Science.gov

Sample records for genomics developing tools

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

    SciTech Connect

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

    2005-03-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  3. 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...

  4. Development and Use of Genomic Tools in Analyzing Spatial Genetic Structure of Lowbush Blueberry Populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The overall aim of the Specialty Crop Research Initiative-funded project, “Generating Genomic Tools for Blueberry Improvement,” is to develop genomic tools for molecular breeding and assessing genetic diversity of blueberry. Two of the objectives are to perform deeper transcriptome sequencing of bl...

  5. Development of applied genomics tools for cucumber breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The past three years have witnessed rapid accumulation of whole genome sequences and other genomics resources in cucumber. So far, draft genomes of three cucumber inbred lines have been released; many cucumber lines are being re-sequenced using next-generation sequencing technologies; nearly three m...

  6. 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...

  7. Functional Genomics Tools for Papaya

    Technology Transfer Automated Retrieval System (TEKTRAN)

    With the genome of papaya (Carica papaya L.) sequenced, the study of gene function is becoming an increasing priority. Our research is to develop an RNA-induced gene silencing tool for the study of functional genomics in papaya. We employed agrobacterium leaf infiltration to induce PTGS in '-glucuro...

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

    PubMed

    Lim, Kwang-il

    2015-01-01

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

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

    PubMed Central

    2011-01-01

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

  10. Overview of USDA-SCRI Project: Cucumber applied genomics: tool development and applications for recessive disease resistance genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A cucumber project was recently funded by the USDA NIFA-SCRI program which is titled “Translational genomics in cucumber - tool development and application for recessive disease resistances”. This grant was the result of a joint effort of the UW public cucumber research community with strong support...

  11. 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. PMID:19172842

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  13. 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.

  14. Developing genomics tools for the western corn rootworm - Progress and promise

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cooperative efforts among a number of interested scientists and institutions in the U.S. and Europe are being undertaken to expand genomics resources for the western corn rootworm (Diabrotica virgifera virgifera). Such resources include development of hundreds of single nucleotide polymorphism (SNP...

  15. 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

  16. Developing molecular tools and insights into the Penstemon genome using genomic reduction and next-generation sequencing

    PubMed Central

    2013-01-01

    Background Penstemon’s unique phenotypic diversity, hardiness, and drought-tolerance give it great potential for the xeric landscaping industry. Molecular markers will accelerate the breeding and domestication of drought tolerant Penstemon cultivars by, creating genetic maps, and clarifying of phylogenetic relationships. Our objectives were to identify and validate interspecific molecular markers from four diverse Penstemon species in order to gain specific insights into the Penstemon genome. Results We used a 454 pyrosequencing and GR-RSC (genome reduction using restriction site conservation) to identify homologous loci across four Penstemon species (P. cyananthus, P. davidsonii, P. dissectus, and P. fruticosus) representing three diverse subgenera with considerable genome size variation. From these genomic data, we identified 133 unique interspecific markers containing SSRs and INDELs of which 51 produced viable PCR-based markers. These markers produced simple banding patterns in 90% of the species × marker interactions (~84% were polymorphic). Twelve of the markers were tested across 93, mostly xeric, Penstemon taxa (72 species), of which ~98% produced reproducible marker data. Additionally, we identified an average of one SNP per 2,890 bp per species and one per 97 bp between any two apparent homologous sequences from the four source species. We selected 192 homologous sequences, meeting stringent parameters, to create SNP markers. Of these, 75 demonstrated repeatable polymorphic marker functionality across the four sequence source species. Finally, sequence analysis indicated that repetitive elements were approximately 70% more prevalent in the P. cyananthus genome, the largest genome in the study, than in the smallest genome surveyed (P. dissectus). Conclusions We demonstrated the utility of GR-RSC to identify homologous loci across related Penstemon taxa. Though PCR primer regions were conserved across a broadly sampled survey of Penstemon species

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

    PubMed

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

    2015-09-01

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

  18. Generating genomic tools for blueberry improvement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Because of their recognized health benefits, there has been increased demand and consumption of blueberries in recent years. Great strides have been made in cultivar development since its domestication using traditional breeding approaches. However, genomic tools are lacking in blueberry, which coul...

  19. 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

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

    PubMed

    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; Vassiliou, George S

    2016-07-01

    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

  1. 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

  2. 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.

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

    PubMed

    Bell, Trevor G; Kramvis, Anna

    2015-02-01

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

  4. 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

  5. GMOL: An Interactive Tool for 3D Genome Structure Visualization.

    PubMed

    Nowotny, Jackson; Wells, Avery; Oluwadare, Oluwatosin; Xu, Lingfei; Cao, Renzhi; Trieu, Tuan; He, Chenfeng; Cheng, Jianlin

    2016-01-01

    It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there still exists a shortage of tools dedicated to visualizing the genome. Creating a tool that can accurately visualize the genome can aid researchers by highlighting structural relationships that may not be obvious when examining the sequence information alone. Here we present a desktop application, known as GMOL, designed to effectively visualize genome structures so that researchers may better analyze genomic data. GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences. Users can also interactively manipulate and measure the whole genome structure and extract static images and machine-readable data files in PDB format from the multi-scale structure. By using GMOL researchers will be able to better understand and analyze genome structure models and the impact their structural relations have on genome activity and DNA function. PMID:26868282

  6. 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.

  7. Genomic sequence analysis tools: a user's guide.

    PubMed

    Fortna, A; Gardiner, K

    2001-03-01

    The wealth of information from various genome sequencing projects provides the biologist with a new perspective from which to analyze, and design experiments with, mammalian systems. The complexity of the information, however, requires new software tools, and numerous such tools are now available. Which type and which specific system is most effective depends, in part, upon how much sequence is to be analyzed and with what level of experimental support. Here we survey a number of mammalian genomic sequence analysis systems with respect to the data they provide and the ease of their use. The hope is to aid the experimental biologist in choosing the most appropriate tool for their analyses. PMID:11226611

  8. 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

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

    PubMed

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

    2016-01-01

    We report an update of the Bovine Genome Database (BGD) (http://BovineGenome.org). The goal of BGD is to support bovine genomics research by providing genome annotation and data mining tools. We have developed new genome and annotation browsers using JBrowse and WebApollo for two Bos taurus genome assemblies, the reference genome assembly (UMD3.1.1) and the alternate genome assembly (Btau_4.6.1). Annotation tools have been customized to highlight priority genes for annotation, and to aid annotators in selecting gene evidence tracks from 91 tissue specific RNAseq datasets. We have also developed BovineMine, based on the InterMine data warehousing system, to integrate the bovine genome, annotation, QTL, SNP and expression data with external sources of orthology, gene ontology, gene interaction and pathway information. BovineMine provides powerful query building tools, as well as customized query templates, and allows users to analyze and download genome-wide datasets. With BovineMine, bovine researchers can use orthology to leverage the curated gene pathways of model organisms, such as human, mouse and rat. BovineMine will be especially useful for gene ontology and pathway analyses in conjunction with GWAS and QTL studies. PMID:26481361

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

    PubMed Central

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

    2016-01-01

    We report an update of the Bovine Genome Database (BGD) (http://BovineGenome.org). The goal of BGD is to support bovine genomics research by providing genome annotation and data mining tools. We have developed new genome and annotation browsers using JBrowse and WebApollo for two Bos taurus genome assemblies, the reference genome assembly (UMD3.1.1) and the alternate genome assembly (Btau_4.6.1). Annotation tools have been customized to highlight priority genes for annotation, and to aid annotators in selecting gene evidence tracks from 91 tissue specific RNAseq datasets. We have also developed BovineMine, based on the InterMine data warehousing system, to integrate the bovine genome, annotation, QTL, SNP and expression data with external sources of orthology, gene ontology, gene interaction and pathway information. BovineMine provides powerful query building tools, as well as customized query templates, and allows users to analyze and download genome-wide datasets. With BovineMine, bovine researchers can use orthology to leverage the curated gene pathways of model organisms, such as human, mouse and rat. BovineMine will be especially useful for gene ontology and pathway analyses in conjunction with GWAS and QTL studies. PMID:26481361

  11. 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. PMID:27014312

  12. 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

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

    PubMed

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

    2016-02-01

    Bluefin tunas are one of the most important fishery resources worldwide. Because of high market values, bluefin tuna farming has been rapidly growing during recent years. At present, the most common form of the tuna farming is based on the stocking of wild-caught fish. Therefore, concerns have been raised about the negative impact of the tuna farming on wild stocks. Recently, the Pacific bluefin tuna (PBT), Thunnus orientalis, has succeeded in completing the reproduction cycle under aquaculture conditions, but production bottlenecks remain to be solved because of very little biological information on bluefin tunas. Functional genomics approaches promise to rapidly increase our knowledge on biological processes in the bluefin tuna. Here, we describe the development of the first 44K PBT oligonucleotide microarray (oligo-array), based on whole-genome shotgun (WGS) sequencing and large-scale expressed sequence tags (ESTs) data. In addition, we also introduce an initial 44K PBT oligo-array experiment using in vitro grown peripheral blood leukocytes (PBLs) stimulated with immunostimulants such as lipopolysaccharide (LPS: a cell wall component of Gram-negative bacteria) or polyinosinic:polycytidylic acid (poly I:C: a synthetic mimic of viral infection). This pilot 44K PBT oligo-array analysis successfully addressed distinct immune processes between LPS- and poly I:C- stimulated PBLs. Thus, we expect that this oligo-array will provide an excellent opportunity to analyze global gene expression profiles for a better understanding of diseases and stress, as well as for reproduction, development and influence of nutrition on tuna aquaculture production. PMID:26477480

  14. The UCSC genome browser and associated tools.

    PubMed

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

    2013-03-01

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

  15. Sequence Maneuverer: tool for sequence extraction from genomes

    PubMed Central

    Yasmin, Tayyaba; Rehman, Inayat Ur; Ansari, Adnan Ahmad; liaqat, Khurrum; khan, Muhammad Irfan

    2012-01-01

    The availability of genomic sequences of many organisms has opened new challenges in many aspects particularly in terms of genome analysis. Sequence extraction is a vital step and many tools have been developed to solve this issue. These tools are available publically but have limitations with reference to the sequence extraction, length of the sequence to be extracted, organism specificity and lack of user friendly interface. We have developed a java based software package having three modules which can be used independently or sequentially. The tool efficiently extracts sequences from large datasets with few simple steps. It can efficiently extract multiple sequences of any desired length from a genome of any organism. The results are crosschecked by published data. Availability URL 1: http://ww3.comsats.edu.pk/bio/ResearchProjects.aspx URL 2: http://ww3.comsats.edu.pk/bio/SequenceManeuverer.aspx PMID:23275734

  16. 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.

  17. 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. PMID:27217183

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

    PubMed

    Gremme, Gordon; Steinbiss, Sascha; Kurtz, Stefan

    2013-01-01

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

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

    DOE PAGESBeta

    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

  20. 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.

  1. mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes.

    PubMed

    Shao, Yucheng; He, Xinyi; Harrison, Ewan M; Tai, Cui; Ou, Hong-Yu; Rajakumar, Kumar; Deng, Zixin

    2010-07-01

    mGenomeSubtractor performs an mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes for investigation of strain variable accessory regions. With parallel computing architecture, mGenomeSubtractor is able to run rapid BLAST searches of the segmented reference genome against multiple subject genomes at the DNA or amino acid level within a minute. In addition to comparison of protein coding sequences, the highly flexible sliding window-based genome fragmentation approach offered can be used to identify short unique sequences within or between genes. mGenomeSubtractor provides powerful schematic outputs for exploration of identified core and accessory regions, including searches against databases of mobile genetic elements, virulence factors or bacterial essential genes, examination of G+C content and binucleotide distribution bias, and integrated primer design tools. mGenomeSubtractor also allows for the ready definition of species-specific gene pools based on available genomes. Pan-genomic arrays can be easily developed using the efficient oligonucleotide design tool. This simple high-throughput in silico 'subtractive hybridization' analytical tool will support the rapidly escalating number of comparative bacterial genomics studies aimed at defining genomic biomarkers of evolutionary lineage, phenotype, pathotype, environmental adaptation and/or disease-association of diverse bacterial species. mGenomeSubtractor is freely available to all users without any login requirement at: http://bioinfo-mml.sjtu.edu.cn/mGS/. PMID:20435682

  2. 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

  3. Gramene, a tool for grass genomics.

    PubMed

    Ware, Doreen H; Jaiswal, Pankaj; Ni, Junjian; Yap, Immanuel V; Pan, Xioakang; Clark, Ken Y; Teytelman, Leonid; Schmidt, Steven C; Zhao, Wei; Chang, Kuan; Cartinhour, Sam; Stein, Lincoln D; McCouch, Susan R

    2002-12-01

    Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice (Oryza sativa). It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, and publications, with a curated database of rice mutants (genes and alleles), molecular markers, and proteins. Gramene curators read and extract detailed information from published sources, summarize that information in a structured format, and establish links to related objects both inside and outside the database, providing seamless connections between independent sources of information. Genetic, physical, and sequence-based maps of rice serve as the fundamental organizing units and provide a common denominator for moving across species and genera within the grass family. Comparative maps of rice, maize (Zea mays), sorghum (Sorghum bicolor), barley (Hordeum vulgare), wheat (Triticum aestivum), and oat (Avena sativa) are anchored by a set of curated correspondences. In addition to sequence-based mappings found in comparative maps and rice genome displays, Gramene makes extensive use of controlled vocabularies to describe specific biological attributes in ways that permit users to query those domains and make comparisons across taxonomic groups. Proteins are annotated for functional significance using gene ontology terms that have been adopted by numerous model species databases. Genetic variants including phenotypes are annotated using plant ontology terms common to all plants and trait ontology terms that are specific to rice. In this paper, we present a brief overview of the search tools available to the plant research community in Gramene. PMID:12481044

  4. GATB: Genome Assembly & Analysis Tool Box

    PubMed Central

    Drezen, Erwan; Rizk, Guillaume; Chikhi, Rayan; Deltel, Charles; Lemaitre, Claire; Peterlongo, Pierre; Lavenier, Dominique

    2014-01-01

    Motivation: Efficient and fast next-generation sequencing (NGS) algorithms are essential to analyze the terabytes of data generated by the NGS machines. A serious bottleneck can be the design of such algorithms, as they require sophisticated data structures and advanced hardware implementation. Results: We propose an open-source library dedicated to genome assembly and analysis to fasten the process of developing efficient software. The library is based on a recent optimized de-Bruijn graph implementation allowing complex genomes to be processed on desktop computers using fast algorithms with low memory footprints. Availability and implementation: The GATB library is written in C++ and is available at the following Web site http://gatb.inria.fr under the A-GPL license. Contact: lavenier@irisa.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24990603

  5. 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.

  6. 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...

  7. Development of Genomic GMACE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The use of genomics to enhance national genetic evaluation systems of dairy cattle is quickly becoming standard practice. The current MACE procedure used by Interbull may not accommodate these new “genomically-enhanced” national evaluations. An important assumption in MACE may no longer be valid in ...

  8. A new set of bioinformatics tools for genome projects.

    PubMed

    Almeida, Luiz G P; Paixão, Roger; Souza, Rangel C; Costa, Gisele C da; Almeida, Darcy F de; Vasconcelos, Ana T R de

    2004-01-01

    A new tool called System for Automated Bacterial Integrated Annotation--SABIA (SABIA being a very well-known bird in Brazil) was developed for the assembly and annotation of bacterial genomes. This system performs automatic tasks of assembly analysis, ORFs identification/analysis, and extragenic region analyses. Genome assembly and contig automatic annotation data are also available in the same working environment. The system integrates several public domains and newly developed software programs capable of dealing with several types of databases, and it is portable to other operational systems. These programs interact with most of the well-known biological database/softwares, such as Glimmer, Genemark, the BLAST family programs, InterPro, COG, Kegg, PSORT, GO, tRNAScan and RBSFinder, and can also be used to identify metabolic pathways. PMID:15100986

  9. Genomics and vaccine development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic-based approaches are driving fundamental changes in our understanding of microbiology. Comparative analysis of microbial strain is providing new insights into pathogen evolution, virulence mechanisms, and host range specificity. Most importantly, gene discovery and genetic variations can now...

  10. 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).

  11. 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...

  12. 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

  13. GRAT--genome-scale rapid alignment tool.

    PubMed

    Kindlund, Ellen; Tammi, Martti T; Arner, Erik; Nilsson, Daniel; Andersson, Björn

    2007-04-01

    Modern alignment methods designed to work rapidly and efficiently with large datasets often do so at the cost of method sensitivity. To overcome this, we have developed a novel alignment program, GRAT, built to accurately align short, highly similar DNA sequences. The program runs rapidly and requires no more memory and CPU power than a desktop computer. In addition, specificity is ensured by statistically separating the true alignments from spurious matches using phred quality values. An efficient separation is especially important when searching large datasets and whenever there are repeats present in the dataset. Results are superior in comparison to widely used existing software, and analysis of two large genomic datasets show the usefulness and scalability of the algorithm. PMID:17292508

  14. 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

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

    PubMed

    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

  16. Comparison of complete mitochondrial genomes of pine wilt nematode Bursaphelenchus xylophilus and Bursaphelenchus mucronatus (Nematoda: Aphelenchoidea) and development of a molecular tool for species identification.

    PubMed

    Sultana, Tahera; Han, Hyerim; Park, Joong-Ki

    2013-05-10

    We determined the complete mitochondrial genome sequences for Bursaphelenchus mucronatus, one species of pinewood nematode. The genome is a circular-DNA molecule of 14,583 bp (195 bp smaller than its congener Bursaphelenchus xylophilus) and contains 12 protein-coding genes (lacking atp8), 22 tRNA genes, and 2 rRNA genes encoded in the same direction, consistent with most other nematodes. Based on sequence comparison of mtDNA genomes, we developed a PCR-based molecular assay to differentiate B. xylophilus (highly pathogenic) and B. mucronatus (relatively less virulent) using species-specific primers. The molecular identification system employs multiplex-PCR and is very effective and reliable for discriminating these Bursaphelenchus species, which are economically important, but difficult to distinguish based on morphology. The comparison of the mitochondrial genomes and molecular identification system of the two species of Bursaphelenchus spp. should provide a rich source of genetic information to support the effective control and management (quarantine) of the pine wilt disease caused by pinewood nematodes. PMID:23434520

  17. 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. PMID:26504547

  18. 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

  19. 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...

  20. Integrons: natural tools for bacterial genome evolution.

    PubMed

    Rowe-Magnus, D A; Mazel, D

    2001-10-01

    Integrons were first identified as the primary mechanism for antibiotic resistance gene capture and dissemination among Gram-negative bacteria. More recently, their role in genome evolution has been extended with the discovery of larger integron structures, the super-integrons, as genuine components of the genomes of many species throughout the gamma-proteobacterial radiation. The functional platforms of these integrons appear to be sedentary, whereas their gene cassette contents are highly variable. Nevertheless, the gene cassettes for which an activity has been experimentally demonstrated encode proteins related to simple adaptive functions and their recruitment is seen as providing the bacterial host with a selective advantage. The widespread occurrence of the integron system among Gram-negative bacteria is discussed, with special focus on the super-integrons. Some of the adaptive functions encoded by these genes are also reviewed, and implications of integron-mediated genome evolution in the emergence of novel bacterial species are highlighted. PMID:11587934

  1. Application of Genomics Tools to Animal Breeding

    PubMed Central

    Dekkers, Jack C.M.

    2012-01-01

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

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

    PubMed

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

    2016-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

  4. 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

  5. Groundnut improvement: use of genetic and genomic tools.

    PubMed

    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 BB

  6. 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

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

    PubMed

    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; Waldron, Levi

    2016-07-01

    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

  8. 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

  9. 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. PMID:26519402

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

    PubMed

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

    2016-07-01

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

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

    PubMed Central

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

    2016-01-01

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

  12. From bacterial genomics to metagenomics: concept, tools and recent advances.

    PubMed

    Sharma, Pooja; Kumari, Hansi; Kumar, Mukesh; Verma, Mansi; Kumari, Kirti; Malhotra, Shweta; Khurana, Jitendra; Lal, Rup

    2008-06-01

    In the last 20 years, the applications of genomics tools have completely transformed the field of microbial research. This has primarily happened due to revolution in sequencing technologies that have become available today. This review therefore, first describes the discoveries, upgradation and automation of sequencing techniques in a chronological order, followed by a brief discussion on microbial genomics. Some of the recently sequenced bacterial genomes are described to explain how complete genome data is now being used to derive interesting findings. Apart from the genomics of individual microbes, the study of unculturable microbiota from different environments is increasingly gaining importance. The second section is thus dedicated to the concept of metagenomics describing environmental DNA isolation, metagenomic library construction and screening methods to look for novel and potentially important genes, enzymes and biomolecules. It also deals with the pioneering studies in the area of metagenomics that are offering new insights into the previously unappreciated microbial world. PMID:23100712

  13. Next generation tools for genomic data generation, distribution, and visualization

    PubMed Central

    2010-01-01

    Background With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing, analyzing, and sharing genomic data. Results Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx); an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub); and a standalone Java Swing application (GWrap) that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser. Conclusions These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See http://sourceforge.net/projects/gnomex/, http://sourceforge.net/projects/genoviz/, and http://sourceforge.net/projects/useq. PMID:20828407

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

    PubMed

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

    2016-01-01

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

  15. 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

  16. 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...

  17. 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

  18. 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

  19. 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...

  20. 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…

  1. Emerging Tools for Synthetic Genome Design

    PubMed Central

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

    2013-01-01

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

  2. Databases and web tools for cancer genomics study.

    PubMed

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

    2015-02-01

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

  3. 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

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

    PubMed

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

    2013-01-01

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

  5. Stacks: an analysis tool set for population genomics

    PubMed Central

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

    2014-01-01

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

  6. 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. PMID:26442252

  7. 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…

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

    Energy Science and Technology Software Center (ESTSC)

    2011-08-01

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

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

    PubMed

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

    2016-06-01

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

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

    PubMed

    Qu, Kun; Garamszegi, Sara; Wu, Felix; 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

    2016-03-01

    Complex biomedical analyses require the use of multiple software tools in concert and remain challenging for much of the biomedical research community. We introduce GenomeSpace (http://www.genomespace.org), a cloud-based, cooperative community resource that currently supports the streamlined interaction of 20 bioinformatics tools and data resources. To facilitate integrative analysis by non-programmers, it offers a growing set of 'recipes', short workflows to guide investigators through high-utility analysis tasks. PMID:26780094

  11. Generating genomic tools for blueberry improvement -- an update of our progress

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is increased demand for and consumption of blueberries worldwide because of their many recognized health benefits. Great strides have been made in blueberry cultivar development since its domestication using traditional breeding approaches. However, genomic tools are lacking in blueberry, whic...

  12. BioViews: Java-based tools for genomic data visualization.

    PubMed

    Helt, G A; Lewis, S; Loraine, A E; Rubin, G M

    1998-03-01

    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

  13. 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

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

    PubMed

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

    2016-01-01

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

  15. 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. PMID:25813238

  16. Revolutions in Neuroscience: Tool Development.

    PubMed

    Bickle, John

    2016-01-01

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

  17. 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

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

    PubMed

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

    2016-04-01

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

  19. 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

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

    PubMed

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

    2014-07-01

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

  1. 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. PMID:27320129

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

    PubMed

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

    2016-01-01

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

  3. 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

  4. 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

  5. Recent developments of genomic research in soybean.

    PubMed

    Chan, Ching; Qi, Xinpeng; Li, Man-Wah; Wong, Fuk-Ling; Lam, Hon-Ming

    2012-07-20

    Soybean is an important cash crop with unique and important traits such as the high seed protein and oil contents, and the ability to perform symbiotic nitrogen fixation. A reference genome of cultivated soybeans was established in 2010, followed by whole-genome re-sequencing of wild and cultivated soybean accessions. These efforts revealed unique features of the soybean genome and helped to understand its evolution. Mapping of variations between wild and cultivated soybean genomes were performed. These genomic variations may be related to the process of domestication and human selection. Wild soybean germplasms exhibited high genomic diversity and hence may be an important source of novel genes/alleles. Accumulation of genomic data will help to refine genetic maps and expedite the identification of functional genes. In this review, we summarize the major findings from the whole-genome sequencing projects and discuss the possible impacts on soybean researches and breeding programs. Some emerging areas such as transcriptomic and epigenomic studies will be introduced. In addition, we also tabulated some useful bioinformatics tools that will help the mining of the soybean genomic data. PMID:22835978

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

    PubMed Central

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

    2014-01-01

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

  7. 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

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

    PubMed

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

    2013-06-01

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

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

    PubMed Central

    2011-01-01

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

  11. 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.

