.; Whinery, L.D.

    1997-04-01

    A spreadsheet-aided engineering design tool has been developed to assist in the parachute design process. The new tool was developed during FY96 and utilized in the design of the flight termination parachute system for a 1900 lb. payload. Many modifications were made during the initial utilization of this tool. Work on the tool continues as the authors attempt to create an application tool for the parachute engineer.