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

    PubMed

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

    2014-01-01

    To facilitate the ongoing research of Vibrio spp., a dedicated platform for the Vibrio research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. We present VibrioBase, a useful resource platform, providing all basic features of a sequence database with the addition of unique analysis tools which could be valuable for the Vibrio research community. VibrioBase currently houses a total of 252 Vibrio genomes developed in a user-friendly manner and useful to enable the analysis of these genomic data, particularly in the field of comparative genomics. Besides general data browsing features, VibrioBase offers analysis tools such as BLAST interfaces and JBrowse genome browser. Other important features of this platform include our newly developed in-house tools, the pairwise genome comparison (PGC) tool, and pathogenomics profiling tool (PathoProT). The PGC tool is useful in the identification and comparative analysis of two genomes, whereas PathoProT is designed for comparative pathogenomics analysis of Vibrio strains. Both of these tools will enable researchers with little experience in bioinformatics to get meaningful information from Vibrio genomes with ease. We have tested the validity and suitability of these tools and features for use in the next-generation database development. PMID:25243218

  14. VibrioBase: A Model for Next-Generation Genome and Annotation Database Development

    PubMed Central

    Choo, Siew Woh; Tan, Tze King; Mutha, Naresh V. R.; Wong, Guat Jah

    2014-01-01

    To facilitate the ongoing research of Vibrio spp., a dedicated platform for the Vibrio research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. We present VibrioBase, a useful resource platform, providing all basic features of a sequence database with the addition of unique analysis tools which could be valuable for the Vibrio research community. VibrioBase currently houses a total of 252 Vibrio genomes developed in a user-friendly manner and useful to enable the analysis of these genomic data, particularly in the field of comparative genomics. Besides general data browsing features, VibrioBase offers analysis tools such as BLAST interfaces and JBrowse genome browser. Other important features of this platform include our newly developed in-house tools, the pairwise genome comparison (PGC) tool, and pathogenomics profiling tool (PathoProT). The PGC tool is useful in the identification and comparative analysis of two genomes, whereas PathoProT is designed for comparative pathogenomics analysis of Vibrio strains. Both of these tools will enable researchers with little experience in bioinformatics to get meaningful information from Vibrio genomes with ease. We have tested the validity and suitability of these tools and features for use in the next-generation database development. PMID:25243218

  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/ PMID:22359434

  16. Genomes correction and assembling: present methods and tools

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  17. AUTOGSCAN: powerful tools for automated genome-wide linkage and linkage disequilibrium analysis.

    PubMed

    Hiekkalinna, Tero; Terwilliger, Joseph D; Sammalisto, Sampo; Peltonen, Leena; Perola, Markus

    2005-02-01

    Genome-wide linkage analysis using multiple traits and statistical software packages is a tedious process which requires a significant amount of manual file manipulation. Different linkage analysis programs require different input file formats, making the task of analyzing data with multiple methods even more time-consuming. We have developed a software tool, AUTOGSCAN, that automates file formatting, the running of statistical analyses, and the summarizing of resulting statistics for whole genome scans with a push of a button, using several independent, and often idiosyncratic, statistical software packages such as MERLIN, SOLAR and GENEHUNTER. We also describe a program, ANALYZE, designed to run qualitative linkage analysis with several different statistical strategies and programs to efficiently screen for linkage and linkage disequilibrium for a given discrete trait. The ANALYZE program can also be used by AUTOGSCAN in a genome-wide sense. PMID:15836805

  18. PREDetector: a new tool to identify regulatory elements in bacterial genomes.

    PubMed

    Hiard, Samuel; Marée, Raphaël; Colson, Séverine; Hoskisson, Paul A; Titgemeyer, Fritz; van Wezel, Gilles P; Joris, Bernard; Wehenkel, Louis; Rigali, Sébastien

    2007-06-15

    In the post-genomic area, the prediction of transcription factor regulons by position weight matrix-based programmes is a powerful approach to decipher biological pathways and to modelize regulatory networks in bacteria. The main difficulty once a regulon prediction is available is to estimate its reliability prior to start expensive experimental validations and therefore trying to find a way how to identify true positive hits from an endless list of potential target genes of a regulatory protein. Here we introduce PREDetector (Prokaryotic Regulatory Elements Detector), a tool developed for predicting regulons of DNA-binding proteins in bacterial genomes that, beside the automatic prediction, scoring and positioning of potential binding sites and their respective target genes in annotated bacterial genomes, it also provides an easy way to estimate the thresholds where to find reliable possible new target genes. PREDetector can be downloaded freely at http://www.montefiore.ulg.ac.be/~hiard/PreDetector/PreDetector.php. PMID:17451648

  19. 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.

  20. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing

    PubMed Central

    Montague, Tessa G.; Cruz, José M.; Gagnon, James A.; Church, George M.; Valen, Eivind

    2014-01-01

    Major advances in genome editing have recently been made possible with the development of the TALEN and CRISPR/Cas9 methods. The speed and ease of implementing these technologies has led to an explosion of mutant and transgenic organisms. A rate-limiting step in efficiently applying TALEN and CRISPR/Cas9 methods is the selection and design of targeting constructs. We have developed an online tool, CHOPCHOP (https://chopchop.rc.fas.harvard.edu), to expedite the design process. CHOPCHOP accepts a wide range of inputs (gene identifiers, genomic regions or pasted sequences) and provides an array of advanced options for target selection. It uses efficient sequence alignment algorithms to minimize search times, and rigorously predicts off-target binding of single-guide RNAs (sgRNAs) and TALENs. Each query produces an interactive visualization of the gene with candidate target sites displayed at their genomic positions and color-coded according to quality scores. In addition, for each possible target site, restriction sites and primer candidates are visualized, facilitating a streamlined pipeline of mutant generation and validation. The ease-of-use and speed of CHOPCHOP make it a valuable tool for genome engineering. PMID:24861617

  1. 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.

  2. Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics

    PubMed Central

    Leggett, Richard M.; Ramirez-Gonzalez, Ricardo H.; Clavijo, Bernardo J.; Waite, Darren; Davey, Robert P.

    2013-01-01

    The processes of quality assessment and control are an active area of research at The Genome Analysis Centre (TGAC). Unlike other sequencing centers that often concentrate on a certain species or technology, TGAC applies expertise in genomics and bioinformatics to a wide range of projects, often requiring bespoke wet lab and in silico workflows. TGAC is fortunate to have access to a diverse range of sequencing and analysis platforms, and we are at the forefront of investigations into library quality and sequence data assessment. We have developed and implemented a number of algorithms, tools, pipelines and packages to ascertain, store, and expose quality metrics across a number of next-generation sequencing platforms, allowing rapid and in-depth cross-platform Quality Control (QC) bioinformatics. In this review, we describe these tools as a vehicle for data-driven informatics, offering the potential to provide richer context for downstream analysis and to inform experimental design. PMID:24381581

  3. 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.

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

    SciTech Connect

    Quake, Steve

    2011-10-12

    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.

  5. 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

    2013-01-22

    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.

  6. 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

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

    PubMed Central

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

    2011-01-01

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

  8. Genomic Editing Tools to Model Human Diseases with Isogenic Pluripotent Stem Cells

    PubMed Central

    Kim, Huen Suk; Bernitz, Jeffrey M.; Lee, Dung-Fang

    2014-01-01

    Patient-specific induced pluripotent stem cells (iPSCs) are considered a versatile resource in the field of biomedicine. As iPSCs are generated on an individual basis, iPSCs may be the optimal cellular material to use for disease modeling, drug discovery, and the development of patient-specific cellular therapies. Recently, to gain an in-depth understanding of human pathologies, patient-specific iPSCs have been used to model human diseases with some iPSC-derived cells recapitulating pathological phenotypes in vitro. However, complex multigenic diseases generally have not resulted in concise conclusions regarding the underlying mechanisms of disease, in large part due to genetic variations between disease-state and control iPSCs. To circumvent this, the use of genomic editing tools to generate perfect isogenic controls is gaining momentum. To date, DNA binding domain-based zinc finger nucleases and transcription activator-like effector nucleases have been utilized to create genetically defined conditions in patient-specific iPSCs, with some examples leading to the successful identification of novel mechanisms of disease. As the feasibility and utility of genomic editing tools in iPSCs improve, along with the introduction of the clustered regularly interspaced short palindromic repeat system, understanding the features and limitations of genomic editing tools and their applications to iPSC technology is critical to expending the field of human disease modeling. PMID:25075441

  9. Genomic Imprinting and Epigenetic Control of Development

    PubMed Central

    Fedoriw, Andrew; Mugford, Joshua; Magnuson, Terry

    2012-01-01

    Epigenetic mechanisms are extensively utilized during mammalian development. Specific patterns of gene expression are established during cell fate decisions, maintained as differentiation progresses, and often augmented as more specialized cell types are required. Much of what is known about these mechanisms comes from the study of two distinct epigenetic phenomena: genomic imprinting and X-chromosome inactivation. In the case of genomic imprinting, alleles are expressed in a parent-of-origin-dependent manner, whereas X-chromosome inactivation in females requires that only one X chromosome is active in each somatic nucleus. As model systems for epigenetic regulation, genomic imprinting and X-chromosome inactivation have identified and elucidated the numerous regulatory mechanisms that function throughout the genome during development. PMID:22687277

  10. Genomic imprinting and epigenetic control of development.

    PubMed

    Fedoriw, Andrew; Mugford, Joshua; Magnuson, Terry

    2012-07-01

    Epigenetic mechanisms are extensively utilized during mammalian development. Specific patterns of gene expression are established during cell fate decisions, maintained as differentiation progresses, and often augmented as more specialized cell types are required. Much of what is known about these mechanisms comes from the study of two distinct epigenetic phenomena: genomic imprinting and X-chromosome inactivation. In the case of genomic imprinting, alleles are expressed in a parent-of-origin-dependent manner, whereas X-chromosome inactivation in females requires that only one X chromosome is active in each somatic nucleus. As model systems for epigenetic regulation, genomic imprinting and X-chromosome inactivation have identified and elucidated the numerous regulatory mechanisms that function throughout the genome during development. PMID:22687277

  11. 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.

  12. 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

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

    PubMed

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

    2016-07-27

    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

  14. 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.

  15. 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…

  16. 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

  17. 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

  18. 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

  19. Analysis of interactions between the epigenome and structural mutability of the genome using Genboree workbench tools

    PubMed Central

    2014-01-01

    Background Interactions between the epigenome and structural genomic variation are potentially bi-directional. In one direction, structural variants may cause epigenomic changes in cis. In the other direction, specific local epigenomic states such as DNA hypomethylation associate with local genomic instability. Methods To study these interactions, we have developed several tools and exposed them to the scientific community using the Software-as-a-Service model via the Genboree Workbench. One key tool is Breakout, an algorithm for fast and accurate detection of structural variants from mate pair sequencing data. Results By applying Breakout and other Genboree Workbench tools we map breakpoints in breast and prostate cancer cell lines and tumors, discriminate between polymorphic breakpoints of germline origin and those of somatic origin, and analyze both types of breakpoints in the context of the Human Epigenome Atlas, ENCODE databases, and other sources of epigenomic profiles. We confirm previous findings that genomic instability in human germline associates with hypomethylation of DNA, binding sites of Suz12, a key member of the PRC2 Polycomb complex, and with PRC2-associated histone marks H3K27me3 and H3K9me3. Breakpoints in germline and in breast cancer associate with distal regulatory of active gene transcription. Breast cancer cell lines and tumors show distinct patterns of structural mutability depending on their ER, PR, or HER2 status. Conclusions The patterns of association that we detected suggest that cell-type specific epigenomes may determine cell-type specific patterns of selective structural mutability of the genome. PMID:25080362

  20. 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

  1. 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.…

  2. ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data

    PubMed Central

    Weddington, Nodin; Stuy, Alexander; Hiratani, Ichiro; Ryba, Tyrone; Yokochi, Tomoki; Gilbert, David M

    2008-01-01

    Background Eukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals) within which replicons are activated relatively synchronously. These domains replicate in a specific temporal order during S-phase and our genome-wide analyses of replication timing have demonstrated that this temporal order of domain replication is a stable property of specific cell types. Results We have developed ReplicationDomain as a web-based database for analysis of genome-wide replication timing maps (replication profiles) from various cell lines and species. This database also provides comparative information of transcriptional expression and is configured to display any genome-wide property (for instance, ChIP-Chip or ChIP-Seq data) via an interactive web interface. Our published microarray data sets are publicly available. Users may graphically display these data sets for a selected genomic region and download the data displayed as text files, or alternatively, download complete genome-wide data sets. Furthermore, we have implemented a user registration system that allows registered users to upload their own data sets. Upon uploading, registered users may choose to: (1) view their data sets privately without sharing; (2) share with other registered users; or (3) make their published or "in press" data sets publicly available, which can fulfill journal and funding agencies' requirements for data sharing. Conclusion ReplicationDomain is a novel and powerful tool to facilitate the comparative visualization of replication timing in various cell types as well as other genome-wide chromatin features and is considerably faster and more convenient than existing browsers when viewing multi-megabase segments of chromosomes. Furthermore, the data upload function with the option of private viewing or sharing of data sets between registered users should be a valuable resource for the scientific community. PMID:19077204

  3. Progress in TILLING as a tool for functional genomics and improvement of crops.

    PubMed

    Chen, Liang; Hao, Liugen; Parry, Martin A J; Phillips, Andrew L; Hu, Yin-Gang

    2014-05-01

    Food security is a global concern and substantial yield increases in crops are required to feed the growing world population. Mutagenesis is an important tool in crop improvement and is free of the regulatory restrictions imposed on genetically modified organisms. Targeting Induced Local Lesions in Genomes (TILLING), which combines traditional chemical mutagenesis with high-throughput genome-wide screening for point mutations in desired genes, offers a powerful way to create novel mutant alleles for both functional genomics and improvement of crops. TILLING is generally applicable to genomes whether small or large, diploid or even allohexaploid, and shows great potential to address the major challenge of linking sequence information to the function of genes and to modulate key traits for plant breeding. TILLING has been successfully applied in many crop species and recent progress in TILLING is summarized below, especially on the developments in mutation detection technology, application of TILLING in gene functional studies and crop breeding. The potential of TILLING/EcoTILLING for functional genetics and crop improvement is also discussed. Furthermore, a small-scale forward strategy including backcross and selfing was conducted to release the potential mutant phenotypes masked in M2 (or M3) plants. PMID:24618006

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

    PubMed Central

    2014-01-01

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

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

    PubMed

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

    2015-01-01

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

  6. Development and application of camelid molecular cytogenetic tools.

    PubMed

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

    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

  7. 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

  8. Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome.

    PubMed

    Arshad, Saadia; Mumtaz, Asia; Ahmad, Freed; Liaquat, Sadia; Nadeem, Shahid; Mehboob, Shahid; Afzal, Muhammad

    2010-01-01

    MicroRNAs (miRNAs) are 22 nucleotides non-coding RNAs that play pivotal regulatory roles in diverse organisms including the humans and are difficult to be identified due to lack of either sequence features or robust algorithms to efficiently identify. Therefore, we made a tool that is Mi-Discoverer for the detection of miRNAs in human genome. The tools used for the development of software are Microsoft Office Access 2003, the JDK version 1.6.0, BioJava version 1.0, and the NetBeans IDE version 6.0. All already made miRNAs softwares were web based; so the advantage of our project was to make a desktop facility to the user for sequence alignment search with already identified miRNAs of human genome present in the database. The user can also insert and update the newly discovered human miRNA in the database. Mi-Discoverer, a bioinformatics tool successfully identifies human miRNAs based on multiple sequence alignment searches. It's a non redundant database containing a large collection of publicly available human miRNAs. PMID:21364831

  9. 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

  10. Fastbreak: a tool for analysis and visualization of structural variations in genomic data

    PubMed Central

    2012-01-01

    Genomic studies are now being undertaken on thousands of samples requiring new computational tools that can rapidly analyze data to identify clinically important features. Inferring structural variations in cancer genomes from mate-paired reads is a combinatorially difficult problem. We introduce Fastbreak, a fast and scalable toolkit that enables the analysis and visualization of large amounts of data from projects such as The Cancer Genome Atlas. PMID:23046488

  11. 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

  12. Interactive Tools to Track Child Development

    MedlinePlus

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

  13. A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

    PubMed Central

    Zhang, Wenyu; Chen, Jiajia; Yang, Yang; Tang, Yifei; Shang, Jing; Shen, Bairong

    2011-01-01

    The advent of next-generation sequencing technologies is accompanied with the development of many whole-genome sequence assembly methods and software, especially for de novo fragment assembly. Due to the poor knowledge about the applicability and performance of these software tools, choosing a befitting assembler becomes a tough task. Here, we provide the information of adaptivity for each program, then above all, compare the performance of eight distinct tools against eight groups of simulated datasets from Solexa sequencing platform. Considering the computational time, maximum random access memory (RAM) occupancy, assembly accuracy and integrity, our study indicate that string-based assemblers, overlap-layout-consensus (OLC) assemblers are well-suited for very short reads and longer reads of small genomes respectively. For large datasets of more than hundred millions of short reads, De Bruijn graph-based assemblers would be more appropriate. In terms of software implementation, string-based assemblers are superior to graph-based ones, of which SOAPdenovo is complex for the creation of configuration file. Our comparison study will assist researchers in selecting a well-suited assembler and offer essential information for the improvement of existing assemblers or the developing of novel assemblers. PMID:21423806

  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. 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.

  15. 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.

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

    PubMed

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

    2016-08-01

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

  17. HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes

    PubMed Central

    Nguyen, Marcus; Ekstrom, Alex; Li, Xueqiong; Yin, Yanbin

    2015-01-01

    Horizontal gene transfer (HGT) is a fast-track mechanism that allows genetically unrelated organisms to exchange genes for rapid environmental adaptation. We developed a new phyletic distribution-based software, HGT-Finder, which implements a novel bioinformatics algorithm to calculate a horizontal transfer index and a probability value for each query gene. Applying this new tool to the Aspergillus fumigatus, Aspergillus flavus, and Aspergillus nidulans genomes, we found 273, 542, and 715 transferred genes (HTGs), respectively. HTGs have shorter length, higher guanine-cytosine (GC) content, and relaxed selection pressure. Metabolic process and secondary metabolism functions are significantly enriched in HTGs. Gene clustering analysis showed that 61%, 41% and 74% of HTGs in the three genomes form physically linked gene clusters (HTGCs). Overlapping manually curated, secondary metabolite gene clusters (SMGCs) with HTGCs found that 9 of the 33 A. fumigatus SMGCs and 31 of the 65 A. nidulans SMGCs share genes with HTGCs, and that HTGs are significantly enriched in SMGCs. Our genome-wide analysis thus presented very strong evidence to support the hypothesis that HGT has played a very critical role in the evolution of SMGCs. The program is freely available at http://cys.bios.niu.edu/HGTFinder/HGTFinder.tar.gz. PMID:26473921

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

    PubMed

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

    2012-01-01

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

  19. 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. PMID:27250347

  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/. PMID:17526516

  1. 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

  2. Development of chloroplast genomic resources for Cynara.

    PubMed

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

    2016-03-01

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

  3. 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.

  4. Genomic resource development for shellfish of conservation concern.

    PubMed

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

    2013-03-01

    Effective conservation of threatened species depends on the ability to assess organism physiology and population demography. To develop genomic resources to better understand the dynamics of two ecologically vulnerable species in the Pacific Northwest of the United States, larval transcriptomes were sequenced for the pinto abalone, Haliotis kamtschatkana kamtschatkana, and the Olympia oyster, Ostrea lurida. Based on comparative species analysis the Ostrea lurida transcriptome (41 136 contigs) is relatively complete. These transcriptomes represent the first significant contribution to genomic resources for both species. Genes are described based on biological function with particular attention to those associated with temperature change, oxidative stress and immune function. In addition, transcriptome-derived genetic markers are provided. Together, these resources provide valuable tools for future studies aimed at conservation of Haliotis kamtschatkana kamtschatkana, Ostrea lurida and related species. PMID:23280275

  5. ICT Tools and Students' Competence Development

    ERIC Educational Resources Information Center

    Fuglestad, Anne Berit

    2004-01-01

    In this paper I will present the rationale that motivates the study in an ongoing three-year project following students in school years 8 to 10. The aim is to develop the students' competence with use of ICT tools in mathematics in such a way that they will be able to choose tools for themselves, not rely just on the teacher telling them what to…

  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. 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.

  7. 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.

  8. 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…

  9. CAGO: A Software Tool for Dynamic Visual Comparison and Correlation Measurement of Genome Organization

    PubMed Central

    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. PMID:22114666

  10. 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

  11. Genomic tools to assist breeding for drought tolerance.

    PubMed

    Langridge, Peter; Reynolds, Matthew P

    2015-04-01

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

  12. The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data

    PubMed Central

    Laulederkind, Stanley J. F.; Shimoyama, Mary; Hayman, G. Thomas; Lowry, Timothy F.; Nigam, Rajni; Petri, Victoria; Smith, Jennifer R.; Wang, Shur-Jen; de Pons, Jeff; Kowalski, George; Liu, Weisong; Rood, Wes; Munzenmaier, Diane H.; Dwinell, Melinda R.; Twigger, Simon N.; Jacob, Howard J.

    2011-01-01

    The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses over 40 000 rat gene records as well as human and mouse orthologs, 1771 rat and 1911 human quantitative trait loci (QTLs) and 2209 rat strains. Biological information curated for these data objects includes disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components. A suite of tools has been developed to aid curators in acquiring and validating data objects, assigning nomenclature, attaching biological information to objects and making connections among data types. The software used to assign nomenclature, to create and edit objects and to make annotations to the data objects has been specifically designed to make the curation process as fast and efficient as possible. The user interfaces have been adapted to the work routines of the curators, creating a suite of tools that is intuitive and powerful. Database URL: http://rgd.mcw.edu PMID:21321022

  13. 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.

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

    PubMed Central

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

    2015-01-01

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

  15. 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. PMID:25853282

  16. Bypassing genomic imprinting allows seed development.

    PubMed

    Nowack, Moritz K; Shirzadi, Reza; Dissmeyer, Nico; Dolf, Andreas; Endl, Elmar; Grini, Paul E; Schnittger, Arp

    2007-05-17

    In developing progeny of mammals the two parental genomes are differentially expressed according to imprinting marks, and embryos with only a uniparental genetic contribution die. Gene expression that is dependent on the parent of origin has also been observed in the offspring of flowering plants, and mutations in the imprinting machinery lead to embryonic lethality, primarily affecting the development of the endosperm-a structure in the seed that nourishes the embryo, analogous to the function of the mammalian placenta. Here we have generated Arabidopsis thaliana seeds in which the endosperm is of uniparental, that is, maternal, origin. We demonstrate that imprinting in developing seeds can be bypassed and viable albeit smaller seedlings can develop from seeds lacking a paternal contribution to the endosperm. Bypassing is only possible if the mother is mutant for any of the FIS-class genes, which encode Polycomb group chromatin-modifying factors. Thus, these data provide functional evidence that the action of the FIS complex balances the contribution of the paternal genome. As flowering plants have evolved a special reproduction system with a parallel fusion of two female with two male gametes, our findings support the hypothesis that only with the evolution of double fertilization did the action of the FIS genes become a requirement for seed development. Furthermore, our data argue for a gametophytic origin of endosperm in flowering plants, thereby supporting a hypothesis raised in 1900 by Eduard Strasburger. PMID:17468744

  17. 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. PMID:25619558

  18. 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

  19. 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

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

    SciTech Connect

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

    1993-02-01

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

  1. Software Tools for Empowering Instructional Developers.

    ERIC Educational Resources Information Center

    Gayeski, Diane M.

    1991-01-01

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

  2. 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.

  3. Spliceosomal introns as tools for genomic and evolutionary analysis

    PubMed Central

    Irimia, Manuel; Roy, Scott William

    2008-01-01

    Over the past 5 years, the availability of dozens of whole genomic sequences from a wide variety of eukaryotic lineages has revealed a very large amount of information about the dynamics of intron loss and gain through eukaryotic history, as well as the evolution of intron sequences. Implicit in these advances is a great deal of information about the structure and evolution of surrounding sequences. Here, we review the wealth of ways in which structures of spliceosomal introns as well as their conservation and change through evolution may be harnessed for evolutionary and genomic analysis. First, we discuss uses of intron length distributions and positions in sequence assembly and annotation, and for improving alignment of homologous regions. Second, we review uses of introns in evolutionary studies, including the utility of introns as indicators of rates of sequence evolution, for inferences about molecular evolution, as signatures of orthology and paralogy, and for estimating rates of nucleotide substitution. We conclude with a discussion of phylogenetic methods utilizing intron sequences and positions. PMID:18263615

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

    PubMed

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

    2015-01-01

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

  5. Snat: a SNP annotation tool for bovine by integrating various sources of genomic information

    PubMed Central

    2011-01-01

    Background Most recently, with maturing of bovine genome sequencing and high throughput SNP genotyping technologies, a large number of significant SNPs associated with economic important traits can be identified by genome-wide association studies (GWAS). To further determine true association findings in GWAS, the common strategy is to sift out most promising SNPs for follow-up replication studies. Hence it is crucial to explore the functional significance of the candidate SNPs in order to screen and select the potential functional ones. To systematically prioritize these statistically significant SNPs and facilitate follow-up replication studies, we developed a bovine SNP annotation tool (Snat) based on a web interface. Results With Snat, various sources of genomic information are integrated and retrieved from several leading online databases, including SNP information from dbSNP, gene information from Entrez Gene, protein features from UniProt, linkage information from AnimalQTLdb, conserved elements from UCSC Genome Browser Database and gene functions from Gene Ontology (GO), KEGG PATHWAY and Online Mendelian Inheritance in Animals (OMIA). Snat provides two different applications, including a CGI-based web utility and a command-line version, to access the integrated database, target any single nucleotide loci of interest and perform multi-level functional annotations. For further validation of the practical significance of our study, SNPs involved in two commercial bovine SNP chips, i.e., the Affymetrix Bovine 10K chip array and the Illumina 50K chip array, have been annotated by Snat, and the corresponding outputs can be directly downloaded from Snat website. Furthermore, a real dataset involving 20 identified SNPs associated with milk yield in our recent GWAS was employed to demonstrate the practical significance of Snat. Conclusions To our best knowledge, Snat is one of first tools focusing on SNP annotation for livestock. Snat confers researchers with a

  6. Visualization tool for advanced laser system development

    NASA Astrophysics Data System (ADS)

    Crockett, Gregg A.; Brunson, Richard L.

    2002-06-01

    Simulation development for Laser Weapon Systems design and system trade analyses has progressed to new levels with the advent of object-oriented software development tools and PC processor capabilities. These tools allow rapid visualization of upcoming laser weapon system architectures and the ability to rapidly respond to what-if scenario questions from potential user commands. These simulations can solve very intensive problems in short time periods to investigate the parameter space of a newly emerging weapon system concept, or can address user mission performance for many different scenario engagements. Equally important to the rapid solution of complex numerical problems is the ability to rapidly visualize the results of the simulation, and to effectively interact with visualized output to glean new insights into the complex interactions of a scenario. Boeing has applied these ideas to develop a tool called the Satellite Visualization and Signature Tool (SVST). This Windows application is based upon a series of C++ coded modules that have evolved from several programs at Boeing-SVS. The SVST structure, extensibility, and some recent results of applying the simulation to weapon system concepts and designs will be discussed in this paper.

  7. 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.

  8. The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development

    PubMed Central

    Chen, Xiao; Bracht, John R.; Goldman, Aaron David; Dolzhenko, Egor; Clay, Derek M.; Swart, Estienne C.; Perlman, David H.; Doak, Thomas G.; Stuart, Andrew; Amemiya, Chris T.; Sebra, Robert P.; Landweber, Laura F.

    2014-01-01

    SUMMARY Programmed DNA rearrangements in the single-celled eukaryote Oxytricha trifallax completely rewire its germline into a somatic nucleus during development. This elaborate, RNA-mediated pathway eliminates noncoding DNA sequences that interrupt gene loci and reorganizes the remaining fragments by inversions and permutations to produce functional genes. Here, we report the Oxytricha germline genome and compare it to the somatic genome to present a global view of its massive scale of genome rearrangements. The remarkably encrypted genome architecture contains >3,500 scrambled genes, as well as >800 predicted germline-limited genes expressed, and some posttranslationally modified, during genome rearrangements. Gene segments for different somatic loci often interweave with each other. Single gene segments can contribute to multiple, distinct somatic loci. Terminal precursor segments from neighboring somatic loci map extremely close to each other, often overlapping. This genome assembly provides a draft of a scrambled genome and a powerful model for studies of genome rearrangement. PMID:25171416

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

    PubMed

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

    2007-01-01

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

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

    PubMed

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

    2015-03-11

    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

  11. 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

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

    PubMed

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

    2003-04-01

    A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits an integrated genome map to be stored, retrieved, viewed, and queried in a stand-alone capacity, in a client/server relationship with the Fungal Genome Database (FGDB), and as a web-browsing tool for the FGDB. In that ODS3 is programmed in Java, the tool promotes platform independence and supports export of integrated genome-mapping data in the extensible markup language (XML) for data interchange with other genome information systems. The tool ODS3 is used to create an initial integrated genome map of the AIDS-related fungal pathogen, Pneumocystis carinii. Contig dynamics would indicate that this physical map is approximately 50% complete with approximately 200 contigs. A total of 10 putative multigene families were found. Two of these putative families were previously characterized in P. carinii, namely the major surface glycoproteins (MSGs) and HSP70 proteins; three of these putative families (not previously characterized in P. carinii) were found to be similar to families encoding the HSP60 in Schizosaccharomyces pombe, the heat-shock psi protein in S. pombe, and the RNA synthetase family (i.e., MES1) in Saccharomyces cerevisiae. Physical mapping data are consistent with the 16S, 5.8S, and 26S rDNA genes being single copy in P. carinii. No other fungus outside this genus is known to have the rDNA genes in single copy. PMID:12702676

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

    PubMed

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

    2011-03-01

    The rapid technological development in the field of parallel sequencing offers new opportunities when tracing and tracking microorganisms in the food and feed chain. If a bioterror organism is deliberately spread it is of crucial importance to get as much information as possible regarding the strain as fast as possible to aid the decision process and select suitable controls, tracing and tracking tools. A lot of efforts have been made to sequence multiple strains of potential bioterror organisms so there is a relatively large set of reference genomes available. This study is focused on how to use parallel sequencing for rapid phylogenomic analysis and screen for genetic modifications. A bioinformatic methodology has been developed to rapidly analyze sequence data with minimal post-processing. Instead of assembling the genome, defining genes, defining orthologous relations and calculating distances, the present method can achieve a similar high resolution directly from the raw sequence data. The method defines orthologous sequence reads instead of orthologous genes and the average similarity of the core genome (ASC) is calculated. The sequence reads from the core and from the non-conserved genomic regions can also be separated for further analysis. Finally, the comparison algorithm is used to visualize the phylogenomic diversity of the bacterial bioterror organisms Bacillus anthracis and Clostridium botulinum using heat plot diagrams. PMID:20826036

  14. 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.

  15. 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.

  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. 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

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

    PubMed

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

    2014-08-01

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

  19. 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.

  20. Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes

    PubMed Central

    Luo, Hao; Zhang, Chun-Ting; Gao, Feng

    2014-01-01

    DNA replication is one of the most basic processes in all three domains of cellular life. With the advent of the post-genomic era, the increasing number of complete archaeal genomes has created an opportunity for exploration of the molecular mechanisms for initiating cellular DNA replication by in vivo experiments as well as in silico analysis. However, the location of replication origins (oriCs) in many sequenced archaeal genomes remains unknown. We present a web-based tool Ori-Finder 2 to predict oriCs in the archaeal genomes automatically, based on the integrated method comprising the analysis of base composition asymmetry using the Z-curve method, the distribution of origin recognition boxes identified by FIMO tool, and the occurrence of genes frequently close to oriCs. The web server is also able to analyze the unannotated genome sequences by integrating with gene prediction pipelines and BLAST software for gene identification and function annotation. The result of the predicted oriCs is displayed as an HTML table, which offers an intuitive way to browse the result in graphical and tabular form. The software presented here is accurate for the genomes with single oriC, but it does not necessarily find all the origins of replication for the genomes with multiple oriCs. Ori-Finder 2 aims to become a useful platform for the identification and analysis of oriCs in the archaeal genomes, which would provide insight into the replication mechanisms in archaea. The web server is freely available at http://tubic.tju.edu.cn/Ori-Finder2/. PMID:25309521

  1. 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.

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

    PubMed

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

    2016-07-01

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

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

    PubMed

    Brohée, Sylvain; Bontempi, Gianluca

    2012-01-01

    ChIP-sequencing is a method of choice to localize the positions of protein binding sites on DNA on a whole genomic scale. The deciphering of the sequencing data produced by this novel technique is challenging and it is achieved by their rigorous interpretation using dedicated tools and adapted visualization programs. Here, we present a bioinformatics tool (D-peaks) that adds several possibilities (including, user-friendliness, high-quality, relative position with respect to the genomic features) to the well-known visualization browsers or databases already existing. D-peaks is directly available through its web interface http://rsat.ulb.ac.be/dpeaks/ as well as a command line tool. PMID:23132505

  4. Developing a mapping tool for tablets

    NASA Astrophysics Data System (ADS)

    Vaughan, Alan; Collins, Nathan; Krus, Mike

    2014-05-01

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

  5. 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

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

    PubMed Central

    Bendahmane, Mohammed

    2013-01-01

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

  7. 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. PMID:27146974

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

    PubMed Central

    Fierst, Janna L.

    2015-01-01

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

  9. 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.

  10. Tandem repeat coupled with endonuclease cleavage (TREC): a seamless modification tool for genome engineering in yeast

    PubMed Central

    Noskov, Vladimir N.; Segall-Shapiro, Thomas H.; Chuang, Ray-Yuan

    2010-01-01

    The complete synthetic Mycoplasma genitalium genome (∼583 kb) has been assembled and cloned as a circular plasmid in the yeast Saccharomyces cerevisiae. Attempts to engineer the cloned genome by standard genetic methods involving the URA3/5-fluoroorotic acid (5-FOA) counter-selection have shown a high background of 5-FOA resistant clones derived from spontaneous deletions of the bacterial genome maintained in yeast. Here, we report a method that can seamlessly modify the bacterial genome in yeast with high efficiency. This method requires two sequential homologous recombination events. First, the target region is replaced with a mutagenesis cassette that consists of a knock-out CORE (an18-bp I-SceI recognition site, the SCEI gene under the control of the GAL1 promoter, and the URA3 marker) and a DNA fragment homologous to the sequence upstream of the target site. The replacement generates tandem repeat sequences flanking the CORE. Second, galactose induces the expression of I-SceI, which generates a double-strand break (DSB) at the recognition site. This DSB promotes intra-molecular homologous recombination between the repeat sequences, and leads to an excision of the CORE. As a result, a seamless modification is generated. This method can be adapted for a variety of genomic modifications and may provide an important tool to modify and design natural or synthetic genomes propagated in yeast. PMID:20228123

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

    PubMed

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

    2016-01-01

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

  12. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    DOE PAGESBeta

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

    2015-01-01

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

  15. 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.

  16. C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison

    PubMed Central

    Minkin, Ilya; Pham, Hoa; Starostina, Ekaterina; Vyahhi, Nikolay; Pham, Son

    2013-01-01

    We present C-Sibelia, a highly accurate and easy-to-use software tool for comparing two closely related bacterial genomes, which can be presented as either finished sequences or fragmented assemblies. C-Sibelia takes as input two FASTA files and produces: (1) a VCF file containing all identified single nucleotide variations and indels; (2) an XMFA file containing alignment information. The software also produces Circos diagrams visualizing high level genomic architecture for rearrangement analyses. C-Sibelia is a part of the Sibelia comparative genomics suite, which is freely available under the GNU GPL v.2 license at http://sourceforge.net/projects/sibelia-bio. C-Sibelia is compatible with Unix-like operating systems. A web-based version of the software is available at http://etool.me/software/csibelia. PMID:25110578

  17. Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences.

    PubMed

    Bose, M; Barber, Robert D

    2006-01-01

    Prophage loci often remain under-annotated or even unrecognized in prokaryotic genome sequencing projects. A PHP application, Prophage Finder, has been developed and implemented to predict prophage loci, based upon clusters of phage-related gene products encoded within DNA sequences. This application provides results detailing several facets of these clusters to facilitate rapid prediction and analysis of prophage sequences. Prophage Finder was tested using previously annotated prokaryotic genomic sequences with manually curated prophage loci as benchmarks. Additional analyses from Prophage Finder searches of several draft prokaryotic genome sequences are available through the Web site (http://bioinformatics.uwp.edu/~phage/DOEResults.php) to illustrate the potential of this application. PMID:16922685

  18. 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.

  19. Development of advanced composite ceramic tool material

    SciTech Connect

    Huang Chuanzhen; Ai Xing

    1996-08-01

    An advanced ceramic cutting tool material has been developed by means of silicon carbide whisker (SiCw) reinforcement and silicon carbide particle (SiCp) dispersion. The material has the advantage of high bending strength and fracture toughness. Compared with the mechanical properties of Al{sub 2}O{sub 3}/SiCp(AP), Al{sub 2}O{sub 3}/SiCw(JX-1), and Al{sub 2}O{sub 3}/SiCp/SiCw(JX-2-I), it confirms that JX-2-I composites have obvious additive effects of both reinforcing and toughening. The reinforcing and toughening mechanisms of JX-2-I composites were studied based on the analysis of thermal expansion mismatch and the observation of microstructure. The cutting performance of JX-2-I composites was investigated primarily.

  20. Development of Fuel Accounting Software Tool

    NASA Astrophysics Data System (ADS)

    Eun, Jong Won; Suk, Juil

    1996-12-01

    A successful spacecraft mission depends on the proper maintenance of the orbit and attitude. One important requirement for the orbit and attitude planning is the accurate estimation of the propellant remaining onboard the spacecraft. For GEO communi-cations satellite, a precise fuel remaining estimation is of particular importance. This paper focuses on the bookkeeping method that was developed for calculating the pro-pellant budget by recording fuel consumption history. In general, the bookkeeping method includes detailed observation of spacecraft maneuver operations throughout the whole mission life. Application of this method is illustrated using a communica-tions satellite. In this the fuel accounting s/w tool, a PC-based spread sheet is utilized to provide an overall view of input/output elements, and to provide strong numerical and graphical merits for analyses.

  1. Solar Array Verification Analysis Tool (SAVANT) Developed

    NASA Technical Reports Server (NTRS)

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

    1999-01-01

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

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

    PubMed Central

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

    2015-01-01

    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. PMID:26304539

  3. Novel Genome-Editing Tools to Model and Correct Primary Immunodeficiencies

    PubMed Central

    Ott de Bruin, Lisa M.; Volpi, Stefano; Musunuru, Kiran

    2015-01-01

    Severe combined immunodeficiency (SCID) and other severe non-SCID primary immunodeficiencies (non-SCID PID) can be treated by allogeneic hematopoietic stem cell (HSC) transplantation, but when histocompatibility leukocyte antigen-matched donors are lacking, this can be a high-risk procedure. Correcting the patient’s own HSCs with gene therapy offers an attractive alternative. Gene therapies currently being used in clinical settings insert a functional copy of the entire gene by means of a viral vector. With this treatment, severe complications may result due to integration within oncogenes. A promising alternative is the use of endonucleases such as ZFNs, TALENs, and CRISPR/Cas9 to introduce a double-stranded break in the DNA and thus induce homology-directed repair. With these genome-editing tools a correct copy can be inserted in a precisely targeted “safe harbor.” They can also be used to correct pathogenic mutations in situ and to develop cellular or animal models needed to study the pathogenic effects of specific genetic defects found in immunodeficient patients. This review discusses the advantages and disadvantages of these endonucleases in gene correction and modeling with an emphasis on CRISPR/Cas9, which offers the most promise due to its efficacy and versatility. PMID:26052330

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

    PubMed

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

    2012-04-01

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

  5. Development of Advanced Tools for Cryogenic Integration

    NASA Astrophysics Data System (ADS)

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

    2004-06-01

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

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

    PubMed

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

    2014-01-01

    Over 95% of all metazoan (animal) species comprise the "invertebrates," but very few genomes from these organisms have been sequenced. We have, therefore, formed a "Global Invertebrate Genomics Alliance" (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture. PMID:24336862

  7. 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

  8. Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era.

    PubMed

    Hu, Zhi-Liang; Park, Carissa A; Wu, Xiao-Lin; Reecy, James M

    2013-01-01

    The Animal QTL database (QTLdb; http://www.animalgenome.org/QTLdb) is designed to house all publicly available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. An earlier version was published in the Nucleic Acids Research Database issue in 2007. Since then, we have continued our efforts to develop new and improved database tools to allow more data types, parameters and functions. Our efforts have transformed the Animal QTLdb into a tool that actively serves the research community as a quality data repository and more importantly, a provider of easily accessible tools and functions to disseminate QTL and gene association information. The QTLdb has been heavily used by the livestock genomics community since its first public release in 2004. To date, there are 5920 cattle, 3442 chicken, 7451 pigs, 753 sheep and 88 rainbow trout data points in the database, and at least 290 publications that cite use of the database. The rapid advancement in genomic studies of cattle, chicken, pigs, sheep and other livestock animals has presented us with challenges, as well as opportunities for the QTLdb to meet the evolving needs of the research community. Here, we report our progress over the recent years and highlight new functions and services available to the general public. PMID:23180796

  9. A Survey of Agent-oriented Development Tools

    NASA Astrophysics Data System (ADS)

    Pokahr, Alexander; Braubach, Lars

    Development tools represent an important additive for the practical realization of software applications, mainly because they help automating development activities and are able to hide complexity from developers. In this chapter, the requirements for tools are generically analyzed by the various tasks that need to be performed in the different development phases. These requirements are the foundation for a detailed investigation of the landscape of available agent-oriented development tools. In order to assess the variety of tools systematically, existing surveys and evaluations have been used to isolate three important categories of tools, which are treated separately: modeling tools, IDEs and phase-specic tools. For each of these categories specic requirements are elaborated, an overview of existing tools is given and one representative tool is presented in more detail.

  10. Development and psychometric evaluation of the genomic nursing concept inventory.

    PubMed

    Ward, Linda D; Haberman, Mel; Barbosa-Leiker, Celestina

    2014-09-01

    Translation of genome science to improve health outcomes requires nurses to develop genomic competency and literacy, and a robust measure of genomic literacy is needed to advance evidence-based nursing education. This study aimed to develop and evaluate the Genomic Nursing Concept Inventory (GNCI), which is a scale to measure understanding of the genetic/genomic concepts most critical to nursing practice. Applying a multistep process, key concepts were drawn from essential nursing genetic/genomic competencies and validated by expert opinion. Surveys and cognitive interviews of baccalaureate nursing (BSN) students informed item development. A 52-item draft inventory was administered to 238 BSN students. Item analysis informed inventory reduction, and the resulting 31-item inventory was tested with 705 BSN students. Scale difficulty was 47%, item difficulty 13% to 84%, and Cronbach’s alpha 0.77. As scale refinement proceeds, the GNCI provides a useful measure of genomic literacy to inform curriculum design and evaluate outcomes in genomic nursing education. PMID:25102130

  11. 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, ...

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

    PubMed Central

    Lemke, Amy A.; Harris-Wai, Julie N.

    2015-01-01

    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. PMID:25764215

  13. 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 ). PMID:26519403

  14. TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data.

    PubMed

    Wintermans, Bastiaan; Brandt, Bernd; Vandenbroucke-Grauls, Christina; Budding, Andries

    2015-01-01

    Next-generation sequencing is not yet commonly used in clinical laboratories because of a lack of simple and intuitive tools. We developed a software tool (TreeSeq) with a quaternary tree search structure for the analysis of sequence data. This permits rapid searches for sequences of interest in large datasets. We used TreeSeq to screen a gut microbiota metagenomic dataset and a whole genome sequencing (WGS) dataset of a strain of Klebsiella pneumoniae for antibiotic resistance genes and compared the results with BLAST and phenotypic resistance determination. TreeSeq was more than thirty times faster than BLAST and accurately detected resistance gene sequences in complex metagenomic data and resistance genes corresponding with the phenotypic resistance pattern of the Klebsiella strain. Resistance genes found by TreeSeq were visualized as a gene coverage heat map, aiding in the interpretation of results. TreeSeq brings analysis of metagenomic and WGS data within reach of clinical diagnostics. PMID:25933115

  15. DNA Microarrays: a Powerful Genomic Tool for Biomedical and Clinical Research

    PubMed Central

    Trevino, Victor; Falciani, Francesco; Barrera-Saldaña, Hugo A

    2007-01-01

    Among the many benefits of the Human Genome Project are new and powerful tools such as the genome-wide hybridization devices referred to as microarrays. Initially designed to measure gene transcriptional levels, microarray technologies are now used for comparing other genome features among individuals and their tissues and cells. Results provide valuable information on disease subcategories, disease prognosis, and treatment outcome. Likewise, they reveal differences in genetic makeup, regulatory mechanisms, and subtle variations and move us closer to the era of personalized medicine. To understand this powerful tool, its versatility, and how dramatically it is changing the molecular approach to biomedical and clinical research, this review describes the technology, its applications, a didactic step-by-step review of a typical microarray protocol, and a real experiment. Finally, it calls the attention of the medical community to the importance of integrating multidisciplinary teams to take advantage of this technology and its expanding applications that, in a slide, reveals our genetic inheritance and destiny. PMID:17660860

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

    PubMed Central

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

    2011-01-01

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

  17. 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.

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

    PubMed

    Bock, Ralph

    2015-01-01

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

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

    PubMed Central

    Han, Na; Qiang, Yujun; Zhang, Wen

    2016-01-01

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

  20. 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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2014-07-22

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

  3. 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

  4. 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.

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

    ScienceCinema

    Goldberg, Robert [UCLA

    2013-01-22

    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.

  6. 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.

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

    PubMed Central

    2012-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  10. 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.

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

    PubMed Central

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

    2010-01-01

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

  12. Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information

    PubMed Central

    2010-01-01

    Background Protein-protein interactions are crucially important for cellular processes. Knowledge of these interactions improves the understanding of cell cycle, metabolism, signaling, transport, and secretion. Information about interactions can hint at molecular causes of diseases, and can provide clues for new therapeutic approaches. Several (usually expensive and time consuming) experimental methods can probe protein - protein interactions. Data sets, derived from such experiments make the development of prediction methods feasible, and make the creation of protein-protein interaction network predicting tools possible. Methods Here we report the development of a simple open source program module (OpenPPI_predictor) that can generate a putative protein-protein interaction network for target genomes. This tool uses the orthologous interactome network data from a related, experimentally studied organism. Results Results from our predictions can be visualized using the Cytoscape visualization software, and can be piped to downstream processing algorithms. We have employed our program to predict protein-protein interaction network for the human parasite roundworm Brugia malayi, using interactome data from the free living nematode Caenorhabditis elegans. Availability The OpenPPI_predictor source code is available from http://tools.neb.com/~posfai/. PMID:20684769

  13. Relation between Science Teachers' Assessment Tools and Students Cognitive Development

    ERIC Educational Resources Information Center

    Ozsevgec, Tuncay; Cepni, Salih

    2006-01-01

    In order to determine students' achievement, science teachers have to develop their own assessment tools. This study attempts to find out the relationship between the teachers' assessment tools and students' cognitive development according to the teachers' teaching experiences. Six open-ended survey questions were developed and delivered to 59…

  14. Relation between Science Teachers' Assessment Tools and Students' Cognitive Development

    ERIC Educational Resources Information Center

    Ozsevgec, Tuncay; Cepni, Salih

    2006-01-01

    In order to determine students' achievement, science teachers have to develop their own assessment tools. This study attempts to find out the relationship between the teachers' assessment tools and students' cognitive development according to the teachers' teaching experiences. Six open-ended survey questions were developed and delivered to 59…

  15. 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).

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

    PubMed

    Wendelsdorf, Katherine; Shah, Sohela

    2015-09-01

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

  17. 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.

  18. Machine tool evaluation and machining operation development

    SciTech Connect

    Morris, T.O.; Kegg, R.

    1997-03-15

    The purpose of this CRADA was to support Cincinnati Milacron`s needs in fabricating precision components, from difficult to machine materials, while maintaining and enhancing the precision manufacturing skills of the Oak Ridge Complex. Oak Ridge and Cincinnati Milacron personnel worked in a team relationship wherein each contributed equally to the success of the program. Process characterization, control technologies, machine tool capabilities, and environmental issues were the primary focus areas. In general, Oak Ridge contributed a wider range of expertise in machine tool testing and monitoring, and environmental testing on machining fluids to the defined tasks while Cincinnati Milacron personnel provided equipment, operations-specific knowledge and shop-floor services to each task. Cincinnati Milacron was very pleased with the results of all of the CRADA tasks. However, some of the environmental tasks were not carried through to a desired completion due to an expanding realization of need as the work progressed. This expansion of the desired goals then exceeded the time length of the CRADA. Discussions are underway on continuing these tasks under either a Work for Others agreement or some alternate funding.

  19. 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…

  20. The Gene-Finder computer tools for analysis of human and model organisms genome sequences.

    PubMed

    Solovyev, V; Salamov, A

    1997-01-01

    We present a complex of new programs for promoter, 3'-processing, splice sites, coding exons and gene structure identification in genomic DNA of several model species. The human gene structure prediction program FGENEH, exon prediction-FEXH and splice site prediction-HSPL have been modified for sequence analysis of Drosophila (FGENED, FEXD and DSPL), C.elegance (FGENEN, FEXN and NSPL), Yeast (FEXY and YSPL) and Plant (FGENEA, FEXA and ASPL) genomic sequences. We recomputed all frequency and discriminant function parameters for these organisms and adjusted organism specific minimal intron lengths. An accuracy of coding region prediction for these programs is similar with the observed accuracy of FEXH and FGENEH. We have developed FEXHB and FGENEHB programs combining pattern recognition features and information about similarity of predicted exons with known sequences in protein databases. These programs have approximately 10% higher average accuracy of coding region recognition. Two new programs for human promoter site prediction (TSSG and TSSW) have been developed which use Gosh (1993) and Wingender (1994) data bases of functional motifs, respectively. POLYAH program was designed for prediction of 3'-processing regions in human genes and CDSB program was developed for bacterial gene prediction. We have developed a new approach to predict multiple genes based on double dynamic programming, that is very important for analysis of long genomic DNA fragments generated by genome sequencing projects. Analysis of uncharacterized sequences based on our methods is available through the University of Houston, Weizmann Institute of Science email servers and several Web pages at Baylor College of Medicine. PMID:9322052

  1. 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

  2. PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences.

    PubMed

    Elnitski, Laura; Riemer, Cathy; Petrykowska, Hanna; Florea, Liliana; Schwartz, Scott; Miller, Webb; Hardison, Ross

    2002-12-01

    Sequence conservation between species is useful both for locating coding regions of genes and for identifying functional noncoding segments. Hence interspecies alignment of genomic sequences is an important computational technique. However, its utility is limited without extensive annotation. We describe a suite of software tools, PipTools, and related programs that facilitate the annotation of genes and putative regulatory elements in pairwise alignments. The alignment server PipMaker uses the output of these tools to display detailed information needed to interpret alignments. These programs are provided in a portable format for use on common desktop computers and both the toolkit and the PipMaker server can be found at our Web site (http://bio.cse.psu.edu/). We illustrate the utility of the toolkit using annotation of a pairwise comparison of the mouse MHC class II and class III regions with orthologous human sequences and subsequently identify conserved, noncoding sequences that are DNase I hypersensitive sites in chromatin of mouse cells. PMID:12504859

  3. 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.

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

    PubMed Central

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

    2016-01-01

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

  5. Development of Regional Excel-Based Stormwater/Nutrient BMP Optimization Tool (Opti-Tool)

    EPA Science Inventory

    During 2014, EPA Region 1 contracted with Tetra Tech, Inc. to work with a regional technical Advisory Committee to develop an Excel-based stormwater/nutrient BMP optimization tool (Opti-Tool) using regional precipitation data and regionally calibrated BMP performance data from UN...

  6. 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)…

  7. 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…

  8. 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.

  9. 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.

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

    PubMed

    Saugeron, Benoit; Sonnier, Pierre; Marchais, Stéphanie

    2016-01-01

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

  11. Mitochondrial insertions into primate nuclear genomes suggest the use of numts as a tool for phylogeny.

    PubMed

    Hazkani-Covo, Einat

    2009-10-01

    Homoplasy-free characters are a valuable and highly desired tool for molecular systematics. Nuclear sequences of mitochondrial origin (numts) are fragments of mitochondrial DNA that have been transferred into the nuclear genome. numts are passively captured into genomes and have no transposition activity, which suggests they may have utility as phylogenetic markers. Here, five fully sequenced primate genomes (human, chimpanzee, orangutan, rhesus macaque, and marmoset) are used to reconstruct the evolutionary dynamics of recent numt accumulation in a phylogenetic context. The status of 367 numt loci is used as categorical data, and a maximum parsimony approach is used to trace numt insertions on different branches of the taxonomically undisputed primate phylogenetic tree. The presence of a given numt in related taxa implies orthologous integration, whereas the absence of a numt indicates the plesiomorphic condition prior to integration. An average rate of 5.65 numts per 1 My is estimated on the tree, but insertion rates vary significantly on different branches. Two instances in which the presence-absence pattern of numts does not agree with the phylogenetic tree were identified. These events may be the result of either lineage sorting or reversal. Using the numts reported here to reconstruct primate phylogeny produces the canonical primate tree topology with high bootstrap support. Moreover, numts identified in gorilla Supercontigs were used to test the human-chimp-gorilla trichotomy, yielding a high level of support for the sister relationship of human and chimpanzee. These analyses suggest that numts are valuable phylogenetic markers that can be used for molecular systematics. It remains to be tested whether numts are useful at deeper phylogenetic levels. PMID:19578158

  12. A genomic atlas of mouse hypothalamic development

    PubMed Central

    Shimogori, Tomomi; Lee, Daniel A; Miranda-Angulo, Ana; Yang, Yanqin; Wang, Hong; Jiang, Lizhi; Yoshida, Aya C; Kataoka, Ayane; Mashiko, Hiromi; Avetisyan, Marina; Qi, Lixin; Qian, Jiang; Blackshaw, Seth

    2014-01-01

    The hypothalamus is a central regulator of many behaviors that are essential for survival, such as temperature regulation, food intake and circadian rhythms. However, the molecular pathways that mediate hypothalamic development are largely unknown. To identify genes expressed in developing mouse hypothalamus, we performed microarray analysis at 12 different developmental time points. We then conducted developmental in situ hybridization for 1,045 genes that were dynamically expressed over the course of hypothalamic neurogenesis. We identified markers that stably labeled each major hypothalamic nucleus over the entire course of neurogenesis and constructed a detailed molecular atlas of the developing hypothalamus. As a proof of concept of the utility of these data, we used these markers to analyze the phenotype of mice in which Sonic Hedgehog (Shh) was selectively deleted from hypothalamic neuroepithelium and found that Shh is essential for anterior hypothalamic patterning. Our results serve as a resource for functional investigations of hypothalamic development, connectivity, physiology and dysfunction. PMID:20436479

  13. 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

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

    PubMed

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

    2016-08-01

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

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

    PubMed Central

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

    2012-01-01

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

  16. 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...

  17. 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.

  18. Development of a fusion approach selection tool

    NASA Astrophysics Data System (ADS)

    Pohl, C.; Zeng, Y.

    2015-06-01

    During the last decades number and quality of available remote sensing satellite sensors for Earth observation has grown significantly. The amount of available multi-sensor images along with their increased spatial and spectral resolution provides new challenges to Earth scientists. With a Fusion Approach Selection Tool (FAST) the remote sensing community would obtain access to an optimized and improved image processing technology. Remote sensing image fusion is a mean to produce images containing information that is not inherent in the single image alone. In the meantime the user has access to sophisticated commercialized image fusion techniques plus the option to tune the parameters of each individual technique to match the anticipated application. This leaves the operator with an uncountable number of options to combine remote sensing images, not talking about the selection of the appropriate images, resolution and bands. Image fusion can be a machine and time-consuming endeavour. In addition it requires knowledge about remote sensing, image fusion, digital image processing and the application. FAST shall provide the user with a quick overview of processing flows to choose from to reach the target. FAST will ask for available images, application parameters and desired information to process this input to come out with a workflow to quickly obtain the best results. It will optimize data and image fusion techniques. It provides an overview on the possible results from which the user can choose the best. FAST will enable even inexperienced users to use advanced processing methods to maximize the benefit of multi-sensor image exploitation.

  19. 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...

  20. Black raspberry genetic and genomic resources development

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  1. 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)

  2. 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.…

  3. 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.

  4. Plasmid Vectors and Molecular Building Blocks for the Development of Genetic Manipulation Tools for Trypanosoma cruzi

    PubMed Central

    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. PMID:24205392

  5. 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. PMID:24205392

  6. 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...

  7. 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

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

    PubMed Central

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

    2013-01-01

    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. PMID:24101620

  9. Surrogate Analysis and Index Developer (SAID) tool

    USGS Publications Warehouse

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

    2015-01-01

    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.

  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. PMID:25989233

  11. 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. PMID:26129944

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

    PubMed

    Ishii, Tetsuya; Araki, Motoko

    2016-07-01

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

  13. 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...

  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. Supporting tools for guideline development and dissemination.

    PubMed

    Quaglini, S; Dazzi, L; Gatti, L; Stefanelli, M; Fassino, C; Tondini, C

    1998-01-01

    This paper describes a methodology for representing clinical practice guidelines and facilitating their introduction into the medical routine. Since this methodology can be exploited in a www environment, it can represent the basis for sharing clinical guidelines both between different institutions and between human and software agents cooperating within a clinical context. In addition, the proposed guideline formalization is intended to deal with patient and organization preferences. This goal is achieved by augmenting the guideline with decision analytic models and by linking the guideline with an organizational model of the clinical setting. The designed framework allows guideline development, tailoring and implementation, real-time access to the guideline prescriptions and guideline validation. PMID:9779886

  16. DIAGNOSTIC TOOL DEVELOPMENT AND APPLICATION THROUGH REGIONAL CASE STUDIES

    EPA Science Inventory

    Case studies are a useful vehicle for developing and testing conceptual models, classification systems, diagnostic tools and models, and stressor-response relationships. Furthermore, case studies focused on specific places or issues of interest to the Agency provide an excellent ...

  17. Tools for Helping Self-Development--Part 2.

    ERIC Educational Resources Information Center

    Hague, Hawdon

    1978-01-01

    The article discusses tools for the self-development of the manager and for the management trainer to use in the organizational setting. These include a range of activities called coaching, delegation, and job rotation for managers. (MF)

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

    PubMed

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

    2015-10-01

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

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

    PubMed Central

    2012-01-01

    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. PMID:23236964

  20. 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

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

    PubMed

    Nikolaichik, Yevgeny; Damienikan, Aliaksandr U

    2016-01-01

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

  2. Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms.

    PubMed

    Quillery, E; Quenez, O; Peterlongo, P; Plantard, O

    2014-03-01

    Assessing the genetic variability of the tick Ixodes ricinus-an important vector of pathogens in Europe-is an essential step for setting up antitick control methods. Here, we report the first identification of a set of SNPs isolated from the genome of I. ricinus, by applying a reduction in genomic complexity, pyrosequencing and new bioinformatics tools. Almost 1.4 million of reads (average length: 528 nt) were generated with a full Roche 454 GS FLX run on two reduced representation libraries of I. ricinus. A newly developed bioinformatics tool (DiscoSnp), which isolates SNPs without requiring any reference genome, was used to obtain 321 088 putative SNPs. Stringent selection criteria were applied in a bioinformatics pipeline to select 1768 SNPs for the development of specific primers. Among 384 randomly SNPs tested by Fluidigm genotyping technology on 464 individuals ticks, 368 SNPs loci (96%) exhibited the presence of the two expected alleles. Hardy-Weinberg equilibrium tests conducted on six natural populations of ticks have shown that from 26 to 46 of the 384 loci exhibited significant heterozygote deficiency. PMID:24119113

  3. 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

  4. 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

  5. Use of the Caulobacter crescentus Genome Sequence To Develop a Method for Systematic Genetic Mapping

    PubMed Central

    West, Lisandra; Yang, Desiree; Stephens, Craig

    2002-01-01

    The functional analysis of sequenced genomes will be facilitated by the development of tools for the rapid mapping of mutations. We have developed a systematic approach to genetic mapping in Caulobacter crescentus that is based on bacteriophage-mediated transduction of strategically placed antibiotic resistance markers. The genomic DNA sequence was used to identify sites distributed evenly around the chromosome at which plasmids could be nondisruptively integrated. DNA fragments from these sites were amplified by PCR and cloned into a kanamycin-resistant (Kanr) suicide vector. Delivery of these plasmids into C. crescentus resulted in integration via homologous recombination. A set of 41 strains containing Kanr markers at 100-kb intervals was thereby generated. These strains serve as donors for generalized transduction using bacteriophage φCr30, which can transduce at least 120 kb of DNA. Transductants are selected with kanamycin and screened for loss of the mutant phenotype to assess linkage between the marker and the site of the mutation. The dependence of cotransduction frequency on sequence distance was evaluated using several markers and mutant strains. With these data as a standard, previously unmapped mutations were readily localized to DNA sequence intervals equivalent to less than 1% of the genome. Candidate genes within the interval were then examined further by subcloning and complementation analysis. Mutations resulting in sensitivity to ampicillin, in nutritional auxotrophies, or temperature-sensitive growth were mapped. This approach to genetic mapping should be applicable to other bacteria with sequenced genomes for which generalized transducing phage are available. PMID:11914347

  6. 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

  7. 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

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

    PubMed Central

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

    2015-01-01

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

  9. 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

    2015-01-01

    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

  10. Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing.

    PubMed

    Eastman, Alexander W; Yuan, Ze-Chun

    2014-01-01

    Advances in sequencing technology have drastically increased the depth and feasibility of bacterial genome sequencing. However, little information is available that details the specific techniques and procedures employed during genome sequencing despite the large numbers of published genomes. Shotgun approaches employed by second-generation sequencing platforms has necessitated the development of robust bioinformatics tools for in silico assembly, and complete assembly is limited by the presence of repetitive DNA sequences and multi-copy operons. Typically, re-sequencing with multiple platforms and laborious, targeted Sanger sequencing are employed to finish a draft bacterial genome. Here we describe a novel strategy based on the identification and targeted sequencing of repetitive rDNA operons to expedite bacterial genome assembly and finishing. Our strategy was validated by finishing the genome of Paenibacillus polymyxa strain CR1, a bacterium with potential in sustainable agriculture and bio-based processes. An analysis of the 38 contigs contained in the P. polymyxa strain CR1 draft genome revealed 12 repetitive rDNA operons with varied intragenic and flanking regions of variable length, unanimously located at contig boundaries and within contig gaps. These highly similar but not identical rDNA operons were experimentally verified and sequenced simultaneously with multiple, specially designed primer sets. This approach also identified and corrected significant sequence rearrangement generated during the initial in silico assembly of sequencing reads. Our approach reduces the required effort associated with blind primer walking for contig assembly, increasing both the speed and feasibility of genome finishing. Our study further reinforces the notion that repetitive DNA elements are major limiting factors for genome finishing. Moreover, we provided a step-by-step workflow for genome finishing, which may guide future bacterial genome finishing projects. PMID

  11. Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing

    PubMed Central

    Eastman, Alexander W.; Yuan, Ze-Chun

    2015-01-01

    Advances in sequencing technology have drastically increased the depth and feasibility of bacterial genome sequencing. However, little information is available that details the specific techniques and procedures employed during genome sequencing despite the large numbers of published genomes. Shotgun approaches employed by second-generation sequencing platforms has necessitated the development of robust bioinformatics tools for in silico assembly, and complete assembly is limited by the presence of repetitive DNA sequences and multi-copy operons. Typically, re-sequencing with multiple platforms and laborious, targeted Sanger sequencing are employed to finish a draft bacterial genome. Here we describe a novel strategy based on the identification and targeted sequencing of repetitive rDNA operons to expedite bacterial genome assembly and finishing. Our strategy was validated by finishing the genome of Paenibacillus polymyxa strain CR1, a bacterium with potential in sustainable agriculture and bio-based processes. An analysis of the 38 contigs contained in the P. polymyxa strain CR1 draft genome revealed 12 repetitive rDNA operons with varied intragenic and flanking regions of variable length, unanimously located at contig boundaries and within contig gaps. These highly similar but not identical rDNA operons were experimentally verified and sequenced simultaneously with multiple, specially designed primer sets. This approach also identified and corrected significant sequence rearrangement generated during the initial in silico assembly of sequencing reads. Our approach reduces the required effort associated with blind primer walking for contig assembly, increasing both the speed and feasibility of genome finishing. Our study further reinforces the notion that repetitive DNA elements are major limiting factors for genome finishing. Moreover, we provided a step-by-step workflow for genome finishing, which may guide future bacterial genome finishing projects. PMID

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. A Tool Set for the Genome-Wide Analysis of Neurospora crassa by RT-PCR.

    PubMed

    Hurley, Jennifer H; Dasgupta, Arko; Andrews, Peter; Crowell, Alexander M; Ringelberg, Carol; Loros, Jennifer J; Dunlap, Jay C

    2015-10-01

    Neurospora crassa is an important model organism for filamentous fungi as well as for circadian biology and photobiology. Although the community-accumulated tool set for the molecular analysis of Neurospora is extensive, two components are missing: (1) dependable reference genes whose level of expression are relatively constant across light/dark cycles and as a function of time of day and (2) a catalog of primers specifically designed for real-time PCR (RT-PCR). To address the first of these we have identified genes that are optimal for use as reference genes in RT-PCR across a wide range of expression levels; the mRNA/transcripts from these genes have potential for use as reference noncycling transcripts outside of Neurospora. In addition, we have generated a genome-wide set of RT-PCR primers, thereby streamlining the analysis of gene expression. In validation studies these primers successfully identified target mRNAs arising from 70% (34 of 49) of all tested genes and from all (28) of the moderately to highly expressed tested genes. PMID:26248984

  17. 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.

  18. Microfield exposure tool enables advances in EUV lithography development

    SciTech Connect

    Naulleau, Patrick

    2009-09-07

    With demonstrated resist resolution of 20 nm half pitch, the SEMATECH Berkeley BUV microfield exposure tool continues to push crucial advances in the areas of BUY resists and masks. The ever progressing shrink in computer chip feature sizes has been fueled over the years by a continual reduction in the wavelength of light used to pattern the chips. Recently, this trend has been threatened by unavailability of lens materials suitable for wavelengths shorter than 193 nm. To circumvent this roadblock, a reflective technology utilizing a significantly shorter extreme ultraviolet (EUV) wavelength (13.5 nm) has been under development for the past decade. The dramatic wavelength shrink was required to compensate for optical design limitations intrinsic in mirror-based systems compared to refractive lens systems. With this significant reduction in wavelength comes a variety of new challenges including developing sources of adequate power, photoresists with suitable resolution, sensitivity, and line-edge roughness characteristics, as well as the fabrication of reflection masks with zero defects. While source development can proceed in the absence of available exposure tools, in order for progress to be made in the areas of resists and masks it is crucial to have access to advanced exposure tools with resolutions equal to or better than that expected from initial production tools. These advanced development tools, however, need not be full field tools. Also, implementing such tools at synchrotron facilities allows them to be developed independent of the availability of reliable stand-alone BUY sources. One such tool is the SEMATECH Berkeley microfield exposure tool (MET). The most unique attribute of the SEMA TECH Berkeley MET is its use of a custom-coherence illuminator made possible by its implementation on a synchrotron beamline. With only conventional illumination and conventional binary masks, the resolution limit of the 0.3-NA optic is approximately 25 nm, however

  19. 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.

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

    PubMed

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

    2015-04-01

    Field pennycress (Thlaspi arvense L.) is being domesticated as a new winter cover crop and biofuel species for the Midwestern United States that can be double-cropped between corn and soybeans. A genome sequence will enable the use of new technologies to make improvements in pennycress. To generate a draft genome, a hybrid sequencing approach was used to generate 47 Gb of DNA sequencing reads from both the Illumina and PacBio platforms. These reads were used to assemble 6,768 genomic scaffolds. The draft genome was annotated using the MAKER pipeline, which identified 27,390 predicted protein-coding genes, with almost all of these predicted peptides having significant sequence similarity to Arabidopsis proteins. A comprehensive analysis of pennycress gene homologues involved in glucosinolate biosynthesis, metabolism, and transport pathways revealed high sequence conservation compared with other Brassicaceae species, and helps validate the assembly of the pennycress gene space in this draft genome. Additional comparative genomic analyses indicate that the knowledge gained from years of basic Brassicaceae research will serve as a powerful tool for identifying gene targets whose manipulation can be predicted to result in improvements for pennycress. PMID:25632110

  1. 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

  2. Open source tools for ATR development and performance evaluation

    NASA Astrophysics Data System (ADS)

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

    2002-07-01

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

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

    SciTech Connect

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

    1999-08-01

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

  4. 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...

  5. 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.

  6. Implications of enterotoxigenic Escherichia coli genomics for vaccine development.

    PubMed

    Sjöling, Åsa; von Mentzer, Astrid; Svennerholm, Ann-Mari

    2015-04-01

    Enterotoxigenic Escherichia coli (ETEC) is a major cause of morbidity and mortality caused by diarrhea in children less than 5 years of age in low- and middle-income countries. Despite a wealth of research elucidating the mechanisms of disease, the immunological responses and vaccine development, ETEC is still relatively uncharacterized when it comes to regulation of virulence and detailed immune mechanisms. The recent emergence of next-generation sequencing now offers the possibility to screen genomes of ETEC strains isolated globally to identify novel vaccine targets in addition to those already established. In this review, we discuss how recent findings on ETEC genomics using novel sequencing techniques will aid in finding novel protective antigens that can be used in vaccine approaches. PMID:25540974

  7. Expression genomics and drug development: towards predictive pharmacology.

    PubMed

    Liu, Edison T

    2005-02-01

    Expression genomics can be defined as the study of the dynamic transciptome and its regulatory elements. Technologies are available that can assess transcripts on a genome-wide scale over time and across many samples. This comprehensive and dynamic database is being used to decipher signalling pathways and to identify new biomarkers and targets. Biomarkers emerging from these studies have prognostic potential and can be used to predict therapeutic outcome. The multiplex nature of this approach not only telescopes the time to discovery, but also allows for detection of complex interactions. Taken together, these capabilities, if carefully used, can speed drug development, enhance the identification of potent drug combinations and identify patient populations that will benefit from these new drugs. PMID:15814022

  8. Infinity: An In-Silico Tool for Genome-Wide Prediction of Specific DNA Matrices in miRNA Genomic Loci

    PubMed Central

    Garibaldi, Francesca; Manni, Isabella; Filligoi, Giancarlo; Piaggio, Giulia; Gurtner, Aymone

    2016-01-01

    Motivation miRNAs are potent regulators of gene expression and modulate multiple cellular processes in physiology and pathology. Deregulation of miRNAs expression has been found in various cancer types, thus, miRNAs may be potential targets for cancer therapy. However, the mechanisms through which miRNAs are regulated in cancer remain unclear. Therefore, the identification of transcriptional factor–miRNA crosstalk is one of the most update aspects of the study of miRNAs regulation. Results In the present study we describe the development of a fast and user-friendly software, named infinity, able to find the presence of DNA matrices, such as binding sequences for transcriptional factors, on ~65kb (kilobase) of 939 human miRNA genomic sequences, simultaneously. Of note, the power of this software has been validated in vivo by performing chromatin immunoprecipitation assays on a subset of new in silico identified target sequences (CCAAT) for the transcription factor NF-Y on colon cancer deregulated miRNA loci. Moreover, for the first time, we have demonstrated that NF-Y, through its CCAAT binding activity, regulates the expression of miRNA-181a, -181b, -21, -17, -130b, -301b in colon cancer cells. Conclusions The infinity software that we have developed is a powerful tool to underscore new TF/miRNA regulatory networks. Availability and Implementation Infinity was implemented in pure Java using Eclipse framework, and runs on Linux and MS Windows machine, with MySQL database. The software is freely available on the web at https://github.com/bio-devel/infinity. The website is implemented in JavaScript, PHP and HTML with all major browsers supported. PMID:27082112

  9. The genomic Echinococcus microsatellite EmsB sequences: from a molecular marker to the epidemiological tool.

    PubMed

    Knapp, J; Bart, J M; Maillard, S; Gottstein, B; Piarroux, R

    2010-03-01

    In the field of molecular and epidemiological parasitology, characterization of fast evolving genetic markers appears as an important challenge to consider the diversity and genetic structure of parasites. The study of respective populations can help us to understand their adaptive strategies to survive and perpetuate the species within different host populations, all trying to resist infection. In the past, the relative monomorphic features of Echinococcus multilocularis, the causative agent of alveolar echinococcosis and a severe human parasitic disease, did not stimulate studies dealing with the genetic variability of Echinococcus species or respective populations. A recently developed, characterized and validated original multilocus microsatellite, named EmsB, tandemly repeated in the genome, offered an additional opportunity for this line of investigation. We have compiled in this review new insights brought by this molecular tracker on the transmission activity of Echinococcus among different hosts and at different geographical scales. PMID:20025824

  10. Development and pilot testing of the collaborative practice assessment tool.

    PubMed

    Schroder, Corinne; Medves, Jennifer; Paterson, Margo; Byrnes, Vaughan; Chapman, Christine; O'Riordan, Anne; Pichora, Deborah; Kelly, Carly

    2011-05-01

    Collaborative practice is receiving increased attention as a model of healthcare delivery that positively influences the effectiveness and efficiency of patient care while improving the work environment of healthcare providers. The collaborative practice assessment tool (CPAT) was developed from the literature to enable interprofessional teams to assess their collaborative practice. The CPAT survey included 56 items across nine domains including: mission and goals; relationships; leadership; role responsibilities and autonomy; communication; decision-making and conflict management; community linkages and coordination; perceived effectiveness and patient involvement; in addition to three open-ended questions. The tool was developed for use in a variety of settings involving a diversity of healthcare providers with the aim of helping teams to identify professional development needs and corresponding educational interventions. The results of two pilot tests indicated that the CPAT is a valid and reliable tool for assessing levels of collaborative practice within teams. This article describes the development of the tool, the pilot testing and validation process, as well as limitations of the tool. PMID:21182434

  11. Cohesin: genomic insights into controlling gene transcription and development

    PubMed Central

    Dorsett, Dale

    2011-01-01

    Over the past decade it has emerged that the cohesin protein complex, which functions in sister chromatid cohesion, chromosome segregation and DNA repair, also regulates gene expression and development. Even minor changes in cohesin activity alter several aspects of development. Genome-wide analysis indicates that cohesin directly regulates transcription of genes involved in cell proliferation, pluripotency, and differentiation through multiple mechanisms. These mechanisms are poorly understood, but involve both partial gene repression in concert with Polycomb group proteins, and facilitating long-range looping, both between enhancers and promoters, and between CTCF protein binding sites. PMID:21324671

  12. Development and psychometric testing of the nursing culture assessment tool.

    PubMed

    Kennerly, Susan M; Yap, Tracey L; Hemmings, Annette; Beckett, Gulbahar; Schafer, John C; Borchers, Andrea

    2012-11-01

    A valid and reliable nursing culture assessment tool aimed at capturing general aspects of nursing culture is needed for use in health care settings to assess and then reshape indicated troubled areas of the nursing culture. This article summarizes the Nursing Culture Assessment Tool's (NCAT) development and reports on a cross-sectional, exploratory investigation of its psychometric properties. The research aims were to test the tool's psychometric properties; discover its dimensionality; and refine the item structure to best represent the construct of nursing culture, an occupational subset of organizational culture. Empirical construct validity was tested using a sample of licensed nurses and nursing assistants (n = 340). Exploratory and confirmatory factor analysis (CFA) and logistical regression yielded a 6-factor, 19-item solution. Evidence supports the tool's validity for assessing nursing culture as a basis for shaping the culture into one that supports change, thereby accelerating, improving, and advancing nursing best practices and care outcomes. PMID:22523245

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

    PubMed

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

    2015-01-01

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

  14. Using competences and competence tools in workforce development.

    PubMed

    Green, Tess; Dickerson, Claire; Blass, Eddie

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

  15. 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.

  16. 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

  17. 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.

  18. PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny

    PubMed Central

    Lei, Runhua; Rowley, Thaine W.; Zhu, Lifeng; Bailey, Carolyn A.; Engberg, Shannon E.; Wood, Mindy L.; Christman, Mary C.; Perry, George H.; Louis, Edward E.; Lu, Guoqing

    2012-01-01

    Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker through comparison of partial genomes of Microcebus and Otolemur. In experimental tests of 20 randomly selected markers, nine markers were successfully amplified by PCR and directly sequenced in all 17 nominal Microcebus species. Phylogenetic analyses of the sequence data obtained for 17 taxa and nine markers confirmed the distinct lineage inferred from previous mtDNA data. PhyloMarker has also been used by other projects including the herons (Ardeidae, Aves) phylogeny and the Wood mice (Muridae, Mammalia) phylogeny. All source code and sample data are made available at http://bioinfo-srv1.awh.unomaha.edu/phylomarker/.

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

    PubMed

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

    2016-01-01

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

  20. Development of a Custom-Designed, Pan Genomic DNA Microarray to Characterize Strain-Level Diversity among Cronobacter spp.

    PubMed Central

    Tall, Ben Davies; Gangiredla, Jayanthi; Gopinath, Gopal R.; Yan, Qiongqiong; Chase, Hannah R.; Lee, Boram; Hwang, Seongeun; Trach, Larisa; Park, Eunbi; Yoo, YeonJoo; Chung, TaeJung; Jackson, Scott A.; Patel, Isha R.; Sathyamoorthy, Venugopal; Pava-Ripoll, Monica; Kotewicz, Michael L.; Carter, Laurenda; Iversen, Carol; Pagotto, Franco; Stephan, Roger; Lehner, Angelika; Fanning, Séamus; Grim, Christopher J.

    2015-01-01

    Cronobacter species cause infections in all age groups; however neonates are at highest risk and remain the most susceptible age group for life-threatening invasive disease. The genus contains seven species:Cronobacter sakazakii, Cronobacter malonaticus, Cronobacter turicensis, Cronobacter muytjensii, Cronobacter dublinensis, Cronobacter universalis, and Cronobacter condimenti. Despite an abundance of published genomes of these species, genomics-based epidemiology of the genus is not well established. The gene content of a diverse group of 126 unique Cronobacter and taxonomically related isolates was determined using a pan genomic-based DNA microarray as a genotyping tool and as a means to identify outbreak isolates for food safety, environmental, and clinical surveillance purposes. The microarray constitutes 19,287 independent genes representing 15 Cronobacter genomes and 18 plasmids and 2,371 virulence factor genes of phylogenetically related Gram-negative bacteria. The Cronobacter microarray was able to distinguish the seven Cronobacter species from one another and from non-Cronobacter species; and within each species, strains grouped into distinct clusters based on their genomic diversity. These results also support the phylogenic divergence of the genus and clearly highlight the genomic diversity among each member of the genus. The current study establishes a powerful platform for further genomics research of this diverse genus, an important prerequisite toward the development of future countermeasures against this foodborne pathogen in the food safety and clinical arenas. PMID:25984509

  1. 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.

  2. 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

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

    PubMed

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

    2016-01-01

    The reference single nucleotide polymorphism (rs) ID in dbSNP (http://www.ncbi.nlm.nih.gov/SNP/) is a key resource identifier, which is widely used in human genetics and genomics studies. However, its application is often complicated by the varied IDs of different versions. Here, we developed a user-friendly tool, SNPTracker, for comprehensively tracking and unifying the rs IDs and genomic coordinates of massive sequence variants at a time. It worked perfectly, and had much higher accuracy and capacity than two alternative utilities in our proof-of-principle examples. SNPTracker will greatly facilitate genetic data exchange and integration in the postgenome-wide association study era. PMID:26585827

  4. 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. PMID:26994965

  5. Development of culturally sensitive dialog tools in diabetes education.

    PubMed

    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

  6. Stress among charge nurses: tool development and stress measurement.

    PubMed

    Admi, Hanna; Moshe-Eilon, Yael

    2010-01-01

    The aim of this study was to develop and implement a tool for measuring the role stress of charge nurses. Tools are lacking regarding measurement of nursing role stressors, particularly for charge nurses. Based on focus groups and in-depth interviews with charge nurses within a large tertiary hospital, a charge nurse stress questionnaire was developed which measures six factors of stress: authority-responsibility conflict, patient-nurse interaction, deficient resources, managerial decision making, role conflict, and overload. The prominent stressors on charge nurses were specific to the role. Mean levels of stress were significantly higher for nurses who attended post-graduate clinical courses than for those who did not. The mean level of stress was higher for department nurse managers than for nurses without a managerial position. This tool was designed to measure charge nurse stress demonstrates reliability, and highlights the specific stressors demanded by the role. Preparation and ongoing support for fulfilling this position are recommended. PMID:20672537

  7. Developing Computational Tools for Application of Toxicogenomics to Environmental Regulations and Risk Assessment

    EPA Science Inventory

    Toxicogenomics is the study of changes in gene expression, protein, and metabolite profiles within cells and tissues, complementary to more traditional toxicological methods. Genomics tools provide detailed molecular data about the underlying biochemical mechanisms of toxicity, a...

  8. Development of a green remediation tool in Japan.

    PubMed

    Yasutaka, Tetsuo; Zhang, Hong; Murayama, Koki; Hama, Yoshihito; Tsukada, Yasuhisa; Furukawa, Yasuhide

    2016-09-01

    The green remediation assessment tool for Japan (GRATJ) presented in this study is a spreadsheet-based software package developed to facilitate comparisons of the environmental impacts associated with various countermeasures against contaminated soil in Japan. This tool uses a life-cycle assessment-based model to calculate inventory inputs/outputs throughout the activity life cycle during remediation. Processes of 14 remediation methods for heavy metal contamination and 12 for volatile organic compound contamination are built into the tool. This tool can evaluate 130 inventory inputs/outputs and easily integrate those inputs/outputs into 9 impact categories, 4 integrated endpoints, and 1 index. Comparative studies can be performed by entering basic data associated with a target site. The integrated results can be presented in a simpler and clearer manner than the results of an inventory analysis. As a case study, an arsenic-contaminated soil remediation site was examined using this tool. Results showed that the integrated environmental impacts were greater with onsite remediation methods than with offsite ones. Furthermore, the contributions of CO2 to global warming, SO2 to urban air pollution, and crude oil to resource consumption were greater than other inventory inputs/outputs. The GRATJ has the potential to improve green remediation and can serve as a valuable tool for decision makers and practitioners in selecting countermeasures in Japan. PMID:26803220

  9. Low voltage resist processes developed for MAPPER tool first exposures

    NASA Astrophysics Data System (ADS)

    Rio, D.; Constancias, C.; van Nieuwstadt, J.; Vijverberg, J.; Derrough, S.; Icard, B.; Pain, L.

    2010-05-01

    The FP7 European project MAGIC [1] aims at designing a multi electron beam machine. In the frame of this project, LETI evaluates a multibeam tool from MAPPER lithography [2]. Each beam has an acceleration voltage of 5kV. A tool has been installed in LETI premises in July 2009. In order to prepare its evaluation, preliminary work was performed on Gaussian beam tools down to 5kV. It aimed at the determination of a stable and robust resist process allowing high resolution at 5kV. Then those results were used to characterize MAPPER tool performances. Meeting the requirements of high resolution and low roughness at low voltage, Dow Corningmolecular glass HSQ (hydrogen silsesquioxane) and MicroChem PMMA (polymethylmethacrylate) were used to test MAPPER tool as negative and positive tone resist references. We did exposures at beam acceleration voltages from 5 kV up to 100 kV. Different post application bake (PAB) temperatures were applied to resist. Several developer concentrations were also tested. The impact of those three parameters on contrast and resolution was checked. Resists chemical characterization was performed with FTIR (Fourier transform infra red) spectroscopy in order to understand the mechanisms leading to the observed variations of contrast and exposure dose as process parameters are changed. The main purpose of this work was to show that high resolution can be achieved at 5kV. First exposures performed with MAPER tool confirmed those results.

  10. CRISPR/cas9, a novel genomic tool to knock down microRNA in vitro and in vivo

    PubMed Central

    Chang, Hong; Yi, Bin; Ma, Ruixia; Zhang, Xiaoguo; Zhao, Hongyou; Xi, Yaguang

    2016-01-01

    MicroRNAs are small and non-coding RNA molecules with the master role in regulation of gene expression at post-transcriptional/translational levels. Many methods have been developed for microRNA loss-of-function study, such as antisense inhibitors and sponges; however, the robustness, specificity, and stability of these traditional strategies are not highly satisfied. CRISPR/cas9 system is emerging as a novel genome editing tool in biology/medicine research, but its indication in microRNA research has not been studied exclusively. In this study, we clone CRISPR/cas9 constructs with single-guide RNAs specifically targeting biogenesis processing sites of selected microRNAs; and we find that CRISPR/cas9 can robustly and specifically reduce the expression of these microRNAs up to 96%. CRISPR/cas9 also shows an exclusive benefit in control of crossing off-target effect on microRNAs in the same family or with highly conserved sequences. More significantly, for the first time, we demonstrate the long term stability of microRNA knockdown phenotype by CRISPR/cas9 in both in vitro and in vivo models. PMID:26924382

  11. CRISPR/cas9, a novel genomic tool to knock down microRNA in vitro and in vivo.

    PubMed

    Chang, Hong; Yi, Bin; Ma, Ruixia; Zhang, Xiaoguo; Zhao, Hongyou; Xi, Yaguang

    2016-01-01

    MicroRNAs are small and non-coding RNA molecules with the master role in regulation of gene expression at post-transcriptional/translational levels. Many methods have been developed for microRNA loss-of-function study, such as antisense inhibitors and sponges; however, the robustness, specificity, and stability of these traditional strategies are not highly satisfied. CRISPR/cas9 system is emerging as a novel genome editing tool in biology/medicine research, but its indication in microRNA research has not been studied exclusively. In this study, we clone CRISPR/cas9 constructs with single-guide RNAs specifically targeting biogenesis processing sites of selected microRNAs; and we find that CRISPR/cas9 can robustly and specifically reduce the expression of these microRNAs up to 96%. CRISPR/cas9 also shows an exclusive benefit in control of crossing off-target effect on microRNAs in the same family or with highly conserved sequences. More significantly, for the first time, we demonstrate the long term stability of microRNA knockdown phenotype by CRISPR/cas9 in both in vitro and in vivo models. PMID:26924382

  12. JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes

    PubMed Central

    Richter, Michael; Lombardot, Thierry; Kostadinov, Ivaylo; Kottmann, Renzo; Duhaime, Melissa Beth; Peplies, Jörg; Glöckner, Frank Oliver

    2008-01-01

    Background Current sequencing technologies give access to sequence information for genomes and metagenomes at a tremendous speed. Subsequent data processing is mainly performed by automatic pipelines provided by the sequencing centers. Although, standardised workflows are desirable and useful in many respects, rational data mining, comparative genomics, and especially the interpretation of the sequence information in the biological context, demands for intuitive, flexible, and extendable solutions. Results The JCoast software tool was primarily designed to analyse and compare (meta)genome sequences of prokaryotes. Based on a pre-computed GenDB database project, JCoast offers a flexible graphical user interface (GUI), as well as an application programming interface (API) that facilitates back-end data access. JCoast offers individual, cross genome-, and metagenome analysis, and assists the biologist in exploration of large and complex datasets. Conclusion JCoast combines all functions required for the mining, annotation, and interpretation of (meta)genomic data. The lightweight software solution allows the user to easily take advantage of advanced back-end database structures by providing a programming and graphical user interface to answer biological questions. JCoast is available at the project homepage. PMID:18380896

  13. 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

  14. Assessment Tool Development for Extracurricular Smet Programs for Girls

    NASA Astrophysics Data System (ADS)

    House, Jody; Johnson, Molly; Borthwick, Geoffrey

    Many different programs have been designed to increase girls' interest in and exposure to science, mathematics, engineering, and technology (SMET). Two of these programs are discussed and contrasted in the dimensions of length, level of science content, pedagogical approach, degree of self- vs. parent-selected participants, and amount of communitybuilding content. Two different evaluation tools were used. For one program, a modified version of the University of Pittsburgh's undergraduate engineering attitude assessment survey was used. Program participants' responses were compared to those from a fifth grade, mixed-sex science class. The only gender difference found was in the area of parental encouragement. The girls in the special class were more encouraged to participate in SMET areas. For the second program, a new age-appropriate tool developed specifically for these types of programs was used, and the tool itself was evaluated. The results indicate that the new tool has construct validity. On the basis of these preliminary results, a long-term plan for the continued development of the assessment tool is outlined.

  15. 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...

  16. solGS: a web-based tool for genomic selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: 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 man...

  17. 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...

  18. 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.

  19. 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…

  20. 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…

  1. Developing an Intranet: Tool Selection and Management Issues.

    ERIC Educational Resources Information Center

    Chou, David C.

    1998-01-01

    Moving corporate systems onto an intranet will increase the data traffic within the corporate network, which necessitates a high-quality management process to the intranet. Discusses costs and benefits of adopting an intranet, tool availability and selection criteria, and management issues for developing an intranet. (Author/AEF)

  2. 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…

  3. DEVELOPING A TOOL FOR ENVIRONMENTALLY PREFERABLE PURCHASING: JOURNAL ARTICLE

    EPA Science Inventory

    NRMRL-CIN-1246 Curran*, M.A. Developing a Tool for Environmentally Preferable Purchasing. Environmental Management and Health (Filho, W.L. (Ed.), MCB University Press) 12 (3):244-253 (2001). EPA/600/J-02/238, http://www.emerald-library.com/ft. 12/04/2000 LCA-based guidance wa...

  4. 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…

  5. Accessing Curriculum Through Technology Tools (ACTTT): A Model Development Project

    ERIC Educational Resources Information Center

    Daytner, Katrina M.; Johanson, Joyce; Clark, Letha; Robinson, Linda

    2012-01-01

    Accessing Curriculum Through Technology Tools (ACTTT), a project funded by the U.S. Office of Special Education Programs (OSEP), developed and tested a model designed to allow children in early elementary school, including those "at risk" and with disabilities, to better access, participate in, and benefit from the general curriculum. Children in…

  6. Transfer of Development Rights: A New Tool for Planners

    ERIC Educational Resources Information Center

    Woodbury, Steven R.

    1975-01-01

    The article focuses on the separation of certain understood rights of ownership and on the provision for the compensation or transfer of those rights to other property. The author reviews the use of this tool and suggests it as a potentially useful device to channel and guide development toward public policy goals. (Author)

  7. DEVELOPMENT OF THE METAL FINISHING FACILITY RISK SCREENING TOOL (MFFRST)

    EPA Science Inventory

    Recently the US EPA completed the development of the first version of the Metal Finishing Facility Risk Screening Tool (MFFRST) and has made this product available to the general public. MFFRST calculates the air emissions from a metal plating line and determines the risk to bot...

  8. 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),…

  9. 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…

  10. 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…

  11. 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…

  12. 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…

  13. 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

  14. 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.

  15. How the proteome packages the genome for cardiovascular development

    PubMed Central

    Karbassi, Elaheh; Vondriska, Thomas M.

    2014-01-01

    The devastating impact of congenital heart defects has made mechanisms of vertebrate heart and vascular development an active area of study. Because myocyte death is a common feature of acquired cardiovascular diseases and the adult heart does not regenerate, the need exists to understand whether features of the developing heart and vasculature—which are more plastic—can be exploited therapeutically in the disease setting. We know that a core network of transcription factors governs commitment to the cardiovascular lineage, and recent studies using genetic loss-of-function approaches and unbiased genomic studies have revealed the role for various chromatin modulatory events. We reason that chromatin structure itself is a causal feature that influences transcriptome complexity along a developmental continuum, and the purpose of this article is to highlight the areas in which ‘omics technologies have the potential to reveal new principles of phenotypic plasticity in development. We review the major mechanisms of chromatin structural regulation, highlighting what is known about their actions to control cardiovascular differentiation. We discuss emergent mechanisms of regulation that have been identified on the basis of genomic and proteomic studies of cardiac nuclei and identify current challenges to an integrated understanding of chromatin structure and cardiovascular phenotype. PMID:25074278

  16. Comparative genetics and genomics of nematodes: genome structure, development, and lifestyle.

    PubMed

    Sommer, Ralf J; Streit, Adrian

    2011-01-01

    Nematodes are found in virtually all habitats on earth. Many of them are parasites of plants and animals, including humans. The free-living nematode, Caenorhabditis elegans, is one of the genetically best-studied model organisms and was the first metazoan whose genome was fully sequenced. In recent years, the draft genome sequences of another six nematodes representing four of the five major clades of nematodes were published. Compared to mammalian genomes, all these genomes are very small. Nevertheless, they contain almost the same number of genes as the human genome. Nematodes are therefore a very attractive system for comparative genetic and genomic studies, with C. elegans as an excellent baseline. Here, we review the efforts that were made to extend genetic analysis to nematodes other than C. elegans, and we compare the seven available nematode genomes. One of the most striking findings is the unexpectedly high incidence of gene acquisition through horizontal gene transfer (HGT). PMID:21721943

  17. HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids

    PubMed Central

    2013-01-01

    Background The analysis of polyploid genomes is problematic because homeologous subgenome sequences are closely related. This relatedness makes it difficult to assign individual sequences to the specific subgenome from which they are derived, and hinders the development of polyploid whole genome assemblies. Results We here present a next-generation sequencing (NGS)-based approach for assignment of subgenome-specific base-identity at sites containing homeolog-specific polymorphisms (HSPs): ‘HSP base Assignment using NGS data through Diploid Similarity’ (HANDS). We show that HANDS correctly predicts subgenome-specific base-identity at >90% of assayed HSPs in the hexaploid bread wheat (Triticum aestivum) transcriptome, thus providing a substantial increase in accuracy versus previous methods for homeolog-specific base assignment. Conclusion We conclude that HANDS enables rapid and accurate genome-wide discovery of homeolog-specific base-identity, a capability having multiple applications in polyploid genomics. PMID:24063258

  18. 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.

  19. 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. PMID:21857199

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci

    PubMed Central

    Buske, Fabian A.; Bauer, Denis C.; Mattick, John S.; Bailey, Timothy L.

    2013-01-01

    Summary: At the heart of many modern biotechnological and therapeutic applications lies the need to target specific genomic loci with pinpoint accuracy. Although landmark experiments demonstrate technological maturity in manufacturing and delivering genetic material, the genomic sequence analysis to find suitable targets lags behind. We provide a computational aid for the sophisticated design of sequence-specific ligands and selection of appropriate targets, taking gene location and genomic architecture into account. Availability: Source code and binaries are downloadable from www.bioinformatics.org.au/triplexator/inspector. Contact: t.bailey@uq.edu.au Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23740745

  6. 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

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND... Industry, Tool Developers, and Food and Drug Administration Staff; Availability AGENCY: Food and Drug... 20993-0002. Send one self-addressed adhesive label to assist that office in processing your request,...

  7. Arenavirus Genome Rearrangement for the Development of Live Attenuated Vaccines

    PubMed Central

    Cheng, Benson Yee Hin; Ortiz-Riaño, Emilio

    2015-01-01

    ABSTRACT Several members of the Arenaviridae family cause hemorrhagic fever disease in humans and pose serious public health problems in their geographic regions of endemicity as well as a credible biodefense threat. To date, there have been no FDA-approved arenavirus vaccines, and current antiarenaviral therapy is limited to an off-label use of ribavirin that is only partially effective. Arenaviruses are enveloped viruses with a bisegmented negative-stranded RNA genome. Each genome segment uses an ambisense coding strategy to direct the synthesis of two viral polypeptides in opposite orientations, separated by a noncoding intergenic region. Here we have used minigenome-based approaches to evaluate expression levels of reporter genes from the nucleoprotein (NP) and glycoprotein precursor (GPC) loci within the S segment of the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV). We found that reporter genes are expressed to higher levels from the NP than from the GPC locus. Differences in reporter gene expression levels from the NP and GPC loci were confirmed with recombinant trisegmented LCM viruses. We then used reverse genetics to rescue a recombinant LCMV (rLCMV) containing a translocated viral S segment (rLCMV/TransS), where the viral NP and GPC open reading frames replaced one another. The rLCMV/TransS showed slower growth kinetics in cultured cells and was highly attenuated in vivo in a mouse model of lethal LCMV infection, but immunization with rLCMV/TransS conferred complete protection against a lethal challenge with wild-type LCMV. Attenuation of rLCMV/TransS was associated with reduced NP expression levels. These results open a new avenue for the development of arenavirus live attenuated vaccines based on rearrangement of their viral genome. IMPORTANCE Several arenaviruses cause severe hemorrhagic fever in humans and also pose a credible bioterrorism threat. Currently, no FDA-licensed vaccines are available to combat arenavirus infections and

  8. 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

  9. Confluence of genes, environment, development, and behavior in a post Genome-Wide Association Study world.

    PubMed

    Vrieze, Scott I; Iacono, William G; McGue, Matt

    2012-11-01

    This article serves to outline a research paradigm to investigate main effects and interactions of genes, environment, and development on behavior and psychiatric illness. We provide a historical context for candidate gene studies and genome-wide association studies, including benefits, limitations, and expected payoffs. Using substance use and abuse as our driving example, we then turn to the importance of etiological psychological theory in guiding genetic, environmental, and developmental research, as well as the utility of refined phenotypic measures, such as endophenotypes, in the pursuit of etiological understanding and focused tests of genetic and environmental associations. Phenotypic measurement has received considerable attention in the history of psychology and is informed by psychometrics, whereas the environment remains relatively poorly measured and is often confounded with genetic effects (i.e., gene-environment correlation). Genetically informed designs, which are no longer limited to twin and adoption studies thanks to ever-cheaper genotyping, are required to understand environmental influences. Finally, we outline the vast amount of individual difference in structural genomic variation, most of which remains to be leveraged in genetic association tests. Although the genetic data can be massive and burdensome (tens of millions of variants per person), we argue that improved understanding of genomic structure and function will provide investigators with new tools to test specific a priori hypotheses derived from etiological psychological theory, much like current candidate gene research but with less confusion and more payoff than candidate gene research has to date. PMID:23062291

  10. A Scaffold Analysis Tool Using Mate-Pair Information in Genome Sequencing

    PubMed Central

    Kim, Pan-Gyu; Cho, Hwan-Gue; Park, Kiejung

    2008-01-01

    We have developed a Windows-based program, ConPath, as a scaffold analyzer. ConPath constructs scaffolds by ordering and orienting separate sequence contigs by exploiting the mate-pair information between contig-pairs. Our algorithm builds directed graphs from link information and traverses them to find the longest acyclic graphs. Using end read pairs of fixed-sized mate-pair libraries, ConPath determines relative orientations of all contigs, estimates the gap size of each adjacent contig pair, and reports wrong assembly information by validating orientations and gap sizes. We have utilized ConPath in more than 10 microbial genome projects, including Mannheimia succiniciproducens and Vibro vulnificus, where we verified contig assembly and identified several erroneous contigs using the four types of error defined in ConPath. Also, ConPath supports some convenient features and viewers that permit investigation of each contig in detail; these include contig viewer, scaffold viewer, edge information list, mate-pair list, and the printing of complex scaffold structures. PMID:18414585

  11. Developing gamma-ray pulsar simulation tools for GLAST

    SciTech Connect

    Razzano, Massimiliano

    2007-07-12

    Pulsars are among the most intriguing sources in the gamma-ray Universe and their high-energy emission remains today quite mysterious. The Gamma-ray Large Area Space Telescope (GLAST) will study the pulsar gamma-ray emission in great detail and will discover a great number of new gamma-ray pulsars. Here are presented the latest developments of the tools that have been created for producing accurate simulations of gamma-ray pulsars emission. The main simulator is called PulsarSpectrum and can reproduce gamma-ray emission with great detail, taking also into account advanced timing effects, e.g. period increase with time, barycentric corrections and higher-order timing noise currently under development. Detailed spectral features can also be simulated with PulsarSpectrum, such as phase-dependent spectra. A suite of ancillary tools have also been built to provide a realistic pulsar population with related timing solutions. Anyway PulsarSpectrum can also simulate pulsar populations coming from external synthesis codes. All these tools are presently used within the GLAST collaboration for testing the LAT Science Analysis Environment tools and for better study of LAT capabilities for pulsar science.

  12. 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.

  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

    2015-12-01

    The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization and distribution of simple sequence repeats (SSRs) remains ambiguous and the use of SSR markers in genomic studies and marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide SSR markers in M. japonicus by genome survey sequencing for application in comparative genomics and breeding. A total of 326 945 perfect SSRs were identifi ed, among which dinucleotide repeats were the most frequent class (44.08%), followed by mononucleotides (29.67%), trinucleotides (18.96%), tetranucleotides (5.66%), hexanucleotides (1.07%), and pentanucleotides (0.56%). In total, 151 541 SSR loci primers were successfully designed. A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population, of which 27 loci (90.0%) were successfully amplifi ed with specifi c products and 24 (80.0%) were polymorphic. For the amplifi ed polymorphic loci, the alleles ranged from 5 to 17 (with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing sequences had signifi cant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identifi ed SSRs signifi cantly contribute to the M. japonicus genomic resources and will facilitate a number of genetic and genomic studies, including high density linkage mapping, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution.

  14. The development of genomics applied to dairy breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic selection (GS) has profoundly changed dairy cattle breeding in the last decade and can be defined as the use of genomic breeding values (GEBV) in selection programs. The GEBV is the sum of the effects of dense DNA markers across the whole genome, capturing all the quantitative trait loci (QT...

  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. 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

  17. 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...

  18. 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

  19. 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.

  20. Microsystem design framework based on tool adaptations and library developments

    NASA Astrophysics Data System (ADS)

    Karam, Jean Michel; Courtois, Bernard; Rencz, Marta; Poppe, Andras; Szekely, Vladimir

    1996-09-01

    Besides foundry facilities, Computer-Aided Design (CAD) tools are also required to move microsystems from research prototypes to an industrial market. This paper describes a Computer-Aided-Design Framework for microsystems, based on selected existing software packages adapted and extended for microsystem technology, assembled with libraries where models are available in the form of standard cells described at different levels (symbolic, system/behavioral, layout). In microelectronics, CAD has already attained a highly sophisticated and professional level, where complete fabrication sequences are simulated and the device and system operation is completely tested before manufacturing. In comparison, the art of microsystem design and modelling is still in its infancy. However, at least for the numerical simulation of the operation of single microsystem components, such as mechanical resonators, thermo-elements, elastic diaphragms, reliable simulation tools are available. For the different engineering disciplines (like electronics, mechanics, optics, etc) a lot of CAD-tools for the design, simulation and verification of specific devices are available, but there is no CAD-environment within which we could perform a (micro-)system simulation due to the different nature of the devices. In general there are two different approaches to overcome this limitation: the first possibility would be to develop a new framework tailored for microsystem-engineering. The second approach, much more realistic, would be to use the existing CAD-tools which contain the most promising features, and to extend these tools so that they can be used for the simulation and verification of microsystems and of the devices involved. These tools are assembled with libraries in a microsystem design environment allowing a continuous design flow. The approach is driven by the wish to make microsystems accessible to a large community of people, including SMEs and non-specialized academic institutions.

  1. 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

  2. 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.

  3. The teaching portfolio as a professional development tool for anaesthetists.

    PubMed

    Sidhu, N S

    2015-05-01

    A teaching portfolio (TP) is a document containing a factual description of a teacher's teaching strengths and accomplishments, allowing clinicians to display them for examination by others. The primary aim of a TP is to improve quality of teaching by providing a structure for self-reflection, which in turn aids professional development in medical education. Contents typically include a personal statement on teaching, an overview of teaching accomplishments and activities, feedback from colleagues and learners, a reflective component and some examples of teaching material. Electronic portfolios are more portable and flexible compared to paper portfolios. Clinicians gain the most benefit from a TP when it is used as a tool for self-reflection of their teaching practice and not merely as a list of activities and achievements. This article explains why and how anaesthetists might use a TP as a tool for professional development in medical education. PMID:25943606

  4. Development of EUV lithography tool technologies at Nikon

    NASA Astrophysics Data System (ADS)

    Murakami, Katsuhiko; Oshino, Tetsuya; Kondo, Hiroyuki; Chiba, Hiroshi; Kawabe, Yoshio; Ono, Takuro; Kandaka, Noriaki; Yamazaki, Atsushi; Yamaguchi, Takashi; Shibata, Ryo; Shiraishi, Masayuki

    2012-03-01

    6-mirror-system EUV projection optics design with NA of 0.4 plus was improved and the residual wavefront error was much reduced. Apodization is an issue for such high-NA EUV projection optics. Broad-band multilayer mirror can solve the problem. Broad-band multilayer mirrors were developed. Measured reflectivity performance of these multilayers was in good agreement with the designed performance. We have decided the measures to control contaminations of optics in HVM EUV exposure tools.

  5. 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.

  6. Application of Genomic and Quantitative Genetic Tools to Identify Candidate Resistance Genes for Brown Rot Resistance in Peach

    PubMed Central

    Martínez-García, Pedro J.; Parfitt, Dan E.; Bostock, Richard M.; Fresnedo-Ramírez, Jonathan; Vazquez-Lobo, Alejandra; Ogundiwin, Ebenezer A.; Gradziel, Thomas M.; Crisosto, Carlos H.

    2013-01-01

    The availability of a complete peach genome assembly and three different peach genome sequences created by our group provide new opportunities for application of genomic data and can improve the power of the classical Quantitative Trait Loci (QTL) approaches to identify candidate genes for peach disease resistance. Brown rot caused by Monilinia spp., is the most important fungal disease of stone fruits worldwide. Improved levels of peach fruit rot resistance have been identified in some cultivars and advanced selections developed in the UC Davis and USDA breeding programs. Whole genome sequencing of the Pop-DF parents lead to discovery of high-quality SNP markers for QTL genome scanning in this experimental population. Pop-DF created by crossing a brown rot moderately resistant cultivar ‘Dr. Davis’ and a brown rot resistant introgression line, ‘F8,1–42’, derived from an initial almond × peach interspecific hybrid, was evaluated for brown rot resistance in fruit of harvest maturity over three seasons. Using the SNP linkage map of Pop-DF and phenotypic data collected with inoculated fruit, a genome scan for QTL identified several SNP markers associated with brown rot resistance. Two of these QTLs were placed on linkage group 1, covering a large (physical) region on chromosome 1. The genome scan for QTL and SNP effects predicted several candidate genes associated with disease resistance responses in other host-pathogen systems. Two potential candidate genes, ppa011763m and ppa026453m, may be the genes primarily responsible for M. fructicola recognition in peach, activating both PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI) responses. Our results provide a foundation for further genetic dissection, marker assisted breeding for brown rot resistance, and development of peach cultivars resistant to brown rot. PMID:24244329

  7. Collaborative socioeconomic tool development to address management and planning needs

    USGS Publications Warehouse

    Richardson, Leslie A.; Huber, Christopher; Cullinane Thomas, Catherine; Donovan, Elizabeth; Koontz, Lynne M.

    2014-01-01

    Public lands and resources managed by the National Park Service (NPS) and other land management agencies provide a wide range of social and economic benefits to both nearby local communities and society as a whole, ranging from job creation, to access to unique recreational opportunities, to subsistence and tribal uses of the land. Over the years, there has been an increased need to identify and analyze the socioeconomic effects of the public’s use of NPS lands and resources, and the wide range of NPS land management decisions. This need stems from laws such as the National Environmental Policy Act (NEPA), increased litigation and appeals on NPS management decisions, as well as an overall need to demonstrate how parks benefit communities and the American public. To address these needs, the U.S. Geological Survey (USGS) and NPS have an ongoing partnership to collaboratively develop socioeconomic tools to support planning needs and resource management. This article discusses two such tools. The first, Assessing Socioeconomic Planning Needs (ASPN), was developed to help NPS planners and managers identify key social and economic issues that can arise as a result of land management actions. The second tool, the Visitor Spending Effects (VSE) model, provides a specific example of a type of analysis that may be recommended by ASPN. The remainder of this article discusses the development, main features, and plans for future versions and applications of both ASPN and the VSE.

  8. Support Tools in Formulation Development for Poorly Soluble Drugs.

    PubMed

    Fridgeirsdottir, Gudrun A; Harris, Robert; Fischer, Peter M; Roberts, Clive J

    2016-08-01

    The need for solubility enhancement through formulation is a well-known but still problematic issue because of the numbers of poorly water-soluble drugs in development. There are several possible routes that can be taken to increase the bioavailability of drugs intended for immediate-release oral formulation. The best formulation strategy for any given drug will depend on numerous factors, including required dose, shelf life, manufacturability, and the properties of the active pharmaceutical ingredient (API). Choosing an optimal formulation and manufacturing route for a new API is therefore not a straightforward process. Currently, there are several approaches that are used in the pharmaceutical industry to select the best formulation strategy. These differ in complexity and efficiency, but most try to predict which route will best suit the API based on selected molecular parameters such as molecular weight, lipophilicity (logP), and solubility. These methods range from using no tools, trial and error methods through a variety of complex tools from small in vitro or in vivo experiments or high throughput screening, guidance maps, and decision trees to the most complex methods based on computational modelling tools. This review aims to list available support tools and explain how they are used. PMID:27368122

  9. Feasibility assessment tool for urban anaerobic digestion in developing countries.

    PubMed

    Lohri, Christian Riuji; Rodić, Ljiljana; Zurbrügg, Christian

    2013-09-15

    This paper describes a method developed to support feasibility assessments of urban anaerobic digestion (AD). The method not only uses technical assessment criteria but takes a broader sustainability perspective and integrates technical-operational, environmental, financial-economic, socio-cultural, institutional, policy and legal criteria into the assessment tool developed. Use of the tool can support decision-makers with selecting the most suitable set-up for the given context. The tool consists of a comprehensive set of questions, structured along four distinct yet interrelated dimensions of sustainability factors, which all influence the success of any urban AD project. Each dimension answers a specific question: I) WHY? What are the driving forces and motivations behind the initiation of the AD project? II) WHO? Who are the stakeholders and what are their roles, power, interests and means of intervention? III) WHAT? What are the physical components of the proposed AD chain and the respective mass and resource flows? IV) HOW? What are the key features of the enabling or disabling environment (sustainability aspects) affecting the proposed AD system? Disruptive conditions within these four dimensions are detected. Multi Criteria Decision Analysis is used to guide the process of translating the answers from six sustainability categories into scores, combining them with the relative importance (weights) attributed by the stakeholders. Risk assessment further evaluates the probability that certain aspects develop differently than originally planned and assesses the data reliability (uncertainty factors). The use of the tool is demonstrated with its application in a case study for Bahir Dar in Ethiopia. PMID:23722149

  10. The Maize TFome – development of a transcription factor open reading frame collection for functional genomics

    PubMed Central

    Burdo, Brett; Gray, John; Goetting-Minesky, Mary P; Wittler, Bettina; Hunt, Matthew; Li, Tai; Velliquette, David; Thomas, Julie; Gentzel, Irene; Brito, Michael dos Santos; Mejía-Guerra, Maria Katherine; Connolly, Layne N; Qaisi, Dalya; Li, Wei; Casas, Maria I; Doseff, Andrea I; Grotewold, Erich

    2014-01-01

    Establishing the architecture of the gene regulatory networks (GRNs) responsible for controlling the transcription of all genes in an organism is a natural development that follows elucidation of the genome sequence. Reconstruction of the GRN requires the availability of a series of molecular tools and resources that so far have been limited to a few model organisms. One such resource consists of collections of transcription factor (TF) open reading frames (ORFs) cloned into vectors that facilitate easy expression in plants or microorganisms. In this study, we describe the development of a publicly available maize TF ORF collection (TFome) of 2034 clones corresponding to 2017 unique gene models in recombination-ready vectors that make possible the facile mobilization of the TF sequences into a number of different expression vectors. The collection also includes several hundred co-regulators (CoREGs), which we classified into well-defined families, and for which we propose here a standard nomenclature, as we have previously done for TFs. We describe the strategies employed to overcome the limitations associated with cloning ORFs from a genome that remains incompletely annotated, with a partial full-length cDNA set available, and with many TF/CoREG genes lacking experimental support. In many instances this required the combination of genome-wide expression data with gene synthesis approaches. The strategies developed will be valuable for developing similar resources for other agriculturally important plants. Information on all the clones generated is available through the GRASSIUS knowledgebase (http://grassius.org/). PMID:25053252

  11. 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.

  12. 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

    2014-01-01

    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. PMID:24759074

  13. Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness

    SciTech Connect

    Wu, L.; Liu, X.; Fields, M.W.; Thompson, D.K.; Bagwell, C.E.; Tiedje, J. M.; Hazen, T.C.; Zhou, J.

    2008-01-15

    The definition and delineation of microbial species are of great importance and challenge due to the extent of evolution and diversity. Whole-genome DNA-DNA hybridization is the cornerstone for defining procaryotic species relatedness, but obtaining pairwise DNA-DNA reassociation values for a comprehensive phylogenetic analysis of procaryotes is tedious and time consuming. A previously described microarray format containing whole-genomic DNA (the community genome array or CGA) was rigorously evaluated as a high-throughput alternative to the traditional DNA-DNA reassociation approach for delineating procaryotic species relationships. DNA similarities for multiple bacterial strains obtained with the CGA-based hybridization were comparable to those obtained with various traditional whole-genome hybridization methods (r=0.87, P<0.01). Significant linear relationships were also observed between the CGA-based genome similarities and those derived from small subunit (SSU) rRNA gene sequences (r=0.79, P<0.0001), gyrB sequences (r=0.95, P<0.0001) or REP- and BOX-PCR fingerprinting profiles (r=0.82, P<0.0001). The CGA hybridization-revealed species relationships in several representative genera, including Pseudomonas, Azoarcus and Shewanella, were largely congruent with previous classifications based on various conventional whole-genome DNA-DNA reassociation, SSU rRNA and/or gyrB analyses. These results suggest that CGA-based DNA-DNA hybridization could serve as a powerful, high-throughput format for determining species relatedness among microorganisms.

  14. 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.

  15. Development and Validation of the Tibetan Primary Care Assessment Tool

    PubMed Central

    Yin, Aitian; Lai, Youwen

    2014-01-01

    Objective. To develop a primary care assessment tool in Tibetan area and assess the primary care quality among different healthcare settings. Methods. Primary care assessment tool-Tibetan version (PCAT-T) was developed to measure seven primary care domains. Data from a cross-sectional survey of 1386 patients was used to conduct validity and reliability analysis of PCAT-T. Analysis of variance was used to conduct comparison of primary care quality among different healthcare settings. Results. A 28-item PCAT-T was constructed which included seven multi-item scales and two single-item scales. All of multi-item scales achieved good internal consistency and item-total correlations. Scaling assumptions tests were well satisfied. The full range of possible scores was observed for all scales, except first contact and continuity. Compared with prefecture hospital (77.42) and county hospital (82.01), township health center achieved highest primary care quality total score (86.64). Conclusions. PCAT-T is a valid and reliable tool to measure patients' experience of primary care in the Tibet Autonomous Region. Township health center has the best primary care performance compared with other healthcare settings, and township health center should play a key role in providing primary care in Tibet. PMID:24967349

  16. 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.

  17. 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.

  18. De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system

    PubMed Central

    2012-01-01

    Background Though genomic-level data are becoming widely available, many of the metazoan species sequenced are laboratory systems whose natural history is not well documented. In contrast, the wide array of species with very well-characterized natural history have, until recently, lacked genomics tools. It is now possible to address significant evolutionary genomics questions by applying high-throughput sequencing to discover the majority of genes for ecologically tractable species, and by subsequently developing microarray platforms from which to investigate gene regulatory networks that function in natural systems. We used GS-FLX Titanium Sequencing (Roche/454-Sequencing) of two normalized libraries of pooled RNA samples to characterize a transcriptome of the dark-eyed junco (Junco hyemalis), a North American sparrow that is a classically studied species in the fields of photoperiodism, speciation, and hormone-mediated behavior. Results From a broad pool of RNA sampled from tissues throughout the body of a male and a female junco, we sequenced a total of 434 million nucleotides from 1.17 million reads that were assembled de novo into 31,379 putative transcripts representing 22,765 gene sets covering 35.8 million nucleotides with 12-fold average depth of coverage. Annotation of roughly half of the putative genes was accomplished using sequence similarity, and expression was confirmed for the majority with a preliminary microarray analysis. Of 716 core bilaterian genes, 646 (90 %) were recovered within our characterized gene set. Gene Ontology, orthoDB orthology groups, and KEGG Pathway annotation provide further functional information about the sequences, and 25,781 potential SNPs were identified. Conclusions The extensive sequence information returned by this effort adds to the growing store of genomic data on diverse species. The extent of coverage and annotation achieved and confirmation of expression, show that transcriptome sequencing provides useful

  19. 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

  20. Continued development of modeling tools and theory for RF heating

    SciTech Connect

    1998-12-01

    Mission Research Corporation (MRC) is pleased to present the Department of Energy (DOE) with its renewal proposal to the Continued Development of Modeling Tools and Theory for RF Heating program. The objective of the program is to continue and extend the earlier work done by the proposed principal investigator in the field of modeling (Radio Frequency) RF heating experiments in the large tokamak fusion experiments, particularly the Tokamak Fusion Test Reactor (TFTR) device located at Princeton Plasma Physics Laboratory (PPPL). An integral part of this work is the investigation and, in some cases, resolution of theoretical issues which pertain to accurate modeling. MRC is nearing the successful completion of the specified tasks of the Continued Development of Modeling Tools and Theory for RF Heating project. The following tasks are either completed or nearing completion. (1) Anisotropic temperature and rotation upgrades; (2) Modeling for relativistic ECRH; (3) Further documentation of SHOOT and SPRUCE. As a result of the progress achieved under this project, MRC has been urged to continue this effort. Specifically, during the performance of this project two topics were identified by PPPL personnel as new applications of the existing RF modeling tools. These two topics concern (a) future fast-wave current drive experiments on the large tokamaks including TFTR and (c) the interpretation of existing and future RF probe data from TFTR. To address each of these topics requires some modification or enhancement of the existing modeling tools, and the first topic requires resolution of certain theoretical issues to produce self-consistent results. This work falls within the scope of the original project and is more suited to the project`s renewal than to the initiation of a new project.

  1. COSTMODL - AN AUTOMATED SOFTWARE DEVELOPMENT COST ESTIMATION TOOL

    NASA Technical Reports Server (NTRS)

    Roush, G. B.

    1994-01-01

    The cost of developing computer software consumes an increasing portion of many organizations' budgets. As this trend continues, the capability to estimate the effort and schedule required to develop a candidate software product becomes increasingly important. COSTMODL is an automated software development estimation tool which fulfills this need. Assimilating COSTMODL to any organization's particular environment can yield significant reduction in the risk of cost overruns and failed projects. This user-customization capability is unmatched by any other available estimation tool. COSTMODL accepts a description of a software product to be developed and computes estimates of the effort required to produce it, the calendar schedule required, and the distribution of effort and staffing as a function of the defined set of development life-cycle phases. This is accomplished by the five cost estimation algorithms incorporated into COSTMODL: the NASA-developed KISS model; the Basic, Intermediate, and Ada COCOMO models; and the Incremental Development model. This choice affords the user the ability to handle project complexities ranging from small, relatively simple projects to very large projects. Unique to COSTMODL is the ability to redefine the life-cycle phases of development and the capability to display a graphic representation of the optimum organizational structure required to develop the subject project, along with required staffing levels and skills. The program is menu-driven and mouse sensitive with an extensive context-sensitive help system that makes it possible for a new user to easily install and operate the program and to learn the fundamentals of cost estimation without having prior training or separate documentation. The implementation of these functions, along with the customization feature, into one program makes COSTMODL unique within the industry. COSTMODL was written for IBM PC compatibles, and it requires Turbo Pascal 5.0 or later and Turbo

  2. In-house developed methodologies and tools for decommissioning projects

    SciTech Connect

    Detilleux, Michel; Centner, Baudouin

    2007-07-01

    The paper describes different methodologies and tools developed in-house by Tractebel Engineering to facilitate the engineering works to be carried out especially in the frame of decommissioning projects. Three examples of tools with their corresponding results are presented: - The LLWAA-DECOM code, a software developed for the radiological characterization of contaminated systems and equipment. The code constitutes a specific module of more general software that was originally developed to characterize radioactive waste streams in order to be able to declare the radiological inventory of critical nuclides, in particular difficult-to-measure radionuclides, to the Authorities. In the case of LLWAA-DECOM, deposited activities inside contaminated equipment (piping, tanks, heat exchangers...) and scaling factors between nuclides, at any given time of the decommissioning time schedule, are calculated on the basis of physical characteristics of the systems and of operational parameters of the nuclear power plant. This methodology was applied to assess decommissioning costs of Belgian NPPs, to characterize the primary system of Trino NPP in Italy, to characterize the equipment of miscellaneous circuits of Ignalina NPP and of Kozloduy unit 1 and, to calculate remaining dose rates around equipment in the frame of the preparation of decommissioning activities; - The VISIMODELLER tool, a user friendly CAD interface developed to ease the introduction of lay-out areas in a software named VISIPLAN. VISIPLAN is a 3D dose rate assessment tool for ALARA work planning, developed by the Belgian Nuclear Research Centre SCK.CEN. Both softwares were used for projects such as the steam generators replacements in Belgian NPPs or the preparation of the decommissioning of units 1 and 2 of Kozloduy NPP; - The DBS software, a software developed to manage the different kinds of activities that are part of the general time schedule of a decommissioning project. For each activity, when relevant

  3. 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.

  4. PrimerDesign-M: A multiple-alignment based multiple-primer design tool for walking across variable genomes

    DOE PAGESBeta

    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

  5. 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.

  6. Measuring vaccine hesitancy: The development of a survey tool.

    PubMed

    Larson, Heidi J; Jarrett, Caitlin; Schulz, William S; Chaudhuri, Mohuya; Zhou, Yuqing; Dube, Eve; Schuster, Melanie; MacDonald, Noni E; Wilson, Rose

    2015-08-14

    In March 2012, the SAGE Working Group on Vaccine Hesitancy was convened to define the term "vaccine hesitancy", as well as to map the determinants of vaccine hesitancy and develop tools to measure and address the nature and scale of hesitancy in settings where it is becoming more evident. The definition of vaccine hesitancy and a matrix of determinants guided the development of a survey tool to assess the nature and scale of hesitancy issues. Additionally, vaccine hesitancy questions were piloted in the annual WHO-UNICEF joint reporting form, completed by National Immunization Managers globally. The objective of characterizing the nature and scale of vaccine hesitancy issues is to better inform the development of appropriate strategies and policies to address the concerns expressed, and to sustain confidence in vaccination. The Working Group developed a matrix of the determinants of vaccine hesitancy informed by a systematic review of peer reviewed and grey literature, and by the expertise of the working group. The matrix mapped the key factors influencing the decision to accept, delay or reject some or all vaccines under three categories: contextual, individual and group, and vaccine-specific. These categories framed the menu of survey questions presented in this paper to help diagnose and address vaccine hesitancy. PMID:25896384

  7. 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.

  8. 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

  9. 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 ...

  10. The Qatar genome: a population-specific tool for precision medicine in the Middle East

    PubMed Central

    Fakhro, Khalid A; Staudt, Michelle R; Ramstetter, Monica Denise; Robay, Amal; Malek, Joel A; Badii, Ramin; Al-Marri, Ajayeb Al-Nabet; Khalil, Charbel Abi; Al-Shakaki, Alya; Chidiac, Omar; Stadler, Dora; Zirie, Mahmoud; Jayyousi, Amin; Salit, Jacqueline; Mezey, Jason G; Crystal, Ronald G; Rodriguez-Flores, Juan L

    2016-01-01

    Reaching the full potential of precision medicine depends on the quality of personalized genome interpretation. In order to facilitate precision medicine in regions of the Middle East and North Africa (MENA), a population-specific genome for the indigenous Arab population of Qatar (QTRG) was constructed by incorporating allele frequency data from sequencing of 1,161 Qataris, representing 0.4% of the population. A total of 20.9 million single nucleotide polymorphisms (SNPs) and 3.1 million indels were observed in Qatar, including an average of 1.79% novel variants per individual genome. Replacement of the GRCh37 standard reference with QTRG in a best practices genome analysis workflow resulted in an average of 7* deeper coverage depth (an improvement of 23%) and 756,671 fewer variants on average, a reduction of 16% that is attributed to common Qatari alleles being present in QTRG. The benefit for using QTRG varies across ancestries, a factor that should be taken into consideration when selecting an appropriate reference for analysis. PMID:27408750

  11. 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...

  12. Methods and tools for comparative genomics of food-borne pathogens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A comparison of protein sequences encoded by a given genome with the database of existing proteins could be an informative approach since proteins with a high degree of similarity are likely to perform similar functions. Here we demonstrate the utility of several DNA and protein sequence comparison...

  13. 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...

  14. Comparative karyotyping as a tool for genome structure analysis of Trypanosoma cruzi.

    PubMed

    Branche, Carole; Ochaya, Stephen; Aslund, Lena; Andersson, Björn

    2006-05-01

    As a part of the Trypanosoma cruzi genome project, 239 genetic markers were hybridised to PFGE separated DNA from T. cruzi, in order to determine the number and size of chromosomes and to aid the assembly of the genome sequence. We used three strains, T. cruzi IIe CL Brener (the genome project reference strain) and two T. cruzi I strains, Sylvio X10/7 and CAI/72, to perform a comparative study of their karyotypes and to determine marker linkage. A densitometry analysis of the separations estimated the total chromosome numbers to be 55 in CL Brener and 57 in the two other strains. In all, 45 markers hybridised to single chromosomal bands and 103 markers to two bands in CL Brener, while the number of markers in Sylvio X10/7 and CAI/72 were 102/68 and 61/105, respectively. Size differences between homologous chromosomes were often large, up to 1900 kb (173%). The average difference was 36% for CL Brener and 23.5% for the T. cruzi I strains. Larger differences in CL Brener are consistent with a recent hybrid origin. Forty markers distributed into 15 linkage groups were found to identify specific chromosomes or chromosomes pairs. While the same markers are generally linked in all three strains, the sizes of the chromosomes vary extensively, indicating large chromosomal rearrangements. These data provide valuable information for the finishing of the CL Brener genome sequence. PMID:16481054

  15. 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...

  16. 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.

  17. Molecular confirmation of the genomic constitution of Douglasdeweya (Triticeae: Poaceae): demonstration of the utility of the 5S rDNA sequence as a tool for haplome identification.

    PubMed

    Baum, Bernard R; Johnson, Douglas A

    2008-06-01

    A new genus Douglasdeweya containing the two species, Douglasdeweya deweyi and D. wangii was published in 2005 by Yen et al. based upon the results of cytogenetical and morphological findings. The genome constitution of Douglasdeweya-PPStSt-allowed its segregation from the genus Pseudoroegneria which contains the StSt or StStStSt genomes. Our previous work had demonstrated the utility of using 5S rDNA units, especially the non-transcribed spacer sequence variation, for the resolution of genomes (haplomes) previously established by cytology. Here, we show that sequence analysis of the 5S DNA units from these species strongly supports the proposed species relationships of Yen et al. (Can J Bot 83:413-419, 2005), i.e., the PP genome from Agropyron and the StSt genome from Pseudoroegneria. Analysis of the 5S rDNA units constitutes a powerful tool for genomic research especially in the Triticeae. PMID:18421479

  18. Development of new tools for studying gene function in fungi based on the Gateway system.

    PubMed

    Shafran, Hadas; Miyara, Itay; Eshed, Ravit; Prusky, Dov; Sherman, Amir

    2008-08-01

    Genomic information of many fungi has been released but large scale functional genomic studies are still limited by a lack of high-throughput methods. The low rates of homologous recombination and low rates of transformation are limiting steps in filamentous fungi, but the molecular tools are also lagging behind. In this paper we describe two new high-throughput functional genomic tools for filamentous fungi that are based on the Gateway technology. One system is the Gateway RNAi vector for fungi that allows gene silencing in a high-throughput manner. The other system is a high-throughput deletion construct system. These systems were tested using the PAC1 gene of Colletotrichum gloeosporioides. Using these types of approaches, large scale functional genomics experiments can be performed in filamentous fungi. PMID:18550398

  19. 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

  20. The Development of a Climate Time Line Information Tool

    NASA Astrophysics Data System (ADS)

    Kowal, D.; McCaffery, M.; Anderson, D.; Habermann, D. E.

    2001-12-01

    The "Climate Time Line" or CTL tool currently in development at the National Geophysical Data Center will provide a climatic and "place-based" context for current weather patterns and a pre-instrumental context for current climate trends. Two audiences-GLOBE students and water managers involved with the Western Water Assessment--are targeted in the pilot project phase to test the CTL as a learning and decision-making support tool. Weather, climate and paleoclimatic observations will be integrated through a web-based interface that can be used for comparing data collected over 10 year, 100 year and 1000+ year periods, and made accessible and meaningful to non-technical users. The Climate Time Line prototype will include the following features: 1) Access to diverse data sets such as NCDC's Historic Climate Network, GLOBE Student Data Archive, World Data Center for Paleoclimatology and historical streamflow data from the USGS; 2) Map Locator/Search Utility for regional inquiries and comparison views; 3) Varying temporal and spatial displays; 4) Tutorial and help sections to guide and support users; 5) Supporting materials including a "Powers of Ten" primer examining variability at various timescales; and 6) Statistical assessment tools. The CTL prototype offers a novel approach in the scientific analysis of climate and hydrology data. It will facilitate inquiries by simplifying access to environmental data. Additionally, it will provide historical timelines for the intended user to compare the development of human cultures in relation to climate trends and variability--promoting an inquiry-rich learning environment. Throughout the pilot project phase, the CTL will undergo evaluation particularly in the area of usability, followed by a pre- and post- assessment of its educational impact on the targeted, non-technical audience. A hypernews workspace has been created to facilitate the development of the CTL. >http://HyperNews.ngdc.noaa.gov/HyperNews/get/ ClimateTimelineProject.html.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. Development of a laboratory extreme-ultraviolet lithography tool

    SciTech Connect

    Tichenor, D.A.; Kubiak, G.D.; Malinowski, M.E.; Stulen, R.H.; Haney, S.J.; Berger, K.W.; Nissen, R.P.; Wilkerson, G.A.; Paul, P.H.; Birtola, S.R.; Jin, P.S.; Arling, R.W.; Ray-Chaudhuri, A.K.; Sweatt, W.C.; Chow, W.W.; Bjorkholm, J.E.; Freeman, R.R.; Himel, M.D.; MacDowell, A.A.; Tennant, D.M.; Fetter, L.A.; Wood, O.R. II; Waskiewicz, W.K.; White, D.L.; Windt, D.L.; Jewell, T.E.

    1994-04-01

    The development of a laboratory EUV lithography tool based on a laser plasma source, a 10x Schwarzchild camera, and a magnetically levitated wafer stage is presented. Interferometric measurements of the camera aberrations are incorporated into physical-optics simulations to estimate the EUV imaging performance of the camera. Experimental results demonstrate the successful matching of five multilayer reflecting surfaces, coated to specification for a wide range of figure and incidence angle requirements. High-resolution, 10x-reduction images of a reflection mask are shown.

  6. 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...

  7. 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…

  8. 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

  9. Genomics of CpG Methylation in Developing and Developed Zebrafish

    PubMed Central

    McGaughey, David M.; Abaan, Hatice Ozel; Miller, Ryan M.; Kropp, Peter A.; Brody, Lawrence C.

    2014-01-01

    DNA methylation is a dynamic process through which specific chromatin modifications can be stably transmitted from parent to daughter cells. A large body of work has suggested that DNA methylation influences gene expression by silencing gene promoters. However, these conclusions were drawn from data focused mostly on promoter regions. Regarding the entire genome, it is unclear how methylation and gene transcription patterns are related during vertebrate development. To identify the genome-wide distribution of CpG methylation, we created series of high-resolution methylome maps of Danio rerio embryos during development and in mature, differentiated tissues. We found that embryonic and terminal tissues have unique methylation signatures in CpG islands and repetitive sequences. Fully differentiated tissues have increased CpG and LTR methylation and decreased SINE methylation relative to embryonic tissues. Unsupervised clustering analyses reveal that the embryonic and terminal tissues can be classified solely by their methylation patterning. Novel analyses also identify a previously undescribed genome-wide exon methylation signature. We also compared whole genome methylation with genome-wide mRNA expression levels using publicly available RNA-seq datasets. These comparisons revealed previously unrecognized relationships between gene expression, alternative splicing, and exon methylation. Surprisingly, we found that exonic methylation is a better predictor of mRNA expression level than promoter methylation. We also found that transcriptionally skipped exons have significantly less methylation than retained exons. Our integrative analyses reveal highly complex interplay between gene expression, alternative splicing, development, and methylation patterning in zebrafish. PMID:24657902

  10. MosaicSolver: a tool for determining recombinants of viral genomes from pileup data

    PubMed Central

    Wood, Graham R.; Ryabov, Eugene V.; Fannon, Jessica M.; Moore, Jonathan D.; Evans, David J.; Burroughs, Nigel

    2014-01-01

    Viral recombination is a key evolutionary mechanism, aiding escape from host immunity, contributing to changes in tropism and possibly assisting transmission across species barriers. The ability to determine whether recombination has occurred and to locate associated specific recombination junctions is thus of major importance in understanding emerging diseases and pathogenesis. This paper describes a method for determining recombinant mosaics (and their proportions) originating from two parent genomes, using high-throughput sequence data. The method involves setting the problem geometrically and the use of appropriately constrained quadratic programming. Recombinants of the honeybee deformed wing virus and the Varroa destructor virus-1 are inferred to illustrate the method from both siRNAs and reads sampling the viral genome population (cDNA library); our results are confirmed experimentally. Matlab software (MosaicSolver) is available. PMID:25120266

  11. 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

  12. Development and validation of the Surgical Outcome Risk Tool (SORT)

    PubMed Central

    Protopapa, K L; Simpson, J C; Smith, N C E; Moonesinghe, S R

    2014-01-01

    Background Existing risk stratification tools have limitations and clinical experience suggests they are not used routinely. The aim of this study was to develop and validate a preoperative risk stratification tool to predict 30-day mortality after non-cardiac surgery in adults by analysis of data from the observational National Confidential Enquiry into Patient Outcome and Death (NCEPOD) Knowing the Risk study. Methods The data set was split into derivation and validation cohorts. Logistic regression was used to construct a model in the derivation cohort to create the Surgical Outcome Risk Tool (SORT), which was tested in the validation cohort. Results Prospective data for 19 097 cases in 326 hospitals were obtained from the NCEPOD study. Following exclusion of 2309, details of 16 788 patients were analysed (derivation cohort 11 219, validation cohort 5569). A model of 45 risk factors was refined on repeated regression analyses to develop a model comprising six variables: American Society of Anesthesiologists Physical Status (ASA-PS) grade, urgency of surgery (expedited, urgent, immediate), high-risk surgical specialty (gastrointestinal, thoracic, vascular), surgical severity (from minor to complex major), cancer and age 65 years or over. In the validation cohort, the SORT was well calibrated and demonstrated better discrimination than the ASA-PS and Surgical Risk Scale; areas under the receiver operating characteristic (ROC) curve were 0·91 (95 per cent c.i. 0·88 to 0·94), 0·87 (0·84 to 0·91) and 0·88 (0·84 to 0·92) respectively (P < 0·001). Conclusion The SORT allows rapid and simple data entry of six preoperative variables, and provides a percentage mortality risk for individuals undergoing surgery. PMID:25388883

  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. PMID:26088539

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

    PubMed

    Guo, Ximing; Ford, Susan E

    2016-03-01

    More and more infectious diseases affect marine molluscs. Some diseases have impacted commercial species including MSX and Dermo of the eastern oyster, QPX of hard clams, withering syndrome of abalone and ostreid herpesvirus 1 (OsHV-1) infections of many molluscs. Although the exact transmission mechanisms are not well understood, human activities and associated environmental changes often correlate with increased disease prevalence. For instance, hatcheries and large-scale aquaculture create high host densities, which, along with increasing ocean temperature, might have contributed to OsHV-1 epizootics in scallops and oysters. A key to understanding linkages between the environment and disease is to understand how the environment affects the host immune system. Although we might be tempted to downplay the role of immunity in invertebrates, recent advances in genomics have provided insights into host and parasite genomes and revealed surprisingly sophisticated innate immune systems in molluscs. All major innate immune pathways are found in molluscs with many immune receptors, regulators and effectors expanded. The expanded gene families provide great diversity and complexity in innate immune response, which may be key to mollusc's defence against diverse pathogens in the absence of adaptive immunity. Further advances in host and parasite genomics should improve our understanding of genetic variation in parasite virulence and host disease resistance. PMID:26880838

  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. Development of an influenza virologic risk assessment tool.

    PubMed

    Trock, Susan C; Burke, Stephen A; Cox, Nancy J

    2012-12-01

    Influenza pandemics pose a continuous risk to human and animal health and may engender food security issues worldwide. As novel influenza A virus infections in humans are identified, pandemic preparedness strategies necessarily involve decisions regarding which viruses should be included for further studies and mitigation efforts. Resource and time limitations dictate that viruses determined to pose the greatest risk to public or animal health should be selected for further research to fill information gaps and, potentially, for development of vaccine candidates that could be put in libraries, manufactured and stockpiled, or even administered to protect susceptible populations of animals or people. A need exists to apply an objective, science-based risk assessment to the process of evaluating influenza viruses. During the past year, the Centers for Disease Control and Prevention began developing a tool to evaluate influenza A viruses that are not circulating in the human population but pose a pandemic risk. The objective is to offer a standardized set of considerations to be applied when evaluating prepandemic viruses. The tool under consideration is a simple, additive model, based on multiattribute decision analysis. The model includes elements that address the properties of the virus itself and population attributes, considers both veterinary and human findings, and integrates both laboratory and field observations. Additionally, each element is assigned a weight such that all elements are not considered of equal importance within the model. PMID:23402136

  17. Development of the Central Dogma Concept Inventory (CDCI) Assessment Tool.

    PubMed

    Newman, Dina L; Snyder, Christopher W; Fisk, J Nick; Wright, L Kate

    2016-01-01

    Scientific teaching requires scientifically constructed, field-tested instruments to accurately evaluate student thinking and gauge teacher effectiveness. We have developed a 23-question, multiple select-format assessment of student understanding of the essential concepts of the central dogma of molecular biology that is appropriate for all levels of undergraduate biology. Questions for the Central Dogma Concept Inventory (CDCI) tool were developed and iteratively revised based on student language and review by experts. The ability of the CDCI to discriminate between levels of understanding of the central dogma is supported by field testing (N= 54), and large-scale beta testing (N= 1733). Performance on the assessment increased with experience in biology; scores covered a broad range and showed no ceiling effect, even with senior biology majors, and pre/posttesting of a single class focused on the central dogma showed significant improvement. The multiple-select format reduces the chances of correct answers by random guessing, allows students at different levels to exhibit the extent of their knowledge, and provides deeper insight into the complexity of student thinking on each theme. To date, the CDCI is the first tool dedicated to measuring student thinking about the central dogma of molecular biology, and version 5 is ready to use. PMID:27055775

  18. 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

  19. 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.

  20. 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

  1. MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models.

    PubMed

    Aurich, Maike K; Fleming, Ronan M T; Thiele, Ines

    2016-01-01

    Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. With the MetaboTools, we make our methods available to the broader scientific community. The MetaboTools consist of a protocol, a toolbox, and tutorials of two use cases. The protocol describes, in a step-wise manner, the workflow of data integration, and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorials explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, the MetaboTools constitute a comprehensive guide to the intra-model analysis of extracellular metabolomic data from microbial, plant, or human cells. This computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community. PMID:27536246

  2. New genome sequence data and molecular tools promote the use of photosynthetic and edible cyanobacteria in bioregenerative systems to support human space exploration.

    NASA Astrophysics Data System (ADS)

    Leys, Natalie; Morin, Nicolas; Janssen, Paul; Mergeay, Max

    Cyanobacteria are daily used as nutritional supplements (e.g. Spirulina) and are considered for promising applications beyond Earth, in space, where they can play a crucial role in closed miniaturised biological waste recycling systems that are currently developed to support future long-term space missions. Cyanobacteria can be cultured with artificial light in controllable photobioreactors, and used for the efficient removal of CO2 from and production of O2 in the at-mosphere of the confined spacecraft, for removal of nitrate from waste water that is recycled to potable water, and as complementary food source. In this context, the filamentous cyanobac-terium Arthrospira sp. PCC 8005 was selected as part of the bio-regenerative life-support system MELiSSA from the European Space Agency. For bioprocess control and optimisation, the access to its genetic information and the development of molecular tools is crucial. Here we report on our efforts to determine the full genome of the cyanobacterium Arthrospira sp. PCC 8005. The obtained sequence data were analysed in detail to gain a better insight in the photosynthetic, nutritive, or potential toxic potential of this strain. In addition, the sensitivity of PCC 8005 to ionizing radiation was investigated because prolonged exposure of PCC 8005 to cosmic radiation in space might have a deleterious effect on its metabolism and oxygenic properties. To our knowledge, of the 6 different research groups across the globe trying to sequence Arthrospira strains, none of them, including us, were yet able to obtain a complete genome sequence. For Arthrospira sp. strain PCC 8005, we obtained 119 contigs (assembled in 16 scaffolds), representing 6,3 Mb, with 5,856 predicted protein-coding sequences (CDSs) and 176 genes encoding RNA. The PCC 8005 genome displays an unusual high number of large repeated sequences, covering around 8% of the genome, which likely hampered the sequenc-ing. The PCC 8005 genome is also ridden by mobile

  3. Genomic Variants and Variations in Malformations of Cortical Development

    PubMed Central

    Jamuar, Saumya S.; Walsh, Christopher A.

    2015-01-01

    Malformations of cortical development (MCD) are a common cause of neurodevelopmental delay and epilepsy and are caused by disruptions in the normal development of the cerebral cortex. Advances in genetic tools have expanded our understanding of the genetics of these malformations over the past few years, with a number of new causative genes identified in patients with MCD. In addition, there has been a vast expansion in the phenotypic characterization of the known genes, with a wide range as well as severity of malformations being reported. There is increasing evidence of role of de novo mutations, including those occurring post fertilization, in MCD. These “somatic” mutations may not be detectable by traditional methods of genetic testing performed on blood DNA. Identification of the genetic etiology can help in guiding families in future pregnancies. Recent work has highlighted how elucidation of key molecular pathway can also allow for targeted therapeutic interventions. PMID:26022163

  4. 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.

  5. The Development of NASA's Low Thrust Trajectory Tool Set

    NASA Technical Reports Server (NTRS)

    Sims, Jon; Artis, Gwen; Kos, Larry

    2006-01-01

    Highly efficient electric propulsion systems can enable interesting classes of missions; unfortunately, they provide only a limited amount of thrust. Low-thrust (LT) trajectories are much more difficult to design than impulsive-type (chemical propulsion) trajectories. Previous low-thrust (LT) trajectory optimization software was often difficult to use, often had difficulties converging, and was somewhat limited in the types of missions it could support. A new state-of-the-art suite (toolbox) of low-thrust (LT) tools along with improved algorithms and methods was developed by NASA's MSFC, JPL, JSC, and GRC to address the needs of our customers to help foster technology development in the areas of advanced LT propulsion systems, and to facilitate generation of similar results by different analysts.

  6. Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development

    NASA Astrophysics Data System (ADS)

    Wang, Jiafeng; Qi, Haigang; Li, Li; Zhang, Guofan

    2014-01-01

    Microsatellites are a ubiquitous component of the eukaryote genome and constitute one of the most popular sources of molecular markers for genetic studies. However, no data are currently available regarding microsatellites across the entire genome in oysters, despite their importance to the aquaculture industry. We present the first genome-wide investigation of microsatellites in the Pacific oyster Crassostrea gigas by analysis of the complete genome, resequencing, and expression data. The Pacific oyster genome is rich in microsatellites. A total of 604 653 repeats were identified, in average of one locus per 815 base pairs (bp). A total of 12 836 genes had coding repeats, and 7 332 were expressed normally, including genes with a wide range of molecular functions. Compared with 20 different species of animals, microsatellites in the oyster genome typically exhibited 1) an intermediate overall frequency; 2) relatively uniform contents of (A)n and (C)n repeats and abundant long (C)n repeats (≥24 bp); 3) large average length of (AG)n repeats; and 4) scarcity of trinucleotide repeats. The microsatellite-flanking regions exhibited a high degree of polymorphism with a heterozygosity rate of around 2.0%, but there was no correlation between heterozygosity and microsatellite abundance. A total of 19 462 polymorphic microsatellites were discovered, and dinucleotide repeats were the most active, with over 26% of loci found to harbor allelic variations. In all, 7 451 loci with high potential for marker development were identified. Better knowledge of the microsatellites in the oyster genome will provide information for the future design of a wide range of molecular markers and contribute to further advancements in the field of oyster genetics, particularly for molecular-based selection and breeding.

  7. 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. PMID:25740473

  8. Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  9. 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.

  10. 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

  11. 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.

  12. Navigating yeast genome maintenance with functional genomics.

    PubMed

    Measday, Vivien; Stirling, Peter C

    2016-03-01

    Maintenance of genome integrity is a fundamental requirement of all organisms. To address this, organisms have evolved extremely faithful modes of replication, DNA repair and chromosome segregation to combat the deleterious effects of an unstable genome. Nonetheless, a small amount of genome instability is the driver of evolutionary change and adaptation, and thus a low level of instability is permitted in populations. While defects in genome maintenance almost invariably reduce fitness in the short term, they can create an environment where beneficial mutations are more likely to occur. The importance of this fact is clearest in the development of human cancer, where genome instability is a well-established enabling characteristic of carcinogenesis. This raises the crucial question: what are the cellular pathways that promote genome maintenance and what are their mechanisms? Work in model organisms, in particular the yeast Saccharomyces cerevisiae, has provided the global foundations of genome maintenance mechanisms in eukaryotes. The development of pioneering genomic tools inS. cerevisiae, such as the systematic creation of mutants in all nonessential and essential genes, has enabled whole-genome approaches to identifying genes with roles in genome maintenance. Here, we review the extensive whole-genome approaches taken in yeast, with an emphasis on functional genomic screens, to understand the genetic basis of genome instability, highlighting a range of genetic and cytological screening modalities. By revealing the biological pathways and processes regulating genome integrity, these analyses contribute to the systems-level map of the yeast cell and inform studies of human disease, especially cancer. PMID:26323482

  13. Searching algorithm for type IV secretion system effectors 1.0: a tool for predicting type IV effectors and exploring their genomic context.

    PubMed

    Meyer, Damien F; Noroy, Christophe; Moumène, Amal; Raffaele, Sylvain; Albina, Emmanuel; Vachiéry, Nathalie

    2013-11-01

    Type IV effectors (T4Es) are proteins produced by pathogenic bacteria to manipulate host cell gene expression and processes, divert the cell machinery for their own profit and circumvent the immune responses. T4Es have been characterized for some bacteria but many remain to be discovered. To help biologists identify putative T4Es from the complete genome of α- and γ-proteobacteria, we developed a Perl-based command line bioinformatics tool called S4TE (searching algorithm for type-IV secretion system effectors). The tool predicts and ranks T4E candidates by using a combination of 13 sequence characteristics, including homology to known effectors, homology to eukaryotic domains, presence of subcellular localization signals or secretion signals, etc. S4TE software is modular, and specific motif searches are run independently before ultimate combination of the outputs to generate a score and sort the strongest T4Es candidates. The user keeps the possibility to adjust various searching parameters such as the weight of each module, the selection threshold or the input databases. The algorithm also provides a GC% and local gene density analysis, which strengthen the selection of T4E candidates. S4TE is a unique predicting tool for T4Es, finding its utility upstream from experimental biology. PMID:23945940

  14. Development of an innovative tool to assess hospital learning environments.

    PubMed

    Chan, D

    2001-11-01

    Nursing as a profession has evolved in response to societal needs for well-prepared practitioners who provide quality care to the needed in episodes of illness, and promote health among all age groups. Clinical practice enables the student to develop competencies in the application of knowledge, skills, and attitudes to clinical field situations. The clinical learning environment is a multidimensional entity with a complex social context. Previous research on clinical learning environment was examined, yet minimal studies have been conducted on hospital learning environments from the psychosocial educational perspective. With the mission to maximize nursing students' clinical learning experiences, the author developed and validated the Clinical Learning Environment Inventory (CLEI) based on the theoretical framework in psychosocial education. It is envisaged that this tool will assist the nurse professional to facilitate nursing students to achieve a productive clinical practice. This paper highlights the need and details the conceptual framework in the development of the CLEI. Although it is not presented as a research based paper, some statistical data are included to verify the reliability and validity of the newly-developed instrument. PMID:11884175

  15. Developing tools and strategies for communicating climate change

    NASA Astrophysics Data System (ADS)

    Bader, D.; Yam, E. M.; Perkins, L.

    2011-12-01

    Research indicates that the public views zoos and aquariums as reliable and trusted sources for information on conservation. Additionally, visiting zoos and aquariums helps people reconsider their connections to conservation issues and solutions. The Aquarium of the Pacific, an AZA-accredited institution that serves the most ethnically diverse population of all aquariums in the nation, is using exhibit space, technology, public programming, and staff professional development to present a model for how aquariums can promote climate literacy. Our newest galleries and programs are designed to immerse our visitors in experiences that connect our live animal collection to larger themes on ocean change. The Aquarium is supporting our new programming with a multifaceted staff professional development that exposes our interpretive staff to current climate science and researchers as well as current social science on public perception of climate science. Our staff also leads workshops for scientists; these sessions allow us to examine learning theory and develop tools to communicate science and controversial subjects effectively. Through our partnerships in the science, social science, and informal science education communities, we are working to innovate and develop best practices in climate communication.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26202110

  17. Development of Antimicrobial Peptide Prediction Tool for Aquaculture Industries.

    PubMed

    Gautam, Aditi; Sharma, Asuda; Jaiswal, Sarika; Fatma, Samar; Arora, Vasu; Iquebal, M A; Nandi, S; Sundaray, J K; Jayasankar, P; Rai, Anil; Kumar, Dinesh

    2016-09-01

    Microbial diseases in fish, plant, animal and human are rising constantly; thus, discovery of their antidote is imperative. The use of antibiotic in aquaculture further compounds the problem by development of resistance and consequent consumer health risk by bio-magnification. Antimicrobial peptides (AMPs) have been highly promising as natural alternative to chemical antibiotics. Though AMPs are molecules of innate immune defense of all advance eukaryotic organisms, fish being heavily dependent on their innate immune defense has been a good source of AMPs with much wider applicability. Machine learning-based prediction method using wet laboratory-validated fish AMP can accelerate the AMP discovery using available fish genomic and proteomic data. Earlier AMP prediction servers are based on multi-phyla/species data, and we report here the world's first AMP prediction server in fishes. It is freely accessible at http://webapp.cabgrid.res.in/fishamp/ . A total of 151 AMPs related to fish collected from various databases and published literature were taken for this study. For model development and prediction, N-terminus residues, C-terminus residues and full sequences were considered. Best models were with kernels polynomial-2, linear and radial basis function with accuracy of 97, 99 and 97 %, respectively. We found that performance of support vector machine-based models is superior to artificial neural network. This in silico approach can drastically reduce the time and cost of AMP discovery. This accelerated discovery of lead AMP molecules having potential wider applications in diverse area like fish and human health as substitute of antibiotics, immunomodulator, antitumor, vaccine adjuvant and inactivator, and also for packaged food can be of much importance for industries. PMID:27141850

  18. Functional genomics of the chicken - a model organism

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The chicken has reached model organism status after genome sequencing and development of high-throughput tools for the exploration of functional elements of the genome. Functional genomics focuses on understanding the function and regulation of genes and gene products on a global or genome-wide scal...

  19. Developing tools for digital radar image data evaluation

    NASA Technical Reports Server (NTRS)

    Domik, G.; Leberl, F.; Raggam, J.

    1986-01-01

    The refinement of radar image analysis methods has led to a need for a systems approach to radar image processing software. Developments stimulated through satellite radar are combined with standard image processing techniques to create a user environment to manipulate and analyze airborne and satellite radar images. One aim is to create radar products for the user from the original data to enhance the ease of understanding the contents. The results are called secondary image products and derive from the original digital images. Another aim is to support interactive SAR image analysis. Software methods permit use of a digital height model to create ortho images, synthetic images, stereo-ortho images, radar maps or color combinations of different component products. Efforts are ongoing to integrate individual tools into a combined hardware/software environment for interactive radar image analysis.

  20. Development of the writing readiness inventory tool in context (WRITIC).

    PubMed

    van Hartingsveldt, Margo J; de Vries, Liesbeth; Cup, Edith H C; de Groot, Imelda J M; Nijhuis-van der Sanden, Maria W G

    2014-11-01

    This article describes the development of the Writing Readiness Inventory Tool in Context (WRITIC), a measurement evaluating writing readiness in Dutch kindergarten children (5 and 6 years old). Content validity was established through 10 expert evaluations in three rounds. Construct validity was established with 251 children following regular education. To identify scale constructs, factor analysis was performed. Discriminative validity was established by examining contrast groups with good (n = 142) and poor (n = 109) performers in paper-and-pencil tasks. Content validity was high with 94.4% agreement among the experts. Two reliable factors were found in the performance of paper-and-pencil tasks with Cronbach's alphas of 0.82 and 0.69 respectively. The contrast groups differed significantly in two WRITIC subdomains: "Sustained attention" and "Task performance". Our findings indicated that the WRITIC is feasible for use in the classroom. PMID:24666171

  1. 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.

  2. Kmasker--a tool for in silico prediction of single-copy FISH probes for the large-genome species Hordeum vulgare.

    PubMed

    Schmutzer, T; Ma, L; Pousarebani, N; Bull, F; Stein, N; Houben, A; Scholz, U

    2014-01-01

    Specific localization of large genomic fragments by fluorescence in situ hybridization (FISH) is challenging in large- genome plant species due to the high content of repetitive sequences. We report the automated work flow (Kmasker) for in silico extraction of unique genomic sequences of large genomic fragments suitable for FISH in barley. This method can be widely used for the integration of genetic and cytogenetic maps in plants and other species with large and complex genomes if the probe sequence (e.g. BACs, sequence contigs) and a low coverage (8-fold) of unassembled sequences of the species of interest are available. Kmasker has been made publicly available as a web tool at http://webblast.ipk-gatersleben.de/kmasker. PMID:24335088

  3. Genome-wide polymorphisms and development of a microarray platform to detect genetic variations in Plasmodium yoelii.

    PubMed

    Nair, Sethu C; Pattaradilokrat, Sittiporn; Zilversmit, Martine M; Dommer, Jennifer; Nagarajan, Vijayaraj; Stephens, Melissa T; Xiao, Wenming; Tan, John C; Su, Xin-Zhuan

    2014-01-01

    The rodent malaria parasite Plasmodium yoelii is an important model for studying malaria immunity and pathogenesis. One approach for studying malaria disease phenotypes is genetic mapping, which requires typing a large number of genetic markers from multiple parasite strains and/or progeny from genetic crosses. Hundreds of microsatellite (MS) markers have been developed to genotype the P. yoelii genome; however, typing a large number of MS markers can be labor intensive, time consuming, and expensive. Thus, development of high-throughput genotyping tools such as DNA microarrays that enable rapid and accurate large-scale genotyping of the malaria parasite will be highly desirable. In this study, we sequenced the genomes of two P. yoelii strains (33X and N67) and obtained a large number of single nucleotide polymorphisms (SNPs). Based on the SNPs obtained, we designed sets of oligonucleotide probes to develop a microarray that could interrogate ∼11,000 SNPs across the 14 chromosomes of the parasite in a single hybridization. Results from hybridizations of DNA samples of five P. yoelii strains or cloned lines (17XNL, YM, 33X, N67 and N67C) and two progeny from a genetic cross (N67×17XNL) to the microarray showed that the array had a high call rate (∼97%) and accuracy (99.9%) in calling SNPs, providing a simple and reliable tool for typing the P. yoelii genome. Our data show that the P. yoelii genome is highly polymorphic, although isogenic pairs of parasites were also detected. Additionally, our results indicate that the 33X parasite is a progeny of 17XNL (or YM) and an unknown parasite. The highly accurate and reliable microarray developed in this study will greatly facilitate our ability to study the genetic basis of important traits and the disease it causes. PMID:24685548

  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. 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.

  6. 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

  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 AN All-Purpose Free Photogrammetric Tool

    NASA Astrophysics Data System (ADS)

    González-Aguilera, D.; López-Fernández, L.; Rodriguez-Gonzalvez, P.; Guerrero, D.; Hernandez-Lopez, D.; Remondino, F.; Menna, F.; Nocerino, E.; Toschi, I.; Ballabeni, A.; Gaiani, M.

    2016-06-01

    Photogrammetry is currently facing some challenges and changes mainly related to automation, ubiquitous processing and variety of applications. Within an ISPRS Scientific Initiative a team of researchers from USAL, UCLM, FBK and UNIBO have developed an open photogrammetric tool, called GRAPHOS (inteGRAted PHOtogrammetric Suite). GRAPHOS allows to obtain dense and metric 3D point clouds from terrestrial and UAV images. It encloses robust photogrammetric and computer vision algorithms with the following aims: (i) increase automation, allowing to get dense 3D point clouds through a friendly and easy-to-use interface; (ii) increase flexibility, working with any type of images, scenarios and cameras; (iii) improve quality, guaranteeing high accuracy and resolution; (iv) preserve photogrammetric reliability and repeatability. Last but not least, GRAPHOS has also an educational component reinforced with some didactical explanations about algorithms and their performance. The developments were carried out at different levels: GUI realization, image pre-processing, photogrammetric processing with weight parameters, dataset creation and system evaluation. The paper will present in detail the developments of GRAPHOS with all its photogrammetric components and the evaluation analyses based on various image datasets. GRAPHOS is distributed for free for research and educational needs.

  9. Facilities as teaching tools: A transformative participatory professional development experience

    NASA Astrophysics Data System (ADS)

    Wilson, Eric A.

    Resource consumption continues to increase as the population grows. In order to secure a sustainable future, society must educate the next generation to become "sustainability natives." Schools play a pivotal role in educating a sustainability-literate society. However, a disconnect exists between the hidden curriculum of the built environment and the enacted curriculum. This study employs a transformative participatory professional development model to instruct teachers on how to use their school grounds as teaching tools for the purpose of helping students make explicit choices in energy consumption, materials use, and sustainable living. Incorporating a phenomenological perspective, this study considers the lived experience of two sustainability coordinators. Grounded theory provides an interpretational context for the participants' interactions with each other and the professional development process. Through a year long professional development experience - commencing with an intense, participatory two-day workshop -the participants discussed challenges they faced with integrating facilities into school curriculum and institutionalizing a culture of sustainability. Two major needs were identified in this study. For successful sustainability initiatives, a hybrid model that melds top-down and bottom-up approaches offers the requisite mix of administrative support, ground level buy-in, and excitement vis-a-vis sustainability. Second, related to this hybrid approach, K-12 sustainability coordinators ideally need administrative capabilities with access to decision making, while remaining connected to students in a meaningful way, either directly in the classroom, as a mentor, or through work with student groups and projects.

  10. Computer vision as a tool to study plant development.

    PubMed

    Spalding, Edgar P

    2009-01-01

    Morphological phenotypes due to mutations frequently provide key information about the biological function of the affected genes. This has long been true of the plant Arabidopsis thaliana, though phenotypes are known for only a minority of this model organism's approximately 25,000 genes. One common explanation for lack of phenotype in a given mutant is that a genetic redundancy masks the effect of the missing gene. Another possibility is that a phenotype escaped detection or manifests itself only in a certain unexamined condition. Addressing this potentially nettlesome alternative requires the development of more sophisticated tools for studying morphological development. Computer vision is a technical field that holds much promise in this regard. This chapter explains in general terms how computer algorithms can extract quantitative information from images of plant structures undergoing development. Automation is a central feature of a successful computer vision application as it enables more conditions and more dependencies to be characterized. This in turn expands the concept of phenotype into a point set in multidimensional condition space. New ways of measuring and thinking about phenotypes, and therefore the functions of genes, are expected to result from expanding the role of computer vision in plant biology. PMID:19588113

  11. AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences

    PubMed Central

    Grau, Jan; Reschke, Maik; Erkes, Annett; Streubel, Jana; Morgan, Richard D.; Wilson, Geoffrey G.; Koebnik, Ralf; Boch, Jens

    2016-01-01

    Transcription activator-like effectors (TALEs) are virulence factors, produced by the bacterial plant-pathogen Xanthomonas, that function as gene activators inside plant cells. Although the contribution of individual TALEs to infectivity has been shown, the specific roles of most TALEs, and the overall TALE diversity in Xanthomonas spp. is not known. TALEs possess a highly repetitive DNA-binding domain, which is notoriously difficult to sequence. Here, we describe an improved method for characterizing TALE genes by the use of PacBio sequencing. We present ‘AnnoTALE’, a suite of applications for the analysis and annotation of TALE genes from Xanthomonas genomes, and for grouping similar TALEs into classes. Based on these classes, we propose a unified nomenclature for Xanthomonas TALEs that reveals similarities pointing to related functionalities. This new classification enables us to compare related TALEs and to identify base substitutions responsible for the evolution of TALE specificities. PMID:26876161

  12. 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.

  13. Development of a multilocus sequence typing tool for Cryptosporidium muris and Cryptosporidium andersoni

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although widely used in the characterization of the transmission of intestinal Cryptosporidium spp., genotyping tools are not available for C. muris and C. andersoni, two most common gastric Cryptosporidium spp. of mammals. In this study, we screened the C. muris whole genome sequencing data for mi...

  14. PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The increasing number of genomic sequences of bacteria makes it possible to select unique SNPs of a particular strain/species at the whole genome level and thus design specific primers based on the SNPs. The high similarity of genomic sequences among phylogenetically-related bacteria requires the id...

  15. Molecular Aspects of Conifer Zygotic and Somatic Embryo Development: A Review of Genome-Wide Approaches and Recent Insights.

    PubMed

    Trontin, Jean-François; Klimaszewska, Krystyna; Morel, Alexandre; Hargreaves, Catherine; Lelu-Walter, Marie-Anne

    2016-01-01

    Genome-wide profiling (transcriptomics, proteomics, metabolomics) is providing unprecedented opportunities to unravel the complexity of coordinated gene expression during embryo development in trees, especially conifer species harboring "giga-genome." This knowledge should be critical for the efficient delivery of improved varieties through seeds and/or somatic embryos in fluctuating markets and to cope with climate change. We reviewed "omics" as well as targeted gene expression studies during both somatic and zygotic embryo development in conifers and tentatively puzzled over the critical processes and genes involved at the specific developmental and transition stages. Current limitations to the interpretation of these large datasets are going to be lifted through the ongoing development of comprehensive genome resources in conifers. Nevertheless omics already confirmed that master regulators (e.g., transcription and epigenetic factors) play central roles. As in model angiosperms, the molecular regulation from early to late embryogenesis may mainly arise from spatiotemporal modulation of auxin-, gibberellin-, and abscisic acid-mediated responses. Omics also showed the potential for the development of tools to assess the progress of embryo development or to build genotype-independent, predictive models of embryogenesis-specific characteristics. PMID:26619863

  16. 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

  17. Genomics and Health Impact Update

    MedlinePlus

    ... Genomics in Practice Newborn Screening Pharmacogenomics Reproductive Health Tools and Databases About the Genomics & Health Impact Update The Office of Public Health Genomics provides updated and credible ...

  18. DEVELOPMENT OF GENOMIC RESOURCES FOR GARLIC AND ONION: GOALS OF A FUNDED USDA-IFAFS GRANT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Enormous genomic resources are being developed for model plants such as Arabidopsis and rice. However, it is not clear how broadly these genomic resources can be applied to the genetic improvement of more distantly related plants. Asparagus, garlic, and onion are the most economically important no...

  19. Draft Genome Sequence of Lactobacillus reuteri Strain CRL 1098, an Interesting Candidate for Functional Food Development

    PubMed Central

    Torres, Andrea C.; Suárez, Nadia E.; Font, Graciela; Saavedra, Lucila

    2016-01-01

    We report here the draft genome sequence of Lactobacillus reuteri strain CRL 1098. This strain represents an interesting candidate for functional food development because of its proven probiotic properties. The draft genome sequence is composed of 1,969,471 bp assembled into 45 contigs and an average G+C content of 38.8%. PMID:27563038

  20. Genome Informatics

    PubMed Central

    Winslow, Raimond L.; Boguski, Mark S.

    2005-01-01

    This article reviews recent advances in genomics and informatics relevant to cardiovascular research. In particular, we review the status of (1) whole genome sequencing efforts in human, mouse, rat, zebrafish, and dog; (2) the development of data mining and analysis tools; (3) the launching of the National Heart, Lung, and Blood Institute Programs for Genomics Applications and Proteomics Initiative; (4) efforts to characterize the cardiac transcriptome and proteome; and (5) the current status of computational modeling of the cardiac myocyte. In each instance, we provide links to relevant sources of information on the World Wide Web and critical appraisals of the promises and the challenges of an expanding and diverse information landscape. PMID:12750305